Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012623.1 Kokia drynarioides strain JFW-HI SEQ_127632, 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: 69468
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:8834 original size:14 final size:13
Alignment explanation
Indices: 8797--8842 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
8787 TGTTATAATG
*
8797 AAAATAATTTTAA
1 AAAATTATTTTAA
8810 AAAATTATTTTAA
1 AAAATTATTTTAA
8823 AAAATTATTTTTAA
1 AAAATTA-TTTTAA
8837 AAAATT
1 AAAATT
8843 TGTCACATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
13 19 0.61
14 12 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AAAATTATTTTAA
Found at i:11766 original size:20 final size:22
Alignment explanation
Indices: 11743--11793 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
11733 TATAAAAATT
11743 CAAGTTTTTCCA-ATAAAA-CC
1 CAAGTTTTTCCATATAAAACCC
**
11763 CAAGTAATTCCATATAAAACCC
1 CAAGTTTTTCCATATAAAACCC
11785 CAAGTTTTT
1 CAAGTTTTT
11794 TCTTTTTCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 10 0.40
21 6 0.24
22 9 0.36
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.31
Consensus pattern (22 bp):
CAAGTTTTTCCATATAAAACCC
Found at i:11779 original size:21 final size:21
Alignment explanation
Indices: 11750--11789 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
11740 ATTCAAGTTT
11750 TTCCAATAAAA-CCCAAGTAA
1 TTCCAATAAAACCCCAAGTAA
11770 TTCCATATAAAACCCCAAGT
1 TTCCA-ATAAAACCCCAAGT
11790 TTTTTCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 7 0.39
ACGTcount: A:0.45, C:0.28, G:0.05, T:0.23
Consensus pattern (21 bp):
TTCCAATAAAACCCCAAGTAA
Found at i:12321 original size:16 final size:16
Alignment explanation
Indices: 12300--12331 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12290 CTTCTTGAAG
*
12300 AATAATTATTGTTCAA
1 AATAATTATTATTCAA
12316 AATAATTATTATTCAA
1 AATAATTATTATTCAA
12332 GTAACTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (16 bp):
AATAATTATTATTCAA
Found at i:31232 original size:22 final size:21
Alignment explanation
Indices: 31204--31269 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
31194 CAATACCTAG
31204 AAAATAATAACAAAATAGTAGC
1 AAAATAATAAC-AAATAGTAGC
* ** *
31226 AATATAATAGTGAAATAATAGC
1 AAAATAATA-ACAAATAGTAGC
* *
31248 AAAACAACAACAAATAGTAGC
1 AAAATAATAACAAATAGTAGC
31269 A
1 A
31270 GAAAAATTTG
Statistics
Matches: 33, Mismatches: 10, Indels: 3
0.72 0.22 0.07
Matches are distributed among these distances:
21 10 0.30
22 23 0.70
ACGTcount: A:0.61, C:0.11, G:0.11, T:0.18
Consensus pattern (21 bp):
AAAATAATAACAAATAGTAGC
Found at i:31924 original size:3 final size:3
Alignment explanation
Indices: 31916--31950 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
31906 TAGGCACTAA
31916 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
31951 GATATAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:32981 original size:20 final size:21
Alignment explanation
Indices: 32956--32996 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
32946 TTTTAAAGCG
*
32956 TTATTTTATT-CTATTAATTA
1 TTATTTTATTACTATAAATTA
*
