Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold99
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: 1377724
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 13826 characters in sequence are not A, C, G, or T
File 5 of 10
Found at i:536599 original size:21 final size:21
Alignment explanation
Indices: 536566--536610 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
536556 TTGCAAGTTG
*
536566 AAATAAAGAAGTTCGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
536588 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
536608 AAA
1 AAA
536611 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.07, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:538435 original size:15 final size:15
Alignment explanation
Indices: 538415--538445 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
538405 TAAAAATGTC
*
538415 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
538430 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
538445 C
1 C
538446 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:540484 original size:20 final size:20
Alignment explanation
Indices: 540459--540536 Score: 66
Period size: 20 Copynumber: 3.6 Consensus size: 20
540449 AATGTCCAAA
540459 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATGTTTCT
* * *
540479 ATGTATCAATACATCTGGAAATTCA
1 ATGTATCGATACA--T-G--TTTCT
*
540504 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATGTTTCT
*
540524 TTGTATCGATACA
1 ATGTATCGATACA
540537 GGGTGATTAT
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
20 27 0.60
22 1 0.02
23 2 0.04
25 15 0.33
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATGTTTCT
Found at i:540700 original size:20 final size:20
Alignment explanation
Indices: 540657--540702 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
540647 AAATCTTTTG
540657 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
540678 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
540698 CAAAA
1 CAAAA
540703 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:543108 original size:13 final size:13
Alignment explanation
Indices: 543090--543115 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
543080 TACAGCAAGT
543090 ATGTATCGATACA
1 ATGTATCGATACA
543103 ATGTATCGATACA
1 ATGTATCGATACA
543116 CAAAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:546098 original size:13 final size:13
Alignment explanation
Indices: 546080--546105 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
546070 CAATTTTTTG
546080 TGTATCGATACAT
1 TGTATCGATACAT
546093 TGTATCGATACAT
1 TGTATCGATACAT
546106 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:546117 original size:32 final size:33
Alignment explanation
Indices: 546060--546123 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
546050 TACAAGCCAA
**
546060 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
546093 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
546124 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:546189 original size:97 final size:97
Alignment explanation
Indices: 546059--546288 Score: 401
Period size: 97 Copynumber: 2.4 Consensus size: 97
546049 TTACAAGCCA
*
546059 ATGTATCGATACAAT-TTTTT-GTGTATCGATACATTGTATCGATACATACTTTGTGTATCGATA
1 ATGTATCGATAC-ATCTTTTTCATGTATCGATACATTGTATCGATACATACTTTGTGTATCGATA
* *
546122 CAAGTTTGGCTACTGCCACGAAATCCCAATGAC
65 CAAGTTTGGCTACTACCAAGAAATCCCAATGAC
*
546155 ATGTATCGATACATCTTTTTCATGTATCGATACATTGTATCGATACATACTTTGTGTATTGATAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGTATCGATACATACTTTGTGTATCGATAC
546220 AAGTTTGGCTACTACCAAGAAATCCCAATGAC
66 AAGTTTGGCTACTACCAAGAAATCCCAATGAC
546252 ATGTATCGATACATCTTTTTCATGTATCGATACATTG
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTG
546289 CAACATGTAT
Statistics
Matches: 128, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
95 2 0.02
96 17 0.13
97 109 0.85
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (97 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGTATCGATACATACTTTGTGTATCGATAC
AAGTTTGGCTACTACCAAGAAATCCCAATGAC
Found at i:546195 original size:13 final size:13
Alignment explanation
Indices: 546177--546202 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
546167 ATCTTTTTCA
546177 TGTATCGATACAT
1 TGTATCGATACAT
546190 TGTATCGATACAT
1 TGTATCGATACAT
546203 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:554960 original size:13 final size:13
Alignment explanation
Indices: 554938--554995 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
554928 GGCAGTAGCT
*
554938 TTGTAGCGATACA
1 TTGTATCGATACA
554951 TTGTATCGATACAACA
1 TTGTATCGAT---ACA
554967 CTTATGTATCGATACA
1 --T-TGTATCGATACA
554983 TTGTATCGATACA
1 TTGTATCGATACA
554996 ATACTTATGT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:554985 original size:32 final size:32
Alignment explanation
Indices: 554939--555016 Score: 138
Period size: 32 Copynumber: 2.4 Consensus size: 32
554929 GCAGTAGCTT
*
554939 TGTAGCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
*
554971 TGTATCGATACATTGTATCGATACAATACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
555003 TGTATCGATACATT
1 TGTATCGATACATT
555017 TACTGTTTGT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAACACTTA
Found at i:555029 original size:21 final size:19
Alignment explanation
Indices: 554951--555036 Score: 76
Period size: 19 Copynumber: 4.7 Consensus size: 19
554941 TAGCGATACA
*
554951 TTGTATCGATACAACACTT
1 TTGTATCGATACAATACTT
*
554970 ATGTATCGATAC---A---
1 TTGTATCGATACAATACTT
554983 TTGTATCGATACAATACTT
1 TTGTATCGATACAATACTT
* *
555002 ATGTATCGATACATTTACTGT
1 TTGTATCGATACA-ATACT-T
555023 TTGTATCGATACAA
1 TTGTATCGATACAA
555037 ATTGTTGAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 11 0.21
16 2 0.04
19 23 0.43
20 4 0.08
21 13 0.25
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (19 bp):
TTGTATCGATACAATACTT
Found at i:558217 original size:50 final size:51
Alignment explanation
Indices: 558123--558218 Score: 133
Period size: 50 Copynumber: 1.9 Consensus size: 51
558113 ATCGATATTC
*
558123 AATGTATCAATACATCTGAGTTAAAAATCAGAATGTATCGATACAATGAAG
1 AATGTATCAATACATCTGAGTTAAAAACCAGAATGTATCGATACAATGAAG
** *
558174 AATGTATTGATACATCTG-G-TAAAAACCCAGAATGTATTGATACAA
1 AATGTATCAATACATCTGAGTTAAAAA-CCAGAATGTATCGATACAA
558219 ACAGTAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
49 6 0.15
50 18 0.45
51 16 0.40
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (51 bp):
AATGTATCAATACATCTGAGTTAAAAACCAGAATGTATCGATACAATGAAG
Found at i:558226 original size:30 final size:30
Alignment explanation
Indices: 558172--558228 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
558162 GATACAATGA
* *
558172 AGAATGTATTGATACATCTGGTAAAAACCC
1 AGAATGTATTGATACAACTAGTAAAAACCC
558202 AGAATGTATTGATACAAAC-AGTAAAAA
1 AGAATGTATTGATAC-AACTAGTAAAAA
558229 TTTAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (30 bp):
AGAATGTATTGATACAACTAGTAAAAACCC
Found at i:558296 original size:21 final size:21
Alignment explanation
Indices: 558255--558329 Score: 120
Period size: 21 Copynumber: 3.7 Consensus size: 21
558245 GTTAGGACCT
*
558255 TGTATCGATACA-TT--CAAA
1 TGTATCGATACATTTAAGAAA
558273 TGTATCGATACATTTAAGAAA
1 TGTATCGATACATTTAAGAAA
558294 TGTATCGATACATTTAAGAAA
1 TGTATCGATACATTTAAGAAA
558315 TGTATCGATACATTT
1 TGTATCGATACATTT
558330 GAACAAAAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
18 12 0.23
19 2 0.04
21 39 0.74
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTAAGAAA
Found at i:561837 original size:51 final size:51
Alignment explanation
Indices: 561779--561890 Score: 170
Period size: 51 Copynumber: 2.2 Consensus size: 51
561769 TTTGCCTGCT
*
561779 TGTATCGATACATCTGGGTAAAAAACCAAAATGTATCGATACAATGAACAA
1 TGTATCGATACATCTAGGTAAAAAACCAAAATGTATCGATACAATGAACAA
* * * * *
561830 TGTATCGATACATCTAGGTAAAAAGCTAGAATGTATTGATACAATGAATAA
1 TGTATCGATACATCTAGGTAAAAAACCAAAATGTATCGATACAATGAACAA
561881 TGTATCGATA
1 TGTATCGATA
561891 AAAACAGTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (51 bp):
TGTATCGATACATCTAGGTAAAAAACCAAAATGTATCGATACAATGAACAA
Found at i:563100 original size:13 final size:13
Alignment explanation
Indices: 563082--563107 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
563072 CAATTTTTTG
563082 TGTATCGATACAT
1 TGTATCGATACAT
563095 TGTATCGATACAT
1 TGTATCGATACAT
563108 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:563803 original size:61 final size:61
Alignment explanation
Indices: 563701--563837 Score: 177
Period size: 61 Copynumber: 2.2 Consensus size: 61
563691 AAAGATGATG
* * * * *
563701 AAGACGAGAAGAGTGATAAAGATGCCAATATGCTAATTCAAGGTCAGCGATATT-GGACTTA
1 AAGATGAGAAGAATGACAAAGATGCAAATATGCTAATTCAAGGCCAGCGATATTGGGA-TTA
* * *
563762 AAGATGAGAAGAATGACAAAGGTGCAAATATGTTGATTCAAGGCCAGCGATATTGGGATTA
1 AAGATGAGAAGAATGACAAAGATGCAAATATGCTAATTCAAGGCCAGCGATATTGGGATTA
*
563823 AAGATGCGAAGAATG
1 AAGATGAGAAGAATG
563838 CCAATGTGCT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
61 63 0.95
62 3 0.05
ACGTcount: A:0.40, C:0.11, G:0.27, T:0.22
Consensus pattern (61 bp):
AAGATGAGAAGAATGACAAAGATGCAAATATGCTAATTCAAGGCCAGCGATATTGGGATTA
Found at i:563919 original size:52 final size:52
Alignment explanation
Indices: 563797--563920 Score: 142
Period size: 52 Copynumber: 2.4 Consensus size: 52
563787 AAATATGTTG
* * * * *
563797 ATTCAAGGCCAGCGATATTGGGATTAAAGATGCGAAGAATGCCAATGTGCTG
1 ATTCAAGGCCAGCGACATTGAGATTAAAGATGAGAAGAATACCAATGTGCTA
* * * * *
563849 ATTCACGACCGGCAACATT-AGACTTGAAGATGAGAAGAATACCAATGTGCTA
1 ATTCAAGGCCAGCGACATTGAGA-TTAAAGATGAGAAGAATACCAATGTGCTA
563901 ATTCAAGGCCAGCGACATTG
1 ATTCAAGGCCAGCGACATTG
563921 GGTTTAAGAA
Statistics
Matches: 56, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
51 2 0.04
52 54 0.96
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.22
Consensus pattern (52 bp):
ATTCAAGGCCAGCGACATTGAGATTAAAGATGAGAAGAATACCAATGTGCTA
Found at i:564071 original size:32 final size:32
Alignment explanation
Indices: 564035--564438 Score: 513
Period size: 32 Copynumber: 12.7 Consensus size: 32
564025 TTAAAAGAGA
*
564035 TGCCACCAACTTGTATGGGCTTTTGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAGGGT
* * *
564067 TGCCATCGACTTTTGTGGGCTTTTGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAGGGT
* * *
564099 TGCCACCGATTTGTGTGGGC-TTTAAGAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGA-AAGGGT
* **
564131 TGCCACCAACTTGTGT-GGATTTTAGAAAATGT
1 TGCCACCAACTTGTGTGGGCTTTT-GAAAGGGT
564163 TGCCACCAACTTGTGTGGGC-TTTGAAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTG-AAAGGGT
*
564195 TGCCACCAACTTGTGTGGGCTTTTG-AAGAGAT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAG-GGT
*
564227 TGCCACCAACTTGTGTGGGCTTTAGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAGGGT
* *
