Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003421.1 Hibiscus syriacus cultivar Beakdansim tig00007204_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: 882701
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 5 of 5
Found at i:797820 original size:59 final size:57
Alignment explanation
Indices: 797633--797801 Score: 144
Period size: 58 Copynumber: 2.9 Consensus size: 57
797623 GCTTTATCTA
* * * * * *
797633 GAAATCCATACACTCAGTATTGA-TTCCCTACCATTTTAGCACATAAAATGCCC-TATCAA
1 GAAATCTATACACTCAGTA-TGATTTCCTTATCA-TTTAGCACACAAAGTGCCCATAT--G
* *** * **
797692 GAAATCCATATTTTCAATATGATTTCCTTATCATTTAGCACACTCAGTGCTCCATATG
1 GAAATCTATACACTCAGTATGATTTCCTTATCATTTAGCACACAAAGTGC-CCATATG
*
797750 GAAATTTATACACTCAGTATGATTTCCTTATCATTTTAGCACACAAAGTGCC
1 GAAATCTATACACTCAGTATGATTTCCTTATCA-TTTAGCACACAAAGTGCC
797802 ATTCGGTAAT
Statistics
Matches: 87, Mismatches: 19, Indels: 9
0.76 0.17 0.08
Matches are distributed among these distances:
58 44 0.51
59 40 0.46
60 3 0.03
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.34
Consensus pattern (57 bp):
GAAATCTATACACTCAGTATGATTTCCTTATCATTTAGCACACAAAGTGCCCATATG
Found at i:802478 original size:51 final size:54
Alignment explanation
Indices: 802404--802532 Score: 158
Period size: 51 Copynumber: 2.4 Consensus size: 54
802394 TTTTCCTTTA
* * *
802404 TGACATCCATTT-AAACCAATTATGAATTTTTGTACA-CTATATATATATCTATG
1 TGACATCC-TTTCAAACCACTTATGAATTGTTGTACATCTATATATATATATATG
* * *
802457 -G-CATCCTTTCATACCACTTATGCATTGTTGTACATTGTATATATATATATATG
1 TGACATCCTTTCAAACCACTTATGAATTGTTGTACA-TCTATATATATATATATG
802510 TGACATCCTTTCAAACCACTTAT
1 TGACATCCTTTCAAACCACTTAT
802533 CCATGGTTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
50 3 0.05
51 25 0.39
52 1 0.02
53 15 0.23
54 1 0.02
55 19 0.30
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.41
Consensus pattern (54 bp):
TGACATCCTTTCAAACCACTTATGAATTGTTGTACATCTATATATATATATATG
Found at i:802843 original size:81 final size:80
Alignment explanation
Indices: 802595--806025 Score: 4332
Period size: 81 Copynumber: 42.8 Consensus size: 80
802585 CATTTAAAAT
* * *
802595 TTCATTTAACTTGCATAA-TGACACATTTATGCCAAATGCACAGCTAGGCCA-TAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACAC-TTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
*
802658 CAACGGTA-TTAACTG
65 CAACGGTATTTAACCG
* * *
802673 TTCATCTAACTAGCATAATTGACACCTTTCTGCCAAATGCACAGTTA-ACCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACA-CTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
802737 CAA-GGTATTTAACCG
65 CAACGGTATTTAACCG
* ** * * *
802752 TTCATATAACTATCATAACTGACACTTTCCTACCAAATGCACATCTAGGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACTTT-CTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
802817 CAACGGTATTTAACCG
65 CAACGGTATTTAACCG
*
802833 TTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCACAGCTAGGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACA-CTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
**
802898 CAACGGTATTTAATTG
65 CAACGGTATTTAACCG
* * * * *
802914 TTCATCTAAATGGCATAATTGAAACATTTCTGCCAAATGCACAGTTAAGCCATTAATCTATTACT
1 TTCATCTAACTGGCATAATTGACAC-TTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
*
802979 CAACGATATTTAACCG
65 CAACGGTATTTAACCG
* * * *
802995 TTCATATAACTGGCATAATTGACACTTTTTTGCAAAATGCACAGCTAGTCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACAC-TTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
*
803060 CAACGGTATTTAACCA
65 CAACGGTATTTAACCG
*
803076 TTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCACAGCTAGGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACA-CTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
* *
803141 CAATGGTATTTAATCG
65 CAACGGTATTTAACCG
* * * *
803157 TTCATCTAACTGGTATAATTGACACCATTCTCCCAAATGCACAGTTAGGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACA-CTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
*
803222 CAACGGTATTTAACCA
65 CAACGGTATTTAACCG
* * *
803238 TTCATCTAACTGGCATAATTGACACCTTACTGCCAAATGCACAGTTAGACCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACA-CTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
* *
803303 CAACGGTATTTAAACA
65 CAACGGTATTTAACCG
* * ** *
803319 TTCATCTAACTGGCATAATTAACACATTTCTACCAAATGCATGGCTAGGCCAATAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACAC-TTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
* * *
803384 CAACGATATTTAATCA
65 CAACGGTATTTAACCG
*
803400 TTCATCTAACTGGCCTAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACA-CTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
*
803465 CAACGGTATTTAACTG
65 CAACGGTATTTAACCG
