Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007016.1 Kokia drynarioides strain JFW-HI SEQ_121622, 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: 49097
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1736 original size:27 final size:27
Alignment explanation
Indices: 1685--1832 Score: 120
Period size: 27 Copynumber: 5.4 Consensus size: 27
1675 ATTCAATAAG
* ** *
1685 TCTGGCTCGAAAGAGCGATGCTCTATT
1 TCTGGCTCGAAAGAGCAATATTCTATA
*
1712 TCTGGCTCGAAAGAGAAATATTCTATA
1 TCTGGCTCGAAAGAGCAATATTCTATA
* ** *
1739 TCTAGCTTAAAAGAGCAATATTC-AGTT
1 TCTGGCTCGAAAGAGCAATATTCTA-TA
* *
1766 TCTGGCTCAAAAGAGCAATATTTTGA-A
1 TCTGGCTCGAAAGAGCAATATTCT-ATA
* * *
1793 CTCTGGCTCGGAAGAGCATTATTCTGTA
1 -TCTGGCTCGAAAGAGCAATATTCTATA
*
1821 TCTGACTCGAAA
1 TCTGGCTCGAAA
1833 TATCATTATT
Statistics
Matches: 95, Mismatches: 21, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
26 1 0.01
27 72 0.76
28 21 0.22
29 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (27 bp):
TCTGGCTCGAAAGAGCAATATTCTATA
Found at i:3259 original size:37 final size:38
Alignment explanation
Indices: 3162--3259 Score: 94
Period size: 38 Copynumber: 2.6 Consensus size: 38
3152 ATTTTCGGAA
* * *
3162 TGCACCCAAGATTGTTGCTGTATAAATATTCTTCAAAT
1 TGCACCCAAGAATGTTGTTGCATAAATATTCTTCAAAT
* * * *
3200 TGCATCCAA-AACTATT-TCTGCATAAGTATTCTT-TAAT
1 TGCACCCAAGAA-TGTTGT-TGCATAAATATTCTTCAAAT
3237 TGCACCCAAGAATGTTGTTGCAT
1 TGCACCCAAGAATGTTGTTGCAT
3260 GAACATGTCC
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
37 20 0.43
38 27 0.57
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (38 bp):
TGCACCCAAGAATGTTGTTGCATAAATATTCTTCAAAT
Found at i:3763 original size:32 final size:32
Alignment explanation
Indices: 3727--3791 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
3717 GATATACTGT
3727 TGATGTTGGGATTTATATGATATCTATTTCAA
1 TGATGTTGGGATTTATATGATATCTATTTCAA
3759 TGATGTTGGGATTTATATGATATCTATTTCAA
1 TGATGTTGGGATTTATATGATATCTATTTCAA
3791 T
1 T
3792 CTTGCTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.28, C:0.06, G:0.18, T:0.48
Consensus pattern (32 bp):
TGATGTTGGGATTTATATGATATCTATTTCAA
Found at i:3778 original size:17 final size:17
Alignment explanation
Indices: 3727--3779 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
3717 GATATACTGT
3727 TGATGTTGGGATTTATA
1 TGATGTTGGGATTTATA
*
3744 TGATATCT---ATTTCA-A
1 TGATGT-TGGGATTT-ATA
3759 TGATGTTGGGATTTATA
1 TGATGTTGGGATTTATA
3776 TGAT
1 TGAT
3780 ATCTATTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
14 1 0.04
15 10 0.36
16 2 0.07
17 14 0.50
18 1 0.04
ACGTcount: A:0.26, C:0.04, G:0.23, T:0.47
Consensus pattern (17 bp):
TGATGTTGGGATTTATA
Found at i:4158 original size:16 final size:16
Alignment explanation
Indices: 4139--4173 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
4129 TTTTAATATC
4139 ATTACATTTTACCTTT
1 ATTACATTTTACCTTT
*
4155 ATTACATTTTATCTTT
1 ATTACATTTTACCTTT
4171 ATT
1 ATT
4174 TTCATATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.14, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTACATTTTACCTTT
Found at i:9422 original size:54 final size:54
Alignment explanation
Indices: 9331--9476 Score: 150
Period size: 54 Copynumber: 2.7 Consensus size: 54
9321 AATCAAATAT
*
9331 CATATAGTGTAAGACATAGTCTGGTGACTATGACATCATATAAGGAATGAAGAC
1 CATATAGTGTAAGACATAGTCTGGTGACTATGACATCATATAAGGAATGAAAAC
* * ** * *
9385 CATATA-TAGTAAGACCTAGTTTGGTGGTTATGGCATCATATGAGGAATGAAAAC