32976 TTATTTTTTTACTATAAATTA
1 TTATTTTATTACTATAAATTA
32997 AACCAATCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATTTTATTACTATAAATTA
Found at i:34444 original size:23 final size:24
Alignment explanation
Indices: 34406--34451 Score: 76
Period size: 23 Copynumber: 1.9 Consensus size: 24
34396 ACTTCGTAAT
34406 ATTGACCAAGCTTCACATTCACAAG
1 ATTGACC-AGCTTCACATTCACAAG
34431 ATTGACC-GCTTCACATTCACA
1 ATTGACCAGCTTCACATTCACA
34452 GTCCTAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 14 0.67
25 7 0.33
ACGTcount: A:0.33, C:0.30, G:0.11, T:0.26
Consensus pattern (24 bp):
ATTGACCAGCTTCACATTCACAAG
Found at i:35739 original size:6 final size:6
Alignment explanation
Indices: 35728--35797 Score: 67
Period size: 6 Copynumber: 12.0 Consensus size: 6
35718 TAATAATTTT
** *
35728 TTTAAA TTTAAA AATAAA TTTAAA TTTATAA -TT-AA TCTAAA TTCT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TT-TAAA
35775 TTTAAA -TTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
35798 AGTAATTTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
4 2 0.04
5 7 0.13
6 40 0.77
7 3 0.06
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:35776 original size:23 final size:23
Alignment explanation
Indices: 35728--35797 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 23
35718 TAATAATTTT
**
35728 TTTAAATTTAAAAATAAATTTAAA
1 TTTAAA-TTAAATCTAAATTTAAA
35752 TTTATAATT-AATCTAAATTCT-AA
1 TTTA-AATTAAATCTAAATT-TAAA
*
35775 TTTAAATTAAATTTAAATTTAAA
1 TTTAAATTAAATCTAAATTTAAA
35798 AGTAATTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
22 5 0.13
23 25 0.64
24 7 0.18
25 2 0.05
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (23 bp):
TTTAAATTAAATCTAAATTTAAA
Found at i:35804 original size:17 final size:18
Alignment explanation
Indices: 35728--35808 Score: 69
Period size: 17 Copynumber: 4.3 Consensus size: 18
35718 TAATAATTTT
*
35728 TTTAAATTTAAAAATAAA
1 TTTAAATTTAAAATTAAA
35746 TTTAAATTTATAATTAATCTAAA
1 TTTAAA-TT-TAA--AAT-TAAA
35769 TTCT-AATTT-AAATTAAA
1 TT-TAAATTTAAAATTAAA
*
35786 TTTAAATTTAAAAGT-AA
1 TTTAAATTTAAAATTAAA
35803 TTTAAA
1 TTTAAA
35809 AGGGGCCTGG
Statistics
Matches: 53, Mismatches: 2, Indels: 17
0.74 0.03 0.24
Matches are distributed among these distances:
16 1 0.02
17 19 0.36
18 13 0.25
19 2 0.04
20 4 0.08
21 1 0.02
22 4 0.08
23 8 0.15
24 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (18 bp):
TTTAAATTTAAAATTAAA
Found at i:36105 original size:6 final size:6
Alignment explanation
Indices: 36080--36149 Score: 76
Period size: 6 Copynumber: 12.0 Consensus size: 6
36070 TAATAATTTT
* *
36080 TTTAAA TTTGAAA -ATAAA TTTAAA TTTAAA ATT-AA TTTAAA TTCT-AA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA
36127 TTTAAA -TTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
36150 AGTAATTTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
5 13 0.24
6 37 0.69
7 4 0.07
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:36116 original size:17 final size:18
Alignment explanation
Indices: 36080--36160 Score: 76
Period size: 17 Copynumber: 4.3 Consensus size: 18
36070 TAATAATTTT
* *
