Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008527.1 Hibiscus syriacus cultivar Beakdansim tig00111402_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 9057482
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 26 of 37
Found at i:6309253 original size:21 final size:22
Alignment explanation
Indices: 6309229--6309271 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
6309219 TTCTGAAACA
6309229 CTAAACTC-TACAATCA-TAATG
1 CTAAACTCATACAA-CATTAATG
*
6309250 CTAAGCTCATACAACATTAATG
1 CTAAACTCATACAACATTAATG
6309272 AACCGCAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.42, C:0.23, G:0.07, T:0.28
Consensus pattern (22 bp):
CTAAACTCATACAACATTAATG
Found at i:6311979 original size:4 final size:4
Alignment explanation
Indices: 6311970--6311997 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
6311960 ACCTAGTAGA
6311970 GAAT GAAT GAAT GAAT GAAT GAAT GAAT
1 GAAT GAAT GAAT GAAT GAAT GAAT GAAT
6311998 AAAATCAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
GAAT
Found at i:6316214 original size:22 final size:22
Alignment explanation
Indices: 6316186--6316227 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
6316176 AAAAAAAAGA
* *
6316186 TGAGAGAGAGGGAGAGAAGTTG
1 TGAGAGAAAGGGAGAAAAGTTG
6316208 TGAGAGAAAGGGAGAAAAGT
1 TGAGAGAAAGGGAGAAAAGT
6316228 AATTTTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.45, T:0.12
Consensus pattern (22 bp):
TGAGAGAAAGGGAGAAAAGTTG
Found at i:6324910 original size:19 final size:19
Alignment explanation
Indices: 6324886--6325009 Score: 149
Period size: 19 Copynumber: 6.2 Consensus size: 19
6324876 GCGATTTTGA
*
6324886 AAAATGTATTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
6324905 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
6324924 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
*
6324943 AAAATGTGTTGCGAGAGTTT
1 AAAATGTGTTGCGATAG-TT
*
6324963 GAAAAACGTGTTGTTGCGATAGTG
1 --AAAA--TG-TGTTGCGATAGTT
* *
6324987 AAAAAGTGTTGCGATAGTG
1 AAAATGTGTTGCGATAGTT
6325006 AAAA
1 AAAA
6325010 ATCCAAAATA
Statistics
Matches: 94, Mismatches: 5, Indels: 12
0.85 0.05 0.11
Matches are distributed among these distances:
19 70 0.74
20 3 0.03
22 8 0.09
24 3 0.03
25 10 0.11
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTT
Found at i:6325466 original size:40 final size:40
Alignment explanation
Indices: 6325404--6325528 Score: 141
Period size: 40 Copynumber: 3.1 Consensus size: 40
6325394 TCGTTGCGAT
* * *
6325404 TTTGGAAAATCGCAACGCGAACTTCGACTATTGCAACGAA
1 TTTGAAAAATCGCAACGTGAACTTGGACTATTGCAACGAA
6325444 TTTGAAAAATCGCAACGTGAACTTGGACTA-T-C-ACGTAAA
1 TTTGAAAAATCGCAACGTGAACTTGGACTATTGCAACG--AA
** *
6325483 TTT-AGAAAATCGCAATATGAACTTGGACTATCGCAACGAA
1 TTTGA-AAAATCGCAACGTGAACTTGGACTATTGCAACGAA
6325523 TTTGAA
1 TTTGAA
6325529 CTTGCGATAG
Statistics
Matches: 72, Mismatches: 6, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
37 3 0.04
38 2 0.03
39 29 0.40
40 33 0.46
41 2 0.03
42 3 0.04
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (40 bp):
TTTGAAAAATCGCAACGTGAACTTGGACTATTGCAACGAA
Found at i:6325675 original size:20 final size:21
Alignment explanation
Indices: 6325624--6325678 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
6325614 GCAATAGTCA
6325624 AAATCGCGTTGCGA-ATCTGG
1 AAATCGCGTTGCGATATCTGG
**
6325644 AAA-CTGATTTGCGATA-CTGG
1 AAATC-GCGTTGCGATATCTGG
6325664 AAATCGCGTTGCGAT
1 AAATCGCGTTGCGAT
6325679 TTAGAGATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
19 1 0.04
20 25 0.89
21 2 0.07
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (21 bp):
AAATCGCGTTGCGATATCTGG
Found at i:6338666 original size:23 final size:23
Alignment explanation
Indices: 6338608--6338676 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
6338598 ACATCTTATA
* * *
6338608 TGGCACTTTGGTGTATTTCTACG
1 TGGCACTTTGATGCAATTCTACG
* * **
6338631 CGGTACTACGATGCAATTCTACG
1 TGGCACTTTGATGCAATTCTACG
*
6338654 TGGCACTTTGATGCAATTATACG
1 TGGCACTTTGATGCAATTCTACG
6338677 AGCTGTGGTG
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (23 bp):
TGGCACTTTGATGCAATTCTACG
Found at i:6343912 original size:141 final size:141
Alignment explanation
Indices: 6343658--6343938 Score: 562
Period size: 141 Copynumber: 2.0 Consensus size: 141
6343648 ATAAAGCATC
6343658 TCCCTATAGTCAATGAACCATTTGTGCACCTAACTAAATAAACTATAACTAATATATTTAAAGGT
1 TCCCTATAGTCAATGAACCATTTGTGCACCTAACTAAATAAACTATAACTAATATATTTAAAGGT
6343723 TGTTAACAATGTCATCCTCACCATGTATGTTATTATAAGGACAACCATACAGTAAAATAATCTTA
66 TGTTAACAATGTCATCCTCACCATGTATGTTATTATAAGGACAACCATACAGTAAAATAATCTTA
6343788 CTTTCATGATT
131 CTTTCATGATT
6343799 TCCCTATAGTCAATGAACCATTTGTGCACCTAACTAAATAAACTATAACTAATATATTTAAAGGT
1 TCCCTATAGTCAATGAACCATTTGTGCACCTAACTAAATAAACTATAACTAATATATTTAAAGGT
6343864 TGTTAACAATGTCATCCTCACCATGTATGTTATTATAAGGACAACCATACAGTAAAATAATCTTA
66 TGTTAACAATGTCATCCTCACCATGTATGTTATTATAAGGACAACCATACAGTAAAATAATCTTA
6343929 CTTTCATGAT
131 CTTTCATGAT
6343939 AAAATCATTA
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
141 140 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.34
Consensus pattern (141 bp):
TCCCTATAGTCAATGAACCATTTGTGCACCTAACTAAATAAACTATAACTAATATATTTAAAGGT
TGTTAACAATGTCATCCTCACCATGTATGTTATTATAAGGACAACCATACAGTAAAATAATCTTA
CTTTCATGATT
Found at i:6353427 original size:23 final size:20
Alignment explanation
Indices: 6353368--6353416 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
6353358 TTTTGGGTCC
6353368 AACAATGGCAATTGACGGTA
1 AACAATGGCAATTGACGGTA
6353388 AACAATGGCAATTGACGGTA
1 AACAATGGCAATTGACGGTA
*
6353408 ATCAATGGC
1 AACAATGGC
6353417 GACAATTGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.20
Consensus pattern (20 bp):
AACAATGGCAATTGACGGTA
Found at i:6357453 original size:15 final size:15
Alignment explanation
Indices: 6357433--6357461 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6357423 ATACATGAAG
6357433 GGACAAAACCCTTCT
1 GGACAAAACCCTTCT
6357448 GGACAAAACCCTTC
1 GGACAAAACCCTTC
6357462 AACATATCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.34, G:0.14, T:0.17
Consensus pattern (15 bp):
GGACAAAACCCTTCT
Found at i:6359019 original size:19 final size:18
Alignment explanation
Indices: 6358995--6359043 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
6358985 ATACTCAAAA
*
6358995 TAATATTATTTTATATATT
1 TAATATTATTTGATAT-TT
*
6359014 TAATATTAATATGATATTT
1 TAATATT-ATTTGATATTT
*
6359033 TAATATCATTT
1 TAATATTATTT
6359044 AATCAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 3 0.12
19 15 0.60
20 7 0.28
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (18 bp):
TAATATTATTTGATATTT
Found at i:6359053 original size:29 final size:27
Alignment explanation
Indices: 6359001--6359054 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 27
6358991 AAAATAATAT
*
6359001 TATTTTATATATTTAATATTAATATGA
1 TATTTTATATATTTAATATAAATATGA
6359028 TATTTTAATATCATTTAATCA-AAATAT
1 TATTTT-ATAT-ATTTAAT-ATAAATAT
6359055 TAATTATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 6 0.26
28 4 0.17
29 12 0.52
30 1 0.04
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (27 bp):
TATTTTATATATTTAATATAAATATGA
Found at i:6359627 original size:24 final size:25
Alignment explanation
Indices: 6359583--6359632 Score: 59
Period size: 24 Copynumber: 2.0 Consensus size: 25
6359573 ATATACGTTA
*
6359583 TTATTTGATATAAATTGTATTAAAT
1 TTATTTGATATAAATTCTATTAAAT
*
6359608 TTATTT-ATAT-AATATCTATTTAAT
1 TTATTTGATATAAAT-TCTATTAAAT
6359632 T
1 T
6359633 CAAAATCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 3 0.14
24 13 0.59
25 6 0.27
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (25 bp):
TTATTTGATATAAATTCTATTAAAT
Found at i:6363227 original size:57 final size:58
Alignment explanation
Indices: 6363058--6363228 Score: 220
Period size: 57 Copynumber: 2.9 Consensus size: 58
6363048 GTCACGGGAG
**
6363058 AATGACCTGTCAGATCTGCTACTACCACCAATTAGCCAGTCATCCCTACCG-CTTTTCGAA
1 AATGACCTGTTTGATCTGCTACT---ACCAATTAGCCAGTCATCCCTACCGCCTTTTCGAA
* * *
6363118 AATGACCTGTTTGATCTGCTACTACCGATTAGCCAGTCATCCCTACCACCTTTT-GGA
1 AATGACCTGTTTGATCTGCTACTACCAATTAGCCAGTCATCCCTACCGCCTTTTCGAA
* * * *
6363175 AATGACCTGTTTGATCTGCTACTGCCAATTAGCCAGTTATCCCGACTGCCTTTT
1 AATGACCTGTTTGATCTGCTACTACCAATTAGCCAGTCATCCCTACCGCCTTTT
6363229 TAACTCTGCG
Statistics
Matches: 99, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
57 73 0.74
58 5 0.05
60 21 0.21
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.31
Consensus pattern (58 bp):
AATGACCTGTTTGATCTGCTACTACCAATTAGCCAGTCATCCCTACCGCCTTTTCGAA
Found at i:6367661 original size:13 final size:13
Alignment explanation
Indices: 6367643--6367680 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
6367633 TCATAACCCG
6367643 ACCCGACCCGTTT
1 ACCCGACCCGTTT
6367656 ACCCGACCCGTTT
1 ACCCGACCCGTTT
6367669 ACCCGACCCGTT
1 ACCCGACCCGTT
6367681 GACCGATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.16, C:0.47, G:0.16, T:0.21
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:6370198 original size:28 final size:23
Alignment explanation
Indices: 6370165--6370254 Score: 117
Period size: 23 Copynumber: 3.8 Consensus size: 23
6370155 TCTGATTTGA
* * *
6370165 ATTCTGTTATGATGTTGACATGG
1 ATTCTGATCTGATATTGACATGG
6370188 ATTCTGATCTGATATTGACATGG
1 ATTCTGATCTGATATTGACATGG
*
6370211 ATTCTGATCTGATACATGACATGG
1 ATTCTGATCTGATA-TTGACATGG
*
6370235 ATTCTGATATGATACTTGAC
1 ATTCTGATCTGATA-TTGAC
