Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002923.1 Kokia drynarioides strain JFW-HI SEQ_115365, 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: 91125
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 6 characters in sequence are not A, C, G, or T
Found at i:6455 original size:19 final size:19
Alignment explanation
Indices: 6424--6473 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
6414 TAAAAAATAT
*
6424 AAAAAAGAAAAC-AATTAG
1 AAAAAATAAAACAAATTAG
6442 AAAAAATAATAACAAATTAG
1 AAAAAATAA-AACAAATTAG
*
6462 TAAAAATTAAAA
1 -AAAAAATAAAA
6474 ATCAAGTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 8 0.30
19 3 0.11
20 8 0.30
21 8 0.30
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.18
Consensus pattern (19 bp):
AAAAAATAAAACAAATTAG
Found at i:16101 original size:2 final size:2
Alignment explanation
Indices: 16094--16127 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
16084 GCATTCAAGC
16094 AT AT AT 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 AT AT AT
16128 TACTTGATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21409 original size:39 final size:39
Alignment explanation
Indices: 21366--21452 Score: 129
Period size: 39 Copynumber: 2.2 Consensus size: 39
21356 GGCCTAGTGA
*
21366 TAGGGGGGATGACCCACCACACCACCATGGACCTGGTGG
1 TAGGGGAGATGACCCACCACACCACCATGGACCTGGTGG
* * * *
21405 TAGGGGAGATGAGCCACTACACCACCCTGGATCTGGTGG
1 TAGGGGAGATGACCCACCACACCACCATGGACCTGGTGG
21444 TAGGGGAGA
1 TAGGGGAGA
21453 GGAACCATCA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.24, C:0.25, G:0.36, T:0.15
Consensus pattern (39 bp):
TAGGGGAGATGACCCACCACACCACCATGGACCTGGTGG
Found at i:23748 original size:18 final size:18
Alignment explanation
Indices: 23727--23769 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
23717 TTTTTCTATC
23727 CTCTTTCTTTGCTCTTTT
1 CTCTTTCTTTGCTCTTTT
* * *
23745 CTCTTTTTTTTCTTTTTT
1 CTCTTTCTTTGCTCTTTT
23763 C-CTTTCT
1 CTCTTTCT
23770 CTCAGTAGAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.00, C:0.26, G:0.02, T:0.72
Consensus pattern (18 bp):
CTCTTTCTTTGCTCTTTT
Found at i:36074 original size:14 final size:14
Alignment explanation
Indices: 36055--36087 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
36045 TATTGCTTAC
36055 TTTTGTTTATTCTA
1 TTTTGTTTATTCTA
36069 TTTTGTTTATTCTA
1 TTTTGTTTATTCTA
36083 TTTTG
1 TTTTG
36088 ATGCTACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.12, C:0.06, G:0.09, T:0.73
Consensus pattern (14 bp):
TTTTGTTTATTCTA
Found at i:48674 original size:31 final size:31
Alignment explanation
Indices: 48636--48697 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
48626 TTGCATAAGT
48636 ATGCCCAGAATTGTCGCTACCTAAACATGTC
1 ATGCCCAGAATTGTCGCTACCTAAACATGTC
48667 ATGCCCAGAATTGTCGCTACCTAAACATGTC
