Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011033.1 Kokia drynarioides strain JFW-HI SEQ_126004, 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: 28464
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Warning! 59 characters in sequence are not A, C, G, or T
Found at i:580 original size:30 final size:29
Alignment explanation
Indices: 544--696 Score: 112
Period size: 30 Copynumber: 5.1 Consensus size: 29
534 CCCTAAAGGT
*
544 CCCTAAACTATCTAAAAATTATATTTTAAC
1 CCCTAAACT-TCTAAAAATTACATTTTAAC
* *
574 CCCTAAACTTCTCCCAAAATTCCATTTTAA-
1 CCCTAAACTTCT--AAAAATTACATTTTAAC
** * *
604 CCCTAATTTTTCCAAAAATTACATTTTTAC
1 CCCTAA-ACTTCTAAAAATTACATTTTAAC
* * *
634 CCCTAAACTT-TCCAAAATTCCATTTTTGAC
1 CCCTAAACTTCT-AAAAATTACA-TTTTAAC
* * *
664 CCCGAAACTTCTTAAAATTACCATTTTATC
1 CCCTAAACTTCTAAAAATTA-CATTTTAAC
694 CCC
1 CCC
697 GGATGTCTAA
Statistics
Matches: 95, Mismatches: 20, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
29 26 0.27
30 50 0.53
31 19 0.20
ACGTcount: A:0.34, C:0.28, G:0.01, T:0.37
Consensus pattern (29 bp):
CCCTAAACTTCTAAAAATTACATTTTAAC
Found at i:660 original size:29 final size:29
Alignment explanation
Indices: 566--690 Score: 119
Period size: 30 Copynumber: 4.2 Consensus size: 29
556 TAAAAATTAT
*
566 ATTTTAACCCCTAAACTTCTCCCAAAATTCC
1 ATTTTTACCCCTAAACTT-T-CCAAAATTCC
* ** *
597 A-TTTTAACCCTAATTTTTCCAAAAATTAC
1 ATTTTTACCCCTAAACTTTCC-AAAATTCC
626 ATTTTTACCCCTAAACTTTCCAAAATTCC
1 ATTTTTACCCCTAAACTTTCCAAAATTCC
* *
655 ATTTTTGACCCCGAAAC-TTCTTAAAATTACC
1 ATTTTT-ACCCCTAAACTTTC-CAAAATT-CC
686 ATTTT
1 ATTTT
691 ATCCCCGGAT
Statistics
Matches: 78, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
28 2 0.03
29 25 0.32
30 43 0.55
31 8 0.10
ACGTcount: A:0.33, C:0.27, G:0.02, T:0.38
Consensus pattern (29 bp):
ATTTTTACCCCTAAACTTTCCAAAATTCC
Found at i:689 original size:60 final size:59
Alignment explanation
Indices: 548--696 Score: 158
Period size: 60 Copynumber: 2.5 Consensus size: 59
538 AAAGGTCCCT
* *
548 AAACTATCTAAAAATTATATTTTAACCCCTAAACTTCTCCCAAAATTCCATTTTAACCCT
1 AAACT-TCTAAAAATTACATTTTAACCCCTAAACTTCTCCCAAAATTCCATTTTAACCCG
** * * *
608 AATTTTTCCAAAAATTACATTTTTACCCCTAAACTT-T-CCAAAATTCCATTTTTGACCCCG
1 AA-ACTTCTAAAAATTACATTTTAACCCCTAAACTTCTCCCAAAATTCCA-TTTT-AACCCG
* *
668 AAACTTCTTAAAATTACCATTTTATCCCC
1 AAACTTCTAAAAATTA-CATTTTAACCCC
697 GGATGTCTAA
Statistics
Matches: 72, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
58 11 0.15
59 15 0.21
60 45 0.62
61 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.01, T:0.37
Consensus pattern (59 bp):
AAACTTCTAAAAATTACATTTTAACCCCTAAACTTCTCCCAAAATTCCATTTTAACCCG
Found at i:715 original size:59 final size:58
Alignment explanation
Indices: 647--869 Score: 223
Period size: 59 Copynumber: 3.7 Consensus size: 58
637 TAAACTTTCC
* * *
647 AAAATTCCATTTTTGACCCCGAAACTTCTTAAAATTACCATTTTATCCCCGGATGTCTA
1 AAAACTCCATTTTTGACCTCGAAACTTCTAAAAATTACCATTTTA-CCCCGGATGTCTA
* * * * * * *
706 AAAACTCCATTTTTTTTTATCTTGAACCTTCCAAAATTTACCATTTTACCCCCGAATGTCTA
1 AAAACTCCA---TTTTTGACCTCGAAACTTCTAAAAATTACCATTTTA-CCCCGGATGTCTA
* * * *
768 AAAACTCCATTTTTGA-TTCGAAACCTTCCAAAAATTACAATTTTACCTCCGGATGTCCA
1 AAAACTCCATTTTTGACCTCGAAA-CTTCTAAAAATTACCATTTTACC-CCGGATGTCTA
* **
827 AAAATTCCATTTTTGACCTCGAGCCTTCTAAAAATTACCATTT
1 AAAACTCCATTTTTGACCTCGAAACTTCTAAAAATTACCATTT
870 CGCCCCCGAG
Statistics
