Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013601.1 Kokia drynarioides strain JFW-HI SEQ_128628, 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: 141783
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 172 characters in sequence are not A, C, G, or T
Found at i:4002 original size:31 final size:30
Alignment explanation
Indices: 3936--4004 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
3926 GTTACATTTA
*
3936 ACAAAACAGTCACTCAACTTAGAAAATGTG
1 ACAAAACAGTCACTCAACTTAGAAAATATG
3966 ACAAAACAGTCACT-AACGTTATCGAAAA-ATG
1 ACAAAACAGTCACTCAAC-TTA--GAAAATATG
3997 ACAAAACA
1 ACAAAACA
4005 ATCAACGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
29 3 0.09
30 17 0.49
31 10 0.29
32 5 0.14
ACGTcount: A:0.51, C:0.20, G:0.12, T:0.17
Consensus pattern (30 bp):
ACAAAACAGTCACTCAACTTAGAAAATATG
Found at i:9507 original size:2 final size:2
Alignment explanation
Indices: 9488--9528 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
9478 AATCAGGAAA
*
9488 AT AT AT A- AT GAT AA 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 AT A
9529 AAAAAATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:10900 original size:26 final size:27
Alignment explanation
Indices: 10869--10924 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
10859 ACCCAATTTT
*
10869 TTTTAATCTATTC-ATAAT-AAATAATA
1 TTTTAATATATTCAATAATAAAATAA-A
10895 TTTTAATATATTCAATAATAAAATAAA
1 TTTTAATATATTCAATAATAAAATAAA
10922 TTT
1 TTT
10925 CAAATAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 12 0.44
27 9 0.33
28 6 0.22
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.46
Consensus pattern (27 bp):
TTTTAATATATTCAATAATAAAATAAA
Found at i:10930 original size:28 final size:26
Alignment explanation
Indices: 10877--10930 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 26
10867 TTTTTTAATC
*
10877 TATTCATAATAAATAATATTTTAATA
1 TATTCATAATAAATAATATTTAAATA
10903 TATTCAATAATAAAATAA-ATTTCAAATA
1 TATTC-ATAAT-AAATAATATTT-AAATA
10931 AAAGAATTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.21
27 9 0.38
28 10 0.42
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.41
Consensus pattern (26 bp):
TATTCATAATAAATAATATTTAAATA
Found at i:27291 original size:6 final size:6
Alignment explanation
Indices: 27280--27314 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
27270 GCCAATTCTT
27280 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
27315 TTGTTATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:27437 original size:90 final size:90
Alignment explanation
Indices: 27293--27457 Score: 321
Period size: 90 Copynumber: 1.8 Consensus size: 90
27283 TTCTTTTTCT
27293 TTTTCTTTTTCTTTTTCTTTTTTTGTTATTTAGTTTTTTAATTACACGTTGGCGCTCTCTTTTTC
1 TTTTCTTTTTCTTTTTCTTTTTTTGTTATTTAGTTTTTTAATTACACGTTGGCGCTCTCTTTTTC
27358 CAAAGGCTTTACCTCCCTTTTGCCA
66 CAAAGGCTTTACCTCCCTTTTGCCA
*
27383 TTTTCTTTTTCTTTTTCTTTTTTTGTTATTTAGTTTTTTAATTACACGTTGGCGCTCTTTTTTTC
1 TTTTCTTTTTCTTTTTCTTTTTTTGTTATTTAGTTTTTTAATTACACGTTGGCGCTCTCTTTTTC
27448 CAAAGGCTTT
66 CAAAGGCTTT
27458 CTTCCCTCCC
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 74 1.00
ACGTcount: A:0.12, C:0.18, G:0.10, T:0.59
Consensus pattern (90 bp):
TTTTCTTTTTCTTTTTCTTTTTTTGTTATTTAGTTTTTTAATTACACGTTGGCGCTCTCTTTTTC
CAAAGGCTTTACCTCCCTTTTGCCA
Found at i:27725 original size:6 final size:6
Alignment explanation
