Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003989.1 Hibiscus syriacus cultivar Beakdansim tig00008679_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: 55896
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:817 original size:18 final size:17
Alignment explanation
Indices: 796--833 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
786 AAAATATAAT
796 AAATAA-AAATTCAAAATA
1 AAATAAGAAATT-AAAA-A
814 AAATAAGAAATTAAAAA
1 AAATAAGAAATTAAAAA
831 AAA
1 AAA
834 CTAACCCTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 10 0.53
19 5 0.26
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (17 bp):
AAATAAGAAATTAAAAA
Found at i:1121 original size:20 final size:20
Alignment explanation
Indices: 1068--1222 Score: 118
Period size: 20 Copynumber: 7.8 Consensus size: 20
1058 TATTTAACTT
*
1068 TCGCGTTACGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
* * *
1088 TCACGCTGCTAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
* *
1108 TCGTGTTACGAATTTGACT-
1 TCGCGTTGCGAATTTGACTA
* *
1127 TCTGTGTTGCG-ATTT-ACAAA
1 TC-GCGTTGCGAATTTGAC-TA
* *
1147 TTCACGTTGCGAATTTGACTT
1 -TCGCGTTGCGAATTTGACTA
* * *
1168 TTGTGTTACGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
* *
1188 TCGCGTTGCGAATTTAACTT
1 TCGCGTTGCGAATTTGACTA
*
1208 TCGCATTGCGAATTT
1 TCGCGTTGCGAATTT
1223 AACTTCAGTG
Statistics
Matches: 103, Mismatches: 26, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
18 2 0.02
19 6 0.06
20 87 0.84
21 6 0.06
22 2 0.02
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:1181 original size:60 final size:61
Alignment explanation
Indices: 1088--1203 Score: 164
Period size: 60 Copynumber: 1.9 Consensus size: 61
1078 AATTTGACTA
* *
1088 TCACGCTGCTAATTTGACTATCGTGTTACGAATTTGACT-TCTGTGTTGCG-ATTTACAAAT
1 TCACGCTGCGAATTTGACTATCGTGTTACGAATTTGACTATC-GCGTTGCGAATTTACAAAT
* * *
1148 TCACGTTGCGAATTTGACTTTTGTGTTACGAATTTGACTATCGCGTTGCGAATTTA
1 TCACGCTGCGAATTTGACTATCGTGTTACGAATTTGACTATCGCGTTGCGAATTTA
1204 ACTTTCGCAT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
60 42 0.86
61 7 0.14
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (61 bp):
TCACGCTGCGAATTTGACTATCGTGTTACGAATTTGACTATCGCGTTGCGAATTTACAAAT
Found at i:1217 original size:60 final size:60
Alignment explanation
Indices: 1098--1227 Score: 156
Period size: 60 Copynumber: 2.2 Consensus size: 60
1088 TCACGCTGCT
* * *
1098 AATTTGACTATCGTGTTACGAATTTGACTTCTGTGTTGCGATTTACAAATTCACGTTGCG
1 AATTTGACTTTCGTGTTACGAATTTGACTTCTGCGTTGCGATTTACAAATTCACATTGCG
* ** *
1158 AATTTGACTTTTGTGTTACGAATTTGACTATC-GCGTTGCGAATTTA-ACTTTCGCATTGCG
1 AATTTGACTTTCGTGTTACGAATTTGACT-TCTGCGTTGCG-ATTTACAAATTCACATTGCG
*
1218 AATTTAACTT
1 AATTTGACTT
1228 CAGTGTTGCG
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
60 53 0.88
61 7 0.12
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42
Consensus pattern (60 bp):
AATTTGACTTTCGTGTTACGAATTTGACTTCTGCGTTGCGATTTACAAATTCACATTGCG
Found at i:1236 original size:20 final size:19
Alignment explanation
Indices: 1098--1242 Score: 87
Period size: 20 Copynumber: 7.3 Consensus size: 19
1088 TCACGCTGCT
* *
1098 AATTTGACTATCGTGTTACG
1 AATTTAACT-TCGTGTTGCG
*
1118 AATTTGACTTCTGTGTTGCG
1 AATTTAACTTC-GTGTTGCG
* **
1138 -ATTTACAAATTCACGTTGCG
1 AATTT--AACTTCGTGTTGCG
* * *
1158 AATTTGACTTTTGTGTTACG
1 AATTTAAC-TTCGTGTTGCG
