Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007697.1 Hibiscus syriacus cultivar Beakdansim tig00109906_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: 338196
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 2
Found at i:186222 original size:43 final size:43
Alignment explanation
Indices: 186157--186248 Score: 159
Period size: 43 Copynumber: 2.1 Consensus size: 43
186147 CTATTCGGTT
186157 CGGATCCATCCTCTCCCTCTAGCTGGCGCTGCCAAAGAGGCTG
1 CGGATCCATCCTCTCCCTCTAGCTGGCGCTGCCAAAGAGGCTG
186200 CGGATCCATCCTC-CCCTCCTAGCTGGCGCTGCCAAAGAGGCTG
1 CGGATCCATCCTCTCCCT-CTAGCTGGCGCTGCCAAAGAGGCTG
*
186243 CTGATC
1 CGGATC
186249 ATCTCGGGAT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
42 4 0.09
43 43 0.91
ACGTcount: A:0.16, C:0.38, G:0.25, T:0.21
Consensus pattern (43 bp):
CGGATCCATCCTCTCCCTCTAGCTGGCGCTGCCAAAGAGGCTG
Found at i:188196 original size:14 final size:14
Alignment explanation
Indices: 188177--188220 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
188167 AATATGTTCG
188177 TTTATGTTCATTCA
1 TTTATGTTCATTCA
*
188191 TTTATG----TTCG
1 TTTATGTTCATTCA
188201 TTTATGTTCATTCA
1 TTTATGTTCATTCA
188215 TTTATG
1 TTTATG
188221 GTCGTTTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
10 9 0.38
14 15 0.62
ACGTcount: A:0.18, C:0.11, G:0.11, T:0.59
Consensus pattern (14 bp):
TTTATGTTCATTCA
Found at i:188197 original size:24 final size:24
Alignment explanation
Indices: 188169--188233 Score: 121
Period size: 24 Copynumber: 2.7 Consensus size: 24
188159 CGTTCGATAA
188169 TATGTTCGTTTATGTTCATTCATT
1 TATGTTCGTTTATGTTCATTCATT
188193 TATGTTCGTTTATGTTCATTCATT
1 TATGTTCGTTTATGTTCATTCATT
*
188217 TATGGTCGTTTATGTTC
1 TATGTTCGTTTATGTTC
188234 GTTTATGTGC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.57
Consensus pattern (24 bp):
TATGTTCGTTTATGTTCATTCATT
Found at i:188479 original size:37 final size:37
Alignment explanation
Indices: 188430--188536 Score: 142
Period size: 37 Copynumber: 2.9 Consensus size: 37
188420 TTTTCATTTA
* * *
188430 CGTTTGTTTATGTTCATTTATTGTGTTCGTTTACGTT
1 CGTTCGTTTATGTTCATTTATTGTGTTCGTTTACATC
*
188467 CGTTCGTTTATGTTCATTTATTGTGTTCTTTTACATC
1 CGTTCGTTTATGTTCATTTATTGTGTTCGTTTACATC
* * *
188504 CGTTCGTTTATGTTCGTTCATTTATGTTCGTTT
1 CGTTCGTTTATGTTCATTTA-TTGTGTTCGTTT
188537 TATCATTTAA
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
37 51 0.84
38 10 0.16
ACGTcount: A:0.11, C:0.14, G:0.17, T:0.58
Consensus pattern (37 bp):
CGTTCGTTTATGTTCATTTATTGTGTTCGTTTACATC
Found at i:188521 original size:14 final size:14
Alignment explanation
Indices: 188504--188535 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
188494 CTTTTACATC
*
188504 CGTTCGTTTATGTT
1 CGTTCATTTATGTT
188518 CGTTCATTTATGTT
1 CGTTCATTTATGTT
188532 CGTT
1 CGTT
188536 TTATCATTTA
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:194433 original size:21 final size:21
Alignment explanation
Indices: 194407--194446 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
194397 CAGAACCCCA
*
194407 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
194428 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
194447 TCAAAGGAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:218981 original size:29 final size:28
Alignment explanation
Indices: 218939--219016 Score: 94
Period size: 23 Copynumber: 2.9 Consensus size: 28
218929 TACCTTATAT
218939 AGATAATAAGAATAATCATAGGGATAGAC
1 AGATAATAAGAATAAT-ATAGGGATAGAC
218968 AGATAATAAG---AATA-A-GGATAGAC
1 AGATAATAAGAATAATATAGGGATAGAC
*
218991 AGATATTAAGAATAATTATAGGGATA
1 AGATAATAAGAATAA-TATAGGGATA
219017 AGATCTTATT
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
23 17 0.40
24 1 0.02
25 1 0.02
26 5 0.12
27 2 0.05
28 1 0.02
29 15 0.36
ACGTcount: A:0.53, C:0.04, G:0.21, T:0.23
Consensus pattern (28 bp):
AGATAATAAGAATAATATAGGGATAGAC
Found at i:221054 original size:2 final size:2
Alignment explanation
Indices: 221047--221077 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
221037 ATCAGAATTT
221047 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
221078 GATGAGTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:222298 original size:31 final size:31
