Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005662.1 Kokia drynarioides strain JFW-HI SEQ_119834, 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: 138052
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 38 characters in sequence are not A, C, G, or T
Found at i:8582 original size:60 final size:60
Alignment explanation
Indices: 8518--8686 Score: 203
Period size: 60 Copynumber: 2.8 Consensus size: 60
8508 ATAAAATTCA
* * *
8518 GAAAAAAAAAATACAATTAAACAAGAACACCTATATTACTCGATTTAATCAATAAATTTT
1 GAAAAAAAAAATAAAATAAAACAAAAACACCTATATTACTCGATTTAATCAATAAATTTT
* * * * * *
8578 GAAAAAAAAAACATAATCAAACAAAAACACCTATATCACTCAATTCAATCAATAAATTTT
1 GAAAAAAAAAATAAAATAAAACAAAAACACCTATATTACTCGATTTAATCAATAAATTTT
* * ** *
8638 GAAAAATAAAATAAAATAAAATAAAAATGCTTATATTACTCGGATTTAA
1 GAAAAAAAAAATAAAATAAAACAAAAACACCTATATTACTC-GATTTAA
8687 GTGTGAAAGT
Statistics
Matches: 90, Mismatches: 18, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
60 85 0.94
61 5 0.06
ACGTcount: A:0.56, C:0.13, G:0.05, T:0.27
Consensus pattern (60 bp):
GAAAAAAAAAATAAAATAAAACAAAAACACCTATATTACTCGATTTAATCAATAAATTTT
Found at i:8583 original size:56 final size:58
Alignment explanation
Indices: 8496--8648 Score: 171
Period size: 60 Copynumber: 2.5 Consensus size: 58
8486 CAATATAAAA
* ** * * * *
8496 TCAATTCAATAAATAAAATTCAGAAAAAAAAAATACAATTAAACAAGAACACCTATATTAC
1 TCAATTCAATCAAT-AAATTTTG-AAAAAAAAACA-AATCAAACAAAAACACCTATATCAC
* *
8557 TCGATTTAATCAATAAATTTTGAAAAAAAAAACATAATCAAACAAAAACACCTATATCAC
1 TCAATTCAATCAATAAATTTTG-AAAAAAAAACA-AATCAAACAAAAACACCTATATCAC
8617 TCAATTCAATCAATAAATTTTGAAAAATAAAA
1 TCAATTCAATCAATAAATTTTGAAAAA-AAAA
8649 TAAAATAAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
59 5 0.06
60 63 0.80
61 11 0.14
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.25
Consensus pattern (58 bp):
TCAATTCAATCAATAAATTTTGAAAAAAAAACAAATCAAACAAAAACACCTATATCAC
Found at i:19220 original size:14 final size:13
Alignment explanation
Indices: 19195--19230 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
19185 TTAACTGATT
19195 TATTTAAAATATA
1 TATTTAAAATATA
*
19208 T-TATAAAATATA
1 TATTTAAAATATA
19220 TATTTAAAATA
1 TATTTAAAATA
19231 ATAAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TATTTAAAATATA
Found at i:19227 original size:25 final size:25
Alignment explanation
Indices: 19195--19264 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
19185 TTAACTGATT
* *
19195 TATTTAAAATATATTATAA-AATATA
1 TATTTAAAATA-ATAAAAATAATATA
19220 TATTTAAAATAATAAAAATAATATA
1 TATTTAAAATAATAAAAATAATATA
* *
19245 TATTTTTAAATAATTAAAAT
1 TA-TTTAAAATAATAAAAAT
19265 GTTAAATATT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
24 5 0.13
25 19 0.49
26 15 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
TATTTAAAATAATAAAAATAATATA
Found at i:19252 original size:27 final size:26
Alignment explanation
Indices: 19210--19264 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
19200 AAAATATATT
19210 ATAAAATATATATTTAAAATAATAAAA
1 ATAAAATATATATTT-AAATAATAAAA
* * *
19237 ATAATATATATTTTTAAATAATTAAA
1 ATAAAATATATATTTAAATAATAAAA
19263 AT
1 AT
19265 GTTAAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
ATAAAATATATATTTAAATAATAAAA
Found at i:19273 original size:26 final size:26
Alignment explanation
Indices: 19217--19274 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
