Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015197.1 Kokia drynarioides strain JFW-HI SEQ_130241, 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: 258806
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 227 characters in sequence are not A, C, G, or T
Found at i:591 original size:4 final size:4
Alignment explanation
Indices: 576--611 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
566 TTTCCTCTCC
*
576 TTCT TCCT TTCT TTCT TTCT TTCCT TTCT TTCT TTC
1 TTCT TTCT TTCT TTCT TTCT TT-CT TTCT TTCT TTC
612 CCGTTTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (4 bp):
TTCT
Found at i:599 original size:17 final size:17
Alignment explanation
Indices: 579--611 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
569 CCTCTCCTTC
579 TTCCTTTCTTTCTTTCT
1 TTCCTTTCTTTCTTTCT
596 TTCCTTTCTTTCTTTC
1 TTCCTTTCTTTCTTTC
612 CCGTTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (17 bp):
TTCCTTTCTTTCTTTCT
Found at i:6394 original size:15 final size:15
Alignment explanation
Indices: 6371--6401 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6361 ATTATCAGAA
*
6371 TTTATAATGAAATTG
1 TTTAAAATGAAATTG
6386 TTTAAAATGAAATTG
1 TTTAAAATGAAATTG
6401 T
1 T
6402 AAGTATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (15 bp):
TTTAAAATGAAATTG
Found at i:23732 original size:23 final size:21
Alignment explanation
Indices: 23706--23753 Score: 51
Period size: 23 Copynumber: 2.2 Consensus size: 21
23696 CTTTTTCTTC
*
23706 ATATTATAATTAATATTTTAATA
1 ATATGATAATTAA-A-TTTAATA
* *
23729 ATATGATTATTAAATTTATTA
1 ATATGATAATTAAATTTAATA
23750 ATAT
1 ATAT
23754 AATTATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 10 0.45
22 1 0.05
23 11 0.50
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
ATATGATAATTAAATTTAATA
Found at i:24856 original size:23 final size:23
Alignment explanation
Indices: 24817--24860 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
24807 TGTTATGGAA
*
24817 ATTTTTTTTTTTATAATTTCAAT
1 ATTTTTTTTTCTATAATTTCAAT
24840 ATTTTTTTTATCT-TAATTTCA
1 ATTTTTTTT-TCTATAATTTCA
24861 GTAACTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (23 bp):
ATTTTTTTTTCTATAATTTCAAT
Found at i:27562 original size:53 final size:51
Alignment explanation
Indices: 27485--27591 Score: 126
Period size: 53 Copynumber: 2.1 Consensus size: 51
27475 ACCATTTAGG
* * * *
27485 AGGGGTGGCCACGAACCCGCAAAGGATTAGTTTCTATGGATAAGAAGCTTGTA
1 AGGGGTAGCCACAAACCCGCAAAGGACTAGTTTCTAT-GATAAGAACCTT-TA
* *
27538 AGGGGTAGCCACAAACCCTG-AAAGGACTAGTTTTTATGATGAGAACCTTTA
1 AGGGGTAGCCACAAACCC-GCAAAGGACTAGTTTCTATGATAAGAACCTTTA
27589 AGG
1 AGG
27592 ATCTATGGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
51 5 0.11
52 10 0.21
53 31 0.66
54 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (51 bp):
AGGGGTAGCCACAAACCCGCAAAGGACTAGTTTCTATGATAAGAACCTTTA
Found at i:27687 original size:59 final size:56
Alignment explanation
Indices: 27593--27716 Score: 167
Period size: 59 Copynumber: 2.2 Consensus size: 56
27583 CCTTTAAGGA
* * * *
27593 TCTATGGATAAGAAATCATTTAGGAGGGGTGGTCACGAACCCTGAAAGGATTAGTT
1 TCTATGGATAAGAAATCATTTAGGAGGGGTAGTCACGAACCCTGAAAAGATTAATC
* *
27649 TCTATGGATAAGAAACCTCCATTTAGGAGTGTTAGTCACGAACCCTGAAAAGATTAATC
1 TCTATGGATAAGAAA--T-CATTTAGGAGGGGTAGTCACGAACCCTGAAAAGATTAATC
27708 TCTATGGAT
1 TCTATGGAT
27717 TATAAAACCA
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
56 15 0.25
58 1 0.02
59 43 0.73
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.28
