Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000448.1 Hibiscus syriacus cultivar Beakdansim tig00000818_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: 88138
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:2271 original size:23 final size:23
Alignment explanation
Indices: 2237--2297 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
2227 ACATCTTATA
*
2237 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
2260 CT-GCACTTCGGTGCAATTCTATG
1 -TGGCACTTCGGTGCAATTCTACG
2283 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
2298 TTTATACGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 1 0.03
23 32 0.94
24 1 0.03
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:7922 original size:23 final size:24
Alignment explanation
Indices: 7862--7932 Score: 83
Period size: 23 Copynumber: 3.0 Consensus size: 24
7852 GACATCTTAT
*
7862 ATGGCACTACGGTGCAATTCTACG
1 ATGGCACTTCGGTGCAATTCTACG
*
7886 AT-GCACTTTGGTGCAATTCTACG
1 ATGGCACTTCGGTGCAATTCTACG
* * *
7909 -TGGCACTTCAGTGCATTTATACG
1 ATGGCACTTCGGTGCAATTCTACG
7932 A
1 A
7933 GCTGTGGTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
22 1 0.03
23 36 0.92
24 2 0.05
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (24 bp):
ATGGCACTTCGGTGCAATTCTACG
Found at i:11189 original size:21 final size:21
Alignment explanation
Indices: 11156--11224 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
11146 TAAACTTTGA
*
11156 TTTATTATTATGGAGTTCAAG
1 TTTATTGTTATGGAGTTCAAG
* *
11177 TTTGTTGTTATGGATTTCAAG
1 TTTATTGTTATGGAGTTCAAG
11198 TTTATTGTTATGG-GTGTCAAG
1 TTTATTGTTATGGAGT-TCAAG
11219 TTTATT
1 TTTATT
11225 AGATAATGCT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
20 1 0.02
21 41 0.98
ACGTcount: A:0.22, C:0.04, G:0.22, T:0.52
Consensus pattern (21 bp):
TTTATTGTTATGGAGTTCAAG
Found at i:13583 original size:22 final size:22
Alignment explanation
Indices: 13558--13600 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
13548 GGGGTGTAGA
13558 TGAGCAGG-CAACTTTGTCTTGT
1 TGAGCAGGTCAA-TTTGTCTTGT
*
13580 TGAGCAGGTGAATTTGTCTTG
1 TGAGCAGGTCAATTTGTCTTG
13601 ATGCTATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.19, C:0.14, G:0.30, T:0.37
Consensus pattern (22 bp):
TGAGCAGGTCAATTTGTCTTGT
Found at i:14116 original size:117 final size:115
Alignment explanation
Indices: 13963--14185 Score: 331
Period size: 117 Copynumber: 1.9 Consensus size: 115
13953 TCCCTTTGGT
* * ** *
13963 TTTGAATCAATTCTGGAAAGGGGATGGGGGGTTATCTTGGTTAATGGGTTCGCTATTGTCATTAT
1 TTTGAATCAATTCTAGAAAGAGGATGGGGGCCTATCTAGGTTAATGGGTTCGCTATTGTCATTAT
* *
14028 CCTTAAGTTT-TATTTTAGAAGTATTCAACAAGTATACTTATCCATTAGGG
66 CCTTAA-TTTATAGTTTAGAAGTATTCAACAAGGATACTTATCCATTAGGG
14078 TTTGAATCAATTCTTAGAAAGAGGATTGGGGGCCTATCTAGGTTAATGGGTTCGCTATTGTCATT
1 TTTGAATCAATTC-TAGAAAGAGGA-TGGGGGCCTATCTAGGTTAATGGGTTCGCTATTGTCATT
* *
14143 ATCCTTCATTTATAGTTTAGAAGTATTCAATAAGGATACTTAT
64 ATCCTTAATTTATAGTTTAGAAGTATTCAACAAGGATACTTAT
14186 AATTTTGCTT
Statistics
Matches: 96, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
115 13 0.14
116 12 0.12
117 71 0.74
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (115 bp):
TTTGAATCAATTCTAGAAAGAGGATGGGGGCCTATCTAGGTTAATGGGTTCGCTATTGTCATTAT
CCTTAATTTATAGTTTAGAAGTATTCAACAAGGATACTTATCCATTAGGG
Found at i:25778 original size:16 final size:16
Alignment explanation
Indices: 25757--25801 Score: 90
Period size: 16 Copynumber: 2.8 Consensus size: 16
25747 AATATACGGT
25757 GTGACCGGTTAAACAA
1 GTGACCGGTTAAACAA
25773 GTGACCGGTTAAACAA
1 GTGACCGGTTAAACAA
25789 GTGACCGGTTAAA
1 GTGACCGGTTAAA
25802 ATTTAGACCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.20
Consensus pattern (16 bp):
GTGACCGGTTAAACAA
Found at i:26400 original size:23 final size:23
Alignment explanation
Indices: 26374--26446 Score: 103
Period size: 23 Copynumber: 3.2 Consensus size: 23
26364 ATATTTTACA
26374 ATATAAGCACTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
* *
