Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003788.1 Hibiscus syriacus cultivar Beakdansim tig00008108_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: 55456
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:3516 original size:20 final size:21
Alignment explanation
Indices: 3487--3526 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
3477 TATAATTATT
3487 TTTTACTTTTT-ATATTTTAAG
1 TTTTACTTTTTGA-ATTTTAAG
3508 TTTTA-TTTTTGAATTTTAA
1 TTTTACTTTTTGAATTTTAA
3527 TACTGTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTTACTTTTTGAATTTTAAG
Found at i:4421 original size:24 final size:24
Alignment explanation
Indices: 4394--4451 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
4384 TAGTAGATGG
* *
4394 TTTTGTTTATATTTATACCATGT-
1 TTTTTTTTATATTTATAACATGTA
*
4417 TTTTTATTTATTTTTATAACATGTA
1 TTTTT-TTTATATTTATAACATGTA
4442 TTTTTTTTAT
1 TTTTTTTTAT
4452 CAGGGTTATC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.13
24 21 0.70
25 5 0.17
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.67
Consensus pattern (24 bp):
TTTTTTTTATATTTATAACATGTA
Found at i:4687 original size:14 final size:13
Alignment explanation
Indices: 4668--4704 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
4658 CGTTCGATAA
4668 TATGTTCGTTCATT
1 TATGTTCGTT-ATT
*
4682 TATGTTCGTTGTT
1 TATGTTCGTTATT
4695 TATGTTCGTT
1 TATGTTCGTT
4705 TGTTTGCGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.59
Consensus pattern (13 bp):
TATGTTCGTTATT
Found at i:4707 original size:14 final size:14
Alignment explanation
Indices: 4668--4709 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
4658 CGTTCGATAA
**
4668 TATGTTCGTTCATT
1 TATGTTCGTTTGTT
4682 TATGTTCG-TTGTT
1 TATGTTCGTTTGTT
4695 TATGTTCGTTTGTT
1 TATGTTCGTTTGTT
4709 T
1 T
4710 GCGTTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.62
Consensus pattern (14 bp):
TATGTTCGTTTGTT
Found at i:4907 original size:10 final size:10
Alignment explanation
Indices: 4885--4923 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
4875 AAAATATATT
4885 TTCATTTATG
1 TTCATTTATG
* *
4895 TTCGTTTACG
1 TTCATTTATG
4905 TTCATTTATG
1 TTCATTTATG
4915 TTCATTTAT
1 TTCATTTAT
4924 TGTGTACGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.18, C:0.13, G:0.10, T:0.59
Consensus pattern (10 bp):
TTCATTTATG
Found at i:4910 original size:20 final size:20
Alignment explanation
Indices: 4885--4922 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4875 AAAATATATT
*
4885 TTCATTTATGTTCGTTTACG
1 TTCATTTATGTTCATTTACG
4905 TTCATTTATGTTCATTTA
1 TTCATTTATGTTCATTTA
4923 TTGTGTACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (20 bp):
TTCATTTATGTTCATTTACG
Found at i:5011 original size:57 final size:57
Alignment explanation
Indices: 4885--5011 Score: 138
Period size: 57 Copynumber: 2.2 Consensus size: 57
4875 AAAATATATT
*
4885 TTCATTTATGTTCGTTTACGTTCATTTATGTTCATTTATTGTGTACGTTTACGATCG
1 TTCATTTATGTTCATTTACGTTCATTTATGTTCATTTATTGTGTACGTTTACGATCG
* * *
4942 TT-TTGTTGTGTTCATTTACGTTCGTTTATTGTCTTCATTTA-TGT-T-CGTTTAC-ATCCG
1 TTCAT-TTATGTTCATTTACGTTCATTTA-TG--TTCATTTATTGTGTACGTTTACGAT-CG
4999 TTCATTTATGTTC
1 TTCATTTATGTTC
5012 GTTCATTTGT
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
56 3 0.05
57 40 0.69
58 4 0.07
59 3 0.05
60 8 0.14
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.55
Consensus pattern (57 bp):
TTCATTTATGTTCATTTACGTTCATTTATGTTCATTTATTGTGTACGTTTACGATCG
Found at i:5014 original size:14 final size:14
Alignment explanation
Indices: 4997--5028 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
4987 CGTTTACATC
4997 CGTTCATTTATGTT
1 CGTTCATTTATGTT
*
5011 CGTTCATTTGTGTT
1 CGTTCATTTATGTT
5025 CGTT
1 CGTT
5029 TATCATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.16, G:0.19, T:0.56
Consensus pattern (14 bp):
CGTTCATTTATGTT
Found at i:5025 original size:24 final size:23
Alignment explanation
Indices: 4885--5031 Score: 120
Period size: 24 Copynumber: 6.4 Consensus size: 23
4875 AAAATATATT
*
4885 TTCATTTATGTTCGTTTA---CG
1 TTCATTTATGTTCGTTTATTGTG
*
4905 TTCATTTATGTTCATTTATTGTG
1 TTCATTTATGTTCGTTTATTGTG
* * * * *
4928 TACGTTTACGATCGTTTTGTTGTG
1 TTCATTTATGTTCG-TTTATTGTG
* *
4952 TTCATTTACGTTCGTTTATTGTC
1 TTCATTTATGTTCGTTTATTGTG
* **
4975 TTCATTTATGTTCGTTTACATCCG
1 TTCATTTATGTTCGTTTA-TTGTG
*