1 ATGCCCAGAATTGTCGCTACCTAAACATGTC
48698 CAGAATGGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (31 bp):
ATGCCCAGAATTGTCGCTACCTAAACATGTC
Found at i:48702 original size:26 final size:26
Alignment explanation
Indices: 48640--48731 Score: 94
Period size: 26 Copynumber: 3.3 Consensus size: 26
48630 ATAAGTATGC
48640 CCAGAATTGTCGCTACCTAAACATGTCAT
1 CCAGAATTGTCGCTACCTAAACATG---T
48669 GCCCAGAATTGTCGCTACCTAAACATGT
1 --CCAGAATTGTCGCTACCTAAACATGT
* * * *
48697 CCAGAATGGTCGCTACATGATCATGT
1 CCAGAATTGTCGCTACCTAAACATGT
*
48723 CTAGAATTG
1 CCAGAATTG
48732 CACCCGAAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
26 29 0.53
28 1 0.02
31 25 0.45
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27
Consensus pattern (26 bp):
CCAGAATTGTCGCTACCTAAACATGT
Found at i:57756 original size:17 final size:18
Alignment explanation
Indices: 57736--57773 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
57726 ATTCCTATTG
*
57736 TCATTACATTT-TAATTT
1 TCATTACATTTCCAATTT
*
57753 TCATTGCATTTCCAATTT
1 TCATTACATTTCCAATTT
57771 TCA
1 TCA
57774 CTGTAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.26, C:0.18, G:0.03, T:0.53
Consensus pattern (18 bp):
TCATTACATTTCCAATTT
Found at i:58870 original size:26 final size:26
Alignment explanation
Indices: 58801--58880 Score: 81
Period size: 26 Copynumber: 3.1 Consensus size: 26
58791 TTATAACTAA
* * *
58801 TGTCGCTGCATGAGTATGCCCAAAAT
1 TGTCGCTGCATAAGCATGTCCAAAAT
* *
58827 TGTCGTTGCTTGAA-CATGTCCAAAAT
1 TGTCGCTGCAT-AAGCATGTCCAAAAT
* *
58853 TGTCGCTACATAAGCATGTCCAGAAT
1 TGTCGCTGCATAAGCATGTCCAAAAT
58879 TG
1 TG
58881 AGCCCAGAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
25 2 0.05
26 40 0.93
27 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (26 bp):
TGTCGCTGCATAAGCATGTCCAAAAT
Found at i:66410 original size:20 final size:20
Alignment explanation
Indices: 66387--66498 Score: 62
Period size: 16 Copynumber: 5.8 Consensus size: 20
66377 TGTGGTCAGC
66387 AAATTATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
66407 AAATTATTTTTTAAAA-TA-T-
1 AAATTA--TTTTAAAATTATTA
* *
66426 -AATTTTTTTTAAATTACTTTA
1 AAATTATTTTAAAATTA--TTA
* * * *
66447 AAATTAATTT-AATTTTTTT
1 AAATTATTTTAAAATTATTA
66466 AAA-TA---TAAAATTATTA
1 AAATTATTTTAAAATTATTA
*
66482 AAATTATTTTTAAATTA
1 AAATTATTTTAAAATTA
66499 CAATTATCAT
Statistics
Matches: 68, Mismatches: 11, Indels: 26
0.65 0.10 0.25
Matches are distributed among these distances:
15 1 0.01
16 16 0.24
17 4 0.06
18 6 0.09
19 5 0.07
20 15 0.22
21 6 0.09
22 15 0.22
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.54
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:66474 original size:26 final size:27
Alignment explanation
Indices: 66444--66504 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
66434 TTAAATTACT
*
