Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009427.1 Kokia drynarioides strain JFW-HI SEQ_124134, 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: 447112
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 11 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:333038 original size:17 final size:16
Alignment explanation
Indices: 333012--333046 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
333002 GGCATAGCAA
*
333012 TTTAATTTAGTTATAAT
1 TTTAACTTAGTT-TAAT
333029 TTTAACTTAGTTTAAT
1 TTTAACTTAGTTTAAT
333045 TT
1 TT
333047 AGTTTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (16 bp):
TTTAACTTAGTTTAAT
Found at i:334866 original size:6 final size:6
Alignment explanation
Indices: 334855--334892 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
334845 GTAACATTCA
334855 CTGGTT CTGGTT CTGGTT CTGGTT CTGGTT CTGGTT CT
1 CTGGTT CTGGTT CTGGTT CTGGTT CTGGTT CTGGTT CT
334893 AGCAAAATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.18, G:0.32, T:0.50
Consensus pattern (6 bp):
CTGGTT
Found at i:360756 original size:50 final size:51
Alignment explanation
Indices: 360615--360756 Score: 169
Period size: 50 Copynumber: 2.8 Consensus size: 51
360605 AAACACTGTT
* * * * **
360615 TGTGGACATGCCACCACTGATTTACAGATAAACTGCCATTGATATCACTTA
1 TGTGGACAAGCCACCATTGATTTGCAGATATACTGCCATTGATATCAAATA
* * * *
360666 TGTGGACAAGCCACCATTGATATGCAGATTTACCGCCATTGAT-TTAAATA
1 TGTGGACAAGCCACCATTGATTTGCAGATATACTGCCATTGATATCAAATA
* *
360716 TGTGAACAAGCCACCATTGATTTGCAGATATACTGTCATTG
1 TGTGGACAAGCCACCATTGATTTGCAGATATACTGCCATTG
360757 CTTCCACTTT
Statistics
Matches: 76, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
50 40 0.53
51 36 0.47
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (51 bp):
TGTGGACAAGCCACCATTGATTTGCAGATATACTGCCATTGATATCAAATA
Found at i:363830 original size:28 final size:28
Alignment explanation
Indices: 363799--363989 Score: 192
Period size: 28 Copynumber: 6.8 Consensus size: 28
363789 TTTGATTCTA
* * *
363799 GCTTAGGTAGAGCGTTACTCTGA-ATCTT
1 GCTTGGGTAGAGCATTATTCT-ACATCTT
363827 GCTT-GGTAAGAGCATTATTCTACATC-T
1 GCTTGGGT-AGAGCATTATTCTACATCTT
* *
363854 GACTCGGGTAGAGCATTATTCTACATCTG
1 G-CTTGGGTAGAGCATTATTCTACATCTT
* * *
363883 GCTCGGGTAGAGCGTTATTCTAAATCTT
1 GCTTGGGTAGAGCATTATTCTACATCTT
*
363911 GCTTGGGTAGAGCATTATTCTACATCTG
1 GCTTGGGTAGAGCATTATTCTACATCTT
* * **
363939 GATCGGGTAGAGTGTTATTCTGA-ATCTT
1 GCTTGGGTAGAGCATTATTCT-ACATCTT
*
363967 GCTTGGGTGGAGCATTATTCTAC
1 GCTTGGGTAGAGCATTATTCTAC
363990 TTCTGGCTCG
Statistics
Matches: 135, Mismatches: 21, Indels: 14
0.79 0.12 0.08
Matches are distributed among these distances:
27 7 0.05
28 123 0.91
29 5 0.04
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (28 bp):
GCTTGGGTAGAGCATTATTCTACATCTT
Found at i:363923 original size:84 final size:84
Alignment explanation
Indices: 363804--363988 Score: 250
Period size: 84 Copynumber: 2.2 Consensus size: 84
363794 TTCTAGCTTA
* *
