Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008243.1 Hibiscus syriacus cultivar Beakdansim tig00110893_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: 10265705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 49
Found at i:529116 original size:64 final size:64
Alignment explanation
Indices: 529047--529267 Score: 234
Period size: 64 Copynumber: 3.5 Consensus size: 64
529037 TTGAAGGTGT
* **
529047 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAACATCGAATGCAATTCATG
1 ATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCAATTCATG
529110 C
64 C
* * **
529111 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGGTGC
1 ATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
* ** * * ** *
529175 ATCGATGCATAAGG-AGTGCATCGAAGCATCCCAGCAATAATAATACATCGAATACCTTTTATGC
1 ATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
*
529239 ACCGATGCATCA-GTAGTGCATCGATGCAT
1 ATCGATGCAT-AGGTAGTGCATCGATGCAT
529268 ACCTTCATTA
Statistics
Matches: 132, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
63 1 0.01
64 125 0.95
65 6 0.05
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (64 bp):
ATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
Found at i:529594 original size:12 final size:12
Alignment explanation
Indices: 529573--529608 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
529563 TATATATGTT
*
529573 CATGTGATATGA
1 CATGTTATATGA
*
529585 TATGTTATATGA
1 CATGTTATATGA
529597 CATGTTATATGA
1 CATGTTATATGA
529609 GAACATGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (12 bp):
CATGTTATATGA
Found at i:536039 original size:64 final size:63
Alignment explanation
Indices: 535956--536139 Score: 235
Period size: 64 Copynumber: 2.9 Consensus size: 63
535946 ACTCTTTTAA
**
535956 AATAA-AAACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCATT
1 AATAATAAACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGC
** *
536018 AATAATGAAACATCGAATGCAATTGGTGCATCGATGCATAAGGAGTGCATCGATGCATCCCAGC
1 AATAAT-AAACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGC
* * ** * * *
536082 AATAATAATACATCAAATACCTTTTATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 AATAATAA-ACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCAT
536140 ACCTTCATTA
Statistics
Matches: 105, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
62 5 0.05
63 2 0.02
64 98 0.93
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.26
Consensus pattern (63 bp):
AATAATAAACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGC
Found at i:536632 original size:15 final size:15
Alignment explanation
Indices: 536614--536646 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
536604 GAGGGTATAA
536614 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
536629 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
536644 TAG
1 TAG
536647 GGGTCCTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.18, G:0.33, T:0.33
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:538553 original size:20 final size:20
Alignment explanation
Indices: 538528--538594 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
538518 TGACTTTTGT
538528 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
*
538548 GTTGCGATTTACAAATTTGC
1 GTTGCGATTTACAAATTCGC
*
538568 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACAAATTCGC
538588 GTTGCGA
1 GTTGCGA
538595 ATTTGAAAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:538611 original size:20 final size:20
Alignment explanation
Indices: 538588--538635 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
538578 ACATATTCGC
538588 GTTGCGAATTTGAAAACTGA
1 GTTGCGAATTTGAAAACTGA
* * *
538608 GTTGCGAATTTGGAACCTGT
1 GTTGCGAATTTGAAAACTGA
538628 GTTGCGAA
1 GTTGCGAA
538636 ATTAAAGTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.31
Consensus pattern (20 bp):
GTTGCGAATTTGAAAACTGA
Found at i:538612 original size:40 final size:40
Alignment explanation
Indices: 538528--538614 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 40
538518 TGACTTTTGT
* *
538528 GTTGCGATTTACAAATTCGCGTTGCGATTTACAAATTTGC
1 GTTGCGATTTACAAATTCGCGTTGCGATTTACAAATCTGA
*
538568 GTTGCGATTTACATATTCGCGTTGCGAATTTGA-AAA-CTGA
1 GTTGCGATTTACAAATTCGCGTTGCG-ATTT-ACAAATCTGA
538608 GTTGCGA
1 GTTGCGA
538615 ATTTGGAACC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
40 34 0.81
41 7 0.17
42 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (40 bp):
GTTGCGATTTACAAATTCGCGTTGCGATTTACAAATCTGA
Found at i:540170 original size:27 final size:28
Alignment explanation
Indices: 540133--540193 Score: 97
Period size: 27 Copynumber: 2.2 Consensus size: 28
540123 GGAAAAAAGA
*
540133 AAAGTAAAACAAGTATTCAGCCACATG-
1 AAAGGAAAACAAGTATTCAGCCACATGC
*
540160 AAAGGAAAACAAGTATTCAGCCGCATGC
1 AAAGGAAAACAAGTATTCAGCCACATGC
540188 AAAGGA
1 AAAGGA
540194 CAGCCATTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 25 0.81
28 6 0.19
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.15
Consensus pattern (28 bp):
AAAGGAAAACAAGTATTCAGCCACATGC
Found at i:543081 original size:17 final size:17
Alignment explanation
Indices: 543059--543093 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
543049 AGGGTAAACT
543059 ATATAAATGGTTATTGA
1 ATATAAATGGTTATTGA
543076 ATATAAATGGTTATTGA
1 ATATAAATGGTTATTGA
543093 A
1 A
543094 GTATGAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (17 bp):
ATATAAATGGTTATTGA
Found at i:545624 original size:59 final size:59
Alignment explanation
Indices: 545525--545661 Score: 177
Period size: 59 Copynumber: 2.3 Consensus size: 59
545515 CAGCAGGCTG
** * *
545525 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
* ** * *
545584 CATATTCGGGACTGTACTTAAGGATACCTAGTACAGATGGTGGACACGACTTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
545643 CATATTCGGG-ATAGCACTA
1 CATATTCGGGAATA-CACTA
545662 CGGTGCTTAT
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
58 1 0.02
59 63 0.98
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
Found at i:545812 original size:44 final size:45
Alignment explanation
Indices: 545762--545880 Score: 150
Period size: 48 Copynumber: 2.6 Consensus size: 45
545752 GTAAGCATAC
*
545762 AAATAAGCTTACGAGCTTTTGGAATAATGGCAAGTATATGGGT-A
1 AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATGGGTAA
* * * *
545806 AAATAAGCTTACGAGCTTATGTAATTTAAATGGTAAGTATTTTGGTAA
1 AAATAAGCTTACGAGCTTATGGAA--T-AATGGCAAGTATATGGGTAA
*
545854 AAATAAGCTTACGAGCTTATGGGATAA
1 AAATAAGCTTACGAGCTTATGGAATAA
545881 ATGGTAAGGG
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
44 22 0.34
45 2 0.03
46 2 0.03
47 15 0.23
48 23 0.36
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATGGGTAA
Found at i:546049 original size:21 final size:21
Alignment explanation
Indices: 546025--546086 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
546015 ATATATTACT
*
546025 TCTCTCTGTTCTGCCGCTGCC
1 TCTCTCTGTGCTGCCGCTGCC
*
546046 TCTCTCTGTGCTGCCGCTGCT
1 TCTCTCTGTGCTGCCGCTGCC
* *
546067 TCTCTCTCTGCTTCCGCTGC
1 TCTCTCTGTGCTGCCGCTGC
546087 TGCTCTAGCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.00, C:0.42, G:0.19, T:0.39
Consensus pattern (21 bp):
TCTCTCTGTGCTGCCGCTGCC
Found at i:546087 original size:21 final size:21
Alignment explanation
Indices: 546023--546131 Score: 85
Period size: 21 Copynumber: 5.2 Consensus size: 21
546013 TGATATATTA
* * *
546023 CTTCTCTCTGTTCTGCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* * *
546044 CCTCTCTCTGTGCTGCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
546065 CTTCTCTCTCTGCTTCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* ** *
546086 CTGCTCTAGCTGCTTCCGCTA
1 CTTCTCTCTCTGCTTCCGCTG
* * *
546107 CTGCTCTATCTGTTTCC-CTTG
1 CTTCTCTCTCTGCTTCCGC-TG
546128 CTTC
1 CTTC
546132 ATTTTCCGCT
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
20 1 0.01
21 73 0.99
ACGTcount: A:0.03, C:0.39, G:0.17, T:0.40
Consensus pattern (21 bp):
CTTCTCTCTCTGCTTCCGCTG
Found at i:554502 original size:83 final size:82
Alignment explanation
Indices: 554415--554617 Score: 237
Period size: 83 Copynumber: 2.4 Consensus size: 82
554405 CTTTTTTGTC
* * * *
554415 AAAACGCCGCCAATTTGCCGCTCTATTACGGCGTTTTGACTCAATCGCCGCAAAATTTATACTCT
1 AAAACGCCGCCAATTTGCC-CTCTATTGCGGCGTTTTGACTAAATCACCGCAAAATTTATAATCT
** *
554480 ATTGTGGCGTTTGTGGTA
65 ATTGAAGCGTTTGTGATA
* * * * *
554498 AAAACGCTGCCAGTTTACCACTATATTGCGGCGTTTTGGCTAAATCACCGCAAAATTTATAATCT
1 AAAACGCCGCCAATTTGCC-CTCTATTGCGGCGTTTTGACTAAATCACCGCAAAATTTATAATCT
554563 ATTGAAGCGTTTGTGATA
65 ATTGAAGCGTTTGTGATA
* *
554581 TAAACGCCGCTAATTTAGCACC-CTATTGCGGCGTTTT
1 AAAACGCCGCCAATTT-GC-CCTCTATTGCGGCGTTTT
554618 TCTAAAAACG
Statistics
Matches: 99, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
83 96 0.97
84 2 0.02
85 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.33
Consensus pattern (82 bp):
AAAACGCCGCCAATTTGCCCTCTATTGCGGCGTTTTGACTAAATCACCGCAAAATTTATAATCTA
TTGAAGCGTTTGTGATA
Found at i:555929 original size:47 final size:45
Alignment explanation
Indices: 555835--555960 Score: 173
Period size: 47 Copynumber: 2.8 Consensus size: 45
555825 GTAAGCATAC
* * *
555835 AAATAAGCTTATGAGCTTTTGGAAT-AATGGCAAGTATATGGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATGGGTA
* *
555879 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATGGGTA
*
555926 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
555961 GGATTTTATA
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
44 22 0.30
45 11 0.15
46 1 0.01
47 39 0.53
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATGGGTA
Found at i:558095 original size:31 final size:31
Alignment explanation
Indices: 558048--558115 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
558038 TCAAACGGTC
558048 GGGGACCATATTGCAAAC-AGACTAAATGTTG
1 GGGGACCATATTGCAAACGA-ACTAAATGTTG
558079 GGGGACCATATTGCAAACGAACTAAATGTTG
1 GGGGACCATATTGCAAACGAACTAAATGTTG
558110 GGGGAC
1 GGGGAC
558116 TGTATTACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
31 35 0.97
32 1 0.03
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.21
Consensus pattern (31 bp):
GGGGACCATATTGCAAACGAACTAAATGTTG
