Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010721.1 Kokia drynarioides strain JFW-HI SEQ_125672, 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: 22958
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:382 original size:130 final size:128
Alignment explanation
Indices: 150--409 Score: 484
Period size: 130 Copynumber: 2.0 Consensus size: 128
140 TGTTCTATTC
150 TTTTCTTCACGAATTTCCTGTTGCCACTATTCTGATGTTTTACCCAAACTAGCATCCTCATTGAC
1 TTTTCTTCACGAATTTCCTGTTGCCACTATTCTGATGTTTTACCCAAACTAGCATCCTCATTGAC
215 AAACAAAGTTTTTTGTAGTCTTTCTTCAGGCTATCGAAATCTTCTTCAACCTTCTTTTTCCCT
66 AAACAAAGTTTTTTGTAGTCTTTCTTCAGGCTATCGAAATCTTCTTCAACCTTCTTTTTCCCT
*
278 NTTTTCTTCACGAATTTCCTGTTGTCACTATTCTGATGTTTTACCCAAACTAGCAGTCCTCATTG
1 -TTTTCTTCACGAATTTCCTGTTGCCACTATTCTGATGTTTTACCCAAACTAGCA-TCCTCATTG
*
343 ACAAACGAAGTTTTTTGTAGTCTTTCTTCAGGCTATCGAAATCTTCTTCAACCTTCTTTTTCCCT
64 ACAAACAAAGTTTTTTGTAGTCTTTCTTCAGGCTATCGAAATCTTCTTCAACCTTCTTTTTCCCT
408 TT
1 TT
410 CCTTAATTTT
Statistics
Matches: 128, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
129 55 0.43
130 73 0.57
ACGTcount: A:0.21, C:0.25, G:0.11, T:0.43
Consensus pattern (128 bp):
TTTTCTTCACGAATTTCCTGTTGCCACTATTCTGATGTTTTACCCAAACTAGCATCCTCATTGAC
AAACAAAGTTTTTTGTAGTCTTTCTTCAGGCTATCGAAATCTTCTTCAACCTTCTTTTTCCCT
Found at i:1430 original size:10 final size:10
Alignment explanation
Indices: 1415--1439 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1405 ATAGTAACAG
1415 ATGCATATGA
1 ATGCATATGA
1425 ATGCATATGA
1 ATGCATATGA
1435 ATGCA
1 ATGCA
1440 AACTTATACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (10 bp):
ATGCATATGA
Found at i:2145 original size:60 final size:62
Alignment explanation
Indices: 2037--2158 Score: 176
Period size: 60 Copynumber: 2.0 Consensus size: 62
2027 AACGAGCATT
* * * ** *
2037 CCTTCGTTGTCAATTTCAAACGTTGAAAAGGGTATTTGATTATTCCGGTTTG-AAGAAAAAA
1 CCTTCGTTGCCAATTTCAAACCTTGAAAAAGGTATTCAATTATTCCGGTTTGCAAAAAAAAA
2098 CCTTCGTTGCCAATTTC-AACCTTGAAAAAGGTATTCAATTATTCCGGTTTGCAAAAAAAAA
1 CCTTCGTTGCCAATTTCAAACCTTGAAAAAGGTATTCAATTATTCCGGTTTGCAAAAAAAAA
2159 ATCGTGCTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
60 30 0.56
61 24 0.44
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Consensus pattern (62 bp):
CCTTCGTTGCCAATTTCAAACCTTGAAAAAGGTATTCAATTATTCCGGTTTGCAAAAAAAAA
Found at i:2586 original size:30 final size:29
Alignment explanation
