Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010908.1 Kokia drynarioides strain JFW-HI SEQ_125876, 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: 118580
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Warning! 61 characters in sequence are not A, C, G, or T
Found at i:2079 original size:27 final size:27
Alignment explanation
Indices: 2035--2097 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
2025 TCTTTTTCTT
* * *
2035 TTTCCTTTATTAGCTTTTTACTTAATA
1 TTTCTTTTATTAGATTTTAACTTAATA
* * *
2062 TTTCTTTTATTATATTTTAACTTACTT
1 TTTCTTTTATTAGATTTTAACTTAATA
2089 TTTCTTTTA
1 TTTCTTTTA
2098 ATTAACCAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.21, C:0.13, G:0.02, T:0.65
Consensus pattern (27 bp):
TTTCTTTTATTAGATTTTAACTTAATA
Found at i:5162 original size:24 final size:22
Alignment explanation
Indices: 5102--5165 Score: 74
Period size: 24 Copynumber: 2.8 Consensus size: 22
5092 TATAATAAAT
* *
5102 ATAAAATTATAAAAAAGAATAC
1 ATAAAATTTTAAAAAAAAATAC
*
5124 ATAAAATTTGAAAAATAAAAATAC
1 ATAAAATTT-TAAAA-AAAAATAC
5148 ATTAAAATTTTAAAAAAA
1 A-TAAAATTTTAAAAAAA
5166 TATATAAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 8 0.23
23 7 0.20
24 12 0.34
25 8 0.23
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (22 bp):
ATAAAATTTTAAAAAAAAATAC
Found at i:5202 original size:20 final size:19
Alignment explanation
Indices: 5149--5218 Score: 77
Period size: 20 Copynumber: 3.6 Consensus size: 19
5139 TAAAAATACA
5149 TTAAAATTTTAAAAAAATAT
1 TTAAAATTTTAAAAAAA-AT
* * *
5169 ATAAAAGTTGAAAAAATAAT
1 TTAAAATTTTAAAAAA-AAT
* *
5189 TTTAAATTTTAAAACAAAT
1 TTAAAATTTTAAAAAAAAT
5208 TTAAAATTTTA
1 TTAAAATTTTA
5219 GAAAGTTACA
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
19 13 0.32
20 26 0.65
21 1 0.03
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (19 bp):
TTAAAATTTTAAAAAAAAT
Found at i:5272 original size:17 final size:17
Alignment explanation
Indices: 5252--5308 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
5242 TAAAAAATTT
5252 AAAATTTAAAAAAATAA
1 AAAATTTAAAAAAATAA
* * **
5269 AAAATTGAAGAAAGGAA
1 AAAATTTAAAAAAATAA
*
5286 AAAATATTATAAAAATTAA
1 AAAAT-TTA-AAAAAATAA
5305 AAAA
1 AAAA
5309 AAACCCAACA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
17 18 0.60
18 2 0.07
19 10 0.33
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (17 bp):
AAAATTTAAAAAAATAA
Found at i:6055 original size:26 final size:27
Alignment explanation
Indices: 6018--6088 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 27
6008 TAAAATTAGA
6018 TTATAT-TATTTTAATATTTAATAATT
1 TTATATATATTTTAATATTTAATAATT
*
6044 TTATATAT-TTTT--TATTTATTAATT
1 TTATATATATTTTAATATTTAATAATT
* *
6068 TTTTATATATTTTAATGTTTA
1 TTATATATATTTTAATATTTA
6089 TATTGTAGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
24 18 0.47
25 4 0.11
26 10 0.26
27 6 0.16
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (27 bp):
TTATATATATTTTAATATTTAATAATT
Found at i:12778 original size:40 final size:40
Alignment explanation
Indices: 12734--12814 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
12724 CATGCAGTTA
12734 CTATAAAGGGATTTCCTTATCGGCCTCTTAAATTTTCCAT
1 CTATAAAGGGATTTCCTTATCGGCCTCTTAAATTTTCCAT
12774 CTATAAAGGGATTTCCTTATCGGCCTCTTAAATTTTCCAT
1 CTATAAAGGGATTTCCTTATCGGCCTCTTAAATTTTCCAT
12814 C
1 C
12815 CATTTTCTCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (40 bp):
CTATAAAGGGATTTCCTTATCGGCCTCTTAAATTTTCCAT