Matches: 133, Mismatches: 25, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
58 6 0.05
59 74 0.56
60 4 0.03
62 49 0.37
ACGTcount: A:0.31, C:0.25, G:0.07, T:0.36
Consensus pattern (58 bp):
AAAACTCCATTTTTGACCTCGAAACTTCTAAAAATTACCATTTTACCCCGGATGTCTA
Found at i:4222 original size:42 final size:44
Alignment explanation
Indices: 4130--4211 Score: 123
Period size: 42 Copynumber: 1.9 Consensus size: 44
4120 TTGAATTTAA
* *
4130 TTTAATAGTTTTATTTTTTATTTTGAAGCAAGTAAGATTACACT
1 TTTAATTGTTTTATTTTTTATTTTGAAGCAAATAAGATTACACT
*
4174 TTTAATTGTTTTA-TTTTTA-TTTGAAGTAAATAAGATTA
1 TTTAATTGTTTTATTTTTTATTTTGAAGCAAATAAGATTA
4212 TTTTTTTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
42 17 0.49
43 6 0.17
44 12 0.34
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.52
Consensus pattern (44 bp):
TTTAATTGTTTTATTTTTTATTTTGAAGCAAATAAGATTACACT
Found at i:4955 original size:41 final size:39
Alignment explanation
Indices: 4898--5024 Score: 155
Period size: 41 Copynumber: 3.1 Consensus size: 39
4888 GAAATTCCAA
4898 AAAAACGCTTCAACGTGAAAGCATTTTTCCTTGATTGAGAC
1 AAAAACGCTTC-ACGTGAAA-CATTTTTCCTTGATTGAGAC
* *
4939 AAAAACGCTCTTACGTGGAAACATTTTTTCTTGATTGAGAC
1 AAAAACGCT-TCACGT-GAAACATTTTTCCTTGATTGAGAC
* * * *
4980 AAAAACGCTTCACGTGAAATCACTTTTCATTGACTGAGAT
1 AAAAACGCTTCACGTGAAA-CATTTTTCCTTGATTGAGAC
5020 AAAAA
1 AAAAA
5025 TACTCTTGCA
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
39 4 0.05
40 25 0.33
41 41 0.55
42 5 0.07
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (39 bp):
AAAAACGCTTCACGTGAAACATTTTTCCTTGATTGAGAC
Found at i:6852 original size:6 final size:6
Alignment explanation
Indices: 6843--6910 Score: 56
Period size: 6 Copynumber: 11.7 Consensus size: 6
6833 GATCCAATAG
*
6843 AATTTA AATTTA AATTT- -ATTTAA AATTTA AATTT- -ATCATA AATTT-
1 AATTTA AATTTA AATTTA AATTT-A AATTTA AATTTA AAT-TTA AATTTA
*
6888 AATTTCA AATTTA AAATTA AATT
1 AATTT-A AATTTA AATTTA AATT
6911 AATGTTCAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
4 6 0.12
5 6 0.12
6 27 0.54
7 11 0.22
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (6 bp):
AATTTA
Found at i:6870 original size:17 final size:16
Alignment explanation
Indices: 6844--6889 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
6834 ATCCAATAGA
6844 ATTTAAATTTAAATTT
1 ATTTAAATTTAAATTT
6860 ATTTAAAATTTAAATTT
1 ATTT-AAATTTAAATTT
*
6877 ATCATAAATTTAA
1 AT-TTAAATTTAA
6890 TTTCAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 4 0.15
17 22 0.81
18 1 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTAAATTTAAATTT
Found at i:6908 original size:24 final size:24
Alignment explanation
Indices: 6881--6926 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
6871 AAATTTATCA
*
6881 TAAATTTAAT-TTCAAATTTAAAAT
1 TAAA-TTAATGTTCAAATATAAAAT
6905 TAAATTAATGTTCAAATATAAA
1 TAAATTAATGTTCAAATATAAA
6927 CACAAGTGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.41
Consensus pattern (24 bp):
TAAATTAATGTTCAAATATAAAAT
Found at i:7713 original size:17 final size:17
Alignment explanation
Indices: 7685--7757 Score: 87
Period size: 17 Copynumber: 4.4 Consensus size: 17
7675 TTGAAAATTG
7685 AATTTA-TTTAAATTTA
1 AATTTATTTTAAATTTA
7701 AGA-TTATTTTAAATTTA
1 A-ATTTATTTTAAATTTA
*
7718 AATTTATTTGAAATTTA
1 AATTTATTTTAAATTTA
* * *
7735 AATTCATTATAAAATTA
1 AATTTATTTTAAATTTA
7752 AATTTA
1 AATTTA
7758 GAAAGTCCAA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
16 5 0.10
