Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002270.1 Hibiscus syriacus cultivar Beakdansim tig00004616_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: 96160
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Found at i:73 original size:21 final size:21
Alignment explanation
Indices: 47--148 Score: 159
Period size: 21 Copynumber: 4.9 Consensus size: 21
37 TCCAAAATCA
*
47 TTGCGATAGCACTGTTCACAG
1 TTGCGATAGCACTGTTCACCG
68 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
**
89 TTGCGATAATACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
**
110 TTGCGATAATACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
131 TTGCGATAGCACTGTTCA
1 TTGCGATAGCACTGTTCA
149 AATTTTCTTT
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 76 1.00
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.31
Consensus pattern (21 bp):
TTGCGATAGCACTGTTCACCG
Found at i:276 original size:13 final size:14
Alignment explanation
Indices: 250--278 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
240 AATAATTTAG
250 AATTTTATTTATTT
1 AATTTTATTTATTT
264 AATTTTA-TTATTT
1 AATTTTATTTATTT
277 AA
1 AA
279 AATTTATAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
AATTTTATTTATTT
Found at i:855 original size:22 final size:22
Alignment explanation
Indices: 827--870 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
817 ACATACTATC
827 GCAAATTCGCAATGTGAACAGT
1 GCAAATTCGCAATGTGAACAGT
849 GCAAATTCGCAATGTGAACAGT
1 GCAAATTCGCAATGTGAACAGT
871 ATCGCCAACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (22 bp):
GCAAATTCGCAATGTGAACAGT
Found at i:902 original size:21 final size:21
Alignment explanation
Indices: 870--963 Score: 154
Period size: 21 Copynumber: 4.5 Consensus size: 21
860 ATGTGAACAG
*
870 TATCGCCAACGGTGATCAGTGC
1 TATCG-CAACGGTGAACAGTGC
892 TATCGCAACGGTG-ACAGTGC
1 TATCGCAACGGTGAACAGTGC
*
912 TATCGCAACGGTGAACAGTGT
1 TATCGCAACGGTGAACAGTGC
933 TATCGCAACGGTGAACAGTGC
1 TATCGCAACGGTGAACAGTGC
954 TATCGCAACG
1 TATCGCAACG
964 CGAATTCGGA
Statistics
Matches: 68, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
20 19 0.28
21 44 0.65
22 5 0.07
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.21
Consensus pattern (21 bp):
TATCGCAACGGTGAACAGTGC
Found at i:921 original size:41 final size:42
Alignment explanation
Indices: 870--963 Score: 154
Period size: 41 Copynumber: 2.2 Consensus size: 42
860 ATGTGAACAG
*
870 TATCGCCAACGGTGATCAGTGCTATCGCAACGGTG-ACAGTGC
1 TATCG-CAACGGTGAACAGTGCTATCGCAACGGTGAACAGTGC
*
912 TATCGCAACGGTGAACAGTGTTATCGCAACGGTGAACAGTGC
1 TATCGCAACGGTGAACAGTGCTATCGCAACGGTGAACAGTGC
954 TATCGCAACG
1 TATCGCAACG
964 CGAATTCGGA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
41 27 0.55
42 22 0.45
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.21
Consensus pattern (42 bp):
TATCGCAACGGTGAACAGTGCTATCGCAACGGTGAACAGTGC
Found at i:1486 original size:19 final size:19
Alignment explanation
Indices: 1428--1487 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
1418 TATTTCATGA
*
1428 TTTTCTTTGATTTATTT-CT
1 TTTTCTTTGA-TTATTTATT
**
1447 TTTTCTATTTTTTATTCTATT
1 TTTTCT-TTGATTATT-TATT
1468 TTTTCTTTGATTATTTATT
1 TTTTCTTTGATTATTTATT
1487 T
1 T
1488 ATTTATTTCT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
19 16 0.48
20 10 0.30
21 7 0.21
ACGTcount: A:0.13, C:0.08, G:0.03, T:0.75
Consensus pattern (19 bp):
TTTTCTTTGATTATTTATT
Found at i:1508 original size:24 final size:23
Alignment explanation
Indices: 1437--1511 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 23
1427 ATTTTCTTTG
* *
1437 ATTTATTTCTTT-TTCTATTTTTT
1 ATTTATTTATTTCTTTTA-TTTTT
*
1460 ATTCTATTT-TTTCTTTGATTATTT
1 ATT-TATTTATTTCTTTTATT-TTT
1484 ATTTATTTATTTCTTGTTATTTTT
1 ATTTATTTATTTCTT-TTATTTTT
1508 ATTT
1 ATTT
1512 TTCTTATTGT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
23 13 0.30
24 27 0.61
25 4 0.09
ACGTcount: A:0.16, C:0.07, G:0.03, T:0.75
Consensus pattern (23 bp):
ATTTATTTATTTCTTTTATTTTT
Found at i:1510 original size:16 final size:16
Alignment explanation
Indices: 1489--1526 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1479 TATTTATTTA
*
1489 TTTATTTCTTGTTATT-
1 TTTATTT-TTCTTATTG
1505 TTTATTTTTCTTATTG
1 TTTATTTTTCTTATTG
1521 TTTATT
1 TTTATT
1527 CTTATGCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.13, C:0.05, G:0.05, T:0.76
Consensus pattern (16 bp):
TTTATTTTTCTTATTG
Found at i:2507 original size:36 final size:36
Alignment explanation
Indices: 2451--2519 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
2441 GTTTGAAATT
*
2451 AGCATGTGGGATAGAGATCATGTTCGGGTAGGAATA
1 AGCATGTGGGATAGAGATCATGTGCGGGTAGGAATA
* *
2487 AGCATGTGAGG-TAGATATCATGTGGGGGTAGGA
1 AGCATGTG-GGATAGAGATCATGTGCGGGTAGGA
2520 TTTTCATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
36 27 0.93
37 2 0.07
ACGTcount: A:0.29, C:0.07, G:0.39, T:0.25
Consensus pattern (36 bp):
AGCATGTGGGATAGAGATCATGTGCGGGTAGGAATA
Found at i:4256 original size:96 final size:96
Alignment explanation
Indices: 4082--4341 Score: 362
Period size: 96 Copynumber: 2.7 Consensus size: 96
4072 AGATTATAAT
* * * *
4082 ATTATATATATACAATAAAGCTTGAGCTGTTCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTA
1 ATTATATATATACAATAAAACTTGAGATGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTA
4147 TGGATAAGATTCAGCTAGCCTGATAAAAGGTG
66 TGGATAAGATTCAGCTAGCCTGAT-AAAGGTG
* * * *
4179 ATTATA-ATGTACAATAAAACTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCTGGCTTTA
1 ATTATATATATACAATAAAACTTGAGATGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTA
* *
4243 TGGATAATATTCAGCTAGCTTGATAAAGGTG
66 TGGATAAGATTCAGCTAGCCTGATAAAGGTG
*
4274 ATTATAATATCTATACAATAATA-TTGAGATGTCCCTCTAGAGCAATTGGTTAAAACGCCCCGAC
1 ATTAT-ATA--TATACAATAAAACTTGAGATGTCCCTCTAGAGCAATTGGTT-AAACGCCCCGAC
4338 TTTA
62 TTTA
4342 GATCCAGCTA
Statistics
Matches: 144, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
95 12 0.08
96 74 0.51
97 7 0.05
98 27 0.19
99 24 0.17
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (96 bp):
ATTATATATATACAATAAAACTTGAGATGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTA
TGGATAAGATTCAGCTAGCCTGATAAAGGTG
Found at i:5622 original size:35 final size:33
Alignment explanation
Indices: 5582--5699 Score: 103
Period size: 35 Copynumber: 3.4 Consensus size: 33
5572 TTGTCTCGCT
5582 TGAGACTAATTTACTC-AAACAAAGTTTTATCTCTC
1 TGAGAC-AATTT-CTCTAAACAAA-TTTTATCTCTC
* *
5617 TGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTC
1 TGAGACAATTTCTC-T-AAACAAATTTTATCTCTC
* * *
5652 TGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTC
1 TGAGACAATTTCTC-T-AAACAAATTTTATCTCTC
*
5687 TTGAGACAGTTTC
1 -TGAGACAATTTC
5700 CCTTGAAACA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
33 3 0.04
34 4 0.05
35 50 0.66
36 19 0.25
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (33 bp):
TGAGACAATTTCTCTAAACAAATTTTATCTCTC
Found at i:5639 original size:36 final size:35
Alignment explanation
Indices: 5598--6035 Score: 338
Period size: 36 Copynumber: 12.5 Consensus size: 35
5588 TAATTTACTC
*
5598 AAACAAAGTTTTATCTCTCTGAGACAGTTTCTCTTG
1 AAACAAA-TTTTGTCTCTCTGAGACAGTTTCTCTTG
*
5634 AAACAAATTTTGTCTCTCTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTGAGACAGTTTCTCTTG
*
5669 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTC-TGAGACAGTTTCTCTTG
* *
5705 AAACAAA----ATCT-T-TGA-ATCTATTTTC-CTT-
1 AAACAAATTTTGTCTCTCTGAGA-C-AGTTTCTCTTG
* * * *
5733 AAACTAATTTCGTCTCCTTTGAGACAGTTTCTTTTG
1 AAACAAATTTTGTCT-CTCTGAGACAGTTTCTCTTG
* *
5769 GAACTAAATTTTCGTCTCCCTTGAGACAGTTTCAT-TTG
1 AAAC-AAATTTT-GTCTCTC-TGAGACAGTTTC-TCTTG
*
5807 AAACAAA-TTCGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAATTTTGTCTCTC-TGAGACAGTTTCTCTTG
* *
5842 AAACGAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTC-TGAGACAGTTTCTCTTG
* * *