66444 TTAAAATTAATT-TAATT-TTTTTAAA
1 TTAAAATTAATTAAAATTATTTTTAAA
66469 TATAAAATT-ATTAAAATTATTTTTAAA
1 T-TAAAATTAATTAAAATTATTTTTAAA
*
66496 TTACAATTA
1 TTAAAATTA
66505 TCATCATCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
25 4 0.13
26 17 0.57
27 9 0.30
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (27 bp):
TTAAAATTAATTAAAATTATTTTTAAA
Found at i:66549 original size:6 final size:6
Alignment explanation
Indices: 66533--66562 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
66523 GGGTTTTTTC
*
66533 CCCCTT TCCCTT CCCCTT CCCCTT CCCCTT
1 CCCCTT CCCCTT CCCCTT CCCCTT CCCCTT
66563 TTGACAGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (6 bp):
CCCCTT
Found at i:67712 original size:28 final size:30
Alignment explanation
Indices: 67670--67735 Score: 111
Period size: 28 Copynumber: 2.3 Consensus size: 30
67660 TAAAAAAATC
67670 AATAA-TTTTATATTTTAAAAAATAA-TTT
1 AATAATTTTTATATTTTAAAAAATAATTTT
67698 AA-AATTTTTATATTTTAAAAAATAATTTT
1 AATAATTTTTATATTTTAAAAAATAATTTT
67727 AATAATTTT
1 AATAATTTT
67736 AAAACAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
27 2 0.06
28 22 0.63
29 5 0.14
30 6 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
AATAATTTTTATATTTTAAAAAATAATTTT
Found at i:72106 original size:26 final size:26
Alignment explanation
Indices: 72076--72210 Score: 87
Period size: 26 Copynumber: 5.0 Consensus size: 26
72066 TTATTGATTC
72076 ATAT-TTTAATAATAATTATATTAAGA
1 ATATATTTAATAATAATTATATTAA-A
* * *
72102 ATATTATTAAATTATATATTATTTTATCAAA
1 ATA-TATTTAA-TA-ATA--ATTATATTAAA
* *
72133 ATTTTATTTAATAATAATTATGTTAAA
1 A-TATATTTAATAATAATTATATTAAA
* *
72160 ATATGA-TTAA-ATTATTTATTATTAAA
1 ATAT-ATTTAATAATAATTA-TATTAAA
* *
72186 TTATATTTAATAATAATTTTATTAA
1 ATATATTTAATAATAATTATATTAA
72211 CATTTAATAA
Statistics
Matches: 82, Mismatches: 16, Indels: 22
0.68 0.13 0.18
Matches are distributed among these distances:
25 7 0.09
26 28 0.34
27 16 0.20
28 4 0.05
29 5 0.06
30 5 0.06
31 8 0.10
32 9 0.11
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (26 bp):
ATATATTTAATAATAATTATATTAAA
Found at i:72127 original size:59 final size:57
Alignment explanation
Indices: 72080--72210 Score: 164
Period size: 52 Copynumber: 2.4 Consensus size: 57
72070 TGATTCATAT
* *
72080 TTTAATAATAATTATATTAAGAATATTATTAAATTATATATTATTTTATCAAAATTTTA
1 TTTAATAATAATTATATTAA-AATATGATTAAATTATATATTATTTTAT-AAAATTATA
* *
72139 TTTAATAATAATTATGTTAAAATATGATTAAA-T-TAT-TTA--TTATTAAATTATA
1 TTTAATAATAATTATATTAAAATATGATTAAATTATATATTATTTTATAAAATTATA
*
72191 TTTAATAATAATTTTATTAA
1 TTTAATAATAATTATATTAA
72211 CATTTAATAA
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
52 25 0.38
53 4 0.06
55 3 0.05
56 3 0.05
57 1 0.02
58 11 0.17
59 19 0.29
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (57 bp):