4999 TTCATTTATGTTCGTTCATTTGTG
1 TTCATTTATGTTCGTTTA-TTGTG
*
5023 TTCGTTTAT
1 TTCATTTAT
5032 CATTTAAATG
Statistics
Matches: 98, Mismatches: 24, Indels: 6
0.77 0.19 0.05
Matches are distributed among these distances:
20 17 0.17
23 34 0.35
24 47 0.48
ACGTcount: A:0.14, C:0.14, G:0.16, T:0.56
Consensus pattern (23 bp):
TTCATTTATGTTCGTTTATTGTG
Found at i:9842 original size:64 final size:64
Alignment explanation
Indices: 9768--9900 Score: 257
Period size: 64 Copynumber: 2.1 Consensus size: 64
9758 TTGTATATCA
9768 GTGATATATAAGAAATGAAAATCTATCTTAATGATCAATCTCAATTAGATAAGATTCTAAAGCT
1 GTGATATATAAGAAATGAAAATCTATCTTAATGATCAATCTCAATTAGATAAGATTCTAAAGCT
*
9832 GTGATATATAAGAAATGAAAATCTATCTTAATGCTCAATCTCAATTAGATAAGATTCTAAAGCT
1 GTGATATATAAGAAATGAAAATCTATCTTAATGATCAATCTCAATTAGATAAGATTCTAAAGCT
9896 GTGAT
1 GTGAT
9901 GAGCCAACTT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 68 1.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (64 bp):
GTGATATATAAGAAATGAAAATCTATCTTAATGATCAATCTCAATTAGATAAGATTCTAAAGCT
Found at i:11208 original size:31 final size:31
Alignment explanation
Indices: 11165--11231 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
11155 TAACGGTAGA
11165 CACCT-AAAATGTAACAGAAAAAA-TGTTAGG
1 CACCTAAAAATGTAACAGAAAAAACT-TTAGG
*
11195 CACCTAAAAATGTAACAGAAAAAACTTTTGG
1 CACCTAAAAATGTAACAGAAAAAACTTTAGG
11226 CACCTA
1 CACCTA
11232 TTTTTAACAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 5 0.15
31 28 0.82
32 1 0.03
ACGTcount: A:0.48, C:0.18, G:0.13, T:0.21
Consensus pattern (31 bp):
CACCTAAAAATGTAACAGAAAAAACTTTAGG
Found at i:19426 original size:267 final size:267
Alignment explanation
Indices: 18951--19493 Score: 1050
Period size: 267 Copynumber: 2.0 Consensus size: 267
18941 GAATGTATTT
18951 TTTAAATGTGTGTTAAAGGTGAAGTGAATTTATGTTAAAGTGTTATATGTTTCATGAACTTTGGC
1 TTTAAATGTGTGTTAAAGGTGAAGTGAATTTATGTTAAAGTGTTATATGTTTCATGAACTTTGGC
* * *
19016 ATTCGCCCATTCCACTCGATATTAATCGGATGGAACTATGCGGTGTTCGACTCTTGGACAATGGA
66 ATTCGCCCATTCCACGCGATATTAATCGGATGGAACTATACGGTGTTCGACTCTCGGACAATGGA
*
19081 ACAATATATGAAAATCAGCTTTGATCGTATTGTATTTCTCGAAAAAATGTATGAAATTATAATAT
131 ACAATATATGAAAACCAGCTTTGATCGTATTGTATTTCTCGAAAAAATGTATGAAATTATAATAT
19146 TACACGTATGGTTATTTATCTATTATTTTTTTCTATTTTGATTATCGATATATTAATTTTATGAC
196 TACACGTATGGTTATTTATCTATTATTTTTTTCTATTTTGATTATCGATATATTAATTTTATGAC
19211 TTAATTA
261 TTAATTA
19218 TTTAAATGTGTGTTAAAGGTGAAGTGAATTTATGTTAAAGTGTTATATGTTTCATGAACTTTGGC
1 TTTAAATGTGTGTTAAAGGTGAAGTGAATTTATGTTAAAGTGTTATATGTTTCATGAACTTTGGC
19283 ATTCGCCCATTCCACGCGATATTAATCGGATGGAACTATACGGTGTTCGACTCTCGGACAATGGA
66 ATTCGCCCATTCCACGCGATATTAATCGGATGGAACTATACGGTGTTCGACTCTCGGACAATGGA
19348 ACAATATATGAAAACCAGCTTTGATCGTATTGTATTTCTCGAAAAAATGTATGAAATTATAATAT
131 ACAATATATGAAAACCAGCTTTGATCGTATTGTATTTCTCGAAAAAATGTATGAAATTATAATAT
19413 TACACGTATGGTTATTTATCTATTATTTTTTTCTATTTTGATTATCGATATATTAATTTTATGAC
196 TACACGTATGGTTATTTATCTATTATTTTTTTCTATTTTGATTATCGATATATTAATTTTATGAC
19478 TTAATTA
261 TTAATTA
19485 TTTAAATGT
1 TTTAAATGT
19494 TATCAATCAA
Statistics
Matches: 272, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
267 272 1.00
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.41
Consensus pattern (267 bp):
TTTAAATGTGTGTTAAAGGTGAAGTGAATTTATGTTAAAGTGTTATATGTTTCATGAACTTTGGC
ATTCGCCCATTCCACGCGATATTAATCGGATGGAACTATACGGTGTTCGACTCTCGGACAATGGA
ACAATATATGAAAACCAGCTTTGATCGTATTGTATTTCTCGAAAAAATGTATGAAATTATAATAT
TACACGTATGGTTATTTATCTATTATTTTTTTCTATTTTGATTATCGATATATTAATTTTATGAC
TTAATTA
Found at i:19815 original size:22 final size:22
Alignment explanation
Indices: 19743--19815 Score: 53
Period size: 22 Copynumber: 3.5 Consensus size: 22
19733 TGGAATTATT
* *
19743 ATAAT-ATT-TTAAAATTAATA
1 ATAATAATTATTATAATAAATA
* * *
19763 ATAA-ATTTTTTATAATAATTA
1 ATAATAATTATTATAATAAATA
* *
19784 ATAATTATTATTATATTAAATA
1 ATAATAATTATTATAATAAATA
*
19806 ATTATAATTA
1 ATAATAATTA
19816 ATCATTTTAA
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
20 6 0.15
21 13 0.33
22 20 0.51
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAATAATTATTATAATAAATA
Found at i:19824 original size:50 final size:49
Alignment explanation
Indices: 19736--19832 Score: 108
Period size: 50 Copynumber: 2.0 Consensus size: 49
19726 TAAAAGGTGG
* * *
19736 AATTATTATAATATTTTAAAATTAATAATAAATTTTTTATAATAATTAAT