17 43 0.90
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:7753 original size:34 final size:33
Alignment explanation
Indices: 7678--7757 Score: 108
Period size: 34 Copynumber: 2.4 Consensus size: 33
7668 GGACCTATTG
* *
7678 AAAATTGAATTTATTTAAATTTAAGATTATTTT
1 AAAATTAAATTTATTTAAATTTAAGATTATTAT
*
7711 AAATTTAAATTTATTTGAAATTTAA-ATTCATTAT
1 AAAATTAAATTTATTT-AAATTTAAGATT-ATTAT
7745 AAAATTAAATTTA
1 AAAATTAAATTTA
7758 GAAAGTCCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
33 17 0.41
34 24 0.59
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (33 bp):
AAAATTAAATTTATTTAAATTTAAGATTATTAT
Found at i:7777 original size:13 final size:14
Alignment explanation
Indices: 7759--7799 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
7749 TTAAATTTAG
7759 AAAGTCCAATTAA-
1 AAAGTCCAATTAAC
7772 AAAGTCCAA--AAC
1 AAAGTCCAATTAAC
7784 AAAGTCCAATT-AC
1 AAAGTCCAATTAAC
7797 AAA
1 AAA
7800 TGGTTCAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 2 0.08
12 9 0.36
13 14 0.56
ACGTcount: A:0.56, C:0.20, G:0.07, T:0.17
Consensus pattern (14 bp):
AAAGTCCAATTAAC
Found at i:7853 original size:15 final size:15
Alignment explanation
Indices: 7805--7853 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
7795 ACAAATGGTT
*
7805 CAATTACAAACGGCC
1 CAATTACAAACGACC
* *
7820 CAAATACAAATGACC
1 CAATTACAAACGACC
*
7835 CAATTACAAGCGACC
1 CAATTACAAACGACC
7850 CAAT
1 CAAT
7854 GGCCCAAAGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.45, C:0.31, G:0.10, T:0.14
Consensus pattern (15 bp):
CAATTACAAACGACC
Found at i:8508 original size:19 final size:19
Alignment explanation
Indices: 8486--8544 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 19
8476 ATAAATATTT
*
8486 TAAATAATATTAATAATAA
1 TAAATAATTTTAATAATAA
*
8505 TAAAT-ATTTTAAAGAATAA
1 TAAATAATTTT-AATAATAA
8524 TAAATAACGTTTTAATAATAA
1 TAAATAA--TTTTAATAATAA
8545 AAAGGGAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 4 0.12
19 17 0.52
20 1 0.03
21 7 0.21
22 4 0.12
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (19 bp):
TAAATAATTTTAATAATAA
Found at i:9630 original size:29 final size:30
Alignment explanation
Indices: 9598--9810 Score: 194
Period size: 29 Copynumber: 7.3 Consensus size: 30
9588 AAAATCCCAT
*
9598 TTTTAACCCT-GAAACTTTTAAAAATTCTA
1 TTTTAACCCTCGAAACTTTCAAAAATTCTA
* *
9627 TTTT-ACCCTCG-AAC-TTCTAAAAATCCCA
1 TTTTAACCCTCGAAACTTTC-AAAAATTCTA
*
9655 TTTTTAACCCT-AAAACTTTCAAAAATTCTA
1 -TTTTAACCCTCGAAACTTTCAAAAATTCTA
* * * *
9685 TTTTTACCC-CTAAAC-TTCTAAAAATCCCA
1 TTTTAACCCTCGAAACTTTC-AAAAATTCTA
*
9714 TTTTAA-CCTCGAAACTTTCAAAAATTATA
1 TTTTAACCCTCGAAACTTTCAAAAATTCTA
* * * *
9743 TTTTTACCCTCG-AACTTCCAAAAATCCCA
1 TTTTAACCCTCGAAACTTTCAAAAATTCTA
9772 TTTTTAA-CCTCGAAACTTTCAAAAATTCTA
1 -TTTTAACCCTCGAAACTTTCAAAAATTCTA
*
9802 TTTTTACCC
1 TTTTAACCC
9811 CTAAAATTTA
Statistics
Matches: 145, Mismatches: 25, Indels: 27
0.74 0.13 0.14
Matches are distributed among these distances:
27 2 0.01
28 21 0.14
29 74 0.51
30 45 0.31
31 3 0.02
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (30 bp):
TTTTAACCCTCGAAACTTTCAAAAATTCTA
Found at i:9657 original size:58 final size:59
Alignment explanation
Indices: 9587--9844 Score: 350
Period size: 58 Copynumber: 4.4 Consensus size: 59
9577 TAAATTACCC
* *
9587 AAAAATCCCATTTTTAACC-CTGAAACTTTTAAAAATTCTA-TTTTA-CCCTCGAACTTCT
1 AAAAATCCCATTTTTAACCTC-GAAACTTTCAAAAATTCTATTTTTACCCCT-AAACTTCT
