Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009585.1 Hibiscus syriacus cultivar Beakdansim tig00116962_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: 8285662
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 35
Found at i:5095360 original size:2 final size:2
Alignment explanation
Indices: 5095317--5095349 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
5095307 AATCCAACAA
5095317 AT AT A- AT A- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5095350 ATTAAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:5104431 original size:2 final size:2
Alignment explanation
Indices: 5104424--5104498 Score: 143
Period size: 2 Copynumber: 38.0 Consensus size: 2
5104414 ATTTTCTTTA
5104424 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5104465 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
5104499 TTGTGTCGGA
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 71 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5108671 original size:21 final size:20
Alignment explanation
Indices: 5108635--5108685 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
5108625 TTTTATATAT
* *
5108635 TATTTTT-TTAATTAAATCAC
1 TATTTTTATTAATTAAA-AAA
5108655 TATTTTTATTGAA-TAAAAAA
1 TATTTTTATT-AATTAAAAAA
5108675 TATTTTTATTA
1 TATTTTTATTA
5108686 TTTCGGGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 1 0.04
20 18 0.67
21 6 0.22
22 2 0.07
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (20 bp):
TATTTTTATTAATTAAAAAA
Found at i:5110433 original size:3 final size:3
Alignment explanation
Indices: 5110425--5110454 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5110415 AAGGTATGCT
5110425 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
5110455 AATGGATTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:5121521 original size:186 final size:190
Alignment explanation
Indices: 5121207--5121584 Score: 719
Period size: 186 Copynumber: 2.0 Consensus size: 190
5121197 TAGACTGTTG
5121207 ACAAACTCAGCATCATTAATCCTAGAAGGAGATGTCCTCGAAGAATTGCTATTTGATCCACCCTT
1 ACAAACTCAGCATCATTAATCCTAGAAGGAGATGTCCTCGAAGAATTGCTATTTGATCCACCCTT
5121272 CTTTCGATGATAATGAGAGCTTCATCCTTAATTTACTTGGTGACATGCCACTCTGAGGTAT-AAA
66 CTTTCGATGATAATGAGAGCTTCATCCTTAATTTACTTGGTGACATGCCACTCTGAGGTATAAAA
5121336 GTATGTGCAAAAAGCTTT-AATTTTAGAACTTTG-TTAAAACCC-ATCAGATAAGAAAAA
131 GTATGTGCAAAAAGCTTTAAATTTTAGAACTTTGTTTAAAACCCAATCAGATAAGAAAAA
5121393 ACAAACTCAGCATCATTAATCCTAGAAGGAGATGTCCTCGAAGAATTGCTATTTGATCCACCCTT
1 ACAAACTCAGCATCATTAATCCTAGAAGGAGATGTCCTCGAAGAATTGCTATTTGATCCACCCTT
5121458 CTTTCGATGATAATGAGAGCTTCATCCTTAATTTACTTGGTGACATGCCACTCTGAGGTATAAAA
66 CTTTCGATGATAATGAGAGCTTCATCCTTAATTTACTTGGTGACATGCCACTCTGAGGTATAAAA
5121523 GTATGTGCAAAAAGCTTTAAATTTTAGAACTTTGTTTAAAACCCATATCAGATAAGAAAAA
131 GTATGTGCAAAAAGCTTTAAATTTTAGAACTTTGTTTAAAACCCA-ATCAGATAAGAAAAA
5121584 A
1 A
5121585 GAAAACCCCA
Statistics
Matches: 187, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
186 126 0.67
187 21 0.11
188 15 0.08
189 9 0.05
191 16 0.09
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.31
Consensus pattern (190 bp):
ACAAACTCAGCATCATTAATCCTAGAAGGAGATGTCCTCGAAGAATTGCTATTTGATCCACCCTT
CTTTCGATGATAATGAGAGCTTCATCCTTAATTTACTTGGTGACATGCCACTCTGAGGTATAAAA
GTATGTGCAAAAAGCTTTAAATTTTAGAACTTTGTTTAAAACCCAATCAGATAAGAAAAA
Found at i:5131577 original size:25 final size:26
Alignment explanation
Indices: 5131543--5131599 Score: 98
Period size: 25 Copynumber: 2.2 Consensus size: 26
5131533 GGACAGTCCA
5131543 CATTTTTCGTACTTTGTCC-ATGTTT
1 CATTTTTCGTACTTTGTCCAATGTTT
5131568 CATTTTTCGTACTTTGTCCATATGTTT
1 CATTTTTCGTACTTTGTCCA-ATGTTT
5131595 CATTT
1 CATTT
5131600 AAGTTCATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 19 0.63
27 11 0.37
ACGTcount: A:0.14, C:0.19, G:0.11, T:0.56
Consensus pattern (26 bp):
CATTTTTCGTACTTTGTCCAATGTTT
Found at i:5145477 original size:35 final size:35
Alignment explanation
Indices: 5145431--5145501 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
5145421 GACTTCAGGT
5145431 AGCCTTCATTTCCAATTTTAGAAATTCTTTATCCA
1 AGCCTTCATTTCCAATTTTAGAAATTCTTTATCCA
5145466 AGCCTTCATTTCCAATTTTAGAAATTCTTTATCCA
1 AGCCTTCATTTCCAATTTTAGAAATTCTTTATCCA
5145501 A
1 A
5145502 ATGCCTCAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.42
Consensus pattern (35 bp):
AGCCTTCATTTCCAATTTTAGAAATTCTTTATCCA
Found at i:5147449 original size:187 final size:179
Alignment explanation
Indices: 5147125--5147490 Score: 660
Period size: 187 Copynumber: 2.0 Consensus size: 179
5147115 AGGTCATGTT
5147125 ATTACATATATGAATATCATTATATCGAATTGTATTTCAAGTTAGTTTCATACTTCTTTTAGTTA
1 ATTACATATATGAATATCATTATATCGAATTGTATTTCAAGTTAGTTTCATACTTCTTTTAGTTA
5147190 TGATAGTTTATTCACTTAGAACATGTTTCATGTTTTTTTATATATAATTATGGGATGTATACAAG
66 TGATAGTTTATTCACTTAGAACATGTTTCATGTTTTTTTATATATAATTATGGGATGTATACAAG
5147255 ACAATATATGTTTAAAGATTCAATCATTTGATAATGAAAGTTTGTATCC
131 ACAATATATGTTTAAAGATTCAATCATTTGATAATGAAAGTTTGTATCC
5147304 ATTACATATATGGAATATCATTATATCGAATTGTATTTCAAGTTAGTTTCATAGACATTCTTTTA
1 ATTACATATAT-GAATATCATTATATCGAATTGTATTTCAAGTTAGTTTCAT--AC-TTCTTTTA
5147369 GTTATGATAGTTTATTTCACTTAAGAACATGTTTCATGTTTTTTTTTATATATAATTATGGGATG
62 GTTATGATAGTTTA-TTCACTT-AGAACATGTTTCATG--TTTTTTTATATATAATTATGGGATG
5147434 TATACAAGACAATATATGTTTAAAGATTCAATCATTTGATAATGAAAGTTTGTATCC
123 TATACAAGACAATATATGTTTAAAGATTCAATCATTTGATAATGAAAGTTTGTATCC
5147491 CTGACATACA
Statistics
Matches: 179, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
179 11 0.06
180 40 0.22
182 2 0.01
183 22 0.12
184 7 0.04
185 15 0.08
187 82 0.46
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.45
Consensus pattern (179 bp):
ATTACATATATGAATATCATTATATCGAATTGTATTTCAAGTTAGTTTCATACTTCTTTTAGTTA
TGATAGTTTATTCACTTAGAACATGTTTCATGTTTTTTTATATATAATTATGGGATGTATACAAG
ACAATATATGTTTAAAGATTCAATCATTTGATAATGAAAGTTTGTATCC
Found at i:5153893 original size:338 final size:337
Alignment explanation
Indices: 5153277--5153953 Score: 1304
Period size: 338 Copynumber: 2.0 Consensus size: 337
5153267 GGCTCCATAA
5153277 AGGATTGGAAATGGAGGCATTGGATTCGTTTGTTGTTCTTGCTCTTCGGGCTCTGCTCAGGCTCA
1 AGGATTGGAAATGGAGGCATTGGATTCGTTTGTTGTTCTTGCTCTTCGGGC-CTGCTCAGGCTCA
5153342 TCTTCGGCTTTCATCGATGTCTCGCATTAATTGCTCAAGCTTGAGATCTTCGTCAGCTTCGGGTG
65 TCTTCGGCTTTCATCGATGTCTCGCATTAATTGCTCAAGCTTGAGATCTTCGTCAGCTTCGGGTG
5153407 GAGCTTGTGAAGAACTAGCTCCCGGAGTATTTGCAGAAGATCGAACCCATTCACCGGTTAATTTT
130 GAGCTTGTGAAGAACTAGCTCCCGGAGTATTTGCAGAAGATCGAACCCATTCACCGGTTAATTTT
5153472 TTCTTAAGGGGAAAAACGACATCTAGACCGACTCTAAGCCCAGCTTTGGAAAACATATTACTCAA
195 TTCTTAAGGGGAAAAACGACATCTAGACCGACTCTAAGCCCAGCTTTGGAAAACATATTACTCAA
5153537 AATACAACCGTAAACAAGAGAGGAACAGAGTTTCTTGTTAGGAACAAGATTTACGGTTTCAACAA
260 AATACAACCGTAAACAAGAGAGGAACAGAGTTTCTTGTTAGGAACAAGATTTACGGTTTCAACAA
5153602 TTTCAGCAAAAAT
325 TTTCAGCAAAAAT
5153615 AGGATTGGAAATATGGAGGCATTGGATTCGTTTGTTGTTCTTGCTCTTCGGG-CTGCTCAGGCTC
1 AGGATTGG-AA-ATGGAGGCATTGGATTCGTTTGTTGTTCTTGCTCTTCGGGCCTGCTCAGGCTC
5153679 ATCTTCGGC-TTCATCGATGTCTCGCATTAATTGCTCAAGCTTGAGATCTTCGTCAGCTTCGGGT
64 ATCTTCGGCTTTCATCGATGTCTCGCATTAATTGCTCAAGCTTGAGATCTTCGTCAGCTTCGGGT
5153743 GGAGCTTGTGAAGAACTAGCTCCCGGAGTATTTGCAGAAGATCGAACCCATTCACCGGTTAATTT
129 GGAGCTTGTGAAGAACTAGCTCCCGGAGTATTTGCAGAAGATCGAACCCATTCACCGGTTAATTT
5153808 GTTTCTTAAGGGGAAAAACGACATCTAGACCGACTCTAAGCCCAGCTTTGGAAAACATATTACTC
194 -TTTCTTAAGGGGAAAAACGACATCTAGACCGACTCTAAGCCCAGCTTTGGAAAACATATTACTC
5153873 AAAATACAACCGTAAACAAGAGAGGAACAGAGTTTCTTGTTAGGAACAAGATTTACGGTTTCAAC
258 AAAATACAACCGTAAACAAGAGAGGAACAGAGTTTCTTGTTAGGAACAAGATTTACGGTTTCAAC
5153938 AATTTCAGCAAAAAT
323 AATTTCAGCAAAAAT
5153953 A
1 A
5153954 ATCTGAGGTA
Statistics
Matches: 336, Mismatches: 0, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
337 120 0.36
338 174 0.52
339 2 0.01
340 40 0.12
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.29
Consensus pattern (337 bp):
AGGATTGGAAATGGAGGCATTGGATTCGTTTGTTGTTCTTGCTCTTCGGGCCTGCTCAGGCTCAT
CTTCGGCTTTCATCGATGTCTCGCATTAATTGCTCAAGCTTGAGATCTTCGTCAGCTTCGGGTGG
AGCTTGTGAAGAACTAGCTCCCGGAGTATTTGCAGAAGATCGAACCCATTCACCGGTTAATTTTT
TCTTAAGGGGAAAAACGACATCTAGACCGACTCTAAGCCCAGCTTTGGAAAACATATTACTCAAA
ATACAACCGTAAACAAGAGAGGAACAGAGTTTCTTGTTAGGAACAAGATTTACGGTTTCAACAAT
TTCAGCAAAAAT
Found at i:5155329 original size:20 final size:21
Alignment explanation
Indices: 5155283--5155343 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
5155273 TTCCCCTGTG
5155283 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
5155306 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
5155326 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
5155344 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:5174996 original size:22 final size:22
Alignment explanation
Indices: 5174942--5174998 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 22
5174932 GCAACGCGAT
*
5174942 TTTGAAAAATGTGTTGCGATAG
1 TTTGAAAAATGTGTTGCGAGAG
5174964 -TT--AAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGAGAG
*
5174983 TTTGAAAAACGTGTTG
1 TTTGAAAAATGTGTTG
5174999 TTGTGATAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 16 0.53
20 2 0.07
21 2 0.07
22 10 0.33
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.35
Consensus pattern (22 bp):
TTTGAAAAATGTGTTGCGAGAG
Found at i:5175458 original size:19 final size:19
Alignment explanation
Indices: 5175436--5175619 Score: 115
Period size: 19 Copynumber: 9.5 Consensus size: 19
5175426 AACTTCGACT
5175436 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
* * **
5175455 ATCGCAACGCGAACTTCGACT
1 ATCGCAA--CGAATTTGGAAA
*
5175476 ATCGCAACGAATTTAGAAA
1 ATCGCAACGAATTTGGAAA
* * **
5175495 ATCGTAACGTGAACTTGGACT
1 ATCGCAAC--GAATTTGGAAA
*
5175516 ATCGTAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
* **
5175535 ATCGCAACGTGAACTTGGACT
1 ATCGCAAC--GAATTTGGAAA
*
5175556 ATCGCAACGAATTTGGACTA
1 ATCGCAACGAATTTGGA-AA
* *
5175576 A-CG-TA--AATTTGAAAA
1 ATCGCAACGAATTTGGAAA
* *
5175591 ATTGCAACGAATTTGTAAA
1 ATCGCAACGAATTTGGAAA
5175610 ATCGCAACGA
1 ATCGCAACGA
5175620 GAACTTGGAC
Statistics
Matches: 124, Mismatches: 30, Indels: 22
0.70 0.17 0.12
Matches are distributed among these distances:
15 2 0.02
16 8 0.06
17 1 0.01
18 1 0.01
19 65 0.52
20 1 0.01
21 46 0.37
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:5175476 original size:40 final size:40
Alignment explanation
Indices: 5175421--5175572 Score: 241
Period size: 40 Copynumber: 3.8 Consensus size: 40
5175411 TTGTGATTTT
5175421 ACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCA
1 ACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCA
* *
5175461 ACGCGAACTTCGACTATCGCAACGAATTTAGAAAATCGTA
1 ACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCA
* * *
5175501 ACGTGAACTTGGACTATCGTAACGAATTTGGAAAATCGCA
1 ACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCA
* *
5175541 ACGTGAACTTGGACTATCGCAACGAATTTGGA
1 ACGCGAACTTCGACTATCGCAACGAATTTGGA
5175573 CTAACGTAAA
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 104 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (40 bp):
ACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCA
Found at i:5175479 original size:21 final size:21
Alignment explanation
Indices: 5175421--5175564 Score: 102
Period size: 21 Copynumber: 7.1 Consensus size: 21
5175411 TTGTGATTTT
