Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014775.1 Kokia drynarioides strain JFW-HI SEQ_129816, 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: 205922
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 27 characters in sequence are not A, C, G, or T
Found at i:987 original size:2 final size:2
Alignment explanation
Indices: 980--1004 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
970 NNNNNNNNNN
980 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1005 CCAGGTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2660 original size:7 final size:7
Alignment explanation
Indices: 2648--2679 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
2638 ACAATATGGT
2648 TTTTATG
1 TTTTATG
2655 TTTTATG
1 TTTTATG
2662 TTTTATG
1 TTTTATG
2669 TTTTATG
1 TTTTATG
2676 TTTT
1 TTTT
2680 TTATTTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.75
Consensus pattern (7 bp):
TTTTATG
Found at i:2686 original size:14 final size:14
Alignment explanation
Indices: 2648--2691 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
2638 ACAATATGGT
*
2648 TTTTATGTTTTATG
1 TTTTATATTTTATG
*
2662 TTTTATGTTTTATG
1 TTTTATATTTTATG
*
2676 TTTTTTATTTT-TG
1 TTTTATATTTTATG
2689 TTT
1 TTT
2692 ATTGTTAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
13 5 0.18
14 23 0.82
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.77
Consensus pattern (14 bp):
TTTTATATTTTATG
Found at i:2686 original size:21 final size:20
Alignment explanation
Indices: 2648--2691 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
2638 ACAATATGGT
*
2648 TTTTATGTTTTATGTTTTATG
1 TTTTATGTTTTATATTTT-TG
*
2669 TTTTATGTTTTTTATTTTTG
1 TTTTATGTTTTATATTTTTG
2689 TTT
1 TTT
2692 ATTGTTAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.77
Consensus pattern (20 bp):
TTTTATGTTTTATATTTTTG
Found at i:5335 original size:17 final size:17
Alignment explanation
Indices: 5315--5361 Score: 85
Period size: 17 Copynumber: 2.8 Consensus size: 17
5305 CCATAACTCG
*
5315 CACATTTACACAGCCCA
1 CACATTGACACAGCCCA
5332 CACATTGACACAGCCCA
1 CACATTGACACAGCCCA
5349 CACATTGACACAG
1 CACATTGACACAG
5362 TTCGCATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.36, C:0.38, G:0.11, T:0.15
Consensus pattern (17 bp):
CACATTGACACAGCCCA
Found at i:5376 original size:17 final size:17
Alignment explanation
Indices: 5356--5521 Score: 167
Period size: 17 Copynumber: 9.9 Consensus size: 17
5346 CCACACATTG
*
5356 ACACAGTTCGCATATAA
1 ACACAGCTCGCATATAA
* *
5373 ACACA--TACACATTTAA
1 ACACAGCT-CGCATATAA
* *
5389 ACATAGCTAGCATATAA
1 ACACAGCTCGCATATAA
*
5406 ATACAGCTCGCATATAA
1 ACACAGCTCGCATATAA
* *
5423 ACATAGCTAGCATAT-A
1 ACACAGCTCGCATATAA
5439 ACACAGCTCGCATATAA
1 ACACAGCTCGCATATAA
* * *
5456 CCACAACTCTCATATAA
1 ACACAGCTCGCATATAA
* *
5473 ACATAGCTAGCATATAA
1 ACACAGCTCGCATATAA
*
5490 ACACAGCTCGTATATAA
1 ACACAGCTCGCATATAA
*
5507 ACACAACTCGCATAT
1 ACACAGCTCGCATAT
5522 TCAAGTAATC
Statistics
Matches: 118, Mismatches: 27, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
15 1 0.01
16 25 0.21
17 91 0.77
18 1 0.01
ACGTcount: A:0.43, C:0.25, G:0.09, T:0.23
Consensus pattern (17 bp):
ACACAGCTCGCATATAA
Found at i:9928 original size:32 final size:31
Alignment explanation
Indices: 9861--9928 Score: 73
Period size: 32 Copynumber: 2.2 Consensus size: 31
9851 GAGATTTTGG
* * * **
9861 TTTAGGTTTCAAATTTTGGGGATTTTCGGGT
1 TTTAGATTTCAAATTTTAGAGATTTTCGGAA
*
9892 TTTAGATTTCAAAATTTTAGAGATTTTTGGAA
1 TTTAGATTTC-AAATTTTAGAGATTTTCGGAA
9924 TTTAG
1 TTTAG
9929 GTTTGGGTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
31 9 0.30
32 21 0.70
ACGTcount: A:0.25, C:0.04, G:0.22, T:0.49
Consensus pattern (31 bp):
TTTAGATTTCAAATTTTAGAGATTTTCGGAA
Found at i:10918 original size:30 final size:29
Alignment explanation
Indices: 10870--10971 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 29
10860 ATTAAAATTA
10870 TTTAATAATTTTATTATTTAAAAAAAATAAT
1 TTTAATAATTTTA-TATTT-AAAAAAATAAT
10901 TTTAATAATTTTATATTT-AAAAAATAAT
