Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012559.1 Kokia drynarioides strain JFW-HI SEQ_127568, 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: 64511
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:68 original size:45 final size:45
Alignment explanation
Indices: 1--777 Score: 851
Period size: 45 Copynumber: 17.2 Consensus size: 45
*
1 ATTATGCTATACGATATGCATGATATGGTCAATATTATTCGATTG
1 ATTATGCTATACGATATGCATGATATGGTAAATATTATTCGATTG
* * ** * *
46 ATTATGTTATACTATACACATGATATGGTAAATTTTATTTGATTG
1 ATTATGCTATACGATATGCATGATATGGTAAATATTATTCGATTG
* * * * *
91 ATTGTGCTACATGATAAGCATGATATGGTAATTATTATGT-GATTTG
1 ATTATGCTATACGATATGCATGATATGGTAAATATTAT-TCGA-TTG
* * * *
137 -TTATGTTATACGATATGAATGATATGGTAATTATTATTCGGTTG
1 ATTATGCTATACGATATGCATGATATGGTAAATATTATTCGATTG
* ** * *
181 ACTATGCTAT-CTGATACACATGATATAGTAAATATTATTTGATTG
1 ATTATGCTATAC-GATATGCATGATATGGTAAATATTATTCGATTG
* * * *
226 ATTATTCTATATGATATGCATGATATGATAAATATT-CTCTGATTG
1 ATTATGCTATACGATATGCATGATATGGTAAATATTATTC-GATTG
* * * *
271 ATTATGCTAAACGGTAGGTATGATATGGTAAATATTATTCGATTG
1 ATTATGCTATACGATATGCATGATATGGTAAATATTATTCGATTG
* * *
316 ATTATGTTATACGATATGCATGATACGCTAAATATTATTCGATTG
1 ATTATGCTATACGATATGCATGATATGGTAAATATTATTCGATTG
** * * *
361 ATTATGCTATACGATGCGCATGATATAGTAAATATTATTTGATTA
1 ATTATGCTATACGATATGCATGATATGGTAAATATTATTCGATTG
* * * ***
406 ATTATGTTATACGATACGCATGATATGGTAAATTTTATTTTTTTG
1 ATTATGCTATACGATATGCATGATATGGTAAATATTATTCGATTG
* * * * * *
451 ATTATGCTACACGATATGCATAATATGGCAATTATTATTCAATTC
1 ATTATGCTATACGATATGCATGATATGGTAAATATTATTCGATTG
* * *
496 ATTATGTTATACGATATGCATGATATGGTAATTATTATTCGACTG
1 ATTATGCTATACGATATGCATGATATGGTAAATATTATTCGATTG
* * * *
541 ACTATGTTATATATGATACGCATGATATGGTAAATATTATTCGATTG
1 ATTATG--CTATACGATATGCATGATATGGTAAATATTATTCGATTG
* * * *
588 AGTATGCTACATGATATGCATGATATGGTAAATATTATTCGGTTG
1 ATTATGCTATACGATATGCATGATATGGTAAATATTATTCGATTG
* * * *
633 ATCATTCTATACGATATGCATGATATGATAAATATTATTTGATTG
1 ATTATGCTATACGATATGCATGATATGGTAAATATTATTCGATTG
* *
678 ATTATGCTATACGATACGCATGATATGGTAAATATTATTTGATTG
1 ATTATGCTATACGATATGCATGATATGGTAAATATTATTCGATTG
* * *
723 ATTACGCTATACGATATGCATGAAATGGTAAATATTATTTGATTG
1 ATTATGCTATACGATATGCATGATATGGTAAATATTATTCGATTG
768 ATTATGCTAT
1 ATTATGCTAT
778 TTGATTAATT
Statistics
Matches: 606, Mismatches: 116, Indels: 20
0.82 0.16 0.03
Matches are distributed among these distances:
44 6 0.01
45 555 0.92
46 6 0.01
47 39 0.06
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (45 bp):
ATTATGCTATACGATATGCATGATATGGTAAATATTATTCGATTG
Found at i:546 original size:24 final size:23
Alignment explanation
Indices: 516--628 Score: 65
Period size: 24 Copynumber: 4.9 Consensus size: 23
506 ACGATATGCA
516 TGATATGGTAATTATTATTCGAC
1 TGATATGGTAATTATTATTCGAC
* * *
539 TGACTAT-GTTATATATGATACG-C
1 TGA-TATGGTAAT-TATTATTCGAC
* *
562 ATGATATGGTAAATATTATTCGAT
1 -TGATATGGTAATTATTATTCGAC
* * *
586 TGAGTATGCTACATGA-TATGC-A-
1 TGA-TATGGTA-ATTATTATTCGAC
*
608 TGATATGGTAAATATTATTCG
1 TGATATGGTAATTATTATTCG
629 GTTGATCATT
Statistics
Matches: 65, Mismatches: 16, Indels: 19
0.65 0.16 0.19
Matches are distributed among these distances:
20 2 0.03
21 10 0.15
22 3 0.05
23 22 0.34
24 26 0.40
25 2 0.03
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.40
Consensus pattern (23 bp):
TGATATGGTAATTATTATTCGAC
Found at i:780 original size:17 final size:17
Alignment explanation
Indices: 758--799 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
748 TGGTAAATAT
*
758 TATTTGATTGATTATGC
1 TATTTGATTAATTATGC
775 TATTTGATTAATTATGC
1 TATTTGATTAATTATGC
*
792 TATATGAT
1 TATTTGAT
800 ATGCACGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.52
Consensus pattern (17 bp):
TATTTGATTAATTATGC