19207 ATTATAAAAT
*
19217 ATATATTTAAAATAATAAAAATAATAT
1 ATAT-TTTAAAATAATAAAAATAATAA
* * **
19244 ATATTTTTAAATAATTAAAATGTTAA
1 ATATTTTAAAATAATAAAAATAATAA
19270 ATATT
1 ATATT
19275 AAATCAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 22 0.85
27 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (26 bp):
ATATTTTAAAATAATAAAAATAATAA
Found at i:30466 original size:23 final size:21
Alignment explanation
Indices: 30439--30483 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
30429 CGGAAAACAT
*
30439 ATAAATATATTAAATATTAAAAA
1 ATAAAAATA-TAAAT-TTAAAAA
*
30462 ATAAAAATATATATTTAAAAA
1 ATAAAAATATAAATTTAAAAA
30483 A
1 A
30484 CGAAAGAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 4 0.20
23 8 0.40
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAAAAATATAAATTTAAAAA
Found at i:39720 original size:20 final size:21
Alignment explanation
Indices: 39687--39725 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
39677 ATTTAATCCA
*
39687 AAAAAATTACAAGAAATGAAC
1 AAAAAATCACAAGAAATGAAC
39708 AAAAAATCA-AAGAAATGA
1 AAAAAATCACAAGAAATGA
39726 GAGAATTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.69, C:0.08, G:0.10, T:0.13
Consensus pattern (21 bp):
AAAAAATCACAAGAAATGAAC
Found at i:44035 original size:12 final size:12
Alignment explanation
Indices: 44000--44036 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
43990 TAATTAAATA
44000 TATTATATTTTT
1 TATTATATTTTT
*
44012 TATTA-ATATTT
1 TATTATATTTTT
44023 TATTATATTTTT
1 TATTATATTTTT
44035 TA
1 TA
44037 GTGTTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TATTATATTTTT
Found at i:44049 original size:24 final size:23
Alignment explanation
Indices: 43992--44036 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
43982 GCATATAATA
43992 ATTAA-ATA-TATTATATTTTTT
1 ATTAATATATTATTATATTTTTT
*
44013 ATTAATATTTTATTATATTTTTT
1 ATTAATATATTATTATATTTTTT
44036 A
1 A
44037 GTGTTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 2 0.10
23 14 0.67
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
ATTAATATATTATTATATTTTTT
Found at i:54682 original size:27 final size:27
Alignment explanation
Indices: 54652--54707 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
54642 CTTTATCTAT
* * *
54652 TAAATCAAATTAATTCAATTGAATTTA
1 TAAATCAAAATAATTAAATTAAATTTA
54679 TAAATCAAAATAATTAAATTAAATTTA
1 TAAATCAAAATAATTAAATTAAATTTA
54706 TA
1 TA
54708 GAATGGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (27 bp):
TAAATCAAAATAATTAAATTAAATTTA
Found at i:57148 original size:27 final size:27
Alignment explanation
Indices: 57116--57173 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
57106 CCATTAAAGA
57116 CTTCAGATGGTGGAGGAAGCAATTAAC
1 CTTCAGATGGTGGAGGAAGCAATTAAC
57143 CTTCAGATGGTGGAGGAAGCAATTAAC
1 CTTCAGATGGTGGAGGAAGCAATTAAC
57170 CTTC
1 CTTC
57174 TTCCTCCCCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (27 bp):
CTTCAGATGGTGGAGGAAGCAATTAAC
Found at i:60893 original size:23 final size:23
Alignment explanation
Indices: 60866--60921 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
60856 TTTGAAATAC
*
60866 ATATAAATATTTAGAAATTTAAA
1 ATATAAATATTTACAAATTTAAA
* * * *
60889 ATATATATTTTTACAATTTTTAA
1 ATATAAATATTTACAAATTTAAA
60912 ATATATAATA
1 ATATA-AATA
60922 CAAATTCGGG
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
23 23 0.92
24 2 0.08
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (23 bp):