Indices: 2552--3002 Score: 369
Period size: 30 Copynumber: 15.2 Consensus size: 29
2542 GGTCAAAACA
*
2552 TAATTTTGGAAAAGTTTAGTGGTAAAAATG
1 TAATTTTGGAAAAGTTTAG-GGTTAAAATG
** * *
2582 TAATTTTGGGTAAGTTTTGGGTCAAAATG
1 TAATTTTGGAAAAGTTTAGGGTTAAAATG
* * * *
2611 TGATTTTAGAGAAA-TCTAGGATTAAAATG
1 TAATTTTGGA-AAAGTTTAGGGTTAAAATG
* * * *
2640 TGA-TTTAGAAAAGGTTT-GAGGTAAAAATA
1 TAATTTTGGAAAA-GTTTAG-GGTTAAAATG
* * *
2669 TGATTTTGAAAAAGTTCGAGGGTTAAAATG
1 TAATTTTGGAAAAGTT-TAGGGTTAAAATG
*
2699 TAATTTTAGG-AAAGTTTAGGGGTCAAAATG
1 TAATTTT-GGAAAAGTTTA-GGGTTAAAATG
2729 TAATTTTGGAAAAGTTTAGAGGTT-AAATG
1 TAATTTTGGAAAAGTTTAG-GGTTAAAATG
*
2758 TAATTTTGGAAAGGTTTAGGGGTTAAAATG
1 TAATTTTGGAAAAGTTTA-GGGTTAAAATG
* *
2788 TAATTTTGGAAAAGTTT-GATGCTAAAATG
1 TAATTTTGGAAAAGTTTAG-GGTTAAAATG
* * *
2817 TAATTTT-AAAAAGGTTTGAGGGTCAAAATA
1 TAATTTTGGAAAA-GTTT-AGGGTTAAAATG
*
2847 TAATTTTGGAAAAGTTTAAGGGTTAAAATA
1 TAATTTTGGAAAAGTTT-AGGGTTAAAATG
* * *
2877 TAATTTTGGAAAGGTTCAAGGGTTAAAATA
1 TAATTTTGGAAAAGTT-TAGGGTTAAAATG
* * *
2907 TAATTTTGGAAAGGTTCAAGGGTT-AAATA
1 TAATTTTGGAAAAGTT-TAGGGTTAAAATG
* *
2936 TAATTTTGGAAAAATTTTAGGGGTTAAAATA
1 TAATTTTGG-AAAAGTTTA-GGGTTAAAATG
* * *
2967 TAATTTTGAAAAAGTTTGGGGTTATAATG
1 TAATTTTGGAAAAGTTTAGGGTTAAAATG
*
2996 TGATTTT
1 TAATTTT
3003 TTGAAGTTTA
Statistics
Matches: 350, Mismatches: 49, Indels: 45
0.79 0.11 0.10
Matches are distributed among these distances:
27 3 0.01
28 12 0.03
29 124 0.35
30 191 0.55
31 20 0.06
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.37
Consensus pattern (29 bp):
TAATTTTGGAAAAGTTTAGGGTTAAAATG
Found at i:2607 original size:59 final size:58
Alignment explanation
Indices: 2542--3002 Score: 396
Period size: 59 Copynumber: 7.8 Consensus size: 58
2532 GAGAATACAA
* * * *
2542 GGTCAAAACATAATTTTGGAAAAGTTTAGTGGTAAAAATGTAATTTTGGGTAAGTTT-TG
1 GGTCAAAATATAATTTTGGAAAAGTTTAG-GGTTAAAATGTAATTTT-GGAAAGTTTAGG
* * * * * * * * *
2601 GGTCAAAATGTGATTTTAGAGAAA-TCTAGGATTAAAATGTGATTTAGAAAAGGTTT-GA
1 GGTCAAAATATAATTTTGGA-AAAGTTTAGGGTTAAAATGTAATTTTGGAAA-GTTTAGG
* * * *
2659 GGTAAAAATATGATTTTGAAAAAGTTCGAGGGTTAAAATGTAATTTTAGGAAAGTTTAGG
1 GGTCAAAATATAATTTTGGAAAAGTT-TAGGGTTAAAATGTAATTTT-GGAAAGTTTAGG
*
2719 GGTCAAAATGTAATTTTGGAAAAGTTTAGAGGTT-AAATGTAATTTTGGAAAGGTTTAGG
1 GGTCAAAATATAATTTTGGAAAAGTTTAG-GGTTAAAATGTAATTTTGGAAA-GTTTAGG
* * * * **
2778 GGTTAAAATGTAATTTTGGAAAAGTTT-GATGCTAAAATGTAATTTTAAAAAGGTTT-GAG