363804 GGTAGAGCGTTACTCTGAATCTTGCTTGGTAAGAGCATTATTCTACATCT-GACTCGGGTAGAGC
1 GGTAGAGCGTTATTCTAAATCTTGCTTGGTAAGAGCATTATTCTACATCTGGA-TCGGGTAGAGC
363868 ATTATTCT-ACATCTGGCTCG
65 ATTATTCTGA-ATCTGGCTCG
*
363888 GGTAGAGCGTTATTCTAAATCTTGCTTGGGT-AGAGCATTATTCTACATCTGGATCGGGTAGAGT
1 GGTAGAGCGTTATTCTAAATCTTGCTT-GGTAAGAGCATTATTCTACATCTGGATCGGGTAGAGC
* * *
363952 GTTATTCTGAATCTTGCTTG
65 ATTATTCTGAATCTGGCTCG
* *
363972 GGTGGAGCATTATTCTA
1 GGTAGAGCGTTATTCTA
363989 CTTCTGGCTC
Statistics
Matches: 90, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
84 84 0.93
85 6 0.07
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (84 bp):
GGTAGAGCGTTATTCTAAATCTTGCTTGGTAAGAGCATTATTCTACATCTGGATCGGGTAGAGCA
TTATTCTGAATCTGGCTCG
Found at i:364007 original size:84 final size:84
Alignment explanation
Indices: 363834--364016 Score: 201
Period size: 84 Copynumber: 2.2 Consensus size: 84
363824 CTTGCTTGGT
*
363834 AAGAGCATTATTCTACATCTGACTCGGGTAGAGCATTATTCTACATCTGGCTCGGGTAGAGCGTT
1 AAGAGCATTATTCTACATCTGACTCGGGTAGAGCATTATTCTACATCTGGCTCGGGTAGAGCATT
* * **
363899 ATTCTAAATCTTGCTTGGG
66 ATTCTAAATCTGGCTCGAA
* ** * * *
363918 TAGAGCATTATTCTACATCTGGA-TCGGGTAGAGTGTTATTCTGA-ATCTTGCTTGGGTGGAGCA
1 AAGAGCATTATTCTACATCT-GACTCGGGTAGAGCATTATTCT-ACATCTGGCTCGGGTAGAGCA
**
363981 TTATTCTACTTCTGGCTCGAA
64 TTATTCTAAATCTGGCTCGAA
364002 AAGAGCGA-TATTCTA
1 AAGAGC-ATTATTCTA
364017 ATTCTAGCTC
Statistics
Matches: 82, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
84 78 0.95
85 4 0.05
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (84 bp):
AAGAGCATTATTCTACATCTGACTCGGGTAGAGCATTATTCTACATCTGGCTCGGGTAGAGCATT
ATTCTAAATCTGGCTCGAA
Found at i:364014 original size:56 final size:56
Alignment explanation
Indices: 363835--364017 Score: 242
Period size: 56 Copynumber: 3.3 Consensus size: 56
363825 TTGCTTGGTA
* * *
363835 AGAGCATTATTCTACATC-TGACTCGGGTAGAGCATTATTCTACATCTGGCTCGGGT
1 AGAGCGTTATTCTAAATCTTG-CTTGGGTAGAGCATTATTCTACATCTGGCTCGGGT
*
363891 AGAGCGTTATTCTAAATCTTGCTTGGGTAGAGCATTATTCTACATCTGGATCGGGT
1 AGAGCGTTATTCTAAATCTTGCTTGGGTAGAGCATTATTCTACATCTGGCTCGGGT
* * * * ***
363947 AGAGTGTTATTCTGAATCTTGCTTGGGTGGAGCATTATTCTACTTCTGGCTCGAAA
1 AGAGCGTTATTCTAAATCTTGCTTGGGTAGAGCATTATTCTACATCTGGCTCGGGT
*
364003 AGAGCGATATTCTAA
1 AGAGCGTTATTCTAA
364018 TTCTAGCTCG
Statistics
Matches: 111, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
56 109 0.98
57 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (56 bp):
AGAGCGTTATTCTAAATCTTGCTTGGGTAGAGCATTATTCTACATCTGGCTCGGGT
Found at i:364126 original size:28 final size:28
Alignment explanation
Indices: 363990--364128 Score: 172
Period size: 28 Copynumber: 5.0 Consensus size: 28
363980 ATTATTCTAC
* *
363990 TTCTGGCTCGAAAAGAGCGATATTCTAA
1 TTCTGGCTCGAAAAGAGCGATATTTTGA
* *
364018 TTCTAGCTCGAAAATAGCGATATTTTGA
1 TTCTGGCTCGAAAAGAGCGATATTTTGA
* * *
364046 TTTTGGTTCGGAAAGAGCGATATTTTGA
1 TTCTGGCTCGAAAAGAGCGATATTTTGA
* *
364074 TTCTGGCTCGAAAATAGTGATATTTTGA
1 TTCTGGCTCGAAAAGAGCGATATTTTGA
*
