Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012452.1 Kokia drynarioides strain JFW-HI SEQ_127456, 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: 68281
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Warning! 40 characters in sequence are not A, C, G, or T
Found at i:578 original size:29 final size:29
Alignment explanation
Indices: 536--592 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
526 TTAGCTTAGA
536 TTCATGTGAGAACAC-GAAGAAAAAACTTC
1 TTCATGTGAGAACACAGAA-AAAAAACTTC
*
565 TTCATGTGAGAACACAGAAAAAGAACTT
1 TTCATGTGAGAACACAGAAAAAAAACTT
593 TAACCCCTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 23 0.88
30 3 0.12
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.21
Consensus pattern (29 bp):
TTCATGTGAGAACACAGAAAAAAAACTTC
Found at i:2875 original size:11 final size:12
Alignment explanation
Indices: 2846--2878 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2836 TCGTTTGTTG
2846 GCTTGTTTATAA
1 GCTTGTTTATAA
*
2858 GCTTGTTTATGA
1 GCTTGTTTATAA
2870 -CTTGTTTAT
1 GCTTGTTTAT
2879 TTATTAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.18, C:0.09, G:0.18, T:0.55
Consensus pattern (12 bp):
GCTTGTTTATAA
Found at i:2954 original size:15 final size:15
Alignment explanation
Indices: 2920--2963 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
2910 AATTAATATT
*
2920 TTTATATATGTATTTA
1 TTTAT-TATTTATTTA
*
2936 TTTATTATTTATTTG
1 TTTATTATTTATTTA
2951 TTTATTATTTATT
1 TTTATTATTTATT
2964 AACATTGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 21 0.81
16 5 0.19
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (15 bp):
TTTATTATTTATTTA
Found at i:2996 original size:24 final size:24
Alignment explanation
Indices: 2969--3014 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2959 TTATTAACAT
*
2969 TGTTTGTGAACACGTTCAATTATA
1 TGTTCGTGAACACGTTCAATTATA
* *
2993 TGTTCGTGAACATGTTCGATTA
1 TGTTCGTGAACACGTTCAATTA
3015 AGTTAAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (24 bp):
TGTTCGTGAACACGTTCAATTATA
Found at i:12441 original size:29 final size:29
Alignment explanation
Indices: 12381--12444 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
12371 TAGTGATCTC
**
12381 ATCAAATTAGTCCCTCTACTATTAAATGA
1 ATCAAATTAGTCCCTCTACTATTAAAAAA
* * * *
12410 ATCAATTTAGTCCTTGTGCTATTAAAAAA
1 ATCAAATTAGTCCCTCTACTATTAAAAAA
12439 ATCAAA
1 ATCAAA
12445 AAAGCCAAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.34
Consensus pattern (29 bp):
ATCAAATTAGTCCCTCTACTATTAAAAAA
Found at i:13492 original size:56 final size:56
Alignment explanation
Indices: 13379--13494 Score: 146
Period size: 56 Copynumber: 2.1 Consensus size: 56
13369 CAATCACAAC
* * *
13379 ATTCTAATGCGAATTCAAATTAAACATTTTATTAACCACGCGACCAGAAACAGAAA
