Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008194.1 Hibiscus syriacus cultivar Beakdansim tig00110813_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: 2426039
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 13
Found at i:1283259 original size:15 final size:15
Alignment explanation
Indices: 1283228--1283266 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1283218 GGTTTTATAT
*
1283228 TTTGGGA-TTTAGTG
1 TTTGGGATTTTAGGG
1283242 TTTGGGATTTTAGGG
1 TTTGGGATTTTAGGG
*
1283257 TTTGTGATTT
1 TTTGGGATTT
1283267 AGAGTTAGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 7 0.32
15 15 0.68
ACGTcount: A:0.13, C:0.00, G:0.33, T:0.54
Consensus pattern (15 bp):
TTTGGGATTTTAGGG
Found at i:1283276 original size:20 final size:20
Alignment explanation
Indices: 1283251--1283292 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1283241 GTTTGGGATT
* *
1283251 TTAGGGTTTGTGATTTAGAG
1 TTAGGGTGTGGGATTTAGAG
1283271 TTAGGGTGTGGGATTTAGAG
1 TTAGGGTGTGGGATTTAGAG
1283291 TT
1 TT
1283293 TGATATTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.38, T:0.43
Consensus pattern (20 bp):
TTAGGGTGTGGGATTTAGAG
Found at i:1283329 original size:28 final size:27
Alignment explanation
Indices: 1283258--1283331 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 27
1283248 ATTTTAGGGT
1283258 TTGTGATTTAGAG-TTAGGGTGTGGGA
1 TTGTGATTTAGAGTTTAGGGTGTGGGA
*
1283284 TT-TAGAGTTT-GATATTTAGGGTGTGGGA
1 TTGT-GA-TTTAGA-GTTTAGGGTGTGGGA
1283312 GTTGTGATTTAGAGTTTAGG
1 -TTGTGATTTAGAGTTTAGG
1283332 ATTTATGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
25 1 0.03
26 6 0.15
27 3 0.08
28 22 0.56
29 6 0.15
30 1 0.03
ACGTcount: A:0.20, C:0.00, G:0.38, T:0.42
Consensus pattern (27 bp):
TTGTGATTTAGAGTTTAGGGTGTGGGA
Found at i:1289160 original size:14 final size:14
Alignment explanation
Indices: 1289141--1289167 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1289131 TCATTCGGTT
1289141 ATGAGTTAGTTAGC
1 ATGAGTTAGTTAGC
1289155 ATGAGTTAGTTAG
1 ATGAGTTAGTTAG
1289168 TGTTAGGTTG
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:0.30, C:0.04, G:0.30, T:0.37
Consensus pattern (14 bp):
ATGAGTTAGTTAGC
Found at i:1295100 original size:20 final size:20
Alignment explanation
Indices: 1295056--1295333 Score: 157
Period size: 20 Copynumber: 13.6 Consensus size: 20
1295046 AATGTCCAAT
* *
1295056 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
1295075 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
1295095 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
1295115 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
1295135 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
1295155 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
1295176 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
1295199 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
1295219 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
1295239 ATAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
1295259 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
1295282 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
1295302 AGAAGCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
*
1295322 AGAATCGCAACG
1 AAAATCGCAACG
1295334 TTAAAAAGAT
Statistics
Matches: 202, Mismatches: 45, Indels: 23
0.75 0.17 0.09
Matches are distributed among these distances:
19 17 0.08
20 142 0.70
21 14 0.07
23 29 0.14
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:1295236 original size:43 final size:43
Alignment explanation
Indices: 1295180--1295320 Score: 189
Period size: 43 Copynumber: 3.3 Consensus size: 43
1295170 GCTTCCAAGT
*
1295180 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAA
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAA
* * * *
1295223 TCGCAATGCGATTT---ATATAATCGCAATGCGATTGAGAGAG
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAA
*
1295263 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAA
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAA
* *
1295306 GCGCAATGCGATTTA
1 TCGCAACGCGATTTA
1295321 TAGAATCGCA
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
40 35 0.42
43 48 0.58
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (43 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAA
Found at i:1295431 original size:6 final size:6
Alignment explanation
Indices: 1295420--1295451 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1295410 GACACGTATT
1295420 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1295452 CGAGACGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1296166 original size:6 final size:6
Alignment explanation
Indices: 1296140--1296205 Score: 111
Period size: 6 Copynumber: 11.5 Consensus size: 6
1296130 TCTCGTCTCG
1296140 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1296185 GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGT
1296206 AATACGTGTC
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 15 0.25
6 45 0.75
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:1296397 original size:83 final size:83
Alignment explanation
Indices: 1296302--1296485 Score: 332
Period size: 83 Copynumber: 2.2 Consensus size: 83
1296292 CGTTGCGACT
* *
1296302 TTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCAATTCTATAAATCGCATTGCGATTCTCTC
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCAATTCTATAAATCGCATTGCGATTCTATC
*
1296367 AGTCGCATTGCGATTTTC
66 AATCGCATTGCGATTTTC
*
1296385 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCAATTCTATAAATCGCATTGCGATTCTATC
1296450 AATCGCATTGCGATTTTC
66 AATCGCATTGCGATTTTC
1296468 TTCTAAATCGCGTTGCGA
1 TTCTAAATCGCGTTGCGA
1296486 ACTTGGAAGC
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 97 1.00
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.36
Consensus pattern (83 bp):
TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCAATTCTATAAATCGCATTGCGATTCTATC
AATCGCATTGCGATTTTC
Found at i:1296461 original size:40 final size:40
Alignment explanation
Indices: 1296305--1296464 Score: 230
Period size: 40 Copynumber: 3.9 Consensus size: 40
1296295 TGCGACTTTC
* *
1296305 TAAATCGCGTTGCGATTCTCTCAATCGCATTGCAATTCTA
1 TAAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTA
* *
1296345 TAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTTTCTTC
1 TAAATCGCATTGCGATTCTCTCAATCGCATTGCGA--TTC-TA
* *
1296388 TAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTA
1 TAAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTA
*
1296428 TAAATCGCATTGCGATTCTATCAATCGCATTGCGATT
1 TAAATCGCATTGCGATTCTCTCAATCGCATTGCGATT
1296465 TTCTTCTAAA
Statistics
Matches: 106, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
40 67 0.63
41 3 0.03
42 3 0.03
43 33 0.31
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (40 bp):
TAAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTA
Found at i:1296562 original size:20 final size:20
Alignment explanation
Indices: 1296292--1296570 Score: 148
Period size: 20 Copynumber: 13.6 Consensus size: 20
1296282 ATCTTTTTAA
*
1296292 CGTTGCGACTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
1296312 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
1296332 CATTGCAATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
1296352 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
1296372 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
1296395 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
1296415 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
1296435 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
1296455 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
1296478 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
1296499 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
1296517 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
1296539 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
1296559 CGTTGCGATTTT
1 CGTTGCGATTTT
1296571 ATTGGTCATT
Statistics
Matches: 203, Mismatches: 45, Indels: 22
0.75 0.17 0.08
Matches are distributed among these distances:
18 2 0.01
20 153 0.75
21 14 0.07
22 6 0.03
23 28 0.14
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:1298780 original size:2 final size:2
Alignment explanation
Indices: 1298773--1298806 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1298763 ATTAAAATCA
1298773 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
1298807 GATAAAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1302853 original size:13 final size:13
Alignment explanation
Indices: 1302835--1302861 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1302825 TAACTAAGTT
1302835 TTATGGCACCCTA
1 TTATGGCACCCTA
1302848 TTATGGCACCCTA
1 TTATGGCACCCTA
1302861 T
1 T
1302862 ATAAAACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (13 bp):
TTATGGCACCCTA
Found at i:1305649 original size:6 final size:7
Alignment explanation
Indices: 1305631--1305660 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
1305621 TTAAAATTAT
1305631 TAAAAAA
1 TAAAAAA
1305638 TAAAAAA
1 TAAAAAA
1305645 TAAAAAAA
1 T-AAAAAA
1305653 TAAAAAA
1 TAAAAAA
1305660 T
1 T
1305661 TATTACATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
TAAAAAA
Found at i:1305652 original size:15 final size:15
Alignment explanation
Indices: 1305632--1305660 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1305622 TAAAATTATT
1305632 AAAAAATAAAAAATA
1 AAAAAATAAAAAATA
1305647 AAAAAATAAAAAAT
1 AAAAAATAAAAAAT
1305661 TATTACATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (15 bp):
AAAAAATAAAAAATA
Found at i:1305993 original size:37 final size:37
Alignment explanation
Indices: 1305917--1305994 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 37
1305907 CAAGTTGAAA
* *
1305917 AAAATTTATATATTTTCTTTAAAAATTTTAAATTCAT
1 AAAATTTATATATTTTCTTTAAAAATTTGAAAATCAT
*
1305954 AAAATTTATATAATTTTTTTTACAAAA-TTGAAAAT-AT
1 AAAATTTATAT-ATTTTCTTTA-AAAATTTGAAAATCAT
1305991 AAAA
1 AAAA
1305995 AGGTTTAATG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 17 0.47
38 15 0.42
39 4 0.11
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (37 bp):
AAAATTTATATATTTTCTTTAAAAATTTGAAAATCAT
Found at i:1306492 original size:60 final size:60
Alignment explanation
Indices: 1306387--1306513 Score: 202
Period size: 60 Copynumber: 2.1 Consensus size: 60
1306377 ATCCTCATTT
1306387 TAAATTGATCCTTAAACTTTTAAACATTCTAACTTCATCCCCAAACCATGACTCTTATTC
1 TAAATTGATCCTTAAACTTTTAAACATTCTAACTTCATCCCCAAACCATGACTCTTATTC
* * * *
1306447 TAAATT-AGTCCTTAAACTTTTGAACATTCTAATTTCTTCCTCAAACCATGACTCTTATTC
1 TAAATTGA-TCCTTAAACTTTTAAACATTCTAACTTCATCCCCAAACCATGACTCTTATTC
1306507 TAAATTG
1 TAAATTG
1306514 GTCTCCAAAC
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
59 1 0.02
60 60 0.98
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (60 bp):
TAAATTGATCCTTAAACTTTTAAACATTCTAACTTCATCCCCAAACCATGACTCTTATTC
Found at i:1306541 original size:60 final size:60
