Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008063.1 Hibiscus syriacus cultivar Beakdansim tig00110560_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: 602526
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 2 of 2
Found at i:431846 original size:33 final size:32
Alignment explanation
Indices: 431764--431846 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 32
431754 TTAGTATTTT
* * * *
431764 TTTAAATAGTTATTATTTTTTATATTAATATA
1 TTTATATAATTATTATTTTATATATTAAAATA
* *
431796 TTTATGTAAATATTATTTTAT-TATTAAAATAA
1 TTTATATAATTATTATTTTATATATTAAAAT-A
431828 TATTATATAATTATTATTT
1 T-TTATATAATTATTATTT
431847 ATTTAGAATT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
31 8 0.20
32 18 0.44
33 15 0.37
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (32 bp):
TTTATATAATTATTATTTTATATATTAAAATA
Found at i:433600 original size:21 final size:21
Alignment explanation
Indices: 433570--433617 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
433560 GCAGGGGTAC
* *
433570 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
433591 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
433612 ATGCCA
1 ATGCCA
433618 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:433647 original size:21 final size:21
Alignment explanation
Indices: 433621--433714 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
433611 TATGCCATCT
* *
433621 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
433642 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
433663 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
433684 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
433705 CCGCAGGGTT
1 CCGCAGGGTT
433715 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:434264 original size:28 final size:28
Alignment explanation
Indices: 434232--434328 Score: 77
Period size: 28 Copynumber: 3.2 Consensus size: 28
434222 GATAAATGTT
*
434232 TTTAAAATACAAATTATATTATTCGAAA
1 TTTAAAATAAAAATTATATTATTCGAAA
* *
434260 TTTAAAATAAAAAAAATAATATTATTCAAATTTAAA
1 TTTAAAAT---AAAAATTATATTATTC-----GAAA
* *
434296 TTTAAAATATAAATTATAGTATTCGAAA
1 TTTAAAATAAAAATTATATTATTCGAAA
434324 TTTAA
1 TTTAA
434329 CATTAAATTT
Statistics
Matches: 54, Mismatches: 7, Indels: 16
0.70 0.09 0.21
Matches are distributed among these distances:
28 16 0.30
31 14 0.26
33 13 0.24
36 11 0.20
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (28 bp):
TTTAAAATAAAAATTATATTATTCGAAA
Found at i:434941 original size:126 final size:126
Alignment explanation
Indices: 434715--435445 Score: 1399
Period size: 126 Copynumber: 5.8 Consensus size: 126
434705 TTTAAGTTAT
*
434715 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
434780 GCGTCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
434841 ACCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
* *
434906 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAGTAGGTACTGATATCTCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
434967 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
435032 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAGTAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
435093 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
435158 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
435219 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
435284 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
435345 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTATCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
435410 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
435446 CCGATTATAG
Statistics
Matches: 596, Mismatches: 9, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
126 596 1.00