Consensus pattern (56 bp):
TCTATGGATAAGAAATCATTTAGGAGGGGTAGTCACGAACCCTGAAAAGATTAATC
Found at i:32825 original size:59 final size:58
Alignment explanation
Indices: 32770--32999 Score: 243
Period size: 58 Copynumber: 3.9 Consensus size: 58
32760 AATTTGGGTT
32770 TAAAAATGGAATTTTTAGACA-TTCGGGGGTAAAAAGGGTATTTTTGAGAGTTTTGGGGG
1 TAAAAATGGAATTTTTAGA-AGTTCGGGGGTAAAAAGGG-ATTTTTGAGAGTTTTGGGGG
* ** * * * *
32829 TAAAAATGGAATTTTTAGAAATTTTAGGGGCAAAATGGAATTTTTGAAAGTTTTGGGGG
1 TAAAAATGGAATTTTTAG-AAGTTCGGGGGTAAAAAGGGATTTTTGAGAGTTTTGGGGG
* * *
32888 TAAAAAT-GAGATTTTTGGAAGTTTGGGGGTAAAATGGGATTTTTG-GAAGTTTT-GGGG
1 TAAAAATGGA-ATTTTTAGAAGTTCGGGGGTAAAAAGGGATTTTTGAG-AGTTTTGGGGG
* * *
32945 TCAAAAATGGGATTTTTAGAAGTTCGAGGGTAAAAATGGGATTTTTTGATAGTTT
1 T-AAAAATGGAATTTTTAGAAGTTCGGGGGTAAAAA-GGGA-TTTTTGAGAGTTT
33000 AGAGACCCTC
Statistics
Matches: 144, Mismatches: 18, Indels: 17
0.80 0.10 0.09
Matches are distributed among these distances:
57 5 0.03
58 58 0.40
59 57 0.40
60 24 0.17
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (58 bp):
TAAAAATGGAATTTTTAGAAGTTCGGGGGTAAAAAGGGATTTTTGAGAGTTTTGGGGG
Found at i:32830 original size:30 final size:30
Alignment explanation
Indices: 32794--32990 Score: 187
Period size: 29 Copynumber: 6.7 Consensus size: 30
32784 TTAGACATTC
32794 GGGGGTAAAAAGGGTATTTTTGAG-AGTTTT
1 GGGGGTAAAAAGGG-ATTTTTGAGAAGTTTT
* *
32824 GGGGGTAAAAATGGAATTTTT-AGAAATTTT
1 GGGGGTAAAAA-GGGATTTTTGAGAAGTTTT
* * * *
32854 AGGGGCAAAATGGAATTTTTGA-AAGTTTT
1 GGGGGTAAAAAGGGATTTTTGAGAAGTTTT
*
32883 GGGGGTAAAAATGAGATTTTTG-GAAG-TTT
1 GGGGGTAAAAA-GGGATTTTTGAGAAGTTTT
*
32912 GGGGGTAAAATGGGATTTTTG-GAAGTTTT
1 GGGGGTAAAAAGGGATTTTTGAGAAGTTTT
*
32941 -GGGGTCAAAAATGGGATTTTT-AGAAG-TTC
1 GGGGGT-AAAAA-GGGATTTTTGAGAAGTTTT
*
32970 GAGGGTAAAAATGGGATTTTT
1 GGGGGTAAAAA-GGGATTTTT
32991 TGATAGTTTA
Statistics
Matches: 141, Mismatches: 16, Indels: 21
0.79 0.09 0.12
Matches are distributed among these distances:
28 18 0.13
29 62 0.44
30 59 0.42
31 2 0.01
ACGTcount: A:0.31, C:0.02, G:0.32, T:0.35
Consensus pattern (30 bp):
GGGGGTAAAAAGGGATTTTTGAGAAGTTTT
Found at i:32991 original size:30 final size:29
Alignment explanation
Indices: 32770--32999 Score: 211
Period size: 30 Copynumber: 7.8 Consensus size: 29
32760 AATTTGGGTT
* *
32770 TAAAAATGGAATTTTTAGACA-TTCGGGGG
1 TAAAAATGGGATTTTTAGA-AGTTTGGGGG
32799 TAAAAA-GGGTATTTTT-GAGAGTTTTGGGGG
1 TAAAAATGGG-ATTTTTAGA-AG-TTTGGGGG
* * *
32829 TAAAAATGGAATTTTTAGAAATTTTAGGGG
1 TAAAAATGGGATTTTTAG-AAGTTTGGGGG
* *
32859 -CAAAATGGAATTTTT-GAAAGTTTTGGGGG
1 TAAAAATGGGATTTTTAG-AAG-TTTGGGGG
* *
32888 TAAAAATGAGATTTTTGGAAGTTTGGGGG
1 TAAAAATGGGATTTTTAGAAGTTTGGGGG
* *
32917 T-AAAATGGGATTTTTGGAAGTTTTGGGG
1 TAAAAATGGGATTTTTAGAAGTTTGGGGG
* *
32945 TCAAAAATGGGATTTTTAGAAGTTCGAGGG
1 T-AAAAATGGGATTTTTAGAAGTTTGGGGG
*
32975 TAAAAATGGGATTTTTTGATAGTTT
1 TAAAAATGGGATTTTTAGA-AGTTT
33000 AGAGACCCTC
Statistics
Matches: 169, Mismatches: 20, Indels: 23
0.80 0.09 0.11
Matches are distributed among these distances:
28 35 0.21
29 59 0.35
30 69 0.41
31 5 0.03
32 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (29 bp):
TAAAAATGGGATTTTTAGAAGTTTGGGGG
Found at i:34173 original size:16 final size:17
Alignment explanation
Indices: 34132--34177 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
34122 TTATATCCAT
34132 TATTATTT-TTATTAAA
1 TATTATTTATTATTAAA
*
34148 TAGTCA-TTATTATT-AA
1 TA-TTATTTATTATTAAA
34164 TATTATTTATTATT
1 TATTATTTATTATT
