Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006776.1 Hibiscus syriacus cultivar Beakdansim tig00017128_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: 74409
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:802 original size:17 final size:16
Alignment explanation
Indices: 735--816 Score: 50
Period size: 17 Copynumber: 5.1 Consensus size: 16
725 CCTTGGCTTG
*
735 CTTTCTCTTTTTGATTT
1 CTTT-TCTTTTTGCTTT
752 CTTTTTCTTTCTT--TTT
1 C-TTTTCTTT-TTGCTTT
768 -TTTTCTGATTTT--TTT
1 CTTTTCT--TTTTGCTTT
783 CTTCTT-TTTTTGTCTTT
1 CTT-TTCTTTTTG-CTTT
800 CTTTTCTTTTTGCTTT
1 CTTTTCTTTTTGCTTT
816 C
1 C
817 CAATTTTGTT
Statistics
Matches: 55, Mismatches: 0, Indels: 21
0.72 0.00 0.28
Matches are distributed among these distances:
14 10 0.18
15 5 0.09
16 15 0.27
17 20 0.36
18 5 0.09
ACGTcount: A:0.02, C:0.17, G:0.05, T:0.76
Consensus pattern (16 bp):
CTTTTCTTTTTGCTTT
Found at i:1153 original size:22 final size:21
Alignment explanation
Indices: 1119--1159 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1109 GTTGCAGAAT
1119 TGATGGTCATGATGGATGAAGA
1 TGATGGTCATGAT-GATGAAGA
**
1141 TGATGGTGTTGATGATGAA
1 TGATGGTCATGATGATGAA
1160 TGGAGATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.29, C:0.02, G:0.37, T:0.32
Consensus pattern (21 bp):
TGATGGTCATGATGATGAAGA
Found at i:4879 original size:20 final size:20
Alignment explanation
Indices: 4850--4903 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
4840 TATATATATG
* *
4850 GCATCATTTCATGCTTTAAT
1 GCATCCTTTCATGCCTTAAT
4870 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
4890 GCATCCTTTCATGC
1 GCATCCTTTCATGC
4904 ATTTTCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.20, C:0.28, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:4922 original size:47 final size:47
Alignment explanation
Indices: 4870--5104 Score: 355
Period size: 47 Copynumber: 5.0 Consensus size: 47
4860 ATGCTTTAAT
4870 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATG
* * * *
4917 GCATCCTTTCATGCCTTAATACTTCCTTTCATTCATTTTCAATTGTG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATG
* * * *
4964 GCAT-TTGTTCATGCCTTAATGCAACCTTTCGTGCATTTTTAATTATG
1 GCATCCT-TTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATG
*
5011 GCATCCTTTCATGCCTTAATGCATCCTTTCATGTATTTTCAATTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATG
* *
5058 GCATCCTTTCATGCCTTAATCCATACTTTCATGCATTTTCAATTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATG
5105 AATTTGATTT
Statistics
Matches: 166, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
46 1 0.01
47 164 0.99
48 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.44
Consensus pattern (47 bp):
GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATG
Found at i:4945 original size:20 final size:20
Alignment explanation
Indices: 4851--4948 Score: 79
Period size: 20 Copynumber: 4.5 Consensus size: 20
4841 ATATATATGG
* * *
4851 CATCATTTCATGCTTTAATG
1 CATCCTTTCATGCCTTAATA
*
4871 CATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATA
*
4891 CATCCTTTCATGCATTTTCAATTA
1 CATCCTTTCATGC--CTT-AA-TA
4915 TGGCATCCTTTCATGCCTTAATA
1 ---CATCCTTTCATGCCTTAATA
*
4938 CTTCCTTTCAT
1 CATCCTTTCAT
4949 TCATTTTCAA
Statistics
Matches: 65, Mismatches: 6, Indels: 14
0.76 0.07 0.16
Matches are distributed among these distances:
20 41 0.63
22 2 0.03
23 4 0.06
24 3 0.05
25 2 0.03
27 13 0.20
ACGTcount: A:0.21, C:0.27, G:0.08, T:0.44
Consensus pattern (20 bp):
CATCCTTTCATGCCTTAATA
Found at i:5683 original size:21 final size:21
Alignment explanation
Indices: 5572--5683 Score: 99
Period size: 21 Copynumber: 5.4 Consensus size: 21
5562 TGTTGCCTGA
5572 TATCGATA-CCCTTACCATGG
1 TATCGATACCCCTTACCATGG
*
5592 TATCGATACTACCC-TACTATGG
1 TATCGATAC--CCCTTACCATGG
*
5614 TACCGATACCCCCTTA-CA--G
1 TATCGATA-CCCCTTACCATGG
* *
5633 TATCGATACACCTTACCATTG
1 TATCGATACCCCTTACCATGG
* *
5654 TATCAATACCCCTTACCATTG
1 TATCGATACCCCTTACCATGG
*
5675 TAGCGATAC
1 TATCGATAC
5684 TGATTGAATC
Statistics