Indices: 27714--27748 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
27704 GCCAATTCTT
27714 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
27749 TTGTTATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:33516 original size:24 final size:23
Alignment explanation
Indices: 33479--33549 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 23
33469 AAATATATAA
* *
33479 AATACATAAATATTTTTTTAAATAT
1 AATA-ATAAATATTATATTAAA-AT
33504 AATAATAAATATTATATTAAAAT
1 AATAATAAATATTATATTAAAAT
33527 -AT--T-AATATTAATATTAAAAT
1 AATAATAAATATT-ATATTAAAAT
33547 AAT
1 AAT
33550 TTTTTTGTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
19 6 0.14
20 11 0.26
21 2 0.05
22 2 0.05
23 2 0.05
24 15 0.36
25 4 0.10
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (23 bp):
AATAATAAATATTATATTAAAAT
Found at i:33526 original size:25 final size:26
Alignment explanation
Indices: 33479--33542 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 26
33469 AAATATATAA
* *
33479 AATACATAAATATT-TTTTTAAATA-T
1 AATA-ATAAATATTATATTAAAATATT
33504 AATAATAAATATTATATTAAAATATT
1 AATAATAAATATTATATTAAAATATT
*
33530 AAT-ATTAATATTA
1 AATAATAAATATTA
33543 AAATAATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 9 0.26
25 21 0.62
26 4 0.12
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
AATAATAAATATTATATTAAAATATT
Found at i:33527 original size:20 final size:21
Alignment explanation
Indices: 33504--33549 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
33494 TTTTAAATAT
33504 AATAATAAATATT-ATATTAA
1 AATAATAAATATTAATATTAA
*
33524 AAT-ATTAATATTAATATTAA
1 AATAATAAATATTAATATTAA
33544 AATAAT
1 AATAAT
33550 TTTTTTGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 8 0.35
20 13 0.57
21 2 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AATAATAAATATTAATATTAA
Found at i:33539 original size:12 final size:13
Alignment explanation
Indices: 33496--33543 Score: 57
Period size: 12 Copynumber: 3.8 Consensus size: 13
33486 AAATATTTTT
33496 TTAAATA-TAATA
1 TTAAATATTAATA
*
33508 ATAAATATT-ATA
1 TTAAATATTAATA
33520 TTAAAATATTAATA
1 TT-AAATATTAATA
33534 TT-AATATTAA
1 TTAAATATTAA
33544 AATAATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 18 0.58
13 8 0.26
14 5 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAATATTAATA
Found at i:45452 original size:21 final size:21
Alignment explanation
Indices: 45411--45449 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
45401 TTTATAAAAA
*
45411 AATTATTTTAATTTTTCAATT
1 AATTATTTTAATTTTTAAATT
*
45432 AATT-TTTTACTTTTTAAA
1 AATTATTTTAATTTTTAAA
45450 ATTTTAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
AATTATTTTAATTTTTAAATT
Found at i:59841 original size:18 final size:18
Alignment explanation
Indices: 59818--59852 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
59808 TTAATCATTT
*
59818 TAAAAAATCAAATTTAAA
1 TAAAAAATAAAATTTAAA
*
59836 TAAAAATTAAAATTTAA
1 TAAAAAATAAAATTTAA
59853 TCTAAAATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAAAATAAAATTTAAA
Found at i:60764 original size:20 final size:20
Alignment explanation
Indices: 60739--60801 Score: 83
Period size: 20 Copynumber: 3.0 Consensus size: 20
60729 TTCTAGCTAT
60739 AAAAATAGGAAAATTATAAA
1 AAAAATAGGAAAATTATAAA
*
60759 AAAAATAGGAAAA-TATATAG
1 AAAAATAGGAAAATTATA-AA
60779 AAAAATAGGAAAAAATTATAAA