Found at i:561079 original size:20 final size:20
Alignment explanation
Indices: 561056--561103 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
561046 GTAGGTTTTG
561056 GATCGATCCTTTAGGCAAAA
1 GATCGATCCTTTAGGCAAAA
* * * *
561076 GATCGATCTTTTTGGGAAGA
1 GATCGATCCTTTAGGCAAAA
561096 GATCGATC
1 GATCGATC
561104 ATTTCAGTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (20 bp):
GATCGATCCTTTAGGCAAAA
Found at i:563884 original size:13 final size:13
Alignment explanation
Indices: 563866--563899 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
563856 ATGTGACAAT
563866 GAGCTATATGAAA
1 GAGCTATATGAAA
563879 GAGCTATATGAAA
1 GAGCTATATGAAA
*
563892 GAACTATA
1 GAGCTATA
563900 AGATTATGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.47, C:0.09, G:0.21, T:0.24
Consensus pattern (13 bp):
GAGCTATATGAAA
Found at i:564173 original size:23 final size:23
Alignment explanation
Indices: 564147--564214 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
564137 AATCTTATAT
* *
564147 GGCACTTTGGTGCATTTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* *
564170 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
*
564193 GGCACTTCGGTGCAATTATACG
1 GGCACTTCGGTGCAATTCTACG
564215 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:564376 original size:14 final size:15
Alignment explanation
Indices: 564353--564385 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
564343 TTCTTTATGG
564353 TGTGAAATGAT-ATA
1 TGTGAAATGATGATA
*
564367 TGTGATATGATGATA
1 TGTGAAATGATGATA
564382 TGTG
1 TGTG
564386 TGTTTCTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.33, C:0.00, G:0.27, T:0.39
Consensus pattern (15 bp):
TGTGAAATGATGATA
Found at i:564495 original size:2 final size:2
Alignment explanation
Indices: 564488--564520 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
564478 AAATGGTATG
564488 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
564521 GCATTTATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:568702 original size:23 final size:23
Alignment explanation
Indices: 568676--568730 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
568666 ATGGCACTTT
*
568676 GGTGCATTTCTACGCGGCACTAC
1 GGTGCAATTCTACGCGGCACTAC
* **
568699 GGTGCAATTCTACGTGGCACTTT
1 GGTGCAATTCTACGCGGCACTAC
568722 GGTGCAATT
1 GGTGCAATT
568731 ATGAGCTGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (23 bp):
GGTGCAATTCTACGCGGCACTAC
Found at i:569007 original size:2 final size:2
Alignment explanation
Indices: 569000--569045 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
568990 GTAAAATGAA
569000 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
569042 AT AT
1 AT AT
569046 GCATTTATGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:570156 original size:19 final size:19
Alignment explanation
Indices: 570132--570179 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
570122 ATTATGTGTA
570132 ACATAACAATTCACAAGTC
1 ACATAACAATTCACAAGTC
*
570151 ACATAACAATTCACAATTC
1 ACATAACAATTCACAAGTC
*
570170 ACATATCAAT
1 ACATAACAAT
570180 AATATATCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.25
Consensus pattern (19 bp):
ACATAACAATTCACAAGTC
Found at i:574612 original size:16 final size:16
Alignment explanation
Indices: 574591--574628 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
574581 ATTAGCAGTG
574591 GAAAGAGAAAGCGGTA
1 GAAAGAGAAAGCGGTA
574607 GAAAGAGAAAGCGGTA
1 GAAAGAGAAAGCGGTA
*
574623 AAAAGA
1 GAAAGA
574629 TCAAAGCCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.55, C:0.05, G:0.34, T:0.05
Consensus pattern (16 bp):
GAAAGAGAAAGCGGTA
Found at i:577047 original size:12 final size:12
Alignment explanation
Indices: 577030--577096 Score: 118
Period size: 12 Copynumber: 5.7 Consensus size: 12
577020 ACATCAATTT
577030 AGTTAGGTGAAG
1 AGTTAGGTGAAG
577042 AGTTAGGTGAAG
1 AGTTAGGTGAAG
*
577054 AATTAGGTGAAG
1 AGTTAGGTGAAG
577066 AGTTAGGTGAAG
1 AGTTAGGTGAAG
577078 AGTTAGGTG-AG
1 AGTTAGGTGAAG
577089 AGTTAGGT
1 AGTTAGGT
577097 ATTTGTATAT
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
11 10 0.19
12 43 0.81
ACGTcount: A:0.33, C:0.00, G:0.40, T:0.27
Consensus pattern (12 bp):
AGTTAGGTGAAG
Found at i:583157 original size:17 final size:18
Alignment explanation
Indices: 583119--583165 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
583109 TGTTTCTAAG
583119 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
583137 GGAATTGGAATCTGT-AA
1 GGAATTGGAATCTGTGAA
583154 GGAATTGGAATC
1 GGAATTGGAATC
583166 CAATTCTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.34, C:0.06, G:0.32, T:0.28
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:583809 original size:27 final size:28
Alignment explanation
Indices: 583751--583811 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
583741 CGACCCGACT
583751 CGACCCGAATATCACACTTAAAAAAAAC
1 CGACCCGAATATCACACTTAAAAAAAAC
* *
583779 CGACCCGAATATCACA-TTTAAAAAACC
1 CGACCCGAATATCACACTTAAAAAAAAC
583806 CGACCC
1 CGACCC
583812 AAACAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 15 0.48
28 16 0.52
ACGTcount: A:0.44, C:0.33, G:0.08, T:0.15
Consensus pattern (28 bp):
CGACCCGAATATCACACTTAAAAAAAAC
Found at i:587654 original size:5 final size:5
Alignment explanation
Indices: 587644--587685 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
587634 TTTTTCACAG
* *
587644 AATAA AATAA AATAA AATAA ACTAA AA-AA ATAAAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AATAA A-ATAA AATAA AA
587686 ATAGGTGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
4 3 0.09
5 26 0.81
6 3 0.09
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (5 bp):
AATAA
Found at i:589518 original size:3 final size:3
Alignment explanation
Indices: 589510--589558 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
589500 TACAAAAATG
589510 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
589558 T
1 T
589559 TTTTTGTAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:589968 original size:131 final size:131
Alignment explanation
Indices: 589748--590474 Score: 841
Period size: 131 Copynumber: 5.6 Consensus size: 131
589738 GTTCTGGTCT
* * * * * *
589748 TCTAAGGGTGACACGGCTCCTATGTGATGAGGAGATCTGGTCGGTGGATGACACTGTTCCTATGT
1 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACAGTTCCTACGC
* * * * * * * * *
589813 GATGAGGATTAAAAACCATATTTAGGGATGATAACATGGTTCCTACATGATGAGGACGGTTGGTT
66 GATGAGGATGACAATCTATCTTTAGGGATGATAACACGGTTCCTACGTGATGAGGACGGCTAGTT
589878 A
131 A
* * *
589879 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTTGATGGATTACACAGTTCCTACGC
1 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACAGTTCCTACGC
* * * * *
589944 GATGAGGACGATATTCTATCTTTAGGGATGATAACACAGTTCCTACGTGATGAGGACGACTAGTT
66 GATGAGGATGACAATCTATCTTTAGGGATGATAACACGGTTCCTACGTGATGAGGACGGCTAGTT
590009 A
131 A
* * * * *
590010 TTTAGGTGTGACACGACTCCTACGTGATGAGGAGTTCTGGTCGGTGGATGACACGGTTCCTA-GC
1 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACAGTTCCTACGC
* * * * * * *
590074 GATGAGGATGACAGGT-TATCTTTAGGGATGATAACGCGATTTCTACATAAAGAGGACGGCTAGT
66 GATGAGGATGACA-ATCTATCTTTAGGGATGATAACACGGTTCCTACGTGATGAGGACGGCTAGT
590138 TA
130 TA
* * * * ** *
590140 TTTAGGTGTGACACAGCTCCTACGTGATGAGGAGGTATGGTCGGTGGATGACATGGTTCCTATGC
1 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACAGTTCCTACGC
* * * * *
590205 GATGAGGATGACAACCCATCTTTAAGGATGATAACACGGTTCCTACGTGATGAGGATGACTAGTT
66 GATGAGGATGACAATCTATCTTTAGGGATGATAACACGGTTCCTACGTGATGAGGACGGCTAGTT
590270 A
131 A
* * **
590271 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAAGTCTGGTCGGTGGATGACATAGTTCCTACAT
1 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACAGTTCCTACGC
* * * * * * *
590336 GATGAGGATGGCAGGT-TATCTTTAGGGATGATAACATGGTTCCTACGCGATGAGAATGGCTGGT
66 GATGAGGATGACA-ATCTATCTTTAGGGATGATAACACGGTTCCTACGTGATGAGGACGGCTAGT
590400 TA
130 TA
* * * *
590402 TCTAGGGGTGACACGGTTCCTACGTGATGAAGAGGTCTGGTCGAG-GGATGACACTGTTCCTACA
1 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCG-GTGGATGACACAGTTCCTACG
590466 CGATGAGGA
65 CGATGAGGA
590475 CGTCTGGCCA
Statistics
Matches: 508, Mismatches: 83, Indels: 10
0.85 0.14 0.02
Matches are distributed among these distances:
130 112 0.22
131 395 0.78
132 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (131 bp):
TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACAGTTCCTACGC
GATGAGGATGACAATCTATCTTTAGGGATGATAACACGGTTCCTACGTGATGAGGACGGCTAGTT
A
Found at i:590201 original size:261 final size:259
Alignment explanation
Indices: 589748--590476 Score: 913
Period size: 261 Copynumber: 2.8 Consensus size: 259
589738 GTTCTGGTCT
* * * *
589748 TCTAAGGGTGACACGGCTCCTATGTGATGAGGAGATCTGGTCGGTGGATGACACTGTTCCTATGT
1 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAG-TCTGGTCGGTGGATGACACAGTTCCTA-GC
* * **** * *
589813 GATGAGGATTAAAAACCATATTTAGGGATGATAACATGGTTCCTACATGATGAGGACGGTTGGTT
64 GATGAGGATGACAGGTTATCTTTAGGGATGATAACATGGTTCCTACATGATGAGGACGGCTGGTT
* * * *
589878 ATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTTGATGGATTACACAGTTCCTACG
129 ATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACA-TGTTCCTACG
* ** * *
589943 CGATGAGGACGATATTCTATCTTTAGGGATGATAACACAGTTCCTACGTGATGAGGACGACTAGT
193 CGATGAGGACGACAACCCATCTTTAAGGATGATAACACAGTTCCTACGTGATGAGGACGACTAGT
590008 TA
258 TA
* * * *
590010 TTTAGGTGTGACACGACTCCTACGTGATGAGGAGTTCTGGTCGGTGGATGACACGGTTCCTAGCG
1 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAG-TCTGGTCGGTGGATGACACAGTTCCTAGCG
** * * * * *
590075 ATGAGGATGACAGGTTATCTTTAGGGATGATAACGCGATTTCTACATAAAGAGGACGGCTAGTTA
65 ATGAGGATGACAGGTTATCTTTAGGGATGATAACATGGTTCCTACATGATGAGGACGGCTGGTTA
* * * * *
590140 TTTAGGTGTGACACAGCTCCTACGTGATGAGGAGGTATGGTCGGTGGATGACATGGTTCCTATGC
130 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACAT-GTTCCTACGC
* * *
590205 GATGAGGATGACAACCCATCTTTAAGGATGATAACACGGTTCCTACGTGATGAGGATGACTAGTT
194 GATGAGGACGACAACCCATCTTTAAGGATGATAACACAGTTCCTACGTGATGAGGACGACTAGTT
590270 A
259 A
*
590271 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAAGTCTGGTCGGTGGATGACATAGTTCCTA-CA
1 TCTAGGGGTGACACGGCTCCTACGTGATGAGG-AGTCTGGTCGGTGGATGACACAGTTCCTAGC-