5878 AAACAAA----ATAT-T-TGA-ACATGTTT-TCCTTA
1 AAACAAATTTTGTCTCTCTGAGACA-GTTTCT-CTTG
** * * *
5907 AAATTAATTTCGTCTCCCTGGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCT-GAGACAGTTTCTCTTG
* **
5943 AAACTAAGTTTTGTCTCTCTTGAGATTGTTTCTCTTG
1 AAAC-AAATTTTGTCTCTC-TGAGACAGTTTCTCTTG
* *
5980 AAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTC-TGAGACAGTTTCTCTTG
6016 AAACAAAATTTTGTCTCTCT
1 AAAC-AAATTTTGTCTCTCT
6036 TGAAACACCA
Statistics
Matches: 324, Mismatches: 45, Indels: 66
0.74 0.10 0.15
Matches are distributed among these distances:
28 10 0.03
29 22 0.07
30 5 0.02
31 2 0.01
32 8 0.02
33 2 0.01
34 7 0.02
35 79 0.24
36 113 0.35
37 52 0.16
38 23 0.07
39 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (35 bp):
AAACAAATTTTGTCTCTCTGAGACAGTTTCTCTTG
Found at i:5652 original size:21 final size:21
Alignment explanation
Indices: 5627--5690 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
5617 TGAGACAGTT
5627 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
* *
5648 TCTC-TGAGAC--A-GTT-TC
1 TCTCTTGAAACAAATTTTGTC
5664 -C-CTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
5683 TCTCTTGA
1 TCTCTTGA
5691 GACAGTTTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 14
0.64 0.08 0.28
Matches are distributed among these distances:
14 1 0.03
15 6 0.19
16 2 0.06
17 3 0.09
18 3 0.09
19 2 0.06
20 6 0.19
21 9 0.28
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTGTC
Found at i:5783 original size:38 final size:37
Alignment explanation
Indices: 5740--5884 Score: 181
Period size: 35 Copynumber: 4.0 Consensus size: 37
5730 CTTAAACTAA
*
5740 TTTCGTCTC-CTTTGAGACAGTTTCTTTTGGAACTAAAT
1 TTTCGTCTCTC-TTGAGACAGTTTCTTTTGAAAC-AAAT
* *
5778 TTTCGTCTCCCTTGAGACAGTTTCATTTGAAACAAA-
1 TTTCGTCTCTCTTGAGACAGTTTCTTTTGAAACAAAT
* *
5814 -TTCGTCTCTCTTGAGACAGTTTCTCTTGAAACGAAT
1 TTTCGTCTCTCTTGAGACAGTTTCTTTTGAAACAAAT
**
5850 TTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTCGTCTCTCTTGAGACAGTTTCTTTTGAAACAAA
5885 ATATTTGAAC
Statistics
Matches: 96, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
35 31 0.32
36 30 0.31
37 5 0.05
38 29 0.30
39 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.39
Consensus pattern (37 bp):
TTTCGTCTCTCTTGAGACAGTTTCTTTTGAAACAAAT
Found at i:5906 original size:173 final size:175
Alignment explanation
Indices: 5611--6183 Score: 726
Period size: 173 Copynumber: 3.4 Consensus size: 175
5601 CAAAGTTTTA
5611 TCTCTC-TGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTC-TGAGACAGTTTCCCTTGAAACA
1 TCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
* *
5674 AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATC-TATTTTCCTT-AAAC
66 AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAA-CATGTTTTCCTTAAAAC
* * *
5737 TAATTTCGTCTCCTTTGAGACAGTTTCTTTTGGAACTAAATTTTCG
130 TAATTTCGTCTCCCTTGAGACAGTTTCATTTGAAACTAAATTTTCG
* * *
5783 TCTCCCTTGAGACAGTTTCAT-TTGAAACAAA-TTCGTCTCTCTTGAGACAGTTTCTCTTGAAAC
1 TCTCTCTTGAGACAGTTTC-TCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
* *
5846 GAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAACATGTTTTCCTTAAAAT
65 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAACATGTTTTCCTTAAAAC
* ** *
5911 TAATTTCGTCTCCCTGGAGACAGTTTCCCTTGAAACTAAGTTTT-G
130 TAATTTCGTCTCCCTTGAGACAGTTTCATTTGAAACTAAATTTTCG
** *
5956 TCTCTCTTGAGATTGTTTCTCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACA
1 TCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-
* *
6021 AAATTTTGTCTCTCTTGA-A-A------C-----AC-CAATATTTGAATATG-TTTCTCTTAAAA
65 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAACATGTTTTC-CTTAAAA
* *
6071 CAAAATTTTGTCTCCCTTGAGACAGTTTCATTTGAAAC-AAA-TTTCG
129 C-TAATTTCGTCTCCCTTGAGACAGTTTCATTTGAAACTAAATTTTCG
* *
6117 TCTCTCTTGAGACAATTTCTCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
1 TCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
6182 AA
66 AA
6184 ATATTTGAAC
Statistics
Matches: 356, Mismatches: 34, Indels: 34
0.84 0.08 0.08
Matches are distributed among these distances:
160 10 0.03
161 82 0.23
162 33 0.09
167 1 0.00
172 16 0.04
173 125 0.35
174 72 0.20
175 17 0.05
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (175 bp):
TCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAACATGTTTTCCTTAAAACT
AATTTCGTCTCCCTTGAGACAGTTTCATTTGAAACTAAATTTTCG
Found at i:5959 original size:37 final size:36
Alignment explanation
Indices: 5912--6038 Score: 164
Period size: 37 Copynumber: 3.5 Consensus size: 36
5902 CCTTAAAATT
* * *
5912 AATTTCGTCTCCCTGGAGACAGTTTCCCTTGAAACTA
1 AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-A
* ** *
5949 AGTTTTGTCTCTCTTGAGATTGTTTCTCTTGAAACA
1 AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
*
5985 AATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAA
1 AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-A
6022 AATTTTGTCTCTCTTGA
1 AATTTTGTCTCTCTTGA
6039 AACACCAATA
Statistics
Matches: 76, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
36 31 0.41
37 45 0.59
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (36 bp):
AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
Found at i:5998 original size:138 final size:135
Alignment explanation
Indices: 5778--6028 Score: 394
Period size: 138 Copynumber: 1.8 Consensus size: 135
5768 GGAACTAAAT
* *
5778 TTTCGTCTCCCTTGAGACAGTTTCATTTGAAACAAATTCGTCTCTCTTGAGACAGTTTCTCTTGA
1 TTTCGTCTCCCTGGAGACAGTTTCACTTGAAACAAATTCGTCTCTCTTGAGACAGTTTCTCTTGA
* *
5843 AACGAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAACATGTTTTCCTTAA
66 AACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT-TTTGAACATGTTTTCCTTAA
5908 AATTAA
130 AATTAA
* * * **
5914 TTTCGTCTCCCTGGAGACAGTTTCCCTTGAAACTAAGTTTTGTCTCTCTTGAGATTGTTTCTCTT
1 TTTCGTCTCCCTGGAGACAGTTTCACTTGAAAC-AA-ATTCGTCTCTCTTGAGACAGTTTCTCTT
5979 GAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTG
64 GAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTG
6029 TCTCTCTTGA
Statistics
Matches: 104, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
136 30 0.29
137 6 0.06
138 68 0.65
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (135 bp):
TTTCGTCTCCCTGGAGACAGTTTCACTTGAAACAAATTCGTCTCTCTTGAGACAGTTTCTCTTGA
AACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGAACATGTTTTCCTTAAA
ATTAA
Found at i:6120 original size:36 final size:35
Alignment explanation
Indices: 6058--6335 Score: 187
Period size: 36 Copynumber: 7.9 Consensus size: 35
6048 ATTTGAATAT
* *
6058 GTTTCTCTTAAAACAAAATTTTGTCTCCCTTGAGACA
1 GTTTCT-TTGAAAC-AAATTTTGTCTCTCTTGAGACA
*
6095 GTTTCATTTGAAACAAATTTCGTCTCTCTTGAGACA
1 GTTTC-TTTGAAACAAATTTTGTCTCTCTTGAGACA
* *
6131 ATTTCTCTTGAAACGAATTTTGTCTCTCTTGAGACA
1 GTTTCT-TTGAAACAAATTTTGTCTCTCTTGAGACA
* * *
6167 GTTTCCCTTGAAACAAA------ATAT-TTGA-ACA
1 GTTT-CTTTGAAACAAATTTTGTCTCTCTTGAGACA
* * ** * * *
6195 TGTTTTCCTTAAAATTAATTTCGTCTCCCTGGAGACA
1 -G-TTTCTTTGAAACAAATTTTGTCTCTCTTGAGACA
* * * **
6232 GTTTCCCTTGAAACTAAGTTTGTCTCTCTTGAGATT
1 GTTT-CTTTGAAACAAATTTTGTCTCTCTTGAGACA
* *
6268 GTTTCTCTTGAAACAAAATTTATCTCTCTT-AGACA
1 GTTTCT-TTGAAACAAATTTTGTCTCTCTTGAGACA
*
6303 GTTTCCCTTGAAACAAAATTTTGTCTCTCTTGA
1 GTTT-CTTTGAAAC-AAATTTTGTCTCTCTTGA
6336 AACACCAATA
Statistics
Matches: 188, Mismatches: 35, Indels: 36
0.73 0.14 0.14
Matches are distributed among these distances:
28 3 0.02
29 14 0.07
30 5 0.03
35 20 0.11
36 129 0.69
37 16 0.09
38 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (35 bp):
GTTTCTTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:6124 original size:161 final size:161
Alignment explanation
Indices: 5874--6190 Score: 451
Period size: 161 Copynumber: 2.0 Consensus size: 161
5864 GACAGTTTCC
** *
5874 CTTGAAACAAAATATTTGAACATGTTTTCCTTAAAATTAATTTCGTCTCCCTGGAGACAGTTTCC
1 CTTGAAACAAAATATTTGAACATGTTTTCCTTAAAAAAAATTTCGTCTCCCTGGAGACAGTTTCA