6370255 TTGAATTATG
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
23 34 0.57
24 26 0.43
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (23 bp):
ATTCTGATCTGATATTGACATGG
Found at i:6370235 original size:24 final size:24
Alignment explanation
Indices: 6370179--6370254 Score: 127
Period size: 24 Copynumber: 3.2 Consensus size: 24
6370169 TGTTATGATG
6370179 TTGACATGGATTCTGATCTGATA-
1 TTGACATGGATTCTGATCTGATAC
6370202 TTGACATGGATTCTGATCTGATAC
1 TTGACATGGATTCTGATCTGATAC
* *
6370226 ATGACATGGATTCTGATATGATAC
1 TTGACATGGATTCTGATCTGATAC
6370250 TTGAC
1 TTGAC
6370255 TTGAATTATG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
23 23 0.47
24 26 0.53
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (24 bp):
TTGACATGGATTCTGATCTGATAC
Found at i:6372608 original size:19 final size:18
Alignment explanation
Indices: 6372568--6372609 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
6372558 ATATAATTAA
**
6372568 AAAT-TAATTAAAAATTT
1 AAATATAATTAAAAAAAT
6372585 AAATATAATTAAAAAAAT
1 AAATATAATTAAAAAAAT
6372603 ATAATAT
1 A-AATAT
6372610 TTATAAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.19
18 12 0.57
19 5 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATATAATTAAAAAAAT
Found at i:6374313 original size:23 final size:23
Alignment explanation
Indices: 6374281--6374341 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
6374271 TTTTGTTGAT
6374281 ATTAT-ATTTTAATTAAATTACA
1 ATTATAATTTTAATTAAATTACA
* * * *
6374303 TTTATAATTTTAACTAATTTATA
1 ATTATAATTTTAATTAAATTACA
6374326 ATTATACA-TTTAATTA
1 ATTATA-ATTTTAATTA
6374342 CTTTTTAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
22 4 0.13
23 26 0.84
24 1 0.03
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTATAATTTTAATTAAATTACA
Found at i:6374672 original size:19 final size:19
Alignment explanation
Indices: 6374650--6374687 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
6374640 AAAAAAGATG
*
6374650 AAATATTTA-AAATTACAAT
1 AAATAATTACAAA-TACAAT
6374669 AAATAATTACAAATACAAT
1 AAATAATTACAAATACAAT
6374688 CGTAAACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATAATTACAAATACAAT
Found at i:6388117 original size:20 final size:20
Alignment explanation
Indices: 6388092--6388131 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
6388082 TTATACGTAT
6388092 TAGTTGGTCGGTTCGTATAC
1 TAGTTGGTCGGTTCGTATAC
6388112 TAGTTGGTCGGTTCGTATAC
1 TAGTTGGTCGGTTCGTATAC
6388132 ATGTACTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.30, T:0.40
Consensus pattern (20 bp):
TAGTTGGTCGGTTCGTATAC
Found at i:6388506 original size:17 final size:18
Alignment explanation
Indices: 6388484--6388518 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
6388474 CTTAATTTTT
*
6388484 TTTTAAAT-TTTTATATA
1 TTTTAAATAATTTATATA
6388501 TTTTAAATAATTTATATA
1 TTTTAAATAATTTATATA
6388519 AATTTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTAAATAATTTATATA
Found at i:6393479 original size:7 final size:7
Alignment explanation
Indices: 6393467--6393589 Score: 246
Period size: 7 Copynumber: 17.6 Consensus size: 7
6393457 CGAGAAGAAC
6393467 TCATTCT
1 TCATTCT
6393474 TCATTCT
1 TCATTCT
6393481 TCATTCT
1 TCATTCT
6393488 TCATTCT
1 TCATTCT
6393495 TCATTCT
1 TCATTCT
6393502 TCATTCT
1 TCATTCT
6393509 TCATTCT
1 TCATTCT
6393516 TCATTCT
1 TCATTCT
6393523 TCATTCT
1 TCATTCT
6393530 TCATTCT
1 TCATTCT
6393537 TCATTCT
1 TCATTCT
6393544 TCATTCT
1 TCATTCT
6393551 TCATTCT
1 TCATTCT
6393558 TCATTCT
1 TCATTCT
6393565 TCATTCT
1 TCATTCT
6393572 TCATTCT
1 TCATTCT
6393579 TCATTCT
1 TCATTCT
6393586 TCAT
1 TCAT
6393590 GCCCTCTGGT
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 116 1.00
ACGTcount: A:0.15, C:0.28, G:0.00, T:0.57
Consensus pattern (7 bp):
TCATTCT
Found at i:6397826 original size:19 final size:20
Alignment explanation
Indices: 6397804--6397841 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
6397794 TAGTTTACAT
*
6397804 TTATGATTATAAAT-TTTCA
1 TTATAATTATAAATATTTCA
*
6397823 TTATAATTTTAAATATTTC
1 TTATAATTATAAATATTTC
6397842 TTTTCAATAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (20 bp):
TTATAATTATAAATATTTCA
Found at i:6406610 original size:23 final size:23
Alignment explanation
Indices: 6406580--6406637 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
6406570 TTTTATATGA
*
6406580 CACTTCGGTGCAATTCTACGCGG
1 CACTTCGGTGCAATTCTACACGG
*
6406603 CACTTCGGTGCAATTCTACATGG
1 CACTTCGGTGCAATTCTACACGG
*
6406626 CACTTAGGTGCA
1 CACTTCGGTGCA
6406638 TTTATACGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.21, C:0.28, G:0.24, T:0.28
Consensus pattern (23 bp):
CACTTCGGTGCAATTCTACACGG
Found at i:6408869 original size:2 final size:2
Alignment explanation
Indices: 6408862--6408899 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6408852 AATTCAAATA
6408862 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6408900 CAAATTAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6410974 original size:2 final size:2
Alignment explanation
Indices: 6410969--6411042 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
6410959 AAAAATATGA
6410969 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6411011 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6411043 TTACAATTAA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6415955 original size:6 final size:6
Alignment explanation
Indices: 6415946--6415972 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
6415936 ATAGAAGCTG
6415946 TCTCTT TCTCTT TCTCTT TCTCTT TCT
1 TCTCTT TCTCTT TCTCTT TCTCTT TCT
6415973 TTCTCTATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (6 bp):
TCTCTT
Found at i:6415975 original size:10 final size:11
Alignment explanation
Indices: 6415946--6415978 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
6415936 ATAGAAGCTG
6415946 TCTCTTTCTCTT
1 TCTCTTTCTC-T
6415958 TCTCTTTCTCT
1 TCTCTTTCTCT
6415969 T-TCTTTCTCT
1 TCTCTTTCTCT
6415979 ATGTCTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 9 0.43
11 2 0.10
12 10 0.48
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (11 bp):
TCTCTTTCTCT
Found at i:6416452 original size:5 final size:5
Alignment explanation
Indices: 6416209--6416448 Score: 390
Period size: 5 Copynumber: 48.0 Consensus size: 5
6416199 CTTGCGAGTG
* * * * *
6416209 GTATT ATATT ATATT ATATT ATATT ATATT GTATT GTATT GTATT GTATT
1 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
6416259 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
1 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
6416309 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
1 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
*
6416359 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT ATATT GTATT
1 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
* * * *
6416409 GTATT ATATT GTATT ATATT GTATT GTATT ATATT ATATT
1 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
6416449 ATATATATAT
Statistics
Matches: 226, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 226 1.00
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (5 bp):
GTATT
Found at i:6426514 original size:5 final size:5
Alignment explanation
Indices: 6426504--6426528 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
6426494 TTGTTTGTTT
6426504 GATTA GATTA GATTA GATTA GATTA
1 GATTA GATTA GATTA GATTA GATTA
6426529 AATTTCAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
GATTA
Found at i:6434342 original size:27 final size:27
Alignment explanation
Indices: 6434300--6434384 Score: 161
Period size: 27 Copynumber: 3.1 Consensus size: 27
6434290 GCCAGAGTTT
*
6434300 TAGCTTCAAGAAGTTGAACCTATCAAC
1 TAGCTTCAAGATGTTGAACCTATCAAC
6434327 TAGCTTCAAGATGTTGAACCTATCAAC
1 TAGCTTCAAGATGTTGAACCTATCAAC
6434354 TAGCTTCAAGATGTTGAACCTATCAAC
1 TAGCTTCAAGATGTTGAACCTATCAAC
6434381 TAGC
1 TAGC
6434385 CTTATAAACT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.28
Consensus pattern (27 bp):
TAGCTTCAAGATGTTGAACCTATCAAC
Found at i:6435768 original size:23 final size:24
Alignment explanation
Indices: 6435742--6435787 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
6435732 TAATTCTACT
*
6435742 ATATTATCTATTTTT-TTTATAAA
1 ATATCATCTATTTTTGTTTATAAA
*
6435765 ATATCATTTATTTTTGTTTATAA
1 ATATCATCTATTTTTGTTTATAA
6435788 TTTATATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (24 bp):
ATATCATCTATTTTTGTTTATAAA
Found at i:6435801 original size:23 final size:23
Alignment explanation
Indices: 6435741--6435801 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 23
6435731 ATAATTCTAC
*
6435741 TATATTATCTATTTTTTTTATAAAA
1 TATATT-TCT-TTTTGTTTATAAAA
* **
6435766 TATCATTTATTTTTGTTTATAATT
1 TAT-ATTTCTTTTTGTTTATAAAA
6435790 TATATTTCTTTT
1 TATATTTCTTTT
6435802 AATATTATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
23 8 0.27
24 14 0.47
25 5 0.17
26 3 0.10
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (23 bp):
TATATTTCTTTTTGTTTATAAAA
Found at i:6448376 original size:20 final size:20
Alignment explanation
Indices: 6448351--6448404 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
6448341 GCGAAATAAA
6448351 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATCTCCAG
** * *
6448371 AATCGCAAATCAATTTCCAG
1 AATCGCAACGCGATCTCCAG
*
6448391 ATTCGCAACGCGAT
1 AATCGCAACGCGAT
6448405 TCTGACTATC
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGATCTCCAG
Found at i:6448464 original size:21 final size:21
Alignment explanation
Indices: 6448413--6448465 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
6448403 ATTCTGACTA
6448413 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * * *
6448434 TCACGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
6448455 TCGCAATGCGA
1 TCGCATTGCGA
6448466 ATACGTAATC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:6452013 original size:14 final size:14
Alignment explanation
Indices: 6451982--6452015 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
6451972 AATGCGAAAT
* *
6451982 GAAAATCGCAATGT
1 GAAAATCGCAACGC
6451996 GAAAATCGCAACGC
1 GAAAATCGCAACGC
6452010 GAAAAT
1 GAAAAT
6452016 GACTATCGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (14 bp):
GAAAATCGCAACGC
Found at i:6452024 original size:34 final size:33
Alignment explanation
Indices: 6451933--6452033 Score: 112
Period size: 34 Copynumber: 3.0 Consensus size: 33
6451923 CTTAATGTCT
* * * * *
6451933 ATCGCAACGCGGAAATTACTATCACAACGAGAGA
1 ATCGCAACGC-GAAATGACTATCGCAATGTGAAA
* **
6451967 ATCGCAATGCGAAATGAAAATCGCAATGTGAAA
1 ATCGCAACGCGAAATGACTATCGCAATGTGAAA
6452000 ATCGCAACGCGAAAATGACTATCGCAATGTGAAA
1 ATCGCAACGCG-AAATGACTATCGCAATGTGAAA
6452034 TGAAAATTGT
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
33 26 0.47
34 29 0.53
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.17
Consensus pattern (33 bp):
ATCGCAACGCGAAATGACTATCGCAATGTGAAA
Found at i:6452067 original size:33 final size:33
Alignment explanation
Indices: 6452020--6452098 Score: 122
Period size: 33 Copynumber: 2.4 Consensus size: 33
6452010 GAAAATGACT
* *
6452020 ATCGCAATGTGAAATGAAAATTGTAACGAGAGA
1 ATCGCAATGCGAAATGAAAATTGCAACGAGAGA
*
6452053 ATCGCAATGCGAAATGAAAATTGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATTGCAACGAGAGA
*
6452086 ATCGCAACGCGAA
1 ATCGCAATGCGAA
6452099 TTTAGTTTCG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.43, C:0.15, G:0.25, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATTGCAACGAGAGA
Found at i:6452126 original size:19 final size:19
Alignment explanation
Indices: 6452104--6452169 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
6452094 GCGAATTTAG
*
6452104 TTTCGCGTTGCGATTCTCA
1 TTTCGCATTGCGATTCTCA
6452123 TTTCGCATTGCGATTCTC-
1 TTTCGCATTGCGATTCTCA
*
6452141 --TCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTCTCA
6452156 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
6452170 AGTCATTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
14 10 0.25
16 3 0.08
17 3 0.08
19 24 0.60
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (19 bp):
TTTCGCATTGCGATTCTCA
Found at i:6452295 original size:14 final size:14
Alignment explanation
Indices: 6452276--6452309 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
6452266 CATCAATTAA
6452276 ACAAATAAACTTTT
1 ACAAATAAACTTTT
* *
6452290 ACAAATCATCTTTT
1 ACAAATAAACTTTT
6452304 ACAAAT
1 ACAAAT
6452310 CAATTAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (14 bp):
ACAAATAAACTTTT
Found at i:6452310 original size:14 final size:14
Alignment explanation
Indices: 6452285--6452311 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6452275 AACAAATAAA
6452285 CTTTTACAAATCAT
1 CTTTTACAAATCAT
6452299 CTTTTACAAATCA
1 CTTTTACAAATCA
6452312 ATTAAACAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (14 bp):
CTTTTACAAATCAT
Found at i:6453727 original size:21 final size:21
Alignment explanation
Indices: 6453663--6453727 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 21
6453653 GAATCGGGCA
*
6453663 CTTGAATGGTGGGA-GGGACCT
1 CTTGAACGGTGGGAGGGGA-CT
* * ** * *
6453684 CTTCAACGATGACAGTGGCCT
1 CTTGAACGGTGGGAGGGGACT
6453705 CTTGAACGGTGGGAGGGGACT
1 CTTGAACGGTGGGAGGGGACT
6453726 CT
1 CT
6453728 CGAGGAATGA
Statistics
Matches: 30, Mismatches: 13, Indels: 2
0.67 0.29 0.04
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.20, C:0.20, G:0.37, T:0.23
Consensus pattern (21 bp):
CTTGAACGGTGGGAGGGGACT
Found at i:6453746 original size:42 final size:42
Alignment explanation
Indices: 6453700--6453779 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
6453690 CGATGACAGT
* * *
6453700 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
6453742 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
6453780 CAGACGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:6454229 original size:94 final size:94
Alignment explanation
Indices: 6454118--6454497 Score: 629
Period size: 94 Copynumber: 4.1 Consensus size: 94
6454108 ATGGATTGCA
* *
6454118 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
6454182 TTAACAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
6454211 TTACTTTCAACCAAAAGACAAAACAAAGACAAATATTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
6454276 TTAGCAGAATTGGCATCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
6454305 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* * * *
6454370 TTAGCATAATTGACAGCAACTGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
6454399 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
6454463 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
6454493 TTACT
1 TTACT
6454498 AAGCAATCTA
Statistics
Matches: 268, Mismatches: 16, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
93 23 0.09
94 245 0.91
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:6456236 original size:19 final size:19
Alignment explanation
Indices: 6456212--6456262 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
6456202 GCAACGAGAG
6456212 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
6456231 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
6456250 AATCGCAATGCGA
1 AATCGCAACGCGA
6456263 TTTTTATTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:6456308 original size:21 final size:21
Alignment explanation
Indices: 6456289--6456361 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
6456279 CGATTCTCTC
6456289 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTTCTCAT
** *
6456309 CGTTGCGATAGTCATTT-TCGT
1 -GTTGCGATTTTCATTTCTCAT
*
6456330 GTTGCGATTTTCATTTTTCAT
1 GTTGCGATTTTCATTTCTCAT
6456351 GTTGCGATTTT
1 GTTGCGATTTT
6456362 AAGTTTAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.12, C:0.16, G:0.19, T:0.52
Consensus pattern (21 bp):
GTTGCGATTTTCATTTCTCAT
Found at i:6456923 original size:20 final size:20
Alignment explanation
Indices: 6456898--6457110 Score: 214
Period size: 20 Copynumber: 10.5 Consensus size: 20
6456888 TTTAAAAATT
6456898 GCGTTGCGATTTACGGATAC
1 GCGTTGCGATTTACGGATAC
* *
6456918 GCGTTGCGATTTTACGTAT-T
1 GCGTTGCGA-TTTACGGATAC
6456938 GTCGTTGCGATTTACGGATAC
1 G-CGTTGCGATTTACGGATAC
** * *
6456959 GTATTGCGATTTACGTATTC
1 GCGTTGCGATTTACGGATAC
* **
6456979 TCGTTGCGATTTACACATAC
1 GCGTTGCGATTTACGGATAC
* *
6456999 GCGTTGCGATTTACGTATTC
1 GCGTTGCGATTTACGGATAC
* *
6457019 TCGTTGCAATTTACGGATAC
1 GCGTTGCGATTTACGGATAC
* *
6457039 GCGTTGCGATTTTACGTAT-T
1 GCGTTGCGA-TTTACGGATAC
6457059 GTCGTTGCGATTTACGGATAC
1 G-CGTTGCGATTTACGGATAC
*
6457080 GCGTTGCGATTTTACAGATAC
1 GCGTTGCGA-TTTACGGATAC
*
6457101 TCGTTGCGAT
1 GCGTTGCGAT
6457111 AGTCAGAATC
Statistics
Matches: 156, Mismatches: 30, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
20 104 0.67
21 52 0.33
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (20 bp):
GCGTTGCGATTTACGGATAC
Found at i:6457144 original size:20 final size:20
Alignment explanation
Indices: 6456898--6457171 Score: 122
Period size: 20 Copynumber: 13.6 Consensus size: 20
6456888 TTTAAAAATT
* ** *
6456898 GCGTTGCGATTTACGGATAC
1 GCGTTGCGATTTTCATATTC
*
6456918 GCGTTGCGATTTTACGTATT-
1 GCGTTGCGATTTT-CATATTC
* ** *
6456938 GTCGTTGCGATTTACGGATAC
1 G-CGTTGCGATTTTCATATTC
** * *
6456959 GTATTGCGATTTACGTATTC
1 GCGTTGCGATTTTCATATTC
* * * *
6456979 TCGTTGCGATTTACACATAC
1 GCGTTGCGATTTTCATATTC
* *
6456999 GCGTTGCGATTTACGTATTC
1 GCGTTGCGATTTTCATATTC
* * * ** *
6457019 TCGTTGCAATTTACGGATAC
1 GCGTTGCGATTTTCATATTC
*
6457039 GCGTTGCGATTTTACGTATT-
1 GCGTTGCGATTTT-CATATTC
* ** *
6457059 GTCGTTGCGATTTACGGATAC
1 G-CGTTGCGATTTTCATATTC
* *
6457080 GCGTTGCGATTTTACAGATAC
1 GCGTTGCGATTTT-CATATTC
* ** * *
6457101 TCGTTGCGATAGTCAGAATC
1 GCGTTGCGATTTTCATATTC
* *
6457121 GCGTTGCGATTTAT-ATGTTT
1 GCGTTGCGATTT-TCATATTC
6457141 GCGTTGCGATTTTCATATTC
1 GCGTTGCGATTTTCATATTC
6457161 GCGTTGCGATT
1 GCGTTGCGATT
6457172 CTGGAAAATA
Statistics
Matches: 197, Mismatches: 48, Indels: 18
0.75 0.18 0.07
Matches are distributed among these distances:
19 1 0.01
20 147 0.75
21 49 0.25
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.38
Consensus pattern (20 bp):
GCGTTGCGATTTTCATATTC
Found at i:6457146 original size:81 final size:82
Alignment explanation
Indices: 6456896--6457171 Score: 300
Period size: 81 Copynumber: 3.4 Consensus size: 82
6456886 GCTTTAAAAA
* *
6456896 TTGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGAT-TTACGGATACG
1 TTGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATATTACGGATACG
**
6456960 TATTGCGATTTACGTAT-T
66 CGTTGCGATTTA--TATGT
* * *
6456978 CT-CGTTGCGATTTACACATACGCGTTGCGA-TTTACGTATTCTCGTTGCAAT-TTACGGATACG
1 TTGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATATTACGGATACG
*
6457040 CGTTGCGATTT-TACGT
66 CGTTGCGATTTATATGT
* * * *
6457056 ATTGTCGTTGCGATTTACGGATACGCGTTGCGATTTTACAG-ATACTCGTTGCGATAGT-CAGA-
1 -TTG-CGTTGCGATTTACAGATACGCGTTGCGATTTTAC-GTATTCTCGTTGCGATATTACGGAT
