Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004203.1 Hibiscus syriacus cultivar Beakdansim tig00009198_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: 49842
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:151 original size:13 final size:14
Alignment explanation
Indices: 106--151 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
96 GATCCTAACT
*
106 TATCACTTATA-CA
1 TATCACATATACCA
*
119 TATCACATATCCCA
1 TATCACATATACCA
133 TATCAC-TATACCA
1 TATCACATATACCA
*
146 TTTCAC
1 TATCAC
152 GAGAAACACA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 20 0.71
14 8 0.29
ACGTcount: A:0.35, C:0.30, G:0.00, T:0.35
Consensus pattern (14 bp):
TATCACATATACCA
Found at i:319 original size:18 final size:18
Alignment explanation
Indices: 296--340 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
286 GCGTAGAATT
*
296 TGTCCCGTAGGACCACTG
1 TGTCCCGAAGGACCACTG
314 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTG
332 TGTCCCGAA
1 TGTCCCGAA
341 CACTATGTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.20, C:0.33, G:0.27, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTG
Found at i:712 original size:13 final size:14
Alignment explanation
Indices: 669--716 Score: 71
Period size: 14 Copynumber: 3.5 Consensus size: 14
659 ATGATTCTTA
*
669 TCTCATACACATGT
1 TCTCATATACATGT
*
683 TCGCATATACATGT
1 TCTCATATACATGT
697 TCTCATATAC-TGT
1 TCTCATATACATGT
710 TCTCATA
1 TCTCATA
717 CAATCCCTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
13 10 0.32
14 21 0.68
ACGTcount: A:0.27, C:0.25, G:0.08, T:0.40
Consensus pattern (14 bp):
TCTCATATACATGT
Found at i:1461 original size:21 final size:21
Alignment explanation
Indices: 1434--1489 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
1424 TATTTGAGAG
1434 TGCATCGATACACATTGAAGA
1 TGCATCGATACACATTGAAGA
*
1455 TGTATCGATACACATTGAAGA
1 TGCATCGATACACATTGAAGA
*
1476 TGCATCGATGCACA
1 TGCATCGATACACA
1490 CAACCCAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.25
Consensus pattern (21 bp):
TGCATCGATACACATTGAAGA
Found at i:2263 original size:45 final size:45
Alignment explanation
Indices: 2195--2368 Score: 251
Period size: 45 Copynumber: 3.9 Consensus size: 45
2185 GGATGTTATA
* * * *
2195 TTTCATGCCTTTAATACACCGTTATGCATTTTAATTATGTCATCCT
1 TTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCAT-CT
* *
2241 TTT-ATGCCTTTAATGCATCGTTATGCATTTCATTTATGGAATCT
1 TTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCT
2285 TTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCT
1 TTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCT
* * *
2330 TTTCATGCCTTTAATGCGCCATTATCCATTTCATTTATG
1 TTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATG
2369 TAATAAAAAC
Statistics
Matches: 116, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
44 5 0.04
45 108 0.93
46 3 0.03
ACGTcount: A:0.22, C:0.21, G:0.11, T:0.46
Consensus pattern (45 bp):
TTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCT
Found at i:2946 original size:21 final size:21
Alignment explanation
Indices: 2916--2971 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
2906 TCGATTCCCA
*
2916 CATCAATATCGATACTAATTG
1 CATCAGTATCGATACTAATTG
2937 CATCAGTATCGATACTAATTG
1 CATCAGTATCGATACTAATTG
2958 CATCAGTATCGATA
1 CATCAGTATCGATA
2972 TTGTTCATCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (21 bp):
CATCAGTATCGATACTAATTG
Found at i:9023 original size:45 final size:45
Alignment explanation
Indices: 8992--9359 Score: 454
Period size: 45 Copynumber: 8.2 Consensus size: 45
8982 TATTCATTAT
* * *
8992 TTTCATTTATAGCATCCTTTCATGCCTTTAAT-ACACAATTGTGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGA-ACCATTATGCA
* * *
9037 TTTCATTTATGGCATTCTTTCATGCCTTTAATGAATCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGAACCATTATGCA
* * * *
9082 TTTCA-TTATGGCATCCTTTCATTCTTTTAATGCACCATTATACA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGAACCATTATGCA
* *
