Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002991.1 Kokia drynarioides strain JFW-HI SEQ_115480, 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: 77957
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.35
Warning! 67 characters in sequence are not A, C, G, or T
Found at i:12257 original size:21 final size:21
Alignment explanation
Indices: 12218--12257 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12208 TCAGAAGCTA
*
12218 TGTCCTCTTTTTTAATTGAAT
1 TGTCCTCTTTTGTAATTGAAT
* *
12239 TGTCTTCTTTTGTAGTTGA
1 TGTCCTCTTTTGTAATTGA
12258 GAGTTCTCCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.57
Consensus pattern (21 bp):
TGTCCTCTTTTGTAATTGAAT
Found at i:20643 original size:24 final size:24
Alignment explanation
Indices: 20615--20685 Score: 88
Period size: 24 Copynumber: 3.0 Consensus size: 24
20605 AGAAATAATC
*
20615 TTTCAGTTAAACTCTTTTTATTTG
1 TTTCAGTTAAACTCTTTTTAGTTG
* *
20639 TTTCAATTAAACTCTATTTAGTTG
1 TTTCAGTTAAACTCTTTTTAGTTG
* * *
20663 TTTGAGTCAAACTCTTATTAGTT
1 TTTCAGTTAAACTCTTTTTAGTT
20686 TAGATTATTT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.25, C:0.13, G:0.10, T:0.52
Consensus pattern (24 bp):
TTTCAGTTAAACTCTTTTTAGTTG
Found at i:27697 original size:17 final size:17
Alignment explanation
Indices: 27675--27708 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
27665 GAAAGCGCAG
27675 CTAAAGGTCAGAGCATT
1 CTAAAGGTCAGAGCATT
*
27692 CTAAAGGTTAGAGCATT
1 CTAAAGGTCAGAGCATT
27709 AGCAGCGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (17 bp):
CTAAAGGTCAGAGCATT
Found at i:27774 original size:24 final size:24
Alignment explanation
Indices: 27726--27770 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
27716 TTTATGGAAA
*
27726 AGCGCCGCTAAAGATTAGAGCATT
1 AGCGCCGCTAAAAATTAGAGCATT
27750 AGCGCCGCTAAAAATTA-AGCA
1 AGCGCCGCTAAAAATTAGAGCA
27771 ATTATTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (24 bp):
AGCGCCGCTAAAAATTAGAGCATT
Found at i:27832 original size:37 final size:34
Alignment explanation
Indices: 27790--27894 Score: 133
Period size: 34 Copynumber: 3.0 Consensus size: 34
27780 AAAAAAATTT
*
27790 AAACTTATATAAACTAATAATATTAAACATTATTTTA
1 AAACTTATATAAACTAA-AAAATT-AA-ATTATTTTA
27827 AAACTTATATAAACTTAAAAAATTCAAA--ATTTTA
1 AAACTTATATAAAC-TAAAAAATT-AAATTATTTTA
27861 AAACTTATATAAACTAAAAAAATTAAATTATTTT
1 AAACTTATATAAACT-AAAAAATTAAATTATTTT
27895 GGTTTTATGT
Statistics
Matches: 62, Mismatches: 2, Indels: 10
0.84 0.03 0.14
Matches are distributed among these distances:
33 4 0.06
34 28 0.45
35 5 0.08
36 1 0.02
37 21 0.34
38 3 0.05
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (34 bp):
AAACTTATATAAACTAAAAAATTAAATTATTTTA
Found at i:30989 original size:43 final size:43
Alignment explanation
Indices: 30941--31038 Score: 135
Period size: 43 Copynumber: 2.3 Consensus size: 43
30931 ATTAGTAGCA
* * *
30941 TTTGTGGGAAAAATACCGCTAAAGACCATGTTCTTTAGCGGCG
1 TTTGTGGGAAAAACACCACTAAAGACCATGGTCTTTAGCGGCG
* * *
30984 TTTGTGGGAAAAGCGCCATTAAAGACCATGGTCTTTAGCGGCG
1 TTTGTGGGAAAAACACCACTAAAGACCATGGTCTTTAGCGGCG
31027 TTTGT-GGAAAAA
1 TTTGTGGGAAAAA
31039 GCGCGGTGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 6 0.12
43 42 0.88
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (43 bp):
TTTGTGGGAAAAACACCACTAAAGACCATGGTCTTTAGCGGCG
Found at i:31039 original size:43 final size:43
Alignment explanation
Indices: 30960--31042 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
30950 AAAATACCGC
* *
30960 TAAAGACCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCAT
