Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001712.1 Kokia drynarioides strain JFW-HI SEQ_113406, 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: 78126
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:3638 original size:18 final size:17
Alignment explanation
Indices: 3609--3645 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
3599 TAAATAATAA
*
3609 AAAATATATTTAAATTT
1 AAAATATATTTAAAATT
3626 AAAATATATTTTAAAATT
1 AAAATATA-TTTAAAATT
3644 AA
1 AA
3646 TTTTTGGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAATATATTTAAAATT
Found at i:9098 original size:15 final size:17
Alignment explanation
Indices: 9074--9105 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
9064 AAAAAGAAAG
9074 AAAATAAAAGAA-AACA
1 AAAATAAAAGAAGAACA
9090 AAAAT-AAAGAAGAACA
1 AAAATAAAAGAAGAACA
9106 CCATTAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.78, C:0.06, G:0.09, T:0.06
Consensus pattern (17 bp):
AAAATAAAAGAAGAACA
Found at i:26389 original size:3 final size:3
Alignment explanation
Indices: 26381--26411 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
26371 CAGTGCATTA
26381 TCT TCT TCT TCT TCT TCT TCT TCT TCAT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TC-T TCT
26412 ATTTCTCTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:39095 original size:37 final size:37
Alignment explanation
Indices: 39054--39205 Score: 209
Period size: 37 Copynumber: 4.1 Consensus size: 37
39044 AATCATCAAG
* * * *
39054 CATTACACTCTAACCAAGACATAATCCTTTCATATAA
1 CATTACACTCTAACCGAGACGTAAGCCTTCCATATAA
* *
39091 CATTACGCTCTAACCGAGATGTAAGCCTTCCATA-AA
1 CATTACACTCTAACCGAGACGTAAGCCTTCCATATAA
*
39127 CATTACACTCTAATCGAGACGTAAGCCTTCCATATAA
1 CATTACACTCTAACCGAGACGTAAGCCTTCCATATAA
*
39164 CATTACGCTCTAACCG-GATCGTAAGCCTTCCATATAA
1 CATTACACTCTAACCGAGA-CGTAAGCCTTCCATATAA
39201 CATTA
1 CATTA
39206 TATCATTTGG
Statistics
Matches: 102, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
36 35 0.34
37 67 0.66
ACGTcount: A:0.35, C:0.28, G:0.10, T:0.28
Consensus pattern (37 bp):
CATTACACTCTAACCGAGACGTAAGCCTTCCATATAA
Found at i:39161 original size:73 final size:74
Alignment explanation
Indices: 39054--39205 Score: 236
Period size: 73 Copynumber: 2.1 Consensus size: 74
39044 AATCATCAAG
* *
39054 CATTACACTCTAACCAAGACATAATCCTTTCATATAACATTACGCTCTAACCGAGAT-GTAAGCC
1 CATTACACTCTAACCAAGACATAAGCCTTCCATATAACATTACGCTCTAACCG-GATCGTAAGCC
39118 TTCCATA-AA
65 TTCCATATAA
* * *
39127 CATTACACTCTAATCGAGACGTAAGCCTTCCATATAACATTACGCTCTAACCGGATCGTAAGCCT
1 CATTACACTCTAACCAAGACATAAGCCTTCCATATAACATTACGCTCTAACCGGATCGTAAGCCT
39192 TCCATATAA
66 TCCATATAA
39201 CATTA
1 CATTA
39206 TATCATTTGG
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
72 3 0.04
73 62 0.86
74 7 0.10
ACGTcount: A:0.35, C:0.28, G:0.10, T:0.28
Consensus pattern (74 bp):
CATTACACTCTAACCAAGACATAAGCCTTCCATATAACATTACGCTCTAACCGGATCGTAAGCCT
