Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011853.1 Kokia drynarioides strain JFW-HI SEQ_126849, 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: 127350
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 177 characters in sequence are not A, C, G, or T
Found at i:332 original size:4 final size:4
Alignment explanation
Indices: 312--373 Score: 63
Period size: 4 Copynumber: 15.2 Consensus size: 4
302 CACATTATCA
* * * *
312 TTCT TTCC TTC- TTCT TTCT TTCCT CTCC TTCT TCCT TTCT TTCT TTCT
1 TTCT TTCT TTCT TTCT TTCT TT-CT TTCT TTCT TTCT TTCT TTCT TTCT
360 TTCCT TTCT TTCT T
1 TT-CT TTCT TTCT T
374 CCCGTTTATT
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
3 3 0.06
4 38 0.79
5 7 0.15
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (4 bp):
TTCT
Found at i:344 original size:17 final size:15
Alignment explanation
Indices: 312--374 Score: 63
Period size: 17 Copynumber: 3.9 Consensus size: 15
302 CACATTATCA
312 TTCTTTCCTTCTTCT
1 TTCTTTCCTTCTTCT
327 TTCTTTCCTCTCCTTCT
1 TTCTTTCCT-T-CTTCT
* *
344 TCCTTTCTTTCTTTCT
1 TTCTTTCCTTC-TTCT
*
360 TTCCTTTCTTTCTTC
1 TT-CTTTCCTTCTTC
375 CCGTTTATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
15 10 0.24
16 10 0.24
17 21 0.51
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (15 bp):
TTCTTTCCTTCTTCT
Found at i:361 original size:29 final size:27
Alignment explanation
Indices: 316--375 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 27
306 TTATCATTCT
316 TTCCTTCTTCTTTCTTTCCTCTCCTTC
1 TTCCTTCTTCTTTCTTTCCTCTCCTTC
* *
343 TTCCTTTCTTTCTTTCTTTCCTTTCTTTC
1 TTCC-TTC-TTCTTTCTTTCCTCTCCTTC
372 TTCC
1 TTCC
376 CGTTTATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 4 0.14
28 3 0.10
29 22 0.76
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (27 bp):
TTCCTTCTTCTTTCTTTCCTCTCCTTC
Found at i:6877 original size:18 final size:18
Alignment explanation
Indices: 6837--6888 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
6827 TTTTCAATTG
*
6837 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAATTTATT
*
6855 CAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
6873 TAATTAA--AAATTTATT
1 TAATTAATTAAATTTATT
6889 CTCATCCCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 9 0.30
17 7 0.23
18 14 0.47
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:8820 original size:23 final size:23
Alignment explanation
Indices: 8684--8833 Score: 107
Period size: 23 Copynumber: 6.4 Consensus size: 23
8674 CGAAGTACTT
8684 AACAGTAAGCACACA-AGTGCTAGGGA
1 AACAGTAAGCACACACAGTGC----GA
8710 AACAGTAAGCACACACAGTGC-A
1 AACAGTAAGCACACACAGTGCGA
* * * * *
8732 ATCAGTAGGCGCACATAGCGC-A
1 AACAGTAAGCACACACAGTGCGA
8754 AATCAGT-AG-ACACACAAGGTGCGA
1 AA-CAGTAAGCACACAC-A-GTGCGA
*
8778 AACAGTAAGCACA-AGAAGTGCGA
1 AACAGTAAGCACACA-CAGTGCGA
*
8801 AACAGTAAGCATACACAGTGCTG-
1 AACAGTAAGCACACACAGTGC-GA
8824 AACAGTAAGC
1 AACAGTAAGC
8834 GCGCTAGCGT
Statistics
Matches: 101, Mismatches: 13, Indels: 23
0.74 0.09 0.17
Matches are distributed among these distances:
21 4 0.04
22 21 0.21
23 44 0.44
24 9 0.09
25 3 0.03
26 15 0.15
27 5 0.05
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (23 bp):
AACAGTAAGCACACACAGTGCGA
Found at i:9454 original size:21 final size:21
Alignment explanation
Indices: 9430--9471 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
9420 CCATATAAAT
9430 TTCA-ATCTCTAATAATTTTTC
1 TTCATATCTCT-ATAATTTTTC
* *
