Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013773.1 Kokia drynarioides strain JFW-HI SEQ_128801, 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: 45570
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1639 original size:24 final size:23
Alignment explanation
Indices: 1612--1681 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
1602 TCATTAACAT
1612 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTA-A
* *
1636 TGTTCATGAACATGTTCATTTAA
1 TGTTCGTGAACATGTTCAATTAA
* *
1659 TGCTCGTGAACATGTTCGATTAA
1 TGTTCGTGAACATGTTCAATTAA
1682 GTTAAATGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 20 0.50
24 20 0.50
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCAATTAA
Found at i:3475 original size:24 final size:24
Alignment explanation
Indices: 3439--3498 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
3429 ACTAATAAGG
* *
3439 GTTTGACTCAAACAAATAAACAGA
1 GTTTAACTGAAACAAATAAACAGA
* *
3463 GTTTAATTGAAACAAATAAATAGA
1 GTTTAACTGAAACAAATAAACAGA
3487 GTTTAACTGAAA
1 GTTTAACTGAAA
3499 GATTAATTCC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.50, C:0.10, G:0.13, T:0.27
Consensus pattern (24 bp):
GTTTAACTGAAACAAATAAACAGA
Found at i:5462 original size:24 final size:24
Alignment explanation
Indices: 5433--5483 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
5423 AGTTTGACTC
*
5433 AAACAAATAAATAGAATTTAATTG
1 AAACAAATAAATAGAATTTAACTG
*
5457 AAACAAATAAATAGAGTTTAACTG
1 AAACAAATAAATAGAATTTAACTG
5481 AAA
1 AAA
5484 GATTGTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.59, C:0.06, G:0.10, T:0.25
Consensus pattern (24 bp):
AAACAAATAAATAGAATTTAACTG
Found at i:6024 original size:17 final size:17
Alignment explanation
Indices: 5994--6028 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5984 AAGAAATTAC
5994 AAGAACATGAAAGGTTA
1 AAGAACATGAAAGGTTA
* *
6011 AAGAAGATGGAAGGTTA
1 AAGAACATGAAAGGTTA
6028 A
1 A
6029 TGGTCAAGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.29, T:0.17
Consensus pattern (17 bp):
AAGAACATGAAAGGTTA
Found at i:11144 original size:17 final size:17
Alignment explanation
Indices: 11114--11148 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
11104 AAGTAGTTAC
*
11114 AAGAATATGAAAGATTA
1 AAGAAGATGAAAGATTA
*
11131 AAGAAGATGGAAGATTA
1 AAGAAGATGAAAGATTA
11148 A
1 A
11149 CGGTTAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.23, T:0.20
Consensus pattern (17 bp):
AAGAAGATGAAAGATTA
Found at i:11285 original size:16 final size:14
Alignment explanation
Indices: 11266--11325 Score: 51
Period size: 14 Copynumber: 4.5 Consensus size: 14
11256 AAACCATTTT
11266 TTATAAATATTATATA
1 TTATAAAT-TT-TATA
11282 TTATAAATTTTATA
1 TTATAAATTTTATA
11296 TTAT---TTTT-TA
1 TTATAAATTTTATA
11306 TT-T-AATTTATATA
1 TTATAAATTT-TATA
11319 TTATAAA
1 TTATAAA
11326 AAATTATAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
9 1 0.03
10 4 0.11
11 7 0.18
12 1 0.03
13 4 0.11
14 9 0.24
15 4 0.11
16 8 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTATAAATTTTATA
Found at i:12890 original size:13 final size:13