Matches: 75, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
18 6 0.08
19 10 0.13
20 8 0.11
21 31 0.41
22 16 0.21
23 4 0.05
ACGTcount: A:0.28, C:0.31, G:0.12, T:0.29
Consensus pattern (21 bp):
TATCGATACCCCTTACCATGG
Found at i:11294 original size:20 final size:19
Alignment explanation
Indices: 11269--11332 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 19
11259 TTTGAAATAC
11269 AAAAATATTCAAATAATCAA
1 AAAAATATT-AAATAATCAA
*
11289 AAAAATATAAAAATAATACAA
1 AAAAATAT-TAAATAAT-CAA
*
11310 ATAAAA-ATTAAATCACTCAA
1 A-AAAATATTAAAT-AATCAA
11330 AAA
1 AAA
11333 TAAATATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
19 2 0.05
20 23 0.62
21 8 0.22
22 4 0.11
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAAATATTAAATAATCAA
Found at i:14002 original size:139 final size:135
Alignment explanation
Indices: 13740--14163 Score: 487
Period size: 138 Copynumber: 3.1 Consensus size: 135
13730 AAAGTTCAGA
* * * *
13740 CTCTAATAATAATCCTAATTAAAATTAAATAATTATGTGATTCGAATAATTAAAGTGGAAACTCG
1 CTCTAATATTAATTCTAATT-AATTTAAATAATTATGTGATTCGAATAATTAAA-TTGAAACTCG
* * ** * ** *
13805 A-CAAAA-AAAGA-AAAAAAAATAATTCACCTAATTTAAGGACTAAATACGAAGTTAGGCCTAAG
64 AGCAAAACAAGGACCAAATTAAGAATTCACCTAATTTAAGGACTAAATGTGAAATTAGGCCTAAG
13867 ATGGAGG
129 ATGGAGG
*
13874 CTCTAATATTAATTCTAGTTGAATTTAAATAAATTATGTGATTCGAATAATTAAATTGAAACATC
1 CTCTAATATTAATTCTAATT-AATTTAAAT-AATTATGTGATTCGAATAATTAAATTGAAAC-TC
* * *
13939 GAGCAAAACCAAGGACCAAATTAAGAATTCACCTATTTTAAGGAATAAATGTGAAATTGGGCCTA
63 GAGCAAAA-CAAGGACCAAATTAAGAATTCACCTAATTTAAGGACTAAATGTGAAATTAGGCCTA
*
14004 AGTTGGAGG
127 AGATGGAGG
* * * * * *
14013 CTCTAATATTAAAAT-TAATTAATTTTAATCAATTATGCGATTTGAATAATTAAATTGGAACCTT
1 CTCTAATATT-AATTCTAATTAATTTAAAT-AATTATGTGATTCGAATAATTAAATT-GAAACTC
* *
14077 GAGCAAAAGCGAGGACCAAATTAAGAATTCACCTAATTTAAGGACTAAATGTGGAATTAGGCCTA
63 GAGCAAAA-CAAGGACCAAATTAAGAATTCACCTAATTTAAGGACTAAATGTGAAATTAGGCCTA
*
14142 AGATAGAGG
127 AGATGGAGG
*
14151 CTCTAATTTTAAT
1 CTCTAATATTAAT
14164 CAATTATTGA
Statistics
Matches: 246, Mismatches: 36, Indels: 13
0.83 0.12 0.04
Matches are distributed among these distances:
134 31 0.13
135 28 0.11
136 5 0.02
137 2 0.01
138 112 0.46
139 65 0.26
140 3 0.01
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (135 bp):
CTCTAATATTAATTCTAATTAATTTAAATAATTATGTGATTCGAATAATTAAATTGAAACTCGAG
CAAAACAAGGACCAAATTAAGAATTCACCTAATTTAAGGACTAAATGTGAAATTAGGCCTAAGAT
GGAGG
Found at i:17374 original size:30 final size:30
Alignment explanation
Indices: 17338--17411 Score: 112
Period size: 30 Copynumber: 2.5 Consensus size: 30
17328 TGGGTCAACT
*
17338 CGTTGACTTTGACCGAGTAAACACGTTGAC
1 CGTTGACTTTGACCGAGTAAACACATTGAC
* * *
17368 CGTTGACTTTGACTGAGTCAACCCATTGAC
1 CGTTGACTTTGACCGAGTAAACACATTGAC
17398 CGTTGACTTTGACC
1 CGTTGACTTTGACC
17412 AAAAAGTCGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.30
Consensus pattern (30 bp):
CGTTGACTTTGACCGAGTAAACACATTGAC
Found at i:17716 original size:20 final size:20
Alignment explanation
Indices: 17674--17718 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
17664 ATTCGATTCA
**
17674 TTTTTCATAATTAAGCTTTG
1 TTTTTCATAATTAAGCTCAG
*
17694 TTTTTCGTAATTAAGCTCAG
1 TTTTTCATAATTAAGCTCAG
17714 TTTTT
1 TTTTT
17719 TATGAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (20 bp):
TTTTTCATAATTAAGCTCAG
Found at i:20224 original size:43 final size:43
Alignment explanation
Indices: 20163--20498 Score: 440
Period size: 43 Copynumber: 7.8 Consensus size: 43
20153 CCGTTACCGT
* * * *
20163 AGGTTCCTTTGCTATGTGCAAGGGTAAGCCTTATAGTTTCCTC
1 AGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
* * *
20206 AGGTTCCTTTGATGTGTGCAAGGGTAAGCCATACAGTTTCCCT
1 AGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
* * * *
20249 ATGTTCCTTTGTTGTGTGAAAGAGTAAGCCTTACAGCTTCCCC
1 AGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
* *
20292 AGGTTCCTTTGATGTGTGCAAGGGTAAGCCTTACAGCTTCCCC
1 AGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
*
20335 AGGTTCCTTTGTTGCGTGCAAGGGTAAGCCTTACAGTTTCTCCC