Alignment explanation
Indices: 1306387--1306542 Score: 174
Period size: 60 Copynumber: 2.6 Consensus size: 60
1306377 ATCCTCATTT
* * * * * *
1306387 TAAATT-GATCCTTAAACTTTTAAACATTCTAACTTCATCCCCAAACCATGACTCTTATTC
1 TAAATTAG-TCCTCAAACTTTTGAACATTCCAATTTCTTCCTCAAACCATGACTCTTATTC
* *
1306447 TAAATTAGTCCTTAAACTTTTGAACATTCTAATTTCTTCCTCAAACCATGACTCTTATTC
1 TAAATTAGTCCTCAAACTTTTGAACATTCCAATTTCTTCCTCAAACCATGACTCTTATTC
* *
1306507 TAAATTGGT-CTCCAAACTTTTTAATC-TTCCAATTTC
1 TAAATTAGTCCT-CAAACTTTTGAA-CATTCCAATTTC
1306543 AACCATAAAT
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
59 2 0.02
60 81 0.95
61 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.40
Consensus pattern (60 bp):
TAAATTAGTCCTCAAACTTTTGAACATTCCAATTTCTTCCTCAAACCATGACTCTTATTC
Found at i:1306838 original size:60 final size:57
Alignment explanation
Indices: 1306691--1306839 Score: 140
Period size: 60 Copynumber: 2.5 Consensus size: 57
1306681 AATTGATAGT
*
1306691 TCAAAAAGTTTGGGAACCAATTTAGAATGAAGATTATAGTTTGGGATGAAACTAAAATG
1 TCAAAAA-TTTGGG-ACCAATTTAGAATGAAGATCATAGTTTGGGATGAAACTAAAATG
* * * *
1306750 TCCAAAATTTTGAGGACTAATCTAGAATGATAG-TCATAGTTTAGGGATGAAATTATAATAT-
1 T-CAAAAATTTG-GGACCAATTTAGAATGA-AGATCATAGTTT-GGGATGAAACTA-AA-ATG
* *
1306811 TTAAAAATTTAGGGACCAATTTGGAATGA
1 TCAAAAATTT-GGGACCAATTTAGAATGA
1306840 GGGTCATGAT
Statistics
Matches: 73, Mismatches: 10, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
59 26 0.36
60 41 0.56
61 4 0.05
62 2 0.03
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (57 bp):
TCAAAAATTTGGGACCAATTTAGAATGAAGATCATAGTTTGGGATGAAACTAAAATG
Found at i:1307598 original size:209 final size:209
Alignment explanation
Indices: 1307238--1307652 Score: 794
Period size: 209 Copynumber: 2.0 Consensus size: 209
1307228 AAAATATATG
*
1307238 GACTAATGCATATGACCAGGGCTGTGGCTGGGGGTGCAAATTGCGCGACCGCGCAGGGTCCCCAA
1 GACTAATGCATATGACCAGGGCCGTGGCTGGGGGTGCAAATTGCGCGACCGCGCAGGGTCCCCAA
* *
1307303 AAAATGGGGCCCAAAAAAATCTATAGTGGCGTTTTACCAATAAACGCCATTATAGATGGACTTAT
66 AAAATGGGGCCAAAAAAAATCTATAGTGGCGTTTTACCAATAAACGCCACTATAGATGGACTTAT
*
1307368 TGCGACGGTTTTTCAAAAACACGCCACTATTATTGCGGTTTTATTGATAAAACGTCATTATAGAT
131 TGCGACGGTTTTTCAAAAACACGCCACTATTATTGCGGTTTTATTGATAAAACGCCATTATAGAT
1307433 GGATTTATTGCTGC
196 GGATTTATTGCTGC
1307447 GACTAATGCATATGACCAGGGCCGTGGCTGGGGGTGCAAATTGCGCGACCGCGCAGGGTCCCCAA
1 GACTAATGCATATGACCAGGGCCGTGGCTGGGGGTGCAAATTGCGCGACCGCGCAGGGTCCCCAA
1307512 AAAATGGGGCCAAAAAAAATCTATAGTGGCGTTTTACCAATAAACGCCACTATAGATGGACTTAT
66 AAAATGGGGCCAAAAAAAATCTATAGTGGCGTTTTACCAATAAACGCCACTATAGATGGACTTAT
1307577 TGCGACGGTTTTTCAAAAACACGCCACTATTATTGCGGTTTTATTGATAAAACGCCATTATAGAT
131 TGCGACGGTTTTTCAAAAACACGCCACTATTATTGCGGTTTTATTGATAAAACGCCATTATAGAT
1307642 GGATTTATTGC
196 GGATTTATTGC
1307653 GGCGTTTGTC
Statistics
Matches: 202, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
209 202 1.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.27
Consensus pattern (209 bp):
GACTAATGCATATGACCAGGGCCGTGGCTGGGGGTGCAAATTGCGCGACCGCGCAGGGTCCCCAA
AAAATGGGGCCAAAAAAAATCTATAGTGGCGTTTTACCAATAAACGCCACTATAGATGGACTTAT
TGCGACGGTTTTTCAAAAACACGCCACTATTATTGCGGTTTTATTGATAAAACGCCATTATAGAT
GGATTTATTGCTGC
Found at i:1308508 original size:108 final size:112
Alignment explanation
Indices: 1308311--1308590 Score: 279
Period size: 108 Copynumber: 2.5 Consensus size: 112
1308301 GTAGCACATT
* ****
1308311 TTTAAAGTTGATGGAGCCTTAGAAATCCGACGATAACAAAATATGTTAATTACTTATTTTGTTAT
1 TTTAAAGCTGATGGAGCCTTAGAAATCCGACGATAACAAAATATGTTAATTA-TTATAACATTAT
** * **
1308376 CAGTATTATAAACATATTAAGTAGCGCCTA-AAATGT-TA-CCAAAG-
65 CACCATAATAAACATAACAAGTAGCGCCTATAAATGTATAGCCAAAGC
1308420 TTT-AAGCTGATGGAGCCTTAGAAATCCGACGATAACAAAATATGTTAATTATTGGA-AACATTA
1 TTTAAAGCTGATGGAGCCTTAGAAATCCGACGATAACAAAATATGTTAATTATT--ATAACATTA
* * * **
1308483 TCAACCATAAT-AACATAACAAGTAGCGCTTATTTAATGTAATAGGCAGCGCC
64 TC-ACCATAATAAACATAACAAGTAGCGCCTA-TAAATGT-ATAGCCAAAG-C
1308535 TATTTAAAGCTGAT-GAGACCTTAGAAATCCGACGATAACAAAATATGTTAATTATT
1 --TTTAAAGCTGATGGAG-CCTTAGAAATCCGACGATAACAAAATATGTTAATTATT
1308591 TTTATTTATT
Statistics
Matches: 142, Mismatches: 15, Indels: 19
0.81 0.09 0.11
Matches are distributed among these distances:
107 2 0.01
108 69 0.49
109 9 0.06
110 5 0.04
112 2 0.01
113 3 0.02
117 6 0.04
118 46 0.32
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (112 bp):
TTTAAAGCTGATGGAGCCTTAGAAATCCGACGATAACAAAATATGTTAATTATTATAACATTATC
ACCATAATAAACATAACAAGTAGCGCCTATAAATGTATAGCCAAAGC
Found at i:1309110 original size:199 final size:200
Alignment explanation
Indices: 1308697--1309127 Score: 562
Period size: 199 Copynumber: 2.1 Consensus size: 200
1308687 CTTATATGAC
* * * * * * *
1308697 AGTATCGATACTTGTACATTTACGCCTATTTTCATTATACCGGTAGAAACATTTACCGTGTACAT
1 AGTATCGATACTTGGACATTTACGACTATTATCAATATATCGATAG--ACTTTTACCGTGTACAT
** * *
1308762 TGTTAATTTGCCTATTACTTTAAAGTAATATGTTTCGAAATTATAAATATTAATACTTTATATAT
64 TGTTAATTAACCTATTACTTTAAAGTAATATATTTCGAAATTACAAATATTAATACTTTATATAT
* * * * ** *
1308827 GTGTATCGATACATTTTGCGTGCAAATTGTTTGAGAAACATATTGGAATAAAAGTATCCTTACCT
129 GTGTATCGATACATTTTGCATGCAAATTGATTGAGAAACATACTAGAATAAAAGTATCAATACCA
*
1308892 ATATAAA
194 ACATAAA
* *
1308899 AGTATCGATACTTGG-TATTTACGACTATTATCAATATATCGATAGACTTTTACCGTTTACATTG
1 AGTATCGATACTTGGACATTTACGACTATTATCAATATATCGATAGACTTTTACCGTGTACATTG
* *
1308963 TTAATTAACCTATTACTTTAAAGTAATATATTTCGAAATTCCAAGTA-TATATACTTTATATATG
66 TTAATTAACCTATTACTTTAAAGTAATATATTTCGAAATTACAAATATTA-ATACTTTATATATG
1309027 TGTATCGATACATTTTGCATGCAAATTGATTGAGAAACATACTAGAATAAAAGTATCAATA-CAA
130 TGTATCGATACATTTTGCATGCAAATTGATTGAGAAACATACTAGAATAAAAGTATCAATACCAA
*
1309091 CATGAGA
195 CAT-AAA
* * *
1309098 AGTGTTGATACTTGGACATTTACGCCTATT
1 AGTATCGATACTTGGACATTTACGACTATT
1309128 TTATTTTACC
Statistics
Matches: 198, Mismatches: 28, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
198 6 0.03
199 142 0.72
200 12 0.06
201 24 0.12
202 14 0.07
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (200 bp):
AGTATCGATACTTGGACATTTACGACTATTATCAATATATCGATAGACTTTTACCGTGTACATTG
TTAATTAACCTATTACTTTAAAGTAATATATTTCGAAATTACAAATATTAATACTTTATATATGT
GTATCGATACATTTTGCATGCAAATTGATTGAGAAACATACTAGAATAAAAGTATCAATACCAAC
ATAAA
Found at i:1309184 original size:20 final size:22
Alignment explanation
Indices: 1309156--1309199 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 22
1309146 TATTAGTAAC
*
1309156 ATTTAAACA-AATCGGTAG-GT
1 ATTTAAACATAATAGGTAGCGT
*
1309176 ATTTTAACATAATAGGTAGCGT
1 ATTTAAACATAATAGGTAGCGT
1309198 AT
1 AT
1309200 ATTTTGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 8 0.40
22 4 0.20
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (22 bp):
ATTTAAACATAATAGGTAGCGT
Found at i:1309250 original size:75 final size:74
Alignment explanation
Indices: 1309124--1309284 Score: 209
Period size: 75 Copynumber: 2.2 Consensus size: 74
1309114 CATTTACGCC
* * *
1309124 TATTTTATTTTACCGTTTACTTTATTAGTAACATTTAAACAAATCGGTAGGT-ATTTTAACATAA
1 TATTTTATTTTACCGTTTACATTATTAGTAACATTTAAACAAACCGATAGGTGA--TTAACATAA
1309188 TAGGTAGCGTA
64 TAGGTAGCGTA
* * *
1309199 TATTTTGTTTTACCGTTTACATTATTAGTAACATTTAAATAAACCGATAGGTGATTAACGTAATA
1 TATTTTATTTTACCGTTTACATTATTAGTAACATTTAAACAAACCGATAGGTGATTAACATAATA
* *
1309264 GGTAAC-TCC
66 GGTAGCGT-A
1309273 TATTTTATTTTA
1 TATTTTATTTTA
1309285 ACCGGTTAAG
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
73 1 0.01
74 26 0.35
75 47 0.63
76 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.43
Consensus pattern (74 bp):
TATTTTATTTTACCGTTTACATTATTAGTAACATTTAAACAAACCGATAGGTGATTAACATAATA
GGTAGCGTA
Found at i:1310391 original size:32 final size:30
Alignment explanation
Indices: 1310351--1310411 Score: 95
Period size: 32 Copynumber: 2.0 Consensus size: 30
1310341 ACATCAATTT
1310351 TTATTAATATTATTATATTATTATAATAATAA
1 TTATTAATATTA-TATATTATT-TAATAATAA
*
1310383 TTATTAATATTATATATTATTTATTAATA
1 TTATTAATATTATATATTATTTAATAATA
1310412 TTACAAAACC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 7 0.25
31 9 0.32
32 12 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
TTATTAATATTATATATTATTTAATAATAA
Found at i:1310408 original size:20 final size:19
Alignment explanation
Indices: 1310351--1310414 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 19
1310341 ACATCAATTT
1310351 TTATTAATATTAT-TA-TA
1 TTATTAATATTATATATTA
*
1310368 TTATT-ATA--ATA-ATAA
1 TTATTAATATTATATATTA
1310383 TTATTAATATTATATATTA
1 TTATTAATATTATATATTA
1310402 TTTATTAATATTA
1 -TTATTAATATTA
1310415 CAAAACCCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
14 3 0.08
15 6 0.16
16 6 0.16
17 5 0.13
18 3 0.08
19 3 0.08
20 12 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATTAATATTATATATTA
Found at i:1312185 original size:20 final size:21
Alignment explanation
Indices: 1312162--1312213 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
1312152 AGAAATTAAA
1312162 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
1312182 AATTCTTTTCTTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
1312204 -ATT-ATTTATT
1 AATTCATTTATT
1312214 GTTTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:1319526 original size:76 final size:76
Alignment explanation
Indices: 1319387--1319532 Score: 186
Period size: 76 Copynumber: 1.9 Consensus size: 76
1319377 ACAAATGTTG
* * * * *
1319387 GGGCATGCTGAAAACCCTTGTCAATCAGAATCAGGAATATTGATGTATCCTGAATGTTTATATCA
1 GGGCATGATGAAAACCCTTGTCAATCAGAATCAAGAATATTGATGTATCCTGAACGCTCATATCA
1319452 GCAAAATGCTA
66 GCAAAATGCTA
* * * **
1319463 GGGCATGATGAAAGCCCCTT-TCAATCAGAATGAAGAATGTTGATGTATTTTGAACGCTCATATC
1 GGGCATGATGAAA-ACCCTTGTCAATCAGAATCAAGAATATTGATGTATCCTGAACGCTCATATC
1319527 AGCAAA
65 AGCAAA
1319533 TATTGGGGCA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
76 54 0.92
77 5 0.08
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (76 bp):
GGGCATGATGAAAACCCTTGTCAATCAGAATCAAGAATATTGATGTATCCTGAACGCTCATATCA
GCAAAATGCTA
Found at i:1320926 original size:22 final size:22
Alignment explanation
Indices: 1320897--1320951 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
1320887 ATCTACACTC
1320897 TTCAAAGATGATAGATTCTCTTT
1 TTCAAAGATGATAGATTCT-TTT
1320920 TT-AAAGATGATAGATTCTTTT
1 TTCAAAGATGATAGATTCTTTT
1320941 TTCAAAGATGA
1 TTCAAAGATGA
1320952 AAGCTTTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.16
22 24 0.77
23 2 0.06
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.42
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTTTT
Found at i:1321780 original size:76 final size:76
Alignment explanation
Indices: 1321628--1322577 Score: 1530
Period size: 76 Copynumber: 12.5 Consensus size: 76
1321618 CTATTTCCCA
* *
1321628 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1321693 ATCCTTAGGGT
66 AGCCTTAGGGT
* *
1321704 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCTGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
1321769 AA-CCTTCGGGT
65 AAGCCTTAGGGT
* * *