Alignment explanation
Indices: 12872--12915 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
12862 AGCAGATGAA
12872 AAATTTATGTAAT
1 AAATTTATGTAAT
* *
12885 AAATTTA--CAAA
1 AAATTTATGTAAT
12896 AAATTTATGTAAT
1 AAATTTATGTAAT
12909 AAATTTA
1 AAATTTA
12916 CAAAAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 9 0.36
13 16 0.64
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (13 bp):
AAATTTATGTAAT
Found at i:12898 original size:24 final size:24
Alignment explanation
Indices: 12870--12926 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
12860 ATAGCAGATG
12870 AAAAATTTATGTAATAAATTTACA
1 AAAAATTTATGTAATAAATTTACA
12894 AAAAATTTATGTAATAAATTTACA
1 AAAAATTTATGTAATAAATTTACA
12918 AAAAATTTA
1 AAAAATTTA
12927 ATATAAAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (24 bp):
AAAAATTTATGTAATAAATTTACA
Found at i:14879 original size:33 final size:33
Alignment explanation
Indices: 14838--14908 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
14828 ATCCAATCTA
*
14838 CGAC-TAGATTGGCCTCCCTCGAGAGATTTAAT
1 CGACTTAGATTGGCCTCCCTCAAGAGATTTAAT
*
14870 CGACTTAGATTGGTCTCCCTCAAGAGATTTAAT
1 CGACTTAGATTGGCCTCCCTCAAGAGATTTAAT
*
14903 CTACTT
1 CGACTT
14909 TGGCTTTAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
32 4 0.11
33 31 0.89
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32
Consensus pattern (33 bp):
CGACTTAGATTGGCCTCCCTCAAGAGATTTAAT
Found at i:18888 original size:51 final size:51
Alignment explanation
Indices: 18757--18894 Score: 176
Period size: 51 Copynumber: 2.7 Consensus size: 51
18747 TGTAAGAAAC
* *
18757 CTAAGGAAGAATCAAGTTCAAGAAAGGCTGAAGAAGATAAATAGGGGCAAA
1 CTAAGGAAGGATCAAGTTCAAGAAAGGTTGAAGAAGATAAATAGGGGCAAA
* *
18808 CTAAGGAAGGATCAAG-TCTAATG-AGGGTTGAAGAAGAT-AATAAGGGGTAAA
1 CTAAGGAAGGATCAAGTTC-AA-GAAAGGTTGAAGAAGATAAAT-AGGGGCAAA
*
18859 CTAAGAAAGGATCAAGTTCAAGAAAGGTTGAA-AAGA
1 CTAAGGAAGGATCAAGTTCAAGAAAGGTTGAAGAAGA
18895 ATGAGCTTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
50 10 0.13
51 63 0.83
52 3 0.04
ACGTcount: A:0.47, C:0.08, G:0.28, T:0.17
Consensus pattern (51 bp):
CTAAGGAAGGATCAAGTTCAAGAAAGGTTGAAGAAGATAAATAGGGGCAAA
Found at i:20682 original size:24 final size:23
Alignment explanation
Indices: 20621--20690 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
20611 TTTATTTAAC
*
20621 TTAATCGAACATGTTCACAAACA
1 TTAATCGAACATGTTCACGAACA
* *
20644 TTAAACGAACATGTTCATGAACA
1 TTAATCGAACATGTTCACGAACA
*
20667 TATAATTGAACATGTTCACGAACA
1 T-TAATCGAACATGTTCACGAACA
20691 ATGTTAATGA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 21 0.52
24 19 0.47
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.27
Consensus pattern (23 bp):
TTAATCGAACATGTTCACGAACA
Found at i:22561 original size:3 final size:3
Alignment explanation
Indices: 22553--22590 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
22543 TTGAGAAATA
22553 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
22591 AAGTAACATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:32664 original size:31 final size:31
Alignment explanation