TTTAATAATAATTATATTAAAATATGATTAAATTATATATTATTTTATAAAATTATA
Found at i:72162 original size:14 final size:14
Alignment explanation
Indices: 72080--72162 Score: 55
Period size: 15 Copynumber: 5.7 Consensus size: 14
72070 TGATTCATAT
72080 TTTAATAATAATTA
1 TTTAATAATAATTA
*
72094 TATTAAGAAT-ATTA
1 T-TTAATAATAATTA
* *
72108 TTAAATTATATATTA
1 TTTAATAATA-ATTA
*
72123 TTTTATCAA-AATTTTA
1 TTTAAT-AATAA--TTA
72139 TTTAATAATAATTA
1 TTTAATAATAATTA
72153 TGTTAA-AATA
1 T-TTAATAATA
72163 TGATTAAATT
Statistics
Matches: 53, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
13 5 0.09
14 15 0.28
15 22 0.42
16 11 0.21
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (14 bp):
TTTAATAATAATTA
Found at i:74110 original size:5 final size:5
Alignment explanation
Indices: 74100--74157 Score: 57
Period size: 5 Copynumber: 11.4 Consensus size: 5
74090 GTTCTTTACC
* *
74100 TTATT TTATT TATTTGT TTGTT TTA-T TTATT TTATT TTATT TTATT TT-TAT
1 TTATT TTATT T-TAT-T TTATT TTATT TTATT TTATT TTATT TTATT TTAT-T
74151 TTATT TT
1 TTATT TT
74158 TAGTACTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
4 5 0.11
5 33 0.73
6 5 0.11
7 2 0.04
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:74114 original size:9 final size:9
Alignment explanation
Indices: 74100--74156 Score: 62
Period size: 9 Copynumber: 6.2 Consensus size: 9
74090 GTTCTTTACC
74100 TTATTTTAT
1 TTATTTTAT
*
74109 TTA-TTTGT
1 TTATTTTAT
*
74117 TTGTTTTAT
1 TTATTTTAT
74126 TTATTTTATT
1 TTATTTTA-T
74136 TTATTTTAT
1 TTATTTTAT
*
74145 TTTTATTTAT
1 TTAT-TTTAT
74155 TT
1 TT
74157 TTAGTACTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
8 6 0.15
9 18 0.45
10 16 0.40
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.79
Consensus pattern (9 bp):
TTATTTTAT
Found at i:74167 original size:25 final size:25
Alignment explanation
Indices: 74120--74170 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
74110 TATTTGTTTG
**
74120 TTTTATTTATTTTATTTTATTTTAT
1 TTTTATTTATTTTATAGTATTTTAT
74145 TTTTATTTATTTT-TAGTACTTTTAT
1 TTTTATTTATTTTATAGTA-TTTTAT
74170 T
1 T
74171 CCGTGCTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (25 bp):
TTTTATTTATTTTATAGTATTTTAT
Found at i:76298 original size:96 final size:96
Alignment explanation
Indices: 76101--76384 Score: 513
Period size: 96 Copynumber: 3.0 Consensus size: 96
76091 GCAATATCTA
* *
76101 AGAATTTGAGTCACACAACTTTAATAATCTCCACCTTCACATGAATTTTCT---C-AACAAGTTC
1 AGAATTTGAGTCACACAACTTTAATAATCTCCACCTTGACACGAATTTTCTCAACGAACAAGTTC
76162 ATCACCACGAACTCTCAACGAACAAGTTCTC
66 ATCACCACGAACTCTCAACGAACAAGTTCTC
76193 AGAATTTGAGTCACACAACTTTAATAATCTCCACCTTGACACGAATTTTCTCAACGAACAAGTTC
1 AGAATTTGAGTCACACAACTTTAATAATCTCCACCTTGACACGAATTTTCTCAACGAACAAGTTC
76258 ATCACCACGAACTCTCAACGAACAAGTTCTC
66 ATCACCACGAACTCTCAACGAACAAGTTCTC
*