ATATAAATATTTACAAATTTAAA
Found at i:63111 original size:6 final size:6
Alignment explanation
Indices: 63102--63148 Score: 94
Period size: 6 Copynumber: 7.8 Consensus size: 6
63092 ACGACTTTAG
63102 CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC CTTTT
1 CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC CTTTT
63149 AATGAATTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
CTTTTC
Found at i:64986 original size:17 final size:17
Alignment explanation
Indices: 64964--65029 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
64954 CACTACCCTA
*
64964 ATTATAATAAATGTTTT
1 ATTATAATAAATATTTT
* * *
64981 ATTATATTGAATTTTTT
1 ATTATAATAAATATTTT
* *
64998 TTTTTAAATAAATATTTT
1 ATTAT-AATAAATATTTT
* *
65016 ATTGTATTAAATAT
1 ATTATAATAAATAT
65030 AATCTTTATA
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
17 25 0.68
18 12 0.32
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.58
Consensus pattern (17 bp):
ATTATAATAAATATTTT
Found at i:65160 original size:24 final size:25
Alignment explanation
Indices: 65133--65181 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
65123 ATTTAGTATA
* *
65133 AATATAAATATATAAT-TATTATTT
1 AATATAAATAAATAATATAATATTT
*
65157 AATATATATAAATAATATAATATTT
1 AATATAAATAAATAATATAATATTT
65182 TTAATAACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AATATAAATAAATAATATAATATTT
Found at i:65166 original size:28 final size:27
Alignment explanation
Indices: 65134--65187 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
65124 TTTAGTATAA
65134 ATATAAAT-ATATAATTATTATTTAATAT
1 ATATAAATAATATAA-TATT-TTTAATAT
65162 ATATAAATAATATAATATTTTTAATA
1 ATATAAATAATATAATATTTTTAATA
65188 ACATAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 7 0.28
28 12 0.48
29 6 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
ATATAAATAATATAATATTTTTAATAT
Found at i:65177 original size:18 final size:19
Alignment explanation
Indices: 65133--65179 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
65123 ATTTAGTATA
65133 AATATAA-ATATATAATTAT
1 AATATAATATATATAA-TAT
* *
65152 TATTTAATATATATAA-AT
1 AATATAATATATATAATAT
65170 AATATAATAT
1 AATATAATAT
65180 TTTTAATAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 10 0.43
19 5 0.22
20 8 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AATATAATATATATAATAT
Found at i:65193 original size:17 final size:17
Alignment explanation
Indices: 65167--65199 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
65157 AATATATATA
*
65167 AATAATATAATATTTTT
1 AATAACATAATATTTTT
65184 AATAACATAATATTTT
1 AATAACATAATATTTT
65200 CGGGTCGAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
AATAACATAATATTTTT
Found at i:68561 original size:38 final size:39
Alignment explanation
Indices: 68519--68601 Score: 96
Period size: 39 Copynumber: 2.2 Consensus size: 39
68509 ATTTGTATTA
* *
68519 AAAAATTAC-CATAAATATAATAAATGTTTTATTATAAT
1 AAAAATCACACATAAATATAATAAATATTTTATTATAAT
* * * * *
68557 AAAAAACACATATAAATATATTAAATATTTTATTGTATT
1 AAAAATCACACATAAATATAATAAATATTTTATTATAAT
68596 AAAAAT
1 AAAAAT
68602 AATAATCGAA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
38 7 0.19
39 29 0.81
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (39 bp):
AAAAATCACACATAAATATAATAAATATTTTATTATAAT
Found at i:71929 original size:13 final size:13
Alignment explanation