Found at i:794 original size:62 final size:62
Alignment explanation
Indices: 713--831 Score: 184
Period size: 62 Copynumber: 1.9 Consensus size: 62
703 TGGTAAATAT
* * *
713 TATTTGATTGATTACGCTATACGATATGCATGAAATGGTAAATATTATTTGATTGATTATGC
1 TATTTGATTAATTACGCTATACGATATGCACGAAATGGCAAATATTATTTGATTGATTATGC
* * *
775 TATTTGATTAATTATGCTATATGATATGCACGATATGGCAAATATTATTTGATTGAT
1 TATTTGATTAATTACGCTATACGATATGCACGAAATGGCAAATATTATTTGATTGAT
832 ATGATATGCA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 51 1.00
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.43
Consensus pattern (62 bp):
TATTTGATTAATTACGCTATACGATATGCACGAAATGGCAAATATTATTTGATTGATTATGC
Found at i:2892 original size:57 final size:55
Alignment explanation
Indices: 2786--2942 Score: 163
Period size: 56 Copynumber: 2.8 Consensus size: 55
2776 TTCCATAACC
* * ** *
2786 TTACACTCTAATTGAGACGTAAGCAGATCATAGCTCTACCCGAGTTGTACATGGAA
1 TTACGCTCTAACTGAGACGTAAGCA-ATCATAGCTCTAATCGAGTTGTACAGGGAA
* *
2842 TTACGCTCTAACTGAGACGTAAGCAATTCCATAGCTCTAATTGAGTTGTACAGGGCA
1 TTACGCTCTAACTGAGACGTAAGCAA-T-CATAGCTCTAATCGAGTTGTACAGGGAA
* * * *
2899 TTATGCTTTAAACAG-GACATAAGCAAATCATAGCTCTAATCGAG
1 TTACGCTCT-AACTGAGACGTAAGC-AATCATAGCTCTAATCGAG
2943 CTGTCCTTTG
Statistics
Matches: 85, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
55 1 0.01
56 39 0.46
57 39 0.46
58 6 0.07
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (55 bp):
TTACGCTCTAACTGAGACGTAAGCAATCATAGCTCTAATCGAGTTGTACAGGGAA
Found at i:4461 original size:25 final size:23
Alignment explanation
Indices: 4429--4490 Score: 70
Period size: 25 Copynumber: 2.6 Consensus size: 23
4419 AAATGCCCAA
* *
4429 ATTTATTTATTTTCAATTTGTATTT
1 ATTTATTTATTAT-AATTT-TATCT
*
4454 ATTTATTTATAAATAATTTTATCT
1 ATTTATTTAT-TATAATTTTATCT
4478 ATTTATTTATTAT
1 ATTTATTTATTAT
4491 TTATAAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 2 0.06
24 14 0.44
25 15 0.47
26 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.65
Consensus pattern (23 bp):
ATTTATTTATTATAATTTTATCT
Found at i:5578 original size:30 final size:30
Alignment explanation
Indices: 5544--5600 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
5534 TGTTATTTTT
5544 AATTCGGCCCTATAATTTCAT-TGGGTTCTC
1 AATTCGGCCCTATAATTTC-TCTGGGTTCTC
5574 AATTCGGCCCTATAATTTCTCTGGGTT
1 AATTCGGCCCTATAATTTCTCTGGGTT
5601 TTCACTACGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (30 bp):
AATTCGGCCCTATAATTTCTCTGGGTTCTC
Found at i:5823 original size:30 final size:30
Alignment explanation
Indices: 5705--6017 Score: 298
Period size: 30 Copynumber: 10.5 Consensus size: 30
5695 TTCTAAACAC
* * *
5705 TCAAATTTGACCC-CACACTTTCGAAAAAT
1 TCAAATTTGACCCATAAACTTTCCAAAAAT
* * * * *
5734 TCCAATTTAACCC-TCTAACATTCCAAATAT
1 TCAAATTTGACCCAT-AAACTTTCCAAAAAT
* * *
5764 TCGAATTTGACCGC-TAAATTTTCAAAAAAT
1 TCAAATTTGACC-CATAAACTTTCCAAAAAT
5794 TCAAATATT-ACCCATAAACTTTCCAAAAAT
1 TCAAAT-TTGACCCATAAACTTTCCAAAAAT
* *
5824 TAAAATTTGATCCC-TTAACTTTCCAAAAAT
1 TCAAATTTGA-CCCATAAACTTTCCAAAAAT
5854 TCAAATTTGACCCATAAACTTTCCAAAAAT
1 TCAAATTTGACCCATAAACTTTCCAAAAAT
*
5884 TCAAATTTGACCCTTAAACTTTCCAAAAAT
1 TCAAATTTGACCCATAAACTTTCCAAAAAT
* * * *
5914 TCAAATTTAACCCTTAAATTTTTCAAAAATT
1 TCAAATTTGACCCATAAACTTTCCAAAAA-T
* * * *
5945 TC-AATTTGAACCTTAAATTTTTCAAAAAT
1 TCAAATTTGACCCATAAACTTTCCAAAAAT
* * *
5974 TCAAATTTTACTCC-TAAAGTTTTCAAAAAT
1 TCAAATTTGAC-CCATAAACTTTCCAAAAAT
6004 TCAAATTTGACCCA
1 TCAAATTTGACCCA
6018 GTTTTCATAT
Statistics
Matches: 241, Mismatches: 32, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
29 22 0.09
30 207 0.86
31 12 0.05
ACGTcount: A:0.41, C:0.21, G:0.04, T:0.35
Consensus pattern (30 bp):
TCAAATTTGACCCATAAACTTTCCAAAAAT
Found at i:17463 original size:50 final size:50