*
5175421 ACGCGAACTTCGACTATCGCA
1 ACGCGAACTTGGACTATCGCA
* **
5175442 A--CGAATTTGGAAAATCGCA
1 ACGCGAACTTGGACTATCGCA
*
5175461 ACGCGAACTTCGACTATCGCA
1 ACGCGAACTTGGACTATCGCA
* * ** *
5175482 A--CGAATTTAGAAAATCGTA
1 ACGCGAACTTGGACTATCGCA
* *
5175501 ACGTGAACTTGGACTATCGTA
1 ACGCGAACTTGGACTATCGCA
* **
5175522 A--CGAATTTGGAAAATCGCA
1 ACGCGAACTTGGACTATCGCA
*
5175541 ACGTGAACTTGGACTATCGCA
1 ACGCGAACTTGGACTATCGCA
5175562 ACG
1 ACG
5175565 AATTTGGACT
Statistics
Matches: 90, Mismatches: 27, Indels: 12
0.70 0.21 0.09
Matches are distributed among these distances:
19 43 0.48
21 47 0.52
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (21 bp):
ACGCGAACTTGGACTATCGCA
Found at i:5175558 original size:80 final size:75
Alignment explanation
Indices: 5175425--5175637 Score: 264
Period size: 80 Copynumber: 2.8 Consensus size: 75
5175415 GATTTTACGC
* * *
5175425 GAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTT
1 GAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGAGAACTTGGACTATCGCAACGAATTT
5175490 AGAAAATCGTAACGT
66 -G--AA-C-TAACGT
* *
5175505 GAACTTGGACTATCGTAACGAATTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAATTT
1 GAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGAGAACTTGGACTATCGCAACGAATTT
*
5175570 GGACTAACGT
66 GAACTAACGT
* * * ** * *
5175580 AAATTTGAAAAATTGCAACGAATTTGTAAAATCGCAACGAGAACTTGGACTATCGCAA
1 GAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGAGAACTTGGACTATCGCAA
5175638 AATCGCGTTG
Statistics
Matches: 119, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
75 55 0.46
76 1 0.01
77 1 0.01
79 1 0.01
80 61 0.51
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (75 bp):
GAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGAGAACTTGGACTATCGCAACGAATTT
GAACTAACGT
Found at i:5175624 original size:75 final size:79
Alignment explanation
Indices: 5175436--5175637 Score: 259
Period size: 75 Copynumber: 2.6 Consensus size: 79
5175426 AACTTCGACT
* *
5175436 ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTAGAAAATCGTA
1 ATCGCAACGAATTTGGAAAATCGCAACGAGAACTTGGACTATCGCAACGAATTTAG-AAATCGTA
* * **
5175501 ACGTGAACTTGGACT
65 ACGTAAACTTGAAAA
* * *
5175516 ATCGTAACGAATTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAATTT-G-GA-C-TAA
1 ATCGCAACGAATTTGGAAAATCGCAACGAGAACTTGGACTATCGCAACGAATTTAGAAATCGTAA
*
5175577 CGTAAATTTGAAAA
66 CGTAAACTTGAAAA
* *
5175591 ATTGCAACGAATTTGTAAAATCGCAACGAGAACTTGGACTATCGCAA
1 ATCGCAACGAATTTGGAAAATCGCAACGAGAACTTGGACTATCGCAA
5175638 AATCGCGTTG
Statistics
Matches: 109, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
75 55 0.50
76 1 0.01
77 1 0.01
79 1 0.01
80 51 0.47
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.24
Consensus pattern (79 bp):
ATCGCAACGAATTTGGAAAATCGCAACGAGAACTTGGACTATCGCAACGAATTTAGAAATCGTAA
CGTAAACTTGAAAA
Found at i:5178692 original size:16 final size:15
Alignment explanation
Indices: 5178671--5178704 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
5178661 AAATATAGAG
*
5178671 ATAATCTTATAGATTT
1 ATAATCTAATA-ATTT
5178687 ATAATCTAATAATTT
1 ATAATCTAATAATTT
5178702 ATA
1 ATA
5178705 TGAAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (15 bp):
ATAATCTAATAATTT
Found at i:5182852 original size:23 final size:23
Alignment explanation
Indices: 5182825--5182877 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
5182815 TGTGAGCTTG
5182825 TTTATGTTTTTAAGGTTAATTTT
1 TTTATGTTTTTAAGGTTAATTTT
5182848 TTTATGTTTTTAAGGTTAATTTT
1 TTTATGTTTTTAAGGTTAATTTT
5182871 TTTATGT
1 TTTATGT
5182878 AAAAGTTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.21, C:0.00, G:0.13, T:0.66
Consensus pattern (23 bp):
TTTATGTTTTTAAGGTTAATTTT
Found at i:5189658 original size:2 final size:2
Alignment explanation
Indices: 5189653--5189680 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5189643 ATACACACAC
5189653 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5189681 TTTTCAGGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5193273 original size:23 final size:23
Alignment explanation
Indices: 5193242--5193305 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
5193232 ATAGGTAAAA
*
5193242 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
5193265 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
5193288 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
5193306 TTGTAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:5193753 original size:23 final size:23
Alignment explanation
Indices: 5193722--5193785 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
5193712 ATAGGTAAAA
* *
5193722 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCACTT
* *
5193745 ATATAATGTAATAGGTATCATTT
1 ATATAATGTAATAGGTAGCACTT
5193768 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
5193786 TTGTAAAGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCACTT
Found at i:5194232 original size:23 final size:23
Alignment explanation
Indices: 5194201--5194264 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
5194191 ATAGGTAAAA
*
5194201 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
5194224 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
5194247 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
5194265 TTGTAAAGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:5194237 original size:479 final size:481
Alignment explanation
Indices: 5192833--5194275 Score: 2779
Period size: 481 Copynumber: 3.0 Consensus size: 481
5192823 TTAAAAAAAA
5192833 TATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTAT
1 TATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTAT
*
5192898 CTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATAATTTATTTTTTACGT
66 CTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGT
5192963 TACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTT
131 TACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTT
5193028 TGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAAT
196 TGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAAT
5193093 TTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAA
261 TTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAA
*
5193158 ATTGAAACATAAATTACATAACTTTAAAAAAAGTGTCGATCCTTTTTATAAAAAGTATGGACACT
326 TTTGAAACATAAATTACATAACTTTAAAAAAAGTGTCGATCCTTTTTATAAAAAGTATGGACACT
5193223 TTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
391 TTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
*
5193288 ATATAATGTAATAGGTAGTTGTAAAA
456 ATATAATGTAATAGGTAGTTGTAAAG
5193314 TATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTAT
1 TATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTAT
*
5193379 CTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACAT
66 CTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGT
5193444 TACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTT
131 TACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTT
5193509 TGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAAT
196 TGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAAT
5193574 TTTTTGTGT-AATGAAATTATT-AATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAA
261 TTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATT-AAAAA
*
5193637 ATTTGAAACATAAATTACATAACTTTAAAAAAAGTGTCGATCCTTTTTATAAAAAGTATGAACAC
325 ATTTGAAACATAAATTACATAACTTTAAAAAAAGTGTCGATCCTTTTTATAAAAAGTATGGACAC
*
5193702 TTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCATT
390 TTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTT
5193767 TATATAATGTAATAGGTAGTTGTAAAG
455 TATATAATGTAATAGGTAGTTGTAAAG
5193794 TATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCATTGTGG-AAA-ATTAATTTAAGGTTAT
1 TATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTAT
5193857 CTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGT
66 CTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGT
5193922 TACGATATATA-TATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTT
131 TACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTT
5193986 TGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAAT
196 TGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAAT
5194051 TTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAA
261 TTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAA
5194116 TTTTGAAACATAAATTACATAACTTTAAAAAAAGTGTCGATCCTTTTTATAAAAAGTATGGACAC
326 -TTTGAAACATAAATTACATAACTTTAAAAAAAGTGTCGATCCTTTTTATAAAAAGTATGGACAC
5194181 TTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTT
390 TTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTT
5194246 TATATAATGTAATAGGTAGTTGTAAAG
455 TATATAATGTAATAGGTAGTTGTAAAG
5194273 TAT
1 TAT
5194276 AGGCGTCTAA
Statistics
Matches: 949, Mismatches: 9, Indels: 10
0.98 0.01 0.01
Matches are distributed among these distances:
477 127 0.13
478 109 0.11
479 232 0.24
480 214 0.23
481 267 0.28
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (481 bp):
TATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTAT
CTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGT
TACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTT
TGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAAT
TTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAA
TTTGAAACATAAATTACATAACTTTAAAAAAAGTGTCGATCCTTTTTATAAAAAGTATGGACACT
TTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
ATATAATGTAATAGGTAGTTGTAAAG
Found at i:5194595 original size:381 final size:381
Alignment explanation
Indices: 5193892--5194656 Score: 1469
Period size: 381 Copynumber: 2.0 Consensus size: 381
5193882 ATTTAGTAAT
5193892 TATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATATTATTAAATTAAAAACAATAAA
1 TATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATATTATTAAATTAAAAACAATAAA
5193957 CATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTAT
66 CATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTAT
5194022 TTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTA
131 TTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTA
**
5194087 GGTGGAAAACATAAAACACTATTAAAAAATTTTGAAACATAAATTACATAACTTTAAAAAAAGTG
196 GGTGGAAAACATAAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTG
5194152 TCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGT
261 TCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGT
*
5194217 AGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTTGTAAAG
326 AGCGCTTATATAATGTAATAGGTATCATTTATATAATGTAATAGGTAGTTGTAAAG
*
5194273 TATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTATTATATTAAAAACAATAA
1 TATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATA-TATTATTAAATTAAAAACAATAA
5194338 ACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTA
65 ACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTA
5194403 TTTTAT-AAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGT
130 TTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGT
*
5194467 AGGTGGAAAACATAAAACACTATTAAAAAAAATTGAAATATAAATTACATAACTTTAAAAAAAGT
195 AGGTGGAAAACATAAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGT
5194532 GTCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGG
260 GTCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGG
5194597 TAGCGCTTATATAATGTAATAGGTATCATTTATATAATGTAATAGGTAGTTGTAAAG