1 AGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTC-CCC
* * * *
20379 AGGTTCCTTTGCTATGTGCAAGGGTAAGCCTTACAGTTTCTCT
1 AGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
*
20422 AGGTTCCTTTGTTGTGTACAAGGGTAAGACCTTACAGTTT-CCC
1 AGGTTCCTTTGTTGTGTGCAAGGGTAAG-CCTTACAGTTTCCCC
* * *
20465 AGGCTCTTTTGTTATGTGCAAGGGTAAGACCTTA
1 AGGTTCCTTTGTTGTGTGCAAGGGTAAG-CCTTA
20499 TCATTTTTTC
Statistics
Matches: 257, Mismatches: 34, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
43 206 0.80
44 51 0.20
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.35
Consensus pattern (43 bp):
AGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
Found at i:20485 original size:173 final size:173
Alignment explanation
Indices: 20163--20498 Score: 480
Period size: 173 Copynumber: 1.9 Consensus size: 173
20153 CCGTTACCGT
* * * *
20163 AGGTTCCTTTGCTATGTGCAAGGGTAAGCCTTATAGTTTCCTCAGGTTCCTTTGATGTGTGCAAG
1 AGGTTCCTTTGCTACGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGATATGTGCAAG
*
20228 GGTAAGCCATACAGTTTCCCTATGTTCCTTTGTTGTGTGAAAGAGTAAGCCTTACAGCTTCCCCA
66 GGTAAGCCATACAGTTTCCCTAGGTTCCTTTGTTGTGTGAAAGAGTAAGCCTTACAGCTTCCCCA
* *
20293 GGTTCCTTTGATGTGTGCAAGGGTAAG-CCTTACAGCTTCCCC
131 GGCTCCTTTGATATGTGCAAGGGTAAGACCTTACAGCTTCCCC
* * *
20335 AGGTTCCTTTGTTGCGTGCAAGGGTAAGCCTTACAGTTTCTCCCAGGTTCCTTTGCTATGTGCAA
1 AGGTTCCTTTGCTACGTGCAAGGGTAAGCCTTACAGTTTC-CCCAGGTTCCTTTGATATGTGCAA
* * * *
20400 GGGTAAGCCTTACAGTTTCTCTAGGTTCCTTTGTTGTGT-ACAAGGGTAAGACCTTACAG-TTTC
65 GGGTAAGCCATACAGTTTCCCTAGGTTCCTTTGTTGTGTGA-AAGAGTAAG-CCTTACAGCTTCC
* *
20463 CCAGGCTCTTTTGTTATGTGCAAGGGTAAGACCTTA
128 CCAGGCTCCTTTGATATGTGCAAGGGTAAGACCTTA
20499 TCATTTTTTC
Statistics
Matches: 144, Mismatches: 16, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
172 37 0.26
173 94 0.65
174 13 0.09
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.35
Consensus pattern (173 bp):
AGGTTCCTTTGCTACGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGATATGTGCAAG
GGTAAGCCATACAGTTTCCCTAGGTTCCTTTGTTGTGTGAAAGAGTAAGCCTTACAGCTTCCCCA
GGCTCCTTTGATATGTGCAAGGGTAAGACCTTACAGCTTCCCC
Found at i:20527 original size:130 final size:125
Alignment explanation
Indices: 20162--20536 Score: 408
Period size: 130 Copynumber: 2.9 Consensus size: 125
20152 ACCGTTACCG
* * * *
20162 TAGGTTCCTTTGCTATGTGCAAGGGTAAGCCTTATAGTTTCCTCAGGTTCCTTTGATGTGTGCAA
1 TAGGTTCCTTTGATGTGTGCAAGGGTAAGCCTTACAGTTTCC-CAGGTTCCTTTGTTGTGTGCAA
* * * * *
20227 GGGTAAGCCATACAGTTTCCCTATGTTCCTTTGTTGTGTGAAAGAGTAAGCCTTACAGCTTCCC
65 GGGTAAGCCTTACATTTTCCC-AT-TTCCTTTCTT-TGTGCAAGGGTAAGCCTTACAGCTTCCC
* * *
20291 CAGGTTCCTTTGATGTGTGCAAGGGTAAGCCTTACAGCTTCCCCAGGTTCCTTTGTTGCGTGCAA
1 TAGGTTCCTTTGATGTGTGCAAGGGTAAGCCTTACAG-TTTCCCAGGTTCCTTTGTTGTGTGCAA
* * * *
20356 GGGTAAGCCTTACAGTTTCTCCCAGGTTCCTTTGCTATGTGCAAGGGTAAGCCTTACAGTTTCTC
65 GGGTAAGCCTTACA-TTT-TCCCA-TTTCCTTT-CTTTGTGCAAGGGTAAGCCTTACAGCTTCCC
* * * * *
20421 TAGGTTCCTTTGTTGTGTACAAGGGTAAGACCTTACAGTTTCCCAGGCTCTTTTGTTATGTGCAA
1 TAGGTTCCTTTGATGTGTGCAAGGGTAAG-CCTTACAGTTTCCCAGGTTCCTTTGTTGTGTGCAA
**
20486 GGGTAAGACCTTATCATTTTTTCATTCTCCTCTTCTTTGTGCATAGGGTAA
65 GGGTAAG-CCTTA-CATTTTCCCATT-TCCT-TTCTTTGTGCA-AGGGTAA
20537 ATATGTTTTA
Statistics
Matches: 207, Mismatches: 28, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
129 67 0.32
130 108 0.52
131 30 0.14
132 2 0.01
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (125 bp):
TAGGTTCCTTTGATGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGTTGTGTGCAAG
GGTAAGCCTTACATTTTCCCATTTCCTTTCTTTGTGCAAGGGTAAGCCTTACAGCTTCCC
Found at i:21819 original size:22 final size:23
Alignment explanation
Indices: 21766--21814 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
21756 TGACTTTTTG
*
21766 GTCAAAGTCAA-AGTCAACACTA
1 GTCAAAGTCAACAGTAAACACTA
*
21788 GTCAAAGTCAACAGTAAACTCTA
1 GTCAAAGTCAACAGTAAACACTA
21811 GTCA
1 GTCA
21815 GGTCAACGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.20
Consensus pattern (23 bp):
GTCAAAGTCAACAGTAAACACTA