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (126 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:435526 original size:8 final size:8
Alignment explanation
Indices: 435513--435553 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
435503 TCACAATCTT
435513 TCAAATTC
1 TCAAATTC
435521 TCAAATTC
1 TCAAATTC
* *
435529 CCAAACTC
1 TCAAATTC
435537 T-AAATTC
1 TCAAATTC
435544 TCAAATTC
1 TCAAATTC
435552 TC
1 TC
435554 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:438572 original size:12 final size:13
Alignment explanation
Indices: 438539--438576 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
438529 AAATACATAA
438539 ATATATTTAATAT
1 ATATATTTAATAT
*
438552 ATTTATTTAATAT
1 ATATATTTAATAT
438565 A-ATATTTAATAT
1 ATATATTTAATAT
438577 TATTAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATATTTAATAT
Found at i:438628 original size:23 final size:23
Alignment explanation
Indices: 438590--438647 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
438580 TAGTTATAAT
438590 TTTTACAT--TATAATCGAAACA
1 TTTTACATAATATAATCGAAACA
438611 TTTTACATAATATAATCGAAACA
1 TTTTACATAATATAATCGAAACA
438634 TTTTACATAATATA
1 TTTTACATAATATA
438648 TTATTAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.23
23 27 0.77
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (23 bp):
TTTTACATAATATAATCGAAACA
Found at i:439407 original size:2 final size:2
Alignment explanation
Indices: 439400--439424 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
439390 AATGTACTCT
439400 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 T
439425 GAATTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:441921 original size:29 final size:29
Alignment explanation
Indices: 441856--441924 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
441846 ATTATATTGT
*
441856 ACTTAT-AAATTTTCAGGGACGAACTTAA
1 ACTTATAAAATTTTCAGGGACAAACTTAA
*
441884 ACTTGTAAAATTTT-AGGGGACAAACTTAA
1 ACTTATAAAATTTTCA-GGGACAAACTTAA
441913 A-TGTATAAAATT
1 ACT-TATAAAATT
441925 CCAGGGGATG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 7 0.20
29 28 0.80
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
ACTTATAAAATTTTCAGGGACAAACTTAA
Found at i:441930 original size:29 final size:29
Alignment explanation
Indices: 441856--441932 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 29
441846 ATTATATTGT
* * *
441856 ACTTATAAATTTTCA-GGGACGAACTTAA
1 ACTTATAAAATTCCAGGGGACAAACTTAA
* **
441884 ACTTGTAAAATTTTAGGGGACAAACTTAA
1 ACTTATAAAATTCCAGGGGACAAACTTAA
441913 A-TGTATAAAATTCCAGGGGA
1 ACT-TATAAAATTCCAGGGGA
441933 TGAATCTTGC
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
28 13 0.32
29 27 0.68
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (29 bp):
ACTTATAAAATTCCAGGGGACAAACTTAA
Found at i:459560 original size:53 final size:53
Alignment explanation
Indices: 459480--459585 Score: 185
Period size: 53 Copynumber: 2.0 Consensus size: 53
459470 AGTGGTCCTC
* * *
459480 CATTTCTGCACCTTTTTTTTGCTTATTTGTACACTTTTATTAAATTCTGTCCA
1 CATTTCTGCACATTTTGTATGCTTATTTGTACACTTTTATTAAATTCTGTCCA
459533 CATTTCTGCACATTTTGTATGCTTATTTGTACACTTTTATTAAATTCTGTCCA
1 CATTTCTGCACATTTTGTATGCTTATTTGTACACTTTTATTAAATTCTGTCCA
459586 GATTCCATTT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.21, C:0.20, G:0.08, T:0.51
Consensus pattern (53 bp):
CATTTCTGCACATTTTGTATGCTTATTTGTACACTTTTATTAAATTCTGTCCA
Found at i:461724 original size:2 final size:2
Alignment explanation
Indices: 461717--461746 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
461707 ATATTAGATA
461717 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
461747 TCATATAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:464043 original size:13 final size:13
Alignment explanation