*
9645 AAAAATCCCATTTTTAACC-CTAAAACTTTCAAAAATTCTATTTTTACCCCTAAACTTCT
1 AAAAATCCCATTTTTAACCTC-GAAACTTTCAAAAATTCTATTTTTACCCCTAAACTTCT
* * *
9704 AAAAATCCCA-TTTTAACCTCGAAACTTTCAAAAATTATATTTTTA-CCCTCGAACTTCC
1 AAAAATCCCATTTTTAACCTCGAAACTTTCAAAAATTCTATTTTTACCCCT-AAACTTCT
*
9762 AAAAATCCCATTTTTAACCTCGAAACTTTCAAAAATTCTATTTTTACCCCTAAAATT-T
1 AAAAATCCCATTTTTAACCTCGAAACTTTCAAAAATTCTATTTTTACCCCTAAACTTCT
*
9820 AAAAAATCCCATTTTTGACCTCGAA
1 -AAAAATCCCATTTTTAACCTCGAA
9845 TTTTCCCAAA
Statistics
Matches: 181, Mismatches: 12, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
57 4 0.02
58 85 0.47
59 84 0.46
60 8 0.04
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (59 bp):
AAAAATCCCATTTTTAACCTCGAAACTTTCAAAAATTCTATTTTTACCCCTAAACTTCT
Found at i:9793 original size:117 final size:117
Alignment explanation
Indices: 9587--9844 Score: 398
Period size: 117 Copynumber: 2.2 Consensus size: 117
9577 TAAATTACCC
* * *
9587 AAAAATCCCATTTTTAACC-CTGAAACTTTTAAAAATTCTATTTTACCCTCGAACTTCTAAAAAT
1 AAAAATCCCATTTTTAACCTC-GAAACTTTCAAAAATTATATTTTACCCTCGAACTTCCAAAAAT
*
9651 CCCATTTTTAACCCTAAAACTTTCAAAAATTCTATTTTTACCCCTAAACTTCT-
65 CCCATTTTTAACCCTAAAACTTTCAAAAATTCTATTTTTACCCCTAAAATT-TA
9704 AAAAATCCCA-TTTTAACCTCGAAACTTTCAAAAATTATATTTTTACCCTCGAACTTCCAAAAAT
1 AAAAATCCCATTTTTAACCTCGAAACTTTCAAAAATTATA-TTTTACCCTCGAACTTCCAAAAAT
*
9768 CCCATTTTTAA-CCTCGAAACTTTCAAAAATTCTATTTTTACCCCTAAAATTTA
65 CCCATTTTTAACCCT-AAAACTTTCAAAAATTCTATTTTTACCCCTAAAATTTA
*
9821 AAAAATCCCATTTTTGACCTCGAA
1 AAAAATCCCATTTTTAACCTCGAA
9845 TTTTCCCAAA
Statistics
Matches: 130, Mismatches: 6, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
116 29 0.22
117 89 0.68
118 12 0.09
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (117 bp):
AAAAATCCCATTTTTAACCTCGAAACTTTCAAAAATTATATTTTACCCTCGAACTTCCAAAAATC
CCATTTTTAACCCTAAAACTTTCAAAAATTCTATTTTTACCCCTAAAATTTA
Found at i:19053 original size:748 final size:738
Alignment explanation
Indices: 17619--19104 Score: 2882
Period size: 748 Copynumber: 2.0 Consensus size: 738
17609 TTAAGAGTTC
17619 CAAGATATCTTTGCGTGGTCTTACCACGATATGCCCGGCTTAAGTACTGACATTGTGGTGCATAA
1 CAAGATATCTTTGCGTGGTCTTACCACGATATGCCCGGCTTAAGTACTGACATTGTGGTGCATAA
17684 ACTCCCTGTAAAGGAAGAAAGCAGGCCTGTGCAGTAAAAACTCCAAAGGATGAGACTGAATGTGT
66 ACTCCCTGTAAAGGAAGAAAGCAGGCCTGTGCAGTAAAAACTCCAAAGGATGAGACTGAATGTGT
17749 TGTTAAAAATAAAAGAAGAAGTCAGGAAACAATTTGACGCCGATTTCCTCTTGGTGGTTAAATAC
131 TGTTAAAAATAAAAGAAGAAGTCAGGAAACAATTTGACGCCGATTTCCTCTTGGTGGTTAAATAC
17814 TCTGAATGGGTAGCTAATATAGTCCCCGTTCCCAAAAAAGATGGAAAGGTGTGTATGTGTGTGGA
196 TCTGAATGGGTAGCTAATATAGTCCCCGTTCCCAAAAAAGATGGAAAGGTGTGTATGTGTGTGGA
17879 CTGTCGAGATTTAAATAAAGCTAGCCCAAAGGATAATTTTTCTTTGCCCCAAATCGACACTCTAG
261 CTGTCGAGATTTAAATAAAGCTAGCCCAAAGGATAATTTTTCTTTGCCCCAAATCGACACTCTAG
17944 TCGACAACACGGCAGGACATTCCCTGTTTTCCTTCATGGATGGCTTCTCTAGGTATAATCAGGTA
326 TCGACAACACGGCAGGACATTCCCTGTTTTCCTTCATGGATGGCTTCTCTAGGTATAATCAGGTA
18009 AGGATGGACCCTGAGGATATGACCAAAACAACTTTTGTCACGCTATGGGGAACATTTTGTTACAA
391 AGGATGGACCCTGAGGATATGACCAAAACAACTTTTGTCACGCTATGGGGAACATTTTGTTACAA
18074 AGTGATGCCCTTCGGACTAAAAAATGTAGGGACAACTTATCAGAGGGCCATGATGACCCTGTTCC
456 AGTGATGCCCTTCGGACTAAAAAATGTAGGGACAACTTATCAGAGGGCCATGATGACCCTGTTCC
18139 ATAACATGATGCACAAAAAGATTAAGGTTTACGTCGATGACATGATTGTGAAATCTCAAACGGAG
521 ATAACATGATGCACAAAAAGATTAAGGTTTACGTCGATGACATGATTGTGAAATCTCAAACGGAG