26397 ATATAAACGCTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
*
26420 ATATAAGCGA-TACCTATTACATC
1 ATATAAGC-ACTACCTATTACATT
26443 ATAT
1 ATAT
26447 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCACTACCTATTACATT
Found at i:26890 original size:23 final size:23
Alignment explanation
Indices: 26864--26936 Score: 103
Period size: 23 Copynumber: 3.2 Consensus size: 23
26854 ATATTTTACA
26864 ATATAAGCACTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
* *
26887 ATATAAACGCTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
*
26910 ATATAAGCGA-TACCTATTACATC
1 ATATAAGC-ACTACCTATTACATT
26933 ATAT
1 ATAT
26937 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCACTACCTATTACATT
Found at i:26962 original size:490 final size:490
Alignment explanation
Indices: 25973--27280 Score: 2457
Period size: 490 Copynumber: 2.7 Consensus size: 490
25963 TTATAATATG
* * * *
25973 TTGAAAGTGTCTATATTTTTTTATAAAAA-AATCGATAATTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATA-CTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
*
26037 TTCAA--TTTTTTAATAGTGTTTCATGTTTTCCACCTACATTATTAATTTAATAATTTCATTTGC
65 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
* * * *
26100 ACAAAATATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAGTA
130 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATA
26165 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
195 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
26230 TATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
260 TATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
26295 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
325 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
26360 ATAGATATTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
390 ATAGATATTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
26425 AGCGATACCTATTACATCATATTTTTACCTATTATA
455 AGCGATACCTATTACATCATATTTTTACCTATTATA
26461 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
26526 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
26591 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATAT
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATAT
26656 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
196 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
26721 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
261 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
26786 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
326 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
26851 TAGATATTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
391 TAGATATTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
26916 GCGATACCTATTACATCATATTTTTACCTATTATA
456 GCGATACCTATTACATCATATTTTTACCTATTATA
26951 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
27016 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
27081 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATAT
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATAT
27146 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAA-TT--TAATAATATAT
196 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
* * *
27208 ACCGTAACGTAAAAAATTAATCATTAGATGCCTATAATTACTAAATTAATATCTTAAAACTCACT
261 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
27273 CAAAAGAT
326 CAAAAGAT
27281 GTACATAGCT
Statistics
Matches: 805, Mismatches: 12, Indels: 7
0.98 0.01 0.01
Matches are distributed among these distances:
487 93 0.12
488 52 0.06
489 2 0.00
490 658 0.82
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (490 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATAT
TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
TAGATATTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
GCGATACCTATTACATCATATTTTTACCTATTATA
Found at i:31332 original size:3 final size:3
Alignment explanation
Indices: 31324--31395 Score: 81
Period size: 3 Copynumber: 24.0 Consensus size: 3
31314 ACTTGTTTGG
* * * *