Indices: 464025--464058 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
464015 TAAACTAACG
464025 ATTAATGTATGTT
1 ATTAATGTATGTT
464038 ATTAATGTATGTT
1 ATTAATGTATGTT
464051 ATTAATGT
1 ATTAATGT
464059 GACGTATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (13 bp):
ATTAATGTATGTT
Found at i:465245 original size:36 final size:36
Alignment explanation
Indices: 465203--465308 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
465193 GCCCTACTGT
*
465203 GTTGGTGGTGTAAGAAAATAGTCCTCCCATTCCACA
1 GTTGGTGGTTTAAGAAAATAGTCCTCCCATTCCACA
465239 GTTGGTGGTTTAAGAAAATAGTCCTCCCATTCCACA
1 GTTGGTGGTTTAAGAAAATAGTCCTCCCATTCCACA
* *
465275 GTTGGTGGTTTAAGAAAATACTCCTTCCATTCCA
1 GTTGGTGGTTTAAGAAAATAGTCCTCCCATTCCA
465309 TTTTTTTTTG
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 67 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (36 bp):
GTTGGTGGTTTAAGAAAATAGTCCTCCCATTCCACA
Found at i:465608 original size:27 final size:28
Alignment explanation
Indices: 465563--465627 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
465553 AGTCCACCCG
*
465563 ACCCGACCC-AAAAATTATAAATCATCC
1 ACCCGACCCGAAAAATTATAAACCATCC
* * *
465590 ACTCGACCCGAAAAA-TATACACCTTCC
1 ACCCGACCCGAAAAATTATAAACCATCC
465617 ACCCGACCCGA
1 ACCCGACCCGA
465628 TTTTGGAGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 27 0.84
28 5 0.16
ACGTcount: A:0.38, C:0.38, G:0.08, T:0.15
Consensus pattern (28 bp):
ACCCGACCCGAAAAATTATAAACCATCC
Found at i:478329 original size:7 final size:7
Alignment explanation
Indices: 478317--478344 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
478307 GCCTAAAGAG
478317 GTCAAAA
1 GTCAAAA
478324 GTCAAAA
1 GTCAAAA
478331 GTCAAAA
1 GTCAAAA
478338 GTCAAAA
1 GTCAAAA
478345 CTCGAAGCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.14
Consensus pattern (7 bp):
GTCAAAA
Found at i:484778 original size:18 final size:19
Alignment explanation
Indices: 484755--484818 Score: 62
Period size: 17 Copynumber: 3.5 Consensus size: 19
484745 TTTATTGAAA
*
484755 AACCGATAAA-CCGAACCG
1 AACCGAAAAACCCGAACCG
484773 AACCGAAAAACCCGAACC-
1 AACCGAAAAACCCGAACCG
*** *
484791 -ATTAAAAAAACCGAACCG
1 AACCGAAAAACCCGAACCG
484809 AACCGAAAAA
1 AACCGAAAAA
484819 GTCAGTTTCG
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
17 13 0.37
18 9 0.26
19 13 0.37
ACGTcount: A:0.53, C:0.30, G:0.12, T:0.05
Consensus pattern (19 bp):
AACCGAAAAACCCGAACCG
Found at i:503792 original size:17 final size:17
Alignment explanation
Indices: 503778--503811 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
503768 GGCAGGAATC
503778 CAGCAAGAACAGGAACA
1 CAGCAAGAACAGGAACA
503795 CAGCAAGAACAGGAACA
1 CAGCAAGAACAGGAACA
503812 ATTGCTGTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.24, G:0.24, T:0.00
Consensus pattern (17 bp):
CAGCAAGAACAGGAACA
Found at i:510844 original size:2 final size:2
Alignment explanation
Indices: 510837--510878 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
510827 TTGGTAAATC
510837 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
510879 GACGCTCTGA
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:517101 original size:64 final size:64
Alignment explanation
Indices: 517033--517257 Score: 208
Period size: 64 Copynumber: 3.5 Consensus size: 64
517023 TTGTTTGAAT
* ** * *
517033 GTGCATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAATAACATCGAATGTAATT
1 GTGCATCGATGCATAGGTAGTGCATCGATGCATC-CCGTTAATAATAA-AACATCAAATGCAATT
517096 C
64 C
* * *
517097 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCGTTAATAATGAAACATCAAATGCAATTG
1 GTGCATCGATGCATAGGTAGTGCATCGATGCATCCCGTTAATAATAAAACATCAAATGCAATTC
*** ** * * * *
517161 GTGCATCGATGCATAAGG-AGTGCATCGATGCATCCCAACAATAATACTACATCGAATAC-CTTT