9126 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGAACCATTATGCA
* * *
9171 TTTCATTTATGGCA-CCTTTTATGCCTTTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGAACCATTATGCA
* * * *
9215 TTTCATTTATGGAATCCTTTCATGCCTTTAATGCACCGTTATACA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGAACCATTATGCA
* * * ** *
9260 TTTCATTTATGGTATTCTTTCATGCCTTTAATGCACTGTTCTGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGAACCATTATGCA
* * *
9305 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCATCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGAACCATTATGCA
9350 TTTCATTTAT
1 TTTCATTTAT
9360 ATAATGAAAA
Statistics
Matches: 289, Mismatches: 31, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
44 79 0.27
45 209 0.72
46 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.11, T:0.45
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCTTTAATGAACCATTATGCA
Found at i:9111 original size:89 final size:90
Alignment explanation
Indices: 8992--9359 Score: 542
Period size: 89 Copynumber: 4.1 Consensus size: 90
8982 TATTCATTAT
* * * * *
8992 TTTCATTTATAGCATCCTTTCATGCCTTTAATACACAATTGTGCATTTCATTTATGGCATTCTTT
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGCATTTCATTTATGGCATCCTTT
* *
9057 CATGCCTTTAATGAATCGTTATGCA
66 CATGCCTTTAATGCACCGTTATGCA
* * *
9082 TTTCA-TTATGGCATCCTTTCATTCTTTTAATGCACCATTATACATTTCATTTATGGCATCCTTT
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGCATTTCATTTATGGCATCCTTT
9146 CATGCCTTTAATGCACCGTTATGCA
66 CATGCCTTTAATGCACCGTTATGCA
* * *
9171 TTTCATTTATGGCA-CCTTTTATGCCTTTAATGCACCGTTATGCATTTCATTTATGGAATCCTTT
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGCATTTCATTTATGGCATCCTTT
*
9235 CATGCCTTTAATGCACCGTTATACA
66 CATGCCTTTAATGCACCGTTATGCA
* * ** *
9260 TTTCATTTATGGTATTCTTTCATGCCTTTAATGCACTGTTCTGCATTTCATTTATGGCATCCTTT
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGCATTTCATTTATGGCATCCTTT
*
9325 CATGCCTTTAATGCATCGTTATGCA
66 CATGCCTTTAATGCACCGTTATGCA
9350 TTTCATTTAT
1 TTTCATTTAT
9360 ATAATGAAAA
Statistics
Matches: 251, Mismatches: 25, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
89 160 0.64
90 91 0.36
ACGTcount: A:0.22, C:0.21, G:0.11, T:0.45
Consensus pattern (90 bp):
TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGCATTTCATTTATGGCATCCTTT
CATGCCTTTAATGCACCGTTATGCA
Found at i:9205 original size:20 final size:20
Alignment explanation
Indices: 9141--9206 Score: 53
Period size: 25 Copynumber: 3.1 Consensus size: 20
9131 TTTATGGCAT
*
9141 CCTTTCATGCCTTTAATGCA
1 CCTTTTATGCCTTTAATGCA
* *
9161 CC-GTTATGCATTTCATTTATGGCA
1 CCTTTTATGCCTTT-A---AT-GCA
9185 CCTTTTATGCCTTTAATGCA
1 CCTTTTATGCCTTTAATGCA
9205 CC
1 CC
9207 GTTATGCATT
Statistics
Matches: 35, Mismatches: 5, Indels: 12
0.67 0.10 0.23
Matches are distributed among these distances:
19 8 0.23
20 8 0.23
21 2 0.06
23 2 0.06
24 6 0.17
25 9 0.26
ACGTcount: A:0.20, C:0.27, G:0.12, T:0.41
Consensus pattern (20 bp):
CCTTTTATGCCTTTAATGCA
Found at i:9213 original size:19 final size:19
Alignment explanation
Indices: 9147--9213 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 19
9137 GCATCCTTTC
9147 ATGCCTTTAATGCACCGTT
1 ATGCCTTTAATGCACCGTT
* *
9166 ATGCATTTCATTTATGGCACCTTTT
1 ATGCCTTT-A---AT-GCACC-GTT
9191 ATGCCTTTAATGCACCGTT
1 ATGCCTTTAATGCACCGTT
9210 ATGC
1 ATGC
9214 ATTTCATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
19 13 0.34
20 6 0.16
21 2 0.05
23 2 0.05
24 6 0.16
25 9 0.24
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (19 bp):
ATGCCTTTAATGCACCGTT
Found at i:9225 original size:134 final size:135
Alignment explanation
Indices: 8992--9359 Score: 569
Period size: 134 Copynumber: 2.7 Consensus size: 135
8982 TATTCATTAT
* * * * *
8992 TTTCATTTATAGCATCCTTTCATGCCTTTAATACACAATTGTGCATTTCATTTATGGCATTCTTT
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACAGTTATGCATTTCATTTATGGCATCCTTT
* * * *
9057 CATGCCTTTAATGAATCGTTATGCATTTCA-TTATGGCATCCTTTCATTCTTTTAATGCACCATT
66 CATGCCTTTAATGCATCGTTATGCATTTCATTTATGGAATCCTTTCATGCCTTTAATGCACCATT
