Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008620.1 Hibiscus syriacus cultivar Beakdansim tig00111582_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: 13158977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 55 of 64
Found at i:11109063 original size:20 final size:20
Alignment explanation
Indices: 11109038--11109093 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
11109028 TGAAACCGAG
11109038 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
*
11109058 AATGACTATCGCAATGCGAA
1 AATGACTATCGCAACGCGAA
**
11109078 TTTGACTATCGCAACG
1 AATGACTATCGCAACG
11109094 AGAGAATCGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:11109180 original size:20 final size:20
Alignment explanation
Indices: 11109138--11109204 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
11109128 GATTCTTGCA
** *
11109138 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCATTTTCGTG
*
11109158 TTGCGATAGTCATTTTAGTG
1 TTGCGATAGTCATTTTCGTG
**
11109178 TTGCGATTTTCATTTTCGTG
1 TTGCGATAGTCATTTTCGTG
11109198 TTGCGAT
1 TTGCGAT
11109205 TTAAAGTTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.18, C:0.15, G:0.24, T:0.43
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGTG
Found at i:11109214 original size:20 final size:20
Alignment explanation
Indices: 11109175--11109214 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
11109165 AGTCATTTTA
** *
11109175 GTGTTGCGATTTTCATTTTC
1 GTGTTGCGATTTAAAGTTTC
11109195 GTGTTGCGATTTAAAGTTTC
1 GTGTTGCGATTTAAAGTTTC
11109215 AGAAACTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.23, T:0.50
Consensus pattern (20 bp):
GTGTTGCGATTTAAAGTTTC
Found at i:11111102 original size:20 final size:20
Alignment explanation
Indices: 11111077--11111203 Score: 167
Period size: 20 Copynumber: 6.7 Consensus size: 20
11111067 AGAATAGTTT
11111077 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
11111097 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
11111117 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
*
11111133 A--ATCACAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
11111151 ATTACCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
11111171 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
11111191 ACTATCGCAATGC
1 ACTATCGCAATGC
11111204 AAATTTAACT
Statistics
Matches: 93, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
14 6 0.06
16 4 0.04
17 4 0.04
18 4 0.04
20 75 0.81
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:11111214 original size:20 final size:20
Alignment explanation
Indices: 11111077--11111220 Score: 122
Period size: 20 Copynumber: 7.5 Consensus size: 20
11111067 AGAATAGTTT
*
11111077 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATA
* *
11111097 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATA
* *
11111117 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATA
* *
11111133 A--ATCACAATGCGAAAATG
1 ACTATCGCAATGCGAAAATA
* * *
11111151 ATTACCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATA
*
11111171 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATA
*
11111191 ACTATCGCAATGC-AAATTTA
1 ACTATCGCAATGCGAAA-ATA
11111211 ACTATCGCAA
1 ACTATCGCAA
11111221 CGAAAGAATC
Statistics
Matches: 107, Mismatches: 10, Indels: 14
0.82 0.08 0.11
Matches are distributed among these distances:
14 6 0.06
16 4 0.04
17 4 0.04
18 4 0.04
19 3 0.03
20 86 0.80
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATA
Found at i:11111273 original size:20 final size:20
Alignment explanation
Indices: 11111248--11111379 Score: 228
Period size: 20 Copynumber: 6.6 Consensus size: 20
11111238 GAAATGAAAA
**
11111248 TCGCATTGCGATAGTCAAAT
1 TCGCATTGCGATAGTCATTT
11111268 TCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
11111288 TCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
11111308 TCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
11111328 TCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
*
11111348 TCGCATTGCGATATTCATTT
1 TCGCATTGCGATAGTCATTT
*
11111368 TCGCGTTGCGAT
1 TCGCATTGCGAT
11111380 TTTAAGTTTC
Statistics
Matches: 108, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 108 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATAGTCATTT
Found at i:11111905 original size:18 final size:19
Alignment explanation
Indices: 11111866--11111907 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
11111856 CTCACATGTC
11111866 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
11111887 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
11111905 ATC
1 ATC
11111908 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:11113341 original size:14 final size:14
Alignment explanation
Indices: 11113322--11113357 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
11113312 ATTGTTTAAT
11113322 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
11113336 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
11113350 TGATTTGT
1 TGATTTGT
11113358 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:11113521 original size:33 final size:33
Alignment explanation
Indices: 11113463--11113558 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
11113453 CATAATTTCG
*
11113463 CGTTGCGATTTTCATTTTCGAATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
11113497 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
** *
11113530 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
11113559 AGTCAATTCC
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 32 0.57
34 24 0.43
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:11113555 original size:20 final size:20
Alignment explanation
Indices: 11113530--11113614 Score: 109
Period size: 20 Copynumber: 4.2 Consensus size: 20
11113520 GCGATTCTCT
11113530 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
11113550 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
* *
11113570 CATTTCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
11113590 TGTTGTGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
11113610 CGTTG
1 CGTTG
11113615 TGATTTCCGT
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 53 0.96
21 2 0.04
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:11115452 original size:24 final size:24
Alignment explanation
Indices: 11115425--11115471 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
11115415 CAAAATCCGA
11115425 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
11115449 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
11115472 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:11115480 original size:24 final size:24
Alignment explanation
Indices: 11115429--11115480 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
11115419 ATCCGAGTAT
** *
11115429 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
11115453 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
11115477 TGAC
1 TGAC
11115481 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:11116345 original size:20 final size:20
Alignment explanation
Indices: 11116322--11116367 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
11116312 TAGAATCTCG
11116322 TTGCGATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCA
11116342 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
11116362 TTGCGA
1 TTGCGA
11116368 ATTAGGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:11116409 original size:21 final size:21
Alignment explanation
Indices: 11116363--11116409 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
11116353 GTATTCGCAT
*
11116363 TGCGAATTAGGAAAATCGCAA
1 TGCGAATTAGGAAAATCGAAA
* * *
11116384 CGCGAATTTGGGAAATCGAAA
1 TGCGAATTAGGAAAATCGAAA
11116405 TGCGA
1 TGCGA
11116410 TAGTTAGAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.19
Consensus pattern (21 bp):
TGCGAATTAGGAAAATCGAAA
Found at i:11118478 original size:16 final size:16
Alignment explanation
Indices: 11118457--11118495 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
11118447 TTGCGTGACT
11118457 GGTTAAACAAATAACC
1 GGTTAAACAAATAACC
* * *
11118473 GGTTAAATAAGTGACC
1 GGTTAAACAAATAACC
11118489 GGTTAAA
1 GGTTAAA
11118496 ATCTATACCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.13, G:0.21, T:0.23
Consensus pattern (16 bp):
GGTTAAACAAATAACC
Found at i:11118846 original size:20 final size:20
Alignment explanation
Indices: 11118817--11118858 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
11118807 TACCTATTAC
*
11118817 TTTATGCTTGTATCGATACT
1 TTTATACTTGTATCGATACT
11118837 TTTATACTTGTATCGATACT
1 TTTATACTTGTATCGATACT
11118857 TT
1 TT
11118859 AGAGGCGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.14, G:0.12, T:0.52
Consensus pattern (20 bp):
TTTATACTTGTATCGATACT
Found at i:11122205 original size:46 final size:46
Alignment explanation
Indices: 11122138--11122230 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
11122128 AATCCAAACA
11122138 TCATGGAGATCTTTACAGTAGGTAA-ATATATCTTGTTTTTTGCACT
1 TCATGGAGATCTTTACAGTAGGTAAGAT-TATCTTGTTTTTTGCACT
11122184 TCATGGAGATCTTTACAGTAGGTAAGATTATCTTGTTTTTTGCACT
1 TCATGGAGATCTTTACAGTAGGTAAGATTATCTTGTTTTTTGCACT
11122230 T
1 T
11122231 TACTTGATCC
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
46 44 0.96
47 2 0.04
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.44
Consensus pattern (46 bp):
TCATGGAGATCTTTACAGTAGGTAAGATTATCTTGTTTTTTGCACT
Found at i:11124310 original size:21 final size:20
Alignment explanation
Indices: 11124279--11124331 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
11124269 ATTCTGGTTC
*
11124279 AAAAGTATCGACACGATTTA
1 AAAAGTATCGACACAATTTA
*
11124299 AAAAGTTATCGACATAATTTA
1 AAAAG-TATCGACACAATTTA
11124320 AAAAGGTATCGA
1 AAAA-GTATCGA
11124332 TACATTATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 5 0.17
21 23 0.79
22 1 0.03
ACGTcount: A:0.47, C:0.11, G:0.15, T:0.26
Consensus pattern (20 bp):
AAAAGTATCGACACAATTTA
Found at i:11124460 original size:221 final size:220
Alignment explanation
Indices: 11124074--11124531 Score: 711
Period size: 221 Copynumber: 2.1 Consensus size: 220
11124064 CACGTGTAAT
* *
11124074 TTTAAAAACGTATCGAAACAATTCAAAAAGGTATTGATATATTATGTTGACCTATTTTCTAATTA
1 TTTAAAAA-GTATCGAAACAATTCAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTA
*
11124139 AACCGATATATTTTTACCAGTTACATTGTAAATTTACCTATTACATTATATATATCGGTTTCGAT
65 AACAGATATATTTTTACCAGTTACATTGTAAATTTACCTATTACATTATATATATCGGTTTCGAT
* *
11124204 GTTTTTGGGATCGATACTTACAATAAATATATCGACACTTGATGTGTGCACCTCGTTGGGCATTC
130 GTTTTTGGGATCGATACTTACAATAAATATATCGACACTTGATGCGTGCAACTCGTTGGGCATTC
** *
11124269 ATTCTGGTTCAAAAGTATCGACACGA
195 ATTCTGGACCAAAAGTATCGACACAA
* * * *
11124295 TTTAAAAAGTTATCGACATAATTTAAAAAGGTATCGATACATTATGTTTACCTATTTTCTAATTA
1 TTTAAAAAG-TATCGAAACAATTCAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTA
** *
11124360 AATCAG-TATATTTTTACTGGTTACATTGTAAATTTATCTATTACATTATATATATCGGTTTCGA
65 AA-CAGATATATTTTTACCAGTTACATTGTAAATTTACCTATTACATTATATATATCGGTTTCGA
* * *
11124424 TGTTTTTGGGATCGATACTTACAATAAATGTATCGACACTTTATGCGTGTAACTCGTTGGGCATT