* *
803481 TTCATCTAACTGGCATAATTGA-TCTTTCTACCAAATGCACAGCTAGGCCATTAATCTTTTACTC
1 TTCATCTAACTGGCATAATTGACACTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTC
*
803545 AACAGTA-TTAACC-
66 AACGGTATTTAACCG
* * * * *
803558 ATCATATAACTGGAATAATTGACACCTTTCCT-CTAAATACACAGCTAGGCCATTAATCTTTTAC
1 TTCATCTAACTGGCATAATTGACA-CTTT-CTGCCAAATGCACAGCTAGGCCATTAATCTTTTAC
* *
803622 TCAACGGTATTTAATCA
64 TCAACGGTATTTAACCG
* *
803639 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTATTTTTTTACT
1 TTCATCTAACTGGCATAATTGACA-CTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
*
803704 CAACGGTATTTAACCA
65 CAACGGTATTTAACCG
* * * *
803720 TTCATCTAACTGGCATAATTGACACATTTCTACCAAATGCATAGCTAGGTCATTAATCATTTACT
1 TTCATCTAACTGGCATAATTGACAC-TTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
*
803785 CAACGGTATTTAACTG
65 CAACGGTATTTAACCG
* * * * * * *
803801 TTAATTTAATTGACATAATTGACACCTTTCTGCCAAATGCTCAACTAGGCTATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACA-CTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
803866 CAACGGTATTTAACCG
65 CAACGGTATTTAACCG
* * *
803882 TTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGTATAGCTAGGCCATTAATATTTTACT
1 TTCATCTAACTGGCATAATTGACAC-TTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
* *
803947 CAACGGTATTTAATCA
65 CAACGGTATTTAACCG
* * * *
803963 TTCATCTAACTGGCATAGTTGACACCTTTCTACAAAATTCACAGCTAGGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACA-CTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
* *
804028 CCACGGTATTTAACTG
65 CAACGGTATTTAACCG
* *
804044 TTCATCTAACTGGCATAATTGACATATTTCTGCCAAATGCATAGCTAAGG-CATTAATCTTTTAC
1 TTCATCTAACTGGCATAATTGACA-CTTTCTGCCAAATGCACAGCT-AGGCCATTAATCTTTTAC
*
804108 TCAATGGTATTTAACCG
64 TCAACGGTATTTAACCG
* * * *
804125 TTCATCTAACTGGTATAATTGATACATTTCTTCCAAATGCACATCTAGGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACAC-TTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
* *
804190 CAACGGTTTTTAACCT
65 CAACGGTATTTAACCG
* *
804206 TTCATCTAACTGGTATAATTGACACCTTTCTAG-CAAATGCATAGCTAGGCCATTAATCTTTTAC
1 TTCATCTAACTGGCATAATTGACA-CTTTCT-GCCAAATGCACAGCTAGGCCATTAATCTTTTAC
** * *
804270 TCAACAATGTTTAACCT
64 TCAACGGTATTTAACCG
** * * * *
804287 TTCATCTAACTACCATAGTTGAAACATTTCTGCCAAATGCACAGTTAAGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACAC-TTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
804352 CAACGGTATTTAACCG
65 CAACGGTATTTAACCG
* * *
804368 TTCATCTAAATGGCATAATTGACACATTTCTACCAAATTCACAGCTAGGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACAC-TTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
*
804433 CAACGGTATTTAACCA
65 CAACGGTATTTAACCG
* *
804449 TTCATCTAACTAGCATAATTGACATATTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACA-CTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
* *
804514 CAATGGTATTTAACTG
65 CAACGGTATTTAACCG
* * *
804530 TTCATCTAATTGGCATAATTGACACATTTCTTCCAAATGCACATCTAGGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACAC-TTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
*
804595 CAACGGTTTTTAACCG
65 CAACGGTATTTAACCG
* *
804611 TTCATCTAACTGGCATAATTGACACATTTCTGCCAAATTCACAGCTAGGCCATTAATATTTTACT
1 TTCATCTAACTGGCATAATTGACAC-TTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
*
804676 CAATGGTATTTAACCG
65 CAACGGTATTTAACCG
* *
804692 TTCATCTAACTGGCATAATTGACACCTTTCTGCTAGATGCA-A-CTAGGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACA-CTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
*
804755 CAACGGTATTTAATCG
65 CAACGGTATTTAACCG
* * * * *
804771 TTGATCTAACTAGCATAATTGACACCTTTCTGCCAAATGGAGATCTAGGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACA-CTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
804836 CAACGGTATTTAACCG
65 CAACGGTATTTAACCG
*
804852 TTCATCTAACTGGCATAATTGACACATTTCTACCAAATGCACAGCTAGGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACAC-TTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
*
804917 CAACGGTATTTAATCG
65 CAACGGTATTTAACCG
* * * *
804933 TTCATCTAACTGGCATAATTGAAATATTTCTGCCAAATGCACAGTTAAGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACA-CTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
* *
804998 CAACGATATTTAATCG
65 CAACGGTATTTAACCG
* * * *
805014 TTCATATAACTGGAATAATTGACACCTTTCTGCAAAATGCACAACTAGGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACA-CTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
* *
805079 CAATGGTATTTAACTG
65 CAACGGTATTTAACCG
* * * *
805095 TTCATCTAACTGGCATAACTGACACCTTTCTACTAAATACACAGCTAGGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACA-CTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
* *