1 AATTATTATAATATTTAAAAATTAATAATAAATATTTTA-AAAAATTAAT
* *
19786 AATTATTATTATA-TTAAATAATT-ATAATTAATCATTTTAAAAAATTA
1 AATTATTATAATATTTAAA-AATTAATAATAAAT-ATTTTAAAAAATTA
19833 CCAATAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
49 19 0.47
50 21 0.52
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (49 bp):
AATTATTATAATATTTAAAAATTAATAATAAATATTTTAAAAAATTAAT
Found at i:23254 original size:125 final size:126
Alignment explanation
Indices: 22992--23747 Score: 959
Period size: 127 Copynumber: 6.0 Consensus size: 126
22982 TACTATTCAC
* * * * * *
22992 GTGAAGGCGCGTTTCTGGGGGCGCACCTTCTATTATTTTGTCAGAAAATATGTTATCATTGTCCT
1 GTGAAAGCGCGTTTCCGGGGG-GCGCCTTCCATTATTTTGTCAGAAAACATGTTATCATTGCCCT
* *
23057 ATTATGTCACTCATGTCACCCGGGGGCACTATTCATTGATGCCCTATTATGGTTGAGGGGACG
65 ATTATGTCACTCATGTC-CCCTGGGGCACTATTCATTGATGCCCTATTATGGTTGAAGGGACG
* *
23120 GTGAAAGCGCGTTTCCGGGGGGTGCCTTCCATTATTTTGTCA-AAGAACATATTATCATTGCCCT
1 GTGAAAGCGCGTTTCCGGGGGGCGCCTTCCATTATTTTGTCAGAA-AACATGTTATCATTGCCCT
* * * *
23184 ATTATGTCACTTATGT-CCCTGGAGCACTATTTATTGATGCCCTATTATGGTTGAAGGGACA
65 ATTATGTCACTCATGTCCCCTGGGGCACTATTCATTGATGCCCTATTATGGTTGAAGGGACG
* * * * *
23245 GTGAAAGCGCGTTTCCGGGGACGCGTCTTCCATTATTTTCTCAGAGAACATGTTATTATTGCCCT
1 GTGAAAGCGCGTTTCCGGGG-GGCGCCTTCCATTATTTTGTCAGAAAACATGTTATCATTGCCCT
* * * *
23310 ATTATGTCACTCATGTCCCCCGAGGCACTATTCATTGATGCCCTATTATAGTT-AAGGGGACT
65 ATTATGTCACTCATGTCCCCTGGGGCACTATTCATTGATGCCCTATTATGGTTGAA-GGGACG
*
23372 GTGAAAGCGCGTTTCCGGGGGGCACCTTCCATTATTTTGTCAGAAAACATGTTATCATTGCCCTA
1 GTGAAAGCGCGTTTCCGGGGGGCGCCTTCCATTATTTTGTCAGAAAACATGTTATCATTGCCCTA
*
23437 TTATGTCACTCATGTCCCCTGGGGCACTATTCA-TGAATGCCCTATTATGATTG-AGAGGACG
66 TTATGTCACTCATGTCCCCTGGGGCACTATTCATTG-ATGCCCTATTATGGTTGAAG-GGACG
* * *
23498 GTGCAAGCACGTTTCCGGGGGG-GCCTTCCATTATTTTGTCAGAGAACATGTTATCATTGCCCTA
1 GTGAAAGCGCGTTTCCGGGGGGCGCCTTCCATTATTTTGTCAGAAAACATGTTATCATTGCCCTA
* * *
23562 TTATGTCACTCGTGTCCCCTGGGGCACTATTTATTGATGCCCTATTATGGTTGAGGGGACG
66 TTATGTCACTCATGTCCCCTGGGGCACTATTCATTGATGCCCTATTATGGTTGAAGGGACG
* * ** * * * **
23623 GTGAAAGCGCGTTTTCGGGGGCGCTCCTTTAATTATTTTGTCAGAAAACATGTAAACGTAACCCT
1 GTGAAAGCGCGTTTCCGGGGG-GCGCCTTCCATTATTTTGTCAGAAAACATGTTATCATTGCCCT
* ** * * * *
23688 ATTATATCACTCATGTCCCCCAGGGTACTATTCA-TGAATGCCTTATTATGTTTGAGGGGA
65 ATTATGTCACTCATGTCCCCTGGGGCACTATTCATTG-ATGCCCTATTATGGTTGAAGGGA
23748 TAAAATGTGA
Statistics
Matches: 548, Mismatches: 67, Indels: 27
0.85 0.10 0.04
Matches are distributed among these distances:
125 173 0.32
126 169 0.31
127 187 0.34
128 19 0.03
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (126 bp):
GTGAAAGCGCGTTTCCGGGGGGCGCCTTCCATTATTTTGTCAGAAAACATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCCTGGGGCACTATTCATTGATGCCCTATTATGGTTGAAGGGACG
Found at i:23444 original size:252 final size:252
Alignment explanation
Indices: 22992--23743 Score: 1003
Period size: 252 Copynumber: 3.0 Consensus size: 252
22982 TACTATTCAC
* * * * * * *
22992 GTGAAGGCGCGTTTCTGGGGGCGCACCTTCTATTATTTTGTCAGAAAATATGTTATCATTGTCCT
1 GTGAAAGCGCGTTTC-CGGGGCGCGCCTTCCATTATTTTGTCAGAGAACATGTTATCATTGCCCT
*
23057 ATTATGTCACTCATGTCACCCGGGGGCACTATTCATTGATGCCCTATTATGGTTGAGGGGACGGT
65 ATTATGTCACTCATGTC-CCCCGGGGCACTATTCATTGATGCCCTATTATGGTTGAGGGGACGGT
** *
23122 GAAAGCGCGTTTCCGGGGGGTGCCTTCCATTATTTTGTCA-AAGAACATATTATCATTGCCCTAT
129 GAAAGCGCGTTTCCGGGGGGCACCTTCCATTATTTTGTCAGAA-AACATGTTATCATTGCCCTAT
* * *
23186 TATGTCACTTATGT-CCCTGGAGCACTATTTATTG-ATGCCCTATTATGGTTGA-AGGGACA
193 TATGTCACTCATGTCCCCTGGAGCACTATTCA-TGAATGCCCTATTATGATTGAGA-GGACA
* * *
23245 GTGAAAGCGCGTTTCCGGGGACGCGTCTTCCATTATTTTCTCAGAGAACATGTTATTATTGCCCT
1 GTGAAAGCGCGTTTCCGGGG-CGCGCCTTCCATTATTTTGTCAGAGAACATGTTATCATTGCCCT
* * * *
23310 ATTATGTCACTCATGTCCCCCGAGGCACTATTCATTGATGCCCTATTATAGTTAAGGGGACTGTG
65 ATTATGTCACTCATGTCCCCCGGGGCACTATTCATTGATGCCCTATTATGGTTGAGGGGACGGTG
23375 AAAGCGCGTTTCCGGGGGGCACCTTCCATTATTTTGTCAGAAAACATGTTATCATTGCCCTATTA
130 AAAGCGCGTTTCCGGGGGGCACCTTCCATTATTTTGTCAGAAAACATGTTATCATTGCCCTATTA
* *
23440 TGTCACTCATGTCCCCTGGGGCACTATTCATGAATGCCCTATTATGATTGAGAGGACG
195 TGTCACTCATGTCCCCTGGAGCACTATTCATGAATGCCCTATTATGATTGAGAGGACA
* * *
23498 GTGCAAGCACGTTTCCGGGG-GGGCCTTCCATTATTTTGTCAGAGAACATGTTATCATTGCCCTA
1 GTGAAAGCGCGTTTCCGGGGCGCGCCTTCCATTATTTTGTCAGAGAACATGTTATCATTGCCCTA
* * *