1 GTGCATCGATGCAT-AGGTAGTGCATCGATGCATCCCGTTAATAATAAAACATCAAATGCAATTC
*
517224 GATGCACCGATGCATCA-GTAGTGCATCGATGCAT
1 G-TGCATCGATGCAT-AGGTAGTGCATCGATGCAT
517258 ACCTTCATTA
Statistics
Matches: 135, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
63 4 0.03
64 124 0.92
65 7 0.05
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (64 bp):
GTGCATCGATGCATAGGTAGTGCATCGATGCATCCCGTTAATAATAAAACATCAAATGCAATTC
Found at i:517581 original size:12 final size:12
Alignment explanation
Indices: 517551--517600 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
517541 ACATGCATAA
517551 GACATGT-ATAT
1 GACATGTGATAT
*
517562 GTTCATGTGATAT
1 G-ACATGTGATAT
*
517575 GATATGTGATAT
1 GACATGTGATAT
517587 GACATGTGATAT
1 GACATGTGATAT
517599 GA
1 GA
517601 GAACACGATA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
11 1 0.03
12 27 0.82
13 5 0.15
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.38
Consensus pattern (12 bp):
GACATGTGATAT
Found at i:517763 original size:15 final size:15
Alignment explanation
Indices: 517745--517791 Score: 94
Period size: 15 Copynumber: 3.1 Consensus size: 15
517735 GATGGTATAA
517745 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
517760 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
517775 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
517790 TA
1 TA
517792 ATGGTCCTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.15, C:0.19, G:0.32, T:0.34
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:537976 original size:2 final size:2
Alignment explanation
Indices: 537969--538007 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
537959 TAAGGGTTGG
537969 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
538008 GTATGTGATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:548895 original size:2 final size:2
Alignment explanation
Indices: 548888--548923 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
548878 TTTTATGATA
548888 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
548924 AATGAATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:571136 original size:36 final size:36
Alignment explanation
Indices: 571089--571171 Score: 139
Period size: 36 Copynumber: 2.3 Consensus size: 36
571079 GGCACAAAAT
*
571089 TCAAATTATTGACGTGATGAGGAAATGGAATTTTGA
1 TCAAATTATTGACGTGATAAGGAAATGGAATTTTGA
* *
571125 TCAAATTATTGAGGTGATAAGGAAATGGGATTTTGA
1 TCAAATTATTGACGTGATAAGGAAATGGAATTTTGA
571161 TCAAATTATTG
1 TCAAATTATTG
571172 GCTAACTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (36 bp):
TCAAATTATTGACGTGATAAGGAAATGGAATTTTGA
Found at i:576992 original size:20 final size:20
Alignment explanation
Indices: 576967--577024 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
576957 TTTGGTTCAC
*
576967 GGAATGTAAGATTATTAGTG
1 GGAATGTAAGATTATCAGTG
*
576987 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTATCAGTG
*
577007 GGAATATAAGATTATCAG
1 GGAATGTAAGATTATCAG
577025 AGAATAGGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.38, C:0.05, G:0.28, T:0.29
Consensus pattern (20 bp):
GGAATGTAAGATTATCAGTG
Found at i:577893 original size:3 final size:3
Alignment explanation
Indices: 577885--577968 Score: 61
Period size: 3 Copynumber: 27.0 Consensus size: 3
577875 CAAATTAAAT
577885 TAA TAA TAAA TAAA TAA -ATA TAA TAA TAA TAA TAA TAA TAA TAA T-A
1 TAA TAA T-AA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
577931 TAA -ATA TAA -ATA TAA TAAA TAA TTAA -AA TAAA TAA TAA
1 TAA TA-A TAA TA-A TAA T-AA TAA -TAA TAA T-AA TAA TAA
577969 ATAAATATAT
Statistics
Matches: 69, Mismatches: 0, Indels: 24
0.74 0.00 0.26
Matches are distributed among these distances:
2 7 0.10
3 43 0.62
4 19 0.28
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:577904 original size:15 final size:15