Indices: 71893--71934 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
71883 CAAAAAACTT
* *
71893 TAAAATATATATTT
1 TAAAA-ATATAATA
71907 TAAAAA-ATAATA
1 TAAAAATATAATA
71919 TAAAAATATAATA
1 TAAAAATATAATA
71932 TAA
1 TAA
71935 TTTTTATACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 10 0.40
13 10 0.40
14 5 0.20
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAAAATATAATA
Found at i:76116 original size:20 final size:20
Alignment explanation
Indices: 76087--76133 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
76077 ATATGCTCGG
76087 ATTAATTTATATTTTAGC-TTA
1 ATTAA-TTATATTTTA-CTTTA
*
76108 ATTAATTATGTTTTACTTTA
1 ATTAATTATATTTTACTTTA
76128 ATTAAT
1 ATTAAT
76134 CAAAATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 18 0.75
21 5 0.21
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.57
Consensus pattern (20 bp):
ATTAATTATATTTTACTTTA
Found at i:79484 original size:15 final size:16
Alignment explanation
Indices: 79464--79493 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
79454 CCAATAATTG
79464 AATCG-AAATTTAAAT
1 AATCGAAAATTTAAAT
79479 AATCGAAAATTTAAA
1 AATCGAAAATTTAAA
79494 AAAAATACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (16 bp):
AATCGAAAATTTAAAT
Found at i:80574 original size:128 final size:128
Alignment explanation
Indices: 80413--80669 Score: 505
Period size: 128 Copynumber: 2.0 Consensus size: 128
80403 AATGGCCGAC
80413 ACCCCTTGTTCTCGGATAAAAAAATTTCAAATTTTTCTGGTGTAGGCCATGCCAACACAAAAAAA
1 ACCCCTTGTTCTCGGATAAAAAAATTTCAAATTTTTCTGGTGTAGGCCATGCCAACACAAAAAAA
80478 TTGCATTTTTTATCTGACAAATGACCGACACCCAAAAATTTGATTTTTTTTTTATTAGATTAA
66 TTGCATTTTTTATCTGACAAATGACCGACACCCAAAAATTTGATTTTTTTTTTATTAGATTAA
*
80541 ACCCCTTGTTCTCGGATAAAAAAATTTCAAATTTTTTTGGTGTAGGCCATGCCAACACAAAAAAA
1 ACCCCTTGTTCTCGGATAAAAAAATTTCAAATTTTTCTGGTGTAGGCCATGCCAACACAAAAAAA
80606 TTGCATTTTTTATCTGACAAATGACCGACACCCAAAAATTTGATTTTTTTTTTATTAGATTAA
66 TTGCATTTTTTATCTGACAAATGACCGACACCCAAAAATTTGATTTTTTTTTTATTAGATTAA
80669 A
1 A
80670 AAGGCAATGG
Statistics
Matches: 128, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
128 128 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.36
Consensus pattern (128 bp):
ACCCCTTGTTCTCGGATAAAAAAATTTCAAATTTTTCTGGTGTAGGCCATGCCAACACAAAAAAA
TTGCATTTTTTATCTGACAAATGACCGACACCCAAAAATTTGATTTTTTTTTTATTAGATTAA
Found at i:81058 original size:19 final size:21
Alignment explanation
Indices: 81024--81062 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
81014 GCGACAGACC
81024 TATAATATATATTATTTTAAA
1 TATAATATATATTATTTTAAA
81045 TATAATA-A-ATTATTTTAA
1 TATAATATATATTATTTTAA
81063 TTATTTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 1 0.06
21 7 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TATAATATATATTATTTTAAA
Found at i:82232 original size:23 final size:23
Alignment explanation
Indices: 82197--82240 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
82187 TCATCATGTC
**
82197 ATTAAAATTTAAATAAA-ATTAAT
1 ATTAAAAAATAAA-AAATATTAAT
82220 ATTAAAAAATAAAAAATATTA
1 ATTAAAAAATAAAAAATATTA
82241 TTTAACATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
ATTAAAAAATAAAAAATATTAAT
Found at i:82559 original size:27 final size:26
Alignment explanation
Indices: 82529--82580 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
82519 TTGCAACGGC
*
82529 TGATTTGATTAATTTGATTTTATTAAT
1 TGATTTGATCAA-TTGATTTTATTAAT