34178 GATTCGTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 2 0.08
16 16 0.64
17 7 0.28
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (17 bp):
TATTATTTATTATTAAA
Found at i:34858 original size:23 final size:22
Alignment explanation
Indices: 34825--34870 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
34815 ATTTGATATT
*
34825 ATTTAAATAAATTTAAGTTTAA
1 ATTTAAATAAATTTAAATTTAA
34847 ATTTATAATAAATTTAAATTTAA
1 ATTTA-AATAAATTTAAATTTAA
34870 A
1 A
34871 ATAAACTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
ATTTAAATAAATTTAAATTTAA
Found at i:34864 original size:17 final size:17
Alignment explanation
Indices: 34842--34900 Score: 82
Period size: 17 Copynumber: 3.5 Consensus size: 17
34832 TAAATTTAAG
*
34842 TTTAAATTTATAATAAA
1 TTTAAATTTAAAATAAA
34859 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* **
34876 CTTATTTTTAAAATAAA
1 TTTAAATTTAAAATAAA
34893 TTTAAATT
1 TTTAAATT
34901 CTGTTGAGCC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:50761 original size:89 final size:88
Alignment explanation
Indices: 50316--50973 Score: 656
Period size: 88 Copynumber: 7.5 Consensus size: 88
50306 GAATCCTGTC
* * ** * *
50316 AGGTTG-CTAGAGTTGAGTGTCTTGTAGTAACAGTTGAATCTATATCCTTGGTGGAGGTTTTGTC
1 AGGTTGAC-AGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCGTGTCC-TGGTTGAGGTTTTGTC
* * * * *
50380 TCCCGACTCTGCCGAGAATCCTGTC
64 TCCTGACTCTACCGAGACTCCTATT
* * *
50405 AGGTTGATAGAGTTGAGTGTCTCGTAGTAACAGGTGAAACCGTGTCGCT-ATCT-AGGTTTTGTC
1 AGGTTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCGTGTC-CTGGT-TGAGGTTTTGTC
* *
50468 TCCCGACTCTACCAAGACTCCTGA-T
64 TCCTGACTCTACCGAGACTCCT-ATT
* * ** * *
50493 AGGTTGACAGAGTTGTGTGTCATGTAGTAACAGGTGAAACTATATCCCCGGTTGAGGTTTTG--T
1 AGGTTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCGTGT-CCTGGTTGAGGTTTTGTCT
* *
50556 -CTGACTCTACAGAGACTCCTGTT
65 CCTGACTCTACCGAGACTCCTATT
* * * ** *
50579 AGGTGGACAAAGTTGAGTGTTTTGTAGTAACAACTGAAACCGTGTCCCT-GTTGAGCTTTTGTCT
1 AGGTTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCGTGT-CCTGGTTGAGGTTTTGTCT
*
50643 -CTCGACTCTATCGAGACTCCTATT
65 CCT-GACTCTACCGAGACTCCTATT
* * * *
50667 CGGTTGTCAGAGTTGAGTGTCTTGTGGTAACAGGTGAAACCGTGTCCTAGGTTGAGGTTTTGTGT
1 AGGTTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCGTGTCCT-GGTTGAGGTTTTGTCT
*
50732 CCTGACTCTACCGAGACTCTTATT
65 CCTGACTCTACCGAGACTCCTATT
* * * * ** *
50756 AGGTTGATAGAGTTGAGTTTCTTGTAGTAACAAGTGAAACCATGTCTCCT-GTCAAGGTTTTGTT
1 AGGTTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACC--GTGTCCTGGTTGAGGTTTTGTC
* * *
50820 TCCCT-ACTTTACTGAGACTCATATT
64 T-CCTGACTCTACCGAGACTCCTATT
* *
50845 AGGTTGACAGAGTTGAGTGTTTTGTAGTAACAGGT-AAACCGTGTCCCTGGTCGAGGTTTTGTCT
1 AGGTTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCGTGT-CCTGGTTGAGGTTTTGTCT
* * *
50909 CCTAACTCTACCGAGAATCCTATC
65 CCTGACTCTACCGAGACTCCTATT
50933 AGGTTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACC
1 AGGTTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACC
50974 ATGTGAAACT
Statistics
Matches: 468, Mismatches: 80, Indels: 42
0.79 0.14 0.07
Matches are distributed among these distances:
85 11 0.02
86 59 0.13
87 13 0.03
88 192 0.41
89 181 0.39
90 6 0.01
91 6 0.01
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (88 bp):
AGGTTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCGTGTCCTGGTTGAGGTTTTGTCTC
CTGACTCTACCGAGACTCCTATT
Found at i:50886 original size:177 final size:176
Alignment explanation
Indices: 50316--50977 Score: 717
