Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000264.1 Hibiscus syriacus cultivar Beakdansim tig00000487_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: 70133
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1214 original size:80 final size:81
Alignment explanation
Indices: 1067--1218 Score: 186
Period size: 80 Copynumber: 1.9 Consensus size: 81
1057 AGTGTATATG
** *
1067 TTTAATATTAAATTTAAAAGATATTATTATATGTTTAAATTTATTTATTAAAAGATATCTGGTTG
1 TTTAATATTAAATTTAAAAGATATTATTATATGTTTAAATTTAGATATTAAAAGAGATCTGGTTG
1132 GAGTAAATTTCTCAGA
66 GAGTAAATTTCTCAGA
* * * *
1148 TTTAATATTTACATTT-AAA-ATATTATTATCTTTTTTAAATTTAGATA-TAAAAGAGATTTAGG
1 TTTAATA-TTAAATTTAAAAGATATTATTAT-ATGTTTAAATTTAGATATTAAAAGAGATCT-GG
1210 -TGGAGTAAA
63 TTGGAGTAAA
1219 ACTCTCTCAA
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
80 29 0.48
81 25 0.41
82 7 0.11
ACGTcount: A:0.40, C:0.03, G:0.11, T:0.45
Consensus pattern (81 bp):
TTTAATATTAAATTTAAAAGATATTATTATATGTTTAAATTTAGATATTAAAAGAGATCTGGTTG
GAGTAAATTTCTCAGA
Found at i:2046 original size:35 final size:33
Alignment explanation
Indices: 1979--2057 Score: 86
Period size: 35 Copynumber: 2.3 Consensus size: 33
1969 CAACACAATC
* *
1979 ATCAATTACATTTTAAACCCCAAAAACTAAAAT
1 ATCAATTACATTCTAAACCCCAAAAACCAAAAT
* * **
2012 ACTTCAATTATATTCTAAACCTCAAATTCCAAAAT
1 A--TCAATTACATTCTAAACCCCAAAAACCAAAAT
2047 ATCAATTACAT
1 ATCAATTACAT
2058 GCCCAATCCC
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
33 10 0.27
35 27 0.73
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.32
Consensus pattern (33 bp):
ATCAATTACATTCTAAACCCCAAAAACCAAAAT
Found at i:6133 original size:35 final size:35
Alignment explanation
Indices: 6066--6133 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 35
6056 GGGGTTGTGC
*
6066 ATGTAATTGAAGTATTTTGGAATTTGATGTTTATG
1 ATGTAATTGAAGTATTTTGGAATTTGAGGTTTATG
6101 ATGTAATTGAAGTATTTTGGAATTT-AGGGTTTA
1 ATGTAATTGAAGTATTTTGGAATTTGA-GGTTTA
6134 AAATATATTG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 1 0.03
35 30 0.97
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (35 bp):
ATGTAATTGAAGTATTTTGGAATTTGAGGTTTATG
Found at i:8251 original size:18 final size:20
Alignment explanation
Indices: 8228--8269 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
8218 CAGTAATTAT
8228 ATTCTC-TTG-TAATCTTAC
1 ATTCTCATTGATAATCTTAC
8246 ATTCTCATTGATAATCTTAC
1 ATTCTCATTGATAATCTTAC
8266 ATTC
1 ATTC
8270 CGTGAACCGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 6 0.27
19 3 0.14
20 13 0.59
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.48
Consensus pattern (20 bp):
ATTCTCATTGATAATCTTAC
Found at i:8835 original size:110 final size:111
Alignment explanation
Indices: 8407--8855 Score: 626
Period size: 109 Copynumber: 4.1 Consensus size: 111
8397 TCGGTTTGTA
** * * * *
8407 TCGATACTTTATAAAAATATATTAATCCATAGCAATATAACAAGTAAAAAAATGA-TAAACCGGC
1 TCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGT-AAAAAATGACAAAACCGGT
*
8471 CTAT-AATGACAAAA-AGGTAAAGCGCTACCGGATATATTGAAAGTG
65 CTATAAATGACAAAACAAGTAAAGCGCTACCGGATATATTGAAAGTG
**
8516 TCGATACTTTATAAAAATATATATATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGT
1 TCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGT-AAAAAATGACAAAACCGGT
8581 CTATAAATGACAAAACAAGTAAAGCGCTACCGGATATATTGAAAGTG
65 CTATAAATGACAAAACAAGTAAAGCGCTACCGGATATATTGAAAGTG
* *
8628 TCGATACTTTATAAAAATGTATCGATCCAT-ACAATATAACAGGT-AAAAATTACAAAACCGGTC
1 TCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAATGACAAAACCGGTC
* *
8691 TATAAATGACAAAACAAGTAAAGCGCTACCGGATATGTTGATAGTG
66 TATAAATGACAAAACAAGTAAAGCGCTACCGGATATATTGAAAGTG
* * *
8737 TCGATACTTTATAAAAATGTATCGATCCATAACAATAAAACATGT-AAAAATGACAAAACCCGGT
1 TCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAATGACAAAA-CCGGT
* * *
8801 CTATAAATGACCAAA-AGGTAAAGCGCTACCGGATATGTT-AATAGTG
65 CTATAAATGACAAAACAAGTAAAGCGCTACCGGATATATTGAA-AGTG
*
8847 TCGCTACTT
1 TCGATACTT
8856 ATTATAAGTA
Statistics
Matches: 314, Mismatches: 20, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
109 144 0.46
110 70 0.22
111 43 0.14
112 57 0.18
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (111 bp):
TCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAATGACAAAACCGGTC
TATAAATGACAAAACAAGTAAAGCGCTACCGGATATATTGAAAGTG
Found at i:9143 original size:4 final size:4
Alignment explanation
Indices: 9134--13184 Score: 6052
Period size: 4 Copynumber: 1043.5 Consensus size: 4
9124 ATTTCAGAAA
9134 GTAT GTAT GT-T GTAT GTAT GTAT GTAT GTAT GTAT GTA- -TAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
9179 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G--T GTAAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT-AT
9226 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G-AT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
9273 GTAT GTAT G--T GTAT -TAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
9318 G-AT GTAT GTAT GTAT GTAT GTAT GTA- GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
9364 GTA- -TAT GTAT GTAT GTAT GTAT G-AT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
9409 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTA- GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
9456 GTAT GTAT GTAT GTAT GTA- -TAT GTAT GTAT GTA- -TAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
9500 GTA- -TAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTA-
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
9545 -TAT GTAT GTAT GTAT GTAT G--T GTAT GTAT GTAT GT-T GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
9589 GTAT GTAT GTAT GTAT GTAT GTA- GTAT GTAT GTAT GTAT GTAT GTA-
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
9635 -TAT GTAT GTAT GTAG GTAT GTAT GTAT GTAT GTAT GTA- GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
9681 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTA- ATAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
9728 GTAT -TAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT -TTT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
9774 GTAT GTAT GTA- G-AT -TAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * *
9819 GTAT GTAT GTAT GTAT GTAT GCAT GCAT GCAT GTA- -TAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * *
9865 GTAT GTAT GCAT GCAT GCAT GCAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
9913 GTAT GTAT GTAT GTAT GTAT GTA- GTAT ATAT GTAT GTA- -TAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
9958 GTAT GTA- -TAT GTAT GTAT GTAT GTA- GTAT GTAT GCAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * * *
10003 GCAT GTAT GTAT GTAT GTAT GTAT GCAT CTAT GCAT GCAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
10051 GTAT GTAT GTAT GTAT GTGT -TGAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GT-AT GTAT GTAT GTAT GTAT GTAT GTAT
10099 GTAT GTAT GTAT GTAT GTAT G--T GTAT G-AT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
10144 GTAT GTAT GTAT GTAT GTAT GTAT GTA- -TAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
10190 GTAT GTAT GTA- GTAT GTAT GTAT GTAT GTAT G-AT GTAT GTA- -TAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* *
10234 GTAT GTAT GTA- GGAG GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTA-
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
10280 -TAT GTAT GTAT GTAT G--T GTAT GTAT GTAT GTAT GTA- -TAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
10323 GTA- -TAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT-T ATAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * *
10368 GCAT GTAT GTA- -TAT GTAT GTA- GTAT GCAT GTAT GTAT GCAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
10413 G-AT GTAT GTAT GTAT GCAT G--T GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
10458 GTTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 G-TAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
10507 GTAT GT-T GTAT GTAT GTAT GTAT GTTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT G-TAT GTAT GTAT GTAT GTAT GTAT
10555 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
10603 GTAT GTAT GTA- GTAT GTAT GTAT GTAT GTAT GTA- GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
10649 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
10697 AGTAT GTAT GTAT GTAT GTAT GTAT GTAT G--T GTAT GTAT -TAT GTAT
1 -GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
10743 GTAT GTAT GTAT GTAT GTAT GTAT GTA- GTAT GGTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT -GTAT GTAT GTAT GTAT
* *
