Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012124.1 Kokia drynarioides strain JFW-HI SEQ_127123, 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: 83826
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:5817 original size:41 final size:41
Alignment explanation
Indices: 5772--5849 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
5762 GGAATGGTCT
*
5772 TGTCCCCTTTACGAGTTTCTTGGTTCTCTTTTCCTTTGTCC
1 TGTCCCCTTTACGAGTTTCTTGCTTCTCTTTTCCTTTGTCC
**
5813 TGTCCCCTTTGTGAGTTTCTTGCTTCTCTTTTCCTTT
1 TGTCCCCTTTACGAGTTTCTTGCTTCTCTTTTCCTTT
5850 TCTTGGCTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.04, C:0.28, G:0.14, T:0.54
Consensus pattern (41 bp):
TGTCCCCTTTACGAGTTTCTTGCTTCTCTTTTCCTTTGTCC
Found at i:11378 original size:20 final size:20
Alignment explanation
Indices: 11353--11401 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
11343 TATTATATTT
11353 TATTTTGAAATATAAATCTA
1 TATTTTGAAATATAAATCTA
11373 TATTTTGAAATATAAATCTA
1 TATTTTGAAATATAAATCTA
11393 TATTTTGAA
1 TATTTTGAA
11402 TAAGCTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (20 bp):
TATTTTGAAATATAAATCTA
Found at i:18421 original size:24 final size:24
Alignment explanation
Indices: 18394--18443 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
18384 AATAATAAAT
*
18394 TTTTTATAGAATA-AAATATGAGTA
1 TTTTTA-AGAATATAAATATAAGTA
*
18418 -TTTTAATAATATAAATATAAGTA
1 TTTTTAAGAATATAAATATAAGTA
18441 TTT
1 TTT
18444 GCTTAGCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
22 5 0.23
23 15 0.68
24 2 0.09
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (24 bp):
TTTTTAAGAATATAAATATAAGTA
Found at i:23451 original size:18 final size:18
Alignment explanation
Indices: 23406--23452 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
23396 TAATTTATTT
23406 TTTATTTTATATTATAGTA
1 TTTATTTT-TATTATAGTA
* *
23425 TTTAATTTTATTATTATTA
1 TTTATTTTTATTA-TAGTA
23444 -TTATTTTTA
1 TTTATTTTTA
23453 CACTAACAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTATTTTTATTATAGTA
Found at i:25605 original size:14 final size:14
Alignment explanation
Indices: 25572--25598 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
25562 ATCTCATTGC
25572 CATTATCATAAATA
1 CATTATCATAAATA
25586 CATTATCATAAAT
1 CATTATCATAAAT
25599 GTTTTATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (14 bp):
CATTATCATAAATA
Found at i:45892 original size:30 final size:31
Alignment explanation
Indices: 45858--45927 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
45848 GTTACATTTA
*
45858 ACAAAACAGTCACTCAA-CTTT-GAAAATGTG
1 ACAAAACAGTCACTAAAGCTTTCGAAAA-GTG
* *
45888 ACAAAACTGTCACTAAAGTTTTCGAAAAGTG
1 ACAAAACAGTCACTAAAGCTTTCGAAAAGTG
45919 ACAAAACAG
1 ACAAAACAG
45928 CCCTCTACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 15 0.44
31 14 0.41
32 5 0.15
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.21