564259 TGCCACCAACTTTTGTGGGC-TTTGAAGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAA-AGGGT
564291 TGCCACCAACTTGTGTGGGC-TTTGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAGGGT
564322 TGCCACCAACTTGTGT-GGCTTTTG-AAGAGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAG-GGT
*
564353 TGCCACCAACTTGTGTGGGC-TTTGAAGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAA-AGGGT
*
564385 TGCCCCCAACTTGTGTGGGC-TTTGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAGGGT
* *
564416 TGCCGCCGACTTGTGTGGGCTTT
1 TGCCACCAACTTGTGTGGGCTTT
564439 GGAGAAGGTT
Statistics
Matches: 327, Mismatches: 30, Indels: 30
0.84 0.08 0.08
Matches are distributed among these distances:
30 6 0.02
31 84 0.26
32 226 0.69
33 11 0.03
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.31
Consensus pattern (32 bp):
TGCCACCAACTTGTGTGGGCTTTTGAAAGGGT
Found at i:564685 original size:28 final size:28
Alignment explanation
Indices: 564620--564691 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
564610 TGTACAGCAA
*
564620 GTGCCACTGA-TTATGGACTTCGAAAAG
1 GTGCCACTGACTTGTGGACTTCGAAAAG
* * *
564647 ATGGCACTGACTTGTGGACTTCGAAGAG
1 GTGCCACTGACTTGTGGACTTCGAAAAG
* *
564675 GTGCCATTGACTAGTGG
1 GTGCCACTGACTTGTGG
564692 GCTTTGAGAA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
27 8 0.22
28 28 0.78
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (28 bp):
GTGCCACTGACTTGTGGACTTCGAAAAG
Found at i:565965 original size:1 final size:1
Alignment explanation
Indices: 565961--566033 Score: 56
Period size: 1 Copynumber: 73.0 Consensus size: 1
565951 GTTGTTGTAG
* * * * * * * * *
565961 TTTTTTTGTGTTTTTTGTTTTTTTTTGTTTTTTTTTGTTTTTATTTTTTTTTGTTTTTGTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
566026 TTTGTTTT
1 TTTTTTTT
566034 ACGAAGGATG
Statistics
Matches: 52, Mismatches: 20, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.01, C:0.01, G:0.11, T:0.86
Consensus pattern (1 bp):
T
Found at i:565973 original size:10 final size:10
Alignment explanation
Indices: 565942--566033 Score: 96
Period size: 10 Copynumber: 9.0 Consensus size: 10
565932 TCTTCCCTTC
*
565942 TTTTTGTTTG
1 TTTTTGTTTT
* *
565952 TTGTTGTAGTT
1 TTTTTGT-TTT
*
565963 TTTTTG-TGT
1 TTTTTGTTTT
565972 TTTTTGTTTT
1 TTTTTGTTTT
565982 TTTTTGTTTT
1 TTTTTGTTTT
565992 TTTTTGTTTT
1 TTTTTGTTTT
*
566002 TATTTTTTTTT
1 T-TTTTGTTTT
*
566013 GTTTTTGTCTT
1 -TTTTTGTTTT
566024 TTTTTGTTTT
1 TTTTTGTTTT
566034 ACGAAGGATG
Statistics
Matches: 67, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
9 7 0.10
10 38 0.57
11 21 0.31
12 1 0.01
ACGTcount: A:0.02, C:0.01, G:0.14, T:0.83
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:565974 original size:7 final size:6
Alignment explanation
Indices: 565942--566033 Score: 51
Period size: 5 Copynumber: 16.7 Consensus size: 6
565932 TCTTCCCTTC
* * *
565942 TTTTTG TTTGTTG TTGTAG -TTTT- TTTGTG TTTTT- TGTTTT- TTTTTG
1 TTTTTG TTT-TTG TTTTTG TTTTTG TTTTTG TTTTTG T-TTTTG TTTTTG
* *
565988 -TTTT- TTTTTG TTTTT- ATTTT- TTTTTG TTTTTG -TCTT- TTTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
566030 TTTT
1 TTTT
566034 ACGAAGGATG
Statistics
Matches: 66, Mismatches: 10, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
5 32 0.48
6 29 0.44
7 5 0.08
ACGTcount: A:0.02, C:0.01, G:0.14, T:0.83
Consensus pattern (6 bp):
TTTTTG
Found at i:565980 original size:17 final size:17
Alignment explanation
Indices: 565960--566033 Score: 71
Period size: 17 Copynumber: 4.3 Consensus size: 17
565950 TGTTGTTGTA
565960 GTTTTTTTGTGTTTTTT
1 GTTTTTTTGTGTTTTTT
*
565977 GTTTTTTTTTGTTTTTT
1 GTTTTTTTGTGTTTTTT
*
565994 -TTTGTTTT-TATTTTTT
1 GTTT-TTTTGTGTTTTTT
* *
566010 TTTGTTTTTGTCTTTTTTT
1 GTT-TTTTTGT-GTTTTTT
566029 GTTTT
1 GTTTT
566034 ACGAAGGATG
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
16 10 0.21
17 26 0.54
18 4 0.08
19 8 0.17
ACGTcount: A:0.01, C:0.01, G:0.12, T:0.85
Consensus pattern (17 bp):
GTTTTTTTGTGTTTTTT
Found at i:565981 original size:16 final size:14
Alignment explanation
Indices: 565961--566033 Score: 76
Period size: 16 Copynumber: 5.0 Consensus size: 14
565951 GTTGTTGTAG
*
565961 TTTTTTTGTGTTTT
1 TTTTTTTTTGTTTT
* *
565975 TTGTTTTTT-TTTG
1 TTTTTTTTTGTTTT
565988 TTTTTTTTTGTTTTT
1 TTTTTTTTTG-TTTT
566003 ATTTTTTTTTGTTTT
1 -TTTTTTTTTGTTTT
566018 TGTCTTTTTTTGTTTT
1 T-T-TTTTTTTGTTTT
566034 ACGAAGGATG
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
13 11 0.22
14 8 0.16
15 8 0.16
16 22 0.45
ACGTcount: A:0.01, C:0.01, G:0.11, T:0.86
Consensus pattern (14 bp):
TTTTTTTTTGTTTT
Found at i:571426 original size:102 final size:104
Alignment explanation
Indices: 571250--571485 Score: 327
Period size: 102 Copynumber: 2.3 Consensus size: 104
571240 TTAAGTTTCT
* * *
571250 CAATTTTTCATAATCGGGGGTACTCCAA-CCTCGGTTTTATTCCTAAAACACTAATTTTCCACAA
1 CAATTTTTCACAATCGGGGATACTCCAACCCTCGGTTTTATTCCTAAAACACCAATTTTCCACAA
* *
571314 TCGGGGATACTCCAACTCCGATTTTATTTTC-AAAACAC
66 TCCGGGATACTCCAACTCCGATTTTATTTGCAAAAACAC
* * * * * *
571352 CAATTTTCCACAATTGGGGATAGTCCAACCCT-GGTTTTATT-TTCAAAACACCAATTTTCTATA
1 CAATTTTTCACAATCGGGGATACTCCAACCCTCGGTTTTATTCCT-AAAACACCAATTTTCCACA
571415 ATCCGGGATACTCCAACTCCGATTTTATTTGCAAAAACAC
65 ATCCGGGATACTCCAACTCCGATTTTATTTGCAAAAACAC
*
571455 CAATTTTTCACAATCGGGGACACTCCAACCC
1 CAATTTTTCACAATCGGGGATACTCCAACCC
571486 CGTTAATCAT
Statistics
Matches: 116, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
101 1 0.01
102 78 0.67
103 37 0.32
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (104 bp):
CAATTTTTCACAATCGGGGATACTCCAACCCTCGGTTTTATTCCTAAAACACCAATTTTCCACAA
TCCGGGATACTCCAACTCCGATTTTATTTGCAAAAACAC
Found at i:571480 original size:52 final size:50
Alignment explanation
Indices: 571250--571485 Score: 269
Period size: 51 Copynumber: 4.6 Consensus size: 50
571240 TTAAGTTTCT
* * * *
571250 CAATTTTTCATAATCGGGGGTACTCCAACCTCGGTTTTA-TTCCTAAAACAC
1 CAATTTTTCACAATCGGGGATACTCCAACC-CGATTTTATTTTC-AAAACAC
* *
571301 TAATTTTCCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACAC
1 CAATTTTTCACAATCGGGGATACTCCAAC-CCGATTTTATTTTCAAAACAC
* * * *
571352 CAATTTTCCACAATTGGGGATAGTCCAACCCTGGTTTTATTTTCAAAACAC
1 CAATTTTTCACAATCGGGGATACTCCAACCC-GATTTTATTTTCAAAACAC
* * *
571403 CAA-TTTTCTATAATCCGGGATACTCCAACTCCGATTTTATTTGCAAAAACAC
1 CAATTTTTC-ACAATCGGGGATACTCCAAC-CCGATTTTATTTTC-AAAACAC
*
571455 CAATTTTTCACAATCGGGGACACTCCAACCC
1 CAATTTTTCACAATCGGGGATACTCCAACCC
571486 CGTTAATCAT
Statistics
Matches: 158, Mismatches: 20, Indels: 14
0.82 0.10 0.07
Matches are distributed among these distances:
50 6 0.04
51 114 0.72
52 33 0.21
53 5 0.03
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (50 bp):
CAATTTTTCACAATCGGGGATACTCCAACCCGATTTTATTTTCAAAACAC
Found at i:571577 original size:79 final size:79
Alignment explanation
Indices: 571494--571779 Score: 419
Period size: 79 Copynumber: 3.6 Consensus size: 79
571484 CCCGTTAATC
* * **
571494 ATCGGGGATACTCCAACCCCGTTATTTCCAAAGGGATACTCCAACCCCGGCTTTATTTTTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAAT
571559 ATTGATTTCTCACA
66 ATTGATTTCTCACA
* *
571573 ATCGGGAATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAAT
571638 ATTGATTTCTCACA
66 ATTGATTTCTCACA
** * *
571652 ATCGGGGATACTCCAACGTCGTTATTTCTGAGGGGATACTCCAACCCCGGTTTTATTCCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAAT
571717 ATTGATTTCTCACA
66 ATTGATTTCTCACA
* * ** ** *
571731 ATCGAGGATACCCCAACCCTATTATTTTTGCGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCG
571780 TTATTTTTGA
Statistics
Matches: 187, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
79 187 1.00
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.30
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAAT
ATTGATTTCTCACA
Found at i:571776 original size:28 final size:28
Alignment explanation
Indices: 571736--571806 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
571726 TCACAATCGA
* *
571736 GGATACCCCAACCCTATTATTTTTGCGG
1 GGATACTCCAACCCTATTATTTTTGAGG
**
571764 GGATACTCCAACCCCGTTATTTTTGAGG
1 GGATACTCCAACCCTATTATTTTTGAGG
*
571792 TGATACTCCAACCCT
1 GGATACTCCAACCCT
571807 GATTTTATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.31
Consensus pattern (28 bp):
GGATACTCCAACCCTATTATTTTTGAGG
Found at i:571847 original size:107 final size:107
Alignment explanation
Indices: 571654--571856 Score: 241
Period size: 107 Copynumber: 1.9 Consensus size: 107
571644 TTCTCACAAT
** * * *
571654 CGGGGATACTCCAACGTCGTTATTTCTGAGGGGATACTCCAACCCCGGTTTTATTCCTAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGATTTTATTCCTAAAACAC
* *
571719 TGATTTCTCACAATCGAGGATACCCCAACCCTATTATTTTTG
66 TAATTTCTCACAATAGAGGATACCCCAACCCTATTATTTTTG
* * * *
571761 CGGGGATACTCCAACCCCGTTATTTTTGAGGTGATACTCCAACCCTGATTTTATT-TTCAAAACA
1 CGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGATTTTATTCCT-AAAACA
* *
571825 CTAATTT-TCTATAATTAG-GGATACTCCAACCC
65 CTAATTTCTC-ACAA-TAGAGGATACCCCAACCC
571857 CAATTTTATT
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
106 3 0.04
107 75 0.94
108 2 0.03
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (107 bp):
CGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGATTTTATTCCTAAAACAC
TAATTTCTCACAATAGAGGATACCCCAACCCTATTATTTTTG
Found at i:571853 original size:51 final size:51
Alignment explanation
Indices: 571793--571908 Score: 153
Period size: 51 Copynumber: 2.3 Consensus size: 51
571783 TTTTTGAGGT
** * *
571793 GATACTCCAACCCTGATTTTATTTTCAAAACA-CTAATTTTCTATAATTAGG
1 GATACTCCAACCCCAATTTTATTTCCAAAACATC-AATTTTCCATAATTAGG
* *
571844 GATACTCCAACCCCAATTTTATTTCCAGAACATCGATTTTCCATAATTAGG
1 GATACTCCAACCCCAATTTTATTTCCAAAACATCAATTTTCCATAATTAGG
*
571895 GATACTCCAGCCCC
1 GATACTCCAACCCC
571909 GTCCTCATCT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
51 56 0.98
52 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.34
Consensus pattern (51 bp):
GATACTCCAACCCCAATTTTATTTCCAAAACATCAATTTTCCATAATTAGG
Found at i:571934 original size:51 final size:51
Alignment explanation
Indices: 571818--571934 Score: 119
Period size: 51 Copynumber: 2.3 Consensus size: 51
571808 ATTTTATTTT
* * * * *
571818 CAAAACACTAATTTTCTATAATTAGGGATACTCCAACCCCAATTTTATTTC
1 CAAAACATTAATTTTCCATAATTAGGGATACTCCAACCCCAATCTCATCTC
* ** * *
571869 CAGAACATCGATTTTCCATAATTAGGGATACTCCAGCCCC-GTCCTCATCTC
1 CAAAACATTAATTTTCCATAATTAGGGATACTCCAACCCCAAT-CTCATCTC
*
571920 CAAAATATTAATTTT
1 CAAAACATTAATTTT
571935 TTTTTGTCGG
Statistics
Matches: 51, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
50 1 0.02
51 50 0.98
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.33
Consensus pattern (51 bp):
CAAAACATTAATTTTCCATAATTAGGGATACTCCAACCCCAATCTCATCTC
Found at i:579901 original size:24 final size:24
Alignment explanation
Indices: 579874--579948 Score: 86
Period size: 23 Copynumber: 3.2 Consensus size: 24
579864 TCTCTTCTAA
*
579874 AAAAAAAACAACAAAAACAAAAGC
1 AAAAAAAACAAAAAAAACAAAAGC