10791 GTAT GTAT GTAG GTAT GTAT GTAT GTCT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
10839 GTAT GTAT GTAT GTAT GGAT GTAT GT-T GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
10886 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
10934 G-AT GTAT GCAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * * * * *
10981 GTAT GTAT GTAT GCAT GCAT G-CT GCAT GCAT GCAT GCAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * * *
11028 GTAT GTAT GTAT GTAT GTAT GCAT GCAT GCAT GCAT GCAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
11076 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G--T GTAT ATAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
11122 GTAT GTAT GTAT GTA- -TAT GTAT GTAT GTAT G-AT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * * *
11167 GTAT GCAT GTAT GTAT GTAT GTAT GCAT CTAT GCAT GCAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
11215 GTAT GTAT GTAT GT-T GTGT -TGAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GT-AT GTAT GTAT GTAT GTAT GTAT GTAT
* *
11262 GTAT GTAT GTAT GTAT GTGT -TGAT GTATT ATAT GTAT G--T GTAT GTA-
1 GTAT GTAT GTAT GTAT GTAT GT-AT GTA-T GTAT GTAT GTAT GTAT GTAT
*
11308 GTAT ATAT GTAT GTAT GTAT G-AT GTAT GTAT GTAT GTAT GTA- -TAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
11353 GTAT GTAT GTA- GTAT GTAT GTAT GTCT GTAT GTA- GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* *
11399 GCAT GCAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G-TAT
11448 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G--T GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
11494 GTAT GTAT G--T GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTA- GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
11539 GTAT GTAT GTAT G--T GTAT GTAT GTAT GTAT GTAT G--T GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
11583 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G-TAT GTAT
* * * * * *
11632 GTAT G-AT GCAT GCAT GCAT GCA- GCAT GCAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * *
11678 GTAT GTAT GTAT GCAT GCAT GCAT GCAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
11726 GTAT GTAT GTAT ATAT GTAT GTA- -TAT GTAT G--T GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
11770 GTAT GTAT GTAT GTAT GTAT GCAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* *
11818 GTAT GTAT GTAT GCAT GCAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
11866 G-AT GTAT GTAT GTAT GTAT GTAT GTAT GT-T G-AT GTAT GTA- -TAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
11909 GTAT GTAT GTTAG GTAT GTAT GTAT GTAT GTAT G--T GTAT GTAT GTAT
1 GTAT GTAT G-TAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
11956 GTAT GTAT GTAT G-AT GTAT GTAT GTAT GTAT ATGAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT-AT GTAT GTAT GTAT
12004 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
12052 GTAT GTAT GTAT GTAT GTA- GTAT GGTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT -GTAT GTAT GTAT GTAT GTAT GTAT
12100 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
12148 ATAT GTA- -TAT GTAT GTAAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GT-AT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* *
12195 GTAT G--T GTAT GTAT GCAT GTAT GTAT GTAT GTAT GTAT GTCTAT GCAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G--TAT GTAT
*
12243 GCAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
12291 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
12339 GTAT GTATT GTAT GTAT GTAT GTA- GTAT GTAT GTAT G-AT GTAT GTAT
1 GTAT GTA-T GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
12386 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTA-
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
12433 GTAT GTAT G--T GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
12479 G--T GTAT GTAT GTAT GTAT GTAT GTAT GTAT G-AT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
12524 GTAT GTAT GTAT GTAT G--T GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
12570 GTAT GTAT GTAT GTAT GTAT GTAT GTAT ATAT GTAT GTAT GTA- -TAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
12616 GTAT GTAT GTAT GTAT GTA- -TAT GTAT GTAT GTAT GTAT GTAT GCAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * *
12662 GTAT GTAT GCAT GTAT GTAT GTAT GTAT GTGCAT CTAT GCAT GCAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT--AT GTAT GTAT GTAT GTAT
* *
12712 GTAT GTAGT ATAT GTAT GTGT G-AT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTA-T GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
12760 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
12808 GTAT GTAT GTAT GTAT GTAT GTA- GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
12855 GTA- -TAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
12901 GTAT GTAT GTAT GTAT GTAT GTAT G--T GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
12947 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
12995 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * *
13043 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GCAT GCAT GCAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * *
13091 GCAT GCAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GCAT GCAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * *
13139 GCAT GCAT GCAT GTAT GTAT GTAT GTAT GTGT -TGAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT-AT GTAT GTAT GT
13185 GTTGATGTAT
Statistics
Matches: 3770, Mismatches: 110, Indels: 334
0.89 0.03 0.08
Matches are distributed among these distances:
2 89 0.02
3 149 0.04
4 3470 0.92
5 55 0.01
6 7 0.00
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.48
Consensus pattern (4 bp):
GTAT
Found at i:14402 original size:12 final size:12
Alignment explanation
Indices: 14385--14419 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
14375 CTTTGTCCTC
14385 TTTTTTCTTTGT
1 TTTTTTCTTTGT
*
14397 TTTTTTCTTTTT
1 TTTTTTCTTTGT
14409 TCTTTTTCTTT
1 T-TTTTTCTTT
14420 CTGCTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (12 bp):
TTTTTTCTTTGT
Found at i:14461 original size:16 final size:14
Alignment explanation
Indices: 14390--14452 Score: 51
Period size: 14 Copynumber: 4.4 Consensus size: 14
14380 TCCTCTTTTT
14390 TCTTTGTTT-TTT-
1 TCTTTGTTTCTTTC
*
14402 TCTTT-TTTCTTTT
1 TCTTTGTTTCTTTC
*
14415 TCTTTCTGCTTATTTTTC
1 TC-TT-TG-TT-TCTTTC
14433 TCTTTGTTTCTTTC
1 TCTTTGTTTCTTTC
14447 TCTTTG
1 TCTTTG
14453 ATTTTCTTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
11 3 0.07
12 8 0.20
13 2 0.05
14 13 0.32
15 3 0.07
16 2 0.05
17 4 0.10
18 6 0.15
ACGTcount: A:0.02, C:0.17, G:0.06, T:0.75
Consensus pattern (14 bp):
TCTTTGTTTCTTTC
Found at i:14478 original size:22 final size:23
Alignment explanation
Indices: 14406--14479 Score: 73
Period size: 22 Copynumber: 3.2 Consensus size: 23
14396 TTTTTTTCTT
14406 TTTTCTTT-TTCTTTCTGCTTATT-
1 TTTTCTTTGTTCTTTC-GCTT-TTA
* *
14429 TTTCTCTTTGTTTCTTTCTCTTTGA
1 TTT-TCTTTG-TTCTTTCGCTTTTA
14454 TTTTCTTTGTTC-TTCGCTTTTA
1 TTTTCTTTGTTCTTTCGCTTTTA
14476 TTTT
1 TTTT
14480 ATCTTTGGAC
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
22 12 0.28
23 6 0.14
24 12 0.28
25 6 0.14
26 7 0.16
ACGTcount: A:0.04, C:0.18, G:0.07, T:0.72
Consensus pattern (23 bp):
TTTTCTTTGTTCTTTCGCTTTTA
Found at i:15116 original size:20 final size:20
Alignment explanation
Indices: 15068--15124 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
15058 AAATGCAATG
* * * *
15068 TTTCAAGGCCGCAAAAAATG
1 TTTCAAGGTCTCAAAGAATA
15088 TTTCAAGGTCTCAAAGAATA
1 TTTCAAGGTCTCAAAGAATA
15108 TTTCAAGGTCTCAAAGA
1 TTTCAAGGTCTCAAAGA
15125 GAGGGAATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.26
Consensus pattern (20 bp):
TTTCAAGGTCTCAAAGAATA
Found at i:18107 original size:14 final size:13
Alignment explanation
Indices: 18083--18116 Score: 59
Period size: 14 Copynumber: 2.5 Consensus size: 13
18073 AGTAAAATTA
18083 ACATAATACACAT
1 ACATAATACACAT
18096 ACATATATACACAT
1 ACATA-ATACACAT
18110 ACATAAT
1 ACATAAT
18117 GGACTAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (13 bp):
ACATAATACACAT
Found at i:19844 original size:3 final size:3
Alignment explanation
Indices: 19836--19890 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
19826 ACATATAAAT
* * * *
19836 TAA TAA TAA TAA TAT TAC TAA TAA TAA TGA TAA TAA TAC TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
19883 TAA -AA TAA
1 TAA TAA TAA
19891 GAAATTAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
2 4 0.09