364102 TTCTGGCTC-AGAAAGAGAGATATTTTG
1 TTCTGGCTCGA-AAAGAGCGATATTTTG
364129 GTACTCAGAA
Statistics
Matches: 94, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
27 1 0.01
28 93 0.99
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.35
Consensus pattern (28 bp):
TTCTGGCTCGAAAAGAGCGATATTTTGA
Found at i:365852 original size:16 final size:16
Alignment explanation
Indices: 365831--365864 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
365821 TGTAGAAGTG
*
365831 AGAAAATGAAATTGGT
1 AGAAAATGAAACTGGT
365847 AGAAAATGAAACTGGT
1 AGAAAATGAAACTGGT
365863 AG
1 AG
365865 TGCTTATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.26, T:0.21
Consensus pattern (16 bp):
AGAAAATGAAACTGGT
Found at i:368577 original size:12 final size:12
Alignment explanation
Indices: 368550--368585 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
368540 ACGTCCACTA
*
368550 TCTTGCTCTT-C
1 TCTTTCTCTTCC
368561 TCTTTCTCTTCC
1 TCTTTCTCTTCC
368573 TCTTTCTCTTCC
1 TCTTTCTCTTCC
368585 T
1 T
368586 TTACTTCCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.00, C:0.39, G:0.03, T:0.58
Consensus pattern (12 bp):
TCTTTCTCTTCC
Found at i:380424 original size:26 final size:26
Alignment explanation
Indices: 380395--380453 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
380385 TACCTCCAGC
380395 AAAATTTAAACGATTTTACCCTT-GAT
1 AAAATTTAAACGATTTTACCCTTCG-T
** *
380421 AAAATTTTGATGATTTTACCCTTCGT
1 AAAATTTAAACGATTTTACCCTTCGT
380447 AAAATTT
1 AAAATTT
380454 TGAAAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 28 0.97
27 1 0.03
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (26 bp):
AAAATTTAAACGATTTTACCCTTCGT
Found at i:380454 original size:26 final size:26
Alignment explanation
Indices: 380406--380456 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
380396 AAATTTAAAC
380406 GATTTTACCCTTGATAAAATTTTGAT
1 GATTTTACCCTTGATAAAATTTTGAT
380432 GATTTTACCCTTCG-TAAAATTTTGA
1 GATTTTACCCTT-GATAAAATTTTGA
380457 AAAAATTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (26 bp):
GATTTTACCCTTGATAAAATTTTGAT
Found at i:391672 original size:30 final size:30
Alignment explanation
Indices: 391636--391708 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
391626 ACGGTCGAAA
* * *
391636 AAGAAAATCAAGATTCACTTTTTTTTTTTC
1 AAGAAAATCAAGATTCACATTCTTGTTTTC
391666 AAGAAAATCAAGATTCACATTCTTGTTTTC
1 AAGAAAATCAAGATTCACATTCTTGTTTTC
391696 AAGAAAATCAAGA
1 AAGAAAATCAAGA
391709 AACCAAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.36
Consensus pattern (30 bp):
AAGAAAATCAAGATTCACATTCTTGTTTTC
Found at i:399616 original size:23 final size:22
Alignment explanation
Indices: 399585--399628 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
399575 AAAGAAATAA
*
399585 AATTAACCCAATTTAATTAATT
1 AATTAACCCAAATTAATTAATT
*
399607 AATTCAACCCAAATTATTTAAT
1 AATT-AACCCAAATTAATTAAT
399629 GAAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAACCCAAATTAATTAATT
Found at i:399889 original size:34 final size:34