9121 ATACA
131 ATACA
*
9126 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCA-CCTTT
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACAGTTATGCATTTCATTTATGGCATCCTTT
* * *
9190 TATGCCTTTAATGCACCGTTATGCATTTCATTTATGGAATCCTTTCATGCCTTTAATGCACCGTT
66 CATGCCTTTAATGCATCGTTATGCATTTCATTTATGGAATCCTTTCATGCCTTTAATGCACCATT
9255 ATACA
131 ATACA
* * * *
9260 TTTCATTTATGGTATTCTTTCATGCCTTTAATGCACTGTTCTGCATTTCATTTATGGCATCCTTT
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACAGTTATGCATTTCATTTATGGCATCCTTT
9325 CATGCCTTTAATGCATCGTTATGCATTTCATTTAT
66 CATGCCTTTAATGCATCGTTATGCATTTCATTTAT
9360 ATAATGAAAA
Statistics
Matches: 213, Mismatches: 19, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
133 31 0.15
134 144 0.68
135 38 0.18
ACGTcount: A:0.22, C:0.21, G:0.11, T:0.45
Consensus pattern (135 bp):
TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACAGTTATGCATTTCATTTATGGCATCCTTT
CATGCCTTTAATGCATCGTTATGCATTTCATTTATGGAATCCTTTCATGCCTTTAATGCACCATT
ATACA
Found at i:9825 original size:22 final size:21
Alignment explanation
Indices: 9774--9829 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
9764 TATGTAATTC
* *
9774 ATGGTATCGATACATTTCTCT
1 ATGGTATCGATACTTTTATCT
*
9795 -TAGTATCGATACTTTTATACT
1 ATGGTATCGATACTTTTAT-CT
9816 ATGGTATCGATACT
1 ATGGTATCGATACT
9830 CCCTTATAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 15 0.52
21 2 0.07
22 12 0.41
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (21 bp):
ATGGTATCGATACTTTTATCT
Found at i:9937 original size:21 final size:21
Alignment explanation
Indices: 9912--9957 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
9902 CCCAGAGCAA
9912 TATCGATACTAATTGCATCAG
1 TATCGATACTAATTGCATCAG
9933 TATCGATACTAATTGCATCAG
1 TATCGATACTAATTGCATCAG
9954 TATC
1 TATC
9958 AATATTGTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.35
Consensus pattern (21 bp):
TATCGATACTAATTGCATCAG
Found at i:20328 original size:14 final size:14
Alignment explanation
Indices: 20320--20358 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
20310 TGATTTTGAT
20320 ATGTCGATTTTAAA
1 ATGTCGATTTTAAA
20334 ATGTCGATTTTAAA
1 ATGTCGATTTTAAA
* *
20348 CTGTTGATTTT
1 ATGTCGATTTT
20359 CAGGCTACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.28, C:0.08, G:0.15, T:0.49
Consensus pattern (14 bp):
ATGTCGATTTTAAA
Found at i:21208 original size:47 final size:46
Alignment explanation
Indices: 21100--21208 Score: 121
Period size: 47 Copynumber: 2.3 Consensus size: 46
21090 ATTGGACATC
*
21100 ACCATCTTATAAGGATGGACCAATCTATAATTCAGTTATTAGACTTT
1 ACCATC-TATAAGGATGGACCAATCTATAATTCAGTTATTAGAATTT
* * * *
21147 ACTATCTATCAAGGATGTATCAATCTGA-AATTCAGTTATTGGAATTT
1 ACCATCTAT-AAGGATGGACCAATCT-ATAATTCAGTTATTAGAATTT
*
21194 ACCCTCCTATAAGGA
1 ACCAT-CTATAAGGA
21209 AGAACTAGTT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
46 3 0.06
47 44 0.85
48 5 0.10
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (46 bp):
ACCATCTATAAGGATGGACCAATCTATAATTCAGTTATTAGAATTT
Found at i:22007 original size:39 final size:37
Alignment explanation
Indices: 21962--22098 Score: 170
Period size: 37 Copynumber: 3.6 Consensus size: 37
21952 TATACATATA
* ***
21962 TATATATATATTATAGTTTGTAAATTGTTTTTGAAAATACG
1 TATATA-ATA-TATAGTTTTTAAAAACTTTTTGAAAAT--G
22003 TATATAATATATAGTTTTTAAAAACTTTTTGAAAATG
1 TATATAATATATAGTTTTTAAAAACTTTTTGAAAATG
*
22040 TATATAATATATAGTTTTTAAAACAC-TTTTGAAAA-C
1 TATATAATATATAGTTTTTAAAA-ACTTTTTGAAAATG
22076 TATATAATATATAGTTTTTAAAA
1 TATATAATATATAGTTTTTAAAA
22099 CATTTTAAAT
Statistics
Matches: 90, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
36 23 0.26
37 33 0.37
38 2 0.02
39 23 0.26
40 3 0.03
41 6 0.07
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (37 bp):
TATATAATATATAGTTTTTAAAAACTTTTTGAAAATG
Found at i:22080 original size:36 final size:37
Alignment explanation
Indices: 21990--22104 Score: 173
Period size: 37 Copynumber: 3.1 Consensus size: 37
21980 TGTAAATTGT