Alignment explanation
Indices: 17388--17529 Score: 178
Period size: 50 Copynumber: 2.8 Consensus size: 50
17378 TATGGAGGAA
* * *
17388 CAAATTGAAGTCGTAATTGCAAATCTCATACACCTAAAGCTGTAGAGGGG
1 CAAATTGAAGTCGCAATGGCGAATCTCATACACCTAAAGCTGTAGAGGGG
* * * *
17438 CAGATTGAAGCCGCAATGGCGAATCTCATTCACCGAAAGCTGTAGAGGGG
1 CAAATTGAAGTCGCAATGGCGAATCTCATACACCTAAAGCTGTAGAGGGG
* * *
17488 CAAATTGAAGTCGCAA-GGACGAATCTTATACTCCTGAAGCTG
1 CAAATTGAAGTCGCAATGG-CGAATCTCATACACCTAAAGCTG
17530 AAATGGAGTG
Statistics
Matches: 77, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
49 2 0.03
50 75 0.97
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (50 bp):
CAAATTGAAGTCGCAATGGCGAATCTCATACACCTAAAGCTGTAGAGGGG
Found at i:17698 original size:84 final size:84
Alignment explanation
Indices: 17593--17748 Score: 217
Period size: 84 Copynumber: 1.9 Consensus size: 84
17583 GAAGTAATGT
**
17593 AATCTTTTACCCTAACTAGAGGGCAAATTGAAGA-TCATTTGATCTCTTACCCCGACCATGGGGC
1 AATCTTTTACCCTAACTAGAGGGCAAATTGAAGACT-ATCCGATCTCTTACCCCGACCATGGGGC
*
17657 AGATTGAATTGATGCAATCC
65 AAATTGAATTGATGCAATCC
* * * *
17677 AATCTTTTACCCTAA-TCAGAGGGTAGATTGAAGACTATCCGATCTTTTACCCCGATCATGGGGC
1 AATCTTTTACCCTAACT-AGAGGGCAAATTGAAGACTATCCGATCTCTTACCCCGACCATGGGGC
17741 AAATTGAA
65 AAATTGAA
17749 GCAATCCAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
83 1 0.02
84 61 0.97
85 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (84 bp):
AATCTTTTACCCTAACTAGAGGGCAAATTGAAGACTATCCGATCTCTTACCCCGACCATGGGGCA
AATTGAATTGATGCAATCC
Found at i:17747 original size:40 final size:40
Alignment explanation
Indices: 17634--17762 Score: 118
Period size: 40 Copynumber: 3.1 Consensus size: 40
17624 AGATCATTTG
* * *
17634 ATCTCTTACCCCGACCATGGGGCAGATTGAATTGATGCAATCCA
1 ATCTTTTACCCCGATCATGGGGCAAATTGAA--GA--CAATCCA
** * * * *
17678 ATCTTTTACCCTAATCA-GAGGGTAGATTGAAGACTATCCG
1 ATCTTTTACCCCGATCATG-GGGCAAATTGAAGACAATCCA
17718 ATCTTTTACCCCGATCATGGGGCAAATTGAAG-CAATCCA
1 ATCTTTTACCCCGATCATGGGGCAAATTGAAGACAATCCA
17757 ATCTTT
1 ATCTTT
17763 CCTTTAAAGT
Statistics
Matches: 70, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
39 11 0.16
40 31 0.44
41 1 0.01
42 2 0.03
43 1 0.01
44 24 0.34
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (40 bp):
ATCTTTTACCCCGATCATGGGGCAAATTGAAGACAATCCA
Found at i:18061 original size:51 final size:51
Alignment explanation
Indices: 17907--18062 Score: 126
Period size: 51 Copynumber: 3.1 Consensus size: 51
17897 TACGAAGGCG
* * **
17907 AATCTTTATCTC-CGTGAAGCAGCAATGGAGCAAGATGAAGCTATGACATCA
1 AATCTTTATCTCTC-TGAAGCTGCAGTGGAGCAAGATGAAGCTACAACATCA
* * * * * * *
17958 AATC-CTATATCTCTGAAGTTGCAGTGG-GTCGAA-TTAAAG-T-CATGAAAGCA
1 AATCTTTATCTCTCTGAAGCTGCAGTGGAG-C-AAGATGAAGCTACA--ACATCA
18008 AATCTTTATCTCTCTGAAGCTGCAGTGGAGCAAGATGAAGCTACAACATCA
1 AATCTTTATCTCTCTGAAGCTGCAGTGGAGCAAGATGAAGCTACAACATCA
18059 AATC
1 AATC
18063 CTATATCCAA
Statistics
Matches: 77, Mismatches: 18, Indels: 20
0.67 0.16 0.17
Matches are distributed among these distances:
49 2 0.03
50 31 0.40
51 40 0.52
52 2 0.03
53 2 0.03
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.26
Consensus pattern (51 bp):
AATCTTTATCTCTCTGAAGCTGCAGTGGAGCAAGATGAAGCTACAACATCA
Found at i:18740 original size:30 final size:29
Alignment explanation
Indices: 18704--19084 Score: 312
Period size: 30 Copynumber: 12.9 Consensus size: 29
18694 TTGATCCTTG
*
18704 AATTTTCCAAAAACTT-GAATTTGACCCTA
1 AATTTTCCAAAAA-TTCAAATTTGACCCTA
* * *
18733 AACTTTT-CAAAAATTCCAATTTAACCCTCT
1 AA-TTTTCCAAAAATTCAAATTTGACCCT-A
* *
18763 AATTTTCTAAAAATTTAAATTTGACTCCTA
1 AATTTTCCAAAAATTCAAATTTGAC-CCTA
* *
18793 AATTTTCTAAAAATTCAAATTTTG-CCCCA
1 AATTTTCCAAAAATTCAAA-TTTGACCCTA
*
18822 AACTTTCC-AAAATTCAAATTTGACCCTTA