805160 CAACGGTAGTTAATCG
65 CAACGGTATTTAACCG
* * * *
805176 TTCATCTAACTGGTATAATTGACATATTTCTCCCAAATGCACAGTTAGGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACA-CTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
*
805241 CAACGGTATCTAACCG
65 CAACGGTATTTAACCG
* * *
805257 TTCATCTAACTGGCATAATTGACACCTTACTACCAAATGCACAGCTAGGCCATTAATATTTTACT
1 TTCATCTAACTGGCATAATTGACA-CTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
* * *
805322 CAAAGTTATTTAACCA
65 CAACGGTATTTAACCG
* **
805338 TTCATCTAACTGGCATAATTGACACATTTCTACCAAATGCATGGCTAGGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACAC-TTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
805403 CAACGGTATTTAACCG
65 CAACGGTATTTAACCG
* * * *
805419 TTCATCTAACTGGTATAATTGACA-TATTTTGCCAAATGCACAACTAGGCCGTTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACT-TTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
*
805483 CAATGGTATTTAACCG
65 CAACGGTATTTAACCG
* * ** *
805499 TTCATCAAACTGACCAT-A---A-A-TTTCAACCAAATGCACTGCTAGGCCATTAATCTTTTACT
1 TTCATCTAACTG-GCATAATTGACACTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
*
805558 CAA-TGTA-TT-ACTCG
65 CAACGGTATTTAAC-CG
*
805572 TTCATCT-ACTGGCATAATTGACACATTTCTGCC-AATGCACAACTAGGCCA-TAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACAC-TTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
* *
805634 CAATGGTA-TTAATCG
65 CAACGGTATTTAACCG
* * * *
805649 TTCATCTAATTGGCATAATTG-CATCTTTCTTCCAAATGCACGGCTTGGCCATTAATC-TTTACT
1 TTCATCTAACTGGCATAATTGACA-CTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
*
805712 CAACGGTATTTAACCA
65 CAACGGTATTTAACCG
* * ** *
805728 TTCATATATAACTGG-A-AATTGACACATTTCTGCCAAATGCATAGCTAGGCGTTTAAGCTTTTA
1 TTC--ATCTAACTGGCATAATTGACAC-TTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTA
*
805791 C-CAACGGTATTT-ACAG
63 CTCAACGGTATTTAACCG
* *
805807 TTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCACAGTTAGACCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACAC-TTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
805872 CAAC-GTA-TTAACCG
65 CAACGGTATTTAACCG
* * * * * *
805886 TTCA--TAACTTGCATTATTG-CACCTTTCT-TCTAATGCACAACTAGGCCATTAATATTTTACT
1 TTCATCTAACTGGCATAATTGACA-CTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
*
805947 CAACGATA-TTAACCG
65 CAACGGTATTTAACCG
* * * *
805962 TTCATCTAACTGGTATAATTGACACCTTTCTGTCAAATGCAGAGCTAGGCCGTTAATCTTTTAC
1 TTCATCTAACTGGCATAATTGACA-CTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTAC
806026 ATTATAACTA
Statistics
Matches: 2919, Mismatches: 365, Indels: 136
0.85 0.11 0.04
Matches are distributed among these distances:
71 3 0.00
72 7 0.00
73 10 0.00
74 3 0.00
75 67 0.02
76 38 0.01
77 81 0.03
78 94 0.03
79 325 0.11
80 171 0.06
81 2107 0.72
82 13 0.00
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (80 bp):
TTCATCTAACTGGCATAATTGACACTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTC
AACGGTATTTAACCG
Found at i:807645 original size:20 final size:20
Alignment explanation
Indices: 807622--807677 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
807612 CCCTAACTGA
*
807622 GGTATAGATACCCTGTCTAT
1 GGTATAGATACCCTGCCTAT
*
807642 GGTATAGATACCCTGCCTCT
1 GGTATAGATACCCTGCCTAT
807662 GGTATAGATACCCTGC
1 GGTATAGATACCCTGC
807678 TAACATTCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.30
Consensus pattern (20 bp):
GGTATAGATACCCTGCCTAT
Found at i:807732 original size:66 final size:66
Alignment explanation
Indices: 807662--807809 Score: 167
Period size: 66 Copynumber: 2.2 Consensus size: 66
807652 CCCTGCCTCT
* *
807662 GGTATAGATACCCTGCTAACATTCTGGAAATTTTCATCTTCAAG-GG-GGTATCGATACACCCT-
1 GGTATCGATACCCTACTAACATTCTGGAAATTTTCAT-TT-AAGAGGAGGTATCGATAC-CCCTA
807724 ATAG
63 ATAG
* * * * *
807728 GGTATCGATACCATATTGACATTCTGTAATTTTTCATTTAAGAGGAGGTATCGATACCCCTACAT
1 GGTATCGATACCCTACTAACATTCTGGAAATTTTCATTTAAGAGGAGGTATCGATACCCCTA-AT
*
807793 AT
65 AG
807795 GGTATCGATACCCTA
1 GGTATCGATACCCTA
807810 TGACCAAAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
64 3 0.04
65 8 0.12
66 41 0.59
67 17 0.25
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (66 bp):
GGTATCGATACCCTACTAACATTCTGGAAATTTTCATTTAAGAGGAGGTATCGATACCCCTAATA
G
Found at i:813797 original size:22 final size:22
Alignment explanation
Indices: 813724--813799 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
813714 GGACCACTAT
*
813724 GTCCCGAATGACCA-TGGATAC
1 GTCCCGAAGGACCACTGGATAC
*
813745 ATCCC-AAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
* ** *
813766 GTTCTTAAGGACCACTGGATAT
1 GTCCCGAAGGACCACTGGATAC
813788 GTCCCGAAGGAC
1 GTCCCGAAGGAC
813800 TACTAAAACC
