Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012738.1 Kokia drynarioides strain JFW-HI SEQ_127749, 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: 77516
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Warning! 352 characters in sequence are not A, C, G, or T
Found at i:9195 original size:28 final size:28
Alignment explanation
Indices: 9140--9195 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
9130 AAGGTCATTA
*
9140 TGGCTGATTCTGATAAAGAAAACTTTTG
1 TGGCTGATTCTGATAAAGAAAACATTTG
* * *
9168 TGGCTGATTCTGTTAAAGGAAGCATTTG
1 TGGCTGATTCTGATAAAGAAAACATTTG
9196 CAACTATCTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.29, C:0.11, G:0.25, T:0.36
Consensus pattern (28 bp):
TGGCTGATTCTGATAAAGAAAACATTTG
Found at i:12769 original size:23 final size:23
Alignment explanation
Indices: 12734--13318 Score: 648
Period size: 23 Copynumber: 25.4 Consensus size: 23
12724 ATCTTAATTC
*
12734 TTTAAGCACAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* * **
12757 TTTAATCGTAAATCATGTTAATA
1 TTTAAGCATAAATCACATTAATA
*
12780 TTTAAGCACAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
*
12803 TTTAAGCATAAACCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* * * * * *
12826 TTTGAGAACAAACCATATAAATA
1 TTTAAGCATAAATCACATTAATA
*
12849 TTTAAGCCTAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* * * *
12872 TTTAAGCATAAATTATACTAACA
1 TTTAAGCATAAATCACATTAATA
* *
12895 TTTAAGCATAAATTACAATAATA
1 TTTAAGCATAAATCACATTAATA
* *
12918 TTTAAACATAAATCACACTAATA
1 TTTAAGCATAAATCACATTAATA
*
12941 TTTAAGCATAAATCATATTAATA
1 TTTAAGCATAAATCACATTAATA
* * * *
12964 TTTGAGTACAAATCATATTAATA
1 TTTAAGCATAAATCACATTAATA
*
12987 TTTAAGAATAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* *
13010 CTTAAGCACAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* *
13033 TTTAATCATAAATCATATTAATA
1 TTTAAGCATAAATCACATTAATA
*
13056 TTTAAGCACAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
*
13079 TTTAAGCATAAATTACATTAATA
1 TTTAAGCATAAATCACATTAATA
* * * *
13102 TTTGATCACAAATCATATTAATA
1 TTTAAGCATAAATCACATTAATA
* *
13125 TTTAAGCACAAATCAAATTAATA
1 TTTAAGCATAAATCACATTAATA
* * * *
13148 TTTGAGCACAAATCATATTAATT
1 TTTAAGCATAAATCACATTAATA
*
13171 TTTAAGCACAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* * * * *
13194 TTTGAGTACAAATCATATGAATA
1 TTTAAGCATAAATCACATTAATA
*
13217 TTTAAGCATAAATAACATTAATA
1 TTTAAGCATAAATCACATTAATA
* * *
13240 CTTAAGCACAAATAACATTAATA
1 TTTAAGCATAAATCACATTAATA
* * *
13263 TTTAATCATAAATCATATTAAAA
1 TTTAAGCATAAATCACATTAATA
*
13286 TTTAAGCACAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
13309 TTTAAGCATA
1 TTTAAGCATA
13319 GATATAAGAA
Statistics
Matches: 468, Mismatches: 94, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 468 1.00
ACGTcount: A:0.48, C:0.13, G:0.05, T:0.34
Consensus pattern (23 bp):
TTTAAGCATAAATCACATTAATA
Found at i:12795 original size:46 final size:46
Alignment explanation
Indices: 12734--13318 Score: 729
