Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003175.1 Hibiscus syriacus cultivar Beakdansim tig00006682_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: 79839
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:315 original size:22 final size:22
Alignment explanation
Indices: 290--331 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
280 CAATTCATTT
290 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
312 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
332 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:1185 original size:39 final size:40
Alignment explanation
Indices: 1140--1228 Score: 121
Period size: 39 Copynumber: 2.3 Consensus size: 40
1130 AATAAAACCC
*
1140 GTTGCGAAATTAAAATTCGTG-TGCAAATTC-GAAAATCGA
1 GTTGCGAAATTAAAATTCGCGTTGCAAATTCAG-AAATCGA
* *
1179 GTTGCGAAAATAAAATTCGCGTTGCGAATTCAGAAATCGA
1 GTTGCGAAATTAAAATTCGCGTTGCAAATTCAGAAATCGA
1219 GTTGC-AAATT
1 GTTGCGAAATT
1229 TGAAATTCAG
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
39 23 0.52
40 20 0.45
41 1 0.02
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.28
Consensus pattern (40 bp):
GTTGCGAAATTAAAATTCGCGTTGCAAATTCAGAAATCGA
Found at i:1204 original size:20 final size:19
Alignment explanation
Indices: 1122--1206 Score: 68
Period size: 18 Copynumber: 4.4 Consensus size: 19
1112 AAATATTTGT
*
1122 GTTGCGAAAATAAAA-CCC
1 GTTGCGAAAATAAAATCGC
* *
1140 GTTGCGAAATTAAAAT-TC
1 GTTGCGAAAATAAAATCGC
* *
1158 GTGTGC-AAATTCGAAAATCGA
1 GT-TGCGAAAAT--AAAATCGC
1179 GTTGCGAAAATAAAATTCGC
1 GTTGCGAAAATAAAA-TCGC
1199 GTTGCGAA
1 GTTGCGAA
1207 TTCAGAAATC
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
18 22 0.41
19 7 0.13
20 19 0.35
21 6 0.11
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (19 bp):
GTTGCGAAAATAAAATCGC
Found at i:1222 original size:20 final size:18
Alignment explanation
Indices: 1140--1228 Score: 54
Period size: 20 Copynumber: 4.6 Consensus size: 18
1130 AATAAAACCC
*
1140 GTTGCGAAATTAAAATTCGT
1 GTTGCG-AATTAAAA-TCGA
*
1160 G-TGCAAATTCGAAAATCGA
1 GTTGCGAATT--AAAATCGA
* *
1179 GTTGCGAAAATAAAATTCGC
1 GTTGCG-AATTAAAA-TCGA
1199 GTTGCGAATTCAGAAATCGA
1 GTTGCGAATT-A-AAATCGA
*
1219 GTTGCAAATT
1 GTTGCGAATT
1229 TGAAATTCAG
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
18 4 0.07
19 14 0.26
20 30 0.56
21 6 0.11
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.28
Consensus pattern (18 bp):
GTTGCGAATTAAAATCGA
Found at i:5213 original size:22 final size:22
Alignment explanation
Indices: 5185--5230 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
5175 ATGGAGTGTT
5185 AATGCT-GAATTTTAATATTAGA
1 AATGCTGGAATTTTAA-ATTAGA
*
5207 AATGCTGGAATTTTAAGTTAGA
1 AATGCTGGAATTTTAAATTAGA
5229 AA
1 AA
5231 GTTGATATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.41, C:0.04, G:0.17, T:0.37
Consensus pattern (22 bp):
AATGCTGGAATTTTAAATTAGA
Found at i:10945 original size:16 final size:16
Alignment explanation
Indices: 10921--10952 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
10911 TCTTGGAAAT
*
10921 TTTTTGAGTTCGAGTC
1 TTTTCGAGTTCGAGTC
10937 TTTTCGAGTTCGAGTC
1 TTTTCGAGTTCGAGTC
10953 GAGTTTCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.16, G:0.25, T:0.47
Consensus pattern (16 bp):
TTTTCGAGTTCGAGTC
Found at i:11577 original size:12 final size:12
Alignment explanation
Indices: 11547--11595 Score: 55
Period size: 13 Copynumber: 3.9 Consensus size: 12
11537 CGCTAGAAGG
11547 TAATTTTTTAAC
1 TAATTTTTTAAC
*
11559 TTCATTTTTTAAC
1 -TAATTTTTTAAC
11572 TAATTTTTTAA-
1 TAATTTTTTAAC
11583 TATATTTATTTAA
1 TA-ATTT-TTTAA
11596 TTTTTTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 2 0.06
12 14 0.44
13 16 0.50
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (12 bp):
TAATTTTTTAAC
Found at i:11612 original size:34 final size:35
Alignment explanation
Indices: 11563--11636 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 35
11553 TTTAACTTCA
11563 TTTTTTAACTAATTTTTTAATATATTTA-TTTAATT
1 TTTTTTAACTAA-TTTTTAATATATTTATTTTAATT
* * * *
11598 TTTTTTATCT-ATTTTTAATCTTTTTATTTTTATT
1 TTTTTTAACTAATTTTTAATATATTTATTTTAATT
11632 TTTTT
1 TTTTT
11637 AGATGGCGCC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
33 13 0.38
34 12 0.35
35 9 0.26
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (35 bp):
TTTTTTAACTAATTTTTAATATATTTATTTTAATT
Found at i:13961 original size:21 final size:18