325 TAGCGCTTATATAATGTAATAGGTATCATTTATATAATGTAATAGGTAGTTGTAAAG
5194654 TAT
1 TAT
5194657 CTATCCTTTT
Statistics
Matches: 378, Mismatches: 5, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
381 285 0.75
382 93 0.25
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (381 bp):
TATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATATTATTAAATTAAAAACAATAAA
CATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTAT
TTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTA
GGTGGAAAACATAAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTG
TCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGT
AGCGCTTATATAATGTAATAGGTATCATTTATATAATGTAATAGGTAGTTGTAAAG
Found at i:5194613 original size:23 final size:23
Alignment explanation
Indices: 5194582--5194645 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
5194572 ATAGGTAAAA
* *
5194582 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCACTT
* *
5194605 ATATAATGTAATAGGTATCATTT
1 ATATAATGTAATAGGTAGCACTT
5194628 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
5194646 TTGTAAAGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCACTT
Found at i:5194865 original size:476 final size:477
Alignment explanation
Indices: 5194273--5195522 Score: 2265
Period size: 476 Copynumber: 2.6 Consensus size: 477
5194263 AGTTGTAAAG
5194273 TATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTATTATATTAAAAACAATAA
1 TATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTA--A-ATTAAAAACAATAA
5194338 ACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTA
63 A-A-ATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTA
5194403 TTTTAT-AAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGT
126 TTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGT
* * *
5194467 AGGTGGAAAACATAAAACACTATTAAAAAAAATTGAAATATAAATTACATAACTTTAAAAAAAGT
191 AGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAATT
* *
5194532 GTCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGG
256 ATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATCTAATAGG
5194597 TAGCGCTTATATAATGTAATAGGTATCATTTATATAATGTAATAGGTAGTTGTAAAGTATCTATC
321 TAGCGCTTATATAATGTAATAGGTATCATTTATATAATGTAATAGGTAGTTGTAAAGTATCTATC
*
5194662 CTTTTTATAAAAGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAG
386 CTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAG
5194727 TGAGTTTTAAGATATTAATTTAGTAAT
451 TGAGTTTTAAGATATTAATTTAGTAAT
*
5194754 TATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTAAATTAAAAATAATAAAAA
1 TATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTAAATTAAAAACAATAAAAA
*
5194819 TATATTACATATTTATTATTATCTTTGATTAATATTGTTAAATTTAAATTCTAAATATTATTTTA
66 TATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTA
5194884 TAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTG
131 TAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTG
5194949 GAAAACATGAAACACTATT-AAAAAAATTGAAACATAAATTACATAACTTTAAAAAAATTATCGA
196 GAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAATTATCGA
* *
5195013 TCCTATTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATCTAATAGGTAGCT
261 TCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATCTAATAGGTAGCG
*
5195078 CTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTTGTAAAGTATCTATCCTTTT
326 CTTATATAATGTAATAGGTATCATTTATATAATGTAATAGGTAGTTGTAAAGTATCTATCCTTTT
*
5195143 TATAAAAGTGTCCATACTTTTTTCACTGTGGAAAATATTAATTTAAGGTTATCTTTTGAGTGAGT
391 TATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGT
5195208 TTTAAGATATTAATTTAGTAAT
456 TTTAAGATATTAATTTAGTAAT
5195230 TATAGGCGTCTAATGATTTA--TTTTACGTTACGATATATATTATTATTAAATTAAAAACAATAA
1 TATAGGCGTCTAATGATTTATTTTTTACGTTACG--ATATA-TATTATTAAATTAAAAACAATAA
*
5195293 CATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTAT
63 -AAATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTAT
5195358 TTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTA
127 TTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTA
*
5195423 GGTGAAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAATTA
192 GGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAATTA
5195488 TCGATCCTTTTTATAAAAAGTATGGACACTTTCAA
257 TCGATCCTTTTTATAAAAAGTATGGACACTTTCAA
5195523 CATATTATAA
Statistics
Matches: 746, Mismatches: 17, Indels: 14
0.96 0.02 0.02
Matches are distributed among these distances:
474 12 0.02
476 344 0.46
477 104 0.14
478 163 0.22
479 76 0.10
481 47 0.06
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.41
Consensus pattern (477 bp):
TATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTAAATTAAAAACAATAAAAA
TATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTA
TAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTG
GAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAATTATCGA
TCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATCTAATAGGTAGCG
CTTATATAATGTAATAGGTATCATTTATATAATGTAATAGGTAGTTGTAAAGTATCTATCCTTTT
TATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGT
TTTAAGATATTAATTTAGTAAT
Found at i:5195092 original size:23 final size:23
Alignment explanation
Indices: 5195066--5195121 Score: 87
Period size: 23 Copynumber: 2.4 Consensus size: 23
5195056 AAATATGATC
5195066 TAATAGGTAGC-TCTTATATAATG
1 TAATAGGTAGCGT-TTATATAATG
*
5195089 TAATAGGTATCGTTTATATAATG
1 TAATAGGTAGCGTTTATATAATG
5195112 TAATAGGTAG
1 TAATAGGTAG
5195122 TTGTAAAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 29 0.97
24 1 0.03
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (23 bp):
TAATAGGTAGCGTTTATATAATG
Found at i:5200316 original size:33 final size:33
Alignment explanation
Indices: 5200247--5200349 Score: 107
Period size: 33 Copynumber: 3.1 Consensus size: 33
5200237 TTAAATGATG
* * ** *
5200247 AACGAACATAAACGAACGCAAATGAACGAACGTA
1 AACGAACATAAAAGAAC-AAAACAAATGAACGTA
* * *
5200281 AACGAACATAAAAGAGCACAAGAAATGAACGTA
1 AACGAACATAAAAGAACAAAACAAATGAACGTA
* *
5200314 AACGAACATAAATGAACAAAACAAATGAACATA
1 AACGAACATAAAAGAACAAAACAAATGAACGTA
5200347 AAC
1 AAC
5200350 CACAACAACA
Statistics
Matches: 57, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
33 42 0.74
34 15 0.26
ACGTcount: A:0.58, C:0.17, G:0.15, T:0.10
Consensus pattern (33 bp):
AACGAACATAAAAGAACAAAACAAATGAACGTA
Found at i:5200473 original size:14 final size:14
Alignment explanation
Indices: 5200454--5200512 Score: 91
Period size: 14 Copynumber: 4.2 Consensus size: 14
5200444 AGATTGAGTT
5200454 AAACATAAATGAAC
1 AAACATAAATGAAC
5200468 AAACATAAATGAAC
1 AAACATAAATGAAC
* * *
5200482 GAACATAGACGAAC
1 AAACATAAATGAAC
5200496 AAACATAAATGAAC
1 AAACATAAATGAAC
5200510 AAA
1 AAA
5200513 TATATTATCA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 39 1.00
ACGTcount: A:0.63, C:0.15, G:0.10, T:0.12
Consensus pattern (14 bp):
AAACATAAATGAAC
Found at i:5203876 original size:47 final size:47
Alignment explanation
Indices: 5203806--5203902 Score: 167
Period size: 47 Copynumber: 2.1 Consensus size: 47
5203796 TATTTTTCCA
* *
5203806 ATTTTTATATGTTAAGTTTTAATTATCACCTCCATCCGAATCCATTT
1 ATTTTTATATGTTAAGTTCTAATTATCACCTCCATCCGAATCCATCT
*
5203853 ATTTTTATATGTTAAGTTCTAATTATCATCTCCATCCGAATCCATCT
1 ATTTTTATATGTTAAGTTCTAATTATCACCTCCATCCGAATCCATCT
5203900 ATT
1 ATT
5203903 GGTAAAAATA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.28, C:0.20, G:0.06, T:0.46
Consensus pattern (47 bp):
ATTTTTATATGTTAAGTTCTAATTATCACCTCCATCCGAATCCATCT
Found at i:5215441 original size:26 final size:23
Alignment explanation
Indices: 5215413--5215463 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
5215403 GTTAAAATTA
* *
5215413 TTATTA-ATATAATATTATTGTAT
1 TTATTATATATAA-ATAATTATAT
5215436 TTATTATATATAAATAATTATAT
1 TTATTATATATAAATAATTATAT
5215459 TTATT
1 TTATT
5215464 TAGTATGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TTATTATATATAAATAATTATAT
Found at i:5218899 original size:21 final size:22
Alignment explanation
Indices: 5218873--5218913 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5218863 CCAAGACAGG
*
5218873 GAGTATCGGTAC-TCCTTTAAT
1 GAGTATCAGTACTTCCTTTAAT
*
5218894 GAGTATTAGTACTTCCTTTA
1 GAGTATCAGTACTTCCTTTA
5218914 TAATATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.41
Consensus pattern (22 bp):
GAGTATCAGTACTTCCTTTAAT
Found at i:5219170 original size:20 final size:20
Alignment explanation
Indices: 5219128--5219173 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
5219118 ACCACGTGAA
* *
5219128 CAGTATCGATACTATTCATG
1 CAGTATCGATACTATTAAAG
5219148 CAGTATCGATACTA-TAAGAG
1 CAGTATCGATACTATTAA-AG
5219168 CAGTAT
1 CAGTAT
5219174 TGGTACTACG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (20 bp):
CAGTATCGATACTATTAAAG
Found at i:5219242 original size:11 final size:11
Alignment explanation
Indices: 5219226--5219262 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5219216 TTTTATGGAC
5219226 TTTGAACTAAT
1 TTTGAACTAAT
*
5219237 TTTGAA--AAC
1 TTTGAACTAAT
5219246 TTTGAACTAAT
1 TTTGAACTAAT
5219257 TTTGAA
1 TTTGAA
5219263 AACTTTGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 8 0.36
11 14 0.64
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (11 bp):
TTTGAACTAAT
Found at i:5219247 original size:20 final size:20
Alignment explanation
Indices: 5219224--5219277 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
5219214 AGTTTTATGG
5219224 ACTTTGAACTAATTTTGAAA
1 ACTTTGAACTAATTTTGAAA
5219244 ACTTTGAACTAATTTTGAAA
1 ACTTTGAACTAATTTTGAAA
*
5219264 ACTTTGAACAAATT
1 ACTTTGAACTAATT
5219278 CAATCAAGTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (20 bp):
ACTTTGAACTAATTTTGAAA
Found at i:5221094 original size:32 final size:33
Alignment explanation
Indices: 5221044--5221136 Score: 136
Period size: 32 Copynumber: 2.8 Consensus size: 33
5221034 TCGATTAAAA
5221044 TATAATATATTTTTAAGTTGTTGTTCAAATTTAAT
1 TATAATATA-TTTTAAGTTGTTGTTCAAA-TTAAT
*
5221079 TATAAT-TA-TTTAAGTTGTTGTTCAAATTATT
1 TATAATATATTTTAAGTTGTTGTTCAAATTAAT
5221110 TATAATATATTTTTAAGTTGTTGTTCA
1 TATAATATA-TTTTAAGTTGTTGTTCA
5221137 TATTCATTTT
Statistics
Matches: 54, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
31 10 0.19
32 20 0.37
34 18 0.33
35 6 0.11
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.55
Consensus pattern (33 bp):
TATAATATATTTTAAGTTGTTGTTCAAATTAAT
Found at i:5221130 original size:34 final size:34
Alignment explanation
Indices: 5221044--5221145 Score: 147
Period size: 34 Copynumber: 3.0 Consensus size: 34
5221034 TCGATTAAAA
*
5221044 TATAATATATTTTTAAGTTGTTGTTCAAATTTAAT
1 TATAATATATTTTTAAGTTGTTGTTCAAA-TTATT
5221079 TATAAT-TA--TTTAAGTTGTTGTTCAAATTATT
1 TATAATATATTTTTAAGTTGTTGTTCAAATTATT
*
5221110 TATAATATATTTTTAAGTTGTTGTTCATATTCATT
1 TATAATATATTTTTAAGTTGTTGTTCAAATT-ATT
5221145 T
1 T
5221146 TCACGTGTGT
Statistics
Matches: 61, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
31 10 0.16
32 20 0.33
34 21 0.34
35 10 0.16
ACGTcount: A:0.31, C:0.04, G:0.09, T:0.56
Consensus pattern (34 bp):
TATAATATATTTTTAAGTTGTTGTTCAAATTATT
Found at i:5225732 original size:32 final size:33
Alignment explanation
Indices: 5225674--5225750 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 33
5225664 AAAAATTGGG
*
5225674 TTCGGGTCGGGTCGAGTTTTTTTAAGTGCGATA
1 TTCGGGTCGGGTCGAGGTTTTTTAAGTGCGATA
*
5225707 TTCGGGTCGGGTCG-GGTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTCGAGGTTTTTTAAGTGCGATA
