Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007931.1 Hibiscus syriacus cultivar Beakdansim tig00110339_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: 2341804
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 12
Found at i:2283552 original size:13 final size:12
Alignment explanation
Indices: 2283534--2283571 Score: 53
Period size: 10 Copynumber: 3.2 Consensus size: 12
2283524 TTTAAATCCT
2283534 TATATTATTATTG
1 TATATTATT-TTG
2283547 TATATTATTTTG
1 TATATTATTTTG
2283559 --TATTATTTTG
1 TATATTATTTTG
2283569 TAT
1 TAT
2283572 TATTTATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
10 10 0.43
12 4 0.17
13 9 0.39
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (12 bp):
TATATTATTTTG
Found at i:2283554 original size:10 final size:10
Alignment explanation
Indices: 2283539--2283576 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
2283529 ATCCTTATAT
* *
2283539 TATTATTGTA
1 TATTATTTTG
2283549 TATTATTTTG
1 TATTATTTTG
2283559 TATTATTTTG
1 TATTATTTTG
2283569 TATTATTT
1 TATTATTT
2283577 ATGTTGATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (10 bp):
TATTATTTTG
Found at i:2293768 original size:22 final size:22
Alignment explanation
Indices: 2293724--2293769 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
2293714 GCCCTAAATT
*
2293724 GAAAAAAGAGGAAAAGAACATAA
1 GAAAAAAGA-GAAAAGAAAATAA
2293747 GAAAAAAGA-AAAAGAAAAATAA
1 GAAAAAAGAGAAAAG-AAAATAA
2293769 G
1 G
2293770 GTGGGTTCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 5 0.24
22 7 0.33
23 9 0.43
ACGTcount: A:0.74, C:0.02, G:0.20, T:0.04
Consensus pattern (22 bp):
GAAAAAAGAGAAAAGAAAATAA
Found at i:2295077 original size:100 final size:104
Alignment explanation
Indices: 2294899--2295126 Score: 252
Period size: 100 Copynumber: 2.2 Consensus size: 104
2294889 CAGAGCCAAT
* ** * * * **
2294899 TTCAACTTCACAACGAAGGATATTGGACCCAAGATAACAGAAGCTCAACTTCACGACGAAGGGGT
1 TTCAACTTCACGACGAAGGATATTAAACCCAAGACAACACAAGCTCAACTTCACGACCAAGGGAC
* *
2294964 GGCTGATTTTCAAC-AA-AATTT-CA-TTC-ATAATCAAA
66 GGCTGACTGTCAACAAATAATTTCCAGTTCTATAA-CAAA
* *
2294999 TTCAACTTCACGACGAAGGATATTAAACTCGAGACAACACAAGCTCAACTTCAC-AGCCAAGGGA
1 TTCAACTTCACGACGAAGGATATTAAACCCAAGACAACACAAGCTCAACTTCACGA-CCAAGGGA
*
2295063 CGGCTGACTGTCAACAAATAATTTCCCAGTTCTATAACTAA
65 CGGCTGACTGTCAACAAATAATTT-CCAGTTCTATAACAAA
*
2295104 TATCAACTTCACGACGGAGGATA
1 T-TCAACTTCACGACGAAGGATA
2295127 ATGGATTCAA
Statistics
Matches: 106, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
99 1 0.01
100 65 0.61
101 2 0.02
102 5 0.05
104 2 0.02
105 7 0.07
106 24 0.23
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (104 bp):
TTCAACTTCACGACGAAGGATATTAAACCCAAGACAACACAAGCTCAACTTCACGACCAAGGGAC
GGCTGACTGTCAACAAATAATTTCCAGTTCTATAACAAA
Found at i:2297167 original size:2 final size:2
Alignment explanation
Indices: 2297160--2297191 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2297150 AGCATTATTA
2297160 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
2297192 TTCTAATTAT
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:2297340 original size:27 final size:23
Alignment explanation
Indices: 2297323--2297389 Score: 89
Period size: 26 Copynumber: 2.7 Consensus size: 23
2297313 TTACCTTTAT
2297323 ATATACATTATATTTTTTTACTTTC
1 ATATA-ATTAT-TTTTTTTACTTTC
2297348 ATATAATTATTTTTTTCTTTACTTTC
1 ATATAATTA--TTTTT-TTTACTTTC
2297374 ATATAATTATTTTTTT
1 ATATAATTATTTTTTT
2297390 CTTTACTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
23 2 0.05
24 9 0.23
25 9 0.23
26 19 0.49
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (23 bp):