Alignment explanation
Indices: 399851--399919 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
399841 AGACATTTAC
399851 TTAGTTTTAACAAGGAATTTAAGTAAAAAGGTGA
1 TTAGTTTTAACAAGGAATTTAAGTAAAAAGGTGA
399885 TTAGTTTTAACAAGGAATTTAAGTAAAAAGGTGA
1 TTAGTTTTAACAAGGAATTTAAGTAAAAAGGTGA
399919 T
1 T
399920 AAATTACGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.43, C:0.03, G:0.20, T:0.33
Consensus pattern (34 bp):
TTAGTTTTAACAAGGAATTTAAGTAAAAAGGTGA
Found at i:405631 original size:12 final size:12
Alignment explanation
Indices: 405614--405638 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
405604 CCATGGAAAC
405614 CTATGCAGATAA
1 CTATGCAGATAA
405626 CTATGCAGATAA
1 CTATGCAGATAA
405638 C
1 C
405639 AGATAACAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (12 bp):
CTATGCAGATAA
Found at i:408653 original size:52 final size:52
Alignment explanation
Indices: 408575--408816 Score: 373
Period size: 52 Copynumber: 4.7 Consensus size: 52
408565 TGGGCCGTAA
408575 ATTAAGAGGTCCGATGACTCTGTGTCATCATGAGTATATGAATCCTTTACGG
1 ATTAAGAGGTCCGATGACTCTGTGTCATCATGAGTATATGAATCCTTTACGG
* *
408627 ATTAAGTGGTCCGATGACTTTGTGTCAT-AGTGAGTATATGAATCCTTTACGG
1 ATTAAGAGGTCCGATGACTCTGTGTCATCA-TGAGTATATGAATCCTTTACGG
* *
408679 ATTAATAGGTCCGATGA--CTGTGTCATCATAAGTATATGAATCCTTTACGG
1 ATTAAGAGGTCCGATGACTCTGTGTCATCATGAGTATATGAATCCTTTACGG
* *
408729 ATTAAGCGGTCCGATGACTCTGTGTCATCGTGAGTATATGAATCCTTTACGG
1 ATTAAGAGGTCCGATGACTCTGTGTCATCATGAGTATATGAATCCTTTACGG
* * *
408781 ATTAAGAGGTCCAAAGACTCTGTGTCATCGTGAGTA
1 ATTAAGAGGTCCGATGACTCTGTGTCATCATGAGTA
408817 ATAAATCTCA
Statistics
Matches: 173, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
50 44 0.25
51 2 0.01
52 127 0.73
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.33
Consensus pattern (52 bp):
ATTAAGAGGTCCGATGACTCTGTGTCATCATGAGTATATGAATCCTTTACGG
Found at i:408753 original size:102 final size:103
Alignment explanation
Indices: 408575--408809 Score: 382
Period size: 102 Copynumber: 2.3 Consensus size: 103
408565 TGGGCCGTAA
* *
408575 ATTAAGAGGTCCGATGACTCTGTGTCATCATGAGTATATGAATCCTTTACGGATTAAGTGGTCCG
1 ATTAAGAGGTCCGATGAC-CTGTGTCATCATAAGTATATGAATCCTTTACGGATTAAGCGGTCCG
*
408640 ATGACTTTGTGTCATAGTGAGTATATGAATCCTTTACGG
65 ATGACTCTGTGTCATAGTGAGTATATGAATCCTTTACGG
*
408679 ATTAATAGGTCCGATGA-CTGTGTCATCATAAGTATATGAATCCTTTACGGATTAAGCGGTCCGA
1 ATTAAGAGGTCCGATGACCTGTGTCATCATAAGTATATGAATCCTTTACGGATTAAGCGGTCCGA
*
408743 TGACTCTGTGTCATCGTGAGTATATGAATCCTTTACGG
66 TGACTCTGTGTCATAGTGAGTATATGAATCCTTTACGG
* *
408781 ATTAAGAGGTCCAAAGACTCTGTGTCATC
1 ATTAAGAGGTCCGATGAC-CTGTGTCATC
408810 GTGAGTAATA
Statistics
Matches: 121, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
102 95 0.79
104 26 0.21
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (103 bp):
ATTAAGAGGTCCGATGACCTGTGTCATCATAAGTATATGAATCCTTTACGGATTAAGCGGTCCGA
TGACTCTGTGTCATAGTGAGTATATGAATCCTTTACGG
Found at i:408857 original size:51 final size:52
Alignment explanation