1 GGTCAAAATATAATTTTGGAAAAGTTTAG-GGTTAAAATGTAATTTTGGAAA-GTTTAG-G
* * *
2837 GGTCAAAATATAATTTTGGAAAAGTTTAAGGGTTAAAATATAATTTTGGAAAGGTTCAAG
1 GGTCAAAATATAATTTTGGAAAAGTTT-AGGGTTAAAATGTAATTTTGGAAA-GTTTAGG
* * * * *
2897 GGTTAAAATATAATTTTGGAAAGGTTCAAGGGTT-AAATATAATTTTGGAAAAATTTTAGG
1 GGTCAAAATATAATTTTGGAAAAGTT-TAGGGTTAAAATGTAATTTTGG--AAAGTTTAGG
* * * * *
2957 GGTTAAAATATAATTTTGAAAAAGTTTGGGGTTATAATGTGATTTT
1 GGTCAAAATATAATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTT
3003 TTGAAGTTTA
Statistics
Matches: 329, Mismatches: 56, Indels: 33
0.79 0.13 0.08
Matches are distributed among these distances:
57 6 0.02
58 44 0.13
59 152 0.46
60 123 0.37
61 4 0.01
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.36
Consensus pattern (58 bp):
GGTCAAAATATAATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTTGGAAAGTTTAGG
Found at i:3024 original size:89 final size:87
Alignment explanation
Indices: 2663--3030 Score: 276
Period size: 89 Copynumber: 4.1 Consensus size: 87
2653 GTTTGAGGTA
* * * * *
2663 AAAATATGATTTTGAAAAAG-TTCGAGGGTTAAAATGTAATTTTAGG-AAAGTTTAGGGGTCAAA
1 AAAATATAATTTTGGAAAAGTTTAG-GGGTTAAAATATAATTTT-GGAAAAGTTT-GGGGTTAAA
* * * *
2726 ATGTAATTTTGGAAAAGTTTAGAGG-T
63 ATGTATTTTTAG-AAGGTTTA-AGGCC
* * * * ** *
2752 TAAATGTAATTTTGGAAAGGTTTAGGGGTTAAAATGTAATTTTGGAAAAGTTTGATGCTAAAATG
1 AAAATATAATTTTGGAAAAGTTTAGGGGTTAAAATATAATTTTGGAAAAGTTTGGGGTTAAAATG
* * * *
2817 TAATTTTAAAAAGGTTTGAGGGTC
66 T-ATTTTTAGAAGGTTT-AAGGCC
* * **
2841 AAAATATAATTTTGGAAAAGTTTAAGGGTTAAAATATAATTTTGGAAAGGTTCAAGGGTTAAAAT
1 AAAATATAATTTTGGAAAAGTTTAGGGGTTAAAATATAATTTTGGAAAAGTT-TGGGGTTAAAAT
* * * * **
2906 ATAATTTTGGAAAGGTTCAAGGGT
65 GTATTTTTAG-AAGGTTTAAGGCC
* * * *
2930 TAAATATAATTTTGGAAAAATTTTAGGGGTTAAAATATAATTTTGAAAAAGTTTGGGGTTATAAT
1 AAAATATAATTTTGG-AAAAGTTTAGGGGTTAAAATATAATTTTGGAAAAGTTTGGGGTTAAAAT
*
2995 GTGATTTTTTGAA-GTTTAAGGACC
65 GT-ATTTTTAGAAGGTTTAAGG-CC
*
3019 AAAATATGATTT
1 AAAATATAATTT
3031 CTAAAAAGTT
Statistics
Matches: 216, Mismatches: 53, Indels: 20
0.75 0.18 0.07
Matches are distributed among these distances:
88 26 0.12
89 134 0.62
90 56 0.26
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (87 bp):
AAAATATAATTTTGGAAAAGTTTAGGGGTTAAAATATAATTTTGGAAAAGTTTGGGGTTAAAATG
TATTTTTAGAAGGTTTAAGGCC
Found at i:3635 original size:3 final size:3
Alignment explanation
