Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 19 of 190
Found at i:5392973 original size:11 final size:11
Alignment explanation
Indices: 5392957--5392987 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
5392947 ATTTGGAAGG
5392957 AAATTGAGAGC
1 AAATTGAGAGC
*
5392968 AAATTGAGAGG
1 AAATTGAGAGC
5392979 AAATTGAGA
1 AAATTGAGA
5392988 AAATAATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.48, C:0.03, G:0.29, T:0.19
Consensus pattern (11 bp):
AAATTGAGAGC
Found at i:5393191 original size:40 final size:40
Alignment explanation
Indices: 5393131--5393209 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
5393121 CAGAGGCGCG
* * *
5393131 CTACGTGGCAGCAAAACGCGTCCACGTCAGCGCGCTTTGC
1 CTACGTGGCAACAAAACGCGTCCAAGTAAGCGCGCTTTGC
*
5393171 CTACGTGGCAACAAAGCGCGTCCAAGTAAGCGCGCTTTG
1 CTACGTGGCAACAAAACGCGTCCAAGTAAGCGCGCTTTG
5393210 TTGCCACGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.23, C:0.32, G:0.28, T:0.18
Consensus pattern (40 bp):
CTACGTGGCAACAAAACGCGTCCAAGTAAGCGCGCTTTGC
Found at i:5394775 original size:30 final size:30
Alignment explanation
Indices: 5394739--5394826 Score: 88
Period size: 31 Copynumber: 2.9 Consensus size: 30
5394729 TTCATTTTTC
5394739 AAATAAAAAATCATAAAAATTATAAAATAA
1 AAATAAAAAATCATAAAAATTATAAAATAA
** * *
5394769 AAATAAAAAAATTGTACAAACTTATTAAAATTA
1 AAAT-AAAAAATCATA-AAAATTA-TAAAATAA
* *
5394802 GAA-AAAAAATCATAAATATTATAAA
1 AAATAAAAAATCATAAAAATTATAAA
5394827 TATTATAAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
29 4 0.09
30 9 0.20
31 18 0.39
32 6 0.13
33 9 0.20
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (30 bp):
AAATAAAAAATCATAAAAATTATAAAATAA
Found at i:5395428 original size:9 final size:9
Alignment explanation
Indices: 5395414--5395528 Score: 81
Period size: 9 Copynumber: 12.0 Consensus size: 9
5395404 TTTTTTAAAT
5395414 TAATTTTTA
1 TAATTTTTA
5395423 TAATTTTTTA
1 TAA-TTTTTA
*
5395433 TAAGTTTATA
1 TAA-TTTTTA
5395443 TAAATTTTGTA
1 T-AATTTT-TA
*
5395454 AATATTTTTA
1 TA-ATTTTTA
5395464 -AATATTTTA
1 TAAT-TTTTA
*
5395473 TTATTTTTA
1 TAATTTTTA
5395482 TAATTTTTA
1 TAATTTTTA
*
5395491 TAAGTTTATA
1 TAA-TTTTTA
5395501 TAAATTTTTA
1 T-AATTTTTA
*
5395511 -ATATTTTAA
1 TA-ATTTTTA
*
5395520 TATTTTTTA
1 TAATTTTTA
5395529 CGATTTCTAT
Statistics
Matches: 85, Mismatches: 11, Indels: 20
0.73 0.09 0.17
Matches are distributed among these distances:
8 3 0.04
9 36 0.42
10 35 0.41
11 11 0.13
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (9 bp):
TAATTTTTA
Found at i:5395430 original size:10 final size:10
Alignment explanation
Indices: 5395417--5395510 Score: 70
Period size: 10 Copynumber: 9.6 Consensus size: 10
5395407 TTTAAATTAA
5395417 TTTTTATAAT
1 TTTTTATAAT
*
5395427 TTTTTATAAG
1 TTTTTATAAT
*
5395437 TTTATATAAAT
1 TTTTTAT-AAT
*
5395448 TTTGTA-AAT
1 TTTTTATAAT
5395457 ATTTTTA-AAT
1 -TTTTTATAAT
* *
5395467 ATTTTATTA-
1 TTTTTATAAT
5395476 TTTTTATAA-
1 TTTTTATAAT
*
5395485 TTTTTATAAG
1 TTTTTATAAT
* *
5395495 TTTATATAAA
1 TTTTTATAAT
5395505 TTTTTA
1 TTTTTA
5395511 ATATTTTAAT
Statistics
Matches: 68, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
9 24 0.35
10 37 0.54
11 7 0.10
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:5395499 original size:58 final size:55
Alignment explanation
Indices: 5395416--5395525 Score: 177
Period size: 58 Copynumber: 1.9 Consensus size: 55
5395406 TTTTAAATTA
5395416 ATTTTTATAATTTTTTATAAGTTTATATAAATTTTGTAAATATTTTTAAATATTTTATT
1 ATTTTTATAATTTTTTATAAGTTTATATAAATTTT-T-AATA-TTTT-AATATTTTATT
5395475 ATTTTTATAA-TTTTTATAAGTTTATATAAATTTTTAATATTTTAATATTTT
1 ATTTTTATAATTTTTTATAAGTTTATATAAATTTTTAATATTTTAATATTTT
5395526 TTACGATTTC
Statistics
Matches: 51, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
54 8 0.16
55 4 0.08
56 4 0.08
57 1 0.02
58 24 0.47
59 10 0.20
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (55 bp):
ATTTTTATAATTTTTTATAAGTTTATATAAATTTTTAATATTTTAATATTTTATT
Found at i:5402395 original size:82 final size:80
Alignment explanation
Indices: 5402295--5402453 Score: 255
Period size: 82 Copynumber: 2.0 Consensus size: 80
5402285 GGGAGGTTCT
* *
5402295 GAATCAAAAGGGAAAACAACTAGAAAATTTAGGTGAAGTTGATGTTGTAGAATACTACAGCAATG
1 GAATCAAAAGGGAAAACAACCAGAAAATTTAGGTGAAGTTGATGTTGTAGAAGACT--AGCAATG
*
5402360 GTAAACTTCTAGTCTGC
64 ATAAACTTCTAGTCTGC
* *
5402377 GAATCAAAAGGGAAAACAACCAGAAAATTTTGGTGAAGTTGATGTTGTAGAAGACTAGCGATGAT
1 GAATCAAAAGGGAAAACAACCAGAAAATTTAGGTGAAGTTGATGTTGTAGAAGACTAGCAATGAT
5402442 AAACTTCTAGTC
66 AAACTTCTAGTC
5402454 GCTTCTGTCA
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
80 19 0.26
82 53 0.74
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.25
Consensus pattern (80 bp):
GAATCAAAAGGGAAAACAACCAGAAAATTTAGGTGAAGTTGATGTTGTAGAAGACTAGCAATGAT
AAACTTCTAGTCTGC
Found at i:5403395 original size:217 final size:217
Alignment explanation
Indices: 5402958--5403369 Score: 747
Period size: 217 Copynumber: 1.9 Consensus size: 217
5402948 AAAGAGGACA
5402958 TCTTGATGGGTAAAAAATTTACAAACTGAAGTTTTGTGAGCACTGCATTTTTGCAAAAAAAAAAA
1 TCTTGATGGGTAAAAAATTTACAAACTGAAGTTTTGTGAGCACTGCATTTTTGCAAAAAAAAAAA
* *
5403023 GAGTTCGATTCTCAAAAAGAAATCCATAACACAAAGGGAACATTGGAGTATATTGATTCTGATAT
66 GAGTTCGATTCACAAAAAGAAATCCATAACACAAAGGGAACATTAGAGTATATTGATTCTGATAT
5403088 GTAGGGGGTCATCCAGAGTGCCTTCGAGAGGTGGAACTAATTATATGCTAACTTTTATTGATGAT
131 GTAGGGGGTCATCCAGAGTGCCTTCGAGAGGTGGAACTAATTATATGCTAACTTTTATTGATGAT
5403153 TTTTTCAGAAAAGGTTGGGCGT
196 TTTTTCAGAAAAGGTTGGGCGT
** *
5403175 TCTTGATGGGTAAAAAATTTACAAACTGAAGTTTTGTGAGCACTGCATTTTTGCAAAGCAAAAGA
1 TCTTGATGGGTAAAAAATTTACAAACTGAAGTTTTGTGAGCACTGCATTTTTGCAAAAAAAAAAA
*
5403240 GAGTTCGATTCAC-AAAAGGAATCCATAACACAAAGGGAACATTAGAGTATATTGATTCTGATAT
66 GAGTTCGATTCACAAAAAGAAATCCATAACACAAAGGGAACATTAGAGTATATTGATTCTGATAT
*
5403304 GT-GGGGGTCATCTAGAGTGCCTTCGAGAGGTGGAACTAATTATATGCTAACTTTTATTGATGAT
131 GTAGGGGGTCATCCAGAGTGCCTTCGAGAGGTGGAACTAATTATATGCTAACTTTTATTGATGAT
5403368 TT
196 TT
5403370 CTTTTTTAAA
Statistics
Matches: 188, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
215 63 0.34
216 51 0.27
217 74 0.39
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (217 bp):
TCTTGATGGGTAAAAAATTTACAAACTGAAGTTTTGTGAGCACTGCATTTTTGCAAAAAAAAAAA
GAGTTCGATTCACAAAAAGAAATCCATAACACAAAGGGAACATTAGAGTATATTGATTCTGATAT
GTAGGGGGTCATCCAGAGTGCCTTCGAGAGGTGGAACTAATTATATGCTAACTTTTATTGATGAT
TTTTTCAGAAAAGGTTGGGCGT
Found at i:5408838 original size:23 final size:23
Alignment explanation
Indices: 5408812--5408864 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
5408802 ATAAGTGCCA
5408812 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
5408835 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
5408858 CACTGAT
1 CACTGAT
5408865 CAATAACACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:5414531 original size:36 final size:36
Alignment explanation
Indices: 5414484--5414592 Score: 182
Period size: 36 Copynumber: 3.0 Consensus size: 36
5414474 GCTAAGCTAC
* *
5414484 CACTTATCACTTTGTCACTTGATTAGATAAGTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
*
5414520 CACTTATCACTTTTTCACTTGATCAGATAAGTATAA
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
*
5414556 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
5414592 C
1 C
5414593 TAAAGCTACC
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 68 1.00
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (36 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
Found at i:5418693 original size:23 final size:23
Alignment explanation
Indices: 5418660--5418711 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
5418650 ATAAGTGCCA
* *
5418660 CACTGATATGTAGTCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
5418683 CACTGAAATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
5418706 CACTGA
1 CACTGA
5418712 TCAATAACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGAAATGTAGCCGAAGCTAC
Found at i:5422313 original size:18 final size:17
Alignment explanation
Indices: 5422292--5422342 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 17
5422282 GTTATATATA
5422292 TATATGATAGAATAATG
1 TATATGATAGAATAATG
*
5422309 CTATA-G-GA-AATAATTG
1 -TATATGATAGAATAA-TG
5422325 TATATGATAGAATAATG
1 TATATGATAGAATAATG
5422342 T
1 T
5422343 CATGAATAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 9
0.71 0.05 0.24
Matches are distributed among these distances:
15 9 0.33
16 4 0.15
17 5 0.19
18 9 0.33
ACGTcount: A:0.45, C:0.02, G:0.18, T:0.35
Consensus pattern (17 bp):
TATATGATAGAATAATG
Found at i:5422916 original size:6 final size:6
Alignment explanation
Indices: 5422905--5422939 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
5422895 TTGTTGTTAC
5422905 CAATGG CAATGG CAATGG CAATGG CAATGG CAATG
1 CAATGG CAATGG CAATGG CAATGG CAATGG CAATG
5422940 AATGATGACG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.34, C:0.17, G:0.31, T:0.17
Consensus pattern (6 bp):
CAATGG
Found at i:5427511 original size:14 final size:15
Alignment explanation
Indices: 5427475--5427511 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
5427465 CTTAAATTCA
*
5427475 TAATTTTTCAACACT
1 TAATTTTTCAACAAT
*
5427490 TAATTTTTCAATAAT
1 TAATTTTTCAACAAT
5427505 TAATTTT
1 TAATTTT
5427512 ACAGTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.35, C:0.11, G:0.00, T:0.54
Consensus pattern (15 bp):
TAATTTTTCAACAAT
Found at i:5430612 original size:33 final size:33
Alignment explanation
Indices: 5430574--5430637 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
5430564 GTACACAAAA
*
5430574 TAAAAGTTCATGA-ATCAAAATATCCATTAAAGC
1 TAAAAGTTCAT-ATATCAAAATATACATTAAAGC
*
5430607 TAAAAGTTCATATATCAAATTATACATTAAA
1 TAAAAGTTCATATATCAAAATATACATTAAA
5430638 ATAAAGTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.04
33 27 0.96
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.31
Consensus pattern (33 bp):
TAAAAGTTCATATATCAAAATATACATTAAAGC
Found at i:5432632 original size:114 final size:113
Alignment explanation
Indices: 5432296--5432945 Score: 980
Period size: 114 Copynumber: 5.7 Consensus size: 113
5432286 GGCGACCTTC
*
5432296 GAAAAACGCCGCTAAATCACACCATTAGCGGCGCATTATACAAAGCGCCGCAAAAAATCTTAACC
1 GAAAAACGCCGCTAAAGCACACCATTAGCGGCGCATTATACAAAGCGCCGCAAAAAATCTTAACC
*
5432361 AAAACGCATCGTTTTGGATTGAGGTATTTTAGAATTAGTGGCGCTTTAA
66 AAAACGCATCGTTTTGGGTTGAGGTATTTTAGAATTAGTGGCGC-TTAA
* * *
5432410 GATAAATGCCGCTAAAGCACACCATTAGCGGCGTATTATACAAAGCGCCGC-AAAAATCTTAACC
1 GAAAAACGCCGCTAAAGCACACCATTAGCGGCGCATTATACAAAGCGCCGCAAAAAATCTTAACC
* *
5432474 AAAACGCATTGTTCTGGGTTGAGGTATTTTAGAATTAGTGGCGCTTAA
66 AAAACGCATCGTTTTGGGTTGAGGTATTTTAGAATTAGTGGCGCTTAA
* *
5432522 GAAAAAACGCCGCTAACGCACACCATTAGCGGCGCATCATACAAAGCGCCGCAAAAAATCTTAAC
1 G-AAAAACGCCGCTAAAGCACACCATTAGCGGCGCATTATACAAAGCGCCGCAAAAAATCTTAAC
* * **
5432587 CGAAACGCATCGTTTTGGGTTGAGGTATATTAGAATTAGTGGCGCTTGCG
65 CAAAACGCATCGTTTTGGGTTGAGGTATTTTAGAATTAGTGGCGCTT-AA
* * * *
5432637 GATAAATGCCACTAAAGCACACCATTAGCGGCGCATTATTCAAAGCGCCGCAAAAAATCTTAACC
1 GAAAAACGCCGCTAAAGCACACCATTAGCGGCGCATTATACAAAGCGCCGCAAAAAATCTTAACC
*
5432702 AAAACGCATCGTTTTGGGTTGAGGTATTTTAGATTTAGTGGCGCTTAA
