Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011397.1 Kokia drynarioides strain JFW-HI SEQ_126379, 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: 23608
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.33
Warning! 454 characters in sequence are not A, C, G, or T
Found at i:590 original size:29 final size:29
Alignment explanation
Indices: 540--966 Score: 329
Period size: 29 Copynumber: 14.6 Consensus size: 29
530 ACCCCTGAAC
* *
540 TTCC-AAAATTTCATTTTAACCCTAAATT
1 TTCCAAAAATTACATTTTTACCCTAAATT
* * *
568 TTCCAAAAAGTACATTTTTACCCCAAACT
1 TTCCAAAAATTACATTTTTACCCTAAATT
* * * * *
597 ATCC-AAAATTCCATTTTTGATCTCGAATTT
1 TTCCAAAAATTACATTTTT-A-CCCTAAATT
* *
627 TTCAAAAAATTACATTTTTACCCTCAAACT
1 TTCCAAAAATTACATTTTTACCCT-AAATT
* * * *
657 TTCC-AAAATTCCATTTTGACCTTGAATT
1 TTCCAAAAATTACATTTTTACCCTAAATT
* *
685 TTCCAAAAATTATATTTTTACCCTTGAATT
1 TTCCAAAAATTACATTTTTACCC-TAAATT
* *
715 TTCC-AAAATTTCATTTTTAACCTCAAATT
1 TTCCAAAAATTACATTTTTACCCT-AAATT
* * *
744 TTCCAAAAATTACATTTCTACCCTTGAACT
1 TTCCAAAAATTACATTTTTACCC-TAAATT
* *
774 TTCC-AAAATTCCATTTTGACCCTAAAATT
1 TTCCAAAAATTACATTTTTACCCT-AAATT
*
803 TT-CAAAAATTACATTTTTACCCCTAAACT
1 TTCCAAAAATTACATTTTTA-CCCTAAATT
* * *
832 TTCC-AAAATTCCATTTTGACCTTAAATT
1 TTCCAAAAATTACATTTTTACCCTAAATT
*
860 TTCCCAAAATT-CATTTTTACCCCGT-AATT
1 TTCCAAAAATTACATTTTTA-CCC-TAAATT
*
889 TTTC-AAAA-TACCATTTTTAACCCTAAATT
1 TTCCAAAAATTA-CATTTTT-ACCCTAAATT
* *
918 TTCCAAAAATATA-TTTTTTACCCTTAAACT
1 TTCCAAAAAT-TACATTTTTACCC-TAAATT
*
948 TTCTAAAAATTACTATTTT
1 TTCCAAAAATTAC-ATTTT
967 ACCTTGAATG
Statistics
Matches: 314, Mismatches: 58, Indels: 51
0.74 0.14 0.12
Matches are distributed among these distances:
27 1 0.00
28 49 0.16
29 168 0.54
30 76 0.24
31 18 0.06
32 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.02, T:0.41
Consensus pattern (29 bp):
TTCCAAAAATTACATTTTTACCCTAAATT
Found at i:708 original size:58 final size:57
Alignment explanation
Indices: 512--1000 Score: 432
Period size: 58 Copynumber: 8.4 Consensus size: 57
502 CCCTAAAATG
* * * * * * *
512 TCCAAAAATCATATTTTGACCCCTGAAC-TTCCAAAATTTCATTTTAACCCTAAATTT
1 TCCAAAAATTACATTTTTACCCC-AAACTTTCCAAAATTCCATTTTGACCTTAAATTT
* * * * *
569 TCCAAAAAGTACATTTTTACCCCAAACTATCCAAAATTCCATTTTTGATCTCGAATTTT
1 TCCAAAAATTACATTTTTACCCCAAACTTTCCAAAATTCCA-TTTTGACCT-TAAATTT
* *
628 TCAAAAAATTACATTTTTACCCTCAAACTTTCCAAAATTCCATTTTGACCTTGAATTT
1 TCCAAAAATTACATTTTTACCC-CAAACTTTCCAAAATTCCATTTTGACCTTAAATTT
* ** * * * *
686 TCCAAAAATTATATTTTTACCCTTGAATTTTCCAAAATTTCATTTTTAACCTCAAATTT
1 TCCAAAAATTACATTTTTACCC-CAAACTTTCCAAAATTCCA-TTTTGACCTTAAATTT
* ** *
745 TCCAAAAATTACATTTCTACCCTTGAACTTTCCAAAATTCCATTTTGACCCTAAAATTT
1 TCCAAAAATTACATTTTTACCC-CAAACTTTCCAAAATTCCATTTTGA-CCTTAAATTT