1321780 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATG-TTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
1321845 AAGCCTTCGGGT
65 AAGCCTTAGGGT
* *
1321857 CATCTATAAGCCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
1321922 AA-CCTTCGGGT
65 AAGCCTTAGGGT
* * *
1321933 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTCAAAAAGCCTTTAGGGAGCTTTTTGATGTTTTC
1 CATCTGTAAGTCCTTCAGTGCATGATG-TTTCCAAAAAGCC-TTCGGGAGCTTTTTGATGTTTTC
*
1321998 AAAACCTTAGGGT
64 AAAGCCTTAGGGT
* * *
1322011 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAACCTTCGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1322076 AGCCTTAGTGT
66 AGCCTTAGGGT
* *
1322087 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1322152 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1322163 CATCTGTAAGT-CTTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTCTCA
1 CATCTGTAAGTCCTT-CAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1322227 AAGCCTTAGGGT
65 AAGCCTTAGGGT
*
1322239 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1322304 AGCCTTAGGGT
66 AGCCTTAGGGT
1322315 CATCTGTAAGT-CTTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTT-CAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1322379 AAGCCTTAGGGT
65 AAGCCTTAGGGT
* *
1322391 CATCTGTAAGTCATGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1322456 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1322467 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTAGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1322532 AGCCTTAGAGT
66 AGCCTTAGGGT
*
1322543 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
1322578 CATTTTCATC
Statistics
Matches: 829, Mismatches: 34, Indels: 22
0.94 0.04 0.02
Matches are distributed among these distances:
75 4 0.00
76 644 0.78
77 148 0.18
78 33 0.04
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:1322719 original size:3 final size:3
Alignment explanation
Indices: 1322711--1322766 Score: 58
Period size: 3 Copynumber: 18.0 Consensus size: 3
1322701 AAATTTAAAT
** * *
1322711 TTA TTA TTA TTA TTA TTA TTA AAA TAA TTA TTA TTA ATA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
1322757 TTA TTTA TTA
1 TTA -TTA TTA
1322767 ATATACAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
3 39 0.87
4 6 0.13
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:1327403 original size:18 final size:18
Alignment explanation
Indices: 1327380--1327420 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1327370 CTATTGTTCC
1327380 TTGACTGA-TCGTTGACCA
1 TTGACTGACT-GTTGACCA
*
1327398 TTGACTGACTGTTGACCG
1 TTGACTGACTGTTGACCA
1327416 TTGAC
1 TTGAC
1327421 CATTGTCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (18 bp):
TTGACTGACTGTTGACCA
Found at i:1327438 original size:25 final size:26
Alignment explanation
Indices: 1327380--1327451 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 26
1327370 CTATTGTTCC
*
1327380 TTGACTGATCGTTGACCATTGACTGA
1 TTGACTGACCGTTGACCATTGACTGA
* * *
1327406 CTG-TTGACCGTTGACCATTGTCT-A
1 TTGACTGACCGTTGACCATTGACTGA
* *
1327430 TTGACTGACTGTTGACCGTTGA
1 TTGACTGACCGTTGACCATTGA
1327452 TCGTTTTCCG
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
24 3 0.08
25 31 0.86
26 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (26 bp):
TTGACTGACCGTTGACCATTGACTGA
Found at i:1328298 original size:39 final size:39
Alignment explanation
Indices: 1328229--1328397 Score: 212
Period size: 39 Copynumber: 4.3 Consensus size: 39
1328219 TCTATGACTT
* * *
1328229 GTAAGTCCTTACCGTAGGCTCTTCGACTTTGTGTTCAGG
1 GTAAGTCCTTACCGTAGGCTCCTCGGCTTTGTGCTCAGG
* * *
1328268 GTAAGTCCTTACCGCAGACTCCTCGGCTTTGTGCTCAAG
1 GTAAGTCCTTACCGTAGGCTCCTCGGCTTTGTGCTCAGG
* *
1328307 GTAAGTCCTTATCGTAGGCTCATCGGCTTTGTGCTCAGG
1 GTAAGTCCTTACCGTAGGCTCCTCGGCTTTGTGCTCAGG
* * * * *
1328346 GTAAGTCCTTATCGAAGGCTCCTCTGCTTTGTGCACATG
1 GTAAGTCCTTACCGTAGGCTCCTCGGCTTTGTGCTCAGG
*
1328385 ATAAGTCCTTACC
1 GTAAGTCCTTACC
1328398 ACATGTCCTT
Statistics
Matches: 112, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 112 1.00
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.33
Consensus pattern (39 bp):
GTAAGTCCTTACCGTAGGCTCCTCGGCTTTGTGCTCAGG
Found at i:1328368 original size:78 final size:78
Alignment explanation
Indices: 1328229--1328397 Score: 239
Period size: 78 Copynumber: 2.2 Consensus size: 78
1328219 TCTATGACTT
* * *
1328229 GTAAGTCCTTACCGTAGGCTCTTCGACTTTGTGTTCAGGGTAAGTCCTTACCGCAGACTCCTCGG
1 GTAAGTCCTTACCGTAGGCTCATCGACTTTGTGCTCAGGGTAAGTCCTTACCGAAGACTCCTCGG
*
1328294 CTTTGTGCTCAAG
66 CTTTGTGCACAAG
* * * * *
1328307 GTAAGTCCTTATCGTAGGCTCATCGGCTTTGTGCTCAGGGTAAGTCCTTATCGAAGGCTCCTCTG
1 GTAAGTCCTTACCGTAGGCTCATCGACTTTGTGCTCAGGGTAAGTCCTTACCGAAGACTCCTCGG
*
1328372 CTTTGTGCACATG
66 CTTTGTGCACAAG
*
1328385 ATAAGTCCTTACC
1 GTAAGTCCTTACC
1328398 ACATGTCCTT
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.33
Consensus pattern (78 bp):
GTAAGTCCTTACCGTAGGCTCATCGACTTTGTGCTCAGGGTAAGTCCTTACCGAAGACTCCTCGG
CTTTGTGCACAAG
Found at i:1329403 original size:33 final size:33
Alignment explanation
Indices: 1329363--1329437 Score: 105
Period size: 33 Copynumber: 2.3 Consensus size: 33
1329353 CTGAAGAGTT
* *
1329363 GGTTGATTGGTCGGGATTTTTCAAAGAGTTGTA
1 GGTTGATTGGTCGAGATTTTCCAAAGAGTTGTA
* * *
1329396 GGTTGATTGGTCGAGATTTTCCGATGAGTTGTT
1 GGTTGATTGGTCGAGATTTTCCAAAGAGTTGTA
1329429 GGTTGATTG
1 GGTTGATTG
1329438 ATCCATATCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.17, C:0.07, G:0.35, T:0.41
Consensus pattern (33 bp):
GGTTGATTGGTCGAGATTTTCCAAAGAGTTGTA
Found at i:1329593 original size:6 final size:6
Alignment explanation
Indices: 1329582--1329622 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
1329572 AGTGGAGTTC
* *
1329582 AAATTG AAATTG AAATTG AAATTG AAATTC AAATTC AAATT
1 AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG AAATT
1329623 TAAGTACTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.34
Consensus pattern (6 bp):
AAATTG
Found at i:1329827 original size:75 final size:75
Alignment explanation
Indices: 1329704--1329909 Score: 279
Period size: 74 Copynumber: 2.8 Consensus size: 75
1329694 TAAAAAATAT
* * * * **
1329704 ACCTTTAAAGAAATCGGTAGGTAGTTTAACGTAATAGGTAGCGTCTATTTTATTTTACCGTTTGT
1 ACCTTTAAAGAAACCGGTAGCTAGTTTAACGTAATAGGTAGTGACTATTTTATTTTACCGTTTAC
1329769 ATTATTATTA
66 ATTATTATTA
* * * *
1329779 ACCTTTAAACAAACCGATAGCTAGTTTAACGTAATAGATAGTGCCTATTTT-TTTTACCGTTTAC
1 ACCTTTAAAGAAACCGGTAGCTAGTTTAACGTAATAGGTAGTGACTATTTTATTTTACCGTTTAC
1329843 ATTATTATTA
66 ATTATTATTA
* * * *
1329853 TCCGTTAAAGAAACCGGTAACTATTTTAACGTAATAGGTAGTGACTATTTTATTTTA
1 ACCTTTAAAGAAACCGGTAGCTAGTTTAACGTAATAGGTAGTGACTATTTTATTTTA
1329910 ACCAGTTAAG
Statistics
Matches: 113, Mismatches: 17, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
74 64 0.57
75 49 0.43
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.41
Consensus pattern (75 bp):
ACCTTTAAAGAAACCGGTAGCTAGTTTAACGTAATAGGTAGTGACTATTTTATTTTACCGTTTAC
ATTATTATTA
Found at i:1330053 original size:20 final size:20
Alignment explanation
Indices: 1330030--1330083 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
1330020 AATTGAAATT
1330030 GATTTTGTCAAATTTCAACC
1 GATTTTGTCAAATTTCAACC
* * *
1330050 GATTTTGTCGATTTTCAATC
1 GATTTTGTCAAATTTCAACC
* *
1330070 GGTTTTTTCAAATT
1 GATTTTGTCAAATT
1330084 CGTTACCTGT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.15, G:0.13, T:0.48
Consensus pattern (20 bp):
GATTTTGTCAAATTTCAACC
Found at i:1330438 original size:12 final size:12
Alignment explanation
Indices: 1330421--1330447 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1330411 TTAGTCAACA
1330421 TTTCCGATAACG
1 TTTCCGATAACG
1330433 TTTCCGATAACG
1 TTTCCGATAACG
1330445 TTT
1 TTT
1330448 AACCGACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (12 bp):
TTTCCGATAACG
Found at i:1334500 original size:17 final size:17
Alignment explanation
Indices: 1334478--1334543 Score: 55
Period size: 16 Copynumber: 3.9 Consensus size: 17
1334468 AATAATTAAT
1334478 TAATAAATTTAAATAAA
1 TAATAAATTTAAATAAA
*
1334495 TAAT-AATTTATATAAA
1 TAATAAATTTAAATAAA
* * *
1334511 T-ATTATTTTTAATAAA
1 TAATAAATTTAAATAAA
* *
1334527 AAATAATATTTATATAA
1 TAATAA-ATTTAAATAA
1334544 TTATATTAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
15 2 0.05
16 21 0.57
17 7 0.19
18 7 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATAAATTTAAATAAA
Found at i:1334504 original size:16 final size:16
Alignment explanation
Indices: 1334478--1334533 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
1334468 AATAATTAAT
1334478 TAATAAATTTAAATAAA
1 TAAT-AATTTAAATAAA
*
1334495 TAATAATTTATATAAA
1 TAATAATTTAAATAAA
* * *
1334511 TATTATTTTTAATAAA
1 TAATAATTTAAATAAA
*
1334527 AAATAAT
1 TAATAAT
1334534 ATTTATATAA
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
16 27 0.87
17 4 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAATTTAAATAAA
Found at i:1334558 original size:32 final size:32
Alignment explanation
Indices: 1334474--1334566 Score: 89
Period size: 32 Copynumber: 2.8 Consensus size: 32
1334464 AAAAAATAAT
* *
1334474 TAATTA-ATAAATTTAAATAAATAATAATTTATA
1 TAATTATATTAATATAAA-AAATAAT-ATTTATA
* **
1334507 TAAATATTATTTTTAATAAAAAATAATATTTATA
1 TAATTA-TATTAAT-ATAAAAAATAATATTTATA
*
1334541 TAATTATATTAATATAAAATATAATA
1 TAATTATATTAATATAAAAAATAATA
1334567 ACTATGTAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
32 12 0.25
33 10 0.21
34 12 0.25
35 10 0.21
36 4 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
TAATTATATTAATATAAAAAATAATATTTATA
Found at i:1334560 original size:30 final size:34
Alignment explanation
Indices: 1334487--1334567 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 34
1334477 TTAATAAATT
*
1334487 TAAATAAATAATAATTTATATAAATATTATTTTTAA
1 TAAA-AAATAATAATTTATAT-AATATTATTATTAA
1334523 TAAAAAATAAT-ATTTATAT-A-ATTA-TATTAA
1 TAAAAAATAATAATTTATATAATATTATTATTAA
1334553 TATAAAATATAATAA
1 TA-AAAA-ATAATAA
1334568 CTATGTAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
30 7 0.17
31 8 0.20
32 6 0.15
33 1 0.02
34 8 0.20
35 7 0.17
36 4 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (34 bp):
TAAAAAATAATAATTTATATAATATTATTATTAA
Found at i:1336372 original size:20 final size:20
Alignment explanation
Indices: 1336349--1336418 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
1336339 GAATCGGTTC
1336349 GAGTCAACTCGAACCGGTAT
1 GAGTCAACTCGAACCGGTAT
* *
1336369 GAGTCAACCCGAACCGGTCT
1 GAGTCAACTCGAACCGGTAT
*
1336389 GAGTCAAC-CTGAACC-GAAT
1 GAGTCAACTC-GAACCGGTAT
1336408 CGAGTCAACTC
1 -GAGTCAACTC
1336419 AGACCGATCT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
19 3 0.07
20 39 0.91
21 1 0.02
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.17
Consensus pattern (20 bp):
GAGTCAACTCGAACCGGTAT
Found at i:1336404 original size:40 final size:40
Alignment explanation
Indices: 1336349--1336435 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 40
1336339 GAATCGGTTC
* *
1336349 GAGTCAACTCGAACCGGTAT-GAGTCAACCC-GAACCGGTCT