1 CATATAGT-GTAAGACATAGTCTGGTGACTATGACATCATATAAGGAATGAAAAC
* * * * * *
9439 CACATCGTATAAGAAATAGTCATGGTGATTATGGCATC
1 CATATAGTGTAAGACATAGTC-TGGTGACTATGACATC
9477 GTATGGAAGA
Statistics
Matches: 75, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
53 1 0.01
54 58 0.77
55 16 0.21
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (54 bp):
CATATAGTGTAAGACATAGTCTGGTGACTATGACATCATATAAGGAATGAAAAC
Found at i:9668 original size:29 final size:28
Alignment explanation
Indices: 9589--9707 Score: 125
Period size: 29 Copynumber: 4.1 Consensus size: 28
9579 ATTTTTCGTA
* *
9589 AAAGTGAAGCCTTAGTGGCTAATTTTGTT
1 AAAGTGAAGCCTTA-TGGCTGATTCTGTT
* *
9618 AAAATG-AGCCTTTGTGGCTGATTCTGTT
1 AAAGTGAAGCC-TTATGGCTGATTCTGTT
*
9646 AAAGTGAAGCCTTCATGGATGATTCTGTT
1 AAAGTGAAGCCTT-ATGGCTGATTCTGTT
*
9675 AAAGTGAAGCCTTTGTGGCTGACTT-TGTT
1 AAAGTGAAGCC-TTATGGCTGA-TTCTGTT
9704 AAAG
1 AAAG
9708 GGGCCTTTGT
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
28 23 0.30
29 49 0.64
30 4 0.05
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (28 bp):
AAAGTGAAGCCTTATGGCTGATTCTGTT
Found at i:9677 original size:57 final size:58
Alignment explanation
Indices: 9589--9707 Score: 163
Period size: 57 Copynumber: 2.1 Consensus size: 58
9579 ATTTTTCGTA
* *
9589 AAAGTGAAGCCTTAGTGGCTAATTTTGTTAAAATG-AGCCTTTGTGGCTGA-TTCTGTT
1 AAAGTGAAGCCTTAGTGGATAATTCTGTTAAAATGAAGCCTTTGTGGCTGACTT-TGTT
* *
9646 AAAGTGAAGCCTTCA-TGGATGATTCTGTTAAAGTGAAGCCTTTGTGGCTGACTTTGTT
1 AAAGTGAAGCCTT-AGTGGATAATTCTGTTAAAATGAAGCCTTTGTGGCTGACTTTGTT
9704 AAAG
1 AAAG
9708 GGGCCTTTGT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
57 29 0.53
58 24 0.44
59 2 0.04
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (58 bp):
AAAGTGAAGCCTTAGTGGATAATTCTGTTAAAATGAAGCCTTTGTGGCTGACTTTGTT
Found at i:14554 original size:17 final size:17
Alignment explanation
Indices: 14532--14585 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
14522 AGATTTAAAC
14532 AAATATATAAAAAAATT
1 AAATATATAAAAAAATT
* *
14549 AAATATACAAAAAATATA
1 AAATATATAAAAAA-ATT
*
14567 AAAGATTAATAAAAAAATT
1 AAATA-T-ATAAAAAAATT
14586 CTAAATTTGC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 13 0.45
18 6 0.21
19 3 0.10
20 7 0.24
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (17 bp):
AAATATATAAAAAAATT
Found at i:15135 original size:20 final size:20
Alignment explanation
Indices: 15111--15191 Score: 76
Period size: 20 Copynumber: 4.0 Consensus size: 20
15101 ATTATATTGT
*
15111 TGTTTTGATGCTTTTTTTAT
1 TGTTTTGATGCTTTTTTTAC
* *
15131 TGTTTTGGTTGCTCTTTTTTGC
1 TGTTTT-GATGCT-TTTTTTAC
15153 TGTTTTTGTAT--TTTTTTTAC
1 TG-TTTTG-ATGCTTTTTTTAC
*
15173 TGTTTTGGTGCTTTTTTTA
1 TGTTTTGATGCTTTTTTTA
15192 AACGTTTTGG
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
18 1 0.02
19 5 0.10
20 23 0.47
21 6 0.12
22 9 0.18
23 5 0.10
ACGTcount: A:0.06, C:0.07, G:0.17, T:0.69
Consensus pattern (20 bp):
TGTTTTGATGCTTTTTTTAC
Found at i:15148 original size:21 final size:20
Alignment explanation
Indices: 15110--15149 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
15100 AATTATATTG
*
15110 TTGTTTTGATGCTTTTTTTA
1 TTGTTTTGATGCTCTTTTTA
*
15130 TTGTTTTGGTTGCTCTTTTT
1 TTGTTTT-GATGCTCTTTTT
15150 TGCTGTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.05, C:0.07, G:0.17, T:0.70
Consensus pattern (20 bp):
TTGTTTTGATGCTCTTTTTA
Found at i:15272 original size:12 final size:12
Alignment explanation