*
579898 AAAAAAAA-AATAAAAACAAAA-C
1 AAAAAAAACAAAAAAAACAAAAGC
*
579920 -AAAAAAACAAAAAAAAAACAAAG-
1 AAAAAAAACAAAAAAAACA-AAAGC
579943 AAAAAA
1 AAAAAA
579949 GAGAGAAAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
21 7 0.16
22 9 0.20
23 15 0.34
24 13 0.30
ACGTcount: A:0.85, C:0.11, G:0.03, T:0.01
Consensus pattern (24 bp):
AAAAAAAACAAAAAAAACAAAAGC
Found at i:579906 original size:11 final size:11
Alignment explanation
Indices: 579874--579948 Score: 75
Period size: 11 Copynumber: 6.9 Consensus size: 11
579864 TCTCTTCTAA
579874 AAAAAAAACAAC
1 AAAAAAAA-AAC
*
579886 AAAAACAAAAGC
1 AAAAA-AAAAAC
*
579898 AAAAAAAAAAT
1 AAAAAAAAAAC
*
579909 AAAAACAAAAC
1 AAAAAAAAAAC
579920 ---AAAAAAAC
1 AAAAAAAAAAC
579928 AAAAAAAAAAC
1 AAAAAAAAAAC
*
579939 AAAGAAAAAA
1 AAAAAAAAAA
579949 GAGAGAAAAG
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
8 7 0.13
11 30 0.58
12 12 0.23
13 3 0.06
ACGTcount: A:0.85, C:0.11, G:0.03, T:0.01
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:579963 original size:1 final size:1
Alignment explanation
Indices: 579872--579948 Score: 55
Period size: 1 Copynumber: 77.0 Consensus size: 1
579862 ATTCTCTTCT
* * * ** * * * *
579872 AAAAAAAAAACAACAAAAACAAAAGCAAAAAAAAAATAAAAACAAAACAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
579937 ACAAAGAAAAAA
1 AAAAAAAAAAAA
579949 GAGAGAAAAG
Statistics
Matches: 55, Mismatches: 21, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.86, C:0.10, G:0.03, T:0.01
Consensus pattern (1 bp):
A
Found at i:581011 original size:61 final size:61
Alignment explanation
Indices: 580916--581578 Score: 736
Period size: 55 Copynumber: 11.4 Consensus size: 61
580906 TCCTTTCACT
*
580916 TTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAATTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACC
580977 TTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTC-AAGCCCACACAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACC
*
581037 TTTCAGTCCTCAAAGAGCAGGACG------CCTTTCAAAGCCCACACAAATTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACC
* *
581092 TTTCAGTCCTCAAAGAGCAGGA---C---ACCTTTCAAAGCCCACACAAGTTGGTGGCA-T
1 TTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACC
* *
581146 TTTCCAGTCCTCAAAGAGCAAGACGCC---T--TTT-AAAGCCCACACAAGTTGGTGGCA-T
1 TTT-CAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACC
* *
581201 TTTCCAGTCCTCCAAGAGCAGGACGCC---T--TTT-AAAGCCCACACAAGTTGGTGGCA-T
1 TTT-CAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACC
* * * *
581256 TTTCCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA-T
1 TTT-CAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACC
* *
581317 TTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTCCAAAGCCCACACGAGTTGGTGGCACC
1 TTTC-AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACC
* * * *
581379 TTTCTGTCCTCAAAAAGTAGGACGCC---T--TTT-AAAGCCCACACGAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACC
* * * * * * *
581434 CTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACATAAGCTGGCGGCGCC
1 TTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACC
** * *
581495 -TTCAGTCCTCAAAGAGCAGGATACCTTTTCCTTT-AAAGCCCATACAAGTTGGTGGC-GC
1 TTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACC
* *
581553 TTCCCAGTCCTCAAAGAGCAAGACGC
1 TT-TCAGTCCTCAAAGAGCAGGACGC
581579 TCCCTCCTTT
Statistics
Matches: 536, Mismatches: 43, Indels: 47
0.86 0.07 0.08
Matches are distributed among these distances:
54 9 0.02
55 238 0.44
56 5 0.01
58 5 0.01
59 19 0.04
60 104 0.19
61 152 0.28
62 4 0.01
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (61 bp):
TTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACC
Found at i:581120 original size:26 final size:26
Alignment explanation
Indices: 581033--581122 Score: 76
Period size: 26 Copynumber: 3.3 Consensus size: 26
581023 AAGTTGGTGG
581033 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCTCAAAGAGCAGGA
* * * **
581059 CGCCTTTCAAAGCCCACACAA-ATTGGTGG-
1 CACCTTTC--AGTCCTCA-AAGA--GCAGGA
581088 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCTCAAAGAGCAGGA
581114 CACCTTTCA
1 CACCTTTCA
581123 AAGCCCACAC
Statistics
Matches: 47, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
25 3 0.06
26 18 0.38
27 7 0.15
28 7 0.15
29 9 0.19
30 3 0.06
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (26 bp):
CACCTTTCAGTCCTCAAAGAGCAGGA
Found at i:581203 original size:27 final size:27
Alignment explanation
Indices: 581173--581258 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
581163 GCAAGACGCC
581173 TTTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTAAAGCCCACACAAGTTGGTGGCA
** ** ** *
581200 TTTTCCAGTCCTC-CA-AGAGCAGGACGCC
1 TTTTAAAG-CC-CACACA-AGTTGGTGGCA
581228 TTTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTAAAGCCCACACAAGTTGGTGGCA
581255 TTTT
1 TTTT
581259 CCAGTCCTCA
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 17 0.43
29 1 0.03
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (27 bp):
TTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:581884 original size:61 final size:57
Alignment explanation
Indices: 581597--581956 Score: 441
Period size: 55 Copynumber: 6.3 Consensus size: 57
581587 TTCGCCCTTT
* * *
581597 AGTCCTCAAAGAGCAGGACGCCT-TTT-AAAGCCCACACAAGTTAGTGGCACTTCCC
1 AGTCCTCAAAGAGCAGGACGCCTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
581652 AGTCCTCAAAGAGCAGGACGCCTC-TT-AAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
581707 AGTCCTTAAAGAGCAGGACG-C-CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* * *
581762 AGTCCTCAAAGAGTAGAACGCCTC-TT-AAAGCCCACATAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* * **
581817 AGTCCTCAAAGAGCAGGATGTTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCC
1 AGTCCTCAAAGAGCAGGACG---CCTCTTT-CAAAGCCCACACAAGTTGGTGGCATTTTCC
* * * *
581878 AATCCTCAAAGAGCAGGACACCTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-T
1 AGTCCTCAAAGAGCAGGACGCC--T-C-TTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
581939 AGTCCTCAAAGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
581957 TGCACTTTAT
Statistics
Matches: 265, Mismatches: 24, Indels: 26
0.84 0.08 0.08
Matches are distributed among these distances:
53 1 0.00
54 3 0.01
55 161 0.61
56 3 0.01
57 1 0.00
58 4 0.02
59 2 0.01
60 1 0.00
61 84 0.32
62 5 0.02
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (57 bp):
AGTCCTCAAAGAGCAGGACGCCTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
Found at i:582822 original size:32 final size:32
Alignment explanation
Indices: 582777--582848 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
582767 ACAAACAGTA
**
582777 AATGTATTGATACATAAGTGTTGTATCGATAC
1 AATGTATCAATACATAAGTGTTGTATCGATAC
* *
582809 AATGTATCAATACATAAGTTTTGTATCGATAT
1 AATGTATCAATACATAAGTGTTGTATCGATAC
582841 AATGTATC
1 AATGTATC
582849 GCTACAAAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (32 bp):
AATGTATCAATACATAAGTGTTGTATCGATAC
Found at i:582891 original size:13 final size:13
Alignment explanation
Indices: 582873--582898 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
582863 ACCAAGGAAA
582873 TGTATCGATACAT
1 TGTATCGATACAT
582886 TGTATCGATACAT
1 TGTATCGATACAT
582899 CGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:584209 original size:21 final size:21
Alignment explanation
Indices: 584183--584301 Score: 168
Period size: 21 Copynumber: 5.7 Consensus size: 21
584173 AAAAAATTCA
584183 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
584204 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
*
584225 AATGCATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
584246 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* * *
584267 AATGTATCGAAACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
584288 AATGTATCGATACA
1 AATGTATCGATACA
584302 GGGTCCCAAC
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
20 3 0.03
21 84 0.97
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:584247 original size:42 final size:42
Alignment explanation
Indices: 584183--584301 Score: 186
Period size: 42 Copynumber: 2.8 Consensus size: 42
584173 AAAAAATTCA
584183 AATGTATCGATACATTTGTAGAATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAGAATGTATCGATACATTTGTGG
*
584225 AATGCATCGATACATTTGTAGAATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAGAATGTATCGATACATTTGTGG
* * *
584267 AATGTATCGAAACA-TTCTACAAATGTATCGATACA
1 AATGTATCGATACATTTGTA-GAATGTATCGATACA
584302 GGGTCCCAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
41 4 0.06
42 67 0.94
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (42 bp):
AATGTATCGATACATTTGTAGAATGTATCGATACATTTGTGG
Found at i:584376 original size:13 final size:13
Alignment explanation
Indices: 584358--584382 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
584348 ACATAAGTTT
584358 TGTATCGATACAA
1 TGTATCGATACAA
584371 TGTATCGATACA
1 TGTATCGATACA
584383 TTTTTCTGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:584409 original size:13 final size:13
Alignment explanation
Indices: 584391--584417 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
584381 CATTTTTCTG
584391 TGTATCGATACAT
1 TGTATCGATACAT
584404 TGTATCGATACAT
1 TGTATCGATACAT
584417 T
1 T
584418 TGGAAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:594303 original size:24 final size:23
Alignment explanation
Indices: 594257--594303 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
594247 AGATAAGTTC
* *
594257 AAATGTTTTTCAAGCCATAAATT
1 AAATGTTTTTCAAGCAAAAAATT
*
594280 AAATGTTTTTCAAGTAAAATAATT
1 AAATGTTTTTCAAGCAAAA-AATT
594304 CAAAGTATCG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.40
Consensus pattern (23 bp):
AAATGTTTTTCAAGCAAAAAATT
Found at i:595096 original size:13 final size:13
Alignment explanation
Indices: 595078--595103 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
595068 CAATTTTTTG
595078 TGTATCGATACAT
1 TGTATCGATACAT
595091 TGTATCGATACAT
1 TGTATCGATACAT
595104 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:595843 original size:21 final size:21
Alignment explanation
Indices: 595802--595845 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
595792 CTCTCCTTTA
* *
595802 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
595823 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
595844 TC
1 TC
595846 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:597667 original size:13 final size:13
Alignment explanation
Indices: 597649--597674 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
597639 ATAATCACCC
597649 TGTATCGATACAA
1 TGTATCGATACAA
597662 TGTATCGATACAA
1 TGTATCGATACAA
597675 AGAAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:599774 original size:15 final size:15
Alignment explanation
Indices: 599754--599784 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
