Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007957.1 Hibiscus syriacus cultivar Beakdansim tig00110384_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8646418
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 32 of 43
Found at i:6504569 original size:54 final size:54
Alignment explanation
Indices: 6504500--6504602 Score: 197
Period size: 54 Copynumber: 1.9 Consensus size: 54
6504490 ATTGTAGTTG
6504500 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
6504554 TATGGATTGATTTATTTTATATAATTTATTAGTATGGATTGATTTATTT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTT
6504603 AAATAATTTA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
Found at i:6504603 original size:58 final size:59
Alignment explanation
Indices: 6504474--6504603 Score: 182
Period size: 54 Copynumber: 2.3 Consensus size: 59
6504464 TATTTTAAAA
***
6504474 TATGGATTGATTTA-TTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTATTGTAGAAATATGGATTGATTTATTTTAAATAATTTATTAG
*
6504532 TATGGATTGATTTA--T-TT-TA-AAATATGGATTGATTTATTTTATATAATTTATTAG
1 TATGGATTGATTTATTTATTGTAGAAATATGGATTGATTTATTTTAAATAATTTATTAG
6504586 TATGGATTGATTTATTTA
1 TATGGATTGATTTATTTA
6504604 AATAATTTAT
Statistics
Matches: 65, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
54 45 0.69
55 2 0.03
56 3 0.05
57 1 0.02
58 14 0.22
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (59 bp):
TATGGATTGATTTATTTATTGTAGAAATATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:6504627 original size:85 final size:84
Alignment explanation
Indices: 6504452--6504687 Score: 367
Period size: 85 Copynumber: 2.8 Consensus size: 84
6504442 TATTTTAAAA
*
6504452 TATGGATTGATTTATTTTAAAATATGGATTGATTTA---T-TAT--TGTAGTTGTATGGATTGAT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTATATAATTTA-TTGTATGGATTGAT
6504511 TTATTTTAAATAATTTATTAG
65 TTA-TTTAAATAATTTATTAG
6504532 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTATATAATTTATTAGTATGGATTGAT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTATATAATTTATT-GTATGGATTGAT
*
6504597 TTATTTAAATAATTTATTTG
65 TTATTTAAATAATTTATTAG
*
6504617 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGAT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTATATAATTTA-TTGTATGGATTGAT
6504682 TTATTT
65 TTATTT
6504688 TAAAATATGG
Statistics
Matches: 145, Mismatches: 3, Indels: 11
0.91 0.02 0.07
Matches are distributed among these distances:
80 36 0.25
83 1 0.01
84 3 0.02
85 85 0.59
86 20 0.14
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (84 bp):
TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTATATAATTTATTGTATGGATTGATT
TATTTAAATAATTTATTAG
Found at i:6504642 original size:22 final size:22
Alignment explanation
Indices: 6504617--6504761 Score: 110
Period size: 22 Copynumber: 6.0 Consensus size: 22
6504607 AATTTATTTG
6504617 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
6504639 TATGGATTGATTTATTTTAAATAA
1 TATGGATTGATTTATTTT-AA-AA
* * *
6504663 TTTATTTGTATGGATTGATTTATTTTAAAA
1 --TA--TGGATTGATTTA-TT---TTAAAA
***
6504693 TATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTA-T-TT-TA-AAA
6504719 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
6504741 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
6504762 TAATTTATTA
Statistics
Matches: 98, Mismatches: 12, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
22 39 0.40
23 4 0.04
24 5 0.05
25 3 0.03
26 27 0.28
27 1 0.01
28 11 0.11
29 2 0.02
30 2 0.02
31 2 0.02
32 2 0.02
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.52
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:6504670 original size:54 final size:53
Alignment explanation
Indices: 6504586--6504770 Score: 299
Period size: 54 Copynumber: 3.5 Consensus size: 53
6504576 AATTTATTAG
6504586 TATGGATTGATTTATTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAA
6504639 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTA-TTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAA
* *
6504693 TATGGATTGATTTA-TT--AT--TGTAGTTGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAA
6504741 TATGGATTGATTTATTTTAAATAATTTATT
1 TATGGATTGATTTA-TTTAAATAATTTATT
6504771 ATTGTAGTTG
Statistics
Matches: 121, Mismatches: 4, Indels: 13
0.88 0.03 0.09
Matches are distributed among these distances:
48 42 0.35
50 4 0.03
52 4 0.03
53 14 0.12
54 57 0.47
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (53 bp):
TATGGATTGATTTATTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAA
Found at i:6504821 original size:31 final size:31
Alignment explanation
Indices: 6504786--6504844 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
6504776 AGTTGTATGG
* * *
6504786 ATTATTTAAATTTTAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
6504817 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
6504845 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:6506484 original size:2 final size:2
Alignment explanation
Indices: 6506477--6506512 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6506467 TAAATGATTC
6506477 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6506513 TCAATCATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6508089 original size:9 final size:10
Alignment explanation
Indices: 6508072--6508101 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
6508062 GATATTTTTA
6508072 TTTCAAAAAT
1 TTTCAAAAAT
6508082 TTTCAAAAAT
1 TTTCAAAAAT
*
6508092 TTTGAAAAAT
1 TTTCAAAAAT
6508102 CTTGTGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (10 bp):
TTTCAAAAAT
Found at i:6508504 original size:23 final size:22
Alignment explanation
Indices: 6508478--6508557 Score: 65
Period size: 23 Copynumber: 3.6 Consensus size: 22
6508468 CATAGCAGAG
*
6508478 TGCATCGGTGCACATTCAATGAA
1 TGCATCGATGCACATTCAATG-A
* * *
6508501 TGCATC-AGTGCACCTT-TATGG
1 TGCATCGA-TGCACATTCAATGA
* *
6508522 TGTATCGATGCACATTCAAGGGA
1 TGCATCGATGCACATTCAA-TGA
6508545 TGCATCGATGCAC
1 TGCATCGATGCAC
6508558 TATCTAGTGT
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
21 12 0.28
22 5 0.12
23 26 0.60
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACATTCAATGA
Found at i:6508549 original size:44 final size:43
Alignment explanation
Indices: 6508476--6508576 Score: 114
Period size: 44 Copynumber: 2.3 Consensus size: 43
6508466 TGCATAGCAG
* * * *
6508476 AGTGCATCGGTGCACATTCAATGAATGCATC-AGTGCACCTTTAT
1 AGTGTATCGATGCACATTCAAGGAATGCATCGA-TGCA-CTATAT
* * *
6508520 GGTGTATCGATGCACATTCAAGGGATGCATCGATGCACTATCT
1 AGTGTATCGATGCACATTCAAGGAATGCATCGATGCACTATAT
6508563 AGTGTATCGATGCA
1 AGTGTATCGATGCA
6508577 TTATGCACAA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
43 17 0.35
44 30 0.62
45 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.29
Consensus pattern (43 bp):
AGTGTATCGATGCACATTCAAGGAATGCATCGATGCACTATAT
Found at i:6513983 original size:35 final size:34
Alignment explanation
Indices: 6513939--6514071 Score: 176
Period size: 35 Copynumber: 3.8 Consensus size: 34
6513929 TTAATCTACG
* *
6513939 TCTGATAACTGTAAAATATCTAATAACTGTAATCA
1 TCTGATAACTGT-AAATATCTGATAACTGAAATCA
* * *
6513974 TCTAATAACTGTAAATATATGATAACTAAAAATCA
1 TCTGATAACTGTAAATATCTGATAACT-GAAATCA
*
6514009 TCTGATAACTGCAAATATCTGATAACTGAAAATCA
1 TCTGATAACTGTAAATATCTGATAACTG-AAATCA
*
6514044 TCTGATAATTGTAAATATCTGATAACTG
1 TCTGATAACTGTAAATATCTGATAACTG
6514072 TAAACATTTA
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
34 13 0.15
35 72 0.85
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.33
Consensus pattern (34 bp):
TCTGATAACTGTAAATATCTGATAACTGAAATCA
Found at i:6514017 original size:52 final size:51
Alignment explanation
Indices: 6513941--6514074 Score: 144
Period size: 52 Copynumber: 2.6 Consensus size: 51
6513931 AATCTACGTC
* * *
6513941 TGATAACTGTAAAATATCTAATAACTGTAATCATCTAATAACTGTAAAT-ATA
1 TGATAACT-AAAAATATCTGATAACTGTAAT-ATCTAATAACTGAAAATCATA
* * *
6513993 TGATAACTAAAAATCATCTGATAACTGCAAATATCTGATAACTGAAAATCATC
1 TGATAACTAAAAAT-ATCTGATAACTG-TAATATCTAATAACTGAAAATCATA
* **
6514046 TGATAATTGTAAATATCTGATAACTGTAA
1 TGATAACTAAAAATATCTGATAACTGTAA
6514075 ACATTTAGAA
Statistics
Matches: 69, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
51 7 0.10
52 46 0.67
53 16 0.23
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.33
Consensus pattern (51 bp):
TGATAACTAAAAATATCTGATAACTGTAATATCTAATAACTGAAAATCATA
Found at i:6514075 original size:17 final size:17
Alignment explanation
Indices: 6513939--6514075 Score: 159
Period size: 17 Copynumber: 7.9 Consensus size: 17
6513929 TTAATCTACG
6513939 TCTGATAACTGTAAAATA
1 TCTGATAACTGT-AAATA
*
6513957 TCTAATAACTGT-AATCA
1 TCTGATAACTGTAAAT-A
*
6513974 TCTAATAACTGTAAATA