804 T-CAAAAATTACATTTTTACCCCTAAACTTTCCAAAATTCCATTTTGACCTTAAATTT
1 TCCAAAAATTACATTTTTACCCC-AAACTTTCCAAAATTCCATTTTGACCTTAAATTT
* * * * * * *
861 TCCCAAAATT-CATTTTTACCCCGTAATTTTTCAAAATACCATTTTTAACCCTAAATTT
1 TCCAAAAATTACATTTTTACCCC-AAACTTTCCAAAATTCCA-TTTTGACCTTAAATTT
* * * * * *
919 TCCAAAAATATA-TTTTTTACCCTTAAACTTTCTAAAAATTACTATTTT-ACCTTGAA-TG
1 TCCAAAAAT-TACATTTTTACCC-CAAACTTTC-CAAAATT-CCATTTTGACCTTAAATTT
* *
977 TCTAAAAATTCCATTTTTAACCCC
1 TCCAAAAATTACATTTTT-ACCCC
1001 GAATCCTTCC
Statistics
Matches: 354, Mismatches: 62, Indels: 31
0.79 0.14 0.07
Matches are distributed among these distances:
56 3 0.01
57 67 0.19
58 136 0.38
59 119 0.34
60 27 0.08
61 2 0.01
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40
Consensus pattern (57 bp):
TCCAAAAATTACATTTTTACCCCAAACTTTCCAAAATTCCATTTTGACCTTAAATTT
Found at i:746 original size:117 final size:117
Alignment explanation
Indices: 540--955 Score: 493
Period size: 117 Copynumber: 3.6 Consensus size: 117
530 ACCCCTGAAC
* * * *
540 TTCCAAAATTTCATTTTAACCCTAAATTTTCCAAAAAGTACATTTTTACCC-CAAACTATCCAAA
1 TTCCAAAATTCCATTTTAACCCTAAATTTTCCAAAAATTACATTTTTACCCTTAAACTTTCCAAA
* * *
604 ATTCCATTTTTGATCTCGAATTTTTCAAAAAATTACATTTTTACCCTCAAACT
66 ATTCCATTTTTGACCTC-AAATTTTCCAAAAATTACATTTTTACCCTCAAACT
* * * * * *
657 TTCCAAAATTCCATTTTGACCTTGAATTTTCCAAAAATTATATTTTTACCCTTGAATTTTCCAAA
1 TTCCAAAATTCCATTTTAACCCTAAATTTTCCAAAAATTACATTTTTACCCTTAAACTTTCCAAA
* * * **
722 ATTTCATTTTTAACCTCAAATTTTCCAAAAATTACATTTCTACCCTTGAACT
66 ATTCCATTTTTGACCTCAAATTTTCCAAAAATTACATTTTTACCCTCAAACT
* *
774 TTCCAAAATTCCATTTTGACCCTAAAATTTT-CAAAAATTACATTTTTACCCCTAAACTTTCCAA
1 TTCCAAAATTCCATTTTAACCCT-AAATTTTCCAAAAATTACATTTTTACCCTTAAACTTTCCAA
* * * *
838 AATTCCA-TTTTGACCTTAAATTTTCCCAAAATT-CATTTTTACCC-CGTAATT
65 AATTCCATTTTTGACCTCAAATTTTCCAAAAATTACATTTTTACCCTC-AAACT
* * * *
889 TTTCAAAATACCATTTTTAACCCTAAATTTTCCAAAAATATA-TTTTTTACCCTTAAACTTTCTA
1 TTCCAAAATTCCA-TTTTAACCCTAAATTTTCCAAAAAT-TACATTTTTACCCTTAAACTTTCCA
953 AAA
64 AAA
956 ATTACTATTT
Statistics
Matches: 255, Mismatches: 38, Indels: 13
0.83 0.12 0.04
Matches are distributed among these distances:
115 31 0.12
116 61 0.24
117 134 0.53
118 29 0.11
ACGTcount: A:0.35, C:0.22, G:0.02, T:0.41
Consensus pattern (117 bp):
TTCCAAAATTCCATTTTAACCCTAAATTTTCCAAAAATTACATTTTTACCCTTAAACTTTCCAAA
ATTCCATTTTTGACCTCAAATTTTCCAAAAATTACATTTTTACCCTCAAACT
Found at i:1024 original size:58 final size:58
Alignment explanation
Indices: 962--1071 Score: 141
Period size: 59 Copynumber: 1.9 Consensus size: 58
952 AAAAATTACT
* *
962 ATTTTA-CCTTGAATGTCTAAAAATTCCATTTTTAACCCCGAATCCTTCCAAAGTTATC
1 ATTTTACCCTCGAATGTCTAAAAACTCCATTTTTAACCCCGAA-CCTTCCAAAGTTATC
** * * *
1020 ATTTTACCCTCGGGTGTCTAAAAACTCCGTTTTTAACCTCGAACTTTCCAAA