Alignment explanation
Indices: 577880--577981 Score: 85
Period size: 15 Copynumber: 7.1 Consensus size: 15
577870 TCTTTCAAAT
*
577880 TAAATTAAT-AATAAA
1 TAAATAAATAAAT-AA
577895 TAAATAAATATAATAA
1 TAAATAAATA-AATAA
577911 T-AAT-AAT-AATAA
1 TAAATAAATAAATAA
577923 T-AATAATATAAAT-A
1 TAAATAA-ATAAATAA
577937 TAAATATAATAAATAA
1 TAAATA-AATAAATAA
*
577953 T-TA-AAATAAATAA
1 TAAATAAATAAATAA
*
577966 TAAATAAATATATAA
1 TAAATAAATAAATAA
577981 T
1 T
577982 TAAAATAGAC
Statistics
Matches: 73, Mismatches: 4, Indels: 20
0.75 0.04 0.21
Matches are distributed among these distances:
12 9 0.12
13 11 0.15
14 9 0.12
15 35 0.48
16 6 0.08
17 3 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAATAAATAAATAA
Found at i:577912 original size:12 final size:12
Alignment explanation
Indices: 577880--577981 Score: 66
Period size: 12 Copynumber: 9.1 Consensus size: 12
577870 TCTTTCAAAT
577880 TAAAT-TAATAA
1 TAAATATAATAA
577891 TAAATA-AATAA
1 TAAATATAATAA
*
577902 -ATATAATAATAA
1 TAAAT-ATAATAA
577914 T-AATAATAATAA
1 TAAAT-ATAATAA
577926 T-AATATAA-ATA
1 TAAATATAATA-A
577937 TAAATATAATAA
1 TAAATATAATAA
577949 -ATAAT-TAA-AA
1 TA-AATATAATAA
577959 T-AA-ATAATAAA
1 TAAATATAAT-AA
577970 TAAATAT-ATAA
1 TAAATATAATAA
577981 T
1 T
577982 TAAAATAGAC
Statistics
Matches: 75, Mismatches: 2, Indels: 28
0.71 0.02 0.27
Matches are distributed among these distances:
9 5 0.07
10 6 0.08
11 27 0.36
12 34 0.45
13 3 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TAAATATAATAA
Found at i:577985 original size:12 final size:12
Alignment explanation
Indices: 577880--577985 Score: 67
Period size: 11 Copynumber: 9.7 Consensus size: 12
577870 TCTTTCAAAT
*
577880 TAAATTAATA-A
1 TAAATAAATATA
*
577891 TAAATAAATAAA
1 TAAATAAATATA
577903 TATAAT-AATA-A
1 TA-AATAAATATA
577914 T-AAT-AATA-A
1 TAAATAAATATA
577923 T-AAT-AATATA
1 TAAATAAATATA
577933 -AATATAAATATAA
1 TAA-ATAAATAT-A
577946 TAAAT-AAT-TA
1 TAAATAAATATA
577956 -AAATAAATA-A
1 TAAATAAATATA
577966 TAAATAAATATA
1 TAAATAAATATA
*
577978 TAATTAAA
1 TAAATAAA
577986 ATAGACATTT
Statistics
Matches: 81, Mismatches: 2, Indels: 23
0.76 0.02 0.22
Matches are distributed among these distances:
9 20 0.25
10 7 0.09
11 23 0.28
12 23 0.28
13 6 0.07
14 2 0.02
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TAAATAAATATA
Found at i:580390 original size:18 final size:17
Alignment explanation
Indices: 580357--580443 Score: 68
Period size: 18 Copynumber: 4.8 Consensus size: 17
580347 TTATTTAAAA
580357 ATATTAATT-TTAATTACT
1 ATATTAATTATT-ATTA-T
*
580375 ATATTATTTATTATTAT
1 ATATTAATTATTATTAT
*
580392 ATTTTAATTAGTTATTAT
1 ATATTAATTA-TTATTAT
* *
580410 ATTAATAATTAATATTATT
1 A-TATTAATTATTATTA-T
*
580429 ATATCTATTTATTAT
1 ATAT-TAATTATTAT
580444 ATTTATTTGT
Statistics
Matches: 55, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
17 9 0.16
18 27 0.49
19 19 0.35
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (17 bp):
ATATTAATTATTATTAT
Found at i:580427 original size:21 final size:19
Alignment explanation
Indices: 580383--580446 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 19
580373 CTATATTATT
*
580383 TATTATTATATTTTAATTA
1 TATTATTATATTATAATTA
*
580402 -GTTATTATATTAATAATTAA
1 TATTATTATATT-ATAATT-A
*
580422 TATTATTATATCTATTTATTA
1 TATTATTATAT-TA-TAATTA
580443 TATT
1 TATT
580447 TATTTGTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
18 10 0.28
19 5 0.14
20 1 0.03
21 15 0.42
22 5 0.14
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
TATTATTATATTATAATTA
Found at i:585899 original size:37 final size:37
Alignment explanation
Indices: 585801--585938 Score: 159
Period size: 37 Copynumber: 3.7 Consensus size: 37
585791 TTCGTCATAC
* * *