Period size: 46 Copynumber: 12.7 Consensus size: 46
12724 ATCTTAATTC
* * **
12734 TTTAAGCACAAATCACATTAATATTTAATCGTAAATCATGTTAATA
1 TTTAAGCACAAATCACATTAATATTTAAGCATAAATCACATTAATA
*
12780 TTTAAGCACAAATCACATTAATATTTAAGCATAAACCACATTAATA
1 TTTAAGCACAAATCACATTAATATTTAAGCATAAATCACATTAATA
* * * * * *
12826 TTTGAGAACAAACCATATAAATATTTAAGCCTAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATATTTAAGCATAAATCACATTAATA
* * * * * * *
12872 TTTAAGCATAAATTATACTAACATTTAAGCATAAATTACAATAATA
1 TTTAAGCACAAATCACATTAATATTTAAGCATAAATCACATTAATA
* * * *
12918 TTTAAACATAAATCACACTAATATTTAAGCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATATTTAAGCATAAATCACATTAATA
* * * *
12964 TTTGAGTACAAATCATATTAATATTTAAGAATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATATTTAAGCATAAATCACATTAATA
* * *
13010 CTTAAGCACAAATCACATTAATATTTAATCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATATTTAAGCATAAATCACATTAATA
*
13056 TTTAAGCACAAATCACATTAATATTTAAGCATAAATTACATTAATA
1 TTTAAGCACAAATCACATTAATATTTAAGCATAAATCACATTAATA
* * * * *
13102 TTTGATCACAAATCATATTAATATTTAAGCACAAATCAAATTAATA
1 TTTAAGCACAAATCACATTAATATTTAAGCATAAATCACATTAATA
* * * *
13148 TTTGAGCACAAATCATATTAATTTTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATATTTAAGCATAAATCACATTAATA
* * * * *
13194 TTTGAGTACAAATCATATGAATATTTAAGCATAAATAACATTAATA
1 TTTAAGCACAAATCACATTAATATTTAAGCATAAATCACATTAATA
* * * * *
13240 CTTAAGCACAAATAACATTAATATTTAATCATAAATCATATTAAAA
1 TTTAAGCACAAATCACATTAATATTTAAGCATAAATCACATTAATA
13286 TTTAAGCACAAATCACATTAATATTTAAGCATA
1 TTTAAGCACAAATCACATTAATATTTAAGCATA
13319 GATATAAGAA
Statistics
Matches: 463, Mismatches: 76, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 463 1.00
ACGTcount: A:0.48, C:0.13, G:0.05, T:0.34
Consensus pattern (46 bp):
TTTAAGCACAAATCACATTAATATTTAAGCATAAATCACATTAATA
Found at i:16247 original size:24 final size:24
Alignment explanation
Indices: 16201--16256 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 24
16191 AATCAATCCA
* *
16201 TTTACTATTAATTTGCTCTGACAT
1 TTTACTATTAATTTGCACCGACAT
16225 TTTA-TATTACATTTGCACCGACAAAT
1 TTTACTATTA-ATTTGCACCGAC--AT
16251 TTTACT
1 TTTACT
16257 CTTTACTCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 5 0.19
24 14 0.54
26 6 0.23
27 1 0.04
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.46
Consensus pattern (24 bp):
TTTACTATTAATTTGCACCGACAT
Found at i:17800 original size:29 final size:30
Alignment explanation
Indices: 17768--17835 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
17758 TTAATTTGGT
* *
17768 CTAATTTAATTCT-TTTAATCGTACATAAA
1 CTAATTTAATTCTATTTAATAGTACAGAAA
* * *
17797 CTAAATTGA-TCTATTTAATAGTAGAGAAA
1 CTAATTTAATTCTATTTAATAGTACAGAAA
17826 CTAATTTAAT
1 CTAATTTAAT
17836 AAGATCTCTA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
28 3 0.10
29 27 0.90
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (30 bp):
CTAATTTAATTCTATTTAATAGTACAGAAA
Found at i:26618 original size:29 final size:25
Alignment explanation