129 TGTTTTTGGGATCGATACTTACAATAAATATATCGACACTTGATGCGTGCAACTCGTTGGGCATT
11124489 CATTCTGGACCAAAAGTATCGACACAA
194 CATTCTGGACCAAAAGTATCGACACAA
11124516 TTTAAAAAGGTATCGA
1 TTTAAAAA-GTATCGA
11124532 TATATTATGT
Statistics
Matches: 216, Mismatches: 18, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
220 1 0.00
221 212 0.98
222 3 0.01
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.38
Consensus pattern (220 bp):
TTTAAAAAGTATCGAAACAATTCAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTAA
ACAGATATATTTTTACCAGTTACATTGTAAATTTACCTATTACATTATATATATCGGTTTCGATG
TTTTTGGGATCGATACTTACAATAAATATATCGACACTTGATGCGTGCAACTCGTTGGGCATTCA
TTCTGGACCAAAAGTATCGACACAA
Found at i:11124648 original size:200 final size:200
Alignment explanation
Indices: 11124299--11125448 Score: 1694
Period size: 200 Copynumber: 5.8 Consensus size: 200
11124289 ACACGATTTA
* * *
11124299 AAAAGTTATCGACATAATTTAAAAAGGTATCGATACATTATGTTTACCTATTTTCTAATTAAATC
1 AAAAG-TATCGACACAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTAAACC
*
11124364 -AGTATATTTTTACTGGTTACATTGTAAATTTATCTATTACATTATATATATCGGTTTCGATGTT
65 GA-TATATTTTTACTGGTTACATTGTAAATTTACCTATTACATTATATATATCGGTTTCGATGTT
* *
11124428 TTTGGGATCGATACTTACAATAAATGTATCGACACTTTATGCGTGTAACTCGTTGGGCATTCATT
129 TTTGGGATCGATACTTACAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATT
11124493 CTGGACC
194 CTGGACC
*
11124500 AAAAGTATCGACACAATTTAAAAAGGTATCGATATATTATGTTGACCTATTTTCTAATTAAACCG
1 AAAAGTATCGACACAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTAAACCG
* **
11124565 ATATATTTTTACCGGTTACATTGTAAATTTACCTATTACATTATATATATTAGTTTCGATGTTTT
66 ATATATTTTTACTGGTTACATTGTAAATTTACCTATTACATTATATATATCGGTTTCGATGTTTT
* * *
11124630 TGGGATCGATTCTTACAATAAATGTATCGACACTTTATCCGTGCACCTCGTTGGGCATTCATTTT
131 TGGGATCGATACTTACAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCT
11124695 GGACC
196 GGACC
*
11124700 AAAAGTATCGACACAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTAAACTG
1 AAAAGTATCGACACAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTAAACCG
** *
11124765 ATATATTTTTACCAGTTACATTGTAAA-TTACCTATTACATTATATATATCGTTTTCGATGTTTT
66 ATATATTTTTACTGGTTACATTGTAAATTTACCTATTACATTATATATATCGGTTTCGATGTTTT
* *
11124829 TGAGATCGATACTTACAATAAATGTATCAACACTTTATGCGTGCACCTCGTTGGGCATTCATTCT
131 TGGGATCGATACTTACAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCT
11124894 GGACC
196 GGACC
* *
11124899 AAAAGTATCGACACAATTTAAAAAGCTATCGATACATTATGTTGACCTATTTTCTAATTAAATCG
1 AAAAGTATCGACACAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTAAACCG
* * * *
11124964 GTATATTTTTACTTGTTACATTTTAAATTTACCTATTATATTATATATATCGGTTTCGATGTTTT
66 ATATATTTTTACTGGTTACATTGTAAATTTACCTATTACATTATATATATCGGTTTCGATGTTTT
* * * *
11125029 TGGGATCAATACTTACATTAAATGTATCGACACTTTATGTGTGCACCTCGTTGGACATTCATTCT
131 TGGGATCGATACTTACAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCT
11125094 GGACC
196 GGACC
* * * * * * * **
11125099 AAAAGTATCGTCATAATTTAAAAA-GTATAGAT-TATTATGTTGACCTATTCTCTCATAAAATGG
1 AAAAGTATCGACACAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTAAACCG
* * *
11125162 GTATATTTTTACTGGTTACATTGTAAATTTACC--TTACTTTATA-ATTATC--ATTCGATG-TT
66 ATATATTTTTACTGGTTACATTGTAAATTTACCTATTACATTATATA-TATCGGTTTCGATGTTT
* ** *
11125221 TTGGGATAGATACTTATGATAAATGTATCGACACTTTATGCGTGCATCTCGTTGGGCATTCATTC
130 TTGGGATCGATACTTACAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTC
11125286 TGGACC
195 TGGACC
* * * * *
11125292 AAAAGTATCAACACAATTTAAAAA-GTATCGATACATTATGTTGACCTATTCTCTCATAAAACCA
1 AAAAGTATCGACACAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTAAACCG
* *
11125356 ATATATTTTTATTGGTTACATTGTAAATTTACCTATTACTTTATA-ATTATCGGTTTCGATGTTT
66 ATATATTTTTACTGGTTACATTGTAAATTTACCTATTACATTATATA-TATCGGTTTCGATGTTT
* *
11125420 TTGGGATCGATACTTATAATAAATATATC
130 TTGGGATCGATACTTACAATAAATGTATC
11125449 AATACATCAA
Statistics
Matches: 865, Mismatches: 75, Indels: 20
0.90 0.08 0.02
Matches are distributed among these distances:
193 93 0.11
194 65 0.08
195 1 0.00
196 28 0.03
198 64 0.07
199 218 0.25
200 390 0.45
201 6 0.01
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40
Consensus pattern (200 bp):
AAAAGTATCGACACAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTAAACCG
ATATATTTTTACTGGTTACATTGTAAATTTACCTATTACATTATATATATCGGTTTCGATGTTTT
TGGGATCGATACTTACAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCT
GGACC
Found at i:11125053 original size:399 final size:397
Alignment explanation
Indices: 11124299--11125448 Score: 1701
Period size: 399 Copynumber: 2.9 Consensus size: 397
11124289 ACACGATTTA
* *
11124299 AAAAGTTATCGACATAATTTAAAAAGGTATCGATACATTATGTTTACCTATTTTCTAATTAAATC
1 AAAAG-TATCGACATAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTAAATG
*
11124364 AGTATATTTTTACTGGTTACATTGTAAATTTATCTATTACATTATATATATCGGTTTCGATGTTT
65 A-TATATTTTTACTGGTTACATTGTAAATTTACCTATTACATTATATATATC-GTTTCGATGTTT
*
11124429 TTGGGATCGATACTTACAATAAATGTATCGACACTTTATGCGTGTAACTCGTTGGGCATTCATTC
128 TTGGGATCGATACTTACAATAAATGTATCGACACTTTATGCGTGCAACTCGTTGGGCATTCATTC
*
11124494 TGGACCAAAAGTATCGACACAATTTAAAAAGGTATCGATATATTATGTTGACCTATTTTCTAATT
193 TGGACCAAAAGTATCGACACAATTTAAAAA-GTATCGATACATTATGTTGACCTATTTTCTAATT
** * **
11124559 AAACCGATATATTTTTACCGGTTACATTGTAAATTTACCTATTACATTATATATATTAGTTTCGA
257 AAACCGATATATTTTTACTTGTTACATTGTAAATTTACCTATTATATTATATATATCGGTTTCGA
* *
11124624 TGTTTTTGGGATCGATTCTTACAATAAATGTATCGACACTTTATCCGTGCACCTCGTTGGGCATT
322 TGTTTTTGGGATCGATACTTACAATAAATGTATCGACACTTTATCCGTGCACCTCGTTGGACATT
*
11124689 CATTTTGGACC
387 CATTCTGGACC
*
11124700 AAAAGTATCGACACAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTAAACTG
1 AAAAGTATCGACATAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTAAA-TG
**
11124765 ATATATTTTTACCAGTTACATTGTAAA-TTACCTATTACATTATATATATCGTTTTCGATGTTTT
65 ATATATTTTTACTGGTTACATTGTAAATTTACCTATTACATTATATATATCG-TTTCGATGTTTT
* * *
11124829 TGAGATCGATACTTACAATAAATGTATCAACACTTTATGCGTGCACCTCGTTGGGCATTCATTCT
129 TGGGATCGATACTTACAATAAATGTATCGACACTTTATGCGTGCAACTCGTTGGGCATTCATTCT
11124894 GGACCAAAAGTATCGACACAATTTAAAAAGCTATCGATACATTATGTTGACCTATTTTCTAATTA
194 GGACCAAAAGTATCGACACAATTTAAAAAG-TATCGATACATTATGTTGACCTATTTTCTAATTA
* * *
11124959 AATCGGTATATTTTTACTTGTTACATTTTAAATTTACCTATTATATTATATATATCGGTTTCGAT
258 AACCGATATATTTTTACTTGTTACATTGTAAATTTACCTATTATATTATATATATCGGTTTCGAT
* * **
11125024 GTTTTTGGGATCAATACTTACATTAAATGTATCGACACTTTATGTGTGCACCTCGTTGGACATTC
323 GTTTTTGGGATCGATACTTACAATAAATGTATCGACACTTTATCCGTGCACCTCGTTGGACATTC
11125089 ATTCTGGACC
388 ATTCTGGACC
* * * * * *
11125099 AAAAGTATCGTCATAATTTAAAAA-GTATAGAT-TATTATGTTGACCTATTCTCTCATAAAATGG
1 AAAAGTATCGACATAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTAAAT-G
* * *
11125162 GTATATTTTTACTGGTTACATTGTAAATTTACC--TTACTTTATA-ATTATC-ATTCGATG-TTT
65 ATATATTTTTACTGGTTACATTGTAAATTTACCTATTACATTATATA-TATCGTTTCGATGTTTT
* ** *
11125222 TGGGATAGATACTTATGATAAATGTATCGACACTTTATGCGTGCATCTCGTTGGGCATTCATTCT
129 TGGGATCGATACTTACAATAAATGTATCGACACTTTATGCGTGCAACTCGTTGGGCATTCATTCT
* * * *
11125287 GGACCAAAAGTATCAACACAATTTAAAAAGTATCGATACATTATGTTGACCTATTCTCTCATAAA
194 GGACCAAAAGTATCGACACAATTTAAAAAGTATCGATACATTATGTTGACCTATTTTCTAATTAA
*
11125352 ACCAATATATTTTTA-TTGGTTACATTGTAAATTTACCTATTACT-TTATA-ATTATCGGTTTCG
259 ACCGATATATTTTTACTT-GTTACATTGTAAATTTACCTATTA-TATTATATA-TATCGGTTTCG
* *
11125414 ATGTTTTTGGGATCGATACTTATAATAAATATATC
321 ATGTTTTTGGGATCGATACTTACAATAAATGTATC
11125449 AATACATCAA
Statistics
Matches: 684, Mismatches: 56, Indels: 27
0.89 0.07 0.04
Matches are distributed among these distances:
391 3 0.00
392 114 0.17
393 92 0.13
394 7 0.01
395 1 0.00
396 14 0.02
397 49 0.07
398 14 0.02
399 304 0.44
400 79 0.12
401 7 0.01
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40
Consensus pattern (397 bp):
AAAAGTATCGACATAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTAAATGA
TATATTTTTACTGGTTACATTGTAAATTTACCTATTACATTATATATATCGTTTCGATGTTTTTG
GGATCGATACTTACAATAAATGTATCGACACTTTATGCGTGCAACTCGTTGGGCATTCATTCTGG
ACCAAAAGTATCGACACAATTTAAAAAGTATCGATACATTATGTTGACCTATTTTCTAATTAAAC
CGATATATTTTTACTTGTTACATTGTAAATTTACCTATTATATTATATATATCGGTTTCGATGTT
TTTGGGATCGATACTTACAATAAATGTATCGACACTTTATCCGTGCACCTCGTTGGACATTCATT
CTGGACC
Found at i:11129217 original size:21 final size:22
Alignment explanation
Indices: 11129180--11129220 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
11129170 TTTCTGGAAA
*
11129180 GGAACCGATTCCCCTGCTACAG
1 GGAACCGATTACCCTGCTACAG
11129202 GGAACCGA-TACCCTGCTAC
1 GGAACCGATTACCCTGCTAC
11129221 GTATAAATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.24, C:0.37, G:0.22, T:0.17
Consensus pattern (22 bp):
GGAACCGATTACCCTGCTACAG
Found at i:11130098 original size:32 final size:32
Alignment explanation
Indices: 11129998--11130104 Score: 101
Period size: 31 Copynumber: 3.4 Consensus size: 32
11129988 TAGGTCCCGA
* * * *
11129998 AGAACCTAGGTAA-AATGTCCATATGGTTCTT
1 AGAACATAGGTAATACTGTCCATATGTTTCAT
** *
11130029 AGAACATAGGT-ATACTGTCCATATGTCCCAA
1 AGAACATAGGTAATACTGTCCATATGTTTCAT
* * *
11130060 AAAACATAGGTAATTCTGTCCATATGTTTCGT
1 AGAACATAGGTAATACTGTCCATATGTTTCAT
*
11130092 AGAACATAAGTAA
1 AGAACATAGGTAA
11130105 ACCCTCGACT
Statistics
Matches: 59, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
30 1 0.02
31 32 0.54
32 26 0.44
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (32 bp):
AGAACATAGGTAATACTGTCCATATGTTTCAT
Found at i:11135290 original size:183 final size:183
Alignment explanation
Indices: 11134970--11135654 Score: 755
Period size: 183 Copynumber: 3.7 Consensus size: 183
11134960 TTATCAAAGT
* * * *
11134970 ATCGAGACATTCAACATATCCGGTAGCA-CTTTACCAGTTTCGTCATAATGAAACCGGTTTTGTC
1 ATCGATACTTTCAACATATCCGGTAG-AGCTTTACCGGTTTTGTCATAATGAAACCGGTTTTGTC
* *
11135034 ATATTTTTACATGTTATATTGTTATGTATCGATACATTTTTATAAAGTATTGATACTTTATAGGC
65 ATATTTTTACCTGTTATATTGTTATGTATCGATACATTTTTATAAAGTATCGATACTTTATAGGC
* * * *
11135099 GTTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTTGATACTTATTTGAATGAA
130 GCTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGGA
* ***
11135153 ATCGATACTTTCAACATATCCGGTAGATCTTTACCGGTTTTGTCATAATGAAATTAGTTTTGTCA
1 ATCGATACTTTCAACATATCCGGTAGAGCTTTACCGGTTTTGTCATAATGAAACCGGTTTTGTCA
*
11135218 TATTTTTACCTGTTATATTATTATGTATCGATACATTTTTATAAAGTATCGATACTTTATAGGCG
66 TATTTTTACCTGTTATATTGTTATGTATCGATACATTTTTATAAAGTATCGATACTTTATAGGCG
11135283 CTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGGA
131 CTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGGA
** ** *** * *
11135336 ATCGATACTTTCAACATATTTGGTATCGCTTTAAATGTTTTGTCATTATGAAACCGGTTTTATCA
1 ATCGATACTTTCAACATATCCGGTAGAGCTTTACCGGTTTTGTCATAATGAAACCGGTTTTGTC-
* * *
11135401 TTATGAAACCGGTTTTATCATTTACCTGTTATATTGTTATGTATCGATATATGTTTAT-AATTGA
65 --AT---A-------T-T--TTTACCTGTTATATTGTTATGTATCGATACATTTTTATAAAGT-A
* * * *
11135465 TCGATACTTTATAGGCTCTATTATTGCTTTTCTTTTAAATTCCAAAAGTGTCGATATTTATTTCA
114 TCGATACTTTATAGGCGCTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAA
11135530 ATGGA
179 ATGGA
* ** * ** * * * *
11135535 ATCGATACTTTTAACATATCCAATAGCGCTTTACCGAATTTGTCATATTGAACCCGATTTTCTCA