Consensus pattern (31 bp):
ACAAAACAGTCACTAAAGCTTTCGAAAAGTG
Found at i:48175 original size:19 final size:19
Alignment explanation
Indices: 48151--48190 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
48141 TCGTTAGGTT
48151 GATGAAAGTAAAAACATAA
1 GATGAAAGTAAAAACATAA
48170 GATGAAAGTAAAAACATAA
1 GATGAAAGTAAAAACATAA
48189 GA
1 GA
48191 ATGTATGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.62, C:0.05, G:0.17, T:0.15
Consensus pattern (19 bp):
GATGAAAGTAAAAACATAA
Found at i:55023 original size:17 final size:18
Alignment explanation
Indices: 54992--55025 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
54982 TAAATTGTTA
54992 AAAAATTTTACTAAAATG
1 AAAAATTTTACTAAAATG
55010 AAAAATTTTA-TAAAAT
1 AAAAATTTTACTAAAAT
55026 TGAGGGCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (18 bp):
AAAAATTTTACTAAAATG
Found at i:58817 original size:22 final size:23
Alignment explanation
Indices: 58786--58839 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
58776 TGCAATCCAA
*
58786 TAGGCACACACAGTGC-AATTAG
1 TAGGCACACACAGCGCAAATTAG
* *
58808 TAGGCGCACATAGCGCAAATTAG
1 TAGGCACACACAGCGCAAATTAG
58831 TAGGCACAC
1 TAGGCACAC
58840 GAGGTGCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 13 0.48
23 14 0.52
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (23 bp):
TAGGCACACACAGCGCAAATTAG
Found at i:58874 original size:23 final size:23
Alignment explanation
Indices: 58829--58906 Score: 88
Period size: 23 Copynumber: 3.4 Consensus size: 23
58819 AGCGCAAATT
* * *
58829 AGTAGGCACACGAGGTGCAAAAC
1 AGTAAGCACACGAAGTGCGAAAC
*
58852 AGTAAGCACACGAAGAGCGAAAC
1 AGTAAGCACACGAAGTGCGAAAC
58875 AGTAAGCACAC-ACAGTGCTG-AAC
1 AGTAAGCACACGA-AGTGC-GAAAC
58898 AGTAAGCAC
1 AGTAAGCAC
58907 GCTAGTGTTC
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
22 1 0.02
23 46 0.96
24 1 0.02
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (23 bp):
AGTAAGCACACGAAGTGCGAAAC
Found at i:59005 original size:24 final size:26
Alignment explanation
Indices: 58967--59014 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
58957 TTTACATGGG
58967 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
58993 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
59015 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:63002 original size:18 final size:19
Alignment explanation
Indices: 62965--63003 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
62955 ATAGGTTGTC
* *
62965 ATTTTATCTTGGTGTTATG
1 ATTTTATCATGGTGTAATG
62984 ATTTTATCAT-GTGTAATG
1 ATTTTATCATGGTGTAATG
63002 AT
1 AT
63004 AAAATTTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.23, C:0.05, G:0.18, T:0.54
Consensus pattern (19 bp):
ATTTTATCATGGTGTAATG
Found at i:64656 original size:29 final size:28
Alignment explanation
Indices: 64563--64652 Score: 135