Alignment explanation
Indices: 13912--13963 Score: 50
Period size: 21 Copynumber: 2.6 Consensus size: 18
13902 CCCTTTATAT
*
13912 ATATTTTTTTTTAATTAA
1 ATATTTTTTTTTAATAAA
13930 ATCATTGTTTTTATTGAATAAAA
1 AT-ATT-TTTTT-TT-AAT-AAA
13953 ATATTTTTTTT
1 ATATTTTTTTT
13964 ATTATTTCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
18 2 0.07
19 3 0.11
20 6 0.21
21 7 0.25
22 6 0.21
23 4 0.14
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.62
Consensus pattern (18 bp):
ATATTTTTTTTTAATAAA
Found at i:14174 original size:261 final size:269
Alignment explanation
Indices: 13668--14226 Score: 866
Period size: 261 Copynumber: 2.1 Consensus size: 269
13658 CTTATTCATA
*
13668 TATTGAATAAAAATATTTTTTTTTATTATTTCAGGTCGGGTCGGGTCGAGTCGGGTTTCTAATTC
1 TATTGAATAAAAATA-TTTTTTTTATTATTTCAGGTCGGAT---GTCGAGTCGGGTTTCTAATTC
*
13733 ATATATTCAGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAGTGTG
62 ATATATTC--GTC-GGTCGGGTCAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAGTGTG
* *
13798 ATATTCAGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCCAAATATATATA
124 ATATTCAGGTCGGGTCGAGTTCGAGTTTAGGGTGAAAAATACCCGACCCGACCCAAATAAATATA
* *
13863 TAATTTTACCTTATATATTTAGGAATAATTATAATAATACCCTTTATATAT-A-TTTTTTTTT-A
189 TAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCTCTATATATAATTTTTTTTTTCA
*
13925 ATTAAATCATTGTTTT
254 ATTAAATCAATGTTTT
*
13941 TATTGAATAAAAATATTTTTTTTATTATTTCAGGTC-GAT-TCGGGTCGGGTTTCTAATTCATAT
1 TATTGAATAAAAATATTTTTTTTATTATTTCAGGTCGGATGTCGAGTCGGGTTTCTAATTCATAT
14004 ATTC-T-GGTCGGGTCAAACTTTATTTTGGTCGGGTCGGGTC-GTTTTTTTAAGTGTGATATTCA
66 ATTCGTCGGTCGGGTCAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCA
* * *
14066 GGTCGGGTCGGGTTCGAGTTTAGGGTGAAAAATACTCGACCCGACTCAAA-AAATATATAATTTT
131 GGTCGGGTCGAGTTCGAGTTTAGGGTGAAAAATACCCGACCCGACCCAAATAAATATATAATTTT
*
14130 ACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTTTTCAATTAAG
196 ACCTTATATATTTAGGAATAATTACAATAATA-CCCTCTATATATAATTTTTTTTTTCAATTAAA
14195 TCAATGTTTT
260 TCAATGTTTT
*
14205 TATTGAATAAAAGTATTTTTTT
1 TATTGAATAAAAATATTTTTTT
14227 ATTTCGAGTC
Statistics
Matches: 269, Mismatches: 13, Indels: 17
0.90 0.04 0.06
Matches are distributed among these distances:
260 44 0.16
261 79 0.29
262 35 0.13
263 9 0.03
264 37 0.14
267 27 0.10
271 2 0.01
272 21 0.08
273 15 0.06
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (269 bp):
TATTGAATAAAAATATTTTTTTTATTATTTCAGGTCGGATGTCGAGTCGGGTTTCTAATTCATAT
ATTCGTCGGTCGGGTCAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCA
GGTCGGGTCGAGTTCGAGTTTAGGGTGAAAAATACCCGACCCGACCCAAATAAATATATAATTTT
ACCTTATATATTTAGGAATAATTACAATAATACCCTCTATATATAATTTTTTTTTTCAATTAAAT
CAATGTTTT
Found at i:17820 original size:59 final size:60
Alignment explanation
Indices: 17756--17877 Score: 158
Period size: 59 Copynumber: 2.0 Consensus size: 60
17746 TTACTAAATA
* * *
17756 ATAACTATCATTCTAAATTGATC-CCAAAC-TTTTGAACATTTTAATTTCATCCTCAAACT
1 ATAACTATCATTATAAATCGATCACCAAACTTTTTGAACATTATAATTTCAT-CTCAAACT
* * * *
17815 ATAACTTTCATTATAGATCGATCACTAAACTTTTTGAGCATTATAATTTCATCTCAAACT
1 ATAACTATCATTATAAATCGATCACCAAACTTTTTGAACATTATAATTTCATCTCAAACT
17875 ATA
1 ATA
17878 CATAGATACT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 19 0.35
60 16 0.30
61 19 0.35
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.39
Consensus pattern (60 bp):
ATAACTATCATTATAAATCGATCACCAAACTTTTTGAACATTATAATTTCATCTCAAACT
Found at i:19583 original size:2 final size:2
Alignment explanation
Indices: 19576--19607 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
19566 TTTTCATCCC
19576 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19608 ATCAACTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34067 original size:20 final size:20
Alignment explanation
Indices: 34042--34134 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
34032 TTTTCCCAAT
*
34042 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* **
34062 TCGCAACGCGAATTGGAAAAA
1 TCGCAATGCGAATAAG-AAAA
*
34083 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* **
34103 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
34124 TCGCAATGCGA
1 TCGCAATGCGA
34135 TACTTACTAT
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:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:34087 original size:41 final size:41
Alignment explanation
Indices: 34042--34134 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