ATATAATTATTTTTTTTACTTTC
Found at i:2297368 original size:26 final size:26
Alignment explanation
Indices: 2297335--2297396 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
2297325 ATACATTATA
2297335 TTTT-TTTACTTTCATATAATTATTT
1 TTTTCTTTACTTTCATATAATTATTT
2297360 TTTTCTTTACTTTCATATAATTATTT
1 TTTTCTTTACTTTCATATAATTATTT
2297386 TTTTCTTTACT
1 TTTTCTTTACT
2297397 ATTATTATAC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 4 0.11
26 32 0.89
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (26 bp):
TTTTCTTTACTTTCATATAATTATTT
Found at i:2297403 original size:21 final size:22
Alignment explanation
Indices: 2297329--2297404 Score: 68
Period size: 26 Copynumber: 3.4 Consensus size: 22
2297319 TTATATATAC
*
2297329 ATTA-TATTTTTTTACTTT-CAT
1 ATTATTATTTTTTT-CTTTACTT
*
2297350 ATAATTATTTTTTTCTTTACTTT
1 ATTATTATTTTTTTCTTTAC-TT
2297373 CATATAATTATTTTTTTCTTTAC-T
1 -AT-T-ATTATTTTTTTCTTTACTT
2297397 ATTATTAT
1 ATTATTAT
2297405 ACTTGCCTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
21 12 0.26
22 11 0.24
23 3 0.07
24 3 0.07
26 17 0.37
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (22 bp):
ATTATTATTTTTTTCTTTACTT
Found at i:2298477 original size:24 final size:24
Alignment explanation
Indices: 2298421--2298477 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
2298411 CCACAGTCGT
* * *
2298421 CATCGTCGTTGTTGTTGTTTTAGA
1 CATCGTTGTTGTTGTTATTGTAGA
* * *
2298445 AATCTTTGTTGTTGTTATTGTAGC
1 CATCGTTGTTGTTGTTATTGTAGA
2298469 CATCGTTGT
1 CATCGTTGT
2298478 CACCATCACC
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.14, C:0.12, G:0.23, T:0.51
Consensus pattern (24 bp):
CATCGTTGTTGTTGTTATTGTAGA
Found at i:2298741 original size:24 final size:24
Alignment explanation
Indices: 2298728--2298795 Score: 136
Period size: 24 Copynumber: 2.8 Consensus size: 24
2298718 CATCATTGGC
2298728 GTTACTGTCATCTTCGTCGTCGGT
1 GTTACTGTCATCTTCGTCGTCGGT
2298752 GTTACTGTCATCTTCGTCGTCGGT
1 GTTACTGTCATCTTCGTCGTCGGT
2298776 GTTACTGTCATCTTCGTCGT
1 GTTACTGTCATCTTCGTCGT
2298796 TACCGTTATC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.43
Consensus pattern (24 bp):
GTTACTGTCATCTTCGTCGTCGGT
Found at i:2301395 original size:20 final size:20
Alignment explanation
Indices: 2301370--2301432 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
2301360 ACATCTTGCT
2301370 CAAAAGACTGACAGATGACC
1 CAAAAGACTGACAGATGACC
* * *
2301390 CAAAAGATTTGAACATCATG-CT
1 CAAAAGA-CTG-ACA-GATGACC
*
2301412 CGAAAGACTGACAGATGACC
1 CAAAAGACTGACAGATGACC
2301432 C
1 C
2301433 GAAGGATTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 8
0.68 0.15 0.17
Matches are distributed among these distances:
19 3 0.09
20 12 0.38
21 4 0.12
22 10 0.31
23 3 0.09
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (20 bp):
CAAAAGACTGACAGATGACC
Found at i:2301405 original size:42 final size:42
Alignment explanation
Indices: 2301359--2301441 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
2301349 CAACGGACAT
*
2301359 AACATCTTGCTCAAAAGACTGACAGATGACCCAAAAGATTTG
1 AACATCATGCTCAAAAGACTGACAGATGACCCAAAAGATTTG
* * *
2301401 AACATCATGCTCGAAAGACTGACAGATGACCCGAAGGATTT
1 AACATCATGCTCAAAAGACTGACAGATGACCCAAAAGATTT
2301442 ACACATTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (42 bp):
AACATCATGCTCAAAAGACTGACAGATGACCCAAAAGATTTG
Found at i:2301909 original size:41 final size:41
Alignment explanation
Indices: 2301864--2301964 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 41
2301854 AAGTCTTACG
* * *
2301864 GATGACCTGAAGGATTTATCATC-TCGCTCGAAAGACTGACA