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
20 7 0.16
21 13 0.30
22 24 0.55
ACGTcount: A:0.29, C:0.28, G:0.24, T:0.20
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGGATAC
Found at i:814347 original size:20 final size:20
Alignment explanation
Indices: 814322--814373 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
814312 CGCTAACTGA
*
814322 GGTATAGATACCCTGTCTAT
1 GGTATAGATACCCTGCCTAT
814342 GGTATAGATACCCTGCCTAT
1 GGTATAGATACCCTGCCTAT
*
814362 GTTATAGATACC
1 GGTATAGATACC
814374 TTGCTAACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (20 bp):
GGTATAGATACCCTGCCTAT
Found at i:815577 original size:20 final size:21
Alignment explanation
Indices: 815549--815600 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 21
815539 GTTAACAATG
* *
815549 GTATTGATACCAT-CTTCGTA
1 GTATCGATACCATGCCTCGTA
* *
815569 GTATCGATA-CATGCCTCTTG
1 GTATCGATACCATGCCTCGTA
815589 GTATCGATACCA
1 GTATCGATACCA
815601 CTGAATCGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 3 0.12
20 21 0.81
21 2 0.08
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (21 bp):
GTATCGATACCATGCCTCGTA
Found at i:825534 original size:22 final size:22
Alignment explanation
Indices: 825508--825591 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 22
825498 TTAGTGCAGA
*
825508 GGGAATAGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
* *
825530 GGGAA-CTGATTCCCCCTTTGAAA
1 GGGAATC-GATACCCCC-TTGAAG
* * * *
825553 GGGAACCGATTCCCCCCTGTAG
1 GGGAATCGATACCCCCTTGAAG
825575 GGGAATCGATACCCCCT
1 GGGAATCGATACCCCCT
825592 GGAGGTTTTG
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
22 30 0.60
23 19 0.38
24 1 0.02
ACGTcount: A:0.25, C:0.30, G:0.25, T:0.20
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:825570 original size:24 final size:23
Alignment explanation
Indices: 825519--825568 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
825509 GGAATAGATA
* *
825519 CCCCC-TTGAAGGGGAACTGATT
1 CCCCCTTTGAAAGGGAACCGATT
825541 CCCCCTTTGAAAGGGAACCGATT
1 CCCCCTTTGAAAGGGAACCGATT
825564 CCCCC
1 CCCCC
825569 CTGTAGGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 5 0.20
23 20 0.80
ACGTcount: A:0.22, C:0.36, G:0.22, T:0.20
Consensus pattern (23 bp):
CCCCCTTTGAAAGGGAACCGATT
Found at i:825980 original size:9 final size:10
Alignment explanation
Indices: 825948--825974 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
825938 AAAACACAAG
825948 AATTTTTCAA
1 AATTTTTCAA
825958 AATTTTTCAA
1 AATTTTTCAA
825968 AATTTTT
1 AATTTTT
825975 GAAATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (10 bp):
AATTTTTCAA
Found at i:827171 original size:18 final size:18
Alignment explanation
Indices: 827150--827189 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
827140 CGACGATGAG
827150 CAAGAACAA-CACGAGGAA
1 CAAGAACAACCA-GAGGAA
*
827168 CAAGCACAACCAGAGGAA
1 CAAGAACAACCAGAGGAA
827186 CAAG
1 CAAG
827190 TACAGCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.53, C:0.25, G:0.23, T:0.00
Consensus pattern (18 bp):
CAAGAACAACCAGAGGAA
Found at i:833184 original size:37 final size:36
Alignment explanation
Indices: 833143--833214 Score: 126
Period size: 37 Copynumber: 2.0 Consensus size: 36
833133 GAAAAAGCCC
*
833143 GAGTGCATCGATGCATGGTTTTGTGCATCGATGCATT
1 GAGTGCATCGATGCATGG-TATGTGCATCGATGCATT
833180 GAGTGCATCGATGCATGGTATGTGCATCGATGCAT
1 GAGTGCATCGATGCATGGTATGTGCATCGATGCAT
833215 AAAATGCATT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 16 0.47
37 18 0.53
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.32
Consensus pattern (36 bp):
GAGTGCATCGATGCATGGTATGTGCATCGATGCATT
Found at i:833187 original size:17 final size:19
Alignment explanation
Indices: 833145--833214 Score: 99
Period size: 17 Copynumber: 3.7 Consensus size: 19
833135 AAAAGCCCGA
*
833145 GTGCATCGATGCATGGTTTT
1 GTGCATCGATGCATGG-TAT
*
833165 GTGCATCGATGCATTG-A-
1 GTGCATCGATGCATGGTAT
833182 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATGGTAT
833201 GTGCATCGATGCAT
1 GTGCATCGATGCAT
833215 AAAATGCATT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
17 15 0.33
18 1 0.02
19 14 0.31
20 15 0.33
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.33
Consensus pattern (19 bp):
GTGCATCGATGCATGGTAT
Found at i:833228 original size:37 final size:37
Alignment explanation
Indices: 833146--833229 Score: 116
Period size: 36 Copynumber: 2.3 Consensus size: 37
833136 AAAGCCCGAG
* ** *
833146 TGCATCGATGCATGGTTTTGTGCATCGATGCATTGAG
1 TGCATCGATGCATGGTTATGTGCATCGATGCATAAAA
833183 TGCATCGATGCATGG-TATGTGCATCGATGCATAAAA
1 TGCATCGATGCATGGTTATGTGCATCGATGCATAAAA
833219 TGCATTCGATG
1 TGCA-TCGATG
833230 TTTGAAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 21 0.50