1 ATTCTAATGCGAATTCAAATTAAACAATTTATTAACCACGCAACAAGAAACAGAAA
* * *
13435 ATTCTAGTGCGAGTTCAAATTAAACAATTTCTTAACCACGCAACGAAGTAAA-A-AAA
1 ATTCTAATGCGAATTCAAATTAAACAATTTATTAACCACGCAAC-AAG-AAACAGAAA
13491 ATTC
1 ATTC
13495 AAAGAATTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
56 46 0.88
57 3 0.06
58 3 0.06
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.26
Consensus pattern (56 bp):
ATTCTAATGCGAATTCAAATTAAACAATTTATTAACCACGCAACAAGAAACAGAAA
Found at i:13545 original size:101 final size:99
Alignment explanation
Indices: 13429--13793 Score: 417
Period size: 101 Copynumber: 3.6 Consensus size: 99
13419 CGACCAGAAA
* *
13429 CAGAAAATTCTAGTGCGAGTTCAAATTAAACAATTTCTTAACCACGCAACGAAGTAAAAAAAATT
1 CAGAAAATTCTAGTGCGAATTCAAATTAAACATTTTCTTAACCACGCAACGAA--AAAAAAAATT
* **
13494 CAAAGAATTTTTTCTTAGTGTTTCTCAGCAAACAAT
64 CAAACAATTTTTTCACAGTGTTTCTCAGCAAACAAT
* * * *
13530 CAGAAATTTCTAGTGCTAATTAAAATT-AACATTTTCTTAACCGCGCAACGAAAATAAAAGAATT
1 CAGAAAATTCTAGTGCGAATTCAAATTAAACATTTTCTTAACCACGCAACGAAAA-AAAA-AATT
* *
13594 CAAACAGTTCTTCTCACAGTGTTTCTCAGCAAACAAT
64 CAAACAATT-TTTTCACAGTGTTTCTCAGCAAACAAT
* * * * * * * **
13631 CAGAAAACTCTAATGCGAATTCGAATCAAACATTTTCTTATCCACGCGACCAAAAATAGGAATTC
1 CAGAAAATTCTAGTGCGAATTCAAATTAAACATTTTCTTAACCACGCAACGAAAAA-AAAAATTC
* * *
13696 AAACAATTTTTCTCAGAGTGTTTCTCAGCAAGCAAA
65 AAACAATTTTT-TCACAGTGTTTCTCAGCAAACAAT
* * *
13732 CAGAAAATTCTAGTGCGAATTCAATTTAAACAGTTTCTTAAACACGCAACGAAAAGAAAAAA
1 CAGAAAATTCTAGTGCGAATTCAAATTAAACATTTTCTTAACCACGCAACGAAAA-AAAAAA
13794 ATTATTCAAA
Statistics
Matches: 216, Mismatches: 41, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
98 2 0.01
99 4 0.02
100 36 0.17
101 149 0.69
102 25 0.12
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (99 bp):
CAGAAAATTCTAGTGCGAATTCAAATTAAACATTTTCTTAACCACGCAACGAAAAAAAAAATTCA
AACAATTTTTTCACAGTGTTTCTCAGCAAACAAT
Found at i:13864 original size:194 final size:192
Alignment explanation
Indices: 13427--13881 Score: 459
Period size: 202 Copynumber: 2.3 Consensus size: 192
13417 CGCGACCAGA
* * * *
13427 AACAGAAAATTCTAGTGCGAGTTCAAATTAAACAATTTCTTAACCACGCAACGAAGTAAAAAAAA
1 AACAGAAAATTCTAATGCGAGTTC-AATCAAACATTTTCTTAACCACGCAAC-AA-AAAAAAAAA
* ** * * *
13492 TTCAAAGAATTTTTTCTTAGTGTTTCTCAGCAAACAATCAGAAATTTCTAGTGCTAATTAAAATT
63 TTCAAACAATTTTTTCAGAGTGTTTCTCAGCAAACAAACAGAAAATTCTAGTGCGAATTAAAATT
* * * * * ** *
13557 AACATTTTCTTAACCGCGCAACGAAAATAAAAGAATTCAAACAGTTCTTCTCACAGTGTTTCTCA
128 AACAGTTTCTTAAACACGCAACG---A-AAAAGAA-T-AAACAATTATTCAAACAGTATTTCTCA
13622 GCAAAC
187 GCAAAC
* * * * * **
13628 AATCAGAAAACTCTAATGCGAATTCGAATCAAACATTTTCTTATCCACGCGACCAAAAATAGGAA
1 AA-CAGAAAATTCTAATGCGAGTTC-AATCAAACATTTTCTTAACCACGC-AACAAAAAAAAAAA
* * *
13693 TTCAAACAATTTTTCTCAGAGTGTTTCTCAGCAAGCAAACAGAAAATTCTAGTGCGAATTCAATT