Period size: 177 Copynumber: 3.8 Consensus size: 176
50306 GAATCCTGTC
* * * *
50316 AGGTTG-CTAGAGTTGAGTGTCTTGTAGTAACAGTTGAATCTATATCCTTGGTGGAGGTTTTGTC
1 AGGTTGAC-AGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCATATCC-TGGTTGAGGTTTTGTC
* * * * * *
50380 TCCCGACTCTGCCGAGAATCCTGTCAGGTTGATAGAGTTGAGTGTCTCGTAGTAACAGGTGAAAC
64 TCCTGACTCTACCGAGAATCCTATCAGGTTGACAGAGTTGAGTGTCTTGTAGTAACAAGTGAAAC
* * * * **
50445 CGTGTCGCTATCTAGGTTTTGTCTCCCGACTCTACCAAGACTCCTGA-T
129 CATGTCCCTGTCAAGGTTTTGTCTCCCGACTCTACTGAGACTCCT-ATT
* * * *
50493 AGGTTGACAGAGTTGTGTGTCATGTAGTAACAGGTGAAACTATATCCCCGGTTGAGGTTTTG--T
1 AGGTTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCATAT-CCTGGTTGAGGTTTTGTCT
* * * * * * * *
50556 -CTGACTCTACAGAGACTCCTGTTAGGTGGACAAAGTTGAGTGTTTTGTAGTAACAACTGAAACC
65 CCTGACTCTACCGAGAATCCTATCAGGTTGACAGAGTTGAGTGTCTTGTAGTAACAAGTGAAACC
* ** * *
50620 GTGTCCCTGTTGAGCTTTTGTCTCTCGACTCTA-TCGAGACTCCTATT
130 ATGTCCCTGTCAAGGTTTTGTCTCCCGACTCTACT-GAGACTCCTATT
* * * * * *
50667 CGGTTGTCAGAGTTGAGTGTCTTGTGGTAACAGGTGAAACCGTGTCCTAGGTTGAGGTTTTGTGT
1 AGGTTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCATATCCT-GGTTGAGGTTTTGTCT
* * * * *
50732 CCTGACTCTACCGAGACTCTTATTAGGTTGATAGAGTTGAGTTTCTTGTAGTAACAAGTGAAACC
65 CCTGACTCTACCGAGAATCCTATCAGGTTGACAGAGTTGAGTGTCTTGTAGTAACAAGTGAAACC
* * * *
50797 ATGTCTCCTGTCAAGGTTTTGTTTCCCTACTTTACTGAGACTCATATT
130 ATGTC-CCTGTCAAGGTTTTGTCTCCCGACTCTACTGAGACTCCTATT
* * * *
50845 AGGTTGACAGAGTTGAGTGTTTTGTAGTAACAGGT-AAACCGTGTCCCTGGTCGAGGTTTTGTCT
1 AGGTTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCATAT-CCTGGTTGAGGTTTTGTCT
* *
50909 CCTAACTCTACCGAGAATCCTATCAGGTTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACC
65 CCTGACTCTACCGAGAATCCTATCAGGTTGACAGAGTTGAGTGTCTTGTAGTAACAAGTGAAACC
50974 ATGT
130 ATGT
50978 GAAACTAAAG
Statistics
Matches: 408, Mismatches: 66, Indels: 22
0.82 0.13 0.04
Matches are distributed among these distances:
173 3 0.01
174 138 0.34
175 1 0.00
176 1 0.00
177 195 0.48
178 69 0.17
179 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (176 bp):
AGGTTGACAGAGTTGAGTGTCTTGTAGTAACAGGTGAAACCATATCCTGGTTGAGGTTTTGTCTC
CTGACTCTACCGAGAATCCTATCAGGTTGACAGAGTTGAGTGTCTTGTAGTAACAAGTGAAACCA
TGTCCCTGTCAAGGTTTTGTCTCCCGACTCTACTGAGACTCCTATT
Found at i:54313 original size:7 final size:6
Alignment explanation
Indices: 54283--54319 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
54273 ATCTCGCCCA
* *
54283 TCTTTT TCTGTT TCTTTT TCTTTT TCTTTT TCCTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT T
54320 AAAAAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (6 bp):
TCTTTT
Found at i:67297 original size:17 final size:17
Alignment explanation
Indices: 67261--67305 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
67251 AAGATAAATA
* *
67261 AATATATTTTATTTATTT
1 AATATA-TTAATTTACTT
67279 AATATATTAATTTACTT
1 AATATATTAATTTACTT
*
67296 AATAAATTAA
1 AATATATTAA
67306 AATTTTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 18 0.75
18 6 0.25
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
AATATATTAATTTACTT
Found at i:68833 original size:22 final size:22
Alignment explanation
Indices: 68805--68848 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
68795 ACTTTTTAAC
*
68805 AGATTTAATGGATAAATTCAAT
1 AGATTTAATGAATAAATTCAAT
68827 AGATTTAATGAATAAATTCAAT
1 AGATTTAATGAATAAATTCAAT
68849 GTTTTGGTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.48, C:0.05, G:0.11, T:0.36