1 ATCGATACTTTCAACATATCCGGTAGAGCTTTACCGGTTTTGTCATAATGAAACCGGTTTTGTCA
* ** * **
11135600 TATGTTTACCTAATATATTGTTATGTATCGATTCATATTTTA-ATTGTATCGATAC
66 TATTTTTACCTGTTATATTGTTATGTATCGATACAT-TTTTATAAAGTATCGATAC
11135655 GTTCCGACAA
Statistics
Matches: 422, Mismatches: 60, Indels: 40
0.81 0.11 0.08
Matches are distributed among these distances:
182 1 0.00
183 254 0.60
184 5 0.01
186 3 0.01
189 1 0.00
193 1 0.00
196 3 0.01
197 1 0.00
198 3 0.01
199 150 0.36
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (183 bp):
ATCGATACTTTCAACATATCCGGTAGAGCTTTACCGGTTTTGTCATAATGAAACCGGTTTTGTCA
TATTTTTACCTGTTATATTGTTATGTATCGATACATTTTTATAAAGTATCGATACTTTATAGGCG
CTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGGA
Found at i:11135395 original size:20 final size:20
Alignment explanation
Indices: 11135372--11135422 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
11135362 CGCTTTAAAT
*
11135372 GTTTTGTCATTATGAAACCG
1 GTTTTATCATTATGAAACCG
11135392 GTTTTATCATTATGAAACCG
1 GTTTTATCATTATGAAACCG
11135412 GTTTTATCATT
1 GTTTTATCATT
11135423 TACCTGTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.45
Consensus pattern (20 bp):
GTTTTATCATTATGAAACCG
Found at i:11135579 original size:199 final size:199
Alignment explanation
Indices: 11135222--11135580 Score: 533
Period size: 199 Copynumber: 1.8 Consensus size: 199
11135212 TTGTCATATT
*
11135222 TTTACCTGTTATATTATTATGTATCGATACATTTTTATAAAGTATCGATACTTTATAGGCGCTAT
1 TTTACCTGTTATATTATTATGTATCGATACATGTTTATAAAGTATCGATACTTTATAGGCGCTAT
11135287 TACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGGAATCGATACTTTCAACA
66 TACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGGAATCGATACTTTCAACA
**** * * *
11135352 TATTTGGTATCGCTTTAAATGTTTTGTCATTATGAAACCGGTTTTATCATTATGAAACCGGTTTT
131 TATCCAATAGCGCTTTAAACGATTTGTCATTATGAAACCGGTTTTATCATTATGAAACCGGTTTT
11135417 ATCA
196 ATCA
* * * *
11135421 TTTACCTGTTATATTGTTATGTATCGATATATGTTTAT-AATTGATCGATACTTTATAGGCTCTA
1 TTTACCTGTTATATTATTATGTATCGATACATGTTTATAAAGT-ATCGATACTTTATAGGCGCTA
* * * *
11135485 TTATTGCTTTTCTTTTAAATTCCAAAAGTGTCGATATTTATTTCAATGGAATCGATACTTTTAAC
65 TTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGGAATCGATACTTTCAAC
*
11135550 ATATCCAATAGCGCTTT-ACCGAATTTGTCAT
130 ATATCCAATAGCGCTTTAAACG-ATTTGTCAT
11135581 ATTGAACCCG
Statistics
Matches: 141, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
198 5 0.04
199 136 0.96
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (199 bp):
TTTACCTGTTATATTATTATGTATCGATACATGTTTATAAAGTATCGATACTTTATAGGCGCTAT
TACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGGAATCGATACTTTCAACA
TATCCAATAGCGCTTTAAACGATTTGTCATTATGAAACCGGTTTTATCATTATGAAACCGGTTTT
ATCA
Found at i:11141651 original size:18 final size:18
Alignment explanation
Indices: 11141628--11141685 Score: 116
Period size: 18 Copynumber: 3.2 Consensus size: 18
11141618 AATAACATTA
11141628 TTATAATAGATTGATACT
1 TTATAATAGATTGATACT
11141646 TTATAATAGATTGATACT
1 TTATAATAGATTGATACT
11141664 TTATAATAGATTGATACT
1 TTATAATAGATTGATACT
11141682 TTAT
1 TTAT
11141686 CTCTATTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (18 bp):
TTATAATAGATTGATACT
Found at i:11143445 original size:26 final size:26
Alignment explanation
Indices: 11143410--11143467 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
11143400 AAGCCCGAAA
11143410 GGGGTTTATAAGCCGAAAGAATATTG
1 GGGGTTTATAAGCCGAAAGAATATTG
11143436 GGGGTTTATAAGCCGAAAGAATATTG
1 GGGGTTTATAAGCCGAAAGAATATTG
11143462 GGGGTT
1 GGGGTT
11143468 CCTAATTCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.31, C:0.07, G:0.34, T:0.28
Consensus pattern (26 bp):
GGGGTTTATAAGCCGAAAGAATATTG
Found at i:11155681 original size:13 final size:13
Alignment explanation
Indices: 11155663--11155688 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11155653 ATAACTCTCA
11155663 GGTACCTGAACAG
1 GGTACCTGAACAG
11155676 GGTACCTGAACAG
1 GGTACCTGAACAG
11155689 TCAGTAGCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.31, T:0.15
Consensus pattern (13 bp):
GGTACCTGAACAG
Found at i:11159352 original size:21 final size:21
Alignment explanation
Indices: 11159305--11159366 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
11159295 TATAATGAAC
11159305 CTTAAACCATAAACCCTAAAA
1 CTTAAACCATAAACCCTAAAA
* ** *
11159326 CATAAACCATAAAGTCTAAAT
1 CTTAAACCATAAACCCTAAAA
*
11159347 CTTAAACTC-TAAATCCTAAA
1 CTTAAAC-CATAAACCCTAAA
11159367 CCCTAAATTG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
21 32 0.97
22 1 0.03
ACGTcount: A:0.50, C:0.24, G:0.02, T:0.24
Consensus pattern (21 bp):
CTTAAACCATAAACCCTAAAA
Found at i:11159374 original size:14 final size:14
Alignment explanation
Indices: 11159341--11159374 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
11159331 ACCATAAAGT
* *
11159341 CTAAATCTTAAACT
1 CTAAATCCTAAACC
11159355 CTAAATCCTAAACC
1 CTAAATCCTAAACC
11159369 CTAAAT
1 CTAAAT
11159375 TGTACTTACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.29
Consensus pattern (14 bp):
CTAAATCCTAAACC
Found at i:11159471 original size:21 final size:21
Alignment explanation
Indices: 11159447--11159502 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
11159437 CCCTATTCTA
*
11159447 TAAACCATAAACCCTAAATCC
1 TAAACCATAAACCCTAAACCC
* *
11159468 TAAACTATAAACCTTAAACCC
1 TAAACCATAAACCCTAAACCC
*
11159489 TAAACCCTAAACCC
1 TAAACCATAAACCC
11159503 AATTATGTGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.20
Consensus pattern (21 bp):
TAAACCATAAACCCTAAACCC
Found at i:11159475 original size:28 final size:28
Alignment explanation
Indices: 11159431--11159500 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
11159421 TGTAATGAAT
**
11159431 CCTAAACCCTATTCTATAAACCATAAAC
1 CCTAAACCCTAAACTATAAACCATAAAC
* *
11159459 CCTAAATCCTAAACTATAAACCTTAAAC
1 CCTAAACCCTAAACTATAAACCATAAAC
11159487 CCTAAACCCTAAAC
1 CCTAAACCCTAAAC
11159501 CCAATTATGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.23
Consensus pattern (28 bp):
CCTAAACCCTAAACTATAAACCATAAAC
Found at i:11159502 original size:7 final size:7
Alignment explanation
Indices: 11159447--11159502 Score: 67
Period size: 7 Copynumber: 8.0 Consensus size: 7
11159437 CCCTATTCTA
*
11159447 TAAACCA
1 TAAACCC
11159454 TAAACCC
1 TAAACCC
*
11159461 TAAATCC
1 TAAACCC
**
11159468 TAAACTA
1 TAAACCC
*
11159475 TAAACCT
1 TAAACCC
11159482 TAAACCC
1 TAAACCC
11159489 TAAACCC
1 TAAACCC
11159496 TAAACCC
1 TAAACCC
11159503 AATTATGTGA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 41 1.00
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.20
Consensus pattern (7 bp):
TAAACCC
Found at i:11162135 original size:17 final size:17
Alignment explanation
Indices: 11162113--11162145 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
11162103 ATTGGAGTTT
11162113 GAGTTCGAGCTTGAATC
1 GAGTTCGAGCTTGAATC
11162130 GAGTTCGAGCTTGAAT
1 GAGTTCGAGCTTGAAT
11162146 TGAGCTCAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.30
Consensus pattern (17 bp):
GAGTTCGAGCTTGAATC
Found at i:11162978 original size:14 final size:14
Alignment explanation
Indices: 11162953--11163003 Score: 70
Period size: 14 Copynumber: 3.7 Consensus size: 14
11162943 TGAATCGGTC
11162953 TGACTATTGACCAT
1 TGACTATTGACCAT
*
11162967 TGATCT-TTGACCGT
1 TGA-CTATTGACCAT
11162981 TGACTATTGA-CAT
1 TGACTATTGACCAT
11162994 TGACTATTGA
1 TGACTATTGA
11163004 ATTTGATCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
13 14 0.42
14 17 0.52
15 2 0.06
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (14 bp):
TGACTATTGACCAT
Found at i:11162998 original size:13 final size:13
Alignment explanation
Indices: 11162953--11163024 Score: 60
Period size: 13 Copynumber: 5.3 Consensus size: 13
11162943 TGAATCGGTC
11162953 TGACTATTGACCAT
1 TGACTATTGA-CAT
*
11162967 TGATCT-TTGACCGT
1 TGA-CTATTGA-CAT
11162981 TGACTATTGACAT
1 TGACTATTGACAT
11162994 TGACTATTGA-ATT
1 TGACTATTGACA-T
11163007 TGA-TCATTGACAAT
1 TGACT-ATTGAC-AT
11163021 TGAC
1 TGAC
11163025 AATTATCTCT
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
12 2 0.04
13 23 0.47
14 21 0.43
15 3 0.06
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (13 bp):
TGACTATTGACAT
Found at i:11163003 original size:20 final size:21
Alignment explanation
Indices: 11162953--11163024 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 21
11162943 TGAATCGGTC
* *
11162953 TGACTATTGACCATTGATCTT
1 TGACTATTGACTATTGATCAT
**
11162974 TGACCGTTGACTATTGA-CAT
1 TGACTATTGACTATTGATCAT
*
11162994 TGACTATTGAAT-TTGATCAT
1 TGACTATTGACTATTGATCAT
*
11163014 TGACAATTGAC
1 TGACTATTGAC
11163025 AATTATCTCT
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
19 4 0.10
20 23 0.56
21 14 0.34
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (21 bp):
TGACTATTGACTATTGATCAT
Found at i:11163657 original size:52 final size:51
Alignment explanation
Indices: 11163594--11163806 Score: 232
Period size: 52 Copynumber: 4.1 Consensus size: 51
11163584 ATCTTTATCT
* *
11163594 TGTTTCATGTTTTCTGTTTTGGGGTTCCTTTTGGAGGGT-ACAGTCCCCATCA
1 TGTTTCTTGTTTTTTGTTTT-GGGTTCCTTTTGGAGGGTAACA-TCCCCATCA
* * * *
11163646 TGTTTCTTGTTTTTTGTTTTGGTTTCCTCTTCGAAGGGTAACATCCTCATCA
1 TGTTTCTTGTTTTTTGTTTTGGGTTCCT-TTTGGAGGGTAACATCCCCATCA
* *
11163698 TGTTTCTTGTTTTTTGTTTTGGGTTCCTTTTCAGAGGGTAACATCCCCACCA
1 TGTTTCTTGTTTTTTGTTTTGGGTTCCTTTT-GGAGGGTAACATCCCCATCA
* * * * * *
11163750 TGTTTCCTATTTTTTGTTTTGGATT-CTTCTTCGGAGGGTAACGTCCTCATCC
1 TGTTTCTTGTTTTTTGTTTTGGGTTCCTT-TT-GGAGGGTAACATCCCCATCA
11163802 TGTTT
1 TGTTT
11163807 ATCTATGGCA
Statistics
Matches: 137, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
51 12 0.09
52 122 0.89
53 3 0.02
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.48
Consensus pattern (51 bp):
TGTTTCTTGTTTTTTGTTTTGGGTTCCTTTTGGAGGGTAACATCCCCATCA
Found at i:11163735 original size:104 final size:104
Alignment explanation
Indices: 11163594--11163806 Score: 295
Period size: 104 Copynumber: 2.0 Consensus size: 104
11163584 ATCTTTATCT
* * * *
11163594 TGTTTCATGTTTTCTGTTTTGGGGTTCCTTTTGGAGGGT-ACAGTCCCCATCATGTTTCTTGTTT
1 TGTTTCATGTTTTCTGTTTTGGGGTTCCTTTTAGAGGGTAACA-TCCCCACCATGTTTCCTATTT
*
11163658 TTTGTTTTGGTTTCCTCTTCGAAGGGTAACATCCTCATCA
65 TTTGTTTTGGATTCCTCTTCGAAGGGTAACATCCTCATCA
* *
11163698 TGTTTCTTGTTTTTTGTTTT-GGGTTCCTTTTCAGAGGGTAACATCCCCACCATGTTTCCTATTT
1 TGTTTCATGTTTTCTGTTTTGGGGTTCCTTTT-AGAGGGTAACATCCCCACCATGTTTCCTATTT
* * * *
11163762 TTTGTTTTGGATTCTTCTTCGGAGGGTAACGTCCTCATCC
65 TTTGTTTTGGATTCCTCTTCGAAGGGTAACATCCTCATCA
11163802 TGTTT
1 TGTTT
11163807 ATCTATGGCA
Statistics
Matches: 96, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
103 11 0.11
104 82 0.85
105 3 0.03
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.48
Consensus pattern (104 bp):
TGTTTCATGTTTTCTGTTTTGGGGTTCCTTTTAGAGGGTAACATCCCCACCATGTTTCCTATTTT
TTGTTTTGGATTCCTCTTCGAAGGGTAACATCCTCATCA
Found at i:11164590 original size:29 final size:29
Alignment explanation
Indices: 11164557--11164622 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
11164547 TTAGATAGAT
11164557 GAATCGATCGAAGTGTGAATGATATATCC
1 GAATCGATCGAAGTGTGAATGATATATCC
* * *
11164586 GAATCGATCTAAGTGTGTATTATATATCC