585801 TAGGATTCAAACTCTTAAAAATAGAATATAATTTTGT
1 TAGGATTTAAACTCCTAAAAATAGGATATAATTTTGT
**
585838 TAAAATTTAAACTCCTAAAAATAGGATATAATTTTGT
1 TAGGATTTAAACTCCTAAAAATAGGATATAATTTTGT
* * * **
585875 TAGGATTTAAACTCCTAAAAATAGGATAGAGTTCTAC
1 TAGGATTTAAACTCCTAAAAATAGGATATAATTTTGT
** *
585912 TATTATTTAAACTCCTAAAGATAGGAT
1 TAGGATTTAAACTCCTAAAAATAGGAT
585939 CCACAAGCAT
Statistics
Matches: 86, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 86 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.36
Consensus pattern (37 bp):
TAGGATTTAAACTCCTAAAAATAGGATATAATTTTGT
Found at i:586427 original size:11 final size:10
Alignment explanation
Indices: 586402--586459 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
586392 TTTTCTTTGC
586402 ATTATTTTAT
1 ATTATTTTAT
*
586412 ATTATTTTCCT
1 ATTATTTT-AT
*
586423 ATTATTATAT
1 ATTATTTTAT
*
586433 A-TA-TATAT
1 ATTATTTTAT
*
586441 ATTATTAT-T
1 ATTATTTTAT
586450 ATTATTTTAT
1 ATTATTTTAT
586460 CTATGTTTAC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
8 6 0.15
9 12 0.30
10 14 0.35
11 8 0.20
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (10 bp):
ATTATTTTAT
Found at i:586491 original size:13 final size:13
Alignment explanation
Indices: 586473--586498 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
586463 TGTTTACTTA
586473 TTTACTATATTTT
1 TTTACTATATTTT
586486 TTTACTATATTTT
1 TTTACTATATTTT
586499 CCTAACGTTA
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:0.08, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTACTATATTTT
Found at i:586499 original size:79 final size:77
Alignment explanation
Indices: 586406--586552 Score: 181
Period size: 79 Copynumber: 1.9 Consensus size: 77
586396 CTTTGCATTA
** * *
586406 TTTTATATTATTTTCCTATTATTATATATATATA-TATTATTATTATTATTTTATCTATGTTTAC
1 TTTTATATTATTTTCCTAACATTATATATATATATTATTATT-TTATTATATT-TCTATGATTAC
586470 TTATTTACTATATTT
64 -TATTTACTATATTT
* * *
586485 TTTTACTA-TATTTTCCTAACGTTATATATATATATTCTTATTTTTTTATATTTCTATGATTACT
1 TTTTA-TATTATTTTCCTAACATTATATATATATATTATTATTTTATTATATTTCTATGATTACT
586549 ATTT
65 ATTT
586553 TTTATTTAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
77 5 0.08
78 10 0.17
79 36 0.61
80 8 0.14
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.62
Consensus pattern (77 bp):
TTTTATATTATTTTCCTAACATTATATATATATATTATTATTTTATTATATTTCTATGATTACTA
TTTACTATATTT
Found at i:586574 original size:77 final size:78
Alignment explanation
Indices: 586408--586574 Score: 173
Period size: 79 Copynumber: 2.1 Consensus size: 78
586398 TTGCATTATT
** * *
586408 TTATATTATTTTCCTATTATTATATATATATATATTATTATTATTATTTTATCTATGTTTACTTA
1 TTATATTATTTTCCTAACATTATATATATATATATTATTATTATTATATTATCTATGATTACTTA
*
586473 TTTACTATATTTTT
66 TTTA-TATATTTTA
* * *
586487 TTACTA-TATTTTCCTAACGTTATATATATATATTCTTATT-TTTTTATATT-TCTATGATTAC-
1 TTA-TATTATTTTCCTAACATTATATATATATA-TATTATTATTATTATATTATCTATGATTACT
*
586548 TATTT-TTTATTTAATA
64 TATTTATATATTT--TA
586564 TTATATTATTT
1 TTATATTATTT
586575 ATTTTTCATT
Statistics
Matches: 74, Mismatches: 9, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
75 6 0.08
76 2 0.03
77 14 0.19
78 10 0.14
79 34 0.46
80 8 0.11
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (78 bp):
TTATATTATTTTCCTAACATTATATATATATATATTATTATTATTATATTATCTATGATTACTTA
TTTATATATTTTA
Found at i:586586 original size:10 final size:10
Alignment explanation
Indices: 586554--586600 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
586544 TTACTATTTT
*
586554 TTATTTAATA
1 TTATTTATTA
586564 TTATATTATTTA
1 TTAT-TTA-TTA
586576 TT-TTTCATTA
1 TTATTT-ATTA
586586 TTATTTATTA
1 TTATTTATTA
586596 TTATT
1 TTATT
586601 ACTATTTAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
10 20 0.62
11 8 0.25