Indices: 15214--15272 Score: 59
Period size: 12 Copynumber: 5.0 Consensus size: 12
15204 ATTGTTTTCG
15214 TGTTATTTTTGC
1 TGTTATTTTTGC
*
15226 TGTTATCTTTG-
1 TGTTATTTTTGC
* *
15237 TTTCTATTTTTGA
1 TGT-TATTTTTGC
*
15250 TGTT-GTTTTGC
1 TGTTATTTTTGC
15261 TGTTATTTTTGC
1 TGTTATTTTTGC
15273 GGCTGTTTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
11 11 0.30
12 24 0.65
13 2 0.05
ACGTcount: A:0.08, C:0.08, G:0.17, T:0.66
Consensus pattern (12 bp):
TGTTATTTTTGC
Found at i:15488 original size:16 final size:16
Alignment explanation
Indices: 15467--15498 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
15457 TTTAATGTTT
*
15467 GTTTTAATGTTTTTAA
1 GTTTTAATATTTTTAA
15483 GTTTTAATATTTTTAA
1 GTTTTAATATTTTTAA
15499 ATGTATTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.62
Consensus pattern (16 bp):
GTTTTAATATTTTTAA
Found at i:16465 original size:20 final size:20
Alignment explanation
Indices: 16440--16488 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
16430 CGAACTCTAA
16440 GTACTTCAAGGATAGTTTAG
1 GTACTTCAAGGATAGTTTAG
16460 GTACTTCAAGGATAGTTTAG
1 GTACTTCAAGGATAGTTTAG
16480 GTACTTCAA
1 GTACTTCAA
16489 TATTTTGAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (20 bp):
GTACTTCAAGGATAGTTTAG
Found at i:21058 original size:2 final size:2
Alignment explanation
Indices: 21051--21093 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
21041 ATCATAACAA
* * *
21051 AC AC AC AC AC GC AC GC AC AC AC AC AC AA AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
21093 A
1 A
21094 TATATATATA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.47, G:0.05, T:0.00
Consensus pattern (2 bp):
AC
Found at i:21072 original size:16 final size:16
Alignment explanation
Indices: 21046--21093 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
21036 ATTGTATCAT
* *
21046 AACAAACACACACACG
1 AACACACACACACACA
* *
21062 CACGCACACACACACA
1 AACACACACACACACA
21078 AACACACACACACACA
1 AACACACACACACACA
21094 TATATATATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.52, C:0.44, G:0.04, T:0.00
Consensus pattern (16 bp):
AACACACACACACACA
Found at i:21694 original size:17 final size:17
Alignment explanation
Indices: 21672--21737 Score: 114
Period size: 17 Copynumber: 3.9 Consensus size: 17
21662 ATATAAATGG
*
21672 AAATGCAATGACAATAA
1 AAATGCAGTGACAATAA
21689 AAATGCAGTGACAATAA
1 AAATGCAGTGACAATAA
21706 AAATGCAGTGACAATAA
1 AAATGCAGTGACAATAA
*
21723 AAATGCAGAGACAAT
1 AAATGCAGTGACAAT
21738 TATACTACAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 47 1.00
ACGTcount: A:0.55, C:0.12, G:0.17, T:0.17
Consensus pattern (17 bp):
AAATGCAGTGACAATAA
Found at i:23263 original size:17 final size:17
Alignment explanation
Indices: 23243--23297 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
23233 GGCAAATGGA
*
23243 AATGCAATGACAATGCG
1 AATGCAATGACAATGAG
* * * * *
23260 AATGTAGTGACTATTAA
1 AATGCAATGACAATGAG
23277 AATGCAATGACAATGAG
1 AATGCAATGACAATGAG
23294 AATG
1 AATG
23298 TGATAACAAT
Statistics
Matches: 27, Mismatches: 11, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.24
Consensus pattern (17 bp):
AATGCAATGACAATGAG
Found at i:23751 original size:21 final size:21
Alignment explanation
Indices: 23725--23764 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
23715 TTTGCCTCGA
*
23725 CTTCTT-TTCCTTCCTCTTGTT
1 CTTCTTGTT-CTTCCACTTGTT
23746 CTTCTTGTTCTTCCACTTG
1 CTTCTTGTTCTTCCACTTG