Indices: 3629--3672 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
3619 GTTATTATTA
3629 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
3673 TCATTGTGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:6665 original size:21 final size:22
Alignment explanation
Indices: 6640--6685 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
6630 GTTCTCTAAA
*
6640 CTTCCATT-CCATTTTCCCCCT
1 CTTCCATTGCCAATTTCCCCCT
*
6661 CTTCCTTTGCCAATTTCCCCCT
1 CTTCCATTGCCAATTTCCCCCT
6683 CTT
1 CTT
6686 GAGAAAGAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.09, C:0.46, G:0.02, T:0.43
Consensus pattern (22 bp):
CTTCCATTGCCAATTTCCCCCT
Found at i:7585 original size:6 final size:6
Alignment explanation
Indices: 7574--7615 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
7564 ATTTAATTTA
7574 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT A-TTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT A
7616 ACTTAGATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 5 0.14
6 30 0.86
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:7586 original size:18 final size:18
Alignment explanation
Indices: 7565--7615 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
7555 TGCATTGGAA
*
7565 TTTAATTTAATTTTTATT
1 TTTAATTTTATTTTTATT
*
7583 TTTATTTTTATTTTTATT
1 TTTAATTTTATTTTTATT
7601 TTT-ATTTTATTTTTA
1 TTTAATTTTATTTTTA
7616 ACTTAGATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 11 0.37
18 19 0.63
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTAATTTTATTTTTATT
Found at i:11875 original size:56 final size:56
Alignment explanation
Indices: 11800--12079 Score: 306
Period size: 56 Copynumber: 5.1 Consensus size: 56
11790 AAAACATTCA
* * * * *
11800 TGGCAAAGTCTGGAAAGGTAAGTCTTTGTGGCAAACCTCTTAAA-TAAACACTTTA
1 TGGCAAACTCTGGAAAGGTAAGCCTTTGTGGCAAACCTCTTAAAGGAAACGCTTTG
* * **
11855 TCGGTAAACTCTGGAAAGGTAAGTCGTTT-TGGCAAACCT-TTAAAGG-AACTTTTTG
1 T-GGCAAACTCTGGAAAGGTAAG-CCTTTGTGGCAAACCTCTTAAAGGAAACGCTTTG
* * *
11910 TGGCAAACTCTAGAAAGGTAAGCCTTTGTGACAAACCTCTTAAAGGAATGCGC-TTG
1 TGGCAAACTCTGGAAAGGTAAGCCTTTGTGGCAAACCTCTTAAAGGAA-ACGCTTTG
* * *
11966 TGGAAAACTCTAGAAAGGTAAGCCTTTATGGCAAACCTCTTAAAGGAAA-GCTTTTG
1 TGGCAAACTCTGGAAAGGTAAGCCTTTGTGGCAAACCTCTTAAAGGAAACGC-TTTG
* *
12022 TGGCAAACTTTGGAAAGGTAAG-CTTTGTGGCAAACCTCTGAAAGGAAA-GCCTTTG
1 TGGCAAACTCTGGAAAGGTAAGCCTTTGTGGCAAACCTCTTAAAGGAAACG-CTTTG
12077 TGG
1 TGG
12080 TGAGCATTAA
Statistics