Indices: 408575--408870 Score: 251
Period size: 52 Copynumber: 5.8 Consensus size: 52
408565 TGGGCCGTAA
* * * * * *
408575 ATTAAGAGGTCCGATGACTCTGTGTCATCATGAGTATATGAATCCTTTACGG
1 ATTAAGAGGTCCAAAGACTATGTGTCATCGTGAGTATATAAATCCTATACGG
* * * * * * *
408627 ATTAAGTGGTCCGATGACTTTGTGTCATAGTGAGTATATGAATCCTTTACGG
1 ATTAAGAGGTCCAAAGACTATGTGTCATCGTGAGTATATAAATCCTATACGG
* * * * * * *
408679 ATTAATAGGTCCGATGAC--TGTGTCATCATAAGTATATGAATCCTTTACGG
1 ATTAAGAGGTCCAAAGACTATGTGTCATCGTGAGTATATAAATCCTATACGG
* * * * * *
408729 ATTAAGCGGTCCGATGACTCTGTGTCATCGTGAGTATATGAATCCTTTACGG
1 ATTAAGAGGTCCAAAGACTATGTGTCATCGTGAGTATATAAATCCTATACGG
*
408781 ATTAAGAGGTCCAAAGACTCTGTGTCATCGTGAGTA-ATAAAT-CTCATACGG
1 ATTAAGAGGTCCAAAGACTATGTGTCATCGTGAGTATATAAATCCT-ATACGG
* * ** *
408832 ATTATGAGGAT-CAATGGTTATGTGTCATCGTAAGTATAT
1 ATTAAGAGG-TCCAAAGACTATGTGTCATCGTGAGTATAT
408871 GAATGAAGTG
Statistics
Matches: 215, Mismatches: 24, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
50 47 0.22
51 38 0.18
52 130 0.60
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (52 bp):
ATTAAGAGGTCCAAAGACTATGTGTCATCGTGAGTATATAAATCCTATACGG
Found at i:414803 original size:17 final size:17
Alignment explanation
Indices: 414781--414814 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
414771 AAAGATATGA
414781 GATACTAGTCAAAAGGT
1 GATACTAGTCAAAAGGT
414798 GATACTAGTCAAAAGGT
1 GATACTAGTCAAAAGGT
414815 AAAGTTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.24
Consensus pattern (17 bp):
GATACTAGTCAAAAGGT
Found at i:415709 original size:52 final size:52
Alignment explanation
Indices: 415624--415816 Score: 193
Period size: 52 Copynumber: 3.8 Consensus size: 52
415614 TAAGCCGTAA
** * *
415624 ATTAAGAGGTCCGAAAATTTTGTGTCATCGTGAGTATATGAATCCTTTACGG
1 ATTAAGAGGTCCGATGACTCTGTGTCATCGTGAGTATATGAATCCTTTACGG
* * * *
415676 ATTAAGAGATCCGATGACTCTGTATCAT--T--GT-GA-GAATCCTTTATGG
1 ATTAAGAGGTCCGATGACTCTGTGTCATCGTGAGTATATGAATCCTTTACGG
* * * *
415722 ATTAAGAGGTCTGATGACTCTGTGTCATCATGAGTATATAAATCCCTTACGG
1 ATTAAGAGGTCCGATGACTCTGTGTCATCGTGAGTATATGAATCCTTTACGG
* * *
415774 ATTATGAGGTCC-AGTGGCTATGTGTCATCGTGAGTATATGAAT
1 ATTAAGAGGTCCGA-TGACTCTGTGTCATCGTGAGTATATGAAT
415817 GAAGTGAATT
Statistics
Matches: 113, Mismatches: 21, Indels: 14
0.76 0.14 0.09
Matches are distributed among these distances:
46 37 0.33
47 1 0.01
48 3 0.03
50 3 0.03
51 2 0.02
52 67 0.59
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (52 bp):
ATTAAGAGGTCCGATGACTCTGTGTCATCGTGAGTATATGAATCCTTTACGG
Found at i:421225 original size:23 final size:23
Alignment explanation
Indices: 421199--421255 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
421189 ATCAAGTGTT
421199 TGTGGCATATT-TGGTAAAACCTA
1 TGTGGCATATTAT-GTAAAACCTA
* * *
421222 TGTGGCTTATTATGTAAAGCCTT
1 TGTGGCATATTATGTAAAACCTA
421245 TGTGGCATATT
1 TGTGGCATATT
421256 CTATAATTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 28 0.97
24 1 0.03
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (23 bp):