1 GATGACCTGAAGGATTTAGCATCAT-ACTCGAAAGACTAACA
* *
2301905 GATGA-CTCGAAAGATTTAAGCATCATACTTGAAAGACTAACA
1 GATGACCT-GAAGGATTT-AGCATCATACTCGAAAGACTAACA
*
2301947 GATGACCCGAAGGATTTA
1 GATGACCTGAAGGATTTA
2301965 AATATCATTG
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
40 2 0.04
41 14 0.29
42 31 0.63
43 2 0.04
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.24
Consensus pattern (41 bp):
GATGACCTGAAGGATTTAGCATCATACTCGAAAGACTAACA
Found at i:2301972 original size:42 final size:42
Alignment explanation
Indices: 2301893--2301972 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
2301883 CATCTCGCTC
* * *
2301893 GAAAGACTGACAGATGACTCGAAAGATTTAAGCATCATACTT
1 GAAAGACTAACAGATGACCCGAAAGATTTAAACATCATACTT
* *
2301935 GAAAGACTAACAGATGACCCGAAGGATTTAAATATCAT
1 GAAAGACTAACAGATGACCCGAAAGATTTAAACATCAT
2301973 TGGGAAATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (42 bp):
GAAAGACTAACAGATGACCCGAAAGATTTAAACATCATACTT
Found at i:2302340 original size:261 final size:260
Alignment explanation
Indices: 2301335--2302342 Score: 1395
Period size: 261 Copynumber: 3.9 Consensus size: 260
2301325 TTCCAAAAGG
* * * * *
2301335 TCTTACGGATGGCCCAACGGACATAACATCTTGCTCAAAAGACTGACAGATGACCCAAAAGATTT
1 TCTTACGGATGACCCAAAGGACTTATCATCTTGCTCAAAAGACTGACAGATGACCCGAAAGATTT
*
2301400 GAA-CATCATGCTCGAAAGACTGACAGATGACCCGAAGGATTTACACATTATTGGGAAATAATTT
66 -AAGCATCATGCTCGAAAGACTGACAGATGACCCGAAGGATTTAAACA-TATTGGGAAATAATTT
* * *
2301464 ACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAGAATTTCATTTTTTGAACATTATA
129 ACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAGAATTTCATTTTCTGAACATTAAA
* *
2301529 TGAGAAACTTTGGTAACCGCTTTCTCATTTTCATGTGAAAATCATGTGTAAACATTCTACCTAAA
194 TGAGAAACTTTGGTAATCGCTTTCTCATTTTCATGTGAAAATCATGTGTAAACATTCTACCTGAA
*
2301594 GG
259 GA
* ** * * *
2301596 TTTTACGGATGACCTGAAGGAATTATCATCTTGCTTAAAAGACTGACAGATGACTCGAAAGATTT
1 TCTTACGGATGACCCAAAGGACTTATCATCTTGCTCAAAAGACTGACAGATGACCCGAAAGATTT
* * *
2301661 AAGCATCATGCTCGAAAAACTGACAGAAGACCCTAAGGATTTAAACATCATTGGGAAATAATTTA
66 AAGCATCATGCTCGAAAGACTGACAGATGACCCGAAGGATTTAAACAT-ATTGGGAAATAATTTA
2301726 CTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAGAATTTCATTTTCTGAACATTAAAT
130 CTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAGAATTTCATTTTCTGAACATTAAAT
*
2301791 GAGAAACTTTGGTAATCGCTTTCTCATTTTCATGTGAAAATCATGTGTAAACATTCTGCCTGAA-
195 GAGAAACTTTGGTAATCGCTTTCTCATTTTCATGTGAAAATCATGTGTAAACATTCTACCTGAAG
2301855 A
260 A
** * * * *
2301856 GTCTTACGGATGACCTGAAGGATTTATCATCTCGCTCGAAAGACTGACAGATGACTCGAAAGATT
1 -TCTTACGGATGACCCAAAGGACTTATCATCTTGCTCAAAAGACTGACAGATGACCCGAAAGATT
* * * *
2301921 TAAGCATCATACTTGAAAGACTAACAGATGACCCGAAGGATTTAAATATCATTGGGAAATAATTT
65 TAAGCATCATGCTCGAAAGACTGACAGATGACCCGAAGGATTTAAACAT-ATTGGGAAATAATTT
*
2301986 ACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAGAATTTGATTTTCTGAACATTAAA
129 ACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAGAATTTCATTTTCTGAACATTAAA
* *
2302051 TGAGAAACTTTGGTAATCAG-TTTCTCATTTTCATGTGAAAATCATGTGTAAACATCCTTCCTGA
194 TGAGAAACTTTGGTAATC-GCTTTCTCATTTTCATGTGAAAATCATGTGTAAACATTCTACCTGA
2302115 AGA
258 AGA
** * * *
2302118 TCTTATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGGATTT
1 TCTTACGGATGACCCAAAGGACTTATCATCTTGCTCAAAAGACTGACAGATGACCCGAAAGA-TT
* * *
2302183 TAA-CATCATGCTCGAAAGACTGACAGATGACCCAAATGG-TTTACAA-AT-TTAGGAAATAGTT
65 TAAGCATCATGCTCGAAAGACTGACAGATGACCCGAA-GGATTTA-AACATATTGGGAAATAATT
* ** *
2302244 TACTGGGTAAGAAACTTTGGAAATCGTTTTCTTACTTTTCAAGAATTTCATTTT-TAGAAAAGAT
128 TACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAGAATTTCATTTTCT-G--AACAT
**
2302308 TAAATGAGAAACTTTGAAAATCG-TTCTCTCATTTT
190 TAAATGAGAAACTTTGGTAATCGCTT-TCTCATTTT
2302343 TCAAAACAAT
Statistics
Matches: 676, Mismatches: 59, Indels: 24
0.89 0.08 0.03
Matches are distributed among these distances:
258 1 0.00
259 62 0.09
260 6 0.01
261 596 0.88
262 11 0.02
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (260 bp):
TCTTACGGATGACCCAAAGGACTTATCATCTTGCTCAAAAGACTGACAGATGACCCGAAAGATTT
AAGCATCATGCTCGAAAGACTGACAGATGACCCGAAGGATTTAAACATATTGGGAAATAATTTAC
TAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAGAATTTCATTTTCTGAACATTAAATG
AGAAACTTTGGTAATCGCTTTCTCATTTTCATGTGAAAATCATGTGTAAACATTCTACCTGAAGA
Found at i:2304349 original size:12 final size:12
Alignment explanation
Indices: 2304328--2304362 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 12
2304318 CATGATATAC
2304328 ATGAATATATGTTA
1 ATGAATATATG--A
2304342 ATGAATATATGA
1 ATGAATATATGA
2304354 ATGAATATA
1 ATGAATATA
2304363 AACGACTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.48
14 11 0.52
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (12 bp):
ATGAATATATGA
Found at i:2307986 original size:16 final size:17
Alignment explanation
Indices: 2307953--2307986 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2307943 AAGATCTATG
2307953 ATATGAACATAAGAGATA
1 ATATGAACAT-AGAGATA
2307971 ATATGAACAT-GAGATA
1 ATATGAACATAGAGATA
2307987 TGTGATTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.53, C:0.06, G:0.18, T:0.24
Consensus pattern (17 bp):
ATATGAACATAGAGATA
Found at i:2308217 original size:18 final size:18
Alignment explanation
Indices: 2308194--2308228 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2308184 AGGGTTCTGC
2308194 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
2308212 GTGGTCCTTCGGGACAT
1 GTGGTCCTTCGGGACAT
2308229 TTCATAGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.23, G:0.34, T:0.29
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:2308490 original size:22 final size:24
Alignment explanation
Indices: 2308452--2308496 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
2308442 GGTTTATTAC
2308452 ATATGTTACATGATATACATGAAT
1 ATATGTTACATGATATACATGAAT
*
2308476 ATATGTTA-ATG-TATATATGAA
1 ATATGTTACATGATATACATGAA
2308497 AGAATATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 3 0.15
24 8 0.40
ACGTcount: A:0.42, C:0.04, G:0.13, T:0.40
Consensus pattern (24 bp):
ATATGTTACATGATATACATGAAT
Found at i:2316540 original size:15 final size:15
Alignment explanation
Indices: 2316517--2316550 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2316507 ATTTTAATAT
*
2316517 AATTTAAAGAAAAAA
1 AATTAAAAGAAAAAA
*
2316532 AATTAAAAGATAAAA
1 AATTAAAAGAAAAAA
2316547 AATT
1 AATT
2316551 GATTTGCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (15 bp):
AATTAAAAGAAAAAA
Found at i:2316865 original size:13 final size:15
Alignment explanation
Indices: 2316836--2316867 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
2316826 ACAAAAATTG
2316836 ATAAATGTATATAAA
1 ATAAATGTATATAAA
2316851 ATAAAT-TAT-TAAA
1 ATAAATGTATATAAA
2316864 ATAA
1 ATAA
2316868 TAAATAGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 3 0.18
15 6 0.35
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
ATAAATGTATATAAA
Found at i:2316989 original size:7 final size:7
Alignment explanation
Indices: 2316974--2317020 Score: 67
Period size: 7 Copynumber: 6.4 Consensus size: 7
2316964 AACCAAAAAT
2316974 AATATTA
1 AATATTA
*
2316981 AAAATTAAA
1 AATATT--A
2316990 AATATTA
1 AATATTA
2316997 AATATTA
1 AATATTA
2317004 AATATTA
1 AATATTA