6457118 ATCGCGTTGCGATTTATATGT
63 A-CGCGTTGCGATTTATATGT
* * *
6457139 TTGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 TTGCGTTGCGATTTACAGATACGCGTTGCGATT
6457172 CTGGAAAATA
Statistics
Matches: 165, Mismatches: 20, Indels: 19
0.81 0.10 0.09
Matches are distributed among these distances:
77 2 0.01
78 1 0.01
79 1 0.01
80 39 0.24
81 79 0.48
82 37 0.22
83 6 0.04
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (82 bp):
TTGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATATTACGGATACG
CGTTGCGATTTATATGT
Found at i:6457163 original size:40 final size:40
Alignment explanation
Indices: 6456895--6457171 Score: 260
Period size: 40 Copynumber: 6.8 Consensus size: 40
6456885 CGCTTTAAAA
*
6456895 ATTGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGT
1 ATTGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGT
** *
6456935 ATTGTCGTTGCGATTTACGGATACGTATTGCGA-TTTACGT
1 ATTG-CGTTGCGATTTACGGATACGCGTTGCGATTTTATGT
* ** *
6456975 ATTCTCGTTGCGATTTACACATACGCGTTGCGA-TTTACGT
1 ATT-GCGTTGCGATTTACGGATACGCGTTGCGATTTTATGT
* * *
6457015 ATTCTCGTTGCAATTTACGGATACGCGTTGCGATTTTACGT
1 ATT-GCGTTGCGATTTACGGATACGCGTTGCGATTTTATGT
*
6457056 ATTGTCGTTGCGATTTACGGATACGCGTTGCGATTTTACAGAT
1 ATTG-CGTTGCGATTTACGGATACGCGTTGCGATTTTA-TG-T
* * *
6457099 ACT-CGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTATATGT
1 ATTGCGTTGCGAT-TTACGGATA-CGCGTTGCGATTT-TATGT
* ** *
6457139 -TTGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 ATTGCGTTGCGATTTACGGATACGCGTTGCGATT
6457172 CTGGAAAATA
Statistics
Matches: 204, Mismatches: 21, Indels: 24
0.82 0.08 0.10
Matches are distributed among these distances:
39 2 0.01
40 101 0.50
41 94 0.46
42 4 0.02
43 3 0.01
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (40 bp):
ATTGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGT
Found at i:6457243 original size:21 final size:20
Alignment explanation
Indices: 6457217--6457283 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
6457207 TGCATTCACA
*
6457217 TTGCGATTCTTCATAATCGCG
1 TTGCGATT-TACATAATCGCG
*
6457238 TTGCGATTTACGTAATCGCG
1 TTGCGATTTACATAATCGCG
* * *
6457258 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACATAATCGCG
6457278 TTGCGA
1 TTGCGA
6457284 ATTAGGAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 34 0.81
21 8 0.19
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.37
Consensus pattern (20 bp):
TTGCGATTTACATAATCGCG
Found at i:6457255 original size:20 final size:20
Alignment explanation
Indices: 6457230--6457283 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
6457220 CGATTCTTCA
6457230 TAATCGCGTTGCGATTTACG
1 TAATCGCGTTGCGATTTACG
6457250 TAATCGCGTTGCGATTTACG
1 TAATCGCGTTGCGATTTACG
* *
6457270 TATTCGCATTGCGA
1 TAATCGCGTTGCGA
6457284 ATTAGGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.35
Consensus pattern (20 bp):
TAATCGCGTTGCGATTTACG
Found at i:6457325 original size:21 final size:21
Alignment explanation
Indices: 6457273--6457325 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
6457263 ATTTACGTAT
*
6457273 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
* * *
6457294 TCGCAACGCGAATTTGGGAAA
1 TCGCAATGCGAATTAGGAAAA
*
6457315 TCGTAATGCGA
1 TCGCAATGCGA
6457326 TAGTCAAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:6470023 original size:6 final size:6
Alignment explanation
Indices: 6470012--6470052 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
6470002 AAAAGAGGAT
* *
6470012 ATATTA ATATTA GTATTA GTATTA ATATTA ATATTA ATATT
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATT
6470053 TTTAATAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (6 bp):
ATATTA
Found at i:6470138 original size:26 final size:26
Alignment explanation
Indices: 6470078--6470139 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
6470068 AAATTAATTT
* *
6470078 TAAAATAATCAAATATTTATTTTTGA
1 TAAAATATTTAAATATTTATTTTTGA
*
6470104 TAAAA-ATTTAAATATTTGTTTTT-A
1 TAAAATATTTAAATATTTATTTTTGA
6470128 TCAAAATATTTA
1 T-AAAATATTTA
6470140 TTTTAGGGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 2 0.06
25 19 0.61
26 10 0.32
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (26 bp):
TAAAATATTTAAATATTTATTTTTGA
Found at i:6471200 original size:43 final size:42
Alignment explanation
Indices: 6471153--6471238 Score: 104
Period size: 42 Copynumber: 2.0 Consensus size: 42
6471143 TTTGTTTAAA
*
6471153 ATTTGGAACTTTGTTGTTTTTCTAAGGA-AAA-TGGATGAATCAC
1 ATTTGG-ACTTTGTTGTTCTTCT--GGAGAAATTGGATGAATCAC
**
6471196 ATTTGGGGTTTGTTGTTCTTCTGGAGAAATTGGATGAATCAC
1 ATTTGGACTTTGTTGTTCTTCTGGAGAAATTGGATGAATCAC
6471238 A
1 A
6471239 AGTTATGAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
40 3 0.08
41 3 0.08
42 26 0.68
43 6 0.16
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.40
Consensus pattern (42 bp):
ATTTGGACTTTGTTGTTCTTCTGGAGAAATTGGATGAATCAC
Found at i:6497194 original size:60 final size:61
Alignment explanation
Indices: 6497098--6497263 Score: 205
Period size: 60 Copynumber: 2.8 Consensus size: 61
6497088 GAATTAGGGG
* ** *
6497098 ATGAAATTGGAATATTCAAAAGTTTGGGGACCAATTTAGAAA-GAGGA-TCATAATTTAGGA
1 ATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTA-AAATGAGGATTCATAATTTAGGA
* * *
6497158 ATGAAATTAGAATGTTCAAAAGTTTAAGGACTAATTTAAAATGA-GATTCATATTTTAGGG
1 ATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAGGATTCATAATTTAGGA
* *
6497218 ATGAAATTATAATATTCAAAAGCTTAAGGA-TCAATTTAAAATGAGG
1 ATGAAATTAGAATATTCAAAAGTTTAAGGACT-AATTTAAAATGAGG
6497264 GTTATAGTTT
Statistics
Matches: 92, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
59 6 0.07
60 85 0.92
61 1 0.01
ACGTcount: A:0.43, C:0.06, G:0.19, T:0.31
Consensus pattern (61 bp):
ATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAGGATTCATAATTTAGGA
Found at i:6498823 original size:19 final size:18
Alignment explanation
Indices: 6498799--6498834 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
6498789 TTAAAGACTA
*
6498799 TTTGTAATCTTTCTCTCTC
1 TTTGTAATATTT-TCTCTC
6498818 TTTGTAATATTTTCTCT
1 TTTGTAATATTTTCTCT
6498835 ATTAGTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.14, C:0.19, G:0.06, T:0.61
Consensus pattern (18 bp):
TTTGTAATATTTTCTCTC
Found at i:6504656 original size:26 final size:26
Alignment explanation
Indices: 6504627--6504680 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
6504617 TAATAAATTA
6504627 TTATCTCCTAAAATTTTAAAATTTTG
1 TTATCTCCTAAAATTTTAAAATTTTG
6504653 TTATCTCCTAAAATTTTAAAATTTTG
1 TTATCTCCTAAAATTTTAAAATTTTG
6504679 TT
1 TT
6504681 CGTTCTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.11, G:0.04, T:0.52
Consensus pattern (26 bp):
TTATCTCCTAAAATTTTAAAATTTTG
Found at i:6514559 original size:34 final size:34
Alignment explanation
Indices: 6514500--6514566 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
6514490 TTATTGAGAG
*
6514500 TTGTTTTCTCCTTTTTATCAAGAGAGAA-TTGTCA
1 TTGTTTTCTCCTTTTGATC-AGAGAGAAGTTGTCA
6514534 TTGTTTTCTCCTTGTTAGATC-GAGAGAAGTTGT
1 TTGTTTTCTCCTT-TT-GATCAGAGAGAAGTTGT
6514567 AATTCATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 20 0.69
35 6 0.21
36 3 0.10
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.46
Consensus pattern (34 bp):
TTGTTTTCTCCTTTTGATCAGAGAGAAGTTGTCA
Found at i:6529170 original size:19 final size:20
Alignment explanation
Indices: 6529140--6529181 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
6529130 AAAAAACTTA
*
6529140 AATTATTTTTTTAATATATG
1 AATTATTTTTTTAATAAATG
*
6529160 AATTA-TTTTTTATTAAATG
1 AATTATTTTTTTAATAAATG
6529179 AAT
1 AAT
6529182 GTTTACATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (20 bp):
AATTATTTTTTTAATAAATG
Found at i:6539111 original size:15 final size:14
Alignment explanation
Indices: 6539091--6539138 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
6539081 GGGAAGTAAT
6539091 TTTTTTTAAAAAAA
1 TTTTTTTAAAAAAA
*
6539105 TTGTTTTCTAAAATAA
1 TT-TTTT-TAAAAAAA
* *
6539121 TTATTTTAAAAATA
1 TTTTTTTAAAAAAA
6539135 TTTT
1 TTTT
6539139 AAAGTTTTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
14 11 0.41
15 7 0.26
16 9 0.33
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (14 bp):
TTTTTTTAAAAAAA
Found at i:6539116 original size:16 final size:15
Alignment explanation
Indices: 6539088--6539138 Score: 50
Period size: 16 Copynumber: 3.4 Consensus size: 15
6539078 GATGGGAAGT
*
6539088 AATTTTTTTTAAAAA
1 AATTTTTTCTAAAAA
*
6539103 AATTGTTTTCTAAAAT
1 AATT-TTTTCTAAAAA
*
6539119 AATTATTT-TAAAAA
1 AATTTTTTCTAAAAA
*
6539133 TATTTT
1 AATTTT
6539139 AAAGTTTTTC
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
14 9 0.31
15 7 0.24
16 13 0.45
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (15 bp):
AATTTTTTCTAAAAA
Found at i:6539391 original size:12 final size:10
Alignment explanation
Indices: 6539355--6539385 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
6539345 TATAATTTAA
6539355 TTTATGATTTT
1 TTTAT-ATTTT
6539366 TTTATATTTT
1 TTTATATTTT
6539376 TTTATATTTT
1 TTTATATTTT
6539386 ATTTTAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.75
11 5 0.25
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (10 bp):
TTTATATTTT
Found at i:6541432 original size:8 final size:8
Alignment explanation
Indices: 6541419--6541456 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
6541409 ACAAAATGTG
6541419 TACATATA
1 TACATATA
6541427 TACATATA
1 TACATATA
*
6541435 TATATATA