Found at i:26109 original size:30 final size:30
Alignment explanation
Indices: 26068--26138 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 30
26058 TTTAAATTAG
26068 TAATAAAAAATTACACTTTAATTTTTTAAAA-
1 TAAT-AAAAATTACA-TTTAATTTTTTAAAAT
**
26099 TAATAAAAATTTGATTTAATTTTTTAAAAT
1 TAATAAAAATTACATTTAATTTTTTAAAAT
*
26129 TTATAAAAAT
1 TAATAAAAAT
26139 ATAAATTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 15 0.42
30 17 0.47
31 4 0.11
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (30 bp):
TAATAAAAATTACATTTAATTTTTTAAAAT
Found at i:41305 original size:64 final size:64
Alignment explanation
Indices: 41204--41328 Score: 207
Period size: 64 Copynumber: 2.0 Consensus size: 64
41194 ATTATTATGT
* *
41204 TTTAACTTCATAACCATATTGTTAACGAAACGTTACAAAAAACATTTAATCTT-ATACTTCAAAA
1 TTTAACTTCATAACCATATTATTAACGAAACGTTACAAAAAA-AATTAATCTTAATACTTCAAAA
*
41268 TTTAACTTCATAACCATATTATTAACGAAATGTTACAAAAAAAATTAATCTTAATACTTCA
1 TTTAACTTCATAACCATATTATTAACGAAACGTTACAAAAAAAATTAATCTTAATACTTCA
41329 TAACCATATT
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
63 9 0.16
64 48 0.84
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.35
Consensus pattern (64 bp):
TTTAACTTCATAACCATATTATTAACGAAACGTTACAAAAAAAATTAATCTTAATACTTCAAAA
Found at i:56373 original size:21 final size:19
Alignment explanation
Indices: 56335--56378 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
56325 AATCAGTTTG
* *
56335 TTTTGCAAATTCTAGTTGT
1 TTTTGCAAATTATAGTTGA
56354 TTTTGCAAACTTTATAGTTGA
1 TTTTGCAAA--TTATAGTTGA
56375 TTTT
1 TTTT
56379 CTGGCAATCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 9 0.43
21 12 0.57
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.55
Consensus pattern (19 bp):
TTTTGCAAATTATAGTTGA
Found at i:59860 original size:73 final size:74
Alignment explanation
Indices: 59750--59892 Score: 229
Period size: 73 Copynumber: 1.9 Consensus size: 74
59740 GTCCTATTTA
*
59750 AATGCTTTGTTGCCTTATTATTTGTCAATTAAAACTGCCTATATTGCTAACAATTCC-CCTTTCT
1 AATGCTTTGTTGCCTTATTATTTGTCAATTAAAACTGCCAATATTGCTAACAA-TCCTCCTTTCT
59814 TTCTTTGTTT
65 TTCTTTGTTT
*
59824 AATGCTTTGTTGCCTTA-TATTTGTCAGA-TAAAACTGCCAATATTGTTAACAATCCTCCTTTCT
1 AATGCTTTGTTGCCTTATTATTTGTCA-ATTAAAACTGCCAATATTGCTAACAATCCTCCTTTCT
59887 TTCTTT
65 TTCTTT
59893 CTTTCTTTCA
Statistics
Matches: 65, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
72 3 0.05
73 44 0.68
74 18 0.28
ACGTcount: A:0.23, C:0.20, G:0.10, T:0.47
Consensus pattern (74 bp):
AATGCTTTGTTGCCTTATTATTTGTCAATTAAAACTGCCAATATTGCTAACAATCCTCCTTTCTT
TCTTTGTTT
Found at i:60651 original size:42 final size:42
Alignment explanation
Indices: 60604--60758 Score: 172
Period size: 42 Copynumber: 3.8 Consensus size: 42
60594 TTCCCCAGTG
*
60604 ACAAGCACAAGCAATAGTATCTTTGGTGGTACATCTGCAACT
1 ACAAGCACAGGCAATAGTATCTTTGGTGGTACATCTGCAACT
* * * * * *
60646 ACAAGCACGGGCACTGGTTTATTTGGTGCTACATCTGCAACT
1 ACAAGCACAGGCAATAGTATCTTTGGTGGTACATCTGCAACT
* * *
60688 ACAAGCACTGGCAATGGCATCTTTGGTGGTACATCTGC-A--
1 ACAAGCACAGGCAATAGTATCTTTGGTGGTACATCTGCAACT
* * *
60727 ACAAGCACAGGTAGTAGTATTTTTGGTGGTAC
1 ACAAGCACAGGCAATAGTATCTTTGGTGGTAC
60759 TTCTTTGCCA
Statistics
Matches: 94, Mismatches: 19, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
39 26 0.28
41 1 0.01
42 67 0.71
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (42 bp):
ACAAGCACAGGCAATAGTATCTTTGGTGGTACATCTGCAACT
Found at i:62603 original size:270 final size:270