Period size: 28 Copynumber: 3.2 Consensus size: 28
64553 AAAATGTGAT
* *
64563 TTTTGGATACTCGGGGGCAAAATGGTAA
1 TTTTGGACACTCGGGGGTAAAATGGTAA
* *
64591 TTTTGGACACTCGGGGGTAAATTGTTAA
1 TTTTGGACACTCGGGGGTAAAATGGTAA
*
64619 TTTTGGACACTCGGGGATAAAATGGTAA
1 TTTTGGACACTCGGGGGTAAAATGGTAA
64647 TTTTGG
1 TTTTGG
64653 GACAGTTCAG
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 55 1.00
ACGTcount: A:0.27, C:0.10, G:0.30, T:0.33
Consensus pattern (28 bp):
TTTTGGACACTCGGGGGTAAAATGGTAA
Found at i:64769 original size:29 final size:29
Alignment explanation
Indices: 64737--64828 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
64727 AAAAATGGAG
64737 TTTTTGGAAGTTCGAGGGTAAAATAGTAA
1 TTTTTGGAAGTTCGAGGGTAAAATAGTAA
* ** * *
64766 TTTTTGAAAAAATCGAGGTTAAAA-ATGGAA
1 TTTTTG-GAAGTTCGAGGGTAAAATA-GTAA
* *
64796 -GTTTGGAAAGTTCGGGGGTAAAAT-GTAA
1 TTTTTGG-AAGTTCGAGGGTAAAATAGTAA
64824 TTTTT
1 TTTTT
64829 AAAAAATTTA
Statistics
Matches: 45, Mismatches: 13, Indels: 10
0.66 0.19 0.15
Matches are distributed among these distances:
28 3 0.07
29 26 0.58
30 16 0.36
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (29 bp):
TTTTTGGAAGTTCGAGGGTAAAATAGTAA
Found at i:64790 original size:59 final size:58
Alignment explanation
Indices: 64722--64888 Score: 178
Period size: 59 Copynumber: 2.8 Consensus size: 58
64712 TGAAAGTTTG
64722 GGGTTAAAAATGG-AGTTTTTGG-AAGTTCGAGGGTAAAATAGTAATTTTTGAAAAAATCGA
1 GGGTTAAAAATGGAAG--TTTGGAAAGTTCGAGGGTAAAAT-GTAATTTTT-AAAAAATCGA
* **
64782 -GGTTAAAAATGGAAGTTTGGAAAGTTCGGGGGTAAAATGTAATTTTTAAAAAATTTA
1 GGGTTAAAAATGGAAGTTTGGAAAGTTCGAGGGTAAAATGTAATTTTTAAAAAATCGA
** * * * *
64839 GGGTTAAAAATATAATTTTGGAGAATTTTGGGGGTCAAAATGTAATTTTT
1 GGGTTAAAAATGGAAGTTTGGA-AAGTTCGAGGGT-AAAATGTAATTTTT
64889 GGACAGGTTA
Statistics
Matches: 94, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
57 8 0.09
58 32 0.34
59 38 0.40
60 16 0.17
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (58 bp):
GGGTTAAAAATGGAAGTTTGGAAAGTTCGAGGGTAAAATGTAATTTTTAAAAAATCGA
Found at i:66103 original size:21 final size:23
Alignment explanation
Indices: 66079--66125 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
66069 TTATTAAGAA
66079 ATAATAAAT-AACA-ATGGTAAT
1 ATAATAAATGAACATATGGTAAT
*
66100 ATAATAAATGAACATATGTTAAT
1 ATAATAAATGAACATATGGTAAT
66123 ATA
1 ATA
66126 TGCATGTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.39
22 4 0.17
23 10 0.43
ACGTcount: A:0.55, C:0.04, G:0.09, T:0.32
Consensus pattern (23 bp):
ATAATAAATGAACATATGGTAAT
Found at i:67483 original size:194 final size:194
Alignment explanation
Indices: 66979--67622 Score: 808
Period size: 194 Copynumber: 3.3 Consensus size: 194
66969 TTTGGTGTCG
* * * * ** *
66979 TTGATTTGGTCTACTTCT-TAGTATCTTATTAGGAAGATGATCGTATCGCTTGTTTCAATCCGCT
1 TTGAGTTGGTATACTTCTCT-GTATCTCATCAGGAAGATGATCGCCTCACTTGTTTCAATCCGCT
* *
