Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004459.1 Hibiscus syriacus cultivar Beakdansim tig00009831_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: 41319
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:697 original size:37 final size:36
Alignment explanation
Indices: 642--1219 Score: 202
Period size: 36 Copynumber: 16.9 Consensus size: 36
632 GGGGTGTTAC
*
642 AGAAACTGTCTCATGGGAGACAAAATTTAGTTCTAAA
1 AGAAACTGTCTCAAGGGAGACAAAATTTAGTT-TAAA
* ** *
679 AGAAAATGTCTCAAGGGAGATGAAA-TTAGTTTCAA
1 AGAAACTGTCTCAAGGGAGACAAAATTTAGTTTAAA
* * *
714 AGAAAACAGAT-TCAA---AG-----ATTTTGTTTCAAG
1 AG-AAACTG-TCTCAAGGGAGACAAAATTTAGTTT-AAA
* *
744 GGAAACTGTCTCAA--GAGACAAAATTT-GTTTCAA
1 AGAAACTGTCTCAAGGGAGACAAAATTTAGTTTAAA
* * * *
777 GGGAACTGTCTCAAGGGAGACAAAATTT-GTTTCTAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTAGTTT-AAA
* * *
813 AGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAA
1 AGAAACTGTCTCAAGGGAGACAAAATTTAGTT-TAAA
* * *
850 AGAAATTGTCTCAAGGGAGACGAAA-TTAGTTT-CA
1 AGAAACTGTCTCAAGGGAGACAAAATTTAGTTTAAA
* ** * *
884 AGAAAACAGAT-T------A-A-ATTATTTTGTTTAAG
1 AG-AAACTG-TCTCAAGGGAGACAAAATTTAGTTTAAA
* * *
913 GGAAACTGTCTCAAGAGAGACAAAATTT-GTTTCAA
1 AGAAACTGTCTCAAGGGAGACAAAATTTAGTTTAAA
* * *
948 GGGAACTGTCTCAAGGGAGAC-AAA-TT-GTTAAAA
1 AGAAACTGTCTCAAGGGAGACAAAATTTAGTTTAAA
* * * **
981 AGAAACTGTCTCAAGAGAGTCAAAACTTAGTTCCAA
1 AGAAACTGTCTCAAGGGAGACAAAATTTAGTTTAAA
* * *
1017 AG-AATTGTCTCAAGGGAGACGAAA-TTAG-TTCAA
1 AGAAACTGTCTCAAGGGAGACAAAATTTAGTTTAAA
* * ** * *
1050 GGAAAAC-AT-TC-------A-ATTATTTTGTTTTCAAG
1 AG-AAACTGTCTCAAGGGAGACAAAATTTAG-TTT-AAA
* ** *
1079 GGAAACTGTCTCAAAAGAGACAAAATTT-GTTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTAGTTT-AAA
* *
1115 GGAAACTGTCTCAAGGGAGACAAAATTTA-TTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTAGTTT-AAA
* * * *
1151 AGAAACTGTCTTAAGAGAGACAAAACTTAGTTCCAAA
1 AGAAACTGTCTCAAGGGAGACAAAATTTAGTT-TAAA
* *
1188 AGAAATTGTCTCAAGGGAGACGAAATTT-GTTT
1 AGAAACTGTCTCAAGGGAGACAAAATTTAGTTT
1220 CAAGGGAAAC
Statistics
Matches: 406, Mismatches: 84, Indels: 104
0.68 0.14 0.18
Matches are distributed among these distances:
25 1 0.00
26 4 0.01
27 2 0.00
28 21 0.05
29 21 0.05
30 6 0.01
33 47 0.12
34 19 0.05
35 77 0.19
36 126 0.31
37 77 0.19
38 5 0.01
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (36 bp):
AGAAACTGTCTCAAGGGAGACAAAATTTAGTTTAAA
Found at i:827 original size:36 final size:36
Alignment explanation
Indices: 733--1229 Score: 343
Period size: 36 Copynumber: 14.5 Consensus size: 36
723 ATTCAAAGAT
*
733 TTTGTTTCAAGGGAAACTGTCTCAA--GAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
*
767 TTTGTTTCAAG-GGAACTGTCTCAAGGGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
* *
802 TTTGTTTCTAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
* * * * *
838 CTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
* * ** *
875 TTAGTTTCAAGA-AAACAGAT-T--A---A-A-TTAT
1 TTTGTTTCAAGAGAAACTG-TCTCAAGGGAGACAAAA
* *
903 TTTGTTT-AAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
*