1 AAAAATAGG--AAAATTATAAA
60801 A
1 A
60802 TTGTAAGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
19 4 0.11
20 23 0.62
22 6 0.16
23 4 0.11
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.19
Consensus pattern (20 bp):
AAAAATAGGAAAATTATAAA
Found at i:60801 original size:9 final size:9
Alignment explanation
Indices: 60789--60849 Score: 52
Period size: 9 Copynumber: 6.6 Consensus size: 9
60779 AAAAATAGGA
60789 AAAAATTAT
1 AAAAATTAT
*
60798 -AAAATTGT
1 AAAAATTAT
60806 AAGAAAGTTAT
1 AA-AAA-TTAT
60817 AAAAATTAT
1 AAAAATTAT
*
60826 AAAGAAATAT
1 AAA-AATTAT
* *
60836 AAAATTTGT
1 AAAAATTAT
60845 AAAAA
1 AAAAA
60850 GAAATTATAA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
8 7 0.17
9 15 0.37
10 14 0.34
11 5 0.12
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:60811 original size:21 final size:20
Alignment explanation
Indices: 60788--60861 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 20
60778 GAAAAATAGG
60788 AAAAAATTATAAAATTGT-A
1 AAAAAATTATAAAATTGTAA
* * *
60807 AGAAAGTTATAAAAAT-TATA
1 AAAAAATTATAAAATTGTA-A
*
60827 AAGAAA-TATAAAATTTGTAA
1 AAAAAATTATAAAA-TTGTAA
60847 AAAGAAATTATAAAA
1 AAA-AAATTATAAAA
60862 AATATCATAT
Statistics
Matches: 41, Mismatches: 8, Indels: 9
0.71 0.14 0.16
Matches are distributed among these distances:
18 1 0.02
19 20 0.49
20 8 0.20
21 5 0.12
22 7 0.17
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (20 bp):
AAAAAATTATAAAATTGTAA
Found at i:60925 original size:17 final size:17
Alignment explanation
Indices: 60903--60935 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
60893 TTTCAATAAC
60903 TTTTAATAATTTTTATT
1 TTTTAATAATTTTTATT
*
60920 TTTTAATTATTTTTAT
1 TTTTAATAATTTTTAT
60936 CACGTGTCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTAATAATTTTTATT
Found at i:61114 original size:29 final size:28
Alignment explanation
Indices: 61070--61148 Score: 74
Period size: 28 Copynumber: 2.8 Consensus size: 28
61060 TTTACGATTT
61070 TTTATATA-TTTT-TTAATTTTTAATGAAA
1 TTTATA-ACTTTTATTAATTTTTAAT-AAA
** *
61098 TTT-TAACTTTTTATTAAAATTTAATAAT
1 TTTATAAC-TTTTATTAATTTTTAATAAA
*
61126 TTTATAACTTTTATTGATTTTTA
1 TTTATAACTTTTATTAATTTTTA
61149 TTTTTTATAG
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
26 1 0.02
27 2 0.05
28 24 0.59
29 14 0.34
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (28 bp):
TTTATAACTTTTATTAATTTTTAATAAA
Found at i:61117 original size:19 final size:18
Alignment explanation
Indices: 61080--61119 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
61070 TTTATATATT
*
61080 TTTTAATTTTTAATGAAA
1 TTTTAATTTTTAATAAAA
*
61098 TTTTAACTTTTTATTAAAA
1 TTTTAA-TTTTTAATAAAA
61117 TTT
1 TTT
61120 AATAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTTAATTTTTAATAAAA
Found at i:61120 original size:18 final size:18
Alignment explanation
Indices: 61081--61122 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
61071 TTATATATTT
*
61081 TTTAATTTTTAATGAAAT
1 TTTAATTTTTAATGAAAA
*
61099 TTTAACTTTTT-ATTAAAA
1 TTTAA-TTTTTAATGAAAA
61117 TTTAAT
1 TTTAAT
61123 AATTTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 15 0.71
19 5 0.24
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (18 bp):
TTTAATTTTTAATGAAAA
Found at i:63845 original size:1 final size:1
Alignment explanation
Indices: 63839--63869 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