1 TTTAATAATTTTATATTTAAAAAAATAAT
* * *
10929 TTAAAAAAATTTATATTTTAAAAAAATAAT
1 TTTAATAATTTTATA-TTTAAAAAAATAAT
*
10959 TTTAATATTTTTA
1 TTTAATAATTTTA
10972 AATCATTTGC
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
28 22 0.35
29 3 0.05
30 24 0.39
31 13 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
TTTAATAATTTTATATTTAAAAAAATAAT
Found at i:10968 original size:28 final size:28
Alignment explanation
Indices: 10875--10968 Score: 95
Period size: 28 Copynumber: 3.3 Consensus size: 28
10865 AATTATTTAA
*
10875 TAAT-TTTATTATTTAAAAAAAATAATTT
1 TAATATTTA-TATTTTAAAAAAATAATTT
10903 TAATAATTT-TATATTT-AAAAAATAATTT
1 TAAT-ATTTATAT-TTTAAAAAAATAATTT
* *
10931 AAAAAAATTTATATTTTAAAAAAATAATTT
1 --TAATATTTATATTTTAAAAAAATAATTT
10961 TAATATTT
1 TAATATTT
10969 TTAAATCATT
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
28 25 0.46
29 9 0.17
30 20 0.37
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TAATATTTATATTTTAAAAAAATAATTT
Found at i:11544 original size:24 final size:25
Alignment explanation
Indices: 11515--11564 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
11505 ATTATAATGT
11515 TTAATA-ATTGATATAC-ATATAATA
1 TTAATATATT-ATATACTATATAATA
*
11539 TTAATATATTATATACTATATGATA
1 TTAATATATTATATACTATATAATA
11564 T
1 T
11565 GATATAGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (25 bp):
TTAATATATTATATACTATATAATA
Found at i:11667 original size:248 final size:256
Alignment explanation
Indices: 11205--11697 Score: 594
Period size: 248 Copynumber: 2.0 Consensus size: 256
11195 TTAATTTTGT
* * *
11205 TATTATACCTATAGATTATAATAACATATATAGTATTACATGATATTATAATATTTAATCATTGA
1 TATTATACATATAGATTATAATAAAATATATAGTATTACATGATATTATAATATTTAATCAAT-A
* * * * * * * *
11270 TGCATATACATTTATATATGTAAAACTATTAATATATTATGTTATATGATGTGGTATTATATAAT
65 TGCATATACATATATATATGTAAAACTATTAATATACTATATGATATGATATAGCATTACATAAT
* * * * *
11335 ATATTAGGAGGACTAACTTTCAACTGTACAAAAAATATATAGATTTAAAGCATATTTTAACTAGT
130 ATAATAGGAGGACTAACTTTCAAATGTACAAAAAATATATAGACTTAAAGCATATTTCAACCAGT
* *
11400 ATAATAATAAACTATAATATATAATAATAAGTAATATATATTGTATTACTATTACATATAAC
195 ATAATAATAAACAATAATATATAATAATAAGTAATATATATTGTACTACTATTACATATAAC
* *
11462 TATTATA-ATATATATTATAATAAAATATATAGTATTACATGATATTATAATGTTTAAT-AAT-T
1 TATTATACATATAGATTATAATAAAATATATAGTATTACATGATATTATAATATTTAATCAATAT
*
11524 G-ATATACATATA-ATAT-TAATA-TATT-ATATACTATATGATATGATATAGCATTACATAATA
66 GCATATACATATATATATGTAAAACTATTAATATACTATATGATATGATATAGCATTACATAATA
* ** * *
11584 TAATAGGA-GATCTAACTTTTAAATGTATGAAAAGTATA-AGAACTTACAA-TATATTTCAACCA
131 TAATAGGAGGA-CTAACTTTCAAATGTACAAAAAATATATAG-ACTTA-AAGCATATTTCAACCA
* * * * *
11646 GTATAATAATAACCAATAATATATGATTATAATTAATATATTTTGTACTACT
193 GTATAATAATAAACAATAATATATAATAATAAGTAATATATATTGTACTACT
11698 CAACTAAAAT
Statistics
Matches: 202, Mismatches: 31, Indels: 15
0.81 0.12 0.06
Matches are distributed among these distances:
247 4 0.02
248 116 0.57
249 6 0.03
250 4 0.02
251 4 0.02
252 10 0.05
253 2 0.01
255 2 0.01
256 47 0.23
257 7 0.03
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.40
Consensus pattern (256 bp):
TATTATACATATAGATTATAATAAAATATATAGTATTACATGATATTATAATATTTAATCAATAT
GCATATACATATATATATGTAAAACTATTAATATACTATATGATATGATATAGCATTACATAATA
TAATAGGAGGACTAACTTTCAAATGTACAAAAAATATATAGACTTAAAGCATATTTCAACCAGTA
TAATAATAAACAATAATATATAATAATAAGTAATATATATTGTACTACTATTACATATAAC
Found at i:22111 original size:20 final size:20
Alignment explanation
Indices: 22088--22137 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
22078 TTTTTTCATG
*
22088 AGTATCGATATTTTTATAA-A
1 AGTATCGATAGTTTTA-AATA
* *
22108 AGTATTGATAGTTTTAAATC
1 AGTATCGATAGTTTTAAATA
22128 AGTATCGATA
1 AGTATCGATA
22138 CCAAATTGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42
Consensus pattern (20 bp):
AGTATCGATAGTTTTAAATA
Found at i:22305 original size:4 final size:4
Alignment explanation
Indices: 22296--22329 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
22286 GAAATGCGTG
*