1 TACATATA
6541443 TA-ATATA
1 TACATATA
6541450 -ACATATA
1 TACATATA
6541457 AGTGAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 1 0.04
7 10 0.36
8 17 0.61
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (8 bp):
TACATATA
Found at i:6541577 original size:203 final size:201
Alignment explanation
Indices: 6541361--6541768 Score: 782
Period size: 203 Copynumber: 2.0 Consensus size: 201
6541351 AAAAAATAAA
6541361 TAATGTAAATAAATATAATAATAAAGAAGTAAACAAATAGGGTAAAATACAAAATGTGTACATAT
1 TAATGTAAATAAATATAATAATAAAGAAGTAAACAAATAGGGTAAAATACAAAATGTGTACATAT
6541426 ATACATATATATATATATAATATAACATATAAGTGAAATAATAATATACTAATAATAAATATATA
66 ATACATATATATATATATAATATAACATATAAGTGAAATAATAATATACTAATAATAAATATATA
6541491 CGAATGTGTAAAAAAAAA-AATAATATAAAATATATATAAATATTATAATGTAATATAAAAAGAT
131 CGAATGTGTAAAAAAAAATAATAATAT-AAA-ATATATAAATATTATAATGTAATAT-AAAAGAT
6541555 AATTAAAAC
193 AATTAAAAC
6541564 TAATGTAAATAAATATAATAATAAAGAAGTAAACAAATAGGGTAAAATACAAAATGTGTACATAT
1 TAATGTAAATAAATATAATAATAAAGAAGTAAACAAATAGGGTAAAATACAAAATGTGTACATAT
6541629 ATACATATATATATATATAATATAACATATAAGTGAAATAATAATATACTAATAATAAATATATA
66 ATACATATATATATATATAATATAACATATAAGTGAAATAATAATATACTAATAATAAATATATA
6541694 CGAATGTGTAAAAAAAAATAATAATATAAAATATATAAATATTATAATGTAATATAAAAGATAAT
131 CGAATGTGTAAAAAAAAATAATAATATAAAATATATAAATATTATAATGTAATATAAAAGATAAT
6541759 TAAAAC
196 TAAAAC
6541765 TAAT
1 TAAT
6541769 ATCCCGAGAA
Statistics
Matches: 204, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
201 20 0.10
202 25 0.12
203 151 0.74
204 8 0.04
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.30
Consensus pattern (201 bp):
TAATGTAAATAAATATAATAATAAAGAAGTAAACAAATAGGGTAAAATACAAAATGTGTACATAT
ATACATATATATATATATAATATAACATATAAGTGAAATAATAATATACTAATAATAAATATATA
CGAATGTGTAAAAAAAAATAATAATATAAAATATATAAATATTATAATGTAATATAAAAGATAAT
TAAAAC
Found at i:6541635 original size:8 final size:8
Alignment explanation
Indices: 6541622--6541659 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
6541612 ACAAAATGTG
6541622 TACATATA
1 TACATATA
6541630 TACATATA
1 TACATATA
*
6541638 TATATATA
1 TACATATA
6541646 TA-ATATA
1 TACATATA
6541653 -ACATATA
1 TACATATA
6541660 AGTGAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 1 0.04
7 10 0.36
8 17 0.61
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (8 bp):
TACATATA
Found at i:6543699 original size:105 final size:104
Alignment explanation
Indices: 6543140--6543700 Score: 898
Period size: 105 Copynumber: 5.4 Consensus size: 104
6543130 GTGTTGTTCC
* * ** *
6543140 GAGTCCGATGTCCTTCGTTGTGAAGTTGAAATTGAATCTG-AA-T--GAAATTTTGTTGACAAGC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTGTTGACAAGC
6543201 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
6543240 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-AAGATTGGGAAGTCGTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA-ATTGAGAAAT-GTTGTTGACAA
*
6543304 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
64 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
6543345 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTGTTGACAAG
6543410 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
6543450 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTT-GTTGACAAG
*
6543515 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
6543555 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTT-GTTGACAAG
* *
6543620 CAGCGGTCCTTTCGTCGTGAAGTTGAACTTACGTTGTCTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
6543660 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
6543701 GTAAAACCTG
Statistics
Matches: 436, Mismatches: 16, Indels: 13
0.94 0.03 0.03
Matches are distributed among these distances:
100 36 0.08
101 1 0.00
102 1 0.00
104 8 0.02
105 388 0.89
106 2 0.00
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (104 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:6544500 original size:1 final size:1
Alignment explanation
Indices: 6544496--6544520 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
6544486 CGTTTTTCTC
6544496 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
6544521 CAACTTAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:6555335 original size:8 final size:8
Alignment explanation
Indices: 6555322--6555359 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
6555312 ACAAAATGTG
6555322 TACATATA
1 TACATATA
6555330 TACATATA
1 TACATATA
*
6555338 TATATATA
1 TACATATA
6555346 TA-ATATA
1 TACATATA
6555353 -ACATATA
1 TACATATA
6555360 AGTGAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 1 0.04
7 10 0.36
8 17 0.61
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (8 bp):
TACATATA
Found at i:6555484 original size:207 final size:200
Alignment explanation
Indices: 6555264--6555674 Score: 759
Period size: 207 Copynumber: 2.0 Consensus size: 200
6555254 AAAAAATAAA
6555264 TAATGTAAATAAATATAATAATAAAGAAGTAAACAAATAGGGTAAAATACAAAATGTGTACATAT
1 TAATGTAAATAAATATAATAATAAAGAAGTAAACAAATAGGGTAAAATACAAAATGTGTACATAT
6555329 ATACATATATATATATATAATATAACATATAAGTGAAATAATAATATACTAATAATAAATATATA
66 ATAC----ATATATATAT-ATATAACATATAAGTGAAATAATAATATACTAATAATAAATATATA
6555394 CGAATGTGTAAAAAAAAATAATAATAATATAAAATATATATAAATATTATAATGTAATATAAAAA
126 CGAATGTGT-AAAAAAAA-AATAATAATATAAAATATATATAAATATTATAATGTAATATAAAAA
6555459 GATAATTAAAAC
189 GATAATTAAAAC
6555471 TAATGTAAATAAATATAATAATAAAGAAGTAAACAAATAGGGTAAAATACAAAATGTGTACATAT
1 TAATGTAAATAAATATAATAATAAAGAAGTAAACAAATAGGGTAAAATACAAAATGTGTACATAT
6555536 ATACATATATATATATATAACATATAAGTGAAATAATAATATACTAATAATAAATATATACGAAT
66 ATACATATATATATATATAACATATAAGTGAAATAATAATATACTAATAATAAATATATACGAAT
6555601 GTGTAAAAAAAAAATAATAATATAAAATATATATAAATATTATAATGTAATATAAAAAGATAATT
131 GTGTAAAAAAAAAATAATAATATAAAATATATATAAATATTATAATGTAATATAAAAAGATAATT
6555666 AAAAC
196 AAAAC
6555671 TAAT
1 TAAT
6555675 ATCCCGAGAA
Statistics
Matches: 204, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
200 62 0.30
201 8 0.04
202 55 0.27
203 10 0.05
207 69 0.34
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.30
Consensus pattern (200 bp):
TAATGTAAATAAATATAATAATAAAGAAGTAAACAAATAGGGTAAAATACAAAATGTGTACATAT
ATACATATATATATATATAACATATAAGTGAAATAATAATATACTAATAATAAATATATACGAAT
GTGTAAAAAAAAAATAATAATATAAAATATATATAAATATTATAATGTAATATAAAAAGATAATT
AAAAC
Found at i:6563476 original size:3 final size:3
Alignment explanation
Indices: 6563468--6563505 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
6563458 AAAAGGGTAC
6563468 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
6563506 AAATTCAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:6575637 original size:25 final size:25
Alignment explanation
Indices: 6575603--6575653 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
6575593 ATGCACCAGC
6575603 TGTGCTCCAAGACTTTTCTCAACTT
1 TGTGCTCCAAGACTTTTCTCAACTT
6575628 TGTGCTCCAAGACTTTTCTCAACTT
1 TGTGCTCCAAGACTTTTCTCAACTT
6575653 T
1 T
6575654 TCTTACTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.20, C:0.27, G:0.12, T:0.41
Consensus pattern (25 bp):
TGTGCTCCAAGACTTTTCTCAACTT
Found at i:6596033 original size:45 final size:45
Alignment explanation
Indices: 6595969--6596061 Score: 141
Period size: 45 Copynumber: 2.1 Consensus size: 45
6595959 AGGGTGTGAG
* * *
6595969 AATGTTTTCAATGGTTAAAAAGATTTTGAATAGATGCTACTTCGT
1 AATGTTTTCAATAGTTAAAAAGATTCTGAATAGATGCTACATCGT
* *
6596014 AATGTTTTTAATAGTTAAAAAGATTCTGAATAGATGTTACATCGT
1 AATGTTTTCAATAGTTAAAAAGATTCTGAATAGATGCTACATCGT
6596059 AAT
1 AAT
6596062 CACTCAGGCT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.40
Consensus pattern (45 bp):
AATGTTTTCAATAGTTAAAAAGATTCTGAATAGATGCTACATCGT
Found at i:6597264 original size:18 final size:17
Alignment explanation
Indices: 6597237--6597280 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 17
6597227 GTCATATATG
*
6597237 TCCCGTAGGACCACTACA
1 TCCCGAAGGA-CACTACA
6597255 TCCCGAAGG--ACTACA
1 TCCCGAAGGACACTACA
6597270 TCCCGAAGGAC
1 TCCCGAAGGAC
6597281 TATTATACCC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 15 0.65
18 8 0.35
ACGTcount: A:0.30, C:0.36, G:0.20, T:0.14
Consensus pattern (17 bp):
TCCCGAAGGACACTACA
Found at i:6597269 original size:15 final size:15
Alignment explanation
Indices: 6597249--6597282 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
6597239 CCGTAGGACC
6597249 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
6597264 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
6597279 ACTA
1 ACTA
6597283 TTATACCCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.35, C:0.32, G:0.18, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:6597414 original size:29 final size:29
Alignment explanation
Indices: 6597363--6597448 Score: 138
Period size: 29 Copynumber: 3.0 Consensus size: 29
6597353 TTATATTCCA
*
6597363 TATGTTCATGTA-CTCATGTCATTTCTCT
1 TATGATCATGTAGCTCATGTCATTTCTCT
6597391 TATGATCATGTAGCTCATGTCATTTCTCT
1 TATGATCATGTAGCTCATGTCATTTCTCT
*
6597420 TGTGATCATGTAGCTCATGTCATGTTCTC
1 TATGATCATGTAGCTCATGTCAT-TTCTC
6597449 ATATCACATA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
28 11 0.20
29 38 0.70
30 5 0.09
ACGTcount: A:0.19, C:0.21, G:0.15, T:0.45
Consensus pattern (29 bp):
TATGATCATGTAGCTCATGTCATTTCTCT
Found at i:6597894 original size:64 final size:63
Alignment explanation
Indices: 6597825--6597981 Score: 169
Period size: 64 Copynumber: 2.5 Consensus size: 63
6597815 TAATGAAGGT