Found at i:23137 original size:26 final size:26
Alignment explanation
Indices: 23101--23272 Score: 137
Period size: 26 Copynumber: 7.3 Consensus size: 26
23091 AAACCAAATA
23101 CATAAATAAAATGCATGAAAGGATGC
1 CATAAATAAAATGCATGAAAGGATGC
* *
23127 CATAAATAAAATGCATGAAATGACG-
1 CATAAATAAAATGCATGAAAGGATGC
* *
23152 CAT---T--AAGGCATGAATGGATGC
1 CATAAATAAAATGCATGAAAGGATGC
*
23173 CATAAATAAAATGCATGAAAGTATG-
1 CATAAATAAAATGCATGAAAGGATGC
* *
23198 CAT---T-AAGT-CATGAAAGGATGT
1 CATAAATAAAATGCATGAAAGGATGC
*
23219 CATAAATAAAATGCATGAAAGGATAC
1 CATAAATAAAATGCATGAAAGGATGC
*
23245 C-T---T--AAGGCATGAAAGGATGC
1 CATAAATAAAATGCATGAAAGGATGC
23265 CATAAATA
1 CATAAATA
23273 TAATTAAATT
Statistics
Matches: 113, Mismatches: 16, Indels: 35
0.69 0.10 0.21
Matches are distributed among these distances:
20 39 0.35
21 10 0.09
22 3 0.03
24 3 0.03
25 10 0.09
26 48 0.42
ACGTcount: A:0.47, C:0.12, G:0.20, T:0.22
Consensus pattern (26 bp):
CATAAATAAAATGCATGAAAGGATGC
Found at i:23180 original size:46 final size:45
Alignment explanation
Indices: 23113--23272 Score: 239
Period size: 46 Copynumber: 3.5 Consensus size: 45
23103 TAAATAAAAT
*
23113 GCATGAAAGGATGCCATAAATAAAATGCATGAAATGACGCATTAAG
1 GCATGAAAGGATGCCATAAATAAAATGCATGAAA-GATGCATTAAG
*
23159 GCATGAATGGATGCCATAAATAAAATGCATGAAAGTATGCATTAAG
1 GCATGAAAGGATGCCATAAATAAAATGCATGAAAG-ATGCATTAAG
* * * *
23205 TCATGAAAGGATGTCATAAATAAAATGCATGAAAGGATACCTTAAG
1 GCATGAAAGGATGCCATAAATAAAATGCATGAAA-GATGCATTAAG
23251 GCATGAAAGGATGCCATAAATA
1 GCATGAAAGGATGCCATAAATA
23273 TAATTAAATT
Statistics
Matches: 103, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
45 1 0.01
46 101 0.98
47 1 0.01
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.22
Consensus pattern (45 bp):
GCATGAAAGGATGCCATAAATAAAATGCATGAAAGATGCATTAAG
Found at i:25400 original size:37 final size:37
Alignment explanation
Indices: 25346--25454 Score: 191
Period size: 37 Copynumber: 2.9 Consensus size: 37
25336 ATAGCGTTAA
25346 AGTTTTACTAGGATTCAAACTCCTAAAAATAGGATAG
1 AGTTTTACTAGGATTCAAACTCCTAAAAATAGGATAG
*
25383 AGTTTTACTAGGTTTCAAACTCCTAAAAATAGGATAG
1 AGTTTTACTAGGATTCAAACTCCTAAAAATAGGATAG
* *
25420 AGTTCTACTATGATTCAAACTCCTAAAAATAGGAT
1 AGTTTTACTAGGATTCAAACTCCTAAAAATAGGAT
25455 CCTGAAGCAT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (37 bp):
AGTTTTACTAGGATTCAAACTCCTAAAAATAGGATAG
Found at i:26060 original size:39 final size:39
Alignment explanation
Indices: 26000--26100 Score: 111
Period size: 39 Copynumber: 2.6 Consensus size: 39
25990 TATATTTTTA
*
26000 TTTT-TTAGATTACATATATATATGTTA-T-TTTTATTATCT
1 TTTTATTA-ATTATATATATATAT-TTACTATTTT-TTATCT
*
26039 ATTTTATTAATT-TATATATATATTTACTATTTTTTATGT
1 -TTTTATTAATTATATATATATATTTACTATTTTTTATCT
*
26078 TTTTATTTATTATATATATATAT
1 TTTTATTAATTATATATATATAT
26101 ATATATATTA
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
38 13 0.24
39 27 0.50
40 11 0.20
41 3 0.06
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (39 bp):
TTTTATTAATTATATATATATATTTACTATTTTTTATCT
Found at i:26124 original size:43 final size:41
Alignment explanation
Indices: 25994--26173 Score: 137
Period size: 41 Copynumber: 4.5 Consensus size: 41
25984 TTAGTATATA
* * * *
25994 TTTTTATTTTTTAGA-TTACATATATATATGTTATTTTTAT
1 TTTTTATTTATTATATTTATATATATATATATTATTTTTAT
* * * *
26034 TATCTATTTTATTA-ATTTATATATATATTTACTATTTTTTAT
1 TTTTTA-TTTATTATATTTATATATATATATATTA-TTTTTAT
* *
26076 GTTTTTATTTATTATATATATATATATATATATTATTTTTAC
1 -TTTTTATTTATTATATTTATATATATATATATTATTTTTAT
* *
26118 CTTTT-TTTATTAT-TTTAT-T-TATAT-T-TTATTTCTTCT
1 TTTTTATTTATTATATTTATATATATATATATTATTT-TTAT
*
26154 TTTTTCTTTATT-T-TTTATAT
1 TTTTTATTTATTATATTTATAT
26174 TTTTTTCTTT
Statistics
Matches: 114, Mismatches: 18, Indels: 19
0.75 0.12 0.13
Matches are distributed among these distances:
35 6 0.05
36 13 0.11
37 12 0.11
38 1 0.01
39 4 0.04
40 13 0.11
41 24 0.21
42 20 0.18
43 21 0.18
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (41 bp):
TTTTTATTTATTATATTTATATATATATATATTATTTTTAT