1 TAAAGACCATGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCAT
31003 TAAAGACCATGGTCTTTAGCGGCGTTTGTGGAAAAAGCGC
1 TAAAGACCATGGTCTTTAGCGGCGTTTGTGGAAAAAGCGC
31043 GGTGTTTGTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (43 bp):
TAAAGACCATGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCAT
Found at i:31059 original size:19 final size:20
Alignment explanation
Indices: 31021--31061 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
31011 ATGGTCTTTA
31021 GCGGCGTTTGTGGAAAAAGC
1 GCGGCGTTTGTGGAAAAAGC
*
31041 GCGGTGTTTGTGG-AAAAGC
1 GCGGCGTTTGTGGAAAAAGC
31060 GC
1 GC
31062 CGCTAAAGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.22, C:0.15, G:0.41, T:0.22
Consensus pattern (20 bp):
GCGGCGTTTGTGGAAAAAGC
Found at i:31639 original size:16 final size:16
Alignment explanation
Indices: 31601--31640 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
31591 TTGAAAATAC
*
31601 ATATTCCAAACACCCA
1 ATATTCTAAACACCCA
31617 ATATTCTAAACACCCA
1 ATATTCTAAACACCCA
31633 ATATTCTA
1 ATATTCTA
31641 TGATAAAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (16 bp):
ATATTCTAAACACCCA
Found at i:32273 original size:35 final size:35
Alignment explanation
Indices: 32232--32317 Score: 154
Period size: 35 Copynumber: 2.5 Consensus size: 35
32222 TTCGAATTCG
* *
32232 AAAATTCAACTCGATTCGAACTCGAAATTTGAAAA
1 AAAATTCAACTTGATTCGAACTCGAAATTCGAAAA
32267 AAAATTCAACTTGATTCGAACTCGAAATTCGAAAA
1 AAAATTCAACTTGATTCGAACTCGAAATTCGAAAA
32302 AAAATTCAACTTGATT
1 AAAATTCAACTTGATT
32318 TGTTTAACTC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 49 1.00
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.28
Consensus pattern (35 bp):
AAAATTCAACTTGATTCGAACTCGAAATTCGAAAA
Found at i:32727 original size:15 final size:15
Alignment explanation
Indices: 32707--32738 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
32697 ATGCATTGAC
*
32707 TTTTGGGTGTTTGGA
1 TTTTGGATGTTTGGA
32722 TTTTGGATGTTTGGA
1 TTTTGGATGTTTGGA
32737 TT
1 TT
32739 ATGTATTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.09, C:0.00, G:0.34, T:0.56
Consensus pattern (15 bp):
TTTTGGATGTTTGGA
Found at i:35712 original size:9 final size:9
Alignment explanation
Indices: 35698--35781 Score: 56
Period size: 9 Copynumber: 9.6 Consensus size: 9
35688 ACATGTGGTA
35698 AAAAATTAT
1 AAAAATTAT
35707 -AAAA--AT
1 AAAAATTAT
35713 -AAAATTCAT
1 AAAAATT-AT
35722 AAAAA-TATT
1 AAAAATTA-T
**
35731 AAATTTTAAT
1 AAAAATT-AT
35741 ATAAAA-TAT
1 A-AAAATTAT
35750 AAAAATTAT
1 AAAAATTAT
35759 AAAAA-TAGT
1 AAAAATTA-T
35768 AAAAATTAT
1 AAAAATTAT
35777 AAAAA
1 AAAAA
35782 AAACGTAAAC
Statistics
Matches: 60, Mismatches: 4, Indels: 22
0.70 0.05 0.26
Matches are distributed among these distances:
6 6 0.10
8 11 0.18
9 30 0.50
10 10 0.17
11 3 0.05
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:35723 original size:15 final size:14
Alignment explanation
Indices: 35699--35755 Score: 55
Period size: 15 Copynumber: 4.0 Consensus size: 14
35689 CATGTGGTAA
35699 AAAATTATAAAAAT
1 AAAATTATAAAAAT
35713 AAAATTCATAAAAAT
1 AAAATT-ATAAAAAT
* *
35728 ATTAAATT-TTAATAT
1 A--AAATTATAAAAAT
35743 AAAA-TATAAAAAT
1 AAAATTATAAAAAT
35756 TATAAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
12 1 0.03
13 8 0.23
14 6 0.17
15 15 0.43
17 5 0.14
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAATTATAAAAAT
Found at i:35772 original size:18 final size:17
Alignment explanation
Indices: 35698--35781 Score: 84