Matches: 191, Mismatches: 24, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
53 4 0.02
54 30 0.16
55 52 0.27
56 101 0.53
57 4 0.02
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (56 bp):
TGGCAAACTCTGGAAAGGTAAGCCTTTGTGGCAAACCTCTTAAAGGAAACGCTTTG
Found at i:11899 original size:27 final size:27
Alignment explanation
Indices: 11813--12079 Score: 165
Period size: 28 Copynumber: 9.7 Consensus size: 27
11803 CAAAGTCTGG
*
11813 AAAGGTAAGTCTTTGTGGCAAACCTCTT
1 AAAGGTAAGCCTTTGTGGCAAACCT-TT
* * * **
11841 AAA--TAAACACTTTATCGGTAAACTCTGG
1 AAAGGTAAGC-CTTTGT-GGCAAAC-CTTT
*
11869 AAAGGTAAGTCGTTT-TGGCAAACCTTT
1 AAAGGTAAG-CCTTTGTGGCAAACCTTT
* **
11896 AAAGG-AA-CTTTTTGTGGCAAACTCTAG
1 AAAGGTAAGC-CTTTGTGGCAAAC-CTTT
*
11923 AAAGGTAAGCCTTTGTGACAAACCTCTT
1 AAAGGTAAGCCTTTGTGGCAAACCT-TT
* **
11951 AAAGG-AATGCGC-TTGTGGAAAACTCTAG
1 AAAGGTAA-GC-CTTTGTGGCAAAC-CTTT
*
11979 AAAGGTAAGCCTTTATGGCAAACCTCTT
1 AAAGGTAAGCCTTTGTGGCAAACCT-TT
* *
12007 AAAGGAAAGCTTTTGTGGCAAA-CTTT
1 AAAGGTAAGCCTTTGTGGCAAACCTTT
*
12033 GGAAAGGTAAG-CTTTGTGGCAAACCTCTG
1 --AAAGGTAAGCCTTTGTGGCAAACCT-TT
*
12062 AAAGGAAAGCCTTTGTGG
1 AAAGGTAAGCCTTTGTGG
12080 TGAGCATTAA
Statistics
Matches: 183, Mismatches: 33, Indels: 46
0.70 0.13 0.18
Matches are distributed among these distances:
24 1 0.01
25 3 0.02
26 15 0.08
27 47 0.26
28 100 0.55
29 10 0.05
30 6 0.03
31 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (27 bp):
AAAGGTAAGCCTTTGTGGCAAACCTTT
Found at i:11998 original size:110 final size:112
Alignment explanation
Indices: 11800--12069 Score: 338
Period size: 110 Copynumber: 2.4 Consensus size: 112
11790 AAAACATTCA
* * *
11800 TGGCAAAGTCTGGAAAGGTAAGTCTTTGTGGCAAACCTCTTAAA-TAAACACTTTATCGGTAAAC
1 TGGCAAACTCTGGAAAGGTAAG-CTTTGTGGCAAACCTCTTAAAGGAAACACTTTATCGGAAAAC
* *
11864 TCTGGAAAGGTAAGTCGTTTTGGCAAACCT-TTAAAGG-AA-CTTTTTG
65 TCTAGAAAGGTAAGTCCTTTTGGCAAACCTCTTAAAGGAAAGC-TTTTG
* * * * *
11910 TGGCAAACTCTAGAAAGGTAAGCCTTTGTGACAAACCTCTTAAAGGAATGCGC-TTGT-GGAAAA
1 TGGCAAACTCTGGAAAGGTAAG-CTTTGTGGCAAACCTCTTAAAGGAA-ACACTTTATCGGAAAA
11973 CTCTAGAAAGGTAAG-CCTTTATGGCAAACCTCTTAAAGGAAAGCTTTTG
64 CTCTAGAAAGGTAAGTCCTTT-TGGCAAACCTCTTAAAGGAAAGCTTTTG
* *
12022 TGGCAAACTTTGGAAAGGTAAGCTTTGTGGCAAACCTCTGAAAGGAAA
1 TGGCAAACTCTGGAAAGGTAAGCTTTGTGGCAAACCTCTTAAAGGAAA
12070 GCCTTTGTGG
Statistics
Matches: 138, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
109 4 0.03