* * ***
5939 CTTGAAACTAAGTTTTGTCTCTCTTGAGATTGTTTCTCTTGAAACAAATTTTATCTCTCTTGAGA
66 CTTGAAACTAAATTTCGTCTCTCTTGAGACAATTTCTCTTGAAACAAATTTTATCTCTCTTGAGA
6004 CAGTTTCCCTTGAAACAAAAT-TTTGTCTCT
131 CAGTTTCCCTTGAAACAAAATATTTGTCTCT
* * * *
6034 CTTGAAACACCAATATTTGAATATG-TTTCTCTTAAAACAAAATTTTGTCTCCCTTGAGACAGTT
1 CTTGAAACA-AAATATTTGAACATGTTTTC-CTTAAAA-AAAATTTCGTCTCCCTGGAGACAGTT
* * *
6098 TCATTTGAAAC-AAATTTCGTCTCTCTTGAGACAATTTCTCTTGAAACGAATTTTGTCTCTCTTG
63 TCACTTGAAACTAAATTTCGTCTCTCTTGAGACAATTTCTCTTGAAACAAATTTTATCTCTCTTG
6162 AGACAGTTTCCCTTGAAACAAAATATTTG
128 AGACAGTTTCCCTTGAAACAAAATATTTG
6191 AACATGTTTT
Statistics
Matches: 138, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
160 13 0.09
161 90 0.65
162 35 0.25
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.39
Consensus pattern (161 bp):
CTTGAAACAAAATATTTGAACATGTTTTCCTTAAAAAAAATTTCGTCTCCCTGGAGACAGTTTCA
CTTGAAACTAAATTTCGTCTCTCTTGAGACAATTTCTCTTGAAACAAATTTTATCTCTCTTGAGA
CAGTTTCCCTTGAAACAAAATATTTGTCTCT
Found at i:6142 original size:88 final size:87
Alignment explanation
Indices: 5958--6126 Score: 225
Period size: 88 Copynumber: 1.9 Consensus size: 87
5948 AAGTTTTGTC
* * *
5958 TCTCTTGAGATTGTTTCTCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TCTCTTGA-ATTGTTTCTCTTAAAACAAATTTTATCTCCCTTGAGACAGTTTCACTTGAAACAAA
*
6023 ATTTTGTCTCTCTTGAAACACCAA
65 ATTTCGTCTCTCTTGAAACA-CAA
* * *
6047 TAT-TTGAATATGTTTCTCTTAAAACAAAATTTTGTCTCCCTTGAGACAGTTTCATTTGAAAC-A
1 TCTCTTGAAT-TGTTTCTCTTAAAAC-AAATTTTATCTCCCTTGAGACAGTTTCACTTGAAACAA
6110 AATTTCGTCTCTCTTGA
64 AATTTCGTCTCTCTTGA
6127 GACAATTTCT
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
87 2 0.03
88 35 0.49
89 34 0.48
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (87 bp):
TCTCTTGAATTGTTTCTCTTAAAACAAATTTTATCTCCCTTGAGACAGTTTCACTTGAAACAAAA
TTTCGTCTCTCTTGAAACACAA
Found at i:6215 original size:299 final size:297
Alignment explanation
Indices: 5618--6404 Score: 1185
Period size: 299 Copynumber: 2.6 Consensus size: 297
5608 TTATCTCTCT
* * ** * *
5618 GAGACAGTTTCTCTTGAAAC-AAATTTTGTCTCTC-TGAGACAGTTTCCCTTGAAACAAATTTTG
1 GAGACAGTTTCCCTTGAAACTAAGTTTTGTCTCTCTTGAGATTGTTTCTCTTGAAACAAATTTTA
* *
5681 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTATTTTCCTT-AAACTAATTTCG
66 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT-TTTG--TC---TCT-CTTGAAAC--A---CC
** * * * * *
5745 TCTCCTTTGAGACA-GTTTCTTTTGGAACTAAATTTTCGTCTCCCTTGAGACAGTTTCATTTGAA
119 AAT-ATTTGA-ATATGTTTCTCTT-AAACAAAATTTT-GTCTCCCTTGAGACAGTTTCATTTGAA
*
5809 ACAAATTCGTCTCTCTTGAGACAGTTTCTCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCC
180 ACAAATTCGTCTCTCTTGAGACAATTTCTCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCC
5874 CTTGAAACAAAATATTTGAACATGTTTTCCTTAAAATTAATTTCGTCTCCCTG
245 CTTGAAACAAAATATTTGAACATGTTTTCCTTAAAATTAATTTCGTCTCCCTG
5927 GAGACAGTTTCCCTTGAAACTAAGTTTTGTCTCTCTTGAGATTGTTTCTCTTGAAACAAATTTTA
1 GAGACAGTTTCCCTTGAAACTAAGTTTTGTCTCTCTTGAGATTGTTTCTCTTGAAACAAATTTTA
5992 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAAACACCAATATTTGAATA
66 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAAACACCAATATTTGAATA
6057 TGTTTCTCTTAAAACAAAATTTTGTCTCCCTTGAGACAGTTTCATTTGAAACAAATTTCGTCTCT
131 TGTTTCTCTT-AAACAAAATTTTGTCTCCCTTGAGACAGTTTCATTTGAAACAAA-TTCGTCTCT
6122 CTTGAGACAATTTCTCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATA
194 CTTGAGACAATTTCTCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATA
6187 TTTGAACATGTTTTCCTTAAAATTAATTTCGTCTCCCTG
259 TTTGAACATGTTTTCCTTAAAATTAATTTCGTCTCCCTG
*
6226 GAGACAGTTTCCCTTGAAACTAAG-TTTGTCTCTCTTGAGATTGTTTCTCTTGAAACAAAATTTA
1 GAGACAGTTTCCCTTGAAACTAAGTTTTGTCTCTCTTGAGATTGTTTCTCTTGAAACAAATTTTA
6290 TCTCTCTT-AGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAAACACCAATA-TTGAATA
66 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAAACACCAATATTTGAATA
*
6353 TGTTTCTCTTAAACAAAATTTTGTCTCCCTGGAGACAGTTTC-TCTTGAAACA
131 TGTTTCTCTTAAACAAAATTTTGTCTCCCTTGAGACAGTTTCAT-TTGAAACA
6405 CAAAAAACCT
Statistics
Matches: 453, Mismatches: 19, Indels: 26
0.91 0.04 0.05
Matches are distributed among these distances:
294 1 0.00
295 39 0.09
296 17 0.04
297 48 0.11
298 81 0.18
299 159 0.35
300 2 0.00
303 1 0.00
304 3 0.01
305 6 0.01
308 2 0.00
309 19 0.04
310 17 0.04
311 58 0.13
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (297 bp):
GAGACAGTTTCCCTTGAAACTAAGTTTTGTCTCTCTTGAGATTGTTTCTCTTGAAACAAATTTTA
TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAAACACCAATATTTGAATA
TGTTTCTCTTAAACAAAATTTTGTCTCCCTTGAGACAGTTTCATTTGAAACAAATTCGTCTCTCT
TGAGACAATTTCTCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATT
TGAACATGTTTTCCTTAAAATTAATTTCGTCTCCCTG
Found at i:6235 original size:137 final size:137
Alignment explanation
Indices: 6034--6325 Score: 385
Period size: 137 Copynumber: 2.1 Consensus size: 137
6024 TTTTGTCTCT
* * * *
6034 CTTGAAACACCAATATTTGAATATGTTTCTCTTAAAACAAAATTTTGTCTCCCTTGAGACAGTTT
1 CTTGAAACA-AAATATTTGAACATGTTTCTCTTAAAACAAAATTTCGTCTCCCTGGAGACAGTTT
* * * *
6099 CATTTGAAAC-AAATTTCGTCTCTCTTGAGACAATTTCTCTTGAAACGAATTTTGTCTCTCTTGA
65 CACTTGAAACTAAATTT-GTCTCTCTTGAGACAATTTCTCTTGAAACAAAATTTATCTCTCTT-A
6163 GACAGTTTCC
128 GACAGTTTCC
**
6173 CTTGAAACAAAATATTTGAACATGTTT-TCCTTAAAA-TTAATTTCGTCTCCCTGGAGACAGTTT
1 CTTGAAACAAAATATTTGAACATGTTTCT-CTTAAAACAAAATTTCGTCTCCCTGGAGACAGTTT
* * ***
6236 CCCTTGAAACTAAGTTTGTCTCTCTTGAGATTGTTTCTCTTGAAACAAAATTTATCTCTCTTAGA
65 CACTTGAAACTAAATTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAATTTATCTCTCTTAGA
6301 CAGTTTCC
130 CAGTTTCC
6309 CTTGAAACAAAAT-TTTG
1 CTTGAAACAAAATATTTG
6326 TCTCTCTTGA
Statistics
Matches: 136, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
135 4 0.03
136 24 0.18
137 71 0.52
138 28 0.21
139 9 0.07
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (137 bp):
CTTGAAACAAAATATTTGAACATGTTTCTCTTAAAACAAAATTTCGTCTCCCTGGAGACAGTTTC
ACTTGAAACTAAATTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAATTTATCTCTCTTAGAC
AGTTTCC
Found at i:6442 original size:30 final size:33
Alignment explanation
Indices: 6391--6472 Score: 109
Period size: 30 Copynumber: 2.5 Consensus size: 33
6381 CTGGAGACAG
6391 TTTCTCTTGAAACACAAAAAACCTTTGAAATCA
1 TTTCTCTTGAAACACAAAAAACCTTTGAAATCA
*
6424 TTTCTCTTG-AA-A-AAAAAACCTTTGAAAAAT-G
1 TTTCTCTTGAAACACAAAAAACCTTTG--AAATCA
6455 TTTCTCTTGAAACACAAA
1 TTTCTCTTGAAACACAAA
6473 GACCTTCGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
30 12 0.28
31 10 0.23
32 8 0.19
33 10 0.23
34 3 0.07
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (33 bp):
TTTCTCTTGAAACACAAAAAACCTTTGAAATCA
Found at i:6459 original size:31 final size:31
Alignment explanation
Indices: 6390--6478 Score: 101
Period size: 33 Copynumber: 2.8 Consensus size: 31
6380 CCTGGAGACA
6390 GTTTCTCTTGAAACACAAAAAACCTTTGAAATC
1 GTTTCTCTTG-AA-ACAAAAAACCTTTGAAATC
*
6423 ATTTCTCTTGAAA-AAAAAACCTTTGAAAAAT-
1 GTTTCTCTTGAAACAAAAAACCTTTG--AAATC
*
6454 GTTTCTCTTGAAACACAAAGACCTT
1 GTTTCTCTTGAAACA-AAAAACCTT
6479 CGAGTTTGAT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
30 12 0.24
31 13 0.27
32 7 0.14
33 17 0.35
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.31
Consensus pattern (31 bp):
GTTTCTCTTGAAACAAAAAACCTTTGAAATC
Found at i:7746 original size:184 final size:181
Alignment explanation
Indices: 7459--7814 Score: 549
Period size: 186 Copynumber: 2.0 Consensus size: 181
7449 ATAATTCAAA
* *
7459 AAAAATAGTTTATAATTAATTTAAATATATATATAAAATAAAAATTTATATAAATTTTTTAATTA
1 AAAAATAATTTACAATTAATTTAAATATATATATAAAATAAAAATTTATATAAATTTTTTAATTA
7524 ATTAATATTAATTTAGGTTTTAAAAGTTATTAGATCTTAAA-T-TTAATTAAGTTTTAAATGATT
66 ATTAATATTAATTTAGGTTTTAAAAGTTATTAGATCTTAAATTATTAATTAAGTTTTAAATGATT
*
7587 TGGA-CTGAGCTCATATGTTATATATAATATATTTAAAATTTTTTAATTTAG