67043 TCTCTGTACCTCATCAGGAAGACGAATTTGGTCTACTTCTCAGTATTTCATCAGGAAGCTAACCA
65 TCTCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATTTCATCAGGAAGCTAACCT
* * * *
67108 TTTTATTGCTTCGACATGCTTCTCAGTATCTTATCAAGAAGCTGAGATTCGAAGATTTACTTACA
130 TTTTATTGCTTCGCCATGCTTCTCAGTATCTCATCAAGAAGCTGAGGTTCGAAGATTT--GT---
*
67173 TCGAGCC
190 TC--GCA
* * * ** **
67180 TTGAGTTAGTATACTTCTCTGTATCTCATCAGGAAAATAACTAC-CC-CGTTTGTTTTGATCCGC
1 TTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGA-T-CGCCTCACTTGTTTCAATCCGC
67243 TTCTCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATTTCATCAGGAAGCTAACC
64 TTCTCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATTTCATCAGGAAGCTAACC
* *
67308 TTTTTATTGCTTCGCCTTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGTTCGC
129 TTTTTATTGCTTCGCCATGCTTCTCAGTATCTCATCAAGAAGCTGAGGTTCGAAGATTTGTTCGC
67373 A
194 A
*
67374 TTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGCTGATCGCCTCACTTGTTTCAATCCGCTT
1 TTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGATCGCCTCACTTGTTTCAATCCGCTT
* * * * *
67439 CTCTGTAACTCATCTGGAAGACAAATTTGGTCCACTTCTCAGTATCTCATCAGGAAACTAACCTT
66 CTCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATTTCATCAGGAAGCTAACCTT
* * * * * * *
67504 TTTATTACTTCGCCCTGCTTCTTAATATCTCATCAAGAAGTTGGGGTTCAAAGATTTGTTCGCA
131 TTTATTGCTTCGCCATGCTTCTCAGTATCTCATCAAGAAGCTGAGGTTCGAAGATTTGTTCGCA
* * ** *
67568 TTGAGTTGGTATACTTATTTGTATCTCATTTGGAAGATGATCACCTCACTTGTTT
1 TTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGATCGCCTCACTTGTTT
67623 GTGGATAATC
Statistics
Matches: 390, Mismatches: 48, Indels: 17
0.86 0.11 0.04
Matches are distributed among these distances:
192 1 0.00
193 3 0.01
194 218 0.56
196 2 0.01
199 1 0.00
201 162 0.42
202 2 0.01
203 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (194 bp):
TTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGATCGCCTCACTTGTTTCAATCCGCTT
CTCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATTTCATCAGGAAGCTAACCTT
TTTATTGCTTCGCCATGCTTCTCAGTATCTCATCAAGAAGCTGAGGTTCGAAGATTTGTTCGCA
Found at i:67701 original size:39 final size:38
Alignment explanation
Indices: 67653--67786 Score: 151
Period size: 39 Copynumber: 3.4 Consensus size: 38
67643 CCGTGATCGA
* * *
67653 GGTAGGAGATTGGTTGACGGTGATATGCCCCAAGCTCGG
1 GGTAAGAGATTGGTTGACGAT-ATCTGCCCCAAGCTCGG
** * * * *
67692 GGTAAGAGATTGAATGGCTATAATCTGCCTCGAGCTCGG
1 GGTAAGAGATTGGTTGACGAT-ATCTGCCCCAAGCTCGG
67731 GGTAAGAGATTGGTTGACGAATATCTGCCCCAAGCTCGG
1 GGTAAGAGATTGGTTGACG-ATATCTGCCCCAAGCTCGG
*
67770 GATAAGAGATTGGTTGA
1 GGTAAGAGATTGGTTGA
67787 TGATGTAATT
Statistics
Matches: 77, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
39 75 0.97
40 2 0.03
ACGTcount: A:0.25, C:0.16, G:0.34, T:0.25
Consensus pattern (38 bp):
GGTAAGAGATTGGTTGACGATATCTGCCCCAAGCTCGG
Found at i:67764 original size:78 final size:78
Alignment explanation