599744 ATTTCGTTTG
*
599754 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
599769 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
599784 G
1 G
599785 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:601617 original size:21 final size:21
Alignment explanation
Indices: 601588--601632 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
601578 AAGTTTTCAT
*
601588 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
601608 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
601630 TTT
1 TTT
601633 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:603867 original size:13 final size:13
Alignment explanation
Indices: 603849--603874 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
603839 CAATTTTTTG
603849 TGTATCGATACAT
1 TGTATCGATACAT
603862 TGTATCGATACAT
1 TGTATCGATACAT
603875 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:604589 original size:20 final size:20
Alignment explanation
Indices: 604564--604618 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
604554 TTTCAAATGC
*
604564 ATTGTATGGATACATTATGT
1 ATTGTATCGATACATTATGT
604584 ATTGTATCGATACATTATGT
1 ATTGTATCGATACATTATGT
*
604604 ATTGTATCCATACAT
1 ATTGTATCGATACAT
604619 AGAAGAGTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.44
Consensus pattern (20 bp):
ATTGTATCGATACATTATGT
Found at i:605778 original size:22 final size:22
Alignment explanation
Indices: 605753--605797 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
605743 GTTTGAAACA
605753 TTTCCTAGTTTGAAACATTTCT
1 TTTCCTAGTTTGAAACATTTCT
605775 TTTCCTAGTTTGAAACATTTCT
1 TTTCCTAGTTTGAAACATTTCT
605797 T
1 T
605798 GATTTTGATT
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:0.22, C:0.18, G:0.09, T:0.51
Consensus pattern (22 bp):
TTTCCTAGTTTGAAACATTTCT
Found at i:605817 original size:26 final size:26
Alignment explanation
Indices: 605787--605865 Score: 79
Period size: 26 Copynumber: 3.0 Consensus size: 26
605777 TCCTAGTTTG
605787 AAACATTTCTTGATTTTGATTAAAAT
1 AAACATTTCTTGATTTTGATTAAAAT
* * * *
605813 GAACATTTCTT-AGTTTTAATTAGAAC
1 AAACATTTCTTGA-TTTTGATTAAAAT
* * *
605839 AAAGATTACTTGCTTTTGATTAAAAT
1 AAACATTTCTTGATTTTGATTAAAAT
605865 A
1 A
605866 GATTTAATTT
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
25 1 0.03
26 39 0.98
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.43
Consensus pattern (26 bp):
AAACATTTCTTGATTTTGATTAAAAT
Found at i:611225 original size:27 final size:27
Alignment explanation
Indices: 611168--611227 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
611158 TTAACAAGTT
**
611168 TAAA-AATAGGGTTGGAGTATCCCCTC
1 TAAATAATAGGGTTGGAGTATCCCCGA
* *
611194 GAAATAATGGGGTTGGAGTATCCCCGA
1 TAAATAATAGGGTTGGAGTATCCCCGA
611221 TAAATAA
1 TAAATAA
611228 AATTTGGTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (27 bp):
TAAATAATAGGGTTGGAGTATCCCCGA
Found at i:616604 original size:20 final size:20
Alignment explanation
Indices: 616579--616650 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 20
616569 TTGAGACATA
*
616579 TATCGATACATTCAC-TTATG
1 TATCGATACATTCACAAT-TG
*
616599 TATCGATACAATCAACAATTG
1 TATCGATACATTC-ACAATTG
616620 TATCGATACATTCACCAATTG
1 TATCGATACATTCA-CAATTG
*
616641 TATTGATACA
1 TATCGATACA
616651 AATTGTAGAC
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
20 13 0.29
21 31 0.69
22 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (20 bp):
TATCGATACATTCACAATTG
Found at i:623286 original size:129 final size:130
Alignment explanation
Indices: 623102--623360 Score: 430
Period size: 130 Copynumber: 2.0 Consensus size: 130
623092 CCTGACATTA
* * *
623102 GACTTTATGCCATGATTATGCTATCATAACATCAGTAACGTCATTGTTTGTATCATGCATTC-CA
1 GACTTTACGCCATGATTATGCTATCATAACATCAATAACGTCATTGTTTGCATCATGCATTCACA
** *
623166 TCATCACTGCATGTCATCATCGCGCCAATCCCGAGTGGAGTAAATCTAAATCCTCCAAATATTTT
66 TCATCACCACATGTCATCATCGCGCCAATCCCCAGTGGAGTAAATCTAAATCCTCCAAATATTTT
*
623231 GACTTTACGCCATGATTATGCTATCATAACATCAATAATGTCATTGTTTGCATCATGCATTCACA
1 GACTTTACGCCATGATTATGCTATCATAACATCAATAACGTCATTGTTTGCATCATGCATTCACA
* *
623296 TCATCACCACATGTCATCATCGTGCCAATCCCCAGTGGAGTAAATCTAAATCCTCCAAATCTTTT
66 TCATCACCACATGTCATCATCGCGCCAATCCCCAGTGGAGTAAATCTAAATCCTCCAAATATTTT
623361 CTCAGAAAAT
Statistics
Matches: 120, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
129 58 0.48
130 62 0.52
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (130 bp):
GACTTTACGCCATGATTATGCTATCATAACATCAATAACGTCATTGTTTGCATCATGCATTCACA
TCATCACCACATGTCATCATCGCGCCAATCCCCAGTGGAGTAAATCTAAATCCTCCAAATATTTT
Found at i:623549 original size:29 final size:29
Alignment explanation
Indices: 623517--624012 Score: 368
Period size: 30 Copynumber: 17.1 Consensus size: 29
623507 TAAGTCAATG
*
623517 ACTCCGTGGCACCCTTTTCAAGGTCCACA
1 ACTCCGTGGCACCCTTTTCAAAGTCCACA
* ** *
623546 ACTCTGTGGCACTTTTTTCTAAAGCCCACA
1 ACTCCGTGGCACCCTTTTC-AAAGTCCACA
* *
623576 A---C-T--CACCTTTTTCAAAGTCCGCA
1 ACTCCGTGGCACCCTTTTCAAAGTCCACA
* * *
623599 GCTCCGTGGCACTCTTTTCAAAATCCACA
1 ACTCCGTGGCACCCTTTTCAAAGTCCACA
*** *
623628 ACTAAATGACACCCTTTT-AAAGTCCACA
1 ACTCCGTGGCACCCTTTTCAAAGTCCACA
* * * *
623656 ACTTCATGGCACCCCTTTTTAAAGTCCATA
1 ACTCCGTGGCA-CCCTTTTCAAAGTCCACA
** * *
623686 ACTCTATGGCACCCCTTTTTAAAGTCCATA
1 ACTCCGTGGCA-CCCTTTTCAAAGTCCACA
* * * *
623716 ATTCTGT-TCACCCTTTTCAAAGTCCATA
1 ACTCCGTGGCACCCTTTTCAAAGTCCACA
** * *
623744 ACTTTGTGACACCTTTTTCTAAAGTCCACA
1 ACTCCGTGGCACCCTTTTC-AAAGTCCACA
*
623774 ACTCCGTGGCAGCCCTTTT-AAAGTTCACA
1 ACTCCGTGGCA-CCCTTTTCAAAGTCCACA
* * *
623803 GCTCTGTGGCACCCTTTTCAAAGTCCATA
1 ACTCCGTGGCACCCTTTTCAAAGTCCACA
** * *
623832 ACTTTGTGGCACCCTTTTTAAAGTCCAAA
1 ACTCCGTGGCACCCTTTTCAAAGTCCACA
* *
623861 ACAT-CATGGCA-CCTTTTTAAAGTCCACA
1 AC-TCCGTGGCACCCTTTTCAAAGTCCACA
* * *
623889 ACAT-CGTGGCACCCCTTTTTAATGTCCATA
1 AC-TCCGTGGCA-CCCTTTTCAAAGTCCACA
** *
623919 ACTCTATGGCACCCTATTCAAAAGTCCACA
1 ACTCCGTGGCACCCTTTTC-AAAGTCCACA
*
623949 ACTCTGTGGCACCCTTTTTCAAAGTCCACA
1 ACTCCGTGGCACCC-TTTTCAAAGTCCACA
* *
623979 ACTCCGTGGCACCCCTTTTTAAAGTCTACA
1 ACTCCGTGGCA-CCCTTTTCAAAGTCCACA
624009 ACTC
1 ACTC
624013 TATGATAACT
Statistics
Matches: 381, Mismatches: 66, Indels: 39
0.78 0.14 0.08
Matches are distributed among these distances:
23 8 0.02
24 9 0.02
26 2 0.01
27 1 0.00
28 72 0.19
29 127 0.33
30 149 0.39
31 13 0.03
ACGTcount: A:0.26, C:0.31, G:0.12, T:0.31
Consensus pattern (29 bp):
ACTCCGTGGCACCCTTTTCAAAGTCCACA
Found at i:623590 original size:53 final size:52
Alignment explanation
Indices: 623526--623630 Score: 129
Period size: 53 Copynumber: 2.0 Consensus size: 52
623516 GACTCCGTGG
* * * *
623526 CACCCTTTTCAAGGTCCACAACTCTGTGGCACTTTTTTCTAAAGCCCACAACT
1 CACCCTTTTCAAAGTCCACAACTCCGTGGCACTCTTTTC-AAAACCCACAACT
* * * *
623579 CACCTTTTTCAAAGTCCGCAGCTCCGTGGCACTCTTTTCAAAATCCACAACT
1 CACCCTTTTCAAAGTCCACAACTCCGTGGCACTCTTTTCAAAACCCACAACT
623631 AAATGACACC
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
52 11 0.25
53 33 0.75
ACGTcount: A:0.25, C:0.34, G:0.11, T:0.30
Consensus pattern (52 bp):
CACCCTTTTCAAAGTCCACAACTCCGTGGCACTCTTTTCAAAACCCACAACT
Found at i:623730 original size:58 final size:60
Alignment explanation
Indices: 623637--624541 Score: 554
Period size: 58 Copynumber: 15.6 Consensus size: 60
623627 AACTAAATGA
*
623637 CACCC-TTTTAAAGTCCACAACTTC-ATGGCACCCCTTTTTAAAGTCCATAACTCTATGG
1 CACCCTTTTTAAAGTCCACAACTTCTGTGGCACCCCTTTTTAAAGTCCATAACTCTATGG
* * * * * *
623695 CACCCCTTTTTAAAGTCCATAA-TTCTGT-TCA-CCCTTTTCAAAGTCCATAACTTTGTGA
1 CA-CCCTTTTTAAAGTCCACAACTTCTGTGGCACCCCTTTTTAAAGTCCATAACTCTATGG
* * * * * * *
623753 CACCTTTTTCTAAAGTCCACAAC-TCCGTGGCAGCCC-TTTTAAAGTTCACAGCTCTGTGG
1 CACCCTTTT-TAAAGTCCACAACTTCTGTGGCACCCCTTTTTAAAGTCCATAACTCTATGG
* * *
623812 CACCCTTTTCAAAGTCCATAACTT-TGTGGCA-CCCTTTTTAAAGTCCAAAACATC-ATGG
1 CACCCTTTTTAAAGTCCACAACTTCTGTGGCACCCCTTTTTAAAGTCCATAAC-TCTATGG
* *
623870 CA-CCTTTTTAAAGTCCACAACATC-GTGGCACCCCTTTTTAATGTCCATAACTCTATGG
1 CACCCTTTTTAAAGTCCACAACTTCTGTGGCACCCCTTTTTAAAGTCCATAACTCTATGG
** * **
623928 CACCCTATTCAAAAGTCCACAAC-TCTGTGGCA-CCCTTTTTCAAAGTCCACAACTCCGTGG
1 CACCCT-TTTTAAAGTCCACAACTTCTGTGGCACCCCTTTTT-AAAGTCCATAACTCTATGG
* *
623988 CACCCCTTTTTAAAGTCTACAACTCTATGATAACTCCGTGGCACCCCTTTTTAAAGTCTATAACT
1 CA-CCCTTTTTAAAGTCCACAA--C--T--T--CT--GTGGCACCCCTTTTTAAAGTCCATAACT
624053 CTATGG
55 CTATGG
* * * * *
624059 CA-CCATTTTAAAGTCCATAAC-TCTGTGGCA-CCCTTTTTCAAAATCCACAACTCTGTGG
1 CACCCTTTTTAAAGTCCACAACTTCTGTGGCACCCCTTTTT-AAAGTCCATAACTCTATGG
* * *
624117 ----C------AAGTCCACAAC-TCTGTGGCA-CCCTTTTTCAAAATCCACAACTCTGTGG
1 CACCCTTTTTAAAGTCCACAACTTCTGTGGCACCCCTTTTT-AAAGTCCATAACTCTATGG
* * * * *
624166 ----C------AAGTCTACAAC-TCTGTGGCA-CCCTTTTCAAAAGTTCACAACT-TCGTGG
1 CACCCTTTTTAAAGTCCACAACTTCTGTGGCACCCCTTTT-TAAAGTCCATAACTCT-ATGG
** * * * * *
624215 CACCCCGTTTAAAGTCCACAACTCCT-TGACACCCATTTTAAAAGTCCATAACTC-GTGG
1 CACCCTTTTTAAAGTCCACAACTTCTGTGGCACCCCTTTTTAAAGTCCATAACTCTATGG
* * * **
624273 CACCCTTTTTCAAAGTCCACAACTTC-ATGGCA-CCCTTTTTCGAAGTCTATAA-TCCGTGG
1 CACCCTTTTT-AAAGTCCACAACTTCTGTGGCACCCCTTTTT-AAAGTCCATAACTCTATGG
* * *
624332 CACCCTTTTCAAAAGTCCACAAC-TCTGTGGCA-CCC-TTTTAAAGTCCATAATTCCATGG
1 CACCCTTTT-TAAAGTCCACAACTTCTGTGGCACCCCTTTTTAAAGTCCATAACTCTATGG
* * * * * * *
624390 CACCCCTTTCAAAGTCCACAAC-TCTATGGC-TCCCTTTTTAAAGTCCACAACACTGTGG
1 CACCCTTTTTAAAGTCCACAACTTCTGTGGCACCCCTTTTTAAAGTCCATAACTCTATGG
* * * * * * *
624448 CACTC-TTTCAAAGTCCACAAC-TCTGTGGCACTCATTTTCAAAGTCCACAACT-TCGTGG
1 CACCCTTTTTAAAGTCCACAACTTCTGTGGCACCCCTTTTTAAAGTCCATAACTCT-ATGG
**
624506 CACCCCTTATCAAAAGTCCACAAC-TCTGTGGCACCC
1 CA-CCCTT-TTTAAAGTCCACAACTTCTGTGGCACCC
624542 TTTCTCAAAG
Statistics
Matches: 694, Mismatches: 93, Indels: 117
0.77 0.10 0.13
Matches are distributed among these distances:
48 1 0.00
49 89 0.13
53 1 0.00
55 1 0.00
57 98 0.14
58 207 0.30
59 139 0.20
60 78 0.11
61 28 0.04
62 2 0.00
67 2 0.00
69 17 0.02
71 23 0.03
72 8 0.01
ACGTcount: A:0.27, C:0.31, G:0.13, T:0.30
Consensus pattern (60 bp):
CACCCTTTTTAAAGTCCACAACTTCTGTGGCACCCCTTTTTAAAGTCCATAACTCTATGG
Found at i:623747 original size:88 final size:87
Alignment explanation
Indices: 623581--624558 Score: 589
Period size: 88 Copynumber: 11.2 Consensus size: 87
623571 CCACAACTCA
* * ** * * * *** *
623581 CCTTTTTCAAAGTCCGCAGCTCCGTGGCACTCTTTTCAAAATCCACAACTAAATGACACCCTTTT
1 CCTTTTT-AAAGTCCACAACTCTATGGCACCCTTTTTAAAGTCCACAACTCTGTGGCACCCTTTT
* *
623646 -AAAGTCCACAACTTCATGGCACC
65 CAAAGTCCATAACTTCGTGGCA-C
* * * *
623669 CCTTTTTAAAGTCCATAACTCTATGGCACCCCTTTTTAAAGTCCATAATTCTGT-TCACCCTTTT
1 CCTTTTTAAAGTCCACAACTCTATGGCA-CCCTTTTTAAAGTCCACAACTCTGTGGCACCCTTTT
* *
623733 CAAAGTCCATAACTTTGTGACAC
65 CAAAGTCCATAACTTCGTGGCAC
* ** * *
623756 CTTTTTCTAAAGTCCACAACTCCGTGGCAGCCC-TTTTAAAGTTCACAGCTCTGTGGCACCCTTT
1 CCTTTT-TAAAGTCCACAACTCTATGGCA-CCCTTTTTAAAGTCCACAACTCTGTGGCACCCTTT
*