22296 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AGAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
22330 TTTAAGTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:28385 original size:20 final size:20
Alignment explanation
Indices: 28339--28408 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
28329 TTTTGAAGTG
* * *
28339 TTAAAATGATTTTGACTTGG
1 TTAAAATTATTTTAACTTGT
* *
28359 TTCAAATTATTTTAACATGT
1 TTAAAATTATTTTAACTTGT
*
28379 TTAAAATCATTTTAACTTGATT
1 TTAAAATTATTTTAACTTG--T
28401 TTAAAATT
1 TTAAAATT
28409 CTTTCAAACT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 31 0.79
22 8 0.21
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.49
Consensus pattern (20 bp):
TTAAAATTATTTTAACTTGT
Found at i:29621 original size:20 final size:20
Alignment explanation
Indices: 29598--29638 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
29588 CTCTTCTATT
*
29598 GATACAATTATAG-TTCTACC
1 GATACAAGTAT-GCTTCTACC
29618 GATACAAGTATGCTTCTACC
1 GATACAAGTATGCTTCTACC
29638 G
1 G
29639 GAACAACTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.32
Consensus pattern (20 bp):
GATACAAGTATGCTTCTACC
Found at i:30469 original size:22 final size:22
Alignment explanation
Indices: 30444--30492 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
30434 CCGACTATTC
30444 TTATTGGAGAACAAGAATGAAG
1 TTATTGGAGAACAAGAATGAAG
30466 TTATTGGAGAACAAGAATGAAG
1 TTATTGGAGAACAAGAATGAAG
30488 TTATT
1 TTATT
30493 TATCCAACCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.43, C:0.04, G:0.24, T:0.29
Consensus pattern (22 bp):
TTATTGGAGAACAAGAATGAAG
Found at i:30745 original size:169 final size:169
Alignment explanation
Indices: 30466--30830 Score: 712
Period size: 169 Copynumber: 2.2 Consensus size: 169
30456 AAGAATGAAG
30466 TTATTGGAGAACAAGAATGAAGTTATTTATCCAACCCAATGATTATGGAGTGTGGAGGATAATCA
1 TTATTGGAGAACAAGAATGAAGTTATTTATCCAACCCAATGATTATGGAGTGTGGAGGATAATCA
30531 CAAACGAGTCATTCATTCCAATGAAGATAGTTGAAGGTGTTAGTGTTCCAAAGGAGGAGAATGAA
66 CAAACGAGTCATTCATTCCAATGAAGATAGTTGAAGGTGTTAGTGTTCCAAAGGAGGAGAATGAA
*
30596 TACTGTAAGACTTCCTCTATTCAATGGCACCGACTATTC
131 TACTGTAAGACCTCCTCTATTCAATGGCACCGACTATTC
*
30635 TTATTGGAGAAAAAGAATGAAGTTATTTATCCAACCCAATGATTATGGAGTGTGGAGGATAATCA
1 TTATTGGAGAACAAGAATGAAGTTATTTATCCAACCCAATGATTATGGAGTGTGGAGGATAATCA
30700 CAAACGAGTCATTCATTCCAATGAAGATAGTTGAAGGTGTTAGTGTTCCAAAGGAGGAGAATGAA
66 CAAACGAGTCATTCATTCCAATGAAGATAGTTGAAGGTGTTAGTGTTCCAAAGGAGGAGAATGAA
30765 TACTGTAAGACCTCCTCTATTCAATGGCACCGACTATTC
131 TACTGTAAGACCTCCTCTATTCAATGGCACCGACTATTC
30804 TTATTGGAGAACAAGAATGAAGTTATT
1 TTATTGGAGAACAAGAATGAAGTTATT
30831 GGAGAACAAA
Statistics
Matches: 193, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
169 193 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (169 bp):
TTATTGGAGAACAAGAATGAAGTTATTTATCCAACCCAATGATTATGGAGTGTGGAGGATAATCA
CAAACGAGTCATTCATTCCAATGAAGATAGTTGAAGGTGTTAGTGTTCCAAAGGAGGAGAATGAA
TACTGTAAGACCTCCTCTATTCAATGGCACCGACTATTC
Found at i:30855 original size:26 final size:22
Alignment explanation
Indices: 30804--30852 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
30794 CCGACTATTC
*
30804 TTATTGGAGAACAAGAATGAAG
1 TTATTGGAGAACAAAAATGAAG
30826 TTATTGGAGAACAAAAATGAAG
1 TTATTGGAGAACAAAAATGAAG
30848 TTATT
1 TTATT
30853 TATCCAACCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.29
Consensus pattern (22 bp):
TTATTGGAGAACAAAAATGAAG
Found at i:37666 original size:16 final size:17
Alignment explanation
Indices: 37645--37686 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
37635 TGATTTATTT
37645 ATTAAATAAATAA-ACAA
1 ATTAAATAAATAATA-AA
*
37662 A-TAAAGAAATAATAAA
1 ATTAAATAAATAATAAA
37678 ATTAAATAA
1 ATTAAATAA
37687 TATACAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (17 bp):
ATTAAATAAATAATAAA
Found at i:42472 original size:8 final size:8
Alignment explanation
Indices: 42459--42489 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
42449 TTCTTGCATT
42459 TGCATTCA
1 TGCATTCA
42467 TGCATTCA
1 TGCATTCA