* *
1178 AATTTGACTATCGCGTTGCG
1 AATTTAACT-TCGTGTTGCG
**
1198 AATTTAACTTTCGCATTGCG
1 AATTTAAC-TTCGTGTTGCG
1218 AATTTAACTTCAGTGTTGCG
1 AATTTAACTTC-GTGTTGCG
1238 -ATTTA
1 AATTTA
1243 CAGATTCGCG
Statistics
Matches: 99, Mismatches: 18, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
19 16 0.16
20 74 0.75
21 9 0.09
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.41
Consensus pattern (19 bp):
AATTTAACTTCGTGTTGCG
Found at i:1236 original size:40 final size:40
Alignment explanation
Indices: 1151--1242 Score: 98
Period size: 40 Copynumber: 2.3 Consensus size: 40
1141 TACAAATTCA
* * ** *
1151 CGTTGCGAATTTGACTTTTGTGTTACGAATTTGACTATCG
1 CGTTGCGAATTTAACTTTCGCATTACGAATTTAACTATCG
*
1191 CGTTGCGAATTTAACTTTCGCATTGCGAATTTAACT-TCAG
1 CGTTGCGAATTTAACTTTCGCATTACGAATTTAACTATC-G
*
1231 TGTTGCG-ATTTA
1 CGTTGCGAATTTA
1243 CAGATTCGCG
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
39 7 0.16
40 37 0.84
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.41
Consensus pattern (40 bp):
CGTTGCGAATTTAACTTTCGCATTACGAATTTAACTATCG
Found at i:1309 original size:20 final size:19
Alignment explanation
Indices: 1260--1313 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
1250 GCGTTGTGAT
1260 ATTCGCGTTGCGAAATTGG
1 ATTCGCGTTGCGAAATTGG
** *
1279 AAACTGGGTTGCGAAATTGG
1 ATTC-GCGTTGCGAAATTGG
1299 AGTTCGCGTTGCGAA
1 A-TTCGCGTTGCGAA
1314 TTTATTGGTC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 24 0.89
21 1 0.04
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.28
Consensus pattern (19 bp):
ATTCGCGTTGCGAAATTGG
Found at i:2203 original size:24 final size:23
Alignment explanation
Indices: 2168--2213 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
2158 GAAAAGTTAG
*
2168 TTGTTTTGCTTTGTTTTTTTCTTA
1 TTGTTTTGCTTT-TTTTATTCTTA
2192 TTGTTTCT-CTTTTTTTATTCTT
1 TTGTTT-TGCTTTTTTTATTCTT
2214 TCATAACTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 9 0.45
24 10 0.50
25 1 0.05
ACGTcount: A:0.04, C:0.11, G:0.09, T:0.76
Consensus pattern (23 bp):
TTGTTTTGCTTTTTTTATTCTTA
Found at i:2774 original size:3 final size:3
Alignment explanation
Indices: 2763--2822 Score: 72
Period size: 3 Copynumber: 21.0 Consensus size: 3
2753 TTTTTTATCG
** *
2763 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2809 TTA TT- TTA TTA TTA
1 TTA TTA TTA TTA TTA
2823 ATATATTACA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 5 0.10
3 43 0.90
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:6309 original size:31 final size:32
Alignment explanation
Indices: 6273--6334 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
6263 ATTTTACATG
*
6273 TACTAACTTATTT-TTCTCTTTTGTTTGTGTA
1 TACTAACTTATTTCCTCTCTTTTGTTTGTGTA
6304 TACTAACTTATTTCCTCTCTTTTGTTTGTGT
1 TACTAACTTATTTCCTCTCTTTTGTTTGTGT
6335 CATTTTGTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 13 0.45
32 16 0.55
ACGTcount: A:0.15, C:0.16, G:0.10, T:0.60
Consensus pattern (32 bp):
TACTAACTTATTTCCTCTCTTTTGTTTGTGTA
Found at i:8494 original size:11 final size:12
Alignment explanation
Indices: 8466--8503 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
8456 AAGAGCAAAG
8466 AGAAAAA-TCAA
1 AGAAAAAGTCAA
*
8477 AGCAAAAGTCAA
1 AGAAAAAGTCAA
8489 AGAAAAAG-CAA
1 AGAAAAAGTCAA
8500 AGAA
1 AGAA
8504 CAAAAGAGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.68, C:0.11, G:0.16, T:0.05