1 GAGTCAACTCGAACC-GAATCGAGTCAACCCAG-ACCGATCT
*
1336389 GAGTCAAC-CTGAACCGAATCGAGTCAACTCAGACCGATCT
1 GAGTCAACTC-GAACCGAATCGAGTCAACCCAGACCGATCT
1336429 GAGTCAA
1 GAGTCAA
1336436 TTAGAATAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
39 4 0.10
40 36 0.88
41 1 0.02
ACGTcount: A:0.31, C:0.29, G:0.23, T:0.17
Consensus pattern (40 bp):
GAGTCAACTCGAACCGAATCGAGTCAACCCAGACCGATCT
Found at i:1345914 original size:19 final size:19
Alignment explanation
Indices: 1345866--1345923 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
1345856 CACTTGACGT
1345866 AAAAATATTAAAA-TA--A
1 AAAAATATTAAAATTATTA
*
1345882 ATAAAT-TT-AAATTATTA
1 AAAAATATTAAAATTATTA
*
1345899 AAAAATATTAAAATTATTT
1 AAAAATATTAAAATTATTA
1345918 AAAAAT
1 AAAAAT
1345924 GTAAAAATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 3 0.09
15 4 0.12
16 5 0.15
17 6 0.18
18 2 0.06
19 14 0.41
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAAATATTAAAATTATTA
Found at i:1345930 original size:19 final size:19
Alignment explanation
Indices: 1345890--1345932 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1345880 AAATAAATTT
*
1345890 AAATTATTAAAAAATATTA
1 AAATTATTAAAAAATATAA
* *
1345909 AAATTATTTAAAAATGTAA
1 AAATTATTAAAAAATATAA
1345928 AAATT
1 AAATT
1345933 GACCCAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
AAATTATTAAAAAATATAA
Found at i:1349625 original size:27 final size:27
Alignment explanation
Indices: 1349593--1349650 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
1349583 TTTGGGTGCC
* * *
1349593 AGAGTCATGGGTGTTTAACATGGTGAT
1 AGAGTCATAGGCGTTGAACATGGTGAT
*
1349620 AGAGTCATAGGCGTTGCACATGGTGAT
1 AGAGTCATAGGCGTTGAACATGGTGAT
1349647 -GAGT
1 AGAGT
1349651 TTTCCATGTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.26, C:0.10, G:0.34, T:0.29
Consensus pattern (27 bp):
AGAGTCATAGGCGTTGAACATGGTGAT
Found at i:1356153 original size:15 final size:15
Alignment explanation
Indices: 1356133--1356194 Score: 124
Period size: 15 Copynumber: 4.1 Consensus size: 15
1356123 GTAGGACCAT
1356133 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
1356148 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
1356163 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
1356178 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
1356193 TA
1 TA
1356195 TTATACCCTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.34, C:0.32, G:0.19, T:0.15
Consensus pattern (15 bp):
TACATCCCGAAGGAC
Found at i:1356356 original size:12 final size:12
Alignment explanation
Indices: 1356339--1356385 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
1356329 TATCATGTTC
* *
1356339 TCATATTACATG
1 TCATATCACATA
1356351 TCATATCACATA
1 TCATATCACATA
1356363 TCATATCACATA
1 TCATATCACATA
1356375 TCATATCACAT
1 TCATATCACAT
1356386 GAACATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.36
Consensus pattern (12 bp):
TCATATCACATA
Found at i:1356802 original size:64 final size:64
Alignment explanation
Indices: 1356694--1356870 Score: 221
Period size: 64 Copynumber: 2.8 Consensus size: 64
1356684 TAATGAAGGT
* * * ** * * **
1356694 ATGCATCGATGCACTACTGATGCATCGGTGCATCAAAGGTATTCGATGTAGT-ATTATTGTTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-GTCACTATTAATGGG
* * *
1356758 ATGCATCGATGCACTCCTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTGTCACTATTAATGGG
*
1356822 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGT
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT
1356871 CTTTATTTAA
Statistics
Matches: 97, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
63 1 0.01
64 96 0.99
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTGTCACTATTAATGGG
Found at i:1356918 original size:63 final size:64
Alignment explanation
Indices: 1356694--1356918 Score: 205
Period size: 64 Copynumber: 3.5 Consensus size: 64
1356684 TAATGAAGGT
* * * * * **
1356694 ATGCATCGATGCACTA-CTGATGCATCGGTGCATCAAA-GGTATTCGATGTAGT-ATTATTGTTG
1 ATGCATCGATGCACTACCT-ATGCATCGATGCA-CAAATTGCATTCGATGT-TTCACTATTAATG
*
1356756 GG
63 AG
** *
1356758 ATGCATCGATGCACT-CCTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACC-TATGCATCGATGCACAAATTGCATTCGATGTTTCACTATTAATGAG
* *
1356822 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTCTTTA-T-TTAAAAT-
1 ATGCATCGATGCACTACCTATGCATCGATGCACAAATTGCATTCGATGT-TTCACTATT--AATG
1356884 AG
63 AG
*
1356886 -TGCATCGATGCACTACCAATGCATCGATGCACA
1 ATGCATCGATGCACTACCTATGCATCGATGCACA
1356919 TTCATATAAT
Statistics
Matches: 137, Mismatches: 16, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
63 36 0.26
64 93 0.68
65 8 0.06
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTATGCATCGATGCACAAATTGCATTCGATGTTTCACTATTAATGAG
Found at i:1363141 original size:15 final size:15
Alignment explanation
Indices: 1363121--1363167 Score: 94
Period size: 15 Copynumber: 3.1 Consensus size: 15
1363111 GTAGGACCAT
1363121 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
1363136 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
1363151 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
1363166 TA
1 TA
1363168 TTATACCCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.34, C:0.32, G:0.19, T:0.15
Consensus pattern (15 bp):
TACATCCCGAAGGAC
Found at i:1363329 original size:12 final size:12
Alignment explanation
Indices: 1363312--1363358 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
1363302 TATCATGTTC
* *
1363312 TCATATTACATG
1 TCATATCACATA
1363324 TCATATCACATA
1 TCATATCACATA
1363336 TCATATCACATA
1 TCATATCACATA
1363348 TCATATCACAT
1 TCATATCACAT
1363359 GAACATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.36
Consensus pattern (12 bp):
TCATATCACATA
Found at i:1363775 original size:64 final size:64
Alignment explanation
Indices: 1363667--1363843 Score: 207
Period size: 64 Copynumber: 2.8 Consensus size: 64
1363657 TAATGAAGGT
* * * ** * * **
1363667 ATGCATCGATGCACTACTGATGCATCGGTGCA-TCAAAGGTATTCGATGTAGT-ATTATTGTTGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACT-GATTGCATTCGATGT-GTCACTATTAATGG
1363730 G
64 G
* *
1363731 ATGCATCGATGCACTCCTTATGCATCGATGCACTGATTGCATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACTGATTGCATTCGATGTGTCACTATTAATGGG
1363795 ATGCATCGATGCACTACTTATGCATCGATGCAC-GAATTGCATTCGATGT
1 ATGCATCGATGCACTACTTATGCATCGATGCACTG-ATTGCATTCGATGT
1363844 CTTTATTTAA
Statistics
Matches: 98, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
63 2 0.02
64 95 0.97
65 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACTGATTGCATTCGATGTGTCACTATTAATGGG
Found at i:1371045 original size:9 final size:10
Alignment explanation
Indices: 1371026--1371118 Score: 55
Period size: 11 Copynumber: 8.7 Consensus size: 10
1371016 TATATATATA
*
1371026 TATAATATTT
1 TATATTATTT
1371036 TATATT-TTT
1 TATATTATTT
1371045 TATATTAATTT
1 TATATT-ATTT
1371056 TATATATAATATT
1 TATAT-T-AT-TT
1371069 T-TATATATTT
1 TATAT-TATTT
*
1371079 TATATTAATTA
1 TATATT-ATTT
* *
1371090 TATATATAATA
1 TATAT-TATTT
*
1371101 TATAATATTTT
1 TATATTA-TTT
1371112 TATATTA
1 TATATTA
1371119 ATTATATAAT
Statistics
Matches: 68, Mismatches: 7, Indels: 15
0.76 0.08 0.17
Matches are distributed among these distances:
9 9 0.13
10 11 0.16
11 35 0.51
12 10 0.15
13 3 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TATATTATTT
Found at i:1371061 original size:34 final size:34
Alignment explanation
Indices: 1371020--1371130 Score: 172
Period size: 34 Copynumber: 3.3 Consensus size: 34
1371010 CGATTATATA
1371020 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
* *
1371054 TTTATATATAATATTTTATATATTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
* *
1371088 TATATATATAATATATAATA-TTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
1371121 TATATA-ATAA
1 TATATATATAA
1371131 AAGCCTTAAG
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
32 4 0.06
33 18 0.25
34 49 0.69
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (34 bp):
TATATATATAATATTTTATATTTTTTATATTAAT
Found at i:1373821 original size:33 final size:33
Alignment explanation
Indices: 1373756--1373856 Score: 177
Period size: 33 Copynumber: 3.1 Consensus size: 33
1373746 AAACTATGAT
*
1373756 AATGAAGCATGCATTACATTATT-GAGAATCTA
1 AATGAAGAATGCATTACATTATTGGAGAATCTA
1373788 AATGAAGAATGCATTACATTATTGGAGAATCTA
1 AATGAAGAATGCATTACATTATTGGAGAATCTA
*
1373821 AATGAAGTATGCATTACATTATTGGAGAATCTA
1 AATGAAGAATGCATTACATTATTGGAGAATCTA
1373854 AAT
1 AAT
1373857 TTTTAATGAT
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 22 0.33
33 44 0.67
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.32
Consensus pattern (33 bp):
AATGAAGAATGCATTACATTATTGGAGAATCTA
Found at i:1377973 original size:33 final size:34
Alignment explanation
Indices: 1377933--1378005 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 34
1377923 TGCAGACTCC
*
1377933 AAAAAGAATATGAATTATTGGTGTGGACAGT-CA
1 AAAAAGAAGATGAATTATTGGTGTGGACAGTACA
1377966 AAAAAGAAGATGAATTATTGGTGTGGACAGTACA
1 AAAAAGAAGATGAATTATTGGTGTGGACAGTACA
1378000 AAAAAG
1 AAAAAG
1378006 TATTATATGT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 30 0.79
34 8 0.21
ACGTcount: A:0.47, C:0.05, G:0.25, T:0.23
Consensus pattern (34 bp):
AAAAAGAAGATGAATTATTGGTGTGGACAGTACA
Found at i:1379164 original size:12 final size:12
Alignment explanation
Indices: 1379147--1379171 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1379137 AAGAAAGCTA
1379147 GGAAATATTAGG
1 GGAAATATTAGG
1379159 GGAAATATTAGG
1 GGAAATATTAGG
1379171 G
1 G
1379172 CAAAGAGGCA
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:0.40, C:0.00, G:0.36, T:0.24
Consensus pattern (12 bp):
GGAAATATTAGG
Found at i:1379498 original size:8 final size:8
Alignment explanation
Indices: 1379473--1379618 Score: 65
Period size: 8 Copynumber: 18.4 Consensus size: 8
1379463 TTGTTTTTAA
1379473 AAAAAATT
1 AAAAAATT
*
1379481 AAAATTATT
1 AAAA-AATT
*
1379490 TAAAAATT
1 AAAAAATT
*
1379498 TAAAAA-T
1 AAAAAATT
1379505 AAAAATATTT
1 AAAAA-A-TT
1379515 AAAAAATT
1 AAAAAATT
1379523 AAAAAATT
1 AAAAAATT
*
1379531 -AAATA-T
1 AAAAAATT
1379537 -AAAAA-T
1 AAAAAATT
* *
1379543 ACTAAAAGT
1 A-AAAAATT
1379552 -AAAAATT
1 AAAAAATT
**
1379559 AAATTATT
1 AAAAAATT
1379567 AAAAAAATAT
1 -AAAAAAT-T
1379577 AAAAAA-T
1 AAAAAATT
* *
1379584 ACTAAAAGT
1 A-AAAAATT
1379593 -AAAAATT
1 AAAAAATT
**
1379600 AAATTATT
1 AAAAAATT
1379608 AAAAAATT
1 AAAAAATT
1379616 AAA
1 AAA
1379619 TATAAATATT
Statistics
Matches: 105, Mismatches: 20, Indels: 26
0.70 0.13 0.17
Matches are distributed among these distances:
6 6 0.06
7 21 0.20
8 51 0.49
9 20 0.19
10 7 0.07
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (8 bp):
AAAAAATT
Found at i:1379509 original size:25 final size:24
Alignment explanation
Indices: 1379474--1379527 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1379464 TGTTTTTAAA
* *
1379474 AAAAATTAAAATTATTTAAAAATTT
1 AAAAA-TAAAAATATTTAAAAAATT
1379499 AAAAATAAAAATATTTAAAAAATT
1 AAAAATAAAAATATTTAAAAAATT
1379523 AAAAA