34032 TTTTCCCAAT
34042 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGAAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGAAAAA
*
34083 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGAAAAA
34124 TCGCAATGCGA
1 TCGCAATGCGA
34135 TACTTACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGAAAAA
Found at i:34147 original size:41 final size:41
Alignment explanation
Indices: 34061--34195 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
34051 GAATAAGTAA
** *
34061 ATCGCAACGCGAATTGGAAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGAAAAATCGCAATGCG-ATACTTACT
*
34102 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGAAAAATCGCAATGCGATACTTACT
* * * * *
34143 ATCGCAATGCGATAAT--ACAAAATCGCAACGAGATACTGACT
1 ATCGCAACGCGA-ATTGGA-AAAATCGCAATGCGATACTTACT
*
34184 TTCGCAACGCGA
1 ATCGCAACGCGA
34196 TTCTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 5 0.06
41 72 0.91
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGAAAAATCGCAATGCGATACTTACT
Found at i:34213 original size:20 final size:20
Alignment explanation
Indices: 34165--34217 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
34155 TAATACAAAA
* *
34165 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
34185 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
34205 TCGCAACGCGATT
1 TCGCAACGCGATT
34218 TACATAGCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:34767 original size:19 final size:19
Alignment explanation
Indices: 34729--34795 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
34719 TTCGAGAATG
34729 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
34749 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
* **
34768 AAAATCGCAATGCGAAACC
1 AAAATCGCAACGCGAAATA
34787 AAAATCGCA
1 AAAATCGCA
34796 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 29 0.73
20 11 0.28
ACGTcount: A:0.48, C:0.24, G:0.16, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:34839 original size:20 final size:19
Alignment explanation
Indices: 34791--34956 Score: 136
Period size: 20 Copynumber: 9.1 Consensus size: 19
34781 GAAACCAAAA
*
34791 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
34810 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
34829 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
* *
34849 TCGTGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
34865 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
34882 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
34896 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
34915 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
34935 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
34955 TC
1 TC
34957 AACCAAAAGA
Statistics
Matches: 120, Mismatches: 14, Indels: 26
0.75 0.09 0.16
Matches are distributed among these distances:
14 20 0.17
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 42 0.35
20 49 0.41
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:34881 original size:33 final size:33
Alignment explanation
Indices: 34844--34931 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
34834 GTTGCGATTT
* * *
34844 TCATTTCGTGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
34877 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
34910 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
34932 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 35 0.70
34 15 0.30
ACGTcount: A:0.11, C:0.24, G:0.25, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:37017 original size:42 final size:42
Alignment explanation
Indices: 36957--37079 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
36947 GCCCGACTCG
* * *
36957 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
36999 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
37041 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
37080 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:37037 original size:21 final size:21
Alignment explanation
Indices: 37013--37079 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
37003 TCATTCCTCG
37013 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
37034 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
37055 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
37076 AGAG
1 AGAG
37080 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:38457 original size:14 final size:14