Indices: 67635--67781 Score: 206
Period size: 78 Copynumber: 1.9 Consensus size: 78
67625 GGATAATCGC
* * * *
67635 AATCTGCCCCGTGATCGAGGTAGGAGATTGGTTGACGGTGATATGCCCCAAGCTCGGGGTAAGAG
1 AATCTGCCCCGAGATCGAGGTAAGAGATTGGTTGACGATGATATGCCCCAAGCTCGGGATAAGAG
67700 ATTGAATGGCTAT
66 ATTGAATGGCTAT
* * * *
67713 AATCTGCCTCGAGCTCGGGGTAAGAGATTGGTTGACGAAT-ATCTGCCCCAAGCTCGGGATAAGA
1 AATCTGCCCCGAGATCGAGGTAAGAGATTGGTTGACG-ATGATATGCCCCAAGCTCGGGATAAGA
67777 GATTG
65 GATTG
67782 GTTGATGATG
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
78 59 0.98
79 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (78 bp):
AATCTGCCCCGAGATCGAGGTAAGAGATTGGTTGACGATGATATGCCCCAAGCTCGGGATAAGAG
ATTGAATGGCTAT
Found at i:68223 original size:50 final size:50
Alignment explanation
Indices: 68169--68727 Score: 256
Period size: 50 Copynumber: 11.3 Consensus size: 50
68159 CCCCTTCAAA
* * *
68169 TCTTCGTGGTACTGGATTCATCGTTGCGATTTTAGATCTTTCCCTTCTTG
1 TCTTCGTGGTACTGGATTCACCGTTGCGATCTTAAATCTTTCCCTTCTTG
* * * * * * * * *
68219 TCTTCTGAGGTACACGG-TTCGCTGTTGTGA-CTTAAACCTTTCCTTTTTTTA
1 TCTTC-GTGGTAC-TGGATTCACCGTTGCGATCTTAAATCTTTCC-CTTCTTG
* * * *
68270 TCTTTGTGGTATTGGATTCACCGTTGCGGTCTTAAATCTTTCCCTTATTG
1 TCTTCGTGGTACTGGATTCACCGTTGCGATCTTAAATCTTTCCCTTCTTG
* * * ** *
68320 TCTTCTATGGTACACGG-TCCGTCGTTGCGAT-TTAAACCTTTCCCTT-TTG
1 TCTTC-GTGGTAC-TGGATTCACCGTTGCGATCTTAAATCTTTCCCTTCTTG
* * * * * * * *
68369 TATCTTTGTCGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCTTTCATG
1 --TCTTCGTGGTACTGGATTCACCGTTGCGATCTTAAATCTTTCCCTTCTTG
* * * * * *
68421 TCTTCATGGTACTGGATTCGCCGTTACG-GCTTAAATTTTTCCCTTATTG
1 TCTTCGTGGTACTGGATTCACCGTTGCGATCTTAAATCTTTCCCTTCTTG
* * * * * *
68470 TCTTC-T-G-A--GG-TACA-CGGTCCG-CCTTAGACCTTTCCCTT-TTG
1 TCTTCGTGGTACTGGATTCACCGTTGCGATCTTAAATCTTTCCCTTCTTG
* * ** * * * *
68511 TATCTTTGTGGTACTGGATCCGTCGTTGAGGTCTTGAATCTTTCCCTTCATG
1 --TCTTCGTGGTACTGGATTCACCGTTGCGATCTTAAATCTTTCCCTTCTTG
* * * *
68563 TCTTCATGGTACTGGATTCGCCGTTGCG-GCTTAAATCTTTCCCTTCGTG
1 TCTTCGTGGTACTGGATTCACCGTTGCGATCTTAAATCTTTCCCTTCTTG
* * * * *
68612 TCTTCTGAGGTACATGG-TCCTACCGTTGAGA-CTTAGATCTTTCCCTTCTGTA
1 TCTTC-GTGGTAC-TGGATTC-ACCGTTGCGATCTTAAATCTTTCCCTTCT-TG
* * * * * **
68664 TCTTTGTGGTATTAGATTCGCCGTTG-TAGTCTTAAATCTTTCCCTTAATG
1 TCTTCGTGGTACTGGATTCACCGTTGCGA-TCTTAAATCTTTCCCTTCTTG
*
68714 TCTTCTTGGTACTG
1 TCTTCGTGGTACTG
68728 AGACCTGTAA
Statistics
Matches: 374, Mismatches: 104, Indels: 62
0.69 0.19 0.11
Matches are distributed among these distances:
41 3 0.01
42 18 0.05
43 6 0.02
44 3 0.01
45 1 0.00
46 2 0.01
47 1 0.00
48 3 0.01
49 53 0.14
50 144 0.39
51 127 0.34
52 13 0.03
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (50 bp):
TCTTCGTGGTACTGGATTCACCGTTGCGATCTTAAATCTTTCCCTTCTTG
Found at i:68309 original size:101 final size:101
Alignment explanation
Indices: 68145--68725 Score: 353