Found at i:26165 original size:34 final size:31
Alignment explanation
Indices: 26118--26182 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 31
26108 TTATTTTTAC
26118 CTTTTTTTATTATTTTATTTATATTTTATTTCTT
1 CTTTTTTTATTA-TTT-TTTATATTTT-TTTCTT
26152 CTTTTTTCT-TTATTTTTTATATTTTTTTCTT
1 CTTTTTT-TATTATTTTTTATATTTTTTTCTT
26183 TATTTTACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
31 6 0.20
32 10 0.33
33 3 0.10
34 10 0.33
35 1 0.03
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (31 bp):
CTTTTTTTATTATTTTTTATATTTTTTTCTT
Found at i:26168 original size:44 final size:44
Alignment explanation
Indices: 26120--26270 Score: 107
Period size: 44 Copynumber: 3.5 Consensus size: 44
26110 ATTTTTACCT
*
26120 TTTTTTATTATTTTATTTATATTTTATTTCTTCTTTTTTCTTTA
1 TTTTTTATTATTTTATTTATATTTTATTTCTTATTTTTTCTTTA
* * * *
26164 TTTTTTA-TATTTTTTTCTTTATTTTACTTAC-TATTTTATCTTT-
1 TTTTTTATTATTTTATT-TATATTTTA-TTTCTTATTTTTTCTTTA
* * * * * * *
26207 TCTTTCT-TTATCTTATCTTTTATTTAATTTGTTTTTTTTTCTTCA
1 T-TTTTTATTATTTTAT-TTATATTTTATTTCTTATTTTTTCTTTA
26252 -TTTTTATT-TATTTATTTAT
1 TTTTTTATTAT-TTTATTTAT
26271 TTATTTCTTA
Statistics
Matches: 81, Mismatches: 17, Indels: 19
0.69 0.15 0.16
Matches are distributed among these distances:
43 19 0.23
44 58 0.72
45 4 0.05
ACGTcount: A:0.16, C:0.09, G:0.01, T:0.75
Consensus pattern (44 bp):
TTTTTTATTATTTTATTTATATTTTATTTCTTATTTTTTCTTTA
Found at i:26201 original size:31 final size:32
Alignment explanation
Indices: 26135--26231 Score: 94
Period size: 32 Copynumber: 3.1 Consensus size: 32
26125 TATTATTTTA
* *
26135 TTTATATTTTATTTCTTCT-TTTTTCTTTATTT
1 TTTATATTTTATTTCTT-TATTTTACTTTATAT
26167 TTTATATTTT-TTTCTTTATTTTAC-TTACTAT
1 TTTATATTTTATTTCTTTATTTTACTTTA-TAT
* * *
26198 TTTATCTTTTCTTTCTTTATCTTATCTTT-TAT
1 TTTATATTTTATTTCTTTATTTTA-CTTTATAT
26230 TT
1 TT
26232 AATTTGTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
30 4 0.07
31 22 0.39
32 27 0.48
33 1 0.02
34 2 0.04
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.74
Consensus pattern (32 bp):
TTTATATTTTATTTCTTTATTTTACTTTATAT
Found at i:26221 original size:28 final size:27
Alignment explanation
Indices: 26155--26229 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 27
26145 ATTTCTTCTT
26155 TTTTCTTTATTTT--TTATA--TT-T-
1 TTTTCTTTATTTTACTTATATTTTATC
26176 TTTTCTTTATTTTACTTACTATTTTATC
1 TTTTCTTTATTTTACTTA-TATTTTATC
* *
26204 TTTTCTTT-CTTTATCTTATCTTTTAT
1 TTTTCTTTATTTTA-CTTATATTTTAT
26230 TTAATTTGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
21 13 0.30
23 3 0.07
24 2 0.05
26 2 0.05
27 12 0.27
28 12 0.27
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (27 bp):
TTTTCTTTATTTTACTTATATTTTATC
Found at i:30445 original size:5 final size:5
Alignment explanation
Indices: 30430--30497 Score: 54
Period size: 5 Copynumber: 13.8 Consensus size: 5
30420 ATTGGAGTGC
* * *
30430 AAAAGG AAAAG AAAAG -ACA- AAAAG AAGAG AAAA- AACAG AAAAG AAGAA-
1 AAAA-G AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA-AAG
30478 AAGAAG AAAAG AAAAG AAAA
1 AA-AAG AAAAG AAAAG AAAA
30498 AGAAGTTCAA
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
4 7 0.14
5 36 0.71
6 8 0.16
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:30452 original size:13 final size:12
Alignment explanation
Indices: 30436--30498 Score: 60
Period size: 13 Copynumber: 5.2 Consensus size: 12
30426 GTGCAAAAGG
30436 AAAAGAAAAGACA
1 AAAAGAAAAGA-A
*
30449 AAAAG--AAGAG
1 AAAAGAAAAGAA
*
30459 AAAA-AACAGAA
1 AAAAGAAAAGAA
30470 AAGAAGAAAAGAA
1 AA-AAGAAAAGAA
30483 GAAAAGAAAAGAA
1 -AAAAGAAAAGAA
30496 AAA
1 AAA
30499 GAAGTTCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
10 4 0.10
11 9 0.22
12 5 0.12
13 21 0.51
14 2 0.05
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAGAA
Found at i:30460 original size:18 final size:19
Alignment explanation
Indices: 30430--30497 Score: 81
Period size: 18 Copynumber: 3.7 Consensus size: 19
30420 ATTGGAGTGC
30430 AAAAGGAAAAGAAAAGACA-
1 AAAA-GAAAAGAAAAGACAG
* *