131 T-GATCTGAGCCCATATGTTATATATAATATATTTAAAATTTTTTAATTTAG
*
7638 AAAAATAATTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTTATATAATTTTTT
1 AAAAATAATTTACAATTAATTT--A-AATATAT-A-TATAAAATAAAAA-TTTATATAAATTTTT
* * *
7703 TAATTAATTAATATTGATTTAGG-TTTAAAAGTTATTGGATCTTAAATTATTAATTGAGTTTTAA
60 TAATTAATTAATATTAATTTAGGTTTTAAAAGTTATTAGATCTTAAATTATTAATTAAGTTTTAA
*
7767 ATGGTTTGATCTGAGCCCATATGTTATATATAATATATTTAAAATTTT
125 ATGATTTGATCTGAGCCCATATGTTATATATAATATATTTAAAATTTT
7815 ATTTAAGATA
Statistics
Matches: 160, Mismatches: 8, Indels: 11
0.89 0.04 0.06
Matches are distributed among these distances:
179 20 0.12
181 1 0.01
182 7 0.04
183 1 0.01
184 35 0.22
185 39 0.24
186 57 0.36
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.47
Consensus pattern (181 bp):
AAAAATAATTTACAATTAATTTAAATATATATATAAAATAAAAATTTATATAAATTTTTTAATTA
ATTAATATTAATTTAGGTTTTAAAAGTTATTAGATCTTAAATTATTAATTAAGTTTTAAATGATT
TGATCTGAGCCCATATGTTATATATAATATATTTAAAATTTTTTAATTTAG
Found at i:13082 original size:38 final size:38
Alignment explanation
Indices: 13047--13120 Score: 123
Period size: 38 Copynumber: 1.9 Consensus size: 38
13037 TATAAGCTAT
*
13047 TTTATCGACT-TGTTCGTTTATGTTCATGAACAAGCTCA
1 TTTATCGACTCT-TTCATTTATGTTCATGAACAAGCTCA
13085 TTTATCGACTCTTTCATTTATGTTCATGAACAAGCT
1 TTTATCGACTCTTTCATTTATGTTCATGAACAAGCT
13121 TGTTTGTAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 33 0.97
39 1 0.03
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (38 bp):
TTTATCGACTCTTTCATTTATGTTCATGAACAAGCTCA
Found at i:18511 original size:54 final size:54
Alignment explanation
Indices: 18432--18968 Score: 752
Period size: 54 Copynumber: 10.0 Consensus size: 54
18422 ATTAAGATGA
* * * * * *
18432 ACACGTAGTGCCTATACTGTCGTTCATCAACACATGATGAATTCTGTGAGTTGC
1 ACACATAGTGCCTGTACGGTTGTTCATCAACTCATGATGAATTCTGTGGGTTGC
* * * *
18486 ACACATAGTGCATGTATGGTTGTTCATCAACTCATGATGAATTTTGTGAGTTGC
1 ACACATAGTGCCTGTACGGTTGTTCATCAACTCATGATGAATTCTGTGGGTTGC
* *
18540 ACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGGTTGC
1 ACACATAGTGCCTGTACGGTTGTTCATCAACTCATGATGAATTCTGTGGGTTGC
* * *
18594 ACACATAGTGCCTGTACGGTTATTCATCAACTAATGATGAATTTTGTGGGTTGC
1 ACACATAGTGCCTGTACGGTTGTTCATCAACTCATGATGAATTCTGTGGGTTGC
* * * *
18648 ACACGTAGTGCCTGTACTGTTGTTCATCAACTCATGATGAATTCCGTGGGTTGT
1 ACACATAGTGCCTGTACGGTTGTTCATCAACTCATGATGAATTCTGTGGGTTGC
18702 ACACATAGTGCCTG-ACGGTTGTTCATCAACTCATGATGAATTCTGTGGGTTGC
1 ACACATAGTGCCTGTACGGTTGTTCATCAACTCATGATGAATTCTGTGGGTTGC
* * *
18755 ACACATAGTGCCTGTACGGTTGTTCATAAACTCATGATGAATTCCGTGAGTTGC
1 ACACATAGTGCCTGTACGGTTGTTCATCAACTCATGATGAATTCTGTGGGTTGC
* * * * * *
18809 ACACATAGTTCCTGTACGGTTTTTCATAAACTTATGATGAATTCCGTGAGTTGC
1 ACACATAGTGCCTGTACGGTTGTTCATCAACTCATGATGAATTCTGTGGGTTGC
* * **
18863 ACACATAGTGTCTGTACGGTTGTTCATCAACTCATGATGAAATCCATGGGTTGC
1 ACACATAGTGCCTGTACGGTTGTTCATCAACTCATGATGAATTCTGTGGGTTGC
* * *
18917 ACACATAGTGCATGTACAGTTGTTCATCAACACATGATGAATTCTGTGGGTT
1 ACACATAGTGCCTGTACGGTTGTTCATCAACTCATGATGAATTCTGTGGGTT
18969 TGAACACTTA
Statistics
Matches: 434, Mismatches: 48, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
53 50 0.12
54 384 0.88
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (54 bp):
ACACATAGTGCCTGTACGGTTGTTCATCAACTCATGATGAATTCTGTGGGTTGC
Found at i:18941 original size:269 final size:269
Alignment explanation
Indices: 18453--18968 Score: 798
Period size: 269 Copynumber: 1.9 Consensus size: 269
18443 CTATACTGTC
* *
18453 GTTCATCAACACATGATGAATTCTGTGAGTTGCACACATAGTGCATGTATGGTTGTTCATCAACT
1 GTTCATCAACACATGATGAATTCTGTGAGTTGCACACATAGTGCATGTACGGTTGTTCATAAACT
** * *
18518 CATGATGAATTTTGTGAGTTGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATT
66 CATGATGAATTCCGTGAGTTGCACACATAGTGCCTGTACGGTTATTCATAAACTCATGATGAATT
* * * ***
18583 CTGTGGGTTGCACACATAGTGCCTGTACGGTTATTCATCAACTAATGATGAATTTTGTGGGTTGC
131 CCGTGAGTTGCACACATAGTGCCTGTACGGTTATTCATCAACTAATGATGAAATCCATGGGTTGC
* * * *
18648 ACACGTAGTGCCTGTACTGTTGTTCATCAACTCATGATGAATTCCGTGGGTTGTACACATAGTGC
196 ACACATAGTGCATGTACAGTTGTTCATCAACACATGATGAATTCCGTGGGTTGTACACATAGTGC
18713 CTGACGGTT
261 CTGACGGTT
* * *
18722 GTTCATCAACTCATGATGAATTCTGTGGGTTGCACACATAGTGCCTGTACGGTTGTTCATAAACT
1 GTTCATCAACACATGATGAATTCTGTGAGTTGCACACATAGTGCATGTACGGTTGTTCATAAACT
* * *
18787 CATGATGAATTCCGTGAGTTGCACACATAGTTCCTGTACGGTTTTTCATAAACTTATGATGAATT
66 CATGATGAATTCCGTGAGTTGCACACATAGTGCCTGTACGGTTATTCATAAACTCATGATGAATT
* * *
18852 CCGTGAGTTGCACACATAGTGTCTGTACGGTTGTTCATCAACTCATGATGAAATCCATGGGTTGC
131 CCGTGAGTTGCACACATAGTGCCTGTACGGTTATTCATCAACTAATGATGAAATCCATGGGTTGC
*
18917 ACACATAGTGCATGTACAGTTGTTCATCAACACATGATGAATTCTGTGGGTT
196 ACACATAGTGCATGTACAGTTGTTCATCAACACATGATGAATTCCGTGGGTT
18969 TGAACACTTA
Statistics
Matches: 221, Mismatches: 26, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
269 221 1.00
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (269 bp):
GTTCATCAACACATGATGAATTCTGTGAGTTGCACACATAGTGCATGTACGGTTGTTCATAAACT
CATGATGAATTCCGTGAGTTGCACACATAGTGCCTGTACGGTTATTCATAAACTCATGATGAATT
CCGTGAGTTGCACACATAGTGCCTGTACGGTTATTCATCAACTAATGATGAAATCCATGGGTTGC
ACACATAGTGCATGTACAGTTGTTCATCAACACATGATGAATTCCGTGGGTTGTACACATAGTGC
CTGACGGTT
Found at i:21084 original size:2 final size:2
Alignment explanation
Indices: 21068--21124 Score: 89
Period size: 2 Copynumber: 29.0 Consensus size: 2
21058 AAGTGACTTA
* *
21068 AT AT AT GT AT GT 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 AT AT AT AT AT AT
21110 AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT
21125 TAATTGTAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
AT
Found at i:21879 original size:17 final size:17
Alignment explanation
Indices: 21853--21885 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
21843 CAATTTATCG
21853 TTTTAATTAAAATTAAT
1 TTTTAATTAAAATTAAT
*
21870 TTTTATTTAAAATTAA
1 TTTTAATTAAAATTAA
21886 AAAACATTTT
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTAATTAAAATTAAT
Found at i:23562 original size:6 final size:6
Alignment explanation
Indices: 23516--23544 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
23506 ATTAACACAT
23516 TTTGCA TTTGCA TTTGCA TTTGCA TTTGC
1 TTTGCA TTTGCA TTTGCA TTTGCA TTTGC
23545 CATCCACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.17, G:0.17, T:0.52
Consensus pattern (6 bp):
TTTGCA
Found at i:27848 original size:7 final size:7
Alignment explanation
Indices: 27838--27933 Score: 67
Period size: 7 Copynumber: 13.1 Consensus size: 7
27828 TGAAAAAATG
27838 AAAAGAA
1 AAAAGAA
27845 AAAAGAGA
1 AAAAGA-A
27853 AAAATGGAA
1 AAAA--GAA
27862 AATGATAGAA
1 AA--A-AGAA
*
27872 AAATG--
1 AAAAGAA
27877 AAAAGAA
1 AAAAGAA
27884 AAAATGAGA
1 AAAA-GA-A
27893 AAAATG--
1 AAAA-GAA
27899 AAAAG-A
1 AAAAGAA
27905 AAAAGAA
1 AAAAGAA
27912 AAAAGAA
1 AAAAGAA
27919 AAAAGAA
1 AAAAGAA
27926 AAAAGAA
1 AAAAGAA
27933 A
1 A
27934 GAGAAAGAGA
Statistics
Matches: 75, Mismatches: 2, Indels: 24
0.74 0.02 0.24
Matches are distributed among these distances:
5 5 0.07
6 9 0.12
7 34 0.45
8 8 0.11
9 10 0.13
10 7 0.09
11 1 0.01
12 1 0.01
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (7 bp):
AAAAGAA
Found at i:27881 original size:32 final size:31
Alignment explanation
Indices: 27845--27952 Score: 110
Period size: 32 Copynumber: 3.4 Consensus size: 31
27835 ATGAAAAGAA
*
27845 AAAAGAGAAAAATGGAAAATGATAGAAAAATG
1 AAAAGAGAAAAATGGAAAATGAAAGAAAAA-G
27877 AAAAGA-AAAAATGAGAAAAATGAAAAGAAAAAG
1 AAAAGAGAAAAATG-G-AAAATG-AAAGAAAAAG
* * * * *
27910 AAAAAAGAAAAAAGAAAAAAGAAAGAGAAAG
1 AAAAGAGAAAAATGGAAAATGAAAGAAAAAG
27941 AGAAAGAGAAAA
1 A-AAAGAGAAAA
27953 TAAAAGGGGG
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
31 17 0.27
32 21 0.33
33 12 0.19
34 14 0.22
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.06
Consensus pattern (31 bp):
AAAAGAGAAAAATGGAAAATGAAAGAAAAAG