76289 AGAATTTGAGTCACACAACTTTAATAATCTCCACCTTGACACAAATTTTCTCAACGAACAAGTTC
1 AGAATTTGAGTCACACAACTTTAATAATCTCCACCTTGACACGAATTTTCTCAACGAACAAGTTC
76354 ATCACCACGAACTCTCAACGAACAAGTTCTC
66 ATCACCACGAACTCTCAACGAACAAGTTCTC
76385 CACCTCTTCC
Statistics
Matches: 185, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
92 49 0.26
95 1 0.01
96 135 0.73
ACGTcount: A:0.36, C:0.28, G:0.10, T:0.27
Consensus pattern (96 bp):
AGAATTTGAGTCACACAACTTTAATAATCTCCACCTTGACACGAATTTTCTCAACGAACAAGTTC
ATCACCACGAACTCTCAACGAACAAGTTCTC
Found at i:76933 original size:59 final size:59
Alignment explanation
Indices: 76867--76984 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
76857 CAGAATCAAC
76867 ATACCCAATGACTCCATCACTAATTCTTCCAAATTGTAAGCAAACATCAATAGTACCTG
1 ATACCCAATGACTCCATCACTAATTCTTCCAAATTGTAAGCAAACATCAATAGTACCTG
76926 ATACCCAATGACTCCATCACTAATTCTTCCAAATTGTAAGCAAACATCAATAGTACCTG
1 ATACCCAATGACTCCATCACTAATTCTTCCAAATTGTAAGCAAACATCAATAGTACCTG
76985 GTAAGTATCT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.37, C:0.27, G:0.08, T:0.27
Consensus pattern (59 bp):
ATACCCAATGACTCCATCACTAATTCTTCCAAATTGTAAGCAAACATCAATAGTACCTG
Found at i:81327 original size:35 final size:35
Alignment explanation
Indices: 81259--81329 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 35
81249 AAGATAATAT
*
81259 ATTTTGTTTAACTTGACTTGCAATCAATCTCTTAG
1 ATTTTGTTTAACTTGACTTGCAATCAATATCTTAG
*
81294 ATTTTGTTTAACTTGACTTGTAAGT-AATATCTTAG
1 ATTTTGTTTAACTTGACTTGCAA-TCAATATCTTAG
81329 A
1 A
81330 ATTTCGGTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 32 0.97
36 1 0.03
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (35 bp):
ATTTTGTTTAACTTGACTTGCAATCAATATCTTAG
Found at i:86755 original size:24 final size:24
Alignment explanation
Indices: 86723--86781 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
86713 AGGATATATA
* * *
86723 TAAAACTCCACGACATTCAGGTGG
1 TAAACCTCCACGACACTCAGGGGG
*
86747 TAAACCTCCACGACACTCGGGGGG
1 TAAACCTCCACGACACTCAGGGGG
86771 TAAACCTCCAC
1 TAAACCTCCAC
86782 ATGTTGAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.31, C:0.32, G:0.20, T:0.17
Consensus pattern (24 bp):
TAAACCTCCACGACACTCAGGGGG
Found at i:86956 original size:24 final size:24
Alignment explanation
Indices: 86924--86983 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
86914 AGGGCACACA
*
86924 TAAACCTCCACAACACTCAGGTGG
1 TAAACCTCCACAACACTCAGGGGG
*
86948 TAAACCTCCACGACACTCAGGGGG
1 TAAACCTCCACAACACTCAGGGGG
86972 TAAACCTCCACA
1 TAAACCTCCACA
86984 TGTTGAAGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.33, C:0.35, G:0.17, T:0.15
Consensus pattern (24 bp):
TAAACCTCCACAACACTCAGGGGG
Found at i:86991 original size:201 final size:201
Alignment explanation
Indices: 86676--87499 Score: 1355
Period size: 201 Copynumber: 4.1 Consensus size: 201
86666 ACATGGGGAA