5225739 TTCGGGTCGGGT
1 TTCGGGTCGGGT
5225751 TTAGGGTGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
32 28 0.67
33 14 0.33
ACGTcount: A:0.12, C:0.12, G:0.38, T:0.39
Consensus pattern (33 bp):
TTCGGGTCGGGTCGAGGTTTTTTAAGTGCGATA
Found at i:5227797 original size:2 final size:2
Alignment explanation
Indices: 5227792--5227821 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5227782 ATCTGTATGA
5227792 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
5227822 GAAGGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5233204 original size:23 final size:22
Alignment explanation
Indices: 5233143--5233211 Score: 59
Period size: 23 Copynumber: 3.1 Consensus size: 22
5233133 AATTTTGAGA
* *
5233143 TTATTTTGAAATTTATGTG-TT
1 TTATTTTTAAATTTATATGATT
* **
5233164 TTCTTTTTAAAAAATATATGATT
1 TTATTTTT-AAATTTATATGATT
*
5233187 TTATTTTTAAATTTTATATAATT
1 TTATTTTTAAA-TTTATATGATT
5233210 TT
1 TT
5233212 TTAAATTTAT
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
21 6 0.17
22 11 0.31
23 19 0.53
ACGTcount: A:0.32, C:0.01, G:0.06, T:0.61
Consensus pattern (22 bp):
TTATTTTTAAATTTATATGATT
Found at i:5236312 original size:25 final size:25
Alignment explanation
Indices: 5236280--5236367 Score: 167
Period size: 25 Copynumber: 3.5 Consensus size: 25
5236270 TTACCATTTT
5236280 TGTGTCAATTTAAAACCTGCAAGTG
1 TGTGTCAATTTAAAACCTGCAAGTG
5236305 TGTGTCAATTTAAAACCTGCAAGTG
1 TGTGTCAATTTAAAACCTGCAAGTG
5236330 TGTGTCAATTTAAAACCTGCAAGTG
1 TGTGTCAATTTAAAACCTGCAAGTG
*
5236355 TTTGTCAATTTAA
1 TGTGTCAATTTAA
5236368 GGCATTCAGT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 62 1.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (25 bp):
TGTGTCAATTTAAAACCTGCAAGTG
Found at i:5236548 original size:16 final size:16
Alignment explanation
Indices: 5236527--5236559 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5236517 TAATAAATAA
5236527 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
5236543 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
5236559 A
1 A
5236560 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:5236640 original size:10 final size:10
Alignment explanation
Indices: 5236625--5236699 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
5236615 CATTTAATAA
5236625 ATAAACGAAC
1 ATAAACGAAC
5236635 ATAAACGAAC
1 ATAAACGAAC
5236645 ----ACGAAC
1 ATAAACGAAC
5236651 ATAAACGAAC
1 ATAAACGAAC
* *
5236661 ATGAAC-ATAA
1 ATAAACGA-AC
5236671 ATGAACACGAAC
1 AT-AA-ACGAAC
*
5236683 ATAAACAAAC
1 ATAAACGAAC
*
5236693 ATCAACG
1 ATAAACG
5236700 TTGGAGACCC
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 34 0.68
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.11, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:5236650 original size:16 final size:16
Alignment explanation
Indices: 5236629--5236693 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
5236619 TAATAAATAA
5236629 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
5236645 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
5236661 ATGAACATAAATGAAC
1 ACGAACATAAACGAAC
*
5236677 ACGAACATAAACAAAC
1 ACGAACATAAACGAAC
5236693 A
1 A
5236694 TCAACGTTGG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.58, C:0.22, G:0.11, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:5237708 original size:24 final size:25
Alignment explanation
Indices: 5237680--5237733 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
5237670 GATTGGGTTA
5237680 AACATAAAT-GAAAGAACATAAACG
1 AACATAAATCGAAAGAACATAAACG
* *
5237704 AACAT-AATCGAACGAATATAAACG
1 AACATAAATCGAAAGAACATAAACG
5237728 AACATA
1 AACATA
5237734 GCCGAACGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 3 0.12
24 23 0.88
ACGTcount: A:0.59, C:0.15, G:0.11, T:0.15
Consensus pattern (25 bp):
AACATAAATCGAAAGAACATAAACG
Found at i:5237717 original size:14 final size:14
Alignment explanation
Indices: 5237700--5237755 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
5237690 AAAGAACATA
*
5237700 AACGAACATAATCG
1 AACGAACATAACCG
*
5237714 AACGAATAT-A---
1 AACGAACATAACCG
*
5237724 AACGAACATAGCCG
1 AACGAACATAACCG
5237738 AACGAACATAACCG
1 AACGAACATAACCG
5237752 AACG
1 AACG
5237756 TTCACGAACG
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 8 0.24
13 1 0.03
14 25 0.74
ACGTcount: A:0.50, C:0.23, G:0.16, T:0.11
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:5237739 original size:24 final size:24
Alignment explanation
Indices: 5237693--5237754 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
5237683 ATAAATGAAA
*
5237693 GAACATAAACGAACATAATCGAAC
1 GAACATAAACGAACATAACCGAAC
* *
5237717 GAATATAAACGAACATAGCCGAAC
1 GAACATAAACGAACATAACCGAAC
*
5237741 GAACATAACCGAAC
1 GAACATAAACGAAC
5237755 GTTCACGAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.52, C:0.23, G:0.15, T:0.11
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:5246106 original size:21 final size:21
Alignment explanation
Indices: 5246077--5246126 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
5246067 GTCTTGATTG
* *
5246077 GAAGAAGCTATTTGTGGGTTC
1 GAAGGAGCTATTCGTGGGTTC
*
5246098 GAAGGAGCTGTTCGTGGGTTC
1 GAAGGAGCTATTCGTGGGTTC
5246119 GAAGGAGC
1 GAAGGAGC
5246127 AATCTCTCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.22, C:0.12, G:0.40, T:0.26
Consensus pattern (21 bp):
GAAGGAGCTATTCGTGGGTTC
Found at i:5250988 original size:66 final size:66
Alignment explanation
Indices: 5250870--5250998 Score: 213
Period size: 66 Copynumber: 2.0 Consensus size: 66
5250860 TATCAATTTC
* * *
5250870 TTAAATCACTCATAATGCATAAAATCAAAACATGGTAGTATAAGAACGTTTATGTCAAATTGAGA
1 TTAAATCACTCATAATCCATAAAATCAAAACATGGTAGCATAAGAACATTTATGTCAAATTGAGA
5250935 T
66 T
* *
5250936 TTAAATCACTCATAATCCATAAACTCAAAACATGGTAGCATAATAACATTTATGTCAAATTGA
1 TTAAATCACTCATAATCCATAAAATCAAAACATGGTAGCATAAGAACATTTATGTCAAATTGA
5250999 AACTACAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (66 bp):
TTAAATCACTCATAATCCATAAAATCAAAACATGGTAGCATAAGAACATTTATGTCAAATTGAGA
T
Found at i:5255807 original size:13 final size:13
Alignment explanation
Indices: 5255782--5255814 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
5255772 AAATAAAAAA
5255782 TATATAATAAATT
1 TATATAATAAATT
5255795 TA-ATAATTAAATT
1 TATATAA-TAAATT
5255808 TATATAA
1 TATATAA
5255815 GCTTAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.22
13 10 0.56
14 4 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TATATAATAAATT
Found at i:5260040 original size:18 final size:18
Alignment explanation
Indices: 5260017--5260053 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
5260007 TAGTCTGAAG
5260017 ATAAATTCAGAATGTTTA
1 ATAAATTCAGAATGTTTA
*
5260035 ATAAATTCATAATGTTTA
1 ATAAATTCAGAATGTTTA
5260053 A
1 A
5260054 AATTTAAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (18 bp):
ATAAATTCAGAATGTTTA
Found at i:5267546 original size:18 final size:18
Alignment explanation
Indices: 5267502--5267547 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
5267492 ATTTTATATA
*
5267502 AAAATATATTAATATAAT
1 AAAATTTATTAATATAAT
5267520 ACAAA-TTATTAAT-TAATT
1 A-AAATTTATTAATATAA-T
5267538 AAAATTTATT
1 AAAATTTATT
5267548 TAAGCATGCG
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 6 0.25
18 15 0.62
19 3 0.12
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
AAAATTTATTAATATAAT
Found at i:5269295 original size:33 final size:30
Alignment explanation
Indices: 5269258--5269318 Score: 95
Period size: 33 Copynumber: 1.9 Consensus size: 30
5269248 ATTTCAAATT
5269258 TAAATATAAAACTACTAAAATATTCAAAATAAA
1 TAAATATAAAA-TACTAAAA-ATT-AAAATAAA
5269291 TAAATATAAAATACTAAAAATTAAAATA
1 TAAATATAAAATACTAAAAATTAAAATA
5269319 CTATTTTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 6 0.21
31 3 0.11
32 8 0.29
33 11 0.39
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (30 bp):
TAAATATAAAATACTAAAAATTAAAATAAA
Found at i:5269315 original size:15 final size:16
Alignment explanation
Indices: 5269259--5269321 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 16
5269249 TTTCAAATTT
5269259 AAATATAAAACTACT-A
1 AAATATAAAA-TACTAA
5269275 AAATATTCAAAATA--AA
1 AAATA-T-AAAATACTAA
5269291 TAAATATAAAATACTAA
1 -AAATATAAAATACTAA
5269308 AAAT-TAAAATACTA
1 AAATATAAAATACTA
5269322 TTTTTGAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
15 16 0.39
16 11 0.27
17 10 0.24
18 4 0.10
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATATAAAATACTAA
Found at i:5272885 original size:19 final size:19
Alignment explanation
Indices: 5272861--5272917 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
5272851 GGTCAGACCA
*
5272861 GTCAAACC-AGTTCATACCG
1 GTCAAACCGA-TTCAAACCG
5272880 GTCAAACCGATTCAAACCG
1 GTCAAACCGATTCAAACCG
*
5272899 GTCGAAACCG-GTCAAACCG
1 GTC-AAACCGATTCAAACCG
5272918 ATTTCCAGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 27 0.79
20 7 0.21
ACGTcount: A:0.33, C:0.32, G:0.19, T:0.16
Consensus pattern (19 bp):
GTCAAACCGATTCAAACCG
Found at i:5272917 original size:9 final size:9
Alignment explanation
Indices: 5272851--5272917 Score: 62
Period size: 9 Copynumber: 7.1 Consensus size: 9
5272841 AGTCGGGTCA
*
5272851 GGTCAGACC
1 GGTCAAACC
*
5272860 AGTCAAACC
1 GGTCAAACC
* *
5272869 AGTTCATACC
1 -GGTCAAACC
5272879 GGTCAAACC
1 GGTCAAACC
*
5272888 GATTCAAACC
1 G-GTCAAACC
5272898 GGTCGAAACC
1 GGTC-AAACC
5272908 GGTCAAACC
1 GGTCAAACC
5272917 G
1 G
5272918 ATTTCCAGCC
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
9 23 0.50
10 23 0.50
ACGTcount: A:0.33, C:0.31, G:0.21, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:5287721 original size:16 final size:17
Alignment explanation
Indices: 5287691--5287722 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5287681 ATATTTATTT
5287691 ATATAAAATATAATATG
1 ATATAAAATATAATATG
5287708 ATATAAAA-ATAATAT
1 ATATAAAATATAATAT
5287723 TATGGTAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
ATATAAAATATAATATG
Found at i:5287760 original size:16 final size:17
Alignment explanation
Indices: 5287741--5287777 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
5287731 TAAAATATTA
5287741 TTTTA-AATAATTAC-AT
1 TTTTACAATAA-TACTAT
5287757 TTTTACAATAATACTAT
1 TTTTACAATAATACTAT
5287774 TTTT
1 TTTT
5287778 TTCATCCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTACAATAATACTAT
Found at i:5295466 original size:6 final size:6
Alignment explanation
Indices: 5295457--5295483 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5295447 CTTTGGAGCT
5295457 TGTCTG TGTCTG TGTCTG TGTCTG TGT
1 TGTCTG TGTCTG TGTCTG TGTCTG TGT
5295484 TCATGTTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.33, T:0.52
Consensus pattern (6 bp):
TGTCTG
Found at i:5303181 original size:15 final size:15
Alignment explanation
Indices: 5303158--5303187 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5303148 TGGTAAAGAT
*
5303158 GAAATGATGAATGAA
1 GAAAAGATGAATGAA
5303173 GAAAAGATGAATGAA
1 GAAAAGATGAATGAA
5303188 AACAAAAACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.27, T:0.17
Consensus pattern (15 bp):
GAAAAGATGAATGAA
Found at i:5305773 original size:20 final size:19
Alignment explanation
Indices: 5305731--5305774 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
5305721 AATCGGAATG
**
5305731 AACCGTTGAACCGGCTGTG
1 AACCGTTGAACCGGCTGAA