1 TCTGATAACTGTAAATA
* **
6513991 TATGATAACTAAAAATCA
1 TCTGATAACTGTAAAT-A
*
6514009 TCTGATAACTGCAAATA
1 TCTGATAACTGTAAATA
*
6514026 TCTGATAACTGAAAATCA
1 TCTGATAACTGTAAAT-A
*
6514044 TCTGATAATTGTAAATA
1 TCTGATAACTGTAAATA
6514061 TCTGATAACTGTAAA
1 TCTGATAACTGTAAA
6514076 CATTTAGAAT
Statistics
Matches: 103, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
16 3 0.03
17 57 0.55
18 43 0.42
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (17 bp):
TCTGATAACTGTAAATA
Found at i:6530060 original size:3 final size:3
Alignment explanation
Indices: 6530052--6530076 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
6530042 GAGGTGATGC
6530052 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
6530077 AGTTGGTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:6534740 original size:22 final size:23
Alignment explanation
Indices: 6534715--6534766 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
6534705 CTCATTCATT
*
6534715 AAAAAAAGCAAAAGAA-AAGAGA
1 AAAAAAAGCAAAAGAAGAAAAGA
*
6534737 AAAAAAAGGAAAAGAAGAAAAGA
1 AAAAAAAGCAAAAGAAGAAAAGA
*
6534760 AGAAAAA
1 AAAAAAA
6534767 TTGTGCAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 15 0.58
23 11 0.42
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (23 bp):
AAAAAAAGCAAAAGAAGAAAAGA
Found at i:6534750 original size:17 final size:17
Alignment explanation
Indices: 6534724--6534757 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
6534714 TAAAAAAAGC
6534724 AAAAGAAAAG-AGAAAA
1 AAAAGAAAAGAAGAAAA
6534740 AAAAGGAAAAGAAGAAAA
1 AAAA-GAAAAGAAGAAAA
6534758 GAAGAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 6 0.38
18 6 0.38
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAGAAGAAAA
Found at i:6534752 original size:15 final size:17
Alignment explanation
Indices: 6534724--6534765 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
6534714 TAAAAAAAGC
6534724 AAAAGAAAAGAGAA-AA
1 AAAAGAAAAGAGAAGAA
*
6534740 AAAAGGAAA-AGAAGAA
1 AAAAGAAAAGAGAAGAA
6534756 AAGAAGAAAA
1 AA-AAGAAAA
6534766 ATTGTGCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 4 0.18
16 12 0.55
17 6 0.27
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAGAGAAGAA
Found at i:6540430 original size:2 final size:2
Alignment explanation
Indices: 6540423--6540452 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6540413 CCAACCCGGT
6540423 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6540453 AATCAGACTT
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):
TA
Found at i:6541517 original size:28 final size:28
Alignment explanation
Indices: 6541485--6541542 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
6541475 CGTTCATGAA
6541485 CAAATTTGTTTAATGTTTGTGAACTGAT
1 CAAATTTGTTTAATGTTTGTGAACTGAT
6541513 CAAATTTGTTTAATGTTTGTGAACTGAT
1 CAAATTTGTTTAATGTTTGTGAACTGAT
6541541 CA
1 CA
6541543 TATGTTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.29, C:0.09, G:0.17, T:0.45
Consensus pattern (28 bp):
CAAATTTGTTTAATGTTTGTGAACTGAT
Found at i:6541555 original size:28 final size:27
Alignment explanation
Indices: 6541491--6541551 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 27
6541481 TGAACAAATT
* *
6541491 TGTTTAATGTTTGTGAACTGATCAAATT
1 TGTTAAATGTTTGTGAACTGATC-AATA
*
6541519 TGTTTAATGTTTGTGAACTGATC-ATA
1 TGTTAAATGTTTGTGAACTGATCAATA
6541545 TGTTAAA
1 TGTTAAA
6541552 AATGGTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 8 0.26
28 23 0.74
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.46
Consensus pattern (27 bp):
TGTTAAATGTTTGTGAACTGATCAATA
Found at i:6542013 original size:3 final size:3
Alignment explanation
Indices: 6542005--6542079 Score: 116
Period size: 3 Copynumber: 25.0 Consensus size: 3
6541995 ATTGATTTAT
6542005 TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
* *
6542050 TAA ATA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6542080 AATATATTAA
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.03
3 61 0.92
4 3 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:6542214 original size:16 final size:16
Alignment explanation
Indices: 6542193--6542234 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
6542183 CCTAGCGCCG
6542193 CAGCCGCCTCTGCCTC
1 CAGCCGCCTCTGCCTC
6542209 CAGCCGCCTCTGCCTC
1 CAGCCGCCTCTGCCTC
6542225 CAGCCGCCTC
1 CAGCCGCCTC
6542235 AGCCAACGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.07, C:0.57, G:0.19, T:0.17
Consensus pattern (16 bp):
CAGCCGCCTCTGCCTC
Found at i:6543443 original size:16 final size:16
Alignment explanation
Indices: 6543422--6543459 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
6543412 TTATGTAGTC
6543422 ATAAATA-TATATATAA
1 ATAAATATTAT-TATAA
*
6543438 ATAAATATTATTTTAA
1 ATAAATATTATTATAA
6543454 ATAAAT
1 ATAAAT
6543460 TATTTTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAATATTATTATAA
Found at i:6545509 original size:2 final size:2
Alignment explanation
Indices: 6545502--6545527 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6545492 TGAGTTAGTG
6545502 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
6545528 GGTAAAATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6545977 original size:17 final size:17
Alignment explanation
Indices: 6545957--6545990 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6545947 TTAATTTTAA
*
6545957 AATTTATTATTTAATTT
1 AATTTACTATTTAATTT
*
6545974 AATTTACTATTTTATTT
1 AATTTACTATTTAATTT
6545991 TCATTGAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
AATTTACTATTTAATTT
Found at i:6546292 original size:20 final size:20
Alignment explanation
Indices: 6546263--6546311 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
6546253 ATGTTATGAT
*
6546263 ATTAAGAAATATATTTA-TAA
1 ATTAATAAAT-TATTTATTAA
*
6546283 ATTAATAAATTTTTTATTAA
1 ATTAATAAATTATTTATTAA
*
6546303 AATAATAAA
1 ATTAATAAA
6546312 AATTTGATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATTAATAAATTATTTATTAA
Found at i:6552499 original size:30 final size:30
Alignment explanation
Indices: 6552410--6552500 Score: 96
Period size: 30 Copynumber: 3.1 Consensus size: 30
6552400 AAAACTTTAA
6552410 AATTTCATAATGCTATTTTGTATTGATATC
1 AATTTCATAATGCTATTTTGTATTGATATC
* * * * * * *
6552440 AATTTTAGAA-CCGATCTAG-AGTAGATATC
1 AATTTCATAATGCTATTTTGTA-TTGATATC
6552469 AATTTCATAATGCTATTTTGTATTGATATC
1 AATTTCATAATGCTATTTTGTATTGATATC
6552499 AA
1 AA
6552501 GTTTAGAATA
Statistics
Matches: 44, Mismatches: 14, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
28 1 0.02
29 20 0.45
30 22 0.50
31 1 0.02
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.43
Consensus pattern (30 bp):
AATTTCATAATGCTATTTTGTATTGATATC
Found at i:6556015 original size:22 final size:22
Alignment explanation
Indices: 6555990--6556034 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
6555980 ATGTTAGCTG
6555990 GATGTATTGATGAAGTGGTAGA
1 GATGTATTGATGAAGTGGTAGA
6556012 GATGTATTGATGAAGTGGTAGA
1 GATGTATTGATGAAGTGGTAGA
6556034 G
1 G
6556035 GAATCATAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.38, T:0.31
Consensus pattern (22 bp):
GATGTATTGATGAAGTGGTAGA
Found at i:6556857 original size:22 final size:21
Alignment explanation
Indices: 6556826--6556867 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
6556816 ATGTTCTCCA
* *
6556826 CTTTTCCTTTTGATTTTTTTAC
1 CTTTTACTTTT-ATATTTTTAC
6556848 CTTTTACTTTTATATTTTTA
1 CTTTTACTTTTATATTTTTA
6556868 GGGATTTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.14, C:0.14, G:0.02, T:0.69
Consensus pattern (21 bp):
CTTTTACTTTTATATTTTTAC
Found at i:6561149 original size:5 final size:5
Alignment explanation
Indices: 6561139--6561165 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
6561129 GTGCCATCTT
6561139 CTCCC CTCCC CTCCC CTCCC CTCCC CT
1 CTCCC CTCCC CTCCC CTCCC CTCCC CT
6561166 GACACAGTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.78, G:0.00, T:0.22
Consensus pattern (5 bp):
CTCCC
Found at i:6570407 original size:21 final size:21
Alignment explanation
Indices: 6570369--6570408 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
6570359 AAAAAATTAC
*
6570369 CTAAAACATTATTATTTTTAT
1 CTAAAACATTAATATTTTTAT
* *
6570390 CTAAAATATTAATGTTTTT
1 CTAAAACATTAATATTTTT
6570409 TTAACATTTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (21 bp):
CTAAAACATTAATATTTTTAT
Found at i:6571305 original size:16 final size:19
Alignment explanation
Indices: 6571258--6571308 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
6571248 TTTGGTTCAC
6571258 GGAATGTAAGATTACCAGTG
1 GGAA-GTAAGATTACCAGTG
6571278 GGAATGTAAGATTACCA-T-
1 GGAA-GTAAGATTACCAGTG
6571296 GGAA-TAAGATTAC
1 GGAAGTAAGATTAC
6571309 TGGCAATGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.29