1 AAAAA
1379528 ATTAAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 22 0.81
25 5 0.19
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (24 bp):
AAAAATAAAAATATTTAAAAAATT
Found at i:1379528 original size:25 final size:24
Alignment explanation
Indices: 1379473--1379529 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 24
1379463 TTGTTTTTAA
*
1379473 AAAAAATTAAAATTATTTAAAAATT
1 AAAAAA-TAAAAATATTTAAAAATT
*
1379498 TAAAAATAAAAATATTTAAAAAATT
1 AAAAAATAAAAATATTT-AAAAATT
1379523 AAAAAAT
1 AAAAAAT
1379530 TAAATATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 10 0.36
25 18 0.64
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (24 bp):
AAAAAATAAAAATATTTAAAAATT
Found at i:1379534 original size:24 final size:23
Alignment explanation
Indices: 1379473--1379536 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 23
1379463 TTGTTTTTAA
1379473 AAAAAATTAAAATTATTTAAAAATT
1 AAAAAATT-AAA-TATTTAAAAATT
* *
1379498 TAAAAATAAAAATATTTAAAAAATT
1 AAAAAAT-TAAATATTT-AAAAATT
1379523 AAAAAATTAAATAT
1 AAAAAATTAAATAT
1379537 AAAAATACTA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
24 11 0.33
25 22 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAAAATTAAATATTTAAAAATT
Found at i:1379542 original size:21 final size:22
Alignment explanation
Indices: 1379516--1379629 Score: 60
Period size: 21 Copynumber: 5.4 Consensus size: 22
1379506 AAAATATTTA
*
1379516 AAAAATTA-AAAAATTAAATAT
1 AAAAATTACAAAAAGTAAATAT
* *
1379537 AAAAA-TACTAAAAGTAAAAAT
1 AAAAATTACAAAAAGTAAATAT
* **
1379558 -TAAATTATTAAAA--AAATAT
1 AAAAATTACAAAAAGTAAATAT
* * *
1379577 AAAAAATACTAAAAGTAAAAATT
1 AAAAATTACAAAAAGTAAATA-T
* *
1379600 AAATTATTA-AAAAATTAAATAT
1 AAA-AATTACAAAAAGTAAATAT
*
1379622 AAATATTA
1 AAAAATTA
1379630 ATCATATTAA
Statistics
Matches: 71, Mismatches: 15, Indels: 14
0.71 0.15 0.14
Matches are distributed among these distances:
19 5 0.07
20 15 0.21
21 27 0.38
22 8 0.11
23 13 0.18
24 3 0.04
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAAATTACAAAAAGTAAATAT
Found at i:1379563 original size:41 final size:42
Alignment explanation
Indices: 1379517--1379624 Score: 150
Period size: 41 Copynumber: 2.5 Consensus size: 42
1379507 AAATATTTAA
1379517 AAAATTAAAAAATTAAATATAAAAATACTAAAAGTAAAAATT
1 AAAATTAAAAAATTAAATATAAAAATACTAAAAGTAAAAATT
*
1379559 -AAATTATTAAAA--AAATATAAAAAATACTAAAAGTAAAAATT
1 AAAATTA-AAAAATTAAATAT-AAAAATACTAAAAGTAAAAATT
1379600 AAATTATTAAAAAATTAAATATAAA
1 AAA--ATTAAAAAATTAAATATAAA
1379625 TATTAATCAT
Statistics
Matches: 57, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
40 6 0.11
41 28 0.49
42 6 0.11
43 4 0.07
44 7 0.12
45 6 0.11
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (42 bp):
AAAATTAAAAAATTAAATATAAAAATACTAAAAGTAAAAATT
Found at i:1379614 original size:40 final size:41
Alignment explanation
Indices: 1379531--1379613 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
1379521 TTAAAAAATT
1379531 AAATAT-AAAAATACTAAAAGTAAAAATTAAATTATTAAAA
1 AAATATAAAAAATACTAAAAGTAAAAATTAAATTATTAAAA
1379571 AAATATAAAAAATACTAAAAGTAAAAATTAAATTATTAAAA
1 AAATATAAAAAATACTAAAAGTAAAAATTAAATTATTAAAA
1379612 AA
1 AA
1379614 TTAAATATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 6 0.14
41 36 0.86
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (41 bp):
AAATATAAAAAATACTAAAAGTAAAAATTAAATTATTAAAA
Found at i:1386664 original size:18 final size:18
Alignment explanation
Indices: 1386641--1386696 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
1386631 ATGTTTTTGT
*
1386641 AGAAAACATACTGTAGAA
1 AGAAAACAGACTGTAGAA
*
1386659 AGAAAACAGACTGTATTG-T
1 AGAAAACAGACTGTA--GAA
1386678 AGAAAACAGACTGTAGAA
1 AGAAAACAGACTGTAGAA
1386696 A
1 A
1386697 ACAGAGAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
17 1 0.03
18 15 0.47
19 15 0.47
20 1 0.03
ACGTcount: A:0.52, C:0.11, G:0.20, T:0.18
Consensus pattern (18 bp):
AGAAAACAGACTGTAGAA
Found at i:1386683 original size:19 final size:19
Alignment explanation
Indices: 1386637--1386692 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 19
1386627 CTGTATGTTT
*
1386637 TTGTAGAAAACATACTGTA
1 TTGTAGAAAACAGACTGTA
*
1386656 --GAAAGAAAACAGACTGTA
1 TTG-TAGAAAACAGACTGTA
1386674 TTGTAGAAAACAGACTGTA
1 TTGTAGAAAACAGACTGTA
1386693 GAAAACAGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 1 0.03
18 14 0.45
19 15 0.48
20 1 0.03
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.23
Consensus pattern (19 bp):
TTGTAGAAAACAGACTGTA
Found at i:1386694 original size:14 final size:14
Alignment explanation
Indices: 1386675--1386701 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1386665 CAGACTGTAT
1386675 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
1386689 TGTAGAAAACAGA
1 TGTAGAAAACAGA
1386702 GAAGTCTGTT
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:0.52, C:0.11, G:0.22, T:0.15
Consensus pattern (14 bp):
TGTAGAAAACAGAC
Found at i:1388670 original size:36 final size:36
Alignment explanation
Indices: 1388617--1388688 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
1388607 TTACCTTCTG
* *
1388617 TTTCAGATGCAATAGGATCCGAATCTGGTTCTTGGC
1 TTTCAGAGGCAACAGGATCCGAATCTGGTTCTTGGC
1388653 TTTCAGAGGCAACAGGATCCGAATCTGGTTCTTGGC
1 TTTCAGAGGCAACAGGATCCGAATCTGGTTCTTGGC
1388689 GAATACTAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (36 bp):
TTTCAGAGGCAACAGGATCCGAATCTGGTTCTTGGC
Found at i:1390801 original size:19 final size:18
Alignment explanation
Indices: 1390755--1390806 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
1390745 ACCTGATACC
*
1390755 ATGTAGAAAACAGGCTGT
1 ATGTAGAAAACAGACTGT
*
1390773 A-GAAAGAAAACAGACTGT
1 ATG-TAGAAAACAGACTGT
1390791 ATTGTAGAAAACAGAC
1 A-TGTAGAAAACAGAC
1390807 AAGTCTGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 1 0.04
18 15 0.54
19 11 0.39
20 1 0.04
ACGTcount: A:0.48, C:0.12, G:0.23, T:0.17
Consensus pattern (18 bp):
ATGTAGAAAACAGACTGT
Found at i:1393350 original size:33 final size:33
Alignment explanation
Indices: 1393308--1393374 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
1393298 AAGCAACGTA
1393308 TGATCTGATACAGGATGATGAAGTAGAATGGTG
1 TGATCTGATACAGGATGATGAAGTAGAATGGTG
1393341 TGATCTGATACAGGATGATGAAGTAGAATGGTG
1 TGATCTGATACAGGATGATGAAGTAGAATGGTG
1393374 T
1 T
1393375 AACGCCCTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.33, C:0.06, G:0.33, T:0.28
Consensus pattern (33 bp):
TGATCTGATACAGGATGATGAAGTAGAATGGTG
Found at i:1393871 original size:2 final size:2
Alignment explanation
Indices: 1393855--1393888 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1393845 TCAAATTATG
* *
1393855 AT AT AT GT AT TT 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
1393889 TTGTAGGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1397965 original size:111 final size:111
Alignment explanation
Indices: 1397766--1397987 Score: 381
Period size: 111 Copynumber: 2.0 Consensus size: 111
1397756 CATCATAAAG
* *
1397766 CTGATGATTGTTGCAGGCACAGGCACTTCTGAGCATCCACCGAAACTACCGACATGGTAATGCTG
1 CTGAAGATTGTTGCAGGCACAGGCACTTCTGAGCATCCACCGAAACTACCAACATGGTAATGCTG
1397831 GAAGAGGCTGAATGTATGAAAAACATCCTTCATTGCGATCCAAGGT
66 GAAGAGGCTGAATGTATGAAAAACATCCTTCATTGCGATCCAAGGT
* * * *
1397877 CTGAAGATTGTTGCATGCATAGGCACTTCTGAGCCTCCTCCGAAACTACCAACATGGTAATGCTG
1 CTGAAGATTGTTGCAGGCACAGGCACTTCTGAGCATCCACCGAAACTACCAACATGGTAATGCTG
*
1397942 GAATAGGCTGAATGTATGAAAAACATCCTTCATTGCGATCCAAGGT
66 GAAGAGGCTGAATGTATGAAAAACATCCTTCATTGCGATCCAAGGT
1397988 TTTGGGTCTA
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
111 104 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (111 bp):
CTGAAGATTGTTGCAGGCACAGGCACTTCTGAGCATCCACCGAAACTACCAACATGGTAATGCTG
GAAGAGGCTGAATGTATGAAAAACATCCTTCATTGCGATCCAAGGT
Found at i:1398818 original size:33 final size:33
Alignment explanation
Indices: 1398771--1398874 Score: 183
Period size: 33 Copynumber: 3.2 Consensus size: 33
1398761 ACAAAGTTTA
* *
1398771 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1398803 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1398836 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1398869 CGATAA
1 CGATAA
1398875 TTGAAACAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 4 0.06
33 65 0.94
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTCCAAGTT
Found at i:1398894 original size:21 final size:21
Alignment explanation
Indices: 1398869--1398910 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1398859 CTTCCAAGTT
1398869 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
1398890 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
1398911 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:1401393 original size:28 final size:27
Alignment explanation
Indices: 1401345--1401399 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
1401335 GGTTTTCCCC
*
1401345 AAATCCGATTTCGGATATTTTTTGTACA
1 AAATCCGATTTCAGA-ATTTTTTGTACA
*
1401373 AAATCGGATATTCAG-ATTTTTTGTACA
1 AAATCCGAT-TTCAGAATTTTTTGTACA
1401400 CCTCTAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 12 0.50
28 8 0.33
29 4 0.17
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.42
Consensus pattern (27 bp):
AAATCCGATTTCAGAATTTTTTGTACA
Found at i:1405987 original size:27 final size:27
Alignment explanation
Indices: 1405949--1406010 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
1405939 GGAAGCCCCG
*
1405949 CATTCAACCGCAAACATATGGCTCTTT
1 CATTCAATCGCAAACATATGGCTCTTT
1405976 CATTCAATCGCAAACATATGGCTCTTT
1 CATTCAATCGCAAACATATGGCTCTTT
1406003 CATTCAAT
1 CATTCAAT
1406011 GACATGTTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.31, C:0.27, G:0.10, T:0.32
Consensus pattern (27 bp):
CATTCAATCGCAAACATATGGCTCTTT
Found at i:1410786 original size:22 final size:21
Alignment explanation
Indices: 1410752--1410792 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1410742 ATAATTATTT
1410752 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
1410773 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
1410793 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:1411001 original size:14 final size:14
Alignment explanation
Indices: 1410984--1411011 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1410974 ATCATAACAA
1410984 AATTATATAACTAT
1 AATTATATAACTAT
1410998 AATTATATAACTAT
1 AATTATATAACTAT
1411012 TCTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:1412374 original size:22 final size:22
Alignment explanation
Indices: 1412342--1412401 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
1412332 AGACCACTAC
* *
1412342 GTCCCGAATGACTACTGGATAT
1 GTCCCGAATGACCACTGAATAT
*
1412364 GTCTCGAATGACCACTGAATAT
1 GTCCCGAATGACCACTGAATAT
*
1412386 GTCCCGAATGATCACT
1 GTCCCGAATGACCACT
1412402 ATAACCTTCG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (22 bp):
GTCCCGAATGACCACTGAATAT
Found at i:1414185 original size:42 final size:41
Alignment explanation
Indices: 1414111--1414274 Score: 193
Period size: 42 Copynumber: 3.9 Consensus size: 41