623820 TCAAAGTCCATAACTTTGTGGCAC
64 TCAAAGTCCATAACTTCGTGGCAC
*
623844 CCTTTTTAAAGTCCAAAACATC-ATGGCA-CCTTTTTAAAGTCCACAACATC-GTGGCACCCCTT
1 CCTTTTTAAAGTCCACAAC-TCTATGGCACCCTTTTTAAAGTCCACAAC-TCTGTGGCA-CCCTT
* * *
623906 TTTAATGTCCATAAC-TCTATGGCAC
63 TTCAAAGTCCATAACTTC-GTGGCAC
** * *
623931 CCTATTCAAAAGTCCACAACTCTGTGGCACCCTTTTTCAAAGTCCACAACTCCGTGGCACCCCTT
1 CCT-TTTTAAAGTCCACAACTCTATGGCACCCTTTTT-AAAGTCCACAACTCTGTGGCA-CCCTT
* *
623996 TTTAAAGTCTACAACTCTATGATAACTCCGTGGCACC
63 TTCAAAG--T----C-C----ATAACTTCGTGGCA-C
* * * *
624033 CCTTTTTAAAGTCTATAACTCTATGGCA-CCATTTTAAAGTCCATAACTCTGTGGCACCCTTTTT
1 CCTTTTTAAAGTCCACAACTCTATGGCACCCTTTTTAAAGTCCACAACTCTGTGGCACCC-TTTT
* *
624097 CAAAATCCACAAC-TCTGTGG---
65 CAAAGTCCATAACTTC-GTGGCAC
* *
624117 -C------AAGTCCACAACTCTGTGGCACCCTTTTTCAAAATCCACAACTCTGTGG---------
1 CCTTTTTAAAGTCCACAACTCTATGGCACCCTTTTT-AAAGTCCACAACTCTGTGGCACCCTTTT
* *
624166 C-AAGTCTACAAC-TCTGTGGCAC
65 CAAAGTCCATAACTTC-GTGGCAC
* * * ** *
624188 CCTTTTCAAAAGTTCACAACT-TCGTGGCACCCCGTTTAAAGTCCACAACTCCT-TGACACCCAT
1 CCTTTT-TAAAGTCCACAACTCT-ATGGCACCCTTTTTAAAGTCCACAACT-CTGTGGCACCC-T
*
624251 TTTAAAAGTCCATAAC-TCGTGGCAC
62 TTTCAAAGTCCATAACTTCGTGGCAC
* * * *
624276 CCTTTTTCAAAGTCCACAACT-TCATGGCACCCTTTTTCGAAGTCTATAA-TCCGTGGCACCCTT
1 CCTTTTT-AAAGTCCACAACTCT-ATGGCACCCTTTTT-AAAGTCCACAACTCTGTGGCACCCTT
*
624339 TTCAAAAGTCCACAAC-TCTGTGGCAC
63 TTC-AAAGTCCATAACTTC-GTGGCAC
* * * * * * * *
624365 CC-TTTTAAAGTCCATAATTCCATGGCACCCCTTTCAAAGTCCACAACTCTATGGCTCCCTTTTT
1 CCTTTTTAAAGTCCACAACTCTATGGCACCCTTTTTAAAGTCCACAACTCTGTGGCACCCTTTTC
* *
624429 AAAGTCCACAAC-ACTGTGGCAC
66 AAAGTCCATAACTTC-GTGGCAC
* * * * *
624451 TC-TTTCAAAGTCCACAACTCTGTGGCACTCATTTTCAAAGTCCACAACT-TCGTGGCACCCCTT
1 CCTTTTTAAAGTCCACAACTCTATGGCAC-CCTTTTTAAAGTCCACAACTCT-GTGGCA-CCCTT
* *
624514 ATCAAAAGTCCACAAC-TCTGTGGCAC
63 TTC-AAAGTCCATAACTTC-GTGGCAC
* *
624540 CCTTTCTCAAAGCCCACAA
1 CCTTT-TTAAAGTCCACAA
624559 AAGTCAGTGG
Statistics
Matches: 709, Mismatches: 113, Indels: 133
0.74 0.12 0.14
Matches are distributed among these distances:
68 16 0.02
69 1 0.00
72 1 0.00
77 17 0.02
78 21 0.03
79 42 0.06
83 1 0.00
85 2 0.00
86 73 0.10
87 160 0.23
88 196 0.28
89 59 0.08
90 32 0.05
91 12 0.02
92 2 0.00
93 1 0.00
96 1 0.00
97 2 0.00
98 3 0.00
99 26 0.04
100 6 0.01
101 30 0.04
102 5 0.01
ACGTcount: A:0.27, C:0.31, G:0.12, T:0.30
Consensus pattern (87 bp):
CCTTTTTAAAGTCCACAACTCTATGGCACCCTTTTTAAAGTCCACAACTCTGTGGCACCCTTTTC
AAAGTCCATAACTTCGTGGCAC
Found at i:624012 original size:30 final size:29
Alignment explanation
Indices: 623581--624013 Score: 385
Period size: 30 Copynumber: 14.8 Consensus size: 29
623571 CCACAACTCA
* * *
623581 CCTTTTTCAAAGTCCGCAGCTCCGTGGCAC
1 CCTTTTT-AAAGTCCACAACTCTGTGGCAC
* * * *** *
623611 TCTTTTCAAAATCCACAACTAAATGACAC
1 CCTTTTTAAAGTCCACAACTCTGTGGCAC
*
623640 CC-TTTTAAAGTCCACAACT-TCATGGCACC
1 CCTTTTTAAAGTCCACAACTCT-GTGGCA-C
* *
623669 CCTTTTTAAAGTCCATAACTCTATGGCACC
1 CCTTTTTAAAGTCCACAACTCTGTGGCA-C
* * *
623699 CCTTTTTAAAGTCCATAATTCTGT-TCAC
1 CCTTTTTAAAGTCCACAACTCTGTGGCAC
* * * *
623727 CCTTTTCAAAGTCCATAACTTTGTGACAC
1 CCTTTTTAAAGTCCACAACTCTGTGGCAC
* *
623756 CTTTTTCTAAAGTCCACAACTCCGTGGCAGC
1 CCTTTT-TAAAGTCCACAACTCTGTGGCA-C
* *
623787 CC-TTTTAAAGTTCACAGCTCTGTGGCAC
1 CCTTTTTAAAGTCCACAACTCTGTGGCAC
* * *
623815 CCTTTTCAAAGTCCATAACTTTGTGGCAC
1 CCTTTTTAAAGTCCACAACTCTGTGGCAC
* *
623844 CCTTTTTAAAGTCCAAAACATC-ATGGCA-
1 CCTTTTTAAAGTCCACAAC-TCTGTGGCAC
623872 CCTTTTTAAAGTCCACAACATC-GTGGCACC
1 CCTTTTTAAAGTCCACAAC-TCTGTGGCA-C
* * *
623902 CCTTTTTAATGTCCATAACTCTATGGCAC
1 CCTTTTTAAAGTCCACAACTCTGTGGCAC
**
623931 CCTATTCAAAAGTCCACAACTCTGTGGCAC
1 CCT-TTTTAAAGTCCACAACTCTGTGGCAC
*
623961 CCTTTTTCAAAGTCCACAACTCCGTGGCACC
1 CCTTTTT-AAAGTCCACAACTCTGTGGCA-C
*
623992 CCTTTTTAAAGTCTACAACTCT
1 CCTTTTTAAAGTCCACAACTCT
624014 ATGATAACTC
Statistics
Matches: 332, Mismatches: 56, Indels: 30
0.79 0.13 0.07
Matches are distributed among these distances:
28 71 0.21
29 99 0.30
30 151 0.45
31 11 0.03
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.31
Consensus pattern (29 bp):
CCTTTTTAAAGTCCACAACTCTGTGGCAC
Found at i:624035 original size:41 final size:41
Alignment explanation
Indices: 623978--624057 Score: 151
Period size: 41 Copynumber: 2.0 Consensus size: 41
623968 CAAAGTCCAC
623978 AACTCCGTGGCACCCCTTTTTAAAGTCTACAACTCTATGAT
1 AACTCCGTGGCACCCCTTTTTAAAGTCTACAACTCTATGAT
*
624019 AACTCCGTGGCACCCCTTTTTAAAGTCTATAACTCTATG
1 AACTCCGTGGCACCCCTTTTTAAAGTCTACAACTCTATG
624058 GCACCATTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.33
Consensus pattern (41 bp):
AACTCCGTGGCACCCCTTTTTAAAGTCTACAACTCTATGAT
Found at i:624051 original size:30 final size:29
Alignment explanation
Indices: 624017--624118 Score: 125
Period size: 30 Copynumber: 3.5 Consensus size: 29
624007 CAACTCTATG
* *
624017 ATAACTCCGTGGCACCCCTTTTTAAAGTCT
1 ATAACTCTGTGGCA-CCCTTTTTAAAGTCC
* *
624047 ATAACTCTATGGCA-CCATTTTAAAGTCC
1 ATAACTCTGTGGCACCCTTTTTAAAGTCC
*
624075 ATAACTCTGTGGCACCCTTTTTCAAAATCC
1 ATAACTCTGTGGCACCCTTTTT-AAAGTCC
*
624105 ACAACTCTGTGGCA
1 ATAACTCTGTGGCA
624119 AGTCCACAAC
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
28 25 0.40
29 6 0.10
30 31 0.50
ACGTcount: A:0.27, C:0.28, G:0.13, T:0.31
Consensus pattern (29 bp):
ATAACTCTGTGGCACCCTTTTTAAAGTCC
Found at i:624141 original size:49 final size:49
Alignment explanation
Indices: 624069--624216 Score: 237
Period size: 49 Copynumber: 3.0 Consensus size: 49
624059 CACCATTTTA
*
624069 AAGTCCATAACTCTGTGGCACCCTTTTTCAAAATCCACAACTCTGTGGC
1 AAGTCCACAACTCTGTGGCACCCTTTTTCAAAATCCACAACTCTGTGGC
624118 AAGTCCACAACTCTGTGGCACCCTTTTTCAAAATCCACAACTCTGTGGC
1 AAGTCCACAACTCTGTGGCACCCTTTTTCAAAATCCACAACTCTGTGGC
* *
624167 AAGTCTACAACTCTGTGGCACCC-TTTTCAAAAGTTCACAACT-TCGTGGC
1 AAGTCCACAACTCTGTGGCACCCTTTTTCAAAA-TCCACAACTCT-GTGGC
624216 A
1 A
624217 CCCCGTTTAA
Statistics
Matches: 94, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
48 10 0.11
49 84 0.89
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.28
Consensus pattern (49 bp):
AAGTCCACAACTCTGTGGCACCCTTTTTCAAAATCCACAACTCTGTGGC
Found at i:624215 original size:30 final size:28
Alignment explanation
Indices: 624167--624558 Score: 351
Period size: 30 Copynumber: 13.4 Consensus size: 28
624157 ACTCTGTGGC
*
624167 AAGTCTACAACTCTGTGGCACCCTTTTCAA
1 AAGTCCACAACTC-GTGGCACCCTTTTC-A
* *
624197 AAGTTCACAACTTCGTGGCACCCCGTTT-A
1 AAGTCCACAAC-TCGTGGCA-CCCTTTTCA
* * *
624226 AAGTCCACAACTCCTTGACACCCATTTTAA
1 AAGTCCACAACT-CGTGGCACCC-TTTTCA
*
624256 AAGTCCATAACTCGTGGCACCCTTTTTCA
1 AAGTCCACAACTCGTGGCACCC-TTTTCA
* *
624285 AAGTCCACAACTTCATGGCACCCTTTTTCG
1 AAGTCCACAAC-TCGTGGCACCC-TTTTCA
* *
624315 AAGTCTATAA-TCCGTGGCACCCTTTTCAA
1 AAGTCCACAACT-CGTGGCACCCTTTTC-A
624344 AAGTCCACAACTCTGTGGCACCCTTTT-A
1 AAGTCCACAACTC-GTGGCACCCTTTTCA
* * * *
624372 AAGTCCATAATTCCATGGCACCCCTTTCA
1 AAGTCCACAACT-CGTGGCACCCTTTTCA
* * *
624401 AAGTCCACAACTCTATGGCTCCCTTTTTA
1 AAGTCCACAACTC-GTGGCACCCTTTTCA
* *
624430 AAGTCCACAACACTGTGGCACTC-TTTCA
1 AAGTCCACAACTC-GTGGCACCCTTTTCA
*
624458 AAGTCCACAACTCTGTGGCACTCATTTTCA
1 AAGTCCACAACTC-GTGGCAC-CCTTTTCA
*
624488 AAGTCCACAACTTCGTGGCACCCCTTATCAA
1 AAGTCCACAAC-TCGTGGCA-CCCTTTTC-A
624519 AAGTCCACAACTCTGTGGCACCCTTTCTCA
1 AAGTCCACAACTC-GTGGCACCCTTT-TCA
*
624549 AAGCCCACAA
1 AAGTCCACAA
624559 AAGTCAGTGG
Statistics
Matches: 300, Mismatches: 42, Indels: 40
0.79 0.11 0.10
Matches are distributed among these distances:
28 57 0.19
29 103 0.34
30 109 0.36
31 31 0.10
ACGTcount: A:0.27, C:0.32, G:0.13, T:0.28
Consensus pattern (28 bp):
AAGTCCACAACTCGTGGCACCCTTTTCA
Found at i:624259 original size:59 final size:58
Alignment explanation
Indices: 624167--624558 Score: 388
Period size: 59 Copynumber: 6.7 Consensus size: 58
624157 ACTCTGTGGC
* *
624167 AAGTCTACAACTCTGTGGCACCCTTTTCAAAAGTTCACAACTTCGTGGCACCCCGTTT-A
1 AAGTCCACAACTCTGTGGCACCCTTTT-AAAAGTCCACAACTTCGTGGCACCCC-TTTCA
* * *
624226 AAGTCCACAACTCCT-TGACACCCATTTTAAAAGTCCATAAC-TCGTGGCACCCTTTTTCA
1 AAGTCCACAACT-CTGTGGCACCC-TTTTAAAAGTCCACAACTTCGTGGCACCC-CTTTCA
* ** * * * *
624285 AAGTCCACAACT-TCATGGCACCCTTTTTCGAAGTCTATAA-TCCGTGGCACCCTTTTCAA
1 AAGTCCACAACTCT-GTGGCACCC-TTTTAAAAGTCCACAACTTCGTGGCACCCCTTTC-A
* *
624344 AAGTCCACAACTCTGTGGCACCCTTTT-AAAGTCCATAA-TTCCATGGCACCCCTTTCA
1 AAGTCCACAACTCTGTGGCACCCTTTTAAAAGTCCACAACTT-CGTGGCACCCCTTTCA
* * * * *
624401 AAGTCCACAACTCTATGGCTCCCTTTTTAAAGTCCACAAC-ACTGTGGCA-CTCTTTCA
1 AAGTCCACAACTCTGTGGCACCCTTTTAAAAGTCCACAACTTC-GTGGCACCCCTTTCA
* *
624458 AAGTCCACAACTCTGTGGCACTCATTTTCAAAGTCCACAACTTCGTGGCACCCCTTATCAA
1 AAGTCCACAACTCTGTGGCAC-CCTTTTAAAAGTCCACAACTTCGTGGCACCCCTT-TC-A
* *
624519 AAGTCCACAACTCTGTGGCACCCTTTCTCAAAGCCCACAA
1 AAGTCCACAACTCTGTGGCACCCTTT-TAAAAGTCCACAA
624559 AAGTCAGTGG
Statistics
Matches: 283, Mismatches: 31, Indels: 36
0.81 0.09 0.10
Matches are distributed among these distances:
57 64 0.23
58 74 0.26
59 98 0.35
60 13 0.05
61 34 0.12
ACGTcount: A:0.27, C:0.32, G:0.13, T:0.28
Consensus pattern (58 bp):
AAGTCCACAACTCTGTGGCACCCTTTTAAAAGTCCACAACTTCGTGGCACCCCTTTCA
Found at i:624648 original size:31 final size:31
Alignment explanation
Indices: 624548--624757 Score: 248
Period size: 31 Copynumber: 6.7 Consensus size: 31
624538 ACCCTTTCTC
* **
624548 AAAGCCCACAAAAGTCAGTGGCAAACTTTTCA
1 AAAGCCCACACAAGTTGGTGG-AAACTTTTCA
* * **
624580 AAAGCCCATATAAGTTGGTGGTATTCTTTCTCA
1 AAAGCCCACACAAGTTGGTGG-AAACTTT-TCA
624613 AAAGCCCACACAAGTTGGTGGAAACTTTTCA
1 AAAGCCCACACAAGTTGGTGGAAACTTTTCA
*
624644 AAAGCCCACACAAGTT-GT-GACAACCCTTTCA
1 AAAGCCCACACAAGTTGGTGGA-AA-CTTTTCA
624675 AAAGCCCACACAAGTTGGTGGAAACTTTTCA
1 AAAGCCCACACAAGTTGGTGGAAACTTTTCA
*
624706 AAAGCCCACACAAGTT-GT-GACAACCCTTTCA
1 AAAGCCCACACAAGTTGGTGGA-AA-CTTTTCA
624737 AAAGCCCACACAAGTTGGTGG
1 AAAGCCCACACAAGTTGGTGG
624758 CATCCTTTCT
Statistics
Matches: 155, Mismatches: 14, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
29 4 0.03
30 8 0.05
31 85 0.55
32 33 0.21
33 25 0.16
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (31 bp):
AAAGCCCACACAAGTTGGTGGAAACTTTTCA
Found at i:624700 original size:62 final size:62
Alignment explanation
Indices: 624538--624757 Score: 305
Period size: 62 Copynumber: 3.5 Consensus size: 62
624528 ACTCTGTGGC
* * ** * * **
624538 ACCCTTTCTCAAAGCCCACAAAAGTCAGTGGCAAACTTTTCAAAAGCCCATATAAGTTGGTGGTA
1 ACCCTTTC-AAAAGCCCACACAAGTTGGTGG-AAACTTTTCAAAAGCCCACACAAGTT-GTGACA
** *
624603 TTCTTTCTCAAAAGCCCACACAAGTTGGTGGAAACTTTTCAAAAGCCCACACAAGTTGTGACA
1 ACCCTT-TCAAAAGCCCACACAAGTTGGTGGAAACTTTTCAAAAGCCCACACAAGTTGTGACA
624666 ACCCTTTCAAAAGCCCACACAAGTTGGTGGAAACTTTTCAAAAGCCCACACAAGTTGTGACA
1 ACCCTTTCAAAAGCCCACACAAGTTGGTGGAAACTTTTCAAAAGCCCACACAAGTTGTGACA
624728 ACCCTTTCAAAAGCCCACACAAGTTGGTGG
1 ACCCTTTCAAAAGCCCACACAAGTTGGTGG
624758 CATCCTTTCT
Statistics
Matches: 140, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