63829 NNNNNNNNNN
63839 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
63870 ACATTCCAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:76663 original size:30 final size:30
Alignment explanation
Indices: 76571--76670 Score: 94
Period size: 30 Copynumber: 3.3 Consensus size: 30
76561 ATAACAACGT
*** *
76571 AAGTAATTAAAATGTAATTTTTTA-AATAT
1 AAGTAATTAAAATGTAATTTAAAATAATAA
* * *
76600 ATGTTGATTAAAATGTATTTTAAAATAAATAA
1 AAG-TAATTAAAATGTAATTTAAAAT-AATAA
*
76632 AAGTAATTAAAATGTAATTTAAGATAATAA
1 AAGTAATTAAAATGTAATTTAAAATAATAA
*
76662 AAGTGATTA
1 AAGTAATTA
76671 TTTTGATAAT
Statistics
Matches: 56, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
29 2 0.04
30 29 0.52
31 19 0.34
32 6 0.11
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (30 bp):
AAGTAATTAAAATGTAATTTAAAATAATAA
Found at i:79926 original size:19 final size:21
Alignment explanation
Indices: 79892--79938 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
79882 TTTTTTAAAG
*
79892 AAAA-TCAAAATAATTT-TCA
1 AAAATTCAAAATAATTTATAA
79911 AAAATTCAAAAT-ATTTATAA
1 AAAATTCAAAATAATTTATAA
79931 AAAATTCA
1 AAAATTCA
79939 TAATTTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAATTCAAAATAATTTATAA
Found at i:85633 original size:17 final size:18
Alignment explanation
Indices: 85600--85633 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
85590 TTCATTTTTT
*
85600 AATATTTTATTAATTAAA
1 AATATTTTATAAATTAAA
85618 AATATTTT-TAAATTAA
1 AATATTTTATAAATTAA
85634 CTCTTATCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AATATTTTATAAATTAAA
Found at i:91938 original size:2 final size:2
Alignment explanation
Indices: 91931--91961 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
91921 TATTGAAGGT
91931 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
91962 TCGTTACGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:92611 original size:91 final size:91
Alignment explanation
Indices: 92456--92637 Score: 346
Period size: 91 Copynumber: 2.0 Consensus size: 91
92446 TGGTTTTTGG
92456 GAATTATTTAGTACAAAAGGGTCCGTCATCTATGTCCCCCTGAGTTAACTGAGTTGGCCCGGACT
1 GAATTATTTAGTACAAAAGGGTCCGTCATCTATGTCCCCCTGAGTTAACTGAGTTGGCCCGGACT
*
92521 CAGTGGACTTTGGTATCAACAAAGGA
66 CAGTGGACTTTGCTATCAACAAAGGA
*
92547 GAATTATTTAGTACAAAAGGGTCTGTCATCTATGTCCCCCTGAGTTAACTGAGTTGGCCCGGACT
1 GAATTATTTAGTACAAAAGGGTCCGTCATCTATGTCCCCCTGAGTTAACTGAGTTGGCCCGGACT
92612 CAGTGGACTTTGCTATCAACAAAGGA
66 CAGTGGACTTTGCTATCAACAAAGGA
92638 AACAAATGTT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 89 1.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (91 bp):
GAATTATTTAGTACAAAAGGGTCCGTCATCTATGTCCCCCTGAGTTAACTGAGTTGGCCCGGACT
CAGTGGACTTTGCTATCAACAAAGGA
Found at i:96167 original size:38 final size:37
Alignment explanation
Indices: 96116--96190 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 37
96106 ACCTAAATAC
*
96116 CTTAAAAAGTATTTAATAAATGAGAAAAATAGGGAAA
1 CTTAAAAAGTATTTAAAAAATGAGAAAAATAGGGAAA
96153 NCTTAAAAAGTATTTAAAAAATGAGAAAAATAGGGAAA
1 -CTTAAAAAGTATTTAAAAAATGAGAAAAATAGGGAAA
96191 AAAAAAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.57, C:0.03, G:0.16, T:0.23
Consensus pattern (37 bp):
CTTAAAAAGTATTTAAAAAATGAGAAAAATAGGGAAA
Found at i:96199 original size:38 final size:38
Alignment explanation
Indices: 96119--96199 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 38