42475 TGCATTCA
1 TGCATTCA
42483 TTGCATT
1 -TGCATT
42490 TACATACATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 16 0.73
9 6 0.27
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.42
Consensus pattern (8 bp):
TGCATTCA
Found at i:50658 original size:50 final size:50
Alignment explanation
Indices: 50603--50761 Score: 151
Period size: 50 Copynumber: 3.2 Consensus size: 50
50593 ATCTTTTACC
* *
50603 CCTAAAGCTATGGAGGTGCAGATTGAAATCGCAATGGCAAATCTCATACA
1 CCTAAAGCTATAGAGGGGCAGATTGAAATCGCAATGGCAAATCTCATACA
* * * ** * *
50653 CCTAAAACTGTAGAGGGGCAGAATT-AAACCGCAATGAAAAAACTCATTCA
1 CCTAAAGCTATAGAGGGGCAG-ATTGAAATCGCAATGGCAAATCTCATACA
* * * * *
50703 CCTAAAGCTATAGAGGGGTAGATTGAAGTCACAA-GGACAAATCTTATACT
1 CCTAAAGCTATAGAGGGGCAGATTGAAATCGCAATGG-CAAATCTCATACA
*
50753 CCTGAAGCT
1 CCTAAAGCT
50762 GAAAAGAAGT
Statistics
Matches: 84, Mismatches: 22, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
49 4 0.05
50 77 0.92
51 3 0.04
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.21
Consensus pattern (50 bp):
CCTAAAGCTATAGAGGGGCAGATTGAAATCGCAATGGCAAATCTCATACA
Found at i:50932 original size:79 final size:79
Alignment explanation
Indices: 50784--50979 Score: 245
Period size: 79 Copynumber: 2.5 Consensus size: 79
50774 AGTTACAACC
* * * *
50784 TCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACCATCTAATCTTTTACCCTAATCAGAGG
1 TCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACAATCCAATCTTTTACCCTAACCAGAGA
50849 GCAGATTGAAGACAA
66 GCAGATTGAAG-CAA
* * * *
50864 TCCAATCTCTTATCCC-AACGATGA-GGTAGATTTAA-ACAATCCAATCTTTTACCTTAACCAGA
1 TCCAATCTCTTA-CCCTAACCA-GAGGGCAGATTGAAGACAATCCAATCTTTTACCCTAACCAGA
50926 GAGCAGATTGAAGCAA
64 GAGCAGATTGAAGCAA
* * *
50942 TCCAGTCTTTTACCCTAACCAGAGGGAAGATTGAAGAC
1 TCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGAC
50980 CATCAGATCT
Statistics
Matches: 98, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
77 5 0.05
78 26 0.27
79 37 0.38
80 25 0.26
81 5 0.05
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (79 bp):
TCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACAATCCAATCTTTTACCCTAACCAGAGA
GCAGATTGAAGCAA
Found at i:50934 original size:39 final size:40
Alignment explanation
Indices: 50784--51034 Score: 241
Period size: 39 Copynumber: 6.4 Consensus size: 40
50774 AGTTACAACC
* *
50784 TCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACCA
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAA
* *
50824 TCTAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACAA
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAA
* * * *
50864 TCCAATCTCTTATCCC-AACGATGA-GGTAGATTTAA-ACAA
1 TCCAATCTTTTA-CCCTAACCA-GAGGGCAGATTGAAGACAA
* *
50903 TCCAATCTTTTACCTTAACCAGAGAGCAGATTGAAG-CAA
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAA
* * *
50942 TCCAGTCTTTTACCCTAACCAGAGGGAAGATTGAAGACCA
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAA
* * * *
50982 T-CAGATCTCTAACCC-GACCA-TGGG-ACGAATTGAA-ACAA
1 TCCA-ATCTTTTACCCTAACCAGAGGGCA-G-ATTGAAGACAA
51020 TCCAATCTTTTACCC
1 TCCAATCTTTTACCC
51035 CTAAAGTTAT
Statistics
Matches: 172, Mismatches: 29, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
37 1 0.01
38 21 0.12
39 76 0.44
40 69 0.40
41 5 0.03
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (40 bp):
TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAA
Found at i:51596 original size:4 final size:4
Alignment explanation
Indices: 51589--51615 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
51579 ATTTATTTGT
51589 TAAA TAAA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAA
51616 TAGAATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:51629 original size:16 final size:16
Alignment explanation
Indices: 51588--51630 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
51578 TATTTATTTG
51588 TTAAATAAATAAATAAA
1 TTAAATAAAT-AATAAA
51605 -TAAATAAATAATAGAA
1 TTAAATAAATAATA-AA
51621 TTAAA-AAATA
1 TTAAATAAATA
51631 TACAAACCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.17