* ** * *
590335 TGATGAGGATGGCAGGTTATCTTTAGGGATGATAACATGGTTCCTACGCGATGAGAATGGCTGGT
64 -GATGAGGATGACAGGTTATCTTTAGGGATGATAACATGGTTCCTACATGATGAGGACGGCTGGT
* *
590400 TATCTAGGGGTGACACGGTTCCTACGTGATGAAGAGGTCTGGTCGAG-GGATGACACTGTTCCTA
128 TATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCG-GTGGATGACA-TGTTCCTA
*
590464 CACGATGAGGACG
191 CGCGATGAGGACG
590477 TCTGGCCATC
Statistics
Matches: 395, Mismatches: 66, Indels: 12
0.84 0.14 0.03
Matches are distributed among these distances:
260 1 0.00
261 219 0.55
262 173 0.44
263 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (259 bp):
TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGTCTGGTCGGTGGATGACACAGTTCCTAGCGA
TGAGGATGACAGGTTATCTTTAGGGATGATAACATGGTTCCTACATGATGAGGACGGCTGGTTAT
CTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACATGTTCCTACGCGA
TGAGGACGACAACCCATCTTTAAGGATGATAACACAGTTCCTACGTGATGAGGACGACTAGTTA
Found at i:590442 original size:43 final size:43
Alignment explanation
Indices: 589850--590474 Score: 169
Period size: 43 Copynumber: 14.4 Consensus size: 43
589840 ATGATAACAT
* *
589850 GGTTCCTACATGATGAGGACGGTTGGTTATCTAGGGG-TGACAC
1 GGTTCCTACGTGATGAGGA-GGCTGGTTATCTAGGGGATGACAC
* *
589893 GGCTCCTACGTGATGAGGAGGTCTGGTTGA--T---GGATTACAC
1 GGTTCCTACGTGATGAGGAGG-CTGGTT-ATCTAGGGGATGACAC
* * * * ** *
589933 AGTTCCTACGCGATGAGGACGATATTCTATCTTTAGGGATGATAACAC
1 GGTTCCTACGTGATGAGGAGGCTGGT-TATC--TAGGG--GATGACAC
* * * * *
589981 AGTTCCTACGTGATGAGGACGACTAGTTATTTAGGTG-TGACAC
1 GGTTCCTACGTGATGAGGA-GGCTGGTTATCTAGGGGATGACAC
** *
590024 GACTCCTACGTGATGAGGAGTTCTGG---TC--GGTGGATGACAC
1 GGTTCCTACGTGATGAGGAG-GCTGGTTATCTAGG-GGATGACAC
* * * *
590064 GGTTCCTA-GCGATGAGGATGACAGGTTATCTTTA-GGGATGATAAC
1 GGTTCCTACGTGATGAGGA-GGCTGGTTATC--TAGGGGATGA-CAC
* * * * * * *
590109 GCGATTTCTACATAAAGAGGACGGCTAGTTATTTAGGTG-TGACAC
1 G-G-TTCCTACGTGATGAGGA-GGCTGGTTATCTAGGGGATGACAC
* * * *
590154 AGCTCCTACGTGATGAGGAGGTATGG---TC--GGTGGATGACAT
1 GGTTCCTACGTGATGAGGAGG-CTGGTTATCTAGG-GGATGACAC
* * * ***** * *
590194 GGTTCCTATGCGATGAGGATGACAACCCATCTTTAAGGATGATAACAC
1 GGTTCCTACGTGATGAGGA-GGCTGGTTATC--T-AGG-GGATGACAC
* *
590242 GGTTCCTACGTGATGAGGATGACTAGTTATCTAGGGG-TGACAC
1 GGTTCCTACGTGATGAGGA-GGCTGGTTATCTAGGGGATGACAC
* * *
590285 GGCTCCTACGTGATGAGGAAGTCTGG---TC--GGTGGATGACAT
1 GGTTCCTACGTGATGAGG-AGGCTGGTTATCTAGG-GGATGACAC
* * * * *
590325 AGTTCCTACATGATGAGGATGGCAGGTTATCTTTAGGGATGATAACAT
1 GGTTCCTACGTGATGAGGA-GGCTGGTTATC--TAGGG--GATGACAC
* *
590373 GGTTCCTACGCGATGAGAATGGCTGGTTATCTAGGGG-TGACAC
1 GGTTCCTACGTGATGAGGA-GGCTGGTTATCTAGGGGATGACAC
* *
590416 GGTTCCTACGTGATGAAGAGGTCTGG---TCGA-GGGATGACAC
1 GGTTCCTACGTGATGAGGAGG-CTGGTTATCTAGGGGATGACAC
* **
590456 TGTTCCTACACGATGAGGA
1 GGTTCCTACGTGATGAGGA
590475 CGTCTGGCCA
Statistics
Matches: 423, Mismatches: 102, Indels: 117
0.66 0.16 0.18
Matches are distributed among these distances:
38 6 0.01
39 25 0.06
40 108 0.26
41 1 0.00
42 10 0.02
43 115 0.27
44 12 0.03
45 9 0.02
46 18 0.04
47 9 0.02
48 107 0.25
49 3 0.01
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (43 bp):
GGTTCCTACGTGATGAGGAGGCTGGTTATCTAGGGGATGACAC
Found at i:590471 original size:40 final size:40
Alignment explanation
Indices: 590405--590481 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
590395 CTGGTTATCT
* ** *
590405 AGGGGTGACACGGTTCCTACGTGATGAAGAGGTCTGGTCG
1 AGGGATGACACGGTTCCTACACGATGAAGACGTCTGGTCG
* *
590445 AGGGATGACACTGTTCCTACACGATGAGGACGTCTGG
1 AGGGATGACACGGTTCCTACACGATGAAGACGTCTGG
590482 CCATCTTTAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.22
Consensus pattern (40 bp):
AGGGATGACACGGTTCCTACACGATGAAGACGTCTGGTCG
Found at i:590744 original size:133 final size:132
Alignment explanation
Indices: 590499--590784 Score: 346
Period size: 133 Copynumber: 2.2 Consensus size: 132
590489 TAGGGATAAT
* ***
590499 GTTTCAAGGGAAACAGACTCAAAGATGATGTTTAAAGGGAAACTGTCTCAAGCGAGACAAAATTT
1 GTTTCAAGGGAAACAGACTCAAAGATGATGTTTAAAGAGAAACTGTCTCAAAAAAGACAAAATTT
* ** * * * *
590564 GTTTTTAAGGGAAATGTTCTCAAAGATCGGTGTTTCATGAAATACTGTCTCAAATGAGACAAAAT
66 GTTTTCAAGGGAAACATACTCAAAGATCGATGTTTCAAGAAATACTGTCTCAAAGGAGACAAAAT
590629 TC
131 TC
* * *
590631 GTTTCAAGGGAAA-TGATCTCAAAGATATATGTTTAAAGAGAAACTGTCTCAAAAAAGACTAAAT
1 GTTTCAAGGGAAACAGA-CTCAAAGAT-GATGTTTAAAGAGAAACTGTCTCAAAAAAGACAAAAT
* *
590695 TTG-TTTCGAGGGAAACATACTCAAAGAT-GATATGTTTCAAGAGAA-ACTGTCTCAAGGGAGAC
64 TTGTTTTCAAGGGAAACATACTCAAAGATCG--ATGTTTCAAGA-AATACTGTCTCAAAGGAGAC
590757 AAAATTC
126 AAAATTC
*
590764 ATTTCAAGGGAAACAGACTCA
1 GTTTCAAGGGAAACAGACTCA
590785 GATATTGGTG
Statistics
Matches: 130, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
131 3 0.02
132 42 0.32
133 81 0.62
134 4 0.03
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.27
Consensus pattern (132 bp):
GTTTCAAGGGAAACAGACTCAAAGATGATGTTTAAAGAGAAACTGTCTCAAAAAAGACAAAATTT
GTTTTCAAGGGAAACATACTCAAAGATCGATGTTTCAAGAAATACTGTCTCAAAGGAGACAAAAT
TC
Found at i:590749 original size:31 final size:30
Alignment explanation
Indices: 590631--590749 Score: 89
Period size: 31 Copynumber: 3.7 Consensus size: 30
590621 GACAAAATTC
*
590631 GTTTCAAGGGAAA-TGATCTCAAAGATATAT
1 GTTTCAAGAGAAACTG-TCTCAAAGATATAT
* *
590661 GTTTAAAGAGAAACTGTCTCAAAAAAGACTAAATTT
1 GTTTCAAGAGAAACTGTCTC---AAAGA-T--ATAT
* * *
590697 GTTTCGAGGGAAACAT-ACTCAAAGATGATAT
1 GTTTCAAGAGAAAC-TGTCTCAAAGAT-ATAT
590728 GTTTCAAGAGAAACTGTCTCAA
1 GTTTCAAGAGAAACTGTCTCAA
590750 GGGAGACAAA
Statistics
Matches: 68, Mismatches: 12, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
30 16 0.24
31 22 0.32
32 1 0.01
33 10 0.15
34 1 0.01
36 17 0.25
37 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (30 bp):
GTTTCAAGAGAAACTGTCTCAAAGATATAT
Found at i:590777 original size:67 final size:65
Alignment explanation
Indices: 590499--590784 Score: 279
Period size: 66 Copynumber: 4.3 Consensus size: 65
590489 TAGGGATAAT
* * ** *
590499 GTTTCAAGGGAAACAGACTCAAAGATGATGTTTAAAGGGAAACTGTCTCAAGCGAGACAAAATTT
1 GTTTCAAGGGAAACATACTCAAAGATGATGTTTAAAGAGAAACTGTCTCAAAAGAGACAAAATTC
* ** * * * * *
590564 GTTTTTAAGGGAAATGTTCTCAAAGATCGGTGTTTCATGA-AATACTGTCTCAAATGAGACAAAA
1 G-TTTCAAGGGAAACATACTCAAAGAT-GATGTTTAAAGAGAA-ACTGTCTCAAAAGAGACAAAA
590628 TTC
63 TTC
* * * *
590631 GTTTCAAGGGAAATGAT-CTCAAAGATATATGTTTAAAGAGAAACTGTCTCAAAAAAGACTAAAT
1 GTTTCAAGGGAAA-CATACTCAAAGAT-GATGTTTAAAGAGAAACTGTCTCAAAAGAGACAAAAT
*
590695 TT
64 TC
* * **
590697 GTTTCGAGGGAAACATACTCAAAGATGATATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAT
1 GTTTCAAGGGAAACATACTCAAAGATG--ATGTTTAAAGAGAAACTGTCTCAAAAGAGACAAAAT
590762 TC
64 TC
* *
590764 ATTTCAAGGGAAACAGACTCA
1 GTTTCAAGGGAAACATACTCA
590785 GATATTGGTG
Statistics
Matches: 177, Mismatches: 36, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
65 3 0.02
66 91 0.51
67 83 0.47
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.27
Consensus pattern (65 bp):
GTTTCAAGGGAAACATACTCAAAGATGATGTTTAAAGAGAAACTGTCTCAAAAGAGACAAAATTC
Found at i:590894 original size:36 final size:36
Alignment explanation
Indices: 590845--590964 Score: 91
Period size: 37 Copynumber: 3.3 Consensus size: 36
590835 AACTGTATCC
* *
590845 AGTGATACGAAATTTATTTTAAGAGAAATTGTCTCA
1 AGTGAGACAAAATTTATTTTAAGAGAAATTGTCTCA
* ***
590881 AGTGAGACAAAATTTGGTTTT-AGAGAAAACCATCTCA
1 AGTGAGACAAAATTT-ATTTTAAGAG-AAATTGTCTCA
* * * *
590918 AGTGAGACAACA-TTAGTTTTTAAGAAAAATTGTATCT
1 AGTGAGACAAAATTTA--TTTTAAGAGAAATTGTCTCA
*
590955 AGCGAGACAA
1 AGTGAGACAA
590965 CACTTTGTTT
Statistics
Matches: 64, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
36 19 0.30
37 42 0.66
38 3 0.05
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (36 bp):
AGTGAGACAAAATTTATTTTAAGAGAAATTGTCTCA
Found at i:590902 original size:37 final size:37
Alignment explanation
Indices: 590861--590964 Score: 102
Period size: 37 Copynumber: 2.8 Consensus size: 37
590851 ACGAAATTTA
*
590861 TTTTAAGAGAAATTGTCTCAAGTGAGACAAAATTTGG
1 TTTTAAGAGAAATTGTCTCAAGTGAGACAAAATTAGG
*** * *
590898 TTTT-AGAGAAAACCATCTCAAGTGAGACAACATTAGT
1 TTTTAAGAG-AAATTGTCTCAAGTGAGACAAAATTAGG
* * * *
590935 TTTTAAGAAAAATTGTATCTAGCGAGACAA
1 TTTTAAGAGAAATTGTCTCAAGTGAGACAA
590965 CACTTTGTTT
Statistics
Matches: 52, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
36 4 0.08
37 45 0.87
38 3 0.06
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (37 bp):
TTTTAAGAGAAATTGTCTCAAGTGAGACAAAATTAGG
Found at i:591334 original size:16 final size:16
Alignment explanation
Indices: 591302--591335 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
591292 TTCATGTGTC
*
591302 ATGTATGTATGTATTG
1 ATGTATGTATATATTG
*
591318 ATGTATGTATATGTTG
1 ATGTATGTATATATTG
591334 AT
1 AT
591336 CTGTGAGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (16 bp):
ATGTATGTATATATTG
Found at i:592374 original size:2 final size:2
Alignment explanation
Indices: 592367--592408 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
592357 GTATACATAC
592367 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
592409 TCCGGGTATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:598517 original size:3 final size:3
Alignment explanation
Indices: 598509--598548 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
598499 ACAAAACATG
* *
598509 TAA TAA TAA T-T TAA TAA TAA TAA TAA TAA TAA TAT TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
598549 TTTTTTTGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 1 0.03
3 31 0.97
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:600336 original size:24 final size:24
Alignment explanation
Indices: 600288--600339 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
600278 TAGCTCGTAT
* ***
600288 AAATTGCACCGAAGTGCCGTGTAG
1 AAATTACACCGAAGTGCCACATAG
600312 AAATTACACCGAAGTGCCACATAG
1 AAATTACACCGAAGTGCCACATAG
600336 AAAT
1 AAAT
600340 GTCCCGAAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (24 bp):
AAATTACACCGAAGTGCCACATAG
Found at i:600385 original size:46 final size:46
Alignment explanation
Indices: 600333--600429 Score: 151
Period size: 46 Copynumber: 2.1 Consensus size: 46
600323 AAGTGCCACA
*
600333 TAGAAATGTCCC-GAAGGACCACATAGTATTGTCCCAAAGGACCGCG