Consensus pattern (12 bp):
AGAAAAAGTCAA
Found at i:10320 original size:36 final size:36
Alignment explanation
Indices: 10268--10385 Score: 150
Period size: 36 Copynumber: 3.3 Consensus size: 36
10258 TGAGAATTTT
* *
10268 AAAACAAATTTTTGTCTCGCTTGAGACAATTTCTTTC
1 AAAACAAA-TTTTGTCTCGATTGAGACAATTTCTTTA
* *
10305 AAAGCAAATTTTGTCTCGATTGAGACAGCTTTC--TA
1 AAAACAAATTTTGTCTCGATTGAGACA-ATTTCTTTA
* *
10340 AAAACAAATTTTGTCTCGTTTGAGACAATTTCTTGA
1 AAAACAAATTTTGTCTCGATTGAGACAATTTCTTTA
10376 AAAACAAATT
1 AAAACAAATT
10386 CCGCCTCACT
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
34 4 0.06
35 26 0.37
36 29 0.41
37 11 0.16
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCGATTGAGACAATTTCTTTA
Found at i:10401 original size:71 final size:72
Alignment explanation
Indices: 10268--10402 Score: 175
Period size: 71 Copynumber: 1.9 Consensus size: 72
10258 TGAGAATTTT
** * ** * *
10268 AAAACAAATTTTTGTCTCGCTTGAGACAATTTCTTTCAAAGCAAATTTTGTCTCGATTGAGACAG
1 AAAACAAATTTTTGTCTCGCTTGAGACAATTTCTTGAAAAACAAATTCCGCCTCGATGGAGACAG
10333 CTTTCTA
66 CTTTCTA
*
10340 AAAACAAA-TTTTGTCTCGTTTGAGACAATTTCTTGAAAAACAAATTCCGCCTC-ACTGGAGACA
1 AAAACAAATTTTTGTCTCGCTTGAGACAATTTCTTGAAAAACAAATTCCGCCTCGA-TGGAGACA
10403 TTTTTCATTG
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
70 1 0.02
71 45 0.83
72 8 0.15
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (72 bp):
AAAACAAATTTTTGTCTCGCTTGAGACAATTTCTTGAAAAACAAATTCCGCCTCGATGGAGACAG
CTTTCTA
Found at i:10569 original size:36 final size:36
Alignment explanation
Indices: 10488--10569 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
10478 ATTTTGTTTT
* * *
10488 GCTTGAGACAATTTCTTTAAAAACAAAGTTTGTATC
1 GCTTGAGACAAATTCTTTAAAAACAAACTTCGTATC
* * *
10524 ACTTAAGACAAATTCTCTT-AAAACAAACTTCGTCTC
1 GCTTGAGACAAATTCT-TTAAAAACAAACTTCGTATC
10560 GCTTGAGACA
1 GCTTGAGACA
10570 TTTTTCCTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
36 35 0.95
37 2 0.05
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.32
Consensus pattern (36 bp):
GCTTGAGACAAATTCTTTAAAAACAAACTTCGTATC
Found at i:10669 original size:105 final size:102
Alignment explanation
Indices: 10543--10781 Score: 290
Period size: 105 Copynumber: 2.3 Consensus size: 102
10533 AAATTCTCTT
* *
10543 AAAACAAACTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAACCTT-GAATTTGATTCAC
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAA-CTTCGAATTTGATTCAC
10607 -TTAAAACAAAATTAATCTCACCTT-AGATTGTTGTTTCTTTC-
65 ATT-AAACAAAATTAATCTCA-CTTGAGATTG-T-TTTC--TCA
* * * *
10648 AAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCACA
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAACTTCGAATTTGATTCACA
* *
10713 TTAAACAAAGTTGATCTCACTTGAGATTGTTTTCTCA
66 TTAAACAAAATTAATCTCACTTGAGATTGTTTTCTCA
*
10750 AAAACAAACTTT-GTCTCGCTTGAGACAATTTC
1 AAAACAAA-TTTCGTCTCGCTTGAGACATTTTC
10782 TCTAAAAACA
Statistics
Matches: 119, Mismatches: 10, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
101 2 0.02
102 26 0.22
103 7 0.06
104 6 0.05
105 76 0.64
106 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (102 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAACTTCGAATTTGATTCACA
TTAAACAAAATTAATCTCACTTGAGATTGTTTTCTCA
Found at i:10789 original size:36 final size:35
Alignment explanation