Alignment explanation
Indices: 62122--62664 Score: 1068
Period size: 270 Copynumber: 2.0 Consensus size: 270
62112 CTTTAAATGG
*
62122 TTTGTAGATTTATAGTTTGTTGAGCTCAAGTATTCTATCATAAATTATAACAGGTTGCGGCATTT
1 TTTGTAGAATTATAGTTTGTTGAGCTCAAGTATTCTATCATAAATTATAACAGGTTGCGGCATTT
62187 TGAAAACCCTTTGGGGCTATTCTTCTCTTTGACATTCATCCTAGGTGGTTCCATGTTTTTGCAAG
66 TGAAAACCCTTTGGGGCTATTCTTCTCTTTGACATTCATCCTAGGTGGTTCCATGTTTTTGCAAG
62252 TAGATACTGGAAAAAGTATTGAAGCTATTAATAGAGAGGCTGATATAAGCAGCGGAATAGAAATG
131 TAGATACTGGAAAAAGTATTGAAGCTATTAATAGAGAGGCTGATATAAGCAGCGGAATAGAAATG
62317 AAAGCTTTTCAGTTGCGGATTTGGCTTGGGCTTGACTGACTTGAATGGAAAATTGCGGCCTTAAT
196 AAAGCTTTTCAGTTGCGGATTTGGCTTGGGCTTGACTGACTTGAATGGAAAATTGCGGCCTTAAT
62382 ATAAAATGAA
261 ATAAAATGAA
62392 TTTGTAGAATTATAGTTTGTTGAGCTCAAGTATTCTATCATAAATTATAACAGGTTGCGGCATTT
1 TTTGTAGAATTATAGTTTGTTGAGCTCAAGTATTCTATCATAAATTATAACAGGTTGCGGCATTT
62457 TGAAAACCCTTTGGGGCTATTCTTCTCTTTGACATTCATCCTAGGTGGTTCCATGTTTTTGCAAG
66 TGAAAACCCTTTGGGGCTATTCTTCTCTTTGACATTCATCCTAGGTGGTTCCATGTTTTTGCAAG
*
62522 TAGTTACTGGAAAAAGTATTGAAGCTATTAATAGAGAGGCTGATATAAGCAGCGGAATAGAAATG
131 TAGATACTGGAAAAAGTATTGAAGCTATTAATAGAGAGGCTGATATAAGCAGCGGAATAGAAATG
62587 AAAGCTTTTCAGTTGCGGATTTGGCTTGGGCTTGACTGACTTGAATGGAAAATTGCGGCCTTAAT
196 AAAGCTTTTCAGTTGCGGATTTGGCTTGGGCTTGACTGACTTGAATGGAAAATTGCGGCCTTAAT
62652 ATAAAATGAA
261 ATAAAATGAA
62662 TTT
1 TTT
62665 TTGGAATTTT
Statistics
Matches: 271, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
270 271 1.00
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.35
Consensus pattern (270 bp):
TTTGTAGAATTATAGTTTGTTGAGCTCAAGTATTCTATCATAAATTATAACAGGTTGCGGCATTT
TGAAAACCCTTTGGGGCTATTCTTCTCTTTGACATTCATCCTAGGTGGTTCCATGTTTTTGCAAG
TAGATACTGGAAAAAGTATTGAAGCTATTAATAGAGAGGCTGATATAAGCAGCGGAATAGAAATG
AAAGCTTTTCAGTTGCGGATTTGGCTTGGGCTTGACTGACTTGAATGGAAAATTGCGGCCTTAAT
ATAAAATGAA
Found at i:67186 original size:158 final size:157
Alignment explanation
Indices: 66899--67188 Score: 447
Period size: 157 Copynumber: 1.8 Consensus size: 157
66889 TATCATGTAA
* * * *
66899 TGCTCACACGAGTTGTGGGTCGAGATGCTGAGCTACATGATGCTGCTCACACGAGCTGTGAAAAA
1 TGCTCACACGAGCTGTGGGTCGAGATGCTAAGCTACACGATGCTGCTCACACGAGCTATGAAAAA
* *
66964 TCCGTATGATTGCTGGATCTCAGCCATCGGTAGGACATCTAAGACCAGCACACATGTAACCTGTA
66 TCCGAATGATTGCTGGATCTCAGCCATCGATAGGACATCTAAGACCAGCACACATGTAACCTGTA
67029 ATGCTCACATGAGCTGTGAAATGGGTC
131 ATGCTCACATGAGCTGTGAAATGGGTC
* * * * *
67056 TGCTCACATGAGCTGTGGGTCGAGATGTTAAGCTACACGATGCTGGTCACACGAGCTATGGAGAA
1 TGCTCACACGAGCTGTGGGTCGAGATGCTAAGCTACACGATGCTGCTCACACGAGCTATGAAAAA
*
67121 TCCGCAATGATTG-TCGGATCTCAGCCATCGATAGGACATCTAAGACCAGCACCCATGTAACCTG
66 TCCG-AATGATTGCT-GGATCTCAGCCATCGATAGGACATCTAAGACCAGCACACATGTAACCTG
67185 TAAT
129 TAAT
67189 CCCAATAACG
Statistics
Matches: 119, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
157 61 0.51
158 58 0.49
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (157 bp):
TGCTCACACGAGCTGTGGGTCGAGATGCTAAGCTACACGATGCTGCTCACACGAGCTATGAAAAA
TCCGAATGATTGCTGGATCTCAGCCATCGATAGGACATCTAAGACCAGCACACATGTAACCTGTA
ATGCTCACATGAGCTGTGAAATGGGTC
Found at i:77873 original size:28 final size:28
Alignment explanation
Indices: 77833--77916 Score: 132
Period size: 28 Copynumber: 3.0 Consensus size: 28
77823 TATATCCGAT
77833 TTACTCCCTGTTGACCCAAAGGTCATGC
1 TTACTCCCTGTTGACCCAAAGGTCATGC
* *
77861 TTACTCCTTGTTGACCCAAAGGTTATGC
1 TTACTCCCTGTTGACCCAAAGGTCATGC
* *