TCCATATAA
Found at i:41875 original size:158 final size:157
Alignment explanation
Indices: 41627--41941 Score: 425
Period size: 158 Copynumber: 2.0 Consensus size: 157
41617 GTAATACTAG
* * * * * *
41627 TGAGCCCAGCTCTAGTTGAATTAACAATAATAATTCTGTCAATTCCTGGCACCTATTGCCTAGCG
1 TGAGCCCAGCTCTAGTTGAATTAACAACAATAATCCCGTCAATTCCTGGCACCCAATGCCTAGCA
* ** * *
41692 GATAAACCGCAATATAAATTGCGCCC-AGCGCTAGTTGGGTAAACCGACGAATGTGTGCCCAACA
66 GATAAACCGCAATATAAATTGCGCCCGA-CGCTAGTCGAATAAAACGACAAATGTGTGCCCAACA
* *
41756 CTAGTAAGTTAAACTGACGAACAATAAT
130 CTAATAAGTTAAACTAACGAACAATAAT
* * *
41784 TGAGCCTAGCTCTAGTTGATTTAACCAACAATAATCCCGTCAATTCTTGGCACCCAATGCCTAGC
1 TGAGCCCAGCTCTAGTTGAATTAA-CAACAATAATCCCGTCAATTCCTGGCACCCAATGCCTAGC
* * *
41849 AGATAAACCGCAATATAATTTGCGCCCGACGCTAGTCGAATAAAACGACAAATGTGTGCCTAGCA
65 AGATAAACCGCAATATAAATTGCGCCCGACGCTAGTCGAATAAAACGACAAATGTGTGCCCAACA
*
41914 CTAATTAGTTAAACTAACGAACAATAAT
130 CTAATAAGTTAAACTAACGAACAATAAT
41942 GGAATCATTT
Statistics
Matches: 136, Mismatches: 20, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
157 22 0.16
158 113 0.83
159 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.25
Consensus pattern (157 bp):
TGAGCCCAGCTCTAGTTGAATTAACAACAATAATCCCGTCAATTCCTGGCACCCAATGCCTAGCA
GATAAACCGCAATATAAATTGCGCCCGACGCTAGTCGAATAAAACGACAAATGTGTGCCCAACAC
TAATAAGTTAAACTAACGAACAATAAT
Found at i:50908 original size:52 final size:52
Alignment explanation
Indices: 50764--50909 Score: 256
Period size: 52 Copynumber: 2.8 Consensus size: 52
50754 TATCCCAATC
*
50764 TTACGGATTATGAGGTCCGATGACTATGTGTCATCGTGAGAATATGAATCCT
1 TTACGGATTATGAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCT
* *
50816 TTACGGATTATAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATGCT
1 TTACGGATTATGAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCT
*
50868 TTACAGATTATGAGGTCCGATGACTATGTGTCATCGTGAGTA
1 TTACGGATTATGAGGTCCGATGACTATGTGTCATCGTGAGTA
50910 ATTCTTTACG
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 89 1.00
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (52 bp):
TTACGGATTATGAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCT
Found at i:68183 original size:58 final size:57
Alignment explanation
Indices: 68014--68175 Score: 234
Period size: 58 Copynumber: 2.8 Consensus size: 57
68004 GGACATCTGG
* * * *
68014 GGGTAAAATGATAATTTTGGAAAAATCGAGGTCAAAATTGGAATTTTTTAAATTTCGG
1 GGGTAAAATGGTAATTTTGGAAAAATCAAGGTCAAAA-TGGAATTTTTTAAAGTTCGA
* *
68072 GGGTAAAATGGTAATTTTGGAAAAATCAGGGTAAAAATGGAATTTTTTAAAGTTCGA
1 GGGTAAAATGGTAATTTTGGAAAAATCAAGGTCAAAATGGAATTTTTTAAAGTTCGA
* *
68129 GGGTAAAATGGTATTTTTGGAAAAAATTAAGGTCAAAATGGAATTTT
1 GGGTAAAATGGTAATTTTGG-AAAAATCAAGGTCAAAATGGAATTTT
68176 GGAAAGTTTA
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
57 37 0.40
58 56 0.60
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.33
Consensus pattern (57 bp):