23562 TTATGTCACTCGTGTCCCCTGGGGCACTATTTATTGATGCCCTATTATGGTTGAGGGGACGGTGA
66 TTATGTCACTCATGTCCCCCGGGGCACTATTCATTGATGCCCTATTATGGTTGAGGGGACGGTGA
* * ** * * * **
23627 AAGCGCGTTTTCGGGGGCGCTCCTTTAATTATTTTGTCAGAAAACATGTAAACGTAACCCTATTA
131 AAGCGCGTTTCCGGGGG-GCACCTTCCATTATTTTGTCAGAAAACATGTTATCATTGCCCTATTA
* * * * *
23692 TATCACTCATGTCCCCCAGG-GTACTATTCATGAATGCCTTATTATGTTTGAG
195 TGTCACTCATGT-CCCCTGGAGCACTATTCATGAATGCCCTATTATGATTGAG
23744 GGGATAAAAT
Statistics
Matches: 442, Mismatches: 50, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
251 114 0.26
252 198 0.45
253 129 0.29
254 1 0.00
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (252 bp):
GTGAAAGCGCGTTTCCGGGGCGCGCCTTCCATTATTTTGTCAGAGAACATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCCCGGGGCACTATTCATTGATGCCCTATTATGGTTGAGGGGACGGTGA
AAGCGCGTTTCCGGGGGGCACCTTCCATTATTTTGTCAGAAAACATGTTATCATTGCCCTATTAT
GTCACTCATGTCCCCTGGAGCACTATTCATGAATGCCCTATTATGATTGAGAGGACA
Found at i:23720 original size:378 final size:380
Alignment explanation
Indices: 22992--23736 Score: 1108
Period size: 378 Copynumber: 2.0 Consensus size: 380
22982 TACTATTCAC
* * * * *
22992 GTGAAGGCGCGTTTCTGGGGGCGCACCTTCTATTATTTTGTCAGAAAATATGTTATCATTGTCCT
1 GTGAAAGCGCGTTTCCGGGGGCGCACCTTCCATTATTTTGTCAGAAAACATGTTATCATTGCCCT
* *
23057 ATTATGTCACTCATGTCACCCGGGGGCACTATTCATTGATGCCCTATTATGGTTGAGGGGACGGT
66 ATTATGTCACTCATGTCACCCGGGGGCACTATTCATTGATGCCCTATTATGATTGAGAGGACGGT
*
23122 GAAAGCGCGTTTCCGGGGGGTGCCTTCCATTATTTTGTCAAAGAACATATTATCATTGCCCTATT
131 GAAAGCACGTTTCCGGGGGGTGCCTTCCATTATTTTGTCAAAGAACATATTATCATTGCCCTATT
*
23187 ATGTCACTTATGTCCCTGGAGCACTATTTATTGATGCCCTATTATGGTTGAAGGGACAGTGAAAG
196 ATGTCACTCATGTCCCTGGAGCACTATTTATTGATGCCCTATTATGGTTGAAGGGACAGTGAAAG
* * * ** ** *
23252 CGCGTTTCCGGGGACGCGTCTTCCATTATTTTCTCAGAGAACATGTTATTATTGCCCTATTATGT
261 CGCGTTTCCGGGGACGCGTCTTCAATTATTTTCTCAGAAAACATGTAAACATAACCCTATTATAT
23317 CACTCATGTCCCCCGAGGCACTATTCATTG-ATGCCCTATTATAGTTAAGGGGACT
326 CACTCATGTCCCCCGAGGCACTATTCA-TGAATGCCCTATTATAGTTAAGGGGACT
23372 GTGAAAGCGCGTTTCCGGGGG-GCACCTTCCATTATTTTGTCAGAAAACATGTTATCATTGCCCT
1 GTGAAAGCGCGTTTCCGGGGGCGCACCTTCCATTATTTTGTCAGAAAACATGTTATCATTGCCCT
*
23436 ATTATGTCACTCATGTC-CCCTGGGGCACTATTCA-TGAATGCCCTATTATGATTGAGAGGACGG
66 ATTATGTCACTCATGTCACCCGGGGGCACTATTCATTG-ATGCCCTATTATGATTGAGAGGACGG
* * *
23499 TGCAAGCACGTTTCCGGGGGG-GCCTTCCATTATTTTGTCAGAGAACATGTTATCATTGCCCTAT
130 TGAAAGCACGTTTCCGGGGGGTGCCTTCCATTATTTTGTCAAAGAACATATTATCATTGCCCTAT
* * * *
23563 TATGTCACTCGTGTCCCCTGGGGCACTATTTATTGATGCCCTATTATGGTTGAGGGGACGGTGAA
195 TATGTCACTCATGT-CCCTGGAGCACTATTTATTGATGCCCTATTATGGTTGAAGGGACAGTGAA
* * * * *
23628 AGCGCGTTTTCGGGGGCGC-TCCTTTAATTATTTTGTCAGAAAACATGTAAACGTAACCCTATTA
259 AGCGCGTTTCCGGGGACGCGT-CTTCAATTATTTTCTCAGAAAACATGTAAACATAACCCTATTA
* *
23692 TATCACTCATGTCCCCC-AGGGTACTATTCATGAATGCCTTATTAT
323 TATCACTCATGTCCCCCGA-GGCACTATTCATGAATGCCCTATTAT
23737 GTTTGAGGGG
Statistics
Matches: 328, Mismatches: 32, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
377 59 0.18
378 193 0.59
379 57 0.17
380 19 0.06
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (380 bp):
GTGAAAGCGCGTTTCCGGGGGCGCACCTTCCATTATTTTGTCAGAAAACATGTTATCATTGCCCT
ATTATGTCACTCATGTCACCCGGGGGCACTATTCATTGATGCCCTATTATGATTGAGAGGACGGT
GAAAGCACGTTTCCGGGGGGTGCCTTCCATTATTTTGTCAAAGAACATATTATCATTGCCCTATT
ATGTCACTCATGTCCCTGGAGCACTATTTATTGATGCCCTATTATGGTTGAAGGGACAGTGAAAG
CGCGTTTCCGGGGACGCGTCTTCAATTATTTTCTCAGAAAACATGTAAACATAACCCTATTATAT
CACTCATGTCCCCCGAGGCACTATTCATGAATGCCCTATTATAGTTAAGGGGACT
Found at i:24364 original size:217 final size:219
Alignment explanation
Indices: 23982--24421 Score: 726
Period size: 217 Copynumber: 2.0 Consensus size: 219
23972 TTTTAACAAG
* * *
23982 ATAATGCAATTTAATTTCAATTTAATTACTGTGAACTATAATTGGAATATAACTTTGAATTTTGA
1 ATAATGCAATTTAATTTCAATTTAAGTACTGTGAACTATAATTGGAATATAACTTTAAATTTCGA
* * * *
24047 TTACAATTTTAAATTTCAATTGGAATATTAAGTTCAATTTGAATTTTTATTTTATAAACTTTTAA
66 ATACAATTTTAAATTTCAATTGGAATATTAAGTTCAATTTGAATTTGTATTTTATAAAATATTAA
*
24112 CAAACATTTAATGTTAAATTTGAATAAAAATAACATTAAAAAA-TT-TTGTAACAACCATTAAAC
131 CAAACATTTAATGTTAAATTTGAATAAAAATAACATTAAAAAATTTGTTCTAACAACCATTAAAC
*
24175 ATTTAAATAACATTACAAAATTAC
196 ATTTAAATAACATAACAAAATTAC
*
24199 ATAATGTAATTTAATTTCAATTTAAGTACTGTGAACTATAATTGGAATATAACTTTAAATTTCGA