9451 TTCATTTTTCTATAATTTTTC
1 TTCATATCTCTATAATTTTTC
9472 AAAGTCAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.24, C:0.17, G:0.00, T:0.60
Consensus pattern (21 bp):
TTCATATCTCTATAATTTTTC
Found at i:13935 original size:26 final size:26
Alignment explanation
Indices: 13906--13955 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
13896 TTATTATATA
13906 AATATATATAATTACT-TTAAAATTTG
1 AATATAT-TAATTACTATTAAAATTTG
* *
13932 AATATATTTATTACTATTTAAATT
1 AATATATTAATTACTATTAAAATT
13956 CGATTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (26 bp):
AATATATTAATTACTATTAAAATTTG
Found at i:27463 original size:21 final size:21
Alignment explanation
Indices: 27433--27475 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
27423 ATTTCAGCTG
27433 TTCTTACTTAAAAACACCACA
1 TTCTTACTTAAAAACACCACA
*
27454 TTCTTCCTTAAAAACACCACA
1 TTCTTACTTAAAAACACCACA
27475 T
1 T
27476 ACTAATACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.30, G:0.00, T:0.30
Consensus pattern (21 bp):
TTCTTACTTAAAAACACCACA
Found at i:41755 original size:366 final size:366
Alignment explanation
Indices: 41068--41799 Score: 1385
Period size: 367 Copynumber: 2.0 Consensus size: 366
41058 GTTTATAGAG
41068 ATGGTAGATGTTTTGAATGTTGATATAGTTAATTTCGATTTCTTTACTTAATATTTTGATGTAAT
1 ATGGTAGATGTTTTGAATGTTGATATAGTTAATTTCGATTTCTTTACTTAATATTTTGATGTAAT
41133 TATTTGATTTTCTTACTAAAAAAAATTATCGGAATAAACAGAATTTATGTTTGTGTAAGAAAATT
66 TATTTGATTTTCTTACTAAAAAAAATTATCGGAATAAACAGAATTTATGTTTGTGTAAGAAAATT
41198 AAAAATTAAGTATTGAATCTTATTTATAAAATACGTATTATTTATAATCAAATATAAATATAATT
131 AAAAATTAAGTATTGAATCTTATTTATAAAATACGTATTATTTATAATCAAATATAAATATAATT
41263 AGATTGTTTAATAAATATAATTTTTAAAATTTTAAAGATAAAATATTTAAAGGGTAATTTTAAAA
196 AGATTGTTTAATAAATATAATTTTTAAAATTTTAAAGATAAAATATTTAAAGGGTAATTTTAAAA
* *
41328 GAAAGAAAATAAAAATGATTTTTTTTTAAAAATCTATAATAAGTGATAAGTTGTCCTTTATCTAT
261 GAAAGAAAATAAAAATGATTTCTTTTAAAAAATCTATAATAAGTGATAAGTTGTCCTTTATCTAT
41393 TTATTATTTTTCACATTTTTTAATGAAAATTTCTATCATGT
326 TTATTATTTTTCACATTTTTTAATGAAAATTTCTATCATGT
*
41434 ATGGTAGATGTTTTGAATGTTGATATGGTTAATTTCGATTTCTTTACTTAATATTTTGATGTAAT
1 ATGGTAGATGTTTTGAATGTTGATATAGTTAATTTCGATTTCTTTACTTAATATTTTGATGTAAT
*
41499 TATTTGATTTTCTTACTAAAAAAAAATTATTGGAATAAACAGAATTTATGTTTGTGTAAGAAAAT
66 TATTTGATTTTCTTACT-AAAAAAAATTATCGGAATAAACAGAATTTATGTTTGTGTAAGAAAAT
*
41564 TAAAAATTAAGTATTGAATTTTATTTATAAAATACGTATTATTTATAATCAAATATAAATATAAT
130 TAAAAATTAAGTATTGAATCTTATTTATAAAATACGTATTATTTATAATCAAATATAAATATAAT
*
41629 TAGATTGTTTGATAAATATAATTTTTAAAATTTTAAAGATAAAATATTTAAAGGGTAATTTTAAA
195 TAGATTGTTTAATAAATATAATTTTTAAAATTTTAAAGATAAAATATTTAAAGGGTAATTTTAAA
*
41694 AGAAAGAAAATAAAAATGA-TTCTTTTAAAAAATCTATATTAAGTGATAAGTTGTCCTTTATCTA
260 AGAAAGAAAATAAAAATGATTTCTTTTAAAAAATCTATAATAAGTGATAAGTTGTCCTTTATCTA
41758 TTTATTATTTTTCACATTTTTTAATGAAAATTTCTATCATGT
325 TTTATTATTTTTCACATTTTTTAATGAAAATTTCTATCATGT
41800 GTTTTTTTAT
Statistics
Matches: 358, Mismatches: 7, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
366 165 0.46
367 193 0.54
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (366 bp):
ATGGTAGATGTTTTGAATGTTGATATAGTTAATTTCGATTTCTTTACTTAATATTTTGATGTAAT
TATTTGATTTTCTTACTAAAAAAAATTATCGGAATAAACAGAATTTATGTTTGTGTAAGAAAATT
AAAAATTAAGTATTGAATCTTATTTATAAAATACGTATTATTTATAATCAAATATAAATATAATT
AGATTGTTTAATAAATATAATTTTTAAAATTTTAAAGATAAAATATTTAAAGGGTAATTTTAAAA
GAAAGAAAATAAAAATGATTTCTTTTAAAAAATCTATAATAAGTGATAAGTTGTCCTTTATCTAT