18204 GAGAAACATGTAAGAATCCTAAGAAGGTTATTTGGAAGGCTAAGGAAATATCAACTAAATTTGAA
586 GAGAAACATGTAAGAATCCTAAGAAGGTTATTTGGAAGGCTAAGGAAATATCAACTAAATTTGAA
18269 TCCAGCAAAATGCACTTTCGGGGCCACATCAGGAAAATTGTTAGGTTTTGAGGTCAGCAAAAGAG
651 TCCAGCAAAATGCACTTTCGGGGCCACATCAGGAAAATTGTTAGGTTTTGAGGTCAGCAAAAGAG
18334 GAATTGAAATAGACCCGGATAAA
716 GAATTGAAATAGACCCGGATAAA
18357 NNNNNNNNNNCAAGATATCTTTGCGTGGTCTTACCACGATATGCCCGGCTTAAGTACTGACATTG
1 ----------CAAGATATCTTTGCGTGGTCTTACCACGATATGCCCGGCTTAAGTACTGACATTG
18422 TGGTGCATAAACTCCCTGTAAAGGAAGAAAGCAGGCCTGTGCAGTAAAAACTCCAAAGGATGAGA
56 TGGTGCATAAACTCCCTGTAAAGGAAGAAAGCAGGCCTGTGCAGTAAAAACTCCAAAGGATGAGA
18487 CTGAATGTGTTGTTAAAAATAAAAGAAGAAGTCAGGAAACAATTTGACGCCGATTTCCTCTTGGT
121 CTGAATGTGTTGTTAAAAATAAAAGAAGAAGTCAGGAAACAATTTGACGCCGATTTCCTCTTGGT
18552 GGTTAAATACTCTGAATGGGTAGCTAATATAGTCCCCGTTCCCAAAAAAGATGGAAAGGTGTGTA
186 GGTTAAATACTCTGAATGGGTAGCTAATATAGTCCCCGTTCCCAAAAAAGATGGAAAGGTGTGTA
18617 TGTGTGTGGACTGTCGAGATTTAAATAAAGCTAGCCCAAAGGATAATTTTTCTTTGCCCCAAATC
251 TGTGTGTGGACTGTCGAGATTTAAATAAAGCTAGCCCAAAGGATAATTTTTCTTTGCCCCAAATC
18682 GACACTCTAGTCGACAACACGGCAGGACATTCCCTGTTTTCCTTCATGGATGGCTTCTCTAGGTA
316 GACACTCTAGTCGACAACACGGCAGGACATTCCCTGTTTTCCTTCATGGATGGCTTCTCTAGGTA
18747 TAATCAGGTAAGGATGGACCCTGAGGATATGACCAAAACAACTTTTGTCACGCTATGGGGAACAT
381 TAATCAGGTAAGGATGGACCCTGAGGATATGACCAAAACAACTTTTGTCACGCTATGGGGAACAT
18812 TTTGTTACAAAGTGATGCCCTTCGGACTAAAAAATGTAGGGACAACTTATCAGAGGGCCATGATG
446 TTTGTTACAAAGTGATGCCCTTCGGACTAAAAAATGTAGGGACAACTTATCAGAGGGCCATGATG
18877 ACCCTGTTCCATAACATGATGCACAAAAAGATTAAGGTTTACGTCGATGACATGATTGTGAAATC
511 ACCCTGTTCCATAACATGATGCACAAAAAGATTAAGGTTTACGTCGATGACATGATTGTGAAATC
18942 TCAAACGGAGGAGAAACATGTAAGAATCCTAAGAAGGTTATTTGGAAGGCTAAGGAAATATCAAC
576 TCAAACGGAGGAGAAACATGTAAGAATCCTAAGAAGGTTATTTGGAAGGCTAAGGAAATATCAAC
19007 TAAATTTGAATCCAGCAAAATGCACTTTCGGGGCCACATCAGGAAAATTGTTAGGTTTTGAGGTC
641 TAAATTTGAATCCAGCAAAATGCACTTTCGGGGCCACATCAGGAAAATTGTTAGGTTTTGAGGTC
19072 AGCAAAAGAGGAATTGAAATAGACCCGGATAAA
706 AGCAAAAGAGGAATTGAAATAGACCCGGATAAA
19105 GTCAAAGCTA
Statistics
Matches: 738, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
748 738 1.00
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (738 bp):
CAAGATATCTTTGCGTGGTCTTACCACGATATGCCCGGCTTAAGTACTGACATTGTGGTGCATAA
ACTCCCTGTAAAGGAAGAAAGCAGGCCTGTGCAGTAAAAACTCCAAAGGATGAGACTGAATGTGT
TGTTAAAAATAAAAGAAGAAGTCAGGAAACAATTTGACGCCGATTTCCTCTTGGTGGTTAAATAC
TCTGAATGGGTAGCTAATATAGTCCCCGTTCCCAAAAAAGATGGAAAGGTGTGTATGTGTGTGGA
CTGTCGAGATTTAAATAAAGCTAGCCCAAAGGATAATTTTTCTTTGCCCCAAATCGACACTCTAG
TCGACAACACGGCAGGACATTCCCTGTTTTCCTTCATGGATGGCTTCTCTAGGTATAATCAGGTA
AGGATGGACCCTGAGGATATGACCAAAACAACTTTTGTCACGCTATGGGGAACATTTTGTTACAA
AGTGATGCCCTTCGGACTAAAAAATGTAGGGACAACTTATCAGAGGGCCATGATGACCCTGTTCC
ATAACATGATGCACAAAAAGATTAAGGTTTACGTCGATGACATGATTGTGAAATCTCAAACGGAG
GAGAAACATGTAAGAATCCTAAGAAGGTTATTTGGAAGGCTAAGGAAATATCAACTAAATTTGAA
TCCAGCAAAATGCACTTTCGGGGCCACATCAGGAAAATTGTTAGGTTTTGAGGTCAGCAAAAGAG
GAATTGAAATAGACCCGGATAAA
Found at i:22720 original size:200 final size:202
Alignment explanation
Indices: 22300--23254 Score: 1065
Period size: 200 Copynumber: 4.7 Consensus size: 202
22290 TATCCACGAG
* * *
22300 CAACGCGGTCATCTTCCTGGTGAGACACTGAGAAGAAGACCCAAACAAGGCTCAAAGTGTGCAAA
1 CAACGCAGTCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACAAGGCTCAAAGTGAGCAAA
*
22365 ATCTTCGAACCCCAACTTCCTGATGAGACACTGAGAAGCAGGTCAAAGCAATAAAAGGTTAGCTT