62 86 0.61
63 7 0.05
64 24 0.17
65 21 0.15
66 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (62 bp):
ACCCTTTCAAAAGCCCACACAAGTTGGTGGAAACTTTTCAAAAGCCCACACAAGTTGTGACA
Found at i:624765 original size:31 final size:31
Alignment explanation
Indices: 624533--624766 Score: 238
Period size: 31 Copynumber: 7.4 Consensus size: 31
624523 CCACAACTCT
* * * **
624533 GTGGCACCCTTTCTCAAAGCCCACAAAAGTCA
1 GTGGCAACCTTTC-AAAAGCCCACACAAGTTG
* * *
624565 GTGGCAAACTTTTCAAAAGCCCATATAAGTTG
1 GTGGC-AACCTTTCAAAAGCCCACACAAGTTG
* * *
624597 GTGGTATTCTTTCTCAAAAGCCCACACAAGTTG
1 GTGGCA-ACCTT-TCAAAAGCCCACACAAGTTG
* *
624630 GTGGAAACTTTTCAAAAGCCCACACAAGTT-
1 GTGGCAACCTTTCAAAAGCCCACACAAGTTG
*
624660 GTGACAACCCTTTCAAAAGCCCACACAAGTTG
1 GTGGCAA-CCTTTCAAAAGCCCACACAAGTTG
* *
624692 GTGGAAACTTTTCAAAAGCCCACACAAGTT-
1 GTGGCAACCTTTCAAAAGCCCACACAAGTTG
*
624722 GTGACAACCCTTTCAAAAGCCCACACAAGTTG
1 GTGGCAA-CCTTTCAAAAGCCCACACAAGTTG
*
624754 GTGGCATCCTTTC
1 GTGGCAACCTTTC
624767 TCGAGGTCCG
Statistics
Matches: 171, Mismatches: 24, Indels: 15
0.81 0.11 0.07
Matches are distributed among these distances:
30 10 0.06
31 92 0.54
32 40 0.23
33 29 0.17
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (31 bp):
GTGGCAACCTTTCAAAAGCCCACACAAGTTG
Found at i:624766 original size:93 final size:96
Alignment explanation
Indices: 624538--624759 Score: 274
Period size: 93 Copynumber: 2.3 Consensus size: 96
624528 ACTCTGTGGC
* * * * * *
624538 ACCCTTTCTCAAAGCCCACAAAAGTCAGTGGCAAACTTTTCAAAAGCCCATATAAGTTGGTGGTA
1 ACCCTTTC-AAAAGCCCACACAAGT-TGTGGCAAACCTTTCAAAAGCCCACACAAGTTGGTGGTA
**
624603 TTCTTTCTCAAAAGCCCACACAAGTTGGTGGAA
64 AACTTTCTCAAAAGCCCACACAAGTTGGTGGAA
* * *
624636 A-CTTTTCAAAAGCCCACACAAGTTGTGACAACCCTTTCAAAAGCCCACACAAGTTGGTGG-AAA
1 ACCCTTTCAAAAGCCCACACAAGTTGTGGCAAACCTTTCAAAAGCCCACACAAGTTGGTGGTAAA
624699 CTTT-TCAAAAGCCCACACAAGTT-GT-GACA
66 CTTTCTCAAAAGCCCACACAAGTTGGTGGA-A
624728 ACCCTTTCAAAAGCCCACACAAGTTGGTGGCA
1 ACCCTTTCAAAAGCCCACACAAGTT-GTGGCA
624760 TCCTTTCTCG
Statistics
Matches: 108, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
91 2 0.02
92 4 0.04
93 41 0.38
94 10 0.09
95 31 0.29
96 14 0.13
97 5 0.05
98 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.23
Consensus pattern (96 bp):
ACCCTTTCAAAAGCCCACACAAGTTGTGGCAAACCTTTCAAAAGCCCACACAAGTTGGTGGTAAA
CTTTCTCAAAAGCCCACACAAGTTGGTGGAA
Found at i:624807 original size:26 final size:27
Alignment explanation
Indices: 624777--624836 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 27
624767 TCGAGGTCCG
*
624777 CACAAGTTGGCAGCACCT-AAAGCCCA
1 CACAAGTTAGCAGCACCTAAAAGCCCA
** *
624803 CACAAGTTAGTGGCACCTAAAAGCCTA
1 CACAAGTTAGCAGCACCTAAAAGCCCA
624830 CACAAGT
1 CACAAGT
624837 CGGTGGCATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 15 0.52
27 14 0.48
ACGTcount: A:0.37, C:0.30, G:0.18, T:0.15
Consensus pattern (27 bp):
CACAAGTTAGCAGCACCTAAAAGCCCA
Found at i:624842 original size:27 final size:26
Alignment explanation
Indices: 624789--624844 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
624779 CAAGTTGGCA
*
624789 GCACCTAAAGCCCACACAAGTTAGTG
1 GCACCTAAAGCCCACACAAGTCAGTG
* *
624815 GCACCTAAAAGCCTACACAAGTCGGTG
1 GCACCT-AAAGCCCACACAAGTCAGTG
624842 GCA
1 GCA
624845 TTTCCTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 6 0.23
27 20 0.77
ACGTcount: A:0.34, C:0.30, G:0.21, T:0.14
Consensus pattern (26 bp):
GCACCTAAAGCCCACACAAGTCAGTG
Found at i:624973 original size:100 final size:103
Alignment explanation
Indices: 624853--625364 Score: 368
Period size: 100 Copynumber: 4.9 Consensus size: 103
624843 CATTTCCTTT
* * * * *
624853 TAAGCCTAATATCGTTGGCCTTAAATCAGCATATTGGCACCTCATCATCTTTAAGCCCAATGCCA
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCATCTTTAAGCCCAATGTCA
*
624918 CTAGCCTTAAATCAGCACATTGGCA-CC-TCTCAT-TC
66 CTAGCCTTAAATCAGCACATTAGCACCCTTCTCATATC
* *
624953 TAAGCCCAATATGGCTGGCCTTGAATCAGCATATTGGCACCTTATCATCTTTAAGCCTAATGTCA
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCATCTTTAAGCCCAATGTCA
* * * *
625018 CTGGCCTTGATTCAGCACATTAGCATCCCTTCTCATATT
66 CTAGCCTTAAATCAGCACATTAGCA-CCCTTCTCATATC
* * * * * ** * * *
625057 TAAGTCCAATATTGCTGACCTTGAATCATCATATTAGCATATTTGTCATCTTTAAGTCCAATATC
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CCTTATCATCTTTAAGCCCAATGTC
* ** ** * * *
625122 GCTAGCCTTAAATCAGCATGTTAGCACATTTTATCATCTT
65 ACTAGCCTTAAATCAGCACATTAGCAC-CCTTCTCATATC
* * * * ** *
625162 TAAGCCCAATGTCGTTGGCCTTAAATCAGCACATTAACA-CTTGTCAAACCTTCTTTCCAAAGCC
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATC--A---TCTTT---AAGCC
* * * * ** * * *
625226 CAATGTCGCTAGCCTTGAATCGGCACATTGGCACATTTATCATCTT
58 CAATGTCACTAGCCTTAAATCAGCACATTAGCACCCTTCTCATATC
* * * * * *
625272 TAAGTCTAATGTCG-TCGGCCTTGAATCAACACATTGGCACCTTTATCATCTTTAAGTCCAATGT
1 TAAGCCCAATATCGCT-GGCCTTGAATCAGCATATTGGCACC-TTATCATCTTTAAGCCCAATGT
** * *
625336 TGCGAGCCTTAAATTAGCACATTAGCACC
64 CACTAGCCTTAAATCAGCACATTAGCACC
625365 TTTATCATCA
Statistics
Matches: 329, Mismatches: 66, Indels: 30
0.77 0.16 0.07
Matches are distributed among these distances:
100 79 0.24
102 2 0.01
103 11 0.03
104 68 0.21
105 78 0.24
107 5 0.02
108 5 0.02
109 1 0.00
110 43 0.13
111 33 0.10
112 4 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (103 bp):
TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCATCTTTAAGCCCAATGTCA
CTAGCCTTAAATCAGCACATTAGCACCCTTCTCATATC
Found at i:625120 original size:52 final size:52
Alignment explanation
Indices: 624851--625197 Score: 213
Period size: 53 Copynumber: 6.7 Consensus size: 52
624841 GGCATTTCCT
* * * * * * *
624851 TTTAAGCCTAATATCGTTGGCCTTAAATCAGCATATTGGCA-CCTCATCATC
1 TTTAAGCCCAATATCGCTGACCTTGAATCAGCATATTAGCATACTTATCATC
** * * * * * *
624902 TTTAAGCCCAATGCCACT-AGCCTTAAATCAGCACATTGGC--ACCTCTCAT-
1 TTTAAGCCCAATATCGCTGA-CCTTGAATCAGCATATTAGCATACTTATCATC
* * * * *
624951 TCTAAGCCCAATATGGCTGGCCTTGAATCAGCATATTGGCA-CCTTATCATC
1 TTTAAGCCCAATATCGCTGACCTTGAATCAGCATATTAGCATACTTATCATC
* * * * * * * * *
625002 TTTAAGCCTAATGTCACTGGCCTTGATTCAGCACATTAGCATCCCTTCTCATA
1 TTTAAGCCCAATATCGCTGACCTTGAATCAGCATATTAGCAT-ACTTATCATC
* * * * *
625055 TTTAAGTCCAATATTGCTGACCTTGAATCATCATATTAGCATATTTGTCATC
1 TTTAAGCCCAATATCGCTGACCTTGAATCAGCATATTAGCATACTTATCATC
* * * * *
625107 TTTAAGTCCAATATCGCT-AGCCTTAAATCAGCATGTTAGCACATTTTATCATC
1 TTTAAGCCCAATATCGCTGA-CCTTGAATCAGCATATTAGCATA-CTTATCATC
* * * * *
625160 TTTAAGCCCAATGTCGTTGGCCTTAAATCAGCACATTA
1 TTTAAGCCCAATATCGCTGACCTTGAATCAGCATATTA
625198 ACACTTGTCA
Statistics
Matches: 230, Mismatches: 57, Indels: 16
0.76 0.19 0.05
Matches are distributed among these distances:
49 31 0.13
50 11 0.05
51 66 0.29
52 42 0.18
53 80 0.35
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (52 bp):
TTTAAGCCCAATATCGCTGACCTTGAATCAGCATATTAGCATACTTATCATC
Found at i:625294 original size:52 final size:52
Alignment explanation
Indices: 624870--625373 Score: 321
Period size: 52 Copynumber: 9.6 Consensus size: 52
624860 AATATCGTTG
* * * * * * *
624870 GCCTTAAATCAGCATATTGGCACC-TCATCATCTTTAAGCCCAATGCCACTA
1 GCCTTGAATCAGCACATTGGCACCTTTATCATCTTTAAGTCCAATGTCGCGA
* * * * * *
624921 GCCTTAAATCAGCACATTGGCACC--TCTCAT-TCTAAGCCCAATATGGCTG-
1 GCCTTGAATCAGCACATTGGCACCTTTATCATCTTTAAGTCCAATGTCGC-GA
* *
624970 GCCTTGAATCAGCATATTGGCACC-TTATCATCTTTAAG-CCTAATGTCACTG-
1 GCCTTGAATCAGCACATTGGCACCTTTATCATCTTTAAGTCC-AATGTCGC-GA
* * * * * * *
625021 GCCTTGATTCAGCACATTAGCATCCCTTCTCATATTTAAGTCCAATATTGCTGA
1 GCCTTGAATCAGCACATTGGCA-CCTTTATCATCTTTAAGTCCAATGTCGC-GA
* * * ** * * *
625075 -CCTTGAATCATCATATTAGCATATTTGTCATCTTTAAGTCCAATATCGCTA
1 GCCTTGAATCAGCACATTGGCACCTTTATCATCTTTAAGTCCAATGTCGCGA
* ** * * * *
625126 GCCTTAAATCAGCATGTTAGCACATTTTATCATCTTTAAGCCCAATGTCGTTG-
1 GCCTTGAATCAGCACATTGGCAC-CTTTATCATCTTTAAGTCCAATGTCG-CGA
* ** * * * *
625179 GCCTTAAATCAGCACATTAACA-CTTGTCAAACCTTCTTTCCAAAGCCCAATGTCGCTA
1 GCCTTGAATCAGCACATTGGCACCTT-T---ATCATCTTT---AAGTCCAATGTCGCGA
* * *
625237 GCCTTGAATCGGCACATTGGCACATTTATCATCTTTAAGTCTAATGTCGTCG-
1 GCCTTGAATCAGCACATTGGCACCTTTATCATCTTTAAGTCCAATGTCG-CGA
* *
625289 GCCTTGAATCAACACATTGGCACCTTTATCATCTTTAAGTCCAATGTTGCGA
1 GCCTTGAATCAGCACATTGGCACCTTTATCATCTTTAAGTCCAATGTCGCGA
* * *
625341 GCCTTAAATTAGCACATTAGCACCTTTATCATC
1 GCCTTGAATCAGCACATTGGCACCTTTATCATC
625374 ATTCAATCTA
Statistics
Matches: 360, Mismatches: 71, Indels: 43
0.76 0.15 0.09
Matches are distributed among these distances:
49 34 0.09
50 11 0.03
51 59 0.16
52 127 0.35
53 79 0.22
54 2 0.01
55 14 0.04
58 32 0.09
59 2 0.01
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (52 bp):
GCCTTGAATCAGCACATTGGCACCTTTATCATCTTTAAGTCCAATGTCGCGA
Found at i:626827 original size:13 final size:13
Alignment explanation
Indices: 626809--626833 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
626799 CATATTGCTT
626809 TGTATCGATACAA
1 TGTATCGATACAA
626822 TGTATCGATACA
1 TGTATCGATACA
626834 TGATCATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:626846 original size:19 final size:19
Alignment explanation
Indices: 626822--626875 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 19
626812 ATCGATACAA
**
626822 TGTATCGATACATGATCAT
1 TGTATCGATACATGAGAAT
*
626841 TGTATCAATACATAGAGAAT
1 TGTATCGATACAT-GAGAAT
*
626861 TATATCGATACATGA
1 TGTATCGATACATGA
626876 AACTGGCAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (19 bp):
TGTATCGATACATGAGAAT
Found at i:628533 original size:19 final size:18
Alignment explanation
Indices: 628482--628603 Score: 95
Period size: 19 Copynumber: 7.1 Consensus size: 18
628472 TTGAATTTCA
628482 ATAA-TTTGTATCGATAC
1 ATAAGTTTGTATCGATAC
* *
628499 AAACAGTAACTGTATCGATAC
1 ATA-AGT--TTGTATCGATAC
628520 ATAAGTGTTGTATCGATAC
1 ATAAGT-TTGTATCGATAC
628539 --AA---TGTATCGATAC
1 ATAAGTTTGTATCGATAC
628552 ATAAGTGTTGTATCGATAC
1 ATAAGT-TTGTATCGATAC
628571 --AA---TGTATCGATAC
1 ATAAGTTTGTATCGATAC
628584 ATAAGTATTGTATCGATAC
1 ATAAGT-TTGTATCGATAC
628603 A
1 A
628604 ATATATCGCT
Statistics
Matches: 84, Mismatches: 5, Indels: 30
0.71 0.04 0.25
Matches are distributed among these distances:
13 22 0.26
15 4 0.05
17 6 0.07
18 1 0.01
19 35 0.42
20 3 0.04
21 13 0.15
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (18 bp):
ATAAGTTTGTATCGATAC
Found at i:628546 original size:13 final size:13
Alignment explanation
Indices: 628528--628584 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
628518 ACATAAGTGT
628528 TGTATCGATACAA
1 TGTATCGATACAA
628541 TGTATCGATACATAA
1 TGTATCGATAC--AA
628556 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
628573 TGTATCGATACA
1 TGTATCGATACA
628585 TAAGTATTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:628550 original size:32 final size:32
Alignment explanation
Indices: 628509--628616 Score: 189
Period size: 32 Copynumber: 3.4 Consensus size: 32
628499 AAACAGTAAC
628509 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