1 TAGAAATGTCCCAG-AGGACCACATAGAATTGTCCCAAAGGACCGCG
* *
600379 TAGAAATGTCCCAGAGGACCACGTAGAATTGTCCCGAAGGACCGCG
1 TAGAAATGTCCCAGAGGACCACATAGAATTGTCCCAAAGGACCGCG
600425 TAGAA
1 TAGAA
600430 CCCTTGACTC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
46 46 0.98
47 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.26, T:0.16
Consensus pattern (46 bp):
TAGAAATGTCCCAGAGGACCACATAGAATTGTCCCAAAGGACCGCG
Found at i:600426 original size:23 final size:23
Alignment explanation
Indices: 600320--600429 Score: 116
Period size: 23 Copynumber: 4.8 Consensus size: 23
600310 AGAAATTACA
*
600320 CCGAAGTG-CCACATAGAAATGTC
1 CCGAAG-GACCACGTAGAAATGTC
* * *
600343 CCGAAGGACCACATAGTATTGTC
1 CCGAAGGACCACGTAGAAATGTC
* *
600366 CCAAAGGACCGCGTAGAAATGTC
1 CCGAAGGACCACGTAGAAATGTC
*
600389 CC-AGAGGACCACGTAGAATTGTC
1 CCGA-AGGACCACGTAGAAATGTC
*
600412 CCGAAGGACCGCGTAGAA
1 CCGAAGGACCACGTAGAA
600430 CCCTTGACTC
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
22 2 0.03
23 71 0.96
24 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.25, T:0.15
Consensus pattern (23 bp):
CCGAAGGACCACGTAGAAATGTC
Found at i:604639 original size:37 final size:37
Alignment explanation
Indices: 604598--604674 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 37
604588 TGAAATTTTT
* *
604598 TTCGAGACGAGTTTATGAAATTACAACTCAAAGTCAA
1 TTCGAGACGAGTTTATAAAATTACAAATCAAAGTCAA
* * *
604635 TTCGAGTCTAGTTTATAAAATTACAAATCGAAGTCAA
1 TTCGAGACGAGTTTATAAAATTACAAATCAAAGTCAA
604672 TTC
1 TTC
604675 AGGTCGAATC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (37 bp):
TTCGAGACGAGTTTATAAAATTACAAATCAAAGTCAA
Found at i:608161 original size:21 final size:21
Alignment explanation
Indices: 608137--608199 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
608127 GTCGAGGGAT
608137 TATATGAGGTCCTTTGGGACA
1 TATATGAGGTCCTTTGGGACA
* * *
608158 TATACGAGGTCCTTCGGGATA
1 TATATGAGGTCCTTTGGGACA
*
608179 TACATGAGGTCCTTTGGGACA
1 TATATGAGGTCCTTTGGGACA
608200 AATTTCACAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (21 bp):
TATATGAGGTCCTTTGGGACA
Found at i:615042 original size:21 final size:21
Alignment explanation
Indices: 615013--615075 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
615003 GTCGAATGAT
615013 TATATGAGGTCCTTCGGGACA
1 TATATGAGGTCCTTCGGGACA
*
615034 TATACGAGGTCCTTCGGGACA
1 TATATGAGGTCCTTCGGGACA
* *
615055 TACATGAGGTCATTCGGGACA
1 TATATGAGGTCCTTCGGGACA
615076 AATTTCACAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (21 bp):
TATATGAGGTCCTTCGGGACA
Found at i:616246 original size:27 final size:25
Alignment explanation
Indices: 616213--616270 Score: 100
Period size: 24 Copynumber: 2.4 Consensus size: 25
616203 TTTGTAGTAT
*
616213 AAAAATAAGATTTATTATAATGAC-
1 AAAAATAATATTTATTATAATGACG
616237 AAAAATAATATTTATTATAATGACG
1 AAAAATAATATTTATTATAATGACG
616262 AAAAATAAT
1 AAAAATAAT
616271 GACACCGTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 23 0.72
25 9 0.28
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (25 bp):
AAAAATAATATTTATTATAATGACG
Found at i:616316 original size:7 final size:7
Alignment explanation
Indices: 616304--616329 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
616294 AACCCGGGTA
616304 GGTTGGT
1 GGTTGGT
616311 GGTTGGT
1 GGTTGGT
616318 GGTTGGT
1 GGTTGGT
616325 GGTTG
1 GGTTG
616330 AACGAGAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.58, T:0.42
Consensus pattern (7 bp):
GGTTGGT
Found at i:616881 original size:25 final size:25
Alignment explanation
Indices: 616853--616911 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
616843 ATTGTAGTAA
616853 AAAAATAATATGT-ATTATAATGACG
1 AAAAATAATAT-TCATTATAATGACG
616878 AAAAATAATATTCATTATAATGACG
1 AAAAATAATATTCATTATAATGACG
616903 AAAAATAAT
1 AAAAATAAT
616912 CGCACCATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 1 0.03
25 32 0.97
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.31
Consensus pattern (25 bp):
AAAAATAATATTCATTATAATGACG
Found at i:622921 original size:12 final size:12
Alignment explanation
Indices: 622904--622952 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
622894 TTGATTGGGC
*
622904 GCCACATCAACT
1 GCCACATCAGCT
*
622916 GCCACATCATC-
1 GCCACATCAGCT
**
622927 GCCATGTCAGCT
1 GCCACATCAGCT
622939 GCCACATCAGCT
1 GCCACATCAGCT
622951 GC
1 GC
622953 TTATTAGATG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
11 8 0.27
12 22 0.73
ACGTcount: A:0.24, C:0.41, G:0.16, T:0.18
Consensus pattern (12 bp):
GCCACATCAGCT
Found at i:625364 original size:24 final size:24
Alignment explanation
Indices: 625323--625601 Score: 139
Period size: 24 Copynumber: 11.9 Consensus size: 24
625313 CAACCTTCGA
* * *
625323 TACCAGTTGAATCTCCACCTCCGG
1 TACCAGTTCACTCCCCACCTCCGG
*
625347 TACCAGTTCACTCCCCACCTCCAG
1 TACCAGTTCACTCCCCACCTCCGG
* * *
625371 TACAAGTCCACTCCCCACCTCCTG
1 TACCAGTTCACTCCCCACCTCCGG
* * *
625395 CACCAGTCCACTCCCCACCTCCTG
1 TACCAGTTCACTCCCCACCTCCGG
* * * * *
625419 TTCCAGTCCATTCTCCACCACC--
1 TACCAGTTCACTCCCCACCTCCGG
625441 -ACCAGTCTTCA--CCCCACCTCCGG
1 TACCAG--TTCACTCCCCACCTCCGG
* * * *
625464 TACCTGTTCAATCTCCACCTCCGA
1 TACCAGTTCACTCCCCACCTCCGG
* *
625488 TACCAG-TCAATTCCCCACCTCTGG
1 TACCAGTTC-ACTCCCCACCTCCGG
* * * * *
625512 TTCCAATCCACTTCCCACCTCCAG
1 TACCAGTTCACTCCCCACCTCCGG
* * * *
625536 TTCCAG-TCAATTCTCCACCACC-G
1 TACCAGTTC-ACTCCCCACCTCCGG
*
625559 T--CAG-TCTTCTCCCCACCTCCGG
1 TACCAGTTC-ACTCCCCACCTCCGG
* *
625581 TACCAGTTCAATCTCCACCTC
1 TACCAGTTCACTCCCCACCTC
625602 AACCACTCCA
Statistics
Matches: 194, Mismatches: 47, Indels: 28
0.72 0.17 0.10
Matches are distributed among these distances:
21 26 0.13
22 6 0.03
23 8 0.04
24 151 0.78
25 3 0.02
ACGTcount: A:0.19, C:0.47, G:0.09, T:0.24
Consensus pattern (24 bp):
TACCAGTTCACTCCCCACCTCCGG
Found at i:625462 original size:117 final size:118
Alignment explanation
Indices: 625337--625623 Score: 379
Period size: 117 Copynumber: 2.5 Consensus size: 118
625327 AGTTGAATCT
* * * *
625337 CCACCTCCGGTACCAGTTCACTCCCCACCTCCAGTACAAGTCCACTCCCCACCTCCT-GCACCAG
1 CCACCTCCGGTACCAGTTCAATCTCCACCTCCAGTACCAGTCCACTCCCCACCTCCTGGCACCAA
* *
625401 TCCACTCCCCACCTCCTGTTCCAGTCCATTCTCCACCACCACCAGTCTTCACC
66 TCCACTCCCCACCTCCAGTTCCAGTCAATTCTCCACCACCACCAGTCTTCACC
* * * **
625454 CCACCTCCGGTACCTGTTCAATCTCCACCTCC-GATACCAGTCAATTCCCCACCT-CTGGTTCCA
1 CCACCTCCGGTACCAGTTCAATCTCCACCTCCAG-TACCAGTCCACTCCCCACCTCCTGGCACCA
* ** *
625517 ATCCACTTCCCACCTCCAGTTCCAGTCAATTCTCCACCACCGTCAGTCTTCTCC
65 ATCCACTCCCCACCTCCAGTTCCAGTCAATTCTCCACCACCACCAGTCTTCACC
*
625571 CCACCTCCGGTACCAGTTCAATCTCCACCT-CA--ACCACTCCACTCCCCACCTCC
1 CCACCTCCGGTACCAGTTCAATCTCCACCTCCAGTACCAGTCCACTCCCCACCTCC
625624 ACCAGTCTTC
Statistics
Matches: 147, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
114 16 0.11
115 1 0.01
116 4 0.03
117 126 0.86
ACGTcount: A:0.19, C:0.50, G:0.08, T:0.23
Consensus pattern (118 bp):
CCACCTCCGGTACCAGTTCAATCTCCACCTCCAGTACCAGTCCACTCCCCACCTCCTGGCACCAA
TCCACTCCCCACCTCCAGTTCCAGTCAATTCTCCACCACCACCAGTCTTCACC
Found at i:625640 original size:21 final size:21
Alignment explanation
Indices: 625592--625644 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
625582 ACCAGTTCAA
*
625592 TCTCCACCTCAACCACTCCAC
1 TCTCCACCTCCACCACTCCAC
* * **
625613 TCCCCACCTCCACCAGTCTTC
1 TCTCCACCTCCACCACTCCAC
625634 TCTCCACCTCC
1 TCTCCACCTCC
625645 GGTACTAATT
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:0.17, C:0.58, G:0.02, T:0.23
Consensus pattern (21 bp):
TCTCCACCTCCACCACTCCAC
Found at i:625686 original size:66 final size:66
Alignment explanation
Indices: 625550--625692 Score: 171
Period size: 66 Copynumber: 2.2 Consensus size: 66
625540 AGTCAATTCT
** *
625550 CCACCACCGTCAGTCTTCTCCCCACCTCCGGTACCAGTTCAATCTCCACCTCAACCACTCCACTC
1 CCACCACCACCAGTCTTCTCCCCACCTCCGGTACCAATTCAATCTCCACCTCAACCACTCCACTC
625615 C
66 C
* * * * * ** *
625616 CCACCTCCACCAGTCTTCTCTCCACCTCCGGTACTAATTCATTCTTCACCTCCGCCAGTCCA-TC
1 CCACCACCACCAGTCTTCTCCCCACCTCCGGTACCAATTCAATCTCCACCTCAACCACTCCACTC
625680 C
66 C
625681 TCCACCACCACC
1 -CCACCACCACC
625693 TGTTCGTTCA
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 3 0.05
66 61 0.95
ACGTcount: A:0.19, C:0.51, G:0.07, T:0.23
Consensus pattern (66 bp):
CCACCACCACCAGTCTTCTCCCCACCTCCGGTACCAATTCAATCTCCACCTCAACCACTCCACTC
C
Found at i:625802 original size:21 final size:21
Alignment explanation
Indices: 625766--625824 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
625756 ACCACTGATA
* *
625766 TACTCTCCGCCGCCACCTGTC
1 TACTCTCCACCTCCACCTGTC
625787 TACTCTCCACCTCCACCTGTC
1 TACTCTCCACCTCCACCTGTC
625808 TACTCTCCACCTCCACC
1 TACTCTCCACCTCCACC
625825 GGTTGTCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.14, C:0.54, G:0.07, T:0.25
Consensus pattern (21 bp):
TACTCTCCACCTCCACCTGTC
Found at i:634102 original size:18 final size:18
Alignment explanation
Indices: 634059--634108 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
634049 TGAATATTTT
*
634059 TCCCGAATGACCA-TATG
1 TCCCGAATGACCACTATA
*
634076 TCTCGAATGACCACTATA
1 TCCCGAATGACCACTATA
634094 TCCCGAATGACCACT
1 TCCCGAATGACCACT
634109 GATAATCCCT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 12 0.41
18 17 0.59
ACGTcount: A:0.30, C:0.32, G:0.14, T:0.24
Consensus pattern (18 bp):
TCCCGAATGACCACTATA
Found at i:638786 original size:21 final size:20
Alignment explanation
Indices: 638762--638861 Score: 78
Period size: 21 Copynumber: 4.9 Consensus size: 20
638752 TTTTAGGGGA
638762 AGGGATCGATCATTTTCATCG
1 AGGGATCGATCATTTTCAT-G
* * *
638783 AGGGGTCGATCTTTTTGATG
1 AGGGATCGATCATTTTCATG
* *
638803 AAGGGATCGATCCTTTTCCTTG
1 -AGGGATCGATCATTTT-CATG
* **
638825 AGGGATCGAAC-TTTTTGTG
1 AGGGATCGATCATTTTCATG
638844 AAGGGATCGAT-ATTTTCA
1 -AGGGATCGATCATTTTCA
638862 AGTTAATTTG
Statistics
Matches: 62, Mismatches: 13, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
19 2 0.03
20 18 0.29
21 40 0.65
22 2 0.03
ACGTcount: A:0.22, C:0.15, G:0.27, T:0.36
Consensus pattern (20 bp):
AGGGATCGATCATTTTCATG
Found at i:638793 original size:42 final size:41
Alignment explanation
Indices: 638741--638861 Score: 145