TGTGGCATATTATGTAAAACCTA
Found at i:426428 original size:9 final size:10
Alignment explanation
Indices: 426407--426461 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
426397 TATATATAGT
426407 TTTTAATAAA
1 TTTTAATAAA
426417 TTTTAA-AAA
1 TTTTAATAAA
*
426426 TTTTAAT-GA
1 TTTTAATAAA
*
426435 TTATTTAT-AA
1 TT-TTAATAAA
426445 TTTCTAATAAA
1 TTT-TAATAAA
426456 TTTTAA
1 TTTTAA
426462 ATGATTCTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 13 0.35
10 19 0.51
11 5 0.14
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (10 bp):
TTTTAATAAA
Found at i:426485 original size:30 final size:29
Alignment explanation
Indices: 426417--426489 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 29
426407 TTTTAATAAA
*
426417 TTTTAAAAATTTTAATGATTATTTATAATT
1 TTTTATAAATTTTAATGATTATTTAT-ATT
* * *
426447 TCTAATAAATTTTAAATGATTCTTCTAT-TT
1 TTTTATAAATTTT-AATGATTATT-TATATT
426477 TTTTATAAATTTT
1 TTTTATAAATTTT
426490 TTTATAATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
30 23 0.66
31 9 0.26
32 3 0.09
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.58
Consensus pattern (29 bp):
TTTTATAAATTTTAATGATTATTTATATT
Found at i:428844 original size:12 final size:14
Alignment explanation
Indices: 428827--428858 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
428817 TGGCTTGAAT
428827 ATAAAA-TTAA-AA
1 ATAAAATTTAAGAA
428839 ATAAAATTTAAGAA
1 ATAAAATTTAAGAA
428853 ATAAAA
1 ATAAAA
428859 GGATTTAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 4 0.22
14 8 0.44
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (14 bp):
ATAAAATTTAAGAA
Found at i:429013 original size:24 final size:24
Alignment explanation
Indices: 428984--429033 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
428974 AATGAAGTTT
428984 ACTTGCTAAATGTAAAGAAGGAAA
1 ACTTGCTAAATGTAAAGAAGGAAA
429008 ACTTGCTAAATGTAAAGAAGGAAA
1 ACTTGCTAAATGTAAAGAAGGAAA
429032 AC
1 AC
429034 AACAACAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.50, C:0.10, G:0.20, T:0.20
Consensus pattern (24 bp):
ACTTGCTAAATGTAAAGAAGGAAA
Found at i:442695 original size:14 final size:13
Alignment explanation
Indices: 442671--442710 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
442661 CCTACGGGTT
*
442671 TTGTGATTTGGAC
1 TTGTAATTTGGAC
*
442684 TTGTATATTTGGAT
1 TTGTA-ATTTGGAC
442698 TTGTAATTTGGAC
1 TTGTAATTTGGAC
442711 ATTTAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.20, C:0.05, G:0.25, T:0.50
Consensus pattern (13 bp):
TTGTAATTTGGAC
Found at i:442726 original size:27 final size:27
Alignment explanation
Indices: 442670--442726 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
442660 GCCTACGGGT
* * *
442670 TTTGTGATTTGGACTTGTATATTTGGA
1 TTTGTAATTTGGACTTGTAAATTTGAA
*
442697 TTTGTAATTTGGACATT-TAAATTTTAA
1 TTTGTAATTTGGAC-TTGTAAATTTGAA
442724 TTT
1 TTT
442727 AAAATCATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.25, C:0.04, G:0.18, T:0.54
Consensus pattern (27 bp):
TTTGTAATTTGGACTTGTAAATTTGAA
Done.