Indices: 26556--26616 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
26546 CATAAACACT
*
26556 AATCATTCATTGCTGAAACAATTTC
1 AATCATTCATTGCCGAAACAATTTC
*
26581 AATCATTCATTGCCGAAACAATTCC
1 AATCATTCATTGCCGAAACAATTTC
*
26606 AGTCATTCATT
1 AATCATTCATT
26617 CAAAAATAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.34, C:0.23, G:0.08, T:0.34
Consensus pattern (25 bp):
AATCATTCATTGCCGAAACAATTTC
Found at i:37321 original size:188 final size:187
Alignment explanation
Indices: 36863--37384 Score: 643
Period size: 188 Copynumber: 2.8 Consensus size: 187
36853 TTTAACATTA
* *
36863 TTTTGACCCACTTCTCTGTACATTACCAGGAAGATGAGATTTGAAGTCTCACTCCACTCCATTGT
1 TTTTGACCCA-TTCTCTGTACCTCACCAGGAAGATGAGATTTGAAGTCTCACTCCACTCCATTGT
* * *
36928 ATCCTTAGGGATGTTGAGATCTACTTCGTTATTTTAATTTGACCCACTGCAACTCAAGGGTATAG
65 ATCCTTAGGGACGTTGAGATCTACTTCGTTATTTTAATCTGACCCACTGCAACTCAGGGGTATAG
* * *
36993 GATTTGGTATTTCACTCCACTCCACTCCATTGTAACATCAAGGACGTTGAGATCTGCTTTG
130 GATTTAGTACTTCACTCCACTCCAC-CC--TGTAACATCAAGGACGTTGAGATCCGCTTTG
* * * * * * *
37054 TTTTGACCCATTTCTTTGTACCTCTCTAAGAAAATGGGATTTGAAGTCTCACTCCATTCCATTGT
1 TTTTGACCCA-TTCTCTGTACCTCACCAGGAAGATGAGATTTGAAGTCTCACTCCACTCCATTGT
* * * * **
37119 ATCATCAAGGACGTTGAGATCTACTTTGTTATTTTTAATCCAACCCACTGCAACTCAGGGGGTAT
65 ATCCTTAGGGACGTTGAGATCTACTTCGTTA-TTTTAATCTGACCCACTGCAACTCA-GGGGTAT
* * * *
37184 AGGATTTAGTACTTCACTCCATTCCA-CC-GTAACCTTAGGGACGTTGAGATCCGCTTTG
128 AGGATTTAGTACTTCACTCCACTCCACCCTGTAACATCAAGGACGTTGAGATCCGCTTTG
* * * * * *
37242 TTTTGACACATTCCTCTGTACCTCACCAGGAAGATGAGATTTGAAGTTTTAGTCCAGTCCACTGT
1 TTTTGACCCATT-CTCTGTACCTCACCAGGAAGATGAGATTTGAAGTCTCACTCCACTCCATTGT
* * * *
37307 ATCCTTAGGGACGTTGAGATCTACTTCGTTGTTTTAATCTGACCCACTACAATTCAGAGGTATAG
65 ATCCTTAGGGACGTTGAGATCTACTTCGTTATTTTAATCTGACCCACTGCAACTCAGGGGTATAG
37372 GATTTAGTACTTC
130 GATTTAGTACTTC
37385 TTGGTCCATT
Statistics
Matches: 280, Mismatches: 48, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
186 21 0.08
187 23 0.08
188 102 0.36
191 83 0.30
192 22 0.08
193 29 0.10
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.35
Consensus pattern (187 bp):
TTTTGACCCATTCTCTGTACCTCACCAGGAAGATGAGATTTGAAGTCTCACTCCACTCCATTGTA
TCCTTAGGGACGTTGAGATCTACTTCGTTATTTTAATCTGACCCACTGCAACTCAGGGGTATAGG
ATTTAGTACTTCACTCCACTCCACCCTGTAACATCAAGGACGTTGAGATCCGCTTTG
Found at i:50671 original size:57 final size:57
Alignment explanation
Indices: 50602--50716 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
50592 TAGGAGGGAC
50602 TAAACTAGAAAATTTCCCTTTTATATTTGTAAAGTTCATCGTCGAAACGATGATGTT
1 TAAACTAGAAAATTTCCCTTTTATATTTGTAAAGTTCATCGTCGAAACGATGATGTT
50659 TAAACTAGAAAATTTCCCTTTTATATTTGTAAAGTTCATCGTCGAAACGATGATGTT
1 TAAACTAGAAAATTTCCCTTTTATATTTGTAAAGTTCATCGTCGAAACGATGATGTT
50716 T
1 T
50717 CAGAGCCACT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (57 bp):
TAAACTAGAAAATTTCCCTTTTATATTTGTAAAGTTCATCGTCGAAACGATGATGTT
Found at i:56490 original size:9 final size:9
Alignment explanation