Indices: 10743--10846 Score: 115
Period size: 36 Copynumber: 3.0 Consensus size: 35
10733 TTGAGATTGT
10743 TTTCTC-AAAAACAAACTTTGTCTCGCTTGAGACAA
1 TTTCTCTAAAAACAAA-TTTGTCTCGCTTGAGACAA
** *
10778 TTTCTCTAAAAACAAATTTTGTCTCATTTGAGACTA
1 TTTCTCTAAAAACAAA-TTTGTCTCGCTTGAGACAA
* *
10814 TATCT-T-AAAGCAAATTTCGTCTCGCTTGAGACA
1 TTTCTCTAAAAACAAATTT-GTCTCGCTTGAGACA
10847 TTTTTCCTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
33 3 0.05
34 19 0.33
35 7 0.12
36 29 0.50
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.36
Consensus pattern (35 bp):
TTTCTCTAAAAACAAATTTGTCTCGCTTGAGACAA
Found at i:10899 original size:273 final size:270
Alignment explanation
Indices: 10376--11008 Score: 787
Period size: 273 Copynumber: 2.3 Consensus size: 270
10366 AATTTCTTGA
* * * * *
10376 AAAACAAATTCCGCCTCACTGGAGACATTTTTCATTGAGATACAAATTTCGAATTTGTTTCACAT
1 AAAACAAATTTCGTCTCACTTGAGACATTTTCCTTTGAGATACAAATTTCGAATTTGTTTCACAT
* * * *
10441 TAAACAAAGTTGATCTCACTTGAGATCGTTTTCTCAAATTTTGTTTTGCTTGAGACAATTTCTTT
66 TAAACAAAGTTGATCTCACTTGAGATCGTTTTCTCAAACTTTGTCTCGCTTGAGACAATTTCTCT
*
10506 AAAAACAAAGTTTGTATCACTTAAGACAAATTCTCTTAAAACAAACTTCGTCTCGCTTGAGACAT
131 AAAAACAAAGTTTGTATCACTTAAGACAAATTATCTTAAAACAAACTTCGTCTCGCTTGAGACAT
10571 TTTTCCTTTGAGATACAAACCTTGAATTTGATTCACTTAAAACAAAATTAATCTCACCTT-AGAT
196 TTTTCCTTTGAGATACAAACCTTGAATTTGATTCACTTAAAAC-AAA-TAATCTCA-CTTGAGAT
*
10635 TGTTGTTTCTTTC
258 TGTTGTTTATTTC
* * *
10648 AAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCACA
1 AAAACAAATTTCGTCTCACTTGAGACATTTT-CCTTTGAGATACAAATTTCGAATTTGTTTCACA
*
10713 TTAAACAAAGTTGATCTCACTTGAGATTGTTTTCTCAAAAACAAACTTTGTCTCGCTTGAGACAA
65 TTAAACAAAGTTGATCTCACTTGAGATCGTTTTCT------CAAACTTTGTCTCGCTTGAGACAA
* * * * * * *
10778 TTTCTCTAAAAACAAATTTTGTCTCATTTGAGAC-TA-TATCTTAAAGCAAATTTCGTCTCGCTT
124 TTTCTCTAAAAACAAAGTTTGTATCACTTAAGACAAATTATCTTAAAACAAACTTCGTCTCGCTT
* ** *
10841 GAGACATTTTTCCTTTGAGATACTAATTTTGAATTTGTTTCACTTAAAAC-AA-AATCTCACTTG
189 GAGACATTTTTCCTTTGAGATACAAACCTTGAATTTGATTCACTTAAAACAAATAATCTCACTTG
*
10904 ATATTGTTGTTTATTTC
254 AGATTGTTGTTTATTTC
* * * * *
10921 GAAACAAATTTCGTTTCACTTGAGACATTTTTCTCTGAGATACAAATTT-AAATTTGTTGT-AC-
1 AAAACAAATTTCGTCTCACTTGAGACATTTTCCTTTGAGATACAAATTTCGAATTTGTT-TCACA
* * *
10983 TTGAAACAAAATTAATATCACTTGAG
65 TT-AAACAAAGTTGATCTCACTTGAG
11009 TTTTTCAAAA
Statistics
Matches: 313, Mismatches: 38, Indels: 21
0.84 0.10 0.06
Matches are distributed among these distances:
270 2 0.01
271 30 0.10
272 45 0.14
273 113 0.36
275 2 0.01
277 70 0.22
278 1 0.00
279 50 0.16
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.39
Consensus pattern (270 bp):
AAAACAAATTTCGTCTCACTTGAGACATTTTCCTTTGAGATACAAATTTCGAATTTGTTTCACAT
TAAACAAAGTTGATCTCACTTGAGATCGTTTTCTCAAACTTTGTCTCGCTTGAGACAATTTCTCT
AAAAACAAAGTTTGTATCACTTAAGACAAATTATCTTAAAACAAACTTCGTCTCGCTTGAGACAT
TTTTCCTTTGAGATACAAACCTTGAATTTGATTCACTTAAAACAAATAATCTCACTTGAGATTGT
TGTTTATTTC
Found at i:11194 original size:29 final size:29
Alignment explanation
Indices: 11160--11257 Score: 139
Period size: 29 Copynumber: 3.5 Consensus size: 29
11150 CTCTTGAGAT
11160 AAATCTTTGAGTCTGTTCCTTTTGAATAA
1 AAATCTTTGAGTCTGTTCCTTTTGAATAA
* *
11189 AAATCTTGGAGTTTGTTCCTTTTGAATAA
1 AAATCTTTGAGTCTGTTCCTTTTGAATAA
* *
11218 ATATCTTTGAGT-TGTTTCTTTTG-A-AA
1 AAATCTTTGAGTCTGTTCCTTTTGAATAA