Period size: 18 Copynumber: 4.8 Consensus size: 17
35688 ACATGTGGTA
35698 AAAAATTAT-AAAA-AT
1 AAAAATTATAAAAATAT
35713 -AAAATTCATAAAAATATT
1 AAAAATT-ATAAAAATA-T
**
35731 AAATTTTAATATAAAATAT
1 AAAAATT-ATA-AAAATAT
35750 AAAAATTATAAAAATAGT
1 AAAAATTATAAAAATA-T
35768 AAAAATTATAAAAA
1 AAAAATTATAAAAA
35782 AAACGTAAAC
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
14 6 0.11
15 2 0.04
16 4 0.07
17 7 0.12
18 19 0.33
19 13 0.23
20 6 0.11
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (17 bp):
AAAAATTATAAAAATAT
Found at i:36042 original size:30 final size:29
Alignment explanation
Indices: 36004--36078 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 29
35994 TTAATACGAT
* *
36004 TATTTTATAATTTTTTACAATTTTTTTTA
1 TATTTTATAATTTTTTACAACTTTTTTAA
**
36033 TATTTTTATAATTTTCTTATGACTTTTTTAA
1 TA-TTTTATAATTTT-TTACAACTTTTTTAA
*
36064 TATTTTAAAATTTTT
1 TATTTTATAATTTTT
36079 CTATATTTCT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
29 3 0.08
30 23 0.59
31 13 0.33
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (29 bp):
TATTTTATAATTTTTTACAACTTTTTTAA
Found at i:36507 original size:93 final size:94
Alignment explanation
Indices: 36353--36525 Score: 201
Period size: 93 Copynumber: 1.9 Consensus size: 94
36343 GGGGCTTAAA
* * *
36353 TGCTTTTTAGAAAAAGTTTGAAAGTATTTTTTATGTATTTTAAAAATTCAAGTATCCAATTGA-C
1 TGCTTTTTAGAAAAAGTTTGAAAGTATTTTTAATATATTTTAAAAATTCAAATATCCAATTGAGC
36417 AGTAAAAAAA-AAAAAGCAGGAGACATAAT
66 A-TAAAAAAATAAAAAGCAGGAGACATAAT
* * * * * *
36446 TGCTTTTTTGAAAAAGTTTGAAGGCT-TTTTTAATATATTTTGACAATTTAAATA-CTTAATTGA
1 TGCTTTTTAGAAAAAGTTTGAAAG-TATTTTTAATATATTTTAAAAATTCAAATATC-CAATTGA
*
36509 GTATAAAAAAATAAAAA
64 GCATAAAAAAATAAAAA
36526 ACTTAATTAC
Statistics
Matches: 66, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
92 1 0.02
93 58 0.88
94 7 0.11
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (94 bp):
TGCTTTTTAGAAAAAGTTTGAAAGTATTTTTAATATATTTTAAAAATTCAAATATCCAATTGAGC
ATAAAAAAATAAAAAGCAGGAGACATAAT
Found at i:37067 original size:17 final size:16
Alignment explanation
Indices: 37041--37086 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
37031 AAAAATTTTT
37041 AATAA-ATAAAATGTAA
1 AATAATATAAAAT-TAA
37057 AA-AATATTAAATATTAA
1 AATAATA-TAAA-ATTAA
37074 AATAATATAAAAT
1 AATAATATAAAAT
37087 AAATATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
15 2 0.08
16 5 0.19
17 13 0.50
18 6 0.23
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (16 bp):
AATAATATAAAATTAA
Found at i:37080 original size:18 final size:17
Alignment explanation
Indices: 37054--37087 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
37044 AAATAAAATG
*
37054 TAAAAAATATTAAATAT
1 TAAAAAATATAAAATAT
37071 TAAAATAATATAAAATA
1 TAAAA-AATATAAAATA
37088 AATATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAAAATATAAAATAT
Found at i:39452 original size:27 final size:27
Alignment explanation
Indices: 39422--39473 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
39412 AAAATGCAGA
* *
39422 TTTTTCTTAATTTTTATGGGATTAGTT
1 TTTTTCTTAATATTTATAGGATTAGTT
* *
39449 TTTTTTTTAATATTTGTAGGATTAG
1 TTTTTCTTAATATTTATAGGATTAG
39474 GCCAATTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.21, C:0.02, G:0.15, T:0.62
Consensus pattern (27 bp):
TTTTTCTTAATATTTATAGGATTAGTT
Found at i:39635 original size:40 final size:40
Alignment explanation
Indices: 39547--39635 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
39537 GAGTTGGACA
* *
39547 CATTTTCCTGCTCTATCAACAAAATGCTTTCAGATGTACG
1 CATTTTTCTGCTCTATCAACAAAATGCTTCCAGATGTACG