1 GAATCGATCGAAGTGTGAATGATATATCC
11164615 GAATCGAT
1 GAATCGAT
11164623 GAGAGACTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (29 bp):
GAATCGATCGAAGTGTGAATGATATATCC
Found at i:11167497 original size:2 final size:2
Alignment explanation
Indices: 11167490--11167525 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
11167480 GATAAGAATA
11167490 AT 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 AT
11167526 TATCGTTGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11168005 original size:3 final size:3
Alignment explanation
Indices: 11167999--11168057 Score: 93
Period size: 3 Copynumber: 19.3 Consensus size: 3
11167989 AAATGAAAAT
11167999 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
11168045 ATA A-A ATA GATA A
1 ATA ATA ATA -ATA A
11168058 ATAAAGATAA
Statistics
Matches: 53, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.04
3 45 0.85
4 6 0.11
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:11168103 original size:19 final size:18
Alignment explanation
Indices: 11168079--11168137 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 18
11168069 TTTGAGTAAG
11168079 AAGAAAAATAATAAAAATA
1 AAGAAAAATAAT-AAAATA
11168098 AAGAAAAAATAATAAAATGA
1 AAG-AAAAATAATAAAAT-A
11168118 AATGAAAAA-AATAAAATA
1 AA-GAAAAATAATAAAATA
11168136 AA
1 AA
11168138 AAATGATCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
18 3 0.08
19 16 0.43
20 17 0.46
21 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (18 bp):
AAGAAAAATAATAAAATA
Found at i:11168128 original size:14 final size:13
Alignment explanation
Indices: 11168082--11168140 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
11168072 GAGTAAGAAG
11168082 AAAAATAATAAAA-
1 AAAAA-AATAAAAT
*
11168095 ATAAAGAA-AAAAT
1 A-AAAAAATAAAAT
* *
11168108 AATAAAATGAAAT
1 AAAAAAATAAAAT
11168121 GAAAAAAATAAAAT
1 -AAAAAAATAAAAT
11168135 AAAAAA
1 AAAAAA
11168141 TGATCAAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
12 8 0.22
13 14 0.39
14 14 0.39
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (13 bp):
AAAAAAATAAAAT
Found at i:11169194 original size:19 final size:20
Alignment explanation
Indices: 11169156--11169206 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
11169146 GAAACCCCTT
11169156 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
11169176 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
11169195 TGAAGATACATG
1 TGAAAATACATG
11169207 TTCTTGGCTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:11169396 original size:25 final size:25
Alignment explanation
Indices: 11169366--11169420 Score: 80
Period size: 22 Copynumber: 2.3 Consensus size: 25
11169356 AGTGCACATG
*
11169366 CTTGAATGATGCACATGGTAGCTTA
1 CTTGAATGATGCACATGGTAGCCTA
11169391 CTTG-A--ATGCACATGGTAGCCTA
1 CTTGAATGATGCACATGGTAGCCTA
11169413 CTTGAATG
1 CTTGAATG
11169421 CACATGGGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 20 0.77
23 1 0.04
24 1 0.04
25 4 0.15
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (25 bp):
CTTGAATGATGCACATGGTAGCCTA
Found at i:11169402 original size:22 final size:22
Alignment explanation
Indices: 11169374--11169427 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
11169364 TGCTTGAATG
*
11169374 ATGCACATGGTAGCTTACTTGA
1 ATGCACATGGTAGCCTACTTGA
11169396 ATGCACATGGTAGCCTACTTGA
1 ATGCACATGGTAGCCTACTTGA
11169418 ATGCACATGG
1 ATGCACATGG
11169428 GTCTTCTTGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (22 bp):
ATGCACATGGTAGCCTACTTGA
Found at i:11170107 original size:24 final size:24
Alignment explanation
Indices: 11170080--11170131 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
11170070 GAATAACATG
11170080 ACATGAGTTAATGAATGA-ATGAAA
1 ACATGAG-TAATGAATGATATGAAA
* * *
11170104 ACATGTGTCATGAATGATATGCAA
1 ACATGAGTAATGAATGATATGAAA
11170128 ACAT
1 ACAT
11170132 AATAAATGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.44, C:0.10, G:0.19, T:0.27
Consensus pattern (24 bp):
ACATGAGTAATGAATGATATGAAA
Found at i:11171215 original size:19 final size:18
Alignment explanation
Indices: 11171164--11171217 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
11171154 GACCTAGACC
11171164 ATAAATAAAA-AAATAAA
1 ATAAATAAAATAAATAAA
* *
11171181 ATTAATAAAATGAAATAAG
1 ATAAATAAAAT-AAATAAA
11171200 ATAAATAAAAATAAATAA
1 ATAAAT-AAAATAAATAA
11171218 TATATATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
17 9 0.29
19 17 0.55
20 5 0.16
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (18 bp):
ATAAATAAAATAAATAAA
Found at i:11171358 original size:110 final size:108
Alignment explanation
Indices: 11171238--11171634 Score: 532
Period size: 110 Copynumber: 3.6 Consensus size: 108
11171228 TATATATATG
* *
11171238 AAAAT-ATTTTAAAACTATATATTATATATA-TATTAAAAAATGTTTTCAAAACTATATATTATA
1 AAAATGATTTCAAAACTATATATTATATA-AGTTTTAAAAAATGTTTTCAAAACTATATATTATA
*
11171301 T-AGTTTTCAAAAATGTTTTAAAACTATTTATTATATATTTTTTC
65 TAAGTTTTC-AAAATGTTTTAAAACTATATATTATATATTTTTTC
* * * *
11171345 AAAAAATGTTTTTAAAACTATATATTATATATGTTTTAAAAAATGTTTTCAAAATTATATATTAT
1 --AAAATGATTTCAAAACTATATATTATATAAGTTTTAAAAAATGTTTTCAAAACTATATATTAT
* *
11171410 ATAAGTTTTCAAAATGATTTCAAAACTATATATTATATAAGTTTTTC
64 ATAAGTTTTCAAAATG-TTTTAAAACTATATATTATAT-ATTTTTTC
** *
11171457 AAAATGATTTCAAAACTATATATTATATAAGTTTTTCAAAATGATTTCAAAACTATATATTATAT
1 AAAATGATTTCAAAACTATATATTATATAAGTTTTAAAAAATGTTTTCAAAACTATATATTATAT
*
11171522 AAGTTTTTAAAATGTTTTCAAAATCTATATATTATATATATATTTTC
66 AAGTTTTCAAAATGTTTT-AAAA-CTATATATTATATAT-T-TTTTC
* *
11171569 AAAATGATTTCAAAACTATATATTATATAAGTTTT-TAAAATGTTTTCAGAAACTATATAATATA
1 AAAATGATTTCAAAACTATATATTATATAAGTTTTAAAAAATGTTTTCA-AAACTATATATTATA
11171633 TA
65 TA
11171635 CATTTTTTAA
Statistics
Matches: 258, Mismatches: 20, Indels: 17
0.87 0.07 0.06
Matches are distributed among these distances:
109 8 0.03
110 136 0.53
111 51 0.20
112 63 0.24
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (108 bp):
AAAATGATTTCAAAACTATATATTATATAAGTTTTAAAAAATGTTTTCAAAACTATATATTATAT
AAGTTTTCAAAATGTTTTAAAACTATATATTATATATTTTTTC
Found at i:11171364 original size:73 final size:72
Alignment explanation
Indices: 11171238--11171648 Score: 513
Period size: 73 Copynumber: 5.6 Consensus size: 72
11171228 TATATATATG
* * ** *
11171238 AAAATATTTT-AAAACTATATATTATATATATATTAAAAAATGTTTTCAAAACTATATATTATAT
1 AAAATGTTTTCAAAACTATATATTATATAT-TTTTTCAAAATGATTTCAAAACTATATATTATAT
11171302 -AGTTTTCA
65 AAGTTTT-A
* * *
11171310 AAAATGTTTT-AAAACTATTTATTATATATTTTTTCAAAAAATGTTTTTAAAACTATATATTATA
1 AAAATGTTTTCAAAACTATATATTATATATTTTTTC--AAAATGATTTCAAAACTATATATTATA
*
11171374 TATGTTTTAA
64 TAAGTTTT-A
* **
11171384 AAAATGTTTTCAAAATTATATATTATATAAGTTTTCAAAATGATTTCAAAACTATATATTATATA
1 AAAATGTTTTCAAAACTATATATTATATATTTTTTCAAAATGATTTCAAAACTATATATTATATA
*
11171449 AGTTTTTC
66 AG-TTTTA
* *
11171457 AAAATGATTTCAAAACTATATATTATATAAGTTTTTCAAAATGATTTCAAAACTATATATTATAT
1 AAAATGTTTTCAAAACTATATATTATAT-ATTTTTTCAAAATGATTTCAAAACTATATATTATAT
*
11171522 AAGTTTTT
65 AAGTTTTA
11171530 AAAATGTTTTCAAAATCTATATATTATATATATATTTTCAAAATGATTTCAAAACTATATATTAT
1 AAAATGTTTTCAAAA-CTATATATTATATAT-T-TTTTCAAAATGATTTCAAAACTATATATTAT
*
11171595 ATAAGTTTTT
63 ATAAGTTTTA
* *
11171605 AAAATGTTTTCAGAAACTATATAATATATACATTTTTTAAAAAT
1 AAAATGTTTTCA-AAACTATAT-AT-TATATATTTTTTCAAAAT
11171649 CGTTTTCTAA
Statistics
Matches: 302, Mismatches: 25, Indels: 21
0.87 0.07 0.06
Matches are distributed among these distances:
71 3 0.01
72 27 0.09
73 100 0.33
74 71 0.24
75 89 0.29
76 6 0.02
77 6 0.02
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.45
Consensus pattern (72 bp):
AAAATGTTTTCAAAACTATATATTATATATTTTTTCAAAATGATTTCAAAACTATATATTATATA
AGTTTTA
Found at i:11171641 original size:37 final size:36
Alignment explanation
Indices: 11171238--11171660 Score: 489
Period size: 37 Copynumber: 11.4 Consensus size: 36
11171228 TATATATATG
* **
11171238 AAAATATTTT-AAAACTATATATTATATATA-TATTAA
1 AAAATGTTTTCAAAACTATATATTATATA-AGT-TTTT
*
11171274 AAAATGTTTTCAAAACTATATATTATAT-AGTTTTCA
1 AAAATGTTTTCAAAACTATATATTATATAAGTTTT-T
* *
11171310 AAAATGTTTT-AAAACTATTTATTATAT-ATTTTTT
1 AAAATGTTTTCAAAACTATATATTATATAAGTTTTT
* * *
11171344 CAAAAAATGTTTTTAAAACTATATATTATATATGTTTTAA
1 ---AAAATGTTTTCAAAACTATATATTATATAAGTTTT-T
* *
11171384 AAAATGTTTTCAAAATTATATATTATATAAGTTTTC
1 AAAATGTTTTCAAAACTATATATTATATAAGTTTTT
*
11171420 AAAATGATTTCAAAACTATATATTATATAAGTTTTT
1 AAAATGTTTTCAAAACTATATATTATATAAGTTTTT
*
11171456 CAAAATGATTTCAAAACTATATATTATATAAGTTTTT
1 -AAAATGTTTTCAAAACTATATATTATATAAGTTTTT
*
11171493 CAAAATGATTTCAAAACTATATATTATATAAGTTTTT
1 -AAAATGTTTTCAAAACTATATATTATATAAGTTTTT
11171530 AAAATGTTTTCAAAATCTATATATTATATATA-TATTTT
1 AAAATGTTTTCAAAA-CTATATATTATATA-AGT-TTTT
*
11171568 CAAAATGATTTCAAAACTATATATTATATAAGTTTTT
1 -AAAATGTTTTCAAAACTATATATTATATAAGTTTTT
* *
11171605 AAAATGTTTTCAGAAACTATATAATATATACATTTTTT
1 AAAATGTTTTCA-AAACTATATATTATATA-AGTTTTT
11171643 AAAAATCGTTTTCTAAAA
1 -AAAAT-GTTTTC-AAAA
11171661 AAAATTCAAA
Statistics
Matches: 346, Mismatches: 21, Indels: 36
0.86 0.05 0.09
Matches are distributed among these distances:
35 24 0.07
36 79 0.23
37 168 0.49
38 42 0.12
39 23 0.07
40 9 0.03
41 1 0.00
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.45
Consensus pattern (36 bp):
AAAATGTTTTCAAAACTATATATTATATAAGTTTTT
Found at i:11171691 original size:2 final size:2
Alignment explanation
Indices: 11171673--11171724 Score: 58
Period size: 2 Copynumber: 27.5 Consensus size: 2
11171663 AATTCAAAAA
*
11171673 AT AT ACT AT AT -T A- AT AT AT AT AT AT AT AT AT AT AT A- AT AA
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11171713 AT A- AT AT AT AT A
1 AT AT AT AT AT AT A
11171725 AAAAATAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
1 4 0.09
2 37 0.86
3 2 0.05
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:11171725 original size:16 final size:16
Alignment explanation
Indices: 11171684--11171732 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
11171674 TATACTATAT
*
11171684 TAATATATAT-ATATA
1 TAATATATATAATAAA
11171699 T-ATATATATAATAAA
1 TAATATATATAATAAA
*
11171714 TAATATATATAAAAAA
1 TAATATATATAATAAA
11171730 TAA
1 TAA
11171733 AATAAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 8 0.27
15 6 0.20
16 16 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATATATATAATAAA
Found at i:11171731 original size:20 final size:20
Alignment explanation
Indices: 11171696--11171733 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
11171686 ATATATATAT
* *
11171696 ATATATATATATAATAAATA
1 ATATATATAAAAAATAAATA
11171716 ATATATATAAAAAATAAA
1 ATATATATAAAAAATAAA
11171734 ATAAAATAAA
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
ATATATATAAAAAATAAATA
Found at i:11172538 original size:85 final size:85
Alignment explanation
Indices: 11172394--11172957 Score: 842
Period size: 85 Copynumber: 6.6 Consensus size: 85
11172384 TAAATTTGAC
* * * * * *
11172394 CTCGAAGGTATTTGTTGATAGATAACCCTTCCCTCCTTGAGTTATGCTGTAAATTTGATATGTCC
1 CTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATG-CC
*
11172459 -TTGAGCTGAATATAATCGAA