938 TTTGTTTCAAG-GGAACTGTCTCAAGGGAGAC-AAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
* * * *
972 -TTG-TTAAAAAGAAACTGTCTCAAGAGAGTCAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
* * * *
1006 CTTAGTTCCAA-AG-AATTGTCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
* * ** *
1041 TTAG-TTCAAG-GAAAAC-AT-TC-----A-A-TTAT
1 TTTGTTTCAAGAG-AAACTGTCTCAAGGGAGACAAAA
* **
1067 TTTGTTTTCAAGGGAAACTGTCTCAAAAGAGACAAAA
1 TTTG-TTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
*
1104 TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
* * *
1140 TTTATTTCAAGAGAAACTGTCTTAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
* * * * *
1176 CTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
*
1213 TTTGTTTCAAGGGAAAC
1 TTTGTTTCAAGAGAAAC
1230 AGATTCAAAT
Statistics
Matches: 359, Mismatches: 68, Indels: 70
0.72 0.14 0.14
Matches are distributed among these distances:
26 4 0.01
27 5 0.01
28 24 0.07
29 3 0.01
30 4 0.01
32 4 0.01
33 41 0.11
34 23 0.06
35 71 0.20
36 115 0.32
37 65 0.18
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
Found at i:862 original size:171 final size:172
Alignment explanation
Indices: 642--1283 Score: 966
Period size: 171 Copynumber: 3.8 Consensus size: 172
632 GGGGTGTTAC
* * * * * *
642 AGAAACTGTCTCATGGGAGACAAAATTTAGTTCTAAAAGAAAATGTCTCAAGGGAGATGAAATTA
1 AGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAATTA
*
707 GTTTCAAAGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTC-AAGAGACAAAATTTG
66 GTTTCAAAGAAAACAGATTCAAATATTTTGTTTCAAGGGAAACTGTCTCAAAGAGACAAAATTTG
*
771 TTTCAAGGGAACTGTCTCAAGGGAGACAAAATTTGTTTCTAG
131 TTTCAAGGGAACTGTCTCAAGGGAGACAAAATTTGTTTCAAG
813 AGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAATTA
1 AGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAATTA
878 GTTTC-AAGAAAACAGATT-AAATTATTTTGTTT-AAGGGAAACTGTCTCAAGAGAGACAAAATT
66 GTTTCAAAGAAAACAGATTCAAA-TATTTTGTTTCAAGGGAAACTGTCTCAA-AGAGACAAAATT
* *
940 TGTTTCAAGGGAACTGTCTCAAGGGAGAC-AAA-TTG-TTAAAA
129 TGTTTCAAGGGAACTGTCTCAAGGGAGACAAAATTTGTTTCAAG
*
981 AGAAACTGTCTCAAGAGAGTCAAAACTTAGTTCC-AAAG-AATTGTCTCAAGGGAGACGAAATTA
1 AGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAATTA
* *
1044 G-TTCAAGGAAAAC--ATTCAATTATTTTGTTTTCAAGGGAAACTGTCTCAAAAGAGACAAAATT
66 GTTTCAAAGAAAACAGATTCAAATATTTTG-TTTCAAGGGAAACTGTCTC-AAAGAGACAAAATT
*
1106 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTATTTCAAG
129 TGTTTCAAGGG-AACTGTCTCAAGGGAGACAAAATTTGTTTCAAG
* *
1151 AGAAACTGTCTTAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAATTT
1 AGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAATTA
* * * *
1216 GTTTCAAGGGAAACAGATTCAAATATTTTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTT
66 GTTTCAAAGAAAACAGATTCAAATATTTTGTTTCAAGGGAAACTGTCTCAA-AGAGACAAAATTT
1281 GTT
130 GTT
1284 GTTTCAAGGG
Statistics
Matches: 430, Mismatches: 23, Indels: 33
0.88 0.05 0.07
Matches are distributed among these distances:
164 10 0.02
165 8 0.02
166 71 0.17
167 24 0.06
168 39 0.09
169 23 0.05
170 62 0.14
171 109 0.25
172 25 0.06
173 13 0.03
174 33 0.08
175 13 0.03