*
5305750 AACCGTTCGAACCGGTTGAA
1 AACCGTT-GAACCGGCTGAA
5305770 AACCG
1 AACCG
5305775 GTTCTGTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (19 bp):
AACCGTTGAACCGGCTGAA
Found at i:5310059 original size:21 final size:21
Alignment explanation
Indices: 5310033--5310072 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5310023 ATGGCTTCAT
*
5310033 TCTTGTTTTCATCTTACTGAG
1 TCTTGTTTTCATCCTACTGAG
*
5310054 TCTTGTTTTCTTCCTACTG
1 TCTTGTTTTCATCCTACTG
5310073 CCTATTGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.23, G:0.12, T:0.55
Consensus pattern (21 bp):
TCTTGTTTTCATCCTACTGAG
Found at i:5314628 original size:30 final size:30
Alignment explanation
Indices: 5314557--5314628 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
5314547 TTTAAAAAAA
* * * *
5314557 TAATTAATTTTAGGGATTAAATTAAAATTT
1 TAATTAAATTTGGGGATCAAAGTAAAATTT
*
5314587 TAATTAAATTTGGGGATCAAAGTGAAATTT
1 TAATTAAATTTGGGGATCAAAGTAAAATTT
5314617 TAATTAAATTTG
1 TAATTAAATTTG
5314629 AATCTAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.42, C:0.01, G:0.14, T:0.43
Consensus pattern (30 bp):
TAATTAAATTTGGGGATCAAAGTAAAATTT
Found at i:5328693 original size:26 final size:25
Alignment explanation
Indices: 5328642--5328695 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
5328632 GAACCGAGTA
* *
5328642 AAACGGTTCGGTTTGGTATGGCTTT
1 AAACGGTTCGGTTTGGTATCGATTT
5328667 AAACGGTTCGGTTTTAGGT-TCGATTT
1 AAACGGTTCGG-TTT-GGTATCGATTT
5328693 AAA
1 AAA
5328696 GGCTTCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 11 0.44
26 11 0.44
27 3 0.12
ACGTcount: A:0.22, C:0.11, G:0.28, T:0.39
Consensus pattern (25 bp):
AAACGGTTCGGTTTGGTATCGATTT
Found at i:5333357 original size:30 final size:30
Alignment explanation
Indices: 5333165--5333346 Score: 355
Period size: 30 Copynumber: 6.1 Consensus size: 30
5333155 TCCGAAGGAC
5333165 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
5333195 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
5333225 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
5333255 CTATCCAGAGGTCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
5333285 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
5333315 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
5333345 CT
1 CT
5333347 GTCTATAGGT
Statistics
Matches: 150, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 150 1.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:5334421 original size:18 final size:19
Alignment explanation
Indices: 5334384--5334420 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5334374 TTTTTCATTA
*
5334384 TGGGGGAATCGGTTCCCCC
1 TGGGGGAATCGATTCCCCC
*
5334403 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
5334421 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.30, G:0.35, T:0.24
Consensus pattern (19 bp):
TGGGGGAATCGATTCCCCC
Found at i:5337710 original size:30 final size:30
Alignment explanation
Indices: 5337561--5337693 Score: 266
Period size: 30 Copynumber: 4.4 Consensus size: 30
5337551 TCCGAATGAC
5337561 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
5337591 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
5337621 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
5337651 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
5337681 CTATCCAGAGGTC
1 CTATCCAGAGGTC
5337694 CCGAAGAACC
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 103 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:5338748 original size:18 final size:19
Alignment explanation
Indices: 5338711--5338747 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5338701 TTTTTCATTA
*
5338711 TGGGGGAATCGGTTCCCCC
1 TGGGGGAATCGATTCCCCC
*
5338730 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
5338748 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.30, G:0.35, T:0.24
Consensus pattern (19 bp):
TGGGGGAATCGATTCCCCC
Found at i:5338798 original size:21 final size:21
Alignment explanation
Indices: 5338774--5338815 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5338764 TTCATATTCG
*
5338774 TTTGAGGGGGAATCGATTCCC
1 TTTGAAGGGGAATCGATTCCC
* *
5338795 TTTGAATGGGTATCGATTCCC
1 TTTGAAGGGGAATCGATTCCC
5338816 CTAGCCCAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (21 bp):
TTTGAAGGGGAATCGATTCCC
Found at i:5345786 original size:12 final size:12
Alignment explanation
Indices: 5345765--5345793 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5345755 TTTAAAAAAT
5345765 AGAA-AAATAGA
1 AGAACAAATAGA
5345776 AGAACAAATAGA
1 AGAACAAATAGA
5345788 AGAACA
1 AGAACA
5345794 GGGATGGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.69, C:0.07, G:0.17, T:0.07
Consensus pattern (12 bp):
AGAACAAATAGA
Found at i:5357939 original size:15 final size:15
Alignment explanation
Indices: 5357916--5357949 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
5357906 TCTATGACTC
*
5357916 TTAATTAATATGTAA
1 TTAACTAATATGTAA
5357931 TTAACTAATATGTAA
1 TTAACTAATATGTAA
5357946 TTAA
1 TTAA
5357950 TTCTAGGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (15 bp):
TTAACTAATATGTAA
Found at i:5359109 original size:6 final size:6
Alignment explanation
Indices: 5359098--5359133 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
5359088 TTAGCTGAAT
*
5359098 TTAAAA TTAAAA TTCAATA TTAAAA TTAAAA TTAAA
1 TTAAAA TTAAAA TT-AAAA TTAAAA TTAAAA TTAAA
5359134 TCGTTTTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (6 bp):
TTAAAA
Found at i:5359119 original size:13 final size:12
Alignment explanation
Indices: 5359098--5359133 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
5359088 TTAGCTGAAT
5359098 TTAAAATTAAAA
1 TTAAAATTAAAA
*
5359110 TTCAATATTAAAA
1 TT-AAAATTAAAA
5359123 TTAAAATTAAA
1 TTAAAATTAAA
5359134 TCGTTTTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (12 bp):
TTAAAATTAAAA
Found at i:5361707 original size:23 final size:23
Alignment explanation
Indices: 5361676--5361764 Score: 151
Period size: 23 Copynumber: 3.9 Consensus size: 23
5361666 CTGAATGATT
*
5361676 CAGTGCTGACTAATTCAGCAAAA
1 CAGTGCTGACTGATTCAGCAAAA
*
5361699 CAGTACTGACTGATTCAGCAAAA
1 CAGTGCTGACTGATTCAGCAAAA
5361722 CAGTGCTGACTGATTCAGCAAAA
1 CAGTGCTGACTGATTCAGCAAAA
*
5361745 CAGTGCTGAATGATTCAGCA
1 CAGTGCTGACTGATTCAGCA
5361765 CAGAAGTACA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 62 1.00
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (23 bp):
CAGTGCTGACTGATTCAGCAAAA
Found at i:5367794 original size:13 final size:13
Alignment explanation
Indices: 5367776--5367802 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5367766 GTCATCTTTC
5367776 ATGTTAACTTTGG
1 ATGTTAACTTTGG
5367789 ATGTTAACTTTGG
1 ATGTTAACTTTGG
5367802 A
1 A
5367803 CAGTAATGCA
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:0.26, C:0.07, G:0.22, T:0.44
Consensus pattern (13 bp):
ATGTTAACTTTGG
Found at i:5372357 original size:18 final size:17
Alignment explanation
Indices: 5372324--5372362 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
5372314 CTAAAAAAAA
5372324 TTTAAATTTTTATATAT
1 TTTAAATTTTTATATAT
*
5372341 TTTAAATATTTTTTATAT
1 TTTAAAT-TTTTATATAT
5372359 TTTA
1 TTTA
5372363 TATTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTAAATTTTTATATAT
Found at i:5373568 original size:24 final size:24
Alignment explanation
Indices: 5373541--5373592 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
5373531 AACGAACATA
*
5373541 TCAAAAATCAAAACATAATCCAGG
1 TCAAAAATCAAAACAAAATCCAGG
** * *
5373565 TCAAGTATCATATCAAAATCCAGG
1 TCAAAAATCAAAACAAAATCCAGG
5373589 TCAA
1 TCAA
5373593 GTATTCGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.21, G:0.10, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAAAATCCAGG
Found at i:5373593 original size:24 final size:24
Alignment explanation
Indices: 5373557--5373702 Score: 172
Period size: 24 Copynumber: 6.1 Consensus size: 24
5373547 ATCAAAACAT
* * *
5373557 AATCCAGGTCAAGTATCATATCAA
1 AATCCATGTCAAGTATCAGATCAG
*
5373581 AATCCAGGTCAAGTATTC-GATCAG
1 AATCCATGTCAAGTA-TCAGATCAG
* * *
5373605 AATCCAAGTCAAATATCATATCAG
1 AATCCATGTCAAGTATCAGATCAG
5373629 AATCCATGTC-AGATATCAGATCAG
1 AATCCATGTCAAG-TATCAGATCAG
5373653 AATCCATGTC-AGATATCAGATCAG
1 AATCCATGTCAAG-TATCAGATCAG
*
5373677 AATTCATGTCAAGTATCAGATCAG
1 AATCCATGTCAAGTATCAGATCAG
5373701 AA
1 AA
5373703 ATCAAATTGA
Statistics
Matches: 109, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
23 3 0.03
24 102 0.94
25 4 0.04
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (24 bp):
AATCCATGTCAAGTATCAGATCAG
Found at i:5373652 original size:12 final size:12
Alignment explanation
Indices: 5373637--5373706 Score: 51
Period size: 12 Copynumber: 5.8 Consensus size: 12
5373627 AGAATCCATG
5373637 TCAGATATCAGA
1 TCAGATATCAGA
5373649 TCAGA-ATCCATG-
1 TCAGATAT-CA-GA
5373661 TCAGATATCAGA
1 TCAGATATCAGA
5373673 TCAGA-ATTCATG-
1 TCAGATA-TCA-GA
5373685 TCA-AGTATCAGA
1 TCAGA-TATCAGA
*
5373697 TCAGAAATCA
1 TCAGATATCA
5373707 AATTGAAAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 20
0.69 0.01 0.29
Matches are distributed among these distances:
11 6 0.13
12 35 0.74
13 6 0.13
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.26
Consensus pattern (12 bp):
TCAGATATCAGA
Found at i:5373719 original size:48 final size:46
Alignment explanation
Indices: 5373571--5373719 Score: 131
Period size: 48 Copynumber: 3.1 Consensus size: 46
5373561 CAGGTCAAGT
* * * *
5373571 ATCATATCAAAATCCAGGTCAAGTATTC-GATCAGAATCCAAGTCAAA
1 ATCAGATCAGAATCCATGTCAAGTA-TCAGATCAGAAT-CAATTCAAA
* * *
5373618 TATCATATCAGAATCCATGTC-AGATATCAGATCAGAATCCATGTCAGAT
1 -ATCAGATCAGAATCCATGTCAAG-TATCAGATCAGAATCAAT-TCA-AA
* *
5373667 ATCAGATCAGAATTCATGTCAAGTATCAGATCAGAAATCAAATTGAAA
1 ATCAGATCAGAATCCATGTCAAGTATCAGATCAG-AATC-AATTCAAA
5373715 ATCAG
1 ATCAG
5373720 GTAAAAAATT
Statistics
Matches: 84, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
47 6 0.07
48 67 0.80
49 9 0.11
50 2 0.02
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.26
Consensus pattern (46 bp):
ATCAGATCAGAATCCATGTCAAGTATCAGATCAGAATCAATTCAAA
Found at i:5377283 original size:9 final size:8
Alignment explanation
Indices: 5377269--5377329 Score: 59
Period size: 9 Copynumber: 6.9 Consensus size: 8
5377259 CATGTGCATG
5377269 TTATTTTT
1 TTATTTTT
5377277 ATTATTTGTT
1 -TTATTT-TT
5377287 TTATTTTT
1 TTATTTTT
*
5377295 ATATTTTTTCT
1 -T-TATTTT-T
5377306 TTATTTTT
1 TTATTTTT
5377314 TTATATTTT
1 TTAT-TTTT
5377323 TTATTTT
1 TTATTTT
5377330 ACTTACTATT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
8 10 0.22
9 26 0.58
10 8 0.18
11 1 0.02
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (8 bp):
TTATTTTT
Found at i:5377324 original size:10 final size:10
Alignment explanation
Indices: 5377290--5377324 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
5377280 ATTTGTTTTA
5377290 TTTTTATATT
1 TTTTTATATT
*
5377300 TTTTCTTTATT
1 TTTT-TATATT
5377311 TTTTTATATT
1 TTTTTATATT
5377321 TTTT
1 TTTT
5377325 ATTTTACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTATATT
Found at i:5377387 original size:21 final size:20
Alignment explanation
Indices: 5377274--5377387 Score: 58
Period size: 20 Copynumber: 5.7 Consensus size: 20
5377264 GCATGTTATT
* *
5377274 TTTATTATTTGTTTTATTT-
1 TTTATTTTTTCTTTTATTTA
*
5377293 TTATATTTTTTC-TTTATTTTT