23765 GATTTCCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.03, C:0.33, G:0.07, T:0.57
Consensus pattern (21 bp):
CTTCTTGTTCTTCCACTTGTT
Found at i:31720 original size:43 final size:43
Alignment explanation
Indices: 31658--31872 Score: 245
Period size: 43 Copynumber: 5.0 Consensus size: 43
31648 GAGTGAGATA
* * * * * *
31658 ATAATTTCAATCTACCCCTACTGGATTAAGAGTAAAAGATTGG
1 ATAACTTCAATATGCCCCTACTAGATTAGGGGTAAAAGATTGG
* * *
31701 ATAACTTTAATTTGCCCCTACTAGATTAGGGGTAAAAGACTGG
1 ATAACTTCAATATGCCCCTACTAGATTAGGGGTAAAAGATTGG
** *
31744 ATGGCTTCAATATGCCCCTACTAGGTTAGGGGTAAAAGATTGG
1 ATAACTTCAATATGCCCCTACTAGATTAGGGGTAAAAGATTGG
* *
31787 ATGACTTCAATCTGCCCCTACTAGATTAGGGGTAAAAGATTGG
1 ATAACTTCAATATGCCCCTACTAGATTAGGGGTAAAAGATTGG
* * * *
31830 ATAGCTTCAATCTACCCCT-CTTA-ACTAGGGGTAAAAGATTGG
1 ATAACTTCAATATGCCCCTAC-TAGATTAGGGGTAAAAGATTGG
31872 A
1 A
31873 AAGTGTCTTC
Statistics
Matches: 150, Mismatches: 21, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
42 20 0.13
43 130 0.87
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (43 bp):
ATAACTTCAATATGCCCCTACTAGATTAGGGGTAAAAGATTGG
Found at i:31956 original size:45 final size:45
Alignment explanation
Indices: 31713--32136 Score: 422
Period size: 45 Copynumber: 9.6 Consensus size: 45
31703 AACTTTAATT
* * * *
31713 TGCCCCTACTAGATTAGGGGTAAAAGACTGG-A--TGGCTTCAATA
1 TGCCCCT-CTTGACTAGGGGTAAAAGATTGGAATGTGGCTTCAATC
* ** *
31756 TGCCCCTACTAGGTTAGGGGTAAAAGATTGG-A--TGACTTCAATC
1 TGCCCCT-CTTGACTAGGGGTAAAAGATTGGAATGTGGCTTCAATC
* * *
31799 TGCCCCTACTAGATTAGGGGTAAAAGATTGG-A--TAGCTTCAATC
1 TGCCCCT-CTTGACTAGGGGTAAAAGATTGGAATGTGGCTTCAATC
* * * *
31842 TACCCCTCTTAACTAGGGGTAAAAGATTGGAAAGTGTCTTCAATC
1 TGCCCCTCTTGACTAGGGGTAAAAGATTGGAATGTGGCTTCAATC
* * **
31887 T-ACCCTCTTGACTAGGGGTAAAAGATTGAAATGTGGCTTTTATC
1 TGCCCCTCTTGACTAGGGGTAAAAGATTGGAATGTGGCTTCAATC
** * *
31931 TGCCGTTCTTGATTAGAGGTAAAAGATTGGAA-GATGGCTTCAATC
1 TGCCCCTCTTGACTAGGGGTAAAAGATTGGAATG-TGGCTTCAATC
** *
31976 TGCCCCTCTTGACTAGGGGTAAAAGATTGGACGGTAGCTTCAATC
1 TGCCCCTCTTGACTAGGGGTAAAAGATTGGAATGTGGCTTCAATC
* * *
32021 TGGCCTTCTTGACTA-GGGTAAAAGATTGGAATGTGACTTCAATC
1 TGCCCCTCTTGACTAGGGGTAAAAGATTGGAATGTGGCTTCAATC
* * *
32065 AGCCCCTCTTGATTAGGGGTAAAAGATTGGAATGTGGCTTCAATA
1 TGCCCCTCTTGACTAGGGGTAAAAGATTGGAATGTGGCTTCAATC
* *
32110 TGCCCCTTTTGACTAAGGGTAAAAGAT
1 TGCCCCTCTTGACTAGGGGTAAAAGAT
32137 GTGGCTATAT
Statistics
Matches: 324, Mismatches: 50, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
42 20 0.06
43 86 0.27
44 74 0.23
45 143 0.44
46 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.29
Consensus pattern (45 bp):
TGCCCCTCTTGACTAGGGGTAAAAGATTGGAATGTGGCTTCAATC
Found at i:31972 original size:89 final size:88
Alignment explanation
Indices: 31773--32136 Score: 354
Period size: 89 Copynumber: 4.1 Consensus size: 88
31763 ACTAGGTTAG
* * *
31773 GGGTAAAAGATT-G--GATGACTTCAATCTGCCCCTACTAGATTAGGGGTAAAAGATTGG-A--T
1 GGGTAAAAGATTGGAAGATGACTTCAATCT-ACCCT-CTTGACTAGGGGTAAAAGATTGGAATGT
* ** * *
31832 AGCTTCAATCTACCCCTCTTAACTA
64 GGCTTCAATCTGGCCTTCTTGACTA
* *
31857 GGGGTAAAAGATTGGAA-AGTGTCTTCAATCTACCCTCTTGACTAGGGGTAAAAGATTGAAATGT
1 -GGGTAAAAGATTGGAAGA-TGACTTCAATCTACCCTCTTGACTAGGGGTAAAAGATTGGAATGT
** *
31921 GGCTTTTATCT-GCCGTTCTTGATTA
64 GGCTTCAATCTGGCC-TTCTTGACTA
* * **
31946 GAGGTAAAAGATTGGAAGATGGCTTCAATCTGCCCCTCTTGACTAGGGGTAAAAGATTGGACGGT
1 G-GGTAAAAGATTGGAAGATGACTTCAATCT-ACCCTCTTGACTAGGGGTAAAAGATTGGAATGT
*