1 AATTTTCCAAAAATTCAAATTTGACCC-TA
* *
18851 AACTTTT-TAGAAATTCAAATTTGACCC-A
1 AA-TTTTCCAAAAATTCAAATTTGACCCTA
* *
18879 AATTTTCAAAAAATTCAAATTTAACCCTCA
1 AATTTTCCAAAAATTCAAATTTGACCCT-A
* *
18909 AACTTTT-AAAAAATTCAAATTTAACCCCTA
1 AA-TTTTCCAAAAATTCAAATTTGA-CCCTA
*
18939 AA-TTTCCAAAAATTCAAATTTGACCCTTG
1 AATTTTCCAAAAATTCAAATTTGACCC-TA
* * * * *
18968 AACTTTCTAGAAATAT-GAATTTGGCCCCTA
1 AATTTTCCAAAAAT-TCAAATTT-GACCCTA
* * *
18998 AATTTACCAAAAATTCTAGTTTGACCCTTA
1 AATTTTCCAAAAATTCAAATTTGACCC-TA
* *
19028 AATTTTCTAAAAATTCTAATTTGACCCATA
1 AATTTTCCAAAAATTCAAATTTGACCC-TA
* *
19058 AAGTTTCCAAAAAATCAAATTTGACCC
1 AATTTTCCAAAAATTCAAATTTGACCC
19085 GATTTTAATG
Statistics
Matches: 288, Mismatches: 42, Indels: 43
0.77 0.11 0.12
Matches are distributed among these distances:
27 8 0.03
28 41 0.14
29 57 0.20
30 162 0.56
31 20 0.07
ACGTcount: A:0.40, C:0.20, G:0.05, T:0.35
Consensus pattern (29 bp):
AATTTTCCAAAAATTCAAATTTGACCCTA
Found at i:18972 original size:59 final size:60
Alignment explanation
Indices: 18707--19084 Score: 361
Period size: 59 Copynumber: 6.4 Consensus size: 60
18697 ATCCTTGAAT
* * * * *
18707 TTTCCAAAAACTT-GAATTTGACCC-TAAACTTTTCAAAAATTCCAATTTAACCCTCT-AAT
1 TTTCCAAAAA-TTCAAATTTGACCCTTAAACTTTTTAAAAATTCAAATTTGACCC-CTAAAC
* *
18766 TTTCTAAAAATTTAAATTTGACTCC-TAAA-TTTTCTAAAAATTCAAATTTTG-CCCC-AAAC
1 TTTCCAAAAATTCAAATTTGAC-CCTTAAACTTTT-TAAAAATTCAAA-TTTGACCCCTAAAC
* *
18825 TTTCC-AAAATTCAAATTTGACCCTTAAACTTTTTAGAAATTCAAATTTGA-CCC-AAAT
1 TTTCCAAAAATTCAAATTTGACCCTTAAACTTTTTAAAAATTCAAATTTGACCCCTAAAC
* * * * *
18882 TTTCAAAAAATTCAAATTTAACCCTCAAACTTTTAAAAAATTCAAATTTAACCCCTAAA-
1 TTTCCAAAAATTCAAATTTGACCCTTAAACTTTTTAAAAATTCAAATTTGACCCCTAAAC
* * * * *
18941 TTTCCAAAAATTCAAATTTGACCCTTGAACTTTCTAGAAATAT-GAATTTGGCCCCTAAA-
1 TTTCCAAAAATTCAAATTTGACCCTTAAACTTTTTAAAAAT-TCAAATTTGACCCCTAAAC
* * * * *
19000 TTTACCAAAAATTCTAGTTTGACCCTTAAA-TTTTCTAAAAATTCTAATTTGACCCATAAAG
1 TTT-CCAAAAATTCAAATTTGACCCTTAAACTTTT-TAAAAATTCAAATTTGACCCCTAAAC
*
19061 TTTCCAAAAAATCAAATTTGACCC
1 TTTCCAAAAATTCAAATTTGACCC
19085 GATTTTAATG
Statistics
Matches: 266, Mismatches: 37, Indels: 31
0.80 0.11 0.09
Matches are distributed among these distances:
57 16 0.06
58 72 0.27
59 89 0.33
60 83 0.31
61 6 0.02
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.35
Consensus pattern (60 bp):
TTTCCAAAAATTCAAATTTGACCCTTAAACTTTTTAAAAATTCAAATTTGACCCCTAAAC
Found at i:19035 original size:60 final size:59
Alignment explanation
Indices: 18707--19084 Score: 346
Period size: 60 Copynumber: 6.4 Consensus size: 59
18697 ATCCTTGAAT
* * ** *
18707 TTTCCAAAAACTT-GAATTTGACCC-TAAACTTTTC-AAAAATTCCAATTTAACCCTCTAAT
1 TTTCCAAAAA-TTCAAATTTGACCCTTAAA-TTTTCTAAAAATTCAAATTTGGCCC-CTAAA
* * *
18766 TTTCTAAAAATTTAAATTTGACTCC-TAAATTTTCTAAAAATTCAAATTTTGCCCC-AAA
1 TTTCCAAAAATTCAAATTTGAC-CCTTAAATTTTCTAAAAATTCAAATTTGGCCCCTAAA
* *
18824 CTTTCC-AAAATTCAAATTTGACCCTTAAACTTTT-TAGAAATTCAAATTT-GACCC-AAA
1 -TTTCCAAAAATTCAAATTTGACCCTTAAA-TTTTCTAAAAATTCAAATTTGGCCCCTAAA
* * * * **
18881 TTTTCAAAAAATTCAAATTTAACCCTCAAACTTTT-AAAAAATTCAAATTTAACCCCTAAA
1 -TTTCCAAAAATTCAAATTTGACCCTTAAA-TTTTCTAAAAATTCAAATTTGGCCCCTAAA
* * * *
18941 TTTCCAAAAATTCAAATTTGACCCTTGAACTTTCTAGAAATAT-GAATTTGGCCCCTAAA
1 TTTCCAAAAATTCAAATTTGACCCTTAAATTTTCTAAAAAT-TCAAATTTGGCCCCTAAA
* * * * *
19000 TTTACCAAAAATTCTAGTTTGACCCTTAAATTTTCTAAAAATTCTAATTTGACCCATAAA
1 TTT-CCAAAAATTCAAATTTGACCCTTAAATTTTCTAAAAATTCAAATTTGGCCCCTAAA
*
19060 GTTTCCAAAAAATCAAATTTGACCC
1 -TTTCCAAAAATTCAAATTTGACCC
19085 GATTTTAATG
Statistics
Matches: 266, Mismatches: 39, Indels: 27
0.80 0.12 0.08
Matches are distributed among these distances:
57 13 0.05
58 79 0.30
59 81 0.30
60 90 0.34
61 3 0.01