1 ATTTTACCCTCGAATGTCTAAAAACTCCATTTTTAACCCCGAACCTTCCAAA
1072 AATCACCATT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
58 14 0.32
59 30 0.68
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.36
Consensus pattern (58 bp):
ATTTTACCCTCGAATGTCTAAAAACTCCATTTTTAACCCCGAACCTTCCAAAGTTATC
Found at i:1089 original size:59 final size:59
Alignment explanation
Indices: 974--1101 Score: 141
Period size: 59 Copynumber: 2.2 Consensus size: 59
964 TTTACCTTGA
* * * * *
974 ATGTCTAAAAATTCCATTTTTAACCCCGAATCCTTCCAAAGTTATCATTTTACCCTCGG
1 ATGTCTAAAAACTCCATTTTTAACCCCGAATCCTTCCAAAATCACCATTATACCCTCGG
* * * * *
1033 GTGTCTAAAAACTCCGTTTTTAACCTCGAA-CTTTCCAAAAATCACCATTATGCCCTCGG
1 ATGTCTAAAAACTCCATTTTTAACCCCGAATCCTTCC-AAAATCACCATTATACCCTCGG
*
1092 ACGTCTAAAA
1 ATGTCTAAAA
1102 TTTTTTTTTT
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
58 5 0.09
59 51 0.91
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.32
Consensus pattern (59 bp):
ATGTCTAAAAACTCCATTTTTAACCCCGAATCCTTCCAAAATCACCATTATACCCTCGG
Found at i:7292 original size:25 final size:24
Alignment explanation
Indices: 7238--7292 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
7228 AATAATATAT
*
7238 TTATTTATTATTTTGATATATTAA
1 TTATTTATTATTTTCATATATTAA
*
7262 TATATTTATTAATTGTTCATTTATT-A
1 T-TATTTATT-ATT-TTCATATATTAA
7288 TTATT
1 TTATT
7293 AGAAATTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 1 0.04
25 12 0.46
26 5 0.19
27 8 0.31
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.64
Consensus pattern (24 bp):
TTATTTATTATTTTCATATATTAA
Found at i:7386 original size:20 final size:20
Alignment explanation
Indices: 7358--7400 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
7348 ACATACCTGC
*
7358 CCCGGCCACTGCCGTCGAAG
1 CCCGACCACTGCCGTCGAAG
* *
7378 CCCGACCACTGCGGTCGGAG
1 CCCGACCACTGCCGTCGAAG
7398 CCC
1 CCC
7401 TGGACGGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.47, G:0.30, T:0.09
Consensus pattern (20 bp):
CCCGACCACTGCCGTCGAAG
Found at i:7687 original size:25 final size:22
Alignment explanation
Indices: 7659--7707 Score: 62
Period size: 25 Copynumber: 2.1 Consensus size: 22
7649 AAAAAGAGGG
7659 ACAGATTCGAAATAACAAAAAGCAA
1 ACAGATTCGAAA-AA-AAAAA-CAA
*
7684 ACAGATTTGAAAAAAAAAACAA
1 ACAGATTCGAAAAAAAAAACAA
7706 AC
1 AC
7708 GTTCTTCTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 5 0.22
23 5 0.22
24 2 0.09
25 11 0.48
ACGTcount: A:0.63, C:0.14, G:0.10, T:0.12
Consensus pattern (22 bp):
ACAGATTCGAAAAAAAAAACAA
Found at i:8500 original size:30 final size:30
Alignment explanation
Indices: 8446--8833 Score: 262
Period size: 30 Copynumber: 13.1 Consensus size: 30
8436 CCTAGGCAAT
8446 CCCC-AAACTTTT-TCAAAA-TACATTTTAA