82556 TGATTTGATCAATTGATTTTATTAA
1 TGATTTGATCAATTGATTTTATTAA
82581 CTGTTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.56
Consensus pattern (26 bp):
TGATTTGATCAATTGATTTTATTAAT
Found at i:82560 original size:13 final size:13
Alignment explanation
Indices: 82529--82590 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
82519 TTGCAACGGC
*
82529 TGATTTGATTAATT
1 TGATTTTATTAA-T
82543 TGATTTTATTAAT
1 TGATTTTATTAAT
* *
82556 TGATTTGATCAAT
1 TGATTTTATTAAT
*
82569 TGATTTTATTAAC
1 TGATTTTATTAAT
82582 TG-TTTTATT
1 TGATTTTATT
82591 TAAAAGTGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
12 7 0.17
13 24 0.57
14 11 0.26
ACGTcount: A:0.27, C:0.03, G:0.11, T:0.58
Consensus pattern (13 bp):
TGATTTTATTAAT
Found at i:92894 original size:10 final size:10
Alignment explanation
Indices: 92879--92912 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
92869 ATTTTTGCAT
*
92879 TTTATTTTAA
1 TTTATTTTTA
92889 TTTATTTTTTA
1 TTTA-TTTTTA
92900 TTTATTTTTA
1 TTTATTTTTA
92910 TTT
1 TTT
92913 TGGTTTTCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:93754 original size:30 final size:29
Alignment explanation
Indices: 93718--93775 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
93708 TTAATATATG
* *
93718 ATAAAATTATATTTTAATCTTTTAAAAATA
1 ATAAAATTATAATTTAAT-TATTAAAAATA
*
93748 ATAAAATTTTAATTTAATTATTAAAAAT
1 ATAAAATTATAATTTAATTATTAAAAAT
93776 GTTACGAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (29 bp):
ATAAAATTATAATTTAATTATTAAAAATA
Found at i:96090 original size:20 final size:19
Alignment explanation
Indices: 96061--96101 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
96051 TTTTTTTATT
*
96061 AATATTAAATAAATAAATA
1 AATATTAAATAAAAAAATA
96080 AATATTTAAATAAAAAAATA
1 AATA-TTAAATAAAAAAATA
96100 AA
1 AA
96102 AAAATATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AATATTAAATAAAAAAATA
Found at i:96539 original size:15 final size:15
Alignment explanation
Indices: 96502--96545 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
96492 TTAATTTTAA
*
96502 TTTTTGTATTATATT
1 TTTTTGTATTATTTT
** *
96517 TTGGTGTATAATTTT
1 TTTTTGTATTATTTT
96532 TTTTTGTATTATTT
1 TTTTTGTATTATTT
96546 ATGTAAAAAA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.11, T:0.70
Consensus pattern (15 bp):
TTTTTGTATTATTTT
Found at i:96696 original size:27 final size:27
Alignment explanation
Indices: 96605--96683 Score: 149
Period size: 27 Copynumber: 2.9 Consensus size: 27
96595 GCAGCTTGCC
*
96605 AGGTAGGCACCTTTGGTGCCGCCTGCA
1 AGGTAGGCACCTTTGGTGCCTCCTGCA
96632 AGGTAGGCACCTTTGGTGCCTCCTGCA
1 AGGTAGGCACCTTTGGTGCCTCCTGCA
96659 AGGTAGGCACCTTTGGTGCCTCCTG
1 AGGTAGGCACCTTTGGTGCCTCCTG
96684 TCAAATATAC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.14, C:0.29, G:0.32, T:0.25
Consensus pattern (27 bp):
AGGTAGGCACCTTTGGTGCCTCCTGCA
Found at i:96875 original size:39 final size:39
Alignment explanation
Indices: 96821--96899 Score: 133
Period size: 39 Copynumber: 2.0 Consensus size: 39
96811 CCCAAATGAC
*
96821 ACCACTCTCCCCAAGTGTTCCATTTTGGTAAATAATGGG
1 ACCACTCTCCCCAAGTGTTCCATTTTGATAAATAATGGG
96860 ACCACTC-CCTCCAAGTGTTCCATTTTGATAAATAATGGG
1 ACCACTCTCC-CCAAGTGTTCCATTTTGATAAATAATGGG
96899 A
1 A
96900 AAAATATATT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
38 2 0.05
39 36 0.95
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.30