Period size: 101 Copynumber: 5.9 Consensus size: 101
68135 TTCACCATTA
* * *** * * * *
68145 CGACTTAAACTTTTCCCCTTCAAATCTTCGTGGTACTGGATTCATCGTTGCGATTTTAGATCTTT
1 CGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTGGATTCACCGTTGCGGTCTTAGATCTTT
*
68210 CCCTTCTTGTCTTCTGA-GGTACACGGTTCG-CTGTTG
66 CCCTTCTTGTCTTCT-ATGGTACACGGTCCGTC-GTTG
* * * * *
68246 TGACTTAAACCTTTCCTTTTTTTATCTTTGTGGTATTGGATTCACCGTTGCGGTCTTAAATCTTT
1 CGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTGGATTCACCGTTGCGGTCTTAGATCTTT
*
68311 CCCTTATTGTCTTCTATGGTACACGGTCCGTCGTTG
66 CCCTTCTTGTCTTCTATGGTACACGGTCCGTCGTTG
* * * *
68347 CGATTTAAACCTTTCCCTTTTGTATCTTTGTCGTACTGGATCCGCCGTTGCGGTCTTAGATCTTT
1 CGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTGGATTCACCGTTGCGGTCTTAGATCTTT
* * * * * *
68412 CCTTTCATGTCTTC-ATGGTAC-TGGATTCGCCGTTA
66 CCCTTCTTGTCTTCTATGGTACACGG-TCCGTCGTTG
* ** * * * * * *
68447 CGGCTTAAATTTTTCCCTTATTG--TC-TTCT-G-A--GG-TACA-CGGT-CCGCCTTAGACCTT
1 CGACTTAAACCTTTCCCTT-TTGTATCTTTGTGGTACTGGATTCACCGTTGCGGTCTTAGATCTT
* *
68502 TCCCTT-TTGTATCTT-TGTGGTAC-TGGATCCGTCGTTG
65 TCCCTTCTTG--TCTTCTATGGTACACGG-TCCGTCGTTG
* * * * * ** * *
68539 AGGTCTTGAATCTTTCCCTTCATG--TCTTCATGGTACTGGATTCGCCGTTGCGG-CTTAAATCT
1 -CGACTTAAACCTTTCCCTT-TTGTATCTTTGTGGTACTGGATTCACCGTTGCGGTCTTAGATCT
* *
68601 TTCCCTTCGTGTCTTCTGA-GGTACATGGTCC-TACCGTTG
64 TTCCCTTCTTGTCTTCT-ATGGTACACGGTCCGT--CGTTG
* * * * * * * ** *
68640 AGACTTAGATCTTTCCCTTCTGTATCTTTGTGGTATTAGATTCGCCGTTGTAGTCTTAAATCTTT
1 CGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTGGATTCACCGTTGCGGTCTTAGATCTTT
**
68705 CCCTTAATGTCTTCT-TGGTAC
66 CCCTTCTTGTCTTCTATGGTAC
68726 TGAGACCTGT
Statistics
Matches: 377, Mismatches: 77, Indels: 52
0.75 0.15 0.10
Matches are distributed among these distances:
90 2 0.01
91 16 0.04
92 24 0.06
93 21 0.06
94 4 0.01
95 1 0.00
96 2 0.01
97 1 0.00
98 5 0.01
99 13 0.03
100 71 0.19
101 192 0.51
102 25 0.07
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.42
Consensus pattern (101 bp):
CGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTGGATTCACCGTTGCGGTCTTAGATCTTT
CCCTTCTTGTCTTCTATGGTACACGGTCCGTCGTTG
Found at i:68564 original size:142 final size:142
Alignment explanation
Indices: 68276--68727 Score: 523
Period size: 142 Copynumber: 3.1 Consensus size: 142
68266 TTTATCTTTG
* *
68276 TGGTATTGGATTCACCGTTGCGGTCTTAAATCTTTCCCTTATTGTCTTCT-ATGGTACACGGTCC
1 TGGTACTGGATTCGCCGTTGCGG-CTTAAATCTTTCCCTTATTGTCTTCTGA-GGTACACGGTCC
* * *
68340 GTCGTTGCGATTTAAACCTTTCCCTTTTGTATCTTTGTCGTACTGGATCCGCCGTTGCGGTCTTA
64 G-C----CG--TTAGACCTTTCCCTTTTGTATCTTTGTGGTACTGGATCCGCCGTTGAGGTCTTA
*
68405 GATCTTTCCTTTCATGTCTTCA
122 -ATCTTTCCCTTCATGTCTTCA
* *
68427 TGGTACTGGATTCGCCGTTACGGCTTAAATTTTTCCCTTATTGTCTTCTGAGGTACACGGTCCGC
1 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTATTGTCTTCTGAGGTACACGGTCCGC
*