11244 AAATCTTTGAGTCT
1 AAATCTTTGAGTCT
11258 ATTTATTTTG
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
26 13 0.21
27 2 0.03
28 10 0.16
29 37 0.60
ACGTcount: A:0.27, C:0.11, G:0.15, T:0.47
Consensus pattern (29 bp):
AAATCTTTGAGTCTGTTCCTTTTGAATAA
Found at i:11241 original size:28 final size:28
Alignment explanation
Indices: 11146--11269 Score: 137
Period size: 29 Copynumber: 4.4 Consensus size: 28
11136 TCTGGAGACA
*
11146 GTTTCTCTTGAGAT-AAATCTTTGAGTCT
1 GTTTCTTTTGA-ATAAAATCTTTGAGTCT
* * *
11174 GTTCCTTTTGAATAAAAATCTTGGAGTTT
1 GTTTCTTTTGAAT-AAAATCTTTGAGTCT
*
11203 GTTCCTTTTGAATAAATATCTTTGAGT-T
1 GTTTCTTTTGAATAAA-ATCTTTGAGTCT
11231 GTTTCTTTTGAA-AAAATCTTTGAGTCT
1 GTTTCTTTTGAATAAAATCTTTGAGTCT
* *
11258 ATTTATTTTGAA
1 GTTTCTTTTGAA
11270 ACAAAGTTTT
Statistics
Matches: 84, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
26 10 0.12
27 16 0.19
28 24 0.29
29 34 0.40
ACGTcount: A:0.26, C:0.10, G:0.15, T:0.48
Consensus pattern (28 bp):
GTTTCTTTTGAATAAAATCTTTGAGTCT
Found at i:11323 original size:50 final size:53
Alignment explanation
Indices: 11266--11366 Score: 163
Period size: 52 Copynumber: 2.0 Consensus size: 53
11256 CTATTTATTT
*
11266 TGAAACAAAGT-TT-TGTCTCTTGAGACAATTTCGTG-AAAAATCTTTGAGTC
1 TGAAACAAAGTGTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
*
11316 TGAAACAAAGTGTTGTCTCTCTTGAGACAATTTTGTGAAAAAATCTTTGAG
1 TGAAACAAAGTGTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAG
11367 ATTGTTTCTT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
50 11 0.24
51 2 0.04
52 20 0.43
53 13 0.28
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.36
Consensus pattern (53 bp):
TGAAACAAAGTGTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
Found at i:11423 original size:29 final size:30
Alignment explanation
Indices: 11354--11417 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 30
11344 AATTTTGTGA
*
11354 AAAAATCTTTGAGATTGTTTCTTTTGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
11384 AAAAATCTTTGAG-TCTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGAT-TGTTTCTTTGGAAAC
11414 AAAA
1 AAAA
11418 TTTTTGTCTC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 1 0.03
30 31 0.97
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (30 bp):
AAAAATCTTTGAGATTGTTTCTTTGGAAAC
Found at i:11507 original size:64 final size:65
Alignment explanation
Indices: 11370--11527 Score: 160
Period size: 64 Copynumber: 2.4 Consensus size: 65
11360 CTTTGAGATT
* * *
11370 GTTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTTGTCTCTCTTAAG
1 GTTTCTTTTG-AA-AAAAATCTTTGAATCTATTTCTTT-GAAACAAAATTTTTGTATCTCTTAAG
*
11435 ATA
63 ACA
* * *
11438 ATTTCTTTTGAAAAAAATCTTTGAATCTATTTCTCTT-AAA-ATGAA-TTTTGTATCTCTTGAGA
1 GTTTCTTTTGAAAAAAATCTTTGAATCTATTTCT-TTGAAACA-AAATTTTTGTATCTCTTAAGA
11500 CA
64 CA
* **
11502 GTTTCTCTTGAAGTAAATCTTTGAAT
1 GTTTCTTTTGAAAAAAATCTTTGAAT
11528 ATGTTCATTT
Statistics
Matches: 77, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
64 39 0.51
65 5 0.06
66 20 0.26
67 4 0.05
68 9 0.12
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (65 bp):
GTTTCTTTTGAAAAAAATCTTTGAATCTATTTCTTTGAAACAAAATTTTTGTATCTCTTAAGACA
Found at i:11696 original size:119 final size:117
Alignment explanation
Indices: 11572--11786 Score: 260
Period size: 119 Copynumber: 1.8 Consensus size: 117