Found at i:27884 original size:39 final size:35
Alignment explanation
Indices: 27830--27939 Score: 129
Period size: 39 Copynumber: 3.1 Consensus size: 35
27820 AGAAGAGATG
27830 AAAAAATGAAAAGAAAAAAGAGAAAAATGGAAAATGA
1 AAAAAATGAAAAGAAAAAAGAGAAAAAT-GAAAA-GA
27867 TAGAAAAATGAAAAGAAAAAATGAGAAAAATGAAAAGA
1 -A-AAAAATGAAAAGAAAAAA-GAGAAAAATGAAAAGA
27905 AAAAGAA--AAAAGAAAAAAGA-AAAAA-GAAAGAGA
1 AAAA-AATGAAAAGAAAAAAGAGAAAAATGAAA-AGA
27938 AA
1 AA
27940 GAGAAAGAGA
Statistics
Matches: 68, Mismatches: 0, Indels: 13
0.84 0.00 0.16
Matches are distributed among these distances:
32 4 0.06
33 10 0.15
34 2 0.03
35 11 0.16
36 3 0.04
37 3 0.04
38 3 0.04
39 23 0.34
40 9 0.13
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.06
Consensus pattern (35 bp):
AAAAAATGAAAAGAAAAAAGAGAAAAATGAAAAGA
Found at i:27914 original size:27 final size:25
Alignment explanation
Indices: 27884--27958 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
27874 ATGAAAAGAA
* *
27884 AAAATGAGAAAAATGAAAAGAAAAAG
1 AAAAAGAGAAAAAAGAAAA-AAAAAG
27910 AAAAA-AGAAAAAAGAAAAAAGAAAG
1 AAAAAGAGAAAAAAGAAAAAA-AAAG
* * *
27935 AGAAAGAG-AAAGAGAAAATAAAAG
1 AAAAAGAGAAAAAAGAAAAAAAAAG
27959 GGGGTTCAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
24 6 0.14
25 30 0.71
26 6 0.14
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (25 bp):
AAAAAGAGAAAAAAGAAAAAAAAAG
Found at i:28329 original size:27 final size:27
Alignment explanation
Indices: 28291--28343 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
28281 CACAATTTTG
28291 GAGATCCTTTTGACAGAAGCTACACTC
1 GAGATCCTTTTGACAGAAGCTACACTC
28318 GAGATCCTTTTGACAGAAGCTACACT
1 GAGATCCTTTTGACAGAAGCTACACT
28344 TGAGTCATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (27 bp):
GAGATCCTTTTGACAGAAGCTACACTC
Found at i:29305 original size:37 final size:36
Alignment explanation
Indices: 29249--29334 Score: 145
Period size: 37 Copynumber: 2.3 Consensus size: 36
29239 TTTGACCTTC
29249 GAAGCAAATCAAACTTAAGCCTTCACAGAAGAGTAGT
1 GAAGCAAATC-AACTTAAGCCTTCACAGAAGAGTAGT
*
29286 GAAGCAAATCATCTATAAGCCTTCACAGAAGAGTAGT
1 GAAGCAAATCAACT-TAAGCCTTCACAGAAGAGTAGT
29323 GAAGCAAATCAA
1 GAAGCAAATCAA
29335 GATTGTTCGA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
36 3 0.07
37 43 0.93
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (36 bp):
GAAGCAAATCAACTTAAGCCTTCACAGAAGAGTAGT
Found at i:29439 original size:55 final size:53
Alignment explanation
Indices: 29333--30013 Score: 498
Period size: 55 Copynumber: 12.6 Consensus size: 53
29323 GAAGCAAATC
* * * * * * **
29333 AAGATTGTTCGAGTTCTATACTCTCTGAAGGAACAAAGAGAGGACAAGTTTTATG
1 AAGATTGTTCGAGTTTTATACTCCCTGAAAGAA-TAGGAGCGGACCTGTTTTA-G
* * *
29388 AAGATTGTTCGAGTTATATACTCCCTGAACGAATAGGAAGCGGACCTGTTTTGCCG
1 AAGATTGTTCGAGTTTTATACTCCCTGAAAGAATAGG-AGCGGACCTGTTTT--AG
* * *
29444 AAGATTGTTCGAGTTTTGTACTCCCTGAATGAATAAGGAGCAGACCCAT-TTTTATG
1 AAGATTGTTCGAGTTTTATACTCCCTGAAAGAAT-AGGAGCGGA-CC-TGTTTTA-G
* * *
29500 AAGA-----C------TATACTCCCTGAAAGAATAGGGAGTGAACTCAT-TTTCAG
1 AAGATTGTTCGAGTTTTATACTCCCTGAAAGAATA-GGAGCGGAC-C-TGTTTTAG
* * *
29544 AAGATTGTTCGAGTTCTATACTCCCTGAAATAATAGGGAGCGGACCCAT-TTTTCG
1 AAGATTGTTCGAGTTTTATACTCCCTGAAAGAATA-GGAGCGGA-CC-TGTTTTAG
* * * * *
29599 AAGATTGTTCAAGTTCTATACTCCCTGAAAGAATAGGGAGTGAACCCGTTTTCAG
1 AAGATTGTTCGAGTTTTATACTCCCTGAAAGAATA-GGAGCGGACCTGTTTT-AG
* *
29654 AAGATTGTTCGAGTTTTATACTCCCTGAAAGAATAAGGAGCGAAACTGTTTTCAG
1 AAGATTGTTCGAGTTTTATACTCCCTGAAAGAAT-AGGAGCGGACCTGTTTT-AG
* * * **
29709 AAGATTGTTCGAGTTATATACTCCATGAAAGAATATGGAGCAGATATGTTTTCAG
1 AAGATTGTTCGAGTTTTATACTCCCTGAAAGAATA-GGAGCGGACCTGTTTT-AG
* * * ** *
29764 AAGATTGTTCGAGTTTTATAATCCCTGAAAAAATAGGGAGCAGACCCATTTCAG
1 AAGATTGTTCGAGTTTTATACTCCCTGAAAGAATA-GGAGCGGACCTGTTTTAG
* * * * *
29818 AAGATTGTTCTAGTTCTATACTCCTTGAAAGAATAAGGAGCGAACCCGTTTTCAG
1 AAGATTGTTCGAGTTTTATACTCCCTGAAAGAAT-AGGAGCGGACCTGTTTT-AG
* * * * *
29873 AAAATTGTTCGA-TTTTATACTCCCTGAAAAAATAAAGAGCGAACTCAT-TTTCAG
1 AAGATTGTTCGAGTTTTATACTCCCTGAAAGAAT-AGGAGCGGAC-C-TGTTTTAG
* * *
29927 AAGATTGTTCGAGTTTTATACTCCGTGAAAGAATAGGGAACGGACCTGTTTTCAA
1 AAGATTGTTCGAGTTTTATACTCCCTGAAAGAATA-GGAGCGGACCTGTTTT-AG
*
29982 AAGATT-TCTCGAGTTTTAT-CTCTCTGAAAGAA
1 AAGATTGT-TCGAGTTTTATACTCCCTGAAAGAA
30014 GAGTGGAGCA
Statistics
Matches: 513, Mismatches: 79, Indels: 69
0.78 0.12 0.10
Matches are distributed among these distances:
44 7 0.01
45 28 0.05
49 1 0.00
51 1 0.00
53 1 0.00
54 110 0.21
55 311 0.61
56 44 0.09
57 9 0.02
58 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (53 bp):
AAGATTGTTCGAGTTTTATACTCCCTGAAAGAATAGGAGCGGACCTGTTTTAG
Found at i:29869 original size:109 final size:109
Alignment explanation
Indices: 29504--30068 Score: 619
Period size: 110 Copynumber: 5.2 Consensus size: 109
29494 TTTATGAAGA
* * * *
29504 CTATACTCCCTGAAAGAATAGGGAGTGAACTCATTTTCAGAAGATTGTTCGAGTTCTATACTCCC
1 CTATACTCCCTGAAAGAATAGGGAGCGAACCCGTTTTCAGAAGATTGTTCGAGTTTTATACTCCC
* * *
29569 TGAAATAATAGGGAGCGGACCCATTTTTC-GAAGATTGTTCAAGTT
66 TGAAAAAATAGGGAGCAGACCCA--TTTCAGAAGATTGTTCGAGTT
*
29614 CTATACTCCCTGAAAGAATAGGGAGTGAACCCGTTTTCAGAAGATTGTTCGAGTTTTATACTCCC
1 CTATACTCCCTGAAAGAATAGGGAGCGAACCCGTTTTCAGAAGATTGTTCGAGTTTTATACTCCC
* * * ***
29679 TGAAAGAATAAGGAGCGAAACTGTTTTCAGAAGATTGTTCGAGTT
66 TGAAAAAATAGGGAGC-AGACCCATTTCAGAAGATTGTTCGAGTT
* * * * *
29724 ATATACTCCATGAAAGAATATGGAGCAGATA--TGTTTTCAGAAGATTGTTCGAGTTTTATAATC
1 CTATACTCCCTGAAAGAATAGGGAGC-GA-ACCCGTTTTCAGAAGATTGTTCGAGTTTTATACTC
*
29787 CCTGAAAAAATAGGGAGCAGACCCATTTCAGAAGATTGTTCTAGTT
64 CCTGAAAAAATAGGGAGCAGACCCATTTCAGAAGATTGTTCGAGTT
* * *
29833 CTATACTCCTTGAAAGAATAAGGAGCGAACCCGTTTTCAGAAAATTGTTCGA-TTTTATACTCCC
1 CTATACTCCCTGAAAGAATAGGGAGCGAACCCGTTTTCAGAAGATTGTTCGAGTTTTATACTCCC
** *
29897 TGAAAAAATAAAGAGC-GAACTCATTTTCAGAAGATTGTTCGAGTT
66 TGAAAAAATAGGGAGCAG-ACCCA-TTTCAGAAGATTGTTCGAGTT
* * * * * * *
29942 TTATACTCCGTGAAAGAATAGGGAACGGACCTGTTTTCAAAAGATT-TCTCGAGTTTTAT-CTCT
1 CTATACTCCCTGAAAGAATAGGGAGCGAACCCGTTTTCAGAAGATTGT-TCGAGTTTTATACTCC
* * * *
30005 CTGAAAGAAGAGTGGAGCATACCCATCTTCAAAAGATT-TCTCGAG-T
65 CTGAAAAAATAG-GGAGCAGACCCAT-TTCAGAAGATTGT-TCGAGTT
30051 CT-TATCTCCCTGAAAGAA
1 CTATA-CTCCCTGAAAGAA
30069 GAGTGGAGTA
Statistics
Matches: 388, Mismatches: 52, Indels: 31
0.82 0.11 0.07
Matches are distributed among these distances:
107 2 0.01
108 34 0.09
109 159 0.41
110 188 0.48
111 4 0.01
112 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Consensus pattern (109 bp):
CTATACTCCCTGAAAGAATAGGGAGCGAACCCGTTTTCAGAAGATTGTTCGAGTTTTATACTCCC
TGAAAAAATAGGGAGCAGACCCATTTCAGAAGATTGTTCGAGTT
Found at i:30067 original size:218 final size:219
Alignment explanation
Indices: 29537--30068 Score: 666
Period size: 218 Copynumber: 2.4 Consensus size: 219
29527 AGTGAACTCA
* * * * * * *
29537 TTTTCAGAAGATTGTTCGAGTTCTATACTCCCTGAAATAATAGGGAGCGGACCCATTTTTC-GAA
1 TTTTCAAAAGATTGTTCGAGTTTTATAATCCCTGAAAAAAGAGGGAGCAGACCCA--TTTCAAAA
* * * *
29601 GATTGTTCAAGTTCTATACTCCCTGAAAGAATAGGGAGTGAACCCGTTTTCAGAAGATTGTTCGA
64 GATTGTTCGAGTTCTATACTCCCTGAAAGAATAAGGAGCGAACCCGTTTTCAGAAAATTGTTCGA
* * *
29666 GTTTTATACTCCCTGAAAGAATAAGGAGCGAAACTGTTTTCAGAAGATTGTTCGAGTTATATACT
129 GTTTTATACTCCCTGAAAAAATAAAGAGCGAAACTATTTTCAGAAGATTGTTCGAGTTATATACT
* * *
29731 CCATGAAAGAATATGGAGCAGATATG
194 CCATGAAAGAATAGGGAACAGACATG
* * *
29757 TTTTCAGAAGATTGTTCGAGTTTTATAATCCCTGAAAAAATAGGGAGCAGACCCATTTCAGAAGA
1 TTTTCAAAAGATTGTTCGAGTTTTATAATCCCTGAAAAAAGAGGGAGCAGACCCATTTCAAAAGA
* *
29822 TTGTTCTAGTTCTATACTCCTTGAAAGAATAAGGAGCGAACCCGTTTTCAGAAAATTGTTCGA-T
66 TTGTTCGAGTTCTATACTCCCTGAAAGAATAAGGAGCGAACCCGTTTTCAGAAAATTGTTCGAGT
*
29886 TTTATACTCCCTGAAAAAATAAAGAGCG-AACTCATTTTCAGAAGATTGTTCGAGTTTTATACTC
131 TTTATACTCCCTGAAAAAATAAAGAGCGAAACT-ATTTTCAGAAGATTGTTCGAGTTATATACTC
* * *
29950 CGTGAAAGAATAGGGAACGGACCTG
195 CATGAAAGAATAGGGAACAGACATG
* * * *