110 69 0.50
111 35 0.25
112 29 0.21
113 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.27
Consensus pattern (112 bp):
TGGCAAACTCTGGAAAGGTAAGCTTTGTGGCAAACCTCTTAAAGGAAACACTTTATCGGAAAACT
CTAGAAAGGTAAGTCCTTTTGGCAAACCTCTTAAAGGAAAGCTTTTG
Found at i:15182 original size:33 final size:33
Alignment explanation
Indices: 15134--15210 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 33
15124 GTTAAGAGAT
* * *
15134 CAAATGGCTCAGATGCAACCGAGCACAGTTGAG
1 CAAATTGCTCAGATGCAACCAAGCACAGTCGAG
*
15167 -ACAATTGCTCAGATGCAAGCAAGCACAGTCGAG
1 CA-AATTGCTCAGATGCAACCAAGCACAGTCGAG
15200 CAAATTGCTCA
1 CAAATTGCTCA
15211 ACTTAAAGCG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 1 0.03
33 36 0.95
34 1 0.03
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (33 bp):
CAAATTGCTCAGATGCAACCAAGCACAGTCGAG
Found at i:15494 original size:14 final size:15
Alignment explanation
Indices: 15467--15498 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
15457 ATTTGAAGTT
15467 ATTGGTTGGATTTGA
1 ATTGGTTGGATTTGA
15482 ATTGGTT-GATTTGA
1 ATTGGTTGGATTTGA
15496 ATT
1 ATT
15499 TACAGGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (15 bp):
ATTGGTTGGATTTGA
Found at i:15786 original size:43 final size:41
Alignment explanation
Indices: 15609--15828 Score: 153
Period size: 43 Copynumber: 5.3 Consensus size: 41
15599 ACATTATTTA
* * * *
15609 TAGCGGAGTTTGTGGGAAAAGCGCTGCTAAAGACGATGATCAT
1 TAGCGGCGTTTGTGGG-AAAGCGC-GCTAAAGACCATGTTCTT
* * *
15652 TAGTGGCATTTGTGAGAAAAGCGTCGCTAAAGACCATGTTCTT
1 TAGCGGCGTTTGTG-GGAAAGCG-CGCTAAAGACCATGTTCTT
* * *
15695 TAGCGACATTTGTGGGAAAAGCAC-C----GCACCATGTTCTT
1 TAGCGGCGTTTGTGGG-AAAGCGCGCTAAAG-ACCATGTTCTT
* * * *
15733 TAACGACGTTTGTGGGAGAAGTGTCGCTGAAGACCATGTTCTT
1 TAGCGGCGTTTGTGGGA-AAGCG-CGCTAAAGACCATGTTCTT
* * * *
15776 TAGCGGCGTTTATGGGAAAGCTCCGCTAGAGACCATGTTCTA
1 TAGCGGCGTTTGTGGGAAAGC-GCGCTAAAGACCATGTTCTT
*
15818 TAGTGGCGTTT
1 TAGCGGCGTTT
15829 TTCCTCATAA
Statistics
Matches: 141, Mismatches: 24, Indels: 25
0.74 0.13 0.13
Matches are distributed among these distances:
37 2 0.01
38 28 0.20
39 1 0.01
40 1 0.01
41 1 0.01
42 31 0.22
43 74 0.52
44 3 0.02
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (41 bp):
TAGCGGCGTTTGTGGGAAAGCGCGCTAAAGACCATGTTCTT
Found at i:21147 original size:89 final size:89
Alignment explanation
Indices: 21032--21197 Score: 233
Period size: 89 Copynumber: 1.9 Consensus size: 89