16 16 0.67
17 4 0.17
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (16 bp):
TTAAATAAATAATAAA
Found at i:55254 original size:27 final size:27
Alignment explanation
Indices: 55216--55292 Score: 127
Period size: 27 Copynumber: 2.9 Consensus size: 27
55206 ATATGAATGG
*
55216 AAATTAGCACTTCGTTGCTCTCTATTC
1 AAATTAGCACTTCGGTGCTCTCTATTC
*
55243 AAATTAGCACTTTGGTGCTCTCTATTC
1 AAATTAGCACTTCGGTGCTCTCTATTC
*
55270 TAATTAGCACTTCGGTGCTCTCT
1 AAATTAGCACTTCGGTGCTCTCT
55293 GATTTGCACT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.40
Consensus pattern (27 bp):
AAATTAGCACTTCGGTGCTCTCTATTC
Found at i:56609 original size:23 final size:23
Alignment explanation
Indices: 56583--56820 Score: 255
Period size: 23 Copynumber: 10.3 Consensus size: 23
56573 ATTATATCTA
* *
56583 TGCTTAAATATTAATATAATTTG
1 TGCTTAAATATTAATGTGATTTG
* * *
56606 TGCTCAAATTTTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
**
56629 TATTTAAATATTAACT-TGATTTG
1 TGCTTAAATATTAA-TGTGATTTG
* *
56652 TGCTTAAATATTAATGTGGTTTAC
1 TGCTTAAATATTAATGTGATTT-G
56676 T-CTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
56698 TGTTTAAATATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
* * *
56721 TGTTTAAATAATAATGTGATCTG
1 TGCTTAAATATTAATGTGATTTG
* *
56744 TACTTAAGTATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* * *
56767 TGCTTAAATATTAATATTATTTA
1 TGCTTAAATATTAATGTGATTTG
* *
56790 TGATTATATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
56813 TGCTTAAA
1 TGCTTAAA
56821 GAATTAAGAT
Statistics
Matches: 173, Mismatches: 38, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
22 2 0.01
23 169 0.98
24 2 0.01
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.49
Consensus pattern (23 bp):
TGCTTAAATATTAATGTGATTTG
Found at i:84165 original size:29 final size:31
Alignment explanation
Indices: 84115--84191 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 31
84105 TCTTATGTTA
* * **
84115 TTATATTATATATAGGTGTGGGCTTT-AT-T
1 TTATATAATATATATGCATGGGCTTTGATGT
*
84144 TTATATAATATATATGCATGGGTTTTGATGT
1 TTATATAATATATATGCATGGGCTTTGATGT
*
84175 TATATATAATAAATATG
1 T-TATATAATATATATG
84192 AGTAGGGTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
29 21 0.54
30 2 0.05
31 2 0.05
32 14 0.36
ACGTcount: A:0.32, C:0.03, G:0.17, T:0.48
Consensus pattern (31 bp):
TTATATAATATATATGCATGGGCTTTGATGT
Found at i:86554 original size:55 final size:57
Alignment explanation
Indices: 86454--86582 Score: 147
Period size: 55 Copynumber: 2.3 Consensus size: 57
86444 CACATTGAGT
* * * * *
86454 CACACGGCCTGAACACATGCCTGTGTGTCTAGCCTATGTGTCTCAAAATAGTATTCA
1 CACACGGTCTGAACACATGCCTGTGTGTCTAGCCCATGTGCCTCAAAACAGTATACA
* *
86511 CACACGGTCTGATACAC-T-CCTGTGTGT-TTGCCCGTGTGCCTCAAAACAGTATACA
1 CACACGGTCTGA-ACACATGCCTGTGTGTCTAGCCCATGTGCCTCAAAACAGTATACA
*
86566 CACACGATCTGACACAC
1 CACACGGTCTGA-ACAC
86583 GCCCATATTC
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
55 37 0.60
56 9 0.15
57 12 0.19
58 4 0.06
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (57 bp):
CACACGGTCTGAACACATGCCTGTGTGTCTAGCCCATGTGCCTCAAAACAGTATACA
Found at i:87755 original size:52 final size:52
Alignment explanation
Indices: 87669--87898 Score: 306
Period size: 52 Copynumber: 4.5 Consensus size: 52
87659 TTTCATTTAG
*
87669 TACTCATGATGACAC--A-TCATCGGACCTCACAATCCGTAAAGGATTCACA
1 TACTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCACA
*
87718 TACTCATGATGACACGTAGTCATCGGACCTCATAATCCGTAAAGGATTC-CTA
1 TACTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAC-A
* ** * * *
87770 TACTCACGATGACACATAGTCATCAAACCTCATAATTCGTAAAGAATTCATA
1 TACTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCACA
* * *
87822 TACTCATGATGACACATAATCATCGGACCTCATAATCCGTAAATGATTCATA
1 TACTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCACA
* *
87874 TACTCACGATGACAAATAGTCATCG
1 TACTCATGATGACACATAGTCATCG
87899 AACCCTTTTA
Statistics
Matches: 158, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
49 15 0.09