Alignment explanation
Indices: 222253--222323 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
222243 ATATATATGT
* * *
222253 ATCACATTAGATATTTTATTAAAAAATAAAG
1 ATCATATTAAATATTTTATTAAAAAACAAAG
* * *
222284 GTCATATTAAATATTTTATTGAAAAACAAAT
1 ATCATATTAAATATTTTATTAAAAAACAAAG
222315 ATCATATTA
1 ATCATATTA
222324 GATCATTTAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.49, C:0.07, G:0.06, T:0.38
Consensus pattern (31 bp):
ATCATATTAAATATTTTATTAAAAAACAAAG
Found at i:231841 original size:30 final size:30
Alignment explanation
Indices: 231793--231887 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
231783 GCACAAATTT
231793 AAACATAAA-GGATTAAAATAATAAAAATAG
1 AAAC-TAAAGGGATTAAAATAATAAAAATAG
* * * * *
231823 AAATTAAAGGGATCAAAATGGAT-GAAATAA
1 AAACTAAAGGGATTAAAAT-AATAAAAATAG
*
231853 AAACTAAAGGGATTAAAATAGTAAAAATAG
1 AAACTAAAGGGATTAAAATAATAAAAATAG
231883 AAACT
1 AAACT
231888 TATGAGTCTA
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
29 5 0.10
30 44 0.86
31 2 0.04
ACGTcount: A:0.61, C:0.04, G:0.15, T:0.20
Consensus pattern (30 bp):
AAACTAAAGGGATTAAAATAATAAAAATAG
Found at i:233661 original size:3 final size:3
Alignment explanation
Indices: 233653--233695 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
233643 TGTAATTAAT
**
233653 TAA TAA TAA TAAA TAA CGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
233696 AAAACCCGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:233907 original size:40 final size:40
Alignment explanation
Indices: 233842--233920 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
233832 TTGGTTGTTG
* *
233842 GGGACGACACTGCTCATACGTGATGAAGAAATCTGGTCAA
1 GGGACGACACGGCTCATACGCGATGAAGAAATCTGGTCAA
* **
233882 GGGATGACACGGCTCATACGCGATGAAGAGTTCTGGTCA
1 GGGACGACACGGCTCATACGCGATGAAGAAATCTGGTCA
233921 TCTTTAAGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.29, C:0.20, G:0.30, T:0.20
Consensus pattern (40 bp):
GGGACGACACGGCTCATACGCGATGAAGAAATCTGGTCAA
Found at i:234019 original size:43 final size:45
Alignment explanation
Indices: 233847--234155 Score: 145
Period size: 43 Copynumber: 6.8 Consensus size: 45
233837 TGTTGGGGAC
* * * *
233847 GACACTGCTCATACGTGATGAAGAAATCTGG---TC-AAGGG-AT
1 GACACGGCTCCTACGTGATGAGGAAGTCTGGTCATCTAAGGGTAT
* * *
233887 GACACGGCTCATACGCGATGAAG-AGTTCTGGTCATCTTTAAGAAGGGTGAT
1 GACACGGCTCCTACGTGATGAGGAAG-TCTGGTCATC--T---AAGGGT-AT
* * * * * * *
233938 AACTCGGTTCCTACGTGATGAGGACGGCTGATTATCTAA-GGT-T
1 GACACGGCTCCTACGTGATGAGGAAGTCTGGTCATCTAAGGGTAT
*
233981 GACACGGCTCCTACGTGATGAGGAAGTCTGGTCGTCTAAGGGTAGAT
1 GACACGGCTCCTACGTGATGAGGAAGTCTGGTCATCTAAGGGT--AT
* * * * * * *
234028 GACATGGTTCATACATGATGAAGAACTCTGGCCATCTTTAGGAAGGGTGAT
1 GACACGGCTCCTACGTGATGAGGAAGTCTGGTCATC--T---AAGGGT-AT
* * * * * *
234079 AACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCTAA-GGT-T
1 GACACGGCTCCTACGTGATGAGGAAGTCTGGTCATCTAAGGGTAT
234122 GACACGGCTCCTACGTGATGAGG-AGATCTGGTCA
1 GACACGGCTCCTACGTGATGAGGAAG-TCTGGTCA
234156 GTTGATGTTG
Statistics
Matches: 200, Mismatches: 46, Indels: 43
0.69 0.16 0.15
Matches are distributed among these distances:
39 1 0.00
40 26 0.13
42 1 0.00
43 61 0.31
44 3 0.01
45 6 0.03
46 4 0.02
47 29 0.14
49 8 0.04
51 54 0.27
52 7 0.04
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (45 bp):
GACACGGCTCCTACGTGATGAGGAAGTCTGGTCATCTAAGGGTAT
Found at i:234094 original size:141 final size:141
Alignment explanation
Indices: 233884--234154 Score: 445
Period size: 141 Copynumber: 1.9 Consensus size: 141
233874 CTGGTCAAGG
* ** *
233884 GATGACACGGCTCATACGCGATGAAGAGTTCTGGTCATCTTTAAGAAGGGTGATAACTCGGTTCC
1 GATGACACGGCTCATACACGATGAAGAACTCTGGCCATCTTTAAGAAGGGTGATAACTCGGTTCC
233949 TACGTGATGAGGACGGCTGATTATCTAAGGTTGACACGGCTCCTACGTGATGAGGA-AGTCTGGT
66 TACGTGATGAGGACGGCTGATTATCTAAGGTTGACACGGCTCCTACGTGATGAGGAGA-TCTGGT
234013 CGTCTAAGGGTA
130 CGTCTAAGGGTA
* * * *
234025 GATGACATGGTTCATACATGATGAAGAACTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCC
1 GATGACACGGCTCATACACGATGAAGAACTCTGGCCATCTTTAAGAAGGGTGATAACTCGGTTCC
*
234090 TACGTGATGAGGACGGCTGGTTATCTAAGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTC
66 TACGTGATGAGGACGGCTGATTATCTAAGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTC
234155 AGTTGATGTT
Statistics
Matches: 120, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
141 119 0.99
142 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (141 bp):
GATGACACGGCTCATACACGATGAAGAACTCTGGCCATCTTTAAGAAGGGTGATAACTCGGTTCC
TACGTGATGAGGACGGCTGATTATCTAAGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTC
GTCTAAGGGTA
Found at i:246986 original size:30 final size:30
Alignment explanation
Indices: 246938--247032 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
246928 GCACAAATTT
246938 AAACATAAA-GGATTAAAATAATAAAAATAG
1 AAAC-TAAAGGGATTAAAATAATAAAAATAG
* * * * *
246968 AAATTAAAGGGATCAAAATGGAT-GAAATAA
1 AAACTAAAGGGATTAAAAT-AATAAAAATAG
*
246998 AAACTAAAGGGATTAAAATAGTAAAAATAG
1 AAACTAAAGGGATTAAAATAATAAAAATAG
247028 AAACT
1 AAACT
247033 TATGAGTCTA
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
29 5 0.10
30 44 0.86
31 2 0.04
ACGTcount: A:0.61, C:0.04, G:0.15, T:0.20
Consensus pattern (30 bp):
AAACTAAAGGGATTAAAATAATAAAAATAG
Found at i:248235 original size:22 final size:22
Alignment explanation
Indices: 248210--248257 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
248200 AAGGTAAAAC
* *
248210 TTTTCTTTCTTCTCTCTCTTTT
1 TTTTCTTTCGTATCTCTCTTTT
*
248232 TTTTGTTTCGTATCTCTCTTTT
1 TTTTCTTTCGTATCTCTCTTTT
248254 TTTT
1 TTTT
248258 TATTCTCTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.02, C:0.21, G:0.04, T:0.73
Consensus pattern (22 bp):
TTTTCTTTCGTATCTCTCTTTT
Found at i:248803 original size:3 final size:3
Alignment explanation
Indices: 248795--248834 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
248785 TGTAATTAAT
**
248795 TAA TAA TAA TAAA TAA CGA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
248835 AAAAACCCGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:248935 original size:17 final size:17
Alignment explanation
Indices: 248913--248951 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
248903 CTTGAAATTT
248913 TATAAGTTCGTCTCTAG
1 TATAAGTTCGTCTCTAG
248930 TATAAGTTCGTCTCTAG
1 TATAAGTTCGTCTCTAG
248947 TATAA
1 TATAA
248952 AATAATTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.41
Consensus pattern (17 bp):
TATAAGTTCGTCTCTAG
Found at i:252838 original size:36 final size:36
Alignment explanation
Indices: 252797--252891 Score: 116
Period size: 28 Copynumber: 2.9 Consensus size: 36
252787 AGTTGAGTAT
*
252797 TATCAGCTTTGGTACATTCTTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
252833 TATCAG---T--T--A-TCGTGTATCAATGTTATCC
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
252861 TATCAGCTTTGGTACATTCGTGTATCAATGT
1 TATCAGCTTTGGTACATTCGTGTATCAATGT
252892 CCAGCACCGT
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
28 23 0.47
29 1 0.02
31 2 0.04
33 2 0.04
35 1 0.02
36 20 0.41
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.43
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:254104 original size:32 final size:32
Alignment explanation
Indices: 254068--254137 Score: 140
Period size: 32 Copynumber: 2.2 Consensus size: 32
254058 AGAAGAGCGA
254068 AACGACCCATCATAACCAAGAACCCTAGTTCT
1 AACGACCCATCATAACCAAGAACCCTAGTTCT
254100 AACGACCCATCATAACCAAGAACCCTAGTTCT
1 AACGACCCATCATAACCAAGAACCCTAGTTCT
254132 AACGAC
1 AACGAC
254138 GATAGAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.39, C:0.34, G:0.10, T:0.17
Consensus pattern (32 bp):
AACGACCCATCATAACCAAGAACCCTAGTTCT
Found at i:255248 original size:75 final size:75
Alignment explanation
Indices: 255126--255348 Score: 432
Period size: 75 Copynumber: 3.0 Consensus size: 75
255116 CTCTTTCCCC
255126 CCCCCCCCCCCCCGAAAGATCAGGACTTAGGTGTTTATATATATGCAGGGTTTTGCAGGAACAAA
1 CCCCCCCCCCCCCGAAAGATCAGGACTTAGGTGTTTATATATATGCAGGGTTTTGCAGGAACAAA
255191 GACAATGCGT
66 GACAATGCGT
255201 CCCCCCCCCCCCCGAAAGATCAGGACTTAGGTGTTTATATATATGCAGGGTTTTGCAGGAACAAA
1 CCCCCCCCCCCCCGAAAGATCAGGACTTAGGTGTTTATATATATGCAGGGTTTTGCAGGAACAAA
255266 GACAATGCGT
66 GACAATGCGT
255276 --CCCCCCCCCCCGAAAGATCAGGACTTAGGTGTTTATATATATGCAGGGTTTTGCAGGAACAAA