68492 C-TTAGACCTTTCCCTTTTGTATCTTTGTGGTACTGGATCCGTCGTTGAGGTCTTGAATCTTTCC
66 CGTTAGACCTTTCCCTTTTGTATCTTTGTGGTACTGGATCCGCCGTTGAGGTCTT-AATCTTTCC
68556 CTTCATGTCTTCA
130 CTTCATGTCTTCA
** * *
68569 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACATGGTCCTA
1 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTATTGTCTTCTGAGGTACACGGTCC-G
* * * *
68634 CCGTTGAGACTTAGATCTTTCCCTTCTGTATCTTTGTGGTATTAGATTCGCCGTTGTA-GTCTTA
65 CCGTT-AGAC------CTTTCCCTTTTGTATCTTTGTGGTACTGGATCCGCCGTTG-AGGTCTT-
* *
68698 AATCTTTCCCTTAATGTCTTCT
121 AATCTTTCCCTTCATGTCTTCA
68720 TGGTACTG
1 TGGTACTG
68728 AGACCTGTAA
Statistics
Matches: 266, Mismatches: 23, Indels: 24
0.85 0.07 0.08
Matches are distributed among these distances:
142 127 0.48
143 3 0.01
144 2 0.01
145 5 0.02
149 1 0.00
150 38 0.14
151 89 0.33
152 1 0.00
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (142 bp):
TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTATTGTCTTCTGAGGTACACGGTCCGC
CGTTAGACCTTTCCCTTTTGTATCTTTGTGGTACTGGATCCGCCGTTGAGGTCTTAATCTTTCCC
TTCATGTCTTCA
Found at i:70734 original size:3 final size:3
Alignment explanation
Indices: 70726--70755 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
70716 TCTACCCCTT
70726 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
70756 AACACGTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:74483 original size:22 final size:22
Alignment explanation
Indices: 74455--74496 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
74445 GTCATCAAGC
74455 TTTATGAAAACAATTTTAAAGT
1 TTTATGAAAACAATTTTAAAGT
74477 TTTATGAAAACAATTTTAAA
1 TTTATGAAAACAATTTTAAA
74497 AACAAATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (22 bp):
TTTATGAAAACAATTTTAAAGT
Found at i:74928 original size:58 final size:59
Alignment explanation
Indices: 74817--75036 Score: 193
Period size: 58 Copynumber: 3.8 Consensus size: 59
74807 TAAAGTTCGA
* *
74817 GTCAAAAATGGAGTTTTTGG-AAGTTTGAGGGT-AAAATGGTAA-TTTTGGAAAAATCAG-G
1 GTCAAAAATGGA-ATTTTGGAAAGTTTGAGGGTAAAAAT-GTAATTTTTAGAAAAAT-AGAG
* *
74875 GTCAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTAG-AAAATTGAG
1 GTCAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAAATGTAATTTTTAGAAAAATAGAG
* * * * * * **
74933 GTTAAAAATGAAATTTTAGAAAGTTTGGGGGTAAAAATATAATTTTCA-AAAAATTTAG
1 GTCAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAAATGTAATTTTTAGAAAAATAGAG
* ** * *
74991 GTTAAAAATATATTTTTGGAGAA-TTATGAGGGTCAAAATGTAATTT
1 GTCAAAAATGGAATTTTGGA-AAGTT-TGAGGGTAAAAATGTAATTT
75037 CTGGATAGTT
Statistics
Matches: 136, Mismatches: 19, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
57 7 0.05
58 100 0.74
59 29 0.21
ACGTcount: A:0.41, C:0.03, G:0.23, T:0.34
Consensus pattern (59 bp):
GTCAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAAATGTAATTTTTAGAAAAATAGAG
Found at i:74976 original size:29 final size:29
Alignment explanation