36080 TTTAAATTTGAAAATAAA
1 TTTAAATTTAAAAATTAA
36098 TTTAAATTT-AAAATTAA
1 TTTAAATTTAAAAATTAA
36115 TTTAAATTCTAATTTAAATTAAA
1 TTTAAATT-TAA---AAATT-AA
*
36138 TTTAAATTT-AAAAGTAA
1 TTTAAATTTAAAAATTAA
36155 TTTAAA
1 TTTAAA
36161 AGGGGCCCGG
Statistics
Matches: 55, Mismatches: 2, Indels: 13
0.79 0.03 0.19
Matches are distributed among these distances:
17 23 0.42
18 14 0.25
19 1 0.02
21 1 0.02
22 6 0.11
23 10 0.18
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.44
Consensus pattern (18 bp):
TTTAAATTTAAAAATTAA
Found at i:36118 original size:11 final size:11
Alignment explanation
Indices: 36102--36148 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
36092 AATAAATTTA
36102 AATTTAAAATT
1 AATTTAAAATT
*
36113 AATTTAAATTCT
1 AATTTAAAAT-T
36125 AATTT-AAATT
1 AATTTAAAATT
*
36135 AAATTTAAATTT
1 -AATTTAAAATT
36147 AA
1 AA
36149 AAGTAATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
10 1 0.03
11 19 0.63
12 10 0.33
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (11 bp):
AATTTAAAATT
Found at i:36122 original size:23 final size:23
Alignment explanation
Indices: 36094--36149 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 23
36084 AATTTGAAAA
36094 TAAATTTAAATTTAAAATT-AATT
1 TAAATTTAAATTT-AAATTAAATT
36117 TAAATTCT-AATTTAAATTAAATT
1 TAAATT-TAAATTTAAATTAAATT
36140 TAAATTTAAA
1 TAAATTTAAA
36150 AGTAATTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
22 6 0.20
23 23 0.77
24 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
TAAATTTAAATTTAAATTAAATT
Found at i:36139 original size:40 final size:41
Alignment explanation
Indices: 36084--36160 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 41
36074 AATTTTTTTA
*
36084 AATTTGAAAATAAATTTAAATTTAAAATTAATTTAAATTCT
1 AATTTGAAAATAAATTTAAATTTAAAAGTAATTTAAATTCT
*
36125 AATTT-AAATTAAATTTAAATTTAAAAGTAATTTAAA
1 AATTTGAAAATAAATTTAAATTTAAAAGTAATTTAAA
36161 AGGGGCCCGG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 29 0.85
41 5 0.15
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (41 bp):
AATTTGAAAATAAATTTAAATTTAAAAGTAATTTAAATTCT
Found at i:36156 original size:352 final size:348
Alignment explanation
Indices: 35514--36209 Score: 1250
Period size: 352 Copynumber: 2.0 Consensus size: 348
35504 GGAGGCTGCA
*
35514 GCAATAGCGATGGCAAGTTGAAGATGGTTAGTTGGCAACTTGGTTGCCGACATGACAGTTTGGTT
1 GCAATAGCGATGGCAAGTTGAAGATGGTTAGTTGGCAACTTGGTTGCCGACATGACACTTTGGTT
35579 GGTGGGGAGATAGGTGGTTGGTAATAATGCAAACGGGAGTAGATTGGGTCAATGAGTTTGAGTTT
66 GGTGGGGAGATAGGTGGTTGGTAATAATGCAAACGGGAGTAGATTGGGTCAATGAGTTTGAGTTT
*
35644 AAAATTTGTGTATAGGTAATTTCGGACCATTGTAAATTTGGACATGTAATTTAGATTTTTATAAT
131 AAAATTTGTGTATAGGTAATTTCGGACCATTGTAAATTTGGACATGTAATTTAAATTTTTATAAT
*
35709 TGGATTTTATAATAATTTTTTTAAATTTAAAAATAAATTTAAATTTATAATTAATCTAAATTCTA
196 TGGATTTTATAATAATTTTTTTAAATTTAAAAATAAATTTAAATTTAAAATTAATCTAAATTCTA
*
35774 ATTTAAATTAAATTTAAATTTAAAAGTAATTTAAAAGGGGCCTGGTGGGCTCCAACACATTGCAC
261 ATTTAAATTAAATTTAAATTTAAAAGTAATTTAAAAGGGGCCCGGTGGGCTCCAACAC--TGCAC
*
35839 ACAAGTTCCACATGTTTATAATAAT
324 ACAAGTTCCACATGTTGATAATAAT
35864 GCAATAGCGATGGCAAGTTGAAGAT-GTATAGTTGGCAACTTGGTTGCCGACATGACACTATCTG