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.35
Consensus pattern (59 bp):
TTTCCAAAAATTCAAATTTGACCCTTAAATTTTCTAAAAATTCAAATTTGGCCCCTAAA
Found at i:20291 original size:3 final size:3
Alignment explanation
Indices: 20283--20322 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
20273 ATGGATTAAT
20283 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
20323 ATATGAATGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:23439 original size:20 final size:19
Alignment explanation
Indices: 23410--23454 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
23400 TAATGGTTAT
*
23410 ATTTTAATATTTAAAATAA
1 ATTTTAATATTCAAAATAA
*
23429 AGTTTTTATATTCAAAATAA
1 A-TTTTAATATTCAAAATAA
23449 ATTTTA
1 ATTTTA
23455 CAAATGATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (19 bp):
ATTTTAATATTCAAAATAA
Found at i:27924 original size:21 final size:21
Alignment explanation
Indices: 27900--27990 Score: 69
Period size: 22 Copynumber: 4.3 Consensus size: 21
27890 ATTATATTGT
*
27900 TGTTTTGGTGTTGTTTTTTGC
1 TGTTTTGGTGTTGTTTTTTAC
* *
27921 TGTTTTGGTTGCTATTTTTTAC
1 TGTTTTGG-TGTTGTTTTTTAC
**
27943 TGTTTCAGTGTTGTGTTTTT-C
1 TGTTTTGGTGTTGT-TTTTTAC
* * *
27964 TAGTTTCGGTGCT-ATTTTTAC
1 T-GTTTTGGTGTTGTTTTTTAC
27985 TGTTTT
1 TGTTTT
27991 TGTTGCTGTT
Statistics
Matches: 55, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
20 9 0.16
21 16 0.29
22 30 0.55
ACGTcount: A:0.07, C:0.09, G:0.22, T:0.63
Consensus pattern (21 bp):
TGTTTTGGTGTTGTTTTTTAC
Found at i:27945 original size:22 final size:22
Alignment explanation
Indices: 27900--28002 Score: 65
Period size: 22 Copynumber: 4.8 Consensus size: 22
27890 ATTATATTGT
* * *
27900 TGTTTTGG-TGTTGTTTTTTGC
1 TGTTTTGGTTGCTATTTTTTAC
27921 TGTTTTGGTTGCTATTTTTTAC
1 TGTTTTGGTTGCTATTTTTTAC
* *
27943 TGTTTCAGTGTTG-T-GTTTTT-C
1 TGTTT-TG-GTTGCTATTTTTTAC
*
27964 TAGTTTCGG-TGCTA-TTTTTAC
1 T-GTTTTGGTTGCTATTTTTTAC
* *
27985 TGTTTTTGTTGCTGTTTT
1 TGTTTTGGTTGCTATTTT
28003 GGTGCTATTT
Statistics
Matches: 64, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
19 2 0.03
20 12 0.19
21 17 0.27
22 27 0.42
23 2 0.03
24 4 0.06
ACGTcount: A:0.06, C:0.09, G:0.22, T:0.63
Consensus pattern (22 bp):
TGTTTTGGTTGCTATTTTTTAC
Found at i:27977 original size:43 final size:42
Alignment explanation
Indices: 27907--27989 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 42
27897 TGTTGTTTTG
*
27907 GTGTTGTTTTTTGCTGTTTTGGTTGCTATTTTTTACTGTTTCA
1 GTGTTGTTTTTTGCTGTTTCGGTTGCTA-TTTTTACTGTTTCA
27950 GTGTTGTGTTTTT-CTAGTTTCGG-TGCTATTTTTACTGTTT
1 GTGTTGT-TTTTTGCT-GTTTCGGTTGCTATTTTTACTGTTT
27990 TTGTTGCTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
42 12 0.32
43 14 0.38
44 11 0.30
ACGTcount: A:0.07, C:0.10, G:0.22, T:0.61
Consensus pattern (42 bp):
GTGTTGTTTTTTGCTGTTTCGGTTGCTATTTTTACTGTTTCA
Found at i:28025 original size:33 final size:32
Alignment explanation
Indices: 27966--28035 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 32
27956 TGTTTTTCTA
* * *
27966 GTTTCGGTGCTATTTTTACTGTTTTTGTTGCT
1 GTTTTGGTGCTATTTTTACTGATTTTGCTGCT
*
27998 GTTTTGGTGCTATTTTTTTACT-ATTTTGCTGTT
1 GTTTTGGTGCTA--TTTTTACTGATTTTGCTGCT
28031 GTTTT
1 GTTTT
28036 TATTTTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
32 11 0.34
33 13 0.41
34 8 0.25
ACGTcount: A:0.07, C:0.10, G:0.20, T:0.63
Consensus pattern (32 bp):
GTTTTGGTGCTATTTTTACTGATTTTGCTGCT
Found at i:28047 original size:12 final size:12
Alignment explanation
Indices: 28027--28095 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 12
28017 ACTATTTTGC
*
28027 TGTTGTTTTTAT
1 TGTTATTTTTAT
* *
28039 TTTTATTTTTGT
1 TGTTATTTTTAT
28051 TGTTATTTTT-T
1 TGTTATTTTTAT
* *
28062 CTATTATTTTTGT
1 -TGTTATTTTTAT
* **
28075 TGTTGTTTTGGT
1 TGTTATTTTTAT