31324 ATC ATC ATC ATC ATC ATC ATC ATT GTC ATC TTC ATC GTC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
31372 ATC ATC TTC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC
31396 GTCAGCTTCA
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.25, C:0.32, G:0.04, T:0.39
Consensus pattern (3 bp):
ATC
Found at i:31396 original size:12 final size:12
Alignment explanation
Indices: 31325--31412 Score: 104
Period size: 12 Copynumber: 7.3 Consensus size: 12
31315 CTTGTTTGGA
* *
31325 TCATCATCATCA
1 TCATCTTCATCG
* *
31337 TCATCATCATTG
1 TCATCTTCATCG
31349 TCATCTTCATCG
1 TCATCTTCATCG
* *
31361 TCATCATCATCA
1 TCATCTTCATCG
31373 TCATCTTCATCG
1 TCATCTTCATCG
31385 TCATCTTCATCG
1 TCATCTTCATCG
* *
31397 TCAGCTTCATCT
1 TCATCTTCATCG
31409 TCAT
1 TCAT
31413 TGACCGCTTA
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.23, C:0.32, G:0.06, T:0.40
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:31410 original size:6 final size:6
Alignment explanation
Indices: 31325--31412 Score: 79
Period size: 6 Copynumber: 14.7 Consensus size: 6
31315 CTTGTTTGGA
* * * * * *
31325 TCATCA TCATCA TCATCA TCAT-T GTCATCT TCATCG TCATCA TCATCA
1 TCATCT TCATCT TCATCT TCATCT -TCATCT TCATCT TCATCT TCATCT
* * *
31373 TCATCT TCATCG TCATCT TCATCG TCAGCT TCATCT TCAT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCAT
31413 TGACCGCTTA
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
6 69 0.99
7 1 0.01
ACGTcount: A:0.23, C:0.32, G:0.06, T:0.40
Consensus pattern (6 bp):
TCATCT
Found at i:33313 original size:200 final size:200
Alignment explanation
Indices: 32893--34255 Score: 2487
Period size: 200 Copynumber: 6.8 Consensus size: 200
32883 AACATTAAAC
* * *
32893 AGTGTCGATACA-TATTATATACCAATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTG
1 AGTGTCGACACATTATT-TAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTG
* *
32957 AAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACAC-TTTTATATAT
65 AAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATAT
33021 GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
130 GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
*
33086 TATAAA
195 TACAAA
*
33092 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTATCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
33157 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
33222 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACATAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
33287 ACAAA
196 ACAAA
33292 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
** *
33357 AAAATTACATATTACATTATACTTTTGAATGTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
33422 GATCGACACTTTATGGTTGCACCTTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
33487 ACAAA
196 ACAAA
33492 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
33557 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCAACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
33622 GATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
33687 ACAAA
196 ACAAA
33692 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
33757 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
33822 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
33887 ACAAA
196 ACAAA
33892 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* *
33957 AAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTATGGGATCGACACATTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* *
34022 GATCGACACTGTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAGAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
*
34087 AAAAA
196 ACAAA
* * *
34092 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTACACTTGTACCGATTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* *
34157 AAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATGTGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
34222 GATCGACACTTTATGGTTGCACCCTGTTTGCCAT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCAT
34256 ATTGTAAATT
Statistics
Matches: 1127, Mismatches: 35, Indels: 3
0.97 0.03 0.00
Matches are distributed among these distances:
199 107 0.09
200 1020 0.91
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.36
Consensus pattern (200 bp):
AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
ACAAA
Found at i:34379 original size:18 final size:18
Alignment explanation
Indices: 34356--34416 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
34346 TCTCATTCAT
*
34356 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
34374 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
34393 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
34412 AATTA
1 AATTA
34417 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:34392 original size:19 final size:19
Alignment explanation
Indices: 34368--34416 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
34358 TTATATTCAC
34368 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
34387 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
34406 ATACAAAATTA
1 ATACAAAATTA
34417 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:36243 original size:33 final size:33
Alignment explanation
Indices: 36206--36271 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
36196 CATCTTAATA
*
36206 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
36239 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
36272 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:36330 original size:21 final size:21
Alignment explanation
Indices: 36305--36369 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
36295 CCCCTTATGC
* *
36305 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
36326 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
36347 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
36368 CT
1 CT
36370 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:38616 original size:17 final size:18
Alignment explanation
Indices: 38594--38636 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
38584 ATATATCCGA
38594 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
38611 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
38631 TATCAT
1 TATCAT
38637 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:38645 original size:20 final size:19
Alignment explanation
Indices: 38599--38645 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
38589 TCCGATATCA
38599 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
38618 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
38639 TTTTACC
1 TTTTACC
38646 TATTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:38807 original size:20 final size:20
Alignment explanation
Indices: 38780--38826 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
38770 TCCGGTAACG
*
38780 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTACCATAT
38799 TTGTTACCGGTTTTACCATAT
1 TT-TTACCGGTTTTACCATAT
38820 TTTTACC
1 TTTTACC
38827 TGGTATATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.17, C:0.19, G:0.11, T:0.53
Consensus pattern (20 bp):
TTTTACCGGTTTTACCATAT
Found at i:38870 original size:181 final size:182
Alignment explanation
Indices: 38566--39038 Score: 662
Period size: 181 Copynumber: 2.6 Consensus size: 182
38556 CGTACTTACG
* * * *
38566 AAAGTATCGACACTTTTAATATATCCGATATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * *
38631 TATCATATTTTTACCTATTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* *
38696 AGGC-GCTAAAACCGCTTCTCTTTTAAATTCACAAAGTGTTGATCCTTATA-T
131 A-CCAGCTAAAACCGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * *
38747 AAAGTATCGAAACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
38812 TACCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** * *
38877 ACCATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 ACCAGCTAAAACCGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * **
38929 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