* * * * *
39587 CGTCTTTCTGCTCTATTAACAAAATGCTTCCAGTTGTATG
1 CATTTTTCTGCTCTATCAACAAAATGCTTCCAGATGTACG
*
39627 TATTTTTCT
1 CATTTTTCT
39636 TTCCTCTTTC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.42
Consensus pattern (40 bp):
CATTTTTCTGCTCTATCAACAAAATGCTTCCAGATGTACG
Found at i:41383 original size:16 final size:16
Alignment explanation
Indices: 41362--41392 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41352 ACATGTGAGC
41362 TGCACACCTAGCAAGT
1 TGCACACCTAGCAAGT
*
41378 TGCACACCTGGCAAG
1 TGCACACCTAGCAAG
41393 CCATACATGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.32, G:0.23, T:0.16
Consensus pattern (16 bp):
TGCACACCTAGCAAGT
Found at i:42649 original size:13 final size:13
Alignment explanation
Indices: 42633--42657 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42623 GGTGGTAAAT
42633 TAAGGTATGAAAA
1 TAAGGTATGAAAA
42646 TAAGGTATGAAA
1 TAAGGTATGAAA
42658 TTATTTACTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (13 bp):
TAAGGTATGAAAA
Found at i:47079 original size:24 final size:23
Alignment explanation
Indices: 47052--47097 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
47042 CCCGCCCCCG
47052 ATTTATAATACTAATTTTATTTTT
1 ATTTATAATACTAATTTT-TTTTT
*
47076 ATTTTTAATACTAATTTTTTTT
1 ATTTATAATACTAATTTTTTTT
47098 ACTTGTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (23 bp):
ATTTATAATACTAATTTTTTTTT
Found at i:47106 original size:22 final size:24
Alignment explanation
Indices: 47057--47107 Score: 70
Period size: 22 Copynumber: 2.2 Consensus size: 24
47047 CCCCGATTTA
* *
47057 TAATACTAATTTTATTTTTATTTT
1 TAATACTAATTTTATTTTTACTTG
47081 TAATACTAA-TTT-TTTTTACTTG
1 TAATACTAATTTTATTTTTACTTG
47103 TAATA
1 TAATA
47108 ATGATTGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 13 0.52
23 3 0.12
24 9 0.36
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (24 bp):
TAATACTAATTTTATTTTTACTTG
Found at i:54389 original size:23 final size:23
Alignment explanation
Indices: 54363--54426 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
54353 TTCATTTAAC
54363 TTAATTGAACATGTTCACAAACA
1 TTAATTGAACATGTTCACAAACA
** *
54386 TTAAACGAACATGTTCACGAACA
1 TTAATTGAACATGTTCACAAACA
*
54409 TATAATTAAACATGTTCA
1 T-TAATTGAACATGTTCA
54427 TGAACAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 21 0.62
24 13 0.38
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.30
Consensus pattern (23 bp):
TTAATTGAACATGTTCACAAACA
Found at i:56296 original size:22 final size:22
Alignment explanation
Indices: 56257--56301 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
56247 ATTTTTGAAT
*
56257 TAAAATTTAATTATAAAATATA
1 TAAAATTAAATTATAAAATATA
56279 TAAAATATAAATTA-AAAATATA
1 TAAAAT-TAAATTATAAAATATA
56301 T
1 T
56302 TTTTAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAAATTAAATTATAAAATATA
Found at i:57343 original size:19 final size:19
Alignment explanation
Indices: 57316--57359 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
57306 TTATCAGTGA
* * *
57316 AGTAAAGATGCATCTATGT
1 AGTATAGATACATCTATGC
57335 AGTATAGATACATCTATGC
1 AGTATAGATACATCTATGC
57354 AGTATA
1 AGTATA
57360 CCACCCATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (19 bp):
AGTATAGATACATCTATGC
Found at i:63149 original size:40 final size:40
Alignment explanation
Indices: 63099--63235 Score: 163
Period size: 40 Copynumber: 3.5 Consensus size: 40
63089 TTTGAAAGAG
*
63099 GGTACCGATATTTTTCAAATATTATCGATACCTTTATCAT
1 GGTATCGATATTTTTCAAATATTATCGATACCTTTATCAT
* * ** *