21022 AAACTTTTCA
* * * * *
21032 AAAATTATATTTTAACCCTTGAACTTTCCAAAACTCACATTTTAACCTTCAAACTTTCCAAAAAT
1 AAAATTACATTTTAACCCTTAAACTTTCCAAAAATCACATTTTAACCCTAAAACTTTCCAAAAAT
*
21097 TACATTTTGACCTCCAAACTACTC
66 CACATTTTGACCTCCAAACTACTC
* * * *
21121 AAAATTACATTTTAACCCTTAAACTTTCTAAAAATTATATTTTAACCCTAAAACTTTCCTAAAAT
1 AAAATTACATTTTAACCCTTAAACTTTCCAAAAATCACATTTTAACCCTAAAACTTTCCAAAAAT
*
21186 CGCATTTTGACC
66 CACATTTTGACC
21198 GTAAACTCTC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
89 66 1.00
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.36
Consensus pattern (89 bp):
AAAATTACATTTTAACCCTTAAACTTTCCAAAAATCACATTTTAACCCTAAAACTTTCCAAAAAT
CACATTTTGACCTCCAAACTACTC
Found at i:21148 original size:59 final size:58
Alignment explanation
Indices: 21000--21175 Score: 212
Period size: 59 Copynumber: 3.0 Consensus size: 58
20990 TTGAACTTTT
* ** *
21000 TCAAAATTACATTTTAACCCTTAAACTTTTCAAAAATTATATTTTAACCCTTGAACTT
1 TCAAAATTACATTTTAACCCTTAAACTTTCCAAAAATTATATTTTAACCCTCAAACTC
* * *
21058 TCCAAAACTCACATTTTAA-CCTTCAAACTTTCCAAAAATTACATTTTGA-CCTCCAAACTAC
1 T-CAAAA-TTACATTTTAACCCTT-AAACTTTCCAAAAATTATATTTTAACCCT-CAAACT-C
* *
21119 TCAAAATTACATTTTAACCCTTAAACTTTCTAAAAATTATATTTTAACCCTAAAACT
1 TCAAAATTACATTTTAACCCTTAAACTTTCCAAAAATTATATTTTAACCCTCAAACT
21176 TTCCTAAAAT
Statistics
Matches: 99, Mismatches: 12, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
58 1 0.01
59 49 0.49
60 48 0.48
61 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.01, T:0.37
Consensus pattern (58 bp):
TCAAAATTACATTTTAACCCTTAAACTTTCCAAAAATTATATTTTAACCCTCAAACTC
Found at i:21175 original size:30 final size:30
Alignment explanation
Indices: 20965--21184 Score: 205
Period size: 30 Copynumber: 7.3 Consensus size: 30
20955 AGCACTTGCT
* * * * *
20965 CTTTTTAAAAATAACAATTTGACCCTTGAA
1 CTTTCTAAAAATTACATTTTAACCCTTAAA
* *
20995 CTTTTTCAAAATTACATTTTAACCCTTAAA
1 CTTTCTAAAAATTACATTTTAACCCTTAAA
* *
21025 CTTT-TCAAAAATTATATTTTAACCCTTGAA
1 CTTTCT-AAAAATTACATTTTAACCCTTAAA
* * *
21055 CTTTCCAAAACTCACATTTTAA-CCTTCAAA
1 CTTTCTAAAAATTACATTTTAACCCTT-AAA
* * *
21085 CTTTCCAAAAATTACATTTTGA-CCTCCAAA
1 CTTTCTAAAAATTACATTTTAACCCT-TAAA
* *
21115 C-TACTCAAAATTACATTTTAACCCTTAAA
1 CTTTCTAAAAATTACATTTTAACCCTTAAA
* *
21144 CTTTCTAAAAATTATATTTTAACCCTAAAA
1 CTTTCTAAAAATTACATTTTAACCCTTAAA
21174 CTTTCCTAAAA
1 CTTT-CTAAAA
21185 TCGCATTTTG
Statistics