* * ** * * * * *
86676 AAACCGCCTCATAGATACCTATTGAGTGTGGAAGTTGAGGATATATATAAAACTCCACGACATTC
1 AAACCTCCTCATAGACACCTATTGAGTGTGGAAGTTGAGGGCACACATAAACCTCCACAACACTC
* *
86741 AGGTGGTAAACCTCCACGACACTCGGGGGGTAAACCTCCACATGTTGAAGGGTTCCCTGCTGGTA
66 AGGTGGTAAACCTCCACGACACTCAGGGGGTAAACCTCCACATGTTGAAGGATTCCCTGCTGGTA
* * *
86806 AACCACCCATGAAGCCATTCCCTGGTGACAAACCATCCAAGGGTAAGGGAAAGGGAGAACCTCAT
131 AGCCACCCATGAAGCCATTCCCCGGTGACAAACCATCAAAGGGTAAGGGAAAGGGAGAACCTCAT
86871 GAACCC
196 GAACCC
*
86877 AAACCTCCTCATCGACACCTATTGAGTGTGGAAGTTGAGGGCACACATAAACCTCCACAACACTC
1 AAACCTCCTCATAGACACCTATTGAGTGTGGAAGTTGAGGGCACACATAAACCTCCACAACACTC
* *
86942 AGGTGGTAAACCTCCACGACACTCAGGGGGTAAACCTCCACATGTTGAAGGATTCCTTGGTGGTA
66 AGGTGGTAAACCTCCACGACACTCAGGGGGTAAACCTCCACATGTTGAAGGATTCCCTGCTGGTA
87007 AGCCACCC-TCGAAGCCATTCCCCGGTGACAAACCATCAAAGGGTAAGGGAAAGGGAGAACCTCA
131 AGCCACCCAT-GAAGCCATTCCCCGGTGACAAACCATCAAAGGGTAAGGGAAAGGGAGAACCTCA
87071 TGAACCC
195 TGAACCC
*
87078 AAACCTCCTCATAGACACCTATTGAGTGTGGAAGTTGATGGCACACATAAACCTCCACAACACTC
1 AAACCTCCTCATAGACACCTATTGAGTGTGGAAGTTGAGGGCACACATAAACCTCCACAACACTC
* * *
87143 AGGTGGTAAACCTCCACGACATTCAGGGGGTAAACCTCCACATGTTGAAGGATTCCCCGATGGTA
66 AGGTGGTAAACCTCCACGACACTCAGGGGGTAAACCTCCACATGTTGAAGGATTCCCTGCTGGTA
* *
87208 AGCCGCCCATGAAGCCATTCCCCGGTGACAAACCATCAAAGGGTAAGGGAAAGGGAGAACCCCAT
131 AGCCACCCATGAAGCCATTCCCCGGTGACAAACCATCAAAGGGTAAGGGAAAGGGAGAACCTCAT
87273 GAACCC
196 GAACCC
*
87279 AAACCTCCTCATAGACACCTATTGAGTGTGGAAGTTGAGGGCACACATAAACCTCCAAAACACTC
1 AAACCTCCTCATAGACACCTATTGAGTGTGGAAGTTGAGGGCACACATAAACCTCCACAACACTC
*
87344 AGGTGGTAAACCTCCACGACACTCAGGGGGTAAACCTCCACATGTTGAAGGATTCCCTTAC-GGT
66 AGGTGGTAAACCTCCACGACACTCAGGGGGTAAACCTCCACATGTTGAAGGATTCCC-TGCTGGT
* ** *
87408 AAGCCACCCATGAAGCCATTTCCCGGTGACAAACCATCCCAGGGTAAGGGAAAGGGAGCACCTCA
130 AAGCCACCCATGAAGCCATTCCCCGGTGACAAACCATCAAAGGGTAAGGGAAAGGGAGAACCTCA
87473 TGAACCC
195 TGAACCC
87480 AAACCTCCTCATAGACACCT
1 AAACCTCCTCATAGACACCT
87500 CTTAAGTGAG
Statistics
Matches: 583, Mismatches: 37, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
200 1 0.00
201 581 1.00
202 1 0.00
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.18
Consensus pattern (201 bp):
AAACCTCCTCATAGACACCTATTGAGTGTGGAAGTTGAGGGCACACATAAACCTCCACAACACTC
AGGTGGTAAACCTCCACGACACTCAGGGGGTAAACCTCCACATGTTGAAGGATTCCCTGCTGGTA
AGCCACCCATGAAGCCATTCCCCGGTGACAAACCATCAAAGGGTAAGGGAAAGGGAGAACCTCAT
GAACCC
Found at i:87157 original size:24 final size:24
Alignment explanation
Indices: 87125--87184 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
87115 ATGGCACACA
*
87125 TAAACCTCCACAACACTCAGGTGG
1 TAAACCTCCACAACACTCAGGGGG
* *
87149 TAAACCTCCACGACATTCAGGGGG
1 TAAACCTCCACAACACTCAGGGGG
87173 TAAACCTCCACA
1 TAAACCTCCACA
87185 TGTTGAAGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.33, C:0.33, G:0.17, T:0.17