1 CCCCCCCCCCCCCGAAAGATCAGGACTTAGGTGTTTATATATATGCAGGGTTTTGCAGGAACAAA
255339 GACAATGCGT
66 GACAATGCGT
255349 TGTGATGAGT
Statistics
Matches: 148, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
73 73 0.49
75 75 0.51
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (75 bp):
CCCCCCCCCCCCCGAAAGATCAGGACTTAGGTGTTTATATATATGCAGGGTTTTGCAGGAACAAA
GACAATGCGT
Found at i:255412 original size:3 final size:3
Alignment explanation
Indices: 255404--255594 Score: 373
Period size: 3 Copynumber: 63.3 Consensus size: 3
255394 ATTTTCAGAC
255404 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
255452 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
255500 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAGG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA-G GAG GAG
255546 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
255594 G
1 G
255595 TAGCCATTGA
Statistics
Matches: 187, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
3 184 0.98
4 3 0.02
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:255714 original size:18 final size:18
Alignment explanation
Indices: 255691--255727 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
255681 GAAGGTTACG
255691 CCTTTCTTTCTGATTTTT
1 CCTTTCTTTCTGATTTTT
255709 CCTTTCTTTCTGATTTTT
1 CCTTTCTTTCTGATTTTT
255727 C
1 C
255728 TTTTTATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.24, G:0.05, T:0.65
Consensus pattern (18 bp):
CCTTTCTTTCTGATTTTT
Found at i:261590 original size:21 final size:21
Alignment explanation
Indices: 261564--261608 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
261554 GATTTCTGGG
* *
261564 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
261585 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
261606 CAA
1 CAA
261609 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:262468 original size:31 final size:31
Alignment explanation
Indices: 262422--262482 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
262412 GGTCGAGGGT
* *
262422 TTACCTATGTCCTTCGGGA-CATATGGACTGA
1 TTACCTAGGTCCTTCGGAATC-TATGGACTGA
*
262453 TTACCTAGGTTCTTCGGAATCTATGGACTG
1 TTACCTAGGTCCTTCGGAATCTATGGACTG
262483 GTCCTTCGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.34
Consensus pattern (31 bp):
TTACCTAGGTCCTTCGGAATCTATGGACTGA
Found at i:264930 original size:33 final size:32
Alignment explanation
Indices: 264883--264994 Score: 179
Period size: 33 Copynumber: 3.4 Consensus size: 32
264873 TTTTAAACTT
264883 TATTTCAATTATCGAACTTGGAAGTTTTTAAG
1 TATTTCAATTATCGAACTTGGAAGTTTTTAAG
*
264915 TATTTGAATTTATCGAACTTGGAAGTTTTTAAG
1 TATTTCAA-TTATCGAACTTGGAAGTTTTTAAG
* *
264948 TATTTGAATTTATCGAACTTGGAAGTATTTAAG
1 TATTTCAA-TTATCGAACTTGGAAGTTTTTAAG
264981 TATTTCAATTATCG
1 TATTTCAATTATCG
264995 TAAACTTTGT
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
32 13 0.17
33 63 0.83
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.45
Consensus pattern (32 bp):
TATTTCAATTATCGAACTTGGAAGTTTTTAAG
Found at i:277223 original size:16 final size:16
Alignment explanation
Indices: 277202--277232 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
277192 GTGTGTGTTT
277202 TAAGTGTGTTTTAAAA
1 TAAGTGTGTTTTAAAA
277218 TAAGTGTGTTTTAAA
1 TAAGTGTGTTTTAAA
277233 GTGATAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.45
Consensus pattern (16 bp):
TAAGTGTGTTTTAAAA
Found at i:294711 original size:20 final size:21
Alignment explanation
Indices: 294686--294778 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
294676 TTTTCCCAAT
*
294686 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
294706 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
294727 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
294747 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
294768 TCGCAATGCGA
1 TCGCAATGCGA
294779 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:294731 original size:41 final size:41
Alignment explanation
Indices: 294686--294778 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
294676 TTTTCCCAAT
294686 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