Alignment explanation
Indices: 38438--38473 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
38428 ATTGTTTAAT
38438 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
38452 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
38466 TGATTTGT
1 TGATTTGT
38474 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:38616 original size:20 final size:20
Alignment explanation
Indices: 38580--38672 Score: 161
Period size: 20 Copynumber: 4.7 Consensus size: 20
38570 AAAAAGTACT
*
38580 ATCGCAATGCG-AAATGAAA
1 ATCGCAACGCGAAAATGAAA
38599 ATCGCAACGCGAAAATGAAA
1 ATCGCAACGCGAAAATGAAA
*
38619 ATCGCAACGTGAAAATGAAA
1 ATCGCAACGCGAAAATGAAA
38639 ATCGCAACGCGAAAATGAAA
1 ATCGCAACGCGAAAATGAAA
38659 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
38673 TTAAATTCGC
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
19 10 0.14
20 60 0.86
ACGTcount: A:0.48, C:0.19, G:0.20, T:0.12
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGAAA
Found at i:38718 original size:33 final size:33
Alignment explanation
Indices: 38675--38770 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 33
38665 ACGCGAAATT
38675 AAATTCGCGTTGCGATTTTCATTTCGCATTGCG
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCG
*
38708 AAATTAGCGTTGCGATTTTCATTTCGCATTGCG
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCG
* *
38741 -ATTCTCTCGTTGCGATTTTCATTTCGCATT
1 AAAT-TCGCGTTGCGATTTTCATTTCGCATT
38771 ACGATAGTAA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
32 2 0.03
33 56 0.97
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.43
Consensus pattern (33 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCG
Found at i:38741 original size:19 final size:19
Alignment explanation
Indices: 38678--38775 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 19
38668 CGAAATTAAA
*
38678 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
38697 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
38711 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
38730 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
38746 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
38763 TTCGCATTACGAT
1 TTCGCATTGCGAT
38776 AGTAATTTCC
Statistics
Matches: 59, Mismatches: 10, Indels: 20
0.66 0.11 0.22
Matches are distributed among these distances:
14 17 0.29
16 7 0.12
17 7 0.12
19 28 0.47
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.43
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:41083 original size:12 final size:12
Alignment explanation
Indices: 41066--41090 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41056 TCTTCGGGGA
41066 CTTTTTCTTCTT
1 CTTTTTCTTCTT
41078 CTTTTTCTTCTT
1 CTTTTTCTTCTT
41090 C
1 C
41091 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:41299 original size:24 final size:24
Alignment explanation
Indices: 41265--41318 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
41255 CTGAAACATC
* *
41265 ATCAAAATCCGTGTATTAACCAAT
1 ATCAAAATCCGGGTATTAACCAAG
* *
41289 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTAACCAAG
41313 ATCAAA
1 ATCAAA
41319 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTAACCAAG
Found at i:42144 original size:33 final size:33
Alignment explanation
Indices: 42102--42164 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
42092 TCATTTGACC
* *
42102 ATCGCAATGCGAAATGCAAATCGCAACGATAGA
1 ATCGCAATGCGAAATGAAAAACGCAACGATAGA
*
42135 ATCGCAATGCGAAATGAAAAAGGCAACGAT
1 ATCGCAATGCGAAATGAAAAACGCAACGAT
42165 GATTAACATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAAACGCAACGATAGA
Found at i:42406 original size:20 final size:20
Alignment explanation
Indices: 42381--42438 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
42371 ATTCATTTGA
42381 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
42401 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
42421 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
42439 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:42524 original size:19 final size:19
Alignment explanation
Indices: 42457--42524 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
42447 GAAATGAAAA
42457 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
*
42473 TCG--TTGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
42490 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
42509 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