Indices: 56472--56526 Score: 52
Period size: 9 Copynumber: 6.9 Consensus size: 9
56462 GTCAATAAAT
56472 AATT-TTAA
1 AATTATTAA
56480 AATTATTAA
1 AATTATTAA
56489 AATTATT--
1 AATTATTAA
*
56496 --TTTTTAA
1 AATTATTAA
56503 AA-TA-TAA
1 AATTATTAA
56510 AATTATTAA
1 AATTATTAA
56519 AATTATTA
1 AATTATTA
56527 TATTATATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
5 4 0.11
7 5 0.13
8 7 0.18
9 22 0.58
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
AATTATTAA
Found at i:56550 original size:37 final size:38
Alignment explanation
Indices: 56472--56568 Score: 135
Period size: 37 Copynumber: 2.6 Consensus size: 38
56462 GTCAATAAAT
* *
56472 AATT-TTAAAATTATTAAAATTATTTTTTTAAAATATAA
1 AATTATTAAAATTATT-ATATTATTATTTTAAAATATAA
*
56510 AATTATTAAAATTATTATATTA-TATTTTGAAATATAA
1 AATTATTAAAATTATTATATTATTATTTTAAAATATAA
*
56547 AATTATTAAAATCATTATATTA
1 AATTATTAAAATTATTATATTA
56569 AATTCTATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
37 34 0.63
38 9 0.17
39 11 0.20
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (38 bp):
AATTATTAAAATTATTATATTATTATTTTAAAATATAA
Found at i:57228 original size:27 final size:27
Alignment explanation
Indices: 57194--57247 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
57184 TTCAAAATCA
57194 AAAACCCTAAACAAAAATCCCCAAATT
1 AAAACCCTAAACAAAAATCCCCAAATT
* * *
57221 AAAACCCTTACCCAAAATCCCCAAATT
1 AAAACCCTAAACAAAAATCCCCAAATT
57248 TGACCACCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (27 bp):
AAAACCCTAAACAAAAATCCCCAAATT
Found at i:57279 original size:23 final size:23
Alignment explanation
Indices: 57230--57279 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
57220 TAAAACCCTT
* *
57230 ACCCAAAATCCCCAAATTTGACC
1 ACCCAAAATCCCCAAATTTAACA
57253 ACCCAAAATCCCC-AATTTCAACA
1 ACCCAAAATCCCCAAATTT-AACA
57276 ACCC
1 ACCC
57280 TAAACAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.40, C:0.42, G:0.02, T:0.16
Consensus pattern (23 bp):
ACCCAAAATCCCCAAATTTAACA
Found at i:57765 original size:29 final size:30
Alignment explanation
Indices: 57724--57793 Score: 108
Period size: 29 Copynumber: 2.4 Consensus size: 30
57714 CGTTCTATTG
57724 TAATAATTTTATATTTCAAAATAA-TAA-TA
1 TAATAATTTTATATTTCAAAA-AATTAATTA
*
57753 TAATAATTTTATATTTCAAAAAATTAATTT
1 TAATAATTTTATATTTCAAAAAATTAATTA
57783 TAATAATTTTA
1 TAATAATTTTA
57794 AAACATCTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
28 2 0.05
29 24 0.63
30 12 0.32
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (30 bp):
TAATAATTTTATATTTCAAAAAATTAATTA
Found at i:58443 original size:34 final size:34
Alignment explanation
Indices: 58404--58469 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
58394 TTATAATATC
*
58404 ACTATCATATTTAATCTCACCACCACCGCTATAA
1 ACTATCATATCTAATCTCACCACCACCGCTATAA
58438 ACTATCATATCTAATCTCACCACCACCGCTAT
1 ACTATCATATCTAATCTCACCACCACCGCTAT
58470 TTTTACACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.29
Consensus pattern (34 bp):
ACTATCATATCTAATCTCACCACCACCGCTATAA