18 4 0.13
19 1 0.03
20 17 0.55
ACGTcount: A:0.39, C:0.10, G:0.25, T:0.25
Consensus pattern (19 bp):
GGAAGTAAGATTACCAGTG
Found at i:6571525 original size:37 final size:37
Alignment explanation
Indices: 6571455--6571526 Score: 92
Period size: 38 Copynumber: 1.9 Consensus size: 37
6571445 GGAAAATATT
* *
6571455 TATATATTTTCTTTAAAAAATTTAAATTCATAAAATC
1 TATATATTTTCTTTAAAAAATTGAAAATCATAAAATC
* *
6571492 TATATAATTTTTTTTACAAAATTGAAAAT-ATAAAA
1 TATAT-ATTTTCTTTAAAAAATTGAAAATCATAAAA
6571527 AGATTTAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 11 0.37
38 19 0.63
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (37 bp):
TATATATTTTCTTTAAAAAATTGAAAATCATAAAATC
Found at i:6573423 original size:16 final size:16
Alignment explanation
Indices: 6573402--6573434 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
6573392 CAAAAAAATT
6573402 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
6573418 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
6573434 T
1 T
6573435 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:6575923 original size:29 final size:31
Alignment explanation
Indices: 6575870--6575929 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
6575860 CAAATTAAGG
6575870 CAAAATGATTTTTGGACTTGAATTGAATTTA
1 CAAAATGATTTTTGGACTTGAATTGAATTTA
6575901 CAAAATG-TTTTTGGACTT-AATTGAATTTA
1 CAAAATGATTTTTGGACTTGAATTGAATTTA
6575930 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (31 bp):
CAAAATGATTTTTGGACTTGAATTGAATTTA
Found at i:6576035 original size:21 final size:21
Alignment explanation
Indices: 6576009--6576087 Score: 92
Period size: 21 Copynumber: 3.7 Consensus size: 21
6575999 AGGGTGTCAA
6576009 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
6576030 AGTGCATCCATGCATCCCAT-C
1 AGTGCATCCATGCA-CCCCTGC
6576051 AGTGCATCCATGCA--CCTGCAC
1 AGTGCATCCATGCACCCCTG--C
6576072 TAGTGCATCCATGCAC
1 -AGTGCATCCATGCAC
6576088 TCAAACACCG
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.04
21 30 0.60
22 18 0.36
ACGTcount: A:0.23, C:0.38, G:0.18, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:6576134 original size:21 final size:21
Alignment explanation
Indices: 6576108--6576170 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
6576098 AATGCAATTA
6576108 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCAAGGCT
* *
6576129 GTGCATCGATGCATC-ATGTT
1 GTGCATCGATGCATCAAGGCT
*
6576149 GTGCATCCATGCA-CGAAGGCT
1 GTGCATCGATGCATC-AAGGCT
6576170 G
1 G
6576171 CAATGGCTAG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.03
20 15 0.43
21 19 0.54
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.25
Consensus pattern (21 bp):
GTGCATCGATGCATCAAGGCT
Found at i:6577402 original size:33 final size:32
Alignment explanation
Indices: 6577360--6577446 Score: 131
Period size: 33 Copynumber: 2.7 Consensus size: 32
6577350 TTGTGATCGT
6577360 TTTTAAGTATTTGAATTTATCGAACTTGGAAG
1 TTTTAAGTATTTGAATTTATCGAACTTGGAAG
*
6577392 ATTTTAAGTATTTGAATTTATCAAACTTGGAAG
1 -TTTTAAGTATTTGAATTTATCGAACTTGGAAG
*
6577425 TATTTAAGTATTTCAA-TTATCG
1 T-TTTAAGTATTTGAATTTATCG
6577447 TAAACTTTGT
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
32 6 0.12
33 44 0.88
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (32 bp):
TTTTAAGTATTTGAATTTATCGAACTTGGAAG
Found at i:6577660 original size:15 final size:17
Alignment explanation
Indices: 6577634--6577665 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
6577624 TTCTATGGGA
6577634 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
6577650 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
6577666 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:6580003 original size:34 final size:30
Alignment explanation
Indices: 6579965--6580033 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
6579955 TTGATATAAC
6579965 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
6579999 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
6580028 AATTTA
1 AATTTA
6580034 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:6580044 original size:29 final size:30
Alignment explanation
Indices: 6579974--6580033 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
6579964 CAATTTAAGG
6579974 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
6580005 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
6580034 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:6580139 original size:21 final size:20
Alignment explanation
Indices: 6580113--6580211 Score: 110
Period size: 21 Copynumber: 4.8 Consensus size: 20
6580103 AGGGTGTCAA
6580113 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCCTGC
*
6580134 AGTGCATTCATGCATCCCTGC
1 AGTGCATCCATGCA-CCCTGC
6580155 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCCATGCACCCTG--C
* * *
6580176 TAGTGCATCGATGCACCATAC
1 -AGTGCATCCATGCACCCTGC
6580197 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
6580212 TCAAACACCG
Statistics
Matches: 67, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
19 4 0.06
20 14 0.21
21 34 0.51
22 13 0.19
23 2 0.03
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.22
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:6580257 original size:20 final size:20
Alignment explanation
Indices: 6580232--6580306 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 20
6580222 AATGCAATTA
*
6580232 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTGCT
**
6580252 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-CTGCT
*
6580273 GTGCATTGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
*
6580293 GTGCATCCATGCAT
1 GTGCATCGATGCAT
6580307 GAAGGCTGCA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 30 0.65
21 16 0.35
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.31
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:6580284 original size:41 final size:41
Alignment explanation
Indices: 6580232--6580314 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
6580222 AATGCAATTA
* *
6580232 GTGCATCGATGCATCCTTCTGTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCCTGCTGTGCATCCATGCATCAAGGCT
* *
6580273 GTGCATTGATGCATCCTGCTGTGCATCCATGCATGAAGGCT
1 GTGCATCGATGCATCCTGCTGTGCATCCATGCATCAAGGCT
6580314 G
1 G
6580315 CAACGGCTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.29
Consensus pattern (41 bp):
GTGCATCGATGCATCCTGCTGTGCATCCATGCATCAAGGCT
Found at i:6583394 original size:2 final size:2
Alignment explanation
Indices: 6583387--6583420 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6583377 AATAAACAAT
6583387 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6583421 CAAACACCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6583697 original size:18 final size:18
Alignment explanation
Indices: 6583656--6583690 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
6583646 GTTTGAACTA
6583656 AATATTTTTAATTTTATT
1 AATATTTTTAATTTTATT
6583674 AATATTTTTAATTTTAT
1 AATATTTTTAATTTTAT
6583691 AATTATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
AATATTTTTAATTTTATT
Found at i:6584031 original size:10 final size:10
Alignment explanation
Indices: 6584016--6584047 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
6584006 CCTGTCAACA
6584016 TTGCTTGGGC
1 TTGCTTGGGC
6584026 TTGCTTGGGC
1 TTGCTTGGGC
6584036 TTGCTTGGGC
1 TTGCTTGGGC
6584046 TT
1 TT
6584048 TTCTACTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.38, T:0.44
Consensus pattern (10 bp):
TTGCTTGGGC
Found at i:6584232 original size:14 final size:14
Alignment explanation
Indices: 6584213--6584242 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
6584203 TTAGAACCAA
6584213 ATTGAGTATAATAT
1 ATTGAGTATAATAT
6584227 ATTGAGTATAATAT
1 ATTGAGTATAATAT
6584241 AT
1 AT
6584243 AAGTATTGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (14 bp):
ATTGAGTATAATAT
Found at i:6584262 original size:20 final size:20
Alignment explanation
Indices: 6584226--6584265 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
6584216 GAGTATAATA
*
6584226 TATTGAGTATAATATATAAG
1 TATTGAGGATAATATATAAG
6584246 TATTGAGGACTAAATATATA
1 TATTGAGGA-T-AATATATA
6584266 TAATTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 1 0.06
22 8 0.47
ACGTcount: A:0.45, C:0.03, G:0.15, T:0.38
Consensus pattern (20 bp):
TATTGAGGATAATATATAAG
Found at i:6585247 original size:7 final size:7
Alignment explanation
Indices: 6585225--6585258 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
6585215 ACAGCTTTTT
6585225 CTTCTT-
1 CTTCTTC
*
6585231 CTTATTC
1 CTTCTTC
6585238 CTTCTTC
1 CTTCTTC
6585245 CTTCTTC
1 CTTCTTC
6585252 CTTCTTC
1 CTTCTTC
6585259 TTGCCAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 5 0.20