Consensus pattern (24 bp):
TAAACCTCCACAACACTCAGGGGG
Found at i:87384 original size:24 final size:24
Alignment explanation
Indices: 87326--87385 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
87316 AGGGCACACA
* *
87326 TAAACCTCCAAAACACTCAGGTGG
1 TAAACCTCCACAACACTCAGGGGG
*
87350 TAAACCTCCACGACACTCAGGGGG
1 TAAACCTCCACAACACTCAGGGGG
87374 TAAACCTCCACA
1 TAAACCTCCACA
87386 TGTTGAAGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.35, C:0.33, G:0.17, T:0.15
Consensus pattern (24 bp):
TAAACCTCCACAACACTCAGGGGG
Found at i:88902 original size:24 final size:23
Alignment explanation
Indices: 88875--88921 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
88865 ATTATACTAC
88875 TAAT-TTTATATTTAAAAATTATTA
1 TAATATTTA-ATTT-AAAATTATTA
*
88899 TAATATTTAATTTAGAATTATTA
1 TAATATTTAATTTAAAATTATTA
88922 ATTAAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 9 0.43
24 8 0.38
25 4 0.19
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TAATATTTAATTTAAAATTATTA
Found at i:88995 original size:18 final size:18
Alignment explanation
Indices: 88953--88986 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
88943 AGAAGTTTCC
88953 ATAATTACACATTTAAAA
1 ATAATTACACATTTAAAA
*
88971 ATAATTAGA-ATTTAAA
1 ATAATTACACATTTAAA
88987 TTATAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (18 bp):
ATAATTACACATTTAAAA
Found at i:89663 original size:176 final size:177
Alignment explanation
Indices: 89474--89823 Score: 549
Period size: 177 Copynumber: 2.0 Consensus size: 177
89464 AAATTACATC
* *
89474 TAAAAATAATTATAATTTAATTGAAAATTATTAGTTAAAAAATTTAACGTAGAAATAAATTGTGT
1 TAAAAATAATTATAATTTAATTGAAAATTATTAGTTAAAAAATTTAACGTAGAAAAAAATTGTGC
*
89539 TAATTTTAAATTTTTAAAA-ATTGTGCAAATTTTATTGATATAAAATAGAGTTATTATTTAAATA
66 TAATTTTAAATTTTTAAAATATTGTGCAAATTTTATTGATATAAAATAGAGTTATTATTTAAACA
* *
89603 GAAGTCTAAGAATAATTTATTTTTCATTATATTCTTAAATTGATGTT
131 AAACTCTAAGAATAATTTATTTTTCATTATATTCTTAAATTGATGTT
* * * *
89650 TAAAAATAATTATAATTTAATTTAAATTTATTAGTTAAAAATTTTAAGGTAGAAAAAAATTGTGC
1 TAAAAATAATTATAATTTAATTGAAAATTATTAGTTAAAAAATTTAACGTAGAAAAAAATTGTGC
* * * * *
89715 TAATTTTAATTTTTTAAAATTTTGTGCAAATTTTATTGATATAAAATAGGGTTATTATTTGAGCA
66 TAATTTTAAATTTTTAAAATATTGTGCAAATTTTATTGATATAAAATAGAGTTATTATTTAAACA
* *
89780 AAACTCTAAGAATAATTTATTTTTCATTATATTTTTTAATTGAT
131 AAACTCTAAGAATAATTTATTTTTCATTATATTCTTAAATTGAT
89824 ATTTTAATTA
Statistics
Matches: 157, Mismatches: 16, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
176 77 0.49
177 80 0.51
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.45
Consensus pattern (177 bp):
TAAAAATAATTATAATTTAATTGAAAATTATTAGTTAAAAAATTTAACGTAGAAAAAAATTGTGC
TAATTTTAAATTTTTAAAATATTGTGCAAATTTTATTGATATAAAATAGAGTTATTATTTAAACA
AAACTCTAAGAATAATTTATTTTTCATTATATTCTTAAATTGATGTT
Done.