29975 TTTTCAAAAGATT-TCTCGAGTTTTAT-CTCTCTGAAAGAAGAGTGGAGCATACCCATCTTCAAA
1 TTTTCAAAAGATTGT-TCGAGTTTTATAATCCCTGAAAAAAGAG-GGAGCAGACCCAT-TTCAAA
30038 AGATT-TCTCGAG-TCT-TATCTCCCTGAAAGAA
63 AGATTGT-TCGAGTTCTATA-CTCCCTGAAAGAA
30069 GAGTGGAGTA
Statistics
Matches: 277, Mismatches: 28, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
217 19 0.07
218 130 0.47
219 77 0.28
220 51 0.18
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (219 bp):
TTTTCAAAAGATTGTTCGAGTTTTATAATCCCTGAAAAAAGAGGGAGCAGACCCATTTCAAAAGA
TTGTTCGAGTTCTATACTCCCTGAAAGAATAAGGAGCGAACCCGTTTTCAGAAAATTGTTCGAGT
TTTATACTCCCTGAAAAAATAAAGAGCGAAACTATTTTCAGAAGATTGTTCGAGTTATATACTCC
ATGAAAGAATAGGGAACAGACATG
Found at i:30089 original size:55 final size:55
Alignment explanation
Indices: 29977--30081 Score: 174
Period size: 55 Copynumber: 1.9 Consensus size: 55
29967 CGGACCTGTT
* * *
29977 TTCAAAAGATTTCTCGAGTTTTATCTCTCTGAAAGAAGAGTGGAGCATACCCATC
1 TTCAAAAGATTTCTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCATC
*
30032 TTCAAAAGATTTCTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGTAGAC
1 TTCAAAAGATTTCTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGAC
30082 TCGTCTTCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (55 bp):
TTCAAAAGATTTCTCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCATC
Found at i:31062 original size:2 final size:2
Alignment explanation
Indices: 31055--31082 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
31045 AATAAGTTAA
31055 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
31083 GTATTTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33723 original size:33 final size:33
Alignment explanation
Indices: 33686--33753 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
33676 ACAATATAAC
*
33686 ATTTTCAGTTACAATCGTAAATCTTATAAATTT
1 ATTTTCAGTTACAATCGAAAATCTTATAAATTT
33719 ATTTTCAGTTACAATCGAAAATCTTATAAATTT
1 ATTTTCAGTTACAATCGAAAATCTTATAAATTT
33752 AT
1 AT
33754 ATAACTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (33 bp):
ATTTTCAGTTACAATCGAAAATCTTATAAATTT
Found at i:35210 original size:21 final size:21
Alignment explanation
Indices: 35180--35337 Score: 112
Period size: 21 Copynumber: 7.6 Consensus size: 21
35170 AATTTACATA
*
35180 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
35201 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
35222 TT--CGTTGTGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* * * *
35241 TTCGCGTTACAATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
35264 TT--TGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
35283 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
**
35306 TT--AATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
35325 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
35338 TTATTCCAAA
Statistics
Matches: 100, Mismatches: 27, Indels: 20
0.68 0.18 0.14
Matches are distributed among these distances:
19 33 0.33
21 49 0.49
23 18 0.18
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:35262 original size:42 final size:42
Alignment explanation
Indices: 35186--35365 Score: 283
Period size: 42 Copynumber: 4.3 Consensus size: 42
35176 CATATTCGCA
35186 TTGCGATAGTCCAAGTTCGCGTTGCGA-TT-TTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
* * * *
35226 TTGTGATAGTCCAAGTTCGCGTTACAATTTATTCCAAATTTG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
**
35268 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTAA
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
35310 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
35352 TTGTGATAGTCCAA
1 TTGCGATAGTCCAA
35366 AATCGCAACG
Statistics
Matches: 126, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 24 0.19
41 2 0.02
42 100 0.79
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:35353 original size:21 final size:20
Alignment explanation
Indices: 35205--35354 Score: 83
Period size: 21 Copynumber: 7.2 Consensus size: 20
35195 TCCAAGTTCG
35205 CGTTGCGATT-TTCCAAATT
1 CGTTGCGATTATTCCAAATT
* * *
35224 CGTTGTGA-TAGTCCAAGTT
1 CGTTGCGATTATTCCAAATT
* *
35243 CGCGTTACAATTTATTCCAAATT
1 --CGTTGCGA-TTATTCCAAATT
* * *
35266 TGTTGCGA-TAGTCCAAGTT
1 CGTTGCGATTATTCCAAATT
35285 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGA-TTATTCCAAATT
** * *
35308 AATTGCGA-TAGTCCAAGTT
1 CGTTGCGATTATTCCAAATT
35327 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGA-TTATTCCAAATT
35350 CGTTG
1 CGTTG
35355 TGATAGTCCA
Statistics
Matches: 94, Mismatches: 24, Indels: 24
0.66 0.17 0.17
Matches are distributed among these distances:
18 1 0.01
19 32 0.34
21 34 0.36
23 27 0.29
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTATTCCAAATT
Found at i:36260 original size:21 final size:21
Alignment explanation
Indices: 36234--36326 Score: 109
Period size: 21 Copynumber: 4.4 Consensus size: 21
36224 CTTGGAATAA
36234 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * * *
36255 ATCGCAA--CAAATTTGGAAT
1 ATCGCAACGCGAACTTCGACT
36274 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
*
36297 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
36318 ATCGCAACG
1 ATCGCAACG
36327 AATTTGAAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
19 8 0.14
21 43 0.73
23 8 0.14
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:36273 original size:42 final size:42
Alignment explanation
Indices: 36225--36304 Score: 160
Period size: 42 Copynumber: 1.9 Consensus size: 42
36215 ATCAAAGAAC
36225 TTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACAAAT
1 TTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACAAAT
36267 TTGGAATAAATCGCAACGCGAACTTCGACTATCGCAAC
1 TTGGAATAAATCGCAACGCGAACTTCGACTATCGCAAC
36305 GCGAACTTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.21
Consensus pattern (42 bp):
TTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACAAAT
Found at i:36322 original size:42 final size:41
Alignment explanation
Indices: 36222--36326 Score: 140
Period size: 42 Copynumber: 2.5 Consensus size: 41
36212 ACTATCAAAG
36222 AACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACA
1 AACTTGGAAT-AATCGCAACGCGAACTTCGACTATCGCAACA
* *
36264 AATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGCG
1 AACTTGGAAT-AATCGCAACGCGAACTTCGACTATCGCAA--CA
*
36308 AACTTGGACT-ATCGCAACG
1 AACTTGGAATAATCGCAACG
36327 AATTTGAAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
42 48 0.84
44 9 0.16
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (41 bp):
AACTTGGAATAATCGCAACGCGAACTTCGACTATCGCAACA
Found at i:36367 original size:21 final size:21
Alignment explanation
Indices: 36338--36388 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
36328 ATTTGAAAAA
*
36338 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
36359 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
*
36380 TTGCGTTGC
1 TCGCGTTGC
36389 AAATCTGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.16, C:0.20, G:0.31, T:0.33
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:37958 original size:2 final size:2
Alignment explanation
Indices: 37953--37990 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
37943 ATTGTATACA
37953 AT AT AT AT 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 AT AT AT AT
37991 TTCTTCATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38148 original size:32 final size:32
Alignment explanation
Indices: 38112--38209 Score: 196
Period size: 32 Copynumber: 3.1 Consensus size: 32
38102 GTACAATTGA
38112 TATACGATGAGTGCATGAATCTTACATACCAT
1 TATACGATGAGTGCATGAATCTTACATACCAT
38144 TATACGATGAGTGCATGAATCTTACATACCAT
1 TATACGATGAGTGCATGAATCTTACATACCAT
38176 TATACGATGAGTGCATGAATCTTACATACCAT
1 TATACGATGAGTGCATGAATCTTACATACCAT
38208 TA
1 TA
38210 ATCGGAGTCG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 66 1.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (32 bp):