37 21 0.50
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (37 bp):
TGCATCGATGCATGGTTATGTGCATCGATGCATAAAA
Found at i:833266 original size:20 final size:20
Alignment explanation
Indices: 833241--833279 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
833231 TTGAAAAATT
833241 AATTGGTGCATCGATGCATG
1 AATTGGTGCATCGATGCATG
*
833261 AATTGGTGCATCGGTGCAT
1 AATTGGTGCATCGATGCAT
833280 CACTTTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (20 bp):
AATTGGTGCATCGATGCATG
Found at i:834365 original size:19 final size:20
Alignment explanation
Indices: 834326--834367 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
834316 ACAAAAAGGT
*
834326 AATATCGGTACTACCATATGA
1 AATATCGATACTA-CATATGA
834347 AATATCGATACTA-ATATGA
1 AATATCGATACTACATATGA
834366 AA
1 AA
834368 AGTAGTATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
21 12 0.60
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (20 bp):
AATATCGATACTACATATGA
Found at i:835204 original size:5 final size:5
Alignment explanation
Indices: 835196--835224 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
835186 GTATATATTA
835196 TAATC TAATC TAATC TAATC TAATC TAAT
1 TAATC TAATC TAATC TAATC TAATC TAAT
835225 TATTTTATTT
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:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATC
Found at i:835237 original size:15 final size:15
Alignment explanation
Indices: 835219--835257 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
835209 TCTAATCTAA
835219 TCTAATTATTTTATT
1 TCTAATTATTTTATT
*
835234 TCTATTTA-TTTATT
1 TCTAATTATTTTATT
*
835248 TATAATTATT
1 TCTAATTATT
835258 ATGTCTCCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TCTAATTATTTTATT
Found at i:837335 original size:30 final size:29
Alignment explanation
Indices: 837248--837335 Score: 88
Period size: 29 Copynumber: 3.0 Consensus size: 29
837238 ATCTTTAATC
* *
837248 TTATTTTTGTCTTAACTTGTTAAATATATT
1 TTATTTTTATCTTAA-TTATTAAATATATT
* *
837278 TTATTTTTATTTTAA-TATAAAAATATATT
1 TTATTTTTATCTTAATTAT-TAAATATATT
* *
837307 TTATTCTTATCTTAATTTTTATAATATAT
1 TTATTTTTATCTTAATTATTA-AATATAT
837336 ATATATTTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
28 2 0.04
29 23 0.49
30 22 0.47
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (29 bp):
TTATTTTTATCTTAATTATTAAATATATT
Found at i:837645 original size:29 final size:29
Alignment explanation
Indices: 837595--837670 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
837585 TTTTTTAAAG
* *
837595 GTTAAGATAAGAATCAAATATATTTTGTAA
1 GTTAAGATAAGAATAAAATATACTTT-TAA
*
837625 GTTAAGA-AATAATAAAATATACTTTTAA
1 GTTAAGATAAGAATAAAATATACTTTTAA
*
837653 GTGAAGATAA-AATTAAAA
1 GTTAAGATAAGAA-TAAAA
837671 CATATATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 11 0.28
29 22 0.55
30 7 0.17
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.33
Consensus pattern (29 bp):
GTTAAGATAAGAATAAAATATACTTTTAA
Found at i:837682 original size:31 final size:28
Alignment explanation
Indices: 837610--837682 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 28
837600 GATAAGAATC
*
837610 AAATATATTTTGTAAGTTAAGAAATAATA
1 AAATATATTTT-TAAGTGAAGAAATAATA
*
837639 AAATATACTTTTAAGTGAAGATAA-AATTAA
1 AAATATATTTTTAAGTGAAGA-AATAA-T-A
837669 AACATATATTTTTA
1 AA-ATATATTTTTA
837683 TATTAAAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 11 0.30
29 13 0.35
30 3 0.08
31 10 0.27
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (28 bp):
AAATATATTTTTAAGTGAAGAAATAATA
Found at i:840912 original size:29 final size:28
Alignment explanation
Indices: 840852--840918 Score: 71
Period size: 29 Copynumber: 2.4 Consensus size: 28
840842 TTTAATGTAT
* *
840852 TAAATTTAGTGAGAAAATTAAAAAAAAT
1 TAAATTTAGTGAGAAAAATAAAAAAAAG
* * *
840880 TAAATTTTAGTGAGAAAAATATAAGAGAG
1 TAAA-TTTAGTGAGAAAAATAAAAAAAAG
*
840909 TAAAATTAGT
1 TAAATTTAGT
840919 AAAGAAAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 9 0.28
29 23 0.72
ACGTcount: A:0.55, C:0.00, G:0.15, T:0.30
Consensus pattern (28 bp):
TAAATTTAGTGAGAAAAATAAAAAAAAG
Found at i:849475 original size:2 final size:2
Alignment explanation
Indices: 849431--849460 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
849421 CCATCAATTA
849431 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
849461 TTGAGTATGA
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:851179 original size:19 final size:19
Alignment explanation
Indices: 851150--851196 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
851140 GGGCAAAAAA
851150 TATTAATTATTAATTATTAT
1 TATT-ATTATTAATTATTAT
*
851170 TATTATTATTATTTATTAT