63 TTCAAACAATTTTT-TCAGAGTGTTTCTCAGCAAACAAACAGAAAATTCTAGTGCGAATTAAAAT
13758 TAAACAGTTTCTTAAACACGCAACG-AAAAGAA-AAA-AATTATTCAAACAGTATTTCAT-AGCA
127 T-AACAGTTTCTTAAACACGCAACGAAAAAGAATAAACAATTATTCAAACAGTATTTC-TCAGCA
13819 AAC
190 AAC
* *
13822 TAACAGAAAGTTCTAATGCGAGTTCAAGCCAAACATTTTCTTAACCACGCAACAAAAAAA
1 -AACAGAAAATTCTAATGCGAGTTCAA-TCAAACATTTTCTTAACCACGCAACAAAAAAA
13882 GAATCTCGCT
Statistics
Matches: 211, Mismatches: 36, Indels: 22
0.78 0.13 0.08
Matches are distributed among these distances:
193 10 0.05
194 61 0.29
195 6 0.03
198 7 0.03
201 20 0.09
202 85 0.40
203 22 0.10
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (192 bp):
AACAGAAAATTCTAATGCGAGTTCAATCAAACATTTTCTTAACCACGCAACAAAAAAAAAAATTC
AAACAATTTTTTCAGAGTGTTTCTCAGCAAACAAACAGAAAATTCTAGTGCGAATTAAAATTAAC
AGTTTCTTAAACACGCAACGAAAAAGAATAAACAATTATTCAAACAGTATTTCTCAGCAAAC
Found at i:24109 original size:16 final size:17
Alignment explanation
Indices: 24076--24112 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
24066 TATTATTACT
*
24076 AATT-TAAAATTTTATA
1 AATTATAAAATATTATA
24092 AATTATAAAATATT-TA
1 AATTATAAAATATTATA
24108 AATTA
1 AATTA
24113 AAATTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTATAAAATATTATA
Found at i:24986 original size:15 final size:15
Alignment explanation
Indices: 24968--25001 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
24958 TTATCTAGAG
24968 AATTTT-TAATATATT
1 AATTTTATAATA-ATT
24983 AATTTTATAATAATT
1 AATTTTATAATAATT
24998 AATT
1 AATT
25002 GAATTGGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
AATTTTATAATAATT
Found at i:25659 original size:23 final size:22
Alignment explanation
Indices: 25622--25665 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
25612 AATTAATAAT
25622 ATATTATTTATATTAATATTTAC
1 ATATTATTTATATTAA-ATTTAC
25645 ATATT-TTTATAATTAAATTTA
1 ATATTATTTAT-ATTAAATTTA
25666 AAAATAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATATTATTTATATTAAATTTAC
Found at i:27560 original size:31 final size:31
Alignment explanation
Indices: 27525--27591 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
27515 AAAAAAGTTC
*
27525 AATAAAGATTTAATTACAGTATAAAGCATAT
1 AATAAAGATTTAATTACAATATAAAGCATAT
*
27556 AATAAAGGTTTAATTACAATATAAAGCATAT
1 AATAAAGATTTAATTACAATATAAAGCATAT
27587 AATAA
1 AATAA
27592 TATTAATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.54, C:0.06, G:0.09, T:0.31
Consensus pattern (31 bp):
AATAAAGATTTAATTACAATATAAAGCATAT
Found at i:29943 original size:31 final size:30
Alignment explanation
Indices: 29886--29958 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 30
29876 TTTGACCTAT
**
29886 AAAATTGATAAAATTTTAATATAATATTTTA
1 AAAATT-ATAAAATTTTAATATAATATAATA
*
29917 AAAATTATAAAATTATTTATCA-AATATAATA
1 AAAATTATAAAATT-TTAAT-ATAATATAATA