Consensus pattern (22 bp):
AGATTTAATGAATAAATTCAAT
Found at i:69534 original size:31 final size:31
Alignment explanation
Indices: 69499--69561 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 31
69489 AACAACTTAG
69499 TGACTTAAA-GAAAAACTTTTAAAT-GATTCAA
1 TGACTTAAATG-AAAACTTTTAAATAG-TTCAA
69530 TGACTTAAATGAAAACTTTTAAATAGTTCAA
1 TGACTTAAATGAAAACTTTTAAATAGTTCAA
69561 T
1 T
69562 AATCATTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.35
Consensus pattern (31 bp):
TGACTTAAATGAAAACTTTTAAATAGTTCAA
Found at i:74982 original size:14 final size:13
Alignment explanation
Indices: 74952--74988 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
74942 TTAACCTATT
74952 ATTAATAAATTAA
1 ATTAATAAATTAA
*
74965 ATTAATTAATTCAA
1 ATTAATAAATT-AA
74979 ATTAATAAAT
1 ATTAATAAAT
74989 AAAAATGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (13 bp):
ATTAATAAATTAA
Found at i:79009 original size:3 final size:3
Alignment explanation
Indices: 79001--79040 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
78991 GTTGAGACGA
*
79001 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG TTG CTG C
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG C
79041 AATTTCTGTA
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:0.00, C:0.33, G:0.33, T:0.35
Consensus pattern (3 bp):
CTG
Found at i:79173 original size:51 final size:51
Alignment explanation
Indices: 79113--79217 Score: 210
Period size: 51 Copynumber: 2.1 Consensus size: 51
79103 CGGCTGCTGT
79113 TGTGACCTCTGGGACAGACTTTGCTGCAACTGTGTCTGTTGCTGTTGGCTC
1 TGTGACCTCTGGGACAGACTTTGCTGCAACTGTGTCTGTTGCTGTTGGCTC
79164 TGTGACCTCTGGGACAGACTTTGCTGCAACTGTGTCTGTTGCTGTTGGCTC
1 TGTGACCTCTGGGACAGACTTTGCTGCAACTGTGTCTGTTGCTGTTGGCTC
79215 TGT
1 TGT
79218 ACAAGGTTAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.11, C:0.23, G:0.30, T:0.36
Consensus pattern (51 bp):
TGTGACCTCTGGGACAGACTTTGCTGCAACTGTGTCTGTTGCTGTTGGCTC
Found at i:79627 original size:30 final size:30
Alignment explanation
Indices: 79570--79627 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
79560 TGCTGCTGCT
* *
79570 GCTGCTGCTGTAGAGGTGGCTGAGGCTGAG
1 GCTGCTGCTGAAGAGGTGACTGAGGCTGAG
* * *
79600 GCTGCTGTTGAAGATGTGACTGTGGCTG
1 GCTGCTGCTGAAGAGGTGACTGAGGCTG
79628 CAGCTGTGAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.14, C:0.16, G:0.43, T:0.28
Consensus pattern (30 bp):
GCTGCTGCTGAAGAGGTGACTGAGGCTGAG
Found at i:88836 original size:2 final size:2
Alignment explanation
Indices: 88829--88858 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
88819 TATCAACTTT
88829 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
88859 ATTCAATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:93791 original size:4 final size:4
Alignment explanation
Indices: 93772--93805 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
93762 CAAAAAGTAT
* *
93772 TACA TATA TGCA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TA
93806 TAAATTAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.47, C:0.21, G:0.03, T:0.29
Consensus pattern (4 bp):
TACA
Found at i:98932 original size:3 final size:3
Alignment explanation
Indices: 98924--98949 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
98914 GAAATCATAT
98924 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
98950 GTCGTAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:101592 original size:299 final size:299
Alignment explanation
Indices: 101054--101659 Score: 1212