1 ATAATGCAATTTAATTTCAATTTAAGTACTGTGAACTATAATTGGAATATAACTTTAAATTTCGA
24264 ATACAATTTTAAATTTCAATTGGAATATTAAGTTCAATTTGAATTTGTA-TTTA-AAAATAATTA
66 ATACAATTTTAAATTTCAATTGGAATATTAAGTTCAATTTGAATTTGTATTTTATAAAAT-ATTA
*
24327 ACAAACATTTAATGTTAAATTTGAATAAAAAATAACATTAAAAAATTTGTTCTAATAACCATTAA
130 ACAAACATTTAATGTTAAATTTGAAT-AAAAATAACATTAAAAAATTTGTTCTAACAACCATTAA
*
24392 ATATTTAAATAACATAACAAAATTAC
194 ACATTTAAATAACATAACAAAATTAC
24418 ATAA
1 ATAA
24422 ATTTCTGAAA
Statistics
Matches: 207, Mismatches: 12, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
215 4 0.02
216 33 0.16
217 126 0.61
218 2 0.01
219 42 0.20
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (219 bp):
ATAATGCAATTTAATTTCAATTTAAGTACTGTGAACTATAATTGGAATATAACTTTAAATTTCGA
ATACAATTTTAAATTTCAATTGGAATATTAAGTTCAATTTGAATTTGTATTTTATAAAATATTAA
CAAACATTTAATGTTAAATTTGAATAAAAATAACATTAAAAAATTTGTTCTAACAACCATTAAAC
ATTTAAATAACATAACAAAATTAC
Found at i:26718 original size:25 final size:24
Alignment explanation
Indices: 26674--26720 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
26664 TAATTAACAC
*
26674 AAATAATAATTAAGTAATAAATTT
1 AAATAATAATTAACTAATAAATTT
26698 AAATAAATAA-TAACTATATAAAT
1 AAAT-AATAATTAACTA-ATAAAT
26721 ATTATTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (24 bp):
AAATAATAATTAACTAATAAATTT
Found at i:26766 original size:11 final size:14
Alignment explanation
Indices: 26737--26771 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
26727 TTAATAAAAA
26737 AATAATATTTATAT
1 AATAATATTTATAT
*
26751 AATAATATTAATAT
1 AATAATATTTATAT
26765 AA-AATAT
1 AATAATAT
26772 AACAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATAATATTTATAT
Found at i:26782 original size:22 final size:21
Alignment explanation
Indices: 26754--26795 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
26744 TTTATATAAT
26754 AATATTAATATAAAATA-TAACA
1 AATATTAA-A-AAAATACTAACA
26776 AATATTAAAAAAATACTAAC
1 AATATTAAAAAAATACTAAC
26796 TTAAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 5 0.26
22 8 0.42
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (21 bp):
AATATTAAAAAAATACTAACA
Found at i:29085 original size:31 final size:31
Alignment explanation
Indices: 29015--29092 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
29005 CTTTTAAAAC
* *
29015 TTACAATACAGTCCCCCAACATTTAGTCTGT
1 TTACAATATAGTCCCCCAACATTTAGTCTAT
29046 TTACAATATAGTCCCCCAACATTTAGTCTAT
1 TTACAATATAGTCCCCCAACATTTAGTCTAT
* *
29077 TTGCAATATGGTCCCC
1 TTACAATATAGTCCCC
29093 GACCGTTTGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.33
Consensus pattern (31 bp):
TTACAATATAGTCCCCCAACATTTAGTCTAT
Found at i:30307 original size:30 final size:31
Alignment explanation
Indices: 30273--30344 Score: 110
Period size: 32 Copynumber: 2.3 Consensus size: 31
30263 GTTCCTAAGA
30273 ACATAGGTAA-CTGTCCATATATCCCGAAGG
1 ACATAGGTAACCTGTCCATATATCCCGAAGG
* *
30303 ACATAGGTAATCCTGTCCATATGTCCCGAATG
1 ACATAGGTAA-CCTGTCCATATATCCCGAAGG
30335 ACATAGGTAA
1 ACATAGGTAA
30345 ATTATTCATA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 10 0.26
32 28 0.74
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.25
Consensus pattern (31 bp):
ACATAGGTAACCTGTCCATATATCCCGAAGG
Found at i:34023 original size:31 final size:31
Alignment explanation
Indices: 33988--34061 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
33978 TCAAACGATC
*
33988 GGGGACCATATTGCAAACAGACTAAATGTTG
1 GGGGACCATATTGCAAACAGACTAAATATTG
* *
34019 GGGGACCATTTTGCAAATAGACTAAATATTG
1 GGGGACCATATTGCAAACAGACTAAATATTG
*
34050 GGGGACTATATT
1 GGGGACCATATT
34062 ATAAGTTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.27
Consensus pattern (31 bp):
GGGGACCATATTGCAAACAGACTAAATATTG
Found at i:42705 original size:26 final size:26
Alignment explanation
Indices: 42669--42751 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 26
42659 CATTGTATTA
* * *
42669 TAATATAATGTAGGAGTTAATGCTTC
1 TAATGTAATGTACGAGTTAATGTTTC
* * *
42695 TAATGTAATGTACTAGTTATTATTTC
1 TAATGTAATGTACGAGTTAATGTTTC
* * *
42721 TGATGTAAAGTATGAGTTAATGTTTC
1 TAATGTAATGTACGAGTTAATGTTTC
*
42747 GAATG
1 TAATG
42752 AAAAAATTAA
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (26 bp):
TAATGTAATGTACGAGTTAATGTTTC
Found at i:46593 original size:84 final size:84
Alignment explanation
Indices: 46468--46832 Score: 500
Period size: 84 Copynumber: 4.3 Consensus size: 84