1 GCAATAGCGATGGCAAGTTGAAGATGGT-TAGTTGGCAACTTGGTTGCCGACATGACACT-T-TG
*
35928 GTTGGTGGGGAGATAGGTGGTTGGTAATAATGCAAATGGGAGTAGATTGGGTCAATGAGTTTGAG
63 GTTGGTGGGGAGATAGGTGGTTGGTAATAATGCAAACGGGAGTAGATTGGGTCAATGAGTTTGAG
* *
35993 TTTAAAATTTGTGTTTAGGTAATTTCGGATCATTGTAAATTTGGACATGTAATTTAAATTTTTAT
128 TTTAAAATTTGTGTATAGGTAATTTCGGACCATTGTAAATTTGGACATGTAATTTAAATTTTTAT
* *
36058 AATTGGATTTTATAATAATTTTTTTAAATTTGAAAATAAATTTAAATTTAAAATTAATTTAAATT
193 AATTGGATTTTATAATAATTTTTTTAAATTTAAAAATAAATTTAAATTTAAAATTAATCTAAATT
36123 CTAATTTAAATTAAATTTAAATTTAAAAGTAATTTAAAAGGGGCCCGGTGGGCTCCAACACTGCA
258 CTAATTTAAATTAAATTTAAATTTAAAAGTAATTTAAAAGGGGCCCGGTGGGCTCCAACACTGCA
36188 CACAAGTTCCACATGTTGATAA
323 CACAAGTTCCACATGTTGATAA
36210 ACTATCTTTA
Statistics
Matches: 333, Mismatches: 10, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
349 2 0.01
350 80 0.24
351 1 0.00
352 250 0.75
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (348 bp):
GCAATAGCGATGGCAAGTTGAAGATGGTTAGTTGGCAACTTGGTTGCCGACATGACACTTTGGTT
GGTGGGGAGATAGGTGGTTGGTAATAATGCAAACGGGAGTAGATTGGGTCAATGAGTTTGAGTTT
AAAATTTGTGTATAGGTAATTTCGGACCATTGTAAATTTGGACATGTAATTTAAATTTTTATAAT
TGGATTTTATAATAATTTTTTTAAATTTAAAAATAAATTTAAATTTAAAATTAATCTAAATTCTA
ATTTAAATTAAATTTAAATTTAAAAGTAATTTAAAAGGGGCCCGGTGGGCTCCAACACTGCACAC
AAGTTCCACATGTTGATAATAAT
Found at i:37400 original size:17 final size:18
Alignment explanation
Indices: 37378--37411 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
37368 AATAAGATTA
*
37378 AAATA-TTATAAATAAAT
1 AAATATTTAAAAATAAAT
37395 AAATATTTAAAAATAAA
1 AAATATTTAAAAATAAA
37412 ATGTGCCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATATTTAAAAATAAAT
Found at i:41910 original size:13 final size:13
Alignment explanation
Indices: 41894--41921 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
41884 AATAAAATAA
41894 AATATATTTTATT
1 AATATATTTTATT
41907 AATATATTTTATT
1 AATATATTTTATT
41920 AA
1 AA
41922 AAAATATACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
AATATATTTTATT
Found at i:41929 original size:17 final size:15
Alignment explanation
Indices: 41891--41928 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
41881 AAAAATAAAA
41891 TAAAATATATTTTAT
1 TAAAATATATTTTAT
41906 T--AATATATTTTAT
1 TAAAATATATTTTAT
*
41919 TAAAAAATAT
1 TAAAATATAT
41929 ACTTTATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
13 13 0.65
15 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAAATATATTTTAT
Found at i:41974 original size:15 final size:15
Alignment explanation
Indices: 41954--41992 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
41944 GTAGAAAAAT
41954 AATTAAAAAATAGAA
1 AATTAAAAAATAGAA
*
41969 AATTAAAGAATAGAA
1 AATTAAAAAATAGAA
*
41984 AAATAAAAA
1 AATTAAAAA
41993 GATGATTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (15 bp):
AATTAAAAAATAGAA
Found at i:43900 original size:20 final size:20
Alignment explanation
Indices: 43875--43913 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
43865 ATTGAGAGGT
43875 TGACGATTGGGAAATAGTAG
1 TGACGATTGGGAAATAGTAG
43895 TGACGATTGGGAAATAGTA