TTATTATTTTTCACATTTTTTAATGAAAATTTCTATCATGT
Found at i:55549 original size:12 final size:12
Alignment explanation
Indices: 55532--55574 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
55522 TTCTATGAAC
55532 ACAAATAAATAA
1 ACAAATAAATAA
*
55544 ACAAAT-GATGAA
1 ACAAATAAAT-AA
55556 CACAAATAAATAA
1 -ACAAATAAATAA
55569 ACAAAT
1 ACAAAT
55575 GATGATAGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 2 0.08
12 14 0.54
13 8 0.31
14 2 0.08
ACGTcount: A:0.67, C:0.12, G:0.05, T:0.16
Consensus pattern (12 bp):
ACAAATAAATAA
Found at i:55557 original size:25 final size:25
Alignment explanation
Indices: 55526--55579 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
55516 CATCTATTCT
55526 ATGAACACAAATAAATAAACAAATG
1 ATGAACACAAATAAATAAACAAATG
55551 ATGAACACAAATAAATAAACAAATG
1 ATGAACACAAATAAATAAACAAATG
55576 ATGA
1 ATGA
55580 TAGCCGCATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.63, C:0.11, G:0.09, T:0.17
Consensus pattern (25 bp):
ATGAACACAAATAAATAAACAAATG
Found at i:59596 original size:29 final size:30
Alignment explanation
Indices: 59546--59620 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 30
59536 TTAAAACTAT
* *
59546 ACATGAACTATGATTTAATGTGTAATTGTAC
1 ACATAAACTTTGATTT-ATGTGTAATTGTAC
* *
59577 ACATAAACTTTGATTT-TGTGTAATTTTAT
1 ACATAAACTTTGATTTATGTGTAATTGTAC
*
59606 ACATGAAATTTTGAT
1 ACAT-AAACTTTGAT
59621 CTGATCCAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 15 0.39
30 9 0.24
31 14 0.37
ACGTcount: A:0.35, C:0.08, G:0.13, T:0.44
Consensus pattern (30 bp):
ACATAAACTTTGATTTATGTGTAATTGTAC
Found at i:61879 original size:29 final size:28
Alignment explanation
Indices: 61844--61925 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 28
61834 ATTTATTAAA
61844 ATTTTAAAAATTCAAAAAAATATAAAATT
1 ATTTTAAAAATT-AAAAAAATATAAAATT
*
61873 ATTTTAAAAAATTAAAAATAGT-TAAAATT
1 ATTTT-AAAAATTAAAAA-AATATAAAATT
* *
61902 A-TTT-AAAATTATAAAATTATAAAA
1 ATTTTAAAAATTAAAAAAATATAAAA
61926 AATAATATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
25 2 0.04
26 15 0.32
28 3 0.06
29 18 0.38
30 9 0.19
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (28 bp):
ATTTTAAAAATTAAAAAAATATAAAATT
Found at i:68504 original size:7 final size:7
Alignment explanation
Indices: 68492--68518 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
68482 CCTCCGACTC
68492 TTCATTT
1 TTCATTT
68499 TTCATTT
1 TTCATTT
68506 TTCATTT
1 TTCATTT
68513 TTCATT
1 TTCATT
68519 AAGTACTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (7 bp):
TTCATTT
Found at i:81234 original size:153 final size:154
Alignment explanation
Indices: 80954--81259 Score: 569
Period size: 153 Copynumber: 2.0 Consensus size: 154
80944 GATCTCGAGT
80954 TTGAATCCCTGGTTCTGTAATCTCTGATCTTAGACTACGATCTCTTTCGTGAGTGTGTGTATGTA
1 TTGAATCCCTGGTTCTGTAATCTCTGATCTTAGACTACGATCTCTTTCGTGAG-GTGTGTATGTA
*
81019 TATAACTCATTGTGCAAACAATATAGTTGAAAGATGTGTGATCGACTGCAGTTAAATCTCATACT
65 TATAACTCATTGTGCAAACAATATAGTTGAAAAATGTGTGATCGACTGCAGTTAAATCTCATACT
*
81084 GTAAAACCCAAGATTGCCCTCTAGC
130 GTAAAACCCAAGATTGCCATCTAGC
*
81109 TTGAATCCCTGGTTCTGTAATCTCTTATCTTAGACTACGATCTCTTTCGTGA-GTGTGTATGTAT
1 TTGAATCCCTGGTTCTGTAATCTCTGATCTTAGACTACGATCTCTTTCGTGAGGTGTGTATGTAT
81173 ATAACTCATTGTGCAAACAATATAGTTGAAAAATGTGTGATCGACTGCAGTTAAATCTCATACTG
66 ATAACTCATTGTGCAAACAATATAGTTGAAAAATGTGTGATCGACTGCAGTTAAATCTCATACTG
81238 TAAAACCCAAGATTGCCATCTA
131 TAAAACCCAAGATTGCCATCTA