1 TT-TATTTTTTCTTTTA-TTTA
* *
5377314 TTATATTTTTTATTTTACTTA
1 TT-TATTTTTTCTTTTATTTA
* *
5377335 -CTATTTTGTT-TTTGT-TTTC
1 TTTATTTT-TTCTTT-TATTTA
* *
5377354 TTTATCTTATCTTTTATTTAA
1 TTTATTTTTTCTTTTATTT-A
5377375 TTTATTTTTTCTT
1 TTTATTTTTTCTT
5377388 CATTTTAATT
Statistics
Matches: 71, Mismatches: 14, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
19 19 0.27
20 24 0.34
21 24 0.34
22 4 0.06
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.75
Consensus pattern (20 bp):
TTTATTTTTTCTTTTATTTA
Found at i:5377387 original size:26 final size:27
Alignment explanation
Indices: 5377358--5377420 Score: 87
Period size: 26 Copynumber: 2.4 Consensus size: 27
5377348 GTTTTCTTTA
5377358 TCTTATCTTTTATTTAATTTATTT-TT
1 TCTTATCTTTTATTTAATTTATTTATT
*
5377384 TCTTCAT-TTTAATTTAATTTATTTATT
1 TCTT-ATCTTTTATTTAATTTATTTATT
5377411 TCTTA-CTTTT
1 TCTTATCTTTT
5377421 TTATCTAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 24 0.75
27 8 0.25
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.70
Consensus pattern (27 bp):
TCTTATCTTTTATTTAATTTATTTATT
Found at i:5381028 original size:36 final size:36
Alignment explanation
Indices: 5380974--5381177 Score: 302
Period size: 36 Copynumber: 5.6 Consensus size: 36
5380964 CTTTGAATAT
* * *
5380974 GTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
**
5381010 GTTTCTTTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
5381046 GTTTCCCATT-AAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCC-TTGAAACAAATTTTGTCTCTCTTGAGACA
* *
5381082 ATTTCCCTTGAAACAAATTTTGTCTCTCTTAAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
5381118 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
*
5381154 GTTTTCCTTGAAACTAAATCTTTG
1 GTTTCCCTTGAAAC-AAAT-TTTG
5381178 AATATGTTTT
Statistics
Matches: 152, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
35 2 0.01
36 140 0.92
37 6 0.04
38 4 0.03
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:5381101 original size:72 final size:72
Alignment explanation
Indices: 5380974--5381343 Score: 434
Period size: 72 Copynumber: 5.2 Consensus size: 72
5380964 CTTTGAATAT
* * * **
5380974 GTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGAAACAAATTTTGTCTCTCT
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCT
*
5381039 TGAGACA
66 TAAGACA
*
5381046 GTTTCCCATT-AAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAATTTTGTCTCTC
1 GTTTCCC-TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTC
5381110 TTAAGACA
65 TTAAGACA
*
5381118 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTTCCTTGAAACTAAA-----TCT-T-
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTC
* * *
5381176 TGAATA-T
65 TTAAGACA
* * * ** * *
5381183 GTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTC
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTC
*
5381248 TTGAGACA
65 TTAAGACA
* *
5381256 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCATTGAAACAAAGTTTTGTCTCTC
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA-TTTTGTCTCTC
*
5381321 TTGAGACA
65 TTAAGACA
*
5381329 GTTTCTCTTGAAACA
1 GTTTCCCTTGAAACA
5381344 TAAAAAACCT
Statistics
Matches: 254, Mismatches: 32, Indels: 23
0.82 0.10 0.07
Matches are distributed among these distances:
65 46 0.18
66 4 0.02
67 1 0.00
68 3 0.01
70 3 0.01
71 3 0.01
72 112 0.44
73 82 0.32
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (72 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCT
TAAGACA
Found at i:5381273 original size:138 final size:137
Alignment explanation
Indices: 5381056--5381305 Score: 394
Period size: 138 Copynumber: 1.8 Consensus size: 137
5381046 GTTTCCCATT
* *
5381056 AAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAATTTTGTCTCTCTTAAGACAGTT
1 AAACAAATTTCGTCTCCCTTGAGACAATTTCCCTTGAAACAAATTTTGTCTCTCTTAAGACAGTT
5381121 TCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTTCC-TTGAAACTAAATCTTTGAATATGT
66 TCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG-TTTCCATTGAAACTAAATCTTTGAATATGT
5381185 TTTCCTTG
130 TTTCCTTG
* ** * * *
5381193 AAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGT
1 AAACAAATTTCGTCTCCCTTGAGACAATTTCCCTTGAAAC-AAATTTTGTCTCTCTTAAGACAGT
*
5381258 TTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCATTGAAAC
65 TTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCATTGAAAC
5381306 AAAGTTTTGT
Statistics
Matches: 102, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
137 39 0.38
138 63 0.62
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (137 bp):
AAACAAATTTCGTCTCCCTTGAGACAATTTCCCTTGAAACAAATTTTGTCTCTCTTAAGACAGTT
TCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCATTGAAACTAAATCTTTGAATATGTT
TTCCTTG
Found at i:5381284 original size:36 final size:36
Alignment explanation
Indices: 5381185--5381343 Score: 232
Period size: 37 Copynumber: 4.4 Consensus size: 36
5381175 TTGAATATGT
* *
5381185 TTTC-CTTGAAACAAATTTCGTCTCCCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * *
5381220 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
5381257 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
5381293 TTTC-CATTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTC-TTGAAACAAA-TTTTGTCTCTCTTGAGACAG
5381330 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
5381344 TAAAAAACCT
Statistics
Matches: 111, Mismatches: 8, Indels: 8
0.87 0.06 0.06
Matches are distributed among these distances:
35 5 0.05
36 42 0.38
37 63 0.57
38 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:5381311 original size:73 final size:73
Alignment explanation
Indices: 5381185--5381343 Score: 257
Period size: 73 Copynumber: 2.2 Consensus size: 73
5381175 TTGAATATGT
** * *
5381185 TTTC-CTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCATTGAAACAAAGTTTTGTCTCTCT
5381249 TGAGACAG
66 TGAGACAG
* *
5381257 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCATTGAAACAAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCATTGAAACAAAGTTTTGTCTCTCT
5381322 TGAGACAG
66 TGAGACAG
5381330 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
5381344 TAAAAAACCT
Statistics
Matches: 80, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
72 4 0.05
73 76 0.95
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (73 bp):
TTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCATTGAAACAAAGTTTTGTCTCTCT
TGAGACAG
Found at i:5381392 original size:36 final size:35
Alignment explanation
Indices: 5381329--5381451 Score: 171
Period size: 36 Copynumber: 3.5 Consensus size: 35
5381319 TCTTGAGACA
*
5381329 GTTTCTCTTG-AA-AC-ATAAAAAACCTTTGAAAT
1 GTTTCTCTTGAAACACAAAAAAAAACCTTTGAAAT
*
5381361 CATTTCTCTTGAAACACAAAAAAAAACCTTTGAAATT
1 -GTTTCTCTTGAAACACAAAAAAAAACCTTTGAAA-T
*
5381398 GTTTCTCTTGAAACACAAAAAAAAACATTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAAAAACCTTTG-AAAT
5381434 GTTTCTCTTGAAACACAA
1 GTTTCTCTTGAAACACAA
5381452 GGACCTTCGA
Statistics
Matches: 81, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
33 9 0.11
34 2 0.02
35 2 0.02
36 64 0.79
37 4 0.05
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (35 bp):
GTTTCTCTTGAAACACAAAAAAAAACCTTTGAAAT
Found at i:5381997 original size:37 final size:37
Alignment explanation
Indices: 5381955--5382062 Score: 180
Period size: 37 Copynumber: 2.9 Consensus size: 37
5381945 AAACAAACGT
* *
5381955 TAGAGTTTTAGTAGGATTCAATCTCCTAAAAATATGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATATGA
5381992 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATATGA
**
5382029 TAGAGTTTTACTATTATTCAAACTCCTAAAAATA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATA
5382063 GGTTCCACAA
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (37 bp):
TAGAGTTTTACTAGGATTCAAACTCCTAAAAATATGA
Found at i:5382713 original size:4 final size:4
Alignment explanation
Indices: 5382667--5382813 Score: 51
Period size: 4 Copynumber: 36.8 Consensus size: 4
5382657 TATTATCTGT
* * *
5382667 TTTA TTAA TTTA TATATA TTTA -CTA TTTT TTTA TGTT- TTTA TTTA TTTA
1 TTTA TTTA TTTA T-T-TA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA
* * * *
5382716 TATA TATA TATA TATTA TTT- TTT- TTTA TATCTA -TTA TTTGT TTTA
1 TTTA TTTA TTTA T-TTA TTTA TTTA TTTA T-T-TA TTTA TTT-A TTTA
* * * *
5382761 TTT- TTATA TTTT TTTC TTTA TTT- TTTC TTTA TTT- TTTA TATA TATT-
1 TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA
5382807 TTTA TTT
1 TTTA TTT
5382814 TACTTACTAT
Statistics
Matches: 110, Mismatches: 16, Indels: 34
0.69 0.10 0.21
Matches are distributed among these distances:
3 22 0.20
4 69 0.63
5 14 0.13
6 5 0.05
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:5382716 original size:37 final size:38
Alignment explanation
Indices: 5382639--5382722 Score: 111
Period size: 37 Copynumber: 2.2 Consensus size: 38
5382629 TATATATATA
5382639 TATATATATGTTATTTTTTATTATCTGTTTTATTAATT
1 TATATATATGTTATTTTTTATTATCTGTTTTATTAATT
* *
5382677 TATATATAT-TTACTATTTTT-TTATGT-TTTTATTTATT
1 TATATATATGTTA-T-TTTTTATTATCTGTTTTATTAATT
5382714 TATATATAT
1 TATATATAT
5382723 ATATATATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
37 22 0.52
38 15 0.36
39 5 0.12
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (38 bp):
TATATATATGTTATTTTTTATTATCTGTTTTATTAATT
Found at i:5382769 original size:45 final size:44
Alignment explanation
Indices: 5382656--5382769 Score: 115
Period size: 43 Copynumber: 2.5 Consensus size: 44
5382646 ATGTTATTTT
* *
5382656 TTATTATCTGTTTTATTAATTTATATATATTTACTATTTTTTTATG
1 TTATTATTTGTTTTATT--TTTATATATATTTACTATTTTTTTATA
* * * * *
5382702 TTTTTATTT-ATTTATATATATATATATATTA-TTTTTTTTTATA
1 TTATTATTTGTTTTATTTTTATATATAT-TTACTATTTTTTTATA
5382745 TCTATTATTTGTTTTATTTTTATAT
1 T-TATTATTTGTTTTATTTTTATAT
5382770 TTTTTTCTTT
Statistics
Matches: 54, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
43 21 0.39
44 10 0.19
45 16 0.30
46 7 0.13
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (44 bp):
TTATTATTTGTTTTATTTTTATATATATTTACTATTTTTTTATA
Found at i:5382770 original size:20 final size:19
Alignment explanation
Indices: 5382690--5382785 Score: 61
Period size: 20 Copynumber: 4.8 Consensus size: 19
5382680 ATATATTTAC
5382690 TATTTTTTTATGTTTT-TATT
1 TATTTTTTTAT-TTTTATA-T
* * *
5382710 TATTTATATATATATATATAT
1 TATTT-T-TTTATTTTTATAT
* *
5382731 TATTTTTTT-TTATATCTAT
1 TATTTTTTTATT-TTTATAT
5382750 TATTTGTTTTATTTTTATAT
1 TATTT-TTTTATTTTTATAT
*
5382770 TTTTTTCTTTATTTTT
1 TATTTT-TTTATTTTT
5382786 TCTTTATTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
18 1 0.02
19 14 0.23
20 28 0.47
21 11 0.18
22 6 0.10
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (19 bp):
TATTTTTTTATTTTTATAT
Found at i:5382781 original size:81 final size:80
Alignment explanation
Indices: 5382624--5382814 Score: 192
Period size: 81 Copynumber: 2.4 Consensus size: 80
5382614 ATATTTTAGA
* * * * * *
5382624 TTATATATATATATATATATATATGTTATTTTTTATTATCTGTTTTATTAATTTATATATATTTA
1 TTATTTATTTATATATATATATATATTATTTTTTATTATATCTATTATTAATTTATATATATTTA
5382689 CTATTTTTTTATGTTT
66 CTATTTTTTTAT-TTT
* ** *
5382705 TTATTTATTTATATATATATATATATTATTTTTTTTTATATCTATTATTTGTTT-TAT-TTTTAT
1 TTATTTATTTATATATATATATATATTATTTTTTATTATATCTATTATTAATTTATATATATT-T
* *
5382768 ATTTTTTTCTTTATTTT
65 ACTATTTT-TTTATTTT
* * *
5382785 TTCTTTATTT-TTTATATATAT-TTTTATTTT