*
6597825 ATGCATCGATGCACTACTTGTGCATC-AGTGCA-TAAAATGCATTCGAT-GTTTTATTATTAATG
1 ATGCATCGATGCACTACTTGTGCATCGA-TGCACT-AAATGCATTCGATCGTTTTATT-TTAA-A
*
6597887 GG
62 AG
* * * *
6597889 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATCTTTTTATTTTAAAAG
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
*
6597952 AGTGCATCGATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACTTGTGCATCGAT
6597982 ACACCTTCAA
Statistics
Matches: 78, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
63 3 0.04
64 65 0.83
65 10 0.13
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
Found at i:6605068 original size:32 final size:32
Alignment explanation
Indices: 6605022--6605086 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
6605012 ACTTAACCCT
* *
6605022 GCTCTCTCGTGCATGGGTTGCATCCATAGCTG
1 GCTCCCTCGTGCATGGATTGCATCCATAGCTG
6605054 GCTCCCTCGTGCATGGATTGCATCCATAGCTG
1 GCTCCCTCGTGCATGGATTGCATCCATAGCTG
6605086 G
1 G
6605087 GAGATTCCTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.14, C:0.29, G:0.28, T:0.29
Consensus pattern (32 bp):
GCTCCCTCGTGCATGGATTGCATCCATAGCTG
Found at i:6605098 original size:23 final size:23
Alignment explanation
Indices: 6605072--6605115 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
6605062 GTGCATGGAT
6605072 TGCATCCATAGCTGGGAGATTCC
1 TGCATCCATAGCTGGGAGATTCC
6605095 TGCATCCATAGCTGGGAGATT
1 TGCATCCATAGCTGGGAGATT
6605116 GTAGCCAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (23 bp):
TGCATCCATAGCTGGGAGATTCC
Found at i:6605573 original size:28 final size:30
Alignment explanation
Indices: 6605533--6605594 Score: 110
Period size: 28 Copynumber: 2.1 Consensus size: 30
6605523 AATTTAGTTA
6605533 ATTAGTTTGTTAGTTTAAG-T-TATATTAT
1 ATTAGTTTGTTAGTTTAAGTTATATATTAT
6605561 ATTAGTTTGTTAGTTTAAGTTATATATTAT
1 ATTAGTTTGTTAGTTTAAGTTATATATTAT
6605591 ATTA
1 ATTA
6605595 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (30 bp):
ATTAGTTTGTTAGTTTAAGTTATATATTAT
Found at i:6605921 original size:20 final size:21
Alignment explanation
Indices: 6605877--6605921 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
6605867 AAATATTGTG
**
6605877 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTAGTGTTAA
*
6605898 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTGTTAA
6605918 TTTA
1 TTTA
6605922 TATTATATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTGTTAA
Found at i:6609127 original size:35 final size:35
Alignment explanation
Indices: 6609086--6609188 Score: 93
Period size: 35 Copynumber: 3.2 Consensus size: 35
6609076 TAAGATTTAA
6609086 TAATGATTAGTAATGATGAAATTATTATTAATATT
1 TAATGATTAGTAATGATGAAATTATTATTAATATT
* *
6609121 TAATGA-T--T--TGAT-AAGA--ATGATT--TA-G
1 TAATGATTAGTAATGATGAA-ATTATTATTAATATT
*
6609146 TAATGATTAGTAATAATGAAATTATTATTAATATT
1 TAATGATTAGTAATGATGAAATTATTATTAATATT
6609181 TAATGATT
1 TAATGATT
6609189 TGATAGTAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 24
0.64 0.06 0.30
Matches are distributed among these distances:
25 6 0.12
26 3 0.06
28 6 0.12
29 2 0.04
30 9 0.18
31 2 0.04
32 6 0.12
34 3 0.06
35 14 0.27
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.45
Consensus pattern (35 bp):
TAATGATTAGTAATGATGAAATTATTATTAATATT
Found at i:6609141 original size:49 final size:49
Alignment explanation
Indices: 6609086--6609478 Score: 336
Period size: 49 Copynumber: 7.2 Consensus size: 49
6609076 TAAGATTTAA
6609086 TAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAAGAATGATTTAG
1 TAATGATTAGTAATGATGAAATTATTATTAATATTTAATGA--T--T-----TGA--TAG
*
6609146 TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
1 TAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAG
* *
6609195 TAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAG
1 TAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAG
* * *
6609244 TAATGATTAGTAATAATGAAATTATTATTAATTTTTTATGATTTGATAG
1 TAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAG
*
6609293 TAATGATTAGTAATGATTACTAATAATGAAATCATTATTAATATTTAATGATTTGATAG
1 TAATGATTAGTAATG----------ATGAAATTATTATTAATATTTAATGATTTGATAG
6609352 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
1 TAATGA-TTAGT-A--A-T-G-----ATGAAATTATTATTAATATTTAATGATTTGATAG
*
6609412 TAATGATTTAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTGATAT
1 TAATGA-TTAGTAATGA-T-G-----A-AA-TTATTATTAATATTTAATGATTTGATAG
6609471 TAATGATT
1 TAATGATT
6609479 TGATAGTAAT
Statistics
Matches: 299, Mismatches: 9, Indels: 52
0.83 0.03 0.14
Matches are distributed among these distances:
49 113 0.38
50 1 0.00
51 4 0.01
52 1 0.00
55 1 0.00
56 2 0.01
57 2 0.01
58 5 0.02
59 71 0.24
60 95 0.32
61 1 0.00
63 1 0.00
64 1 0.00
65 1 0.00
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.46
Consensus pattern (49 bp):
TAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAG
Found at i:6609151 original size:60 final size:59
Alignment explanation
Indices: 6609079--6609479 Score: 522
Period size: 60 Copynumber: 7.1 Consensus size: 59
6609069 GTATTTATAA
* *
6609079 GATTTAATAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAAGAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGAT-AGAAT
6609139 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGA--T--T----T
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGAAT
*
6609190 GA--TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGA--T--T----T
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGAAT
* *
6609239 GA--TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTTATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG-AAT
* *
6609297 GA-TTAGTAATGATTACTAATAATGAAATCATTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG-AAT
6609356 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG-AAT
* *
6609416 GATTTAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATA-GAAT
6609475 GATTT
1 GATTT
6609480 GATAGTAATG
Statistics
Matches: 317, Mismatches: 12, Indels: 25
0.90 0.03 0.07
Matches are distributed among these distances:
49 91 0.29
51 4 0.01
53 1 0.00
56 1 0.00
58 4 0.01
59 91 0.29
60 125 0.39
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.46
Consensus pattern (59 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGAAT
Found at i:6609249 original size:98 final size:105
Alignment explanation
Indices: 6609086--6609426 Score: 390
Period size: 109 Copynumber: 3.1 Consensus size: 105
6609076 TAAGATTTAA
* * * *
6609086 TAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAAGAATGATTTAGTAATG
1 TAATGATTAGTAATAATGAAATCATTATTAATATTT-ATGATATGAT-A-TATGA-TTAGTAATG
6609151 ATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
62 ATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
*
6609195 TAATGATTAGTAATAATGAAATTATTATTAAT-TTT-T-A-ATGAT-T-TGA-TAGTAATGATTA
1 TAATGATTAGTAATAATGAAATCATTATTAATATTTATGATATGATATATGATTAGTAATGATTA
*
6609253 GTAATAATGAAATTATTATTAATTTTTTATGATTTGATAGTAATGATTAG
66 GTAATAATGAAATTATTATTAA-TATTTA--A--TGAT--T--TGA-TAG
* *
6609303 TAATGATTACTAATAATGAAATCATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATG
1 TAATGATTAGTAATAATGAAATCATTATTAATATTT-ATGATATGATA-T-ATGA-TTAGTAATG
6609368 ATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
62 ATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
6609412 TAATGATTTAGTAAT
1 TAATGA-TTAGTAAT
6609427 GATTAGTAAT
Statistics
Matches: 201, Mismatches: 9, Indels: 43
0.79 0.04 0.17
Matches are distributed among these distances:
98 34 0.17
99 5 0.02
100 3 0.01
101 1 0.00
103 4 0.02
104 4 0.02
105 2 0.01
106 1 0.00
107 3 0.01
108 36 0.18
109 43 0.21
110 10 0.05
111 1 0.00
112 2 0.01
113 4 0.02
114 4 0.02
115 1 0.00
116 1 0.00
117 3 0.01
118 5 0.02
119 34 0.17
ACGTcount: A:0.41, C:0.01, G:0.13, T:0.45
Consensus pattern (105 bp):
TAATGATTAGTAATAATGAAATCATTATTAATATTTATGATATGATATATGATTAGTAATGATTA
GTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
Found at i:6609303 original size:10 final size:10
Alignment explanation
Indices: 6609290--6609436 Score: 53
Period size: 10 Copynumber: 14.7 Consensus size: 10
6609280 TATGATTTGA
6609290 TAGTAATGAT
1 TAGTAATGAT
6609300 TAGTAATGAT
1 TAGTAATGAT
* *
6609310 TACTAAT-AA
1 TAGTAATGAT
* *
6609319 T-GAAATCAT
1 TAGTAATGAT
*
6609328 TATTAAT-AT
1 TAGTAATGAT
6609337 T--TAATGATTT
1 TAGTAATGA--T
6609347 GATAGTAATGATT
1 --TAGTAATGA-T
6609360 TAGTAATGAT
1 TAGTAATGAT
*
6609370 TAGTAAT-AA
1 TAGTAATGAT
* *
6609379 T-GAAATTAT
1 TAGTAATGAT
*
6609388 TATTAAT-AT
1 TAGTAATGAT
6609397 T--TAATGATTT
1 TAGTAATGA--T
6609407 GATAGTAATGATT
1 --TAGTAATGA-T
6609420 TAGTAATGAT
1 TAGTAATGAT
6609430 TAGTAAT
1 TAGTAAT
6609437 AATAATTTAT
Statistics
Matches: 107, Mismatches: 12, Indels: 36
0.69 0.08 0.23
Matches are distributed among these distances:
7 8 0.07
8 9 0.08
9 14 0.13
10 40 0.37
11 18 0.17
12 2 0.02
13 4 0.04
14 12 0.11
ACGTcount: A:0.41, C:0.01, G:0.14, T:0.44
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:6609373 original size:21 final size:20
Alignment explanation
Indices: 6609349--6609437 Score: 67
Period size: 21 Copynumber: 4.4 Consensus size: 20
6609339 AATGATTTGA
6609349 TAGTAATGATTTAGTAATGAT
1 TAGTAAT-ATTTAGTAATGAT
* * *
6609370 TAGTAATA-AT-GAAATTAT
1 TAGTAATATTTAGTAATGAT
* * *
6609388 TATTAATATTTAATGATTTGA-
1 TAGTAATATTTAGT-A-ATGAT
6609409 TAGTAATGATTTAGTAATGAT
1 TAGTAAT-ATTTAGTAATGAT
6609430 TAGTAATA
1 TAGTAATA
6609438 ATAATTTATT
Statistics