294727 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
294768 TCGCAATGCGA
1 TCGCAATGCGA
294779 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:294791 original size:41 final size:41
Alignment explanation
Indices: 294705--294839 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
294695 GAATAAGTAA
* *
294705 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
294746 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
294787 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
294828 TTCGCAACGCGA
1 ATCGCAACGCGA
294840 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:294792 original size:20 final size:20
Alignment explanation
Indices: 294767--294861 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
294757 AATTGGGAAA
*
294767 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
294787 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
294808 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
294828 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
294848 TTCGCAACGCGATA
1 ATCGCAACGCGATA
294862 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:295077 original size:22 final size:22
Alignment explanation
Indices: 295049--295092 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
295039 CACTCTCTCA
295049 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
295071 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
295093 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:295381 original size:20 final size:20
Alignment explanation
Indices: 295356--295393 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
295346 CGATTCTCTC
295356 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
295376 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
295394 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:296733 original size:18 final size:18
Alignment explanation
Indices: 296712--296756 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
296702 TCCACTTCGG
*
296712 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
296730 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
296748 GAGCCATCA
1 GAGCCATCA
296757 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:297162 original size:6 final size:6
Alignment explanation
Indices: 297153--297199 Score: 67
Period size: 6 Copynumber: 7.7 Consensus size: 6
297143 TTTGTTAGTA
* *
297153 TTTGTT TTTGGT TTTGTT TTTGGT TTTGTT TTTGTT TTTGTCT TTTG
1 TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TTTGT-T TTTG
297200 GTTGAAGTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
6 31 0.86
7 5 0.14
ACGTcount: A:0.00, C:0.02, G:0.21, T:0.77
Consensus pattern (6 bp):
TTTGTT
Found at i:297170 original size:12 final size:12
Alignment explanation
Indices: 297153--297202 Score: 82
Period size: 12 Copynumber: 4.1 Consensus size: 12
297143 TTTGTTAGTA
297153 TTTGTTTTTGGT
1 TTTGTTTTTGGT
297165 TTTGTTTTTGGT
1 TTTGTTTTTGGT
*
297177 TTTGTTTTTGTT
1 TTTGTTTTTGGT
297189 TTTGTCTTTTGGT
1 TTTGT-TTTTGGT
297202 T
1 T
297203 GAAGTAATGC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
12 28 0.80
13 7 0.20
ACGTcount: A:0.00, C:0.02, G:0.22, T:0.76
Consensus pattern (12 bp):
TTTGTTTTTGGT
Found at i:297310 original size:19 final size:20
Alignment explanation
Indices: 297267--297322 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
297257 CGTAACACGA
297267 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
297287 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
297306 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
297323 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:297330 original size:14 final size:14
Alignment explanation
Indices: 297311--297400 Score: 90
Period size: 14 Copynumber: 5.9 Consensus size: 14
297301 ATGCGAAATG
297311 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
297325 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
297341 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
297357 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
297373 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
297389 AAAATCGCAACG
1 AAAATCGCAACG