Period size: 299 Copynumber: 2.0 Consensus size: 299
101044 ACCCCAGTCG
101054 CATTATTCGGATAAAGGTACAAGAGCATGATCCCCATATATGTAATTCTCTTCTATTGCCTAAAT
1 CATTATTCGGATAAAGGTACAAGAGCATGATCCCCATATATGTAATTCTCTTCTATTGCCTAAAT
101119 CTCACACCATTTCTTTTTAAGTTTTTCATATTCAGATGCTACATTAATGTCAGAGCATCTATGCT
66 CTCACACCATTTCTTTTTAAGTTTTTCATATTCAGATGCTACATTAATGTCAGAGCATCTATGCT
101184 AACCTCTTTCTTCATTTTTTCTTTCAAGCACTAACAAGCATTAACAATGAGAGCTCGGAATGAAC
131 AACCTCTTTCTTCATTTTTTCTTTCAAGCACTAACAAGCATTAACAATGAGAGCTCGGAATGAAC
101249 ATAACTCTCATACACTAGAAGACTACGAAAAATATCAAAAGAATCACTTAAAAAAATCAGCTTGC
196 ATAACTCTCATACACTAGAAGACTACGAAAAATATCAAAAGAATCACTTAAAAAAATCAGCTTGC
101314 AATGTGATTCTAATATCAGCAATTCAAATTCCAGTATTA
261 AATGTGATTCTAATATCAGCAATTCAAATTCCAGTATTA
101353 CATTATTCGGATAAAGGTACAAGAGCATGATCCCCATATATGTAATTCTCTTCTATTGCCTAAAT
1 CATTATTCGGATAAAGGTACAAGAGCATGATCCCCATATATGTAATTCTCTTCTATTGCCTAAAT
101418 CTCACACCATTTCTTTTTAAGTTTTTCATATTCAGATGCTACATTAATGTCAGAGCATCTATGCT
66 CTCACACCATTTCTTTTTAAGTTTTTCATATTCAGATGCTACATTAATGTCAGAGCATCTATGCT
101483 AACCTCTTTCTTCATTTTTTCTTTCAAGCACTAACAAGCATTAACAATGAGAGCTCGGAATGAAC
131 AACCTCTTTCTTCATTTTTTCTTTCAAGCACTAACAAGCATTAACAATGAGAGCTCGGAATGAAC
101548 ATAACTCTCATACACTAGAAGACTACGAAAAATATCAAAAGAATCACTTAAAAAAATCAGCTTGC
196 ATAACTCTCATACACTAGAAGACTACGAAAAATATCAAAAGAATCACTTAAAAAAATCAGCTTGC
101613 AATGTGATTCTAATATCAGCAATTCAAATTCCAGTATTA
261 AATGTGATTCTAATATCAGCAATTCAAATTCCAGTATTA
101652 CATTATTC
1 CATTATTC
101660 TACAAGATTA
Statistics
Matches: 307, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
299 307 1.00
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.33
Consensus pattern (299 bp):
CATTATTCGGATAAAGGTACAAGAGCATGATCCCCATATATGTAATTCTCTTCTATTGCCTAAAT
CTCACACCATTTCTTTTTAAGTTTTTCATATTCAGATGCTACATTAATGTCAGAGCATCTATGCT
AACCTCTTTCTTCATTTTTTCTTTCAAGCACTAACAAGCATTAACAATGAGAGCTCGGAATGAAC
ATAACTCTCATACACTAGAAGACTACGAAAAATATCAAAAGAATCACTTAAAAAAATCAGCTTGC
AATGTGATTCTAATATCAGCAATTCAAATTCCAGTATTA
Found at i:111309 original size:22 final size:22
Alignment explanation
Indices: 111282--111326 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
111272 AAGTCCGCAC
111282 ATATTATTATT-TTTAAATATTT
1 ATATTA-TATTATTTAAATATTT
*
111304 ATATTATATTATTTTAATATTT
1 ATATTATATTATTTAAATATTT
111326 A
1 A
111327 ATAATTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
ATATTATATTATTTAAATATTT
Found at i:117054 original size:2 final size:2
Alignment explanation
Indices: 117047--117073 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
117037 ATTTACATTT
117047 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
117074 AAGCTAGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:128937 original size:108 final size:108
Alignment explanation
Indices: 128748--128959 Score: 406
Period size: 108 Copynumber: 2.0 Consensus size: 108
128738 ACTTGAATTT
128748 TTTTTGGTCCAAGTTAATTCCCACATTGAGGCCTAAACTTAAAAAAGTTCAGGTCTTAAAGTGGG
1 TTTTTGGTCCAAGTTAATTCCCACATTGAGGCCTAAACTTAAAAAAGTTCAGGTCTTAAAGTGGG
128813 AACAATTACCAAGTTCAGGGATTAACTTAGACAAAAAAAAAAA
66 AACAATTACCAAGTTCAGGGATTAACTTAGACAAAAAAAAAAA
*
128856 TTTTTGGTCCAAGTTAATTCCGACATTGAGGCCTAAACTTAAAAAAGTTCAGGTCTTAAAGTGGG
1 TTTTTGGTCCAAGTTAATTCCCACATTGAGGCCTAAACTTAAAAAAGTTCAGGTCTTAAAGTGGG
*
128921 AACAATTACCAAGTTCAGGGATTAACTTGGACAAAAAAA
66 AACAATTACCAAGTTCAGGGATTAACTTAGACAAAAAAA
128960 GTTCAAGCCC
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
108 102 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (108 bp):