2317011 AATATTA
1 AATATTA
2317018 AAT
1 AAT
2317021 TAGAGGATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
7 30 0.83
9 6 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AATATTA
Found at i:2318370 original size:25 final size:25
Alignment explanation
Indices: 2318324--2318371 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
2318314 CTTCGGGTTC
* *
2318324 TTGTAAATGGGCCTTCATATTTGCT
1 TTGTAAATGGGCCTCCAGATTTGCT
* *
2318349 TTGTAACTGGGGCTCCAGATTTG
1 TTGTAAATGGGCCTCCAGATTTG
2318372 TCTTCAATTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.40
Consensus pattern (25 bp):
TTGTAAATGGGCCTCCAGATTTGCT
Found at i:2319794 original size:3 final size:3
Alignment explanation
Indices: 2319786--2319856 Score: 70
Period size: 3 Copynumber: 23.7 Consensus size: 3
2319776 CGTCACTGCC
* * * * * * *
2319786 ACA ACA ACA AGA ACA TCG ACA ACA TCA ACA ACA GCG ACA ACA TCA ACA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
*
2319834 ACA TCA ACA ACA ACA ACA ACA AC
1 ACA ACA ACA ACA ACA ACA ACA AC
2319857 GAAAAAAAAT
Statistics
Matches: 52, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.56, C:0.32, G:0.06, T:0.06
Consensus pattern (3 bp):
ACA
Found at i:2319809 original size:18 final size:18
Alignment explanation
Indices: 2319786--2319854 Score: 93
Period size: 18 Copynumber: 3.8 Consensus size: 18
2319776 CGTCACTGCC
*
2319786 ACAACAACAAGAACATCG
1 ACAACAACAACAACATCG
* *
2319804 ACAACATCAACAACAGCG
1 ACAACAACAACAACATCG
* *
2319822 ACAACATCAACAACATCA
1 ACAACAACAACAACATCG
2319840 ACAACAACAACAACA
1 ACAACAACAACAACA
2319855 ACGAAAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.57, C:0.32, G:0.06, T:0.06
Consensus pattern (18 bp):
ACAACAACAACAACATCG
Found at i:2319856 original size:9 final size:9
Alignment explanation
Indices: 2319786--2319854 Score: 84
Period size: 9 Copynumber: 7.7 Consensus size: 9
2319776 CGTCACTGCC
*
2319786 ACAACAACA
1 ACAACATCA
* *
2319795 AGAACATCG
1 ACAACATCA
2319804 ACAACATCA
1 ACAACATCA
* *
2319813 ACAACAGCG
1 ACAACATCA
2319822 ACAACATCA
1 ACAACATCA
2319831 ACAACATCA
1 ACAACATCA
*
2319840 ACAACAACA
1 ACAACATCA
2319849 ACAACA
1 ACAACA
2319855 ACGAAAAAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 50 1.00
ACGTcount: A:0.57, C:0.32, G:0.06, T:0.06
Consensus pattern (9 bp):
ACAACATCA
Found at i:2319895 original size:24 final size:24
Alignment explanation
Indices: 2319878--2319938 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
2319868 GCAATGGCAG
2319878 CAAAAACAACAACAGCAACGGTAA
1 CAAAAACAACAACAGCAACGGTAA
*
2319902 CAAAAACAACAACAACAACGGTAA
1 CAAAAACAACAACAGCAACGGTAA
2319926 CAAAAACAACAAC
1 CAAAAACAACAAC
2319939 GGCATGGATA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.62, C:0.26, G:0.08, T:0.03
Consensus pattern (24 bp):
CAAAAACAACAACAGCAACGGTAA
Found at i:2319927 original size:18 final size:18
Alignment explanation
Indices: 2319906--2319940 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2319896 CGGTAACAAA
*
2319906 AACAACAACAACAACGGT
1 AACAAAAACAACAACGGT
2319924 AACAAAAACAACAACGG
1 AACAAAAACAACAACGG
2319941 CATGGATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.26, G:0.11, T:0.03
Consensus pattern (18 bp):
AACAAAAACAACAACGGT
Found at i:2320008 original size:25 final size:26
Alignment explanation
Indices: 2319963--2320012 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
2319953 TATTATTTTG
*
2319963 AATTTAAAATACAATCATTTTAATAT
1 AATTTAAAATAAAATCATTTTAATAT
2319989 AATTTAAAA-AAAATCATTTTAATA
1 AATTTAAAATAAAATCATTTTAATA
2320013 CAATGTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (26 bp):