77889 TTACTCCCTATTGACCTAAAGGTCATGC
1 TTACTCCCTGTTGACCCAAAGGTCATGC
77917 CTGTTACCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.32
Consensus pattern (28 bp):
TTACTCCCTGTTGACCCAAAGGTCATGC
Found at i:81414 original size:2 final size:2
Alignment explanation
Indices: 81407--81431 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
81397 GATTTTAACG
81407 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 A
81432 GAATTTGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:83575 original size:24 final size:24
Alignment explanation
Indices: 83508--83828 Score: 273
Period size: 24 Copynumber: 13.0 Consensus size: 24
83498 TGTAAATAGA
*
83508 TATACATGCTGACGAGCGTAAACA
1 TATACATGCTGACGAGCGTAAACG
* * * *
83532 TAGATATATGCTGGCTAGCGTAAATG
1 T--ATACATGCTGACGAGCGTAAACG
83558 TATACATGCTGACGAGCGTAAACG
1 TATACATGCTGACGAGCGTAAACG
*
83582 TATACATGCTGATGAGCGTAAACG
1 TATACATGCTGACGAGCGTAAACG
* *
83606 TAAATACATGCTGGCGAGTGTAAACG
1 T--ATACATGCTGACGAGCGTAAACG
** *
83632 TATACATGCTGGTGAGCGTAAACA
1 TATACATGCTGACGAGCGTAAACG
** *
83656 TATACATGCTGATAAGCGTAAACATT
1 TATACATGCTGACGAGCGTAAAC--G
* *
83682 TATACATGCTGATGAGCATAAACG
1 TATACATGCTGACGAGCGTAAACG
* * *
83706 TAGATATATGCTGGCGAGCGTAAACC
1 T--ATACATGCTGACGAGCGTAAACG
** * * *
83732 TATACATATTGGCGAGTGTAAATG
1 TATACATGCTGACGAGCGTAAACG
* * * *
83756 TATACATTCTGGCAAGCGTAAACA
1 TATACATGCTGACGAGCGTAAACG
* * *
83780 TAAACATGCTGATGAGCGTAAATG
1 TATACATGCTGACGAGCGTAAACG
83804 TATATACATGCTGACGAGCGTAAAC
1 --TATACATGCTGACGAGCGTAAAC
83829 ATAGATATAT
Statistics
Matches: 238, Mismatches: 49, Indels: 18
0.78 0.16 0.06
Matches are distributed among these distances:
24 138 0.58
26 100 0.42
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.26
Consensus pattern (24 bp):
TATACATGCTGACGAGCGTAAACG
Found at i:83629 original size:74 final size:73
Alignment explanation
Indices: 83508--83855 Score: 311
Period size: 74 Copynumber: 4.7 Consensus size: 73
83498 TGTAAATAGA
* * *
83508 TATACATGCTGACGAGCGTAAACATAGATATATGCTGGCTAGCGTAAATGTATACATGCTGACGA
1 TATACATGCTGACGAGCGTAAACATA-ATACATGCTGGCGAGCGTAAACGTATACATGCTGACGA
83573 GCGTAAACG
65 GCGTAAACG
* * * **
83582 TATACATGCTGATGAGCGTAAACGTAAATACATGCTGGCGAGTGTAAACGTATACATGCTGGTGA
1 TATACATGCTGACGAGCGTAAACAT-AATACATGCTGGCGAGCGTAAACGTATACATGCTGACGA
*
83647 GCGTAAACA
65 GCGTAAACG
** * ** * * *
83656 TATACATGCTGATAAGCGTAAACATTTATACATGCTGATGAGCATAAACGTAGATATATGCTGGC
1 TATACATGCTGACGAGCGTAAACA-TAATACATGCTGGCGAGCGTAAACGT--ATACATGCTGAC
*
83721 GAGCGTAAACC
63 GAGCGTAAACG
** * * ** * * * * *
83732 TATACATATTGGCGAGTGTAAATGT-ATACATTCTGGCAAGCGTAAACATAAACATGCTGATGAG
1 TATACATGCTGACGAGCGTAAACATAATACATGCTGGCGAGCGTAAACGTATACATGCTGACGAG
*
83796 CGTAAATG
66 CGTAAACG
* * **
83804 TATATACATGCTGACGAGCGTAAACATAGATATATGTTGGTAAGCGTAAACG
1 --TATACATGCTGACGAGCGTAAACATA-ATACATGCTGGCGAGCGTAAACG
83856 CATATTAGCT
Statistics
Matches: 216, Mismatches: 50, Indels: 14
0.77 0.18 0.05
Matches are distributed among these distances:
72 17 0.08
74 142 0.66
75 3 0.01
76 54 0.25
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (73 bp):
TATACATGCTGACGAGCGTAAACATAATACATGCTGGCGAGCGTAAACGTATACATGCTGACGAG
CGTAAACG
Found at i:83737 original size:124 final size:123
Alignment explanation
Indices: 83508--83854 Score: 396
Period size: 124 Copynumber: 2.8 Consensus size: 123
83498 TGTAAATAGA
* * * *
83508 TATACATGCTGACGAGCGTAAACATAGATATATGCTGGCTAGCGT-AAATGTATACATGCTGACG