28087 TGTTATTTT
1 TGTTATTTT
28096 GGTTGTTTGG
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 1 0.02
12 44 0.96
13 1 0.02
ACGTcount: A:0.09, C:0.01, G:0.14, T:0.75
Consensus pattern (12 bp):
TGTTATTTTTAT
Found at i:28054 original size:24 final size:23
Alignment explanation
Indices: 28010--28102 Score: 87
Period size: 24 Copynumber: 3.8 Consensus size: 23
28000 TTTGGTGCTA
*
28010 TTTTTTTACTATTTTGCTGTTGTTT
1 TTTTTTTA-T-TTTTGTTGTTGTTT
*
28035 TTATTTTTATTTTTGTTGTTATTT
1 TT-TTTTTATTTTTGTTGTTGTTT
*
28059 TTTCTATTATTTTTGTTGTTGTTT
1 TTT-TTTTATTTTTGTTGTTGTTT
* * *
28083 TGGTTGTTATTTTGGTTGTT
1 T-TTTTTTATTTTTGTTGTT
28103 TGGATGTTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
23 1 0.02
24 47 0.81
25 4 0.07
26 6 0.10
ACGTcount: A:0.09, C:0.03, G:0.15, T:0.73
Consensus pattern (23 bp):
TTTTTTTATTTTTGTTGTTGTTT
Found at i:28082 original size:48 final size:46
Alignment explanation
Indices: 27999--28102 Score: 118
Period size: 48 Copynumber: 2.2 Consensus size: 46
27989 TTTGTTGCTG
* * * *
27999 TTTTGGTGCTATTTTTTTACTATTTTGCTGTTGTTTTTATTTTTAT
1 TTTTGTTGTTATTTTTTTACTATTTTGCTGTTGTTTTGATTGTTAT
* * *
28045 TTTTGTTGTTATTTTTTCTATTATTTTTGTTGTTGTTTTGGTTGTTAT
1 TTTTGTTGTTATTTTTT-TACTA-TTTTGCTGTTGTTTTGATTGTTAT
*
28093 TTTGGTTGTT
1 TTTTGTTGTT
28103 TGGATGTTAT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
46 15 0.31
47 4 0.08
48 29 0.60
ACGTcount: A:0.09, C:0.04, G:0.16, T:0.71
Consensus pattern (46 bp):
TTTTGTTGTTATTTTTTTACTATTTTGCTGTTGTTTTGATTGTTAT
Found at i:28096 original size:12 final size:12
Alignment explanation
Indices: 28041--28102 Score: 63
Period size: 12 Copynumber: 5.2 Consensus size: 12
28031 GTTTTTATTT
*
28041 TTATTTTTGTTG
1 TTATTTTGGTTG
* *
28053 TTATTTT-TTCTA
1 TTATTTTGGT-TG
*
28065 TTATTTTTGTTG
1 TTATTTTGGTTG
*
28077 TTGTTTTGGTTG
1 TTATTTTGGTTG
28089 TTATTTTGGTTG
1 TTATTTTGGTTG
28101 TT
1 TT
28103 TGGATGTTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
11 1 0.02
12 39 0.95
13 1 0.02
ACGTcount: A:0.08, C:0.02, G:0.18, T:0.73
Consensus pattern (12 bp):
TTATTTTGGTTG
Found at i:28110 original size:20 final size:21
Alignment explanation
Indices: 28076--28115 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
28066 TATTTTTGTT
*
28076 GTTGTTTTGGTTGTTATTTTG
1 GTTGTTTTGGATGTTATTTTG
28097 GTTG-TTTGGATGTTATTTT
1 GTTGTTTTGGATGTTATTTT
28116 TATGCGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.07, C:0.00, G:0.28, T:0.65
Consensus pattern (21 bp):
GTTGTTTTGGATGTTATTTTG
Found at i:28766 original size:18 final size:18
Alignment explanation
Indices: 28729--28780 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
28719 TTTTCAGTTG
*
28729 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAATTTATT
28747 TAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
*
28765 TATTTAA--AAATTTATT
1 TAATTAATTAAATTTATT
28781 CTCATCCCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 9 0.29
17 7 0.23
18 15 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:31213 original size:31 final size:31
Alignment explanation
Indices: 31175--31234 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
31165 AAATCAAACA
*
31175 TGAAAATGCAACTTTCCAAGGATTTTAATGG
1 TGAAAATGCAACTTTCCAAGAATTTTAATGG
*
31206 TGAAAATGCAACTTTTCAAGAATTTTAAT
1 TGAAAATGCAACTTTCCAAGAATTTTAAT
31235 CAATACTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (31 bp):
TGAAAATGCAACTTTCCAAGAATTTTAATGG
Found at i:36118 original size:24 final size:24
Alignment explanation
Indices: 36086--36133 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
36076 CACCCTATAC
36086 GTATCACATGTGATAATAAGTAAA
1 GTATCACATGTGATAATAAGTAAA
36110 GTATCACATGTGATAATAAGTAAA
1 GTATCACATGTGATAATAAGTAAA