21990 TTTTGAAAATACGTATATAATATATAGTTTTTAAAA-AC
1 TTTTGAAAAT-C-TATATAATATATAGTTTTTAAAACAC
*
22028 TTTTTGAAAATGTATATAATATATAGTTTTTAAAACAC
1 -TTTTGAAAATCTATATAATATATAGTTTTTAAAACAC
22066 TTTTGAAAA-CTATATAATATATAGTTTTTAAAACA-
1 TTTTGAAAATCTATATAATATATAGTTTTTAAAACAC
22101 TTTT
1 TTTT
22105 AAATATTTTT
Statistics
Matches: 73, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
35 4 0.05
36 25 0.34
37 32 0.44
38 2 0.03
39 10 0.14
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (37 bp):
TTTTGAAAATCTATATAATATATAGTTTTTAAAACAC
Found at i:22126 original size:23 final size:23
Alignment explanation
Indices: 22100--22144 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
22090 TTTTTAAAAC
22100 ATTTTAAATATTT-TTATTTATTT
1 ATTTTAAAT-TTTATTATTTATTT
**
22123 ATTTTTCATTTTATTATTTATT
1 ATTTTAAATTTTATTATTTATT
22145 GTTTTCTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (23 bp):
ATTTTAAATTTTATTATTTATTT
Found at i:23418 original size:23 final size:23
Alignment explanation
Indices: 23367--23424 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
23357 TTTATTTCCC
*
23367 TTTATATTTATTTTATTTCTTTA
1 TTTATTTTTATTTTATTTCTTTA
* *
23390 TCTATTTTTATTTTA-TTCTTGTT
1 TTTATTTTTATTTTATTTCTT-TA
23413 TTTATTTATTAT
1 TTTATTT-TTAT
23425 ATATATTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 5 0.17
23 20 0.69
24 4 0.14
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (23 bp):
TTTATTTTTATTTTATTTCTTTA
Found at i:26226 original size:95 final size:95
Alignment explanation
Indices: 26117--26370 Score: 343
Period size: 94 Copynumber: 2.7 Consensus size: 95
26107 ATAATAATAT
* * *
26117 ATATGCAATAAAGCTTGAGCTGTCCCTCTAAAGCAATTGGTTAAACGCCCTGGCTTTATGGATAA
1 ATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCTGGCTTTATGGATAA
*
26182 GATTTAGATAGCCTGATAAAGGTGATTATA
66 GATTCAGATAGCCTGATAAAGGTGATTATA
*
26212 ATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCC-GTCTTTATGGATAA
1 ATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCTGGCTTTATGGATAA
* * *
26276 TATTCAGCTAGCCTGATTAAGGTGATTATA
66 GATTCAGATAGCCTGATAAAGGTGATTATA
* * *
26306 ATATATAA-ACAATGATATTAAGTTGTCCCTCTAGAGCAATTGGTTAAACG-CCTCGGCTTTATG
1 ATATACAATA-AA-G--CTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCT-GGCTTTATG
26369 GA
61 GA
26371 ATCAGCTAGC
Statistics
Matches: 141, Mismatches: 12, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
93 1 0.01
94 48 0.34
95 48 0.34
96 2 0.01
97 32 0.23
98 10 0.07
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (95 bp):
ATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCTGGCTTTATGGATAA
GATTCAGATAGCCTGATAAAGGTGATTATA
Found at i:26382 original size:97 final size:92
Alignment explanation
Indices: 26117--26383 Score: 288
Period size: 95 Copynumber: 2.8 Consensus size: 92
26107 ATAATAATAT
* * * * *
26117 ATATGCAATAAAGCTTGAGCTGTCCCTCTAAAGCAATTGGTTAAACGCCCTGGCTTTATGG-ATA
1 ATATACAATAAAGATTAAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCC-GGCTTTATGGAAT-
*
26181 AGATTTAGATAGCCTGATAAAGGTGATTATA
64 AG--TTAGCTAGCCTGATAAAGGTGATTATA
* * *
26212 ATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCGTCTTTATGGATAAT
1 ATATACAATAAAGATTAAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCGGCTTTATGG--AAT
*
26277 A-TTCAGCTAGCCTGATTAAGGTGATTATA
64 AGTT-AGCTAGCCTGATAAAGGTGATTATA
*
26306 ATATATAA-ACAATGATATTAAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCTCGGCTTTATGG
1 ATATACAATA-AA-G--ATTAAGTTGTCCCTCTAGAGCAATTGGTTAAACGCC-CGGCTTTATGG
*
26370 AATCAGCTAGCTAG
61 AAT-AGTTAGCTAG
26384 ACAATGGCAA
Statistics
Matches: 150, Mismatches: 11, Indels: 20
0.83 0.06 0.11
Matches are distributed among these distances:
93 3 0.02
94 41 0.27
95 48 0.32
96 4 0.03
97 43 0.29
98 11 0.07
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (92 bp):
ATATACAATAAAGATTAAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCGGCTTTATGGAATAG
TTAGCTAGCCTGATAAAGGTGATTATA
Found at i:27660 original size:84 final size:84