GGGTAAAATGGTAATTTTGGAAAAATCAAGGTCAAAATGGAATTTTTTAAAGTTCGA
Found at i:68240 original size:29 final size:29
Alignment explanation
Indices: 68026--68242 Score: 121
Period size: 29 Copynumber: 7.5 Consensus size: 29
68016 GTAAAATGAT
*
68026 AATTTTGGAAAA-ATCGAGGTCAAAATTGG
1 AATTTTGGAAAAGTTCGAGGTCAAAA-TGG
** * *
68055 AATTTT-TTAAATTTCGGGGGT-AAAATGG
1 AATTTTGGAAAAGTTC-GAGGTCAAAATGG
* *
68083 TAATTTTGGAAAA-ATC-AGGGTAAAAATGG
1 -AATTTTGGAAAAGTTCGA-GGTCAAAATGG
**
68112 AATTTT-TTAAAGTTCGAGGGT-AAAATGG
1 AATTTTGGAAAAGTTCGA-GGTCAAAATGG
* * *
68140 TATTTTTGGAAAAAATT-AAGGTCAAAATGG
1 -AATTTTGG-AAAAGTTCGAGGTCAAAATGG
* * ** *
68170 AATTTTGG-AAAGTTTAGGGGAAAAAATGA
1 AATTTTGGAAAAG-TTCGAGGTCAAAATGG
*
68199 AATTTT-TAGAAAGTTCGAGGTCAAAATGG
1 AATTTTGGA-AAAGTTCGAGGTCAAAATGG
68228 AATTTTGGAAAAGTT
1 AATTTTGGAAAAGTT
68243 TAAGGGGTCA
Statistics
Matches: 141, Mismatches: 30, Indels: 34
0.69 0.15 0.17
Matches are distributed among these distances:
27 6 0.04
28 26 0.18
29 84 0.60
30 20 0.14
31 5 0.04
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.32
Consensus pattern (29 bp):
AATTTTGGAAAAGTTCGAGGTCAAAATGG
Found at i:68246 original size:87 final size:88
Alignment explanation
Indices: 68072--68256 Score: 218
Period size: 87 Copynumber: 2.1 Consensus size: 88
68062 TAAATTTCGG
* * *
68072 GGGT-AAAATGGTAATTTTGGAAAAATCAGGGTAAAAATGGAATTTTTTAAAGTTCGAGGGTAAA
1 GGGTCAAAATGGTAATTTTGGAAAAATCAGGGAAAAAATGAAATTTTTGAAAGTTCGAGGGTAAA
*
68136 ATGGTATTTTTGGAAAAAATTAA
66 ATGGTAATTTTGGAAAAAATTAA
** *
68159 -GGTCAAAATGG-AATTTTGGAAAGTTTAGGGGAAAAAATGAAATTTTTAGAAAGTTCGA-GGTC
1 GGGTCAAAATGGTAATTTTGGAAAAATCA-GGGAAAAAATGAAATTTTT-GAAAGTTCGAGGGT-
**
68221 AAAATGG-AATTTTGGAAAAGTTTAA
63 AAAATGGTAATTTTGGAAAAAATTAA
68246 GGGGTCAAAAT
1 -GGGTCAAAAT
68257 ATGATTCTGG
Statistics
Matches: 83, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
86 16 0.19
87 42 0.51
88 16 0.19
89 9 0.11
ACGTcount: A:0.41, C:0.03, G:0.25, T:0.30
Consensus pattern (88 bp):
GGGTCAAAATGGTAATTTTGGAAAAATCAGGGAAAAAATGAAATTTTTGAAAGTTCGAGGGTAAA
ATGGTAATTTTGGAAAAAATTAA
Found at i:69396 original size:3 final size:3
Alignment explanation
Indices: 69390--69425 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
69380 TTTTTATTTG
69390 TTA TTA TTA TTA TTA TTA TTA TTA -TA TTCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA
69426 ATAATAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:70215 original size:6 final size:6
Alignment explanation
Indices: 70163--70247 Score: 54
Period size: 6 Copynumber: 14.8 Consensus size: 6
70153 GACTTTGAAA
* * * * *
70163 TTAAAT TTAAAG TTAAGT TTAAA- AT-CAT TTCAAAT TTAAA- CTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TT-AAAT TTAAAT TTAAAT
** *
70209 TTAAAT TTAAA- ACAAAT TTAAAT TTAAA- ATAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
70248 GTCAATATAA
Statistics
Matches: 57, Mismatches: 16, Indels: 12
0.67 0.19 0.14