1 TGACGATTGGGAAATAGTA
43914 ATAACACTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.05, G:0.33, T:0.26
Consensus pattern (20 bp):
TGACGATTGGGAAATAGTAG
Found at i:46939 original size:6 final size:6
Alignment explanation
Indices: 46914--46949 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
46904 GTAAATGAAA
*
46914 CATTTC TCATTTC CACTTC CATTTC CATTTC CATTT
1 CATTTC -CATTTC CATTTC CATTTC CATTTC CATTT
46950 TGAGAAATCC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (6 bp):
CATTTC
Found at i:54826 original size:81 final size:80
Alignment explanation
Indices: 54695--54938 Score: 258
Period size: 80 Copynumber: 3.0 Consensus size: 80
54685 TGAGATAAGA
* * * * * * * *
54695 ACCCTCCGATGGCTAAGACTC-TGCATACGATACAGTTTCTTATCAACTTGTGTGAGCAACATCG
1 ACCCTCCGATGACTAAGA-TCAAGCATATGTTGCAGATTCTTATCAGCTTGTGTGAGCAACATCA
*
54759 TGAGTGGATAAATAAGG
65 TGAGTGGAT-AATATGG
* * * **
54776 ACCCTTCGATGACTAAGATCAAGCATATGTTGCGGATTCTTATTAGCTTGTGTGAGCAGTATCAT
1 ACCCTCCGATGACTAAGATCAAGCATATGTTGCAGATTCTTATCAGCTTGTGTGAGCAACATCAT
*
54841 GAGTGGATTATATGG
66 GAGTGGATAATATGG
** * ** *
54856 ACCCTCCGATGGTTGAGATCCTGCATATGTTGCAGATTCTTGA-CAGCTTGTGTGAGCATCATCA
1 ACCCTCCGATGACTAAGATCAAGCATATGTTGCAGATTCTT-ATCAGCTTGTGTGAGCAACATCA
54920 TGAGTGGATAATATGG
65 TGAGTGGATAATATGG
54936 ACC
1 ACC
54939 ATATTGATGG
Statistics
Matches: 135, Mismatches: 26, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
80 77 0.57
81 58 0.43
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (80 bp):
ACCCTCCGATGACTAAGATCAAGCATATGTTGCAGATTCTTATCAGCTTGTGTGAGCAACATCAT
GAGTGGATAATATGG
Found at i:54991 original size:81 final size:80
Alignment explanation
Indices: 54738--54992 Score: 280
Period size: 80 Copynumber: 3.2 Consensus size: 80
54728 AGTTTCTTAT
* * * ** * *
54738 CAACTTGTGTGAGCAACATCGTGAGTGGATAAATAAGGACCCTTCGATGACTAAGATCAAGCATA
1 CAACTTGTGTGAGCATCATCATGAGTGGAT-AATATGGACCCTTCGATGGTTGAGATCATGCATA
* *
54803 TGTTGCGGATT-CTTA
65 TGTTGCAGATTCCTGA
* * * * *
54818 TTAGCTTGTGTGAGCAGT-ATCATGAGTGGATTATATGGACCCTCCGATGGTTGAGATCCTGCAT
1 -CAACTTGTGTGAGCA-TCATCATGAGTGGATAATATGGACCCTTCGATGGTTGAGATCATGCAT
*
54882 ATGTTGCAGATTCTTGA
64 ATGTTGCAGATTCCTGA
* * * *
54899 CAGCTTGTGTGAGCATCATCATGAGTGGATAATATGGACCATATTGATGGTTGGGATCATGCATA
1 CAACTTGTGTGAGCATCATCATGAGTGGATAATATGGACCCT-TCGATGGTTGAGATCATGCATA
*
54964 TGTTGCAGTTTCCTGA
65 TGTTGCAGATTCCTGA
54980 CAACTTGTGTGAG
1 CAACTTGTGTGAG
54993 TAGTATCTTA
Statistics
Matches: 145, Mismatches: 25, Indels: 8
0.81 0.14 0.04
Matches are distributed among these distances:
79 1 0.01
80 73 0.50
81 71 0.49
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (80 bp):
CAACTTGTGTGAGCATCATCATGAGTGGATAATATGGACCCTTCGATGGTTGAGATCATGCATAT
GTTGCAGATTCCTGA
Found at i:55095 original size:25 final size:25
Alignment explanation
Indices: 55028--55084 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
55018 GTTTTGGTTT
* * *
55028 GTAAGAGCAATATACTATCTGGCTC
1 GTAAGAGCAACATTCTGTCTGGCTC
55053 GTAAGAGCAACATTCTGTCTGGCTC
1 GTAAGAGCAACATTCTGTCTGGCTC
55078 GTAAGAG
1 GTAAGAG
55085 TGTGATTCTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (25 bp):