1 TATACATGCTGGCGAGCGTAAACAT--ATACATGCT-GATAGCGTAAAATATATACATGCTGACG
* * * *
83572 AGCGTAAACGT--ATACATGCTGATGAGCGTAAACGTAAATACATGCTGGCGAGTGTAAACG
63 AGCGTAAACGTAGATATATGCTGGTGAGCGTAAACCT-AATACATACTGGCGAGTGTAAACG
* * *
83632 TATACATGCTGGTGAGCGTAAACATATACATGCTGATAAGCGTAAACATTTATACATGCTGATGA
1 TATACATGCTGGCGAGCGTAAACATATACATGCTGAT-AGCGTAAA-ATATATACATGCTGACGA
* * * *
83697 GCATAAACGTAGATATATGCTGGCGAGCGTAAACCT-ATACATATTGGCGAGTGTAAATG
64 GCGTAAACGTAGATATATGCTGGTGAGCGTAAACCTAATACATACTGGCGAGTGTAAACG
* * * *
83756 TATACATTCTGGCAAGCGTAAACATAAACATGCTGATGAGCGTAAATGTATATACATGCTGACGA
1 TATACATGCTGGCGAGCGTAAACATATACATGCTGAT-AGCGTAAA-ATATATACATGCTGACGA
* * *
83821 GCGTAAACATAGATATATGTTGGTAAGCGTAAAC
64 GCGTAAACGTAGATATATGCTGGTGAGCGTAAAC
83855 GCATATTAGC
Statistics
Matches: 190, Mismatches: 28, Indels: 10
0.83 0.12 0.04
Matches are distributed among these distances:
121 2 0.01
122 13 0.07
123 2 0.01
124 153 0.81
126 20 0.11
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (123 bp):
TATACATGCTGGCGAGCGTAAACATATACATGCTGATAGCGTAAAATATATACATGCTGACGAGC
GTAAACGTAGATATATGCTGGTGAGCGTAAACCTAATACATACTGGCGAGTGTAAACG
Found at i:83877 original size:24 final size:24
Alignment explanation
Indices: 83850--83925 Score: 107
Period size: 24 Copynumber: 3.2 Consensus size: 24
83840 TTGGTAAGCG
83850 TAAACGCATATTAGCTGGCGAGCA
1 TAAACGCATATTAGCTGGCGAGCA
* *
83874 TAAATGCATATTAGCTGGCAAGCA
1 TAAACGCATATTAGCTGGCGAGCA
* **
83898 TAAACGCATATTAGTTGATGAGCA
1 TAAACGCATATTAGCTGGCGAGCA
83922 TAAA
1 TAAA
83926 TGTACTAAAC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (24 bp):
TAAACGCATATTAGCTGGCGAGCA
Found at i:83892 original size:124 final size:123
Alignment explanation
Indices: 83558--83902 Score: 295
Period size: 124 Copynumber: 2.8 Consensus size: 123
83548 AGCGTAAATG
* * * *** * *
83558 TATACATGCTGACGAGCGTAAACGT--ATACATGCTGATGAGCGTAAACGTAAATACATGCTGGC
1 TATACATGCTGACGAGCATAAACATAGATATATGCTGGCAAGCGTAAACCT--ATACATACTGGC
** * * * ** * *
83621 GAGTGTAAACGTATACATGCTGGTGAGCGTAAACATATACATGCTGATAAGCGTAAACATT
64 GAGCATAAATGCATA-ATTCTGGCAAGCGTAAACATAAACATGCTGATAAGCGTAAACATA
* * * *
83682 TATACATGCTGATGAGCATAAACGTAGATATATGCTGGCGAGCGTAAACCTATACATATTGGCGA
1 TATACATGCTGACGAGCATAAACATAGATATATGCTGGCAAGCGTAAACCTATACATACTGGCGA
** * * **
83747 GTGTAAATGTATACATTCTGGCAAGCGTAAACATAAACATGCTGATGAGCGTAAATGTA
66 GCATAAATGCATA-ATTCTGGCAAGCGTAAACATAAACATGCTGATAAGCGTAAACATA
* * * *
83806 TATACATGCTGACGAGCGTAAACATAGATATATGTTGGTAAGCGTAAACGC-ATA-TTAGCTGGC
1 TATACATGCTGACGAGCATAAACATAGATATATGCTGGCAAGCGTAAAC-CTATACATA-CTGGC
*
83869 GAGCATAAATGCAT-ATTAGCTGGCAAGCATAAAC
64 GAGCATAAATGCATAATT--CTGGCAAGCGTAAAC
83903 GCATATTAGT
Statistics
Matches: 186, Mismatches: 29, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
122 3 0.02
123 2 0.01
124 160 0.86
125 1 0.01
126 20 0.11
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (123 bp):
TATACATGCTGACGAGCATAAACATAGATATATGCTGGCAAGCGTAAACCTATACATACTGGCGA
GCATAAATGCATAATTCTGGCAAGCGTAAACATAAACATGCTGATAAGCGTAAACATA
Found at i:85855 original size:20 final size:21
Alignment explanation
Indices: 85816--85855 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
85806 TGCGATCATT
* *
85816 TCTTGTTGTATGGTTAAATGG
1 TCTTGTAGTATGGCTAAATGG
85837 TCTTGTAGT-TGGCTAAATG
1 TCTTGTAGTATGGCTAAATG
85856 CATGTATTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.20, C:0.07, G:0.28, T:0.45
Consensus pattern (21 bp):