12 4 0.12
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (10 bp):
TTATTTATTA
Found at i:586623 original size:29 final size:27
Alignment explanation
Indices: 586567--586665 Score: 78
Period size: 29 Copynumber: 3.6 Consensus size: 27
586557 TTTAATATTA
*
586567 TATTATTTATTTT-TCATTATTATT-TAT
1 TATTATTAATTTTAT-ATT-TTATTATAT
*
586594 TATTATTACTATTTAGTATTTTATTATAT
1 TATTATTAAT-TTTA-TATTTTATTATAT
* *
586623 TATACATAAATTTTATATTTTATATATAT
1 TAT-TATTAATTTTATATTTTAT-TATAT
*
586652 TTTTATT-ATTTTAT
1 TATTATTAATTTTAT
586666 TATACTATTT
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
27 15 0.26
28 18 0.31
29 20 0.34
30 5 0.09
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (27 bp):
TATTATTAATTTTATATTTTATTATAT
Found at i:586638 original size:18 final size:18
Alignment explanation
Indices: 586617--586660 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
586607 TAGTATTTTA
586617 TTATATTATACATAAATT
1 TTATATTATACATAAATT
* * *
586635 TTATATTTTATATATATT
1 TTATATTATACATAAATT
586653 TT-TATTAT
1 TTATATTAT
586661 TTTATTATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATATTATACATAAATT
Found at i:586661 original size:20 final size:20
Alignment explanation
Indices: 586550--586693 Score: 86
Period size: 20 Copynumber: 7.2 Consensus size: 20
586540 ATGATTACTA
*
586550 TTTT-TTATTTAATATTATAT
1 TTTTATTATTTTATA-TATAT
*
586570 TATTTATT-TTTCAT-TAT-T
1 T-TTTATTATTTTATATATAT
* *
586588 ATTTATTATTATTACTATTTAGT
1 TTTTATTATT-TTA-TATATA-T
* * *
586611 ATTTTATTATATTATACATAAA
1 -TTTTATTATTTTATATAT-AT
586633 TTTTA-TATTTTATATATAT
1 TTTTATTATTTTATATATAT
586652 TTTTATTATTTTAT-TATACT
1 TTTTATTATTTTATATATA-T
* *
586672 ATTTATTATTTCAT-TATAT
1 TTTTATTATTTTATATATAT
586691 TTT
1 TTT
586694 AGTTTCTTTG
Statistics
Matches: 97, Mismatches: 15, Indels: 25
0.71 0.11 0.18
Matches are distributed among these distances:
17 6 0.06
18 3 0.03
19 18 0.19
20 37 0.38
21 15 0.15
22 5 0.05
23 5 0.05
24 8 0.08
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (20 bp):
TTTTATTATTTTATATATAT
Found at i:593335 original size:21 final size:22
Alignment explanation
Indices: 593298--593362 Score: 116
Period size: 21 Copynumber: 3.0 Consensus size: 22
593288 CTCGTATAAA
593298 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
593320 TGCACCGAAG-GCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
593341 TGCACCGAAGTG-CCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
593362 T
1 T
593363 TTGTCCATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
21 31 0.74
22 11 0.26
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.18
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:593696 original size:29 final size:29
Alignment explanation
Indices: 593654--593725 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
593644 TTTTCTGCAT
**
593654 ATTCATGTCATGTAATACATATAAGATGA
1 ATTCATGTCATGTAATACATATAAGACAA
* *
593683 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAAGACAA
593712 ATTCATGTCATGTA
1 ATTCATGTCATGTA
593726 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAAGACAA
Found at i:594158 original size:66 final size:66
Alignment explanation
Indices: 594024--594170 Score: 201
Period size: 65 Copynumber: 2.3 Consensus size: 66
594014 TTTTTCTCAT
* * *
594024 GGGGGAATCGGTT-CCCCCCTGGGGTATCGATTCCCCTTAAGCAATCTGGAATTCATATACGATG
1 GGGGGTATCGGTTCCCCCCCTGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGATG
594088 A
66 A
* * *
594089 GGGGGTATCGGTTCCCCCCCTGGGGTACCGATT-CCCTCT-AGCATTCTGGAAATCATATTCGTT
1 GGGGGTATCGGTTCCCCCCCTGGGGTACCGATTCCCCT-TAAGCAATCTGGAAATCATATACGAT
594152 GA
65 GA
*
594154 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
594171 TTGAATGGGT
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