29948 AAAATATATAA
1 AAAAT-TATAA
29959 CTCAATTTCC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
30 8 0.22
31 22 0.61
32 6 0.17
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (30 bp):
AAAATTATAAAATTTTAATATAATATAATA
Found at i:39157 original size:23 final size:23
Alignment explanation
Indices: 39131--39294 Score: 131
Period size: 23 Copynumber: 7.1 Consensus size: 23
39121 TGCTGGGTAA
*
39131 CAGAGGGCATACAAAGTGCTAAT
1 CAGAGGGCACACAAAGTGCTAAT
*
39154 CAGAGGGCACACGAAGTGCTAAT
1 CAGAGGGCACACAAAGTGCTAAT
*
39177 AACAGAGGGCACACAAAGTGCTGAT
1 --CAGAGGGCACACAAAGTGCTAAT
* *
39202 CAGAGGGCACGA-AATGTGCTAAA
1 CAGAGGGCAC-ACAAAGTGCTAAT
* *
39225 CAGAGAGCACA-AATAGTGCTAAA
1 CAGAGGGCACACAA-AGTGCTAAT
* * *
39248 CAGA-AGCACACACAGTGTTGAA-
1 CAGAGGGCACACAAAGTGCT-AAT
* * *
39270 CAGA-AGCACACACAGTGCTGAT
1 CAGAGGGCACACAAAGTGCTAAT
39292 CAG
1 CAG
39295 TAAGCGCGCT
Statistics
Matches: 121, Mismatches: 13, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
21 1 0.01
22 35 0.29
23 63 0.52
24 1 0.01
25 21 0.17
ACGTcount: A:0.40, C:0.21, G:0.26, T:0.13
Consensus pattern (23 bp):
CAGAGGGCACACAAAGTGCTAAT
Found at i:39180 original size:48 final size:48
Alignment explanation
Indices: 39106--39251 Score: 151
Period size: 48 Copynumber: 3.1 Consensus size: 48
39096 AAATACTTAA
* ** *
39106 CAGAGGGCACATAAGTGCTGGGTAACAGAGGGCATACAAAGTGCTAAT
1 CAGAGGGCACAGAAGTGCTGAATAACAGAGGGCACACAAAGTGCTAAT
*
39154 CAGAGGGCACACGAAGTGCT-AATAACAGAGGGCACACAAAGTGCTGAT
1 CAGAGGGCACA-GAAGTGCTGAATAACAGAGGGCACACAAAGTGCTAAT
* *
39202 CAGAGGGCAC-GAAATGTGCT--A-AACAGAGAGCACA-AATAGTGCTAAA
1 CAGAGGGCACAG-AA-GTGCTGAATAACAGAGGGCACACAA-AGTGCTAAT
39248 CAGA
1 CAGA
39252 AGCACACACA
Statistics
Matches: 86, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
45 2 0.02
46 24 0.28
47 3 0.03
48 50 0.58
49 7 0.08
ACGTcount: A:0.39, C:0.18, G:0.29, T:0.14
Consensus pattern (48 bp):
CAGAGGGCACAGAAGTGCTGAATAACAGAGGGCACACAAAGTGCTAAT
Found at i:39188 original size:25 final size:25
Alignment explanation
Indices: 39103--39246 Score: 126
Period size: 23 Copynumber: 6.0 Consensus size: 25
39093 CCGAAATACT
* **
39103 TAACAGAGGGCACA-TAAGTGCTGGG
1 TAACAGAGGGCACACAAAGTGCT-AA
*
39128 TAACAGAGGGCATACAAAGTGCTAA
1 TAACAGAGGGCACACAAAGTGCTAA
*
39153 T--CAGAGGGCACACGAAGTGCTAA
1 TAACAGAGGGCACACAAAGTGCTAA
*
39176 TAACAGAGGGCACACAAAGTGCTGA
1 TAACAGAGGGCACACAAAGTGCTAA
*
39201 T--CAGAGGGCACGA-AATGTGCT-A
1 TAACAGAGGGCAC-ACAAAGTGCTAA
*
39223 -AACAGAGAGCACA-AATAGTGCTAA
1 TAACAGAGGGCACACAA-AGTGCTAA
39247 ACAGAAGCAC
Statistics
Matches: 100, Mismatches: 11, Indels: 17
0.78 0.09 0.13
Matches are distributed among these distances:
22 4 0.04
23 52 0.52
24 2 0.02
25 35 0.35
26 7 0.07
ACGTcount: A:0.39, C:0.18, G:0.28, T:0.15