Consensus pattern (39 bp):
ACCACTCTCCCCAAGTGTTCCATTTTGATAAATAATGGG
Found at i:97562 original size:9 final size:9
Alignment explanation
Indices: 97548--97578 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
97538 ATAATACATC
97548 AAAAACACT
1 AAAAACACT
97557 AAAAACACT
1 AAAAACACT
*
97566 AAAAACATT
1 AAAAACACT
97575 AAAA
1 AAAA
97579 TAAATATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.71, C:0.16, G:0.00, T:0.13
Consensus pattern (9 bp):
AAAAACACT
Found at i:105450 original size:18 final size:17
Alignment explanation
Indices: 105403--105455 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
105393 TTATCATTGT
*
105403 TTTTTTTAATTTAATAA
1 TTTTTTTAATTTTATAA
**
105420 TTTTTAGACATTTTATATA
1 TTTTTTTA-ATTTTATA-A
105439 TTTTTTTAATTTT-TAA
1 TTTTTTTAATTTTATAA
105455 T
1 T
105456 ATTTGTAACA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
16 2 0.07
17 8 0.28
18 12 0.41
19 7 0.24
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (17 bp):
TTTTTTTAATTTTATAA
Found at i:108711 original size:21 final size:21
Alignment explanation
Indices: 108687--108727 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
108677 GTTTATGTAA
108687 TTTTA-TTTTTAGGAATTTAATT
1 TTTTACTTTTTA--AATTTAATT
108709 TTTTACTTTTTAAATTTAA
1 TTTTACTTTTTAAATTTAA
108728 AAAATCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 5 0.28
23 6 0.33
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.63
Consensus pattern (21 bp):
TTTTACTTTTTAAATTTAATT
Found at i:109455 original size:31 final size:29
Alignment explanation
Indices: 109420--109485 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 29
109410 CAATTGAATC
** *
109420 TAAATTTTTAAATCTGAAAAGTATATAAAAT
1 TAAATTTTTAAAAAT-AAAAATATA-AAAAT
109451 TAAATTTTTAAAAATAAAAATATAAAAAT
1 TAAATTTTTAAAAATAAAAATATAAAAAT
109480 TAAATT
1 TAAATT
109486 CCAAATTACA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 11 0.34
30 8 0.25
31 13 0.41
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (29 bp):
TAAATTTTTAAAAATAAAAATATAAAAAT
Found at i:115705 original size:28 final size:29
Alignment explanation
Indices: 115668--115724 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
115658 AAATTGTTTA
*
115668 GAGGAGCTAAA-ATAAAATTATAAAATTTT
1 GAGGAGCTAAAGATAAAACT-TAAAATTTT
*
115697 GAGG-GCTAAAGTTAAAACTTAAAATTTT
1 GAGGAGCTAAAGATAAAACTTAAAATTTT
115725 CATGTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 15 0.60
29 10 0.40
ACGTcount: A:0.47, C:0.05, G:0.16, T:0.32
Consensus pattern (29 bp):
GAGGAGCTAAAGATAAAACTTAAAATTTT
Found at i:117274 original size:18 final size:19
Alignment explanation
Indices: 117253--117290 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
117243 TTAAATTAAG
*
117253 TTATTACTTTAA-ATTTTT
1 TTATAACTTTAATATTTTT
*
117271 TTATAATTTTAATATTTTT
1 TTATAACTTTAATATTTTT
117290 T
1 T
117291 GGAATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATAACTTTAATATTTTT
Found at i:122450 original size:58 final size:59
Alignment explanation
Indices: 122353--122463 Score: 179
Period size: 59 Copynumber: 1.9 Consensus size: 59
122343 CTAATGTGGG
* * *
122353 AACATTTGTCAAGTTCAAGATCTAACTTCGACAAAAAAAAATTCAAACCCTAACGTAAA
1 AACAATTGTCAAGTTCAAGATCTAACCTCGAAAAAAAAAAATTCAAACCCTAACGTAAA
*
122412 AACAATTGTCAAGTTCAAGATCTAACCT-GAAAAAAAAAAATTCAAATCCTAA
1 AACAATTGTCAAGTTCAAGATCTAACCTCGAAAAAAAAAAATTCAAACCCTAA