AATTTAAAATAAAATCATTTTAATAT
Found at i:2321957 original size:18 final size:19
Alignment explanation
Indices: 2321934--2321977 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
2321924 CCAGTAATCC
*
2321934 TATTCC-CTGGTAATCTTT
1 TATTCCACTGGTAATCTTA
2321952 TATTCCCACTGGTAATCTTA
1 TATT-CCACTGGTAATCTTA
2321972 TATTCC
1 TATTCC
2321978 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 15 0.65
ACGTcount: A:0.20, C:0.25, G:0.09, T:0.45
Consensus pattern (19 bp):
TATTCCACTGGTAATCTTA
Found at i:2321965 original size:20 final size:20
Alignment explanation
Indices: 2321940--2321977 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2321930 ATCCTATTCC
*
2321940 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTATATTCCCA
2321960 CTGGTAATCTTATATTCC
1 CTGGTAATCTTATATTCC
2321978 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTATATTCCCA
Found at i:2328112 original size:23 final size:24
Alignment explanation
Indices: 2328080--2328127 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
2328070 CGATACCACC
2328080 TTGAAGGGGAACTGATTCCC-CCT
1 TTGAAGGGGAACTGATTCCCTCCT
*
2328103 TTGAATGGGAACTGATTCCCTCCT
1 TTGAAGGGGAACTGATTCCCTCCT
2328127 T
1 T
2328128 GAGGGAATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (24 bp):
TTGAAGGGGAACTGATTCCCTCCT
Found at i:2331948 original size:20 final size:19
Alignment explanation
Indices: 2331923--2331960 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
2331913 TAAATCGTTG
2331923 TGCAAATATTTTCAATTTTC
1 TGCAAATATTTTC-ATTTTC
2331943 TGCAAATATTTTCATTTT
1 TGCAAATATTTTCATTTT
2331961 GCAAAGCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.29, C:0.13, G:0.05, T:0.53
Consensus pattern (19 bp):
TGCAAATATTTTCATTTTC
Found at i:2332084 original size:13 final size:13
Alignment explanation
Indices: 2332066--2332099 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
2332056 GAGTTAGGAC
2332066 AATAGATGAGTGA
1 AATAGATGAGTGA
*
2332079 AATAGATTAGTGA
1 AATAGATGAGTGA
2332092 AATAGATG
1 AATAGATG
2332100 GTTGAGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.26
Consensus pattern (13 bp):
AATAGATGAGTGA
Found at i:2332582 original size:2 final size:2
Alignment explanation
Indices: 2332575--2332608 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2332565 TAACTTCTTA
2332575 AT 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 AT
2332609 CTAAATAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2336809 original size:36 final size:36
Alignment explanation
Indices: 2336768--2336843 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
2336758 ATTTTCGGGA
*
2336768 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
2336804 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
2336840 TTTT
1 TTTT
2336844 TTAGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:2337283 original size:15 final size:15
Alignment explanation
Indices: 2337263--2337292 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2337253 TATCACAATC
2337263 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
2337278 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
2337293 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:2341773 original size:36 final size:36
Alignment explanation
Indices: 2341732--2341804 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
2341722 ATTTTCGGGA
*
2341732 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
2341768 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
2341804 T
1 T
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Done.