96109 TAAATACCTT
* ****
96119 AAAAAGTATTTAATAAATGAGAAAAATAGGGAAANCTT
1 AAAAAGTATTTAAAAAATGAGAAAAATAGGGAAAAAAA
96157 AAAAAGTATTTAAAAAATGAGAAAAATAGGGAAAAAAA
1 AAAAAGTATTTAAAAAATGAGAAAAATAGGGAAAAAAA
96195 AAAAA
1 AAAAA
96200 AGTCTTCAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.64, C:0.01, G:0.15, T:0.19
Consensus pattern (38 bp):
AAAAAGTATTTAAAAAATGAGAAAAATAGGGAAAAAAA
Found at i:105791 original size:16 final size:18
Alignment explanation
Indices: 105766--105804 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
105756 GAATTGTGAA
*
105766 ATTACCAAAAAAA-AAAT
1 ATTACAAAAAAAATAAAT
105783 -TTACAAAAAAAATAAAT
1 ATTACAAAAAAAATAAAT
105800 ATTAC
1 ATTAC
105805 TTCAAGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 11 0.58
17 4 0.21
18 4 0.21
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (18 bp):
ATTACAAAAAAAATAAAT
Found at i:120273 original size:31 final size:29
Alignment explanation
Indices: 120202--120283 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 29
120192 AAACTGTTGA
* * **
120202 ATAATTTAGTGATCAAATTGTAAATTTTT
1 ATAATTTAGTGATCAAAATGAAAATTTCC
* *
120231 TTAATTAAGTGATCAAAATGAAAATTTAACC
1 ATAATTTAGTGATCAAAATGAAAATTT--CC
*
120262 ATAATTTAGTGATAAAAATGAA
1 ATAATTTAGTGATCAAAATGAA
120284 GTTTACCCAA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 23 0.55
31 19 0.45
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (29 bp):
ATAATTTAGTGATCAAAATGAAAATTTCC
Found at i:125620 original size:42 final size:38
Alignment explanation
Indices: 125573--125665 Score: 100
Period size: 38 Copynumber: 2.3 Consensus size: 38
125563 ACATTAAAAA
*
125573 TTATTTAGATTAAAAAACACTATAATAAA-AGTAATAAATGTT
1 TTATTT-GATT-AAAAACAC-A-AATAAATA-TAATAAATATT
*
125615 TTATTTTATTAAAAACACAAATAAATATAATAAATATT
1 TTATTTGATTAAAAACACAAATAAATATAATAAATATT
125653 TTATTCT-ATTAAA
1 TTATT-TGATTAAA
125666 TATAAAATAT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
38 27 0.57
39 3 0.06
40 8 0.17
41 3 0.06
42 6 0.13
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (38 bp):
TTATTTGATTAAAAACACAAATAAATATAATAAATATT
Found at i:125646 original size:38 final size:40
Alignment explanation
Indices: 125585--125665 Score: 114
Period size: 38 Copynumber: 2.1 Consensus size: 40
125575 ATTTAGATTA
* *
125585 AAAAACACTATAATAAAAGTAATAAATGTTTTATTTTATT
1 AAAAACACTATAATAAAAGTAATAAATATTTTATTCTATT
125625 AAAAACAC-A-AATAAATA-TAATAAATATTTTATTCTATT
1 AAAAACACTATAATAAA-AGTAATAAATATTTTATTCTATT
125663 AAA
1 AAA
125666 TATAAAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 28 0.74
39 2 0.05
40 8 0.21
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.37
Consensus pattern (40 bp):
AAAAACACTATAATAAAAGTAATAAATATTTTATTCTATT
Found at i:130205 original size:61 final size:61
Alignment explanation
Indices: 130120--130252 Score: 241
Period size: 61 Copynumber: 2.2 Consensus size: 61
130110 AAGTTAAAAT
*
130120 TTGCTA-TTTCCAAAATCTTATGCCACAAACATATTATCACGTTTGTAATTCTATGCCAAC
1 TTGCTATTTTCAAAAATCTTATGCCACAAACATATTATCACGTTTGTAATTCTATGCCAAC
*
130180 TTGCTATTTTCAAAAATCTTATGCCACAAACATGTTATCACGTTTGTAATTCTATGCCAAC
1 TTGCTATTTTCAAAAATCTTATGCCACAAACATATTATCACGTTTGTAATTCTATGCCAAC
130241 TTGCTATTTTCA
1 TTGCTATTTTCA
130253 CACAATGCTT
Statistics
Matches: 70, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
60 6 0.09
61 64 0.91