11562 TTAACAAAAT
* * *
11572 CATCTTTGAGTCTATTTC-TTTAAAAC-AAATGTTGTCTCTCTT-GAGACAATTTCTAATT-AAA
1 CATCTTTGAGTATATTTCTTTTAAAACAAAAT-TT-TATCTCTTAAAGACAATTTCT-ATTGAAA
11633 AACTAA-CTTTTGAGATTGTTTCATTTGAAACAAATTTGGTCTTACTTAAGATGTAATC
63 AA--AATC-TTTGAGATTGTTTCATTTGAAA-AAATTTGGTCTTACTTAAGATGTAATC
* * *
11691 CATCTTTGAGTATGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAA
1 CATCTTTGAGTATATTTCTTTTAAAACAAAATTTTATCTCTTAAAGACAATTTCTATTGAAAAAA
* *
11756 ATCTTTGAGTTTGTTTCCTTTGAAAAAATTT
66 ATCTTTGAGATTGTTTCATTTGAAAAAATTT
11787 CTCGAGACAA
Statistics
Matches: 83, Mismatches: 8, Indels: 12
0.81 0.08 0.12
Matches are distributed among these distances:
117 6 0.07
118 22 0.27
119 26 0.31
120 25 0.30
121 4 0.05
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (117 bp):
CATCTTTGAGTATATTTCTTTTAAAACAAAATTTTATCTCTTAAAGACAATTTCTATTGAAAAAA
ATCTTTGAGATTGTTTCATTTGAAAAAATTTGGTCTTACTTAAGATGTAATC
Found at i:12402 original size:28 final size:28
Alignment explanation
Indices: 12371--12432 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
12361 TAAAAATATC
*
12371 ATCTTTGAGTTTATTTTTTTTGAAACAA
1 ATCTTTGAGTTTATTTCTTTTGAAACAA
* *
12399 ATCTTTGGGTTTGTTTCTTTTGAAACAA
1 ATCTTTGAGTTTATTTCTTTTGAAACAA
12427 ATCTTT
1 ATCTTT
12433 AATTTGGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.24, C:0.10, G:0.13, T:0.53
Consensus pattern (28 bp):
ATCTTTGAGTTTATTTCTTTTGAAACAA
Found at i:12442 original size:28 final size:28
Alignment explanation
Indices: 12371--12452 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
12361 TAAAAATATC
* * *
12371 ATCTTTGAGTTTATTTTTTTTGAAACAA
1 ATCTTTGAATTTGTTTCTTTTGAAACAA
**
12399 ATCTTTGGGTTTGTTTCTTTTGAAACAA
1 ATCTTTGAATTTGTTTCTTTTGAAACAA
*
12427 ATCTTT-AATTTGGTTTCTCTTGAAAC
1 ATCTTTGAATTT-GTTTCTTTTGAAAC
12453 CATAACTCCT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 3 0.06
28 44 0.94
ACGTcount: A:0.24, C:0.11, G:0.13, T:0.51
Consensus pattern (28 bp):
ATCTTTGAATTTGTTTCTTTTGAAACAA
Found at i:12536 original size:40 final size:40
Alignment explanation
Indices: 12481--12675 Score: 153
Period size: 40 Copynumber: 4.7 Consensus size: 40
12471 CCAGCCGTCC
*
12481 TCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCT
1 TCATCACGTAGGAACCGTGTCATCCCCAGACCAGATCTCT
* ** * *
12521 TCATCACGTAGGAACCGTGTCAACCATAGATAACCAG-CCGTCC
1 TCATCACGTAGGAACCGTGTCATCCCCAG---ACCAGATC-TCT
* * * *
12564 TCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTAGGAACCGTGTCATC-CC--CAGA---CCAGATCTCT
* *
12610 TCATCACGTATGAGCCGTGTCATTCCCC-GACCAGATCTCT
1 TCATCACGTAGGAACCGTGTCA-TCCCCAGACCAGATCTCT
*
12650 TCATCACGTAGGAGCCGTGTCA-CCCC
1 TCATCACGTAGGAACCGTGTCATCCCC
12676 TAGATAACTA
Statistics
Matches: 124, Mismatches: 19, Indels: 26
0.73 0.11 0.15
Matches are distributed among these distances:
38 4 0.03
40 55 0.44
42 1 0.01
43 31 0.25
44 1 0.01
46 29 0.23
47 3 0.02
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.24
Consensus pattern (40 bp):
TCATCACGTAGGAACCGTGTCATCCCCAGACCAGATCTCT
Found at i:12791 original size:134 final size:129
Alignment explanation
Indices: 12481--12926 Score: 592
Period size: 134 Copynumber: 3.4 Consensus size: 129
12471 CCAGCCGTCC
* * * * *
12481 TCATCATGTAGGAACCGTGTCATCCC-CAGACCAGATCTCTTCATCACGTAGGAACCGTGTCAAC
1 TCATCACGTATGAGCCGTGTCATCCCTC-GACCAGATCTCTTCATCACGTAGGAGCCGTGTCACC