3 39 0.91
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:19857 original size:15 final size:15
Alignment explanation
Indices: 19830--19879 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
19820 AATGTAACAT
19830 ATAA-ATTAATAATA
1 ATAATATTAATAATA
*
19844 ATAATATTACTAATA
1 ATAATATTAATAATA
19859 ATAATGA-TAATAATA
1 ATAAT-ATTAATAATA
*
19874 CTAATA
1 ATAATA
19880 AAATAAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
14 5 0.16
15 25 0.81
16 1 0.03
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (15 bp):
ATAATATTAATAATA
Found at i:20382 original size:3 final size:3
Alignment explanation
Indices: 20374--20456 Score: 85
Period size: 3 Copynumber: 27.0 Consensus size: 3
20364 ATTAATTTAT
* *
20374 TTA TTA TTA TTA TTA TTA TTA TTA TTAA ATA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
* * * * *
20420 TAA TTA CTA ATA TTA TTA TTTA TTA CTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
20457 ATAAAAAATT
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
3 61 0.92
4 5 0.08
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:20399 original size:25 final size:25
Alignment explanation
Indices: 20370--20444 Score: 87
Period size: 25 Copynumber: 2.9 Consensus size: 25
20360 CCATATTAAT
*
20370 TTATTTATTATTATTATTATTATTA
1 TTATTTAATATTATTATTATTATTA
* *
20395 TTATTAAATATTATTATTATAATTA
1 TTATTTAATATTATTATTATTATTA
*
20420 TAATTACTAATATTATTATTTATTA
1 TTATT--TAATATTATTA-TTATTA
20445 CTAATATTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
25 26 0.63
27 10 0.24
28 5 0.12
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (25 bp):
TTATTTAATATTATTATTATTATTA
Found at i:20458 original size:9 final size:9
Alignment explanation
Indices: 20363--20459 Score: 76
Period size: 9 Copynumber: 10.9 Consensus size: 9
20353 TTTTTACCCA
20363 TATTAAT-T
1 TATTAATAT
20371 TATT--TAT
1 TATTAATAT
*
20378 TATTATTAT
1 TATTAATAT
*
20387 TATTATTAT
1 TATTAATAT
20396 TATTAAATAT
1 TATT-AATAT
*
20406 TATTATTAT
1 TATTAATAT
*
20415 AATT-ATAAT
1 TATTAAT-AT
*
20424 TACTAATAT
1 TATTAATAT
*
20433 TATTATTTAT
1 TATTA-ATAT
*
20443 TACTAATAT
1 TATTAATAT
20452 TATTAATA
1 TATTAATA
20460 AAAAATTACA
Statistics
Matches: 71, Mismatches: 11, Indels: 13
0.75 0.12 0.14
Matches are distributed among these distances:
6 1 0.01
7 5 0.07
8 5 0.07
9 43 0.61
10 17 0.24
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (9 bp):
TATTAATAT
Found at i:20491 original size:13 final size:13
Alignment explanation
Indices: 20473--20502 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
20463 AATTACAAGC
20473 CCCAGTCAACCAG
1 CCCAGTCAACCAG
20486 CCCAGTCAACCAG
1 CCCAGTCAACCAG
20499 CCCA
1 CCCA
20503 AACCAAACTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.50, G:0.13, T:0.07
Consensus pattern (13 bp):
CCCAGTCAACCAG
Found at i:22121 original size:16 final size:17
Alignment explanation
Indices: 22086--22119 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
22076 TCCTTTTCTG
22086 ATATTTTTTTTAAATAA
1 ATATTTTTTTTAAATAA
22103 ATATTTTTTTTAAATAA
1 ATATTTTTTTTAAATAA
22120 TAGGATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATTTTTTTTAAATAA
Found at i:24703 original size:179 final size:181
Alignment explanation
Indices: 24403--24769 Score: 663
Period size: 179 Copynumber: 2.0 Consensus size: 181
24393 TCGTCTGAGT
24403 TCGCATTCCACAGCAAAAATTATAAAAAATATCATGACAGCCGTTACAGCTTGGAAAACAACTTT
1 TCGCATTCCACAGCAAAAATTATAAAAAATATCATGACAGCCGTTACAGCTTGGAAAACAACTTT
24468 TGTATCCGAGCTAAAGCAGCAAAAGAAATGCTAACTCCTGATTATGAAGAATGGAGATC-GCCAG
66 TGTATCCGAGCTAAAGCAGCAAAAGAAATGCTAACTCCTGATTATGAAGAATGGAGATCAGCCAG
24532 AAAAAATG-AAAT-TCCTCTACCAGATC-AAATGAGGACATTTCTATGGAAGA
131 -AAAAATGAAAATATCCTCTACCAGATCAAAATGAGGACA-TTCTATGGAAGA
24582 TCGCATTCCACAGCAAAAATTATAAAAGAATATCATGACAGCCGTTACAGCTTGGAAAACAAC-T
1 TCGCATTCCACAGCAAAAATTATAAAA-AATATCATGACAGCCGTTACAGCTTGGAAAACAACTT
24646 TTGTATCCGAGCTAAAGCAGCAAAAGAAATGCTAACTCCTGATTATGAAGAATGGAGATCAGCCA
65 TTGTATCCGAGCTAAAGCAGCAAAAGAAATGCTAACTCCTGATTATGAAGAATGGAGATCAGCCA
*
24711 GAAAAATGAAAATATTCTCTACCAGATCAAAATGAGGACATTCTATGGAAGA
130 GAAAAATGAAAATATCCTCTACCAGATCAAAATGAGGACATTCTATGGAAGA
24763 TCGCATT
1 TCGCATT
24770 AAGGTAGTTC
Statistics
Matches: 182, Mismatches: 1, Indels: 8