Consensus pattern (25 bp):
TAACAGAGGGCACACAAAGTGCTAA
Found at i:39255 original size:22 final size:22
Alignment explanation
Indices: 39217--39288 Score: 90
Period size: 22 Copynumber: 3.2 Consensus size: 22
39207 GGCACGAAAT
*
39217 GTGCTAAACAGAGAGCACAAATA
1 GTGCTAAACAGA-AGCACAAACA
*
39240 GTGCTAAACAGAAGCACACACA
1 GTGCTAAACAGAAGCACAAACA
* * *
39262 GTGTTGAACAGAAGCACACACA
1 GTGCTAAACAGAAGCACAAACA
39284 GTGCT
1 GTGCT
39289 GATCAGTAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 32 0.73
23 12 0.27
ACGTcount: A:0.42, C:0.22, G:0.22, T:0.14
Consensus pattern (22 bp):
GTGCTAAACAGAAGCACAAACA
Found at i:43857 original size:44 final size:44
Alignment explanation
Indices: 43794--43881 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
43784 ATAATTTGGA
43794 AAGAGATTACCCCACCTATCATTAGCTAAACCCCGTTCAAGCCT
1 AAGAGATTACCCCACCTATCATTAGCTAAACCCCGTTCAAGCCT
43838 AAGAGATTACCCCACCTATCATTAGCTAAACCCCGTTCAAGCCT
1 AAGAGATTACCCCACCTATCATTAGCTAAACCCCGTTCAAGCCT
43882 TTCTTTAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.32, C:0.34, G:0.11, T:0.23
Consensus pattern (44 bp):
AAGAGATTACCCCACCTATCATTAGCTAAACCCCGTTCAAGCCT
Found at i:45675 original size:12 final size:12
Alignment explanation
Indices: 45658--45683 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
45648 ATAACAGGAC
45658 AAAGAAGAAAAG
1 AAAGAAGAAAAG
45670 AAAGAAGAAAAG
1 AAAGAAGAAAAG
45682 AA
1 AA
45684 GGGAAACTGC
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:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAAGAAGAAAAG
Found at i:45737 original size:24 final size:25
Alignment explanation
Indices: 45689--45737 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
45679 AAGAAGGGAA
*
45689 ACTGCGAAATTACAGAAAAAACGAG
1 ACTGCGAAAGTACAGAAAAAACGAG
*
45714 ACTGCGAAAGTGCAG-AAAAACGAG
1 ACTGCGAAAGTACAGAAAAAACGAG
45738 TCAAAAGATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.49, C:0.16, G:0.24, T:0.10
Consensus pattern (25 bp):
ACTGCGAAAGTACAGAAAAAACGAG
Found at i:57626 original size:22 final size:22
Alignment explanation
Indices: 57600--57653 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
57590 ATATCCAAAC
57600 AATAACAACAAAATAGTAGCAA
1 AATAACAACAAAATAGTAGCAA
* * * * *
57622 TATAATATCGAAATATTAGCAA
1 AATAACAACAAAATAGTAGCAA
57644 AATAACAACA
1 AATAACAACA
57654 TAACAGCAGT
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.59, C:0.13, G:0.07, T:0.20
Consensus pattern (22 bp):
AATAACAACAAAATAGTAGCAA
Found at i:58078 original size:22 final size:22
Alignment explanation
Indices: 58052--58105 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
58042 ATATCCAAAC
58052 AATAACAACAAAATAGTAGCAA
1 AATAACAACAAAATAGTAGCAA
* * * * *
58074 TATAATATCGAAATATTAGCAA
1 AATAACAACAAAATAGTAGCAA