122464 TATGAAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
58 22 0.46
59 26 0.54
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (59 bp):
AACAATTGTCAAGTTCAAGATCTAACCTCGAAAAAAAAAAATTCAAACCCTAACGTAAA
Found at i:122472 original size:59 final size:59
Alignment explanation
Indices: 122353--122476 Score: 171
Period size: 59 Copynumber: 2.1 Consensus size: 59
122343 CTAATGTGGG
* * * *
122353 AACATTTGTCAAGTTCAAGATCTAACTTCGACAAAAAAAAATTCAAACCCTAACGTAAA
1 AACAATTGTCAAGTTCAAGATCTAACCTCGAAAAAAAAAAATTCAAACCCTAACATAAA
* *
122412 AACAATTGTCAAGTTCAAGATCTAACCT-GAAAAAAAAAAATTCAAATCCTAATATGAAA
1 AACAATTGTCAAGTTCAAGATCTAACCTCGAAAAAAAAAAATTCAAACCCTAACAT-AAA
122471 AA-AATT
1 AACAATT
122477 ACCAAATTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
58 27 0.47
59 31 0.53
ACGTcount: A:0.51, C:0.17, G:0.08, T:0.24
Consensus pattern (59 bp):
AACAATTGTCAAGTTCAAGATCTAACCTCGAAAAAAAAAAATTCAAACCCTAACATAAA
Found at i:122491 original size:59 final size:59
Alignment explanation
Indices: 122369--122492 Score: 135
Period size: 58 Copynumber: 2.1 Consensus size: 59
122359 TGTCAAGTTC
* * * ** * *
122369 AAGATCTAACTTCGACAAAAAAAAATTCAAACCCTAACGTAAAAACAATTGTCAAGTTC
1 AAGATCTAACCTCGAAAAAAAAAAATTCAAACCCTAACATAAAAACAATTACCAAATTA
* *
122428 AAGATCTAACCT-GAAAAAAAAAAATTCAAATCCTAATATGAAAAA-AATTACCAAATTAA
1 AAGATCTAACCTCGAAAAAAAAAAATTCAAACCCTAACAT-AAAAACAATTACCAAATT-A
122487 AAGATC
1 AAGATC
122493 AAAATGTGAT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
58 32 0.59
59 22 0.41
ACGTcount: A:0.54, C:0.17, G:0.07, T:0.22
Consensus pattern (59 bp):
AAGATCTAACCTCGAAAAAAAAAAATTCAAACCCTAACATAAAAACAATTACCAAATTA
Found at i:126866 original size:12 final size:12
Alignment explanation
Indices: 126849--126874 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
126839 AATATTATAC
126849 ATAGTTAAACAA
1 ATAGTTAAACAA
126861 ATAGTTAAACAA
1 ATAGTTAAACAA
126873 AT
1 AT
126875 CCTACAAGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.27
Consensus pattern (12 bp):
ATAGTTAAACAA
Found at i:129843 original size:3 final size:3
Alignment explanation
Indices: 129837--129862 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
129827 GAAAAAAAAA
129837 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
129863 AAGCGGATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:130335 original size:139 final size:138
Alignment explanation
Indices: 130085--130363 Score: 425
Period size: 139 Copynumber: 2.0 Consensus size: 138
130075 TGTCAATTAA
** *
130085 ATCTTAGTTTGATTGGCAGAGATATTGTTGCCAACATAGAAGGATGGAAATTCGAGTGCGCTGAA
1 ATCTTAGTTCAATTGGCAGAGATATTGTTGCCAACATAGAAGGATGGAAATTCGAATGCGCTGAA
* * *
130150 GCGCATTATCCTCTTATTTATAGGTTGGGAAGAGGCTATGGATAATTCTAAGCATTGTGTAATAA
66 GCGCATTATCCTCCTATTTATAGGTTGAGAAGAGGCTATGGATAATTCTAAACATTGTGTAA-AA
*
130215 AAAATAGAT
130 AAAACAGAT
* * *
130224 ATCTTAGTTCAATTTGCAGAGGTATTGTTGCCAACATAGGAGGATGGAAATTCGAATGCGCTGAA
1 ATCTTAGTTCAATTGGCAGAGATATTGTTGCCAACATAGAAGGATGGAAATTCGAATGCGCTGAA
* *
130289 GCGTATTATCCTCCTATTTATAGGTTGAGAATGA-GCTATGGATAATTCTAAACATTGTGTGAAA
66 GCGCATTATCCTCCTATTTATAGGTTGAGAA-GAGGCTATGGATAATTCTAAACATTGTGTAAAA
130353 AAAACAGAT
130 AAAACAGAT
130362 AT
1 AT
130364 GATCAGAACC
Statistics
Matches: 127, Mismatches: 12, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
138 12 0.09
139 113 0.89
140 2 0.02
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (138 bp):