51 2 0.01
52 141 0.89
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (52 bp):
TACTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCACA
Found at i:98281 original size:14 final size:14
Alignment explanation
Indices: 98262--98310 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
98252 AAAGTAAACA
98262 AAAATAAATTAGAT
1 AAAATAAATTAGAT
* *
98276 AAAATAAA-AACA-
1 AAAATAAATTAGAT
98288 AAAATAAATTAGAT
1 AAAATAAATTAGAT
98302 AAAATAAAT
1 AAAATAAAT
98311 AAATCGTGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 8 0.28
13 4 0.14
14 17 0.59
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.22
Consensus pattern (14 bp):
AAAATAAATTAGAT
Found at i:98293 original size:26 final size:26
Alignment explanation
Indices: 98257--98309 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
98247 TATTAAAAGT
98257 AAACAAAAATAAATTAGATAAAATAA
1 AAACAAAAATAAATTAGATAAAATAA
98283 AAACAAAAATAAATTAGATAAAATAA
1 AAACAAAAATAAATTAGATAAAATAA
98309 A
1 A
98310 TAAATCGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.19
Consensus pattern (26 bp):
AAACAAAAATAAATTAGATAAAATAA
Found at i:102538 original size:14 final size:14
Alignment explanation
Indices: 102504--102534 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
102494 CGAATTATTT
102504 CCTCTTTCTTCTTC
1 CCTCTTTCTTCTTC
102518 CCTCTTTC-TCTTC
1 CCTCTTTCTTCTTC
102531 CCTC
1 CCTC
102535 CTTTTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (14 bp):
CCTCTTTCTTCTTC
Found at i:103909 original size:41 final size:41
Alignment explanation
Indices: 103857--104035 Score: 225
Period size: 41 Copynumber: 4.4 Consensus size: 41
103847 GAGTCATAAA
* * * * * *
103857 TCTTCCTTTAATCATATTCTTATTTTCATCTCAAGACATTAG
1 TCTTCC-TTATTCATAATCTCATTCTCATCTCGAGACATGAG
* * *
103899 TTTTCCTTAATCA-AATCTCATTCTCATTTCGAGACATGAG
1 TCTTCCTTATTCATAATCTCATTCTCATCTCGAGACATGAG
* *
103939 TCTCCCTTATTCATAATCTAATTCTCATCTCGAGACATGAG
1 TCTTCCTTATTCATAATCTCATTCTCATCTCGAGACATGAG
* *
103980 TCTTCGTTATTCATAATTTCATTCTCATCTCGAGACATGAG
1 TCTTCCTTATTCATAATCTCATTCTCATCTCGAGACATGAG
104021 TCTTCCTTATTCATA
1 TCTTCCTTATTCATA
104036 CACCAAGTAT
Statistics
Matches: 119, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
40 31 0.26
41 83 0.70
42 5 0.04
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.42
Consensus pattern (41 bp):
TCTTCCTTATTCATAATCTCATTCTCATCTCGAGACATGAG
Found at i:104873 original size:22 final size:21
Alignment explanation
Indices: 104826--104873 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
104816 GACTTTCATA
*
104826 ATTAACTTAATTAATCATCTT
1 ATTAACTTAATTAATCATATT
* *
104847 TTTAACATTAATTAATCCTATT
1 ATTAAC-TTAATTAATCATATT
104869 ATTAA
1 ATTAA
104874 TCAATATTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTAACTTAATTAATCATATT
Found at i:110362 original size:23 final size:23
Alignment explanation
Indices: 110336--110642 Score: 407
Period size: 23 Copynumber: 13.3 Consensus size: 23
110326 CTTATATCTA
*
110336 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* * *
110359 TGCTCAAATTTTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
110382 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
110405 TGCTTAAATATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
110428 TGCTTAAATAATAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
110451 TGCTTAAATAATAATTTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* * *
110474 TGTTTAAATATTAATTTGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
110497 TGCTTAAATAATAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
110520 TGCTTAAATATTAATCTAATTTG
1 TGCTTAAATATTAATGTGATTTG
110543 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
** * * * *
110566 TAATTAAATAATAATATTATTTA
1 TGCTTAAATATTAATGTGATTTG
**
110589 TAATTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
110612 TGCTTAAATATTAATGTGATTCG
1 TGCTTAAATATTAATGTGATTTG
110635 TGCTTAAA
1 TGCTTAAA
110643 GAATTAAGAT
Statistics
Matches: 248, Mismatches: 36, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 248 1.00