1 CCCCTAAACTTTTCT-AAAATTACATTTTAA
8474 CCCCTAAACTTTTCTAAAATTACATTTTAA
1 CCCCTAAACTTTTCTAAAATTACATTTTAA
* * * *
8504 CCCCCAAGCTTTTTTAAAATTACATTTGAA
1 CCCCTAAACTTTTCTAAAATTACATTTTAA
* * * *
8534 CTCCTCGAACTTCTTC-AAAATTACCTTTTGA
1 CCCCT-AAACTT-TTCTAAAATTACATTTTAA
* * ** * * *
8565 TCTC-AATTTTTTTCCAAAACTACATTTTGA
1 CCCCTAA-ACTTTTCTAAAATTACATTTTAA
8595 CCCCT-AAC-TTTCTCAAAATTACATTTTAA
1 CCCCTAAACTTTTCT-AAAATTACATTTTAA
* * * *
8624 CACCTAAACTTCTCTAAAAATACATTTTGA
1 CCCCTAAACTTTTCTAAAATTACATTTTAA
* *
8654 -CCCTCAAACTTCTCTAAAATTACATGTTAA
1 CCCCT-AAACTTTTCTAAAATTACATTTTAA
* * * *
8684 CCCTTAAACTTTCCCTGAAATCACATTTTAA
1 CCCCTAAACTTT-TCTAAAATTACATTTTAA
* * * *
8715 CCCTTAAACTTTTCTAAAATCATAATTTAA
1 CCCCTAAACTTTTCTAAAATTACATTTTAA
* *
8745 -CCCTAAAC-TTTCTCAAAATCACATTTTGA
1 CCCCTAAACTTTTCT-AAAATTACATTTTAA
* * * * *
8774 CCTC-AAACTTTTCCAAATTTGCATTTTGA
1 CCCCTAAACTTTTCTAAAATTACATTTTAA
* **
8803 --CCTAAACTTTTCCAAAATTATGTTTTAA
1 CCCCTAAACTTTTCTAAAATTACATTTTAA
8831 CCC
1 CCC
8834 AGAATTCTCC
Statistics
Matches: 280, Mismatches: 60, Indels: 38
0.74 0.16 0.10
Matches are distributed among these distances:
27 1 0.00
28 33 0.12
29 71 0.25
30 123 0.44
31 50 0.18
32 2 0.01
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (30 bp):
CCCCTAAACTTTTCTAAAATTACATTTTAA
Found at i:8684 original size:60 final size:58
Alignment explanation
Indices: 8586--8784 Score: 212
Period size: 61 Copynumber: 3.4 Consensus size: 58
8576 TTCCAAAACT
*
8586 ACATTTTGACCC-CTAACTTTCTCAAAATTACATTTTAACACCTAAACTTCTCTAAAAAT-
1 ACATTTTGACCCTCAAACTTTCT-AAAATTACA-TTTAAC-CCTAAACTTCTCTAAAAATC
* *
8645 ACATTTTGACCCTCAAACTTCTCTAAAATTACATGTTAACCCTTAAACTTTCCCT-GAAATC
1 ACATTTTGACCCTCAAACTT-TCTAAAATTACAT-TTAACCC-TAAAC-TTCTCTAAAAATC
* * *
8706 ACATTTTAACCCTTAAACTTTTCTAAAATCATA-ATTTAACCCTAAACTT-TCTCAAAATC
1 ACATTTTGACCCTCAAAC-TTTCTAAAAT--TACATTTAACCCTAAACTTCTCTAAAAATC
8765 ACATTTTGA-CCTCAAACTTT
1 ACATTTTGACCCTCAAACTTT
8785 TCCAAATTTG
Statistics
Matches: 121, Mismatches: 9, Indels: 22
0.80 0.06 0.14
Matches are distributed among these distances:
57 3 0.02
58 9 0.07
59 30 0.25
60 34 0.28
61 39 0.32
62 4 0.03
63 2 0.02
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.36
Consensus pattern (58 bp):
ACATTTTGACCCTCAAACTTTCTAAAATTACATTTAACCCTAAACTTCTCTAAAAATC
Found at i:8828 original size:28 final size:28
Alignment explanation
Indices: 8701--8820 Score: 98
Period size: 29 Copynumber: 4.1 Consensus size: 28
8691 ACTTTCCCTG
* * *
8701 AAATCACATTTTAACCCTTAAACTTTTCTA
1 AAATCATATTTTGA-CC-TAAACTTTTCCA
* *
8731 AAATCATAATTTAACCCTAAAC-TTTCTCA
1 AAATCATATTTTGA-CCTAAACTTTTC-CA
*
8760 AAATCACATTTTGACCTCAAACTTTTCCA
1 AAATCATATTTTGACCT-AAACTTTTCCA
* ***
8789 AATTTGCATTTTGACCTAAACTTTTCCA
1 AAATCATATTTTGACCTAAACTTTTCCA