36134 ATGTTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.17, T:0.29
Consensus pattern (24 bp):
GTATCACATGTGATAATAAGTAAA
Found at i:40107 original size:13 final size:13
Alignment explanation
Indices: 40089--40115 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40079 GTGTGGATAA
40089 ATCATTTAAAAAT
1 ATCATTTAAAAAT
40102 ATCATTTAAAAAT
1 ATCATTTAAAAAT
40115 A
1 A
40116 AAACATGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (13 bp):
ATCATTTAAAAAT
Found at i:41636 original size:25 final size:25
Alignment explanation
Indices: 41585--41636 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
41575 ATATATATTT
* * *
41585 AAAAATTATATAAAAATATTTTCAA
1 AAAAATTATATAAAAATAATATAAA
*
41610 AAAAATTATATAAAACTAATATAAA
1 AAAAATTATATAAAAATAATATAAA
41635 AA
1 AA
41637 TTGTAATACG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (25 bp):
AAAAATTATATAAAAATAATATAAA
Found at i:41917 original size:30 final size:30
Alignment explanation
Indices: 41881--41943 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
41871 AATGAAAACC
*
41881 TTTGAATTGTTTAGTGATCATATTGTAATA
1 TTTGAATAGTTTAGTGATCATATTGTAATA
41911 TTTGAATAGTTTAGTGATCATATTGTAATA
1 TTTGAATAGTTTAGTGATCATATTGTAATA
41941 TTT
1 TTT
41944 TAAAATTAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.30, C:0.03, G:0.16, T:0.51
Consensus pattern (30 bp):
TTTGAATAGTTTAGTGATCATATTGTAATA
Found at i:54686 original size:30 final size:29
Alignment explanation
Indices: 54640--54828 Score: 189
Period size: 29 Copynumber: 6.3 Consensus size: 29
54630 GGGGGAATGA
* * *
54640 AAGTTTTGGGGTAAAAAATGGAACTTTTAG
1 AAGTTTAGGGGT-AAAAATGGAATTTTTGG
* * * *
54670 AGGTTTAGGCGTAAAAATAGAAGTTTTGG
1 AAGTTTAGGGGTAAAAATGGAATTTTTGG
* *
54699 AAGTTTTAGGGTTGAAAATGGAATTTTTGG
1 AAG-TTTAGGGGTAAAAATGGAATTTTTGG
* *
54729 AAGTTTGGGGGTAAAAATGGAATTTTTAG
1 AAGTTTAGGGGTAAAAATGGAATTTTTGG
*
54758 AAGTTTTGGGGTCAAAAATGGGAATTTTTGG
1 AAGTTTAGGGGT-AAAAAT-GGAATTTTTGG
* ** *
54789 AAGTTTGGGGGTAAAAATATAATTTTTGA
1 AAGTTTAGGGGTAAAAATGGAATTTTTGG
54818 ACAGTTTAGGG
1 A-AGTTTAGGG
54829 ACCTTCAGGG
Statistics
Matches: 132, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
29 58 0.44
30 53 0.40
31 21 0.16
ACGTcount: A:0.33, C:0.02, G:0.30, T:0.35
Consensus pattern (29 bp):
AAGTTTAGGGGTAAAAATGGAATTTTTGG
Found at i:54719 original size:59 final size:59
Alignment explanation
Indices: 54640--54816 Score: 228
Period size: 59 Copynumber: 3.0 Consensus size: 59
54630 GGGGGAATGA
* * * * * *
54640 AAGTTTTGGGGTAAAAAATGGAACTTTTAGAGGTTTAGGCGTAAAAATAGAAGTTTTGG
1 AAGTTTTGGGGTAAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATAGAATTTTTGG
* ** * *
54699 AAGTTTTAGGGTTGAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTAG
1 AAGTTTTGGGGTAAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATAGAATTTTTGG
* *
54758 AAGTTTTGGGGTCAAAAATGGGAATTTTTGGAAGTTTGGGGGTAAAAATATAATTTTTG
1 AAGTTTTGGGGTAAAAAAT-GGAATTTTTGGAAGTTTGGGGGTAAAAATAGAATTTTTG
54817 AACAGTTTAG
Statistics
Matches: 100, Mismatches: 17, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
59 64 0.64
60 36 0.36
ACGTcount: A:0.33, C:0.02, G:0.29, T:0.36
Consensus pattern (59 bp):
AAGTTTTGGGGTAAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATAGAATTTTTGG
Found at i:56715 original size:6 final size:6
Alignment explanation
Indices: 56704--56788 Score: 60
Period size: 6 Copynumber: 15.0 Consensus size: 6
56694 ATTATTTAAA
56704 TAAATT TAAATT TAAATT TATAA-- TAAATT TAAATTT TAAA-- TAAA-T
1 TAAATT TAAATT TAAATT TA-AATT TAAATT TAAA-TT TAAATT TAAATT
* * *
56749 TAAATT TCAAA-- TAAACT TAATTT TAAA-A TAAATT TAAATT
1 TAAATT T-AAATT TAAATT TAAATT TAAATT TAAATT TAAATT
56789 CTGTTGGGCC
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