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.47
Consensus pattern (23 bp):
TGCTTAAATATTAATGTGATTTG
Found at i:116948 original size:3 final size:3
Alignment explanation
Indices: 116942--116981 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
116932 TAAAGGTTAA
* * *
116942 ATT ATT ATT ATT AAT AAT AAT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
116982 GTTACTTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:117860 original size:2 final size:2
Alignment explanation
Indices: 117853--117880 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
117843 ATTTTGGTTT
117853 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
117881 AATTCTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:117921 original size:18 final size:18
Alignment explanation
Indices: 117900--117940 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
117890 TCCTTTTTCA
117900 ATTTCAGATTTCAATTTT
1 ATTTCAGATTTCAATTTT
* **
117918 ATTTTAGATTTTGATTTT
1 ATTTCAGATTTCAATTTT
117936 ATTTC
1 ATTTC
117941 TCTTTCTTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.61
Consensus pattern (18 bp):
ATTTCAGATTTCAATTTT
Found at i:118004 original size:86 final size:85
Alignment explanation
Indices: 117851--118012 Score: 218
Period size: 86 Copynumber: 1.9 Consensus size: 85
117841 AGATTTTGGT
*
117851 TTTCTCTCTCTCTCTCTCTCTCTCTCTCTCAATTCTTTTTCCTTTTTCAATTTCAGATTTCAATT
1 TTTCTCTCTCTCTCTCTCTCTCTCTCTCTCAATTCTTTTTCCTTTCTCAATTTCAGATTTCAATT
117916 TTATTTTAGATTTTGATTTTA
66 TTA-TTTAGATTTTGATTTTA
* * * * * * * *
117937 TTTCTCTTTCTTTCTTTCTTTCTGTCTCTCGATTCTTTTTCCTTTCTCAATTTCAG-TTTTATTT
1 TTTCTCTCTCTCTCTCTCTCTCTCTCTCTCAATTCTTTTTCCTTTCTCAATTTCAGATTTCA-AT
118001 TTTATTTAGATT
65 TTTATTTAGATT
118013 GTGGTACCAT
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
85 12 0.18
86 54 0.82
ACGTcount: A:0.13, C:0.22, G:0.04, T:0.61
Consensus pattern (85 bp):
TTTCTCTCTCTCTCTCTCTCTCTCTCTCTCAATTCTTTTTCCTTTCTCAATTTCAGATTTCAATT
TTATTTAGATTTTGATTTTA
Found at i:119054 original size:30 final size:31
Alignment explanation
Indices: 119020--119092 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 31
119010 ATTACATTTA
*
119020 ACAAAACAGTCACTCAACTT-T-GAAAATGTG
1 ACAAAACAGTCACTAAACTTATCGAAAA-GTG
* * *
119050 ACAAAACAATTACTAAAGTTATCGAAAAGTG
1 ACAAAACAGTCACTAAACTTATCGAAAAGTG
119081 ACAAAACAGTCA
1 ACAAAACAGTCA
119093 TCTACTTACT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
30 16 0.46
31 14 0.40
32 5 0.14
ACGTcount: A:0.49, C:0.18, G:0.12, T:0.21
Consensus pattern (31 bp):
ACAAAACAGTCACTAAACTTATCGAAAAGTG
Found at i:121709 original size:12 final size:11
Alignment explanation
Indices: 121689--121763 Score: 51
Period size: 12 Copynumber: 6.2 Consensus size: 11
121679 TTAGTATTAC
121689 TTTTGAAAAGT
1 TTTTGAAAAGT
*
121700 GTTTTTAAAAGT
1 -TTTTGAAAAGT
*
121712 TTGATGGAAAAGTT
1 TT--TTGAAAAG-T
*
121726 CTTTTGAGAAGT
1 -TTTTGAAAAGT
121738 ATTTTGAAAAGT
1 -TTTTGAAAAGT
*
121750 GTTTTTAAAAGT
1 -TTTTGAAAAGT
121762 TT
1 TT
121764 GATGGAAAAG
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
11 4 0.08
12 31 0.62
13 12 0.24
14 1 0.02
15 2 0.04
ACGTcount: A:0.33, C:0.01, G:0.20, T:0.45
Consensus pattern (11 bp):
TTTTGAAAAGT
Found at i:121755 original size:13 final size:12
Alignment explanation
Indices: 121689--121802 Score: 70
Period size: 13 Copynumber: 9.1 Consensus size: 12
121679 TTAGTATTAC
121689 TTTTGAAAAGTGT
1 TTTTGAAAAGT-T
121702 TTTT-AAAAGTT
1 TTTTGAAAAGTT
* *
121713 TGATGGAAAAGTT
1 T-TTTGAAAAGTT
* *
121726 CTTTTGAGAAGTA
1 -TTTTGAAAAGTT
121739 TTTTGAAAAGTGT
1 TTTTGAAAAGT-T
121752 TTTT-AAAAGTT
1 TTTTGAAAAGTT
* *
121763 TGATGGAAAAGTT
1 T-TTTGAAAAGTT
* *
121776 CTTTTGAGAAGTAC
1 -TTTTGAAAAGT-T
*
121790 TTTTAAAAAGTT
1 TTTTGAAAAGTT
121802 T
1 T
121803 GGTTAAAGAT
Statistics
Matches: 76, Mismatches: 17, Indels: 17
0.69 0.15 0.15
Matches are distributed among these distances:
11 4 0.05
12 25 0.33
13 45 0.59
14 2 0.03