TCTTGTAGTATGGCTAAATGG
Found at i:87578 original size:32 final size:32
Alignment explanation
Indices: 87513--87579 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
87503 TTCATTTGAA
*
87513 TTCTTCCTCTTCTTTTCTCTCTGAAACTCTTC
1 TTCTTCCTCTTCTTTTCTCTCTCAAACTCTTC
*
87545 TTCTTCTTCTTCTTTT-TCTTCTCAAA-TCTTTC
1 TTCTTCCTCTTCTTTTCTC-TCTCAAACTC-TTC
87577 TTC
1 TTC
87580 ACTTGAGTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 4 0.13
32 27 0.87
ACGTcount: A:0.09, C:0.31, G:0.01, T:0.58
Consensus pattern (32 bp):
TTCTTCCTCTTCTTTTCTCTCTCAAACTCTTC
Found at i:95193 original size:9 final size:9
Alignment explanation
Indices: 95176--95219 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
95166 ATTTCTCTTT
*
95176 AAAAGTCTC
1 AAAATTCTC
95185 AAAATTCTC
1 AAAATTCTC
**
95194 TAAAGCTCTC
1 -AAAATTCTC
95204 AAAATTCTC
1 AAAATTCTC
95213 AAAATTC
1 AAAATTC
95220 GTTTAGTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
9 22 0.76
10 7 0.24
ACGTcount: A:0.43, C:0.23, G:0.05, T:0.30
Consensus pattern (9 bp):
AAAATTCTC
Found at i:95203 original size:19 final size:18
Alignment explanation
Indices: 95177--95212 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
95167 TTTCTCTTTA
95177 AAAGTCTCAAAATTCTCT
1 AAAGTCTCAAAATTCTCT
95195 AAAGCTCTCAAAATTCTC
1 AAAG-TCTCAAAATTCTC
95213 AAAATTCGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.39, C:0.25, G:0.06, T:0.31
Consensus pattern (18 bp):
AAAGTCTCAAAATTCTCT
Found at i:98270 original size:21 final size:21
Alignment explanation
Indices: 98242--98299 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
98232 ATAGTACAAA
98242 CTTCTACCGAAACAAGTGACAG
1 CTTCTACCGAAACAAGTGAC-G
* *
98264 C-TCTACC-AATATAAGTGACT
1 CTTCTACCGAA-ACAAGTGACG
98284 CTTCTACCGAAACAAG
1 CTTCTACCGAAACAAG
98300 AATTTTACCT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
20 3 0.10
21 24 0.80
22 3 0.10
ACGTcount: A:0.36, C:0.28, G:0.14, T:0.22
Consensus pattern (21 bp):
CTTCTACCGAAACAAGTGACG
Found at i:99090 original size:52 final size:52
Alignment explanation
Indices: 99010--99248 Score: 334
Period size: 52 Copynumber: 4.6 Consensus size: 52
99000 ATTTCATTTA
* * * * *
99010 ATACTCACGATGATACATAGTCACCGGACCTCTTAATCCGTGAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * *
99062 ATACTCACGATAACACATAGTCATCGGACCTCATAATCCGTAAAAGATTCTT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * *
99114 ATACTCACGAAGACACATAATCATCGGACTTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * * * *
99166 ATACTCACGATGACACGTAGTAATTGGAACTCATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
99218 ATACTCACGATGACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
99249 TTTTCATTTA
Statistics
Matches: 161, Mismatches: 26, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 161 1.00
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:100146 original size:21 final size:21
Alignment explanation
Indices: 100118--100165 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
100108 ACTTTCATCA
*
100118 TTAACCTTACTTAATCA-CTC
1 TTAACCTTAATTAATCACCTC
100138 TTAATCCTTAATTAATCATCCTC
1 TTAA-CCTTAATTAATCA-CCTC
100161 TTAAC
1 TTAAC
100166 ACCTAAATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 4 0.17
21 12 0.50
22 1 0.04
23 7 0.29
ACGTcount: A:0.31, C:0.27, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAACCTTAATTAATCACCTC
Found at i:100537 original size:18 final size:18