32011 AGCTTCAATCTGGCCTTCTTGACTA
64 GGCTTCAATCTGGCCTTCTTGACTA
*
32036 GGGTAAAAGATTGGAATG-TGACTTCAATC-AGCCCCTCTTGATTAGGGGTAAAAGATTGGAATG
1 GGGTAAAAGATTGGAA-GATGACTTCAATCTA--CCCTCTTGACTAGGGGTAAAAGATTGGAATG
* *
32099 TGGCTTCAATATGCCCCTT-TTGACTAA
63 TGGCTTCAATCTG-GCCTTCTTGACT-A
32126 GGGTAAAAGAT
1 GGGTAAAAGAT
32137 GTGGCTATAT
Statistics
Matches: 233, Mismatches: 29, Indels: 29
0.80 0.10 0.10
Matches are distributed among these distances:
85 12 0.05
86 21 0.09
87 6 0.03
88 14 0.06
89 112 0.48
90 65 0.28
91 3 0.01
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (88 bp):
GGGTAAAAGATTGGAAGATGACTTCAATCTACCCTCTTGACTAGGGGTAAAAGATTGGAATGTGG
CTTCAATCTGGCCTTCTTGACTA
Found at i:31991 original size:134 final size:134
Alignment explanation
Indices: 31773--32136 Score: 440
Period size: 134 Copynumber: 2.8 Consensus size: 134
31763 ACTAGGTTAG
* * *
31773 GGGTAAAAGATTG-GA--TGACTTCAATCTGCCCCTACTAGATTAGGGGTAAAAGATT-G--GAT
1 GGGTAAAAGATTGAAATGTGACTTCAATCAGCCCCT-CTTGATTAGGGGTAAAAGATTGGAAGAT
* * *
31832 AGCTTCAATCTACCCCTCTTAACTAGGGGTAAAAGATTGGAAAGT-GTCTTCAATCT-ACCCTCT
65 GGCTTCAATCTGCCCCTCTTGACTAGGGGTAAAAGATTGGAAAGTAG-CTTCAATCTGACCCTCT
31895 TGACTA
129 TGACTA
* ** * ** *
31901 GGGGTAAAAGATTGAAATGTGGCTTTTATCTGCCGTTCTTGATTAGAGGTAAAAGATTGGAAGAT
1 -GGGTAAAAGATTGAAATGTGACTTCAATCAGCCCCTCTTGATTAGGGGTAAAAGATTGGAAGAT
** * *
31966 GGCTTCAATCTGCCCCTCTTGACTAGGGGTAAAAGATTGGACGGTAGCTTCAATCTGGCCTTCTT
65 GGCTTCAATCTGCCCCTCTTGACTAGGGGTAAAAGATTGGAAAGTAGCTTCAATCTGACCCTCTT
32031 GACTA
130 GACTA
*
32036 GGGTAAAAGATTGGAATGTGACTTCAATCAGCCCCTCTTGATTAGGGGTAAAAGATTGGAATG-T
1 GGGTAAAAGATTGAAATGTGACTTCAATCAGCCCCTCTTGATTAGGGGTAAAAGATTGGAA-GAT
* * *
32100 GGCTTCAATATGCCCCTTTTGACTAAGGGTAAAAGAT
65 GGCTTCAATCTGCCCCTCTTGACTAGGGGTAAAAGAT
32137 GTGGCTATAT
Statistics
Matches: 200, Mismatches: 26, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
129 13 0.06
130 1 0.00
131 19 0.09
132 14 0.07
134 140 0.70
135 13 0.06
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (134 bp):
GGGTAAAAGATTGAAATGTGACTTCAATCAGCCCCTCTTGATTAGGGGTAAAAGATTGGAAGATG
GCTTCAATCTGCCCCTCTTGACTAGGGGTAAAAGATTGGAAAGTAGCTTCAATCTGACCCTCTTG
ACTA
Found at i:33684 original size:17 final size:17
Alignment explanation
Indices: 33664--33718 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
33654 GACAAATGGA
*
33664 AATGCAATGACAATGCG
1 AATGCAATGACAATGAG
* ** *
33681 AATGTAGGGACAATGAA
1 AATGCAATGACAATGAG
33698 AATGCAATGACAATGAG
1 AATGCAATGACAATGAG
33715 AATG
1 AATG
33719 TGATAACAAT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.45, C:0.11, G:0.25, T:0.18
Consensus pattern (17 bp):
AATGCAATGACAATGAG
Found at i:34270 original size:48 final size:48
Alignment explanation
Indices: 34212--34304 Score: 168
Period size: 48 Copynumber: 1.9 Consensus size: 48
34202 AGCACCCGAA
* *
34212 ATGTAGGTAGTGAGGTTGCTATTGTGTATAGCAACCGGACGATTAAGT
1 ATGTAAGTAGTGAGGTTGCTATTGTGTATAGCAACCGAACGATTAAGT
34260 ATGTAAGTAGTGAGGTTGCTATTGTGTATAGCAACCGAACGATTA
1 ATGTAAGTAGTGAGGTTGCTATTGTGTATAGCAACCGAACGATTA
34305 TGTTAAGGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.31
Consensus pattern (48 bp):
ATGTAAGTAGTGAGGTTGCTATTGTGTATAGCAACCGAACGATTAAGT
Found at i:42214 original size:43 final size:43
Alignment explanation
Indices: 42150--42404 Score: 287
Period size: 43 Copynumber: 5.9 Consensus size: 43
42140 AGATAATTGT
* *
42150 TTCAATTTGCCCCTATTGGATT-AGGAGTAAAAGACTGGATAGC