66 ATCTTCGAACCCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTT
* * * *
22430 TCTAATGAGATACTGAAG-AGTCAACCAAGTTCACCTTCCTAATGAGATACAGAGAAGCGAGTTG
131 CCTGATGAGATACTGAAGAAGTCAACCAAATTCGCCTTCCTAATGAGATACAGAGAAGCGAGTTG
22494 AAACAAA
196 AAACAAA
* * *
22501 CAACGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGATCCAAAAAAGGCTCAAAGTGAGCAAA
1 CAACGCAGTCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACAAGGCTCAAAGTGAGCAAA
*
22566 ATCTTCGAACCCCAGC-TCCTTGATGAGACA-TCGAGAAGCAGGTCGAAGCAAT-AAAGGTTAGC
66 ATCTTCGAACCCCAACTTCC-TGATGAGACACT-GAGAAGCAGGTCGAAGCAATAAAAGGTTAGC
*
22628 TTCCTGATGAGATACTGAAG-AGTCAACCAAATCCGCCTTCCTAATGAGATACAGAGAAGCGAGT
129 TTCCTGATGAGATACTGAAGAAGTCAACCAAATTCGCCTTCCTAATGAGATACAGAGAAGCGAGT
*
22692 TGAAACCAA
194 TGAAACAAA
*
22701 CAACGCAGTCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACAAGGCTTAAAGTGCA-CAA
1 CAACGCAGTCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACAAGGCTCAAAGTG-AGCAA
* *
22765 AATCTTCAAACCCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCGATAAAAGGTTAGCT
65 AATCTTCGAACCCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCT
* * * *
22830 TCCTGATGAGATACTG-AGAAGTGAACCAAATTCGTCTTCCTAATGAGATACAGAGGAGCGAATT
130 TCCTGATGAGATACTGAAGAAGTCAACCAAATTCGCCTTCCTAATGAGATACAGAGAAGCGAGTT
22894 GAAACAAA
195 GAAACAAA
* * * *
22902 CAGCG-ATGTGATCATCTTCCTGATGAGGCACTGAGAAGAAGTCCCAAACGAGGCTCGAAA-TGA
1 CAACGCA---G-TCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACAAGGCTC-AAAGTGA
* * * * * * **
22965 GCGAAATCTTCGAACCCCAGCTT-CT--T--G--ATTGAGAGGTAGGTTGAAGCAATAAAATTAT
61 GCAAAATCTTCGAACCCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA-GGT
* * * * ** * * *
23023 TAGATTCTTGATGAAATACT-ACGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAGC
125 TAGCTTCCTGATGAGATACTGAAGAAGTCAACCAAATTCGCCTTCCTAATGAGATACAGAGAAGC
23087 GTA-TTGAAACAAA
190 G-AGTTGAAACAAA
* * * * * * *
23100 CGATGCAGTCGTCTTCCTGATAAGATACTGAGAAGAAGACCAAAACAAACCCGCGCTCGATA-TG
1 CAACGCAGTCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAAC-AA---G-GCTC-AAAGTG
* * * * *
23164 AGC-AAATCTTCGAA-CCCAAGTATCTTGGTGAGATACT-AGGAAGCAGGTCGAAGTAATAAAAC
60 AGCAAAATCTTCGAACCCCAACT-TCCTGATGAGACACTGA-GAAGCAGGTCGAAGCAATAAAA-
* * *
23226 GGTTAGCTCCCAGATGAGATATTG-AGAAG
122 GGTTAGCTTCCTGATGAGATACTGAAGAAG
23255 AAAGCCAAGT
Statistics
Matches: 645, Mismatches: 77, Indels: 59
0.83 0.10 0.08
Matches are distributed among these distances:
195 32 0.05
196 2 0.00
197 22 0.03
198 74 0.11
199 16 0.02
200 199 0.31
201 189 0.29
202 1 0.00
203 4 0.01
204 63 0.10
205 4 0.01
206 39 0.06
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (202 bp):
CAACGCAGTCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACAAGGCTCAAAGTGAGCAAA
ATCTTCGAACCCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTT
CCTGATGAGATACTGAAGAAGTCAACCAAATTCGCCTTCCTAATGAGATACAGAGAAGCGAGTTG
AAACAAA
Found at i:23616 original size:17 final size:17
Alignment explanation
Indices: 23588--23660 Score: 94
Period size: 17 Copynumber: 4.4 Consensus size: 17
23578 TTGGAAATTG
23588 AATTTA-TTTAAATTTA
1 AATTTATTTTAAATTTA
*
23604 AGTTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
23621 AATTTATTTGAAATTTA
1 AATTTATTTTAAATTTA
* * *
23638 AATTCATTATAAAATTA
1 AATTTATTTTAAATTTA
23655 AATTTA
1 AATTTA
23661 GAAAGTTCAA
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
16 5 0.10