Matches are distributed among these distances:
4 1 0.02
5 13 0.23
6 39 0.68
7 4 0.07
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (6 bp):
TTAAAT
Found at i:70242 original size:17 final size:17
Alignment explanation
Indices: 70170--70247 Score: 95
Period size: 17 Copynumber: 4.6 Consensus size: 17
70160 AAATTAAATT
* *
70170 TAAAGTTAAGTTTAAAA
1 TAAATTTAAATTTAAAA
* *
70187 T-CATTTCAAATTTAAAC
1 TAAATTT-AAATTTAAAA
70204 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
70221 CAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
70238 TAAATTTAAA
1 TAAATTTAAA
70248 GTCAATATAA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
16 3 0.06
17 44 0.86
18 4 0.08
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:70257 original size:17 final size:17
Alignment explanation
Indices: 70204--70271 Score: 64
Period size: 17 Copynumber: 4.0 Consensus size: 17
70194 AAATTTAAAC
* *
70204 TAAATTTAAATTTAAAA
1 TAAATTTAAAATCAAAA
* * *
70221 CAAATTTAAATTTAAAA
1 TAAATTTAAAATCAAAA
* *
70238 TAAATTTAAAGTCAATA
1 TAAATTTAAAATCAAAA
*
70255 TAAACTTAAAATCAAAA
1 TAAATTTAAAATCAAAA
70272 GTTTGATCCA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 43 1.00
ACGTcount: A:0.59, C:0.06, G:0.01, T:0.34
Consensus pattern (17 bp):
TAAATTTAAAATCAAAA
Found at i:70258 original size:28 final size:28
Alignment explanation
Indices: 70193--70266 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 28
70183 AAAATCATTT
* *
70193 CAAATTTAAAC-TAAATTTAAATTTAAAA
1 CAAATATAAACTTAAA-ATAAATTTAAAA
* * *
70221 CAAATTTAAATTTAAAATAAATTTAAAGT
1 CAAATATAAACTTAAAATAAATTTAAA-A
70250 C-AATATAAACTTAAAAT
1 CAAATATAAACTTAAAAT
70267 CAAAAGTTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
28 34 0.87
29 5 0.13
ACGTcount: A:0.57, C:0.07, G:0.01, T:0.35
Consensus pattern (28 bp):
CAAATATAAACTTAAAATAAATTTAAAA
Found at i:70745 original size:3 final size:3
Alignment explanation
Indices: 70737--70773 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
70727 TTTGCAATTC
70737 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
70774 AATTTCAGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:72901 original size:28 final size:29
Alignment explanation
Indices: 72863--72937 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 29
72853 TTTCCTTTAC
*
72863 AAAGATAGCCACAAAGGC-TTCATTTAAT
1 AAAGATCGCCACAAAGGCATTCATTTAAT
* *
72891 AGAGATCGCCACAAAGGCATTTCCTTTAAT
1 AAAGATCGCCACAAAGGCA-TTCATTTAAT
* *
72921 AAAGATCACCACGAAGG
1 AAAGATCGCCACAAAGG
72938 TGTTTCCATT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 16 0.41
30 23 0.59
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.21
Consensus pattern (29 bp):
AAAGATCGCCACAAAGGCATTCATTTAAT
Found at i:72944 original size:30 final size:30
Alignment explanation
Indices: 72853--72937 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 30
72843 CACGAAGTCG
*
72853 TTTCCTTT-ACAAAGAT-AGCCACAAAGGC-