81260 TTCTCCGATC
Statistics
Matches: 148, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
153 97 0.66
155 51 0.34
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (154 bp):
TTGAATCCCTGGTTCTGTAATCTCTGATCTTAGACTACGATCTCTTTCGTGAGGTGTGTATGTAT
ATAACTCATTGTGCAAACAATATAGTTGAAAAATGTGTGATCGACTGCAGTTAAATCTCATACTG
TAAAACCCAAGATTGCCATCTAGC
Found at i:90752 original size:40 final size:39
Alignment explanation
Indices: 90684--90761 Score: 138
Period size: 40 Copynumber: 2.0 Consensus size: 39
90674 TACTTTTTTG
*
90684 AAATTTAAAAATTAGTTTTTATATTTTAAATAAAAATTT
1 AAATTTAAAAATTAATTTTTATATTTTAAATAAAAATTT
90723 AAATTTAAAAATTATATTTTTATATTTTAAATAAAAATT
1 AAATTTAAAAATTA-ATTTTTATATTTTAAATAAAAATT
90762 ATGAAAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 14 0.38
40 23 0.62
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (39 bp):
AAATTTAAAAATTAATTTTTATATTTTAAATAAAAATTT
Found at i:90773 original size:40 final size:38
Alignment explanation
Indices: 90690--90774 Score: 109
Period size: 40 Copynumber: 2.2 Consensus size: 38
90680 TTTGAAATTT
* *
90690 AAAAATTAGTTTTTATATTTTAAATAAAAATTTAAATTT
1 AAAAATTAATTTTTATATTTTAAATAAAAATTTAAA-TA
90729 AAAAATTATATTTTTATATTTTAAATAAAAATTATGAAA-A
1 AAAAATTA-ATTTTTATATTTTAAATAAAAATT-T-AAATA
90769 AAAAAT
1 AAAAAT
90775 ATGAAAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
39 8 0.20
40 29 0.71
41 1 0.02
42 3 0.07
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (38 bp):
AAAAATTAATTTTTATATTTTAAATAAAAATTTAAATA
Found at i:90777 original size:13 final size:13
Alignment explanation
Indices: 90755--90784 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
90745 TATTTTAAAT
*
90755 AAAAATTATGAAA
1 AAAAAATATGAAA
90768 AAAAAATATGAAA
1 AAAAAATATGAAA
90781 AAAA
1 AAAA
90785 TATTTCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.17
Consensus pattern (13 bp):
AAAAAATATGAAA
Found at i:90794 original size:22 final size:23
Alignment explanation
Indices: 90769--90819 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
90759 ATTATGAAAA
*
90769 AAAAATATG-AAAAAAATATTTC
1 AAAAATACGAAAAAAAATATTTC
90791 -AAAATACGAAAAAAAATATTTC
1 AAAAATACGAAAAAAAATATTTC
90813 AGAAAAT
1 A-AAAAT
90820 TCTAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 7 0.28
22 13 0.52
24 5 0.20
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (23 bp):
AAAAATACGAAAAAAAATATTTC
Found at i:90827 original size:24 final size:22
Alignment explanation
Indices: 90770--90813 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
90760 TTATGAAAAA
*
90770 AAAATATG-AAAAAAATATTTC
1 AAAATACGAAAAAAAATATTTC
90791 AAAATACGAAAAAAAATATTTC
1 AAAATACGAAAAAAAATATTTC
90813 A
1 A
90814 GAAAATTCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.25
Consensus pattern (22 bp):
AAAATACGAAAAAAAATATTTC
Found at i:91736 original size:32 final size:34
Alignment explanation
Indices: 91666--91736 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 34
91656 ATATTTATTT
91666 TTAAA-ATTTTAAATTTTATTTAAAATATAAAAA
1 TTAAATATTTTAAATTTTATTTAAAATATAAAAA
* * * *
91699 ATAAATATTTT-AA-TTTGTTTAAAATATGAAGA
1 TTAAATATTTTAAATTTTATTTAAAATATAAAAA
91731 TTAAAT
1 TTAAAT
91737 TCAAAAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
32 21 0.66
33 6 0.19
34 5 0.16
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (34 bp):
TTAAATATTTTAAATTTTATTTAAAATATAAAAA
Found at i:92232 original size:39 final size:39