GTAAGAGCAACATTCTGTCTGGCTC
Found at i:57257 original size:23 final size:20
Alignment explanation
Indices: 57231--57283 Score: 52
Period size: 24 Copynumber: 2.4 Consensus size: 20
57221 CTTTATTTAA
57231 TAAATTATTTTGATATAATAAAT
1 TAAATT-TTTTGA-AT-ATAAAT
*
57254 TAAAATGTTTTTGAATATAAGT
1 T-AAAT-TTTTTGAATATAAAT
57276 TAAATTTT
1 TAAATTTT
57284 GACAAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
20 3 0.11
21 4 0.15
22 6 0.22
23 3 0.11
24 10 0.37
25 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (20 bp):
TAAATTTTTTGAATATAAAT
Found at i:57756 original size:20 final size:20
Alignment explanation
Indices: 57731--57778 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
57721 TATCGATCCG
*
57731 GTATCGATACTCTTGAAAAA
1 GTATCGATAATCTTGAAAAA
* * *
57751 GTATCGATAATTTTGTACAA
1 GTATCGATAATCTTGAAAAA
57771 GTATCGAT
1 GTATCGAT
57779 TTTTTATATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (20 bp):
GTATCGATAATCTTGAAAAA
Found at i:57809 original size:18 final size:18
Alignment explanation
Indices: 57783--57818 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
57773 ATCGATTTTT
* *
57783 TATATGCTCCAACGGTCA
1 TATACGCTCCAACAGTCA
57801 TATACGCTCCAACAGTCA
1 TATACGCTCCAACAGTCA
57819 CTAGATTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.14, T:0.25
Consensus pattern (18 bp):
TATACGCTCCAACAGTCA
Found at i:68200 original size:59 final size:58
Alignment explanation
Indices: 68127--68557 Score: 532
Period size: 59 Copynumber: 7.4 Consensus size: 58
68117 GGAGTGGCAG
* * *
68127 AATGGT-AGTTTTGGAATG-TTCGGAATCAAAAATAGGATTTTTGGAAGTTCGAGGGTAA
1 AATGGTAATTTTTGGAA-GATTCGG-GTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAA
* * *
68185 AATGGTAATTTTTGGAAGATTCGGGGCTAAAATGGGATTTTTGGAAGTT-TAGGAGTAA
1 AATGGTAATTTTTGGAAGATTCGGGTCAAAAATGGGATTTTTGGAAGTTCGAGG-GTAA
* *
68243 AATAGTAATTTTTGGAAGATTCGGGGTTAAAAATGGGATTTTTGGAAGTTC-AGGGGTAA
1 AATGGTAATTTTTGGAAGATTC-GGGTCAAAAATGGGATTTTTGGAAGTTCGA-GGGTAA
* * * *
68302 AATGATAATTTTTGGAAGATTTAGGGT-TAAAATGGGATTTTTGGAAGTT-TAGGGGTAA
1 AATGGTAATTTTTGGAAGA-TTCGGGTCAAAAATGGGATTTTTGGAAGTTCGA-GGGTAA
* * * **
68360 GATGGTAATTTTTAGAAGGTTCGGGGTTTAAAATGGGATTTTTGGAAGTTCGAGGGTAA
1 AATGGTAATTTTTGGAAGATTC-GGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAA
* * * *
68419 AATAGTAATTTTTGGAAGATTCGGTATCAAAAATGGGATTTTTGGAAGTTTGGGGGTAA
1 AATGGTAATTTTTGGAAGATTCGG-GTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAA
*
68478 AATAGTAATTTTTGGAAGATTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAA
1 AATGGTAATTTTTGGAAGATTCG-GGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAA
68537 AATGGTAATTTTTGGAAGATT
1 AATGGTAATTTTTGGAAGATT
68558 TAGGGACCTC
Statistics
Matches: 327, Mismatches: 33, Indels: 25
0.85 0.09 0.06
Matches are distributed among these distances:
57 5 0.02
58 103 0.31
59 213 0.65
60 6 0.02
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (58 bp):
AATGGTAATTTTTGGAAGATTCGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAA
Found at i:68341 original size:117 final size:117
Alignment explanation