42525 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.22
16 3 0.07
17 3 0.07
19 29 0.64
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:44580 original size:20 final size:19
Alignment explanation
Indices: 44545--44600 Score: 85
Period size: 20 Copynumber: 2.9 Consensus size: 19
44535 GAAACTTAAA
44545 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
44564 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
*
44584 ATCGCAATGCGAAATGA
1 ATCGCAACGCGAAATGA
44601 AAATTGCAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:44623 original size:14 final size:14
Alignment explanation
Indices: 44600--44657 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
44590 ATGCGAAATG
*
44600 AAAATTGCAACGAC
1 AAAATCGCAACGAC
*
44614 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
*
44630 ATGAAATTGCAACGAC
1 A--AAATCGCAACGAC
44646 AAAATCGCAACG
1 AAAATCGCAACG
44658 CGAAACACAA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
14 19 0.54
16 8 0.23
18 8 0.23
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:44642 original size:32 final size:33
Alignment explanation
Indices: 44584--44662 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
44574 GGAAATGGCT
*
44584 ATCGCAATGCGAAATGAAAATTGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATTGCAACGACAAA
44617 ATCGCAACGCGAAATG-AAATTGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATTGCAACGACAAA
44649 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
44663 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATTGCAACGACAAA
Found at i:44691 original size:19 final size:19
Alignment explanation
Indices: 44669--44750 Score: 104
Period size: 18 Copynumber: 4.6 Consensus size: 19
44659 GAAACACAAA
44669 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
44688 TCGCGTTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
44706 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
44722 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
44739 TCGCATTGCGAT
1 TCGCATTGCGAT
44751 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
14 6 0.11
15 3 0.06
16 4 0.07
17 4 0.07
18 20 0.37
19 17 0.31
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:44769 original size:20 final size:19
Alignment explanation
Indices: 44735--44789 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
44725 TTGCGATTTT
*
44735 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
44754 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
44774 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
44790 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:44778 original size:39 final size:34
Alignment explanation
Indices: 44669--44770 Score: 102
Period size: 33 Copynumber: 2.8 Consensus size: 34
44659 GAAACACAAA
44669 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTCATT
1 TCGCATTGCGA---TCATTTCGCGTTGCGATTTCATT
44706 TCGCATTGCGAT--TTT-GTCGTTGCGATTTTCATT
1 TCGCATTGCGATCATTTCG-CGTTGCGA-TTTCATT
44739 TCGCATTGCGATAGCCATTTCCGCGTTGCGAT
1 TCGCATTGCGAT---CATTT-CGCGTTGCGAT
44771 AGTCATTTTC
Statistics
Matches: 56, Mismatches: 0, Indels: 17
0.77 0.00 0.23
Matches are distributed among these distances:
31 1 0.02
32 11 0.20
33 19 0.34
34 1 0.02
37 11 0.20
38 4 0.07
39 8 0.14
40 1 0.02
ACGTcount: A:0.14, C:0.23, G:0.22, T:0.42
Consensus pattern (34 bp):
TCGCATTGCGATCATTTCGCGTTGCGATTTCATT
Found at i:45293 original size:18 final size:18
Alignment explanation
Indices: 45267--45311 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
45257 GTCGATCAGA
*
45267 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
45285 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
45303 TGATGGCTC
1 TGATGGCTC
45312 CCGAAGTGGA
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:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:46656 original size:20 final size:20
Alignment explanation
Indices: 46631--46668 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
46621 AATAGTTTCT
46631 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
46651 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
46669 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:47188 original size:20 final size:20
Alignment explanation
Indices: 47163--47215 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
47153 GATTATGTAT
*