Alignment explanation
Indices: 92189--92266 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
92179 TACTAGATCA
92189 CCATTTTCATCTATAAAATCCATAAAAGCTCTCATTCAC
1 CCATTTTCATCTATAAAATCCATAAAAGCTCTCATTCAC
92228 CCATTTTCATCTATAAAATCCATAAAAGCTCTCATTCAC
1 CCATTTTCATCTATAAAATCCATAAAAGCTCTCATTCAC
92267 AATACTCCTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (39 bp):
CCATTTTCATCTATAAAATCCATAAAAGCTCTCATTCAC
Found at i:101861 original size:24 final size:25
Alignment explanation
Indices: 101820--101868 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
101810 AATATTTATA
101820 TTATATAATTTTAATATTTAATAAAT
1 TTATATAATTTT-ATATTTAATAAAT
*
101846 TTATATAATTTT-TATTTATTAAA
1 TTATATAATTTTATATTTAATAAA
101869 AACTTTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.45
26 12 0.55
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TTATATAATTTTATATTTAATAAAT
Found at i:104625 original size:2 final size:2
Alignment explanation
Indices: 104614--104679 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
104604 AAGTATCAAT
104614 TA TA -A 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 TA TA
104655 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
104680 TTAATAGAGT
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 62 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:105158 original size:3 final size:3
Alignment explanation
Indices: 105137--105187 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
105127 CATATATTTT
* * *
105137 ATA ATA ATCT ATA AT- ATA ATA ATA ATA ATA ATA ATT ATA AAA ATAA
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
105183 ATA AT
1 ATA AT
105188 TAAAAAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
2 2 0.05
3 32 0.82
4 5 0.13
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:109324 original size:18 final size:18
Alignment explanation
Indices: 109301--109346 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
109291 GTATTTATAT
*
109301 TATTGAATTTTTTAATAA
1 TATTGAATTTTATAATAA
*
109319 TATTGAATATTTATATTAA
1 TATTGAAT-TTTATAATAA
*
109338 AATTGAATT
1 TATTGAATT
109347 ATTAATGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (18 bp):
TATTGAATTTTATAATAA
Found at i:113814 original size:29 final size:29
Alignment explanation
Indices: 113780--113840 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
113770 GTTAGAGTTT
**
113780 TTTACTAATTTAATACAAAAAAA-TATTTA
1 TTTACTAAAATAATA-AAAAAAATTATTTA
113809 TTTACTAAAATAATAAAAAAAATTATTTA
1 TTTACTAAAATAATAAAAAAAATTATTTA
113838 TTT
1 TTT
113841 TATTTGACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 7 0.24
29 22 0.76
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (29 bp):
TTTACTAAAATAATAAAAAAAATTATTTA
Found at i:114636 original size:23 final size:23
Alignment explanation
Indices: 114610--114706 Score: 100
Period size: 23 Copynumber: 4.5 Consensus size: 23
114600 AGTGCTGGGC
114610 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
114633 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
* *
114652 -AC--TGAGCACACAAAGTACTA
1 AACAGAGAGCACACAAAGTGCTA
* *
114672 ATCAGAGAGCACACGAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
114695 AACAGAGAGCAC
1 AACAGAGAGCAC
114707 GCTAGTGTTC
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
16 10 0.17
18 2 0.03
19 1 0.02
20 1 0.02
21 2 0.03
23 42 0.72
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.10