7 20 0.80
ACGTcount: A:0.03, C:0.38, G:0.00, T:0.59
Consensus pattern (7 bp):
CTTCTTC
Found at i:6590540 original size:16 final size:16
Alignment explanation
Indices: 6590516--6590549 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
6590506 TATCGCCGAC
*
6590516 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
6590532 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
6590548 CG
1 CG
6590550 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:6591556 original size:19 final size:18
Alignment explanation
Indices: 6591528--6591589 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 18
6591518 GGATTTTATC
6591528 AATT-TAAATATAATAAA
1 AATTATAAATATAATAAA
*
6591545 AATATATAAATACAAATAAA
1 AAT-TATAAATA-TAATAAA
* * *
6591565 AATTATAATTATAATTAT
1 AATTATAAATATAATAAA
6591583 AATTATA
1 AATTATA
6591590 TGCATTAGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
17 3 0.08
18 12 0.32
19 13 0.35
20 9 0.24
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
AATTATAAATATAATAAA
Found at i:6591574 original size:6 final size:6
Alignment explanation
Indices: 6591565--6591589 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6591555 TACAAATAAA
6591565 AATTAT AATTAT AATTAT AATTAT A
1 AATTAT AATTAT AATTAT AATTAT A
6591590 TGCATTAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTAT
Found at i:6592257 original size:36 final size:35
Alignment explanation
Indices: 6592214--6592296 Score: 115
Period size: 30 Copynumber: 2.5 Consensus size: 35
6592204 TTGGTAATGC
6592214 AATGCTCATTGAATATTGATATTGGAAAATTAGGT
1 AATGCTCATTGAATATTGATATTGGAAAATTAGGT
6592249 AAATGCTCATTG---A---ATATTGGAAAATTAGGT
1 -AATGCTCATTGAATATTGATATTGGAAAATTAGGT
6592279 AATGCTCATTGAATATTG
1 AATGCTCATTGAATATTG
6592297 GAAAATAGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
29 11 0.27
30 17 0.41
32 1 0.02
33 1 0.02
36 11 0.27
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.36
Consensus pattern (35 bp):
AATGCTCATTGAATATTGATATTGGAAAATTAGGT
Found at i:6592318 original size:28 final size:29
Alignment explanation
Indices: 6592228--6592336 Score: 186
Period size: 29 Copynumber: 3.8 Consensus size: 29
6592218 CTCATTGAAT
6592228 ATTG-ATATTGGAAAATTAGGTAAATGCTC
1 ATTGAATATTGGAAAATTAGGT-AATGCTC
6592257 ATTGAATATTGGAAAATTAGGTAATGCTC
1 ATTGAATATTGGAAAATTAGGTAATGCTC
6592286 ATTGAATATTGGAAAA-TAGGTAATGCTC
1 ATTGAATATTGGAAAATTAGGTAATGCTC
*
6592314 TTTGAATATTGGAAAATTAGGTA
1 ATTGAATATTGGAAAATTAGGTA
6592337 TTTCCACTAG
Statistics
Matches: 77, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
28 27 0.35
29 33 0.43
30 17 0.22
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.35
Consensus pattern (29 bp):
ATTGAATATTGGAAAATTAGGTAATGCTC
Found at i:6592319 original size:57 final size:58
Alignment explanation
Indices: 6592228--6592336 Score: 186
Period size: 57 Copynumber: 1.9 Consensus size: 58
6592218 CTCATTGAAT
6592228 ATTGATATTGGAAAATTAGGTAAATGCTCATTGAATATTGGAAAATTAGGTAATGCTC
1 ATTGATATTGGAAAATTAGGTAAATGCTCATTGAATATTGGAAAATTAGGTAATGCTC
*
6592286 ATTGAATATTGGAAAA-TAGGT-AATGCTCTTTGAATATTGGAAAATTAGGTA
1 ATTG-ATATTGGAAAATTAGGTAAATGCTCATTGAATATTGGAAAATTAGGTA
6592337 TTTCCACTAG
Statistics
Matches: 49, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
57 29 0.59
58 9 0.18
59 11 0.22
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.35
Consensus pattern (58 bp):
ATTGATATTGGAAAATTAGGTAAATGCTCATTGAATATTGGAAAATTAGGTAATGCTC
Found at i:6594238 original size:2 final size:2
Alignment explanation
Indices: 6594231--6594266 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6594221 AGGGATTAAA
6594231 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6594267 TAAATTAGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6596481 original size:44 final size:46
Alignment explanation
Indices: 6596366--6596492 Score: 206
Period size: 46 Copynumber: 2.8 Consensus size: 46
6596356 TTAAGTATTG
*
6596366 AAAAAATTAAACTTTTAATAACAAATATTAGAAAAAAAATATTGGC
1 AAAAAATTAAACCTTTAATAACAAATATTAGAAAAAAAATATTGGC
6596412 AAAAAATTAAACCTTTAATAACAAATATTAGAAAAAAAATATTGGC
1 AAAAAATTAAACCTTTAATAACAAATATTAGAAAAAAAATATTGGC
*
6596458 AAAAAGTTAAACAC-TT-AT-ACAAATATTAGAAAAAA
1 AAAAAATTAAAC-CTTTAATAACAAATATTAGAAAAAA
6596493 TAAATTATAA
Statistics
Matches: 78, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
44 17 0.22
45 2 0.03
46 58 0.74
47 1 0.01
ACGTcount: A:0.60, C:0.08, G:0.06, T:0.26
Consensus pattern (46 bp):
AAAAAATTAAACCTTTAATAACAAATATTAGAAAAAAAATATTGGC
Found at i:6598980 original size:17 final size:17
Alignment explanation
Indices: 6598958--6598992 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
6598948 TCAGAATGCA
6598958 TTTCCTCGCAAAATTTT
1 TTTCCTCGCAAAATTTT
6598975 TTTCCTCGCAAAATTTT
1 TTTCCTCGCAAAATTTT
6598992 T
1 T
6598993 GATAGATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.06, T:0.49
Consensus pattern (17 bp):
TTTCCTCGCAAAATTTT
Found at i:6600320 original size:36 final size:36
Alignment explanation
Indices: 6600273--6600383 Score: 213
Period size: 36 Copynumber: 3.1 Consensus size: 36
6600263 GAGTTCGTGG
6600273 TGGTGGTGGCGAATTTGGTGGTACTGCTGGTGGAGA
1 TGGTGGTGGCGAATTTGGTGGTACTGCTGGTGGAGA
6600309 TGGTGGTGGCGAATTTGGTGGTACTGCTGGTGGAGA
1 TGGTGGTGGCGAATTTGGTGGTACTGCTGGTGGAGA
*
6600345 TGGTGGTGGCGAATTTGGTGGTACTGCTGGTGGTGA
1 TGGTGGTGGCGAATTTGGTGGTACTGCTGGTGGAGA
6600381 TGG
1 TGG
6600384 CGGAGTTGAA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 74 1.00
ACGTcount: A:0.13, C:0.08, G:0.48, T:0.32
Consensus pattern (36 bp):
TGGTGGTGGCGAATTTGGTGGTACTGCTGGTGGAGA
Found at i:6600535 original size:18 final size:18
Alignment explanation
Indices: 6600514--6600577 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
6600504 CGAAGATGGA
6600514 GGTGGTGAGGAATTTTGT
1 GGTGGTGAGGAATTTTGT
** * *
6600532 GGTGGTGGAGGTGAAAATGGA
1 GGTGGT-GA-G-GAATTTTGT
*
6600553 GGTGGCGAGGAATTTTGT
1 GGTGGTGAGGAATTTTGT
6600571 GGTGGTG
1 GGTGGTG
6600578 GAGGTGGCGA
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
18 17 0.52
19 3 0.09
20 3 0.09
21 10 0.30
ACGTcount: A:0.19, C:0.02, G:0.50, T:0.30
Consensus pattern (18 bp):
GGTGGTGAGGAATTTTGT
Found at i:6600579 original size:27 final size:27
Alignment explanation
Indices: 6600549--6600610 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
6600539 GAGGTGAAAA
*
6600549 TGGAGGTGGCGAGGAATTTTGTGGTGG
1 TGGAGGTGGCGAGGAATTTCGTGGTGG
*
6600576 TGGAGGTGGCGATGAATTTCGTGGTGG
1 TGGAGGTGGCGAGGAATTTCGTGGTGG
*
6600603 TGGTGGTG
1 TGGAGGTG
6600611 ATGGCCTGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.13, C:0.05, G:0.52, T:0.31
Consensus pattern (27 bp):
TGGAGGTGGCGAGGAATTTCGTGGTGG
Found at i:6600582 original size:39 final size:39
Alignment explanation
Indices: 6600495--6600583 Score: 151
Period size: 39 Copynumber: 2.3 Consensus size: 39
6600485 TAGTTGGTGC
* * *
6600495 TGGTGGAGGCGAAGATGGAGGTGGTGAGGAATTTTGTGG
1 TGGTGGAGGTGAAAATGGAGGTGGCGAGGAATTTTGTGG
6600534 TGGTGGAGGTGAAAATGGAGGTGGCGAGGAATTTTGTGG
1 TGGTGGAGGTGAAAATGGAGGTGGCGAGGAATTTTGTGG
6600573 TGGTGGAGGTG
1 TGGTGGAGGTG
6600584 GCGATGAATT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.20, C:0.02, G:0.52, T:0.26
Consensus pattern (39 bp):
TGGTGGAGGTGAAAATGGAGGTGGCGAGGAATTTTGTGG
Found at i:6608198 original size:2 final size:2
Alignment explanation
Indices: 6608193--6608222 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6608183 AAAAAACATA
6608193 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
6608223 TAATTTAAAT
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:6608924 original size:16 final size:16
Alignment explanation
Indices: 6608902--6608943 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
6608892 TCGGGGGTTG
**
6608902 ATTTCGGTTTGAGTTA
1 ATTTCGGTTCAAGTTA
*
6608918 TTTTCGGTTCAAGTTA
1 ATTTCGGTTCAAGTTA
6608934 ATTTCGGTTC
1 ATTTCGGTTC
6608944 GGGTAAGTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.17, C:0.12, G:0.21, T:0.50
Consensus pattern (16 bp):
ATTTCGGTTCAAGTTA
Found at i:6610930 original size:23 final size:23
Alignment explanation
Indices: 6610876--6610934 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
6610866 TCTAGAATAC
**
6610876 TGACTGGAAATTCTGGAAGTTGG
1 TGACTGGACCTTCTGGAAGTTGG
6610899 TGACTGGACCTTCTGGAAGTTGG
1 TGACTGGACCTTCTGGAAGTTGG
6610922 TGACTGGACCTTC
1 TGACTGGACCTTC
6610935 AAGAAGCTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.17, G:0.32, T:0.31
Consensus pattern (23 bp):
TGACTGGACCTTCTGGAAGTTGG
Found at i:6610940 original size:23 final size:23
Alignment explanation
Indices: 6610891--6610940 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