17 43 0.90
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:23636 original size:7 final size:6
Alignment explanation
Indices: 23593--23641 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
23583 AATTGAATTT
* *
23593 ATTTAA ATTTAA GTTT-A TTTTAA ATTTAA ATTT-- ATTTGAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA
23639 ATT
1 ATT
23642 CATTATAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
4 4 0.11
5 4 0.11
6 24 0.67
7 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (6 bp):
ATTTAA
Found at i:23656 original size:34 final size:33
Alignment explanation
Indices: 23582--23660 Score: 104
Period size: 34 Copynumber: 2.4 Consensus size: 33
23572 GACCTATTGG
* * * *
23582 AAATTGAATTTATTTAAATTTAAGTTTATTTTA
1 AAATTAAATTTATTTAAATTTAAATTCATTATA
*
23615 AATTTAAATTTATTTGAAATTTAAATTCATTATA
1 AAATTAAATTTATTT-AAATTTAAATTCATTATA
23649 AAATTAAATTTA
1 AAATTAAATTTA
23661 GAAAGTTCAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 13 0.33
34 26 0.67
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (33 bp):
AAATTAAATTTATTTAAATTTAAATTCATTATA
Found at i:23712 original size:15 final size:15
Alignment explanation
Indices: 23692--23746 Score: 92
Period size: 15 Copynumber: 3.7 Consensus size: 15
23682 AAAACAAAGT
23692 CCAATTACAAATGGC
1 CCAATTACAAATGGC
*
23707 CCAATTACAAACGGC
1 CCAATTACAAATGGC
*
23722 CCAATTACAAATGAC
1 CCAATTACAAATGGC
23737 CCAATTACAA
1 CCAATTACAA
23747 GCGACCCAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.44, C:0.29, G:0.09, T:0.18
Consensus pattern (15 bp):
CCAATTACAAATGGC
Found at i:23726 original size:30 final size:30
Alignment explanation
Indices: 23692--23756 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
23682 AAAACAAAGT
* *
23692 CCAATTACAAATGGCCCAATTACAAACGGC
1 CCAATTACAAATGACCCAATTACAAACGAC
*
23722 CCAATTACAAATGACCCAATTACAAGCGAC
1 CCAATTACAAATGACCCAATTACAAACGAC
23752 CCAAT
1 CCAAT
23757 GGCCCAAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.42, C:0.31, G:0.11, T:0.17
Consensus pattern (30 bp):
CCAATTACAAATGACCCAATTACAAACGAC
Found at i:23752 original size:15 final size:15
Alignment explanation
Indices: 23692--23756 Score: 85
Period size: 15 Copynumber: 4.3 Consensus size: 15
23682 AAAACAAAGT
* *
23692 CCAATTACAAATGGC
1 CCAATTACAAACGAC
*
23707 CCAATTACAAACGGC
1 CCAATTACAAACGAC
*
23722 CCAATTACAAATGAC
1 CCAATTACAAACGAC
*
23737 CCAATTACAAGCGAC
1 CCAATTACAAACGAC
23752 CCAAT
1 CCAAT
23757 GGCCCAAAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.42, C:0.31, G:0.11, T:0.17
Consensus pattern (15 bp):
CCAATTACAAACGAC
Found at i:24309 original size:3 final size:3
Alignment explanation
Indices: 24301--24386 Score: 172
Period size: 3 Copynumber: 28.7 Consensus size: 3
24291 ATAAATGTAT
24301 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
24349 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
24387 GCAACGTTAA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 83 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:24475 original size:19 final size:19
Alignment explanation
Indices: 24453--24513 Score: 88
Period size: 19 Copynumber: 3.2 Consensus size: 19
24443 AAATATTTTT
24453 AATAATTTTAATAATAATA
1 AATAATTTTAATAATAATA
*
24472 AATATTTTTAATAATAATA
1 AATAATTTTAATAATAATA
24491 AATAACGTTTTAATAATAA-A
1 AATAA--TTTTAATAATAATA
24511 AAT
1 AAT
24514 GGAAATTGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 22 0.58