1 TTTCCTTTAATAAAGATCA-CCACAAAGGCA
* * *
72881 -TTCATTTAATAGAGATCGCCACAAAGGCA
1 TTTCCTTTAATAAAGATCACCACAAAGGCA
*
72910 TTTCCTTTAATAAAGATCACCACGAAGG
1 TTTCCTTTAATAAAGATCACCACAAAGG
72938 TGTTTCCATT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
27 6 0.13
28 16 0.36
30 23 0.51
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.26
Consensus pattern (30 bp):
TTTCCTTTAATAAAGATCACCACAAAGGCA
Found at i:73019 original size:28 final size:28
Alignment explanation
Indices: 72988--73111 Score: 108
Period size: 28 Copynumber: 4.4 Consensus size: 28
72978 TTTAAAAAAA
72988 TTTCCAAAAAGGCATTCTTAATAGAGGT
1 TTTCCAAAAAGGCATTCTTAATAGAGGT
* *
73016 TTTCCAAACAGGCGTTCTTAATAGAGGT
1 TTTCCAAAAAGGCATTCTTAATAGAGGT
* * * * * *
73044 TTGCCACAAAGTCGTTCTTAACAGAGAT
1 TTTCCAAAAAGGCATTCTTAATAGAGGT
* * *
73072 TTGCCATAAAGG-AGTTCTTGATAGA-GT
1 TTTCCAAAAAGGCA-TTCTTAATAGAGGT
*
73099 TTTGCCACAAAGG
1 TTT-CCAAAAAGG
73112 TGTTCTTACC
Statistics
Matches: 78, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
27 3 0.04
28 75 0.96
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (28 bp):
TTTCCAAAAAGGCATTCTTAATAGAGGT
Found at i:73096 original size:56 final size:55
Alignment explanation
Indices: 73002--73139 Score: 170
Period size: 56 Copynumber: 2.5 Consensus size: 55
72992 CAAAAAGGCA
* * * *
73002 TTCTTAATAGAGGTTTTCCAAACAGGCGTTCTTAATAGAGGTTTGCCACAAA-GTCG
1 TTCTTAACAGAGATTTGCCAAA-AGGAGTTCTTAATAGAGGTTTGCCACAAAGGT-G
* *
73058 TTCTTAACAGAGATTTGCCATAAAGGAGTTCTTGATAGAGTTTTGCCACAAAGGTG
1 TTCTTAACAGAGATTTGCCA-AAAGGAGTTCTTAATAGAGGTTTGCCACAAAGGTG
*
73114 TTCTTACCAGAGATTTGCCACAAAGG
1 TTCTTAACAGAGATTTGCCA-AAAGG
73140 CATGTCCTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
56 68 0.94
57 4 0.06
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (55 bp):
TTCTTAACAGAGATTTGCCAAAAGGAGTTCTTAATAGAGGTTTGCCACAAAGGTG
Found at i:73116 original size:28 final size:28
Alignment explanation
Indices: 73002--73139 Score: 145
Period size: 28 Copynumber: 4.9 Consensus size: 28
72992 CAAAAAGGCA
* * *
73002 TTCTTAATAGAGGTTTTCCA-AACAGGCG
1 TTCTTAATAGAGATTTGCCACAA-AGGTG
*
73030 TTCTTAATAGAGGTTTGCCACAAA-GTCG
1 TTCTTAATAGAGATTTGCCACAAAGGT-G
* * *
73058 TTCTTAACAGAGATTTGCCATAAAGGAG
1 TTCTTAATAGAGATTTGCCACAAAGGTG
* *
73086 TTCTTGATAGAGTTTTGCCACAAAGGTG
1 TTCTTAATAGAGATTTGCCACAAAGGTG
**
73114 TTCTTACCAGAGATTTGCCACAAAGG
1 TTCTTAATAGAGATTTGCCACAAAGG
73140 CATGTCCTTT
Statistics
Matches: 92, Mismatches: 15, Indels: 6
0.81 0.13 0.05
Matches are distributed among these distances:
27 1 0.01
28 88 0.96
29 3 0.03
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (28 bp):
TTCTTAATAGAGATTTGCCACAAAGGTG
Found at i:75219 original size:25 final size:25
Alignment explanation
Indices: 75174--75221 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
75164 AGATAGGAGG
75174 GGAATAAAAGTTTTGGAGGGAAAGT
1 GGAATAAAAGTTTTGGAGGGAAAGT
*