628541 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
628573 TGTATCGATACATAAGTATTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
628605 TATATCGCTACA
1 TGTATCGATACA
628617 AAGCTACTGC
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 73 1.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:629596 original size:33 final size:32
Alignment explanation
Indices: 629559--629626 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
629549 CGTTACAAGC
**
629559 CAATGTATCGATACATTTTATGATGTATCGATA
1 CAATGTATCGATACATACTATG-TGTATCGATA
*
629592 CAATGTATCGATACATACTGTGTGTATCGATA
1 CAATGTATCGATACATACTATGTGTATCGATA
629624 CAA
1 CAA
629627 GTTTAGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATACTATGTGTATCGATA
Found at i:629599 original size:13 final size:13
Alignment explanation
Indices: 629581--629606 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
629571 ACATTTTATG
629581 ATGTATCGATACA
1 ATGTATCGATACA
629594 ATGTATCGATACA
1 ATGTATCGATACA
629607 TACTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:629674 original size:20 final size:20
Alignment explanation
Indices: 629649--629699 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
629639 CCAATGACTT
* **
629649 GTATCGATATATTTTTTCAA
1 GTATCGATACATTTAGTCAA
*
629669 GTATCGATACATTTAGTCAT
1 GTATCGATACATTTAGTCAA
629689 GTATCGATACA
1 GTATCGATACA
629700 ATGTATCGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (20 bp):
GTATCGATACATTTAGTCAA
Found at i:629705 original size:13 final size:13
Alignment explanation
Indices: 629687--629711 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
629677 ACATTTAGTC
629687 ATGTATCGATACA
1 ATGTATCGATACA
629700 ATGTATCGATAC
1 ATGTATCGATAC
629712 TGTGCAACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:630310 original size:22 final size:21
Alignment explanation
Indices: 630267--630310 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
630257 TTTTCTTTTC
* *
630267 TCTCCCCCTTAATCAAACATT
1 TCTCCCCCTTAATAAAAAATT
*
630288 TCTCCCCCTTAGTAAAATAATT
1 TCTCCCCCTTAATAAAA-AATT
630310 T
1 T
630311 AACACTTTCG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.30, C:0.32, G:0.02, T:0.36
Consensus pattern (21 bp):
TCTCCCCCTTAATAAAAAATT
Found at i:630358 original size:23 final size:23
Alignment explanation
Indices: 630331--630401 Score: 81
Period size: 23 Copynumber: 3.0 Consensus size: 23
630321 CACATTAACC
*
630331 ATTTCTTTCTCCCCCTTAATCAT
1 ATTTCTTACTCCCCCTTAATCAT
**
630354 ATTTCTTACTCCCTATTAATCACAT
1 ATTTCTTACTCCCCCTTAAT--CAT
*
630379 ATTTCTTACT-CTCCTTAATCAT
1 ATTTCTTACTCCCCCTTAATCAT
630401 A
1 A
630402 AATTTATTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
22 4 0.10
23 17 0.43
24 6 0.15
25 13 0.32
ACGTcount: A:0.24, C:0.30, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTCTTACTCCCCCTTAATCAT
Found at i:630406 original size:24 final size:22
Alignment explanation
Indices: 630343--630402 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 22
630333 TTCTTTCTCC
630343 CCCTTAATCAT-ATTTCTTACT
1 CCCTTAATCATAATTTCTTACT
*
630364 CCCTATTAATCACATATTTCTTACT
1 CCC--TTAATCATA-ATTTCTTACT
630389 CTCCTTAATCATAA
1 C-CCTTAATCATAA
630403 ATTTATTTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
21 3 0.09
23 8 0.25
24 8 0.25
25 11 0.34
26 2 0.06
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.43
Consensus pattern (22 bp):
CCCTTAATCATAATTTCTTACT
Found at i:632050 original size:20 final size:21
Alignment explanation
Indices: 632021--632061 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
632011 TTTTTTTGAT
632021 GATGATTTTG-A-TGAAAAAC
1 GATGATTTTGAAGTGAAAAAC
632040 GATGTATTTTGAAGTGAAAAAC
1 GATG-ATTTTGAAGTGAAAAAC
632062 AAGAAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 1 0.05
22 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (21 bp):
GATGATTTTGAAGTGAAAAAC
Found at i:638408 original size:13 final size:13
Alignment explanation
Indices: 638390--638415 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
638380 ACATTTTATG
638390 ATGTATCGATACA
1 ATGTATCGATACA
638403 ATGTATCGATACA
1 ATGTATCGATACA
638416 TACTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:638511 original size:20 final size:20
Alignment explanation
Indices: 638467--638514 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
638457 GCCAATGACT
*
638467 TGTATCGATACAGTTTTTCA
1 TGTATCGATACAGTTTGTCA
*
638487 AGTATCGATACA-TTTAGTCA
1 TGTATCGATACAGTTT-GTCA
638507 TGTATCGA
1 TGTATCGA
638515 GACAATGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.40
Consensus pattern (20 bp):
TGTATCGATACAGTTTGTCA
Found at i:649064 original size:79 final size:78
Alignment explanation
Indices: 648930--649101 Score: 227
Period size: 79 Copynumber: 2.2 Consensus size: 78
648920 GATGACGATG
* * * * *
648930 GGGTTGGAGTACCCCTGATTATGGAAAATCGGTGTTCTGAAAATAAAATCGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCTAATTATAGAAAATCGGTGTTCTGAAAATAAAATCAGGGTTAGAGTATCC
** *
648995 CCTTGGAAATAATA
66 CCACGAAAATAA-A
* *
649009 GGGTTGGAGTATCCCTAATTATAGAAAATTGGTGTTTTGAAAATAAAATCAGGGTTAGAGTATCC
1 GGGTTGGAGTATCCCTAATTATAGAAAATCGGTGTTCTGAAAATAAAATCAGGGTTAGAGTATCC
*
649074 CCACGAAAATAAC
66 CCACGAAAATAAA
649087 GGCGTTGGAGTATCC
1 GG-GTTGGAGTATCC
649102 TCGATTGTGA
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
78 2 0.02
79 79 0.98
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (78 bp):
GGGTTGGAGTATCCCTAATTATAGAAAATCGGTGTTCTGAAAATAAAATCAGGGTTAGAGTATCC
CCACGAAAATAAA
Found at i:649133 original size:79 final size:77
Alignment explanation
Indices: 649050--649264 Score: 315
Period size: 79 Copynumber: 2.7 Consensus size: 77
649040 GTGTTTTGAA
* * *
649050 AATAAAATCAGGGTTAGAGTATCCCCACGAAAATAACG-GCGTTGGAGTATCCTCGATTGTGAGA
1 AATAAAA-CGGGGTT-GAGTATCCCCTCGAAAATAACGAG-GTTGGAGTATCCCCGATTGTGAGA
649114 AATCAATATTTTAGG
63 AATCAATATTTTAGG
649129 AATAAAACTGGGGTTGCAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCGATTGTGAGAA
1 AATAAAAC-GGGGTTG-AGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCGATTGTGAGAA
649194 ATCAATATTTTAGG
64 ATCAATATTTTAGG
* *
649208 AATAAAGCCGGGGTTGGAGTATCCCCTCGGAAATAACGAGGTTGGAGTATCCCCGAT
1 AATAAA-ACGGGGTT-GAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCGAT
649265 GATTAACGAG
Statistics
Matches: 126, Mismatches: 5, Indels: 10
0.89 0.04 0.07
Matches are distributed among these distances:
78 2 0.02
79 121 0.96
80 3 0.02
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (77 bp):
AATAAAACGGGGTTGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCGATTGTGAGAAAT
CAATATTTTAGG
Found at i:649251 original size:28 final size:27
Alignment explanation
Indices: 649219--649290 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
649209 ATAAAGCCGG
**
649219 GGTTGGAGTATCCCCTCGGAAATAACGA
1 GGTTGGAGTATCCCCGAGG-AATAACGA
* *
649247 GGTTGGAGTATCCCCGATGATTAACGA
1 GGTTGGAGTATCCCCGAGGAATAACGA
*
649274 GGTTGGAGTGTCCCCGA
1 GGTTGGAGTATCCCCGA
649291 TTATGAGAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 23 0.59
28 16 0.41
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.24
Consensus pattern (27 bp):
GGTTGGAGTATCCCCGAGGAATAACGA
Found at i:649354 original size:52 final size:51
Alignment explanation
Indices: 649275--649453 Score: 236
Period size: 51 Copynumber: 3.5 Consensus size: 51
649265 GATTAACGAG
*
649275 GTTGGAGTGTCCCCGATTATGAGAAATTGGTGTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGA-AAATTGGTGTTTTTGGAAATAAAATCGGA
* *
649327 GTTGGAGTATCCTCGATTATAGAAAATTGGTG-TTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTAT-GAAAATTGGTGTTTTTGGAAATAAAATCGGA
* * * * *
649378 GTTGGAGTATCCCCAATTATGAAAAATTAGTGTTTTAGG-AATAAAACCGGG
1 GTTGGAGTATCCCCGATTATG-AAAATTGGTGTTTTTGGAAATAAAATCGGA
*
649429 GTTGGAGTACCCCCGATTATGAAAA
1 GTTGGAGTATCCCCGATTATGAAAA
649454 ATTGAGAAAC
Statistics
Matches: 112, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
50 5 0.04
51 74 0.66
52 31 0.28
53 2 0.02
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAATTGGTGTTTTTGGAAATAAAATCGGA
Found at i:651828 original size:13 final size:13
Alignment explanation
Indices: 651810--651835 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
651800 ACAAAGATCG
651810 ATGTATCGATACA
1 ATGTATCGATACA
651823 ATGTATCGATACA
1 ATGTATCGATACA
651836 TTTCCTTGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:651901 original size:32 final size:32
Alignment explanation
Indices: 651859--651931 Score: 119
Period size: 32 Copynumber: 2.3 Consensus size: 32
651849 AACTTCGTAG
*
651859 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTAATGTAT
* *
651891 CGATATATTGTATCGATACAACACTAATGTAT
1 CGATACATTGTATCGATACAAAACTAATGTAT
651923 CGATACATT
1 CGATACATT
651932 TACTATTTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTAATGTAT
Found at i:652318 original size:62 final size:62
Alignment explanation
Indices: 652139--652324 Score: 347
Period size: 62 Copynumber: 3.0 Consensus size: 62
652129 AAAAACCATT
*
652139 TTCAAGTTGTCGAAAATGAATTCATCCCCACATATGTCCAATCCTCCACCTACTAACTAGGC
1 TTCAAGTTGTCGAAAATGAATTCATCCCCACATATGTCCAATCCTCCACCTACTAGCTAGGC
652201 TTCAAGTTGTCGAAAATGAATTCATCCCCACATATGTCCAATCCTCCACCTACTAGCTAGGC
1 TTCAAGTTGTCGAAAATGAATTCATCCCCACATATGTCCAATCCTCCACCTACTAGCTAGGC
*
652263 TTCAAGTTGTCGAAAATGAATTCATCCCTACATATGTCCAATCCTCCACCTACTAGCT-GGC
1 TTCAAGTTGTCGAAAATGAATTCATCCCCACATATGTCCAATCCTCCACCTACTAGCTAGGC
652324 T
1 T
652325 CGGACAAAAT
Statistics
Matches: 122, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
61 4 0.03
62 118 0.97
ACGTcount: A:0.29, C:0.30, G:0.12, T:0.28
Consensus pattern (62 bp):
TTCAAGTTGTCGAAAATGAATTCATCCCCACATATGTCCAATCCTCCACCTACTAGCTAGGC
Found at i:656991 original size:5 final size:5
Alignment explanation
Indices: 656977--657024 Score: 62
Period size: 5 Copynumber: 9.4 Consensus size: 5
656967 CGTCTTCCGT
*
656977 AAAA- AAAAC AAAAC AAAAC AAAAC AAAAA AAAAC AAACAAC AAAAC AA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC -AA-AAC AAAAC AA
657025 CAAAAAGGGT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
4 4 0.10
5 28 0.72
6 4 0.10
7 3 0.08
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:657029 original size:22 final size:24
Alignment explanation
Indices: 656977--657030 Score: 76
Period size: 22 Copynumber: 2.3 Consensus size: 24
656967 CGTCTTCCGT
656977 AAAAAAAACAAAACAAAACAAAACA
1 AAAAAAAACAAAAC-AAACAAAACA
657002 AAAAAAAAC-AAAC-AACAAAACA
1 AAAAAAAACAAAACAAACAAAACA
*
657024 ACAAAAA
1 AAAAAAA
657031 GGGTCCGGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 15 0.54
24 4 0.14
25 9 0.32
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (24 bp):
AAAAAAAACAAAACAAACAAAACA
Found at i:658566 original size:29 final size:29
Alignment explanation
Indices: 658466--658810 Score: 475
Period size: 29 Copynumber: 12.0 Consensus size: 29
658456 TTTCTCACCT