0.95 0.01 0.04
Matches are distributed among these distances:
179 95 0.52
180 44 0.24
181 32 0.18
182 11 0.06
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (181 bp):
TCGCATTCCACAGCAAAAATTATAAAAAATATCATGACAGCCGTTACAGCTTGGAAAACAACTTT
TGTATCCGAGCTAAAGCAGCAAAAGAAATGCTAACTCCTGATTATGAAGAATGGAGATCAGCCAG
AAAAATGAAAATATCCTCTACCAGATCAAAATGAGGACATTCTATGGAAGA
Found at i:33439 original size:17 final size:17
Alignment explanation
Indices: 33419--33451 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
33409 ATTATGCTTG
33419 AAGAAAA-AAGAAAAAGA
1 AAGAAAAGAA-AAAAAGA
33436 AAGAAAAGAAAAAAAG
1 AAGAAAAGAAAAAAAG
33452 GGGGGGTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAGAAAAGAAAAAAAGA
Found at i:33801 original size:16 final size:18
Alignment explanation
Indices: 33782--33827 Score: 69
Period size: 16 Copynumber: 2.6 Consensus size: 18
33772 CTATTTCAAG
33782 TTCAATTTATTT-GAAA-
1 TTCAATTTATTTCGAAAT
33798 TTCAATTTATTTTCGAAAT
1 TTCAATTTA-TTTCGAAAT
33817 TTCAATTTATT
1 TTCAATTTATT
33828 CTTCTATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.33
17 3 0.11
18 6 0.22
19 9 0.33
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.54
Consensus pattern (18 bp):
TTCAATTTATTTCGAAAT
Found at i:33822 original size:19 final size:17
Alignment explanation
Indices: 33782--33827 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 17
33772 CTATTTCAAG
33782 TTCAATTTA-TTTGAAA
1 TTCAATTTATTTTGAAA
33798 TTCAATTTATTTTCGAAA
1 TTCAATTTATTTT-GAAA
33816 TTTCAATTTATT
1 -TTCAATTTATT
33828 CTTCTATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.33
17 3 0.11
18 4 0.15
19 11 0.41
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.54
Consensus pattern (17 bp):
TTCAATTTATTTTGAAA
Found at i:34796 original size:82 final size:84
Alignment explanation
Indices: 34494--35045 Score: 922
Period size: 82 Copynumber: 6.7 Consensus size: 84
34484 GAACAAATGT
34494 AATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAACCA
1 AATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGACAGAACCA
34558 ATCATTGAATTTAGAAGATG
65 ATCATTGAATTTAGAAGATG
*
34578 AATGTGCTCATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAACCAA
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGACAGAACCAA
34642 TCATTGAATTTAGAAGATG
66 TCATTGAATTTAGAAGATG
* *
34661 AATGTGCTCATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAATCAA
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGACAGAACCAA
34725 TCATTGAATTT-GAAGATG
66 TCATTGAATTTAGAAGATG
* *
34743 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTTGG-CAGAATCAA
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGACAGAACCAA
34807 TCATTGAATTT-GAAGATG
66 TCATTGAATTTAGAAGATG
* **
34825 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT-GTCAGAATTAA
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGACAGAACCAA
34889 TCATTGAATTT-GAAGATG
66 TCATTGAATTTAGAAGATG
*
34907 AATGTGCTCATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGACAGAACCAA
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGACAGAACCAA
34972 TCATTGAATTTAGAAGATG
66 TCATTGAATTTAGAAGATG
* * * *
34991 AATTTTCCCATAGCATCTTCTGGAAGTGATCTTTGAGTTATCTGATCTGGTTTGG
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
35046 TAGGAACTAC
Statistics
Matches: 449, Mismatches: 15, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
81 1 0.00
82 217 0.48
83 161 0.36
84 70 0.16
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (84 bp):
AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGACAGAACCAA
TCATTGAATTTAGAAGATG
Found at i:35970 original size:113 final size:113
Alignment explanation
Indices: 35772--36892 Score: 1761
Period size: 113 Copynumber: 9.8 Consensus size: 113
35762 GCAAAGATTT
*
35772 AAATCCATCATCTGATGGATCAGCATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
35837 AAGGAAGAAGAAATTCATAATGAGGAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
35885 AAATCCATCATCTGATGGATCAGCTTTTCTAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAG
35950 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
35998 AAATCCATCATCTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAG
36063 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * *
36111 AAATCCATCATCTGATGGATCATCTTTTCTAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAA
1 AAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
36176 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTAGCTC
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
36224 AAATCCATCATCTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAG
36289 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
36337 AAATCCATTATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAG
36402 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
36450 AAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAG
36515 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
36563 AAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG-A-
1 AAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAG
* ** * *
36626 AAGAGAAGAA-AAAGTTCACAATGAGAAGAGCTTATTCAACCTTTCGCAT-
66 AAG-GAAGAAGAAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGC-TC
* ** * *
36675 AATTCTATCACAGAAGCAGATAGATTAGCATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAA
1 AA----ATC-C---ATCATCT-GA-T-GGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAA
* * *
36740 CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACAT-
55 CTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC-TC
* * * * * *
36799 GAATTCATCAAT-TGATGGATCAACCTTGCCAGAAAGAGTTCATAATGAGAAGAACTCATC-GAA
1 AAATCCATC-ATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG-A
* *
36862 AGAAGGATGAAGAAGTTCATAATGAGAAGAA
64 AGAAGGAAGAAGAAATTCATAATGAGAAGAA
36893 CTCATCAAGA
Statistics
Matches: 946, Mismatches: 43, Indels: 38
0.92 0.04 0.04
Matches are distributed among these distances:
111 6 0.01
112 38 0.04
113 794 0.84
114 1 0.00
115 2 0.00
116 6 0.01
117 2 0.00
119 1 0.00
120 6 0.01
121 2 0.00
122 1 0.00
123 44 0.05
124 38 0.04
125 5 0.01
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.27
Consensus pattern (113 bp):
AAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:37164 original size:3 final size:3
Alignment explanation
Indices: 37156--37235 Score: 79
Period size: 3 Copynumber: 26.0 Consensus size: 3
37146 ATTAATTTAT
* * *
37156 TTA TTA TTA TTA TTA TTA TTA TTAA ATA TTA TTA TTA TAA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA
* * * *
37202 TTA CTA ATA TTA TTA TTTA TTA CTA ATA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
37236 ATAAAAAATT
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
3 58 0.92
4 5 0.08
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:37185 original size:19 final size:19
Alignment explanation
Indices: 37172--37236 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
37162 TTATTATTAT
* *
37172 TATTATTAAATATTATTAT
1 TATTATTAAATATTACTAA
* *
37191 TATAATTATA-ATTACTAA
1 TATTATTAAATATTACTAA
**
37209 TATTATTATTTATTACTAA
1 TATTATTAAATATTACTAA
37228 TATTATTAA
1 TATTATTAA
37237 TAAAAAATTA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
18 14 0.37
19 24 0.63
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTATTAAATATTACTAA
Found at i:38878 original size:17 final size:18
Alignment explanation
Indices: 38856--38890 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
38846 TCCTTTTCTG
38856 ATATTTTTTTT-AAATAA
1 ATATTTTTTTTGAAATAA
38873 ATATTTTTTTTGAAATAA
1 ATATTTTTTTTGAAATAA
38891 TAGGATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
ATATTTTTTTTGAAATAA
Found at i:44045 original size:21 final size:21
Alignment explanation
Indices: 44020--44060 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
44010 CAAAAGACTG
44020 AAACATACTCAAAACGACCCC
1 AAACATACTCAAAACGACCCC
44041 AAACATACTCAAAACGACCC
1 AAACATACTCAAAACGACCC
44061 AAATGAGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.37, G:0.05, T:0.10
Consensus pattern (21 bp):
AAACATACTCAAAACGACCCC
Found at i:44840 original size:142 final size:142
Alignment explanation
Indices: 44584--44867 Score: 559
Period size: 142 Copynumber: 2.0 Consensus size: 142
44574 CCGATCAATG
*
44584 GAAATGATTAAGACCTTATGTTTGGATCAATCCTTTGGTGCCTCTGGATAGAGAGAAAAAAATTC
1 GAAATGATTAAGACCTTATGTTTGGATCAATCCTTTGGTGCCTCTAGATAGAGAGAAAAAAATTC
44649 ATCTTTGACTCGGAGTTTATCGAAACAGAAAGTGTGTTGTAGCGTGGACGGAGACTATGTGAACA
66 ATCTTTGACTCGGAGTTTATCGAAACAGAAAGTGTGTTGTAGCGTGGACGGAGACTATGTGAACA
44714 GGTTGCTCGTGC
131 GGTTGCTCGTGC