65 TTTGAGCTGAATGTAATCGAA
* *
11172479 ATCGAAGGTCTTTGTTGACAGATAGCCCTTATCGCCTTGAGCTATGCTGTAAATTTGATATGCCT
1 CTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCT
*
11172544 TTGAGCTGAATGTAATCCAA
66 TTGAGCTGAATGTAATCGAA
* * * *
11172564 CTCGAAGGTCTTTGTTGATAGATAGCCCTTATCGCCTTGAGTTATGCTGTAAATTTGATATGCAT
1 CTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCT
*
11172629 TTGAGTTGAATGTAATCGAA
66 TTGAGCTGAATGTAATCGAA
11172649 CTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCT
1 CTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCT
11172714 TTGAGCTGAATGTAATCGAA
66 TTGAGCTGAATGTAATCGAA
* * *
11172734 CTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCACCTTAAGCTATGCTGTAAATTTGATATACCT
1 CTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCT
* * *
11172799 TTGAACTAAATGTAATTGAA
66 TTGAGCTGAATGTAATCGAA
* * *
11172819 CTCGAAGGTCTTTTTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATACGCCT
1 CTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCT
*
11172884 TTGAGCTGAATGTAATCAAA
66 TTGAGCTGAATGTAATCGAA
* * * **
11172904 CTCGAAGGTCTTTGCTGACAGACAACCCTTCTCGCCTTGATTTATGCTGTAAAT
1 CTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAAT
11172958 AGTTCCTTTA
Statistics
Matches: 436, Mismatches: 42, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
84 2 0.00
85 434 1.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (85 bp):
CTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCT
TTGAGCTGAATGTAATCGAA
Found at i:11174390 original size:83 final size:85
Alignment explanation
Indices: 11174182--11174392 Score: 293
Period size: 84 Copynumber: 2.5 Consensus size: 85
11174172 GGCTAGCTAA
* * * * *
11174182 ATCCTTAAAGTCGGGGCGTTTAACCAATTGCTCTAGATGGACA-ACGCAATATTATAATCACCTT
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTTTAGAGGGATAGACACAATATTATAATCACCTT
* *
11174246 TATCAGGCTAGTTAAATATT
66 TATCAGGCTAGCTAAATACT
* * *
11174266 ATCTATAAAGTCGGGGTGTTTAACCAATTGTTTTAGAGGGATAGA-ACAATATTATAATCACCTT
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTTTAGAGGGATAGACACAATATTATAATCACCTT
11174330 TATCAGGCTAGCTAAAT-CT
66 TATCAGGCTAGCTAAATACT
* *
11174349 ATCCATAAAGCCGGGGCGTTTAACCAATTACTTTAGAGGGATAG
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTTTAGAGGGATAG
11174393 CTCAAGCTTT
Statistics
Matches: 111, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
83 40 0.36
84 70 0.63
85 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (85 bp):
ATCCATAAAGTCGGGGCGTTTAACCAATTGCTTTAGAGGGATAGACACAATATTATAATCACCTT
TATCAGGCTAGCTAAATACT
Found at i:11174485 original size:99 final size:98
Alignment explanation
Indices: 11174314--11174519 Score: 306
Period size: 99 Copynumber: 2.1 Consensus size: 98
11174304 GGATAGAACA
*
11174314 ATATTATAATCACCTTTATCAGGCTAGCTAAATCTATCCATAAAGCCGGGGCGTTTAACCAATTA
1 ATATTATAATCACCTTTATCAGGCTAGCTAAATCTATCCATAAAGCCGGGGAGTTTAACCAATTA
* * * *
11174379 CTTTAGAGGGATAGCTCAAGCTTTATTATATAG
66 CTCTAGAGGAAGAACTCAAGCTTTATTATATAG
* *
11174412 ATATTATAATCACCTTTATCAGGCTAGTTGAATCTTATCCATAAAGCCGGGGAGTTTAACCAATT
1 ATATTATAATCACCTTTATCAGGCTAGCTAAATC-TATCCATAAAGCCGGGGAGTTTAACCAATT
* * *
11174477 GCTCTAGAGGAAGAACTCAAGCTTTATTGTATAT
65 ACTCTAGAGGAAGAACTCAAGCTTTATTATATAG
11174511 ATA-TATAAT
1 ATATTATAAT
11174520 ATTATAATCT
Statistics
Matches: 97, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
98 38 0.39
99 59 0.61
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Consensus pattern (98 bp):
ATATTATAATCACCTTTATCAGGCTAGCTAAATCTATCCATAAAGCCGGGGAGTTTAACCAATTA
CTCTAGAGGAAGAACTCAAGCTTTATTATATAG
Found at i:11178257 original size:17 final size:18
Alignment explanation
Indices: 11178221--11178257 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
11178211 AAAATATAAT
11178221 AATAATAATAATAAAATA
1 AATAATAATAATAAAATA
11178239 AATAA-AATAGAT-AAATA
1 AATAATAATA-ATAAAATA
11178256 AA
1 AA
11178258 GATAAAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (18 bp):
AATAATAATAATAAAATA
Found at i:11178302 original size:20 final size:21
Alignment explanation
Indices: 11178277--11178325 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
11178267 GAGTAAGAAG
11178277 AAAAATAATAAAA-ATAAA-GA
1 AAAAATAATAAAATA-AAACGA
11178297 AAAAATAATAAAATAAAACGA
1 AAAAATAATAAAATAAAACGA
11178318 AAAAATAA
1 AAAAATAA
11178326 AATAAAAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.14
Consensus pattern (21 bp):
AAAAATAATAAAATAAAACGA
Found at i:11179507 original size:9 final size:9
Alignment explanation
Indices: 11179467--11179519 Score: 61
Period size: 9 Copynumber: 5.7 Consensus size: 9
11179457 CCTGAACCAC
11179467 AAATAAAAT
1 AAATAAAAT
*
11179476 TAATAAAAT
1 AAATAAAAT
*
11179485 TAATAAAAT
1 AAATAAAAT
*
11179494 GAAATAATAT
1 -AAATAAAAT
11179504 AAATAAAAAT
1 AAAT-AAAAT
11179514 AAATAA
1 AAATAA
11179520 TATATATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
9 23 0.61
10 15 0.39
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (9 bp):
AAATAAAAT
Found at i:11179508 original size:19 final size:18
Alignment explanation
Indices: 11179467--11179523 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 18
11179457 CCTGAACCAC
* *
11179467 AAATAAAATTAATAAAAT
1 AAATAAAATAAATAATAT
*
11179485 TAATAAAATGAAATAATAT
1 AAATAAAAT-AAATAATAT
11179504 AAATAAAAATAAATAATAT
1 AAAT-AAAATAAATAATAT
11179523 A
1 A
11179524 TATATATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 8 0.24
19 20 0.61
20 5 0.15
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (18 bp):
AAATAAAATAAATAATAT
Found at i:11179556 original size:25 final size:24
Alignment explanation
Indices: 11179528--11179575 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
11179518 AATATATATA
*
11179528 TATATATTTTAAAATATTTTAAAAC
1 TATATATTAT-AAATATTTTAAAAC
*
11179553 TATATATTATATATATTTTAAAA
1 TATATATTATAAATATTTTAAAA
11179576 AATGTTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TATATATTATAAATATTTTAAAAC
Found at i:11179598 original size:37 final size:35
Alignment explanation
Indices: 11179519--11179910 Score: 385
Period size: 37 Copynumber: 10.6 Consensus size: 35
11179509 AAAATAAATA
*
11179519 ATATATATATATATATTTT-AAAATATTTT-AAAACT
1 ATATAT-TATATA-ATTTTAAAAATGTTTTCAAAACT
11179554 ATATATTATATATATTTTAAAAAATGTTTTCAAAACT
1 ATATATTATATA-ATTTT-AAAAATGTTTTCAAAACT
*
11179591 ATATATTATATAATTTTCAAATATGTTTT-AAAACT
1 ATATATTATATAATTTT-AAAAATGTTTTCAAAACT
* *
11179626 ATATATTATATATGTTTTCAAAAAATGTTTTTAAAACT
1 ATATATTATATA-ATTTT--AAAAATGTTTTCAAAACT
* *
11179664 ATATATTATATATGTTTTCAAAAATGTTTTCAAAATT
1 ATATATTATATA-ATTTT-AAAAATGTTTTCAAAACT
*
11179701 ATATATTATATAAGTTTTCAAAAATGATTTCAAAACT
1 ATATATTATATAA-TTTT-AAAAATGTTTTCAAAACT
* *
11179738 ATATATTATATAAGTTTTTCAAAATGATTTCAAAACT
1 ATATATTATATAA--TTTTAAAAATGTTTTCAAAACT
* * *
11179775 ATATATTATATAAGTTTTTAAAATGTTTTTAAAAATT
1 ATATATTATATAA-TTTTAAAAATG-TTTTCAAAACT
* ** *
11179812 ATATTATATATATATATATTTCAAAATAATTTCAAAATT
1 ATA-TAT-TATATA-AT-TTTAAAAATGTTTTCAAAACT
* *
11179851 ATATATTATATAAGTTTTTAAAATGTTTTAAAAACT
1 ATATATTATATAA-TTTTAAAAATGTTTTCAAAACT
*
11179887 ATATAATATATACATTTTCAAAAA
1 ATATATTATATA-ATTTT-AAAAA
11179911 ATCATTTTCT
Statistics
Matches: 311, Mismatches: 30, Indels: 30
0.84 0.08 0.08
Matches are distributed among these distances:
34 12 0.04
35 24 0.08
36 70 0.23
37 143 0.46
38 34 0.11
39 19 0.06
40 9 0.03
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (35 bp):
ATATATTATATAATTTTAAAAATGTTTTCAAAACT
Found at i:11179691 original size:74 final size:71
Alignment explanation
Indices: 11179519--11179909 Score: 448
Period size: 74 Copynumber: 5.3 Consensus size: 71
11179509 AAAATAAATA
*
11179519 ATATATATATATATATTTT-AAAATATTTTAAAACTATATATTATATATA-TTTTAAAAAATGTT
1 ATATAT-TATATATATTTTCAAAATGTTTTAAAACTATATATTATATA-AGTTTT-AAAAATGTT
11179582 TTCAAAACT
63 TTCAAAACT
*
11179591 ATATATTATATA-ATTTTCAAATATGTTTTAAAACTATATATTATATATGTTTTCAAAAAATGTT
1 ATATATTATATATATTTTCAAA-ATGTTTTAAAACTATATATTATATAAGTTTT--AAAAATGTT
*
11179655 TTTAAAACT
63 TTCAAAACT
* * *
11179664 ATATATTATATATGTTTTCAAAAATGTTTTCAAAATTATATATTATATAAGTTTTCAAAAATGAT
1 ATATATTATATATATTTTC-AAAATGTTTT-AAAACTATATATTATATAAGTTTT-AAAAATGTT
11179729 TTCAAAACT
63 TTCAAAACT
* *
11179738 ATATATTATATA-AGTTTTTCAAAATGATTTCAAAACTATATATTATATAAGTTTTTAAAATGTT
1 ATATATTATATATA--TTTTCAAAATG-TTTTAAAACTATATATTATATAAGTTTTAAAAATG-T
* *
11179802 TTTAAAAATT
62 TTTCAAAACT
* * * *
11179812 ATATTATATATATATATATTTCAAAATAATTTCAAAATTATATATTATATAAGTTTTTAAAATGT
1 ATA-TAT-TATATATAT-TTTCAAAAT-GTTTTAAAACTATATATTATATAAGTTTTAAAAATGT
*
11179877 TTTAAAAACT
62 TTTCAAAACT
* *
11179887 ATATAATATATACATTTTCAAAA
1 ATATATTATATATATTTTCAAAA
11179910 AATCATTTTC
Statistics
Matches: 282, Mismatches: 21, Indels: 32
0.84 0.06 0.10
Matches are distributed among these distances:
70 5 0.02
71 9 0.03
72 42 0.15
73 44 0.16
74 82 0.29
75 50 0.18
76 49 0.17
77 1 0.00
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (71 bp):
ATATATTATATATATTTTCAAAATGTTTTAAAACTATATATTATATAAGTTTTAAAAATGTTTTC
AAAACT
Found at i:11179926 original size:15 final size:14
Alignment explanation
Indices: 11179899--11179941 Score: 61
Period size: 13 Copynumber: 3.0 Consensus size: 14
11179889 ATAATATATA
11179899 CATTTTCAAAAAAT
1 CATTTTCAAAAAAT
11179913 CATTTTCTAAAAAAAT
1 CATTTTC--AAAAAAT
11179929 -ATTTTCAAAAAAT
1 CATTTTCAAAAAAT
11179942 ATACTATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 7 0.26
14 7 0.26
15 6 0.22
16 7 0.26
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (14 bp):
CATTTTCAAAAAAT
Found at i:11179927 original size:16 final size:14
Alignment explanation
Indices: 11179900--11179940 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
11179890 TAATATATAC
11179900 ATTTTC-AAAAAAT
1 ATTTTCAAAAAAAT
11179913 CATTTTCTAAAAAAAT
1 -ATTTTC-AAAAAAAT
11179929 ATTTTCAAAAAA
1 ATTTTCAAAAAA
11179941 TATACTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
16 7 0.28
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.37
Consensus pattern (14 bp):
ATTTTCAAAAAAAT
Found at i:11180664 original size:20 final size:20
Alignment explanation
Indices: 11180617--11180698 Score: 58
Period size: 20 Copynumber: 4.0 Consensus size: 20
11180607 AACGCGATTC
* *
11180617 TCCAAATTCACGATG-TGAAC
1 TCCAAATTCACGACGCT-AAT
*
11180637 TCCCAATTCACGACGCTAAT
1 TCCAAATTCACGACGCTAAT
* * * *
11180657 TCCAAATTCGCAACGCGATT
1 TCCAAATTCACGACGCTAAT
* *
11180677 CTCCAAATTTATGACGCTAAT
1 -TCCAAATTCACGACGCTAAT
11180698 T
1 T
11180699 TATATTTTAA
Statistics
Matches: 46, Mismatches: 14, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
20 31 0.67
21 15 0.33
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.28
Consensus pattern (20 bp):
TCCAAATTCACGACGCTAAT
Found at i:11180920 original size:20 final size:20
Alignment explanation
Indices: 11180897--11180964 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
11180887 AATCAAGTGT
11180897 CGAATTTAGAGTCTGCGTTG
1 CGAATTTAGAGTCTGCGTTG
* ** *
11180917 CGAATTTGGAAACTGTGTTG
1 CGAATTTAGAGTCTGCGTTG
* * *
11180937 TGAAATTGGAGT-TCGCGTTG
1 CGAATTTAGAGTCT-GCGTTG
11180957 CGAATTTA
1 CGAATTTA