66 AAAACGCATCGTTTTGGGTTGAGGTATTTTAGAATTAGTGGCGCTTAA
* * * *
5432750 GGATAAATGCCGCTAAAGCACACCATTAGCGGTGCATTATACAAAGCGCCGCAAAAAATCATAAC
1 -GAAAAACGCCGCTAAAGCACACCATTAGCGGCGCATTATACAAAGCGCCGCAAAAAATCTTAAC
* *
5432815 CAAAACGCATCGTTTTTGGTTGAGGTATTTTTAGAATTAGTAGCGC-TATA
65 CAAAACGCATCGTTTTGGGTTGAGGTA-TTTTAGAATTAGTGGCGCTTA-A
* * *
5432865 GTAAAACGCCGCTAAAGTACATCATTAGCGGCGCATTATACAAAGCGCCGCAAACAAATCTTAAC
1 GAAAAACGCCGCTAAAGCACACCATTAGCGGCGCATTATACAAAGCGCCGCAAA-AAATCTTAAC
5432930 CAAAACGCATCGTTTT
65 CAAAACGCATCGTTTT
5432946 AAACCGAAAC
Statistics
Matches: 486, Mismatches: 43, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
112 5 0.01
113 99 0.20
114 339 0.70
115 43 0.09
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.24
Consensus pattern (113 bp):
GAAAAACGCCGCTAAAGCACACCATTAGCGGCGCATTATACAAAGCGCCGCAAAAAATCTTAACC
AAAACGCATCGTTTTGGGTTGAGGTATTTTAGAATTAGTGGCGCTTAA
Found at i:5433416 original size:21 final size:21
Alignment explanation
Indices: 5433355--5433417 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
5433345 TTTATGGGCC
*
5433355 ATGGTTTAAGGGTTAGGGTTTA
1 ATGG-TTAAGGGTTAGGGGTTA
*
5433377 AT-G-TATAGGTGTTATGGGTTA
1 ATGGTTA-AGG-GTTAGGGGTTA
5433398 ATGGTTAAGGGTTAGGGGTT
1 ATGGTTAAGGGTTAGGGGTT
5433418 TAGGGTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
19 2 0.06
20 3 0.09
21 21 0.62
22 6 0.18
23 2 0.06
ACGTcount: A:0.22, C:0.00, G:0.38, T:0.40
Consensus pattern (21 bp):
ATGGTTAAGGGTTAGGGGTTA
Found at i:5433424 original size:21 final size:20
Alignment explanation
Indices: 5433360--5433424 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 20
5433350 GGGCCATGGT
*
5433360 TTAAGGGTTAGGGTTTAATG
1 TTAAGGGTTAGGGTTTAAGG
5433380 -TATAGGTGTTATGGG-TTAATGG
1 TTA-AGG-GTTA-GGGTTTAA-GG
*
5433402 TTAAGGGTTAGGGGTTTAGGG
1 TTAAGGGTTA-GGGTTTAAGG
5433423 TT
1 TT
5433425 TATAGTTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
19 2 0.06
20 3 0.08
21 19 0.53
22 10 0.28
23 2 0.06
ACGTcount: A:0.22, C:0.00, G:0.38, T:0.40
Consensus pattern (20 bp):
TTAAGGGTTAGGGTTTAAGG
Found at i:5433442 original size:50 final size:50
Alignment explanation
Indices: 5433357--5433485 Score: 120
Period size: 50 Copynumber: 2.6 Consensus size: 50
5433347 TATGGGCCAT
* * * * * *
5433357 GGTTTA-AGGGTTAGGGTTTAATG-TATAGGTGTTATGGGTTAATGGTTAAG
1 GGTTTACAGGTTTAGGGTTTAAAGAT-TATGTTTTATGAGTCAA-GGTTAAG
** * * *
5433407 GG-TTAGGGGTTTAGGGTTTATAGTTTATGTTTTATGAGTCAAGGTTTAG
1 GGTTTACAGGTTTAGGGTTTAAAGATTATGTTTTATGAGTCAAGGTTAAG
5433456 GGTTTACAGGTTTAGGGTTTAAAGATTATG
1 GGTTTACAGGTTTAGGGTTTAAAGATTATG
5433486 GTTTGTGTAC
Statistics
Matches: 63, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
49 11 0.17
50 51 0.81
51 1 0.02
ACGTcount: A:0.23, C:0.02, G:0.33, T:0.42
Consensus pattern (50 bp):
GGTTTACAGGTTTAGGGTTTAAAGATTATGTTTTATGAGTCAAGGTTAAG
Found at i:5433466 original size:15 final size:15
Alignment explanation
Indices: 5433448--5433476 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5433438 TTATGAGTCA
5433448 AGGTTTAGGGTTTAC
1 AGGTTTAGGGTTTAC
5433463 AGGTTTAGGGTTTA
1 AGGTTTAGGGTTTA
5433477 AAGATTATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.03, G:0.34, T:0.41
Consensus pattern (15 bp):
AGGTTTAGGGTTTAC
Found at i:5434672 original size:191 final size:190
Alignment explanation
Indices: 5434316--5434694 Score: 578
Period size: 191 Copynumber: 2.0 Consensus size: 190
5434306 TACAAATCCC
* ** *
5434316 TAGACCTTTCACCTTTTCAACGACGATTCCCCTCTTCTCGGTCGAATATCGCTTCTCGTCTGGGC
1 TAGACCATTCACCCCTTCAACGACGATTCCCCTCTTCTCGATCGAATATCGCTTCTCGTCTGGGC
* * *
5434381 TGACTGGTAAAAAACTTTCCAAATCCCTAATTTCTCCGTTGACTCCGTATATAGCTGTTCATTTT
66 TGACTGGTAAAAAACTTTCCAAATCCCTAATGTCTCCGTTGACTACGTATATAGCTATTCATTTT
* *
5434446 TATGTTCGATTTTTTCTTTCTGTAATGCCCGCTTTGTTTTTCCTTTCTCTTTAAATTCCA
131 TATGTTCGATTTTTTCTTTCTCTAATGCCCGCTTTGTTTTTCCTTTCGCTTTAAATTCCA
* *
5434506 TAGACCATTCACCCCTTCAACGACGATTTCCCCTCTTTTCGATCGAATATTGCTTCTCGTCTGGG
1 TAGACCATTCACCCCTTCAACGACGA-TTCCCCTCTTCTCGATCGAATATCGCTTCTCGTCTGGG
* * * *
5434571 CTGACTGGTAAAAATCTTTCCAAATCCCTAATGTCTTCGTTGATTACGTATATGGCTATTCATTT
65 CTGACTGGTAAAAAACTTTCCAAATCCCTAATGTCTCCGTTGACTACGTATATAGCTATTCATTT
* * **
5434636 TTCTGTTTGATTTTTTCTTTCTCTAATGTTCGCTTTGTTTTTCCTTTCGCTTTAAATTC
130 TTATGTTCGATTTTTTCTTTCTCTAATGCCCGCTTTGTTTTTCCTTTCGCTTTAAATTC
5434695 TGTGTTGCTT
Statistics
Matches: 169, Mismatches: 19, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
190 23 0.14
191 146 0.86
ACGTcount: A:0.18, C:0.25, G:0.13, T:0.43
Consensus pattern (190 bp):
TAGACCATTCACCCCTTCAACGACGATTCCCCTCTTCTCGATCGAATATCGCTTCTCGTCTGGGC
TGACTGGTAAAAAACTTTCCAAATCCCTAATGTCTCCGTTGACTACGTATATAGCTATTCATTTT
TATGTTCGATTTTTTCTTTCTCTAATGCCCGCTTTGTTTTTCCTTTCGCTTTAAATTCCA
Found at i:5436276 original size:27 final size:27
Alignment explanation
Indices: 5436234--5436466 Score: 239
Period size: 27 Copynumber: 8.8 Consensus size: 27
5436224 TAACTTGTAT
*
5436234 ATAAGCTTGCATAACTTACATAAATTAA
1 ATAA-CTTACATAACTTACATAAATTAA
5436262 ATAACTTACATAACTTACATAAATTAA
1 ATAACTTACATAACTTACATAAATTAA
* *
5436289 GTAACTTACATAAACTTGCATAAATTAA
1 ATAACTTACAT-AACTTACATAAATTAA
*
5436317 TTAACTTACATAACTT--AT--A-T--
1 ATAACTTACATAACTTACATAAATTAA
* * * * *
5436337 A-AACTTGCATAAATTAAATAACTTAC
1 ATAACTTACATAACTTACATAAATTAA
*
5436363 ATAACTTACATAACCTACATAAATTAA
1 ATAACTTACATAACTTACATAAATTAA
*
5436390 ATAACTTACATAACCTACATAAATTAA
1 ATAACTTACATAACTTACATAAATTAA
* **
5436417 ATAACTTACATAACATACATAAACTTGC
1 ATAACTTACATAACTTACATAAA-TTAA
* *
5436445 ATAAATTAAATAACTTACATAA
1 ATAACTTACATAACTTACATAA
5436467 CTTACANNNN
Statistics
Matches: 175, Mismatches: 20, Indels: 20
0.81 0.09 0.09
Matches are distributed among these distances:
19 12 0.07
21 2 0.01
22 1 0.01
23 1 0.01
24 1 0.01
25 2 0.01
26 1 0.01
27 105 0.60
28 50 0.29
ACGTcount: A:0.49, C:0.16, G:0.03, T:0.32
Consensus pattern (27 bp):
ATAACTTACATAACTTACATAAATTAA
Found at i:5436310 original size:10 final size:10
Alignment explanation
Indices: 5436246--5436472 Score: 174
Period size: 9 Copynumber: 24.8 Consensus size: 10
5436236 AAGCTTGCAT
5436246 AACTTACATA
1 AACTTACATA
*
5436256 AA-TTAAAT-
1 AACTTACATA
5436264 AACTTACAT-
1 AACTTACATA
5436273 AACTTACATA
1 AACTTACATA
5436283 AA-TTA-AGT-
1 AACTTACA-TA
5436291 AACTTACATA
1 AACTTACATA
*
5436301 AACTTGCATA
1 AACTTACATA
*
5436311 AA-TTA-ATT
1 AACTTACATA
5436319 AACTTACAT-
1 AACTTACATA
*
5436328 AACTTATATA
1 AACTTACATA
*
5436338 AACTTGCATA
1 AACTTACATA
*
5436348 AA-TTAAAT-
1 AACTTACATA
5436356 AACTTACAT-
1 AACTTACATA
5436365 AACTTACAT-
1 AACTTACATA
*
5436374 AACCTACATA
1 AACTTACATA
*
5436384 AA-TTAAAT-
1 AACTTACATA
5436392 AACTTACAT-
1 AACTTACATA
*
5436401 AACCTACATA
1 AACTTACATA
*
5436411 AA-TTAAAT-
1 AACTTACATA
5436419 AACTTACAT-
1 AACTTACATA
*
5436428 AACATACATA
1 AACTTACATA
*
5436438 AACTTGCATA
1 AACTTACATA
*
5436448 AA-TTAAAT-
1 AACTTACATA
5436456 AACTTACAT-
1 AACTTACATA
5436465 AACTTACA
1 AACTTACA
5436473 NNNNNNNNNN
Statistics
Matches: 176, Mismatches: 25, Indels: 33
0.75 0.11 0.14
Matches are distributed among these distances:
8 17 0.10
9 117 0.66
10 42 0.24
ACGTcount: A:0.50, C:0.16, G:0.02, T:0.32
Consensus pattern (10 bp):
AACTTACATA
Found at i:5436311 original size:37 final size:35
Alignment explanation
Indices: 5436244--5436472 Score: 215
Period size: 37 Copynumber: 6.5 Consensus size: 35
5436234 ATAAGCTTGC
* * *
5436244 ATAACTTACATAAATTAAATAACTTACATAACTTA
1 ATAACTTACATAACTTACATAACTTACATAAATTA
* *
5436279 CATAAATTA-AGTAACTTACATAAACTTGCATAAATTA
1 -ATAACTTACA-TAACTTACAT-AACTTACATAAATTA
* *
5436316 ATTAACTTACATAACTTATATAAACTTGCATAAATTAA
1 A-TAACTTACATAACTTACAT-AACTTACATAAATT-A
*
5436354 ATAACTTACATAACTTACATAACCTACATAAA-T-
1 ATAACTTACATAACTTACATAACTTACATAAATTA
*
5436387 -T-A---A-ATAACTTACATAACCTACATAAATTAA
1 ATAACTTACATAACTTACATAACTTACATAAATT-A
* *
5436417 ATAACTTACATAACATACATAAACTTGCATAAATTAA
1 ATAACTTACATAACTTACAT-AACTTACATAAATT-A
5436454 ATAACTTACATAACTTACA
1 ATAACTTACATAACTTACA
5436473 NNNNNNNNNN
Statistics
Matches: 164, Mismatches: 14, Indels: 29
0.79 0.07 0.14
Matches are distributed among these distances:
27 23 0.14
28 2 0.01
31 2 0.01
32 2 0.01
35 3 0.02
36 36 0.22
37 93 0.57
38 3 0.02
ACGTcount: A:0.50, C:0.16, G:0.02, T:0.32
Consensus pattern (35 bp):
ATAACTTACATAACTTACATAACTTACATAAATTA
Found at i:5442206 original size:21 final size:21
Alignment explanation
Indices: 5442180--5442248 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
5442170 CAACAACTTA
* *
5442180 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGAG
* * *
5442201 AAGCAGAGGTTACAGAGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
5442222 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
5442243 AAGCAG
1 AAGCAG
5442249 CGAGAGAAAC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.36, C:0.16, G:0.43, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGAG
Found at i:5442248 original size:12 final size:12
Alignment explanation
Indices: 5442233--5442272 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
5442223 AGCAGAGGCT
5442233 GCAGCGAGAGAA
1 GCAGCGAGAGAA
5442245 GCAGCGAGAGAA
1 GCAGCGAGAGAA
* *
5442257 ACAGCGATAGAA
1 GCAGCGAGAGAA
5442269 GCAG
1 GCAG
5442273 AGGTTCAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.42, C:0.17, G:0.38, T:0.03
Consensus pattern (12 bp):
GCAGCGAGAGAA
Found at i:5442715 original size:42 final size:42
Alignment explanation
Indices: 5442667--5442914 Score: 335
Period size: 42 Copynumber: 5.9 Consensus size: 42
5442657 TTTGTGAAAT
**
5442667 AAGCGCCGCTAAAGAACACT-A-CTGTTAGCGGCG-TTTTTGAA
1 AAGCGCCGCTAAAGAACA-TGATCT-TTAGCGGCGTTTTTTCCA
* *
5442708 CAAGCGCCGCTATAGAACATTA-CTTTTAGCGGCGTTTTCTTCCA
1 -AAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTTT-TTCCA
*
5442752 AAGCGCCGCTAAAGATCATGATCTTTAGCGGCGTTTTTTCCA
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCA
* *
5442794 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTCCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCA
*
5442836 AAGCGCCGCTAAAGAACATGATCTTTAGCGGC-TTTTTTTCA
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCA
*
5442877 TAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT
5442915 CTGTAAGCGC
Statistics
Matches: 188, Mismatches: 12, Indels: 12
0.89 0.06 0.06
Matches are distributed among these distances:
41 39 0.21
42 109 0.58
43 36 0.19
44 4 0.02
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.30
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCA
Found at i:5442798 original size:85 final size:84
Alignment explanation
Indices: 5442667--5442914 Score: 335
Period size: 85 Copynumber: 3.0 Consensus size: 84
5442657 TTTGTGAAAT
** * *
5442667 AAGCGCCGCTAAAGAACACT-A-CTGTTAGCGGCG-TTTTTGAACAAGCGCCGCTATAGAACATT
1 AAGCGCCGCTAAAGAACA-TGATCT-TTAGCGGCGTTTTTTCCA-AAGCGCCGCTAAAGAACATG
5442729 A-CTTTTAGCGGCGTTTTCTTCCA
63 ATC-TTTAGCGGCGTTTT-TTCCA
*
5442752 AAGCGCCGCTAAAGATCATGATCTTTAGCGGCGTTTTTTCCAAAGCGCCGCTAAAGAACATGATC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCAAAGCGCCGCTAAAGAACATGATC
* *
5442817 TTTAGCGGCATTTTTTCCT
66 TTTAGCGGCGTTTTTTCCA
* *