*
12545 CATAGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCT
65 CATAGATAACCAGACGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCT
12610 TCATCACGTATGAGCCGTGTCATTCCC-CGACCAGATCTCTTCATCACGTAGGAGCCGTGTCACC
1 TCATCACGTATGAGCCGTGTCA-TCCCTCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCACC
* *
12674 CCTAGATAACTAGACGTCCTCATCACGTAGGAACCATGTTATTGC-CCTTCCTAAAGATGGCCAG
65 CATAGATAACCAGACGTCCTCATCACGTAGGAACCATGTTA-T-CACCTT--T--AGATGGCCAG
12738 AACTCT
124 AACTCT
* * * *
12744 TCATCACGTATGAGTCGTGTCATCCCTTGACCAGATTTCCTCATCACGTAGGAGCCGTGTCACCC
1 TCATCACGTATGAGCCGTGTCATCCCTCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCACCC
* * **
12809 TTAGATAACCAGTCGTCCTCATCACGTAGGAACTGTGTTATCACCTTTAGATGGCCAAGAACTCT
66 ATAGATAACCAGACGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCC-AGAACTCT
** *** *
12874 TCATCATATATGAGTAATGTCATCCCTCGACCAGATTTCTTCATCACGTAGGA
1 TCATCACGTATGAGCCGTGTCATCCCTCGACCAGATCTCTTCATCACGTAGGA
12927 ATTGTGTCAC
Statistics
Matches: 284, Mismatches: 23, Indels: 19
0.87 0.07 0.06
Matches are distributed among these distances:
129 99 0.35
130 65 0.23
131 2 0.01
132 2 0.01
133 9 0.03
134 107 0.38
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (129 bp):
TCATCACGTATGAGCCGTGTCATCCCTCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCACCC
ATAGATAACCAGACGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCT
Found at i:13150 original size:3 final size:3
Alignment explanation
Indices: 13139--13192 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
13129 TTTTTTATCG
** *
13139 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
13184 TTA TTA TTA
1 TTA TTA TTA
13193 ATATATTACA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
2 5 0.12
3 37 0.88
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:13169 original size:32 final size:31
Alignment explanation
Indices: 13133--13192 Score: 102
Period size: 32 Copynumber: 1.9 Consensus size: 31
13123 GGGTTTTTTT
*
13133 TTATCGTTATTTTATTATTATTATTATTATTA
1 TTATCGTTATCTTATTATT-TTATTATTATTA
13165 TTATCGTTATCTTATTATTTTATTATTA
1 TTATCGTTATCTTATTATTTTATTATTA
13193 ATATATTACA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 9 0.33
32 18 0.67
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.65
Consensus pattern (31 bp):
TTATCGTTATCTTATTATTTTATTATTATTA
Found at i:27288 original size:22 final size:22
Alignment explanation
Indices: 27263--27304 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
27253 GATTTTTAAC
27263 TAATATATAATTATAA-GTTTAT
1 TAATATATAATT-TAATGTTTAT
*
27285 TAATTTATAATTTAATGTTT
1 TAATATATAATTTAATGTTT
27305 TATAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
TAATATATAATTTAATGTTTAT
Found at i:28563 original size:3 final size:3
Alignment explanation
Indices: 28555--28587 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
28545 ATGTTATTTC
28555 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
28588 TGTTTGACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:29959 original size:151 final size:151
Alignment explanation
Indices: 29683--29980 Score: 336
Period size: 151 Copynumber: 2.0 Consensus size: 151
29673 TTAAAAAGTA
* * * *
29683 GTTATCAAAATGAAGAATTGAAGATACATAGTTATTCTAAAATGGTTTAGGAGTATTGGTTCAAA
1 GTTATCAAAATGAAGAATTGAAGATACATAGGTATTCTAAAATGGTTTAGGAGCAATGGCTCAAA