38994 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
39039 AATTTGGATC
Statistics
Matches: 257, Mismatches: 33, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
180 1 0.00
181 159 0.62
182 97 0.38
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (182 bp):
AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
ACCAGCTAAAACCGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:39441 original size:38 final size:38
Alignment explanation
Indices: 39399--39547 Score: 167
Period size: 40 Copynumber: 3.9 Consensus size: 38
39389 TTTTAGACCG
* * *
39399 TTTTTGAAAACATATAATATATAGTTTTTTAAAATTTC
1 TTTTTGAAAACATATAATATATAGTTTTTAAAAATATA
* * * *
39437 TTTTTAAAAACGTATATATAATATAATTTTTAAAAACATA
1 TTTTTGAAAACATATA-AT-ATATAGTTTTTAAAAATATA
*
39477 TTTTTGAAAACATATAATATATAGTTTTTTAAAA-ATA
1 TTTTTGAAAACATATAATATATAGTTTTTAAAAATATA
** *
39514 TTTTTGAAAACATATAGCATATA-ATTTTAAAAAT
1 TTTTTGAAAACATATAATATATAGTTTTTAAAAAT
39548 GTTTTTTTTG
Statistics
Matches: 93, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
36 8 0.09
37 24 0.26
38 28 0.30
39 4 0.04
40 29 0.31
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.45
Consensus pattern (38 bp):
TTTTTGAAAACATATAATATATAGTTTTTAAAAATATA
Found at i:39481 original size:14 final size:14
Alignment explanation
Indices: 39462--39491 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39452 ATATAATATA
39462 ATTTTTAAAAACAT
1 ATTTTTAAAAACAT
*
39476 ATTTTTGAAAACAT
1 ATTTTTAAAAACAT
39490 AT
1 AT
39492 AATATATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (14 bp):
ATTTTTAAAAACAT
Found at i:39536 original size:39 final size:38
Alignment explanation
Indices: 39399--39529 Score: 174
Period size: 40 Copynumber: 3.4 Consensus size: 38
39389 TTTTAGACCG
** *
39399 TTTTTGAAAACATATAATATATAGTTTTTTAAAATTTC
1 TTTTTGAAAACATATAATATATAGTTTTTTAAAACATA
* * * *
39437 TTTTTAAAAACGTATATATAATATAATTTTTAAAAACATA
1 TTTTTGAAAACATATA-AT-ATATAGTTTTTTAAAACATA
39477 TTTTTGAAAACATATAATATATAGTTTTTTAAAA-ATA
1 TTTTTGAAAACATATAATATATAGTTTTTTAAAACATA
39514 TTTTTGAAAACATATA
1 TTTTTGAAAACATATA
39530 GCATATAATT
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
37 19 0.24
38 28 0.35
39 4 0.05
40 29 0.36
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.46
Consensus pattern (38 bp):
TTTTTGAAAACATATAATATATAGTTTTTTAAAACATA
Found at i:39555 original size:37 final size:37
Alignment explanation
Indices: 39399--39547 Score: 142
Period size: 37 Copynumber: 3.9 Consensus size: 37
39389 TTTTAGACCG
* * *
39399 TTTTTGAAAACATATAATATATAGTTTTTTAAAATTTC
1 TTTTTGAAAACATATAATATATAG-ATTTTAAAAATTA
* * *
39437 TTTTTAAAAACGTATATATAATATA-ATTTTTAAAAACATA
1 TTTTTGAAAACATATA-AT-ATATAGA-TTTTAAAAA-TTA
*
39477 TTTTTGAAAACATATAATATATAGTTTTTTAAAAA-TA
1 TTTTTGAAAACATATAATATATAG-ATTTTAAAAATTA
**
39514 TTTTTGAAAACATATAGCATATA-ATTTTAAAAAT
1 TTTTTGAAAACATATAATATATAGATTTTAAAAAT
39548 GTTTTTTTTG
Statistics
Matches: 92, Mismatches: 12, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
35 9 0.10
37 23 0.25
38 19 0.21
39 21 0.23
40 20 0.22
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.45
Consensus pattern (37 bp):
TTTTTGAAAACATATAATATATAGATTTTAAAAATTA
Found at i:39611 original size:18 final size:17
Alignment explanation
Indices: 39573--39621 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 17
39563 TATACATTAG
*
39573 TATTTTATTTTCCATTTTT
1 TATTTTATTTT-TA-TTTT
39592 TATTTTTATTTTTATTTT
1 TA-TTTTATTTTTATTTT
39610 TATTTTATTTTT
1 TATTTTATTTTT
39622 TCTTATTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 10 0.36
18 6 0.21
19 3 0.11
20 9 0.32
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (17 bp):
TATTTTATTTTTATTTT
Found at i:39622 original size:12 final size:13
Alignment explanation
Indices: 39573--39622 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 13
39563 TATACATTAG
*
39573 TATTTTAT-TTTC
1 TATTTTATATTTT
* *
39585 CATTTTTTATTTT
1 TATTTTATATTTT
39598 TATTTT-TATTTT
1 TATTTTATATTTT
39610 TATTTTAT-TTTT
1 TATTTTATATTTT
39622 T