5442836 AAGCGCCGCTAAAGAACATGATCTTTAGCGGC-TTTTTTTCATAGCGCCGCTAAAGAACATGATC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCAAAGCGCCGCTAAAGAACATGATC
5442900 TTTAGCGGCGTTTTT
66 TTTAGCGGCGTTTTT
5442915 CTGTAAGCGC
Statistics
Matches: 148, Mismatches: 11, Indels: 10
0.88 0.07 0.06
Matches are distributed among these distances:
83 44 0.30
84 36 0.24
85 59 0.40
86 9 0.06
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.30
Consensus pattern (84 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCAAAGCGCCGCTAAAGAACATGATC
TTTAGCGGCGTTTTTTCCA
Found at i:5446253 original size:2 final size:2
Alignment explanation
Indices: 5446246--5446275 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5446236 TTTAAACTTA
5446246 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
5446276 GCATGCTCAT
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:5452124 original size:18 final size:18
Alignment explanation
Indices: 5452103--5452137 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5452093 AAAAGAAGGA
5452103 AATTAAAGAAAATTAAAG
1 AATTAAAGAAAATTAAAG
**
5452121 AATTAAATTAAATTAAA
1 AATTAAAGAAAATTAAA
5452138 TTGTTGAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (18 bp):
AATTAAAGAAAATTAAAG
Found at i:5453637 original size:177 final size:174
Alignment explanation
Indices: 5453336--5453852 Score: 759
Period size: 177 Copynumber: 2.9 Consensus size: 174
5453326 GAGTCATAAG
* * *
5453336 CTATTTGTGAAGTTAAAATTGTTTTTCAATCCAAACCCAACAGCTATTGTGTTTGAAAAAAAAAA
1 CTATTTTTGAAGTTAAAATTGATTTTCAATCCAAACCCAAAAGCTATTGTGTTTGAAAAAAAAAA
* * *
5453401 ACACTTTTGGAGTCAAAAGATGTTTTTAACTCTTATTTATAATCTAATGTATTTTATATAATATT
66 ACACTTTTGGAGTCAAAGGATATTTTTAACTCTTATTTATAATCTAATATATTTTATATAATATT
* *
5453466 TATATTGGATCTGAATTTATTGAGTCATAAGCAATACAAAACAGA
131 TATATTGGA-CTAAATTTATTGAGCCATAAGCAATACAAAACAGA
* **
5453511 TTATTTTTGAAGTTAAAATTGATTTTCAATCCAAACCCAAAAGCTATTACGTTTGTAAAAAAAAA
1 CTATTTTTGAAGTTAAAATTGATTTTCAATCCAAACCCAAAAGCTATTGTGTTTG--AAAAAAAA
*
5453576 AAACACTTTTGGAGTCCAAGGATATTTTTAACTCTTATTTATAATCTAATATATTTTATATAATA
64 AAACACTTTTGGAGTCAAAGGATATTTTTAACTCTTATTTATAATCTAATATATTTTATATAATA
***
5453641 TTTATATTGGACCTAAATTTATTGAGCCATAAGCAACGTAAAACAGA
129 TTTATATTGGA-CTAAATTTATTGAGCCATAAGCAATACAAAACAGA
* * *
5453688 CCATTTTTGAAATT-AAATTTATTTTTCAATCCAAACCCAAAAGCTATTGTGTTTGAAAAAAAAA
1 CTATTTTTGAAGTTAAAATTGA-TTTTCAATCCAAACCCAAAAGCTATTGTGTTTGAAAAAAAAA
* * *
5453752 AACA-TTTTCGGAGTCAAAGAATCTTTTTAACTCTTATTTATAATTTAATATATTTTATATAATA
65 AACACTTTT-GGAGTCAAAGGATATTTTTAACTCTTATTTATAATCTAATATATTTTATATAATA
*
5453816 TTTGTATTGGACTTAAATTTATTGAGCCATAAGCAAT
129 TTTATATTGGAC-TAAATTTATTGAGCCATAAGCAAT
5453853 GCTAAACACA
Statistics
Matches: 309, Mismatches: 28, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
174 5 0.02
175 146 0.47
176 6 0.02
177 152 0.49
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (174 bp):
CTATTTTTGAAGTTAAAATTGATTTTCAATCCAAACCCAAAAGCTATTGTGTTTGAAAAAAAAAA
ACACTTTTGGAGTCAAAGGATATTTTTAACTCTTATTTATAATCTAATATATTTTATATAATATT
TATATTGGACTAAATTTATTGAGCCATAAGCAATACAAAACAGA
Found at i:5477104 original size:421 final size:417
Alignment explanation
Indices: 5476315--5477104 Score: 1053
Period size: 421 Copynumber: 1.9 Consensus size: 417
5476305 ATATCGTTAT
* * * * *
5476315 ATCCCTCCGCCAAGAGGACATATGTCAACCCAATAGACATTGTTGACTATGCATTTATTTCCTAA
1 ATCCCTCCACCAAGAGGACATATGTCAACCCAAGAGACATCGTTGACTATGCATTGACTTCCTAA
* * * * * * *
5476380 ACATGACTACTCGTCCCATTTCAAATGGAACTATCACTCGTGTTTAAAGTAGAATGCTATCCTAA
66 ACATGACCACCCGTCCCACTTCAAATGGAACTACCACCCGAGTTTAAAGGAGAATGCTATCCTAA
* * *
5476445 TGTGAACACACTTCCAAGATAACAAGGAGTCTTTAGATTAACTACCTCATACTGATAGAATCTCA
131 TGTGAACACACTTCCAAGACAACAAAGAGTCTTTAGATTAACTACCTCAGACTGATAGAATCTCA
* *
5476510 TAATATATGCCTATGATTATTCATTACACATTTAACGAGATTAAACATTTGTATAGCCAATTTTA
196 TAATATATGCCTATGATTATTCATTACACATTTAACGAGATTAAACATTTATATAGCCAATATTA
* * * * * * *
5476575 TACCAATGGACAAGGGGACCTTTTTTATAAATACCTTGGGAAGCTATGAATAGGGGATTGACTTT
261 TACCAATGGACAAGAGGACCTTTTCTATAAATACCTTGGAAAACTAGGAACAGGGGATCGACTTT
* * * * *
5476640 TTAGTACTCTTAAGTTACTCTCAGCATTTATCCTCTCAATCAGCTTGTCCTTTTGTCCTTGTTTT
326 TTAGCACCCTAAAGTCACTCTCAACATTTATCCTCTCAATCAGCTTGTCCTTTTGTCCTTGTTTT
5476705 GGCTCTCAGCATTTACAGGTCAACTAA
391 GGCTCTCAGCATTTACAGGTCAACTAA
* * *
5476732 ATCCCTTCACCAAGAGGACATGTGTCAACCCAAGAGACATCGTTGACTATGCATTGACTTCCTGA
1 ATCCCTCCACCAAGAGGACATATGTCAACCCAAGAGACATCGTTGACTATGCATTGACTTCCTAA
* * *
5476797 GCATTACCACCCGTCCCACTTCAAATGGAACCTACCACCCGAGTTTAAAGGAGAATGTTATCCTA
66 ACATGACCACCCGTCCCACTTCAAATGGAA-CTACCACCCGAGTTTAAAGGAGAATGCTATCCTA
* * * * * *
5476862 ATTTGAACATACTTCCAATG-CAATAAATAGTCTATTTAGGCTTGACTACCTCAGACTGATAGAA
130 ATGTGAACACACTTCCAA-GACAACAAAGAGTC--TTTA-GATTAACTACCTCAGACTGATAGAA
* * * *
5476926 TCTCATAATATGTGTCTATGATTATTCATTACACATTTAACGAGATTAAATATTTATCTAGCCAA
191 TCTCATAATATATGCCTATGATTATTCATTACACATTTAACGAGATTAAACATTTATATAGCCAA
* * *
5476991 TATTATACCAGTGGATAAGAGGA-CTTTTCCTATAAATATCTTGGAAAACTAGGAACAGGGGATC
256 TATTATACCAATGGACAAGAGGACCTTTT-CTATAAATACCTTGGAAAACTAGGAACAGGGGATC
* * *
5477055 GCCTTTTTAGCACCCTAAAGTCACTCTCAACATTTATCCTTTTAATCAGC
320 GACTTTTTAGCACCCTAAAGTCACTCTCAACATTTATCCTCTCAATCAGC
5477105 CTGTTTCCTA
Statistics
Matches: 316, Mismatches: 51, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
417 82 0.26
418 53 0.17
419 1 0.00
420 9 0.03
421 171 0.54
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.32
Consensus pattern (417 bp):
ATCCCTCCACCAAGAGGACATATGTCAACCCAAGAGACATCGTTGACTATGCATTGACTTCCTAA
ACATGACCACCCGTCCCACTTCAAATGGAACTACCACCCGAGTTTAAAGGAGAATGCTATCCTAA
TGTGAACACACTTCCAAGACAACAAAGAGTCTTTAGATTAACTACCTCAGACTGATAGAATCTCA
TAATATATGCCTATGATTATTCATTACACATTTAACGAGATTAAACATTTATATAGCCAATATTA
TACCAATGGACAAGAGGACCTTTTCTATAAATACCTTGGAAAACTAGGAACAGGGGATCGACTTT
TTAGCACCCTAAAGTCACTCTCAACATTTATCCTCTCAATCAGCTTGTCCTTTTGTCCTTGTTTT
GGCTCTCAGCATTTACAGGTCAACTAA
Found at i:5477173 original size:92 final size:92
Alignment explanation
Indices: 5477016--5477200 Score: 334
Period size: 92 Copynumber: 2.0 Consensus size: 92
5477006 TAAGAGGACT
*
5477016 TTTCCTATAAATATCTTGGAAAACTAGGAACAGGGGATCGCCTTTTTAGCACCCTAAAGTCACTC
1 TTTCCTATAAATATCTTGGAAAACTAGGAACAAGGGATCGCCTTTTTAGCACCCTAAAGTCACTC
5477081 TCAACATTTATCCTTTTAATCAGCCTG
66 TCAACATTTATCCTTTTAATCAGCCTG
*
5477108 TTTCCTATAAATATCTTGGAAAACTATGAACAAGGGATCGCCTTTTTAGCACCCTAAAGTCACTC
1 TTTCCTATAAATATCTTGGAAAACTAGGAACAAGGGATCGCCTTTTTAGCACCCTAAAGTCACTC
* *
5477173 TCAACATTTATCTTTTTAATTAGCCTG
66 TCAACATTTATCCTTTTAATCAGCCTG
5477200 T
1 T
5477201 CCTCTTGTCC
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 89 1.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.35
Consensus pattern (92 bp):
TTTCCTATAAATATCTTGGAAAACTAGGAACAAGGGATCGCCTTTTTAGCACCCTAAAGTCACTC
TCAACATTTATCCTTTTAATCAGCCTG
Found at i:5484055 original size:26 final size:26
Alignment explanation
Indices: 5484019--5484081 Score: 126
Period size: 26 Copynumber: 2.4 Consensus size: 26
5484009 ATAAATCATA
5484019 AGAAAATTTATGAAATGACTCAGATG
1 AGAAAATTTATGAAATGACTCAGATG
5484045 AGAAAATTTATGAAATGACTCAGATG
1 AGAAAATTTATGAAATGACTCAGATG
5484071 AGAAAATTTAT
1 AGAAAATTTAT
5484082 ATTGGAGAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.29
Consensus pattern (26 bp):
AGAAAATTTATGAAATGACTCAGATG
Found at i:5491386 original size:12 final size:12
Alignment explanation
Indices: 5491369--5491400 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
5491359 CATATAGCTA
5491369 GCCACACGACCG
1 GCCACACGACCG
5491381 GCCACACGACCG
1 GCCACACGACCG
5491393 GCCACACG
1 GCCACACG
5491401 CTCGTGTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.25, C:0.50, G:0.25, T:0.00
Consensus pattern (12 bp):
GCCACACGACCG
Found at i:5495411 original size:20 final size:22
Alignment explanation
Indices: 5495382--5495423 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
5495372 TTTGCTTTAG
*
5495382 TTTTCTTAGGTTTTC-TATTTT
1 TTTTCTTAGGGTTTCTTATTTT
5495403 TTTTC-TAGGGTTTCTTATTTT
1 TTTTCTTAGGGTTTCTTATTTT
5495424 CCACATTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.10, C:0.10, G:0.12, T:0.69
Consensus pattern (22 bp):
TTTTCTTAGGGTTTCTTATTTT
Found at i:5525976 original size:24 final size:25
Alignment explanation
Indices: 5525919--5525976 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
5525909 GGATAAAAGG
* * *
5525919 AGATGAAAGGTTTAAGGAATATGGA
1 AGATGAAAGGTTTAAAGAAAATGAA
* *
5525944 AGGTTAAAGG-TTAAAGAAAATGAA
1 AGATGAAAGGTTTAAAGAAAATGAA
5525968 AGATGAAAG
1 AGATGAAAG
5525977 ATTGAACATC
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
24 18 0.69
25 8 0.31
ACGTcount: A:0.50, C:0.00, G:0.29, T:0.21
Consensus pattern (25 bp):
AGATGAAAGGTTTAAAGAAAATGAA
Found at i:5527227 original size:28 final size:28
Alignment explanation
Indices: 5527195--5527280 Score: 84
Period size: 28 Copynumber: 3.0 Consensus size: 28
5527185 AAACATATAT
*
5527195 TTTTAAAAAAATTAAAAAAATGTTAGAA
1 TTTTAAAAAAATTAAAAAAATATTAGAA
* *
5527223 TTTTATAAAAATCGTAAAAAAATATTTAAAA
1 TTTTAAAAAAAT--TAAAAAAATA-TTAGAA
* **
5527254 TATTAAAATTA-TAAAAAAATATTAGAA
1 TTTTAAAAAAATTAAAAAAATATTAGAA
5527281 ATTGAAAATT
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
27 5 0.11
28 21 0.45
30 9 0.19
31 12 0.26
ACGTcount: A:0.60, C:0.01, G:0.05, T:0.34
Consensus pattern (28 bp):
TTTTAAAAAAATTAAAAAAATATTAGAA
Found at i:5527288 original size:19 final size:19
Alignment explanation
Indices: 5527250--5527288 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5527240 AAAAATATTT
*
5527250 AAAATATTAAAATTATAAA
1 AAAATATTAAAATTAGAAA
5527269 AAAATATTAGAAATT-GAAA
1 AAAATATTA-AAATTAGAAA
5527288 A
1 A
5527289 TTATTGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (19 bp):
AAAATATTAAAATTAGAAA
Found at i:5527288 original size:27 final size:28
Alignment explanation
Indices: 5527237--5527292 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
5527227 ATAAAAATCG
*
5527237 TAAAAAAATATTTAAAATATTAAAATTA
1 TAAAAAAATATTTAAAATATGAAAATTA
5527265 TAAAAAAATA-TTAGAAAT-TGAAAATTA
1 TAAAAAAATATTTA-AAATATGAAAATTA
5527292 T
1 T
5527293 TGTAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 12 0.46
28 14 0.54
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (28 bp):
TAAAAAAATATTTAAAATATGAAAATTA
Found at i:5528549 original size:20 final size:20
Alignment explanation
Indices: 5528523--5528563 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5528513 TATAATTTTA
5528523 TAATTTTTT-T-TCTATTTG
1 TAATTTTTTATATCTATTTG
*
5528541 TAATTTTTTATATCTTTTTG
1 TAATTTTTTATATCTATTTG
5528561 TAA
1 TAA
5528564 ATCTTTTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 1 0.05
20 10 0.50
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (20 bp):
TAATTTTTTATATCTATTTG
Found at i:5529181 original size:40 final size:40
Alignment explanation
Indices: 5529106--5529181 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
5529096 GCACTTTACC
** *
5529106 CGTGTCAGCAAAAGCACGTTGACGTGGGCATGCTTTGCCA
1 CGTGTCAGCAAAAGCACGTTGACGTGAACACGCTTTGCCA
* *
5529146 CGTGTCAGCAAAAGCGCGTTGACGTGAACGCGCTTT
1 CGTGTCAGCAAAAGCACGTTGACGTGAACACGCTTT
5529182 ACCCCGTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.22, C:0.25, G:0.30, T:0.22