1 TATTATTATTAATTATTAT
*
851189 TAATATTA
1 TATTATTA
851197 ATTGATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 21 0.84
20 4 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTATTATTAATTATTAT
Found at i:851205 original size:19 final size:18
Alignment explanation
Indices: 851150--851208 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 18
851140 GGGCAAAAAA
851150 TATTAATTATTAATTATTAT
1 TATTAA-TATTAATTA-TAT
*
851170 TATTATTATT-ATT-TAT
1 TATTAATATTAATTATAT
851186 TATTAATATTAATTGATAT
1 TATTAATATTAATT-ATAT
851205 TATT
1 TATT
851209 TTACATGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
16 12 0.35
17 3 0.09
18 3 0.09
19 11 0.32
20 5 0.15
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
TATTAATATTAATTATAT
Found at i:851208 original size:3 final size:3
Alignment explanation
Indices: 851150--851196 Score: 58
Period size: 3 Copynumber: 14.7 Consensus size: 3
851140 GGGCAAAAAA
*
851150 TAT TAAT TAT TAAT TAT TAT TAT TAT TAT TATT TAT TAT TAA TAT TA
1 TAT T-AT TAT T-AT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TA
851197 ATTGATATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
3 30 0.77
4 9 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:853653 original size:30 final size:30
Alignment explanation
Indices: 853617--853688 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
853607 CCCGAAGGAC
*
853617 CTATCCAGAGGTCATAAAGATCATCGGTAA
1 CTATCCAGAGGTCATAAAGATCATCGGCAA
*
853647 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCATAAAGATCATCGGCAA
* *
853677 CTGTCCATAGGT
1 CTATCCAGAGGT
853689 TTCGAAGAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCATCGGCAA
Found at i:853794 original size:63 final size:62
Alignment explanation
Indices: 853676--853802 Score: 184
Period size: 63 Copynumber: 2.0 Consensus size: 62
853666 ATCCTCGGCA
* * *
853676 ACTGTCCATAGGTTTCGAAGAACCTAGGTAAATTGTCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATAGGTCTCGAAGAACATAGGTAAATTGTCCATATGTTCCGTAGAACATAGGTAT
* *
853738 ACTGTCCATATGTCTCGAA-AGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAT
1 ACTGTCCATAGGTCTCGAAGA-ACATAGGTAAAT-TGTCCATATGTTCCGTAGAACATAGGTAT
853801 AC
1 AC
853803 CCTCGACTCT
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
61 1 0.02
62 27 0.47
63 30 0.52
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (62 bp):
ACTGTCCATAGGTCTCGAAGAACATAGGTAAATTGTCCATATGTTCCGTAGAACATAGGTAT
Found at i:853795 original size:32 final size:32
Alignment explanation
Indices: 853677--853799 Score: 128
Period size: 31 Copynumber: 3.9 Consensus size: 32
853667 TCCTCGGCAA
* * * * *
853677 CTGTCCATAGGTTTCGAAGAACCTAGGTAAAT
1 CTGTCCATATGTTCCGTAGAACATAGGTAATT
* *
853709 -TGTCCATATGTTCCTTAGAACATAGGT-ATA
1 CTGTCCATATGTTCCGTAGAACATAGGTAATT
*
853739 CTGTCCATATG-TCTCG-AAAGACATAGGTAATT
1 CTGTCCATATGTTC-CGTAGA-ACATAGGTAATT
853771 CTGTCCATATGTTCCGTAGAACATAGGTA
1 CTGTCCATATGTTCCGTAGAACATAGGTA
853800 TACCCTCGAC
Statistics
Matches: 74, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
30 5 0.07
31 41 0.55
32 24 0.32
33 4 0.05
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32
Consensus pattern (32 bp):
CTGTCCATATGTTCCGTAGAACATAGGTAATT
Found at i:862971 original size:86 final size:85
Alignment explanation
Indices: 862822--862980 Score: 230
Period size: 86 Copynumber: 1.9 Consensus size: 85
862812 ATATTCGACT
* * *
862822 GAGGATATACCACATGGTTTTCCTGTAAAGGGGAGTCATCTAAAGATTATCTCACTTGGTTCAGA
1 GAGGATATACCACATGGTTTTCCTATAAAGGGGAGTCATCCAAAGATTATCTCACTCGGTTCAGA
862887 CCCACTAAGGGGAACCACCC
66 CCCACTAAGGGGAACCACCC
* * *
862907 GAGGAATATACCACATGGTTTTCCTATGAAGTGGAGTCATCCAAA-ATTCATCTTACTCGGTTCA
1 GAGG-ATATACCACATGGTTTTCCTATAAAGGGGAGTCATCCAAAGATT-ATCTCACTCGGTTCA
*
862971 GACCCGCTAA
64 GACCCACTAA
862981 TCACCTGAGG
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
85 7 0.11
86 58 0.89
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (85 bp):
GAGGATATACCACATGGTTTTCCTATAAAGGGGAGTCATCCAAAGATTATCTCACTCGGTTCAGA
CCCACTAAGGGGAACCACCC
Found at i:863053 original size:80 final size:80
Alignment explanation
Indices: 862822--863009 Score: 200
Period size: 86 Copynumber: 2.3 Consensus size: 80
862812 ATATTCGACT
* * * * * *
862822 GAGG-ATATACCACATGGTTTTCCTGTAAAGGGGAGTCATCTAAAGATT-ATCTCACTTGGTTCA
1 GAGGAATATACCACATGGTTTTCCTATGAAGTGGAGTCATCCAAA-ATTAATCTTACTCGGTTCA
* *
862885 GACCCACTAAGGGGAACCACCC
65 GACCCGCT------AATCACCC
*
862907 GAGGAATATACCACATGGTTTTCCTATGAAGTGGAGTCATCCAAAATTCATCTTACTCGGTTCAG
1 GAGGAATATACCACATGGTTTTCCTATGAAGTGGAGTCATCCAAAATTAATCTTACTCGGTTCAG
*
862972 ACCCGCTAATCACCT
66 ACCCGCTAATCACCC
*
862987 GAGGAATATACTACATGGTTTTC