75199 GGAAGTAAAAGTTTTTG-GGGAAA
1 GGAA-TAAAAGTTTTGGAGGGAAA
75222 ATTAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.40, C:0.00, G:0.35, T:0.25
Consensus pattern (25 bp):
GGAATAAAAGTTTTGGAGGGAAAGT
Found at i:75319 original size:24 final size:23
Alignment explanation
Indices: 75283--75328 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
75273 ATACGGTTTA
* *
75283 TTCAAGTTATTCGAATTCGAAAG
1 TTCAACTTATTCGAACTCGAAAG
75306 TTCAACTTGATTCGAACTCGAAA
1 TTCAACTT-ATTCGAACTCGAAA
75329 TTCGAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (23 bp):
TTCAACTTATTCGAACTCGAAAG
Found at i:76252 original size:21 final size:23
Alignment explanation
Indices: 76209--76270 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 23
76199 AAAGAAATAA
*
76209 TAAAAATATTTACAAAAA-GTATTT
1 TAAAAA-A-TTACAAAAATTTATTT
76233 T-AAAAATT-CAAAAATTTATTT
1 TAAAAAATTACAAAAATTTATTT
76254 TAAAAAATTACAAAAAT
1 TAAAAAATTACAAAAAT
76271 AATTAAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
20 6 0.18
21 8 0.24
22 8 0.24
23 11 0.32
24 1 0.03
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (23 bp):
TAAAAAATTACAAAAATTTATTT
Found at i:76262 original size:22 final size:22
Alignment explanation
Indices: 76218--76270 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
76208 ATAAAAATAT
*
76218 TTACAAAAA-GTATTTTAAAAA
1 TTACAAAAATTTATTTTAAAAA
76239 TT-CAAAAATTTATTTTAAAAAA
1 TTACAAAAATTTATTTT-AAAAA
76261 TTACAAAAAT
1 TTACAAAAAT
76271 AATTAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 6 0.21
21 8 0.29
22 7 0.25
23 7 0.25
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.36
Consensus pattern (22 bp):
TTACAAAAATTTATTTTAAAAA
Found at i:76276 original size:20 final size:20
Alignment explanation
Indices: 76203--76317 Score: 67
Period size: 20 Copynumber: 5.6 Consensus size: 20
76193 TTTTTTAAAG
76203 AAATAA-TAAAAATATTTACAA
1 AAATAATTAAAAA-A-TTACAA
* *
76224 AAAGTATTTTAAAAATT-CAA
1 AAA-TAATTAAAAAATTACAA
*
76244 AAATTTATTTTAAAAAATTACAA
1 AAA--TA-ATTAAAAAATTACAA
*
76267 AAATAATT-AAAAA-TAGAA
1 AAATAATTAAAAAATTACAA
* * *
76285 AAAAAATTATAAAATAACAA
1 AAATAATTAAAAAATTACAA
*
76305 AAACAATATAAAA
1 AAATAAT-TAAAA
76318 CTTTTACTAA
Statistics
Matches: 74, Mismatches: 12, Indels: 16
0.73 0.12 0.16
Matches are distributed among these distances:
18 11 0.15
19 9 0.12
20 17 0.23
21 13 0.18
22 13 0.18
23 11 0.15
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (20 bp):
AAATAATTAAAAAATTACAA
Found at i:76279 original size:21 final size:22
Alignment explanation
Indices: 76234--76279 Score: 51
Period size: 21 Copynumber: 2.1 Consensus size: 22
76224 AAAGTATTTT
* *
76234 AAAAATT-CAAAAATTTATTTTA
1 AAAAATTACAAAAA-TTAATTAA
76256 AAAAATTACAAAAA-TAATTAA
1 AAAAATTACAAAAATTAATTAA
76277 AAA
1 AAA
76280 TAGAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
21 8 0.38
22 7 0.33
23 6 0.29
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (22 bp):