* ** * * *
29748 TTTGGTAAAAGATGGACTTAAAATGAACACGGAATTGAAGCAATACGAAATCATGCAAAGTTGAG
66 TTTGGTAAAAAAAAGACTTAAAATGAACACGGAATTGAAGCAATAAGAAATCATACAAAGTTGAA
29813 GGACTAAATTGAAAAAAATTT
131 GGACTAAATTGAAAAAAATTT
* *
29834 GTTATCAAAAAT-AA-AATTGAAGATACATAGGTGTT-TGAAAATGTTTTAGGAGCACATGGCTC
1 GTTATC-AAAATGAAGAATTGAAGATACATAGGTATTCT-AAAATGGTTTAGGAGCA-ATGGCTC
* * * * * *
29896 AAAATTT-GTAAAAAAAATACTTAAAATGAAGA-GGAATTGAAGGAGTAATAGAATCATATAAAG
63 -AAATTTGGTAAAAAAAAGACTTAAAATGAACACGGAATTGAAGCAATAAGA-AATCATACAAAG
* *
29959 TTGAAGGACTAAGTTTAAAAAA
126 TTGAAGGACTAAATTGAAAAAA
29981 TATTAAATTT
Statistics
Matches: 122, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
149 1 0.01
150 48 0.39
151 62 0.51
152 11 0.09
ACGTcount: A:0.45, C:0.07, G:0.20, T:0.28
Consensus pattern (151 bp):
GTTATCAAAATGAAGAATTGAAGATACATAGGTATTCTAAAATGGTTTAGGAGCAATGGCTCAAA
TTTGGTAAAAAAAAGACTTAAAATGAACACGGAATTGAAGCAATAAGAAATCATACAAAGTTGAA
GGACTAAATTGAAAAAAATTT
Found at i:36921 original size:12 final size:10
Alignment explanation
Indices: 36893--36917 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
36883 GGAACAACTA
36893 TTTTTATATT
1 TTTTTATATT
36903 TTTTTATATT
1 TTTTTATATT
36913 TTTTT
1 TTTTT
36918 TTATGAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTATATT
Found at i:44784 original size:23 final size:25
Alignment explanation
Indices: 44740--44785 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
44730 ACGAAGGATT
*
44740 AACTTGTGTGATTGTATTTAAAAAA
1 AACTTGTGTGATTGTATATAAAAAA
44765 AACTTGTGTGATTG-A-ATAAAA
1 AACTTGTGTGATTGTATATAAAA
44786 TTCAGTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 1 0.05
25 14 0.70
ACGTcount: A:0.41, C:0.04, G:0.17, T:0.37
Consensus pattern (25 bp):
AACTTGTGTGATTGTATATAAAAAA
Found at i:47273 original size:30 final size:30
Alignment explanation
Indices: 47237--47308 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 30
47227 CCTGCAGGAC
47237 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
47267 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
47297 CTGTCCATAGGT
1 CTATCCAGAGGT
47309 TCCGAAGAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:47333 original size:31 final size:30
Alignment explanation
Indices: 47292--47419 Score: 116
Period size: 31 Copynumber: 4.1 Consensus size: 30
47282 AAAGATCCTC
*
47292 GGTAACTGTCCATAGGTTCCGAAGAACCTA
1 GGTAACTGTCCATAGGTTCCGAAGAACATA
* **
47322 GGTGAACTGTCCATATGTTCCTTAGAACATA
1 GGT-AACTGTCCATAGGTTCCGAAGAACATA
*
47353 GGTATACTGTCCATATG-TCTCGAA-AGACATA
1 GGTA-ACTGTCCATAGGTTC-CGAAGA-ACATA
* * *
47384 GGTAATTATGTCCATATGTTCCGTAGAACATA
1 GGTAA--CTGTCCATAGGTTCCGAAGAACATA
47416 GGTA
1 GGTA
47420 TCCTCGACTC
Statistics
Matches: 82, Mismatches: 8, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
30 8 0.10
31 49 0.60
32 22 0.27
33 3 0.04
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (30 bp):
GGTAACTGTCCATAGGTTCCGAAGAACATA
Found at i:48722 original size:21 final size:21
Alignment explanation
Indices: 48696--48739 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
48686 ATTTTATTCG
* *
48696 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
48717 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
48738 CT
1 CT
48740 AGCCCAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Done.