Period size: 42 Copynumber: 2.9 Consensus size: 41
638731 GTTTCAAGAA
*
638741 AGGGATCGATCTTTTAGGGGAAGGGATCGATCATTTTCATCG
1 AGGGATCGATCTTTT-GGTGAAGGGATCGATCATTTTCATCG
* * * * *
638783 AGGGGTCGATCTTTTTGATGAAGGGATCGATCCTTTTCCTTG
1 AGGGATCGATC-TTTTGGTGAAGGGATCGATCATTTTCATCG
* *
638825 AGGGATCGAACTTTTTGTGAAGGGATCGAT-ATTTTCA
1 AGGGATCGATCTTTTGGTGAAGGGATCGATCATTTTCA
638862 AGTTAATTTG
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
40 5 0.08
41 17 0.26
42 40 0.61
43 4 0.06
ACGTcount: A:0.22, C:0.14, G:0.29, T:0.35
Consensus pattern (41 bp):
AGGGATCGATCTTTTGGTGAAGGGATCGATCATTTTCATCG
Found at i:640760 original size:4 final size:4
Alignment explanation
Indices: 640751--640775 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
640741 AAATATGTAA
640751 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
640776 GAGAGATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:647866 original size:85 final size:85
Alignment explanation
Indices: 647723--647891 Score: 338
Period size: 85 Copynumber: 2.0 Consensus size: 85
647713 TGTCCTCAAC
647723 GACTAAGGCCCCGTTTGGTTCATGGAATATTTCATTCCTACGGGGAATGTTTTTTTTCGGGTTGA
1 GACTAAGGCCCCGTTTGGTTCATGGAATATTTCATTCCTACGGGGAATGTTTTTTTTCGGGTTGA
647788 AGATACCCACGTTTGGTTTT
66 AGATACCCACGTTTGGTTTT
647808 GACTAAGGCCCCGTTTGGTTCATGGAATATTTCATTCCTACGGGGAATGTTTTTTTTCGGGTTGA
1 GACTAAGGCCCCGTTTGGTTCATGGAATATTTCATTCCTACGGGGAATGTTTTTTTTCGGGTTGA
647873 AGATACCCACGTTTGGTTT
66 AGATACCCACGTTTGGTTT
647892 CTCCACCTTC
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (85 bp):
GACTAAGGCCCCGTTTGGTTCATGGAATATTTCATTCCTACGGGGAATGTTTTTTTTCGGGTTGA
AGATACCCACGTTTGGTTTT
Found at i:651110 original size:15 final size:15
Alignment explanation
Indices: 651090--651120 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
651080 CAACAAATAG
651090 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
651105 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
651120 A
1 A
651121 TTTAGAATTT
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:651316 original size:20 final size:20
Alignment explanation
Indices: 651280--651317 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
651270 ATCCTATTCC
**
651280 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
651300 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
651318 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:659794 original size:17 final size:17
Alignment explanation
Indices: 659772--659810 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
659762 TGAATCAAAT
659772 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
659789 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
659806 -AATTA
1 TAATTA
659811 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:662118 original size:23 final size:23
Alignment explanation
Indices: 662086--662146 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
662076 CTCATATAAA
662086 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
662109 TGCACTGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
662132 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
662147 TATAAGATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:667567 original size:23 final size:23
Alignment explanation
Indices: 667510--667570 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
667500 CTCATATAAC
667510 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* ** *
667533 TACAATGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
667556 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
667571 TATAAGATGT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:668041 original size:15 final size:15
Alignment explanation
Indices: 668017--668051 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
668007 ACTCATATAA
* *
668017 CTTATTATCACATAT
1 CTTATAATCACATAC
668032 CTTATAATCACATAC
1 CTTATAATCACATAC
668047 CTTAT
1 CTTAT
668052 TTCATTTCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.34, C:0.23, G:0.00, T:0.43
Consensus pattern (15 bp):
CTTATAATCACATAC
Found at i:670971 original size:35 final size:35
Alignment explanation
Indices: 670901--671308 Score: 385
Period size: 35 Copynumber: 11.4 Consensus size: 35
670891 TTTTTTTAAA
* * * *
670901 TATATGTTTTCAAAATCGTTTTAAAAAAATCATATTT
1 TATATGTTTTCAAAACCATTTT-AAAAACT-ATATAT
* * *
670938 TATACGTTTTCAAAACCATTTCAAAAAATATAT-T
1 TATATGTTTTCAAAACCATTTTAAAAACTATATAT
* *
670972 ATATATGTTTTCAAAACCATTTTTAAGACTATATAT
1 -TATATGTTTTCAAAACCATTTTAAAAACTATATAT
* **
671008 TATACGTTTTCAAAATTATTTTAAAAA-TATAT-T
1 TATATGTTTTCAAAACCATTTTAAAAACTATATAT
*
671041 ATATATGTTTTCAAAACTAATTTT--AAACTATATAT
1 -TATATGTTTTCAAAAC-CATTTTAAAAACTATATAT
** *
671076 TATATGTTTTCAAAATTATTTTAAAAACTATATAC
1 TATATGTTTTCAAAACCATTTTAAAAACTATATAT
* *
671111 TATATGTTTTCAAAACCGTTTTCAAAACTATATAT
1 TATATGTTTTCAAAACCATTTTAAAAACTATATAT
* * *
671146 TATACGTTTTCAAAACTATTTTTTTAAAAAAACTATACAT
1 TATATGTTTTCAAAACCA---TTTT--AAAAACTATATAT
** *
671186 TATATGTTTTCAAAATTATTTTAAAAACTATATAC
1 TATATGTTTTCAAAACCATTTTAAAAACTATATAT
*
671221 TATATGTTTTCAAAACCATTTTAAAAATTATATAT
1 TATATGTTTTCAAAACCATTTTAAAAACTATATAT
** ** *
671256 TATACATTTTCAAAAATAAGTTTCCAAAAACTATATAT
1 TATATGTTTTC-AAAACCA-TTT-TAAAAACTATATAT
*
671294 TATATATTTTCAAAA
1 TATATGTTTTCAAAA
671309 ATTATATTTG
Statistics
Matches: 310, Mismatches: 45, Indels: 32
0.80 0.12 0.08
Matches are distributed among these distances:
33 9 0.03
34 40 0.13
35 166 0.54
36 13 0.04
37 29 0.09
38 26 0.08
40 27 0.09
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.44
Consensus pattern (35 bp):
TATATGTTTTCAAAACCATTTTAAAAACTATATAT
Found at i:671102 original size:138 final size:143
Alignment explanation
Indices: 670901--671322 Score: 441
Period size: 138 Copynumber: 2.9 Consensus size: 143
670891 TTTTTTTAAA
** * * * *
670901 TATATGTTTTCAAAATCGTTTTAAAAAAATCATATTTTATACGTTTTCAAAACCATTTCAAAAAA
1 TATATGTTTTCAAAATAATTTT--AAAACT-ATATATTATATGTTTTCAAAACCATTTTAAAAAA
* *
670966 TATATTATATATGTTTTCAAAACCATTTTTAAGACTATATATTATACGTTTTC-AAA-ATTATTT
63 TATATTATATATGTTTTCAAAACCATTTTCAAAACTATATATTATACGTTTTCAAAACATTATTT
* *
671029 TAAAAATA-TAT-TA-
128 TAAAAAAACTATACAT
** *
671042 TATATGTTTTCAAAACTAATTTT-AAACTATATATTATATGTTTTCAAAATTATTTTAAAAACTA
1 TATATGTTTTCAAAA-TAATTTTAAAACTATATATTATATGTTTTCAAAACCATTTTAAAAAATA
* *
671106 TA-TACTATATGTTTTCAAAACCGTTTTCAAAACTATATATTATACGTTTTCAAAACTATTTTTT
65 TATTA-TATATGTTTTCAAAACCATTTTCAAAACTATATATTATACGTTTTCAAAAC-ATTATTT
671170 TAAAAAAACTATACAT
128 TAAAAAAACTATACAT
* *
671186 TATATGTTTTCAAAATTATTTTAAAAACTATATACTATATGTTTTCAAAACCATTTTAAAAATTA
1 TATATGTTTTCAAAATAATTTT-AAAACTATATATTATATGTTTTCAAAACCATTTTAAAAA--A
* ** * **
671251 TATATTATACA--TTTTCAAAAATAAGTTTCCAAAAACTATATATTATATATTTTCAAAA-ATTA
63 TATATTATATATGTTTTC-AAAACCA-TTTTC-AAAACTATATATTATACGTTTTCAAAACATTA
*
671313 TATTTGAAAA
125 T-TTTAAAAA
671323 GCTCCTGGTC
Statistics
Matches: 235, Mismatches: 29, Indels: 28
0.80 0.10 0.10
Matches are distributed among these distances:
137 2 0.01
138 75 0.32
139 7 0.03
141 28 0.12
142 8 0.03
143 7 0.03
144 15 0.06
145 40 0.17
146 8 0.03
147 18 0.08
148 27 0.11
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.44
Consensus pattern (143 bp):
TATATGTTTTCAAAATAATTTTAAAACTATATATTATATGTTTTCAAAACCATTTTAAAAAATAT
ATTATATATGTTTTCAAAACCATTTTCAAAACTATATATTATACGTTTTCAAAACATTATTTTAA
AAAAACTATACAT
Found at i:671196 original size:110 final size:108
Alignment explanation
Indices: 670901--671322 Score: 468
Period size: 110 Copynumber: 3.9 Consensus size: 108
670891 TTTTTTTAAA
* * * *
670901 TATATGTTTTCAAAATCGTTTTAAAAAAATCATATTTTATACGTTTTCAAAAC-CA-TTTCAAAA
1 TATATGTTTTCAAAACCATTTT-AAAAAAT-ATATATTATACGTTTTCAAAACTAATTTTCAAAA
** * * *
670964 AA-TATAT-TATATATGTTTTCAAAACCATTTTTAAGACTATATAT
64 AACTATATAT-TATATGTTTTCAAAATTATTTTAAAAACTATATAC
* ** *
671008 TATACGTTTTCAAAATTATTTT-AAAAATATAT-TATATATGTTTTCAAAACTAATTTT----AA
1 TATATGTTTTCAAAACCATTTTAAAAAATATATAT-TATACGTTTTCAAAACTAATTTTCAAAAA
671067 ACTATATATTATATGTTTTCAAAATTATTTTAAAAACTATATAC
65 ACTATATATTATATGTTTTCAAAATTATTTTAAAAACTATATAC
* * * * *
671111 TATATGTTTTCAAAACCGTTTTCAAAACTATATATTATACGTTTTCAAAACTATTTTTTTAAAAA
1 TATATGTTTTCAAAACCATTTTAAAAAATATATATTATACGTTTTCAAAACTA--ATTTTCAAAA
*
671176 AACTATACATTATATGTTTTCAAAATTATTTTAAAAACTATATAC
64 AACTATATATTATATGTTTTCAAAATTATTTTAAAAACTATATAC
* * * * *
671221 TATATGTTTTCAAAACCATTTTAAAAATTATATATTATACATTTTCAAAAATAAGTTTCCAAAAA
1 TATATGTTTTCAAAACCATTTTAAAAAATATATATTATACGTTTTCAAAACTAATTTTCAAAAAA
* *
671286 CTATATATTATATATTTTCAAAAATTATATTTGAAAA
66 CTATATATTATATGTTTTC-AAAATTAT-TTTAAAAA
671323 GCTCCTGGTC
Statistics
Matches: 270, Mismatches: 30, Indels: 27
0.83 0.09 0.08
Matches are distributed among these distances:
102 3 0.01
103 54 0.20
104 46 0.17
105 8 0.03
106 7 0.03
107 19 0.07
108 25 0.09
109 8 0.03
110 100 0.37
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.44
Consensus pattern (108 bp):
TATATGTTTTCAAAACCATTTTAAAAAATATATATTATACGTTTTCAAAACTAATTTTCAAAAAA
CTATATATTATATGTTTTCAAAATTATTTTAAAAACTATATAC
Found at i:672744 original size:20 final size:20
Alignment explanation
Indices: 672719--672764 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
672709 CCTGATTGAA
672719 GGACCTTTGCAGTGGTCCTT
1 GGACCTTTGCAGTGGTCCTT
672739 GGACCTTTGCAGTGGTCCTT
1 GGACCTTTGCAGTGGTCCTT
672759 GGACCT
1 GGACCT
672765 CTAAAGTGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.11, C:0.26, G:0.30, T:0.33
Consensus pattern (20 bp):
GGACCTTTGCAGTGGTCCTT
Found at i:672772 original size:20 final size:20
Alignment explanation
Indices: 672729--672773 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
672719 GGACCTTTGC
* **
672729 AGTGGTCCTTGGACCTTTGC
1 AGTGGTCCTTGGACCTCTAA
672749 AGTGGTCCTTGGACCTCTAA
1 AGTGGTCCTTGGACCTCTAA
672769 AGTGG
1 AGTGG
672774 CCTCCTCATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.22, G:0.31, T:0.31
Consensus pattern (20 bp):
AGTGGTCCTTGGACCTCTAA
Found at i:675243 original size:15 final size:15
Alignment explanation
Indices: 675219--675258 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
675209 CGGTGAGTAT