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (61 bp):
TTGCTATTTTCAAAAATCTTATGCCACAAACATATTATCACGTTTGTAATTCTATGCCAAC
Found at i:139086 original size:215 final size:215
Alignment explanation
Indices: 138634--139671 Score: 1541
Period size: 215 Copynumber: 4.9 Consensus size: 215
138624 CTGTGAGCCT
* *
138634 TGAGATAAAACCCGAAGCAGAATTAAGACACATCAGTATATATCCATTTGTATATCTCAATATAT
1 TGAGATAAAACCCGAAGCAGAATTGAGACACATCAATATATATCCATTTGTATATCTCAATATAT
* * * ** *
138699 ACACATACATATGCATGTCTAGTTAGAATATTAGGACAAGTTGTCGGCCACCTTATCTGTAAAAT
66 --ATATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGTAAAAT
* * *
138764 GTGATCCA-TTTGGCAAATATTCCATATTTAAGAACTTTCCTGGAATATTTTCTGAAACTATGAC
129 GTGAT-CATTTTAGCAAATATTCCAT-CTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGAC
*
138828 CCATCAAGGCTCTTAGCAGAATCG
192 CCATCAAGACTCTTAGCAGAATCG
*
138852 TGAGATAAAACCTGAAGCAGAATTGAGACACATCAATATATATCCATTTGTATATCTCAATATAT
1 TGAGATAAAACCCGAAGCAGAATTGAGACACATCAATATATATCCATTTGTATATCTCAATATAT
* * * *
138917 ATATACATACGCGTGTGTAGTTAGAATATTTGGACAAGTTGTCGTCTGCCTTATCTGTAAAATGT
66 ATATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGTAAAATGT
* *
138982 GATCATTTTAGCAAATATTCCATCTTAAGAACTTTACTGGAAAATTTTCTGATACTATGACCCAT
131 GATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGACCCAT
*
139047 CAAGACTCTTAGCAGAATGG
196 CAAGACTCTTAGCAGAATCG
* * *
139067 TGAGATAAAACCCGAAGCAGAATTGAGACACTTCAATATATATCCAATTGTAAATCTC--TATAT
1 TGAGATAAAACCCGAAGCAGAATTGAGACACATCAATATATATCCATTTGTATATCTCAATATAT
* * * *
139130 ATAAACATACGCATGTCTAGTTAGACTATTTGGACAAGCTGTCATCTAACTTATCTGTAAAATGT
66 ATATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGTAAAATGT
*
139195 GATTATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGACCCAT
131 GATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGACCCAT
*
139260 CAAGACTCTTAGCAGAGTCG
196 CAAGACTCTTAGCAGAATCG
* ** *
139280 TGAGATAGAACCCGAAGCAGAATTGAGATGCATCAATATGTATCCATTTG------T---TATAT
1 TGAGATAAAACCCGAAGCAGAATTGAGACACATCAATATATATCCATTTGTATATCTCAATATAT
* *
139336 ATATACATACGCATGTCTAGTTAGAATATTTGGACAACTTGTCATCTACCATATCTGTAAAATGT
66 ATATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGTAAAATGT
*
139401 GATCATTTTGGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGACCCAT
131 GATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGACCCAT
* *
139466 CAAGGCTCTTAGCAGAGTCG
196 CAAGACTCTTAGCAGAATCG
*
139486 TGAGATAAAACCCGAAGCAGAATTGAGCCACATCAATATATATTTATCCATTTGTATATCTCAAT
1 TGAGATAAAACCCGAAGCAGAATTGAGACACATC-A-ATATA--TATCCATTTGTATATCTCAAT
139551 -T-TATATACATACGCATGTCTAG-TAGAAT-TTTGGACAAGTTGTCATCTACCTTATCTGTAAA
62 ATATATATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGTAAA
139612 ATGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACT
127 ATGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACT
139672 CTTTTTCCCC
Statistics
Matches: 748, Mismatches: 58, Indels: 31
0.89 0.07 0.04
Matches are distributed among these distances:
206 176 0.24
207 2 0.00
208 4 0.01
210 10 0.01
213 186 0.25
215 202 0.27
216 83 0.11
217 21 0.03
218 63 0.08
219 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (215 bp):
TGAGATAAAACCCGAAGCAGAATTGAGACACATCAATATATATCCATTTGTATATCTCAATATAT
ATATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGTAAAATGT
GATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGACCCAT
CAAGACTCTTAGCAGAATCG
Done.