58096 AATAACAACA
1 AATAACAACA
58106 TAACAACAGT
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.59, C:0.13, G:0.07, T:0.20
Consensus pattern (22 bp):
AATAACAACAAAATAGTAGCAA
Found at i:58103 original size:452 final size:452
Alignment explanation
Indices: 57259--58172 Score: 1747
Period size: 452 Copynumber: 2.0 Consensus size: 452
57249 TTTAATTAAT
*
57259 GTCAAACTTGACATGCACGAACTAGAGCTGATCATGGATCGAGCTAGTGTAAAAAATCAAGTTCA
1 GTCAAACTTGACATGCACGAACTAGAGCTGATCATGGATCGAGCTAGTGTAAAAAATCAAGTCCA
57324 TTTTCTAGGTTAGCCTGAATAAAAAATACTAAACCTGACCCAGCCTAGCCACATTAAATTTTTTA
66 TTTTCTAGGTTAGCCTGAATAAAAAATACTAAACCTGACCCAGCCTAGCCACATTAAATTTTTTA
*
57389 GATTATTATTTTTATATAAAATAAATTTAAAAAATATAATATATCAAATAAAATGAAAACATTAA
131 GATTATTATTTTTATATAAAATAAATTTAAAAAATATAATACATCAAATAAAATGAAAACATTAA
*
57454 AATAAATACATTCCAACAAATTGGAAATACATATAAAAAAAAGTTTTATACTTAAATAACAGTAA
196 AATAAATACATTCCAACAAATTGGAAATACATATAAAAAAAAGTTTTATACTTAAATAACAATAA
57519 CATAATTGCAACTTAACAAGCATGTGTCTTTAAAATAGTATTAAAATTAACAATAAAATAAGAAT
261 CATAATTGCAACTTAACAAGCATGTGTCTTTAAAATAGTATTAAAATTAACAATAAAATAAGAAT
57584 TATATAATATCCAAACAATAACAACAAAATAGTAGCAATATAATATCGAAATATTAGCAAAATAA
326 TATATAATATCCAAACAATAACAACAAAATAGTAGCAATATAATATCGAAATATTAGCAAAATAA
*
57649 CAACATAACAGCAGTAAACAATGACAGACAACAACAGAATTTTTTTGTCAAATTCGAGTCGG
391 CAACATAACAACAGTAAACAATGACAGACAACAACAGAATTTTTTTGTCAAATTCGAGTCGG
*
57711 GTCAAACTTGACATGCACGAACTAGAGCTGATCATGGGTCGAGCTAGTGTAAAAAATCAAGTCCA
1 GTCAAACTTGACATGCACGAACTAGAGCTGATCATGGATCGAGCTAGTGTAAAAAATCAAGTCCA
**
57776 TTTTCTAGGTTAGCCTGAATAAAAAATACTAAACCTGGTCCAGCCTAGCCACATTAAATTTTTTA
66 TTTTCTAGGTTAGCCTGAATAAAAAATACTAAACCTGACCCAGCCTAGCCACATTAAATTTTTTA
57841 GATTATTATTTTTATATAAAATAAATTTAAAAAATATAATACATCAAATAAAATGAAAACATTAA
131 GATTATTATTTTTATATAAAATAAATTTAAAAAATATAATACATCAAATAAAATGAAAACATTAA
*
57906 AATAAATGCATTCCAACAAATTGGAAATACATATAAAAAAAAGTTTTATACTTAAATAACAATAA
196 AATAAATACATTCCAACAAATTGGAAATACATATAAAAAAAAGTTTTATACTTAAATAACAATAA
57971 CATAATTGCAACTTAACAAGCATGTGTCTTTAAAATAGTATTAAAATTAACAATAAAATAAGAAT
261 CATAATTGCAACTTAACAAGCATGTGTCTTTAAAATAGTATTAAAATTAACAATAAAATAAGAAT
58036 TATATAATATCCAAACAATAACAACAAAATAGTAGCAATATAATATCGAAATATTAGCAAAATAA
326 TATATAATATCCAAACAATAACAACAAAATAGTAGCAATATAATATCGAAATATTAGCAAAATAA
58101 CAACATAACAACAGTAAACAATGACAGACAACAACAGAATTTTTTTGTCAAATTCGAGTCGG
391 CAACATAACAACAGTAAACAATGACAGACAACAACAGAATTTTTTTGTCAAATTCGAGTCGG
*
58163 GTCAATCTTG
1 GTCAAACTTG
58173 GGTCAAAAAA
Statistics
Matches: 453, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
452 453 1.00
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.28
Consensus pattern (452 bp):
GTCAAACTTGACATGCACGAACTAGAGCTGATCATGGATCGAGCTAGTGTAAAAAATCAAGTCCA
TTTTCTAGGTTAGCCTGAATAAAAAATACTAAACCTGACCCAGCCTAGCCACATTAAATTTTTTA