1 TTCAATCTGCCCCTACTGGATTAAGG-GTAAAAGACTGGATAGC
* * * * *
42193 TTTAATTTGCCCCTACCGGATTAAGGGTAAAAGACTAGATGGC
1 TTCAATCTGCCCCTACTGGATTAAGGGTAAAAGACTGGATAGC
* * * * * *
42236 GTCAATCTGCCCCTATTGGATTAGGGGTAAAAGATTTGATTGC
1 TTCAATCTGCCCCTACTGGATTAAGGGTAAAAGACTGGATAGC
* * * *
42279 TTCAATATGCCCCTACTAGATTAAGGGTAAAAGACTAGATAGT
1 TTCAATCTGCCCCTACTGGATTAAGGGTAAAAGACTGGATAGC
* * * *
42322 TTCAATCTGTCCCTACTGGATTAAAGGTAAAAGATTGGATCGC
1 TTCAATCTGCCCCTACTGGATTAAGGGTAAAAGACTGGATAGC
* *
42365 TTCAATCTGCCCCTAATGGATTAAGGGTAAAGGACTGGAT
1 TTCAATCTGCCCCTACTGGATTAAGGGTAAAAGACTGGAT
42405 GGTGGCTTCA
Statistics
Matches: 175, Mismatches: 36, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
43 172 0.98
44 3 0.02
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (43 bp):
TTCAATCTGCCCCTACTGGATTAAGGGTAAAAGACTGGATAGC
Found at i:42301 original size:86 final size:87
Alignment explanation
Indices: 42150--42534 Score: 375
Period size: 86 Copynumber: 4.4 Consensus size: 87
42140 AGATAATTGT
* * * * * *
42150 TTCAATTTGCCCCTATTGGATTAGGAGTAAAAGACTGGATAGCTTTAATTTGCCCCTACCGGATT
1 TTCAATCTGCCCCTATTGGATTAGGGGTAAAAGATTGGATTGCTTCAATTTGCCCCTACTGGATT
42215 AAGGGTAAAAGACT-AGATGGC
66 AAGGGTAAAAGACTGAGATGGC
* * * *
42236 GTCAATCTGCCCCTATTGGATTAGGGGTAAAAGATTTGATTGCTTCAATATGCCCCTACTAGATT
1 TTCAATCTGCCCCTATTGGATTAGGGGTAAAAGATTGGATTGCTTCAATTTGCCCCTACTGGATT
* *
42301 AAGGGTAAAAGACT-AGATAGT
66 AAGGGTAAAAGACTGAGATGGC
* * ** * * *
42322 TTCAATCTGTCCCTACTGGATTAAAGGTAAAAGATTGGATCGCTTCAATCTGCCCCTAATGGATT
1 TTCAATCTGCCCCTATTGGATTAGGGGTAAAAGATTGGATTGCTTCAATTTGCCCCTACTGGATT
* *
42387 AAGGGTAAAGGACTGGATGGTGGC
66 AAGGGTAAAAGACT-GA-GATGGC
* * * * * * * *
42411 TTCAATCTACCCATCTT-GATTAGGGGTAAAAGATTAGAATGACTTCAATTTACCCCT-CTTGAC
1 TTCAATCTGCCCCTATTGGATTAGGGGTAAAAGATTGGATTG-CTTCAATTTGCCCCTACTGGAT
* * *
42474 TAGGGGTAAAAGATTGAAATGTGAC
65 TAAGGGTAAAAGACTGAGATG-G-C
* * *
42499 TTCAATTTGCCCCTCTT-GATTAGGGGTAGAAGATTG
1 TTCAATCTGCCCCTATTGGATTAGGGGTAAAAGATTG
42535 AAAGATGGCT
Statistics
Matches: 242, Mismatches: 51, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
86 144 0.60
87 3 0.01
88 67 0.28
89 28 0.12
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (87 bp):
TTCAATCTGCCCCTATTGGATTAGGGGTAAAAGATTGGATTGCTTCAATTTGCCCCTACTGGATT
AAGGGTAAAAGACTGAGATGGC
Found at i:42385 original size:129 final size:129
Alignment explanation
Indices: 42145--42395 Score: 335
Period size: 129 Copynumber: 1.9 Consensus size: 129
42135 GAGTGAGATA
* * * * * *
42145 ATTGTTTCAATTTGCCCCTATTGGATTAGGAGTAAAAGACTGGATAGCTTTAATTTGCCCCTACC
1 ATTGCTTCAATATGCCCCTACTAGATTAGGAGTAAAAGACTAGATAGCTTTAATCTGCCCCTACC
* * * *
42210 GGATTAAGGGTAAAAGACTAGATGGCGTCAATCTGCCCCTATTGGATTAGGGGTAAAAGATTTG
66 GGATTAAAGGTAAAAGACTAGATCGCGTCAATCTGCCCCTAATGGATTAAGGGTAAAAGATTTG
*
42274 ATTGCTTCAATATGCCCCTACTAGATTAAGG-GTAAAAGACTAGATAG-TTTCAATCTGTCCCTA
1 ATTGCTTCAATATGCCCCTACTAGATT-AGGAGTAAAAGACTAGATAGCTTT-AATCTGCCCCTA
* * * *
42337 CTGGATTAAAGGTAAAAGATTGGATCGCTTCAATCTGCCCCTAATGGATTAAGGGTAAA
64 CCGGATTAAAGGTAAAAGACTAGATCGCGTCAATCTGCCCCTAATGGATTAAGGGTAAA
42396 GGACTGGATG
Statistics
Matches: 105, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
128 3 0.03
129 99 0.94
130 3 0.03
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (129 bp):
ATTGCTTCAATATGCCCCTACTAGATTAGGAGTAAAAGACTAGATAGCTTTAATCTGCCCCTACC
GGATTAAAGGTAAAAGACTAGATCGCGTCAATCTGCCCCTAATGGATTAAGGGTAAAAGATTTG
Found at i:42438 original size:45 final size:44