Indices: 32606--32665 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
32596 TTAATATATT
* *
32606 ATTTGGTACCTAAATTTGACTTTAATGTTCA
1 ATTTGGTAACTAAATTTGACTTCAATGTTCA
* * *
32637 ATTTGGTAACTGAGTTTGGCTTCAATGTT
1 ATTTGGTAACTAAATTTGACTTCAATGTT
32666 GACTTTGTTA
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:0.25, C:0.12, G:0.18, T:0.45
Consensus pattern (31 bp):
ATTTGGTAACTAAATTTGACTTCAATGTTCA
Found at i:32902 original size:32 final size:32
Alignment explanation
Indices: 32860--32929 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
32850 TTGGTCTGGA
32860 TACC-AAATTGAA-TCTTGAAACCAAACTCAGG
1 TACCAAAATTGAACT-TTGAAACCAAACTCAGG
* *
32891 TACCAAAATTGAACTTTGAAGCGAAACTCAGG
1 TACCAAAATTGAACTTTGAAACCAAACTCAGG
*
32923 TATCAAA
1 TACCAAA
32930 TGATACATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 4 0.12
32 29 0.85
33 1 0.03
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (32 bp):
TACCAAAATTGAACTTTGAAACCAAACTCAGG
Found at i:35818 original size:30 final size:31
Alignment explanation
Indices: 35773--35899 Score: 109
Period size: 30 Copynumber: 4.2 Consensus size: 31
35763 AAATTACTTT
* * *
35773 TTTGACTCTCAAATTTTTC-AAAAATTCTAA
1 TTTGACCCTTAAATTTTTCAAAAAATTCCAA
* *
35803 TTCGACCCTTAAATTTTCCAAAAAATTCCAA
1 TTTGACCCTTAAATTTTTCAAAAAATTCCAA
* * *
35834 TTTGA-CCTCTAAA-CTTTCTAAAACTTCCAA
1 TTTGACCCT-TAAATTTTTCAAAAAATTCCAA
* * **
35864 TTTGACCCCTAAAATTTT-AAAAAATTTAAA
1 TTTGACCCTTAAATTTTTCAAAAAATTCCAA
35894 TTTGAC
1 TTTGAC
35900 TCGGTTTTAA
Statistics
Matches: 77, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
30 54 0.70
31 23 0.30
ACGTcount: A:0.38, C:0.20, G:0.04, T:0.38
Consensus pattern (31 bp):
TTTGACCCTTAAATTTTTCAAAAAATTCCAA
Found at i:40524 original size:20 final size:19
Alignment explanation
Indices: 40476--40566 Score: 69
Period size: 21 Copynumber: 4.5 Consensus size: 19
40466 CGGATTCGGT
40476 AAGGAAGAAATAAAAAAAAA
1 AAGGAA-AAATAAAAAAAAA
**
40496 AGACAAAAAATTAAAAAAAAA
1 A-AGGAAAAA-TAAAAAAAAA
40517 AAGGAAAAA-AGAGAAAAAGAA
1 AAGGAAAAATA-A-AAAAA-AA
*
40538 AAGGAAAAAGAAGAAAATAAA
1 AAGGAAAAATAA-AAAA-AAA
40559 AA-GAAAAA
1 AAGGAAAAA
40567 GGGGAGGTTG
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
18 1 0.02
19 1 0.02
20 21 0.35
21 35 0.58
22 2 0.03
ACGTcount: A:0.79, C:0.01, G:0.15, T:0.04
Consensus pattern (19 bp):
AAGGAAAAATAAAAAAAAA
Found at i:40524 original size:21 final size:21
Alignment explanation
Indices: 40487--40566 Score: 76
Period size: 21 Copynumber: 3.8 Consensus size: 21
40477 AGGAAGAAAT
* *
40487 AAAAAAAAAAGACAAAAAATTA-
1 AAAAAAAAAAG-GAAAAAA-GAG
40509 AAAAAAAAAAGGAAAAAAGAG
1 AAAAAAAAAAGGAAAAAAGAG
*
40530 AAAAAGAAAAGG-AAAAAGAAG
1 AAAAAAAAAAGGAAAAAAG-AG
*
40551 AAAATAAAAA-GAAAAA
1 AAAAAAAAAAGGAAAAA
40567 GGGGAGGTTG
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
20 8 0.16
21 31 0.62
22 11 0.22
ACGTcount: A:0.81, C:0.01, G:0.14, T:0.04
Consensus pattern (21 bp):
AAAAAAAAAAGGAAAAAAGAG
Found at i:40547 original size:12 final size:13
Alignment explanation