297401 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
14 30 0.47
16 16 0.25
18 18 0.28
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:297353 original size:32 final size:32
Alignment explanation
Indices: 297295--297410 Score: 214
Period size: 32 Copynumber: 3.6 Consensus size: 32
297285 GGAAATGGCT
297295 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
297328 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAATCGCAACGACAAA
297360 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAATCGCAACGACAAA
*
297392 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
297411 ATCGTAATGC
Statistics
Matches: 82, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
32 66 0.80
33 16 0.20
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAATCGCAACGACAAA
Found at i:297453 original size:14 final size:14
Alignment explanation
Indices: 297434--297490 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 14
297424 TTGTGTTTCG
297434 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
297448 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
297464 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
297480 CGTTGCGATTT
1 CGTTGCGATTT
297491 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.11, C:0.18, G:0.25, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:297472 original size:32 final size:32
Alignment explanation
Indices: 297429--297506 Score: 147
Period size: 32 Copynumber: 2.4 Consensus size: 32
297419 GCGATTTGTG
*
297429 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTCA
297461 TTTCGCATTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTCA
297493 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
297507 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.46
Consensus pattern (32 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTCA
Found at i:297525 original size:20 final size:19
Alignment explanation
Indices: 297491--297545 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
297481 GTTGCGATTT
*
297491 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
297510 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
297530 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
297546 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:300132 original size:24 final size:24
Alignment explanation
Indices: 300105--300158 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
300095 GTATTCGAAA
* *
300105 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
300129 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
300153 TTTGAT
1 TTTGAT
300159 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:300350 original size:12 final size:12
Alignment explanation
Indices: 300333--300357 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
300323 ATATAATCCT
300333 GAAGAAGAAAAA
1 GAAGAAGAAAAA
300345 GAAGAAGAAAAA
1 GAAGAAGAAAAA
300357 G
1 G
300358 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:302672 original size:19 final size:19
Alignment explanation
Indices: 302650--302741 Score: 69
Period size: 19 Copynumber: 5.4 Consensus size: 19
302640 GGAAATTATT
302650 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
302669 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
302683 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* * *
302702 ATCG-AA-ACG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
302716 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
302735 ATCGCAA
1 ATCGCAA
302742 CGAGGGAATC
Statistics
Matches: 53, Mismatches: 10, Indels: 20
0.64 0.12 0.24
Matches are distributed among these distances:
14 15 0.28
15 4 0.08
16 4 0.08
17 4 0.08
18 4 0.08
19 22 0.42
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:302673 original size:39 final size:37
Alignment explanation
Indices: 302630--302743 Score: 118
Period size: 33 Copynumber: 3.2 Consensus size: 37
302620 CTTAATGTCC
*
302630 ATCGCAACGCGGAAATTATTATCGCAATGCGAAATGAAA
1 ATCGCAACGC-G-AATAATTATCGCAATGCGAAATGAAA
* *
302669 ATCGCAACGAG-A-GA--ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAATAATTATCGCAATGCGAAATGAAA
*