6610881 GGAAATTCTG
**
6610891 GAAGTTGGTGACTGGACCTTCTG
1 GAAGTTGGTGACTGGACCTTCAA
6610914 GAAGTTGGTGACTGGACCTTCAA
1 GAAGTTGGTGACTGGACCTTCAA
6610937 GAAG
1 GAAG
6610941 CTACAACGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.34, T:0.26
Consensus pattern (23 bp):
GAAGTTGGTGACTGGACCTTCAA
Found at i:6613208 original size:175 final size:172
Alignment explanation
Indices: 6612917--6613258 Score: 540
Period size: 175 Copynumber: 2.0 Consensus size: 172
6612907 TCTCACTCTC
*
6612917 AAATTTTAAATGAAATCAATTTTAGGATTACACTTAGTAGGATACATTTTTAAAAAAATTATCGA
1 AAATTTTAAATGAAATCAATTTTAGGATTACACTTAGTAGGATACATTTTTAAAAAAATCATCGA
* * * * *
6612982 AAATGATTTTTTTATACCTTAAGACAATCACTTCAAAGTAATTTTAAATTAAAATGATATTACTC
66 AAATGACTTTCTTATACATTAAGACAACCACTTCAAAGGAATTTTAAATTAAAATGATATTACTC
6613047 TTAATCTAATTATTTTTACACAGAATAATTACACAGTTCAGTCTT
131 TTAATCT-A--ATTTTTACACAGAATAATTACACAGTTCAGTCTT
* ** *
6613092 AAATTTTAAATGAAATCAATTTTAGGATTACACTTAGTAGGATACTTTTTTTTAAAAATCATCGG
1 AAATTTTAAATGAAATCAATTTTAGGATTACACTTAGTAGGATACATTTTTAAAAAAATCATCGA
* **
6613157 AAATTACTTTCTTATACATTAAGACAACCACTTCACTGGAATTTTAAATTAAAATGATATTACTC
66 AAATGACTTTCTTATACATTAAGACAACCACTTCAAAGGAATTTTAAATTAAAATGATATTACTC
6613222 TTAATCTAATTTTTACACAGAATAATTACACAGTTCA
131 TTAATCTAATTTTTACACAGAATAATTACACAGTTCA
6613259 CATAATTTAT
Statistics
Matches: 154, Mismatches: 13, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
172 29 0.19
174 1 0.01
175 124 0.81
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (172 bp):
AAATTTTAAATGAAATCAATTTTAGGATTACACTTAGTAGGATACATTTTTAAAAAAATCATCGA
AAATGACTTTCTTATACATTAAGACAACCACTTCAAAGGAATTTTAAATTAAAATGATATTACTC
TTAATCTAATTTTTACACAGAATAATTACACAGTTCAGTCTT
Found at i:6615671 original size:18 final size:18
Alignment explanation
Indices: 6615648--6615682 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6615638 CAACAGCCAC
*
6615648 CGCAACCATTTATGATGT
1 CGCAACCATATATGATGT
6615666 CGCAACCATATATGATG
1 CGCAACCATATATGATG
6615683 CCACCGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (18 bp):
CGCAACCATATATGATGT
Found at i:6616020 original size:9 final size:9
Alignment explanation
Indices: 6616008--6616049 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
6615998 ACCTACTCAG
*
6616008 GACGACGAA
1 GACGACGAT
6616017 GACGACGAT
1 GACGACGAT
*
6616026 GACGACGAC
1 GACGACGAT
*
6616035 GACGATGAT
1 GACGACGAT
6616044 GACGAC
1 GACGAC
6616050 AGCGAGGAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.36, C:0.24, G:0.33, T:0.07
Consensus pattern (9 bp):
GACGACGAT
Found at i:6616035 original size:15 final size:15
Alignment explanation
Indices: 6616011--6616049 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
6616001 TACTCAGGAC
*
6616011 GACGAAGACGACGAT
1 GACGACGACGACGAT
6616026 GACGACGACGACGAT
1 GACGACGACGACGAT
*
6616041 GATGACGAC
1 GACGACGAC
6616050 AGCGAGGAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.36, C:0.23, G:0.33, T:0.08
Consensus pattern (15 bp):
GACGACGACGACGAT
Found at i:6616234 original size:26 final size:25
Alignment explanation
Indices: 6616165--6616234 Score: 60
Period size: 26 Copynumber: 2.8 Consensus size: 25
6616155 ATATTTGTAT
6616165 TTACTTTATTTTGTTAAATTATAATA
1 TTACTTTATTTTGTTAAATT-TAATA
*
6616191 -T--TTTATTATT-TCT-CATTTAATA
1 TTACTTTATT-TTGT-TAAATTTAATA
6616213 CTTACTTTATTTTGTTAAATTT
1 -TTACTTTATTTTGTTAAATTT
6616235 GTTGGACTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 16
0.65 0.04 0.31
Matches are distributed among these distances:
22 5 0.15
23 10 0.29
24 4 0.12
25 4 0.12
26 11 0.32
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.61
Consensus pattern (25 bp):
TTACTTTATTTTGTTAAATTTAATA
Found at i:6619623 original size:16 final size:14
Alignment explanation
Indices: 6619603--6619649 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 14
6619593 TATTTTTTTT
6619603 AAATAATCATAATAA
1 AAATAAT-ATAATAA
6619618 ACAATAAGTATAATAA
1 A-AATAA-TATAATAA
6619634 AAA-AATTATAATAA
1 AAATAA-TATAATAA
6619648 AA
1 AA
6619650 TTTATAACGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 12 0.41
15 3 0.10
16 13 0.45
17 1 0.03
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (14 bp):
AAATAATATAATAA
Found at i:6619645 original size:14 final size:15
Alignment explanation
Indices: 6619611--6619649 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
6619601 TTAAATAATC
6619611 ATAATAAACAATAAGT
1 ATAATAAA-AATAAGT
*
6619627 ATAATAAAAA-AATT
1 ATAATAAAAATAAGT
6619641 ATAATAAAA
1 ATAATAAAA
6619650 TTTATAACGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.55
15 2 0.09
16 8 0.36
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (15 bp):
ATAATAAAAATAAGT
Found at i:6623569 original size:20 final size:20
Alignment explanation
Indices: 6623543--6623647 Score: 121
Period size: 20 Copynumber: 5.5 Consensus size: 20
6623533 GATAGGAGGC
*
6623543 AGTCTTGCTGAATCCAGCAG
1 AGTCTTGCTGAATCAAGCAG
* * **
6623563 TGTCTTGCT-CATGTA-CA-
1 AGTCTTGCTGAATCAAGCAG
6623580 -GTCTTGCTGAATCAAGCAG
1 AGTCTTGCTGAATCAAGCAG
6623599 AGTCTTGCTGAATCAAGCAG
1 AGTCTTGCTGAATCAAGCAG
6623619 AGTCTTGCTGAATCAAGCAG
1 AGTCTTGCTGAATCAAGCAG
6623639 CA-TCTTGCT
1 -AGTCTTGCT
6623648 CATGTGCAAT
Statistics
Matches: 73, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
16 8 0.11
17 3 0.04
18 4 0.05
19 3 0.04
20 54 0.74
21 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (20 bp):
AGTCTTGCTGAATCAAGCAG
Found at i:6623589 original size:36 final size:36
Alignment explanation
Indices: 6623542--6623652 Score: 125
Period size: 36 Copynumber: 3.0 Consensus size: 36
6623532 TGATAGGAGG
* *
6623542 CAGTCTTGCTGAATCCAGCAGTGTCTTGCTCATGTA
1 CAGTCTTGCTGAATCAAGCAGAGTCTTGCTCATGTA
* *
6623578 CAGTCTTGCTGAATCAAGCAGAGTCTTGCTGAATCAAGCA
1 CAGTCTTGCTGAATCAAGCAGAGTCTTGC----TCATGTA
*
6623618 GAGTCTTGCTGAATCAAGCAGCA-TCTTGCTCATGT
1 CAGTCTTGCTGAATCAAGCAG-AGTCTTGCTCATGT
6623653 GCAATCCTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
36 31 0.49
40 31 0.49
41 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (36 bp):
CAGTCTTGCTGAATCAAGCAGAGTCTTGCTCATGTA
Found at i:6624861 original size:34 final size:30
Alignment explanation
Indices: 6624783--6624869 Score: 90
Period size: 31 Copynumber: 2.8 Consensus size: 30
6624773 TTTTTTTTTA
6624783 TTATT-TCGGGTCGGGT-CGGGTGAAACCT
1 TTATTCTCGGGTCGGGTCCGGGTGAAACCT
*
6624811 TAATTTCGTCGGGTCGGGTCACGGGTGAAAAACCCT
1 TTA-TTC-TCGGGTCGGGTC-CGGGTG--AAA-CCT
6624847 TTATTCTCGGGTCGGGT-CGGGTG
1 TTATTCTCGGGTCGGGTCCGGGTG
6624870 GCCCAAAAAC
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
28 2 0.04
29 2 0.04
31 11 0.22
32 6 0.12
33 6 0.12
34 11 0.22
35 6 0.12
36 5 0.10
ACGTcount: A:0.15, C:0.20, G:0.36, T:0.30
Consensus pattern (30 bp):
TTATTCTCGGGTCGGGTCCGGGTGAAACCT
Found at i:6634732 original size:64 final size:64
Alignment explanation
Indices: 6634664--6634844 Score: 204
Period size: 65 Copynumber: 2.8 Consensus size: 64
6634654 TTGGAACACT
* ** *
6634664 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAA-ATAGCC
1 TGATGCATCGATGCATGAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAT-GCA
*** * *
6634728 TGATGCATCGATGCATGTCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA
1 TGATGCATCGATGCATGAAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATATGCA
* * * *
6634793 T-AGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 TGA-TGCATCGATGCATGAAGTGTGCATCGATGCATGAAATGCATTCGATGTT
6634845 CAATTAATTC
Statistics
Matches: 98, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
64 46 0.47
65 50 0.51
66 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (64 bp):
TGATGCATCGATGCATGAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATATGCA
Found at i:6634818 original size:19 final size:18
Alignment explanation
Indices: 6634794--6634842 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
6634784 AAATATTCAT
6634794 AGTGCATCGATGCATGGA
1 AGTGCATCGATGCATGGA
*
6634812 GAGTGCATCGGTGCATGGA
1 -AGTGCATCGATGCATGGA
6634831 A-TGCATTCGATG
1 AGTGCA-TCGATG
6634843 TTCAATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 4 0.15
18 6 0.22
19 17 0.63
ACGTcount: A:0.24, C:0.16, G:0.35, T:0.24
Consensus pattern (18 bp):
AGTGCATCGATGCATGGA
Found at i:6635524 original size:17 final size:17
Alignment explanation
Indices: 6635502--6635545 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
6635492 AATAGTCAAG
*
6635502 CATCCAAATATCATAAA
1 CATCCAAATAACATAAA
*
6635519 CATCCAAACAAACATAAA
1 CATCCAAA-TAACATAAA
6635537 CATCCAAAT
1 CATCCAAAT
6635546 CAAAAAGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.55, C:0.27, G:0.00, T:0.18
Consensus pattern (17 bp):
CATCCAAATAACATAAA