1 GAGGAATATACCACATGGTTTTC
863010 TCGTGAATGG
Statistics
Matches: 91, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
80 28 0.31
85 7 0.08
86 56 0.62
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (80 bp):
GAGGAATATACCACATGGTTTTCCTATGAAGTGGAGTCATCCAAAATTAATCTTACTCGGTTCAG
ACCCGCTAATCACCC
Found at i:863466 original size:85 final size:85
Alignment explanation
Indices: 863143--863471 Score: 322
Period size: 85 Copynumber: 3.9 Consensus size: 85
863133 TTAGTAGAAA
* * * *
863143 AACTCAAGACGAGAAGAGTTATCTGTCATCCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAG
1 AACTCAAGGCGAGAAGAGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTC-AAG
*
863208 G-CACATCAAATTTACAGCAT
65 GACATATCAAATTTACAGCAT
* * * * *
863228 AACTCAAGGCGAGAAAAGTTATCTGTCAGCAAGAGACCTTTGAGTTCGATTCCATTTAGCTCAAG
1 AACTCAAGGCGAGAAGAGTTATCTGTCAACAA-AGACCTTCGAGTTCGATTACATTCAGCTCAAG
* **
863293 GACA-ACCAAATGCACAGCAT
65 GACATATCAAATTTACAGCAT
* * * * * * * *
863313 AGCTTAAGGCAAGAAGGGTCATCTGTCAACACAA-ACCTTCGAGTTTGATTACATTCAGTTCCAG
1 AACTCAAGGCGAGAAGAGTTATCTGTCAACA-AAGACCTTCGAGTTCGATTACATTCAGCTCAAG
* * *
863377 GACATGTCAAGTTTATAGCAT
65 GACATATCAAATTTACAGCAT
* * * * * * * *
863398 AACTCAAGGCGAGAAGGGTTATCTGTCAACAAACACCTTCAAGTTTGATTCCATTCAACTCGATG
1 AACTCAAGGCGAGAAGAGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAGG
863463 ACATATCAA
66 ACATATCAA
863472 CTACATGGTA
Statistics
Matches: 198, Mismatches: 41, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
84 30 0.15
85 140 0.71
86 28 0.14
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.25
Consensus pattern (85 bp):
AACTCAAGGCGAGAAGAGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAGG
ACATATCAAATTTACAGCAT
Found at i:864230 original size:46 final size:46
Alignment explanation
Indices: 864036--864333 Score: 199
Period size: 46 Copynumber: 6.6 Consensus size: 46
864026 CCAGCCTTCC
* **
864036 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTATGAGTCGTGTTATCACCTTTAGATGGCCAGAACTCT
* * * * * * *
864082 TAATCACGTATGAGCCGTGTCATCACC---CGA---CCTGATCTCC
1 TCATCACGTATGAGTCGTGTTATCACCTTTAGATGGCCAGAACTCT
* * * * * *
864122 TCATCACGTAGGAGTTGTGTCA--ACCTTT-GA-GAACCAG-CCGTCC
1 TCATCACGTATGAGTCGTGTTATCACCTTTAGATG-GCCAGAAC-TCT
* * **
864165 TCATCACATAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTATGAGTCGTGTTATCACCTTTAGATGGCCAGAACTCT
* * * **
864211 TCATTACATATGAGTCGTGTATGTGTCAATCC-TT-GATAACCAGAACTCT
1 TCATCACGTATGAGTCGTG--T-TATC-A-CCTTTAGATGGCCAGAACTCT
*
864260 TCATCACGTATGAGTCGTGTTATCACCTTTAGATGGCCATAACTCT
1 TCATCACGTATGAGTCGTGTTATCACCTTTAGATGGCCAGAACTCT
*
864306 TCATCACGTATGAGTCGTGTCATCACCT
1 TCATCACGTATGAGTCGTGTTATCACCT
864334 GACTTGATCT
Statistics
Matches: 197, Mismatches: 36, Indels: 38
0.73 0.13 0.14
Matches are distributed among these distances:
38 3 0.02
40 27 0.14
42 1 0.01
43 25 0.13
44 2 0.01
45 9 0.05
46 88 0.45
47 3 0.02
48 1 0.01
49 33 0.17
50 3 0.02
51 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (46 bp):
TCATCACGTATGAGTCGTGTTATCACCTTTAGATGGCCAGAACTCT
Found at i:864487 original size:40 final size:40
Alignment explanation
Indices: 864432--864527 Score: 122
Period size: 40 Copynumber: 2.4 Consensus size: 40
864422 TGGCCTGCCG
* * * *
864432 TCCTCAACACGTAGGAACCGTGTCATTTCCC-GACCTGATT
1 TCCTCATCACGTAGGAACCGTGTCA-ATCCCTGACCAGATC
*
864472 TCCTCATCACGTAGGAACTGTGTCAATCCCTGACCAGATC
1 TCCTCATCACGTAGGAACCGTGTCAATCCCTGACCAGATC
*
864512 TCCTCATCATGTAGGA
1 TCCTCATCACGTAGGA
864528 GTTGTGTCAC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
39 4 0.08
40 45 0.92
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (40 bp):
TCCTCATCACGTAGGAACCGTGTCAATCCCTGACCAGATC
Found at i:864744 original size:7 final size:7
Alignment explanation
Indices: 864732--864775 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
864722 CGAGAAAAAA
864732 TATTAAT
1 TATTAAT
864739 TATTAAT
1 TATTAAT
864746 TATTAAT
1 TATTAAT
864753 TATT-AT
1 TATTAAT
864759 TATT-AT
1 TATTAAT
*
864765 TATTATT
1 TATTAAT
864772 TATT
1 TATT
864776 GTTAATATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
6 12 0.34
7 23 0.66
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TATTAAT
Found at i:864750 original size:3 final size:3
Alignment explanation
Indices: 864732--864785 Score: 54
Period size: 3 Copynumber: 16.7 Consensus size: 3
864722 CGAGAAAAAA
* *
864732 TAT TAAT TAT TAAT TAT TAAT TAT TAT TAT TAT TAT TATT TAT TGT TAA
1 TAT T-AT TAT T-AT TAT T-AT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
864781 TAT TA
1 TAT TA
864786 ATTGATATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
3 31 0.72
4 12 0.28