302702 ATCGAAACGC---TAATT-TCGCAATGCGAAATGAAA
1 ATCGCAACGCGAATAATTATCGCAATGCGAAATGAAA
302735 ATCGCAACG
1 ATCGCAACG
302744 AGGGAATCGC
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
32 1 0.02
33 53 0.80
35 1 0.02
36 1 0.02
38 1 0.02
39 9 0.14
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.18
Consensus pattern (37 bp):
ATCGCAACGCGAATAATTATCGCAATGCGAAATGAAA
Found at i:302692 original size:33 final size:33
Alignment explanation
Indices: 302650--302761 Score: 154
Period size: 33 Copynumber: 3.4 Consensus size: 33
302640 GGAAATTATT
302650 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* **
302683 ATCGCAATGCGAAATGAAAATCGAAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
302715 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
302749 ATCGCAACGCGAA
1 ATCGCAATGCGAA
302762 TTTAATTTCG
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
32 1 0.01
33 65 0.97
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:302779 original size:19 final size:20
Alignment explanation
Indices: 302757--302799 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
302747 GAATCGCAAC
302757 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
302776 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
302796 GCGA
1 GCGA
302800 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:302784 original size:14 final size:14
Alignment explanation
Indices: 302785--302818 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
302775 TGCGATTTTC
302785 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
302799 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
302813 ATTTTC
1 ATTTTC
302819 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:302959 original size:14 final size:14
Alignment explanation
Indices: 302940--302976 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
302930 CATCAATTAA
302940 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
302954 ACAAATCACCTTTT
1 ACAAATCAACTTTT
302968 ACAAATCAA
1 ACAAATCAA
302977 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:304398 original size:21 final size:21
Alignment explanation
Indices: 304329--304398 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
304319 CATGTGAATC
*
304329 GGACTCTTGAATGGTGGGA-G
1 GGACTCTTGAACGGTGGGAGG
* * ** *
304349 GGACCTCTTCAACGATGACAGT
1 GGA-CTCTTGAACGGTGGGAGG
*
304371 GGCCTCTTGAACGGTGGGAGG
1 GGACTCTTGAACGGTGGGAGG
304392 GGACTCT
1 GGACTCT
304399 CGAGGAATGA
Statistics
Matches: 35, Mismatches: 13, Indels: 3
0.69 0.25 0.06
Matches are distributed among these distances:
20 3 0.09
21 30 0.86
22 2 0.06
ACGTcount: A:0.20, C:0.20, G:0.37, T:0.23
Consensus pattern (21 bp):
GGACTCTTGAACGGTGGGAGG
Found at i:304417 original size:42 final size:41
Alignment explanation
Indices: 304332--304454 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
304322 GTGAATCGGA
* * * *
304332 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAATGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
*
304374 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAATGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
304416 CTCTTCAATGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAATGGTGGGAGGGGACTCTCGA-GGATGATAGG
304455 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.24
Consensus pattern (41 bp):
CTCTTGAATGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:306537 original size:33 final size:33
Alignment explanation
Indices: 306480--306578 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
306470 ACGAGATAAT
*
306480 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
306514 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
306547 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
306579 GCGAAATGAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:306572 original size:19 final size:19
Alignment explanation
Indices: 306455--306620 Score: 145
Period size: 20 Copynumber: 9.1 Consensus size: 19
306445 TCTTTTGGTT
*
306455 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
306474 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
306494 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