63139 GGTATTGATATTTTTCAGATATTATCGATA-CTGAAATCTT
1 GGTATCGATATTTTTCAAATATTATCGATACCT-TTATCAT
*
63179 GGTATCGATATTTATCAAATATTATCGATACCTTTGA--AT
1 GGTATCGATATTTTTCAAATATTATCGATACCTTT-ATCAT
*
63218 GGGATCGATATTTTTCAA
1 GGTATCGATATTTTTCAA
63236 CTGTTTCAAA
Statistics
Matches: 80, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
39 19 0.24
40 58 0.73
41 3 0.04
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (40 bp):
GGTATCGATATTTTTCAAATATTATCGATACCTTTATCAT
Found at i:65577 original size:10 final size:9
Alignment explanation
Indices: 65552--65579 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
65542 TCGTAAGAAT
65552 GGGTTTTTG
1 GGGTTTTTG
65561 GGGTTTTTG
1 GGGTTTTTG
65570 GGGTTTTTG
1 GGGTTTTTG
65579 G
1 G
65580 TGAATGTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.46, T:0.54
Consensus pattern (9 bp):
GGGTTTTTG
Found at i:65729 original size:41 final size:40
Alignment explanation
Indices: 65649--65739 Score: 103
Period size: 41 Copynumber: 2.2 Consensus size: 40
65639 TTTTTCCCCG
* *
65649 AGTATCGATAATTTTGTAAAATTATCGATACCTTAAAAAC
1 AGTATCGATAATTTTGTAAAAATATCGATAACTTAAAAAC
* * * *
65689 GGGTATCGAT-ATTTTTTGAAAAATATCGATAATTTTAAAAC
1 -AGTATCGATAATTTTGT-AAAAATATCGATAACTTAAAAAC
65730 AGTATCGATA
1 AGTATCGATA
65740 CCAAATCTGC
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
40 14 0.34
41 27 0.66
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (40 bp):
AGTATCGATAATTTTGTAAAAATATCGATAACTTAAAAAC
Found at i:65735 original size:20 final size:20
Alignment explanation
Indices: 65649--65739 Score: 64
Period size: 20 Copynumber: 4.5 Consensus size: 20
65639 TTTTTCCCCG
*
65649 AGTATCGATAATTTTGTAAA
1 AGTATCGATAATTTTGAAAA
* **
65669 ATTATCGAT-ACCTT-AAAA
1 AGTATCGATAATTTTGAAAA
*
65687 ACGGGTATCGATATTTTTTGAAAA
1 A---GTATCGATA-ATTTTGAAAA
65711 A-TATCGATAATTTT-AAAA
1 AGTATCGATAATTTTGAAAA
65729 CAGTATCGATA
1 -AGTATCGATA
65740 CCAAATCTGC
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
18 8 0.15
19 8 0.15
20 24 0.44
21 7 0.13
23 2 0.04
24 5 0.09
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (20 bp):
AGTATCGATAATTTTGAAAA
Found at i:72440 original size:40 final size:40
Alignment explanation
Indices: 72355--72453 Score: 130
Period size: 40 Copynumber: 2.5 Consensus size: 40
72345 TTTTGAAAGA
* * *
72355 GGGTATCAAAATTTTTCAAATATTTTCGATACCTTTATCAT
1 GGGTATCGATATTTTTCAAATATTATCGATACCTTTA-CAT
*
72396 -GGTATCGATATTTATCAAATATTATCGATACCTTTGA-AT
1 GGGTATCGATATTTTTCAAATATTATCGATACCTTT-ACAT
72435 GGGTATCGATATTTTTCAA
1 GGGTATCGATATTTTTCAA
72454 CTGTTTCAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
39 2 0.04
40 48 0.94
41 1 0.02
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.42
Consensus pattern (40 bp):
GGGTATCGATATTTTTCAAATATTATCGATACCTTTACAT
Found at i:76670 original size:47 final size:48
Alignment explanation
Indices: 76561--76681 Score: 113
Period size: 50 Copynumber: 2.5 Consensus size: 48
76551 TTTTTTACTT
* * * * *
76561 TTTTTATAA-ATTTAAAATTTAATAATTTTATTTTTAAGAATATTTAGA
1 TTTTTATAATATTTAAAAATTAA-AACTTAATTATTAAGAATATTTACA
* * *
76609 TTTTTATTGTATATTTAAAAATTAAAACTTAATTATTAATATTA-TTACA
1 TTTTTA-T-AATATTTAAAAATTAAAACTTAATTATTAAGAATATTTACA
*
76658 TTTTTATAATATTTTAAAA-TAAAA
1 TTTTTATAATATTTAAAAATTAAAA
76682 TAAAAAAACA
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
46 5 0.08
47 10 0.17
48 7 0.12
49 11 0.18
50 15 0.25
51 12 0.20
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (48 bp):
TTTTTATAATATTTAAAAATTAAAACTTAATTATTAAGAATATTTACA
Done.