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (172 bp):
AGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAATTA
GTTTCAAAGAAAACAGATTCAAATATTTTGTTTCAAGGGAAACTGTCTCAAAGAGACAAAATTTG
TTTCAAGGGAACTGTCTCAAGGGAGACAAAATTTGTTTCAAG
Found at i:1139 original size:134 final size:131
Alignment explanation
Indices: 938--1183 Score: 300
Period size: 134 Copynumber: 1.9 Consensus size: 131
928 AGAGACAAAA
** *
938 TTTGTTTCAAGGGAACTGTCTCAAGGGAGACAAATTGTTAAAAAGAAACTGTCTCAAGAGAGTCA
1 TTTGTTTCAAGGGAACTGTCTCAAAAGAGACAAATTGTTAAAAAGAAACTGTCTCAAGAGAGACA
* * *
1003 AAACTTAGTTCCAA-AG-AATTGTCTCAAGGGAGACGAAA-TTAGTTCAAGGAAAACATTCAATT
66 AAACTTA-TTCCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCAAGGAAAACATTCAATT
1065 AT
130 AT
* ** *
1067 TTTGTTTTCAAGGGAAACTGTCTCAAAAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGGG
1 TTTG-TTTCAAGGG-AACTGTCTCAAAAGAGAC-AAA-TTG-TTAAAAAGAAACTGTCTCAAGAG
* * *
1132 AGACAAAATTTATTTCAAGAGAAACTGTCTTAAGAGAGACAAAACTTAGTTC
61 AGACAAAACTTATTCCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTC
1184 CAAAAGAAAT
Statistics
Matches: 96, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
129 4 0.04
130 9 0.09
131 16 0.17
132 3 0.03
133 8 0.08
134 31 0.32
135 18 0.19
136 7 0.07
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (131 bp):
TTTGTTTCAAGGGAACTGTCTCAAAAGAGACAAATTGTTAAAAAGAAACTGTCTCAAGAGAGACA
AAACTTATTCCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCAAGGAAAACATTCAATTA
T
Found at i:1249 original size:29 final size:29
Alignment explanation
Indices: 1213--1326 Score: 113
Period size: 29 Copynumber: 3.6 Consensus size: 29
1203 GGAGACGAAA
1213 TTTGTTTCAAGGGAAACAGATTCAAATAT
1 TTTGTTTCAAGGGAAACAGATTCAAATAT
*
1242 TTTGTTTCAAGGGAAAC-TATCTCAAGAGAGATAAAATT
1 TTTGTTTCAAGGGAAACAGAT-TC---A-A-AT---A-T
1280 TGTTGTTTCAAGGGAAACAGATTCAAATAT
1 T-TTGTTTCAAGGGAAACAGATTCAAATAT
1310 TTTGTTTCAAGGGAAAC
1 TTTGTTTCAAGGGAAAC
1327 TATCTCAAGA
Statistics
Matches: 71, Mismatches: 2, Indels: 24
0.73 0.02 0.25
Matches are distributed among these distances:
28 2 0.03
29 35 0.49
30 2 0.03
31 1 0.01
32 1 0.01
33 1 0.01
34 4 0.06
35 1 0.01
36 1 0.01
37 1 0.01
38 2 0.03
39 18 0.25
40 2 0.03
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (29 bp):
TTTGTTTCAAGGGAAACAGATTCAAATAT
Found at i:1293 original size:39 final size:39
Alignment explanation
Indices: 1243--1384 Score: 171
Period size: 39 Copynumber: 3.9 Consensus size: 39
1233 TTCAAATATT
1243 TTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTG
1 TTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTG
*
1282 TTGTTTCAAGGGAAACAGAT-TC---A-A-AT---A-TT-
1 TTGTTTCAAGGGAAAC-TATCTCAAGAGAGATAAAATTTG
1311 TTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTG
1 TTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTG
* *
1350 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAA
1385 CTTGGAAAAT
Statistics
Matches: 87, Mismatches: 4, Indels: 24
0.76 0.03 0.21
Matches are distributed among these distances:
28 2 0.02
29 18 0.21
30 2 0.02
31 1 0.01
32 1 0.01
33 1 0.01
34 4 0.05
35 1 0.01
36 1 0.01
37 1 0.01