1 TTATTTATTTATATATATATATATATTATTTT
5382815 ACTTACTATT
Statistics
Matches: 93, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
78 8 0.09
79 13 0.14
80 22 0.24
81 50 0.54
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.70
Consensus pattern (80 bp):
TTATTTATTTATATATATATATATATTATTTTTTATTATATCTATTATTAATTTATATATATTTA
CTATTTTTTTATTTT
Found at i:5382784 original size:11 final size:11
Alignment explanation
Indices: 5382770--5382797 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
5382760 ATTTTTATAT
5382770 TTTTTTCTTTA
1 TTTTTTCTTTA
5382781 TTTTTTCTTTA
1 TTTTTTCTTTA
5382792 TTTTTT
1 TTTTTT
5382798 ATATATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTCTTTA
Found at i:5388643 original size:76 final size:76
Alignment explanation
Indices: 5388517--5388668 Score: 268
Period size: 76 Copynumber: 2.0 Consensus size: 76
5388507 CAATAACTAA
* *
5388517 ATGAAGCCAAAGTTAGAGATGAAACACATTGTGATGAAGACTGGTTAAGGTGAAGACTTAACTAC
1 ATGAAGCCAAAGTTAGAGACGAAACACATAGTGATGAAGACTGGTTAAGGTGAAGACTTAACTAC
5388582 GATTGATAGTT
66 GATTGATAGTT
* *
5388593 ATGAAGCCAAAGTTAGAGACGAAACACCTAGTGATGAAGACTGGTTAAGGTGAAGACTTATCTAC
1 ATGAAGCCAAAGTTAGAGACGAAACACATAGTGATGAAGACTGGTTAAGGTGAAGACTTAACTAC
5388658 GATTGATAGTT
66 GATTGATAGTT
5388669 GTGTATGCCG
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.26
Consensus pattern (76 bp):
ATGAAGCCAAAGTTAGAGACGAAACACATAGTGATGAAGACTGGTTAAGGTGAAGACTTAACTAC
GATTGATAGTT
Found at i:5394570 original size:88 final size:87
Alignment explanation
Indices: 5394418--5394592 Score: 325
Period size: 88 Copynumber: 2.0 Consensus size: 87
5394408 AATAAGAAGT
5394418 ACAAGTAATGTTTGGCCTGAATCTTGTATAGTTTCTCGATAACAAAACAAAATAAACAGAATCCA
1 ACAAGTAATGTTTGGCCTGAATCTTGTATAGTTTCTCGATAACAAAACAAAATAAACAGAATCCA
5394483 AAATTATTACATAGAAATCACAAG
66 AAA--ATTACATAGAAATCACAAG
5394507 ACAAGTAATGTTTGGCCTGAATCTTGTATAG-TTCTCGATAACAAAACAAAATAAACAGAATCCA
1 ACAAGTAATGTTTGGCCTGAATCTTGTATAGTTTCTCGATAACAAAACAAAATAAACAGAATCCA
5394571 AAAATTACATAGAAATCACAAG
66 AAAATTACATAGAAATCACAAG
5394593 TTCAAATTCG
Statistics
Matches: 86, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
86 19 0.22
88 36 0.42
89 31 0.36
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.26
Consensus pattern (87 bp):
ACAAGTAATGTTTGGCCTGAATCTTGTATAGTTTCTCGATAACAAAACAAAATAAACAGAATCCA
AAAATTACATAGAAATCACAAG
Found at i:5395466 original size:59 final size:58
Alignment explanation
Indices: 5395299--5395467 Score: 178
Period size: 60 Copynumber: 2.8 Consensus size: 58
5395289 AGTATGACCC
* * * * *
5395299 TCATTCTAAAATGATCCCTGAATTTTTAAATATTTCAATTTCATCCGTGAATTATGACTA
1 TCATTCTAAAATGGTCCCTAAAATTTTAAATATTTCAATTTCATCC--CAACTATGACTA
* * * *
5395359 TCATTCTAAAATAGTCCTTAAACTTTTGAATATTTCAATTTCATTCCCAACTATGAC-A
1 TCATTCTAAAATGGTCCCTAAAATTTTAAATATTTCAATTTCA-TCCCAACTATGACTA
* * *
5395417 TTCATTCTAAATTGGTCCCTAAAAATTTTAAACATTCCAATTTCATCCCAA
1 -TCATTCTAAAATGGTCCCT-AAAATTTTAAATATTTCAATTTCATCCCAA
5395468 GATATATATA
Statistics
Matches: 91, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
58 1 0.01
59 30 0.33
60 57 0.63
61 3 0.03
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (58 bp):
TCATTCTAAAATGGTCCCTAAAATTTTAAATATTTCAATTTCATCCCAACTATGACTA
Found at i:5396902 original size:25 final size:25
Alignment explanation
Indices: 5396865--5396921 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
5396855 TTGTCGCTTA
5396865 TATGT-TTCCAAAGAACAAAAATAT
1 TATGTGTTCCAAAGAACAAAAATAT
5396889 TATGTGTTCCAAAGAACAAAAATAT
1 TATGTGTTCCAAAGAACAAAAATAT
*
5396914 AATGTGTT
1 TATGTGTT
5396922 GTCGTTTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 5 0.16
25 26 0.84
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.32
Consensus pattern (25 bp):
TATGTGTTCCAAAGAACAAAAATAT
Found at i:5397122 original size:25 final size:25
Alignment explanation
Indices: 5397088--5397146 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
5397078 GGTTTGTCGC
*
5397088 TTATATGTTCCAAAGAACAAAAATA
1 TTATGTGTTCCAAAGAACAAAAATA
5397113 TTATGTGTTCCAAAGAACAAAAATA
1 TTATGTGTTCCAAAGAACAAAAATA
*
5397138 TAATGTGTT
1 TTATGTGTT
5397147 TGTCGTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (25 bp):
TTATGTGTTCCAAAGAACAAAAATA
Found at i:5397145 original size:225 final size:223
Alignment explanation
Indices: 5396754--5397203 Score: 841
Period size: 225 Copynumber: 2.0 Consensus size: 223
5396744 GGTGATGGGT
5396754 TTGAGACCTTACCCGCCCCGCATCCGCCTGCCTCACGTATGTTTGGCCACTAAATACCTATTAAA
1 TTGAGACCTTACCCGCCCCGCATCCGCCTGCCTCACGTATGTTTGGCCACTAAATACCTATTAAA
5396819 ATTTGGATTATTATAAATTTAGGTATAATTTTAAGGTTGTCGCTTATATGTTTCCAAAGAACAAA
66 ATTTGGATTATTATAAATTTAGGTATAATTTTAAGGTTGTCGCTTATATGTTTCCAAAGAACAAA
5396884 AATATTATGTGTTCCAAAGAACAAAAATATAATGTG-TTGTCGTTTATATGTTTCTATGCTTTAA
131 AATATTATGTGTTCCAAAGAACAAAAATATAATGTGTTTGTCG-TT-TATGTTTCTATGCTTTAA
5396948 TTATGTCTTTTATTATGAGGTTTTTATATAC
194 TTATGTCTTTTATTATGAGG-TTTTATATAC
5396979 TTGAGACCTTACCCGCCCCGCATCCGCCTGCCTCACGTATGTTTGGCCACTAAATACCTATTAAA
1 TTGAGACCTTACCCGCCCCGCATCCGCCTGCCTCACGTATGTTTGGCCACTAAATACCTATTAAA
5397044 ATTTGGATTATTATAAATTTAGGTATAATTTTAAGGTTTGTCGCTTATATG-TTCCAAAGAACAA
66 ATTTGGATTATTATAAATTTAGGTATAATTTTAAGG-TTGTCGCTTATATGTTTCCAAAGAACAA
5397108 AAATATTATGTGTTCCAAAGAACAAAAATATAATGTGTTTGTCGTTTATGTTTCTATGCTTTAAT
130 AAATATTATGTGTTCCAAAGAACAAAAATATAATGTGTTTGTCGTTTATGTTTCTATGCTTTAAT
*
5397173 TATGTCTTTTATTATGATGTTTTATATAC
195 TATGTCTTTTATTATGAGGTTTTATATAC
5397202 TT
1 TT
5397204 TAAGATCTAT
Statistics
Matches: 222, Mismatches: 1, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
223 12 0.05
224 37 0.17
225 153 0.69
226 20 0.09
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (223 bp):
TTGAGACCTTACCCGCCCCGCATCCGCCTGCCTCACGTATGTTTGGCCACTAAATACCTATTAAA
ATTTGGATTATTATAAATTTAGGTATAATTTTAAGGTTGTCGCTTATATGTTTCCAAAGAACAAA
AATATTATGTGTTCCAAAGAACAAAAATATAATGTGTTTGTCGTTTATGTTTCTATGCTTTAATT
ATGTCTTTTATTATGAGGTTTTATATAC
Found at i:5400025 original size:47 final size:50
Alignment explanation
Indices: 5399955--5400055 Score: 145
Period size: 47 Copynumber: 2.1 Consensus size: 50
5399945 TTTATTTTCG
*
5399955 TTTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGG-TTTAT
1 TTTTTTCGAATAAATGCATGCGAACTAGATATCATGCAGTTAGGATTTAT
* * *
5400004 TTTTTTTGAAT-AA-GCATGCGAATTAGATATCATGCAGTTAGGATTTCT
1 TTTTTTCGAATAAATGCATGCGAACTAGATATCATGCAGTTAGGATTTAT
5400052 TTTT
1 TTTT
5400056 GTGGATAACA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
47 27 0.57
48 10 0.21
49 10 0.21
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.43
Consensus pattern (50 bp):
TTTTTTCGAATAAATGCATGCGAACTAGATATCATGCAGTTAGGATTTAT
Found at i:5409739 original size:24 final size:24
Alignment explanation
Indices: 5409724--5409799 Score: 65
Period size: 24 Copynumber: 3.3 Consensus size: 24
5409714 AAAAGAGAAA
5409724 AAAAATGAGAAAATAAGAAAAAAG
1 AAAAATGAGAAAATAAGAAAAAAG
*
5409748 AAAAATGATGGAAAA-AA-CAAAAAG
1 AAAAATGA--GAAAATAAGAAAAAAG
*
5409772 --AAA-GA-AAAAGAAGAAAAAATG
1 AAAAATGAGAAAATAAGAAAAAA-G
5409793 AAAAATG
1 AAAAATG
5409800 GAAGAGAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 16
0.70 0.03 0.27
Matches are distributed among these distances:
18 4 0.10
19 2 0.05
20 5 0.12
21 3 0.07
22 3 0.07
23 3 0.07
24 15 0.36
25 2 0.05
26 5 0.12
ACGTcount: A:0.74, C:0.01, G:0.17, T:0.08
Consensus pattern (24 bp):
AAAAATGAGAAAATAAGAAAAAAG
Found at i:5409752 original size:16 final size:16
Alignment explanation
Indices: 5409723--5409854 Score: 53
Period size: 17 Copynumber: 7.9 Consensus size: 16
5409713 TAAAAGAGAA
5409723 AAAAAATGAGAAAATAAG
1 AAAAAA-GA-AAAATAAG
*
5409741 AAAAAAGAAAAATGATG
1 AAAAAAGAAAAAT-AAG
* *
5409758 GAAAAA-ACAAA-AAG
1 AAAAAAGAAAAATAAG
*
5409772 ---AAAGAAAAAGAAG
1 AAAAAAGAAAAATAAG
5409785 AAAAAATGAAAAATGGAAG
1 AAAAAA-GAAAAAT--AAG
*
5409804 AGAACAAATGGAAAAAGGAAG
1 A-AA-AAA--GAAAAA-TAAG
5409825 AAAAAGAGAAAAAT--G
1 AAAAA-AGAAAAATAAG
*
5409840 AAAAAAGAGAAATAA
1 AAAAAAGAAAAATAA
5409855 AAGGAGGGTT
Statistics
Matches: 88, Mismatches: 10, Indels: 34
0.67 0.08 0.26
Matches are distributed among these distances:
11 3 0.03
12 4 0.05
13 3 0.03
14 9 0.10
15 6 0.07
16 12 0.14
17 15 0.17
18 12 0.14
19 6 0.07
20 5 0.06
21 7 0.08
22 6 0.07
ACGTcount: A:0.72, C:0.02, G:0.20, T:0.07
Consensus pattern (16 bp):
AAAAAAGAAAAATAAG
Found at i:5409807 original size:21 final size:21
Alignment explanation
Indices: 5409783--5409839 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
5409773 AAGAAAAAGA
5409783 AGAAAAAATGAAAAATGGAAG
1 AGAAAAAATGAAAAATGGAAG
*
5409804 AGAACAAATGGAAAAA-GGAAG
1 AGAAAAAAT-GAAAAATGGAAG
*
5409825 A-AAAAGA-GAAAAATG
1 AGAAAAAATGAAAAATG
5409840 AAAAAAGAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 6 0.19
19 1 0.03
20 4 0.13
21 14 0.45
22 6 0.19
ACGTcount: A:0.67, C:0.02, G:0.25, T:0.07
Consensus pattern (21 bp):
AGAAAAAATGAAAAATGGAAG
Found at i:5409850 original size:24 final size:24
Alignment explanation
Indices: 5409724--5409851 Score: 68
Period size: 27 Copynumber: 5.1 Consensus size: 24
5409714 AAAAGAGAAA
*
5409724 AAAAATGAGAAAATAAGAAAAAAGA-
1 AAAAA-GAGAAAA-ATGAAAAAAGAG
* ** *
5409749 AAAATGATGGAAAAAACAAAAAGAAAG
1 AAAAAGA--GAAAAATGAAAAA-AGAG
*
5409776 AAAAAGAAGAAAAAATGAAAAATG-G
1 AAAAAG-AG-AAAAATGAAAAAAGAG
*
5409801 ---AAGAGAACAAATGGAAAAAGGAAG
1 AAAAAGAGAA-AAAT-GAAAAAAG-AG
5409825 AAAAAGAGAAAAATGAAAAAAGAG
1 AAAAAGAGAAAAATGAAAAAAGAG
5409849 AAA
1 AAA
5409852 TAAAAGGAGG
Statistics
Matches: 80, Mismatches: 10, Indels: 27
0.68 0.09 0.23
Matches are distributed among these distances:
20 2 0.03
21 6 0.08
22 10 0.12
24 8 0.10
25 19 0.24
26 12 0.15
27 22 0.28
28 1 0.01
ACGTcount: A:0.72, C:0.02, G:0.20, T:0.06
Consensus pattern (24 bp):
AAAAAGAGAAAAATGAAAAAAGAG
Found at i:5411750 original size:110 final size:108
Alignment explanation
Indices: 5411180--5411951 Score: 589
Period size: 102 Copynumber: 7.3 Consensus size: 108
5411170 TTGTTGAAGA
* * *
5411180 TTGAG-TCTTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-GAGTCCT
1 TTGAGTTC-TATACTCCCTGAACGAATAGGGAGCGGACAAGTTCGTTGAAGATTGTTCGAGTTCT
* *
5411240 ATACTCTCTGAATGAATAGGGAGCGGACA-AGTTCGTTGAAGA---
65 ATACTCTCTGAAGGAATAGGGAGCGGACACA-TT-TTTGAAGATTG
* * * *
5411282 TTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-GAGTCCTA
1 TTGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACAAGTTCGTTGAAGATTGTTCGAGTTCTA
* *
5411343 TACTCTCTGAATGAATAGGGAGCGGACA-AGTTCGTTGAAGA---
66 TACTCTCTGAAGGAATAGGGAGCGGACACA-TT-TTTGAAGATTG
* * * * *
5411384 TTGAGTCCTATACTCTCTAAAGGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-GAGTCCTA
1 TTGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACAAGTTCGTTGAAGATTGTTCGAGTTCTA
*
5411445 TACTCTCTGAAGGAATAGGGAGCGGACA-AGTTCGTTGAAGA---
66 TACTCTCTGAAGGAATAGGGAGCGGACACA-TT-TTTGAAGATTG
* * * *
5411486 TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-GAGTCCTA
1 TTGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACAAGTTCGTTGAAGATTGTTCGAGTTCTA
*
5411547 TACTCTCTGAAGGAATAGGGAGCGGACA-AGTTCGTTGAAGA---
66 TACTCTCTGAAGGAATAGGGAGCGGACACA-TT-TTTGAAGATTG
* * * * * * *
5411588 TTGAGTCCTATACTCTCTGAAGGAATAAGGAGCGGGCAAGTTCGTTGAAGATTGTTCAAGTTATA
1 TTGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACAAGTTCGTTGAAGATTGTTCGAGTTCTA
* *
5411653 TACTCTCTGAAGGATTAGAGAGCGGACACATTTTATGAAGATTG