Alignment explanation
Indices: 27540--27710 Score: 238
Period size: 84 Copynumber: 2.0 Consensus size: 84
27530 TCTGTCAGCC
* * *
27540 AAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCACAACATTTGC-AGCATACCTCAAGGCGA
1 AAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACAACATTTGCTA-CATAACTCAAGGCAA
* *
27604 GAAGGGTTATCTT-CCAACAA
65 GAAGGGCTAT-TTGCAAACAA
* **
27624 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATTATTTGCTACATAACTCAAGGCAAG
1 AAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACAACATTTGCTACATAACTCAAGGCAAG
27689 AAGGGCTATTTGCAAACAA
66 AAGGGCTATTTGCAAACAA
27708 AAG
1 AAG
27711 TGTCGAAACG
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
83 2 0.03
84 74 0.96
85 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (84 bp):
AAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACAACATTTGCTACATAACTCAAGGCAAG
AAGGGCTATTTGCAAACAA
Found at i:32151 original size:84 final size:83
Alignment explanation
Indices: 31424--32175 Score: 773
Period size: 84 Copynumber: 9.0 Consensus size: 83
31414 ATCATCTACA
* * *
31424 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCGAAGGCACATCATTTGCAGCATAGCTCAAGGTG
1 AAAAGACCTTCGAGTTCGACTACGCTCAGCTC-AAGGCACATCATTTACAACATAGCTCAAGGCG
* *
31489 AGAAAGGCTATCTACCAAC
65 AGAAGGGCTATCTGCCAAC
* * *
31508 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAGCTAAAGGCA
1 AAAAGACCTTCGAGTTCGACTACGCTCAGCT-CAAGGCACATCATTTACAACATAGCTCAAGGCG
* *
31573 AGAAGGGCTATTTGCCAAT
65 AGAAGGGCTATCTGCCAAC
* *
31592 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGTACATCATTTACACCATAGCTCAAGGCG
1 AAAAGACCTTCGAGTTCGACTACGCTCAGCT-CAAGGCACATCATTTACAACATAGCTCAAGGCG
* *
31657 AGAAGGGCTATCTTCCAAA
65 AGAAGGGCTATCTGCCAAC
* * * **
31676 AAAAGAACTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGAT
1 AAAAGACCTTCGAGTTCGACTACGCTCAGCT-CAAGGCACATCATTTACAACATAGCTCAAGGCG
* * *
31741 AGAAGGGTTATTTTCCAAC
65 AGAAGGGCTATCTGCCAAC
* *
31760 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAACATAACTCAAGGCT
1 AAAAGACCTTCGAGTTCGACTACGCTCAGCT-CAAGGCACATCATTTACAACATAGCTCAAGGCG
* ** * *
31825 AAAAGGATTATATGTCAAC
65 AGAAGGGCTATCTGCCAAC
* * * * * * ** * *
31844 -AAAGGCCTTCGAGTTAGATTACACTCAGCTCAAAGACACATCATTTGCAGTATAGCTTAAGTCG
1 AAAAGACCTTCGAGTTCGACTACGCTCAGCTC-AAGGCACATCATTTACAACATAGCTCAAGGCG
* *
31908 ATAAGGGCTATATGCCAAC
65 AGAAGGGCTATCTGCCAAC
* ** * * * *
31927 CAAAGACCTTCGAGTTATATTACACTCAGCTCAAGGGCACATCATTTACAACATAACTCAAGGCT
1 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCAA-GGCACATCATTTACAACATAGCTCAAGGCG
* **
31992 AGAAGGGTTATCTGTTAAC
65 AGAAGGGCTATCTGCCAAC
* * * * *
32011 -CAAGACCTTCAAGTTCGATTACACTCAG----AGGCACATCATTTACAGCATAGCTCAAGGCGA
1 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAGGCACATCATTTACAACATAGCTCAAGGCGA
32071 GAAGGGCTATCTGCCAAC
66 GAAGGGCTATCTGCCAAC
* *** * **
32089 AAAAGACCTTCGAGTTCGATTATATTCAGCTCAAAG-ACATCAAATTTACAGTATAGCTCAAGGC
1 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAGGCACATC--ATTTACAACATAGCTCAAGGC
* *
32153 -ATGAAGGGATATCTGTCAAC
64 GA-GAAGGGCTATCTGCCAAC
32173 AAA
1 AAA
32176 GTTATCGAGT
Statistics
Matches: 573, Mismatches: 83, Indels: 24
0.84 0.12 0.04
Matches are distributed among these distances:
78 43 0.08
79 25 0.04
82 6 0.01
83 94 0.16
84 404 0.71
85 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (83 bp):
AAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAGGCACATCATTTACAACATAGCTCAAGGCGA
GAAGGGCTATCTGCCAAC
Found at i:32750 original size:2 final size:2
Alignment explanation
Indices: 32743--32774 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
32733 ACATACATAC
32743 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32775 TTGCAAACAG
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):
AT
Found at i:32839 original size:37 final size:37
Alignment explanation
Indices: 32755--33018 Score: 227
Period size: 37 Copynumber: 7.2 Consensus size: 37
32745 ATATATATAT
* **