8817 AAAT
1 AAAT
8821 TATGTTTTAA
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
28 21 0.27
29 37 0.48
30 19 0.25
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.38
Consensus pattern (28 bp):
AAATCATATTTTGACCTAAACTTTTCCA
Found at i:15851 original size:30 final size:30
Alignment explanation
Indices: 15790--15932 Score: 134
Period size: 29 Copynumber: 4.9 Consensus size: 30
15780 GAGAAATTGA
* * *
15790 GGTTAAAATGT-AATTTTGTAAAAATTT-AG
1 GGTTAAAATGTGATTTTTG-GAAAGTTTAAG
**
15819 GGTCGAAATGTGATTTTTGGAAAGTTTAAG
1 GGTTAAAATGTGATTTTTGGAAAGTTTAAG
*
15849 GGTTAAAATGT-ATTTTTGGAAAGTTTAGG
1 GGTTAAAATGTGATTTTTGGAAAGTTTAAG
* * * * *
15878 GGAT-AAATTTGAATTTTTAGAAA-ATTAGG
1 GGTTAAAATGTG-ATTTTTGGAAAGTTTAAG
15907 GGTTAAAATGTGATTTTTGGAAAGTT
1 GGTTAAAATGTGATTTTTGGAAAGTT
15933 CTGGGACCTC
Statistics
Matches: 92, Mismatches: 16, Indels: 11
0.77 0.13 0.09
Matches are distributed among these distances:
28 5 0.05
29 53 0.58
30 34 0.37
ACGTcount: A:0.35, C:0.01, G:0.24, T:0.40
Consensus pattern (30 bp):
GGTTAAAATGTGATTTTTGGAAAGTTTAAG
Found at i:17858 original size:15 final size:15
Alignment explanation
Indices: 17834--17874 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
17824 CATCTTGATC
17834 TCTCATTTTTTGTTTT
1 TCTCATTTTTT-TTTT
*
17850 T-TTATTTTTTTTTT
1 TCTCATTTTTTTTTT
17864 TCTCATTTTTT
1 TCTCATTTTTT
17875 AGGTGAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 5 0.23
15 16 0.73
16 1 0.05
ACGTcount: A:0.07, C:0.10, G:0.02, T:0.80
Consensus pattern (15 bp):
TCTCATTTTTTTTTT
Found at i:18692 original size:13 final size:13
Alignment explanation
Indices: 18674--18698 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18664 TAACTTTACT
18674 TTTTTTTCTTTTC
1 TTTTTTTCTTTTC
18687 TTTTTTTCTTTT
1 TTTTTTTCTTTT
18699 TTTNNNNNNN
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTCTTTTC
Found at i:18990 original size:14 final size:14
Alignment explanation
Indices: 18968--19005 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
18958 TTCGTCTTAA
*
18968 CTTTACTTTTTTTT
1 CTTTTCTTTTTTTT
18982 CTTTTC-TTTTTTT
1 CTTTTCTTTTTTTT
18995 CTTTT-TTTTTT
1 CTTTTCTTTTTT
19006 GTGTTGGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 17 0.77
14 5 0.23
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (14 bp):
CTTTTCTTTTTTTT
Found at i:18993 original size:13 final size:12
Alignment explanation
Indices: 18974--19005 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
18964 TTAACTTTAC
18974 TTTTTTTTCTTT
1 TTTTTTTTCTTT
18986 TCTTTTTTTCTTT
1 T-TTTTTTTCTTT
18999 TTTTTTT
1 TTTTTTT
19006 GTGTTGGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (12 bp):
TTTTTTTTCTTT
Found at i:23432 original size:30 final size:29