11180965 TTGGTTATTT
Statistics
Matches: 35, Mismatches: 12, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
19 1 0.03
20 34 0.97
ACGTcount: A:0.24, C:0.12, G:0.29, T:0.35
Consensus pattern (20 bp):
CGAATTTAGAGTCTGCGTTG
Found at i:11189190 original size:105 final size:105
Alignment explanation
Indices: 11188856--11189416 Score: 966
Period size: 105 Copynumber: 5.3 Consensus size: 105
11188846 TGTTTCGTGG
* * *** * *
11188856 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAACCGGGAAAT-TACTTGTTGGCAACCA
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGT--TTGTTGACAACCA
*
11188920 GCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGT
64 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
11188962 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAA-TGTTTGTTGACAACCAG
11189027 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
65 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
11189068 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTAGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGC
11189133 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
11189173 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTCGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGC
*
11189238 GGTCCCTTCGTCGCGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
11189278 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGC
11189343 GGTCCCTTCGTCGTGAAGTTGAACTT--GTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
11189381 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
11189417 GGTAAAACCT
Statistics
Matches: 440, Mismatches: 13, Indels: 7
0.96 0.03 0.02
Matches are distributed among these distances:
103 48 0.11
105 249 0.57
106 141 0.32
107 1 0.00
108 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.33
Consensus pattern (105 bp):
CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGC
GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
Found at i:11189640 original size:1 final size:1
Alignment explanation
Indices: 11189634--11189664 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
11189624 ACATTCTGGG
11189634 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
11189665 GGAGATGCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:11190235 original size:1 final size:1
Alignment explanation
Indices: 11190229--11190253 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
11190219 CACCCAAACG
11190229 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
11190254 CAACTTAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:11201992 original size:12 final size:11
Alignment explanation
Indices: 11201970--11202016 Score: 53
Period size: 12 Copynumber: 4.4 Consensus size: 11
11201960 GGGCCCTGTA
*
11201970 ATAAATATAAT
1 ATAATTATAAT
11201981 ATAATTTATAAT
1 ATAA-TTATAAT
*
11201993 ATAAATAT-AT
1 ATAATTATAAT
11202003 AT-ATTATAAT
1 ATAATTATAAT
11202013 ATAA
1 ATAA
11202017 GGACGAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
9 4 0.13
10 8 0.27
11 8 0.27
12 10 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
ATAATTATAAT
Found at i:11202009 original size:20 final size:23
Alignment explanation
Indices: 11201970--11202016 Score: 73
Period size: 20 Copynumber: 2.2 Consensus size: 23
11201960 GGGCCCTGTA
11201970 ATAAATATAATATAATTTATAAT
1 ATAAATATAATATAATTTATAAT
11201993 ATAAATAT-ATAT-A-TTATAAT
1 ATAAATATAATATAATTTATAAT
11202013 ATAA
1 ATAA
11202017 GGACGAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.46
21 1 0.04
22 4 0.17
23 8 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
ATAAATATAATATAATTTATAAT
Found at i:11204352 original size:26 final size:26
Alignment explanation
Indices: 11204317--11204369 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
11204307 TGACCCAAAG
*
11204317 TACCTCCAAGC-CTTGAAATGACTAAA
1 TACCTCCAAGCTC-TGAAATGAATAAA
*
11204343 TACCTTCAAGCTCTGAAATGAATAAA
1 TACCTCCAAGCTCTGAAATGAATAAA
11204369 T
1 T
11204370 CAACTAGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (26 bp):
TACCTCCAAGCTCTGAAATGAATAAA
Found at i:11206069 original size:2 final size:2
Alignment explanation
Indices: 11206062--11206091 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11206052 GACATGTGTC
11206062 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
11206092 TTAAAATTTT
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
Found at i:11206163 original size:15 final size:16
Alignment explanation
Indices: 11206139--11206171 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11206129 GGTCGTTTGG
11206139 TTCTAG-AAAAATATT
1 TTCTAGAAAAAATATT
*
11206154 TTCTATAAAAAATATT
1 TTCTAGAAAAAATATT
11206170 TT
1 TT
11206172 ATGTTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (16 bp):
TTCTAGAAAAAATATT
Found at i:11223698 original size:32 final size:32
Alignment explanation
Indices: 11223662--11223729 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
11223652 ACTCTCAGTA
*
11223662 AAGAGACATATGTTAAACAAGAAAGGAATTGG
1 AAGAGACATATGTTAAACAAGAAAGGAAATGG
*
11223694 AAGAGACATATGTTAAACAAGAAATGAAATGG
1 AAGAGACATATGTTAAACAAGAAAGGAAATGG
11223726 AAGA
1 AAGA
11223730 AACAACAGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.53, C:0.06, G:0.24, T:0.18
Consensus pattern (32 bp):
AAGAGACATATGTTAAACAAGAAAGGAAATGG
Found at i:11225217 original size:19 final size:19
Alignment explanation
Indices: 11225195--11225236 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
11225185 TAGAGTATAG
11225195 ATCAGACATCATAATAGAA
1 ATCAGACATCATAATAGAA
* *
11225214 ATCAGAGATCATAATAGAT
1 ATCAGACATCATAATAGAA
11225233 ATCA
1 ATCA
11225237 CAGTTCATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.50, C:0.14, G:0.12, T:0.24
Consensus pattern (19 bp):
ATCAGACATCATAATAGAA
Found at i:11225244 original size:19 final size:19
Alignment explanation
Indices: 11225202--11225255 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
11225192 TAGATCAGAC
*
11225202 ATCATAATAGAAATCAGAG
1 ATCATAATAGAAATCACAG
*
11225221 ATCATAATAGATATCACAG
1 ATCATAATAGAAATCACAG
* * *
11225240 TTCATGACAGAAATCA
1 ATCATAATAGAAATCA
11225256 GAGGTCAGAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.48, C:0.15, G:0.13, T:0.24
Consensus pattern (19 bp):
ATCATAATAGAAATCACAG
Found at i:11226906 original size:14 final size:14
Alignment explanation
Indices: 11226889--11226922 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
11226879 AGTCAACGAT
11226889 TTGACTCA-AACGGG
1 TTGACTCAGAA-GGG
11226903 TTGACTCAGAAGGG
1 TTGACTCAGAAGGG
11226917 TTGACT
1 TTGACT
11226923 TGGCTCAGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.89
15 2 0.11
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.26
Consensus pattern (14 bp):
TTGACTCAGAAGGG
Found at i:11227800 original size:2 final size:2
Alignment explanation
Indices: 11227795--11227823 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11227785 AAGGAAATGC
11227795 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11227824 AGATCATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11232299 original size:2 final size:2
Alignment explanation
Indices: 11232287--11232315 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
11232277 TAAAGTCGAA
11232287 AT AT A- 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
11232316 TATTAAGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11244505 original size:2 final size:2
Alignment explanation
Indices: 11244498--11244528 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11244488 GTAATATAAT
11244498 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
11244529 TCCAACTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:11246975 original size:2 final size:2
Alignment explanation
Indices: 11246968--11247012 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
11246958 TCACTCTCCC
11246968 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11247010 TA T
1 TA T
11247013 GTCATCACAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11250784 original size:314 final size:314
Alignment explanation
Indices: 11250015--11251267 Score: 2303
Period size: 314 Copynumber: 4.0 Consensus size: 314
11250005 ATGGATTAAT
* * * *
11250015 TAATGTCAGAATGTCCTATGGACA-CCGACATTAACAGGTTACTTTATACCATCCGTATT-C---
1 TAATGTCAGAATGTCCTAAGGACATCGGA-ATTCACAGGTTACTTTATACCATCCATATTCCATA
*
11250075 -CACCACTATTAAAAGAAGTGAATGCCATTCATCACATTGCAATCCCCGACTTGAATATATTAGC
65 ACACCACTACTAAAAGAAGTGAATGCCATTCATCACATTGCAATCCCCGACTTGAATATATTAGC
11250139 ATGGAACTTCAAAACCTTTTAAATTTCAGCATATTCTGATACTTCAGTCCAATGCATATAGTTAA
130 ATGGAACTTCAAAACCTTTTAAATTTCAGCATATTCTGATACTTCAGTCCAATGCATATAGTTAA
11250204 TTCAGATAAAACGATGTATCAGTCATACAAAAGAACCTCATGCTCCGGAGAGAATCAAGTTGGCA
195 TTCAGATAAAACGATGTATCAGTCATACAAAAGAACCTCATGCTCCGGAGAGAATCAAGTTGGCA
11250269 ATTAAGCAAATTGTAGTAGAGTGATGTACAATAACCCTGGTATATAAGCTACAAG
260 ATTAAGCAAATTGTAGTAGAGTGATGTACAATAACCCTGGTATATAAGCTACAAG
11250324 TAATGTCAGAATGTCCTAAGGACATCGGAATTCACAGGTTACTTTATACCATCCATATTCCATAA
1 TAATGTCAGAATGTCCTAAGGACATCGGAATTCACAGGTTACTTTATACCATCCATATTCCAT-A
11250389 ACACCACTACTAAAAGAAGTGAATGCCATTCATCACATTGCAATCCCCGACTTGAATATATTAGC
65 ACACCACTACTAAAAGAAGTGAATGCCATTCATCACATTGCAATCCCCGACTTGAATATATTAGC
11250454 ATGGAACTTC-AAACCTTTTAAATTTCAGCATATTCTGATACTTCAGTCCAATGCATATAGTTAA
130 ATGGAACTTCAAAACCTTTTAAATTTCAGCATATTCTGATACTTCAGTCCAATGCATATAGTTAA
*
11250518 TTCAGATAAAACGATGTATCAGTTTATAC-AAAGAACCTCATGCTCC-GAGAGAATCAAGTTGGC
195 TTCAGATAAAACGATGTATCAG-TCATACAAAAGAACCTCATGCTCCGGAGAGAATCAAGTTGGC
11250581 AATTAAGCAAATTGTAGTAGAGTGATGTACAATAACCCTGGTATATAAGCTACAAG
259 AATTAAGCAAATTGTAGTAGAGTGATGTACAATAACCCTGGTATATAAGCTACAAG
11250637 TAATGTCAGAATGTCCTAAGGACATCGGAATTCACAGGTTACTTTATACCATCCATATTCCATAA
1 TAATGTCAGAATGTCCTAAGGACATCGGAATTCACAGGTTACTTTATACCATCCATATTCCAT-A
11250702 ACACCACTACTAAAAGAAGTGAATGCCATTCATCACATTGCAATCCCCGACTTGAATATATTAGC
65 ACACCACTACTAAAAGAAGTGAATGCCATTCATCACATTGCAATCCCCGACTTGAATATATTAGC
11250767 ATGGAACTTCAAAACCTTTTAAATTTCAGCATATTCTGATACTTCAGTCCAATGCATATAGTTAA
130 ATGGAACTTCAAAACCTTTTAAATTTCAGCATATTCTGATACTTCAGTCCAATGCATATAGTTAA
*
11250832 TTCAGATAAAACGATGTATCAGTTATACAAAAGAACCTCATGCTCCGGAGAGAATCAAGTTGGCA
195 TTCAGATAAAACGATGTATCAGTCATACAAAAGAACCTCATGCTCCGGAGAGAATCAAGTTGGCA
11250897 ATTAAGCAAATTGTAGTAGAGTGATGTACAATAACCCTGGTATATAAGCTACAAG
260 ATTAAGCAAATTGTAGTAGAGTGATGTACAATAACCCTGGTATATAAGCTACAAG
11250952 TAATGTCAGAATGTCCTAAGGACATCGGAATTCACAGGTTACTTTATACCATCCATATTCCATAA
1 TAATGTCAGAATGTCCTAAGGACATCGGAATTCACAGGTTACTTTATACCATCCATATTCCATAA
11251017 CACCACTACTAAAAGAAGTGAATGCCATTCATCACATTGCAATCCCCGACTTGAATATATTAGCA
66 CACCACTACTAAAAGAAGTGAATGCCATTCATCACATTGCAATCCCCGACTTGAATATATTAGCA
* *
11251082 TGGAACTTCAAAACCTTTTAAATTGCAGCATATTCTGATACTTCAGTCCAATGCATATAATTAAT
131 TGGAACTTCAAAACCTTTTAAATTTCAGCATATTCTGATACTTCAGTCCAATGCATATAGTTAAT
11251147 TCAGATAAAACGATGTATCAGTCATACAAAAGAACCTCATGCTCCGGAGAGAATCAAGTTGGCAA
196 TCAGATAAAACGATGTATCAGTCATACAAAAGAACCTCATGCTCCGGAGAGAATCAAGTTGGCAA
11251212 TTAAGCAAATTGTAGTAGAGTGATGT--AATAACCCTGGGTATATAAGCTACAAG