675219 ATGGATGATGAGAAC
1 ATGGATGATGAGAAC
*
675234 GATGGA-GATGAGCAC
1 -ATGGATGATGAGAAC
675249 ATGGATGATG
1 ATGGATGATG
675259 CTCATGACGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 5 0.23
15 12 0.55
16 5 0.23
ACGTcount: A:0.35, C:0.07, G:0.38, T:0.20
Consensus pattern (15 bp):
ATGGATGATGAGAAC
Found at i:676028 original size:30 final size:30
Alignment explanation
Indices: 675994--676053 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
675984 TTGTAAAATT
* * *
675994 GATTTTGGACTTAATTGAATTTATTAAAAA
1 GATTTTAGACTTAATTAAATTTATCAAAAA
676024 GATTTTAGACTTAATTAAATTTATCAAAAA
1 GATTTTAGACTTAATTAAATTTATCAAAAA
676054 CATACTCGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.42
Consensus pattern (30 bp):
GATTTTAGACTTAATTAAATTTATCAAAAA
Found at i:677200 original size:155 final size:155
Alignment explanation
Indices: 676928--677243 Score: 555
Period size: 155 Copynumber: 2.0 Consensus size: 155
676918 GTTCATCATT
676928 TCTTTTTAAGAATTAATTCTTCCGTTTTGCTACTTCATTTAATTTATGAGAGTATGATGGTGTCC
1 TCTTTTTAAGAATTAATTCTTCCGTTTTGCTACTTCATTTAATTTATGAGAGTATGATGGTGTCC
676993 CTTTATGAATAATATCACACTATTGACCAATTATAGTTCATTATTCACCACCATAATCA-TTCTT
66 CTTTATGAATAATATCACACTATTGACCAATTATAGTTCATTATT--CCACCATAATCACTTCTT
677057 ATTATCTTAATATTTTT-TTAAGTTGA
129 ATTATCTTAATATTTTTATTAAGTTGA
677083 TCTTTTTAAGAATTAATTCTTCCGTTTTGCTACTTCATTTAATTTATGAGAGTATGATGGTGTCC
1 TCTTTTTAAGAATTAATTCTTCCGTTTTGCTACTTCATTTAATTTATGAGAGTATGATGGTGTCC
677148 CTTTATGAATAATATCACACTATTGACCAATTAATAGTTCAATTTATTCACCACCATAATCACTT
66 CTTTATGAATAATATCACACTATTGACCAATT-ATAGTTC-A-TTATT--CCACCATAATCACTT
677213 CTTATTATCTTAATATTTTTATTAAGTTGA
126 CTTATTATCTTAATATTTTTATTAAGTTGA
677243 T
1 T
677244 TTTCAACTTT
Statistics
Matches: 156, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
155 97 0.62
156 7 0.04
157 1 0.01
158 19 0.12
159 22 0.14
160 10 0.06
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.46
Consensus pattern (155 bp):
TCTTTTTAAGAATTAATTCTTCCGTTTTGCTACTTCATTTAATTTATGAGAGTATGATGGTGTCC
CTTTATGAATAATATCACACTATTGACCAATTATAGTTCATTATTCCACCATAATCACTTCTTAT
TATCTTAATATTTTTATTAAGTTGA
Found at i:679003 original size:5 final size:5
Alignment explanation
Indices: 678993--679021 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
678983 ACTCGTAAGT
678993 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
679022 TGCGGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:685416 original size:4 final size:4
Alignment explanation
Indices: 685407--685452 Score: 92
Period size: 4 Copynumber: 11.5 Consensus size: 4
685397 TACATGGAAT
685407 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
685453 GCACATATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:686434 original size:9 final size:10
Alignment explanation
Indices: 686399--686431 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
686389 GGACCGGCTG
686399 AAAACCGGAA
1 AAAACCGGAA
*
686409 AAAATCGGAA
1 AAAACCGGAA
686419 AAAACCGGAA
1 AAAACCGGAA
686429 AAA
1 AAA
686432 CCGCCAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.64, C:0.15, G:0.18, T:0.03
Consensus pattern (10 bp):
AAAACCGGAA
Found at i:688213 original size:21 final size:21
Alignment explanation
Indices: 688166--688214 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
688156 AGTATCTAAC
* **
688166 AATAACAAAATTCGTAAAAAA
1 AATAATAAAATTAATAAAAAA
*
688187 AATAATAAAATTAATAAAAAT
1 AATAATAAAATTAATAAAAAA
688208 AATAATA
1 AATAATA
688215 TTTTCGATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.24
Consensus pattern (21 bp):
AATAATAAAATTAATAAAAAA
Found at i:693188 original size:11 final size:11
Alignment explanation
Indices: 693174--693198 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
693164 CATTTACTCG
693174 TTTTTTATTTT
1 TTTTTTATTTT
693185 TTTTTTATTTT
1 TTTTTTATTTT
693196 TTT
1 TTT
693199 ACATTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTATTTT
Found at i:694465 original size:21 final size:21
Alignment explanation
Indices: 694440--694483 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
694430 TTGCGGTCGC
694440 CGCGGACGCTATTACGGCCGT
1 CGCGGACGCTATTACGGCCGT
*
694461 CGCGGACGCTATTGCGGCCGT
1 CGCGGACGCTATTACGGCCGT
694482 CG
1 CG
694484 AGGATAACTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.11, C:0.34, G:0.36, T:0.18
Consensus pattern (21 bp):
CGCGGACGCTATTACGGCCGT
Found at i:695167 original size:23 final size:23
Alignment explanation
Indices: 695138--695187 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
695128 GTTTGGTTTA
695138 TTTAGATTTTGTAAACATGTTCG
1 TTTAGATTTTGTAAACATGTTCG
695161 TTTAGATTTTGTAAACATGTTCG
1 TTTAGATTTTGTAAACATGTTCG
695184 TTTA
1 TTTA
695188 AATGTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.26, C:0.08, G:0.16, T:0.50
Consensus pattern (23 bp):
TTTAGATTTTGTAAACATGTTCG
Found at i:695348 original size:12 final size:12
Alignment explanation
Indices: 695331--695363 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
695321 GAGAACCAAG
695331 TAAACAAGCTTA
1 TAAACAAGCTTA
*
695343 TAAACAAGTTTA
1 TAAACAAGCTTA
695355 TAAACAAGC
1 TAAACAAGC
695364 CAATAAATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.52, C:0.15, G:0.09, T:0.24
Consensus pattern (12 bp):
TAAACAAGCTTA
Found at i:695376 original size:24 final size:23
Alignment explanation
Indices: 695331--695385 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
695321 GAGAACCAAG
**
695331 TAAACAAGCTTATAAACAAGTTT
1 TAAACAAGCCAATAAACAAGTTT
**
695354 ATAAACAAGCCAATAAATGAGTTT
1 -TAAACAAGCCAATAAACAAGTTT
695378 TCAAACAA
1 T-AAACAA
695386 ATTTGTTCGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.51, C:0.15, G:0.09, T:0.25
Consensus pattern (23 bp):
TAAACAAGCCAATAAACAAGTTT
Found at i:696251 original size:4 final size:4
Alignment explanation
Indices: 696229--696266 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
696219 TCTTCCTCCT
* *
696229 TACA TACA TGCA TAGA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TA
696267 ATTTCATAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.47, C:0.21, G:0.05, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:696294 original size:13 final size:13
Alignment explanation
Indices: 696276--696301 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
696266 AATTTCATAG
696276 TTCTGAACATTTC
1 TTCTGAACATTTC
696289 TTCTGAACATTTC
1 TTCTGAACATTTC
696302 CGGTGAAACA
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:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (13 bp):
TTCTGAACATTTC
Found at i:701516 original size:30 final size:31
Alignment explanation
Indices: 701459--701540 Score: 96
Period size: 31 Copynumber: 2.7 Consensus size: 31
701449 AATAAAAAAA
* **
701459 TTAAAGGACCAAAATAG-TATTAATAGAAAC
1 TTAAAGGACCAAAATAGAAAAAAATAGAAAC
* *
701489 TT-GAGGACCAAAATAGAAAAAAATAGAAAT
1 TTAAAGGACCAAAATAGAAAAAAATAGAAAC
*
701519 TTAAAGGACTAAAATAGAAAAA
1 TTAAAGGACCAAAATAGAAAAA
701541 TATAAAGTTG
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 13 0.30
30 13 0.30
31 17 0.40
ACGTcount: A:0.59, C:0.07, G:0.15, T:0.20
Consensus pattern (31 bp):
TTAAAGGACCAAAATAGAAAAAAATAGAAAC
Found at i:701554 original size:29 final size:30
Alignment explanation
Indices: 701459--701560 Score: 91
Period size: 29 Copynumber: 3.4 Consensus size: 30
701449 AATAAAAAAA
* * ** *
701459 TTAAAGGACCAAAATAGTATTAATAGAAAC
1 TTAAAGGACTAAAATAGAAAAAATAGAAAG
* * *
701489 TT-GAGGACCAAAATAGAAAAAAATAGAAAT
1 TTAAAGGACTAAAATAG-AAAAAATAGAAAG
*
701519 TTAAAGGACTAAAATAG-AAAAATATAAAG
1 TTAAAGGACTAAAATAGAAAAAATAGAAAG
*
701548 TTGAAGGACTAAA
1 TTAAAGGACTAAA
701561 CAATAATTAT
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
29 35 0.58
30 13 0.22
31 12 0.20
ACGTcount: A:0.57, C:0.07, G:0.16, T:0.21
Consensus pattern (30 bp):
TTAAAGGACTAAAATAGAAAAAATAGAAAG
Found at i:704282 original size:10 final size:10
Alignment explanation
Indices: 704267--704297 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
704257 ATTTAAATAA
*
704267 ATAAACGATC
1 ATAAACGAAC
704277 ATAAACGAAC
1 ATAAACGAAC
704287 ATAAACGAAC
1 ATAAACGAAC
704297 A
1 A
704298 ACACAAACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.58, C:0.19, G:0.10, T:0.13
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:712740 original size:20 final size:20
Alignment explanation
Indices: 712684--712741 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
712674 TGAGGTTGTA
*
712684 GTATCGATATCAGATGATTG
1 GTATCGATATCAGATGCTTG
* *
712704 GTACCGATA-CTGGATGCTTG
1 GTATCGATATC-AGATGCTTG
712724 GTATCGATATCAGATGCT
1 GTATCGATATCAGATGCT
712742 CGATATTGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (20 bp):
GTATCGATATCAGATGCTTG
Found at i:712825 original size:21 final size:21
Alignment explanation
Indices: 712801--712851 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
712791 AGAGGACTGA
712801 TATCCATACCA-AATGAGTTGG
1 TATCCATACCATAA-GAGTTGG
*
712822 TATCCATA-CATAAGATTTGG
1 TATCCATACCATAAGAGTTGG
712842 TATCCATACC
1 TATCCATACC
712852 GAAAGCTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (21 bp):
TATCCATACCATAAGAGTTGG
Found at i:715724 original size:164 final size:173
Alignment explanation
Indices: 715445--715769 Score: 517
Period size: 164 Copynumber: 1.9 Consensus size: 173
715435 AGTTAATGCG
* *
715445 ATAAGCTGATGAAGATTAAAAAAACGACACAATCATTAAATTTATCAAATAATAACAATTTGGTA
1 ATAAGCTGATGAAGATTAAAAAAAC-AAACAATCATTAAA-TTATCAAATAATAACAATTTGGAA
715510 TTTAAATACAACAAACTTACAATAAGATTAAATGGTAAATGATAACCAAATTACAATAACTGATA
64 TTTAAATACAACAAACTTACAATAAGATTAAATGGTAAATGATAACCAAATTACAATAACTGATA
715575 TTAAATGGTAAT-AACAAAATT-ACTGAAATTAATGTCATTCATA
129 TTAAATGGTAATAAACAAAATTAACTGAAATTAATGTCATTCATA
*
715618 ATAAGCT-ATTAAGATTAAAAAAA-AAACAAT-ATTAAA-TA-CAAATAATAACAATTTGGAATT
1 ATAAGCTGATGAAGATTAAAAAAACAAACAATCATTAAATTATCAAATAATAACAATTTGGAATT
*
715678 TAAA-A-AA-AAAGTTACAATAAGAATTAAATGGTAAATGATAACCAAATTACAATAACTGATAT
66 TAAATACAACAAACTTACAATAAG-ATTAAATGGTAAATGATAACCAAATTACAATAACTGATAT
715740 TAAATGGTAATAAACAAAATTAACTGAAAT
130 TAAATGGTAATAAACAAAATTAACTGAAAT
715770 ATATCAAAAA
Statistics
Matches: 145, Mismatches: 4, Indels: 13