47163 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
47183 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
47203 TATCTCGTTGCGA
1 TATCGCGTTGCGA
47216 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:47249 original size:20 final size:20
Alignment explanation
Indices: 47143--47254 Score: 82
Period size: 20 Copynumber: 5.5 Consensus size: 20
47133 CGCTTTGAAA
*
47143 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
47164 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
47184 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
47204 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
47225 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
47245 ATCGCATTGC
1 ATCGCATTGC
47255 AATTTTCCCA
Statistics
Matches: 73, Mismatches: 16, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
19 2 0.03
20 47 0.64
21 24 0.33
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:47260 original size:41 final size:41
Alignment explanation
Indices: 47183--47260 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
47173 CGAAAGTCAG
* * * *
47183 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCAATTTTTTAT
* *
47224 TATCGCATTGCGATAGTCAGTATCGCATTGCAATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCAATTTT
47261 CCCAATTCGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCAATTTTTTAT
Found at i:47275 original size:21 final size:21
Alignment explanation
Indices: 47246--47338 Score: 91
Period size: 20 Copynumber: 4.5 Consensus size: 21
47236 ATAGTCAGTA
*
47246 TCGCATTGCAATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
47267 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
47287 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
47308 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
47328 TCGCATTGCGA
1 TCGCATTGCGA
47339 ATTGGGAAAA
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.56
21 25 0.44
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:47276 original size:41 final size:41
Alignment explanation
Indices: 47246--47341 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 41
47236 ATAGTCAGTA
* *
47246 TCGCATTGCAATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCAATTTTCCCAATTCGCGTTGCGATTCACGTAT
* * *
47287 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCAATTTTCCCAATTCGCGTTGCGATTCACGTAT
47328 TCGCATTGCGAATT
1 TCGCATTGC-AATT
47342 GGGAAAATCG
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
41 49 0.94
42 3 0.06
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.41
Consensus pattern (41 bp):
TCGCATTGCAATTTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:47290 original size:20 final size:20
Alignment explanation
Indices: 47265--47338 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
47255 AATTTTCCCA
*
47265 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
* **
47285 ATTCGCATTGCGATTTTCCCA
1 ATTCGCATTGCGA-TTTACTT
*
47306 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
47326 ATTCGCATTGCGA
1 ATTCGCATTGCGA
47339 ATTGGGAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACTT
Found at i:51194 original size:44 final size:44
Alignment explanation
Indices: 51131--51231 Score: 166
Period size: 44 Copynumber: 2.3 Consensus size: 44
51121 TGGTGCATCG
* * *
51131 GTGCATCAGTGTAAAATTCAAATATTTTGACCGTTGGACCCTTA
1 GTGCATCGGTGCAAAATTCAAATATTTTAACCGTTGGACCCTTA
*
51175 GTGCATCGGTGCAAAATTCAAATATTTTAATCGTTGGACCCTTA
1 GTGCATCGGTGCAAAATTCAAATATTTTAACCGTTGGACCCTTA
51219 GTGCATCGGTGCA
1 GTGCATCGGTGCA
51232 CTAAGAGTGC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (44 bp):
GTGCATCGGTGCAAAATTCAAATATTTTAACCGTTGGACCCTTA
Found at i:51371 original size:65 final size:65
Alignment explanation
Indices: 51238--51397 Score: 200
Period size: 65 Copynumber: 2.5 Consensus size: 65
51228 TGCACTAAGA
* * *
51238 GTGCATCGATGCATCAAGTGTATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
* * * *
51302 GTGCATCGGTGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGCT
*
51365 AT
65 -G
*
51367 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
51398 CAATTTAATT
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 27 0.33
65 53 0.64
66 3 0.04
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
Found at i:51436 original size:65 final size:63
Alignment explanation
Indices: 51238--51447 Score: 196
Period size: 65 Copynumber: 3.3 Consensus size: 63