Matches: 50, Mismatches: 12, Indels: 13
0.67 0.16 0.17
Matches are distributed among these distances:
18 13 0.26
19 2 0.04
20 5 0.10
21 22 0.44
22 8 0.16
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.44
Consensus pattern (20 bp):
TAGTAATATTTAGTAATGAT
Found at i:6609381 original size:119 final size:119
Alignment explanation
Indices: 6609241--6609479 Score: 408
Period size: 119 Copynumber: 2.0 Consensus size: 119
6609231 AATGATTTGA
* *
6609241 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTTATGATTTGATAGTAATGA-TTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
6609305 ATGATTACTAATAATGAAATCATTATTAATATTTAATGATTTGATAGTAATGATT
66 ATGATTACTAATAAT-AAATCATTATTAATATTTAATGATTTGATAGTAATGATT
6609360 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
* * * *
6609425 ATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTGATATTAATGATT
66 ATGATTACTAATAATAAATCATTATTAATATTTAATGATTTGATAGTAATGATT
6609479 T
1 T
6609480 GATAGTAATG
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
119 93 0.82
120 20 0.18
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.46
Consensus pattern (119 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
ATGATTACTAATAATAAATCATTATTAATATTTAATGATTTGATAGTAATGATT
Found at i:6609465 original size:21 final size:22
Alignment explanation
Indices: 6609436--6609479 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
6609426 TGATTAGTAA
6609436 TAATAATTT-ATTATTAAT-ATT
1 TAATAATTTGA-TATTAATGATT
*
6609457 TAATGATTTGATATTAATGATT
1 TAATAATTTGATATTAATGATT
6609479 T
1 T
6609480 GATAGTAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.55
Consensus pattern (22 bp):
TAATAATTTGATATTAATGATT
Found at i:6609473 original size:14 final size:14
Alignment explanation
Indices: 6609456--6609493 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
6609446 TTATTAATAT
6609456 TTAATGATTTGATA
1 TTAATGATTTGATA
6609470 TTAATGATTTGATA
1 TTAATGATTTGATA
*
6609484 GTAATGATTT
1 TTAATGATTT
6609494 ACGACTTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (14 bp):
TTAATGATTTGATA
Found at i:6609479 original size:59 final size:60
Alignment explanation
Indices: 6609241--6609479 Score: 410
Period size: 59 Copynumber: 4.0 Consensus size: 60
6609231 AATGATTTGA
* *
6609241 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTTATGATTTGATAGTAATGA-T
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATT
* *
6609300 TAGTAATGATTACTAATAATGAAATCATTATTAATATTTAATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATT
6609360 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATT
* *
6609420 TAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGATATTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATT
6609479 T
1 T
6609480 GATAGTAATG
Statistics
Matches: 171, Mismatches: 8, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
59 92 0.54
60 79 0.46
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.46
Consensus pattern (60 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATT
Found at i:6612079 original size:22 final size:21
Alignment explanation
Indices: 6612041--6612081 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
6612031 TTTATGTATA
*
6612041 ATATAACTTAAACTAACAATC
1 ATATAACCTAAACTAACAATC
*
6612062 ATATAACCCTAAATTAACAA
1 ATATAA-CCTAAACTAACAA
6612082 ACTAATTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.54, C:0.20, G:0.00, T:0.27
Consensus pattern (21 bp):
ATATAACCTAAACTAACAATC
Found at i:6612273 original size:26 final size:26
Alignment explanation
Indices: 6612227--6612284 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
6612217 CCCTTTCTTT
*
6612227 CTTTC-TCGGCTGCAATTTCTTCTCC
1 CTTTCTTCGGCTGCAATCTCTTCTCC
*
6612252 CTTTCTTCTGCTGCAATCTCTTCTCC
1 CTTTCTTCGGCTGCAATCTCTTCTCC
6612278 CTTTCTT
1 CTTTCTT
6612285 TCTTTTATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 5 0.17
26 25 0.83
ACGTcount: A:0.07, C:0.36, G:0.09, T:0.48
Consensus pattern (26 bp):
CTTTCTTCGGCTGCAATCTCTTCTCC
Found at i:6612372 original size:33 final size:33
Alignment explanation
Indices: 6612330--6612396 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
6612320 ATAATTTAGG
6612330 TGTCACCGGCTGCCTCAATTATTTCACCAATAA
1 TGTCACCGGCTGCCTCAATTATTTCACCAATAA
6612363 TGTCACCGGCTGCCTCAATTATTTCACCAATAA
1 TGTCACCGGCTGCCTCAATTATTTCACCAATAA
6612396 T
1 T
6612397 TGTGCAATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.31
Consensus pattern (33 bp):
TGTCACCGGCTGCCTCAATTATTTCACCAATAA
Found at i:6612625 original size:29 final size:29
Alignment explanation
Indices: 6612554--6612630 Score: 118
Period size: 29 Copynumber: 2.7 Consensus size: 29
6612544 TCGCCGAGAC
***
6612554 TGCTTGGCGACCTACAAGGTCGCTGGGAG
1 TGCTTGGCGACCTTGTAGGTCGCTGGGAG
*
6612583 TGCATGGCGACCTTGTAGGTCGCTGGGAG
1 TGCTTGGCGACCTTGTAGGTCGCTGGGAG
6612612 TGCTTGGCGACCTTGTAGG
1 TGCTTGGCGACCTTGTAGG
6612631 GGTGTTGGGG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.14, C:0.22, G:0.39, T:0.25
Consensus pattern (29 bp):
TGCTTGGCGACCTTGTAGGTCGCTGGGAG
Found at i:6615569 original size:38 final size:38
Alignment explanation
Indices: 6615525--6615620 Score: 165
Period size: 38 Copynumber: 2.5 Consensus size: 38
6615515 TATGAAAAAT
* * *
6615525 ATAATCATATTCAAATATGTATCAAATACGTACATTCA
1 ATAATCATATTCGAATATGTAGCAAATACATACATTCA
6615563 ATAATCATATTCGAATATGTAGCAAATACATACATTCA
1 ATAATCATATTCGAATATGTAGCAAATACATACATTCA
6615601 ATAATCATATTCGAATATGT
1 ATAATCATATTCGAATATGT
6615621 GTCTGTTTCG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 55 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (38 bp):
ATAATCATATTCGAATATGTAGCAAATACATACATTCA
Found at i:6619421 original size:35 final size:35
Alignment explanation
Indices: 6619375--6619448 Score: 130
Period size: 35 Copynumber: 2.1 Consensus size: 35
6619365 CAAAACCTAT
*
6619375 TCAAGACAGTAGAATGATAAATCAAGCCAAGCCCA
1 TCAAGACAGTAGAAGGATAAATCAAGCCAAGCCCA
*
6619410 TCAAGACAGTAGAAGGATAAATCAAGGCAAGCCCA
1 TCAAGACAGTAGAAGGATAAATCAAGCCAAGCCCA
6619445 TCAA
1 TCAA
6619449 CATTCATGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.46, C:0.22, G:0.19, T:0.14
Consensus pattern (35 bp):
TCAAGACAGTAGAAGGATAAATCAAGCCAAGCCCA
Found at i:6623416 original size:20 final size:20
Alignment explanation
Indices: 6623393--6623527 Score: 112
Period size: 20 Copynumber: 6.7 Consensus size: 20
6623383 GAATTGGAAA
6623393 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
6623413 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
6623433 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
6623454 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
6623474 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* ** *
6623494 TTCGCAACACGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
6623514 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
6623528 TTTCAAAGCG
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
19 4 0.04
20 65 0.69
21 23 0.24
22 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:6623458 original size:61 final size:61
Alignment explanation
Indices: 6623373--6623527 Score: 186
Period size: 61 Copynumber: 2.6 Consensus size: 61
6623363 GAATAAGTAA
* ** * *
6623373 ATCGCAACACGA-ATTGGAAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACT
1 ATCGCAACACGATAATACAAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACT
** * * * *
6623433 ATCGCAATGCGATAATACAAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACT
1 ATCGCAACACGATAATACAAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACT
* *
6623494 TTCGCAACACGATAATACATAATCGCAATGCGAT
1 ATCGCAACACGATAATACAAAATCGCAATGCGAT
6623528 TTTCAAAGCG
Statistics
Matches: 77, Mismatches: 17, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
60 10 0.13
61 67 0.87
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (61 bp):
ATCGCAACACGATAATACAAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACT
Found at i:6624251 original size:25 final size:24
Alignment explanation
Indices: 6624197--6624251 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
6624187 TGTTTATTAT
* *
6624197 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
6624221 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
6624247 TGTTT
1 TGTTT
6624252 ATTATTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:6625401 original size:18 final size:18
Alignment explanation
Indices: 6625380--6625424 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
6625370 TCCACTTCGG
*
6625380 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
6625398 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
6625416 GAGCCATCA
1 GAGCCATCA
6625425 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:6625959 original size:19 final size:20
Alignment explanation
Indices: 6625916--6625960 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
6625906 AGCAACACGA
6625916 AAATGACTATCGCAACGCAG
1 AAATGACTATCGCAACGCAG
* *
6625936 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCAG
6625955 AAATGA
1 AAATGA
6625961 AAATCACAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (20 bp):
AAATGACTATCGCAACGCAG
Found at i:6625979 original size:14 final size:14
Alignment explanation
Indices: 6625960--6626017 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
6625950 ATGCGAAATG
*
6625960 AAAATCACAACGAC
1 AAAATCGCAACGAC
*
6625974 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