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:864768 original size:19 final size:19
Alignment explanation
Indices: 864732--864785 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
864722 CGAGAAAAAA
864732 TATTAATTATTAATTATTAAT
1 TATT-ATTATT-ATTATTAAT
*
864753 TATTATTATTATTATTATT
1 TATTATTATTATTATTAAT
* *
864772 TATTGTTAATATTA
1 TATTATTATTATTA
864786 ATTGATATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 20 0.67
20 6 0.20
21 4 0.13
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
TATTATTATTATTATTAAT
Found at i:864794 original size:29 final size:28
Alignment explanation
Indices: 864737--864796 Score: 51
Period size: 26 Copynumber: 2.3 Consensus size: 28
864727 AAAAATATTA
864737 ATTATTA-ATTATTAATT-ATTATT-ATT
1 ATTATTATATTATT-ATTAATTATTAATT
*
864763 ATTATTAT-TTATTGTTAA-TATTAATT
1 ATTATTATATTATTATTAATTATTAATT
864789 GA-TATTAT
1 -ATTATTAT
864797 TTTACATGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
25 6 0.21
26 22 0.76
27 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (28 bp):
ATTATTATATTATTATTAATTATTAATT
Found at i:864797 original size:29 final size:28
Alignment explanation
Indices: 864731--864797 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
864721 CCGAGAAAAA
864731 ATATTAATTATTAATTATTAATTATTATT
1 ATATT-ATTATTAATTATTAATTATTATT
* *
864760 ATTATTATTATTTATTGTTAA-TATTAATT
1 A-TATTATTATTAATTATTAATTATT-ATT
864789 GATATTATT
1 -ATATTATT
864798 TTACATGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 4 0.12
29 24 0.73
30 5 0.15
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (28 bp):
ATATTATTATTAATTATTAATTATTATT
Found at i:875046 original size:34 final size:30
Alignment explanation
Indices: 875008--875076 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
874998 TTGATATAAC
*
875008 AATTTAAGGCAAAATGGTTTTTGGACTTAAATTG
1 AATTTAA--CAAAAT-GTATTTGGACTT-AATTG
875042 AATTT-ACAAAATGTATTTGGACTTAATTG
1 AATTTAACAAAATGTATTTGGACTTAATTG
875071 AATTTA
1 AATTTA
875077 TTCAAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 11 0.33
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.41
Consensus pattern (30 bp):
AATTTAACAAAATGTATTTGGACTTAATTG
Found at i:875084 original size:31 final size:31
Alignment explanation
Indices: 875017--875076 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
875007 CAATTTAAGG
*
875017 CAAAATGGTTTTTGGACTTAAATTGAATTTA
1 CAAAATGGTATTTGGACTTAAATTGAATTTA
875048 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTAAATTGAATTTA
875077 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTAAATTGAATTTA
Found at i:875168 original size:19 final size:19
Alignment explanation
Indices: 875141--875207 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
875131 AATGTTTTTA
*
875141 TGAATAGTAATTTACTATT
1 TGAACAGTAATTTACTATT
875160 TGAACAGT-ATATTACTATT
1 TGAACAGTAAT-TTACTATT
* * * *
875179 TGACCAGTAAATCACTGTT
1 TGAACAGTAATTTACTATT
875198 TGAACAGTAA
1 TGAACAGTAA
875208 CCGAGGCTCA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
18 2 0.05
19 37 0.93
20 1 0.03
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.37
Consensus pattern (19 bp):
TGAACAGTAATTTACTATT
Found at i:875336 original size:21 final size:21
Alignment explanation
Indices: 875312--875353 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
875302 ATTTGAATAT
**
875312 TATGAAGGGGTATTGATTCCC
1 TATGAAGGGGTACCGATTCCC
875333 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
875354 CCCATTCTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:880976 original size:39 final size:38
Alignment explanation
Indices: 880885--880979 Score: 129
Period size: 38 Copynumber: 2.5 Consensus size: 38
880875 CTTTATTTTA
** *
880885 GTCGGGTCGGATC-AATTTTTTTAAGTGTGATATTCGG
1 GTCGGGTCGGATCGGGTTTTTTTAAGTGTGATATTCAG
880922 GTCGGGTCGGATCGGGTTTTTTTAAGTGTGATATTCAG
1 GTCGGGTCGGATCGGGTTTTTTTAAGTGTGATATTCAG
* *
880960 GTTGGGTTGGATTCGGGTTT
1 GTCGGGTCGGA-TCGGGTTT
880980 AGGGTGAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
37 13 0.25
38 30 0.59
39 8 0.16
ACGTcount: A:0.15, C:0.09, G:0.35, T:0.41
Consensus pattern (38 bp):
GTCGGGTCGGATCGGGTTTTTTTAAGTGTGATATTCAG
Found at i:882570 original size:22 final size:23
Alignment explanation
Indices: 882532--882582 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 23
882522 CTCTTTTTCT
*
882532 ATTTAGGTGCTTTTTTTTGGTTA
1 ATTTAGGTGCTTTTTTTTGGTCA
*
882555 ATTTAGGTG-TTTTTTTTTGTCA
1 ATTTAGGTGCTTTTTTTTGGTCA
882577 ATTTAG
1 ATTTAG
882583 ATGTCTAACG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 17 0.65
23 9 0.35
ACGTcount: A:0.16, C:0.04, G:0.20, T:0.61
Consensus pattern (23 bp):
ATTTAGGTGCTTTTTTTTGGTCA
Done.