30449 AAAAGAAGAGAAAAAACAG
1 AAAAGAAAAGAAAAGACAG
30468 AAAAG--AAGAAAAGA-AG
1 AAAAGAAAAGAAAAGACAG
30484 AAAAGAAAAGAAAA
1 AAAAGAAAAGAAAA
30498 AGAAGTTCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
16 7 0.17
17 7 0.17
18 19 0.45
19 9 0.21
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAGAAAAGACAG
Found at i:30470 original size:27 final size:26
Alignment explanation
Indices: 30430--30502 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 26
30420 ATTGGAGTGC
30430 AAAAGGAAAAGAAAAGACA-AAAAGAAG
1 AAAA-GAAAAGAAAAGA-AGAAAAGAAG
30457 AGAAA-AAACAGAAAAGAAGAAAAGAAG
1 A-AAAGAAA-AGAAAAGAAGAAAAGAAG
30484 AAAAGAAAAGAAAAAGAAG
1 AAAAGAAAAG-AAAAGAAG
30503 TTCAAAAAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
26 9 0.22
27 29 0.71
28 3 0.07
ACGTcount: A:0.75, C:0.03, G:0.22, T:0.00
Consensus pattern (26 bp):
AAAAGAAAAGAAAAGAAGAAAAGAAG
Found at i:30473 original size:16 final size:15
Alignment explanation
Indices: 30454--30501 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
30444 AGACAAAAAG
30454 AAGAGAAAAAACAGAA
1 AAGAGAAAAAA-AGAA
*
30470 AAGAAGAAAAGAAGAA
1 AAG-AGAAAAAAAGAA
*
30486 AAGAAAAGAAAAAGAA
1 AAGAGAA-AAAAAGAA
30502 GTTCAAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 3 0.11
16 17 0.63
17 7 0.26
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAGAAAAAAAGAA
Found at i:30477 original size:8 final size:8
Alignment explanation
Indices: 30438--30490 Score: 54
Period size: 8 Copynumber: 6.2 Consensus size: 8
30428 GCAAAAGGAA
30438 AAGAAAAG
1 AAGAAAAG
30446 ACA-AAAAG
1 A-AGAAAAG
*
30454 AAGAGAAAAA
1 -A-AGAAAAG
30464 ACAGAAAAG
1 A-AGAAAAG
30473 AAGAAAAG
1 AAGAAAAG
30481 AAGAAAAG
1 AAGAAAAG
30489 AA
1 AA
30491 AAGAAAAAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
8 23 0.61
9 11 0.29
10 4 0.11
ACGTcount: A:0.75, C:0.04, G:0.21, T:0.00
Consensus pattern (8 bp):
AAGAAAAG
Found at i:38657 original size:94 final size:95
Alignment explanation
Indices: 38504--38681 Score: 261
Period size: 94 Copynumber: 1.9 Consensus size: 95
38494 GGTAGTATTG
* *
38504 ATACCATGGTGAGGGTATCGATACCAAGTACCATAAAATCTAATTTTGGTATCGATACCGG-AAG
1 ATACCATGGTGAGGGTATCGATACCAAGTACCATAAAATATAATTTTGGTATCAATACCGGAAAG
* *
38568 GGGTATCGGTACCGTAGTATATTAGTATCA
66 GGGTATCGATACCATAGTATATTAGTATCA
* * **
38598 ATACCATGGTGAGGGTATCGATGCCAAGATA-TATCGAATATAATTTTGGTATCAATACCGGAAA
1 ATACCATGGTGAGGGTATCGATACCAAG-TACCATAAAATATAATTTTGGTATCAATACCGGAAA
38662 GGGGTATCGATACCATAGTA
65 GGGGTATCGATACCATAGTA
38682 GGGTAGTATC
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
94 52 0.70
95 22 0.30
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (95 bp):
ATACCATGGTGAGGGTATCGATACCAAGTACCATAAAATATAATTTTGGTATCAATACCGGAAAG
GGGTATCGATACCATAGTATATTAGTATCA
Found at i:39113 original size:59 final size:59
Alignment explanation
Indices: 39038--39441 Score: 668
Period size: 59 Copynumber: 6.9 Consensus size: 59
39028 GAATTACCAA
39038 AGGGCACTTCGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTCGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
*
39097 AGGGCACTTCGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAAAT
1 AGGGCACTTCGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* *
39156 AGGGAACTTCGTGTGCTAAAATGGTAAGGAAGTCATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTCGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
*
39215 AGGGCACTTCGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* *
39274 AGGGCACTTCGTGTGTTAAAATGGTAAGGAAATCATACTAA-TATATGAATTTCCAGAT
1 AGGGCACTTCGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * * * *
39332 AGGGCACTTTGTGTGCGAAAATGGAAAGGAAATCAAACTAAGTGTATGAATTTCCAAAT
1 AGGGCACTTCGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* *
39391 AAGGCACTTCGTGTGCTAAAATGATAAGGAAATCATACTAA-TCGTATGAAT
1 AGGGCACTTCGTGTGCTAAAATGGTAAGGAAATCATACTAAGT-GTATGAAT
39442 ATACTATTGA
Statistics
Matches: 320, Mismatches: 23, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
58 52 0.16
59 268 0.84