20 4 0.11
21 12 0.32
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (19 bp):
AATAATTTTAATAATAATA
Found at i:25609 original size:29 final size:30
Alignment explanation
Indices: 25565--25820 Score: 251
Period size: 30 Copynumber: 8.7 Consensus size: 30
25555 CTAAATTACC
* * *
25565 CAAAAAATCTATTTTTAACCTCGAAACTTT
1 CAAAAATTCTATTTTTAACCCCTAAACTTT
25595 CAAAAATTCTA-TTTT-ACCCCTAAAC-TT
1 CAAAAATTCTATTTTTAACCCCTAAACTTT
*
25622 CTAAAAA-TCTCATTTTTAACCCCGAAACTTT
1 C-AAAAATTCT-ATTTTTAACCCCTAAACTTT
*
25653 CAAAAATTATA-TTTT-ACCCCTAAACTTT
1 CAAAAATTCTATTTTTAACCCCTAAACTTT
* * * *
25681 TAAAAATCCCATTTTTAACCCCAAAACTTT
1 CAAAAATTCTATTTTTAACCCCTAAACTTT
* * * *
25711 TAAAAATTCAATTTTT-ACCCCCAAACTTC
1 CAAAAATTCTATTTTTAACCCCTAAACTTT
*
25740 CAAAAA-TCTCATTTTTAACCCCAAAACTTT
1 CAAAAATTCT-ATTTTTAACCCCTAAACTTT
* *
25770 CAAAAATTTTATTTCT-ACCCCTAAACTTT
1 CAAAAATTCTATTTTTAACCCCTAAACTTT
* * *
25799 CAAAAATCCCATTTTTGACCCC
1 CAAAAATTCTATTTTTAACCCC
25821 GAATTTTCCC
Statistics
Matches: 188, Mismatches: 26, Indels: 24
0.79 0.11 0.10
Matches are distributed among these distances:
27 6 0.03
28 35 0.19
29 62 0.33
30 78 0.41
31 7 0.04
ACGTcount: A:0.38, C:0.26, G:0.01, T:0.36
Consensus pattern (30 bp):
CAAAAATTCTATTTTTAACCCCTAAACTTT
Found at i:25648 original size:58 final size:58
Alignment explanation
Indices: 25567--25823 Score: 356
Period size: 58 Copynumber: 4.4 Consensus size: 58
25557 AAATTACCCA
*
25567 AAAAATCT-ATTTTTAACCTCGAAACTTTCAAAAATTCTATTTTACCCCTAAACTTCT
1 AAAAATCTCATTTTTAACCCCGAAACTTTCAAAAATTCTATTTTACCCCTAAACTTCT
* *
25624 AAAAATCTCATTTTTAACCCCGAAACTTTCAAAAATTATATTTTACCCCTAAACTTTT
1 AAAAATCTCATTTTTAACCCCGAAACTTTCAAAAATTCTATTTTACCCCTAAACTTCT
* * * * * *
25682 AAAAATCCCATTTTTAACCCCAAAACTTTTAAAAATTCAATTTTTACCCCCAAACTTCC
1 AAAAATCTCATTTTTAACCCCGAAACTTTCAAAAATTCTA-TTTTACCCCTAAACTTCT
* *
25741 AAAAATCTCATTTTTAACCCCAAAACTTTCAAAAATTTTATTTCTACCCCTAAACTT-T
1 AAAAATCTCATTTTTAACCCCGAAACTTTCAAAAATTCTATTT-TACCCCTAAACTTCT
* *
25799 CAAAAATCCCATTTTTGACCCCGAA
1 -AAAAATCTCATTTTTAACCCCGAA
25824 TTTTCCCAAA
Statistics
Matches: 176, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
57 8 0.05
58 84 0.48
59 84 0.48
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (58 bp):
AAAAATCTCATTTTTAACCCCGAAACTTTCAAAAATTCTATTTTACCCCTAAACTTCT
Found at i:25756 original size:59 final size:59
Alignment explanation
Indices: 25567--25820 Score: 343
Period size: 59 Copynumber: 4.4 Consensus size: 59
25557 AAATTACCCA
* * *
25567 AAAAATCT-ATTTTTAACCTCGAAACTTTCAAAAATTCTA-TTTTACCCCTAAACTTCT
1 AAAAATCTCATTTTTAACCCCAAAACTTTCAAAAATTCTATTTTTACCCCTAAACTTCC
* * **
25624 AAAAATCTCATTTTTAACCCCGAAACTTTCAAAAATTATA-TTTTACCCCTAAACTTTT
1 AAAAATCTCATTTTTAACCCCAAAACTTTCAAAAATTCTATTTTTACCCCTAAACTTCC
* * * *
25682 AAAAATCCCATTTTTAACCCCAAAACTTTTAAAAATTCAATTTTTACCCCCAAACTTCC
1 AAAAATCTCATTTTTAACCCCAAAACTTTCAAAAATTCTATTTTTACCCCTAAACTTCC
* * *
25741 AAAAATCTCATTTTTAACCCCAAAACTTTCAAAAATTTTATTTCTACCCCTAAACTTTC
1 AAAAATCTCATTTTTAACCCCAAAACTTTCAAAAATTCTATTTTTACCCCTAAACTTCC
* *
25800 AAAAATCCCATTTTTGACCCC
1 AAAAATCTCATTTTTAACCCC
25821 GAATTTTCCC
Statistics
Matches: 175, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
57 8 0.05
58 81 0.46
59 86 0.49
ACGTcount: A:0.37, C:0.26, G:0.01, T:0.36
Consensus pattern (59 bp):
AAAAATCTCATTTTTAACCCCAAAACTTTCAAAAATTCTATTTTTACCCCTAAACTTCC
Done.