46458 GACAGTTTCC
* * * * * *
46468 TGTTGGCAGATAGCTCTTCTCGCCTTGAGTTATGTTGCAAATGATGTGCGTTTAAGCTGAGTGTA
1 TGTTGGCAGATAACTCTTCTCGCCTTGAGATAAGCTGCAAATGATGTGCCTTTGAGCTGAGTGTA
46533 ATCGAACTCGAAGGTCTTT
66 ATCGAACTCGAAGGTCTTT
* * *
46552 TGTTGGCAGATAACCCTTCTTGCCTTGAGATAAGCTGCAAATAATGTGCCTTTGAGCTGAGTGTA
1 TGTTGGCAGATAACTCTTCTCGCCTTGAGATAAGCTGCAAATGATGTGCCTTTGAGCTGAGTGTA
*
46617 ATCGAACTCGAAGGTTTTT
66 ATCGAACTCGAAGGTCTTT
* * * * *
46636 TGTTGGCAGATAACTCTTCTCACCTTAAGCTATGCTGCAAATGATGTACCTTTGAGCTGAGTGTA
1 TGTTGGCAGATAACTCTTCTCGCCTTGAGATAAGCTGCAAATGATGTGCCTTTGAGCTGAGTGTA
46701 ATCGAACTCGAAGGTCTTT
66 ATCGAACTCGAAGGTCTTT
* * ** * *
46720 TGCTGGCAGATAACTCTTCTCGCCTTAAGCTATAA--TATAAATGATGTGCCTTTGAGTTGAGCG
1 TGTTGGCAGATAACTCTTCTCGCCTTGAG--ATAAGCTGCAAATGATGTGCCTTTGAGCTGAGTG
46783 TAATCGAACTCGAAGGTCTTT
64 TAATCGAACTCGAAGGTCTTT
*
46804 TGTTGGCAGATAACTCTTCTTGCCTTGAG
1 TGTTGGCAGATAACTCTTCTCGCCTTGAG
46833 CAATGATGTG
Statistics
Matches: 248, Mismatches: 31, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
84 246 0.99
86 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (84 bp):
TGTTGGCAGATAACTCTTCTCGCCTTGAGATAAGCTGCAAATGATGTGCCTTTGAGCTGAGTGTA
ATCGAACTCGAAGGTCTTT
Found at i:47648 original size:124 final size:123
Alignment explanation
Indices: 46930--47277 Score: 489
Period size: 124 Copynumber: 2.8 Consensus size: 123
46920 GAACACGATA
* * * * * * *
46930 TCCTTCGTCGTGAAGTTGAAATCGCGGAGGGCCCATTCGTTGTGAAGTTGAGCCTTTATTTAGAT
1 TCCTTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTGGAT
* * *
46995 ATACTTCGTCGTGAAGTTGAAATCCAATCTGAAGATGAATGTTGTTGGTGGGCACAAT
66 ATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGGGCACAAT
47053 TCCATTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTGGA
1 TCC-TTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTGGA
* * * * *
47118 TATCCTTCGTCGTGAAGTTGAAATCCAATATAAAGATAAATGTTACTGGTGAGCACGAT
65 TATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGGGCACAAT
* * *
47177 TCCCTTCGTTGTGAAGTTAAAACCGTGGATGACCCATTCGGTGTGAAGTTGAGCCTTGAATTGGA
1 T-CCTTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTGGA
* *
47242 TATCATTCGTCGTGAAGTTGAAATTCAATCTCAAAG
65 TATCCTTCGTCGTGAAGTTGAAATCCAATCT-AAAG
47278 GTCTTTTGTT
Statistics
Matches: 201, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
123 3 0.01
124 192 0.96
125 6 0.03
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (123 bp):
TCCTTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTGGAT
ATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGGGCACAAT
Found at i:47659 original size:124 final size:124
Alignment explanation
Indices: 47407--47801 Score: 537
Period size: 124 Copynumber: 3.2 Consensus size: 124
47397 AATGAACACG
* * * * * * *
47407 ATATCCTTCGTCGTGAAGTTGAAATCGCGGAGGGCCCATTCGTTGTGAAGTTGAGCCTTTATTTA
1 ATATCCTTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTG
* * * *
47472 GATATACTTCGTCGTGAAGTTGAAATCCAATCTGAAGATGAATGTTGTTGGTGGGCACA
66 GATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGAGCACA
47531 AT-TCCATTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATT
1 ATATCC-TTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATT
* * * *
47595 GGATATCCTTCGTCGTGAAGTTGAAATCCAATATAAAGATAAATGTTACTGGTGAGCACG
65 GGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGAGCACA
* * *
47655 AT-TCCCTTCGTTGTGAAGTTAAAACCGTGGATGACCCATTCGGTGTGAAGTTGAGCCTTGAATT
1 ATAT-CCTTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATT
* * * *
47719 GGATATCATTCGTCGTGAAGTTGAAATTCAATCTCAAGATGAATGTTGCT-TTGAGTCA-A
65 GGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGAG-CACA
47778 ATATCCTTCGTCGTGAAGTTGAAA
1 ATATCCTTCGTCGTGAAGTTGAAA
47802 TTGGTTCTGA
Statistics
Matches: 239, Mismatches: 28, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
123 27 0.11
124 210 0.88
125 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (124 bp):
ATATCCTTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTG
GATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGAGCACA
Found at i:47696 original size:480 final size:480
Alignment explanation
Indices: 46795--47755 Score: 1922
Period size: 480 Copynumber: 2.0 Consensus size: 480
46785 ATCGAACTCG
46795 AAGGTCTTTTGTTGGCAGATAACTCTTCTTGCCTTGAGCAATGATGTGCATTTAAACTAAGTATA