Alignment explanation
Indices: 42237--42579 Score: 184
Period size: 43 Copynumber: 7.8 Consensus size: 44
42227 CTAGATGGCG
* *
42237 TCAATCTGCCCCTATTGGATTAGGGGTAAAAGATTTG-AT-TG-CT
1 TCAATCTACCCCTCTT-GATTAGGGGTAAAAGA-TTGAATATGACT
* * * * * *
42280 TCAATATGCCCCTACTAGATTAAGGGTAAAAGACT-AGATA-G-TT
1 TCAATCTACCCCT-CTTGATTAGGGGTAAAAGATTGA-ATATGACT
** * ** * *
42323 TCAATCTGTCCCTACTGGATTAAAGGTAAAAGATTGGAT-CG-CT
1 TCAATCTACCCCT-CTTGATTAGGGGTAAAAGATTGAATATGACT
* * * * * * * * *
42366 TCAATCTGCCCCTAATGGATTAAGGGTAAAGGACTGGATGGTGGCT
1 TCAATCTACCCCT-CTTGATTAGGGGTAAAAGATTGAAT-ATGACT
*
42412 TCAATCTACCCATCTTGATTAGGGGTAAAAGATT-AGA-ATGACT
1 TCAATCTACCCCTCTTGATTAGGGGTAAAAGATTGA-ATATGACT
* * *
42455 TCAATTTACCCCTCTTGACTAGGGGTAAAAGATTGAAATGTGACT
1 TCAATCTACCCCTCTTGATTAGGGGTAAAAGATTG-AATATGACT
* * * * *
42500 TCAATTTGCCCCTCTTGATTAGGGGTAGAAGATTGAAAGATGGCT
1 TCAATCTACCCCTCTTGATTAGGGGTAAAAGATTG-AATATGACT
* * * **
42545 TCAATCTAGCCCTTTTGACTACAGGTAAAAGATTG
1 TCAATCTACCCCTCTTGATTAGGGGTAAAAGATTG
42580 GACGATAGCT
Statistics
Matches: 240, Mismatches: 47, Indels: 24
0.77 0.15 0.08
Matches are distributed among these distances:
42 1 0.00
43 134 0.56
44 2 0.01
45 90 0.38
46 13 0.05
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (44 bp):
TCAATCTACCCCTCTTGATTAGGGGTAAAAGATTGAATATGACT
Found at i:42465 original size:43 final size:44
Alignment explanation
Indices: 42410--42579 Score: 191
Period size: 45 Copynumber: 3.8 Consensus size: 44
42400 TGGATGGTGG
* *
42410 CTTCAATCTACCCATCTTGATTAGGGGTAAAAGATT-AGAA-TGA
1 CTTCAATTTACCCCTCTTGATTAGGGGTAAAAGATTGA-AAGTGA
*
42453 CTTCAATTTACCCCTCTTGACTAGGGGTAAAAGATTGAAATGTGA
1 CTTCAATTTACCCCTCTTGATTAGGGGTAAAAGATTGAAA-GTGA
* * *
42498 CTTCAATTTGCCCCTCTTGATTAGGGGTAGAAGATTGAAAGATGG
1 CTTCAATTTACCCCTCTTGATTAGGGGTAAAAGATTGAAAG-TGA
* * * * **
42543 CTTCAATCTAGCCCTTTTGACTACAGGTAAAAGATTG
1 CTTCAATTTACCCCTCTTGATTAGGGGTAAAAGATTG
42580 GACGATAGCT
Statistics
Matches: 108, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
43 35 0.32
44 2 0.02
45 71 0.66
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (44 bp):
CTTCAATTTACCCCTCTTGATTAGGGGTAAAAGATTGAAAGTGA
Found at i:42481 original size:88 final size:90
Alignment explanation
Indices: 42410--42576 Score: 212
Period size: 88 Copynumber: 1.9 Consensus size: 90
42400 TGGATGGTGG
* *
42410 CTTCAATCTACCCATCTTGATTAGGGGTAAAAGATT-AGA-ATGACTTCAATTTACCCCTCTTGA
1 CTTCAATCTACCCATCTTGATTAGGGGTAAAAGATTGAAAGATGACTTCAATCTACCCCTCTTGA
*
42473 CTAGGGGTAAAAGATTGAAATGTGA
66 CTAGGGGTAAAAGACTGAAATGTGA
* * * * * * *
42498 CTTCAATTTGCCCCTCTTGATTAGGGGTAGAAGATTGAAAGATGGCTTCAATCTAGCCCTTTTGA
1 CTTCAATCTACCCATCTTGATTAGGGGTAAAAGATTGAAAGATGACTTCAATCTACCCCTCTTGA
**
42563 CTACAGGTAAAAGA
66 CTAGGGGTAAAAGA
42577 TTGGACGATA
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
88 32 0.48
89 2 0.03
90 32 0.48
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (90 bp):
CTTCAATCTACCCATCTTGATTAGGGGTAAAAGATTGAAAGATGACTTCAATCTACCCCTCTTGA
CTAGGGGTAAAAGACTGAAATGTGA
Found at i:43488 original size:7 final size:7
Alignment explanation
Indices: 43474--43510 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
43464 TTTTCTTCTA
43474 TTTT-CT
1 TTTTCCT
43480 TTTTCC-
1 TTTTCCT
43486 TTTTCCT
1 TTTTCCT
43493 TTTTCCT
1 TTTTCCT
*
43500 TTTTACT
1 TTTTCCT
43507 TTTT
1 TTTT
43511 TTCTTTCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 10 0.36
7 18 0.64