Found at i:6635536 original size:18 final size:19
Alignment explanation
Indices: 6635513--6635549 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
6635503 ATCCAAATAT
6635513 CATAAACATCCAAA-CAAA
1 CATAAACATCCAAATCAAA
6635531 CATAAACATCCAAATCAAA
1 CATAAACATCCAAATCAAA
6635550 AAGTTTAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (19 bp):
CATAAACATCCAAATCAAA
Found at i:6641270 original size:22 final size:21
Alignment explanation
Indices: 6641228--6641267 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
6641218 GAGTTTGTTT
*
6641228 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
6641249 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
6641268 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:6643263 original size:64 final size:64
Alignment explanation
Indices: 6643195--6643375 Score: 218
Period size: 64 Copynumber: 2.8 Consensus size: 64
6643185 TTGGAACACT
* **
6643195 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
1 TGATGCATCGATGCATGAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
*** * * **
6643259 TGATGCATCGATGCATGTCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTAAAAATATTC
1 TGATGCATCGATGCATGAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
* * * * *
6643323 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 TGA-TGCATCGATGCATGAAGTGTGCATCGATGCATGAAATGCATTCGATGTT
6643376 CAATTAATTC
Statistics
Matches: 98, Mismatches: 18, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
64 56 0.57
65 42 0.43
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (64 bp):
TGATGCATCGATGCATGAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
Found at i:6643347 original size:19 final size:19
Alignment explanation
Indices: 6643323--6643373 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
6643313 AAAAATATTC
6643323 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
6643342 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
6643361 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
6643374 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:6643358 original size:65 final size:64
Alignment explanation
Indices: 6643216--6643424 Score: 217
Period size: 64 Copynumber: 3.2 Consensus size: 64
6643206 TGCACCAAGT
* ** * ****
6643216 GTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGATGCATCGATGCATGTCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAAATATTCAGATGCATCGATGCATGGAGA
* *
6643280 GTGCATCGATGCATCAAATGCATTCGATGTTTTAAAAATATTCAGAGTGCATCGATGCATGGAGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAAATATTCAGA-TGCATCGATGCATGGAGA
* * **
6643345 GTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTA-ATTCATCGATGCATCGATGCATGGAC
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAAATATTCA--GATGCATCGATGCATGGA-
6643408 TGA
63 -GA
*
6643411 -TGCATCGGTGCATG
1 GTGCATCGATGCATG
6643425 CCTTTGAATA
Statistics
Matches: 125, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
63 5 0.04
64 62 0.50
65 56 0.45
66 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAAATATTCAGATGCATCGATGCATGGAGA
Found at i:6649743 original size:23 final size:23
Alignment explanation
Indices: 6649712--6649774 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
6649702 TTCGTATTCG
* * *
6649712 ATTCATTTAGCATTCACGAACAT
1 ATTCGTTTAACATTCACAAACAT
* **
6649735 ATTCGTTTAACGTTCGTAAACAT
1 ATTCGTTTAACATTCACAAACAT
*
6649758 ATTCGTTTAACGTTCAC
1 ATTCGTTTAACATTCAC
6649775 TCTCTTTTCT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (23 bp):
ATTCGTTTAACATTCACAAACAT
Found at i:6652598 original size:31 final size:31
Alignment explanation
Indices: 6652557--6652663 Score: 108
Period size: 31 Copynumber: 3.4 Consensus size: 31
6652547 TAGTTTTTAT
6652557 TTTTTAAATTTGATTAATTTTATTTAGGTAC
1 TTTTTAAATTTGATTAATTTTATTTAGGTAC
* * * ** *
6652588 TTTTTGAATTTTAAGTTATACATTTATTT-TTTAT
1 TTTTT-AAATTTGA-TTA-A-TTTTATTTAGGTAC
6652622 TTTTTAAATTTGATTAATTTTATTTAGGTAC
1 TTTTTAAATTTGATTAATTTTATTTAGGTAC
*
6652653 TTTTTGAATTT
1 TTTTTAAATTT
6652664 TAAAATATCA
Statistics
Matches: 58, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
30 7 0.12
31 18 0.31
32 9 0.16
33 9 0.16
34 8 0.14
35 7 0.12
ACGTcount: A:0.27, C:0.03, G:0.08, T:0.62
Consensus pattern (31 bp):
TTTTTAAATTTGATTAATTTTATTTAGGTAC
Found at i:6652608 original size:65 final size:65
Alignment explanation
Indices: 6652534--6652666 Score: 257
Period size: 65 Copynumber: 2.0 Consensus size: 65
6652524 TTGTTATGTG
6652534 TAAGTTATACATTTAGTTTTTATTTTTTAAATTTGATTAATTTTATTTAGGTACTTTTTGAATTT
1 TAAGTTATACATTTAGTTTTTATTTTTTAAATTTGATTAATTTTATTTAGGTACTTTTTGAATTT
*
6652599 TAAGTTATACATTTATTTTTTATTTTTTAAATTTGATTAATTTTATTTAGGTACTTTTTGAATTT
1 TAAGTTATACATTTAGTTTTTATTTTTTAAATTTGATTAATTTTATTTAGGTACTTTTTGAATTT
6652664 TAA
1 TAA
6652667 AATATCACTC
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.29, C:0.03, G:0.08, T:0.60
Consensus pattern (65 bp):
TAAGTTATACATTTAGTTTTTATTTTTTAAATTTGATTAATTTTATTTAGGTACTTTTTGAATTT
Found at i:6656741 original size:57 final size:58
Alignment explanation
Indices: 6656671--6656785 Score: 180
Period size: 58 Copynumber: 2.0 Consensus size: 58
6656661 CGTAATCGTC
* * *
6656671 TGCAAAATTAT-A-AGAAATTATATCAGCTCAGATAAAATCATTTACCCAGAATCTGAA
1 TGCAAAATAATAAGAGAAACTATATCAGCTCAGAT-AAAGCATTTACCCAGAATCTGAA
6656728 TGCAAAATAATAAGAGAAACTATATCAGCTCAGATAAAGCATTTACCCAGAATCTGAA
1 TGCAAAATAATAAGAGAAACTATATCAGCTCAGATAAAGCATTTACCCAGAATCTGAA
6656786 CTTTTTCAGT
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
57 10 0.19
58 23 0.43
59 20 0.38
ACGTcount: A:0.46, C:0.17, G:0.12, T:0.25
Consensus pattern (58 bp):
TGCAAAATAATAAGAGAAACTATATCAGCTCAGATAAAGCATTTACCCAGAATCTGAA
Found at i:6658138 original size:18 final size:18
Alignment explanation
Indices: 6658115--6658149 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
6658105 GAGACATGTG
6658115 AAAAAATAAAATAAAATT
1 AAAAAATAAAATAAAATT
6658133 AAAAAATAAAATAAAAT
1 AAAAAATAAAATAAAAT
6658150 CACAACATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAAAATAAAATAAAATT
Found at i:6658639 original size:28 final size:28
Alignment explanation
Indices: 6658582--6658637 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
6658572 TTATTGTCTT
* *
6658582 TGCTTCTGTGCCTTTTGTTTTATTTGGG
1 TGCTTCTGTGCCTTTGGTTTGATTTGGG
* *
6658610 TGCTGTCTGTTCCTTTGGTTTGCTTTGG
1 TGCT-TCTGTGCCTTTGGTTTGATTTGG
6658638 TGTGTGGCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.02, C:0.16, G:0.27, T:0.55
Consensus pattern (28 bp):
TGCTTCTGTGCCTTTGGTTTGATTTGGG
Found at i:6663077 original size:20 final size:20
Alignment explanation
Indices: 6663022--6663082 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
6663012 AATTTATAAA
*
6663022 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* * * *
6663042 TCGTAACGCGATAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
6663062 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
6663082 T
1 T
6663083 TGCGAATTTG
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.43, C:0.23, G:0.15, T:0.20
Consensus pattern (20 bp):
TCGCAACACAAAAGTCAAAT
Found at i:6663156 original size:20 final size:19
Alignment explanation
Indices: 6663117--6663181 Score: 69
Period size: 20 Copynumber: 3.4 Consensus size: 19
6663107 ATAGTTAAAC
6663117 TCGCAACTGAATTTCAAAT
1 TCGCAACTGAATTTCAAAT
* *
6663136 TCGCAACTCGATTTTCGAAT
1 TCGCAACT-GAATTTCAAAT
* *
6663156 TCGCAACACGAATTT-AATT
1 TCGCAAC-TGAATTTCAAAT
6663175 TCGCAAC
1 TCGCAAC
6663182 AGGTTTTAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
19 17 0.45
20 21 0.55
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.31
Consensus pattern (19 bp):
TCGCAACTGAATTTCAAAT
Found at i:6663182 original size:19 final size:19
Alignment explanation
Indices: 6663155--6663201 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
6663145 GATTTTCGAA
6663155 TTCGCAACACGAATTTAAT
1 TTCGCAACACGAATTTAAT
**
6663174 TTCGCAACA-GGTTTTAAT
1 TTCGCAACACGAATTTAAT
*
6663192 TTTGCAACAC
1 TTCGCAACAC
6663202 AAATGTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (19 bp):
TTCGCAACACGAATTTAAT
Found at i:6663356 original size:14 final size:15
Alignment explanation
Indices: 6663337--6663374 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
6663327 TCCTCATCTC
6663337 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
6663351 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
6663367 TAATTTTT
1 TAATTTTT
6663375 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:6663990 original size:12 final size:12
Alignment explanation
Indices: 6663969--6664002 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6663959 ACCACATTTC
*
6663969 CAATACCAAACA