TTTTTGGTCCAAGTTAATTCCCACATTGAGGCCTAAACTTAAAAAAGTTCAGGTCTTAAAGTGGG
AACAATTACCAAGTTCAGGGATTAACTTAGACAAAAAAAAAAA
Found at i:133932 original size:48 final size:49
Alignment explanation
Indices: 133879--133980 Score: 147
Period size: 48 Copynumber: 2.1 Consensus size: 49
133869 TACTAAAACG
* *
133879 TATTATTATCTTATTTATAAAAT-A-AAAAAAATATGATTAATTTTAAGA
1 TATTATTAT-ATATTTATAAAATGAGAAAAAAATATGATTAATTTTAAAA
*
133927 TATTA-TATATATTTATAAAATGAGAAAAAATTATGATTAATTTTAAAA
1 TATTATTATATATTTATAAAATGAGAAAAAAATATGATTAATTTTAAAA
133975 TATTAT
1 TATTAT
133981 ACAAATAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
46 12 0.25
47 4 0.08
48 32 0.67
ACGTcount: A:0.50, C:0.01, G:0.05, T:0.44
Consensus pattern (49 bp):
TATTATTATATATTTATAAAATGAGAAAAAAATATGATTAATTTTAAAA
Found at i:139766 original size:6 final size:6
Alignment explanation
Indices: 139727--139763 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
139717 TTACACACAC
* *
139727 ACATAT ACATAT ACATAT ACATAT ATATAT ATATAT A
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT A
139764 TATTAATGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (6 bp):
ACATAT
Found at i:149629 original size:5 final size:5
Alignment explanation
Indices: 149619--149646 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
149609 TTTTTCACAT
149619 GGTTA GGTTA GGTTA GGTTA GGTTA GGT
1 GGTTA GGTTA GGTTA GGTTA GGTTA GGT
149647 AGCTAATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.43, T:0.39
Consensus pattern (5 bp):
GGTTA
Found at i:154577 original size:20 final size:20
Alignment explanation
Indices: 154548--154590 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
154538 TCATCAGTTA
*
154548 TATATCTATATTATTATTAC
1 TATATCTATACTATTATTAC
*
154568 TATATTTATACTATTATTAC
1 TATATCTATACTATTATTAC
154588 TAT
1 TAT
154591 TTATTAAGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (20 bp):
TATATCTATACTATTATTAC
Found at i:163650 original size:29 final size:29
Alignment explanation
Indices: 163573--163686 Score: 120
Period size: 29 Copynumber: 3.9 Consensus size: 29
163563 TAGAAATAAT
163573 ACAAATACAGTTACAGATACAGTCATGTC
1 ACAAATACAGTTACAGATACAGTCATGTC
* * * * *
163602 ATAGATACAATTATAGATACAATCATGTC
1 ACAAATACAGTTACAGATACAGTCATGTC
* * *
163631 ACAAATATAGTTACAAATACAGTCATATC
1 ACAAATACAGTTACAGATACAGTCATGTC
** * *
163660 ACATGTACAGTTACAGATGCAGACATG
1 ACAAATACAGTTACAGATACAGTCATG
163687 ATACCCCCTA
Statistics
Matches: 65, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (29 bp):
ACAAATACAGTTACAGATACAGTCATGTC
Found at i:163818 original size:40 final size:40
Alignment explanation
Indices: 163774--163924 Score: 230
Period size: 40 Copynumber: 3.8 Consensus size: 40
163764 ATGACACATC
*
163774 GCAGTGTTTATAGTGTCACTGTCGATTCAGTTGAAATCTT
1 GCAGTGTTAATAGTGTCACTGTCGATTCAGTTGAAATCTT
163814 GCAGTGTTAATAGTGTCACTGTCGATTCAGTTGAAATCTT
1 GCAGTGTTAATAGTGTCACTGTCGATTCAGTTGAAATCTT
*
163854 GCAGTGTTAATAGTGTCACTGTCAATTCAGTTGAAATCTT
1 GCAGTGTTAATAGTGTCACTGTCGATTCAGTTGAAATCTT
*** * * *
163894 ATTGTGTTAACAGTGTCACTGCCAATTCAGT
1 GCAGTGTTAATAGTGTCACTGTCGATTCAGT
163925 AAATATTCTC
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 104 1.00
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (40 bp):
GCAGTGTTAATAGTGTCACTGTCGATTCAGTTGAAATCTT
Found at i:165613 original size:41 final size:41
Alignment explanation
Indices: 165555--165638 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
165545 CTTCATCTTG
*