38 2 0.02
39 51 0.59
40 2 0.02
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (39 bp):
TTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTG
Found at i:1302 original size:68 final size:68
Alignment explanation
Indices: 1214--1365 Score: 304
Period size: 68 Copynumber: 2.2 Consensus size: 68
1204 GAGACGAAAT
1214 TTGTTTCAAGGGAAACAGATTCAAATATTTTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAAT
1 TTGTTTCAAGGGAAACAGATTCAAATATTTTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAAT
1279 TTG
66 TTG
1282 TTGTTTCAAGGGAAACAGATTCAAATATTTTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAAT
1 TTGTTTCAAGGGAAACAGATTCAAATATTTTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAAT
1347 TTG
66 TTG
1350 TTGTTTCAAGGGAAAC
1 TTGTTTCAAGGGAAAC
1366 TGTCTCAAGA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 84 1.00
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.32
Consensus pattern (68 bp):
TTGTTTCAAGGGAAACAGATTCAAATATTTTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAAT
TTG
Found at i:2284 original size:32 final size:32
Alignment explanation
Indices: 2217--2310 Score: 136
Period size: 32 Copynumber: 2.9 Consensus size: 32
2207 ATTCCCAAAG
*
2217 ATGCCCCAATATTCGATGTTGAATCT-AAAAA
1 ATGCCCCAATATTTGATGTTGAATCTCAAAAA
*
2248 ATGCCCCAATATTTGATGTTAAATCTCAAAAA
1 ATGCCCCAATATTTGATGTTGAATCTCAAAAA
**
2280 ATGCCCCAGCATTTGATGTTGAATCTTCAAA
1 ATGCCCCAATATTTGATGTTGAATC-TCAAA
2311 GATGCCGTCA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 24 0.43
32 27 0.48
33 5 0.09
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (32 bp):
ATGCCCCAATATTTGATGTTGAATCTCAAAAA
Found at i:2316 original size:32 final size:31
Alignment explanation
Indices: 2212--2316 Score: 129
Period size: 32 Copynumber: 3.3 Consensus size: 31
2202 ATTTAATTCC
* *
2212 CAAAGATGCCCCAATATTCGATGTTGAATCT
1 CAAAAATGCCCCAATATTTGATGTTGAATCT
* *
2243 AAAAAATGCCCCAATATTTGATGTTAAATCT
1 CAAAAATGCCCCAATATTTGATGTTGAATCT
**
2274 CAAAAAATGCCCCAGCATTTGATGTTGAATCTT
1 C-AAAAATGCCCCAATATTTGATGTTGAATC-T
*
2307 CAAAGATGCC
1 CAAAAATGCC
2317 GTCATTGTTC
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
31 27 0.43
32 34 0.54
33 2 0.03
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (31 bp):
CAAAAATGCCCCAATATTTGATGTTGAATCT
Found at i:3304 original size:60 final size:62
Alignment explanation
Indices: 3228--3355 Score: 163
Period size: 68 Copynumber: 2.0 Consensus size: 62
3218 TGTCTCTCTC
3228 TTGATGCTCTATGATCTTC-AAGTGG-AGTGATTCAGAAATGATTGTGCTTGATCAATCTCAT
1 TTGATGCTCTATGATCTTCGAAGTGGTAGTGATTCAGAAATGATTGTGCTTGATC-ATCTCAT
*
3289 TTGA-GCTCTATGATCTTCGAGTGAAGTGGTTCAGTGATTCAGAAATTATTGTGCTTGATCATCT
1 TTGATGCTCTATGATCTTC----GAAGTGG-T-AGTGATTCAGAAATGATTGTGCTTGATCATCT
3353 CAT
60 CAT
3356 AGTTTGAATC
Statistics
Matches: 58, Mismatches: 1, Indels: 10
0.84 0.01 0.14
Matches are distributed among these distances:
60 14 0.24
61 4 0.07
65 6 0.10
67 7 0.12
68 27 0.47
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (62 bp):
TTGATGCTCTATGATCTTCGAAGTGGTAGTGATTCAGAAATGATTGTGCTTGATCATCTCAT