306512 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
306528 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
306546 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
306561 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
306581 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
306600 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
306619 GA
1 GA
306621 TTTTGGTTTC
Statistics
Matches: 121, Mismatches: 13, Indels: 26
0.76 0.08 0.16
Matches are distributed among these distances:
14 19 0.16
15 3 0.02
16 2 0.02
17 1 0.01
18 4 0.03
19 44 0.36
20 46 0.38
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:306638 original size:19 final size:19
Alignment explanation
Indices: 306616--306663 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
306606 AAAATCGCAA
*
306616 TGCGATTTTGGTTT-CGCGT
1 TGCGATTTT-ATTTCCGCGT
*
306635 TGCGATAGTTATTTCCGCGT
1 TGCGAT-TTTATTTCCGCGT
306655 TGCGATTTT
1 TGCGATTTT
306664 CATTCTCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.10, C:0.17, G:0.27, T:0.46
Consensus pattern (19 bp):
TGCGATTTTATTTCCGCGT
Found at i:307222 original size:20 final size:21
Alignment explanation
Indices: 307173--307225 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
307163 GCGCTATGTA
307173 AATCG-CGTTGCGAAAGCCAG
1 AATCGTCGTTGCGAAAGCCAG
*
307193 AATCGT-GTTGCGAAAGTCAG
1 AATCGTCGTTGCGAAAGCCAG
*
307213 TATC-TCGTTGCGA
1 AATCGTCGTTGCGA
307226 TTTTGTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (21 bp):
AATCGTCGTTGCGAAAGCCAG
Found at i:307399 original size:21 final size:21
Alignment explanation
Indices: 307338--307391 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
307328 ACTGTATACC
307338 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGATTTCCAACT
307359 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGATTTCCAACT
307380 ATCGCAACGCGA
1 ATCGCAACGCGA
307392 AATGCAACGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATTTCCAACT
Found at i:310994 original size:20 final size:20
Alignment explanation
Indices: 310971--311021 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
310961 CACAGAATGT
*
310971 AAGATTATCAGTGAGAATAA
1 AAGATTACCAGTGAGAATAA
*
310991 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGAGAATAA
311011 AAGATTACCAG
1 AAGATTACCAG
311022 AGAATAAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.47, C:0.10, G:0.22, T:0.22
Consensus pattern (20 bp):
AAGATTACCAGTGAGAATAA
Found at i:315123 original size:21 final size:21
Alignment explanation
Indices: 315093--315140 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
315083 TAATTTTCAA
*
315093 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
315114 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
315135 ACATTG
1 ACATTG
315141 CAATATTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:319764 original size:21 final size:21
Alignment explanation
Indices: 319734--319782 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
319724 TAATTTTCAA
*
319734 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
319755 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
319776 ACATTGT
1 ACATTGT
319783 AATATTAGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:322552 original size:30 final size:30
Alignment explanation
Indices: 322508--322566 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
322498 GGTGAAGAAT
*
322508 CTAAAGACGCCATGTACTCTGGCCGTCTTA
1 CTAAAAACGCCATGTACTCTGGCCGTCTTA
* *
322538 CTAAAAACGTCATGTGCTCTGGCCGTCTT
1 CTAAAAACGCCATGTACTCTGGCCGTCTT
322567 CCGGAGTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (30 bp):
CTAAAAACGCCATGTACTCTGGCCGTCTTA
Found at i:337276 original size:18 final size:18
Alignment explanation
Indices: 337253--337293 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
337243 AGGCATTTGA
* *
337253 TCCTCTGGTTGTGCTTGT
1 TCCTCTGCTCGTGCTTGT
337271 TCCTCTGCTCGTGCTTGT
1 TCCTCTGCTCGTGCTTGT
337289 TCCTC
1 TCCTC
337294 ATGTTGTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.00, C:0.32, G:0.22, T:0.46
Consensus pattern (18 bp):
TCCTCTGCTCGTGCTTGT
Done.