Consensus pattern (40 bp):
CGTGTCAGCAAAAGCACGTTGACGTGAACACGCTTTGCCA
Found at i:5531789 original size:103 final size:103
Alignment explanation
Indices: 5531544--5531902 Score: 551
Period size: 103 Copynumber: 3.5 Consensus size: 103
5531534 GGTGGATTCC
* ** *
5531544 GCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGGGAATCAGCACT
1 GCACTTAGCAACCACCAATGAATAGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACT
** * *
5531609 TAGCAACCCCC-TTCACATTTCAAAGATGTGGTGGAATTA
66 TAGCAACCCCCTTTCACATTT-AAA-ATACGGTGGGATCA
*
5531648 GCACTTAGCAACCACCAATGAATAGGGGAATTAGCACTTAGCAACCCCTCGGGGGAATCAGCACT
1 GCACTTAGCAACCACCAATGAATAGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACT
5531713 TAGCAACCCCCTTTCACATTTAAAATACGGTGGGATCA
66 TAGCAACCCCCTTTCACATTTAAAATACGGTGGGATCA
* *
5531751 GCACTTAGCAACCACCAAT-AGGTAGGGGAATCAACACTTAGCAACCCCTCGGGGGAATCAGCAC
1 GCACTTAGCAACCACCAATGA-ATAGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCAC
5531815 TTAGCAACCCCCTTTCACATTTAAAATACGGTGGGATCA
65 TTAGCAACCCCCTTTCACATTTAAAATACGGTGGGATCA
* **
5531854 GCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GCACTTAGCAACCACCAATGAATAGGGGAATCAGCACTTAGCAACCCCT
5531903 TTATATGCAA
Statistics
Matches: 235, Mismatches: 17, Indels: 7
0.91 0.07 0.03
Matches are distributed among these distances:
102 1 0.00
103 150 0.64
104 75 0.32
105 9 0.04
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.19
Consensus pattern (103 bp):
GCACTTAGCAACCACCAATGAATAGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACT
TAGCAACCCCCTTTCACATTTAAAATACGGTGGGATCA
Found at i:5544128 original size:114 final size:113
Alignment explanation
Indices: 5543983--5544293 Score: 297
Period size: 114 Copynumber: 2.7 Consensus size: 113
5543973 TGGTCATAAA
* * *
5543983 CGCCGCAAAAACTGTTAAGAAAAC-ACTGTCGTTTTCAGTTTAGGTTTTGGGGACTTTAGTGGTG
1 CGCCGC-AAAACTGTTAAGAAAACGA-TGTCGTTTTCA-TTTAGGTTTTAGAGACTTTAGTGGCG
* *
5544047 CTTACT-GAAAAACGCCGCTA-TAGTC-AAGAATTAGCGGCGCTTTATTATAAC
63 CTT-CTCGAAAAACGCCGC-AGTAG-CGAAGAATTAGCGGCGCTTTATCACAAC
* * ** * * *
5544098 CGTCGCAAAACTGTTAAGAAAACGTTGTCGTTTTTCATTTATCTTTTCGAGACGTTAGTGGCGAT
1 CGCCGCAAAACTGTTAAGAAAACGATGTCG-TTTTCATTTAGGTTTTAGAGACTTTAGTGGCGCT
* * * ** * *
5544163 TTTCGGAAAGCGCCGCAGTAGCGAAGCTTTAGTGGCGCTTTATCACAAG
65 TCTCGAAAAACGCCGCAGTAGCGAAGAATTAGCGGCGCTTTATCACAAC
* * *
5544212 TGCCGTAAAACTGTTAAGAAAACGATGTCGTTTTTAATTTAGGTTTTAGAGACTTTAGTGGCGCT
1 CGCCGCAAAACTGTTAAGAAAACGATGTCG-TTTTCATTTAGGTTTTAGAGACTTTAGTGGCGCT
* * *
5544277 TGTCTAAAAATGCCGCA
65 TCTCGAAAAACGCCGCA
5544294 AAATATAGGA
Statistics
Matches: 158, Mismatches: 33, Indels: 11
0.78 0.16 0.05
Matches are distributed among these distances:
113 3 0.02
114 144 0.91
115 11 0.07
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (113 bp):
CGCCGCAAAACTGTTAAGAAAACGATGTCGTTTTCATTTAGGTTTTAGAGACTTTAGTGGCGCTT
CTCGAAAAACGCCGCAGTAGCGAAGAATTAGCGGCGCTTTATCACAAC
Found at i:5544988 original size:14 final size:14
Alignment explanation
Indices: 5544971--5545029 Score: 75
Period size: 14 Copynumber: 4.2 Consensus size: 14
5544961 TTAAGGATTG
5544971 GGGTTAAGGGTTTA
1 GGGTTAAGGGTTTA
*
5544985 GGGTTTAAGGGTTAA
1 GGG-TTAAGGGTTTA
*
5545000 GGGTTAAGGG-TTG
1 GGGTTAAGGGTTTA
*
5545013 GGGTTAGGGGTTTA
1 GGGTTAAGGGTTTA
5545027 GGG
1 GGG
5545030 GTTTATAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
13 10 0.26
14 15 0.39
15 13 0.34
ACGTcount: A:0.19, C:0.00, G:0.49, T:0.32
Consensus pattern (14 bp):
GGGTTAAGGGTTTA
Found at i:5544994 original size:15 final size:15
Alignment explanation
Indices: 5544974--5545034 Score: 65
Period size: 15 Copynumber: 4.2 Consensus size: 15
5544964 AGGATTGGGG
5544974 TTAAGGGTTTAGGGT
1 TTAAGGGTTTAGGGT
*
5544989 TTAAGGGTTAAGGG-
1 TTAAGGGTTTAGGGT
*
5545003 TTAAGGG-TT-GGGG
1 TTAAGGGTTTAGGGT
*
5545016 TTAGGGGTTTAGGGGT
1 TTAAGGGTTTA-GGGT
5545032 TTA
1 TTA
5545035 TAATTAATGT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
12 3 0.08
13 7 0.18
14 9 0.24
15 13 0.34
16 6 0.16
ACGTcount: A:0.20, C:0.00, G:0.44, T:0.36
Consensus pattern (15 bp):
TTAAGGGTTTAGGGT
Found at i:5545034 original size:8 final size:7
Alignment explanation
Indices: 5544971--5545029 Score: 66
Period size: 7 Copynumber: 8.4 Consensus size: 7
5544961 TTAAGGATTG
5544971 GGGTTAA
1 GGGTTAA
*
5544978 GGGTTTA
1 GGGTTAA
5544985 GGGTTTAA
1 GGG-TTAA
5544993 GGGTTAA
1 GGGTTAA
5545000 GGGTTAA
1 GGGTTAA
*
5545007 GGGTT-G
1 GGGTTAA
*
5545013 GGGTTAG
1 GGGTTAA
*
5545020 GGGTTTA
1 GGGTTAA
5545027 GGG
1 GGG
5545030 GTTTATAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
6 5 0.11
7 34 0.76
8 6 0.13
ACGTcount: A:0.19, C:0.00, G:0.49, T:0.32
Consensus pattern (7 bp):
GGGTTAA
Found at i:5545225 original size:28 final size:29
Alignment explanation
Indices: 5545193--5545258 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
5545183 GGCTTATGGA
*
5545193 TTATGGTTTAAAAGTTAGG-GTTAAGGGT
1 TTATGGGTTAAAAGTTAGGTGTTAAGGGT
** *
5545221 TTATGGGTTAAGGGTTAGGTGTTAGGGGT
1 TTATGGGTTAAAAGTTAGGTGTTAAGGGT
*
5545250 TTAGGGGTT
1 TTATGGGTT
5545259 TATAGTTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 16 0.50
29 16 0.50
ACGTcount: A:0.21, C:0.00, G:0.39, T:0.39
Consensus pattern (29 bp):
TTATGGGTTAAAAGTTAGGTGTTAAGGGT
Found at i:5545230 original size:15 final size:14
Alignment explanation
Indices: 5545207--5545255 Score: 64
Period size: 15 Copynumber: 3.4 Consensus size: 14
5545197 GGTTTAAAAG
5545207 TTAGGGTTAAGGGT
1 TTAGGGTTAAGGGT
5545221 TTATGGGTTAAGGG-
1 TTA-GGGTTAAGGGT
*
5545235 TTAGGTGTTAGGGGT
1 TTAGG-GTTAAGGGT
5545250 TTAGGG
1 TTAGGG
5545256 GTTTATAGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
13 2 0.06
14 14 0.45
15 15 0.48
ACGTcount: A:0.18, C:0.00, G:0.45, T:0.37
Consensus pattern (14 bp):
TTAGGGTTAAGGGT
Found at i:5547125 original size:27 final size:29
Alignment explanation
Indices: 5547071--5547126 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
5547061 ATTTAATTTA
* *
5547071 TATTAAGTTGATTGTTACTTTATCAATTAT
1 TATTAAGTTGATTGTTA-GTGATCAATTAT
5547101 TATTAAGTTGATTGTT-GTGAT-AATTA
1 TATTAAGTTGATTGTTAGTGATCAATTA
5547127 AAATTGATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.21
28 3 0.12
30 16 0.67
ACGTcount: A:0.30, C:0.04, G:0.14, T:0.52
Consensus pattern (29 bp):
TATTAAGTTGATTGTTAGTGATCAATTAT
Found at i:5548058 original size:19 final size:19
Alignment explanation
Indices: 5548034--5548077 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
5548024 ATATATTTTT
*
5548034 TTTTAAATATGA-TTTAATA
1 TTTTAAATAT-ATTTTAAAA
5548053 TTTTAAATATATTTTAAAA
1 TTTTAAATATATTTTAAAA
5548072 TTTTAA
1 TTTTAA
5548078 TTTAACTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 1 0.04
19 22 0.96
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
TTTTAAATATATTTTAAAA
Found at i:5548318 original size:40 final size:40
Alignment explanation
Indices: 5548261--5548337 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
5548251 TATATTTTTA
5548261 AAAATTGATACAATACATAACTTGCATAACCTACATACAT
1 AAAATTGATACAATACATAACTTGCATAACCTACATACAT
*
5548301 AAAATTGATACATTACATAACTTGCATAACCTACATA
1 AAAATTGATACAATACATAACTTGCATAACCTACATA
5548338 AAATTAAGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.47, C:0.19, G:0.05, T:0.29
Consensus pattern (40 bp):
AAAATTGATACAATACATAACTTGCATAACCTACATACAT
Found at i:5548358 original size:20 final size:20
Alignment explanation
Indices: 5548335--5548373 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5548325 CATAACCTAC
5548335 ATAAAATTAAGATAACTTAT
1 ATAAAATTAAGATAACTTAT
*
5548355 ATAATATTAAGATAACTTA
1 ATAAAATTAAGATAACTTA
5548374 CATTCTACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (20 bp):
ATAAAATTAAGATAACTTAT
Found at i:5548400 original size:25 final size:24
Alignment explanation
Indices: 5548366--5548444 Score: 95
Period size: 25 Copynumber: 3.2 Consensus size: 24
5548356 TAATATTAAG
* *
5548366 ATAACTTACATTCTACAGAACTTAC
1 ATAAC-TACATTATACATAACTTAC
*
5548391 ATAACATACATAATACATAACTTAC
1 ATAAC-TACATTATACATAACTTAC
*
5548416 ATAACTAACATTATACATAGCTTAC
1 ATAACT-ACATTATACATAACTTAC
5548441 ATAA
1 ATAA
5548445 TACTCAACTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
24 1 0.02
25 46 0.98
ACGTcount: A:0.47, C:0.20, G:0.03, T:0.30
Consensus pattern (24 bp):
ATAACTACATTATACATAACTTAC
Found at i:5548407 original size:16 final size:16
Alignment explanation
Indices: 5548388--5548419 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5548378 CTACAGAACT
5548388 TACATAACATACATAA
1 TACATAACATACATAA
*
5548404 TACATAACTTACATAA
1 TACATAACATACATAA
5548420 CTAACATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (16 bp):
TACATAACATACATAA
Found at i:5548455 original size:66 final size:65
Alignment explanation
Indices: 5548370--5548553 Score: 192
Period size: 66 Copynumber: 2.8 Consensus size: 65
5548360 ATTAAGATAA
** * * * * *
5548370 CTTACATTCTACAGAACTTACATAACATACATAATACATAACTTACATAACTAA-C-ATTATACA
1 CTTACATAATACACAACTTACATAGCTTACATAATAAATAACTTACATAA--AATCAACT-TACA
5548433 TAG
63 TAG
* * *
5548436 CTTACATAATACTCAACTTACTTAGCTTACATAATAAATAACTTGCATAAAATTCAACTTACATA
1 CTTACATAATACACAACTTACATAGCTTACATAATAAATAACTTACATAAAA-TCAACTTACATA
5548501 G
65 G
** * *
5548502 CTTACATTCTACACAATTTACGTAGCTTACATAATAAATAACTTACATAAAA
1 CTTACATAATACACAACTTACATAGCTTACATAATAAATAACTTACATAAAA
5548554 AAGTGAACAA
Statistics
Matches: 99, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
64 2 0.02
66 95 0.96
67 2 0.02
ACGTcount: A:0.44, C:0.20, G:0.04, T:0.32
Consensus pattern (65 bp):
CTTACATAATACACAACTTACATAGCTTACATAATAAATAACTTACATAAAATCAACTTACATAG
Found at i:5548485 original size:41 final size:41
Alignment explanation
Indices: 5548391--5548508 Score: 130
Period size: 41 Copynumber: 2.9 Consensus size: 41
5548381 CAGAACTTAC
* * * * *
5548391 ATAACATACATAATACAT-AACTTACATAACTAACATTATAC
1 ATAACTTACATAATAC-TCAACTTACATAGCTTACATAATAA
* *
5548432 ATAGCTTACATAATACTCAACTTACTTAGCTTACATAATAA
1 ATAACTTACATAATACTCAACTTACATAGCTTACATAATAA
* * *
5548473 ATAACTTGCATAAAATTCAACTTACATAGCTTACAT
1 ATAACTTACATAATACTCAACTTACATAGCTTACAT
5548509 TCTACACAAT
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 1 0.02
41 63 0.98
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.32
Consensus pattern (41 bp):
ATAACTTACATAATACTCAACTTACATAGCTTACATAATAA
Found at i:5548547 original size:25 final size:25
Alignment explanation
Indices: 5548490--5548550 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
5548480 GCATAAAATT
** *
5548490 CAACTTACATAGCTTACATTCTACA
1 CAACTTACATAGCTTACATAATAAA
* *
5548515 CAATTTACGTAGCTTACATAATAAA
1 CAACTTACATAGCTTACATAATAAA
*
5548540 TAACTTACATA
1 CAACTTACATA
5548551 AAAAAGTGAA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33
Consensus pattern (25 bp):
CAACTTACATAGCTTACATAATAAA
Found at i:5554071 original size:21 final size:21
Alignment explanation
Indices: 5554045--5554115 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
5554035 CTACAACTTA
*
5554045 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* * *
5554066 AAGCAGTGACTACAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