TATACGATGAGTGCATGAATCTTACATACCAT
Found at i:40727 original size:42 final size:42
Alignment explanation
Indices: 40681--40801 Score: 199
Period size: 42 Copynumber: 2.9 Consensus size: 42
40671 CGAATCATTG
*
40681 GGTGAATCATTGGAATTTCCAATAGGATTATTA-AATGTATTA
1 GGTGAATCATTGGAATTTCCAATAGAATTATTAGAA-GTATTA
*
40723 GGTGAATCATTGAAATTTCCAATAGAATTATTAGAAGTATTA
1 GGTGAATCATTGGAATTTCCAATAGAATTATTAGAAGTATTA
*
40765 GGTGAATCATTGGAATTTCCAATCGAATTATTAGAAG
1 GGTGAATCATTGGAATTTCCAATAGAATTATTAGAAG
40802 GTTTAATCAG
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
42 72 0.97
43 2 0.03
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.36
Consensus pattern (42 bp):
GGTGAATCATTGGAATTTCCAATAGAATTATTAGAAGTATTA
Found at i:41242 original size:84 final size:84
Alignment explanation
Indices: 41136--41417 Score: 458
Period size: 84 Copynumber: 3.3 Consensus size: 84
41126 CCACTGTTTT
*
41136 TTTTTTCTCATCAAACTAAGTTTGTCACTACACAATCAAAATTCAAACAATCAAACAAGCCTATA
1 TTTTTTCTCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAACAATCAAACAAGCC-ATA
41201 AACTCAATATTTAGCCATTG
65 AACTCAATATTTAGCCATTG
*
41221 TTTTTT-TCATCAAACTAAGTTTGCCACTACACAATCAAAATTTAAACAATCAAACAAGTCCATA
1 TTTTTTCTCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAACAATCAAACAAG-CCATA
*
41285 AACTCAATATTTAGCCACTG
65 AACTCAATATTTAGCCATTG
* *
41305 TTTTTTCCCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAACAATCAAACAAACCCATA
1 TTTTTTCTCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAACAATCAAAC-AAGCCATA
*
41370 AACTCAATATTTAGCCACTGTT
65 AACTCAATATTTAGCCA-T-TG
41392 TTTTTTCTCATCAAACTAAGTTTGCC
1 TTTTTTCTCATCAAACTAAGTTTGCC
41418 TCAGTGTGAC
Statistics
Matches: 183, Mismatches: 9, Indels: 8
0.92 0.05 0.04
Matches are distributed among these distances:
84 78 0.43
85 77 0.42
86 2 0.01
87 26 0.14
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.32
Consensus pattern (84 bp):
TTTTTTCTCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAACAATCAAACAAGCCATAA
ACTCAATATTTAGCCATTG
Found at i:41353 original size:85 final size:85
Alignment explanation
Indices: 41117--41417 Score: 473
Period size: 85 Copynumber: 3.5 Consensus size: 85
41107 CTTGAACGAA
*
41117 AATATTTAGCCACTGTTTTTTTTTTCTCATCAAACTAAGTTTGTCACTACACAATCAAAATTCAA
1 AATATTTAGCCACTG---TTTTTTTCTCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAA
41182 ACAATCAAACAAGCCTATAAACTC
63 ACAATCAAACAAGCC-ATAAACTC
* *
41206 AATATTTAGCCATTG-TTTTTT-TCATCAAACTAAGTTTGCCACTACACAATCAAAATTTAAACA
1 AATATTTAGCCACTGTTTTTTTCTCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAACA
41269 ATCAAACAAGTCCATAAACTC
66 ATCAAACAAG-CCATAAACTC
*
41290 AATATTTAGCCACTG-TTTTTTCCCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAACA
1 AATATTTAGCCACTGTTTTTTTCTCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAACA
*
41354 ATCAAACAAACCCATAAACTC
66 ATCAAAC-AAGCCATAAACTC
41375 AATATTTAGCCACTGTTTTTTTTCTCATCAAACTAAGTTTGCC
1 AATATTTAGCCACTG-TTTTTTTCTCATCAAACTAAGTTTGCC
41418 TCAGTGTGAC
Statistics
Matches: 199, Mismatches: 8, Indels: 12
0.91 0.04 0.05
Matches are distributed among these distances:
84 78 0.39
85 80 0.40
86 2 0.01
87 25 0.13
89 14 0.07
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (85 bp):
AATATTTAGCCACTGTTTTTTTCTCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAACA
ATCAAACAAGCCATAAACTC
Found at i:41549 original size:23 final size:23
Alignment explanation
Indices: 41519--41575 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
41509 ATTCTCAATC
*
41519 AGAATATGATTCAAACATTTGTT
1 AGAATATGATTCAAACAGTTGTT
41542 AGAATATGATTCAAACAGTTGTT
1 AGAATATGATTCAAACAGTTGTT
41565 AGAATATGATT
1 AGAATATGATT
41576 AAAATTGATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (23 bp):
AGAATATGATTCAAACAGTTGTT
Found at i:48052 original size:31 final size:31
Alignment explanation
Indices: 48012--48076 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
48002 GATCCTCAGT
* *
48012 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATAGGTCCCGAAGAACATAGGTA
* * **
48043 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATAGGTCCCGAAGAACATAGGTA
48074 AAC
1 AAC
48077 CCTCGACTCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (31 bp):
AACTATCCATAGGTCCCGAAGAACATAGGTA
Found at i:49433 original size:14 final size:15
Alignment explanation
Indices: 49414--49443 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
49404 GAAGGAAATG
49414 AAGAAG-AAGAAGAA
1 AAGAAGAAAGAAGAA
49428 AAGAAGAAAGAAGAA
1 AAGAAGAAAGAAGAA
49443 A
1 A
49444 GCTTTGGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (15 bp):
AAGAAGAAAGAAGAA
Found at i:49438 original size:18 final size:17
Alignment explanation
Indices: 49408--49442 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
49398 GATACGGAAG
*
49408 GAAATGAAGAAGAAGAA
1 GAAAAGAAGAAGAAGAA
49425 GAAAAGAAGAAAGAAGAA
1 GAAAAGAAG-AAGAAGAA
49443 AGCTTTGGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.03
Consensus pattern (17 bp):
GAAAAGAAGAAGAAGAA
Found at i:53488 original size:29 final size:29
Alignment explanation
Indices: 53446--53526 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
53436 TTTTATATGT
53446 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
53474 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
53503 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
53527 ATATCACATA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 7 0.14
29 39 0.76
30 5 0.10
ACGTcount: A:0.17, C:0.22, G:0.16, T:0.44
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:53974 original size:64 final size:64
Alignment explanation
Indices: 53905--54059 Score: 165
Period size: 64 Copynumber: 2.4 Consensus size: 64
53895 ATGAAGGTAC
* * **
53905 GCATCGATGCACTACTTGTGCATCGGTGTA-TAAAATGCATTCGAT-GTTTTATTATTAATTG-G
1 GCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCGATCGTTTTATT-TTAAAAGAG
53967 AT
64 -T
* * * *
53969 GCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATCTTTTTATTTTAAAAGAGT
1 GCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAGAGT
*
54033 GCATCGATGCACTACCTGTGCATCGAT
1 GCATCGATGCACTACTTGTGCATCGAT
54060 ACACCTTCAA
Statistics
Matches: 75, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
63 1 0.01
64 64 0.85
65 10 0.13
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (64 bp):
GCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAGAGT
Found at i:60882 original size:29 final size:29
Alignment explanation
Indices: 60843--60923 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
60833 CTGTCTGGCG
60843 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
60871 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
60900 TCATATAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
60924 ATATCATATA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 7 0.14
29 38 0.76
30 5 0.10
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.44
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:67266 original size:60 final size:60
Alignment explanation
Indices: 67170--67286 Score: 155
Period size: 60 Copynumber: 1.9 Consensus size: 60
67160 CTCCACGATG
* ** *
67170 TCGACATTTAGGTCGAACAAGCTGGTGGTTGCATGCCTTCCCCTT-GAACTTGAAGGCCTC
1 TCGACATTGAGGTCGAACAAGCTGGCAGTTGAATGCC-TCCCCTTGGAACTTGAAGGCCTC
* * *
67230 TCGACATTGAGGTCGAAGAAGCTTGCAGTTGAATGCCTCCCCTTGGAATTTGAAGGC
1 TCGACATTGAGGTCGAACAAGCTGGCAGTTGAATGCCTCCCCTTGGAACTTGAAGGC
67287 ATCGTGTCAA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
59 7 0.14
60 42 0.86
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.27
Consensus pattern (60 bp):
TCGACATTGAGGTCGAACAAGCTGGCAGTTGAATGCCTCCCCTTGGAACTTGAAGGCCTC
Found at i:68208 original size:21 final size:19
Alignment explanation