Alignment explanation
Indices: 100510--100552 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
100500 ATCTCATCAA
* *
100510 AGCTTCTGTCTCGCATGT
1 AGCTTCTGTCTCCCACGT
*
100528 AGCTTTTGTCTCCCACGT
1 AGCTTCTGTCTCCCACGT
100546 AGCTTCT
1 AGCTTCT
100553 TCAAGCCCGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.12, C:0.30, G:0.19, T:0.40
Consensus pattern (18 bp):
AGCTTCTGTCTCCCACGT
Found at i:107002 original size:17 final size:17
Alignment explanation
Indices: 106963--107040 Score: 61
Period size: 17 Copynumber: 4.5 Consensus size: 17
106953 TTAAACCCAT
*
106963 TTTAACATTTATTTTAAGA
1 TTTAA-ATTGATTTTAA-A
*
106982 -TTAAATTGATTTTGAA
1 TTTAAATTGATTTTAAA
*
106998 TTTAAATTTATTTTAAA
1 TTTAAATTGATTTTAAA
* *
107015 TTTGAATTTAGA-TTTATA
1 TTT-AAATT-GATTTTAAA
107033 TTTAAATT
1 TTTAAATT
107041 TAAAACTTAT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
16 1 0.02
17 30 0.62
18 16 0.33
19 1 0.02
ACGTcount: A:0.37, C:0.01, G:0.06, T:0.55
Consensus pattern (17 bp):
TTTAAATTGATTTTAAA
Found at i:107005 original size:6 final size:6
Alignment explanation
Indices: 106996--107044 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
106986 ATTGATTTTG
* * * *
106996 AATTTA AATTT- ATTTTA AATTTG AATTTA GATTTA TATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
107043 AA
1 AA
107045 ACTTATTATA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
5 4 0.11
6 31 0.89
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (6 bp):
AATTTA
Found at i:107018 original size:23 final size:24
Alignment explanation
Indices: 106992--107041 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
106982 TTAAATTGAT
106992 TTTGAATTTAAATTTAT-TTTAAA
1 TTTGAATTTAAATTTATATTTAAA
*
107015 TTTGAATTTAGATTTATATTTAAA
1 TTTGAATTTAAATTTATATTTAAA
107039 TTT
1 TTT
107042 AAAACTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (24 bp):
TTTGAATTTAAATTTATATTTAAA
Found at i:107466 original size:16 final size:17
Alignment explanation
Indices: 107427--107470 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
107417 GACCTACATG
*
107427 TTTTCAAAACGATTTTTT
1 TTTTAAAAACGA-TTTTT
107445 TATTTAAAAACGA-TTTT
1 T-TTTAAAAACGATTTTT
107462 TTTTAAAAA
1 TTTTAAAAA
107471 AAATCGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 8 0.33
17 5 0.21
18 1 0.04
19 10 0.42
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.50
Consensus pattern (17 bp):
TTTTAAAAACGATTTTT
Found at i:107473 original size:19 final size:19
Alignment explanation
Indices: 107432--107472 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
107422 ACATGTTTTC
**
107432 AAAACGATTTTTTTATTTA
1 AAAACGATTTTTTTATAAA
107451 AAAACGATTTTTTT-TAAA
1 AAAACGATTTTTTTATAAA
107469 AAAA
1 AAAA
107473 ATCGTTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (19 bp):
AAAACGATTTTTTTATAAA
Found at i:117285 original size:115 final size:115
Alignment explanation
Indices: 117074--117285 Score: 291
Period size: 115 Copynumber: 1.8 Consensus size: 115
117064 TCAAAGCGAA
* * * *
117074 CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGAAATAAAATGGTTA
1 CAAATCTTCGAACCCCAGCTTCCTGATGAGATAATGAGAAGCAGGGCGAAGAAATAAAACGGTCA
* *
117139 GCTTCCTGATGAGATACAGAGAAGTATACCAACTCAAGGCTCGATGTGAG
66 GCTTCCTGATGAGACACAGAGAAGTAGACCAACTCAAGGCTCGATGTGAG
* * * **
117189 CAAATCTTCGAATCCCAGCTTCCTGATGAGATAATGAGAAGCAGGGCGAAGCAGTAAGGCGGTCA
1 CAAATCTTCGAACCCCAGCTTCCTGATGAGATAATGAGAAGCAGGGCGAAGAAATAAAACGGTCA
* *