1 AAGGTCTTTTGTTGGCAGATAACTCTTCTTGCCTTGAGCAATGATGTGCATTTAAACTAAGTATA
46860 ATCGAACTTGAAGGTATTTGTTGGTAGATAACCCTTTTAGCCTTGAGTTATGCTGTAAATGAACA
66 ATCGAACTTGAAGGTATTTGTTGGTAGATAACCCTTTTAGCCTTGAGTTATGCTGTAAATGAACA
46925 CGATATCCTTCGTCGTGAAGTTGAAATCGCGGAGGGCCCATTCGTTGTGAAGTTGAGCCTTTATT
131 CGATATCCTTCGTCGTGAAGTTGAAATCGCGGAGGGCCCATTCGTTGTGAAGTTGAGCCTTTATT
46990 TAGATATACTTCGTCGTGAAGTTGAAATCCAATCTGAAGATGAATGTTGTTGGTGGGCACAATTC
196 TAGATATACTTCGTCGTGAAGTTGAAATCCAATCTGAAGATGAATGTTGTTGGTGGGCACAATTC
47055 CATTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATA
261 CATTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATA
47120 TCCTTCGTCGTGAAGTTGAAATCCAATATAAAGATAAATGTTACTGGTGAGCACGATTCCCTTCG
326 TCCTTCGTCGTGAAGTTGAAATCCAATATAAAGATAAATGTTACTGGTGAGCACGATTCCCTTCG
47185 TTGTGAAGTTAAAACCGTGGATGACCCATTCGGTGTGAAGTTGAGCCTTGAATTGGATATCATTC
391 TTGTGAAGTTAAAACCGTGGATGACCCATTCGGTGTGAAGTTGAGCCTTGAATTGGATATCATTC
47250 GTCGTGAAGTTGAAATTCAATCTCA
456 GTCGTGAAGTTGAAATTCAATCTCA
47275 AAGGTCTTTTGTTGGCAGATAACTCTTCTTGCCTTGAGCAATGATGTGCATTTAAACTAAGTATA
1 AAGGTCTTTTGTTGGCAGATAACTCTTCTTGCCTTGAGCAATGATGTGCATTTAAACTAAGTATA
47340 ATCGAACTTGAAGGTATTTGTTGGTAGATAACCCTTTTAGCCTTGAGTTATGCTGTAAATGAACA
66 ATCGAACTTGAAGGTATTTGTTGGTAGATAACCCTTTTAGCCTTGAGTTATGCTGTAAATGAACA
47405 CGATATCCTTCGTCGTGAAGTTGAAATCGCGGAGGGCCCATTCGTTGTGAAGTTGAGCCTTTATT
131 CGATATCCTTCGTCGTGAAGTTGAAATCGCGGAGGGCCCATTCGTTGTGAAGTTGAGCCTTTATT
47470 TAGATATACTTCGTCGTGAAGTTGAAATCCAATCTGAAGATGAATGTTGTTGGTGGGCACAATTC
196 TAGATATACTTCGTCGTGAAGTTGAAATCCAATCTGAAGATGAATGTTGTTGGTGGGCACAATTC
47535 CATTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATA
261 CATTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATA
47600 TCCTTCGTCGTGAAGTTGAAATCCAATATAAAGATAAATGTTACTGGTGAGCACGATTCCCTTCG
326 TCCTTCGTCGTGAAGTTGAAATCCAATATAAAGATAAATGTTACTGGTGAGCACGATTCCCTTCG
47665 TTGTGAAGTTAAAACCGTGGATGACCCATTCGGTGTGAAGTTGAGCCTTGAATTGGATATCATTC
391 TTGTGAAGTTAAAACCGTGGATGACCCATTCGGTGTGAAGTTGAGCCTTGAATTGGATATCATTC
47730 GTCGTGAAGTTGAAATTCAATCTCA
456 GTCGTGAAGTTGAAATTCAATCTCA
47755 A
1 A
47756 GATGAATGTT
Statistics
Matches: 481, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
480 481 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (480 bp):
AAGGTCTTTTGTTGGCAGATAACTCTTCTTGCCTTGAGCAATGATGTGCATTTAAACTAAGTATA
ATCGAACTTGAAGGTATTTGTTGGTAGATAACCCTTTTAGCCTTGAGTTATGCTGTAAATGAACA
CGATATCCTTCGTCGTGAAGTTGAAATCGCGGAGGGCCCATTCGTTGTGAAGTTGAGCCTTTATT
TAGATATACTTCGTCGTGAAGTTGAAATCCAATCTGAAGATGAATGTTGTTGGTGGGCACAATTC
CATTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATA
TCCTTCGTCGTGAAGTTGAAATCCAATATAAAGATAAATGTTACTGGTGAGCACGATTCCCTTCG
TTGTGAAGTTAAAACCGTGGATGACCCATTCGGTGTGAAGTTGAGCCTTGAATTGGATATCATTC
GTCGTGAAGTTGAAATTCAATCTCA
Found at i:47875 original size:64 final size:64
Alignment explanation
Indices: 47769--48001 Score: 288
Period size: 64 Copynumber: 3.6 Consensus size: 64
47759 GAATGTTGCT
* * ** * *
47769 TTGAGTCAAATATCCTTCG-TCGTGAAGTTGAAATTGGTTCTGAATGAAACTGGGAAGCCGTTTG
1 TTGAGTCCAATATCATTCGCT-GTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTCGTTTG
* * *
47833 TTGAGTTCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATTAAACTAGAAAGTCGTTTG
1 TTGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTCGTTTG
* * * * * *
47897 TTGAGTCCAATATCATTCACTGTGAAGTTAAAATTGACTTTGAATGAAACTGAAAAGTTGTTTA
1 TTGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTCGTTTG
* * *
47961 TTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTAACTCT
1 TTGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCT
48002 AAAAACTGCA
Statistics
Matches: 144, Mismatches: 24, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
64 143 0.99
65 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (64 bp):
TTGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTCGTTTG
Found at i:49212 original size:12 final size:12
Alignment explanation
Indices: 49195--49219 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49185 ACTGCCACAA
49195 TTTCAAACATAT
1 TTTCAAACATAT
49207 TTTCAAACATAT
1 TTTCAAACATAT
49219 T
1 T
49220 GAAAAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (12 bp):
TTTCAAACATAT
Found at i:49939 original size:22 final size:22
Alignment explanation
Indices: 49914--49971 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
49904 ATGTTGATGT