1414101 TTCAAAATTC
* * *
1414111 CATAGTGCTTTAACTATTAAATTACATGGCTTTGTCTTGTTG
1 CATAGTGCGTTAATTATTAAATT-TATGGCTTTGTCTTGTTG
* * * * * *
1414153 AATAATGTGTTAATTATTAAATTCTATTGCTTTGTCTTATTC
1 CATAGTGCGTTAATTATTAAATT-TATGGCTTTGTCTTGTTG
*
1414195 CATAGTGCCTTAATTATTAAAGTTTATGGCTTTGTCTTGTTG
1 CATAGTGCGTTAATTATTAAA-TTTATGGCTTTGTCTTGTTG
*
1414237 CATAGTGCGTTACTTATTAAATTTCATGGCTTTGTCTT
1 CATAGTGCGTTAATTATTAAATTT-ATGGCTTTGTCTT
1414275 CTCCCTTCAA
Statistics
Matches: 101, Mismatches: 19, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
41 3 0.03
42 96 0.95
43 2 0.02
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.48
Consensus pattern (41 bp):
CATAGTGCGTTAATTATTAAATTTATGGCTTTGTCTTGTTG
Found at i:1414213 original size:84 final size:84
Alignment explanation
Indices: 1414107--1414274 Score: 232
Period size: 84 Copynumber: 2.0 Consensus size: 84
1414097 AAAGTTCAAA
* *
1414107 ATTCCATAGTGCTTTAACTATTAAA-TTACATGGCTTTGTCTTGTTGAATAATGTGTTAATTATT
1 ATTCCATAGTGCCTTAACTATTAAAGTT-CATGGCTTTGTCTTGTTGAATAATGCGTTAATTATT
*
1414171 AAA-TTCTATTGCTTTGTCTT
65 AAATTTC-ATGGCTTTGTCTT
* * * * *
1414191 ATTCCATAGTGCCTTAATTATTAAAGTTTATGGCTTTGTCTTGTTGCATAGTGCGTTACTTATTA
1 ATTCCATAGTGCCTTAACTATTAAAGTTCATGGCTTTGTCTTGTTGAATAATGCGTTAATTATTA
1414256 AATTTCATGGCTTTGTCTT
66 AATTTCATGGCTTTGTCTT
1414275 CTCCCTTCAA
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
84 69 0.93
85 5 0.07
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.48
Consensus pattern (84 bp):
ATTCCATAGTGCCTTAACTATTAAAGTTCATGGCTTTGTCTTGTTGAATAATGCGTTAATTATTA
AATTTCATGGCTTTGTCTT
Found at i:1415982 original size:31 final size:31
Alignment explanation
Indices: 1415884--1415974 Score: 159
Period size: 31 Copynumber: 3.0 Consensus size: 31
1415874 CAATTTAAGG
1415884 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1415915 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
*
1415946 CAAAAT-GTTTTTAGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1415975 TTCAAAATTT
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
29 11 0.19
30 11 0.19
31 37 0.63
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:1418361 original size:13 final size:13
Alignment explanation
Indices: 1418338--1418375 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1418328 CAATCAGAAC
1418338 AAAAAAG-AAAAA
1 AAAAAAGCAAAAA
*
1418350 AGAAAAGCAAAAA
1 AAAAAAGCAAAAA
*
1418363 AAAAAAACAAAAA
1 AAAAAAGCAAAAA
1418376 CAAAGGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 6 0.27
13 16 0.73
ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAGCAAAAA
Found at i:1418367 original size:19 final size:20
Alignment explanation
Indices: 1418335--1418379 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
1418325 ATCCAATCAG
*
1418335 AACAAAAAAGAAAAAAGAAA
1 AACAAAAAAGAAAAAACAAA
*
1418355 AGCAAAAAA-AAAAAACAAA
1 AACAAAAAAGAAAAAACAAA
1418374 AACAAA
1 AACAAA
1418380 GGAAAAAGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (20 bp):
AACAAAAAAGAAAAAACAAA
Found at i:1419465 original size:33 final size:32
Alignment explanation
Indices: 1419409--1419483 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 32
1419399 AGGAACAATG
1419409 GGGGCATCTTTGAAAATTCAACATCAAATGATT
1 GGGGCATCTTTGAAAATTCAACATCAAAT-ATT
*** * **
1419442 GGGGCATCTTTGGCGATTTAACATTGAATATT
1 GGGGCATCTTTGAAAATTCAACATCAAATATT
1419474 GGGGCATCTT
1 GGGGCATCTT
1419484 CGGGGACTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 13 0.36
33 23 0.64
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (32 bp):
GGGGCATCTTTGAAAATTCAACATCAAATATT
Found at i:1422851 original size:42 final size:41
Alignment explanation
Indices: 1422804--1422967 Score: 159
Period size: 42 Copynumber: 3.9 Consensus size: 41
1422794 TTCAAAATTC
* *
1422804 CATAGTGCTTTAACTATTAAATTACATGGCTTTGTCTTGTTG
1 CATAGTGCGTTAACTATTAAATT-CATGGCTTTGTCTTGTTA
* * * * *
1422846 CATAGTGCGTCAATTATTAAATTCTATTGCTTTGTCTTATTC
1 CATAGTGCGTTAACTATTAAATTC-ATGGCTTTGTCTTGTTA
* * * * *
1422888 CATAATGCCTTAATTATTAAAGTTTATGGCTTTGTCTTGATA
1 CATAGTGCGTTAACTATTAAA-TTCATGGCTTTGTCTTGTTA
*
1422930 CCTAGTGCGTT-ACTTATTAAATTTCATGGCTTTGTCTT
1 CATAGTGCGTTAAC-TATTAAA-TTCATGGCTTTGTCTT
1422968 CTCCCTTCAA
Statistics
Matches: 99, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
41 2 0.02
42 95 0.96
43 2 0.02
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (41 bp):
CATAGTGCGTTAACTATTAAATTCATGGCTTTGTCTTGTTA
Found at i:1422947 original size:84 final size:84
Alignment explanation
Indices: 1422800--1422967 Score: 214
Period size: 84 Copynumber: 2.0 Consensus size: 84
1422790 AAAGTTCAAA
* * * *
1422800 ATTCCATAGTGCTTTAACTATTAAATTACATGGCTTTGTCTTGTTGCATAGTGCGTCAATTATTA
1 ATTCCATAATGCCTTAACTATTAAATTACATGGCTTTGTCTTGATACATAGTGCGTCAATTATTA
*
1422865 AA-TTCTATTGCTTTGTCTT
66 AATTTC-ATGGCTTTGTCTT
* * * * *
1422884 ATTCCATAATGCCTTAATTATTAAAGTT-TATGGCTTTGTCTTGATACCTAGTGCGTTACTTATT
1 ATTCCATAATGCCTTAACTATTAAA-TTACATGGCTTTGTCTTGATACATAGTGCGTCAATTATT
1422948 AAATTTCATGGCTTTGTCTT
65 AAATTTCATGGCTTTGTCTT
1422968 CTCCCTTCAA
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
84 67 0.93
85 5 0.07
ACGTcount: A:0.24, C:0.15, G:0.14, T:0.46
Consensus pattern (84 bp):
ATTCCATAATGCCTTAACTATTAAATTACATGGCTTTGTCTTGATACATAGTGCGTCAATTATTA
AATTTCATGGCTTTGTCTT
Found at i:1424009 original size:24 final size:22
Alignment explanation
Indices: 1423959--1424016 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 22
1423949 AATGAAGGTA
*
1423959 TGCATCGATGCACTCTATAGTG
1 TGCATCGATGCACTCCATAGTG
*
1423981 T--ATCGATGCATTCCATAACGTG
1 TGCATCGATGCACTCCAT-A-GTG
1424003 TGCATCGATGCACT
1 TGCATCGATGCACT
1424017 ACCTGTGCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 13 0.45
21 1 0.03
22 5 0.17
24 10 0.34
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (22 bp):
TGCATCGATGCACTCCATAGTG
Found at i:1424078 original size:64 final size:64
Alignment explanation
Indices: 1424002--1424159 Score: 174
Period size: 64 Copynumber: 2.5 Consensus size: 64
1423992 TCCATAACGT
** * * *
1424002 GTGCATCGATGCACTACCTGTGCATCGATGCACAAATCACCTTCGATGTTTTAATCTTAAGGGG
1 GTGCATCGATGCACTACCTGTGCATCGATAAACAAATCACATTCGATGTTTTAATCTTAAAGGA
** ** * *
1424066 GTGCATCGATGCACTA-CTAGTGCATCGATAAACTTATGGCATTCGATGTTTTTATTTTAAAGGA
1 GTGCATCGATGCACTACCT-GTGCATCGATAAACAAATCACATTCGATGTTTTAATCTTAAAGGA
* * *
1424130 GTGCATCGATACACTTCATGTGCATCGATA
1 GTGCATCGATGCACTACCTGTGCATCGATA
1424160 GACCTTGAAC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
63 2 0.03
64 75 0.96
65 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCACTACCTGTGCATCGATAAACAAATCACATTCGATGTTTTAATCTTAAAGGA
Found at i:1430312 original size:22 final size:22
Alignment explanation
Indices: 1430284--1430342 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
1430274 GACCACTACA
*
1430284 TCCCGAAGAACCATTGGATATG
1 TCCCGAAGAACCACTGGATATG
1430306 TCCCGAA-AGACCACTGGATATG
1 TCCCGAAGA-ACCACTGGATATG
*
1430328 TCCCGAAGGACCACT
1 TCCCGAAGAACCACT
1430343 ATAACCCTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 1 0.03
22 32 0.97
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.19
Consensus pattern (22 bp):
TCCCGAAGAACCACTGGATATG
Found at i:1430991 original size:16 final size:18
Alignment explanation
Indices: 1430956--1430992 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1430946 CTTAATGAGG
1430956 TGCATCGATGCACTACTTA
1 TGCATCGAT-CACTACTTA
1430975 TGCATCGAT-AC-ACTTA
1 TGCATCGATCACTACTTA
1430991 TG
1 TG
1430993 GCATTCGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.39
17 2 0.11
19 9 0.50
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.32
Consensus pattern (18 bp):
TGCATCGATCACTACTTA
Found at i:1431000 original size:64 final size:64
Alignment explanation
Indices: 1430891--1431051 Score: 182
Period size: 64 Copynumber: 2.5 Consensus size: 64
1430881 TCCATAACGT
* *
1430891 GTGCATCGATGCACTACTTGTGCATC-AGTACACAAATCACCTTCGATGTTTTAATCTT-AATGA
1 GTGCATCGATGCACTACTTGTGCATCGA-TACACAAATCACATTCGATGTTTTAATCTTAAAGGA
* ** ** * *
1430954 GGTGCATCGATGCACTACTTATGCATCGATACACTTATGGCATTCGATGTTTTTATTTTAAAGGA
1 -GTGCATCGATGCACTACTTGTGCATCGATACACAAATCACATTCGATGTTTTAATCTTAAAGGA
* * *
1431019 GTGCATCGATACACTTCATGTGCATCGATACAC
1 GTGCATCGATGCACTACTTGTGCATCGATACAC
1431052 CTTAAACAAT
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
64 77 0.94
65 5 0.06
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (64 bp):
GTGCATCGATGCACTACTTGTGCATCGATACACAAATCACATTCGATGTTTTAATCTTAAAGGA
Found at i:1434039 original size:35 final size:34
Alignment explanation
Indices: 1433993--1434105 Score: 154
Period size: 35 Copynumber: 3.2 Consensus size: 34
1433983 AAAACAATCC
*
1433993 TCAATTTCATTCTAAACCACAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACC-CAAATTCCAAAATAAT
1434028 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCCAAAATAAT
* * * *
1434063 TCAATTACATTCTAAAACCTAAATTCTAAAATACT
1 TCAATTTCATTCT-AAACCCAAATTCCAAAATAAT
1434098 TCAATTTC
1 TCAATTTC
1434106 TATCTTTTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
34 1 0.01
35 64 0.91
36 5 0.07
ACGTcount: A:0.42, C:0.22, G:0.01, T:0.35
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:1435205 original size:35 final size:34
Alignment explanation
Indices: 1435157--1435268 Score: 161
Period size: 35 Copynumber: 3.2 Consensus size: 34
1435147 ATTCCTCCTT
*
1435157 AAATTGAAATATTTTAGAATTTGGGTTTTAGAATG
1 AAATTGAATTATTTTAGAATTTGGG-TTTAGAATG
* *
1435192 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTAGAATTT-GGGTTTAGAATG
*
1435227 AAATTGAATTACTTTAGAATTTGGGGTTTAGAATG
1 AAATTGAATTATTTTAGAATTT-GGGTTTAGAATG
1435262 AAATTGA
1 AAATTGA
1435269 TGAATGTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
35 66 0.96
36 3 0.04
ACGTcount: A:0.36, C:0.01, G:0.21, T:0.42
Consensus pattern (34 bp):
AAATTGAATTATTTTAGAATTTGGGTTTAGAATG
Found at i:1436161 original size:2 final size:2
Alignment explanation
Indices: 1436154--1436192 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1436144 ATTTAATGAT
1436154 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1436193 GATAGGTTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1436867 original size:23 final size:23
Alignment explanation
Indices: 1436841--1436886 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1436831 AATTAAAACA
*
1436841 AAAATAAA-AGAAATAATAAATAT
1 AAAATAAATA-AAATAAAAAATAT
1436864 AAAATAAATAAAATAAAAAATAT
1 AAAATAAATAAAATAAAAAATAT
1436887 CGGATCAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (23 bp):
AAAATAAATAAAATAAAAAATAT
Found at i:1436939 original size:17 final size:17
Alignment explanation
Indices: 1436918--1436954 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1436908 ATAATGGCCT
*
1436918 TAAAAATAT-AATTAAA
1 TAAAAACATGAATTAAA
1436934 TAAAAACATGAATTAAA
1 TAAAAACATGAATTAAA
1436951 TAAA
1 TAAA
1436955 GAAAGGATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.27
Consensus pattern (17 bp):
TAAAAACATGAATTAAA