1 CAATATCAAACA
6663981 CAATATCAAACA
1 CAATATCAAACA
*
6663993 CAATCTCAAA
1 CAATATCAAA
6664003 ACCCACAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:6675788 original size:20 final size:20
Alignment explanation
Indices: 6675746--6675814 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
6675736 AAATCGTAAC
* * *
6675746 GCGAATTTGAATTTTGCTTT
1 GCGAATTTGACTTTCGCGTT
*
6675766 GCGAATTTGACTTTCGCGAT
1 GCGAATTTGACTTTCGCGTT
*
6675786 GCGAATTT-ACCTTTCGTGTT
1 GCGAATTTGA-CTTTCGCGTT
6675806 GCGAATTTG
1 GCGAATTTG
6675815 TACCTTCAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.02
20 40 0.98
ACGTcount: A:0.19, C:0.16, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTGACTTTCGCGTT
Found at i:6675924 original size:66 final size:64
Alignment explanation
Indices: 6675848--6675991 Score: 252
Period size: 66 Copynumber: 2.2 Consensus size: 64
6675838 AATTTAAAAC
6675848 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCGAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGC-AAAAAATAATTCTTATTTACACATC-AATT
6675913 A
64 A
* *
6675914 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
6675978 AACAAATCAACTTT
1 AACAAATCAACTTT
6675992 CAATGTAAAA
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
64 19 0.25
65 23 0.30
66 34 0.45
ACGTcount: A:0.50, C:0.18, G:0.02, T:0.30
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
Found at i:6677398 original size:21 final size:20
Alignment explanation
Indices: 6677374--6677467 Score: 89
Period size: 21 Copynumber: 4.5 Consensus size: 20
6677364 GAGGGACCCA
*
6677374 TTGAACGATGACAGGGGCCTC
1 TTGAACGAT-AGAGGGGCCTC
* *
6677395 TTGAATGGTAGGAGGGGCCTC
1 TTGAACGATA-GAGGGGCCTC
* *
6677416 TTGAATGATGAGAGGAGCCTC
1 TTGAACGAT-AGAGGGGCCTC
**
6677437 TTGAACGATAGGAGGCACCTC
1 TTGAACGATA-GAGGGGCCTC
6677458 TTGAACGATA
1 TTGAACGATA
6677468 ACAGGTGAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
20 2 0.03
21 59 0.95
22 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.33, T:0.22
Consensus pattern (20 bp):
TTGAACGATAGAGGGGCCTC
Found at i:6677409 original size:42 final size:42
Alignment explanation
Indices: 6677350--6677472 Score: 149
Period size: 42 Copynumber: 2.9 Consensus size: 42
6677340 GTGAATCAGG
* *
6677350 CTCTTGAACGGTGGGAGGGACC-CATTGAACGATGACAGGGGC
1 CTCTTGAACGGTAGGAGGGACCTC-TTGAACGATGACAGGAGC
* * * *
6677392 CTCTTGAATGGTAGGAGGGGCCTCTTGAATGATGAGAGGAGC
1 CTCTTGAACGGTAGGAGGGACCTCTTGAACGATGACAGGAGC
* * *
6677434 CTCTTGAACGATAGGAGGCACCTCTTGAACGATAACAGG
1 CTCTTGAACGGTAGGAGGGACCTCTTGAACGATGACAGG
6677473 TGAATCGTGC
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
42 66 0.99
43 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.34, T:0.20
Consensus pattern (42 bp):
CTCTTGAACGGTAGGAGGGACCTCTTGAACGATGACAGGAGC
Found at i:6677848 original size:63 final size:65
Alignment explanation
Indices: 6677781--6677920 Score: 157
Period size: 63 Copynumber: 2.2 Consensus size: 65
6677771 GTAAAGTAGA
* * *
6677781 TACCTCATCACGTAGC-GCACCATTATCATCACGTAAAATATCC-ACCTCATCATGTAAAG-ACC
1 TACCTCATCACGTACCAGCACCATTATCATCACGTAAAATA-CCGACCTCATCACGCAAAGCACC
6677843 G
65 G
* * * *
6677844 TACCTCATCAC--ACCATGCACCATTGTCTTCACGTAAAGTACCGACCTCATGACGCAAAGCACC
1 TACCTCATCACGTACCA-GCACCATTATCATCACGTAAAATACCGACCTCATCACGCAAAGCACC
6677907 G
65 G
6677908 -ACCTCATCACGTA
1 TACCTCATCACGTA
6677921 ACTCCCCTAA
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
61 2 0.03
62 2 0.03
63 55 0.86
64 4 0.06
65 1 0.02
ACGTcount: A:0.31, C:0.34, G:0.12, T:0.22
Consensus pattern (65 bp):
TACCTCATCACGTACCAGCACCATTATCATCACGTAAAATACCGACCTCATCACGCAAAGCACCG
Found at i:6679625 original size:20 final size:20
Alignment explanation
Indices: 6679602--6679676 Score: 56
Period size: 20 Copynumber: 4.1 Consensus size: 20
6679592 ACTTAAACTT
6679602 GCAACACGAAAATGAAAATC
1 GCAACACGAAAATGAAAATC
6679622 GC-A-ACG---A-GAAAATC
1 GCAACACGAAAATGAAAATC
**
6679636 GCAATGCGAAAATGAAAATC
1 GCAACACGAAAATGAAAATC
* * *
6679656 ACAACGCGAAACT-AAAATC
1 GCAACACGAAAATGAAAATC
6679675 GC
1 GC
6679677 GTTGCGATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
14 9 0.20
15 2 0.05
16 2 0.05
18 3 0.07
19 9 0.20
20 19 0.43
ACGTcount: A:0.51, C:0.21, G:0.17, T:0.11
Consensus pattern (20 bp):
GCAACACGAAAATGAAAATC
Found at i:6680079 original size:22 final size:22
Alignment explanation
Indices: 6680052--6680099 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
6680042 GGAGATAGAT
6680052 GGATTTCGTCGGAGATGGGGAC
1 GGATTTCGTCGGAGATGGGGAC
6680074 GGATTTCGTCGGAGATGGGGAC
1 GGATTTCGTCGGAGATGGGGAC
6680096 GGAT
1 GGAT
6680100 GTCGCCGTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.19, C:0.12, G:0.46, T:0.23
Consensus pattern (22 bp):
GGATTTCGTCGGAGATGGGGAC
Found at i:6680111 original size:22 final size:22
Alignment explanation
Indices: 6680052--6680111 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
6680042 GGAGATAGAT
* *
6680052 GGATTTCGTCGGAGATGGGGAC
1 GGATGTCGCCGGAGATGGGGAC
* *
6680074 GGATTTCGTCGGAGATGGGGAC
1 GGATGTCGCCGGAGATGGGGAC
*
6680096 GGATGTCGCCGTAGAT
1 GGATGTCGCCGGAGAT
6680112 AGTGAGAGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.18, C:0.15, G:0.43, T:0.23
Consensus pattern (22 bp):
GGATGTCGCCGGAGATGGGGAC
Found at i:6680302 original size:20 final size:20
Alignment explanation
Indices: 6680279--6680486 Score: 145
Period size: 20 Copynumber: 10.3 Consensus size: 20
6680269 GACTATCGCA
6680279 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTTTGTG
* ***
6680299 TTGCGAATTTGAAATTCAATG
1 TTGCGAATTTG-ACTTTTGTG
* ***
6680320 TTGCGAATTTGAAATTCAATG
1 TTGCGAATTTG-ACTTTTGTG
6680341 TTGCGAATTTGA-TTATTGTG
1 TTGCGAATTTGACTT-TTGTG
* *
6680361 GTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTTTGTG
*
6680381 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTTTGTG
* * *
6680401 TTGCG-ATTT-ACAGATTCGCG
1 TTGCGAATTTGAC--TTTTGTG
* * **
6680421 TTGCGAATTTAACTTTCGCA
1 TTGCGAATTTGACTTTTGTG
* *
6680441 TTGCGAATTTGACTATAGAT-
1 TTGCGAATTTGACTTTTG-TG
*
6680461 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTTTGTG
6680481 TTGCGA
1 TTGCGA
6680487 TTTACATATT
Statistics
Matches: 155, Mismatches: 24, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
18 2 0.01
19 7 0.05
20 101 0.65
21 43 0.28
22 2 0.01
ACGTcount: A:0.23, C:0.12, G:0.23, T:0.42
Consensus pattern (20 bp):
TTGCGAATTTGACTTTTGTG
Found at i:6680323 original size:21 final size:21
Alignment explanation
Indices: 6680297--6680352 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
6680287 TTGACTTTTG
6680297 TGTTGCGAATTTGAAATTCAA
1 TGTTGCGAATTTGAAATTCAA
6680318 TGTTGCGAATTTGAAATTCAA
1 TGTTGCGAATTTGAAATTCAA
6680339 TGTTGCGAATTTGA
1 TGTTGCGAATTTGA
6680353 TTATTGTGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.39
Consensus pattern (21 bp):
TGTTGCGAATTTGAAATTCAA
Found at i:6680424 original size:40 final size:39
Alignment explanation
Indices: 6680380--6680511 Score: 124
Period size: 40 Copynumber: 3.3 Consensus size: 39
6680370 TGACTTCTGT
*
6680380 GTTGCGAATTTGACTTATGTGTTGCGATTTACAGATTCGC
1 GTTGCGAATTTGACTT-TGTGTTGCGATTTACATATTCGC
* ** * *
6680420 GTTGCGAATTTAACTTTCGCATTGCGAATTTGAC-TA-TAGA
1 GTTGCGAATTTGACTTT-GTGTTGCG-ATTT-ACATATTCGC
*
6680460 TTTGCGAATTTGACTTCTGTGTTGCGATTTACATATTCGC
1 GTTGCGAATTTGACTT-TGTGTTGCGATTTACATATTCGC
* *
6680500 GTTTCGATTTTG
1 GTTGCGAATTTG
6680512 GAAACTGGGT
Statistics
Matches: 71, Mismatches: 15, Indels: 12
0.72 0.15 0.12
Matches are distributed among these distances:
38 2 0.03
39 7 0.10
40 54 0.76
41 6 0.08
42 2 0.03
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.42
Consensus pattern (39 bp):
GTTGCGAATTTGACTTTGTGTTGCGATTTACATATTCGC
Found at i:6682193 original size:15 final size:15
Alignment explanation
Indices: 6682173--6682207 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
6682163 ATATGCTCTA
6682173 TGTTTGTCACTCATC
1 TGTTTGTCACTCATC
6682188 TGTTTGTCACTCATC
1 TGTTTGTCACTCATC
6682203 TGTTT
1 TGTTT
6682208 TATTCTATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.11, C:0.23, G:0.14, T:0.51
Consensus pattern (15 bp):
TGTTTGTCACTCATC
Found at i:6689092 original size:111 final size:112
Alignment explanation
Indices: 6688893--6689225 Score: 517
Period size: 111 Copynumber: 3.0 Consensus size: 112
6688883 TTGTCGGTTT
* ** *
6688893 GTGTCGATACTTTATAAAAATATATTAATCGATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
6688958 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
* *
6689005 GTGTCGATAATTTATAAAAATGTATCGATCCATAATAATATAACAGGT-AAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * * *
6689069 GGGT-TATAAATGACAAAACAGGTAAATCACTATCGGATATATTGAAA