6625990 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
6626006 AAAATCGCAACG
1 AAAATCGCAACG
6626018 CGAAATAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.50, C:0.24, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:6625986 original size:33 final size:33
Alignment explanation
Indices: 6625944--6626030 Score: 140
Period size: 32 Copynumber: 2.7 Consensus size: 33
6625934 AGAAATGGCT
6625944 ATCGCAATGCGAAATGAAAATCACAACGACAAA
1 ATCGCAATGCGAAATGAAAATCACAACGACAAA
*
6625977 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCACAACGACAAA
* *
6626009 ATCGCAACGCGAAATAAAAATC
1 ATCGCAATGCGAAATGAAAATC
6626031 GCAATGCGAT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
32 29 0.58
33 21 0.42
ACGTcount: A:0.49, C:0.22, G:0.16, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCACAACGACAAA
Found at i:6626051 original size:19 final size:18
Alignment explanation
Indices: 6626046--6626171 Score: 98
Period size: 19 Copynumber: 6.9 Consensus size: 18
6626036 GCGATTTGTG
*
6626046 TTTCGCGTTGCGATTTCA
1 TTTCGCATTGCGATTTCA
6626064 TTTCGCATTGCGATTT--
1 TTTCGCATTGCGATTTCA
*
6626080 TGTCG--TTGCGATTTTCA
1 TTTCGCATTGCGA-TTTCA
*
6626097 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGA-TTTCA
**
6626116 TTTCGCATTGCGATAGCCA
1 TTTCGCATTGCGAT-TTCA
* *
6626135 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCATTGCGAT-TTCA
*
6626155 TTTTCGCGTTGCGATTT
1 -TTTCGCATTGCGATTT
6626172 TAACTTTCGT
Statistics
Matches: 91, Mismatches: 9, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
14 6 0.07
15 3 0.03
16 4 0.04
17 4 0.04
18 16 0.18
19 30 0.33
20 25 0.27
21 3 0.03
ACGTcount: A:0.13, C:0.21, G:0.22, T:0.44
Consensus pattern (18 bp):
TTTCGCATTGCGATTTCA
Found at i:6626092 original size:32 final size:33
Alignment explanation
Indices: 6626051--6626113 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
6626041 TTGTGTTTCG
6626051 CGTTGCGA-TTTCATTTCGCATTGCGATTTTGT
1 CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
*
6626083 CGTTGCGATTTTCATTTCGCGTTGCGATTTT
1 CGTTGCGATTTTCATTTCGCATTGCGATTTT
6626114 CATTTCGCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 8 0.28
33 21 0.72
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
Found at i:6626148 original size:20 final size:19
Alignment explanation
Indices: 6626083--6626169 Score: 102
Period size: 19 Copynumber: 4.5 Consensus size: 19
6626073 GCGATTTTGT
**
6626083 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
**
6626102 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
6626121 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
6626141 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
6626161 CGTTGCGAT
1 CGTTGCGAT
6626170 TTTAACTTTC
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
19 32 0.53
20 25 0.42
21 3 0.05
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.40
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:6626156 original size:39 final size:39
Alignment explanation
Indices: 6626095--6626169 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
6626085 TTGCGATTTT
**
6626095 CATTTCGCGTTGCGATTTTCA-TTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGTCATTTTCGCATTGCGATAGC
*
6626133 CATTTCCGCGTTGCGATAGTCATTTTCGCGTTGCGAT
1 CATTT-CGCGTTGCGATAGTCATTTTCGCATTGCGAT
6626170 TTTAACTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 5 0.16
39 14 0.44
40 13 0.41
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.39
Consensus pattern (39 bp):
CATTTCGCGTTGCGATAGTCATTTTCGCATTGCGATAGC
Found at i:6626156 original size:58 final size:53
Alignment explanation
Indices: 6626046--6626172 Score: 152
Period size: 52 Copynumber: 2.3 Consensus size: 53
6626036 GCGATTTGTG
**
6626046 TTTCGCGTTGCGA-TTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTCA-
1 TTTCGCGTTGCGATTTTCATTTCGCATTGCGATTTTGTCGTTGCGATAGTCAT
6626097 TTTCGCGTTGCGATTTTCATTTCGCATTGCGATAGCCATTTCCG-CGTTGCGATAGTCAT
1 TTTCGCGTTGCGATTTTCATTTCGCATTGCGAT-----TTT--GTCGTTGCGATAGTCAT
6626156 TTTCGCGTTGCGATTTT
1 TTTCGCGTTGCGATTTT
6626173 AACTTTCGTG
Statistics
Matches: 65, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
51 13 0.20
52 19 0.29
57 3 0.05
58 12 0.18
59 18 0.28
ACGTcount: A:0.13, C:0.21, G:0.22, T:0.44
Consensus pattern (53 bp):
TTTCGCGTTGCGATTTTCATTTCGCATTGCGATTTTGTCGTTGCGATAGTCAT
Found at i:6626179 original size:20 final size:19
Alignment explanation
Indices: 6626046--6626188 Score: 127
Period size: 20 Copynumber: 7.7 Consensus size: 19
6626036 GCGATTTGTG
6626046 TTTCGCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTCA
*
6626064 TTTCGCATTGCGA-TTT--
1 TTTCGCGTTGCGATTTTCA
*
6626080 TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
6626097 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* ***
6626116 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGATTTTCA
**
6626135 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCGTTGCGATTTTCA
*
6626155 TTTTCGCGTTGCGATTTTAA
1 -TTTCGCGTTGCGATTTTCA
*
6626175 CTTTCGTGTTGCGA
1 -TTTCGCGTTGCGA
6626189 AAGTAAACTA
Statistics
Matches: 103, Mismatches: 15, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
14 7 0.07
15 3 0.03
16 2 0.02
17 2 0.02
18 15 0.15
19 32 0.31
20 39 0.38
21 3 0.03
ACGTcount: A:0.13, C:0.21, G:0.22, T:0.43
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:6626631 original size:41 final size:42
Alignment explanation
Indices: 6626535--6626622 Score: 124
Period size: 41 Copynumber: 2.1 Consensus size: 42
6626525 GACTCACATG
* *
6626535 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
* * *
6626577 TCCTCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
6626618 TCATC
1 TCATC
6626623 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 22 0.55
42 18 0.45
ACGTcount: A:0.22, C:0.43, G:0.15, T:0.20
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
Found at i:6628057 original size:14 final size:14
Alignment explanation
Indices: 6628038--6628073 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
6628028 ATTGTTTAAT
6628038 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
6628052 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
6628066 TGATTTGT
1 TGATTTGT
6628074 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:6628234 original size:19 final size:19
Alignment explanation
Indices: 6628210--6628277 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
6628200 ATCGCAACGA
6628210 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
6628229 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
6628248 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
6628262 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
6628278 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:6628321 original size:20 final size:20
Alignment explanation
Indices: 6628296--6628371 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
6628286 TCGCATTGCG
*
6628296 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
* ***
6628316 ATTTTCGCGTTGCGATTTTTC
1 ATTTTCGAGTTGCGA-TAGCC
*
6628337 A-TTTCGAATTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
6628356 ATTTTCGCGTTGCGAT
1 ATTTTCGAGTTGCGAT
6628372 TTCCCCGTTG
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
19 3 0.07
20 36 0.86
21 3 0.07
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.42
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:6628329 original size:34 final size:34
Alignment explanation
Indices: 6628284--6628387 Score: 109
Period size: 40 Copynumber: 2.9 Consensus size: 34
6628274 GCGATTTTCA
*
6628284 TTTCGCATTGCGATTTTCTAGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCTAGTTGCGATAGCCAT
*
6628318 TTTCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCAT
1 TTTCGCGTTGCGA-TTTTC---T--AGTTGCGATAGCCAT
* **
6628358 TTTCGCGTTGCGATTTCCCCGTTGCGATAG
1 TTTCGCGTTGCGATTTTCTAGTTGCGATAG
6628388 TCAAATGAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
34 21 0.36
35 5 0.09
38 1 0.02
39 4 0.07
40 27 0.47
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.40
Consensus pattern (34 bp):
TTTCGCGTTGCGATTTTCTAGTTGCGATAGCCAT
Found at i:6628610 original size:20 final size:20
Alignment explanation
Indices: 6628585--6628676 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
6628575 TTGAAGATGA
6628585 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
6628605 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
* **
6628625 TTGCGATTTTGTATTATCTCG
1 TTGCGATTTT-CAGAATCTCG
** * * *
6628646 TTGCGATAGTCAGTATCGCA
1 TTGCGATTTTCAGAATCTCG
6628666 TTGCGATTTTC
1 TTGCGATTTTC
6628677 CAAATTCGCA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:6629512 original size:24 final size:24
Alignment explanation
Indices: 6629485--6629538 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
6629475 GTATTCAAAA
*
6629485 TTTGATCTTGGTCAATACTCGGAC
1 TTTGATATTGGTCAATACTCGGAC
*
6629509 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACTCGGAC
6629533 TTTGAT
1 TTTGAT
6629539 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATATTGGTCAATACTCGGAC
Found at i:6629730 original size:12 final size:12
Alignment explanation
Indices: 6629713--6629737 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6629703 ATATAATCCT
6629713 GAAGAAGAAAAA
1 GAAGAAGAAAAA
6629725 GAAGAAGAAAAA
1 GAAGAAGAAAAA
6629737 G
1 G
6629738 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Done.