Indices: 68183--68221 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
68173 ATTTATTCAA
68183 ATAATCATATATAAAATAAAT
1 ATAAT-ATA-ATAAAATAAAT
*
68204 ATAATATAATATAATAAA
1 ATAATATAATAAAATAAA
68222 AAATAGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAATATAATAAAATAAAT
Found at i:69755 original size:7 final size:7
Alignment explanation
Indices: 69747--69780 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
69737 ATATTAAAAG
*
69747 TTTAAAG
1 TTTAAAT
*
69754 TTCAAAT
1 TTTAAAT
69761 TTTAAAT
1 TTTAAAT
69768 TTTAAAT
1 TTTAAAT
69775 TTTAAA
1 TTTAAA
69781 AGCTAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (7 bp):
TTTAAAT
Found at i:78298 original size:24 final size:24
Alignment explanation
Indices: 78270--78336 Score: 98
Period size: 26 Copynumber: 2.7 Consensus size: 24
78260 TCTTTTCCTC
78270 ATATACTGCCTGTTATTTATATAT
1 ATATACTGCCTGTTATTTATATAT
78294 ATATACACTGCCTGTTATTTATATAT
1 ATAT--ACTGCCTGTTATTTATATAT
* *
78320 ATACACTGCTTGTTATT
1 ATATACTGCCTGTTATT
78337 GATTTATGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
24 16 0.41
26 23 0.59
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.48
Consensus pattern (24 bp):
ATATACTGCCTGTTATTTATATAT
Found at i:78305 original size:26 final size:25
Alignment explanation
Indices: 78274--78336 Score: 101
Period size: 24 Copynumber: 2.5 Consensus size: 25
78264 TTCCTCATAT
78274 ACTGCCTGTTATTTATATATATATAC
1 ACTGCCTGTTATTT-TATATATATAC
78300 ACTGCCTGTTA-TTTATATATATAC
1 ACTGCCTGTTATTTTATATATATAC
*
78324 ACTGCTTGTTATT
1 ACTGCCTGTTATT
78337 GATTTATGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
24 21 0.60
25 3 0.09
26 11 0.31
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.48
Consensus pattern (25 bp):
ACTGCCTGTTATTTTATATATATAC
Found at i:78456 original size:60 final size:61
Alignment explanation
Indices: 78361--78541 Score: 192
Period size: 60 Copynumber: 3.0 Consensus size: 61
78351 ATTGTATATT
* * * *
78361 TTCAAATTACGACTATCATTTTAAATTGATATTTAAA-TTTCTAAATATTCTAATTTTAT-C
1 TTCAAATTATGACTATCATTATAAATTAATATTTAAACTTT-TAAATATTCTAATTTCATCC
* * *
78421 TTCAAATTATGACTTTCATTATAAATTAATTTTTAAACTTTTGAATATTCTAATTTCATCC
1 TTCAAATTATGACTATCATTATAAATTAATATTTAAACTTTTAAATATTCTAATTTCATCC
* * * * *
78482 TT-AAATTATGA-TCATCTTTCTAAATTGATCA-TCAAACTTTAAAATATTCTAATTTCATCC
1 TTCAAATTATGACT-ATCATTATAAATTAAT-ATTTAAACTTTTAAATATTCTAATTTCATCC
78542 CCGAATTCAT
Statistics
Matches: 102, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
59 1 0.01
60 95 0.93
61 6 0.06
ACGTcount: A:0.36, C:0.14, G:0.03, T:0.47
Consensus pattern (61 bp):
TTCAAATTATGACTATCATTATAAATTAATATTTAAACTTTTAAATATTCTAATTTCATCC
Found at i:78486 original size:29 final size:29
Alignment explanation
Indices: 78453--78541 Score: 72
Period size: 29 Copynumber: 3.0 Consensus size: 29
78443 AAATTAATTT
78453 TTAAACTTTTGAATATTCTAATTTCATCC
1 TTAAACTTTTGAATATTCTAATTTCATCC
* * * * *
78482 TTAAA-TTATGATCATCTTTCTAAATTGATCA
1 TTAAACTTTTGA--AT-ATTCTAATTTCATCC
* **
78513 TCAAACTTTAAAATATTCTAATTTCATCC
1 TTAAACTTTTGAATATTCTAATTTCATCC
78542 CCGAATTCAT
Statistics
Matches: 43, Mismatches: 13, Indels: 8
0.67 0.20 0.12
Matches are distributed among these distances:
28 5 0.12
29 16 0.37
30 4 0.09
31 15 0.35
32 3 0.07
ACGTcount: A:0.35, C:0.17, G:0.03, T:0.45
Consensus pattern (29 bp):
TTAAACTTTTGAATATTCTAATTTCATCC
Found at i:81740 original size:21 final size:21
Alignment explanation
Indices: 81715--81755 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
81705 CTGACTATCG
81715 CATTGCGATTTTCCGAATTCA
1 CATTGCGATTTTCCGAATTCA
81736 CATTGCGATTTTCCGAATTC
1 CATTGCGATTTTCCGAATTC
81756 GCAATACGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (21 bp):
CATTGCGATTTTCCGAATTCA
Found at i:81801 original size:20 final size:20
Alignment explanation
Indices: 81754--81809 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
81744 TTTTCCGAAT
*
81754 TCGCAATACGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
81774 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
*
81794 TCGCAATGCGATTATG
1 TCGCAATGCGAATATG
81810 ACTATCGCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.27
Consensus pattern (20 bp):
TCGCAATGCGAATATGTAAA
Found at i:81816 original size:20 final size:20
Alignment explanation
Indices: 81773--81866 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 20
81763 GAATATGTAA
* *
81773 ATCGCAATGCGAATATGTA-A
1 ATCGCAATGCGATTATG-ACT
81793 ATCGCAATGCGATTATGACT
1 ATCGCAATGCGATTATGACT
* * *
81813 ATCGCAACGAGATTCTGACT
1 ATCGCAATGCGATTATGACT
* **
81833 ATCGCAACGCGATGCTGACT
1 ATCGCAATGCGATTATGACT
81853 ATCGCAATGCGATT
1 ATCGCAATGCGATT
81867 TTCAAAGCGC
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
19 1 0.02
20 63 0.98
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGATTATGACT
Found at i:82493 original size:20 final size:20
Alignment explanation
Indices: 82428--82495 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
82418 AGAATCGCAA
* *
82428 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCATTTTCGTGT
**
82447 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGTGT
82467 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGTGT
82487 TGCGATTTT
1 TGCGATTTT
82496 AAGTTTCAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 7 0.17
20 35 0.83
ACGTcount: A:0.12, C:0.15, G:0.24, T:0.50
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGTGT
Found at i:84245 original size:24 final size:24
Alignment explanation
Indices: 84211--84264 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
84201 CTGAAACATC
84211 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
84235 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
84259 ATCAAA
1 ATCAAA
84265 TTTAGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:85165 original size:20 final size:20
Alignment explanation
Indices: 85078--85165 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
85068 GAAATTCAGT
*
85078 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
85098 GTTGCGATAGTCAGAATCTC
1 GTTGCGATAGTCAGAATCGC
*
85118 GTTGCGATAATCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* *
85138 GTTGCGATCGTCATAATCGC
1 GTTGCGATAGTCAGAATCGC
*
85158 ATTGCGAT
1 GTTGCGAT
85166 TTACATATTC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:85205 original size:21 final size:21
Alignment explanation
Indices: 85181--85220 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
85171 TATTCGCATT
85181 GCGAATTCGGAAAATCGCAGC
1 GCGAATTCGGAAAATCGCAGC
*
85202 GCGAATTTGGAAAATCGCA
1 GCGAATTCGGAAAATCGCA
85221 ATGCGATAGT
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:0.35, C:0.20, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTCGGAAAATCGCAGC
Found at i:85226 original size:21 final size:21
Alignment explanation
Indices: 85174--85226 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
85164 ATTTACATAT
*
85174 TCGCATTGCGAATTCGGAAAA
1 TCGCAATGCGAATTCGGAAAA
** *
85195 TCGCAGCGCGAATTTGGAAAA
1 TCGCAATGCGAATTCGGAAAA
85216 TCGCAATGCGA
1 TCGCAATGCGA
85227 TAGTCAGAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTCGGAAAA
Found at i:94139 original size:60 final size:59
Alignment explanation
Indices: 94029--94142 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 59
94019 ACTATCATTT
* * * **
94029 CATTTTAAATTGATCCTTAAATTTTAAATATTCCAATTTCATTCCAAAACTATAGCTTG
1 CATTCTAAATTAATCCTTAAATTTTAAATATTACAATTTCACCCCAAAACTATAGCTTG
* * * *
94088 CATTCTAAATTAATCCTTAAACTTTTGAATATTATATTTTCACCCCTAAACTATA
1 CATTCTAAATTAATCCTTAAA-TTTTAAATATTACAATTTCACCCCAAAACTATA
94143 ACCTATTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
59 19 0.42
60 26 0.58
ACGTcount: A:0.36, C:0.18, G:0.04, T:0.42
Consensus pattern (59 bp):
CATTCTAAATTAATCCTTAAATTTTAAATATTACAATTTCACCCCAAAACTATAGCTTG
Done.