261 TTAAGCAAATTGTAGTAGAGTGATGTACAATAACCCT-GGTATATAAGCTACAAG
11251265 TAA
1 TAA
11251268 ATAAATATAC
Statistics
Matches: 923, Mismatches: 9, Indels: 20
0.97 0.01 0.02
Matches are distributed among these distances:
309 51 0.06
310 4 0.00
312 9 0.01
313 239 0.26
314 406 0.44
315 214 0.23
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (314 bp):
TAATGTCAGAATGTCCTAAGGACATCGGAATTCACAGGTTACTTTATACCATCCATATTCCATAA
CACCACTACTAAAAGAAGTGAATGCCATTCATCACATTGCAATCCCCGACTTGAATATATTAGCA
TGGAACTTCAAAACCTTTTAAATTTCAGCATATTCTGATACTTCAGTCCAATGCATATAGTTAAT
TCAGATAAAACGATGTATCAGTCATACAAAAGAACCTCATGCTCCGGAGAGAATCAAGTTGGCAA
TTAAGCAAATTGTAGTAGAGTGATGTACAATAACCCTGGTATATAAGCTACAAG
Found at i:11253095 original size:21 final size:20
Alignment explanation
Indices: 11253064--11253102 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
11253054 TTGTCAAAAA
11253064 ATAAAAATAAAAGAATAACT
1 ATAAAAATAAAAGAATAACT
*
11253084 ATAAAAACTAAAATAATAA
1 ATAAAAA-TAAAAGAATAA
11253103 TTTGAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.21
Consensus pattern (20 bp):
ATAAAAATAAAAGAATAACT
Found at i:11260484 original size:30 final size:30
Alignment explanation
Indices: 11260406--11260491 Score: 93
Period size: 32 Copynumber: 2.8 Consensus size: 30
11260396 AACTTTACAA
* *
11260406 AATAGTTAATAAA-TTTATCAAACTGTTAC
1 AATAGTCATTAAATTTTATCAAACTGTTAC
* * *
11260435 AAAATGATCGTTGAATTTTATCAAACTGTTAC
1 AATA-G-TCATTAAATTTTATCAAACTGTTAC
*
11260467 AATAGTCATTAAATTTTATCGAACT
1 AATAGTCATTAAATTTTATCAAACT
11260492 TTTATATTGT
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
29 3 0.07
30 18 0.40
31 5 0.11
32 19 0.42
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (30 bp):
AATAGTCATTAAATTTTATCAAACTGTTAC
Found at i:11261922 original size:20 final size:20
Alignment explanation
Indices: 11261893--11261933 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
11261883 CCCGCTTGGA
11261893 TGTTAAGACCAAATCTAGGC
1 TGTTAAGACCAAATCTAGGC
*
11261913 TGTTATGACCAAATCTAGGC
1 TGTTAAGACCAAATCTAGGC
11261933 T
1 T
11261934 ATTACATATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (20 bp):
TGTTAAGACCAAATCTAGGC
Found at i:11269783 original size:31 final size:28
Alignment explanation
Indices: 11269718--11269791 Score: 78
Period size: 31 Copynumber: 2.5 Consensus size: 28
11269708 ACGAATTACA
*
11269718 TAACTTTTTAAAATTATACTTTGATCCT
1 TAACTTTTTAAAATTATACTTTGATACT
* *
11269746 TAAACTTTTCTAAAGTTTATACTTTGGCTACT
1 T-AACTTTT-TAAA-ATTATACTTT-GATACT
11269778 TAAC-TTTTAAAATT
1 TAACTTTTTAAAATT
11269792 TACATTTTGG
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
28 3 0.08
29 11 0.29
30 7 0.18
31 12 0.32
32 5 0.13
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.49
Consensus pattern (28 bp):
TAACTTTTTAAAATTATACTTTGATACT
Found at i:11285214 original size:24 final size:24
Alignment explanation
Indices: 11285187--11285264 Score: 122
Period size: 24 Copynumber: 3.2 Consensus size: 24
11285177 TAGTACCGTG
11285187 TAGAATTGCACATATAA-TGTCACA
1 TAGAATTGCACATA-AAGTGTCACA
11285211 TAGAATTGCACATAAAGTGTCACA
1 TAGAATTGCACATAAAGTGTCACA
* *
11285235 TGGAATTGCACATAAAGTGTCGCA
1 TAGAATTGCACATAAAGTGTCACA
11285259 TAGAAT
1 TAGAAT
11285265 GTACACGAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
23 2 0.04
24 48 0.96
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (24 bp):
TAGAATTGCACATAAAGTGTCACA
Found at i:11289797 original size:60 final size:60
Alignment explanation
Indices: 11289673--11289785 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
11289663 AATATAATAA
* * * * *
11289673 ATAGTCAGGTGACCATTTTGTAACTTTTAATAGTCAAGGGACTCAACAAAGTAACTCTTT
1 ATAGTCAGGGGACCATTTTATAACTTTTAATAATCAAGGGACTCAACAAAATAACTCTCT
* *
11289733 ATAGTCAGGGGACTATTTTATAACTTTTAATAATC-GGGGCACTCAACAAAATA
1 ATAGTCAGGGGACCATTTTATAACTTTTAATAATCAAGGG-ACTCAACAAAATA
11289786 GTATCCTATA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 3 0.07
60 43 0.93
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (60 bp):
ATAGTCAGGGGACCATTTTATAACTTTTAATAATCAAGGGACTCAACAAAATAACTCTCT
Found at i:11290882 original size:60 final size:60
Alignment explanation
Indices: 11290811--11290940 Score: 179
Period size: 60 Copynumber: 2.2 Consensus size: 60
11290801 ACCTTAATTT
* * * * * * *
11290811 TAAATTGGTCTTTAAACTTTTGAATATTTTAATTTTATCCCTAAACTATTACTCTCCTTC
1 TAAATTAGTCTTTAAACTTTTGAACATTCTAATTTCATACCTAAACTATGACCCTCCTTC
* *
11290871 TAAATTAGTCTTTAAACTTTTGAACATTCTAATTTCATACCTAAACTATGGCCCTCTTTC
1 TAAATTAGTCTTTAAACTTTTGAACATTCTAATTTCATACCTAAACTATGACCCTCCTTC
11290931 TAAATTAGTC
1 TAAATTAGTC
11290941 CCCAAGCTTC
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.30, C:0.19, G:0.06, T:0.45
Consensus pattern (60 bp):
TAAATTAGTCTTTAAACTTTTGAACATTCTAATTTCATACCTAAACTATGACCCTCCTTC
Found at i:11290965 original size:60 final size:60
Alignment explanation
Indices: 11290824--11290968 Score: 155
Period size: 60 Copynumber: 2.4 Consensus size: 60
11290814 ATTGGTCTTT
* * * * * * ***
11290824 AAACTTTTGAATATTTTAATTTTATCCCTAAACTATTACTCTCCTTCTAAATTAGTCTTT
1 AAACTTCTGAATATTCTAATTTCATACCTAAACTATGACCCTCCTTCTAAATTAGTCCCC
* * * *
11290884 AAACTTTTGAACATTCTAATTTCATACCTAAACTATGGCCCTCTTTCTAAATTAGTCCCC
1 AAACTTCTGAATATTCTAATTTCATACCTAAACTATGACCCTCCTTCTAAATTAGTCCCC
* *
11290944 AAGCTTCTGAATATTCCAATTTCAT
1 AAACTTCTGAATATTCTAATTTCAT
11290969 CCTCCAAATC
Statistics
Matches: 70, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 70 1.00
ACGTcount: A:0.30, C:0.22, G:0.06, T:0.42
Consensus pattern (60 bp):
AAACTTCTGAATATTCTAATTTCATACCTAAACTATGACCCTCCTTCTAAATTAGTCCCC
Found at i:11291966 original size:60 final size:59
Alignment explanation
Indices: 11291835--11291987 Score: 182
Period size: 60 Copynumber: 2.6 Consensus size: 59
11291825 GCATCATATG
* * * * * *
11291835 TCCTCAAACTATGACACTCATTCTAAATTAGTCTTTATATTTTTAATATTCTAATTTAA
1 TCCTTAAACTATGACACTCATTTTAAATTAGTCCTTACATTTTGAACATTCTAATTTAA
* *
11291894 T-CTTCAAACTATGATACTCATTTTAAATTAGTCCTTACACTTTTGAACATTCTAATTTTA
1 TCCTT-AAACTATGACACTCATTTTAAATTAGTCCTTACA-TTTTGAACATTCTAATTTAA
* * *
11291954 TCCTTAAACTATGACCCTTATTTTAAATTGGTCC
1 TCCTTAAACTATGACACTCATTTTAAATTAGTCC
11291988 CCAAACTTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
58 2 0.03
59 31 0.39
60 43 0.54
61 3 0.04
ACGTcount: A:0.31, C:0.19, G:0.05, T:0.44
Consensus pattern (59 bp):
TCCTTAAACTATGACACTCATTTTAAATTAGTCCTTACATTTTGAACATTCTAATTTAA
Found at i:11292174 original size:29 final size:29
Alignment explanation
Indices: 11292141--11292235 Score: 75
Period size: 31 Copynumber: 3.2 Consensus size: 29
11292131 ATATACATAT
11292141 AGTTTGGGATGAAATTAAAATGTTGAAAA
1 AGTTTGGGATGAAATTAAAATGTTGAAAA
** * * ** * *
11292170 AGTTTGGGGACCAATTTAGAATGAAGGATAT
1 AGTTT-GGGATGAAATTAAAATG-TTGAAAA
*
11292201 AGTTTGGAGATGAAACTAAAATGTT-AAAA
1 AGTTTGG-GATGAAATTAAAATGTTGAAAA
11292230 AGTTTG
1 AGTTTG
11292236 AGGACAAATT
Statistics
Matches: 46, Mismatches: 17, Indels: 6
0.67 0.25 0.09
Matches are distributed among these distances:
29 13 0.28
30 15 0.33
31 18 0.39
ACGTcount: A:0.41, C:0.03, G:0.25, T:0.31
Consensus pattern (29 bp):
AGTTTGGGATGAAATTAAAATGTTGAAAA
Found at i:11292265 original size:60 final size:60
Alignment explanation
Indices: 11292137--11292251 Score: 187
Period size: 60 Copynumber: 1.9 Consensus size: 60
11292127 TAGTATATAC
* * *
11292137 ATATAGTTTGGGATGAAATTAAAATGTTGAAAAAGTTTGGGGACCAATTTAGAATGAAGG
1 ATATAGTTTGGGATGAAACTAAAATGTTGAAAAAGTTTGAGGACAAATTTAGAATGAAGG
11292197 ATATAGTTTGGAGATGAAACTAAAATGTT-AAAAAGTTTGAGGACAAATTTAGAAT
1 ATATAGTTTGG-GATGAAACTAAAATGTTGAAAAAGTTTGAGGACAAATTTAGAAT
11292252 AGTAGTCATA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
60 35 0.69
61 16 0.31
ACGTcount: A:0.43, C:0.03, G:0.23, T:0.30
Consensus pattern (60 bp):
ATATAGTTTGGGATGAAACTAAAATGTTGAAAAAGTTTGAGGACAAATTTAGAATGAAGG
Found at i:11292273 original size:60 final size:58
Alignment explanation
Indices: 11292137--11292309 Score: 183
Period size: 60 Copynumber: 2.9 Consensus size: 58
11292127 TAGTATATAC
*
11292137 ATATAGTTTGGGATGAAATTAAAATGTTGAAAAAGTTTGGGGACCAATTTAGAATGAAGG
1 ATATAGTTTGGGATGAAATTAAAATGTT-AAAAAGTTTGAGGA-CAATTTAGAATGAAGG
* *
11292197 ATATAGTTTGGAGATGAAACTAAAATGTTAAAAAGTTTGAGGACAAATTTAGAAT--AGT
1 ATATAGTTTGG-GATGAAATTAAAATGTTAAAAAGTTTGAGGAC-AATTTAGAATGAAGG
* * *
11292255 AGTCATAGTTTAAGGATGAAATTTAAAA-ATTAAAAA-TTTAAGGATCAATTTAGAA
1 A-T-ATAGTTT-GGGATGAAA-TTAAAATGTTAAAAAGTTTGAGGA-CAATTTAGAA
11292310 AAAAATCATA
Statistics
Matches: 99, Mismatches: 7, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
58 3 0.03
59 18 0.18
60 56 0.57
61 22 0.22
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.31
Consensus pattern (58 bp):
ATATAGTTTGGGATGAAATTAAAATGTTAAAAAGTTTGAGGACAATTTAGAATGAAGG
Found at i:11294310 original size:2 final size:2
Alignment explanation
Indices: 11294303--11294353 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
11294293 AGGTATACCC
11294303 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11294345 TA TA TA TA T
1 TA TA TA TA T
11294354 TCAATGTTCC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11295274 original size:2 final size:2
Alignment explanation
Indices: 11295267--11295291 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11295257 TGAGAAGATA
11295267 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
11295292 CTTACAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11295904 original size:19 final size:19
Alignment explanation
Indices: 11295865--11295906 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
11295855 GCTCGACATG
* *
11295865 ACTTGACTCGAATTTATAA
1 ACTTGACTCGAATTGAAAA
*
11295884 ACTTGACTCGACTTGAAAA
1 ACTTGACTCGAATTGAAAA
11295903 ACTT
1 ACTT
11295907 TCAAGTCAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (19 bp):
ACTTGACTCGAATTGAAAA
Found at i:11300291 original size:117 final size:118
Alignment explanation
Indices: 11300137--11300442 Score: 488
Period size: 117 Copynumber: 2.6 Consensus size: 118
11300127 AGTGTTGATG
* * *
11300137 TTGATCCAACTCCTTATGTGATGGAATCAAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTT
1 TTGATCCAACTCCTTTTGTGATAGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTT
*
11300202 CTTCTCCCTTATCGGTTGAGTTCTTCTCATTATGAACTC-TCCATTAGAAATA
66 CTTCTCCCTTATCGGGTGAGTTCTTCTCATTATGAACTCTTCCATTAGAAATA
* * *
11300254 TTGATCCATCTCCTTTTGTAATAGAATCGAGCTAAGGTTGAATAAGTTCTTCTCATTATGAACTT
1 TTGATCCAACTCCTTTTGTGATAGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTT
* * *
11300319 TTTCTCCTTTATCGGGTGAGTTCTTCTCATTATGAACTCTTCCATTGGAAATA
66 CTTCTCCCTTATCGGGTGAGTTCTTCTCATTATGAACTCTTCCATTAGAAATA
* * *
11300372 TTGATCCACCTCCTTTTGTGATAGAATCGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTT
1 TTGATCCAACTCCTTTTGTGATAGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTT
11300437 CTTCTC
66 CTTCTC
11300443 ATTATGAACT
Statistics
Matches: 172, Mismatches: 16, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
117 95 0.55
118 77 0.45
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (118 bp):
TTGATCCAACTCCTTTTGTGATAGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTT
CTTCTCCCTTATCGGGTGAGTTCTTCTCATTATGAACTCTTCCATTAGAAATA
Found at i:11300451 original size:96 final size:96
Alignment explanation
Indices: 11300339--11300538 Score: 287
Period size: 96 Copynumber: 2.1 Consensus size: 96
11300329 ATCGGGTGAG
* *
11300339 TTCTTCTCATTATGAACTCT-TCCATTGGAAATATTGATCCACCTCCTTTTGTGATAGAATC-GA
1 TTCTTCTCATTATGAACTCTCT-CATTGGAAATATTGATCCACCTCATTCTGTGATAGAATCAG-
*
11300402 ACCAAGGTTGAACAAGTTCTTCTCATTATGAAC
64 ACCAAGGTTGAACAAGTTATTCTCATTATGAAC
* * *
11300435 TTCTTCTCATTATGAACTCTCTCATTGGAAATGTTGATCCACCTCATTCTGTGATGGAATCAGGC
1 TTCTTCTCATTATGAACTCTCTCATTGGAAATATTGATCCACCTCATTCTGTGATAGAATCAGAC
* *
11300500 TAAGGTTGAATAAGTTATTCTCATTATGAAC
66 CAAGGTTGAACAAGTTATTCTCATTATGAAC
*
11300531 TTTTTCTC
1 TTCTTCTC
11300539 CCTCATCGGA
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
96 91 0.98
97 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (96 bp):
TTCTTCTCATTATGAACTCTCTCATTGGAAATATTGATCCACCTCATTCTGTGATAGAATCAGAC
CAAGGTTGAACAAGTTATTCTCATTATGAAC
Found at i:11300459 original size:15 final size:17
Alignment explanation
Indices: 11300418--11300460 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
11300408 GTTGAACAAG
11300418 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
11300435 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
11300452 -TC-TCTCATT
1 TTCTTCTCATT
11300461 GGAAATGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.27
16 2 0.08
17 17 0.65
ACGTcount: A:0.21, C:0.26, G:0.05, T:0.49
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:11300808 original size:119 final size:119
Alignment explanation
Indices: 11300663--11300986 Score: 384
Period size: 119 Copynumber: 2.7 Consensus size: 119
11300653 AATTTAAACA
* *
11300663 AAAAGGTCGAACAATTTCTTCTCATTATGAACTTATTCTTCCTCCTCGGACGAGTTCTTCTCATT
1 AAAAGGTCGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTCCTCGGATGAGTTCTTCTCATT
* * * **
11300728 ATGAGCCATTCCATTGGAAATGA-CGATCCACCTCCTTCTGTGATGGATTTGAG
66 ATGAACCATTCCATTGGAAATGATCGACCCACCTCCTTCTGTGATGGAATCAAG
* * * * * *
11300781 TAAAAGGTCGAACACGGTCTTCGCATTATGAACTTCTTCTTCCTTCTTGGATGAGTTCTTCTCAT
1 -AAAAGGTCGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTCCTCGGATGAGTTCTTCTCAT
* * * * * *
11300846 TATGAACTC-TTTCTTTGTAAGT-ATTGACCCACCTCCTTTTGTGATGGAATCAAG
65 TATGAAC-CATTCCATTGGAAATGATCGACCCACCTCCTTCTGTGATGGAATCAAG
* * * * *
11300900 CAAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCATCGGATGAGTTCTTCTCATT
1 AAAAGGTCGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTCCTCGGATGAGTTCTTCTCATT
*
11300965 ATGAACCATTCCAATGGAAATG
66 ATGAACCATTCCATTGGAAATG
11300987 TTGACTGGTT
Statistics
Matches: 167, Mismatches: 34, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
117 1 0.01
118 70 0.42
119 95 0.57
120 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (119 bp):
AAAAGGTCGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTCCTCGGATGAGTTCTTCTCATT
ATGAACCATTCCATTGGAAATGATCGACCCACCTCCTTCTGTGATGGAATCAAG
Found at i:11303525 original size:9 final size:9
Alignment explanation
Indices: 11303500--11303543 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
11303490 CTTCTTTCAA
*
11303500 TTTTCTTCC
1 TTTTTTTCC
11303509 TCTTTTTTCC
1 T-TTTTTTCC
*
11303519 TTTTTTTTC
1 TTTTTTTCC
*
11303528 TTTTTTTTC
1 TTTTTTTCC
11303537 TTTTTTT
1 TTTTTTT
11303544 TTTTCTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
9 24 0.75
10 8 0.25
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTTCC
Found at i:11303534 original size:18 final size:18
Alignment explanation
Indices: 11303511--11303608 Score: 69
Period size: 18 Copynumber: 5.5 Consensus size: 18
11303501 TTTCTTCCTC
*
11303511 TTTTTTCCTTTTTTTTCT
1 TTTTTTCCTTTTTTTTAT
*
11303529 TTTTTTTCTTTTTTTT-T
1 TTTTTTCCTTTTTTTTAT
*
11303546 TTCTTATT-CTTTTTTATAT
1 TT-TT-TTCCTTTTTTTTAT
* *
11303565 ATTTTTT-CTTTTATTCA-
1 -TTTTTTCCTTTTTTTTAT
* * *
11303582 TTTTTTCATTTTTCTTAA
1 TTTTTTCCTTTTTTTTAT
11303600 TTTTTTCCT
1 TTTTTTCCT
11303609 CTTTAGGTGT
Statistics
Matches: 64, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
16 6 0.09
17 9 0.14
18 42 0.66
19 5 0.08
20 2 0.03
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTTCCTTTTTTTTAT
Found at i:11303544 original size:9 final size:9
Alignment explanation
Indices: 11303511--11303576 Score: 71
Period size: 9 Copynumber: 7.3 Consensus size: 9
11303501 TTTCTTCCTC
*
11303511 TTTTTTCCT
1 TTTTTTTCT
11303520 TTTTTTTCT
1 TTTTTTTCT
11303529 TTTTTTTCT
1 TTTTTTTCT
11303538 TTTTTTT-T
1 TTTTTTTCT
*
11303546 TTCTTATTCT
1 TT-TTTTTCT
* *
11303556 TTTTTATAT
1 TTTTTTTCT
*
11303565 ATTTTTTCT
1 TTTTTTTCT
11303574 TTT
1 TTT
11303577 ATTCATTTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
8 3 0.07
9 40 0.87
10 3 0.07
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:11303569 original size:27 final size:26
Alignment explanation
Indices: 11303511--11303587 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 26
11303501 TTTCTTCCTC
* * * *
11303511 TTTTTTCCTTTTTTTTCTTTTTTTTCTT
1 TTTTTT-C-TTTTATTCTTTTTTATATA
*
11303539 TTTTTTTTTCTTATTCTTTTTTATATA
1 TTTTTTCTT-TTATTCTTTTTTATATA
11303566 TTTTTTCTTTTATTCATTTTTT
1 TTTTTTCTTTTATTC-TTTTTT
11303588 CATTTTTCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
26 8 0.20
27 27 0.66
28 6 0.15
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (26 bp):
TTTTTTCTTTTATTCTTTTTTATATA
Found at i:11324371 original size:42 final size:42
Alignment explanation
Indices: 11324308--11324389 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
11324298 TTCTGTGCAC
11324308 TTAGTACCGATAATGTACATCCAGCACCAATACTGTTCTTTG
1 TTAGTACCGATAATGTACATCCAGCACCAATACTGTTCTTTG
* * * * * *
11324350 TTAGTATCGATATTGTTCATCCAGTACCGATAGTGTTCTT
1 TTAGTACCGATAATGTACATCCAGCACCAATACTGTTCTT
11324390 GCAACCTCGG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.38
Consensus pattern (42 bp):
TTAGTACCGATAATGTACATCCAGCACCAATACTGTTCTTTG
Found at i:11327049 original size:18 final size:18
Alignment explanation
Indices: 11327026--11327072 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
11327016 ATGCTAAAAT
11327026 GGTATCGATACCATATAC
1 GGTATCGATACCATATAC
11327044 GGTATCGATACCATATAC
1 GGTATCGATACCATATAC
* *
11327062 GATATCAATAC
1 GGTATCGATAC
11327073 TACTTATTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (18 bp):
GGTATCGATACCATATAC
Found at i:11330554 original size:13 final size:12
Alignment explanation
Indices: 11330532--11330588 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
11330522 CTAGGGTTTT
*
11330532 GGTTTTGGTCCTG
1 GGTTTGGGT-CTG
*
11330545 GGTTTGGGTCTT
1 GGTTTGGGTCTG
*
11330557 GTTTTGGGTCTG
1 GGTTTGGGTCTG
* * *
11330569 GGTTTCGGTTTC
1 GGTTTGGGTCTG
11330581 GGTTTGGG
1 GGTTTGGG
11330589 CCCATGTATT
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
12 27 0.77
13 8 0.23
ACGTcount: A:0.00, C:0.11, G:0.42, T:0.47
Consensus pattern (12 bp):
GGTTTGGGTCTG
Found at i:11330586 original size:24 final size:24
Alignment explanation
Indices: 11330529--11330588 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
11330519 AGGCTAGGGT
* *
11330529 TTTGGTTTTGGTCCTGGGTTTGGG
1 TTTGGTTTGGGTCCTGGGTTTCGG
*
11330553 TCTTGTTTTGGGT-CTGGGTTTCGG
1 T-TTGGTTTGGGTCCTGGGTTTCGG
11330577 TTTCGGTTTGGG
1 TTT-GGTTTGGG
11330589 CCCATGTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 2 0.07
24 19 0.63
25 9 0.30
ACGTcount: A:0.00, C:0.10, G:0.40, T:0.50
Consensus pattern (24 bp):
TTTGGTTTGGGTCCTGGGTTTCGG
Found at i:11331679 original size:14 final size:14
Alignment explanation
Indices: 11331662--11331688 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11331652 TATTTTAAAA
11331662 TATTTTTAATTTTC
1 TATTTTTAATTTTC
11331676 TATTTTTAATTTT
1 TATTTTTAATTTT
11331689 TTTACTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (14 bp):
TATTTTTAATTTTC
Found at i:11332263 original size:20 final size:20
Alignment explanation
Indices: 11332238--11332275 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
11332228 GCGTCTTCTG
11332238 CCTACTCGGCTACTCCTAAT
1 CCTACTCGGCTACTCCTAAT
11332258 CCTACTCGGCTACTCCTA
1 CCTACTCGGCTACTCCTA
11332276 CTCGTGTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.42, G:0.11, T:0.29
Consensus pattern (20 bp):
CCTACTCGGCTACTCCTAAT
Found at i:11335539 original size:169 final size:170
Alignment explanation
Indices: 11335260--11335598 Score: 662
Period size: 169 Copynumber: 2.0 Consensus size: 170
11335250 AGTTTAATTC
11335260 AATAAATTTAGTTTTTTAATCAAATAATAACATATATCATTATCTAATTAGATACATTTTCTTTT
1 AATAAATTTAGTTTTTTAATCAAATAATAACATATATCATTATCTAATTAGATACATTTTCTTTT
11335325 AAATTTTAATTTATTTAATTCAATAAAAATCTTAAACTCATTTTTAATCAATTATTAGATTT-TT
66 AAATTTTAATTTATTTAATTCAATAAAAATCTTAAACTCATTTTTAATCAATTATTAGATTTGTT
*
11335389 TTAATGATTTATATGTTCTCATACTCCTTAGTAAGTCTAG
131 TTAATGATTTATATGTTCTCATACTCCCTAGTAAGTCTAG
11335429 AATAAATTTAGTTTTTTAATCAAATAATAACATATATCATTATCTAATTAGATACATTTTCTTTT
1 AATAAATTTAGTTTTTTAATCAAATAATAACATATATCATTATCTAATTAGATACATTTTCTTTT
11335494 AAATTTTAATTTATTTAATTCAATAAAAATCTTAAACTCATTTTTAATCAATTATTAGATTTGTT
66 AAATTTTAATTTATTTAATTCAATAAAAATCTTAAACTCATTTTTAATCAATTATTAGATTTGTT
11335559 TTAATGATTTATATGTTCTCATACTCCCTAGTAAGTCTAG
131 TTAATGATTTATATGTTCTCATACTCCCTAGTAAGTCTAG
11335599 GCTTGAATAA
Statistics
Matches: 168, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
169 127 0.76
170 41 0.24
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.47
Consensus pattern (170 bp):
AATAAATTTAGTTTTTTAATCAAATAATAACATATATCATTATCTAATTAGATACATTTTCTTTT
AAATTTTAATTTATTTAATTCAATAAAAATCTTAAACTCATTTTTAATCAATTATTAGATTTGTT
TTAATGATTTATATGTTCTCATACTCCCTAGTAAGTCTAG
Found at i:11336144 original size:15 final size:15
Alignment explanation
Indices: 11336120--11336152 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
11336110 AGGGTTTTGA
11336120 AGGATTTATA-TTTT
1 AGGATTTATAGTTTT
11336134 AGGACTTTATAGTTTT
1 AGGA-TTTATAGTTTT
11336150 AGG
1 AGG
11336153 GAGATTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 6 0.35
16 7 0.41
ACGTcount: A:0.27, C:0.03, G:0.21, T:0.48
Consensus pattern (15 bp):
AGGATTTATAGTTTT
Found at i:11338885 original size:20 final size:20
Alignment explanation
Indices: 11338862--11338913 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
11338852 AACGCGATCC
11338862 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
11338882 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
11338902 CCAAAATCGCAA
1 CCAGAATCGCAA
11338914 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:11338930 original size:21 final size:20
Alignment explanation
Indices: 11338903--11339001 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
11338893 AATCAGTTTC
11338903 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
11338924 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
11338945 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
11338965 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
11338986 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
11339002 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Done.