32755 ATATATATATATATATA-TATTTGCAAACAGTTTTTGAAA
1 ATATATATA-ATATATAGTTTTTAAAAACA--TTTTGAAA
32794 ATAAGTATATAATATATAGTTTTTAAAAACATTTTGAAA
1 AT-A-TATATAATATATAGTTTTTAAAAACATTTTGAAA
* *
32833 ATGTATATAATATATAATTTTT-AAAACACTTTTGAAA
1 ATATATATAATATATAGTTTTTAAAAACA-TTTTGAAA
*
32870 A-CTATATAATATATAGTTTTT-AAAACATTTTAGAAA
1 ATATATATAATATATAGTTTTTAAAAACATTTT-GAAA
*
32906 ATATATATAATATATAG-TTTTGAAAACA--TT----
1 ATATATATAATATATAGTTTTTAAAAACATTTTGAAA
32936 -TATATAT--TATATAGTTTTTTAAAAAACATTTTTGAAA
1 ATATATATAATATATAG-TTTTT-AAAAACA-TTTTGAAA
* *
32973 A-CT-TATAATATATATTTTTTAAAAAACATTTTGGAAA
1 ATATATATAATATATAGTTTTT-AAAAACATTTT-GAAA
33010 ATATATATA
1 ATATATATA
33019 GTTTTAAAAT
Statistics
Matches: 190, Mismatches: 12, Indels: 46
0.77 0.05 0.19
Matches are distributed among these distances:
27 7 0.04
29 11 0.06
30 6 0.03
33 2 0.01
35 6 0.03
36 46 0.24
37 66 0.35
38 7 0.04
39 16 0.08
40 8 0.04
41 15 0.08
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTTAAAAACATTTTGAAA
Found at i:32876 original size:36 final size:35
Alignment explanation
Indices: 32799--33099 Score: 197
Period size: 37 Copynumber: 8.7 Consensus size: 35
32789 TGAAAATAAG
32799 TATATAATATATAGTTTTTAAAA-ACATTTTGAAAA
1 TATATAATATATAGTTTTTAAAACAC-TTTTGAAAA
*
32834 TGTATATAATATATAATTTTTAAAACACTTTTGAAAA
1 --TATATAATATATAGTTTTTAAAACACTTTTGAAAA
32871 CTATATAATATATAGTTTTTAAAACA-TTTTAGAAAATA
1 -TATATAATATATAGTTTTTAAAACACTTTT-G-AAA-A
*
32909 TATATAATATATAGTTTTGAAAACA--TTT----A
1 TATATAATATATAGTTTTTAAAACACTTTTGAAAA
*
32938 TATAT--TATATAGTTTTTTAAAAAACATTTTTGAAAA
1 TATATAATATATAG-TTTTT--AAAACACTTTTGAAAA
* * *
32974 CT-TATAATATATATTTTTTAAAAAACATTTTG-GAA
1 -TATATAATATATAGTTTTTAAAACAC-TTTTGAAAA
* *
33009 -A-AT-ATATATAG-TTTTAAAATAGTTTTTGAAAA
1 TATATAATATATAGTTTTTAAAACA-CTTTTGAAAA
* * * *
33041 TATAT--TATATGGTTTTGAAAAGCATTTTTAAAATCA
1 TATATAATATATAGTTTTTAAAA-CACTTTTGAAA--A
* * *
33077 TATATAAAATATAATTTTAAAAA
1 TATATAATATATAGTTTTTAAAA
33100 AAAATTAATT
Statistics
Matches: 215, Mismatches: 21, Indels: 55
0.74 0.07 0.19
Matches are distributed among these distances:
27 7 0.03
28 4 0.02
29 6 0.03
30 6 0.03
31 14 0.07
32 12 0.06
33 9 0.04
34 17 0.08
35 12 0.06
36 43 0.20
37 64 0.30
38 21 0.10
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (35 bp):
TATATAATATATAGTTTTTAAAACACTTTTGAAAA
Found at i:32939 original size:25 final size:28
Alignment explanation
Indices: 32897--32953 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
32887 TTTTAAAACA
*
32897 TTTTAG-AAA-ATATATATAATATATAG
1 TTTTAGAAAACATATATATATTATATAG
*
32923 TTTT-GAAAACATTTATATATTATATAG
1 TTTTAGAAAACATATATATATTATATAG
32950 TTTT
1 TTTT
32954 TTAAAAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 1 0.04
26 7 0.26
27 19 0.70
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (28 bp):
TTTTAGAAAACATATATATATTATATAG
Found at i:32955 original size:29 final size:28
Alignment explanation
Indices: 32909--32966 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 28
32899 TTAGAAAATA
*
32909 TATATAATATATAGTTTT-GAAAACATT
1 TATATAATATATAGTTTTAAAAAACATT
*
32936 TATATATTATATAGTTTTTTAAAAAACATT
1 TATATAATATATAG--TTTTAAAAAACATT
32966 T
1 T
32967 TTGAAAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 13 0.50
29 4 0.15
30 9 0.35
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.48
Consensus pattern (28 bp):
TATATAATATATAGTTTTAAAAAACATT
Found at i:32999 original size:67 final size:64
Alignment explanation
Indices: 32872--33003 Score: 160
Period size: 67 Copynumber: 2.0 Consensus size: 64
32862 TTTTGAAAAC
*
32872 TATATAATATATAGTTTTTAAAACATTTTAGAAAATATATATAATATATAGTTTTGAAAACATT
1 TATATAATATATAGTTTTTAAAACATTTTAGAAAATATATATAATATATAGTTTTAAAAACATT
* * * *
32936 TATATATTATATAGTTTTTTAAAAAACATTTTTGAAAA-CT-TATAATATATATTTTTTAAAAAA
1 TATATAATATATAG-TTTTT--AAAACATTTTAGAAAATATATATAATATATA-GTTTT-AAAAA
32999 CATT
61 CATT
33003 T
1 T
33004 TGGAAAATAT
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
64 13 0.22
65 16 0.28