Matches: 157, Mismatches: 26, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
29 25 0.16
30 126 0.80
31 6 0.04
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.38
Consensus pattern (30 bp):
CTTTCTAAAAATTACATTTTAACCCTTAAA
Found at i:22090 original size:322 final size:323
Alignment explanation
Indices: 21479--22062 Score: 791
Period size: 322 Copynumber: 1.8 Consensus size: 323
21469 AATAATTTCA
**
21479 AAACTGAGGCAACATCTTATCGTGAGAAAATCTCGAAAAATTATGCCCTAACGTGCTGGGTGTGA
1 AAACTGAGGCAACATCTTATCGTGAGAAAATCTCGAAAAATTATGCCCTAACGTGCTGGGTAAGA
* * * * *
21544 TTTTTCATATAATTCGTGTGATCGAATATCCTCTTTAAAACTTTTCAAAGAGTCCTTCAATTTCG
66 TTTTTCATATAATTCGCGCGACCAAATATCCTCTTTAAAACTTCTCAAAGAGTCCTTCAATTTCG
** * *
21609 AAATTCCGAGAACATCGTGCCCTAACGTGTTGGATACGACTTCAATTCTCTGGGAAATTCGAAAC
131 AAATTCAAAGAACATCGTGCCCTAACGTGTTGGACACGACTTCAATTCTCTGAGAAATTCGAAAC
* * *** *
21674 ACGCGGGCATTTTTCTTCAAATCTAACTTTTAAAATTCACGAGAAATAAGTTATTTGTCTGAGGA
196 ACGCGGGCATTTTTCTTCAAATCTAACTTTTAAAATTCAAGAGAAATAAGTTATGTGTAAAAAGA
*
21739 TCATATGTTAAACTTCATTCGAAATTTCAAGTTCTCAGAAAATATATAAATAATTTTAAACAC
261 TCATATGTTAAACTTCACTCGAAATTTCAAGTTCTCAGAAAATATATAAATAATTTTAAACAC
* * *
21802 AAAC-GAGGCAATATCTTTTCGTGTGAAAA-CTTCGAAAAATTATGCCCTAACGTGCTGGGTAAG
1 AAACTGAGGCAACATCTTATCGTGAGAAAATC-TCGAAAAATTATGCCCTAACGTGCTGGGTAAG
* * * *
21865 ATTTTTCGTATAATTCGCGCGACCAAATATTCTCTTTAAAACTTCTCAAAGTGTCCTTCAATTTT
65 ATTTTTCATATAATTCGCGCGACCAAATATCCTCTTTAAAACTTCTCAAAGAGTCCTTCAATTTC
* * * * *
21930 GAAATTCAAAGAACGTCGTGCCTTAACTTGTTGGACATGTCTTCAATTCTAC-GAGAAATTCGAA
130 GAAATTCAAAGAACATCGTGCCCTAACGTGTTGGACACGACTTCAATTCT-CTGAGAAATTCGAA
* * * *
21994 ACACGCGGGCATTTTTCTTCAAATTTGATTTTTGAAAA-TCAAGCA-AAATGAGTTATGTGTAAA
194 ACACGCGGGCATTTTTCTTCAAATCTAACTTTT-AAAATTCAAG-AGAAATAAGTTATGTGTAAA
22057 AAGATC
257 AAGATC
22063 GTATTTTACA
Statistics
Matches: 224, Mismatches: 33, Indels: 9
0.84 0.12 0.03
Matches are distributed among these distances:
321 1 0.00
322 213 0.95
323 10 0.04
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (323 bp):
AAACTGAGGCAACATCTTATCGTGAGAAAATCTCGAAAAATTATGCCCTAACGTGCTGGGTAAGA
TTTTTCATATAATTCGCGCGACCAAATATCCTCTTTAAAACTTCTCAAAGAGTCCTTCAATTTCG
AAATTCAAAGAACATCGTGCCCTAACGTGTTGGACACGACTTCAATTCTCTGAGAAATTCGAAAC
ACGCGGGCATTTTTCTTCAAATCTAACTTTTAAAATTCAAGAGAAATAAGTTATGTGTAAAAAGA
TCATATGTTAAACTTCACTCGAAATTTCAAGTTCTCAGAAAATATATAAATAATTTTAAACAC
Done.