Found at i:60837 original size:153 final size:153
Alignment explanation
Indices: 60559--61027 Score: 841
Period size: 153 Copynumber: 3.1 Consensus size: 153
60549 ATATCTTTAA
*
60559 AATATTGTATTAAAATCAATTTATACGAAATAAACATACCCTTGCCTTTTCAACTATTAATCTTC
1 AATATTGTATTAAAATCAATTTATATGAAATAAACATACCCTTGCCTTTTCAACTATTAATCTTC
*
60624 AAGAAGAGATTGATTTAAGTAAGGCTGGATTGTGAACTTTCAAACCTTATCTCCACTTTTTCTTT
66 AAGAAGAGACTGATTTAAGTAAGGCTGGATTGTGAACTTTCAAACCTTATCTCCACTTTTTCTTT
60689 TTGAATTTAGACCAAGTAAGATG
131 TTGAATTTAGACCAAGTAAGATG
*
60712 AATATTGTATTAAAATCAATTTATATGAAATAAACATACCCTTGCCTTTTCAACTATTACTCTTC
1 AATATTGTATTAAAATCAATTTATATGAAATAAACATACCCTTGCCTTTTCAACTATTAATCTTC
*
60777 AAGAAGAGACTGATTTAAGTAAGGCTGGATTGTGAACTTTCAAACCTTATCTCTACTTTTTCTTT
66 AAGAAGAGACTGATTTAAGTAAGGCTGGATTGTGAACTTTCAAACCTTATCTCCACTTTTTCTTT
*
60842 TTGAATTTAGACTAAGTAAGATG
131 TTGAATTTAGACCAAGTAAGATG
* * *
60865 AGTAGTGTATTAAAATCAATTTATATGAAATAAACATACCCTTGCCTTTTCAAGTATTAATCTTC
1 AATATTGTATTAAAATCAATTTATATGAAATAAACATACCCTTGCCTTTTCAACTATTAATCTTC
*
60930 AAGAAGAGACTGATTTAAGTAAGGCTGGATTGTGAACTTTCAAACCTTATCTCCACGTTTTCTTT
66 AAGAAGAGACTGATTTAAGTAAGGCTGGATTGTGAACTTTCAAACCTTATCTCCACTTTTTCTTT
60995 TTGAATTTAGACCAAGTAAGATG
131 TTGAATTTAGACCAAGTAAGATG
61018 AAGT-TTGTAT
1 AA-TATTGTAT
61028 ATTCCATCAG
Statistics
Matches: 301, Mismatches: 14, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
153 300 1.00
154 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (153 bp):
AATATTGTATTAAAATCAATTTATATGAAATAAACATACCCTTGCCTTTTCAACTATTAATCTTC
AAGAAGAGACTGATTTAAGTAAGGCTGGATTGTGAACTTTCAAACCTTATCTCCACTTTTTCTTT
TTGAATTTAGACCAAGTAAGATG
Found at i:67581 original size:33 final size:35
Alignment explanation
Indices: 67544--67626 Score: 98
Period size: 40 Copynumber: 2.3 Consensus size: 35
67534 TCTTGATGTA
*
67544 ATTTGTTTATATT-T-GTTAGAAATTACATCTTAT
1 ATTTGTTTATATTATGGTTAGAAATTACAGCTTAT
67577 ATTTGTTTATATTAAAAGATGGTTAGAAATTACAGCTTAT
1 ATTTGTTTATATT-----ATGGTTAGAAATTACAGCTTAT
67617 ATTTGTTTAT
1 ATTTGTTTAT
67627 CACTTTATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
33 13 0.31
39 1 0.02
40 28 0.67
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.51
Consensus pattern (35 bp):
ATTTGTTTATATTATGGTTAGAAATTACAGCTTAT
Found at i:68278 original size:33 final size:33
Alignment explanation
Indices: 68234--68317 Score: 141
Period size: 33 Copynumber: 2.5 Consensus size: 33
68224 AGAAATCTAT
* *
68234 CAAACACCAGAAAATATTTTACATAGATTCATC
1 CAAACATCAGAAAATATTTTACACAGATTCATC
*
68267 CAAACATCAGAAAATATTTTACACAGGTTCATC
1 CAAACATCAGAAAATATTTTACACAGATTCATC
68300 CAAACATCAGAAAATATT
1 CAAACATCAGAAAATATT
68318 AACTTTTCCA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.46, C:0.20, G:0.07, T:0.26
Consensus pattern (33 bp):
CAAACATCAGAAAATATTTTACACAGATTCATC
Found at i:73794 original size:21 final size:21
Alignment explanation
Indices: 73764--73843 Score: 63
Period size: 21 Copynumber: 3.6 Consensus size: 21