66 5 0.09
67 24 0.41
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (64 bp):
TATATAATATATAGTTTTTAAAACATTTTAGAAAATATATATAATATATAGTTTTAAAAACATT
Found at i:33015 original size:30 final size:30
Alignment explanation
Indices: 32979--33045 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
32969 GAAAACTTAT
*
32979 AATATATAT-TTTTTAAAAAACATTTTGGAA
1 AATATATATAGTTTTAAAAAA-ATTTTGGAA
* * *
33009 AATATATATAGTTTTAAAATAGTTTTTGAA
1 AATATATATAGTTTTAAAAAAATTTTGGAA
33039 AATATAT
1 AATATAT
33046 TATATGGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 23 0.72
31 9 0.28
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.45
Consensus pattern (30 bp):
AATATATATAGTTTTAAAAAAATTTTGGAA
Found at i:33122 original size:7 final size:7
Alignment explanation
Indices: 33107--33163 Score: 78
Period size: 7 Copynumber: 8.0 Consensus size: 7
33097 AAAAAAATTA
*
33107 ATTTTTT
1 ATTTATT
33114 ATTTATT
1 ATTTATT
33121 ATTTATT
1 ATTTATT
33128 ATTTATT
1 ATTTATT
33135 ATTTATTT
1 ATTTA-TT
*
33143 ATTTGTT
1 ATTTATT
*
33150 ATTTGTT
1 ATTTATT
33157 ATTTATT
1 ATTTATT
33164 GTTTTATCTT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
7 40 0.87
8 6 0.13
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.74
Consensus pattern (7 bp):
ATTTATT
Found at i:33125 original size:11 final size:11
Alignment explanation
Indices: 33107--33163 Score: 57
Period size: 11 Copynumber: 5.3 Consensus size: 11
33097 AAAAAAATTA
*
33107 ATTTTTTATTT
1 ATTTATTATTT
33118 A-TTATT-TATT
1 ATTTATTAT-TT
33128 ATTTATTATTT
1 ATTTATTATTT
33139 ATTTATT-TGTT
1 ATTTATTAT-TT
*
33150 ATTTGTTATTT
1 ATTTATTATTT
33161 ATT
1 ATT
33164 GTTTTATCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 1 0.03
10 8 0.21
11 28 0.72
12 2 0.05
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.74
Consensus pattern (11 bp):
ATTTATTATTT
Found at i:34418 original size:20 final size:20
Alignment explanation
Indices: 34383--34440 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 20
34373 CTATCATTCT
34383 TTTTCTTTTATTTATTTTCCC
1 TTTTCTTTT-TTTATTTTCCC
34404 TTTTCTTTTTTTA-TTTCCC
1 TTTTCTTTTTTTATTTTCCC
*
34423 TTTATATTTATTTTATTT
1 TTT-TCTTT-TTTTATTT
34441 CTTTATCTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 9 0.27
20 8 0.24
21 14 0.42
22 2 0.06
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTCTTTTTTTATTTTCCC
Found at i:34422 original size:19 final size:20
Alignment explanation
Indices: 34381--34458 Score: 81
Period size: 19 Copynumber: 3.9 Consensus size: 20
34371 TACTATCATT
*
34381 CTTTTTCTTTTATTTATTTTCC
1 CTTTATCTTTT-TTTA-TTTCC
34403 CTTT-TCTTTTTTTATTTCC
1 CTTTATCTTTTTTTATTTCC
*
34422 CTTTATATTTATTTTATTT--
1 CTTTATCTTT-TTTTATTTCC
*
34441 CTTTATCTATTTTTATTT
1 CTTTATCTTTTTTTATTT
34459 TATTCTTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
18 8 0.16
19 17 0.33
20 8 0.16
21 14 0.27
22 4 0.08
ACGTcount: A:0.13, C:0.14, G:0.00, T:0.73
Consensus pattern (20 bp):
CTTTATCTTTTTTTATTTCC
Found at i:34472 original size:27 final size:29
Alignment explanation
Indices: 34423--34478 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
34413 TTTATTTCCC
34423 TTTATATTTATTTTATTTCTTTATCTATT
1 TTTATATTTATTTTATTTCTTTATCTATT
*
34452 TTTAT-TTTATTCTT-TTT-TTTATTTATT
1 TTTATATTTATT-TTATTTCTTTATCTATT
34479 GTATATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 9 0.36
28 9 0.36
29 7 0.28
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (29 bp):
TTTATATTTATTTTATTTCTTTATCTATT
Found at i:34474 original size:23 final size:23
Alignment explanation
Indices: 34423--34573 Score: 64
Period size: 23 Copynumber: 6.4 Consensus size: 23
34413 TTTATTTCCC
*
34423 TTTATATTTATTTTATTTCTTTA
1 TTTATTTTTATTTTATTTCTTTA
*
34446 TCTATTTTTATTTTA-TTCTTT-
1 TTTATTTTTATTTTATTTCTTTA
* * *
34467 TTT-TTATTTATTGTATATATATTA
1 TTTATT-TTTATTTTATTTCT-TTA
* * *
34491 -TCATTTTCT-TTGT-TTTCTTTG
1 TTTATTTT-TATTTTATTTCTTTA
*
34512 TTCT-TTTTTATTTTATTTTCATTTCT
1 TT-TATTTTTATTTTA-TTTC-TTT-A
*