Alignment explanation
Indices: 23368--23574 Score: 161
Period size: 30 Copynumber: 7.0 Consensus size: 29
23358 CAAGAATTTG
* *
23368 GGGTTAAAATATAATTTTATA-AAAATTT-A
1 GGGTTAAAAT-GAATTTT-TAGAAAGTTTAA
*
23397 GGGTTAAAATGAGATCTTTAGAAAGTTTAA
1 GGGTTAAAATGA-ATTTTTAGAAAGTTTAA
* *
23427 GGGTTAAAATGTAATTTTTGGAAAGTTT-G
1 GGGTTAAAATG-AATTTTTAGAAAGTTTAA
* * * *
23456 GGGCTAAATCTAAATTTTTTGAAAGTTTAA
1 GGGTTAAA-ATGAATTTTTAGAAAGTTTAA
* * *
23486 GGGTTAAAATGTAATTTTTGGAAAATTTTA
1 GGGTTAAAATG-AATTTTTAGAAAGTTTAA
* * *
23516 GGGTTGAATTCAAATTTTTAGAAAGTTTAA
1 GGGTTAAAAT-GAATTTTTAGAAAGTTTAA
*
23546 GGGTTAAAATGTGATTTTT-GAAAAGTTTA
1 GGGTTAAAATG-AATTTTTAG-AAAGTTTA
23575 GGGAGTAATA
Statistics
Matches: 141, Mismatches: 27, Indels: 19
0.75 0.14 0.10
Matches are distributed among these distances:
28 3 0.02
29 44 0.31
30 93 0.66
31 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.20, T:0.40
Consensus pattern (29 bp):
GGGTTAAAATGAATTTTTAGAAAGTTTAA
Found at i:23435 original size:59 final size:58
Alignment explanation
Indices: 23368--23577 Score: 260
Period size: 59 Copynumber: 3.6 Consensus size: 58
23358 CAAGAATTTG
* * * * *
23368 GGGTTAAAATATAATTTTAT-AAAAATTTAGGGTTAAAATGAGATCTTTAGAAAGTTTAA
1 GGGTTAAAATGTAATTTT-TGAAAAGTTTAGGGTT-AAATCAAATTTTTAGAAAGTTTAA
* * * *
23427 GGGTTAAAATGTAATTTTTGGAAAGTTTGGGGCTAAATCTAAATTTTTTGAAAGTTTAA
1 GGGTTAAAATGTAATTTTTGAAAAGTTTAGGGTTAAATC-AAATTTTTAGAAAGTTTAA
* *
23486 GGGTTAAAATGTAATTTTTGGAAAATTTTAGGGTTGAATTCAAATTTTTAGAAAGTTTAA
1 GGGTTAAAATGTAATTTTT-GAAAAGTTTAGGGTT-AAATCAAATTTTTAGAAAGTTTAA
*
23546 GGGTTAAAATGTGATTTTTGAAAAGTTTAGGG
1 GGGTTAAAATGTAATTTTTGAAAAGTTTAGGG
23578 AGTAATAAAC
Statistics
Matches: 130, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
58 5 0.04
59 74 0.57
60 47 0.36
61 4 0.03
ACGTcount: A:0.37, C:0.02, G:0.21, T:0.40
Consensus pattern (58 bp):
GGGTTAAAATGTAATTTTTGAAAAGTTTAGGGTTAAATCAAATTTTTAGAAAGTTTAA
Found at i:23563 original size:60 final size:60
Alignment explanation
Indices: 23413--23577 Score: 246
Period size: 60 Copynumber: 2.8 Consensus size: 60
23403 AAATGAGATC
*
23413 TTTAGAAAGTTTAAGGGTTAAAATGTAATTTTTGG-AAAGTTTGGGGCTAAATCTAAATT
1 TTTAGAAAGTTTAAGGGTTAAAATGTAATTTTTGGAAAAGTTTAGGGCTAAATCTAAATT
* * * *
23472 TTTTGAAAGTTTAAGGGTTAAAATGTAATTTTTGGAAAATTTTAGGGTTGAAT-TCAAATT
1 TTTAGAAAGTTTAAGGGTTAAAATGTAATTTTTGGAAAAGTTTAGGGCTAAATCT-AAATT
*
23532 TTTAGAAAGTTTAAGGGTTAAAATGTGATTTTT-GAAAAGTTTAGGG
1 TTTAGAAAGTTTAAGGGTTAAAATGTAATTTTTGGAAAAGTTTAGGG
23578 AGTAATAAAC
Statistics
Matches: 96, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
59 47 0.49
60 49 0.51
ACGTcount: A:0.35, C:0.02, G:0.22, T:0.41
Consensus pattern (60 bp):
TTTAGAAAGTTTAAGGGTTAAAATGTAATTTTTGGAAAAGTTTAGGGCTAAATCTAAATT
Done.