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:114678 original size:39 final size:39
Alignment explanation
Indices: 114616--114690 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
114606 GGGCAACAGA
* *
114616 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTACTAAACAGAGAGCACACAAAGTACT
* *
114655 GAGCACACAAAGTACTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTACTAAACAGAGAGCACACAAAGT
114691 GCTAAACAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAGTACTAAACAGAGAGCACACAAAGTACT
Found at i:118336 original size:5 final size:5
Alignment explanation
Indices: 118323--118365 Score: 77
Period size: 5 Copynumber: 8.6 Consensus size: 5
118313 ACTTACTAAC
*
118323 AAATT AAATA AAATT AAATT AAATT AAATT AAATT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAA
118366 AATAACCGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (5 bp):
AAATT
Found at i:119044 original size:4 final size:4
Alignment explanation
Indices: 118984--119082 Score: 87
Period size: 4 Copynumber: 25.0 Consensus size: 4
118974 AAATTATTAC
* * * * * * *
118984 CTTT CTCT CGTT C-TT CTTT TTTT CCTCT CTTT C-TT CCTT CATT CCTT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT
*
119031 CTTTT TTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT C-TT
1 C-TTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
119079 CTTT
1 CTTT
119083 GGTGTCGTTT
Statistics
Matches: 78, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
3 9 0.12
4 65 0.83
5 4 0.05
ACGTcount: A:0.01, C:0.28, G:0.01, T:0.70
Consensus pattern (4 bp):
CTTT
Found at i:123982 original size:82 final size:81
Alignment explanation
Indices: 123831--124073 Score: 197
Period size: 84 Copynumber: 2.9 Consensus size: 81
123821 TTTTAATGGA
* * * * * **
123831 CCAAAATATAAGTTTATTATATATTAATTTATAATTTCATTATTTCTGAACGGATTAAATAT-TT
1 CCAAAGTATAATTTTATTATATATTAATTTATAA-TTCTTTATTTAT-AAAGGATTAAATATAAC
123895 TTTTTTATTTTTAAG-GGG
64 TTTTTTA-TTTTAAGAGGG
** * * *
123913 TTAAATTGTAATTTTATTATATATTAATTTATAATCTCTTTATTTATAATAGGATTGAAT-TGAA
1 CCAAAGTATAATTTTATTATATATTAATTTATAAT-TCTTTATTTATAA-AGGATTAAATAT-AA
*
123977 CTTTTTTCATTTTGAGAGGG
63 CTTTTTT-ATTTTAAGAGGG
* * * *
123997 CCAAAGTATAATTTCACTATATATTGATTTATAATTTTTCTATTTATAAGAGGATTAAA-ATGAA
1 CCAAAGTATAATTTTATTATATATTAATTTATAATTCTT-TATTTATAA-AGGATTAAATAT--A
*
124061 AATTTTTTATTTT
62 ACTTTTTTATTTT
124074 TGGGAGCGCA
Statistics
Matches: 128, Mismatches: 24, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
81 4 0.03
82 46 0.36
83 15 0.12
84 55 0.43
85 8 0.06
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.50
Consensus pattern (81 bp):
CCAAAGTATAATTTTATTATATATTAATTTATAATTCTTTATTTATAAAGGATTAAATATAACTT
TTTTATTTTAAGAGGG
Found at i:125311 original size:18 final size:16
Alignment explanation
Indices: 125277--125312 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
125267 TGTTTGTTTG
125277 TATTTTAAAAATTAAT
1 TATTTTAAAAATTAAT
125293 TATTTTAAATAATTTAAT
1 TATTTTAAA-AA-TTAAT
125311 TA
1 TA
125313 AAGTTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 2 0.11
18 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTTTAAAAATTAAT
Found at i:125488 original size:2 final size:2
Alignment explanation
Indices: 125483--125510 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
125473 TAAATAATTA
125483 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
125511 TGATTAAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.