49914 TGTTTTATTTTAATTTAGTCAC
1 TGTTTTATTTTAATTTAGTCAC
* * *
49936 TG-TTAATTTCTGATTTAGTTAC
1 TGTTTTATTT-TAATTTAGTCAC
49958 --TTTTATTTTAATTT
1 TGTTTTATTTTAATTT
49972 TTGCATGTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
20 5 0.17
21 12 0.41
22 12 0.41
ACGTcount: A:0.22, C:0.07, G:0.09, T:0.62
Consensus pattern (22 bp):
TGTTTTATTTTAATTTAGTCAC
Found at i:50250 original size:27 final size:26
Alignment explanation
Indices: 50214--50272 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
50204 TTTTTTATAT
*
50214 ATTTTGTTATTTCTTTTAGATATTAAC
1 ATTTTCTTATTTCTTTTA-ATATTAAC
* * *
50241 ATTTTCTTATTTTTTTTATTTTTAAC
1 ATTTTCTTATTTCTTTTAATATTAAC
50267 ATTTTC
1 ATTTTC
50273 ATCATTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 12 0.43
27 16 0.57
ACGTcount: A:0.22, C:0.08, G:0.03, T:0.66
Consensus pattern (26 bp):
ATTTTCTTATTTCTTTTAATATTAAC
Found at i:50265 original size:26 final size:28
Alignment explanation
Indices: 50236--50289 Score: 85
Period size: 26 Copynumber: 2.0 Consensus size: 28
50226 CTTTTAGATA
*
50236 TTAACATTTTC-TTATTTTT-TTTATTT
1 TTAACATTTTCATCATTTTTATTTATTT
50262 TTAACATTTTCATCATTTTTATTTATTT
1 TTAACATTTTCATCATTTTTATTTATTT
50290 ATATTGTGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 11 0.44
27 7 0.28
28 7 0.28
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (28 bp):
TTAACATTTTCATCATTTTTATTTATTT
Found at i:52588 original size:21 final size:20
Alignment explanation
Indices: 52559--52611 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
52549 AAAATGAAAA
52559 AAAT-AAAATAACAGT-AGCT
1 AAATCAAAATAACAGTGA-CT
52578 AAATCAGAAATTAACAGTGACT
1 AAATCA-AAA-TAACAGTGACT
*
52600 AAATTAAAATAA
1 AAATCAAAATAA
52612 AACAACATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 4 0.14
20 4 0.14
21 6 0.21
22 14 0.48
23 1 0.03
ACGTcount: A:0.58, C:0.09, G:0.09, T:0.23
Consensus pattern (20 bp):
AAATCAAAATAACAGTGACT
Found at i:54061 original size:124 final size:122
Alignment explanation
Indices: 53851--54206 Score: 498
Period size: 124 Copynumber: 2.9 Consensus size: 122
53841 CACGATATTA
* * **
53851 TTCGTCGTGAAGTTGAAATCATGG-TAGACCCCTTTGTTGTGAAGTTGAGCCTTGAATTGGATAT
1 TTCGTCGTGAAGTTGAAACCGTGGAT-GA-CCCTTCATTGTGAAGTTGAGCCTTGAATTGGATAT
* * *
53915 CCTTCGTCGTGAAGTTAAAATCCAATCTGAAAATGAATGTTGCTGGTGGGCACGATTCCC
64 CATTCGTCGTGAAGTTGAAATCCAATCT-AAAATGAATGTTGCTGGTGAGCACGATTCCC
*
53975 TTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCATTGTGAAGTTGAGCCTTGAATTGGATATC
1 TTCGTCGTGAAGTTGAAACCGTGGATGACCC-TTCATTGTGAAGTTGAGCCTTGAATTGGATATC
* * * *
54040 TTTCGTCGTGAAGTTGAAATCCAATCTAAAGATAAATATTACTGGTGAGCACGATTCCC
65 ATTCGTCGTGAAGTTGAAATCCAATCTAAA-ATGAATGTTGCTGGTGAGCACGATTCCC
* * *
54099 TTGGTTGTGAAGTTGAAACCGTGGATGACCTCTTCATTGTGAAGTTGAGCATTGAATTGGATATC
1 TTCGTCGTGAAGTTGAAACCGTGGATGACC-CTTCATTGTGAAGTTGAGCCTTGAATTGGATATC
*
54164 ATTCGTCGTGAAGTTGAAATCCAATCTCAAGATGAATGTTGCT
65 ATTCGTCGTGAAGTTGAAATCCAATCT-AAAATGAATGTTGCT
54207 TCGAGTCCAA
Statistics
Matches: 207, Mismatches: 20, Indels: 10
0.87 0.08 0.04
Matches are distributed among these distances:
123 6 0.03
124 197 0.95
125 4 0.02
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (122 bp):
TTCGTCGTGAAGTTGAAACCGTGGATGACCCTTCATTGTGAAGTTGAGCCTTGAATTGGATATCA
TTCGTCGTGAAGTTGAAATCCAATCTAAAATGAATGTTGCTGGTGAGCACGATTCCC
Found at i:54283 original size:64 final size:64
Alignment explanation
Indices: 54247--54439 Score: 314
Period size: 64 Copynumber: 3.0 Consensus size: 64
54237 AAATTAGTTT
* * * *
54247 TGAATGAAACTGGGAAGCCGTTTGTTGAGTCCAATATCCTTCGCTGTGAATTTGAAATTGACTC
1 TGAATGAAACTGGAAAGTCGTTTGTTGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTC
* *
54311 TGAATGAAATTGGAAAGTCGTTTGTTGAGTCCAATAGCATTCGCTGTGAAGTTGAAATTGACTC
1 TGAATGAAACTGGAAAGTCGTTTGTTGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTC
* *
54375 TGAATGAAACTGGAAAGTTGTTTGTTGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGACTC
1 TGAATGAAACTGGAAAGTCGTTTGTTGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTC
54439 T
1 T
54440 AAAAACATCA
Statistics
Matches: 119, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 119 1.00
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.34
Consensus pattern (64 bp):
TGAATGAAACTGGAAAGTCGTTTGTTGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTC
Done.