Indices: 40523--40565 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
40513 AAAAAAGGAA
40523 AAAAGAGAAAAAG
1 AAAAGAGAAAAAG
40536 AAAAG-GAAAAAG
1 AAAAGAGAAAAAG
* *
40548 AAGAAAATAAAAAG
1 AA-AAGAGAAAAAG
40562 AAAA
1 AAAA
40566 AGGGGAGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 9 0.35
13 9 0.35
14 8 0.31
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (13 bp):
AAAAGAGAAAAAG
Found at i:41613 original size:50 final size:50
Alignment explanation
Indices: 41472--41645 Score: 152
Period size: 50 Copynumber: 3.5 Consensus size: 50
41462 CGATAGAATA
** * * * *
41472 ACAAATCTTTTACCCCTAAAGCTGTGGAGGTGCAGATTGAAACCGCAATG
1 ACAAATCTCATACACCTAAAGCTGTAGAGGAGCAGATTGAAGCCGCAATG
* * * *
41522 ACAAATTTCATACACTTAAAGCTGTAGA-GAGGCAGAATGAAGCTGCAATG
1 ACAAATCTCATACACCTAAAGCTGTAGAGGA-GCAGATTGAAGCCGCAATG
* * * * * *
41572 GCAAATCTCATTCACCTAAAGCTGTAGAGGAGAAGATTGAAGTCACAAGG
1 ACAAATCTCATACACCTAAAGCTGTAGAGGAGCAGATTGAAGCCGCAATG
* * * *
41622 ACGAATCTTATACTCCTGAAGCTG
1 ACAAATCTCATACACCTAAAGCTG
41646 AAATGAAGCG
Statistics
Matches: 96, Mismatches: 26, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
49 1 0.01
50 93 0.97
51 2 0.02
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.23
Consensus pattern (50 bp):
ACAAATCTCATACACCTAAAGCTGTAGAGGAGCAGATTGAAGCCGCAATG
Found at i:41798 original size:80 final size:80
Alignment explanation
Indices: 41667--42081 Score: 688
Period size: 80 Copynumber: 5.2 Consensus size: 80
41657 AGTTACAACC
* *
41667 TCCAATCTTTTACCCTAACCAGAGGGTAAGATTGAAGATCATCCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
*
41732 GGTAGATTGAAGAAA
66 GGCAGATTGAAGAAA
* * * ** * *
41747 TCTAATCTTTTACCCTAACTAGAGGGCAAGATTGAAAACCATCTTATCTTTTACCCTGATCATGA
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
*
41812 GGCAGATTTAAGAAA
66 GGCAGATTGAAGAAA
41827 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
41892 GGCAGATTGAAGAAA
66 GGCAGATTGAAGAAA
*
41907 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCTGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
*
41972 GACAGATTGAAGAAA
66 GGCAGATTGAAGAAA
*
41987 TCCAATCTTTTATCCC-AACCAGAGGGCAAGATTGAAGACCATCCAATCTTTTACCCCGATCATG
1 TCCAATCTTTTA-CCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATG
42051 GGGCAGATTGAAGAAA
65 GGGCAGATTGAAGAAA
42067 TCCAATCTTTTACCC
1 TCCAATCTTTTACCC
42082 CGACTATGGG
Statistics
Matches: 310, Mismatches: 24, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
79 3 0.01
80 304 0.98
81 3 0.01
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.27
Consensus pattern (80 bp):
TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
GGCAGATTGAAGAAA
Found at i:42177 original size:79 final size:78
Alignment explanation
Indices: 41735--42198 Score: 264
Period size: 80 Copynumber: 5.8 Consensus size: 78
41725 ATCATGGGGT
* ** * * * **
41735 AGATTGAAGAAATCTAATCTTTTACCCTAACTA-GAGGGCAAGATTGAAAACCATCTTATCTTTT
1 AGATTGAAGAAATCCAATCTTTTACCCCGACCATG-GAGC-AGATTG-AAACAATCCAATCTTTT
* * *
41799 ACCCTGATCATG-AGGC
63 ACCTTAACCA-GAAGGC
* ** * * *
41815 AGATTTAAGAAATCCAATCTTTTACCCTAACCA-GAGGGCAAGATTGAAGACCATCCGATCTTTT