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTCCT
Found at i:47062 original size:43 final size:43
Alignment explanation
Indices: 46872--47090 Score: 271
Period size: 43 Copynumber: 5.1 Consensus size: 43
46862 GAAAATCGCT
* * *
46872 GCTATAGAACATGATCTTTAACGATGCTTT-CCCATAAACGCC
1 GCTAAAGAACATGGTCTTTAACGATGCTTTCCCCACAAACGCC
* * *
46914 GCT-ATGAACATGGTCTTTAACGACGCTTTCCCCACAAACCCC
1 GCTAAAGAACATGGTCTTTAACGATGCTTTCCCCACAAACGCC
**
46956 GCTAAAGAACATGGTCTTTAACGGCGCTTTCCCCACAAACGCC
1 GCTAAAGAACATGGTCTTTAACGATGCTTTCCCCACAAACGCC
* *
46999 GCTAAAGAACATGATCTTTAGCGATGCTTTCCCCACAAACGCC
1 GCTAAAGAACATGGTCTTTAACGATGCTTTCCCCACAAACGCC
* ** * * * *
47042 GCTAAAGAATATGGTCTTTAGTGGTACTTTTCCCACAAACGCT
1 GCTAAAGAACATGGTCTTTAACGATGCTTTCCCCACAAACGCC
47085 GCTAAA
1 GCTAAA
47091 AAACTTTCCC
Statistics
Matches: 155, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
41 22 0.14
42 16 0.10
43 117 0.75
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (43 bp):
GCTAAAGAACATGGTCTTTAACGATGCTTTCCCCACAAACGCC
Found at i:47140 original size:68 final size:69
Alignment explanation
Indices: 47025--47162 Score: 197
Period size: 68 Copynumber: 2.0 Consensus size: 69
47015 TTTAGCGATG
* ** * *
47025 CTTTCCCCACAAACGCCGCTAAAGAATATGGTCTTTAGTGGTACTTTTCCCACAAACGCTGCTAA
1 CTTTCCCCACAAACGCCGCTAAAGAACATGGTCTTTAACGGCACTTTTCCCACAAACGCCGCTAA
47090 AAAA
66 AAAA
* * *
47094 CTTT-CCCACAAACGCTGCTAAAGAACATGGTCTTTAACGGCGCTTTTCCCTCAAACGCCGCTAA
1 CTTTCCCCACAAACGCCGCTAAAGAACATGGTCTTTAACGGCACTTTTCCCACAAACGCCGCTAA
47158 AAAA
66 AAAA
47162 C
1 C
47163 ATGGTCTTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
68 57 0.93
69 4 0.07
ACGTcount: A:0.31, C:0.30, G:0.14, T:0.25
Consensus pattern (69 bp):
CTTTCCCCACAAACGCCGCTAAAGAACATGGTCTTTAACGGCACTTTTCCCACAAACGCCGCTAA
AAAA
Found at i:47157 original size:43 final size:43
Alignment explanation
Indices: 47095--47195 Score: 166
Period size: 43 Copynumber: 2.3 Consensus size: 43
47085 GCTAAAAAAC
* * *
47095 TTTCCCACAAACGCTGCTAAAGAACATGGTCTTTAACGGCGCT
1 TTTCCCACAAACGCCGCTAAAAAACATGGTCTTTAACGACGCT
*
47138 TTTCCCTCAAACGCCGCTAAAAAACATGGTCTTTAACGACGCT
1 TTTCCCACAAACGCCGCTAAAAAACATGGTCTTTAACGACGCT
47181 TTTCCCACAAACGCC
1 TTTCCCACAAACGCC
47196 TCTACTATTA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 53 1.00
ACGTcount: A:0.29, C:0.32, G:0.15, T:0.25
Consensus pattern (43 bp):
TTTCCCACAAACGCCGCTAAAAAACATGGTCTTTAACGACGCT
Found at i:47183 original size:111 final size:112
Alignment explanation
Indices: 46982--47194 Score: 293
Period size: 111 Copynumber: 1.9 Consensus size: 112
46972 TTTAACGGCG
* *
46982 CTTTCCCCACAAACGCCGCTAAAGAACATGATCTTTAGCGATGCTTTCCCCACAAACGCCGCTAA
1 CTTTCCCCACAAACGCCGCTAAAGAACATGATCTTTAACGACGCTTTCCCCACAAACGCCGCTAA
* * ** **
47047 AGAATATGGTCTTTAGTGGTACTTTTCCCACAAACGCTGCTAAAAAA
66 AAAACATGGTCTTTAACGACACTTTTCCCACAAACGCTGCTAAAAAA
* * * * *
47094 CTTT-CCCACAAACGCTGCTAAAGAACATGGTCTTTAACGGCGCTTTTCCCTCAAACGCCGCTAA
1 CTTTCCCCACAAACGCCGCTAAAGAACATGATCTTTAACGACGCTTTCCCCACAAACGCCGCTAA
*
47158 AAAACATGGTCTTTAACGACGCTTTTCCCACAAACGC
66 AAAACATGGTCTTTAACGACACTTTTCCCACAAACGC
47195 CTCTACTATT
Statistics
Matches: 87, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
111 83 0.95
112 4 0.05
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (112 bp):
CTTTCCCCACAAACGCCGCTAAAGAACATGATCTTTAACGACGCTTTCCCCACAAACGCCGCTAA
AAAACATGGTCTTTAACGACACTTTTCCCACAAACGCTGCTAAAAAA
Done.