Found at i:3425 original size:27 final size:27
Alignment explanation
Indices: 3393--3453 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
3383 CATCTTGTCT
3393 TCTTTTTTCTTTAAT-TTTCCTTTTTTTC
1 TCTTTTTT-TTT-ATCTTTCCTTTTTTTC
* *
3421 -CTTTTTTTTTCTCTTTGCTTTTTTTC
1 TCTTTTTTTTTATCTTTCCTTTTTTTC
3447 TCTTTTT
1 TCTTTTT
3454 GTTCTGATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 1 0.03
26 15 0.52
27 13 0.45
ACGTcount: A:0.03, C:0.18, G:0.02, T:0.77
Consensus pattern (27 bp):
TCTTTTTTTTTATCTTTCCTTTTTTTC
Found at i:3454 original size:17 final size:17
Alignment explanation
Indices: 3415--3454 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
3405 AATTTTCCTT
* *
3415 TTTTTCCTTTTTTTTTC
1 TTTTTGCTTTTTTTCTC
*
3432 TCTTTGCTTTTTTTCTC
1 TTTTTGCTTTTTTTCTC
3449 TTTTTG
1 TTTTTG
3455 TTCTGATTGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.78
Consensus pattern (17 bp):
TTTTTGCTTTTTTTCTC
Found at i:5407 original size:17 final size:18
Alignment explanation
Indices: 5382--5415 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5372 GATGCAAACG
*
5382 AAAACAAAT-AAAAGAGA
1 AAAAAAAATGAAAAGAGA
5399 AAAAAAAATGAAAAGAG
1 AAAAAAAATGAAAAGAG
5416 GTTAGTGAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.76, C:0.03, G:0.15, T:0.06
Consensus pattern (18 bp):
AAAAAAAATGAAAAGAGA
Found at i:6522 original size:28 final size:24
Alignment explanation
Indices: 6486--6548 Score: 63
Period size: 28 Copynumber: 2.4 Consensus size: 24
6476 AAAAACTAAC
*
6486 AAAATATAAAACTAATGAAATAGAGAAG
1 AAAA-ATAAAACAAAT-AAA-AGA-AAG
6514 ATAAAATAAAACAAATAAAAGAAAG
1 A-AAAATAAAACAAATAAAAGAAAG
*
6539 AAAAAGAAAA
1 AAAAATAAAA
6549 GAATAATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 8 0.25
25 4 0.12
26 3 0.09
27 3 0.09
28 11 0.34
29 3 0.09
ACGTcount: A:0.73, C:0.03, G:0.11, T:0.13
Consensus pattern (24 bp):
AAAAATAAAACAAATAAAAGAAAG
Found at i:6805 original size:2 final size:2
Alignment explanation
Indices: 6798--6830 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6788 CGAAATGATA
6798 AT 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 AT A
6831 AAATAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7048 original size:14 final size:15
Alignment explanation
Indices: 7029--7067 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
7019 AAATGTGCGT
*
7029 ATAAATAAAATTA-A
1 ATAAATAAAATAATA
7043 ATAAATAAAATAATA
1 ATAAATAAAATAATA
*
7058 ATAATTAAAA
1 ATAAATAAAA
7068 CGTAAATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
ATAAATAAAATAATA
Found at i:28693 original size:2 final size:2
Alignment explanation
Indices: 28686--28718 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
28676 CTTTGTAAGG
28686 AT 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 AT A
28719 CACTCAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33665 original size:20 final size:20
Alignment explanation
Indices: 33642--33683 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
33632 CAACACGAAC
* *
33642 TCCAATTTCGCAACACAGTT
1 TCCAAATTCACAACACAGTT
*
33662 TCCAAATTCACAACTCAGTT