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.29
Consensus pattern (59 bp):
AGGGCACTTCGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
Found at i:53567 original size:29 final size:28
Alignment explanation
Indices: 53534--53662 Score: 84
Period size: 29 Copynumber: 4.4 Consensus size: 28
53524 TGAAGGGGTA
53534 CTAAAATGTAAATAATAAAATATAAAGTG
1 CTAAAATGTAAATAATAAAATA-AAAGTG
* * *
53563 CTAAAATATTGATAA-AATGAAATAAAGGTG
1 CTAAAAT-GT-A-AATAATAAAATAAAAGTG
* * * *
53593 CTAATATATAAATAAAGGAAAATAAAA-TA
1 CTAAAATGTAAAT-AA-TAAAATAAAAGTG
*
53622 CTATAATGTAAATAAAGTAAAATAAAA-TG
1 CTAAAATGTAAAT-AA-TAAAATAAAAGTG
*
53651 CTAAAAAGTAAA
1 CTAAAATGTAAA
53663 AATGCAAAAA
Statistics
Matches: 78, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
27 2 0.03
28 1 0.01
29 45 0.58
30 19 0.24
31 9 0.12
32 2 0.03
ACGTcount: A:0.60, C:0.04, G:0.11, T:0.26
Consensus pattern (28 bp):
CTAAAATGTAAATAATAAAATAAAAGTG
Found at i:53798 original size:21 final size:22
Alignment explanation
Indices: 53747--53798 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
53737 GAATCGAAAT
53747 AATATAAAAGTTAGTGAGTCGG
1 AATATAAAAGTTAGTGAGTCGG
53769 AATATAAAAGTTAGTGAGTCGG
1 AATATAAAAGTTAGTGAGTCGG
53791 AA-ATAAAA
1 AATATAAAA
53799 TAAGGAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 6 0.20
22 24 0.80
ACGTcount: A:0.48, C:0.04, G:0.23, T:0.25
Consensus pattern (22 bp):
AATATAAAAGTTAGTGAGTCGG
Found at i:55275 original size:50 final size:50
Alignment explanation
Indices: 55170--55276 Score: 112
Period size: 50 Copynumber: 2.1 Consensus size: 50
55160 TCACACTCCA
* * * *
55170 ATTTGCCTTTTCATCGCGACTAGGAGGGTTGGTTAGAGCCATATTATCGT
1 ATTTTCCTTTTCATCGCGACTAGGAGGGTTGGATAGAGACATATCATCGT
* *
55220 GTTTTCCTTTTCATTGCGACTAGGAGGGCTT-GATAG-GACATTATCCATCG-
1 ATTTTCCTTTTCATCGCGACTAGGAGGG-TTGGATAGAGACA-TAT-CATCGT
55270 ATTTTCC
1 ATTTTCC
55277 ATATATCTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
49 3 0.06
50 38 0.81
51 6 0.13
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (50 bp):
ATTTTCCTTTTCATCGCGACTAGGAGGGTTGGATAGAGACATATCATCGT
Found at i:55755 original size:8 final size:8
Alignment explanation
Indices: 55742--55806 Score: 60
Period size: 8 Copynumber: 8.0 Consensus size: 8
55732 GCTATTTTTA
55742 AAAAAAAC
1 AAAAAAAC
55750 AAAAAAAC
1 AAAAAAAC
*
55758 AAAAACAAA
1 AAAAA-AAC
*
55767 AAAAAAAG
1 AAAAAAAC
**
55775 GCAAAAAC
1 AAAAAAAC
*
55783 AAAAAAAT
1 AAAAAAAC
55791 AAAAAAA-
1 AAAAAAAC
55798 ATAAAAAAC
1 A-AAAAAAC
55807 CCAAAATTTC
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
7 1 0.02
8 38 0.83
9 7 0.15
ACGTcount: A:0.85, C:0.09, G:0.03, T:0.03
Consensus pattern (8 bp):
AAAAAAAC
Found at i:55773 original size:25 final size:25
Alignment explanation
Indices: 55740--55805 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
55730 TTGCTATTTT
55740 TAAAAAAAACAAAAAAACAAAAACAA
1 TAAAAAAAACAAAAAAACAAAAA-AA
***
55766 -AAAAAAAAGGCAAAAACAAAAAAA
1 TAAAAAAAACAAAAAAACAAAAAAA
*
55790 TAAAAAAAATAAAAAA
1 TAAAAAAAACAAAAAA
55806 CCCAAAATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
24 2 0.06
25 31 0.94
ACGTcount: A:0.85, C:0.08, G:0.03, T:0.05
Consensus pattern (25 bp):
TAAAAAAAACAAAAAAACAAAAAAA
Found at i:55781 original size:33 final size:32
Alignment explanation
Indices: 55744--55805 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
55734 TATTTTTAAA
55744 AAAAACAAAAAAACAAAAACAAAAAAAAAAGGC
1 AAAAACAAAAAAACAAAAA-AAAAAAAAAAGGC
* *
55777 AAAAACAAAAAAATAAAAAAAATAAAAAA
1 AAAAACAAAAAAACAAAAAAAAAAAAAAA
55806 CCCAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 9 0.33
33 18 0.67
ACGTcount: A:0.85, C:0.08, G:0.03, T:0.03
Consensus pattern (32 bp):
AAAAACAAAAAAACAAAAAAAAAAAAAAAGGC
Found at i:57485 original size:21 final size:21
Alignment explanation
Indices: 57444--57485 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
57434 TTCAGTGAAC
* *
57444 ATTACCAAGGTACTTCATCCT
1 ATTACCAAGGTAATCCATCCT
*
57465 ATTACCAAGGTAATCCTTCCT
1 ATTACCAAGGTAATCCATCCT