1 T
39623 CTTATTTCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 23 0.72
13 9 0.28
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (13 bp):
TATTTTATATTTT
Found at i:39630 original size:7 final size:6
Alignment explanation
Indices: 39588--39621 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
39578 TATTTTCCAT
39588 TTTTTA TTTTTA TTTTTA TTTTTA -TTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
39622 TCTTATTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:40526 original size:64 final size:65
Alignment explanation
Indices: 40374--40535 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 65
40364 GAATAAATTG
* * * * * * ** *
40374 AACATCAAATGCAGTTTATGCATCGATGTACTCTCCATGCATCGATGCACTCAAGTTTTAATGAA
1 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATACACTCAAGGCTTAATCAA
* *
40439 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATACACT-TAGGCTTATTCAA
1 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATACACTCAAGGCTTAATCAA
*
40503 AACATCGAATGCATTTTATGCATCGGTGCACAC
1 AACATCGAATGCATTTTATGCATCGATGCACAC
40536 TTAGTGCACC
Statistics
Matches: 85, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
64 40 0.47
65 45 0.53
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.29
Consensus pattern (65 bp):
AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATACACTCAAGGCTTAATCAA
Found at i:48995 original size:20 final size:20
Alignment explanation
Indices: 48966--49003 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
48956 TTTTAAAGGG
*
48966 ATGCACCGATGCACCAATCC
1 ATGCACCGATGAACCAATCC
*
48986 ATGCATCGATGAACCAAT
1 ATGCACCGATGAACCAAT
49004 GAATAAATTA
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:0.34, C:0.32, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGAACCAATCC
Found at i:49055 original size:19 final size:19
Alignment explanation
Indices: 49031--49103 Score: 137
Period size: 19 Copynumber: 3.8 Consensus size: 19
49021 AAAACAGTTT
*
49031 ATGCATCGATGGACTCTCC
1 ATGCATCGATGCACTCTCC
49050 ATGCATCGATGCACTCTCC
1 ATGCATCGATGCACTCTCC
49069 ATGCATCGATGCACTCTCC
1 ATGCATCGATGCACTCTCC
49088 ATGCATCGATGCACTC
1 ATGCATCGATGCACTC
49104 AAGTTTTAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 53 1.00
ACGTcount: A:0.22, C:0.34, G:0.18, T:0.26
Consensus pattern (19 bp):
ATGCATCGATGCACTCTCC
Found at i:49139 original size:65 final size:64
Alignment explanation
Indices: 49069--49234 Score: 201
Period size: 64 Copynumber: 2.6 Consensus size: 64
49059 TGCACTCTCC
* ** * *
49069 ATGCATCGATGCACTC-TCCATGCATCGATGCACTCAAGTTTTAATGATAACATCGAATGCATTT
1 ATGCATCGATGCACACAT-CATGCATCGATGCACT-AAGGCTTAATCAAAACATCGAATGCATTT
49133 T
64 T
* *
49134 ATGCATCGATGCACACATCATGCATCGATGCACTTAGGCTTATTCAAAACATCGAATGCATTTT
1 ATGCATCGATGCACACATCATGCATCGATGCACTAAGGCTTAATCAAAACATCGAATGCATTTT
* * *
49198 ATGCATCGATGTACAC-TTAGTGCACCGATGCACTAAG
1 ATGCATCGATGCACACATCA-TGCATCGATGCACTAAG
49235 TGTTCCAACG
Statistics
Matches: 88, Mismatches: 11, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
63 2 0.02
64 54 0.61
65 31 0.35
66 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (64 bp):
ATGCATCGATGCACACATCATGCATCGATGCACTAAGGCTTAATCAAAACATCGAATGCATTTT
Found at i:55892 original size:21 final size:22
Alignment explanation
Indices: 55871--55912 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
55861 TAGATTGCCC
55871 AGAGGGAACCGATTCCCCCCCA
1 AGAGGGAACCGATTCCCCCCCA
* * *
55893 AGGGGGTACTGATTCCCCCC
1 AGAGGGAACCGATTCCCCCC
55913 TGAATGGTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.21, C:0.38, G:0.26, T:0.14
Consensus pattern (22 bp):
AGAGGGAACCGATTCCCCCCCA
Found at i:59394 original size:200 final size:201
Alignment explanation
Indices: 58970--59475 Score: 647
Period size: 200 Copynumber: 2.5 Consensus size: 201
58960 TGTAGTATAA
* * * * * *
58970 CTCAAGGCGAGAAGGGCTATCTATCCATAGAGACTTTCGAGTTCGATTTCATTAAGCTCGATGAC
1 CTCAAGGCGAGAAGGGCTATCTATCAACAAAAACTTTCGAGTTCGATTCCATTCAGCTCGATGAC
* * *