44726 GAAATGATTAAGACCTTATGTTTGGATCAATCCTTTGGTGCCTCTAGATAGAGAGAAAAAAATTC
1 GAAATGATTAAGACCTTATGTTTGGATCAATCCTTTGGTGCCTCTAGATAGAGAGAAAAAAATTC
44791 ATCTTTGACTCGGAGTTTATCGAAACAGAAAGTGTGTTGTAGCGTGGACGGAGACTATGTGAACA
66 ATCTTTGACTCGGAGTTTATCGAAACAGAAAGTGTGTTGTAGCGTGGACGGAGACTATGTGAACA
44856 GGTTGCTCGTGC
131 GGTTGCTCGTGC
44868 TCGAGTGGCT
Statistics
Matches: 141, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
142 141 1.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (142 bp):
GAAATGATTAAGACCTTATGTTTGGATCAATCCTTTGGTGCCTCTAGATAGAGAGAAAAAAATTC
ATCTTTGACTCGGAGTTTATCGAAACAGAAAGTGTGTTGTAGCGTGGACGGAGACTATGTGAACA
GGTTGCTCGTGC
Found at i:55408 original size:19 final size:19
Alignment explanation
Indices: 55378--55427 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
55368 CCATGGGTGG
55378 CACCATTTATGCCGAAAATA
1 CACCA-TTATGCCGAAAATA
*
55398 TACCATTATGCCGAAAATA
1 CACCATTATGCCGAAAATA
55417 CACCATTATGC
1 CACCATTATGC
55428 ATTGAACAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 24 0.86
20 4 0.14
ACGTcount: A:0.38, C:0.26, G:0.10, T:0.26
Consensus pattern (19 bp):
CACCATTATGCCGAAAATA
Found at i:60758 original size:12 final size:12
Alignment explanation
Indices: 60741--60765 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
60731 TTGTAAATGC
60741 ACATGGCGTTGG
1 ACATGGCGTTGG
60753 ACATGGCGTTGG
1 ACATGGCGTTGG
60765 A
1 A
60766 GAACCATCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (12 bp):
ACATGGCGTTGG
Found at i:62671 original size:23 final size:21
Alignment explanation
Indices: 62632--62703 Score: 83
Period size: 23 Copynumber: 3.4 Consensus size: 21
62622 TGCTATATAT
*
62632 CGATACACTATGAATGTGTAC
1 CGATACACTCTGAATGTGTAC
* *
62653 CGATACATTCCTTGAATGTGTAT
1 CGATACACT-C-TGAATGTGTAC
62676 CGATACACTCTGAA-GTGTAC
1 CGATACACTCTGAATGTGTAC
*
62696 CAATACAC
1 CGATACAC
62704 CCGTCGGGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
20 12 0.28
21 12 0.28
22 1 0.02
23 18 0.42
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (21 bp):
CGATACACTCTGAATGTGTAC
Found at i:63778 original size:15 final size:15
Alignment explanation
Indices: 63758--63787 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
63748 GCTAGGACAT
63758 TTGGTTTAGATAACG
1 TTGGTTTAGATAACG
63773 TTGGTTTAGATAACG
1 TTGGTTTAGATAACG
63788 AGAGAAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.27, T:0.40
Consensus pattern (15 bp):
TTGGTTTAGATAACG
Found at i:64953 original size:25 final size:25
Alignment explanation
Indices: 64922--64980 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
64912 GGGGAGTAAT
64922 TTTTCAAAATTGATTTCAAAAATAA
1 TTTTCAAAATTGATTTCAAAAATAA
64947 TTTTCAAAATTGATTTCAAAAATAA
1 TTTTCAAAATTGATTTCAAAAATAA
64972 TTTTCAAAA
1 TTTTCAAAA
64981 AGAAAATCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
TTTTCAAAATTGATTTCAAAAATAA
Found at i:64974 original size:12 final size:13
Alignment explanation
Indices: 64922--64981 Score: 70
Period size: 12 Copynumber: 4.8 Consensus size: 13
64912 GGGGAGTAAT
* *
64922 TTTTCAAAATTGA
1 TTTTCAAAAATAA
64935 -TTTCAAAAATAA
1 TTTTCAAAAATAA
* *
64947 TTTTCAAAATTGA
1 TTTTCAAAAATAA
64960 -TTTCAAAAATAA
1 TTTTCAAAAATAA
64972 TTTTCAAAAA
1 TTTTCAAAAA
64982 GAAAATCTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
12 20 0.51
13 19 0.49
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.40
Consensus pattern (13 bp):
TTTTCAAAAATAA
Found at i:66684 original size:83 final size:81
Alignment explanation
Indices: 66541--66701 Score: 241
Period size: 83 Copynumber: 2.0 Consensus size: 81
66531 GAATTTCGAG
* *
66541 AGAGTTTTACTCCAACTAAAACTATTTTAATATCTAAATTTAAACATATAATAATATCTTTTAAA
1 AGAGTTTTACTCCAACCAAAACTATTTTAATATCTAAATTTAAAAATATAATAATATCTTTTAAA
66606 TTTTAAATATTAAACCTA
66 -TTT-AATATTAAACCTA
* * * * *
66624 AGAGTTTTACTTCAACCAAAATTCTTTTAATATCTAAATTTAAAAATATTATAATGTCTTTTAAA
1 AGAGTTTTACTCCAACCAAAACTATTTTAATATCTAAATTTAAAAATATAATAATATCTTTTAAA
66689 TTTAATATTAAAC
66 TTTAATATTAAAC
66702 ATATATTTTC
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
81 10 0.14
82 3 0.04
83 58 0.82
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.42
Consensus pattern (81 bp):
AGAGTTTTACTCCAACCAAAACTATTTTAATATCTAAATTTAAAAATATAATAATATCTTTTAAA
TTTAATATTAAACCTA
Done.