658466 TTTCCAAAGCCCACAAGTCAGTGGCAT-C
1 TTTCCAAAGCCCACAAGTCAGTGGCATCC
*
658494 TTTCCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCCAAAGCCCACAAGTCAGTGGCATCC
*
658523 TTTTCTAAAGCCCACAAGTCAGTGGCATCC
1 -TTTCCAAAGCCCACAAGTCAGTGGCATCC
658553 TTTCCAAAGCCCACAAGTCAGTGGCATCC
1 TTTCCAAAGCCCACAAGTCAGTGGCATCC
658582 TTTCCAAAGCCCACAAGTCAGTGGCATCC
1 TTTCCAAAGCCCACAAGTCAGTGGCATCC
*
658611 TTTCCAAAGCCCACAAGTCAGTGGCAACC
1 TTTCCAAAGCCCACAAGTCAGTGGCATCC
* * *
658640 -TTCAAAAGCCTACAAGTCAGTGGCATCT
1 TTTCCAAAGCCCACAAGTCAGTGGCATCC
*
658668 TTTCCAAAGCCCACAAGTCAGTGGCAACC
1 TTTCCAAAGCCCACAAGTCAGTGGCATCC
*
658697 -TTCAAAAGCCCACAAGTCAGTGGCA-CC
1 TTTCCAAAGCCCACAAGTCAGTGGCATCC
* *
658724 TTTTTCCAAAGCCCACAAGTCAGTGGTATCT
1 --TTTCCAAAGCCCACAAGTCAGTGGCATCC
* * *
658755 TTTCAAAAGCCCACAAGTTAGTGGCAACC
1 TTTCCAAAGCCCACAAGTCAGTGGCATCC
* * **
658784 -TTCAAAAGCACACAAGTTGGTGGCATC
1 TTTCCAAAGCCCACAAGTCAGTGGCATC
658811 TTCTTCTAAG
Statistics
Matches: 285, Mismatches: 25, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
27 2 0.01
28 98 0.34
29 134 0.47
30 50 0.18
31 1 0.00
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.21
Consensus pattern (29 bp):
TTTCCAAAGCCCACAAGTCAGTGGCATCC
Found at i:658925 original size:49 final size:49
Alignment explanation
Indices: 658864--659166 Score: 282
Period size: 49 Copynumber: 6.2 Consensus size: 49
658854 CATCTTTGAA
658864 CCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGT
*
658913 CCAATATCGCTGGCCTTGAATCAGCATATTGGCA----C--CTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGT
* *
658956 CCAATGTCG-TCGGCCTTGAATCAGCACATTGGTATCTTCATCTTTAAGT
1 CCAATATCGCT-GGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGT
* * * * * *
659005 CCGATATCGTTGGCCTTGAATCAGCATATTGGCATCTTTAATATTACTAAGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCATC-TTCATCTT--TAAGT
* ** * *
659057 CCAATGTCGCTGGCCTTGTCTCAGCACATTGGCA--TTCTTCTTCAAGT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGT
* * * * * ** *
659104 CTAATGTCGCTGGCCATGAATCAACACATTGTCATTCTTCGCATCTTCGAGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCA-TCTT--CATCTTTAAGT
659156 CCAATATCGCT
1 CCAATATCGCT
659167 AGCCGCATAT
Statistics
Matches: 205, Mismatches: 33, Indels: 29
0.77 0.12 0.11
Matches are distributed among these distances:
42 1 0.00
43 37 0.18
45 1 0.00
47 32 0.16
49 76 0.37
50 9 0.04
52 49 0.24
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.33
Consensus pattern (49 bp):
CCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGT
Found at i:658971 original size:43 final size:43
Alignment explanation
Indices: 658902--659045 Score: 173
Period size: 43 Copynumber: 3.2 Consensus size: 43
658892 TTGGCATCTT
658902 CATCTTTAAGTCCAATATCG-CTGGCCTTGAATCAGCATATTGG
1 CATCTTTAAGTCCAATATCGTC-GGCCTTGAATCAGCATATTGG
* * *
658945 CACCTTTAAGTCCAATGTCGTCGGCCTTGAATCAGCACATTGG
1 CATCTTTAAGTCCAATATCGTCGGCCTTGAATCAGCATATTGG
* *
658988 TATCTTCATCTTTAAGTCCGATATCGTTGGCCTTGAATCAGCATATTGG
1 ------CATCTTTAAGTCCAATATCGTCGGCCTTGAATCAGCATATTGG
659037 CATCTTTAA
1 CATCTTTAA
659046 TATTACTAAG
Statistics
Matches: 86, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
43 47 0.55
44 1 0.01
49 38 0.44
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (43 bp):
CATCTTTAAGTCCAATATCGTCGGCCTTGAATCAGCATATTGG
Found at i:659001 original size:92 final size:90
Alignment explanation
Indices: 658804--659045 Score: 373
Period size: 92 Copynumber: 2.7 Consensus size: 90
658794 CACAAGTTGG
*
658804 TGGCATCTTC-T-TCTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTTGAACCA
1 TGGCATCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTT-AACCA
658867 ATATCGCTGGCCTTGAATCAGCACAT
65 ATATCGCTGGCCTTGAATCAGCACAT
*
658893 TGGCATCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCC
1 TGGCATCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTTAA--CC
*
658958 AATGTCG-TCGGCCTTGAATCAGCACAT
64 AATATCGCT-GGCCTTGAATCAGCACAT
* * *
658985 TGGTATCTTCATCTTTAAGTCCGATATCGTTGGCCTTGAATCAGCATATTGGCATCTTTAA
1 TGGCATCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTTAA
659046 TATTACTAAG
Statistics
Matches: 141, Mismatches: 7, Indels: 7
0.91 0.05 0.05
Matches are distributed among these distances:
89 10 0.07
90 3 0.02
91 45 0.32
92 83 0.59
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.33
Consensus pattern (90 bp):
TGGCATCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTTAACCAA
TATCGCTGGCCTTGAATCAGCACAT
Found at i:659874 original size:19 final size:19
Alignment explanation
Indices: 659850--659908 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
659840 AAATAGTAAC
659850 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
659869 TGTATCGATAC--AA----
1 TGTATCGATACATAAGTGT
*
659882 TGTATCGATACATAGGTGT
1 TGTATCGATACATAAGTGT
659901 TGTATCGA
1 TGTATCGA
659909 CACAATGTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
13 11 0.33
15 1 0.03
17 2 0.06
19 19 0.58
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:659887 original size:13 final size:13
Alignment explanation
Indices: 659869--659893 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
659859 ACATAAGTGT
659869 TGTATCGATACAA
1 TGTATCGATACAA
659882 TGTATCGATACA
1 TGTATCGATACA
659894 TAGGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:659891 original size:32 final size:32
Alignment explanation
Indices: 659850--659925 Score: 125
Period size: 32 Copynumber: 2.4 Consensus size: 32
659840 AAATAGTAAC
*
659850 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGACACAA
*
659882 TGTATCGATACATAGGTGTTGTATCGACACAA
1 TGTATCGATACATAAGTGTTGTATCGACACAA
*
659914 TGTATCGCTACA
1 TGTATCGATACA
659926 AAGCTACTGC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGACACAA
Found at i:659967 original size:20 final size:20
Alignment explanation
Indices: 659942--659996 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
659932 CTGCCAAGGA
659942 AATGTATCGATACATT-ATTC
1 AATGTATCGATACATTGA-TC
*
659962 AATGTATCGATACGTTGATC
1 AATGTATCGATACATTGATC
**
659982 TTTGTATCGATACAT
1 AATGTATCGATACAT
659997 CTAGGAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
AATGTATCGATACATTGATC
Found at i:664897 original size:20 final size:21
Alignment explanation
Indices: 664857--664898 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
664847 TTCTACGATT
*
664857 TGTATCGATACAATTAGTGAA
1 TGTATCGATACAATAAGTGAA
664878 TGTATCGATAC-ATAAGTGAA
1 TGTATCGATACAATAAGTGAA
664898 T
1 T
664899 ATATTAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (21 bp):
TGTATCGATACAATAAGTGAA
Found at i:664984 original size:20 final size:20
Alignment explanation
Indices: 664959--665010 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
664949 GTTGAAAAAT
*
664959 TGTATCGATACATAAGTAAA
1 TGTATCGATACATAACTAAA
* **
664979 TGTATCGATGCATTTCTAAA
1 TGTATCGATACATAACTAAA
*
664999 TGTATCAATACA
1 TGTATCGATACA
665011 ATTGGCTTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (20 bp):
TGTATCGATACATAACTAAA
Found at i:666485 original size:13 final size:13
Alignment explanation
Indices: 666467--666491 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
666457 CATAAAGTGT
666467 TGTATCGATACAA
1 TGTATCGATACAA
666480 TGTATCGATACA
1 TGTATCGATACA
666492 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:666489 original size:33 final size:33
Alignment explanation
Indices: 666447--666511 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
666437 TTCAACGATT
666447 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
666480 TGTATCGATACATATTTTTTTGTATCGATACA
1 TGTATCGATACATAAAGTGTTGTATCGATACA
666512 TATTTTTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:666505 original size:20 final size:20
Alignment explanation
Indices: 666480--666535 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
666470 ATCGATACAA
666480 TGTATCGATACATATTTTTT
1 TGTATCGATACATATTTTTT
666500 TGTATCGATACATATTTTTT
1 TGTATCGATACATATTTTTT
666520 TGTATCGATACA-ATTT
1 TGTATCGATACATATTT
666536 AAGCTACTGC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 4 0.11
20 32 0.89
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.52
Consensus pattern (20 bp):
TGTATCGATACATATTTTTT
Found at i:666575 original size:21 final size:21
Alignment explanation
Indices: 666550--666608 Score: 118
Period size: 21 Copynumber: 2.8 Consensus size: 21
666540 TACTGCCAAA
666550 AAATGTATCGATACATTACTC
1 AAATGTATCGATACATTACTC
666571 AAATGTATCGATACATTACTC
1 AAATGTATCGATACATTACTC
666592 AAATGTATCGATACATT
1 AAATGTATCGATACATT
666609 GTATCAATAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (21 bp):
AAATGTATCGATACATTACTC
Found at i:676761 original size:18 final size:18
Alignment explanation
Indices: 676717--676761 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
676707 ATGCAAGCCC
*
676717 AAATTATGAAGCTCATGG
1 AAATTATGTAGCTCATGG
676735 AAATTATGTAGCTCATGG
1 AAATTATGTAGCTCATGG
676753 AAATTATGT
1 AAATTATGT
676762 CGGCATCCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (18 bp):
AAATTATGTAGCTCATGG
Found at i:683890 original size:9 final size:9
Alignment explanation
Indices: 683876--683946 Score: 72
Period size: 9 Copynumber: 7.4 Consensus size: 9
683866 CTTTGTACCC
683876 AAAAAAACA
1 AAAAAAACA
683885 AAAAAAA-A
1 AAAAAAACA
683893 GAAAAAAACCA
1 -AAAAAAA-CA
683904 AAAAAAACA
1 AAAAAAACA
*
683913 AAAAAACCA
1 AAAAAAACA
*
683922 AGAAAAAATA
1 A-AAAAAACA
683932 GCAAAAAAACA
1 --AAAAAAACA
683943 AAAA
1 AAAA
683947 GGGGTCCAGA
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
8 1 0.02
9 29 0.56
10 13 0.25
11 8 0.15
12 1 0.02
ACGTcount: A:0.83, C:0.11, G:0.04, T:0.01
Consensus pattern (9 bp):
AAAAAAACA
Found at i:683899 original size:18 final size:18
Alignment explanation
Indices: 683876--683946 Score: 88
Period size: 18 Copynumber: 3.7 Consensus size: 18
683866 CTTTGTACCC
683876 AAAAAAACAAAAAAAAAG
1 AAAAAAACAAAAAAAAAG
* *
683894 AAAAAAACCAAAAAAAAC
1 AAAAAAACAAAAAAAAAG
683912 AAAAAAACCAAGAAAAAATAG
1 AAAAAAA-CAA-AAAAAA-AG
683933 CAAAAAAACAAAAA
1 -AAAAAAACAAAAA
683947 GGGGTCCAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
18 23 0.51
19 2 0.04
20 9 0.20
21 4 0.09
22 7 0.16
ACGTcount: A:0.83, C:0.11, G:0.04, T:0.01
Consensus pattern (18 bp):
AAAAAAACAAAAAAAAAG
Found at i:683941 original size:30 final size:27
Alignment explanation
Indices: 683874--683946 Score: 101
Period size: 30 Copynumber: 2.6 Consensus size: 27
683864 TCCTTTGTAC
683874 CCAAAAAAACAAAAAAAAAGAAAAAAA
1 CCAAAAAAACAAAAAAAAAGAAAAAAA
683901 CCAAAAAAAACAAAAAAACCAAGAAAAAATA
1 CC-AAAAAAACAAAAAAA--AAGAAAAAA-A
*
683932 GCAAAAAAACAAAAA
1 CCAAAAAAACAAAAA
683947 GGGGTCCAGA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
27 2 0.05
28 15 0.37
30 22 0.54
31 2 0.05
ACGTcount: A:0.81, C:0.14, G:0.04, T:0.01
Consensus pattern (27 bp):
CCAAAAAAACAAAAAAAAAGAAAAAAA
Done.