ACGTcount: A:0.34, C:0.03, G:0.20, T:0.43
Consensus pattern (12 bp):
TTTTGAAAAGTT
Found at i:121760 original size:50 final size:51
Alignment explanation
Indices: 121686--121800 Score: 214
Period size: 50 Copynumber: 2.3 Consensus size: 51
121676 AGTTTAGTAT
121686 TACTTTTGAAAAGTGTTTTTAAAAGTTTGATGGAAAAGTTCTTTTGAGAAG
1 TACTTTTGAAAAGTGTTTTTAAAAGTTTGATGGAAAAGTTCTTTTGAGAAG
121737 TA-TTTTGAAAAGTGTTTTTAAAAGTTTGATGGAAAAGTTCTTTTGAGAAG
1 TACTTTTGAAAAGTGTTTTTAAAAGTTTGATGGAAAAGTTCTTTTGAGAAG
*
121787 TACTTTTAAAAAGT
1 TACTTTTGAAAAGT
121801 TTGGTTAAAG
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
50 50 0.81
51 12 0.19
ACGTcount: A:0.35, C:0.03, G:0.20, T:0.42
Consensus pattern (51 bp):
TACTTTTGAAAAGTGTTTTTAAAAGTTTGATGGAAAAGTTCTTTTGAGAAG
Found at i:121780 original size:25 final size:25
Alignment explanation
Indices: 121693--121774 Score: 98
Period size: 25 Copynumber: 3.3 Consensus size: 25
121683 TATTACTTTT
121693 GAAAAGTGTTTTTAAAAGTTTGATG
1 GAAAAGTGTTTTTAAAAGTTTGATG
* *
121718 GAAAAGT-TCTTTTGAGAAGTATT--TT
1 GAAAAGTGT-TTTT-AAAAGT-TTGATG
121743 GAAAAGTGTTTTTAAAAGTTTGATG
1 GAAAAGTGTTTTTAAAAGTTTGATG
121768 GAAAAGT
1 GAAAAGT
121775 TCTTTTGAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
23 2 0.04
24 6 0.13
25 31 0.66
26 6 0.13
27 2 0.04
ACGTcount: A:0.37, C:0.01, G:0.23, T:0.39
Consensus pattern (25 bp):
GAAAAGTGTTTTTAAAAGTTTGATG
Found at i:131508 original size:18 final size:18
Alignment explanation
Indices: 131485--131520 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
131475 TTAAAAATAT
131485 TAGTTAGTCTTCCTCCAC
1 TAGTTAGTCTTCCTCCAC
*
131503 TAGTTAGTGTTCCTCCAC
1 TAGTTAGTCTTCCTCCAC
131521 CTCATCCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.31, G:0.14, T:0.39
Consensus pattern (18 bp):
TAGTTAGTCTTCCTCCAC
Found at i:149750 original size:14 final size:14
Alignment explanation
Indices: 149731--149764 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
149721 TAATTTGGTC
*
149731 ATTTTTAATATTTGT
1 ATTTTTAA-ATTTCT
149746 ATTTTTAAATTTCT
1 ATTTTTAAATTTCT
149760 ATTTT
1 ATTTT
149765 ATCTAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (14 bp):
ATTTTTAAATTTCT
Found at i:152537 original size:16 final size:16
Alignment explanation
Indices: 152516--152568 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
152506 GGGTGGAAAG
152516 AAAATTAGAAAGATGA
1 AAAATTAGAAAGATGA
*
152532 AAAATT-GAAGGGAT-A
1 AAAATTAGAA-AGATGA
152547 TAAAATTAGAAAGATAGA
1 -AAAATTAGAAAGAT-GA
152565 AAAA
1 AAAA
152569 GTTTTTCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
15 4 0.13
16 18 0.60
17 7 0.23
18 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.19, T:0.19
Consensus pattern (16 bp):
AAAATTAGAAAGATGA
Found at i:155768 original size:7 final size:7
Alignment explanation
Indices: 155753--155787 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
155743 ATTTAAATAT
*
155753 TCAAAAC
1 TCAACAC
155760 TCAACAC
1 TCAACAC
155767 TCAACAC
1 TCAACAC
155774 TCAACAC
1 TCAACAC
155781 TCAACAC
1 TCAACAC
155788 AATTGATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.46, C:0.40, G:0.00, T:0.14
Consensus pattern (7 bp):
TCAACAC
Found at i:187479 original size:36 final size:38
Alignment explanation
Indices: 187411--187489 Score: 99
Period size: 36 Copynumber: 2.1 Consensus size: 38
187401 GAGCCAACCA
* *
187411 ACCCAAACCAGAAGCCCAAATTTGAGATCCAATATCTG
1 ACCCAAACCAGAAGCCCAAATTTGAGACCCAATACCTG
* *
187449 ACCCAAACCA-AGGCCCAATTTTG-GACCCAATACCTG
1 ACCCAAACCAGAAGCCCAAATTTGAGACCCAATACCTG
*
187485 GCCCA
1 ACCCA
187490 TTTTAATACC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
36 15 0.42
37 11 0.31
38 10 0.28
ACGTcount: A:0.35, C:0.34, G:0.14, T:0.16
Consensus pattern (38 bp):
ACCCAAACCAGAAGCCCAAATTTGAGACCCAATACCTG
Found at i:205889 original size:2 final size:2
Alignment explanation
Indices: 205882--205922 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
205872 TACAGCTTCT
*
205882 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.