1 AGATTGAAGAAATCCAATCTTTTACCCCGACCATG-GAGC-AGATTGAA-ACAATCCAATCTTTT
*** * *
41879 ACCCCGATCATG-GGGC
63 ACCTTAACCA-GAAGGC
** * * **
41895 AGATTGAAGAAATCCAATCTTTTACCCTAACCA-GAGGGCAAGATTGAAGACCATCTGATCTTTT
1 AGATTGAAGAAATCCAATCTTTTACCCCGACCATG-GAGC-AGATTGAA-ACAATCCAATCTTTT
*** *
41959 ACCCCGATCATG--GGAC
63 ACCTTAACCA-GAAGG-C
* * * *
41975 AGATTGAAGAAATCCAATCTTTTATCCCAACCA-GAGGGCAAGATTGAAGACCATCCAATCTTTT
1 AGATTGAAGAAATCCAATCTTTTACCCCGACCATG-GAGC-AGATTGAA-ACAATCCAATCTTTT
*** * *
42039 ACCCCGATCATG-GGGC
63 ACCTTAACCA-GAAGGC
* * * *
42055 AGATTGAAGAAATCCAATCTTTTACCCCGACTATGGGGTAGATTGAAGCAATCCAATCTTTTACC
1 AGATTGAAGAAATCCAATCTTTTACCCCGACCATGGAGCAGATTGAAACAATCCAATCTTTTACC
42120 TTAACCAGAAGGC
66 TTAACCAGAAGGC
* *
42133 AGATTGAAGACCAT-CAGATCTTTTACCCCGACCATGGAGCAGATTGAAATAATCCAATCTTTTA
1 AGATTGAAGA-AATCCA-ATCTTTTACCCCGACCATGGAGCAGATTGAAACAATCCAATCTTTTA
42197 CC
64 CC
42199 CCTAAAACTA
Statistics
Matches: 347, Mismatches: 30, Indels: 15
0.89 0.08 0.04
Matches are distributed among these distances:
77 1 0.00
78 34 0.10
79 58 0.17
80 251 0.72
81 3 0.01
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (78 bp):
AGATTGAAGAAATCCAATCTTTTACCCCGACCATGGAGCAGATTGAAACAATCCAATCTTTTACC
TTAACCAGAAGGC
Found at i:42852 original size:57 final size:57
Alignment explanation
Indices: 42735--42891 Score: 167
Period size: 57 Copynumber: 2.6 Consensus size: 57
42725 ATTTTTATTT
*
42735 ATTTATTTATTATTATTTTCATAAATATAAATAAATAATAAAACAAAATTAATATTATTTTAC
1 ATTTATTTA-T-TTA-TTTCATAAA-ATAAATAAAT-A-AATACAAAATTAATATTATTTTAC
* *
42798 ATTTATTTATTTATATTCATAAAAT-AATAAATAAATATAAAA-TAATATTTATTTTAT
1 ATTTATTTATTTAT-TTCATAAAATAAATAAATAAATACAAAATTAATA-TTATTTTAC
* *
42855 ATTTATTTA-TTATTTTATGAATATAAATAAATAAATA
1 ATTTATTTATTTATTTCAT-AAAATAAATAAATAAATA
42892 AATAACAAAC
Statistics
Matches: 85, Mismatches: 5, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
55 4 0.05
56 13 0.15
57 36 0.42
58 1 0.01
59 7 0.08
60 3 0.04
61 11 0.13
62 1 0.01
63 9 0.11
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.48
Consensus pattern (57 bp):
ATTTATTTATTTATTTCATAAAATAAATAAATAAATACAAAATTAATATTATTTTAC
Found at i:42872 original size:61 final size:60
Alignment explanation
Indices: 42723--42895 Score: 176
Period size: 61 Copynumber: 2.8 Consensus size: 60
42713 AATTTTCTTA
*
42723 TTATTTT-TATTTATTTATTTATTATTATTTTCATAAAT-ATAAATAAATAATAAAACAAAAT
1 TTATTTTATATTTATTTA-TTATT-TTATATTCATAAATAATAAATAAAT-ATAAAACAAAAT
* * * *
42784 TAATATTAT-TTTACATTTATT-TATTTATATTCATAAAATAATAAATAAATATAAAATAATAT
1 TTATTTTATATTT--ATTTATTAT-TTTATATTCAT-AAATAATAAATAAATATAAAACAAAAT
*
42846 TTATTTTATATTTATTTATTATTTTATGAAT-ATAAATAAATAAATAAATA
1 TTATTTTATATTTATTTATTATTTTAT-ATTCATAAAT-AATAAATAAATA
42896 ACAAACCAAA
Statistics
Matches: 94, Mismatches: 8, Indels: 20
0.77 0.07 0.16
Matches are distributed among these distances:
60 4 0.04
61 44 0.47
62 28 0.30
63 18 0.19
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (60 bp):
TTATTTTATATTTATTTATTATTTTATATTCATAAATAATAAATAAATATAAAACAAAAT
Done.