57486 CATCTTCTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.33
Consensus pattern (21 bp):
ATTACCAAGGTAATCCATCCT
Found at i:61414 original size:18 final size:19
Alignment explanation
Indices: 61383--61425 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
61373 TGCAATCATC
61383 TTTTGCCACATCCACCTCA
1 TTTTGCCACATCCACCTCA
*
61402 TTTT-CCACCTCCACCTCA
1 TTTTGCCACATCCACCTCA
*
61420 TATTGC
1 TTTTGC
61426 TTTTGTGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.19, C:0.42, G:0.05, T:0.35
Consensus pattern (19 bp):
TTTTGCCACATCCACCTCA
Found at i:64751 original size:95 final size:95
Alignment explanation
Indices: 64588--64810 Score: 304
Period size: 95 Copynumber: 2.3 Consensus size: 95
64578 TACTGATGAG
* *
64588 GTAGTATCGATGCCATGGTGAGGGTATCGATACCAGGTAACATCGAACCTAATTTTGGTATCGAT
1 GTAGTATCGATACCATGGTGAGGGTATCGATACCAGATAACATCGAACCTAATTTTGGTATCGAT
* * * *
64653 ACCGGAAGGGCGTATCGGTACCCTAGTATA
66 ACCGAAAGGGCGTATCGATACCATAGTAGA
* *
64683 GTAGTATTGATACCATGGTGAGGGTATCGATACCAAGAT-ACATCGAAGCTAATTTTGGTATCGA
1 GTAGTATCGATACCATGGTGAGGGTATCGATACC-AGATAACATCGAACCTAATTTTGGTATCGA
* *
64747 TACCGAAAGGGGGTATCGATACCATAGTAGG
65 TACCGAAAGGGCGTATCGATACCATAGTAGA
* ** *
64778 GTAGTATCAATACCATATTAAGGGTATCGATAC
1 GTAGTATCGATACCATGGTGAGGGTATCGATAC
64811 TAAAGGGCCA
Statistics
Matches: 112, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
95 109 0.97
96 3 0.03
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (95 bp):
GTAGTATCGATACCATGGTGAGGGTATCGATACCAGATAACATCGAACCTAATTTTGGTATCGAT
ACCGAAAGGGCGTATCGATACCATAGTAGA
Found at i:64779 original size:19 final size:19
Alignment explanation
Indices: 64739--64810 Score: 56
Period size: 22 Copynumber: 3.6 Consensus size: 19
64729 AGCTAATTTT
* *
64739 GGTATCGATACCGAAAG-GG
1 GGTATCGATACC-ATAGTAG
64758 GGTATCGATACCATAGTAGG
1 GGTATCGATACCATAGTA-G
* *
64778 GTAGTATCAATACCATATTAAG
1 G--GTATCGATACCATAGT-AG
64800 GGTATCGATAC
1 GGTATCGATAC
64811 TAAAGGGCCA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
18 3 0.07
19 12 0.28
20 11 0.26
22 16 0.37
23 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.25
Consensus pattern (19 bp):
GGTATCGATACCATAGTAG
Found at i:64790 original size:22 final size:23
Alignment explanation
Indices: 64759--64803 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
64749 CCGAAAGGGG
*
64759 GTATCGATACCATAGT-AGGGTA
1 GTATCAATACCATAGTAAGGGTA
*
64781 GTATCAATACCATATTAAGGGTA
1 GTATCAATACCATAGTAAGGGTA
64804 TCGATACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (23 bp):
GTATCAATACCATAGTAAGGGTA
Found at i:64810 original size:20 final size:20
Alignment explanation
Indices: 64757--64810 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 20
64747 TACCGAAAGG
*
64757 GGGTATCGATACCATAGTAG
1 GGGTATCGATACCATAGTAA
* *
64777 GGTAGTATCAATACCATATTAA
1 GG--GTATCGATACCATAGTAA
64799 GGGTATCGATAC
1 GGGTATCGATAC
64811 TAAAGGGCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 11 0.39
22 17 0.61
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (20 bp):
GGGTATCGATACCATAGTAA
Found at i:65362 original size:59 final size:59
Alignment explanation
Indices: 65133--65350 Score: 355
Period size: 59 Copynumber: 3.7 Consensus size: 59
65123 GAATTACCAA
*
65133 AGGGCACTTCGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATAAATTTCCAGAT
1 AGGGCACTTCGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * *
65192 AGGGCATTTCCTTTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTCGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * *
65251 AGAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCTAGAT
1 AGGGCACTTCGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* *
65310 AGGGCACTTCATGTGCTAAAATGATAAGGAAATCATACTAA
1 AGGGCACTTCGTGTGCTAAAATGGTAAGGAAATCATACTAA
65351 TCGTATTAAT
Statistics
Matches: 145, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 145 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (59 bp):
AGGGCACTTCGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
Done.