Found at i:1438595 original size:2 final size:2
Alignment explanation
Indices: 1438588--1438636 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1438578 TGATAACTTT
1438588 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
1438630 TA TA TA T
1 TA TA TA T
1438637 TGTCATACTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1438729 original size:2 final size:2
Alignment explanation
Indices: 1438722--1438759 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1438712 ATACTAACTC
1438722 AT 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 AT
1438760 TGTCATACTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1438775 original size:123 final size:123
Alignment explanation
Indices: 1438599--1438862 Score: 474
Period size: 123 Copynumber: 2.1 Consensus size: 123
1438589 ATATATATAT
1438599 ATATATATATATATATATATATATATATATATATATATTGTCATACTCATAATTTGATATCCAAC
1 ATATATATATATATATATATATATATATATATATATATTGTCATACTCATAATTTGATATCCAAC
* * *
1438664 TATTCTAGAAATATATAAAACTAAAAATTGTACATTAAATATAAGTGAATACTAACTC
66 TATTCTAAAAAAATATAAAACTAAAAATTGTACATTAAATATAAGTAAATACTAACTC
1438722 ATATATATATATATATATATATATATATATATATATATTGTCATACTCATAATTTGATATCCAAC
1 ATATATATATATATATATATATATATATATATATATATTGTCATACTCATAATTTGATATCCAAC
* * *
1438787 TATTCTAAAAAAATATAAAACTAAAATTTTTACATTAAGTATAAGTAAATACTAACTC
66 TATTCTAAAAAAATATAAAACTAAAAATTGTACATTAAATATAAGTAAATACTAACTC
1438845 ATATATATATATATATAT
1 ATATATATATATATATAT
1438863 TGTCATACTC
Statistics
Matches: 135, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
123 135 1.00
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (123 bp):
ATATATATATATATATATATATATATATATATATATATTGTCATACTCATAATTTGATATCCAAC
TATTCTAAAAAAATATAAAACTAAAAATTGTACATTAAATATAAGTAAATACTAACTC
Found at i:1441181 original size:121 final size:120
Alignment explanation
Indices: 1440967--1442301 Score: 1081
Period size: 121 Copynumber: 10.9 Consensus size: 120
1440957 GTCGATCTAT
* * * *
1440967 TGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCTTTCGTTGTGAAGTTGAGCT
1 TGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCC
** * * * *
1441032 TTGAATTGGATATTATTCGACGTAAAGTTGAAATCCAAGGGTTGCATTGCTGCTTG
66 TTGAATTGGATATCCTTCGTCATGAAGTTGAAATCCAAGGGTTG-ATTGTTGCTTG
*
1441088 TGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGCC
1 TGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCC
* ** * *
1441153 TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGC-TG
66 TTGAATTGGATATCCTTCGTCATGAAGTTGAAATCC-A---AGGGTTGATTGTTGCTTG
* * * * * * * * *
1441211 ATGGACACAATATCCTTCATCGTGAAGTTGAAATAGTAGAT-AGCTCATTCGTTGTGAAGTTAAA
1 -TGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGA-CCCCTTCGTTGTGAAGTTGAG
* * * * **
1441275 CTTTGAATTGGATACCCTTCGTCGTGAATTTGAAATCCAA-TCTTG-TGTAAGTTACGTCATT-
64 CCTTGAATTGGATATCCTTCGTCATGAAGTTGAAATCCAAGGGTTGAT-T--GTT--G-C-TTG
* * *
1441336 TCGAGTC-CAATATCCTTCG-CTGTGAAGTTGAAATTAACTCTGAATGAAACTGGGAAGCCCCTT
1 T-G-GGCACGATATCCTTCGTC-GTGAAGTTG--A--AA-TC-G--TG-GA-T--G-A-CCCCTT
* * * * * **
1441399 CGCTGTGAAGTTGGGCTTTGAATTGAATATCATTCGTTGTGAAGTTGAAATCC-A------A-TG
49 CGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCATGAAGTTGAAATCCAAGGGTTGATTG
* *
1441456 CTGCTTA
114 TTGCTTG
* * * * * * *
1441463 TGAGCACGATATCATTCGTCGTGAAGTTAAAATCATGGATGTCCCTTTCGTTGTGAAGTTGAGTC
1 TGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCC
* * * ** *
1441528 TTGAATTAGATATTCTTCGTCGTGAAGTTGAAATCCAA-TCTTG-TGTAAGTTGTATTG
66 TTGAATTGGATATCCTTCGTCATGAAGTTGAAATCCAAGGGTTGAT-T--GTTG-CTTG
* * * ** * *
1441585 TTTCGAGTC-CAATATCCTTCGCCGTGAAGTTGAAATTATGGATGGCCTCTTCGTTGTGAAGTTG
1 --T-G-GGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTG
* * * * *
1441649 AGCTTTGAATTGGATATCATTCGTCAT-TAGTTGAAATCCAAGGGTTACATTGTTGCTGG
62 AGCCTTGAATTGGATATCCTTCGTCATGAAGTTGAAATCCAAGGGTT-GATTGTTGCTTG
* * *
1441708 TGGACACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCATCGTGAAGTTGAGCC
1 TGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCC
* * * * * * *
1441773 TCGAATTGGATATCCTTCTTCTTGAAGTTGAAATTCAATCTAA-AGATGAATGTTGCTGG
66 TTGAATTGGATATCCTTCGTCATGAAGTTGAAA-TC---C-AAGGGTTGATTGTTGCTTG
* * * * * *
1441832 TGGGTACGATATCATTCGTCGTGAAGGTGAAATCGTTGATGGCCCCATCGTTGTGAAGTTGAGCC
1 TGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCC
* * *
1441897 TCGAATTGGATATCCTTCATCATGAAGTTGAAATCCAAGGGTTGAATTGATGCTTG
66 TTGAATTGGATATCCTTCGTCATGAAGTTGAAATCCAAGGGTTG-ATTGTTGCTTG
* * *
1441953 TGAGCACGATATGCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTCGTGAAGTTGAGCC
1 TGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCC
* *
1442018 TTGAATTGGATATCCTTCATCATGAATTTGAAATCCAAGGGTTGCATTGTTGCTTG
66 TTGAATTGGATATCCTTCGTCATGAAGTTGAAATCCAAGGGTTG-ATTGTTGCTTG
* * * * * * *
1442074 TGAGCACGATATCATTCGTCATGAAGTTGAAATCGTGGATGGCCCCTACGTCGTGAAGTTGAGCA
1 TGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCC
* * ** * * *
1442139 TTGAATTGGATATCATTCTTCATGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGG
66 TTGAATTGGATATCCTTCGTCATGAAGTTGAAATCC-A---AGGGTTGATTGTTGCTTG
* *
1442198 TGGACACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCT
1 TGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCC
* *
1442263 TTGAATTGGATATCATTCGTTATGAAGTTGAAATCCAAG
66 TTGAATTGGATATCCTTCGTCATGAAGTTGAAATCCAAG
1442302 TATTGTTTCA
Statistics
Matches: 987, Mismatches: 161, Indels: 133
0.77 0.13 0.10
Matches are distributed among these distances:
112 49 0.05
113 1 0.00
114 1 0.00
116 1 0.00
117 1 0.00
118 2 0.00
119 8 0.01
120 76 0.08
121 318 0.32
122 8 0.01
123 10 0.01
124 313 0.32
125 104 0.11
126 28 0.03
127 5 0.01
128 1 0.00
129 2 0.00
130 3 0.00
131 1 0.00
132 1 0.00
133 1 0.00
134 1 0.00
135 1 0.00
138 1 0.00
139 50 0.05
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (120 bp):
TGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCC
TTGAATTGGATATCCTTCGTCATGAAGTTGAAATCCAAGGGTTGATTGTTGCTTG
Found at i:1441281 original size:124 final size:124
Alignment explanation
Indices: 1440971--1442300 Score: 1008
Period size: 124 Copynumber: 10.8 Consensus size: 124
1440961 ATCTATTGGG
* * *
1440971 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCTTTCGTTGTGAAGTTGAGCTTTGA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCTTTGA
** * * * ** * * * *
1441036 ATTGGATATTATTCGACGTAAAGTTGAAATCC-A---AGGGTTGCATTGCTGCTTG-TGGG
66 ATTGGATATCCTTCGTCATGAAGTTGAAATCCAATCTAAAGATG-AATGTTGC-TGATGGA
* *
1441092 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCTTTGA
*
1441157 ATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGATGGA
66 ATTGGATATCCTTCGTCATGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGATGGA
* * * * * * * *
1441216 CACAATATCCTTCATCGTGAAGTTGAAATAGTAGAT-AGCTCATTCGTTGTGAAGTTAAACTTTG
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGA-CCCCTTCGTTGTGAAGTTGAGCTTTG
* * * * * *
1441280 AATTGGATACCCTTCGTCGTGAATTTGAAATCCAATCT--TG-TGTAA-GTTACGTCATTTCGAG
65 AATTGGATATCCTTCGTCATGAAGTTGAAATCCAATCTAAAGATG-AATGTTGC-TGA--T-G-G
*
1441341 T
124 A
* * *
1441342 C-CAATATCCTTCG-CTGTGAAGTTGAAATTAACTCTGAATGAAACTGGGAAGCCCCTTCGCTGT
1 CACGATATCCTTCGTC-GTGAAGTTG--A--AA-TC-G--TG-GA-T--G-A-CCCCTTCGTTGT
* * * ** * *
1441405 GAAGTTGGGCTTTGAATTGAATATCATTCGTTGTGAAGTTGAAATCCAA--T---GCTG---CTT
51 GAAGTTGAGCTTTGAATTGGATATCCTTCGTCATGAAGTTGAAATCCAATCTAAAGATGAATGTT
*
1441462 -ATGA--G-
116 GCTGATGGA
* * * * *
1441467 CACGATATCATTCGTCGTGAAGTTAAAATCATGGATGTCCCTTTCGTTGTGAAGTTGAG-TCTTG
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCT-TTG
* * * * * * * *
1441531 AATTAGATATTCTTCGTCGTGAAGTTGAAATCCAATCTTGTGTAAGTTGTATTGTTTC-GA--GT
65 AATTGGATATCCTTCGTCATGAAGTTGAAATCCAATC---T-AAAGATG-AATGTTGCTGATGGA
* * ** * *
1441593 C-CAATATCCTTCGCCGTGAAGTTGAAATTATGGATGGCCTCTTCGTTGTGAAGTTGAGCTTTGA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCTTTGA
* * ** * * *
1441657 ATTGGATATCATTCGTCAT-TAGTTGAAATCCAAGGGT-TACAT---TGTTGCTGGTGGA
66 ATTGGATATCCTTCGTCATGAAGTTGAAATCCAA-TCTAAAGATGAATGTTGCTGATGGA
* * * *
1441712 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCATCGTGAAGTTGAGCCTCGA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCTTTGA
* * * * *
1441777 ATTGGATATCCTTCTTCTTGAAGTTGAAATTCAATCTAAAGATGAATGTTGCTGGTGGG
66 ATTGGATATCCTTCGTCATGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGATGGA
* * * * * * * *
1441836 TACGATATCATTCGTCGTGAAGGTGAAATCGTTGATGGCCCCATCGTTGTGAAGTTGAGCCTCGA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCTTTGA
* * *
1441901 ATTGGATATCCTTCATCATGAAGTTGAAATCCAAGGGT-TGAA-TTG-ATGCTTG-TGA--G-
66 ATTGGATATCCTTCGTCATGAAGTTGAAATCCAA---TCTAAAGATGAATG-TTGCTGATGGA
* * *
1441957 CACGATATGCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTCGTGAAGTTGAGCCTTGA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCTTTGA
* * ** * *
1442022 ATTGGATATCCTTCATCATGAATTTGAAATCC-A---AGGGTTGCATTGTTGCT--TGTGA
66 ATTGGATATCCTTCGTCATGAAGTTGAAATCCAATCTAAAGATG-AATGTTGCTGATG-GA
* * * * * *
1442077 GCACGATATCATTCGTCATGAAGTTGAAATCGTGGATGGCCCCTACGTCGTGAAGTTGAGCATTG
1 -CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCTTTG
* * *
1442142 AATTGGATATCATTCTTCATGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGGA
65 AATTGGATATCCTTCGTCATGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGATGGA
1442202 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCTTTGA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCTTTGA
* *
1442267 ATTGGATATCATTCGTTATGAAGTTGAAATCCAA
66 ATTGGATATCCTTCGTCATGAAGTTGAAATCCAA
1442301 GTATTGTTTC
Statistics
Matches: 980, Mismatches: 153, Indels: 149
0.76 0.12 0.12
Matches are distributed among these distances:
111 1 0.00
112 51 0.05
114 1 0.00
116 9 0.01
117 6 0.01
118 5 0.01
119 3 0.00
120 73 0.07
121 290 0.30
122 11 0.01
123 3 0.00
124 319 0.33
125 110 0.11
126 28 0.03
127 3 0.00
129 2 0.00
130 1 0.00
131 1 0.00
132 2 0.00
133 1 0.00
134 3 0.00
135 1 0.00
136 1 0.00
137 3 0.00
139 52 0.05
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.34
Consensus pattern (124 bp):
CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCTTTGA
ATTGGATATCCTTCGTCATGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGATGGA
Found at i:1441928 original size:245 final size:243
Alignment explanation
Indices: 1441467--1442296 Score: 921
Period size: 245 Copynumber: 3.4 Consensus size: 243
1441457 TGCTTATGAG
* * * * * * *
1441467 CACGATATCATTCGTCGTGAAGTTAAAATCATGGATGTCCCTTTCGTTGTGAAGTTGAGTCTTGA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTCGTGAAGTTGAGCCTTGA
* * * * * * * * * *
1441532 ATTAGATATTCTTCGTCGTGAAGTTGAAATCCAATCT--TGTGTAA-GTTGTATTGTTTCGAGTC
66 ATTGGATATCCTTCTTCATGAAGTTGAAATTCAATCTAAAGTGCAATGTTG--CTG-GT-GAGTA
* * * ** * *
1441594 CAATATCCTTCGCCGTGAAGTTGAAATTATGGATGGCCTCTTCGTTGTGAAGTTGAGCTTTGAAT
127 CGATATCATTCGTCGTGAAGTTGAAATCGTGGATGGCC-CCTCGTTGTGAAGTTGAGCATTGAAT
* *
1441659 TGGATATCATTCGTCAT-TAGTTGAAATCCAAGGGTTACATTGTTGCTGGTGGA
191 TGGATATCATTCATCATGAAGTTGAAATCCAAGGGTTA-ATTGTTGCTGGTGGA
* *