AAAAATTACAAAAATTAATTAA
Found at i:76280 original size:19 final size:19
Alignment explanation
Indices: 76256--76317 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 19
76246 ATTTATTTTA
*
76256 AAAAATTACAAAAATAATT
1 AAAAATTACAAAAAAAATT
*
76275 AAAAA-TAGAAAAAAAATT
1 AAAAATTACAAAAAAAATT
* *
76293 ATAAAATAACAAAAACAATAT
1 A-AAAATTACAAAAAAAAT-T
76314 AAAA
1 AAAA
76318 CTTTTACTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 12 0.34
19 9 0.26
20 12 0.34
21 2 0.06
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (19 bp):
AAAAATTACAAAAAAAATT
Found at i:76286 original size:18 final size:19
Alignment explanation
Indices: 76265--76317 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
76255 AAAAAATTAC
*
76265 AAAAATAATTA-AAAATAG
1 AAAAAAAATTATAAAATAG
76283 AAAAAAAATTATAAAATA-
1 AAAAAAAATTATAAAATAG
76301 ACAAAAACAA-TATAAAA
1 A-AAAAA-AATTATAAAA
76318 CTTTTACTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 11 0.35
19 18 0.58
20 2 0.06
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.19
Consensus pattern (19 bp):
AAAAAAAATTATAAAATAG
Found at i:76602 original size:27 final size:28
Alignment explanation
Indices: 76590--76654 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
76580 AATATTTATA
76590 TTTTATATTTTTTATATAATTTTATAAT
1 TTTTATATTTTTTATATAATTTTATAAT
* *
76618 TTTTCTA-TTTTTAAATAATTTTAATAAT
1 TTTTATATTTTTTATATAATTTT-ATAAT
76646 TTTTA-ATTT
1 TTTTATATTT
76655 AAATTTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 15 0.47
28 17 0.53
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (28 bp):
TTTTATATTTTTTATATAATTTTATAAT
Found at i:76648 original size:19 final size:17
Alignment explanation
Indices: 76589--76654 Score: 53
Period size: 19 Copynumber: 3.7 Consensus size: 17
76579 AAATATTTAT
*
76589 ATTTTATATTTTTTATATA
1 ATTTTATA-ATTTTA-ATA
**
76608 ATTTTATAATTTTTCTA
1 ATTTTATAATTTTAATA
*
76625 TTTTTAAATAATTTTAATA
1 ATTTT--ATAATTTTAATA
76644 ATTTT-TAATTT
1 ATTTTATAATTT
76655 AAATTTTTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
16 6 0.16
17 6 0.16
18 4 0.11
19 22 0.58
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTATAATTTTAATA
Found at i:77219 original size:31 final size:30
Alignment explanation
Indices: 77153--77226 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
77143 TCTCAAAATT
* *
77153 ATATATAAATTTTATTTTAATGTATAATTTG
1 ATATATAAATTTTAATTTAATG-ATAATTTC
*
77184 ATATATAAATTTTAATTTGATG-TAATTATAC
1 ATATATAAATTTTAATTTAATGATAATT-T-C
77215 ATATA-AAATTTT
1 ATATATAAATTTT
77227 GATTGTGGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
29 5 0.13
30 8 0.21
31 25 0.66
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.51
Consensus pattern (30 bp):
ATATATAAATTTTAATTTAATGATAATTTC
Found at i:77639 original size:16 final size:16
Alignment explanation
Indices: 77618--77650 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