59035 ATATCAACCGTATGGTAGCAGCGAATAACTACTTTCCGGTTGAAGCTTAAACTGAGTTCTTTAAG
66 ATATCAACCGCATGGTAGCAGCGAGTAACTACTTTCTGGTTGAAGCTTAAACTGAGTTCTTTAAG
* * *
59100 TCAAGAAGAAGACCTAGGCGGGCTGCGATTTAGCAACAAGGAACTATCTCTCAGTTAAAATTACA
131 TCAAGAAGAAGACCTAGGCGGGCTGCGATTTAGCAACAAGGAACTATATCCCAGTCAAAATTACA
*
59165 TCATAG
196 GCATAG
* * * *
59171 CTCCAGGCGATAAGGGCTATCTATCAACAAAAAATTTCGAGTTCGATCCCATTCAGCTCGATGAC
1 CTCAAGGCGAGAAGGGCTATCTATCAACAAAAACTTTCGAGTTCGATTCCATTCAGCTCGATGAC
* * *
59236 ATATTAACCGCATGGTAGCAGCGAGGAACTACTTTCTGGTT-AAGTTTAAACTGAAG-TCTTTAA
66 ATATCAACCGCATGGTAGCAGCGAGTAACTACTTTCTGGTTGAAGCTTAAACTG-AGTTCTTTAA
* * * ** *
59299 GTCAATAAGAAGACTTGGGTTGGCTGCGATTTAGCAACAAGGAACTATATCCCAGTCAAATTTAC
130 GTCAAGAAGAAGACCTAGGCGGGCTGCGATTTAGCAACAAGGAACTATATCCCAGTCAAAATTAC
59364 AGCATAG
195 AGCATAG
* * * * * * * *
59371 CTCAAGGTGAGAAGGGTTATCTATCAACAAAAACCTTCGAGTTCTATTCAATTCAGCTTGAGGGC
1 CTCAAGGCGAGAAGGGCTATCTATCAACAAAAACTTTCGAGTTCGATTCCATTCAGCTCGATGAC
* * * *
59436 ATATCAGCCACATGGTAGCATCGAGTAACTACTTTTTGGT
66 ATATCAACCGCATGGTAGCAGCGAGTAACTACTTTCTGGT
59476 CAAATTTTCA
Statistics
Matches: 260, Mismatches: 44, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
200 167 0.64
201 93 0.36
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (201 bp):
CTCAAGGCGAGAAGGGCTATCTATCAACAAAAACTTTCGAGTTCGATTCCATTCAGCTCGATGAC
ATATCAACCGCATGGTAGCAGCGAGTAACTACTTTCTGGTTGAAGCTTAAACTGAGTTCTTTAAG
TCAAGAAGAAGACCTAGGCGGGCTGCGATTTAGCAACAAGGAACTATATCCCAGTCAAAATTACA
GCATAG
Found at i:59981 original size:37 final size:36
Alignment explanation
Indices: 59841--60094 Score: 275
Period size: 34 Copynumber: 6.9 Consensus size: 36
59831 GGTCTTACTT
*
59841 ACATTTCGAAAATATATATAAATATATAGTTTTTGAAA
1 ACATTTTGAAAATATATAT-AATATATAG-TTTTGAAA
*
59879 ACATTTTGAATATATATATAATATATAGTTTTGAAA
1 ACATTTTGAAAATATATATAATATATAGTTTTGAAA
**
59915 ACATTTTG-AAA-ATATATAATATACGGTTTTGAAA
1 ACATTTTGAAAATATATATAATATATAGTTTTGAAA
*
59949 ATATTTTGAAAAATATATATAATATATAGTTTTGAAA
1 ACATTTTG-AAAATATATATAATATATAGTTTTGAAA
*
59986 ACATTTTGAAAAAAATACATATAATATATAGTTTTTGAAA
1 ACATTTTG---AAAATATATATAATATATAG-TTTTGAAA
* * *
60026 ACATTTTAAAAAATATATATATAATATATAATTTT-AGA
1 ACATTTT--GAAA-ATATATATAATATATAGTTTTGAAA
* *
60064 ACGTTTTTG-AAA-ACATATAATATATAGTTTT
1 AC-ATTTTGAAAATATATATAATATATAGTTTT
60095 TTTTTAAAAA
Statistics
Matches: 188, Mismatches: 18, Indels: 24
0.82 0.08 0.10
Matches are distributed among these distances:
34 45 0.24
35 3 0.02
36 21 0.11
37 37 0.20
38 21 0.11
39 31 0.16
40 30 0.16
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (36 bp):
ACATTTTGAAAATATATATAATATATAGTTTTGAAA
Found at i:60234 original size:6 final size:6
Alignment explanation
Indices: 60219--60270 Score: 61
Period size: 6 Copynumber: 8.3 Consensus size: 6
60209 TACATTAGTA
*
60219 TTTTAT TTTTCAT TTTTAT TTTTAT TTTTA- TTTTAT TTATTTT TTCTTAT
1 TTTTAT TTTT-AT TTTTAT TTTTAT TTTTAT TTTTAT TT-TTAT TT-TTAT
60269 TT
1 TT
60271 CAGGTCCAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
5 5 0.12
6 19 0.47
7 16 0.40
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTAT
Found at i:60237 original size:13 final size:12
Alignment explanation
Indices: 60219--60270 Score: 61
Period size: 13 Copynumber: 4.2 Consensus size: 12
60209 TACATTAGTA
60219 TTTTATTTTTCAT
1 TTTTATTTTT-AT
60232 TTTTATTTTTAT
1 TTTTATTTTTAT
60244 TTTTA-TTTTAT
1 TTTTATTTTTAT
*
60255 TTATTTTTTCTTAT
1 TT-TTATTT-TTAT
60269 TT
1 TT
60271 CAGGTCCAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
11 8 0.23
12 9 0.26
13 12 0.34
14 6 0.17
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTATTTTTAT
Found at i:60240 original size:12 final size:11
Alignment explanation
Indices: 60217--60262 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
60207 TATACATTAG
60217 TATTTTATTTT
1 TATTTTATTTT
60228 TCATTTTTATTTT
1 T-A-TTTTATTTT
60241 TATTTT-TATTT
1 TATTTTAT-TTT
60252 TA-TTTATTTT
1 TATTTTATTTT
60262 T
1 T
60263 TCTTATTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