1 TCCAAATTCACAACACAGTT
33682 TC
1 TC
33684 TGCAATCATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.31, G:0.07, T:0.31
Consensus pattern (20 bp):
TCCAAATTCACAACACAGTT
Found at i:33853 original size:20 final size:20
Alignment explanation
Indices: 33830--33878 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
33820 ATTTTCTAAA
**
33830 TCGCAACACGAATTTTGTTT
1 TCGCAACACGAATTTTGAAT
* *
33850 TCGCAACTCGATTTTTGAAT
1 TCGCAACACGAATTTTGAAT
33870 TCGCAACAC
1 TCGCAACAC
33879 AAATGTTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (20 bp):
TCGCAACACGAATTTTGAAT
Found at i:33998 original size:21 final size:21
Alignment explanation
Indices: 33967--34026 Score: 86
Period size: 21 Copynumber: 2.8 Consensus size: 21
33957 TATCACTCTC
33967 TCCAGCGACATCCATTCCTATA
1 TCCA-CGACATCCATTCCTATA
33989 TCCACGACATCCATTCCTATA
1 TCCACGACATCCATTCCTATA
*
34010 TCTAACGACATCC-TTCC
1 TC-CACGACATCCATTCC
34027 CCATCTCTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
21 23 0.64
22 13 0.36
ACGTcount: A:0.27, C:0.38, G:0.07, T:0.28
Consensus pattern (21 bp):
TCCACGACATCCATTCCTATA
Found at i:34688 original size:12 final size:12
Alignment explanation
Indices: 34667--34700 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
34657 ACCACATTTC
*
34667 CAATACCAAACA
1 CAATATCAAACA
34679 CAATATCAAACA
1 CAATATCAAACA
*
34691 CAATCTCAAA
1 CAATATCAAA
34701 ACCCATAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:34853 original size:24 final size:23
Alignment explanation
Indices: 34825--34878 Score: 90
Period size: 24 Copynumber: 2.3 Consensus size: 23
34815 AGTATTCGAA
34825 ATTTGATCTTGGTCAATACCCGG
1 ATTTGATCTTGGTCAATACCCGG
*
34848 ACTTTGATCTTGGTCAATACTCGG
1 A-TTTGATCTTGGTCAATACCCGG
34872 ATTTGAT
1 ATTTGAT
34879 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 7 0.24
24 22 0.76
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (23 bp):
ATTTGATCTTGGTCAATACCCGG
Found at i:37441 original size:39 final size:39
Alignment explanation
Indices: 37384--37458 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
37374 GTGAATGCAT
37384 ACATTTTCAGTTAGACATGCATTAGTAACTTGAGTTTGA
1 ACATTTTCAGTTAGACATGCATTAGTAACTTGAGTTTGA
37423 ACATTTTCAGTT-GAACATGCATTAGTAACTTGAGTT
1 ACATTTTCAGTTAG-ACATGCATTAGTAACTTGAGTT
37459 AAATTCGCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
38 1 0.03
39 34 0.97
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (39 bp):
ACATTTTCAGTTAGACATGCATTAGTAACTTGAGTTTGA
Found at i:37572 original size:20 final size:20
Alignment explanation
Indices: 37533--37577 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
37523 TGCGATTGTT
* *
37533 GCAAAAGTCAAATTCGCAAC
1 GCAAAAATCAAATTCACAAC
*
37553 GCAAAAATCAAATTTACAAC
1 GCAAAAATCAAATTCACAAC
*
37573 ACAAA
1 GCAAA
37578 TTTGACTATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.53, C:0.22, G:0.09, T:0.16
Consensus pattern (20 bp):
GCAAAAATCAAATTCACAAC
Found at i:37644 original size:20 final size:19
Alignment explanation
Indices: 37601--37645 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
37591 ATAATCGTAA
*