66 -GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
*
6689116 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * *
6689181 GGTCTATAAATAACAAAACAGGTAAAGCGCTACCATATATGTTGA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGA
6689226 TAGTAAGTAT
Statistics
Matches: 198, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
111 104 0.53
112 94 0.47
ACGTcount: A:0.47, C:0.13, G:0.15, T:0.25
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
Found at i:6689536 original size:182 final size:182
Alignment explanation
Indices: 6689229--6689728 Score: 750
Period size: 182 Copynumber: 2.8 Consensus size: 182
6689219 ATGTTGATAG
*
6689229 TAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAATAAAGTGTCGATACTT
1 TAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTT
* * *
6689294 TATAAAAATGTATCGATCCATTACAATATAACAGGTAAAAAAATGATAAAACCGGTCTCGAAATG
66 TATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAATCGGTCTCGAAATG
* * * *
6689359 GCAAAACCGATAAAGAGCTACCGGATATGTTAAAAGTGTCGATATTTTATTA
131 ACAAAACCGATAAAGAACTACCGAATATGTTAAAAGTGTCGATACTTTATTA
* * *
6689411 TAAGTATTGACACTTTTGGAATTTAAAAGAGAATAAGTTATAACGCCAATAAAGTGTCGATACTT
1 TAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTT
* * *
6689476 TATAAAAATGTATCAATCTATAACAATATAACAGGTAAAAATATGACAAAATCGGTCTCGAAATG
66 TATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAATCGGTCTCGAAATG
* * *
6689541 ACAAAATCGGTAAAGAACTACCGAATATGTTGAAAGTGTCGATACTTTATTA
131 ACAAAACCGATAAAGAACTACCGAATATGTTAAAAGTGTCGATACTTTATTA
* * * * * *
6689593 TAAGTATCGATATTTTTGAAATTTAAAAGAAAAGATGTTATAGCGTCAATAAAGTGTCGATACTT
1 TAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTT
** *
6689658 TAT-AAAATGTATCGATCCATAACAATATAACATTTAAAAATATGATAAAATTGGTCTCGAAATG
66 TATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAATCGGTCTCGAAATG
*
6689722 ATAAAAC
131 ACAAAAC
6689729 TGGTAGTAAA
Statistics
Matches: 284, Mismatches: 34, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
181 60 0.21
182 224 0.79
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.30
Consensus pattern (182 bp):
TAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTT
TATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAATCGGTCTCGAAATG
ACAAAACCGATAAAGAACTACCGAATATGTTAAAAGTGTCGATACTTTATTA
Found at i:6690926 original size:23 final size:23
Alignment explanation
Indices: 6690895--6690951 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
6690885 GTTCGTGTTC
* *
6690895 GTTCATTTAGCGTTCG-TAAACAT
1 GTTCGTTTAACGTTCGAT-AACAT
*
6690918 GTTCGTTTAACTTTCGATAACAT
1 GTTCGTTTAACGTTCGATAACAT
*
6690941 GTTTGTTTAAC
1 GTTCGTTTAAC
6690952 ATTAAATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 28 0.97
24 1 0.03
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.44
Consensus pattern (23 bp):
GTTCGTTTAACGTTCGATAACAT
Found at i:6692135 original size:60 final size:58
Alignment explanation
Indices: 6692039--6692228 Score: 161
Period size: 59 Copynumber: 3.2 Consensus size: 58
6692029 TTGTATCATA
** * * *
6692039 CATCCCTAATCTATGACCCTCATT-TCAAATTGGTCCTTAAACTTTTAAATATTTCAATTT
1 CATCCCTAAAATATGA-CTTCATTCT-AAATTGGTCCTCAAA-TTTTAAACATTTCAATTT
* *
6692099 CATCCCTAAAATATGACTATCATTCTAAATTAGTCCTCAAATATTT-AACATTTCATTTT
1 CATCCCTAAAATATGACT-TCATTCTAAATTGGTCCTCAAAT-TTTAAACATTTCAATTT
* * * * *
6692158 TATCCCCAAATTATGATCTTTATTCTAAATTGGTCCCCAAATTTTTTAAAACATTTCAATTT
1 CATCCCTAAAATATGA-CTTCATTCTAAATTGGTCCTCAAA--TTTT-AAACATTTCAATTT
*
6692220 AAT-CCTAAA
1 CATCCCTAAA
6692229 TTATACGTAT
Statistics
Matches: 106, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
59 45 0.42
60 40 0.38
61 7 0.07
62 14 0.13
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.41
Consensus pattern (58 bp):
CATCCCTAAAATATGACTTCATTCTAAATTGGTCCTCAAATTTTAAACATTTCAATTT
Found at i:6692443 original size:60 final size:60
Alignment explanation
Indices: 6692353--6692537 Score: 205
Period size: 60 Copynumber: 3.1 Consensus size: 60
6692343 TATTTGGATG
* * * *
6692353 AATTTGGGGATAAAATT-GAA-GATGCAAAAGTTTAAGGACCAATTTAGAATGATATTCAT
1 AATTTGGGGATGAAATTGGAATG-TTCAAAAGTTTAAGGACCAATTTAGAATGAGAGTCAT
* * * *
6692412 AGTTTGGGGGTGAAATTTGAATGTTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCAT
1 AATTTGGGGATGAAATTGGAATGTTCAAAAGTTTAAGGACCAATTTAGAATGAGAGTCAT
* * * * * *
6692472 AATTTTGGGATGAAATTGGAATGTTTAAAAGTTTAA-GAGCTAATTTAAAATGAGGGTTAT
1 AATTTGGGGATGAAATTGGAATGTTCAAAAGTTTAAGGA-CCAATTTAGAATGAGAGTCAT
6692532 AATTTG
1 AATTTG
6692538 AACACATGAT
Statistics
Matches: 107, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
59 16 0.15
60 90 0.84
61 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.34
Consensus pattern (60 bp):
AATTTGGGGATGAAATTGGAATGTTCAAAAGTTTAAGGACCAATTTAGAATGAGAGTCAT
Found at i:6699643 original size:14 final size:15
Alignment explanation
Indices: 6699624--6699653 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
6699614 ATTTATAATT
6699624 AAATCATAC-TTAAA
1 AAATCATACTTTAAA
6699638 AAATCATACTTTAAA
1 AAATCATACTTTAAA
6699653 A
1 A
6699654 TAATAATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATCATACTTTAAA
Found at i:6702435 original size:18 final size:18
Alignment explanation
Indices: 6702400--6702444 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
6702390 TTCTCTTATT
*
6702400 TTTATTTAAATTATTTTTA
1 TTTATTT-AATTACTTTTA
*
6702419 TTTATTTAATTGCTTTTA
1 TTTATTTAATTACTTTTA
6702437 -TTATTTAA
1 TTTATTTAA
6702445 ATATCTCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 8 0.33
18 9 0.38
19 7 0.29
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTATTTAATTACTTTTA
Found at i:6713261 original size:30 final size:30
Alignment explanation
Indices: 6713205--6713261 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
6713195 TTGATGAAAA
* *
6713205 ATTAATTTTATGTTCAAATATCAATTAAAG
1 ATTAATTTAATGTTCAAACATCAATTAAAG
*
6713235 ATTAATTTAATTGTTCGAACAT-AATTA
1 ATTAATTTAA-TGTTCAAACATCAATTA
6713262 TTTTTCAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 14 0.61
31 9 0.39
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (30 bp):
ATTAATTTAATGTTCAAACATCAATTAAAG
Found at i:6717254 original size:21 final size:20
Alignment explanation
Indices: 6717230--6717278 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
6717220 CTCTATTCTC
*
6717230 TTATTTTTATTTAAATTGCTT
1 TTATTTTTATTT-AATCGCTT
6717251 TTA--TTTATTTAATCGCTT
1 TTATTTTTATTTAATCGCTT
6717269 TTATTATTTA
1 TTATT-TTTA
6717279 AATATCTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 10 0.42
19 7 0.29
21 7 0.29
ACGTcount: A:0.24, C:0.06, G:0.04, T:0.65
Consensus pattern (20 bp):
TTATTTTTATTTAATCGCTT
Found at i:6717270 original size:18 final size:18
Alignment explanation
Indices: 6717235--6717279 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
6717225 TTCTCTTATT
*
6717235 TTTATTTAAATTGCTTTTA
1 TTTATTT-AATCGCTTTTA
6717254 TTTATTTAATCGCTTTTA
1 TTTATTTAATCGCTTTTA
6717272 -TTATTTAA
1 TTTATTTAA
6717280 ATATCTCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 8 0.32
18 10 0.40
19 7 0.28
ACGTcount: A:0.27, C:0.07, G:0.04, T:0.62
Consensus pattern (18 bp):
TTTATTTAATCGCTTTTA
Found at i:6717824 original size:94 final size:94
Alignment explanation
Indices: 6717661--6717883 Score: 308
Period size: 94 Copynumber: 2.4 Consensus size: 94
6717651 GGTACCAACA
*
6717661 AGGTAGTATCGATACCATGGTAAGGGTATCGATACCAAGTAACATCAAACCTAATTTTGGTATCG
1 AGGTAGTATCGATACCATGGTAAGGGTATCGATACCAAGCAACATCAAACCTAATTTTGGTATCG
** *
6717726 ATACCAG-AGAGGGTATCGGTACTATAGAAT
66 ATACCAGAAGAGGGTATCAATACCAT--AAT
* * *
6717756 A-GTAGTATCGATACCATGGTAAGGGTATCGATACCAAGCCACATCGAATCTAATTTTGGTATCG
1 AGGTAGTATCGATACCATGGTAAGGGTATCGATACCAAGCAACATCAAACCTAATTTTGGTATCG
* *
6717820 ATACCGGAAGGGGGTATCAATACCATAAT
66 ATACCAGAAGAGGGTATCAATACCATAAT
6717849 AGGGTAGTATCGATACCATGGT-AGGAGTATCGATA
1 A-GGTAGTATCGATACCATGGTAAGG-GTATCGATA
6717884 GTGAAGAACC
Statistics
Matches: 115, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
93 4 0.03
94 68 0.59
95 43 0.37
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (94 bp):
AGGTAGTATCGATACCATGGTAAGGGTATCGATACCAAGCAACATCAAACCTAATTTTGGTATCG
ATACCAGAAGAGGGTATCAATACCATAAT
Found at i:6717864 original size:22 final size:20
Alignment explanation
Indices: 6717833--6717883 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 20
6717823 CCGGAAGGGG
*
6717833 GTATCAATACCATAATAGGGTA
1 GTATCGATACCATAATA-GG-A
**
6717855 GTATCGATACCATGGTAGGA
1 GTATCGATACCATAATAGGA
6717875 GTATCGATA
1 GTATCGATA
6717884 GTGAAGAACC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 10 0.38
21 2 0.08
22 14 0.54
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (20 bp):
GTATCGATACCATAATAGGA
Done.