1441712 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCATCGTGAAGTTGAGCCTCGA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTCGTGAAGTTGAGCCTTGA
* *
1441777 ATTGGATATCCTTCTTCTTGAAGTTGAAATTCAATCTAAAGATG-AATGTTGCTGGTGGGTACGA
66 ATTGGATATCCTTCTTCATGAAGTTGAAATTCAATCTAAAG-TGCAATGTTGCTGGTGAGTACGA
* * * *
1441841 TATCATTCGTCGTGAAGGTGAAATCGTTGATGGCCCCATCGTTGTGAAGTTGAGCCTCGAATTGG
130 TATCATTCGTCGTGAAGTTGAAATCGTGGATGGCCCC-TCGTTGTGAAGTTGAGCATTGAATTGG
* * *
1441906 ATATCCTTCATCATGAAGTTGAAATCCAAGGGTTGAATTGATGCTTGT-GA
194 ATATCATTCATCATGAAGTTGAAATCCAAGGGTT-AATTGTTGCTGGTGGA
*
1441956 GCACGATATGCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTCGTGAAGTTGAGCCTTG
1 -CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTCGTGAAGTTGAGCCTTG
* * * * * *
1442021 AATTGGATATCCTTCATCATGAATTTGAAA-TC---C-AAGGGTTGCATTGTTGCTTGTGAGCAC
65 AATTGGATATCCTTCTTCATGAAGTTGAAATTCAATCTAA-AG-TGCAATGTTGCTGGTGAGTAC
* *
1442081 GATATCATTCGTCATGAAGTTGAAATCGTGGATGGCCCCTACGTCGTGAAGTTGAGCATTGAATT
128 GATATCATTCGTCGTGAAGTTGAAATCGTGGATGGCCCCT-CGTTGTGAAGTTGAGCATTGAATT
* ** *
1442146 GGATATCATTCTTCATGAAGTTGAAATCCAA-TCTAAAGATGAATGTTGCTGGTGGA
192 GGATATCATTCATCATGAAGTTGAAATCCAAGGGT-TA-AT---TGTTGCTGGTGGA
* *
1442202 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCTTTGA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTCGTGAAGTTGAGCCTTGA
*
1442267 ATTGGATATCATTCGTT-ATGAAGTTGAAAT
66 ATTGGATATCCTTC-TTCATGAAGTTGAAAT
1442297 CCAAGTATTG
Statistics
Matches: 501, Mismatches: 65, Indels: 37
0.83 0.11 0.06
Matches are distributed among these distances:
240 2 0.00
241 7 0.01
242 102 0.20
243 1 0.00
244 75 0.15
245 299 0.60
246 6 0.01
247 3 0.01
248 6 0.01
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.34
Consensus pattern (243 bp):
CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTCGTGAAGTTGAGCCTTGA
ATTGGATATCCTTCTTCATGAAGTTGAAATTCAATCTAAAGTGCAATGTTGCTGGTGAGTACGAT
ATCATTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTCGTTGTGAAGTTGAGCATTGAATTGGAT
ATCATTCATCATGAAGTTGAAATCCAAGGGTTAATTGTTGCTGGTGGA
Found at i:1442112 original size:366 final size:369
Alignment explanation
Indices: 1441467--1442301 Score: 1137
Period size: 366 Copynumber: 2.3 Consensus size: 369
1441457 TGCTTATGAG
* * * * *
1441467 CACGATATCATTCGTCGTGAAGTTAAAATCATGGATGTCCCTTTCGTTGTGAAGTTGAGTCTTGA
1 CACGATATCATTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCCTTGA
* * * * *
1441532 ATTAGATATTCTTCGTCGTGAAGTTGAAATCCAATCTTGTGTAAGTTGTATTGTTTCGAGTCCAA
66 ATTGGATATCCTTCGTCATGAAGTTGAAATCCAAGCGTGTGTAAGTTGTATTGTTTCGAGTCCAA
* * * * *
1441597 TATCCTTCGCCGTGAAGTTGAAATTATGGATGGCCTCTTCGTTGTGAAGTTGAGCTTTGAATTGG
131 TATCCTTCGCCGTGAAGTTGAAATCATGGATGACCCCTTCGTCGTGAAGTTGAGCCTTGAATTGG
* * *
1441662 ATATCATTCGTCATTAGTTGAAATCCAAGGGTTACATTGTTGCTGGTGGACACGATATCCTTCGT
196 ATATCATTCATCATAAGTTGAAATCCAAGGGTTACATTGTTGCTGGTGGACACGATATCATTCGT
* * * *
1441727 CGTGAAGTTGAAATCGTGGATGACCCCTTCATCGTGAAGTTGAGCCTCGAATTGGATATCCTTCT
261 CATGAAGTTGAAATCGTGGATGACCCCTACATCGTGAAGTTGAGCATCGAATTGGATATCATTCT
* * *
1441792 TCTTGAAGTTGAAATTCAATCTAAAGATGAATGTTGCTGGTGGG
326 TCATGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGGA
* * * * * *
1441836 TACGATATCATTCGTCGTGAAGGTGAAATCGTTGATGGCCCCATCGTTGTGAAGTTGAGCCTCGA
1 CACGATATCATTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCCTTGA
* *
1441901 ATTGGATATCCTTCATCATGAAGTTGAAATCCAAGGGT-TG-AA-TTG-A-TGCTTGT-GAG-CA
66 ATTGGATATCCTTCGTCATGAAGTTGAAATCCAAGCGTGTGTAAGTTGTATTG-TT-TCGAGTC-
* * * *
1441959 CGATATGCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTCGTGAAGTTGAGCCTTGAAT
128 CAATATCCTTCGCCGTGAAGTTGAAATCATGGATGACCCCTTCGTCGTGAAGTTGAGCCTTGAAT
* * * *
1442024 TGGATATCCTTCATCATGAATTTGAAATCCAAGGGTTGCATTGTTGCTTGT-GAGCACGATATCA
193 TGGATATCATTCATCAT-AAGTTGAAATCCAAGGGTTACATTGTTGCTGGTGGA-CACGATATCA
* * *
1442088 TTCGTCATGAAGTTGAAATCGTGGATGGCCCCTACGTCGTGAAGTTGAGCATTGAATTGGATATC
256 TTCGTCATGAAGTTGAAATCGTGGATGACCCCTACATCGTGAAGTTGAGCATCGAATTGGATATC
1442153 ATTCTTCATGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGGA
321 ATTCTTCATGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGGA
* *
1442202 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCTTTGA
1 CACGATATCATTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCCTTGA
* *
1442267 ATTGGATATCATTCGTTATGAAGTTGAAATCCAAG
66 ATTGGATATCCTTCGTCATGAAGTTGAAATCCAAG
1442302 TATTGTTTCA
Statistics
Matches: 407, Mismatches: 54, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
364 3 0.01
365 79 0.19
366 235 0.58
367 2 0.00
368 2 0.00
369 86 0.21
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.34
Consensus pattern (369 bp):
CACGATATCATTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCCTTGA
ATTGGATATCCTTCGTCATGAAGTTGAAATCCAAGCGTGTGTAAGTTGTATTGTTTCGAGTCCAA
TATCCTTCGCCGTGAAGTTGAAATCATGGATGACCCCTTCGTCGTGAAGTTGAGCCTTGAATTGG
ATATCATTCATCATAAGTTGAAATCCAAGGGTTACATTGTTGCTGGTGGACACGATATCATTCGT
CATGAAGTTGAAATCGTGGATGACCCCTACATCGTGAAGTTGAGCATCGAATTGGATATCATTCT
TCATGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGGA
Found at i:1446963 original size:30 final size:30
Alignment explanation
Indices: 1446913--1446979 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
1446903 AGGAAAAAAT
*
1446913 AGAAATTTAAAGTACCAAAATAGCATAAAC
1 AGAAATTTAAAGAACCAAAATAGCATAAAC
** * * *
1446943 AGAAATTTAAAGAATTAAAATAGTATTAAT
1 AGAAATTTAAAGAACCAAAATAGCATAAAC
1446973 AGAAATT
1 AGAAATT
1446980 AGAATGACCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.06, G:0.10, T:0.27
Consensus pattern (30 bp):
AGAAATTTAAAGAACCAAAATAGCATAAAC
Found at i:1447272 original size:5 final size:5
Alignment explanation
Indices: 1447262--1447286 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1447252 ATAAAGCTCC
1447262 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
1447287 ACGTAGAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:1454804 original size:31 final size:32
Alignment explanation
Indices: 1454769--1454836 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
1454759 TAGGCTTTGT
* *
1454769 GGCCCTAAGATCA-TTCTTGGGTAGTCCCCGC
1 GGCCCTAAGATCAGTTCTTAGGTAGGCCCCGC
* *
1454800 GGCCCTAAGATGAGTTCTTAGGTAGGCCCCGT
1 GGCCCTAAGATCAGTTCTTAGGTAGGCCCCGC
1454832 GGCCC
1 GGCCC
1454837 CGAACTTTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 12 0.38
32 20 0.62
ACGTcount: A:0.16, C:0.31, G:0.29, T:0.24
Consensus pattern (32 bp):
GGCCCTAAGATCAGTTCTTAGGTAGGCCCCGC
Found at i:1459901 original size:31 final size:32
Alignment explanation
Indices: 1459866--1459933 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
1459856 TAGGCTTTGT
* *
1459866 GGCCCTAAGATCA-TTCTTGGGTAGTCCCCGC
1 GGCCCTAAGATCAGTTCTTAGGTAGGCCCCGC
* *
1459897 GGCCCTAAGATGAGTTCTTAGGTAGGCCCCGT
1 GGCCCTAAGATCAGTTCTTAGGTAGGCCCCGC
1459929 GGCCC
1 GGCCC
1459934 CGAACTTTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 12 0.38
32 20 0.62
ACGTcount: A:0.16, C:0.31, G:0.29, T:0.24
Consensus pattern (32 bp):
GGCCCTAAGATCAGTTCTTAGGTAGGCCCCGC
Found at i:1468796 original size:20 final size:21
Alignment explanation
Indices: 1468752--1468807 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
1468742 CAGTTTCCAA
* *
1468752 ATTCGCAACGCGAATATCCAG
1 ATTCGCAACGCGATTATCAAG
*
1468773 ATTCGCAACGCGATTGT-AAG
1 ATTCGCAACGCGATTATCAAG
*
1468793 ATTCGCAACTCGATT
1 ATTCGCAACGCGATT
1468808 TTGAAAAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (21 bp):
ATTCGCAACGCGATTATCAAG
Found at i:1468848 original size:37 final size:39
Alignment explanation
Indices: 1468807--1468883 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 39
1468797 GCAACTCGAT
* *
1468807 TTTGAAAAA-TG-TGTTGCGATAGTTAAAATGTGTTGCG
1 TTTGAAAAACTGTTGTTGCGATAGTGAAAAAGTGTTGCG
*
1468844 TTTGAAAAACGTGTTGTTGGGATAGTGAAAAAGTGTTGCG
1 TTTGAAAAAC-TGTTGTTGCGATAGTGAAAAAGTGTTGCG
1468884 ATAGTGAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
37 9 0.26
39 2 0.06
40 23 0.68
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (39 bp):
TTTGAAAAACTGTTGTTGCGATAGTGAAAAAGTGTTGCG
Found at i:1468894 original size:19 final size:20
Alignment explanation
Indices: 1468809--1468895 Score: 92
Period size: 19 Copynumber: 4.4 Consensus size: 20
1468799 AACTCGATTT
1468809 TGAAAAATGTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
* *
1468829 T-TAAAATGTGTTGCG-T-T
1 TGAAAAATGTGTTGCGATAG
*
1468846 TGAAAAACGTGTTGTTGGGATAG
1 TGAAAAA--TG-TGTTGCGATAG
1468869 TGAAAAA-GTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
1468888 TGAAAAAT
1 TGAAAAAT
1468896 CCAAAATAAG
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
17 1 0.02
18 5 0.09
19 30 0.56
20 4 0.07
21 6 0.11
22 1 0.02
23 7 0.13
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (20 bp):
TGAAAAATGTGTTGCGATAG
Found at i:1469882 original size:21 final size:21
Alignment explanation
Indices: 1469856--1469895 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1469846 CTAATTTTTA
1469856 AATATT-AAATAAAATATATAT
1 AATATTAAAAT-AAATATATAT
1469877 AATATTAAAATAAATATAT
1 AATATTAAAATAAATATAT
1469896 TTATATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AATATTAAAATAAATATATAT
Found at i:1474428 original size:16 final size:16
Alignment explanation
Indices: 1474404--1474434 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1474394 TATATATATA
1474404 ATATAATGGATTATTT
1 ATATAATGGATTATTT
*
1474420 ATATTATGGATTATT
1 ATATAATGGATTATT
1474435 AGATTTTGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (16 bp):
ATATAATGGATTATTT
Found at i:1475203 original size:20 final size:20
Alignment explanation
Indices: 1475178--1475216 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1475168 GAGGATTAGG
**
1475178 AACCGATTTTTAGGTCTTCC
1 AACCGATTTACAGGTCTTCC
1475198 AACCGATTTACAGGTCTTC
1 AACCGATTTACAGGTCTTC
1475217 TAAATAAGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (20 bp):
AACCGATTTACAGGTCTTCC
Found at i:1477700 original size:23 final size:23
Alignment explanation
Indices: 1477670--1477743 Score: 103
Period size: 23 Copynumber: 3.2 Consensus size: 23
1477660 GAGTCGAAGG
*
1477670 TTCTACGCGGTCCTTCGGGATAT
1 TTCTACGCGGTCCTTCGGGACAT
*
1477693 TTCTACGCGGTCCTTCGGGACAA
1 TTCTACGCGGTCCTTCGGGACAT
* * *
1477716 TACTATGTGGTCCTTCGGGACAT
1 TTCTACGCGGTCCTTCGGGACAT
1477739 TTCTA
1 TTCTA
1477744 TGTGACACTT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.16, C:0.26, G:0.24, T:0.34
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGGACAT
Found at i:1478649 original size:26 final size:26
Alignment explanation
Indices: 1478610--1478669 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
1478600 GCACGGGGAC
1478610 GGCGAGTCCAATTACGATGGTGGCGA
1 GGCGAGTCCAATTACGATGGTGGCGA
* * *
1478636 GGTGAGTCCGATTACGATGGTGGTGA
1 GGCGAGTCCAATTACGATGGTGGCGA
1478662 GGCGAGTC
1 GGCGAGTC
1478670 GATGACCAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.20, C:0.17, G:0.42, T:0.22
Consensus pattern (26 bp):
GGCGAGTCCAATTACGATGGTGGCGA
Done.