65 54 0.74
66 19 0.26
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCCCTGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGATG
A
Found at i:594180 original size:21 final size:21
Alignment explanation
Indices: 594150--594192 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
594140 ATCATATTCG
* *
594150 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
594171 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
594192 T
1 T
594193 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:594185 original size:66 final size:65
Alignment explanation
Indices: 594025--594192 Score: 198
Period size: 65 Copynumber: 2.6 Consensus size: 65
594015 TTTTCTCATG
* * * *
594025 GGGGAATCGGTTCCCCCCTGGGGTATCGATTCCCCTTAAGCAATCTGGAATTCATATACGATGAG
1 GGGGTATCGGTTCCCCCCTGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGATGAA
* * *
594090 GGGGTATCGGTTCCCCCCCTGGGGTACCGATT-CCCTCT-AGCATTCTGGAAATCATATTCGTTG
1 GGGGTATCGGTT-CCCCCCTGGGGTACCGATTCCCCT-TAAGCAATCTGGAAATCATATACGATG
594153 AA
64 AA
*
594155 GGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGTATCGGTTCCCCCCTG---GGGTACCGATTCCCCT
594193 AACCCAGAAA
Statistics
Matches: 89, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
63 6 0.07
65 49 0.55
66 30 0.34
67 4 0.04
ACGTcount: A:0.19, C:0.27, G:0.26, T:0.28
Consensus pattern (65 bp):
GGGGTATCGGTTCCCCCCTGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGATGAA
Found at i:600213 original size:21 final size:20
Alignment explanation
Indices: 600154--600216 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 20
600144 AGCTCGTATA
600154 AATGCACCGAAGTGCCGTAG
1 AATGCACCGAAGTGCCGTAG
600174 AATTGCACCGAAGTGCCGTAG
1 AA-TGCACCGAAGTGCCGTAG
600195 AATGCACCGAAGTGCCCGTAG
1 AATGCACCGAAGTG-CCGTAG
600216 A
1 A
600217 TTTTGTCCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
20 14 0.34
21 27 0.66
ACGTcount: A:0.30, C:0.25, G:0.29, T:0.16
Consensus pattern (20 bp):
AATGCACCGAAGTGCCGTAG
Found at i:600571 original size:29 final size:28
Alignment explanation
Indices: 600504--600572 Score: 95
Period size: 28 Copynumber: 2.4 Consensus size: 28
600494 TTTCTGCATA
*
600504 TCATGTCATGTAATACATATAGATGAAT
1 TCATGTCATGTAATACATATAGATAAAT
*
600532 TCATGTCATGTAATACATTTA-ATACAAAT
1 TCATGTCATGTAATACATATAGAT--AAAT
600561 TCATGTCATGTA
1 TCATGTCATGTA
600573 TCATAATATG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 2 0.05
28 20 0.54
29 15 0.41
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.38
Consensus pattern (28 bp):
TCATGTCATGTAATACATATAGATAAAT
Found at i:600980 original size:61 final size:60
Alignment explanation
Indices: 600869--600987 Score: 161
Period size: 61 Copynumber: 2.0 Consensus size: 60
600859 TTTTTCTCAT
* *
600869 GGGGGAATCGGTTCCCCCCCTGGGGTATCGATTCCCTTAAGCAATCTGGAATTCATATGA
1 GGGGGAATCGGTTCCCCCCCTGGGGTACCGATTCCCTTAAGCAATCTGGAAATCATATGA
* *
600929 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCT-AGC-ATTTGGAAATCATAT
1 GGGGGAATCGGTTCCCCCCCT-GGGGTACCGATT-CCCT-TAAGCAATCTGGAAATCATAT
600988 TCGTTGAAGG
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
60 20 0.38
61 24 0.46
62 7 0.13
63 1 0.02
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (60 bp):
GGGGGAATCGGTTCCCCCCCTGGGGTACCGATTCCCTTAAGCAATCTGGAAATCATATGA
Found at i:601028 original size:19 final size:20
Alignment explanation
Indices: 600992--601031 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
600982 TCATATTCGT
* *
600992 TGAAGGGGTATCGGTTCCCC
1 TGAAGGGGTACCGATTCCCC
601012 TGAA-GGGTACCGATTCCCC
1 TGAAGGGGTACCGATTCCCC
601031 T
1 T
601032 AACCCAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.17, C:0.28, G:0.30, T:0.25
Consensus pattern (20 bp):
TGAAGGGGTACCGATTCCCC
Done.