117254 GCTTCCTTATGAGACACTA-AGAAGTGGACCAA
66 GCTTCCTGATGAGACAC-AGAGAAGTAGACCAA
117286 ATTCGTCTTC
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
115 82 0.99
116 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.21
Consensus pattern (115 bp):
CAAATCTTCGAACCCCAGCTTCCTGATGAGATAATGAGAAGCAGGGCGAAGAAATAAAACGGTCA
GCTTCCTGATGAGACACAGAGAAGTAGACCAACTCAAGGCTCGATGTGAG
Found at i:117491 original size:201 final size:201
Alignment explanation
Indices: 117140--117577 Score: 777
Period size: 201 Copynumber: 2.2 Consensus size: 201
117130 AAATGGTTAG
117140 CTTCCTGATGAGATACAGAGAAGTATACCAACTCAAGGCTCGATGTGAGCAAATCTTCGAATCCC
1 CTTCCTGATGAGATACAGAGAAGTATACCAACTCAAGGCTCGATGTGAGCAAATCTTCGAATCCC
*
117205 AGCTTCCTGATGAGATAATGAGAAGCAGGGCGAAGCAGTAAGGCGGTCAGCTTCCTTATGAGACA
66 AGCTTCCTGATGAGATAATGAGAAGCAGGGCGAAGCAGTAAGGCGGTCAGCTTCCTGATGAGACA
* *
117270 CTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGTGGATTGAAACAAGTGAGGC
131 CTAAGAAGTGGACAAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGAGGC
117335 GGTCAT
196 GGTCAT
* ** * *
117341 CTTCTTGATGAGATTTAGAGAAGTATACCAACTCAGGGCTCGATGTGAGCAAATCTTCGAATCCT
1 CTTCCTGATGAGATACAGAGAAGTATACCAACTCAAGGCTCGATGTGAGCAAATCTTCGAATCCC
*
117406 AGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAGTAAGGCGGTCAGCTTCCTGATGAGACA
66 AGCTTCCTGATGAGATAATGAGAAGCAGGGCGAAGCAGTAAGGCGGTCAGCTTCCTGATGAGACA
* *
117471 CTGAGAAGTGGACAAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTTAGGC
131 CTAAGAAGTGGACAAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGAGGC
117536 GGTCAT
196 GGTCAT
117542 CTTCCTGATGAGATACAGAGAAGTATACCAACTCAA
1 CTTCCTGATGAGATACAGAGAAGTATACCAACTCAA
117578 TGTGGATTAA
Statistics
Matches: 222, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
201 222 1.00
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (201 bp):
CTTCCTGATGAGATACAGAGAAGTATACCAACTCAAGGCTCGATGTGAGCAAATCTTCGAATCCC
AGCTTCCTGATGAGATAATGAGAAGCAGGGCGAAGCAGTAAGGCGGTCAGCTTCCTGATGAGACA
CTAAGAAGTGGACAAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGAGGC
GGTCAT
Found at i:117563 original size:86 final size:85
Alignment explanation
Indices: 117408--117565 Score: 219
Period size: 86 Copynumber: 1.8 Consensus size: 85
117398 CGAATCCTAG
* * *
117408 CTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAGTAAGGCGGTCAGCTTCCTGATGAGACACT
1 CTTCCTGATGAGATACAGAGAAGCAGGGCGAAACAGTAAGGCGGTCAGCTTCCTGATGAGACACA
117473 GAGAAGTGGACAAAATTCGT
66 GAGAAGTGGACAAAATTCGT
** * * *
117493 CTTCCTGATGAGATACAGAGAAGC-GGATTGAAACAAGTTAGGCGGTCATCTTCCTGATGAGATA
1 CTTCCTGATGAGATACAGAGAAGCAGG-GCGAAAC-AGTAAGGCGGTCAGCTTCCTGATGAGACA
117557 CAGAGAAGT
64 CAGAGAAGT
117566 ATACCAACTC
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
84 2 0.03
85 27 0.43
86 34 0.54
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.22
Consensus pattern (85 bp):
CTTCCTGATGAGATACAGAGAAGCAGGGCGAAACAGTAAGGCGGTCAGCTTCCTGATGAGACACA
GAGAAGTGGACAAAATTCGT
Found at i:118432 original size:13 final size:13
Alignment explanation
Indices: 118416--118458 Score: 58
Period size: 12 Copynumber: 3.6 Consensus size: 13
118406 AATAAATGGC
118416 ATTAATAAATATT
1 ATTAATAAATATT
118429 ATTAA-AAA-A-T
1 ATTAATAAATATT
118439 ATTAAT-AATATT
1 ATTAATAAATATT
118451 ATTAATAA
1 ATTAATAA
118459 TAATAAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
10 8 0.31
11 2 0.08
12 10 0.38
13 6 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATTAATAAATATT
Done.