5554087 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
5554108 AAGCAGAG
1 AAGCAGAG
5554116 CAGAGCAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.34, C:0.18, G:0.44, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:5554542 original size:43 final size:43
Alignment explanation
Indices: 5554462--5554643 Score: 242
Period size: 43 Copynumber: 4.3 Consensus size: 43
5554452 AACAAACAAA
* *
5554462 TAGCGGCGTTTGTGG-AAGAGTGCCGCTAAAGAACATGATCTT
1 TAGCGGCGTTTGTGGAAAGAGCGCCGCTAAAGAACATGACCTT
* *
5554504 TAGCGGCGTTTGTGGAAAGAGCGCCGCTAAAGATCATGATCTT
1 TAGCGGCGTTTGTGGAAAGAGCGCCGCTAAAGAACATGACCTT
* * *
5554547 TAGTGGCGTTTCTAGAAAGAGCGCCGCTAAAGAACATGACCTT
1 TAGCGGCGTTTGTGGAAAGAGCGCCGCTAAAGAACATGACCTT
* * *
5554590 TAGTGGCGTTTGTAGGAAA-AGCGCCGCTAAAGACCCTGACCTT
1 TAGCGGCGTTTGT-GGAAAGAGCGCCGCTAAAGAACATGACCTT
*
5554633 TAGCGCCGTTT
1 TAGCGGCGTTT
5554644 TTTTTGTTGC
Statistics
Matches: 125, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
42 15 0.12
43 106 0.85
44 4 0.03
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGAAAGAGCGCCGCTAAAGAACATGACCTT
Found at i:5556246 original size:22 final size:23
Alignment explanation
Indices: 5556212--5556255 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
5556202 GTGATGAGGT
**
5556212 TATCTTATGAATACGTT-AAATC
1 TATCTTAAAAATACGTTGAAATC
*
5556234 TATCTTAAAAATATGTTGAAAT
1 TATCTTAAAAATACGTTGAAAT
5556256 GGATTGGTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (23 bp):
TATCTTAAAAATACGTTGAAATC
Found at i:5556823 original size:156 final size:156
Alignment explanation
Indices: 5556536--5556835 Score: 428
Period size: 156 Copynumber: 1.9 Consensus size: 156
5556526 ATCCAGCTAG
* * *
5556536 GAGCTTTTTTAGTATTTTTGCTGACAGTGCATCCTACTTGAAGCGTTTTTCAACCCTAACTATCA
1 GAGCTTTTTTAGTACTTTTGCTGACAGTACATCCTACTTGAAACGTTTTTCAACCCTAACTATCA
* *
5556601 GATTTCCCGTGAATCCCAGGATTTTTTTTTCAAAACCATCTTCTCAAAAATATTTTTCAAAATCA
66 GATTTCCCGTGAATCCCAGGATTATTTTTTCAAAACCATCTTCACAAAAATATTTTTCAAAATCA
*
5556666 ACATTACAAAAAAAACGTCTAGGTGA
131 ACAGTACAAAAAAAACGTCTAGGTGA
*
5556692 GAGCTTTTTTAGTACTTTTGCTGACAGTACATCCTACTTGAAACGTTTTTCAA-CCTCAATTATC
1 GAGCTTTTTTAGTACTTTTGCTGACAGTACATCCTACTTGAAACGTTTTTCAACCCT-AACTATC
* * *
5556756 AGATTTCCCAG-GAATCCC-GAGA-TATTTTTTCGAAACCATCTTCACAAAATTATATTTTCAGA
65 AGATTTCCC-GTGAATCCCAG-GATTATTTTTTCAAAACCATCTTCACAAAAATAT-TTTTCAAA
* *
5556818 TTCAACAGTACAGAAAAA
127 ATCAACAGTACAAAAAAA
5556836 GTCCAGTTGG
Statistics
Matches: 128, Mismatches: 12, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
155 31 0.24
156 96 0.75
157 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (156 bp):
GAGCTTTTTTAGTACTTTTGCTGACAGTACATCCTACTTGAAACGTTTTTCAACCCTAACTATCA
GATTTCCCGTGAATCCCAGGATTATTTTTTCAAAACCATCTTCACAAAAATATTTTTCAAAATCA
ACAGTACAAAAAAAACGTCTAGGTGA
Found at i:5557069 original size:27 final size:28
Alignment explanation
Indices: 5557009--5557070 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
5556999 TAAACCATAG
*
5557009 ACCCTAAACCTTAATTTATTTTTTAAAA
1 ACCCTAAACCCTAATTTATTTTTTAAAA
* *
5557037 ATCCTAAACCCTAATTT-TTTTTTCAAA
1 ACCCTAAACCCTAATTTATTTTTTAAAA
5557064 ACCCTAA
1 ACCCTAA
5557071 GCACTAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 15 0.50
28 15 0.50
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (28 bp):
ACCCTAAACCCTAATTTATTTTTTAAAA
Found at i:5557077 original size:27 final size:28
Alignment explanation
Indices: 5557009--5557078 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
5556999 TAAACCATAG
5557009 ACCCTAAAC-CTTAATTTATTTTTTAAAA
1 ACCCTAAACAC-TAATTTATTTTTTAAAA
* * *
5557037 ATCCTAAACCCTAATTT-TTTTTTCAAA
1 ACCCTAAACACTAATTTATTTTTTAAAA
*
5557064 ACCCTAAGCACTAAT
1 ACCCTAAACACTAAT
5557079 ATGCAAATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 21 0.58
28 14 0.39
29 1 0.03
ACGTcount: A:0.37, C:0.23, G:0.01, T:0.39
Consensus pattern (28 bp):
ACCCTAAACACTAATTTATTTTTTAAAA
Found at i:5558786 original size:38 final size:38
Alignment explanation
Indices: 5558743--5558824 Score: 103
Period size: 38 Copynumber: 2.1 Consensus size: 38
5558733 TTAAATTTTG
5558743 AAAAAAATATAAAAACTAAAATTCAAA-AAATAAAAAAAT
1 AAAAAAATA-AAAAA-TAAAATTCAAACAAATAAAAAAAT
* * * *
5558782 AAAAAAATAAAAAATTAAATTTAAACAAATTAAAATAT
1 AAAAAAATAAAAAATAAAATTCAAACAAATAAAAAAAT
5558820 AAAAA
1 AAAAA
5558825 TTAAATTAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 9 0.24
38 20 0.53
39 9 0.24
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.21
Consensus pattern (38 bp):
AAAAAAATAAAAAATAAAATTCAAACAAATAAAAAAAT
Found at i:5558822 original size:30 final size:29
Alignment explanation
Indices: 5558733--5558831 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 29
5558723 GACTAAAATT
*
5558733 TTAAATTTTGAAAAAAATATAAAAACT-AAAA
1 TTAAA-TTT-AAAAAAATA-AAAAAATAAAAA
**
5558764 TTCAAAAAATAAAAAAATAAAAAAATAAAAAA
1 TT--AAATTTAAAAAAATAAAAAAAT-AAAAA
* * *
5558796 TTAAATTTAAACAAATTAAAATATAAAAA
1 TTAAATTTAAAAAAATAAAAAAATAAAAA
5558825 TTAAATT
1 TTAAATT
5558832 AACAGAATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
29 12 0.21
30 23 0.41
31 11 0.20
32 7 0.12
33 3 0.05
ACGTcount: A:0.69, C:0.03, G:0.01, T:0.27
Consensus pattern (29 bp):
TTAAATTTAAAAAAATAAAAAAATAAAAA
Found at i:5558827 original size:14 final size:14
Alignment explanation
Indices: 5558746--5558829 Score: 56
Period size: 14 Copynumber: 6.2 Consensus size: 14
5558736 AATTTTGAAA
*
5558746 AAAATATAAAAACT
1 AAAATATAAAAATT
*
5558760 AAAAT-TCAAAAAAT
1 AAAATAT-AAAAATT
5558774 AAAA-A-AATAAA--
1 AAAATATAA-AAATT
5558785 AAAATA-AAAAATT
1 AAAATATAAAAATT
*
5558798 -AAATTTAAACAAATT
1 AAAATAT-AA-AAATT
5558813 AAAATATAAAAATT
1 AAAATATAAAAATT
5558827 AAA
1 AAA
5558830 TTAACAGAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 20
0.71 0.04 0.25
Matches are distributed among these distances:
11 7 0.12
12 9 0.16
13 4 0.07
14 25 0.44
15 7 0.12
16 5 0.09
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:5558828 original size:23 final size:22
Alignment explanation
Indices: 5558746--5558829 Score: 64
Period size: 23 Copynumber: 3.8 Consensus size: 22
5558736 AATTTTGAAA
* *
5558746 AAAATATAAAAACTAAAATTCAA-
1 AAAATATAAAAATTAAAA--AAAT
*
5558769 AAAATA-AAAAAATAAAAAAAT
1 AAAATATAAAAATTAAAAAAAT
* * * *
5558790 AAAAAATTAAATTTAAACAAATT
1 AAAATATAAAAATTAAA-AAAAT
5558813 AAAATATAAAAATTAAA
1 AAAATATAAAAATTAAA
5558830 TTAACAGAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
20 2 0.04
21 5 0.10
22 17 0.35
23 24 0.50
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.23
Consensus pattern (22 bp):
AAAATATAAAAATTAAAAAAAT
Found at i:5561537 original size:30 final size:31
Alignment explanation
Indices: 5561489--5561547 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
5561479 TGCTTATAAT
* *
5561489 ATAATTTTTATAACTTAAA-CTTGTATGAAA
1 ATAATTTTTATAAATTAAATCATGTATGAAA
5561519 ATAATTTTT-TAAAATTAAATCATGTATGA
1 ATAATTTTTAT-AAATTAAATCATGTATGA
5561548 GTGTCTAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 1 0.04
30 16 0.64
31 8 0.32
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (31 bp):
ATAATTTTTATAAATTAAATCATGTATGAAA
Found at i:5565015 original size:22 final size:24
Alignment explanation
Indices: 5564980--5565025 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
5564970 CTTCTTCTTT
*
5564980 TTTTAGGTTATATATTTTATTTTA
1 TTTTAGGTTATATATATTATTTTA
5565004 TTTTAGG-T-TATATATTATTTTA
1 TTTTAGGTTATATATATTATTTTA
5565026 CTATATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.62
23 1 0.05
24 7 0.33
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (24 bp):
TTTTAGGTTATATATATTATTTTA
Found at i:5577281 original size:40 final size:39
Alignment explanation
Indices: 5577237--5577372 Score: 148
Period size: 40 Copynumber: 3.4 Consensus size: 39
5577227 ACAGGGGCAC
* *
5577237 GTATGTGCATTCAGGGGTACCAAAGTACAAATAGGGATA
1 GTATGTGCATTCAGGGGTACCGAAGTACAAATAGGGACA
* * *
5577276 TGTATGTGCATTTAGGGATACCGAAGTACAAATAGGGGCA
1 -GTATGTGCATTCAGGGGTACCGAAGTACAAATAGGGACA
* * * *
5577316 CGCATTTGCATTTAGGGGTACCGAAGTATAAATAGGAGCACA
1 -GTATGTGCATTCAGGGGTACCGAAGTACAAATAGG-G-ACA
5577358 -TATGTGCATTCAGGG
1 GTATGTGCATTCAGGG
5577373 ACATTTTCCT
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 77 0.96
41 1 0.01
42 2 0.03
ACGTcount: A:0.32, C:0.14, G:0.29, T:0.25
Consensus pattern (39 bp):
GTATGTGCATTCAGGGGTACCGAAGTACAAATAGGGACA
Found at i:5578308 original size:15 final size:14
Alignment explanation
Indices: 5578275--5578314 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
5578265 ATACCTTATT
*
5578275 TTTATTTTATTTCA
1 TTTATTTAATTTCA
*
5578289 TTTATTTAAGTTTTA
1 TTTATTTAA-TTTCA
5578304 TTTATTTAATT
1 TTTATTTAATT
5578315 ACAAGTTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (14 bp):
TTTATTTAATTTCA
Found at i:5601724 original size:6 final size:6
Alignment explanation
Indices: 5601713--5601743 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
5601703 ACCAAAATAG
5601713 ACTGGT ACTGGT ACTGGT ACTGGT ACTGGT A
1 ACTGGT ACTGGT ACTGGT ACTGGT ACTGGT A
5601744 GAAAAGCAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.16, G:0.32, T:0.32
Consensus pattern (6 bp):
ACTGGT
Found at i:5603651 original size:26 final size:24
Alignment explanation
Indices: 5603615--5603692 Score: 79
Period size: 26 Copynumber: 3.1 Consensus size: 24
5603605 CCTCAATTTA
5603615 AAAAAAAATTAAATTATTAATCTTTT
1 AAAAAAAATTAAATTATT-AT-TTTT
*
5603641 AAAAAGAATTAAATTATTATTTTT
1 AAAAAAAATTAAATTATTATTTTT
*
5603665 AACGAAAATATT-AATTAATT-TTTTT
1 AA--AAAAAATTAAATT-ATTATTTTT
5603690 AAA
1 AAA
5603693 CATGACAATC
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
23 1 0.02
24 6 0.13
25 13 0.28
26 26 0.57
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (24 bp):
AAAAAAAATTAAATTATTATTTTT
Found at i:5606462 original size:51 final size:51
Alignment explanation
Indices: 5606402--5606737 Score: 344
Period size: 51 Copynumber: 6.6 Consensus size: 51
5606392 GATGAACACG
* * * *
5606402 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGATCACA
* * * * * * * * *
5606453 TGTGTAGTACTAAGTGAATGCTACTATGTATACCAAGAAGTTTTGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGATCACA
* *
5606504 TGTGTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATGA-TGAACACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT-ATTGATCACA
* * * *
5606555 TGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAAGCT-TTGGTCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAA--TATTGATCACA
* * *
5606606 TGTGTAGTACTATGTGAAGGCTACTATGTGAACCG-TAAA-ATTTGATCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATA-TTGATCACA
* * *
5606656 CGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGATCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATA-TTGATCACA
*
5606706 TGTGTAGTACTATGTGAAGACTACTACGTGTA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTA
5606738 TCGAATGATA
Statistics
Matches: 241, Mismatches: 37, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
50 87 0.36
51 153 0.63
52 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (51 bp):
TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGATCACA
Found at i:5606578 original size:102 final size:100
Alignment explanation
Indices: 5606398--5606737 Score: 418
Period size: 102 Copynumber: 3.4 Consensus size: 100
5606388 TATCGATGAA
* * *
5606398 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT-ATGATCACATGTGTAGTAC
*
5606463 TAAGTGAATGCTACTATGTATACC-AAGAAGTTTTGGT
65 TAAGTGAAGGCTACTATGTATACCGAA-AAG-TTTGGT
* * *
5606500 CACATGTGTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATGATGAACACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT-ATGATCACATGTGTAGTAC
*
5606565 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
65 TAAGTGAAGGCTACTATGTATACCGAAAAG-TTTGGT
* * * **
5606602 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCG-TAAAATTTGATCACGCGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGAT-AAATATGATCACATGTGTAGTAC
* * * *
5606666 TATGTGAAGGCTACTACGTGA-ACCGTAAAA-CTTGAT
65 TAAGTGAAGGCTACTATGT-ATACCG-AAAAGTTTGGT
*
5606702 CACGTGTGTAGTACTATGTGAAGACTACTACGTGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
5606738 TCGAATGATA
Statistics
Matches: 210, Mismatches: 24, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
100 37 0.18
101 37 0.18
102 134 0.64
103 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (100 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATGATCACATGTGTAGTACT
AAGTGAAGGCTACTATGTATACCGAAAAGTTTGGT
Found at i:5610608 original size:16 final size:16
Alignment explanation
Indices: 5610567--5610614 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
5610557 ATTCCATTTC
5610567 ATAATCTCAATTCA-A
1 ATAATCTCAATTCACA
5610582 ATAATCATCAATTCACA
1 ATAATC-TCAATTCACA
** *
5610599 ATCTTCTCAAATCACA
1 ATAATCTCAATTCACA
5610615 TAAAAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 6 0.21
16 17 0.61
17 5 0.18
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAATCTCAATTCACA
Found at i:5621052 original size:98 final size:98
Alignment explanation
Indices: 5620878--5621074 Score: 340
Period size: 98 Copynumber: 2.0 Consensus size: 98
5620868 GTGCAATAAA
* *
5620878 ACTTTAAAAGAATATCCATTTATCAAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTTATCAAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
*
5620943 CCTCTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
* *
5620976 ACTTTAAAAGAACATCCACTTATCCAATATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTTATCAAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
*
5621041 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
5621074 A
1 A
5621075 TGATTTTTAA
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.29
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCAAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:5621771 original size:25 final size:25
Alignment explanation
Indices: 5621741--5621788 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
5621731 TATAAATATT
5621741 AAAATATTCATTAAAAAAATATAGG
1 AAAATATTCATTAAAAAAATATAGG
* * *
5621766 AAAATATTCGTTTAAAATATATA
1 AAAATATTCATTAAAAAAATATA
5621789 TATATATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.33
Consensus pattern (25 bp):
AAAATATTCATTAAAAAAATATAGG
Found at i:5622443 original size:23 final size:22
Alignment explanation
Indices: 5622398--5622455 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
5622388 AAAGGGTATC
* *
5622398 TACAAATTAAATC-TCTAAAAT
1 TACAAATCATATCTTCTAAAAT
*
5622419 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAAAT
*
5622442 TACATATCATATCT
1 TACAAATCATATCT
5622456 AGGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAAAT
Found at i:5622461 original size:19 final size:19
Alignment explanation
Indices: 5622434--5622487 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
5622424 AATCATATCT
*
5622434 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
*
5622453 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
5622472 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
5622488 CTCAAAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:5629705 original size:42 final size:42
Alignment explanation
Indices: 5629646--5629729 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
5629636 GACATCGTAT
5629646 GTTAGCCTACCTTTAGGCCTCATTCGGCACCTAAGGTCATAA
1 GTTAGCCTACCTTTAGGCCTCATTCGGCACCTAAGGTCATAA
5629688 GTTAGCCTACCTTTAGGCCTCATTCGGCACCTAAGGTCATAA
1 GTTAGCCTACCTTTAGGCCTCATTCGGCACCTAAGGTCATAA
5629730 AAGAACTCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.29
Consensus pattern (42 bp):
GTTAGCCTACCTTTAGGCCTCATTCGGCACCTAAGGTCATAA
Found at i:5632186 original size:16 final size:16
Alignment explanation
Indices: 5632167--5632198 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5632157 TATTTGGTTT
*
5632167 ATTTTTAGTTTAATTA
1 ATTTTTAGGTTAATTA
5632183 ATTTTTAGGTTAATTA
1 ATTTTTAGGTTAATTA
5632199 GGTTAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.59
Consensus pattern (16 bp):
ATTTTTAGGTTAATTA
Found at i:5632646 original size:22 final size:22
Alignment explanation
Indices: 5632621--5632665 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
5632611 TGATTCAGTG
5632621 TATGACTCGAAGTGGAATTCTT
1 TATGACTCGAAGTGGAATTCTT
*
5632643 TATGACTCGGAGTGGAATTCTT
1 TATGACTCGAAGTGGAATTCTT
5632665 T
1 T
5632666 CTATCGAGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.38
Consensus pattern (22 bp):
TATGACTCGAAGTGGAATTCTT
Found at i:5636179 original size:18 final size:18
Alignment explanation
Indices: 5636156--5636191 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5636146 TTAGAGATCG
5636156 ACTCGACAGTGTATGAGT
1 ACTCGACAGTGTATGAGT
5636174 ACTCGACAGTGTATGAGT
1 ACTCGACAGTGTATGAGT
5636192 TTTACGCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (18 bp):
ACTCGACAGTGTATGAGT
Found at i:5636353 original size:25 final size:25
Alignment explanation
Indices: 5636319--5636371 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
5636309 ATGCTCCATA
*
5636319 CTATGTTTCTGATGCATTGGACGTG
1 CTATGTTTCTGATGCATTAGACGTG
5636344 CTATGTTTCTGATGCATTAGACGTG
1 CTATGTTTCTGATGCATTAGACGTG
5636369 CTA
1 CTA
5636372 GATATTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.40
Consensus pattern (25 bp):
CTATGTTTCTGATGCATTAGACGTG
Found at i:5637271 original size:19 final size:19
Alignment explanation
Indices: 5637247--5637288 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
5637237 GGATACAAGC
5637247 GTCGTCACACCGAACATAG
1 GTCGTCACACCGAACATAG
*
5637266 GTCGTCACACCGAACATGG
1 GTCGTCACACCGAACATAG
5637285 GTCG
1 GTCG
5637289 AGGGAAGGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.26, C:0.31, G:0.26, T:0.17
Consensus pattern (19 bp):
GTCGTCACACCGAACATAG
Found at i:5640248 original size:16 final size:16
Alignment explanation
Indices: 5640227--5640258 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5640217 TAATTGGTTG
*
5640227 ATTTTTAGTTTAATTA
1 ATTTTTAGATTAATTA
5640243 ATTTTTAGATTAATTA
1 ATTTTTAGATTAATTA
5640259 GATTAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.59
Consensus pattern (16 bp):
ATTTTTAGATTAATTA
Found at i:5640724 original size:13 final size:12
Alignment explanation
Indices: 5640686--5640728 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
5640676 TACGTTCCTC
5640686 TTTTTTTTCTT-
1 TTTTTTTTCTTA
5640697 TTCTTTTTTCATTA
1 TT-TTTTTTC-TTA
5640711 TATTTTTTTCTTA
1 T-TTTTTTTCTTA
5640724 TTTTT
1 TTTTT
5640729 ATCTTCTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
11 2 0.07
12 11 0.39
13 6 0.21
14 8 0.29
15 1 0.04
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTTTTTCTTA
Found at i:5641253 original size:43 final size:43
Alignment explanation
Indices: 5641206--5641293 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
5641196 AATCCCTCGA
5641206 CTAAGTATTAGAAGGAGCAGAAGCTTGTTTCGTTTACTTTTTT
1 CTAAGTATTAGAAGGAGCAGAAGCTTGTTTCGTTTACTTTTTT
5641249 CTAAGTATTAGAAGGAGCAGAAGCTTGTTTCGTTTACTTTTTT
1 CTAAGTATTAGAAGGAGCAGAAGCTTGTTTCGTTTACTTTTTT
5641292 CT
1 CT
5641294 TCTTTTTTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.42
Consensus pattern (43 bp):
CTAAGTATTAGAAGGAGCAGAAGCTTGTTTCGTTTACTTTTTT
Found at i:5643011 original size:15 final size:15
Alignment explanation
Indices: 5642991--5643019 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5642981 ATTTCACACC
5642991 TCTTCTGTTGCAATG
1 TCTTCTGTTGCAATG
5643006 TCTTCTGTTGCAAT
1 TCTTCTGTTGCAAT
5643020 CAAAAACTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.48
Consensus pattern (15 bp):
TCTTCTGTTGCAATG
Found at i:5646892 original size:3 final size:3
Alignment explanation
Indices: 5646884--5646946 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
5646874 TTAATCCATC
5646884 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5646932 ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA
5646947 GATTTTTGCC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5649163 original size:9 final size:9
Alignment explanation
Indices: 5649147--5649176 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
5649137 TTAATTGAAA
5649147 AATTAATTT
1 AATTAATTT
*
5649156 AGTTAATTT
1 AATTAATTT
5649165 AATTAATTT
1 AATTAATTT
5649174 AAT
1 AAT
5649177 GAATAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (9 bp):
AATTAATTT
Found at i:5650585 original size:43 final size:43
Alignment explanation
Indices: 5650534--5650720 Score: 259
Period size: 43 Copynumber: 4.3 Consensus size: 43
5650524 CAACGCCGCT
*
5650534 AACATGATCTTTAGCGGCGCTTTACCCACAAATGCCGCTAAAG
1 AACATGATCTTTAGCGGCGCTTTACCCACAAACGCCGCTAAAG
*
5650577 AACATGATCTTTAGCGGCGCATTACCCACAAACGCCGCTAAAG
1 AACATGATCTTTAGCGGCGCTTTACCCACAAACGCCGCTAAAG
* * *
5650620 ATCATGTTCTTTAGCGGCGCTTTAGCCACAAACGCCGCTAAAG
1 AACATGATCTTTAGCGGCGCTTTACCCACAAACGCCGCTAAAG
* * * * *
5650663 ATCATGTTCTTTAGCGACGCTTT-CTCTACAAACGCCACTAAAG
1 AACATGATCTTTAGCGGCGCTTTAC-CCACAAACGCCGCTAAAG
*
5650706 AACATGACCTTTAGC
1 AACATGATCTTTAGC
5650721 AGCGTTTTTG
Statistics
Matches: 130, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
43 130 1.00
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (43 bp):
AACATGATCTTTAGCGGCGCTTTACCCACAAACGCCGCTAAAG
Found at i:5655132 original size:105 final size:103
Alignment explanation
Indices: 5654789--5655182 Score: 395
Period size: 105 Copynumber: 3.7 Consensus size: 103
5654779 GCAAATTTTT
** * *
5654789 TTCATTTTGAACAAAACGACGTCGTTTTGCTATTCTAAAA-TTTTT-TTATTTTTTTTATAAATT
1 TTCATTTTGAACAAAACGACACCGTTTTGCTATGCTAAAATTTTTTATTTTTTTTTTTATAAATT
* *
5654852 GATTTATTTTTTGCGG-TTTTTTTATAAAAAACGCCGCTAT
66 GATTTATTTTTTGCGGCGTTTTTTAT---AAACGCCGCTAA
* * ******
5654892 TTCATTTTGAACAAAATGACACTGTTTTGCTATGCTAAAATTATTTTATTTTATTTTTTGCGGCG
1 TTCATTTTGAACAAAACGACACCGTTTTGCTATGCTAAAATT-TTTTATTTT-TTTTTTTATAAA
* * * *
5654957 TT--TTT-TCTTTTGCGGCGTTTTTCATAAAAACGCCACAAA
64 TTGATTTATTTTTTGCGGCGTTTTT--TATAAACGCCGCTAA
* * *
5654996 TTTTTTTTCATTTTAAACAAAACGACGCCGTTTTGCTATTCTAAATATTTTTTATTTTGTTTTTT
1 ------TTCATTTTGAACAAAACGACACCGTTTTGCTATGCTAAA-ATTTTTTATTTT-TTTTTT
5655061 TATAAATTGATTTATTTTTTGCGGCGTTTTTTATAAACGCCGCTAA
58 TATAAATTGATTTATTTTTTGCGGCGTTTTTTATAAACGCCGCTAA
* *
5655107 TTCATTTTGAACAAAATGACACCGTTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTATAAAT
1 TTCATTTTGAACAAAACGACACCGTTTTGCTATGCT-AAAATTTTTTATTTTTTTTTTTATAAAT
5655172 TGATTTATTTT
65 TGATTTATTTT
5655183 CACCGTTTTG
Statistics
Matches: 234, Mismatches: 39, Indels: 35
0.76 0.13 0.11
Matches are distributed among these distances:
103 35 0.15
104 42 0.18
105 56 0.24
106 6 0.03
107 10 0.04
110 51 0.22
111 15 0.06
112 3 0.01
113 16 0.07
ACGTcount: A:0.27, C:0.12, G:0.11, T:0.50
Consensus pattern (103 bp):
TTCATTTTGAACAAAACGACACCGTTTTGCTATGCTAAAATTTTTTATTTTTTTTTTTATAAATT
GATTTATTTTTTGCGGCGTTTTTTATAAACGCCGCTAA
Found at i:5655156 original size:215 final size:210
Alignment explanation
Indices: 5654751--5655165 Score: 647
Period size: 215 Copynumber: 1.9 Consensus size: 210
5654741 TATTGCTTAC
* * *
5654751 CTTTAGCGGCGTTTTTATGAAAAACGCCGCAAATTTTTTTCATTTTGAACAAAACGACGTCGTTT
1 CTTTAGCGGCGTTTTTATGAAAAACGCCACAAATTTTTTTCATTTTAAACAAAACGACGCCGTTT
*
5654816 TGCTATTCTAAAATTTTTTTATTTTTTTTATAAATTGATTTATTTTTTGCGGTTTTTTTATAAAA
66 TGCTATTCTAAAATTTTTTTATTTTTTTTATAAATTGATTTATTTTTTGCGGGTTTTTTAT--AA
* *
5654881 AACGCCGCTATTTCATTTTGAACAAAATGACACTGTTTTGCTATGCTAAAATTATTTTATTTTAT
129 AACGCCGCTAATTCATTTTGAACAAAATGACACCGTTTTGCTATGCTAAAATTATTTTATTTTAT
5654946 TTTTTGCGGCGTTTTTT
194 TTTTTGCGGCGTTTTTT
*
5654963 CTTTTGCGGCGTTTTTCAT-AAAAACGCCACAAATTTTTTTTCATTTTAAACAAAACGACGCCGT
1 CTTTAGCGGCGTTTTT-ATGAAAAACGCCACAAA-TTTTTTTCATTTTAAACAAAACGACGCCGT
*
5655027 TTTGCTATTCTAAATATTTTTTATTTTGTTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTT
64 TTTGCTATTCTAAA-A-TTTTT-TTAT-TTTTTTTATAAATTGATTTATTTTTTGCGG-GTTTTT
5655092 TAT-AAACGCCGCTAATTCATTTTGAACAAAATGACACCGTTTTGCTATGCTAAAAATT-TTTTA
124 TATAAAACGCCGCTAATTCATTTTGAACAAAATGACACCGTTTTGCTATGCT-AAAATTATTTTA
5655155 TTTTATTTTTT
188 TTTTATTTTTT
5655166 ATAAATTGAT
Statistics
Matches: 187, Mismatches: 8, Indels: 13
0.90 0.04 0.06
Matches are distributed among these distances:
212 28 0.15
213 44 0.24
214 1 0.01
215 67 0.36
216 9 0.05
217 30 0.16
218 8 0.04
ACGTcount: A:0.26, C:0.13, G:0.12, T:0.48
Consensus pattern (210 bp):
CTTTAGCGGCGTTTTTATGAAAAACGCCACAAATTTTTTTCATTTTAAACAAAACGACGCCGTTT
TGCTATTCTAAAATTTTTTTATTTTTTTTATAAATTGATTTATTTTTTGCGGGTTTTTTATAAAA
CGCCGCTAATTCATTTTGAACAAAATGACACCGTTTTGCTATGCTAAAATTATTTTATTTTATTT
TTTGCGGCGTTTTTT
Found at i:5655282 original size:40 final size:40
Alignment explanation
Indices: 5655217--5655295 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
5655207 ACGCCGCAAA
* *
5655217 CGCCGCTATTGATTATCTTTTGCGGCGTTTTTATAAAAAC
1 CGCCGCTATTGATTACCTTTAGCGGCGTTTTTATAAAAAC
* * *
5655257 CGCCGCTATTGCTTACCTTTAGCGGCTTTTTTGTAAAAA
1 CGCCGCTATTGATTACCTTTAGCGGCGTTTTTATAAAAA
5655296 ACGCTGCAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.39
Consensus pattern (40 bp):
CGCCGCTATTGATTACCTTTAGCGGCGTTTTTATAAAAAC
Found at i:5655383 original size:15 final size:15
Alignment explanation
Indices: 5655352--5655389 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
5655342 CTATGCTAAA
5655352 ATTTTTTAT--TTTG
1 ATTTTTTATAATTTG
5655365 -TTTTTTATAATTTG
1 ATTTTTTATAATTTG
5655379 ATTTTTTATAA
1 ATTTTTTATAA
5655390 AATAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 8 0.36
14 4 0.18
15 10 0.45
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (15 bp):
ATTTTTTATAATTTG
Found at i:5656060 original size:13 final size:14
Alignment explanation
Indices: 5656041--5656081 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
5656031 NNNCCTTAAA
5656041 CCATAATCCCTAAT
1 CCATAATCCCTAAT
5656055 -CATAATCCCTAAAT
1 CCATAATCCCT-AAT
*
5656069 CCATACTCCCTAA
1 CCATAATCCCTAA
5656082 ACCCTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 10 0.42
14 5 0.21
15 9 0.38
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.27
Consensus pattern (14 bp):
CCATAATCCCTAAT
Found at i:5656347 original size:15 final size:15
Alignment explanation
Indices: 5656268--5656352 Score: 52
Period size: 15 Copynumber: 5.8 Consensus size: 15
5656258 CCCTAACTTT
*
5656268 TAATCCCTAAACCCT
1 TAATCCCTAAACCCA
* *
5656283 TAA-CCCTCTAACCCC
1 TAATCCCT-AAACCCA
* *
5656298 TAAACCTTAAATCCC-
1 TAATCCCTAAA-CCCA
* *
5656313 -AACCCCT-AATCCA
1 TAATCCCTAAACCCA
5656326 TAATCCCTAAACCCA
1 TAATCCCTAAACCCA
*
5656341 TACTCCCTAAAC
1 TAATCCCTAAAC
5656353 TTTAAAATAT
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
12 2 0.04
13 2 0.04
14 15 0.28
15 29 0.54
16 6 0.11
ACGTcount: A:0.35, C:0.42, G:0.00, T:0.22
Consensus pattern (15 bp):
TAATCCCTAAACCCA
Found at i:5656844 original size:113 final size:114
Alignment explanation
Indices: 5656601--5656852 Score: 420
Period size: 114 Copynumber: 2.2 Consensus size: 114
5656591 TAAATTATTT
* *
5656601 TTAGCGGCGCTTT-TCCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCGTTGGGC
1 TTAGCGGCGCTTTCT-TAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCGTTGGAC
*
5656665 TTAGGTTTTTTTGCGGCGCTTTCTAGAAAACGCCGCTAAAGCCCTGAACA
65 TTAGGTTTTTTTGCGGCGCTTTCCAGAAAACGCCGCTAAAGCCCTGAACA
*
5656715 TTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGACT
1 TTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCGTTGGACT
*
5656780 TAGG-TTTTTTGCGGCGCTTTCCCA-AAAACGCCGCTAAAGCCCTGAGCA
66 TAGGTTTTTTTGCGGCGCTTT-CCAGAAAACGCCGCTAAAGCCCTGAACA
5656828 TTAGCGGCGCTTTCTTAAAAACGCC
1 TTAGCGGCGCTTTCTTAAAAACGCC
5656853 AGAGTATTAG
Statistics
Matches: 131, Mismatches: 5, Indels: 5
0.93 0.04 0.04
Matches are distributed among these distances:
113 64 0.49
114 66 0.50
115 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.24
Consensus pattern (114 bp):
TTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCGTTGGACT
TAGGTTTTTTTGCGGCGCTTTCCAGAAAACGCCGCTAAAGCCCTGAACA
Found at i:5662440 original size:42 final size:41
Alignment explanation
Indices: 5662310--5662578 Score: 274
Period size: 43 Copynumber: 6.4 Consensus size: 41
5662300 ACGTCGCTAA
* * * *
5662310 CTTTAGCGGCGCTTACAGGAAAAAAGCTGCTACAGAACATGTT
1 CTTTAGCGGCGCTT--AGGAAAAACGCCGCTAAAGATCATGTT
* * *
5662353 CTTTAGCGGCGCTAAGGAAATAAACGCCGCTAAAGAACATATT
1 CTTTAGCGGCGCTTAGG-AA-AAACGCCGCTAAAGATCATGTT
*
5662396 CTTTAGCGGCGCTTAGTAAAACACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAA-ACGCCGCTAAAGATCATGTT
* * *
5662438 CTTCAGCGGCG-TTTGGAAAAATCGCCACTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAA-CGCCGCTAAAGATCATGTT
*
5662479 CTTTAGCGGCGCTTAGGAAGAAAACGCCGCTAAA-AGTAATGTT
1 CTTTAGCGGCGCTTAGG-A-AAAACGCCGCTAAAGA-TCATGTT
* * *
5662522 CTATAGCGGCGCTTGGTGAAAAACGCCGCTAAA-ATTAGTGTT
1 CTTTAGCGGCGCTTAG-GAAAAACGCCGCTAAAGATCA-TGTT
*
5662564 CTTTAGTGGCGCTTA
1 CTTTAGCGGCGCTTA
5662579 TTTCAAAAAT
Statistics
Matches: 193, Mismatches: 23, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
40 1 0.01
41 42 0.22
42 68 0.35
43 77 0.40
44 5 0.03
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.25
Consensus pattern (41 bp):
CTTTAGCGGCGCTTAGGAAAAACGCCGCTAAAGATCATGTT
Found at i:5663027 original size:12 final size:12
Alignment explanation
Indices: 5663010--5663061 Score: 77
Period size: 12 Copynumber: 4.3 Consensus size: 12
5663000 TTTTGAACCT
*
5663010 CTGCTTCTATCA
1 CTGCTTCTCTCA
5663022 CTGCTTCTCTCA
1 CTGCTTCTCTCA
* *
5663034 CTGCTTCTTTCG
1 CTGCTTCTCTCA
5663046 CTGCTTCTCTCA
1 CTGCTTCTCTCA
5663058 CTGC
1 CTGC
5663062 GGCCTCTGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.08, C:0.38, G:0.12, T:0.42
Consensus pattern (12 bp):
CTGCTTCTCTCA
Found at i:5663037 original size:24 final size:24
Alignment explanation
Indices: 5663010--5663061 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
5663000 TTTTGAACCT
5663010 CTGCTTCTATCACTGCTTCTCTCA
1 CTGCTTCTATCACTGCTTCTCTCA
* *
5663034 CTGCTTCTTTCGCTGCTTCTCTCA
1 CTGCTTCTATCACTGCTTCTCTCA
5663058 CTGC
1 CTGC
5663062 GGCCTCTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.08, C:0.38, G:0.12, T:0.42
Consensus pattern (24 bp):
CTGCTTCTATCACTGCTTCTCTCA
Found at i:5663076 original size:21 final size:21
Alignment explanation
Indices: 5663046--5663135 Score: 90
Period size: 21 Copynumber: 4.3 Consensus size: 21
5663036 GCTTCTTTCG
5663046 CTGCTTCTCTCACTGCGGCCT
1 CTGCTTCTCTCACTGCGGCCT
* *
5663067 CTGTTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCACTGCGGCCT
* ** *
5663088 CTGCTTCTTTCGTTGCAGCCT
1 CTGCTTCTCTCACTGCGGCCT
* ** *
5663109 CTGCTTCCCTCGTTGCCGCCT
1 CTGCTTCTCTCACTGCGGCCT
5663130 CTGCTT
1 CTGCTT
5663136 GAAGTTGTTG
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 60 1.00
ACGTcount: A:0.02, C:0.40, G:0.20, T:0.38
Consensus pattern (21 bp):
CTGCTTCTCTCACTGCGGCCT
Found at i:5663094 original size:42 final size:42
Alignment explanation
Indices: 5663046--5663135 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 42
5663036 GCTTCTTTCG
* * * *
5663046 CTGCTTCTCTCACTGCGGCCTCTGTTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCACTGCAGCCTCTGCTTCCCTCGCTGCCGCCT
* ** *
5663088 CTGCTTCTTTCGTTGCAGCCTCTGCTTCCCTCGTTGCCGCCT
1 CTGCTTCTCTCACTGCAGCCTCTGCTTCCCTCGCTGCCGCCT
5663130 CTGCTT
1 CTGCTT
5663136 GAAGTTGTTG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.02, C:0.40, G:0.20, T:0.38
Consensus pattern (42 bp):
CTGCTTCTCTCACTGCAGCCTCTGCTTCCCTCGCTGCCGCCT
Found at i:5665745 original size:44 final size:44
Alignment explanation
Indices: 5665695--5665788 Score: 109
Period size: 44 Copynumber: 2.1 Consensus size: 44
5665685 GTCTTCTTTG
* * *
5665695 GAAGGAGGTGATGGAAGGATTTCGGATTTCAAGAAATTCGG-CAA
1 GAAGGAGGCGATGGAAGAATTTCGGAATTCAAGAAATT-GGCCAA
** * *
5665739 GAAGGAGGCGATTTACGAATTTGGGAATTCAAGAAATTGGCCAA
1 GAAGGAGGCGATGGAAGAATTTCGGAATTCAAGAAATTGGCCAA
5665783 GAAGGA
1 GAAGGA
5665789 CGCAGGAATT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
43 2 0.05
44 40 0.95
ACGTcount: A:0.36, C:0.10, G:0.33, T:0.21
Consensus pattern (44 bp):
GAAGGAGGCGATGGAAGAATTTCGGAATTCAAGAAATTGGCCAA
Found at i:5667539 original size:115 final size:112
Alignment explanation
Indices: 5667323--5668049 Score: 443
Period size: 115 Copynumber: 6.3 Consensus size: 112
5667313 ATGCATGGTT
* * * *
5667323 AAGACCAAAACTG-TGCGTTTTGGTAAAGATCTCTTGCGGCGCTTATAAAAAAGCGCCGCTAATA
1 AAGA-CAAAAC-GCTGCGTTTTGGTTAACATATCTTGCGGCGCTTA-AATAAAGCGCCGCTAATA
* * * ** *
5667387 TTATGATTTAGCGGCGATTTCTCGTAAACGCCACTAATTCCAGTATACATC
63 TGAT-ATTTAGCGGCGTTTTCTCGTAAGCGCCACTAATTATATTATACATC
** * * *
5667438 AAGATTTAAACGCAGCGTTTCGGTTAATATATCTTGCGGCGCTTCAAATAAAGCGCCGCTAATAG
1 AAGA-CAAAACGCTGCGTTTTGGTTAACATATCTTGCGGCGCTT-AAATAAAGCGCCGCTAATA-
* * * *
5667503 TGATATTTAGCGGCGTTTTGTTGTAAGCTCCACTAATGATATTATACATC
63 TGATATTTAGCGGCGTTTTCTCGTAAGCGCCACTAATTATATTATACATC
* * * * * * ****
5667553 AAGACCAAAACGTTGAGTTTTGGTTAAGAAATATAGCGGCGCTTCTCCAAACGCGCCGCTAATAA
1 AAGA-CAAAACGCTGCGTTTTGGTTAACATATCTTGCGGCGCTTAAATAAA-GCGCCGCTAAT-A
* * ** * * *
5667618 T-ACTCTTTAGCGGCG-CTTCTCCAAACGCGCCACTAATTCTAATATACCTC
63 TGA-TATTTAGCGGCGTTTTCTCGTAA-GCGCCACTAATTATATTATACATC
* * * * * *
5667668 AATACCAAACCCTGCGTTTTGGTGT-GCATATCTTGCGGCGCTTAACTGAAAGCGCCGCGAATAC
1 AAGACAAAACGCTGCGTTTTGGT-TAACATATCTTGCGGCGCTTAAAT-AAAGCGCCGCTAATA-
* * *
5667732 TGATATTTAGCGGCGTTTTGTTGTAAGCGCCAGTAATTATATTATACATC
63 TGATATTTAGCGGCGTTTTCTCGTAAGCGCCACTAATTATATTATACATC
* * * * * * * *
5667782 AAGACCAAAACGTTGAGTTTTGGTTAAGAAATATAGCGGCGCTTCTCAA-AACGCGCCGCTAATA