4 9 0.14
5 11 0.17
6 33 0.52
7 11 0.17
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (6 bp):
TAAATT
Found at i:56732 original size:17 final size:17
Alignment explanation
Indices: 56710--56788 Score: 92
Period size: 17 Copynumber: 4.7 Consensus size: 17
56700 TAAATAAATT
56710 TAAATTTAAATTTATAA
1 TAAATTTAAATTTATAA
56727 TAAATTTAAATTT-TAAA
1 TAAATTTAAATTTAT-AA
56744 TAAA-TTAAATTTCA-AA
1 TAAATTTAAATTT-ATAA
* * *
56760 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTATAA
56777 TAAATTTAAATT
1 TAAATTTAAATT
56789 CTGTTGGGCC
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
16 16 0.30
17 38 0.70
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:56732 original size:23 final size:23
Alignment explanation
Indices: 56697--56788 Score: 82
Period size: 23 Copynumber: 3.8 Consensus size: 23
56687 ATTGGACATT
56697 ATTTAAATAAATTTAAA-TTTAA
1 ATTTAAATAAATTTAAATTTTAA
56719 ATTTATAATAAATTTAAATTTTAA
1 ATTTA-AATAAATTTAAATTTTAA
*
56743 A--TAAATTAAATTTCAAATAAACTTAA
1 ATTTAAA-TAAATTT-AAAT---TTTAA
*
56769 TTTTAAAATAAATTTAAATT
1 ATTT-AAATAAATTTAAATT
56789 CTGTTGGGCC
Statistics
Matches: 57, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
21 2 0.04
22 14 0.25
23 16 0.28
24 6 0.11
26 4 0.07
27 4 0.07
28 8 0.14
29 3 0.05
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
ATTTAAATAAATTTAAATTTTAA
Found at i:56752 original size:33 final size:34
Alignment explanation
Indices: 56710--56788 Score: 110
Period size: 33 Copynumber: 2.4 Consensus size: 34
56700 TAAATAAATT
*
56710 TAAATTTAAATTT-ATAATAAATTTAAATTTT-AAA
1 TAAATTTAAATTTCA-AATAAACTT-AATTTTAAAA
56744 TAAA-TTAAATTTCAAATAAACTTAATTTTAAAA
1 TAAATTTAAATTTCAAATAAACTTAATTTTAAAA
56777 TAAATTTAAATT
1 TAAATTTAAATT
56789 CTGTTGGGCC
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
32 6 0.15
33 23 0.56
34 12 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (34 bp):
TAAATTTAAATTTCAAATAAACTTAATTTTAAAA
Found at i:57332 original size:25 final size:25
Alignment explanation
Indices: 57294--57343 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
57284 CTTAGAGGTA
*
57294 CTTAGATTCGACCAATTACACAAGT
1 CTTAGATTCAACCAATTACACAAGT
57319 CTTAGATTCAACCAATTACACAAGT
1 CTTAGATTCAACCAATTACACAAGT
57344 GCATACCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.28
Consensus pattern (25 bp):
CTTAGATTCAACCAATTACACAAGT
Found at i:58289 original size:31 final size:31
Alignment explanation
Indices: 58230--58289 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
58220 ACTTACTATC
* ** *
58230 TCAATTACTTAAATAAAAACTTTTAAATAGT
1 TCAATAACTTAAATAAAAACCATCAAATAGT
*
58261 TCAATAACTTAAATGAAAACCATCAAATA
1 TCAATAACTTAAATAAAAACCATCAAATA
58290 ATTTAGTAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.52, C:0.13, G:0.03, T:0.32
Consensus pattern (31 bp):
TCAATAACTTAAATAAAAACCATCAAATAGT
Found at i:63468 original size:21 final size:20
Alignment explanation
Indices: 63444--63500 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
63434 CTCTAAATTG
*
63444 TAAATATTAAAATTTAAACCT
1 TAAAT-TTAAAATTTAAACAT
* * *
63465 TAAACTCAAAATCATAAACAT
1 TAAATTTAAAAT-TTAAACAT
63486 TAAATTTAAAATTTA
1 TAAATTTAAAATTTA
63501 TTAATATTTA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
20 8 0.29
21 20 0.71
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAATTTAAAATTTAAACAT
Found at i:63550 original size:22 final size:21
Alignment explanation
Indices: 63508--63550 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
63498 TTATTAATAT
* *
63508 TTATTTATTGTAGTTACATTA
1 TTATTTATTATAGTTAAATTA
*
63529 TTATTTAATTATATTTAAATTA
1 TTATTT-ATTATAGTTAAATTA
63551 ATTTATGAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (21 bp):
TTATTTATTATAGTTAAATTA
Done.