10 8 0.26
11 11 0.35
12 2 0.06
13 10 0.32
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.80
Consensus pattern (11 bp):
TATTTTATTTT
Found at i:60270 original size:19 final size:19
Alignment explanation
Indices: 60220--60270 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 19
60210 ACATTAGTAT
*
60220 TTTA-TTTTTCAT-TTTTA
1 TTTATTTTTTCTTATTTTA
*
60237 TTT-TTATTT-TTATTTTA
1 TTTATTTTTTCTTATTTTA
60254 TTTATTTTTTCTTATTT
1 TTTATTTTTTCTTATTT
60271 CAGGTCCAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 1 0.04
17 15 0.56
18 5 0.19
19 6 0.22
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTATTTTTTCTTATTTTA
Found at i:60301 original size:17 final size:18
Alignment explanation
Indices: 60267--60301 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
60257 ATTTTTTCTT
60267 ATTTCAGGTCCAACTCCA
1 ATTTCAGGTCCAACTCCA
*
60285 ATTTTAGGTCC-ACTCCA
1 ATTTCAGGTCCAACTCCA
60302 GCCCAGAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.26, C:0.31, G:0.11, T:0.31
Consensus pattern (18 bp):
ATTTCAGGTCCAACTCCA
Found at i:74671 original size:13 final size:13
Alignment explanation
Indices: 74653--74688 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
74643 TTTTAAGATT
74653 TTGAAATCAAGTG
1 TTGAAATCAAGTG
*
74666 TTGAAATCAAGTT
1 TTGAAATCAAGTG
74679 TTGAAATCAA
1 TTGAAATCAA
74689 AAAGACATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (13 bp):
TTGAAATCAAGTG
Found at i:76985 original size:23 final size:21
Alignment explanation
Indices: 76938--77017 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
76928 AGTACCCCAG
* ***
76938 GGGGGTATCGATTCCCCTGTG
1 GGGGGAATCGATTCCCCTCAA
76959 GGGGGAATCGATTCCCCTTCAAA
1 GGGGGAATCGATTCCCC-TC-AA
* *
76982 GGGGGAATCGGTT-CCCTCAT
1 GGGGGAATCGATTCCCCTCAA
*
77002 GGGGGGATCGATTCCC
1 GGGGGAATCGATTCCC
77018 TCTGCACCAA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
20 12 0.25
21 20 0.42
22 4 0.08
23 12 0.25
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
GGGGGAATCGATTCCCCTCAA
Found at i:77011 original size:20 final size:20
Alignment explanation
Indices: 76959--77019 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
76949 TTCCCCTGTG
*
76959 GGGGGAATCGATTCCCCTTCAAA
1 GGGGGAATCGATT-CCC-TC-AT
*
76982 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
77002 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
77020 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 12 0.35
ACGTcount: A:0.18, C:0.26, G:0.33, T:0.23
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:80828 original size:22 final size:21
Alignment explanation
Indices: 80786--80825 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
80776 GAGCTTATTT
*
80786 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
80807 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
80826 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:86379 original size:32 final size:32
Alignment explanation
Indices: 86338--86399 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
86328 AGTTTGATAT
86338 TATTTTTAACTTCAAAATTTTAAAAATTTACA
1 TATTTTTAACTTCAAAATTTTAAAAATTTACA
*
86370 TATTTTTAACTTCAAAATTTTAAAATTTTA
1 TATTTTTAACTTCAAAATTTTAAAAATTTA
86400 AAAATTTACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (32 bp):
TATTTTTAACTTCAAAATTTTAAAAATTTACA
Found at i:86429 original size:40 final size:40
Alignment explanation
Indices: 86335--86431 Score: 122
Period size: 40 Copynumber: 2.4 Consensus size: 40
86325 AAAAGTTTGA
* *
86335 TATTATTTTTAACTTCAAAATTTTAAAAATTTACATATTTT
1 TATT-TTTTTAATTTTAAAATTTTAAAAATTTACATATTTT
** ***
86376 TAACTTCAAAATTTTAAAATTTTAAAAATTTACATATTTT
1 TATTTTTTTAATTTTAAAATTTTAAAAATTTACATATTTT
86416 TATTTTTTTAATTTTA
1 TATTTTTTTAATTTTA
86432 TTAACTACAC
Statistics
Matches: 44, Mismatches: 12, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
40 42 0.95
41 2 0.05
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (40 bp):
TATTTTTTTAATTTTAAAATTTTAAAAATTTACATATTTT
Done.