51228 TGCACTAAGA
* * * * *
51238 GTGCATCGATGCATCAAGTGTATTCGATGTTTCA-AAATAGC-CAGAGTGCATCGATGCATGGCT
1 GTGCATCGGTGCATCAAATGCATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGGTT
51301 G
63 G
*
51302 GTGCATCGGTGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCATCGGTGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGT-T
51367 -
63 G
* * ** *
51367 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCGTCGATGCATGGAT
1 GTGCATCGGTGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-T
51430 TG
62 TG
51432 GTGCATCGGTGCATCA
1 GTGCATCGGTGCATCA
51448 CTATGAAAAA
Statistics
Matches: 122, Mismatches: 14, Indels: 19
0.79 0.09 0.12
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 46 0.38
65 64 0.52
66 5 0.04
67 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.31
Consensus pattern (63 bp):
GTGCATCGGTGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTG
Found at i:52456 original size:21 final size:21
Alignment explanation
Indices: 52432--52475 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
52422 GAGCTGGAGG
* *
52432 AGGAGGAGCACGAGAGGAGCT
1 AGGAGCAGCACGAGAGGAACT
* *
52453 AGGAGCAGCTCGTGAGGAACT
1 AGGAGCAGCACGAGAGGAACT
52474 AG
1 AG
52476 CTCCCGGAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.43, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAGGAACT
Found at i:59859 original size:17 final size:19
Alignment explanation
Indices: 59817--59854 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
59807 TTGGACCCTT
*
59817 AGTGCATCGGTGCACTAAG
1 AGTGCATCGATGCACTAAG
*
59836 AGTGCATCGATGCATTAAG
1 AGTGCATCGATGCACTAAG
59855 TGCATTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (19 bp):
AGTGCATCGATGCACTAAG
Found at i:59924 original size:20 final size:19
Alignment explanation
Indices: 59882--59969 Score: 85
Period size: 20 Copynumber: 4.7 Consensus size: 19
59872 AATAGCCAGA
**
59882 GTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGAATG
59901 GTGCATCGATGCATGAAATG
1 GTGCATCGATGCATG-AATG
*
59921 GTGCATCGAT---T-CATG
1 GTGCATCGATGCATGAATG
*
59936 GTGCATCGATGCATGGATTG
1 GTGCATCGATGCAT-GAATG
*
59956 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
59970 CACTCTGAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
15 13 0.23
17 1 0.02
18 1 0.02
19 15 0.26
20 27 0.47
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.28
Consensus pattern (19 bp):
GTGCATCGATGCATGAATG
Found at i:59938 original size:15 final size:15
Alignment explanation
Indices: 59918--59951 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
59908 GATGCATGAA
*
59918 ATGGTGCATCGATTC
1 ATGGTGCATCGATGC
59933 ATGGTGCATCGATGC
1 ATGGTGCATCGATGC
59948 ATGG
1 ATGG
59952 ATTGGTGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (15 bp):
ATGGTGCATCGATGC
Found at i:62895 original size:3 final size:3
Alignment explanation
Indices: 62889--62914 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
62879 GATGATGATG
62889 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
62915 TTTTCATCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:67972 original size:38 final size:38
Alignment explanation
Indices: 67930--68004 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
67920 GTTTTTTAAC
* *
67930 AAATTGAAAAATATTTATAT-ATTTTTTTTAAAAAATTT
1 AAATTCAAAAA-ATTTATATAATTGTTTTTAAAAAATTT
* *
67968 AAATTCATAAAATTTATATAATTGTTTTTACAAAATT
1 AAATTCAAAAAATTTATATAATTGTTTTTAAAAAATT
68005 GAAAATATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 8 0.25
38 24 0.75
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (38 bp):
AAATTCAAAAAATTTATATAATTGTTTTTAAAAAATTT
Found at i:70022 original size:68 final size:62
Alignment explanation
Indices: 69934--70057 Score: 144
Period size: 62 Copynumber: 1.9 Consensus size: 62
69924 ACTAGTTATA
69934 TTTTAATATTCAAATGTAAACATATAATAATATCTTTTAATTT-AAAATATTCAAAAAATATAGA
1 TTTTAATATTCAAATGTAAAC--A-AAT-ATA--TTTTAATTTGAAAATATT-AAAAAATATAGA
69998 CTCC
59 CTCC
* *
70002 TTTTACTATTCAAACT-TAAACAAATATATTTTAATTTGGAAATATTAAAAAATATA
1 TTTTAATATTCAAA-TGTAAACAAATATATTTTAATTTGAAAATATTAAAAAATATA
70058 TAATTATCTT
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
62 19 0.37
63 7 0.13
64 3 0.06
65 3 0.06
66 1 0.02
68 18 0.35
69 1 0.02
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.40
Consensus pattern (62 bp):
TTTTAATATTCAAATGTAAACAAATATATTTTAATTTGAAAATATTAAAAAATATAGACTCC
Done.