0.90 0.02 0.08
Matches are distributed among these distances:
163 13 0.09
164 53 0.37
165 10 0.07
166 33 0.23
167 2 0.01
169 6 0.04
170 6 0.04
172 15 0.10
173 7 0.05
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.28
Consensus pattern (173 bp):
ATAAGCTGATGAAGATTAAAAAAACAAACAATCATTAAATTATCAAATAATAACAATTTGGAATT
TAAATACAACAAACTTACAATAAGATTAAATGGTAAATGATAACCAAATTACAATAACTGATATT
AAATGGTAATAAACAAAATTAACTGAAATTAATGTCATTCATA
Found at i:715760 original size:35 final size:35
Alignment explanation
Indices: 715684--715761 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 35
715674 AATTTAAAAA
715684 AAAAGTTACAATAAGAATTAAATGGTAAATGATAAC
1 AAAA-TTACAATAAGAATTAAATGGTAAATGATAAC
*
715720 CAAATTACAATAACTGATATTAAATGGT-AAT-A-AAC
1 AAAATTACAATAA--GA-ATTAAATGGTAAATGATAAC
715755 AAAATTA
1 AAAATTA
715762 ACTGAAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
35 18 0.49
36 4 0.11
37 5 0.14
38 10 0.27
ACGTcount: A:0.55, C:0.08, G:0.10, T:0.27
Consensus pattern (35 bp):
AAAATTACAATAAGAATTAAATGGTAAATGATAAC
Found at i:716834 original size:111 final size:111
Alignment explanation
Indices: 716692--717024 Score: 560
Period size: 111 Copynumber: 3.0 Consensus size: 111
716682 ATTACAAAAA
*
716692 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACAAATTATTACTAATAATTTAAATTA
1 TTAATTTTTAATCTAATAATCATGCATTAAATAAATCAACAAATTATTACTAATAATTTAAATTA
*
716757 AATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTATCGATATAT
66 AATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTATCGAGATAT
**
716803 TTAATTTTTAATCTAATAATCATGCATTAAATAAATCAATTAATTATTACTAATAATTTAAATTA
1 TTAATTTTTAATCTAATAATCATGCATTAAATAAATCAACAAATTATTACTAATAATTTAAATTA
* * *
716868 AATTAAAACGTTAAAATGTTACTGTATTAGCAAAATGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTATCGAGATAT
716914 TTAATTTTTAATCTAATAATCATGCATTAAATAAATCAACTAAA-TATTACTAATAATTTAAATT
1 TTAATTTTTAATCTAATAATCATGCATTAAATAAATCAAC-AAATTATTACTAATAATTTAAATT
* * *
716978 AAATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
65 AAATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTATCGAGATAT
717025 ATGATTTCCA
Statistics
Matches: 208, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
111 206 0.99
112 2 0.01
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.38
Consensus pattern (111 bp):
TTAATTTTTAATCTAATAATCATGCATTAAATAAATCAACAAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTATCGAGATAT
Found at i:717682 original size:48 final size:49
Alignment explanation
Indices: 717607--717702 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 49
717597 AAACCCTAAC
717607 TGATGTATATATATAATGTCATATTTT-AAATATATAATATATTAATTA
1 TGATGTATATATATAATGTCATATTTTAAAATATATAATATATTAATTA
*
717655 TGATGTATATATATAATGTCATTTTTTAAAATATATAATATATTAATT
1 TGATGTATATATATAATGTCATATTTTAAAATATATAATATATTAATT
717703 TTTACTCTGA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 26 0.57
49 20 0.43
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (49 bp):
TGATGTATATATATAATGTCATATTTTAAAATATATAATATATTAATTA
Found at i:718437 original size:12 final size:12
Alignment explanation
Indices: 718402--718474 Score: 53
Period size: 12 Copynumber: 5.9 Consensus size: 12
718392 TCTATAAAAA
*
718402 TATTTTATTGTAT
1 TATTTTATTAT-T
718415 TA-TTTATTTATT
1 TATTTTA-TTATT
718427 TATTTTATTA-T
1 TATTTTATTATT
718438 TATTATTATTATT
1 TATT-TTATTATT
*
718451 AATATTTT-TTTTT
1 --TATTTTATTATT
*
718464 TATTTTTTTAT
1 TATTTTATTAT
718475 AGGCCCCATA
Statistics
Matches: 50, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
11 11 0.22
12 19 0.38
13 14 0.28
14 2 0.04
15 4 0.08
ACGTcount: A:0.25, C:0.00, G:0.01, T:0.74
Consensus pattern (12 bp):
TATTTTATTATT
Found at i:719380 original size:4 final size:4
Alignment explanation
Indices: 719371--719412 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
719361 TTTTGGCCAT
*
719371 TTTA TTTA TTTA TTTA TTTA TTTA CTTT- TTTA ATT- TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTT
719413 TATCTTCCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
3 5 0.15
4 25 0.76
5 3 0.09
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:723687 original size:110 final size:108
Alignment explanation
Indices: 723530--723788 Score: 328
Period size: 110 Copynumber: 2.4 Consensus size: 108
723520 GCTTCCCAAT
* * *
723530 TTCAGAGCCAATTTCAACTTCAC-AGCGAATGATATTGGACCCAAGACAACACAAGCTCAACTTC
1 TTCAGAGCCAATTTCAACTTCACGA-CGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTC
* * *
723594 AC-GACGAAAGGGCGGCTGATTGTCAACAAAAAACTTTTCAATTTC
65 ACAG-CGAAAGGGCGGCTGACTGTCAACAAAAAA-TTTCCAAGTTC
* *
723639 ATTCAGAGTCAATTTCAACTTCACGACGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTC
1 -TTCAGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTC
* * *
723704 ACAGCGAAGGGGCGGCTGACTGTCAACAAATAATTTCCCAGTTC
65 ACAGCGAAAGGGCGGCTGACTGTCAACAAAAAATTTCCAAGTTC
* * *
723748 --CAGAGCCAATTTTAACTTCACGGCGGAGGATATTGGACTCG
1 TTCAGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCG
723789 GAACAATTCA
Statistics
Matches: 131, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
106 36 0.27
109 8 0.06
110 85 0.65
111 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (108 bp):
TTCAGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
CAGCGAAAGGGCGGCTGACTGTCAACAAAAAATTTCCAAGTTC
Found at i:724113 original size:258 final size:257
Alignment explanation
Indices: 723748--724220 Score: 637
Period size: 258 Copynumber: 1.8 Consensus size: 257
723738 TTCCCAGTTC
* * * **
723748 CAGAGCCAATTTTAACTTCACGGCGGAGGATATTGGACTCGGAACAATTCAACTTACTTGGATTT
1 CAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACTCGAAACAACACAACTTACTTGGATTT
* * * *
723813 CAACTTCACGATGAAGGATATCCAATTACCAGGCTCAACTTCACGACG-AATGAGCCACT-CACG
66 CAACTTCACGACGAAGGATATCCAACTACCAGGCTCAACTTCACAAAGAAATGA-CCA-TACACG
* * * * * *
723876 GTTTCAACTTCACGATGAAGGGAATCGTACACATAAGCAACATCCATCTCTAGAATGGATTTCAA
129 ATTTCAACTTCACGACGAAGGGAATCATACACACAAGCAACATCAACCTCTAGAATGGATTTCAA
723941 CTTCACAACGAAGGATATCCAACTCAAAGAAGGAGTGGCTGTCAATAAACTTTCTAATTTCATT
194 CTTCACAACGAAGGATATCCAACTCAAAGAAGGAGTGGCTGTCAATAAACTTTCTAATTTCATT
* *
724005 CAGAGTCAATTTCAACTTCACGGCGAAGGATATTGGACTCGAAACAGCACAACTTACATTGGATT
1 CAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACTCGAAACAACACAACTTAC-TTGGATT
* * * *
724070 TCAACTTCACGACGAAGGATATCCAACT-CCAAGGTTTAACTTCACAAAGAAATGACCATATATG
65 TCAACTTCACGACGAAGGATATCCAACTACC-AGGCTCAACTTCACAAAGAAATGACCATACACG
* * * * * *
724134 ATTTCAACTTCACGACGAAGGGAATCATGCTCACCAGCAACATTAACCTTTAGATTGGATTTCAA
129 ATTTCAACTTCACGACGAAGGGAATCATACACACAAGCAACATCAACCTCTAGAATGGATTTCAA
*
724199 CTTCACGACGAAGGATATCCAA
194 CTTCACAACGAAGGATATCCAA
724221 TTCCATGCTC
Statistics
Matches: 184, Mismatches: 28, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
257 53 0.29
258 126 0.68
259 5 0.03
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.25
Consensus pattern (257 bp):
CAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACTCGAAACAACACAACTTACTTGGATTT
CAACTTCACGACGAAGGATATCCAACTACCAGGCTCAACTTCACAAAGAAATGACCATACACGAT
TTCAACTTCACGACGAAGGGAATCATACACACAAGCAACATCAACCTCTAGAATGGATTTCAACT
TCACAACGAAGGATATCCAACTCAAAGAAGGAGTGGCTGTCAATAAACTTTCTAATTTCATT
Found at i:724453 original size:84 final size:84
Alignment explanation
Indices: 724288--724458 Score: 209
Period size: 84 Copynumber: 2.0 Consensus size: 84
724278 GATATCGTGT
* * * * * * *
724288 TCATTTGCAATATAGCTCAAGGCAAGAAGGGTTATTTGCCAACCAAATACCTTCGAGTTCGACTA
1 TCATTTGCAACACAGCTCAAGGCAAAAAAGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
* * *
724353 CGCTCAGCTCCAAGGCACA
66 CACTCAACTCCAAGGCAAA
* *
724372 TCATTTGCAACACAGCTCCAGGCAAAAAAGGCTATCTGCCAACCAAAGACCTTCGAGTTCGATTA
1 TCATTTGCAACACAGCTCAAGGCAAAAAAGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
*
724437 CATTCAACT-CAGAGGCAAA
66 CACTCAACTCCA-AGGCAAA
724456 TCA
1 TCA
724459 AATTTACAGC
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
83 2 0.03
84 71 0.97
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (84 bp):
TCATTTGCAACACAGCTCAAGGCAAAAAAGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
CACTCAACTCCAAGGCAAA
Found at i:724669 original size:23 final size:24
Alignment explanation
Indices: 724616--724681 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 24
724606 GGTCTACAAA
*
724616 AATATTTTATTGTATTATTTATTTAT
1 AATATTTTA-T-TATTATTTATTAAT
*
724642 -TTATTTTATTATTA-TTATTAAT
1 AATATTTTATTATTATTTATTAAT
* *
724664 AATATTTTTTTATAATTT
1 AATATTTTATTATTATTT
724682 TTGTAGGCCC
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
22 7 0.21
23 16 0.48
24 3 0.09
25 7 0.21
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
AATATTTTATTATTATTTATTAAT
Found at i:726445 original size:112 final size:113
Alignment explanation
Indices: 726248--726472 Score: 443
Period size: 112 Copynumber: 2.0 Consensus size: 113
726238 TTTCGGACCC
726248 ACCCGAAAGACAATTCTGACATATATGAAAACTGGTAACATATCCCTCAATCCAACAGAAAAACT
1 ACCCGAAAGACAATTCTGACATATATGAAAACTGGTAACATATCCCTCAATCCAACAGAAAAACT
726313 CAAACCCAATTATGGTGTTTTTAACCCATCAAC-CCTCCTCCTGGTGT
66 CAAACCCAATTATGGTGTTTTTAACCCATCAACGCCTCCTCCTGGTGT
726360 ACCCGAAAGACAATTCTGACATATATGAAAACTGGTAACATATCCCTCAATCCAACAGAAAAACT
1 ACCCGAAAGACAATTCTGACATATATGAAAACTGGTAACATATCCCTCAATCCAACAGAAAAACT
726425 CAAACCCAATTATGGTGTTTTTAACCCATCAACGCCTCCTCCTGGTGT
66 CAAACCCAATTATGGTGTTTTTAACCCATCAACGCCTCCTCCTGGTGT
726473 GTCTCAATGA
Statistics
Matches: 112, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
112 98 0.88
113 14 0.12
ACGTcount: A:0.36, C:0.28, G:0.12, T:0.25
Consensus pattern (113 bp):
ACCCGAAAGACAATTCTGACATATATGAAAACTGGTAACATATCCCTCAATCCAACAGAAAAACT
CAAACCCAATTATGGTGTTTTTAACCCATCAACGCCTCCTCCTGGTGT
Found at i:730204 original size:38 final size:38
Alignment explanation
Indices: 730162--730248 Score: 113
Period size: 38 Copynumber: 2.3 Consensus size: 38
730152 CTACAATTAG
* * *
730162 TGTTTTTTCCTTGACA-TGATGTTCTAGTTGTATTTCTC
1 TGTTTATTCCTTGAAATTG-TGTACTAGTTGTATTTCTC
*
730200 TGTTTATTCCTTGAAATTGTGTACTTGTTGTATTTCTC
1 TGTTTATTCCTTGAAATTGTGTACTAGTTGTATTTCTC
*
730238 TGTTTCTTCCT