37601 TGCGAATTTGACTTTGTAT
1 TGCGAATTTGACTTTGCAT
*
37620 TGCGAATTTGACTTTCGCGT
1 TGCGAATTTGACTTT-GCAT
37640 TGCGAA
1 TGCGAA
37646 AGTGTACCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (19 bp):
TGCGAATTTGACTTTGCAT
Found at i:38973 original size:21 final size:21
Alignment explanation
Indices: 38947--39060 Score: 90
Period size: 21 Copynumber: 5.5 Consensus size: 21
38937 GTGAATCGGG
38947 CTCTTGAACGGT-AGGAGGGAC
1 CTCTTGAACGGTGA-GAGGGAC
* *
38968 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGGTGAGAGGGAC
* *
38989 CTCTTGAACGGGGGGAGAGG-C
1 CTCTTGAACGGTGAGAG-GGAC
* * * *
39010 CTCTTAAAAGATGAGAGGGGC
1 CTCTTGAACGGTGAGAGGGAC
* * *
39031 CTC-TGAATGATGAGAGGGGC
1 CTCTTGAACGGTGAGAGGGAC
39051 CTCTTGAACG
1 CTCTTGAACG
39061 ATAGGAGAAG
Statistics
Matches: 76, Mismatches: 13, Indels: 8
0.78 0.13 0.08
Matches are distributed among these distances:
20 20 0.26
21 53 0.70
22 3 0.04
ACGTcount: A:0.25, C:0.18, G:0.38, T:0.19
Consensus pattern (21 bp):
CTCTTGAACGGTGAGAGGGAC
Found at i:39013 original size:42 final size:41
Alignment explanation
Indices: 38947--39081 Score: 139
Period size: 42 Copynumber: 3.2 Consensus size: 41
38937 GTGAATCGGG
*
38947 CTCTTGAACGGTAGGAGGGACCTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGGTGGGAGGG-CCTCTTGAACGATGAGAGGGGC
* * *
38989 CTCTTGAACGGGGGGAGAGGCCTCTTAAAAGATGAGAGGGGC
1 CTCTTGAACGGTGGGAG-GGCCTCTTGAACGATGAGAGGGGC
* * * **
39031 CTC-TGAATGATGAGAGGGGCCTCTTGAACGAT-AGGAGAAGC
1 CTCTTGAACGGTGGGA-GGGCCTCTTGAACGATGA-GAGGGGC
39072 CTCTTGAACG
1 CTCTTGAACG
39082 AGACAGGTGA
Statistics
Matches: 76, Mismatches: 13, Indels: 8
0.78 0.13 0.08
Matches are distributed among these distances:
40 1 0.01
41 29 0.38
42 44 0.58
43 2 0.03
ACGTcount: A:0.26, C:0.19, G:0.36, T:0.19
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGCCTCTTGAACGATGAGAGGGGC
Found at i:41176 original size:19 final size:20
Alignment explanation
Indices: 41138--41181 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
41128 AAACTTAAAT
*
41138 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATCAAAA
41158 TCGCAACGCG-AAATCAAAA
1 TCGCAACGCGAAAATCAAAA
41177 TCGCA
1 TCGCA
41182 TTGCGAATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.45, C:0.25, G:0.18, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAATCAAAA
Found at i:41211 original size:14 final size:14
Alignment explanation
Indices: 41192--41225 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
41182 TTGCGAATTC
41192 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
*
41206 ATTTTCGTGTTGCG
1 ATTTTCGCGTTGCG
*
41220 AATTTC
1 ATTTTC
41226 AATTTTTGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:41236 original size:21 final size:21
Alignment explanation
Indices: 41206--41245 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
41196 TCGCGTTGCG
41206 ATTTTCGTGTTGCGAATTTCA
1 ATTTTCGTGTTGCGAATTTCA
*
41227 ATTTTTGTGTTGCGAATTT
1 ATTTTCGTGTTGCGAATTT
41246 AAGTTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.10, G:0.20, T:0.53
Consensus pattern (21 bp):
ATTTTCGTGTTGCGAATTTCA
Done.