ATCTTAGTTCAATTGGCAGAGATATTGTTGCCAACATAGAAGGATGGAAATTCGAATGCGCTGAA
GCGCATTATCCTCCTATTTATAGGTTGAGAAGAGGCTATGGATAATTCTAAACATTGTGTAAAAA
AAACAGAT
Found at i:131935 original size:20 final size:20
Alignment explanation
Indices: 131910--131947 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
131900 CTTCCTATCA
131910 AATTATTT-ATGTATATTTTT
1 AATTATTTAATG-ATATTTTT
131930 AATTATTTAATGATATTT
1 AATTATTTAATGATATTT
131948 CAAGAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
AATTATTTAATGATATTTTT
Found at i:132072 original size:21 final size:21
Alignment explanation
Indices: 132048--132087 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
132038 ACCCCTGACT
*
132048 CTTAAGGTTCAATG-TTTAAGA
1 CTTAAAGTTC-ATGATTTAAGA
132069 CTTAAAGTTCATGATTTAA
1 CTTAAAGTTCATGATTTAA
132088 AATTCTGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (21 bp):
CTTAAAGTTCATGATTTAAGA
Found at i:137212 original size:44 final size:41
Alignment explanation
Indices: 137138--137224 Score: 97
Period size: 44 Copynumber: 2.0 Consensus size: 41
137128 AAAACGCATA
*
137138 AAAAATAACATCCAAACAACAAAAATAACAACCAAAACAGTAGC
1 AAAAATAACATCAAAACAACAAAAATAACAA-CAAAA-A-TAGC
*
137182 AAAAATAACAGT-AAAACAACATTAAA-AACAACAAAAATAGC
1 AAAAATAACA-TCAAAACAACA-AAAATAACAACAAAAATAGC
137223 AA
1 AA
137225 TAAAAATAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
41 6 0.15
42 1 0.03
43 5 0.13
44 23 0.59
45 4 0.10
ACGTcount: A:0.67, C:0.18, G:0.05, T:0.10
Consensus pattern (41 bp):
AAAAATAACATCAAAACAACAAAAATAACAACAAAAATAGC
Found at i:137273 original size:20 final size:19
Alignment explanation
Indices: 137246--137289 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
137236 CGAAAATAAC
*
137246 AATC-AAAACAATAAAAAA
1 AATCAAAAACAACAAAAAA
*
137264 AACTCAAAAACAGCAAAAAA
1 AA-TCAAAAACAACAAAAAA
137284 AATCAA
1 AATCAA
137290 CCAAAACAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 6 0.27
20 14 0.64
ACGTcount: A:0.73, C:0.16, G:0.02, T:0.09
Consensus pattern (19 bp):
AATCAAAAACAACAAAAAA
Found at i:137283 original size:22 final size:21
Alignment explanation
Indices: 137238--137306 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 21
137228 AAATAACACG
* * **
137238 AAAATAACAATCAAAACAATA
1 AAAAAAACAACCAAAACAGCA
* *
137259 AAAAAAAC-TCAAAAACAGCA
1 AAAAAAACAACCAAAACAGCA
*
137279 AAAAAAATCAACCAAAACAGTA
1 AAAAAAA-CAACCAAAACAGCA
137301 AAAAAA
1 AAAAAA
137307 GCACCTAAAC
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
20 14 0.38
21 8 0.22
22 15 0.41
ACGTcount: A:0.72, C:0.16, G:0.03, T:0.09
Consensus pattern (21 bp):
AAAAAAACAACCAAAACAGCA
Found at i:137316 original size:20 final size:21
Alignment explanation
Indices: 137270--137317 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
137260 AAAAAACTCA
* *
137270 AAAACAGCAAAAAAAATCAACC
1 AAAACAG-TAAAAAAAGCAACC
137292 AAAACAGTAAAAAAAGC-ACC
1 AAAACAGTAAAAAAAGCAACC
*
137312 TAAACA
1 AAAACA
137318 ACAATATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 8 0.35
21 8 0.35
22 7 0.30
ACGTcount: A:0.67, C:0.21, G:0.06, T:0.06
Consensus pattern (21 bp):
AAAACAGTAAAAAAAGCAACC
Found at i:138020 original size:2 final size:2
Alignment explanation
Indices: 138015--138052 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
138005 TTTACATCCT
138015 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.