1 TGTTTATTCCT
730249 GAGATGCTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
38 41 0.95
39 2 0.05
ACGTcount: A:0.13, C:0.16, G:0.15, T:0.56
Consensus pattern (38 bp):
TGTTTATTCCTTGAAATTGTGTACTAGTTGTATTTCTC
Found at i:730970 original size:43 final size:42
Alignment explanation
Indices: 730847--731111 Score: 300
Period size: 42 Copynumber: 6.2 Consensus size: 42
730837 AAGAAAATTA
* * * *
730847 GCGGCGTTTGTATCCCAAAACGCTGCTATATATCTGATCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTGACCTTTT
*
730890 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATATGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
* * * *
730932 GTGGCATTTGTTCCAAAAAATGCCGCTATAGATCTGACCTATT
1 GCGGCGTTTGTTCC-AAAAACGCCGCTATAGATCTGACCTTTT
* * * *
730975 GCGGCATTTGTTCCAAAAACGCCACTATAGATGTCATCCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGA-CCTTTT
* * *
731018 GCGGCGTTTGTTCCAAAAATGCCACTATAGAT-TCATCCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGA-CCTTTT
*
731060 GCGGCGTTTGTTCCAAAAACACCGCTATAGATCTTGA-CTTATT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATC-TGACCTT-TT
*
731103 GCGACGTTT
1 GCGGCGTTT
731112 TTAGTTCTCA
Statistics
Matches: 194, Mismatches: 23, Indels: 10
0.85 0.10 0.04
Matches are distributed among these distances:
42 98 0.51
43 94 0.48
44 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (42 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
Found at i:730996 original size:85 final size:85
Alignment explanation
Indices: 730847--731091 Score: 305
Period size: 85 Copynumber: 2.9 Consensus size: 85
730837 AAGAAAATTA
* * * * * *
730847 GCGGCGTTTGTATCCCAAAACGCTGCTATATATCTGATCTTTTGCGGCGTTTGTTCCAAAAACGC
1 GCGGCATTTGT-TCCAAAAATGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGC
*
730912 CGCTATAGATATGA-CCTTTT
65 CGCTATAGATATCATCCTTTT
* * *
730932 GTGGCATTTGTTCCAAAAAATGCCGCTATAGATCTGACCTATTGCGGCATTTGTTCCAAAAACGC
1 GCGGCATTTGTTCC-AAAAATGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGC
* *
730997 CACTATAGATGTCATCCTTTT
65 CGCTATAGATATCATCCTTTT
* * * *
731018 GCGGCGTTTGTTCCAAAAATGCCACTATAGAT-TCATCCTTTTGCGGCGTTTGTTCCAAAAACAC
1 GCGGCATTTGTTCCAAAAATGCCGCTATAGATCTGA-CCTTTTGCGGCGTTTGTTCCAAAAACGC
731082 CGCTATAGAT
65 CGCTATAGAT
731092 CTTGACTTAT
Statistics
Matches: 137, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
84 5 0.04
85 114 0.83
86 18 0.13
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.33
Consensus pattern (85 bp):
GCGGCATTTGTTCCAAAAATGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGCC
GCTATAGATATCATCCTTTT
Found at i:735924 original size:21 final size:21
Alignment explanation
Indices: 735898--735951 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
735888 TATGGGCTAT
735898 TGCATCGATGCACATCCGAGG
1 TGCATCGATGCACATCCGAGG
735919 TGCATCGATGCACATCCGAGG
1 TGCATCGATGCACATCCGAGG
*
735940 TGCACCGATGCA
1 TGCATCGATGCA
735952 TCAAGGGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.24, C:0.30, G:0.28, T:0.19
Consensus pattern (21 bp):
TGCATCGATGCACATCCGAGG
Found at i:737208 original size:2 final size:2
Alignment explanation
Indices: 737197--737250 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
737187 TATAGGAAAA
737197 AT AT AT -T AT AT AT AT AT AT AT AT AT AT A- 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
737237 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
737251 GAATATGAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 48 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:737229 original size:23 final size:23
Alignment explanation
Indices: 737197--737247 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
737187 TATAGGAAAA
*
737197 ATATATTATATATATATATATAT
1 ATATAATATATATATATATATAT
737220 ATATAATATATATATATATATAT
1 ATATAATATATATATATATATAT
737243 ATATA
1 ATATA
737248 TATGAATATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATATAATATATATATATATATAT
Found at i:737831 original size:16 final size:17
Alignment explanation
Indices: 737810--737843 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
737800 GTGCACAACC
737810 TCTATAG-ACTCACATA
1 TCTATAGTACTCACATA
*
737826 TCTATAGTTCTCACATA
1 TCTATAGTACTCACATA
737843 T
1 T
737844 GTACATGGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (17 bp):
TCTATAGTACTCACATA
Found at i:741191 original size:22 final size:22
Alignment explanation
Indices: 741166--741207 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
741156 GTCAAAGAAA
741166 GTCAACGGTCCGGTCGGGTCGG
1 GTCAACGGTCCGGTCGGGTCGG
*
741188 GTCAACGGTCGGGTCGGGTC
1 GTCAACGGTCCGGTCGGGTC
741208 AGACCGGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.10, C:0.26, G:0.45, T:0.19
Consensus pattern (22 bp):
GTCAACGGTCCGGTCGGGTCGG
Found at i:741198 original size:17 final size:17
Alignment explanation
Indices: 741176--741208 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
741166 GTCAACGGTC
741176 CGGTCGGGTCGGGTCAA
1 CGGTCGGGTCGGGTCAA
741193 CGGTCGGGTCGGGTCA
1 CGGTCGGGTCGGGTCA
741209 GACCGGTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.09, C:0.24, G:0.48, T:0.18
Consensus pattern (17 bp):
CGGTCGGGTCGGGTCAA
Found at i:741228 original size:19 final size:19
Alignment explanation
Indices: 741206--741303 Score: 92
Period size: 19 Copynumber: 5.1 Consensus size: 19
741196 TCGGGTCGGG
741206 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
741225 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
741244 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
* *
741263 TCAAATCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* * *
741283 TGAAAACCGGTTAAACCGGT
1 T-CAGACCGGTCAAACCGGT
741303 T
1 T
741304 TCCAGCAGCC
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
18 3 0.05
19 38 0.58
20 17 0.26
21 8 0.12
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.18
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:741234 original size:10 final size:10
Alignment explanation
Indices: 741206--741254 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
741196 TCGGGTCGGG
741206 TCAGACCGG-
1 TCAGACCGGT
*
741215 TCAAACCGGT
1 TCAGACCGGT
741225 TCAGACCGG-
1 TCAGACCGGT
*
741234 TCAAACCGGT
1 TCAGACCGGT
741244 TC-GAACCGGT
1 TCAG-ACCGGT
741254 T
1 T
741255 GAAACCGGTC
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
9 16 0.48
10 17 0.52
ACGTcount: A:0.24, C:0.31, G:0.27, T:0.18
Consensus pattern (10 bp):
TCAGACCGGT
Found at i:741260 original size:10 final size:10
Alignment explanation
Indices: 741210--741303 Score: 90
Period size: 9 Copynumber: 9.7 Consensus size: 10
741200 GTCGGGTCAG
741210 ACCGG-TCAA
1 ACCGGTTCAA
*
741219 ACCGGTTCAG
1 ACCGGTTCAA
741229 ACCGG-TCAA
1 ACCGGTTCAA
*
741238 ACCGGTTCGA
1 ACCGGTTCAA
*
741248 ACCGGTTGAA
1 ACCGGTTCAA
741258 ACCGG-TCAA
1 ACCGGTTCAA
*
741267 ATCGG-TCAGA
1 ACCGGTTCA-A
*
741277 ACCGGTTGAAA
1 ACCGGTT-CAA
741288 ACCGGTT-AA
1 ACCGGTTCAA
741297 ACCGGTT
1 ACCGGTT
741304 TCCAGCAGCC
Statistics
Matches: 71, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
9 32 0.45
10 29 0.41
11 9 0.13
12 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.18
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:741261 original size:29 final size:28
Alignment explanation
Indices: 741205--741302 Score: 115
Period size: 29 Copynumber: 3.4 Consensus size: 28
741195 GTCGGGTCGG
* * *
741205 GTCAGACCGGTCAAACCGGTTCAGACCG
1 GTCAAACCGGTCAAACCGGTTGAAACCG
*
741233 GTCAAACCGGTTCGAACCGGTTGAAACCG
1 GTCAAACCGG-TCAAACCGGTTGAAACCG
*
741262 GTCAAATCGGTCAGAACCGGTTGAAAACCG
1 GTCAAACCGGTCA-AACCGGTTG-AAACCG
*
741292 GTTAAACCGGT
1 GTCAAACCGGT
741303 TTCCAGCAGC
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
28 11 0.19
29 33 0.56
30 15 0.25
ACGTcount: A:0.29, C:0.27, G:0.28, T:0.17
Consensus pattern (28 bp):
GTCAAACCGGTCAAACCGGTTGAAACCG
Found at i:748438 original size:21 final size:22
Alignment explanation
Indices: 748401--748441 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
748391 ACGGTCAACA
748401 GTCAACGGTCCGGTCGGGTCGG
1 GTCAACGGTCCGGTCGGGTCGG
*
748423 GTCAAC-GTCGGGTCGGGTC
1 GTCAACGGTCCGGTCGGGTC
748442 AGACCGGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.10, C:0.27, G:0.44, T:0.20
Consensus pattern (22 bp):
GTCAACGGTCCGGTCGGGTCGG
Found at i:751647 original size:28 final size:28
Alignment explanation
Indices: 751615--751750 Score: 105
Period size: 28 Copynumber: 4.9 Consensus size: 28
751605 ATCAGGGCGT
*
751615 GGAATAACTCTCATACAAAATACATCAG
1 GGAATAAATCTCATACAAAATACATCAG
** * * *
751643 GGAATAAATCTTGTATAGAATATATCAG
1 GGAATAAATCTCATACAAAATACATCAG
* * * *
751671 GGAAGAAATCTCATACAAAACAGATCTG
1 GGAATAAATCTCATACAAAATACATCAG
* * * * *
751699 GGAATAAATCCCATACAGAACAGAT-TG
1 GGAATAAATCTCATACAAAATACATCAG
*
751726 GAGAATAAATCCCATACAAAA-ACAT
1 G-GAATAAATCTCATACAAAATACAT
751751 GAATGTATCA
Statistics
Matches: 88, Mismatches: 19, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
27 6 0.07
28 82 0.93
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (28 bp):
GGAATAAATCTCATACAAAATACATCAG
Found at i:755947 original size:26 final size:27
Alignment explanation
Indices: 755916--755967 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
755906 TGGAGATGTT
755916 TGGATGA-TACACTAT-TTTATGTTTAA
1 TGGATGATTA-ACTATATTTATGTTTAA
*
755942 TGGATGATTAAGTATATTTATGTTTA
1 TGGATGATTAACTATATTTATGTTTA
755968 TTATTGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.31, C:0.04, G:0.17, T:0.48
Consensus pattern (27 bp):
TGGATGATTAACTATATTTATGTTTAA
Found at i:756488 original size:22 final size:21
Alignment explanation
Indices: 756463--756530 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 21
756453 GAACTCGAAC
756463 ATTTTTTGCCTTAGCAACTTTT
1 ATTTTTTGCCTTAGCAA-TTTT
* *
756485 ATTTATT-CACTCTTGCAA--TT
1 ATTTTTTGC-CT-TAGCAATTTT
*
756505 AATTTTTGCCTTAGCAATTTTT
1 ATTTTTTGCCTTAGCAA-TTTT
756527 ATTT
1 ATTT
756531 GTTTACTATT
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
19 5 0.15
20 9 0.26
21 2 0.06
22 13 0.38
23 5 0.15
ACGTcount: A:0.22, C:0.16, G:0.07, T:0.54
Consensus pattern (21 bp):
ATTTTTTGCCTTAGCAATTTT
Done.