Indices: 68154--68562 Score: 601
Period size: 117 Copynumber: 3.5 Consensus size: 117
68144 GTTCGGAATC
* * ** *
68154 AAAAATAGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGATTCGGGGCTAAAATG
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGATAATTTTTGGAAGATTTAGGGTTAAAATG
*
68219 GGATTTTTGGAAGTTTAGGAGTAAAATAGTAATTTTTGGAAGATTCGGGGTT
66 GGATTTTTGGAAGTTTAGGGGTAAAATAGTAATTTTTGGAAGATTCGGGGTT
68271 AAAAATGGGATTTTTGGAAGTTC-AGGGGTAAAATGATAATTTTTGGAAGATTTAGGGTTAAAAT
1 AAAAATGGGATTTTTGGAAGTTCGA-GGGTAAAATGATAATTTTTGGAAGATTTAGGGTTAAAAT
* * * *
68335 GGGATTTTTGGAAGTTTAGGGGTAAGATGGTAATTTTTAGAAGGTTCGGGGTT
65 GGGATTTTTGGAAGTTTAGGGGTAAAATAGTAATTTTTGGAAGATTCGGGGTT
* *
68388 TAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAT-AGTAATTTTTGGAAGA-TT-CGGTATCAAA
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGA-TAATTTTTGGAAGATTTAGGGT-T--AA
* * *
68450 AATGGGATTTTTGGAAGTTTGGGGGTAAAATAGTAATTTTTGGAAGATTCGAGGTC
62 AATGGGATTTTTGGAAGTTTAGGGGTAAAATAGTAATTTTTGGAAGATTCGGGGTT
*
68506 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGATTTAGGG
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGATAATTTTTGGAAGATTTAGGG
68563 ACCTCCGGGG
Statistics
Matches: 261, Mismatches: 22, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
115 3 0.01
116 5 0.02
117 150 0.57
118 99 0.38
119 2 0.01
120 2 0.01
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (117 bp):
AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGATAATTTTTGGAAGATTTAGGGTTAAAATG
GGATTTTTGGAAGTTTAGGGGTAAAATAGTAATTTTTGGAAGATTCGGGGTT
Found at i:68562 original size:29 final size:28
Alignment explanation
Indices: 68163--68562 Score: 290
Period size: 29 Copynumber: 13.6 Consensus size: 28
68153 CAAAAATAGG
*
68163 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
1 ATTTTTGGAAGTT-TAGGGTAAAATGGTA
** *
68192 ATTTTTGGAAGATTCGGGGCTAAAATGG-G
1 ATTTTTGGAAG-TTTAGGG-TAAAATGGTA
*
68221 ATTTTTGGAAGTTTAGGAGTAAAATAGTA
1 ATTTTTGGAAGTTTAGG-GTAAAATGGTA
** *
68250 ATTTTTGGAAGATTCGGGGTTAAAAATGG-G
1 ATTTTTGGAAG-TTTAGGG-T-AAAATGGTA
* *
68280 ATTTTTGGAAGTTCAGGGGTAAAATGATA
1 ATTTTTGGAAGTTTA-GGGTAAAATGGTA
*
68309 ATTTTTGGAAGATTTAGGGTTAAAATGG-G
1 ATTTTTGGAAG-TTTAGGG-TAAAATGGTA
*
68338 ATTTTTGGAAGTTTAGGGGTAAGATGGTA
1 ATTTTTGGAAGTTTA-GGGTAAAATGGTA
* ** *
68367 ATTTTTAGAAGGTTCGGGGTTTAAAATGG-G
1 ATTTTTGGAA-GTTTAGGG--TAAAATGGTA
* *
68397 ATTTTTGGAAGTTCGAGGGTAAAATAGTA
1 ATTTTTGGAAGTT-TAGGGTAAAATGGTA
* * * *
68426 ATTTTTGGAAGATTCGGTATCAAAAATGG-G
1 ATTTTTGGAAGTTTAGG-GT--AAAATGGTA
* *
68456 ATTTTTGGAAGTTTGGGGGTAAAATAGTA
1 ATTTTTGGAAGTTT-AGGGTAAAATGGTA
* * *
68485 ATTTTTGGAAGATTCGAGGTCAAAAATGG-G
1 ATTTTTGGAAGTTTAG-GGT--AAAATGGTA
*
68515 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
1 ATTTTTGGAAGTT-TAGGGTAAAATGGTA
68544 ATTTTTGGAAGATTTAGGG
1 ATTTTTGGAAG-TTTAGGG
68563 ACCTCCGGGG
Statistics
Matches: 293, Mismatches: 49, Indels: 58
0.73 0.12 0.14
Matches are distributed among these distances:
28 51 0.17
29 129 0.44
30 85 0.29
31 28 0.10
ACGTcount: A:0.31, C:0.03, G:0.30, T:0.35
Consensus pattern (28 bp):
ATTTTTGGAAGTTTAGGGTAAAATGGTA
Done.