77608 GGTAAAATAT
77618 TTTCTGCATTTTCCTG
1 TTTCTGCATTTTCCTG
77634 TTTCTGCATTTTCCTG
1 TTTCTGCATTTTCCTG
77650 T
1 T
77651 GTTTGTTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.24, G:0.12, T:0.58
Consensus pattern (16 bp):
TTTCTGCATTTTCCTG
Found at i:77670 original size:22 final size:22
Alignment explanation
Indices: 77645--77688 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
77635 TTCTGCATTT
77645 TCCTGTGTTTGTTTCACAGCAA
1 TCCTGTGTTTGTTTCACAGCAA
77667 TCCTGTGTTTGTTTCACAGCAA
1 TCCTGTGTTTGTTTCACAGCAA
77689 ACAGCTTGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (22 bp):
TCCTGTGTTTGTTTCACAGCAA
Found at i:77925 original size:21 final size:21
Alignment explanation
Indices: 77876--77925 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
77866 AAATCAAACT
77876 TAATA-TTATTATATTGATAA
1 TAATATTTATTATATTGATAA
* **
77896 TAA-ATTTTATTTTATTTTTAA
1 TAATA-TTTATTATATTGATAA
77917 TAATATTTA
1 TAATATTTA
77926 AAATTATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
19 1 0.04
20 3 0.12
21 19 0.79
22 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
TAATATTTATTATATTGATAA
Found at i:77993 original size:21 final size:21
Alignment explanation
Indices: 77967--78014 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
77957 ATTTTTCAAT
77967 ATTATTAAATAAACCTATTTA
1 ATTATTAAATAAACCTATTTA
77988 ATTATTAAATAAACCTATTTA
1 ATTATTAAATAAACCTATTTA
78009 ATTATT
1 ATTATT
78015 TATATTTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTATTAAATAAACCTATTTA
Found at i:78070 original size:17 final size:16
Alignment explanation
Indices: 78029--78070 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
78019 TTTAATCATA
78029 TAATAAA-TTATTAAT
1 TAATAAATTTATTAAT
*
78044 TAATATAATTTATTATTT
1 TAATA-AATTTATTA-AT
78062 TAATAAATT
1 TAATAAATT
78071 ATTTAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 5 0.22
16 2 0.09
17 10 0.43
18 6 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATAAATTTATTAAT
Found at i:78087 original size:33 final size:31
Alignment explanation
Indices: 78029--78098 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 31
78019 TTTAATCATA
78029 TAATAAATTATTAATTAATATAATTTATTATTT
1 TAATAAATTATTAATTAATATAA-TT-TTATTT
*
78062 TAATAAATTATTTAA-T-ATTTCAATTTTATTT
1 TAATAAATTA-TTAATTAATAT-AATTTTATTT
78093 TAATAA
1 TAATAA
78099 TAAATTTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
31 12 0.35
32 5 0.15
33 13 0.38
34 4 0.12
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (31 bp):
TAATAAATTATTAATTAATATAATTTTATTT
Found at i:78121 original size:15 final size:16
Alignment explanation
Indices: 78094--78124 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
78084 ATTTTATTTT
78094 AATAATAAATTTTAAA
1 AATAATAAATTTTAAA
78110 AATAAT-AATTTTAAA
1 AATAATAAATTTTAAA
78125 TA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAATAAATTTTAAA
Done.