66 TACTCTCTGAAGGAATAGGGAGCGGACACATTTT-TGAAGATTG
* **
5411697 TTCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACTCA-TTTATTGAAGATT-TTCTGAGTT
1 TT-GAGTTCTATACTCCCTGAACGAATAGGGAGCGGAC-AAGTTCGTTGAAGATTGTTC-GAGTT
* * *
5411760 CTATACTCTCTAAAGGAATAGAGAGCGGATC-CGTTTTATTGAAGATTG
63 CTATACTCTCTGAAGGAATAGGGAGCGGA-CAC-ATTT-TTGAAGATTG
* * * * ** *
5411808 TTCAAG-TCTTATACTCCCTG-ACTGAATAGGGAGCAGACACGTTTGCCGAAGATTGTTTGAG-T
1 TT-GAGTTC-TATACTCCCTGAAC-GAATAGGGAGCGGACAAGTTCGTTGAAGATTGTTCGAGTT
* ** * * **
5411870 CTTATACTCCCTGACTGAATAGGGAGCAGACACGTTTGCCGAAGATTG
63 C-TATACTCTCTGAAGGAATAGGGAGCGGACACATTT-TTGAAGATTG
*
5411918 TTTGAG-TCTTATACTCCCTGAAAGAATAGGGAGC
1 -TTGAGTTC-TATACTCCCTGAACGAATAGGGAGC
5411952 AGACCCGCCA
Statistics
Matches: 600, Mismatches: 46, Indels: 40
0.87 0.07 0.06
Matches are distributed among these distances:
102 348 0.58
103 1 0.00
105 3 0.00
106 39 0.06
107 1 0.00
109 5 0.01
110 117 0.19
111 83 0.14
112 3 0.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.28
Consensus pattern (108 bp):
TTGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACAAGTTCGTTGAAGATTGTTCGAGTTCTA
TACTCTCTGAAGGAATAGGGAGCGGACACATTTTTGAAGATTG
Found at i:5411788 original size:55 final size:51
Alignment explanation
Indices: 5411172--5411788 Score: 880
Period size: 51 Copynumber: 11.9 Consensus size: 51
5411162 AAATTCGTTT
* *
5411172 GTTGAAGATTGAGTCTTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
5411223 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
5411274 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
5411325 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
5411376 GTTGAAGATTGAGTCCTATACTCTCTAAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
5411427 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
5411478 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
5411529 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* *
5411580 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAAGGAGCGGGCAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
** * *
5411631 GTTGAAGATTGTTCAAGTTATATACTCTCTGAAGGATTAGAGAGCGGACACA-TT-
1 GTTGAAGATTG----AGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA-AGTTC
* * * * * *
5411685 TTATGAAGATTGTTCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACTCA-TTT
1 GT-TGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC-AAGTTC
* * * *
5411741 ATTGAAGATTTTCTGAGTTCTATACTCTCTAAAGGAATAGAGAGCGGA
1 GTTGAAGA---T-TGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGA
5411789 TCCGTTTTAT
Statistics
Matches: 528, Mismatches: 25, Indels: 22
0.92 0.04 0.04
Matches are distributed among these distances:
51 413 0.78
54 1 0.00
55 108 0.20
56 3 0.01
58 2 0.00
59 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (51 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
Found at i:5411874 original size:55 final size:55
Alignment explanation
Indices: 5411800--5411955 Score: 276
Period size: 55 Copynumber: 2.8 Consensus size: 55
5411790 CCGTTTTATT
**
5411800 GAAGATTGTTCAAGTCTTATACTCCCTGACTGAATAGGGAGCAGACACGTTTGCC
1 GAAGATTGTTTGAGTCTTATACTCCCTGACTGAATAGGGAGCAGACACGTTTGCC
5411855 GAAGATTGTTTGAGTCTTATACTCCCTGACTGAATAGGGAGCAGACACGTTTGCC
1 GAAGATTGTTTGAGTCTTATACTCCCTGACTGAATAGGGAGCAGACACGTTTGCC
**
5411910 GAAGATTGTTTGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGAC
1 GAAGATTGTTTGAGTCTTATACTCCCTGACTGAATAGGGAGCAGAC
5411956 CCGCCATTTG
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 97 1.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (55 bp):
GAAGATTGTTTGAGTCTTATACTCCCTGACTGAATAGGGAGCAGACACGTTTGCC
Found at i:5411916 original size:166 final size:166
Alignment explanation
Indices: 5411632--5411951 Score: 373
Period size: 166 Copynumber: 1.9 Consensus size: 166
5411622 GGCAAGTTCG
* * * * *
5411632 TTGAAGATTGTTCAAGTTATATACTCTCTGAAGGATTAGAGAGCGGACACATTTTATGAAGATTG
1 TTGAAGATTGTTCAAGTTATATACTCCCTGAAGGAATAGAGAGCAGACACATTTGACGAAGATTG
* * **
5411697 TTCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACTCATTTATTGAAGATT-TTCTGAGT-T
66 TTCGAGTTCTATACTCCCTGAACGAATAGGGAGCAGACACATTTACCGAAGATTGTT-TGAGTCT
*
5411760 CTATACTCTCT-AAAGGAATAGAGAGCGGATCCGTTTTA
130 -TATACTCCCTGAAA-GAATAGAGAGCGGATCCGTTTTA
** * * *
5411798 TTGAAGATTGTTCAAGTCT-TATACTCCCTGACTGAATAGGGAGCAGACACGTTTGCCGAAGATT
1 TTGAAGATTGTTCAAGT-TATATACTCCCTGAAGGAATAGAGAGCAGACACATTTGACGAAGATT
* * *
5411862 GTTTGAG-TCTTATACTCCCTG-ACTGAATAGGGAGCAGACACGTTTGCCGAAGATTGTTTGAGT
65 GTTCGAGTTC-TATACTCCCTGAAC-GAATAGGGAGCAGACACATTTACCGAAGATTGTTTGAGT
*
5411925 CTTATACTCCCTGAAAGAATAGGGAGC
128 CTTATACTCCCTGAAAGAATAGAGAGC
5411952 AGACCCGCCA
Statistics
Matches: 129, Mismatches: 19, Indels: 12
0.81 0.12 0.08
Matches are distributed among these distances:
165 4 0.03
166 118 0.91
167 7 0.05
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.31
Consensus pattern (166 bp):
TTGAAGATTGTTCAAGTTATATACTCCCTGAAGGAATAGAGAGCAGACACATTTGACGAAGATTG
TTCGAGTTCTATACTCCCTGAACGAATAGGGAGCAGACACATTTACCGAAGATTGTTTGAGTCTT
ATACTCCCTGAAAGAATAGAGAGCGGATCCGTTTTA
Found at i:5411971 original size:55 final size:52
Alignment explanation
Indices: 5411180--5411955 Score: 250
Period size: 51 Copynumber: 14.7 Consensus size: 52
5411170 TTGTTGAAGA
* * * * * ** * *
5411180 TTGAGTCTTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGA-AGA
1 TTGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTGAAGATTGT
* * * * * * ** * *
5411231 TTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGA-AGA
1 TTGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTGAAGATTGT
* * * * * * ** * *
5411282 TTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGA-AGA
1 TTGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTGAAGATTGT
* * * * * * ** * *
5411333 TTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGA-AGA
1 TTGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTGAAGATTGT
* * * * * ** * *
5411384 TTGAGTCCTATACTCTCT-AAAGGAATAGGGAGCGGACAAGTTCGTTGA-AGA
1 TTGAGTCTTATACTCCCTGAAA-GAATAGGGAGCAGACACGTTTGAAGATTGT
* * * * * * ** * *
5411435 TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGA-AGA
1 TTGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTGAAGATTGT
* * * * * * ** * *
5411486 TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGA-AGA
1 TTGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTGAAGATTGT
* * * * * * ** * *
5411537 TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGA-AGA
1 TTGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTGAAGATTGT
* * * * * * *
5411588 TTGAGTCCTATACTCTCTGAAGGAATAAGGAGCGGGCAAGTTCGTTGAAGATTGT
1 TTGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACG-T--TTGAAGATTGT
** * * * * * *
5411643 TCAAGT-TATATACTCTCTGAAGGATTAGAGAGCGGACACATTTTATGAAGATTGT
1 TTGAGTCT-TATACTCCCTGAAAGAATAGGGAGCAGACAC--GTT-TGAAGATTGT
* * * **
5411698 TCGAGT-TCTATACTCCCTGAACGAATAGGGAGCGGACTCATTTATTGAAGATT-T
1 TTGAGTCT-TATACTCCCTGAAAGAATAGGGAGCAGA--CACGT-TTGAAGATTGT
* * *
5411752 TCTGAGT-TCTATACTCTCT-AAAGGAATAGAGAGCGGATC-CGTTTTATTGAAGATTGT
1 T-TGAGTCT-TATACTCCCTGAAA-GAATAGGGAGCAGA-CACG---T-TTGAAGATTGT
** **
5411809 TCAAGTCTTATACTCCCTGACTGAATAGGGAGCAGACACGTTTGCCGAAGATTGT
1 TTGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTT---GAAGATTGT
**
5411864 TTGAGTCTTATACTCCCTGACTGAATAGGGAGCAGACACGTTTGCCGAAGATTGT
1 TTGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTT---GAAGATTGT
5411919 TTGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGAC
1 TTGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGAC
5411956 CCGCCATTTG
Statistics
Matches: 657, Mismatches: 43, Indels: 46
0.88 0.06 0.06
Matches are distributed among these distances:
50 2 0.00
51 386 0.59
52 5 0.01
53 1 0.00
54 11 0.02
55 207 0.32
56 39 0.06
57 6 0.01
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.28
Consensus pattern (52 bp):
TTGAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTGAAGATTGT
Found at i:5414535 original size:2 final size:2
Alignment explanation
Indices: 5414528--5414571 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
5414518 CGTCATCCTT
5414528 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
5414570 TA
1 TA
5414572 AGTCGCCATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5420507 original size:5 final size:5
Alignment explanation
Indices: 5420497--5420524 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
5420487 GGAGCCTTTG
5420497 TAAAA TAAAA TAAAA TAAAA TAAAA TAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAA
5420525 TAGAGCCGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:5423527 original size:36 final size:36
Alignment explanation
Indices: 5423480--5423555 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
5423470 AATTCTGGAG
* * *
5423480 TATGCAGGTTCAGCTCCGATCAAGCTGGTAATTTCT
1 TATGCAGGTTCAACACCGATCAAGCTGGTAATTCCT
*
5423516 TATGCAGGTTCAACACCGATCAAGTTGGTAATTCCT
1 TATGCAGGTTCAACACCGATCAAGCTGGTAATTCCT
5423552 TATG
1 TATG
5423556 GACCTAAGGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (36 bp):
TATGCAGGTTCAACACCGATCAAGCTGGTAATTCCT
Found at i:5423696 original size:23 final size:23
Alignment explanation
Indices: 5423666--5423712 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
5423656 TTATTGGGTA
5423666 AGTCCTTATGGGCCTGAGGGAAC
1 AGTCCTTATGGGCCTGAGGGAAC
5423689 AGTCCTTATGGGCCTGAGGGAAC
1 AGTCCTTATGGGCCTGAGGGAAC
5423712 A
1 A
5423713 CCCCTCAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.23, C:0.21, G:0.34, T:0.21
Consensus pattern (23 bp):
AGTCCTTATGGGCCTGAGGGAAC
Found at i:5426508 original size:16 final size:16
Alignment explanation
Indices: 5426487--5426529 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
5426477 AATTAAGCGC
*
5426487 TGAATGATTCAAATGT
1 TGAATGATTCAAATAT
*
5426503 TGAATGGTTCAAATAT
1 TGAATGATTCAAATAT
5426519 TGAATGATTCA
1 TGAATGATTCA
5426530 GAGGCTCTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (16 bp):
TGAATGATTCAAATAT
Found at i:5428972 original size:21 final size:20
Alignment explanation
Indices: 5428946--5429044 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
5428936 AATCAGTTTC
5428946 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
5428967 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
5428988 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
5429008 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
5429029 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
5429045 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 16 0.26
21 45 0.74
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:5429060 original size:40 final size:40
Alignment explanation
Indices: 5429011--5429165 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
5429001 CGATTTTCCA
* ** *
5429011 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
* * *
5429051 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATC-CGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACAT
* ** *
5429091 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
5429131 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
5429166 TATTTAAAGC
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.01
40 62 0.65
41 33 0.34
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
Done.