73754 ATCAATTCAA
73764 AAACA-ATCAATTTGCATACC
1 AAACACATCAATTTGCATACC
* *
73784 AAACACATCAATAATTCTCATAATTC
1 AAACACATCAAT--TT-GCAT-A-CC
* *
73810 AAAAACAATCAATTTGCATGCC
1 AAACAC-ATCAATTTGCATACC
73832 AAACACATCAAT
1 AAACACATCAAT
73844 AATTCTCATA
Statistics
Matches: 46, Mismatches: 7, Indels: 13
0.70 0.11 0.20
Matches are distributed among these distances:
20 5 0.11
21 12 0.26
22 6 0.13
23 2 0.04
24 6 0.13
25 3 0.07
26 6 0.13
27 6 0.13
ACGTcount: A:0.47, C:0.24, G:0.04, T:0.25
Consensus pattern (21 bp):
AAACACATCAATTTGCATACC
Found at i:73805 original size:24 final size:24
Alignment explanation
Indices: 73778--73860 Score: 84
Period size: 24 Copynumber: 3.5 Consensus size: 24
73768 AATCAATTTG
73778 CATACCAAACACATCAATAATTCT
1 CATACCAAACACATCAATAATTCT
*
73802 CATAATTCAAA-A-A-CAATCAATT-T
1 CAT-A-CCAAACACATCAAT-AATTCT
*
73825 GCATGCCAAACACATCAATAATTCT
1 -CATACCAAACACATCAATAATTCT
73850 CATACCAAACA
1 CATACCAAACA
73861 GCTTGTTTAC
Statistics
Matches: 47, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
22 4 0.09
23 6 0.13
24 26 0.55
25 7 0.15
26 4 0.09
ACGTcount: A:0.47, C:0.27, G:0.02, T:0.24
Consensus pattern (24 bp):
CATACCAAACACATCAATAATTCT
Found at i:73817 original size:48 final size:48
Alignment explanation
Indices: 73757--73853 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
73747 GCATATAATC
73757 AATTCAAAAACAATCAATTTGCATACCAAACACATCAATAATTCTCAT
1 AATTCAAAAACAATCAATTTGCATACCAAACACATCAATAATTCTCAT
*
73805 AATTCAAAAACAATCAATTTGCATGCCAAACACATCAATAATTCTCAT
1 AATTCAAAAACAATCAATTTGCATACCAAACACATCAATAATTCTCAT
73853 A
1 A
73854 CCAAACAGCT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.47, C:0.23, G:0.03, T:0.27
Consensus pattern (48 bp):
AATTCAAAAACAATCAATTTGCATACCAAACACATCAATAATTCTCAT
Found at i:73934 original size:14 final size:15
Alignment explanation
Indices: 73904--74030 Score: 107
Period size: 15 Copynumber: 8.7 Consensus size: 15
73894 TCACATGAAC
* *
73904 AGTTCACACATAAAT
1 AGTTCACATACAAAT
*
73919 AGTTTACATA-AAAT
1 AGTTCACATACAAAT
* *
73933 AGTTCACATATAAAC
1 AGTTCACATACAAAT
*
73948 AGTTCGCATACAAAT
1 AGTTCACATACAAAT
* * **
73963 AGTTCACAAATAAGC
1 AGTTCACATACAAAT
**
73978 AGTTCGTATAC-AAT
1 AGTTCACATACAAAT
*
73992 AGTTCACATATAAAT
1 AGTTCACATACAAAT
*
74007 AGTTCGCATAC-AAT
1 AGTTCACATACAAAT
74021 AGTTCACATA
1 AGTTCACATA
74031 TAAACAGTTT
Statistics
Matches: 86, Mismatches: 24, Indels: 5
0.75 0.21 0.04
Matches are distributed among these distances:
14 34 0.40
15 52 0.60
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.29
Consensus pattern (15 bp):
AGTTCACATACAAAT
Found at i:74046 original size:29 final size:29
Alignment explanation
Indices: 73904--74047 Score: 189
Period size: 29 Copynumber: 4.9 Consensus size: 29
73894 TCACATGAAC
* * ** *
73904 AGTTCACACATAAATAGTTTACATAAAAT
1 AGTTCACATATAAACAGTTCGCATACAAT
73933 AGTTCACATATAAACAGTTCGCATACAAAT
1 AGTTCACATATAAACAGTTCGCATAC-AAT
* * *
73963 AGTTCACAAATAAGCAGTTCGTATACAAT