Indices: 74837--75036 Score: 115
Period size: 29 Copynumber: 6.9 Consensus size: 29
74827 GAGTTTTTGG
* *
74837 AAGTTTGAGGGT-AAAATGGTAATTTTGGA
1 AAGTTTGAGGGTAAAAAT-ATAATTTTAGA
** * ** *
74866 AA-AATCAGGGTCAAAAATGGAATTTTGGA
1 AAGTTTGAGGGT-AAAAATATAATTTTAGA
* *
74895 AAGTTCGAGGGTAAAAATGTAATTTTTAGA
1 AAGTTTGAGGGTAAAAATATAA-TTTTAGA
* *
74925 AA-ATTGAGGTTAAAAATGA-AATTTTAGA
1 AAGTTTGAGGGTAAAAAT-ATAATTTTAGA
* *
74953 AAGTTTGGGGGTAAAAATATAATTTTCAAA
1 AAGTTTGAGGGTAAAAATATAATTTT-AGA
* * * *
74983 AAATTT-AGGTTAAAAATATATTTTTGGA
1 AAGTTTGAGGGTAAAAATATAATTTTAGA
* *
75011 GAA-TTATGAGGGTCAAAATGTAATTT
1 -AAGTT-TGAGGGTAAAAATATAATTT
75037 CTGGATAGTT
Statistics
Matches: 132, Mismatches: 28, Indels: 21
0.73 0.15 0.12
Matches are distributed among these distances:
28 19 0.14
29 74 0.56
30 39 0.30
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.34
Consensus pattern (29 bp):
AAGTTTGAGGGTAAAAATATAATTTTAGA
Found at i:76807 original size:17 final size:17
Alignment explanation
Indices: 76780--76873 Score: 98
Period size: 17 Copynumber: 5.5 Consensus size: 17
76770 TTCAATATTT
* *
76780 ATAAATCTAAATTTATA
1 ATAAATTTAAATTTAAA
*
76797 TTAAATTTAAATTTTAAA
1 ATAAATTTAAA-TTTAAA
*
76815 ACAAATTTAAATTTAAA
1 ATAAATTTAAATTTAAA
* *
76832 ATAAATTTATATTCAAA
1 ATAAATTTAAATTTAAA
**
76849 ATAAATTTAACCTTAAA
1 ATAAATTTAAATTTAAA
*
76866 ACAAATTT
1 ATAAATTT
76874 TAAAATGAGT
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
17 49 0.78
18 14 0.22
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAAATTTAAATTTAAA
Found at i:81284 original size:3 final size:3
Alignment explanation
Indices: 81276--81307 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
81266 AAATAATTGC
81276 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
81308 ACTTTATCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:81863 original size:4 final size:4
Alignment explanation
Indices: 81854--81911 Score: 57
Period size: 4 Copynumber: 14.5 Consensus size: 4
81844 AAATAAACGG
* *
81854 GAAA GAAA GAAAA GAAA GAAA GAAA G-AA GAAG GAGAG GAAA GAAA G-AA
1 GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA GAAA
*
81902 GAAT GAAA GA
1 GAAA GAAA GA
81912 TATGTAATGT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
3 6 0.13
4 32 0.70
5 8 0.17
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:81894 original size:20 final size:18
Alignment explanation
Indices: 81853--81904 Score: 70
Period size: 20 Copynumber: 2.8 Consensus size: 18
81843 CAAATAAACG
81853 GGAAAGAAAGAA-AAGAA
1 GGAAAGAAAGAAGAAGAA
*
81870 AGAAAGAAAGAAGAAGGAGA
1 GGAAAGAAAGAAGAA-GA-A
81890 GGAAAGAAAGAAGAA
1 GGAAAGAAAGAAGAA
81905 TGAAAGATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 11 0.37
18 2 0.07
19 2 0.07
20 15 0.50
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (18 bp):
GGAAAGAAAGAAGAAGAA
Done.