34538 TTTATTTTCTTTCTTTATTTTCTTTA
1 TTTATTTT-TAT-TTTA-TTTCTTTA
34564 TTTCATTTTT
1 TTT-ATTTTT
34574 TTTCCTCCAA
Statistics
Matches: 96, Mismatches: 15, Indels: 31
0.68 0.11 0.22
Matches are distributed among these distances:
20 2 0.02
21 13 0.14
22 19 0.20
23 22 0.23
24 7 0.07
25 4 0.04
26 10 0.10
27 10 0.10
28 9 0.09
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (23 bp):
TTTATTTTTATTTTATTTCTTTA
Found at i:34552 original size:14 final size:14
Alignment explanation
Indices: 34522--34577 Score: 69
Period size: 14 Copynumber: 4.0 Consensus size: 14
34512 TTCTTTTTTA
34522 TTTTATTTTCATTTC
1 TTTTATTTTC-TTTC
34537 TTTTATTTTCTTTC
1 TTTTATTTTCTTTC
*
34551 -TTTATTTTCTTTA
1 TTTTATTTTCTTTC
* *
34564 TTTCATTTTTTTTC
1 TTTTATTTTCTTTC
34578 CTCCAATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
13 12 0.33
14 14 0.39
15 10 0.28
ACGTcount: A:0.11, C:0.12, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTATTTTCTTTC
Found at i:34559 original size:9 final size:9
Alignment explanation
Indices: 34493--34566 Score: 50
Period size: 9 Copynumber: 8.4 Consensus size: 9
34483 ATATATTATC
34493 ATTTTCTTT
1 ATTTTCTTT
*
34502 GTTTTC-TT
1 ATTTTCTTT
*
34510 -TGTTCTTT
1 ATTTTCTTT
34518 -TTTAT-TTT
1 ATTT-TCTTT
34526 ATTTTCATTT
1 ATTTTC-TTT
* *
34536 CTTTTATTT
1 ATTTTCTTT
34545 -TCTTTCTTT
1 AT-TTTCTTT
34554 ATTTTCTTT
1 ATTTTCTTT
34563 ATTT
1 ATTT
34567 CATTTTTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
7 4 0.08
8 11 0.21
9 29 0.56
10 8 0.15
ACGTcount: A:0.09, C:0.11, G:0.03, T:0.77
Consensus pattern (9 bp):
ATTTTCTTT
Found at i:36006 original size:20 final size:20
Alignment explanation
Indices: 35983--36021 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
35973 AATATGAATA
35983 TATTAAAAATATTAAAAAAC
1 TATTAAAAATATTAAAAAAC
* * *
36003 TATTACAATTTTTAAAAAA
1 TATTAAAAATATTAAAAAA
36022 TAAAATATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
TATTAAAAATATTAAAAAAC
Found at i:36057 original size:25 final size:26
Alignment explanation
Indices: 36015--36067 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
36005 TTACAATTTT
**
36015 TAAAAAATAAAATATATTCCAAACTA
1 TAAAAAATAAAATATATTAAAAACTA
36041 TAAAATAAT-AAAT-TATTAAAAACTA
1 TAAAA-AATAAAATATATTAAAAACTA
36066 TA
1 TA
36068 TATAATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 12 0.50
26 9 0.38
27 3 0.12
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (26 bp):
TAAAAAATAAAATATATTAAAAACTA
Found at i:45238 original size:60 final size:61
Alignment explanation
Indices: 45145--45303 Score: 230
Period size: 60 Copynumber: 2.6 Consensus size: 61
45135 ACCGTAGTGC
* * *
45145 TATGACATATAAAGTGGTGCCCACCACCTGCACTAAGTTTACACTCTAGTGCTAATCCG-A
1 TATGACACATAAGGTCGTGCCCACCACCTGCACTAAGTTTACACTCTAGTGCTAATCCGAA
* * * *
45205 TATGACACATAAGGTCGTGCCCACCTCATGCACTAAGTTTACACTCTAGTGTTGATCCGAA
1 TATGACACATAAGGTCGTGCCCACCACCTGCACTAAGTTTACACTCTAGTGCTAATCCGAA
* *
45266 TAAGGCACATAAGGTCGTGCCCACCACCTGCACTAAGT
1 TATGACACATAAGGTCGTGCCCACCACCTGCACTAAGT
45304 GTCCTTACAC
Statistics
Matches: 87, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
60 52 0.60
61 35 0.40
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (61 bp):
TATGACACATAAGGTCGTGCCCACCACCTGCACTAAGTTTACACTCTAGTGCTAATCCGAA
Found at i:46769 original size:19 final size:19
Alignment explanation
Indices: 46734--46776 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
46724 AAAATAATCC
*
46734 AATTTCACATTCTAACATA
1 AATTTCACACTCTAACATA
*
46753 AATTTCA-ACTCTCAACATT
1 AATTTCACACTCT-AACATA
46772 AATTT
1 AATTT
46777 ACAGCATAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.40
Consensus pattern (19 bp):
AATTTCACACTCTAACATA
Found at i:48956 original size:2 final size:2
Alignment explanation
Indices: 48949--48978 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
48939 TTAATCTTCC
48949 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48979 TAATGTGACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.