1 AGTTCACATATAAACAGTTCGCATACAAT
*
73992 AGTTCACATATAAATAGTTCGCATACAAT
1 AGTTCACATATAAACAGTTCGCATACAAT
*
74021 AGTTCACATATAAACAGTTTGCATACA
1 AGTTCACATATAAACAGTTCGCATACA
74048 TATAAGCAAA
Statistics
Matches: 100, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
29 74 0.74
30 26 0.26
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.29
Consensus pattern (29 bp):
AGTTCACATATAAACAGTTCGCATACAAT
Found at i:74245 original size:43 final size:43
Alignment explanation
Indices: 74184--74288 Score: 156
Period size: 43 Copynumber: 2.4 Consensus size: 43
74174 AATAGCCATA
* *
74184 TAAGTGTAGCACGAATGCTTGTACTCTCCGAATACACTGCCTG
1 TAAGTGTAGCACGAATGCTTGTACTCTCCAAAAACACTGCCTG
* * * *
74227 TAAGTGCAGCACAAATGCTTGTACTCTCTAAAAACACTGCTTG
1 TAAGTGTAGCACGAATGCTTGTACTCTCCAAAAACACTGCCTG
74270 TAAGTGTAGCACGAATGCT
1 TAAGTGTAGCACGAATGCT
74289 CACATCGAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.28
Consensus pattern (43 bp):
TAAGTGTAGCACGAATGCTTGTACTCTCCAAAAACACTGCCTG
Found at i:74477 original size:75 final size:76
Alignment explanation
Indices: 74316--74477 Score: 182
Period size: 75 Copynumber: 2.1 Consensus size: 76
74306 CACACATTTC
* * * * * * *
74316 AATCTGTCGTCTCGGATTGCCAAGCAATGATGAACTACCACCTCAGATTGCTCAGTAACAATGGT
1 AATCTGTCATCCCAGATTGCCAAGCAACGATGAACTACCAACTCAGATTCCCCAGTAACAATGGT
**
74381 TTATTGAATCA
66 TTATCAAATCA
* * * * **
74392 AATCTATCATCCCAGATTGCCCAGCAACGATGACCTACCAACT-GGATTCCCCAGTAATGATGGT
1 AATCTGTCATCCCAGATTGCCAAGCAACGATGAACTACCAACTCAGATTCCCCAGTAACAATGGT
74456 TTATCAAATCA
66 TTATCAAATCA
74467 AATCTGTCATC
1 AATCTGTCATC
74478 TTAAGTTGTC
Statistics
Matches: 70, Mismatches: 16, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
75 35 0.50
76 35 0.50
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (76 bp):
AATCTGTCATCCCAGATTGCCAAGCAACGATGAACTACCAACTCAGATTCCCCAGTAACAATGGT
TTATCAAATCA
Found at i:75179 original size:21 final size:21
Alignment explanation
Indices: 75144--75217 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
75134 TACCATATGT
* * *
75144 AAGAGGTCACACAACATGTAA
1 AAGAGTTCGCACAACATATAA
* *
75165 AAGTGTTCGCACAACATCTAA
1 AAGAGTTCGCACAACATATAA
* *
75186 AAAAGTTCGCATAACATATAA
1 AAGAGTTCGCACAACATATAA
75207 AAGAGTTCGCA
1 AAGAGTTCGCA
75218 TATGCATGTA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.45, C:0.19, G:0.16, T:0.20
Consensus pattern (21 bp):
AAGAGTTCGCACAACATATAA
Found at i:76932 original size:29 final size:29
Alignment explanation
Indices: 76874--76958 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 29
76864 AACATGCGAC
* *
76874 AACACAACACAGAATAAGATCATA-ATAAT
1 AACACAACACAGAATAATATCACACA-AAT
* *
76903 AACACAACTCAGAATAATATGACACAAAT
1 AACACAACACAGAATAATATCACACAAAT
* * *
76932 AACTCAACAAAGAGTAATATCACACAA
1 AACACAACACAGAATAATATCACACAA
76959 CAAAATGTAT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
29 45 0.98
30 1 0.02
ACGTcount: A:0.56, C:0.20, G:0.07, T:0.16
Consensus pattern (29 bp):
AACACAACACAGAATAATATCACACAAAT
Done.