1 AAGA-CAAAACGCTGCGTTTTGGTTAACATATCTTGCGGCGC-T-TAAATAAAGCGCCGCTAAT-
* * * ** * *
5667846 AT-ACTCTTTAGCGGCG-CTTCTAC-AAACGCGCCACTAATCCTAATATACCTC
62 ATGA-TATTTAGCGGCGTTTTCT-CGTAA-GCGCCACTAATTATATTATACATC
* * * * * *
5667897 AAGACCAAACTCTGCGTTTTGGTGT-GCATATCTTGCGGCGATTCTAAA-AAATCGCCGCTAATT
1 AAGACAAAACGCTGCGTTTTGGT-TAACATATCTTGCGGCG-CT-TAAATAAAGCGCCGCTAATA
* * * * *
5667960 TTATACTTTAGCGGCGTTTT-TGCCTAA-CGCCACTAACTGTACTATACATC
63 TGATA-TTTAGCGGCGTTTTCT-CGTAAGCGCCACTAATTATATTATACATC
* * * *
5668010 GAGACCAAACCGCTGCGTTTTGGTTAACATTTTTTGCGGC
1 AAGA-CAAAACGCTGCGTTTTGGTTAACATATCTTGCGGC
5668050 ACTTCTATTA
Statistics
Matches: 461, Mismatches: 123, Indels: 57
0.72 0.19 0.09
Matches are distributed among these distances:
113 25 0.05
114 173 0.38
115 254 0.55
116 7 0.02
117 2 0.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (112 bp):
AAGACAAAACGCTGCGTTTTGGTTAACATATCTTGCGGCGCTTAAATAAAGCGCCGCTAATATGA
TATTTAGCGGCGTTTTCTCGTAAGCGCCACTAATTATATTATACATC
Found at i:5667741 original size:114 final size:114
Alignment explanation
Indices: 5667588--5668033 Score: 361
Period size: 114 Copynumber: 3.9 Consensus size: 114
5667578 AAGAAATATA
* * * *
5667588 GCGGCGCTTCTCCAAACGCGCCGCTAATAATACTCTTTAGCGGCGCTTCTCCAAACGCGCCACTA
1 GCGGCGCTTCTCAAAACGCGCCGCGAATAATACTATTTAGCGGCGCTTCTACAAACGCGCCACTA
*
5667653 ATTCTAATATACCTCAATACCAAACCCTGCGTTTTGGTGTGCATATCTT
66 ATTCTAATATACCTCAAGACCAAACCCTGCGTTTTGGTGTGCATATCTT
* * * * ***
5667702 GCGGCGCTTAACT-GAAA-GCGCCGCGAATACTGA-TATTTAGCGGCGTTTTGTTGTAA-GCGCC
1 GCGGCGCTT--CTCAAAACGCGCCGCGAATAAT-ACTATTTAGCGGCG-CTTCTACAAACGCGCC
* * * * ** * * * *
5667763 AGTAATTATATTATACATCAAGACCAAAACGTTGAGTTTTGGT-TAAG-AAATATA
62 ACTAATTCTAATATACCTCAAGACC-AAACCCTGCGTTTTGGTGT--GCATATCTT
* *
5667817 GCGGCGCTTCTCAAAACGCGCCGCTAATAATACTCTTTAGCGGCGCTTCTACAAACGCGCCACTA
1 GCGGCGCTTCTCAAAACGCGCCGCGAATAATACTATTTAGCGGCGCTTCTACAAACGCGCCACTA
* *
5667882 ATCCTAATATACCTCAAGACCAAACTCTGCGTTTTGGTGTGCATATCTT
66 ATTCTAATATACCTCAAGACCAAACCCTGCGTTTTGGTGTGCATATCTT
* * ** * ** * * * *
5667931 GCGGCGATTCTAAAAAATCGCCGCTAATTTTA-TACTTTAGCGGCGTTTTTGCCTAA--CGCCAC
1 GCGGCGCTTCTCAAAACGCGCCGCGAATAATACTA-TTTAGCGGCGCTTCT-ACAAACGCGCCAC
* * * * *
5667993 TAACTGTACTATACATCGAGACCAAACCGCTGCGTTTTGGT
64 TAATTCTAATATACCTCAAGACCAAACC-CTGCGTTTTGGT
5668034 TAACATTTTT
Statistics
Matches: 258, Mismatches: 58, Indels: 32
0.74 0.17 0.09
Matches are distributed among these distances:
113 31 0.12
114 136 0.53
115 88 0.34
116 3 0.01
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (114 bp):
GCGGCGCTTCTCAAAACGCGCCGCGAATAATACTATTTAGCGGCGCTTCTACAAACGCGCCACTA
ATTCTAATATACCTCAAGACCAAACCCTGCGTTTTGGTGTGCATATCTT
Found at i:5667777 original size:229 final size:229
Alignment explanation
Indices: 5667466--5668036 Score: 850
Period size: 229 Copynumber: 2.5 Consensus size: 229
5667456 TTCGGTTAAT
* *
5667466 ATATCTTGCGGCGCTTCAAATAAAGCGCCGCTAATAGTGATATTTAGCGGCGTTTTGTTGTAAGC
1 ATATCTTGCGGCGCTTCAAATAAAGCGCCGCGAATACTGATATTTAGCGGCGTTTTGTTGTAAGC
*
5667531 TCCACTAATGATATTATACATCAAGACCAAAACGTTGAGTTTTGGTTAAGAAATATAGCGGCGCT
66 GCCACTAATGATATTATACATCAAGACCAAAACGTTGAGTTTTGGTTAAGAAATATAGCGGCGCT
* * *
5667596 TCTCCAAACGCGCCGCTAATAATACTCTTTAGCGGCGCTTCTCCAAACGCGCCACTAATTCTAAT
131 TCTCAAAACGCGCCGCTAATAATACTCTTTAGCGGCGCTTCTACAAACGCGCCACTAATCCTAAT
*
5667661 ATACCTCAATACCAAACCCTGCGTTTTGGTGTGC
196 ATACCTCAAGACCAAACCCTGCGTTTTGGTGTGC
*
5667695 ATATCTTGCGGCGCTT-AACTGAAAGCGCCGCGAATACTGATATTTAGCGGCGTTTTGTTGTAAG
1 ATATCTTGCGGCGCTTCAAAT-AAAGCGCCGCGAATACTGATATTTAGCGGCGTTTTGTTGTAAG
* *
5667759 CGCCAGTAATTATATTATACATCAAGACCAAAACGTTGAGTTTTGGTTAAGAAATATAGCGGCGC
65 CGCCACTAATGATATTATACATCAAGACCAAAACGTTGAGTTTTGGTTAAGAAATATAGCGGCGC
5667824 TTCTCAAAACGCGCCGCTAATAATACTCTTTAGCGGCGCTTCTACAAACGCGCCACTAATCCTAA
130 TTCTCAAAACGCGCCGCTAATAATACTCTTTAGCGGCGCTTCTACAAACGCGCCACTAATCCTAA
*
5667889 TATACCTCAAGACCAAACTCTGCGTTTTGGTGTGC
195 TATACCTCAAGACCAAACCCTGCGTTTTGGTGTGC
* * * * *
5667924 ATATCTTGCGGCGATTCTAAA-AAATCGCCGCTAAT-TTTATACTTTAGCGGCG-TTT-TTGCCT
1 ATATCTTGCGGCGCTTC-AAATAAAGCGCCGCGAATACTGATA-TTTAGCGGCGTTTTGTTG--T
* * * * *
5667985 AA-CGCCACTAACTG-TACTATACATCGAGACCAAACCGCTGCGTTTTGGTTAA
62 AAGCGCCACTAA-TGATATTATACATCAAGACCAAAACGTTGAGTTTTGGTTAA
5668037 CATTTTTTGC
Statistics
Matches: 311, Mismatches: 24, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
227 3 0.01
228 51 0.16
229 255 0.82
231 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (229 bp):
ATATCTTGCGGCGCTTCAAATAAAGCGCCGCGAATACTGATATTTAGCGGCGTTTTGTTGTAAGC
GCCACTAATGATATTATACATCAAGACCAAAACGTTGAGTTTTGGTTAAGAAATATAGCGGCGCT
TCTCAAAACGCGCCGCTAATAATACTCTTTAGCGGCGCTTCTACAAACGCGCCACTAATCCTAAT
ATACCTCAAGACCAAACCCTGCGTTTTGGTGTGC
Found at i:5668146 original size:75 final size:75
Alignment explanation
Indices: 5667985--5668146 Score: 189
Period size: 75 Copynumber: 2.2 Consensus size: 75
5667975 GTTTTTGCCT
* * * * * *
5667985 AACGCCACTAACTGTACTATACATCGAGACCAAACCGCTGCGTTTTGGTTAACATTTTTTGCGGC
1 AACGCCACTAATTCTAATATACATCAAGACCAAAACGCTGCGTTTTGGTTAACATATTTTGCGGC
*
5668050 ACTTCTATTA
66 ACTTCTAGTA
* * * * *
5668060 AGCGCCACTAATTCTAATATACATCAAGATCAAAACTCTGCGTTTTGGTTATCATATTTTGTGGC
1 AACGCCACTAATTCTAATATACATCAAGACCAAAACGCTGCGTTTTGGTTAACATATTTTGCGGC
* *
5668125 GCTTTTAGTA
66 ACTTCTAGTA
*
5668135 AACGCCGCTAAT
1 AACGCCACTAAT
5668147 ACTTGTTTTA
Statistics
Matches: 71, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (75 bp):
AACGCCACTAATTCTAATATACATCAAGACCAAAACGCTGCGTTTTGGTTAACATATTTTGCGGC
ACTTCTAGTA
Found at i:5669243 original size:49 final size:49
Alignment explanation
Indices: 5669130--5669367 Score: 275
Period size: 49 Copynumber: 4.8 Consensus size: 49
5669120 ACCGAAAAAA
* * *
5669130 ATGAATGCAACAAAAACAAACAATGAAGCATAATTAGAAACACCACTTTATTT
1 ATGAATGCAAC-AAAACAATCAATGAAACATAAATA-AAACA--ACTTTATTT
* *
5669183 ATGAATACAACAAAACAATCAATGAAGCATAAATAAAACAACTTTATTT
1 ATGAATGCAACAAAACAATCAATGAAACATAAATAAAACAACTTTATTT
* *
5669232 ATGAATGCAACAAAACAATCAATGAAATATAAATAAAACAATTTTATTT
1 ATGAATGCAACAAAACAATCAATGAAACATAAATAAAACAACTTTATTT
* * * *
5669281 ATGAATGCAAC-AATCAATGAA-GCATAA-GTAAAGAAAACACAACTTTATTT
1 ATGAATGCAACAAAACAATCAATG-A-AACATAAA-TAAA-ACAACTTTATTT
*
5669331 ATGAATGCAACAAAACATTCAATGAAACATAAATAAA
1 ATGAATGCAACAAAACAATCAATGAAACATAAATAAA
5669368 TAAAAAAACA
Statistics
Matches: 161, Mismatches: 17, Indels: 17
0.83 0.09 0.09
Matches are distributed among these distances:
47 1 0.01
48 13 0.08
49 70 0.43
50 27 0.17
51 17 0.11
52 23 0.14
53 10 0.06
ACGTcount: A:0.54, C:0.14, G:0.08, T:0.24
Consensus pattern (49 bp):
ATGAATGCAACAAAACAATCAATGAAACATAAATAAAACAACTTTATTT
Found at i:5684419 original size:9 final size:9
Alignment explanation
Indices: 5684405--5684441 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
5684395 TATAGTTTGA
5684405 TATTCGAAT
1 TATTCGAAT
5684414 TATTCGAAT
1 TATTCGAAT
*
5684423 TATTCGAGT
1 TATTCGAAT
5684432 TATTCGAAT
1 TATTCGAAT
5684441 T
1 T
5684442 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:5709933 original size:27 final size:28
Alignment explanation
Indices: 5709890--5709945 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 28
5709880 GATATTATAA
5709890 AGGAAAAGAAAGAAAAAAA-AATAGAGAG
1 AGGAAAAGAAAGAAAAAAATAA-AGAGAG
*
5709918 AGGAAAA-ATAGAAAAAAATAAAGAGAG
1 AGGAAAAGAAAGAAAAAAATAAAGAGAG
5709945 A
1 A
5709946 AATAAAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 17 0.65
28 9 0.35
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.05
Consensus pattern (28 bp):
AGGAAAAGAAAGAAAAAAATAAAGAGAG
Found at i:5709955 original size:25 final size:25
Alignment explanation
Indices: 5709890--5709955 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 25
5709880 GATATTATAA
*
5709890 AGGAAAAGAAAGAAAAAAAAATAGAGAG
1 AGGAAAA-AAAG--AAAAAAATAAAGAG
*
5709918 AGGAAAAATAGAAAAAAATAAAGAG
1 AGGAAAAAAAGAAAAAAATAAAGAG
5709943 A-GAAATAAAAGAA
1 AGGAAA-AAAAGAA
5709956 TTAATTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 4 0.12
25 20 0.59
27 3 0.09
28 7 0.21
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (25 bp):
AGGAAAAAAAGAAAAAAATAAAGAG
Found at i:5711090 original size:12 final size:12
Alignment explanation
Indices: 5711073--5711102 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5711063 TGAAAAAAAT
5711073 ACAATTTGACTA
1 ACAATTTGACTA
5711085 ACAATTTGACTA
1 ACAATTTGACTA
5711097 A-AATTT
1 ACAATTT
5711103 AAAATTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (12 bp):
ACAATTTGACTA
Found at i:5724837 original size:22 final size:21
Alignment explanation
Indices: 5724799--5724839 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
5724789 CGTATTGTAA
**
5724799 AACAAAGAGAATTATAAAATG
1 AACAAAGAGAAAAATAAAATG
5724820 AACAAAGGAGAAAAATAAAA
1 AACAAA-GAGAAAAATAAAA
5724840 GGATACTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.68, C:0.05, G:0.15, T:0.12
Consensus pattern (21 bp):
AACAAAGAGAAAAATAAAATG
Found at i:5725815 original size:20 final size:21
Alignment explanation
Indices: 5725787--5725831 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
5725777 AAAAAATAAT
5725787 TTTTAATTATTT-TCT-TTTA
1 TTTTAATTATTTCTCTCTTTA
5725806 TTTTACATTATTTCTCTCTTTA
1 TTTTA-ATTATTTCTCTCTTTA
5725828 TTTT
1 TTTT
5725832 TCTATTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.22
20 7 0.30
21 3 0.13
22 8 0.35
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTAATTATTTCTCTCTTTA
Found at i:5728100 original size:69 final size:69
Alignment explanation
Indices: 5727989--5728123 Score: 216
Period size: 69 Copynumber: 2.0 Consensus size: 69
5727979 TTGGTTTTGC
* * * *
5727989 CTTGTGAATTTAGATTTTTCTCAATTCTGGGTTGTTGCCCTTTTAGCTTTGAGGTCTCTCATATG
1 CTTGTGAAATTAGATTTTTCTCAATTCTGGGTTGTTACCCTTTTAGCTGTGAGGTCTATCATATG
5728054 ATTT
66 ATTT
* *
5728058 CTTGTGAAATTAGATTTTTCTCAGTTCTGGGTTGTTACCCTTTTTGCTGTGAGGTCTATCATATG
1 CTTGTGAAATTAGATTTTTCTCAATTCTGGGTTGTTACCCTTTTAGCTGTGAGGTCTATCATATG
5728123 A
66 A
5728124 CTTTTTGAAG
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.17, C:0.16, G:0.20, T:0.47
Consensus pattern (69 bp):
CTTGTGAAATTAGATTTTTCTCAATTCTGGGTTGTTACCCTTTTAGCTGTGAGGTCTATCATATG
ATTT
Found at i:5731118 original size:123 final size:123
Alignment explanation
Indices: 5730899--5731124 Score: 362
Period size: 123 Copynumber: 1.8 Consensus size: 123
5730889 GGGAGCTTGA
* **
5730899 GAAATCAAATAGGAAAATGGATGATACATTAGGCAATGTGAAGGAAGATGGGTCATGTAGGAAGA
1 GAAATCAAATAGGAAAATGGATGATACACTAGGCAATGCAAAGGAAGATGGGTCATGTAGGAAGA
* * *
5730964 AATTGTAACGACCCGACTTTTTTTGGTGTCGAAAAATGCGGTTTCGGAACCCCATTTC
66 AATTGTAACGACCCAACTTTTGTCGGTGTCGAAAAATGCGGTTTCGGAACCCCATTTC
* *
5731022 GAAATCAAATAGGAAAATGGATGATACACTAGGCAATGCAAAGGAAGATGGGTCATGTAGGGATA
1 GAAATCAAATAGGAAAATGGATGATACACTAGGCAATGCAAAGGAAGATGGGTCATGTAGGAAGA
* *
5731087 AATTGTAATGACCCAACTTTTGTCGGTGTCGAGAAATG
66 AATTGTAACGACCCAACTTTTGTCGGTGTCGAAAAATG
5731125 AGATTTCAGA
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
123 93 1.00
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.25
Consensus pattern (123 bp):
GAAATCAAATAGGAAAATGGATGATACACTAGGCAATGCAAAGGAAGATGGGTCATGTAGGAAGA
AATTGTAACGACCCAACTTTTGTCGGTGTCGAAAAATGCGGTTTCGGAACCCCATTTC
Done.