GATTATTATTTTTATATAAAATAAATTTAAAAAATATAATACATCAAATAAAATGAAAACATTAA
AATAAATACATTCCAACAAATTGGAAATACATATAAAAAAAAGTTTTATACTTAAATAACAATAA
CATAATTGCAACTTAACAAGCATGTGTCTTTAAAATAGTATTAAAATTAACAATAAAATAAGAAT
TATATAATATCCAAACAATAACAACAAAATAGTAGCAATATAATATCGAAATATTAGCAAAATAA
CAACATAACAACAGTAAACAATGACAGACAACAACAGAATTTTTTTGTCAAATTCGAGTCGG
Found at i:60221 original size:19 final size:18
Alignment explanation
Indices: 60199--60260 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
60189 AAAAACAATC
60199 TATAATTTAAAAAATTCAA
1 TATAATTTAAAAAATT-AA
* *
60218 TATAAATAATAAAAATTAA
1 TATAATTTA-AAAAATTAA
* *
60237 TTTAATTT-TAAAATTAA
1 TATAATTTAAAAAATTAA
60254 TAATAAT
1 T-ATAAT
60261 AAATCTAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
17 9 0.26
18 4 0.12
19 14 0.41
20 7 0.21
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
TATAATTTAAAAAATTAA
Found at i:60273 original size:27 final size:27
Alignment explanation
Indices: 60224--60277 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
60214 TCAATATAAA
* * *
60224 TAATAAAAATTAATTTAATTTTAAAAT
1 TAATAAAAATAAATCTAAATTTAAAAT
*
60251 TAATAATAATAAATCTAAATTTAAAAT
1 TAATAAAAATAAATCTAAATTTAAAAT
60278 GATTTTTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (27 bp):
TAATAAAAATAAATCTAAATTTAAAAT
Found at i:60752 original size:20 final size:19
Alignment explanation
Indices: 60719--60770 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
60709 TGGATCTCAA
60719 ATTAATT-ATATTATTATATT
1 ATTAATTAAT-TTA-TATATT
*
60739 ATTAATTAATTTATATTTT
1 ATTAATTAATTTATATATT
*
60758 ATTCATTTAATTT
1 ATT-AATTAATTT
60771 TAAAAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 8 0.29
20 18 0.64
21 2 0.07
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTAATTAATTTATATATT
Found at i:60767 original size:24 final size:24
Alignment explanation
Indices: 60718--60769 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
60708 CTGGATCTCA
*
60718 AATTAATTATATTATTATATTATT
1 AATTAATTATATTATTATATCATT
60742 AATTAATTTATATT-TTAT-TCATTT
1 AATTAA-TTATATTATTATATCA-TT
60766 AATT
1 AATT
60770 TTAAAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 2 0.08
24 16 0.64
25 7 0.28
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
AATTAATTATATTATTATATCATT
Found at i:66372 original size:20 final size:21
Alignment explanation
Indices: 66347--66399 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
66337 TTGGTACAAT
66347 ATTAATATTTAAAAAACTT-A
1 ATTAATATTTAAAAAACTTCA
* * **
66367 ATTAATTTTTTAAAATTTTCA
1 ATTAATATTTAAAAAACTTCA
66388 ATTAA-ATTTAAA
1 ATTAATATTTAAA
66400 TTTAAAATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 20 0.77
21 6 0.23
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTAATATTTAAAAAACTTCA
Done.