165555 AACCTCGAATCCAGAATTCGAACATAAAATCTTAAACCCTA
1 AACCTCGAATCCAGAATTCAAACATAAAATCTTAAACCCTA
** *
165596 AACCTCGAATCTTGAATTCAAACATCAAATCTTAAACCCTA
1 AACCTCGAATCCAGAATTCAAACATAAAATCTTAAACCCTA
165637 AA
1 AA
165639 TATTAATCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.44, C:0.26, G:0.06, T:0.24
Consensus pattern (41 bp):
AACCTCGAATCCAGAATTCAAACATAAAATCTTAAACCCTA
Found at i:165665 original size:40 final size:41
Alignment explanation
Indices: 165581--165673 Score: 93
Period size: 41 Copynumber: 2.3 Consensus size: 41
165571 TTCGAACATA
* * *
165581 AAATCTTAAACCCTAAACCTCGAATCTTGAATTCAAACATC
1 AAATCTTAAACCCTAAACATCGAATCTTGAACTCAAACACC
* * *
165622 AAATCTTAAACCCTAAATAT-TAATCTTGACCCTCAAAC-CC
1 AAATCTTAAACCCTAAACATCGAATCTTGA-ACTCAAACACC
165662 AAATAC-TAAACC
1 AAAT-CTTAAACC
165674 TCAAATCTTG
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
40 19 0.43
41 25 0.57
ACGTcount: A:0.43, C:0.28, G:0.03, T:0.26
Consensus pattern (41 bp):
AAATCTTAAACCCTAAACATCGAATCTTGAACTCAAACACC
Found at i:165744 original size:21 final size:21
Alignment explanation
Indices: 165693--165744 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
165683 GAGTTTGGGA
165693 TTCAA-GTTCAAGGTTCAAAG
1 TTCAAGGTTCAAGGTTCAAAG
* * *
165713 TTC-AGGATTCATGGTTCTATG
1 TTCAAGG-TTCAAGGTTCAAAG
165734 TTCAAGGTTCA
1 TTCAAGGTTCA
165745 GAGTAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 1 0.04
20 4 0.15
21 18 0.69
22 3 0.12
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (21 bp):
TTCAAGGTTCAAGGTTCAAAG
Found at i:169666 original size:14 final size:14
Alignment explanation
Indices: 169624--169667 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
169614 TTTTACCAAA
169624 AAAAAAATATTATAT
1 AAAAAAATATTA-AT
* *
169639 TAACAAAT-TTAAT
1 AAAAAAATATTAAT
169652 AAAAAAATATTAAT
1 AAAAAAATATTAAT
169666 AA
1 AA
169668 TTAGACGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 8 0.33
14 10 0.42
15 6 0.25
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (14 bp):
AAAAAAATATTAAT
Found at i:171129 original size:29 final size:29
Alignment explanation
Indices: 171068--171139 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
171058 ATCCAAAAGT
** **
171068 ACCTAGTTGGTACTTGAACTTTTTTTGGT
1 ACCTAGTTGGTACTTGAACTTCATTTGCC
171097 ACCTAGTTGGTACTTGAACTTGCATTT-CC
1 ACCTAGTTGGTACTTGAACTT-CATTTGCC
171126 ACCTAAGTTGGTAC
1 ACCT-AGTTGGTAC
171140 CTTTGCACTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 25 0.68
30 12 0.32
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (29 bp):
ACCTAGTTGGTACTTGAACTTCATTTGCC
Found at i:173094 original size:234 final size:234
Alignment explanation
Indices: 172685--173139 Score: 802
Period size: 234 Copynumber: 1.9 Consensus size: 234
172675 TGAGACGAAT
* *
172685 TTTCGAGACGGAAAACATGTATATATATTTGAAGTTTGGGAATTTTGAGTTTAGAGATTAGATAT
1 TTTCGAGACCGAAAACATGTATATATATTTGAAGTATGGGAATTTTGAGTTTAGAGATTAGATAT
* * *
172750 GCCGGTCTATGTTTTTATTGAGCTCTATATGGTTCATGGGATTGTTTTGAAAGTGCAGAAGTTGT
66 GCCGGTCTATGTTTTTATTGAGCTCTACATGGATCATAGGATTGTTTTGAAAGTGCAGAAGTTGT
172815 GAACTTGCTGTGACTAGTGGTTGAGTATTAGTGTATTCCGGGGTTAGTATCGAGCTTGATTTAAT
131 GAACTTGCTGTGACTAGTGGTTGAGTATTAGTGTATTCCGGGGTTAGTATCGAGCTTGATTTAAT
172880 GTTGTGATGCTAAAGTTCATTCTTTTCTCTACAACTATA
196 GTTGTGATGCTAAAGTTCATTCTTTTCTCTACAACTATA
* *
172919 TTTCGAGCCCGAAAACATGTATATATATTTTAAGTATGGGAATTTTGAGTTTAGAGATTAGATAT
1 TTTCGAGACCGAAAACATGTATATATATTTGAAGTATGGGAATTTTGAGTTTAGAGATTAGATAT
* * *
172984 GCTGGTCTATGTTTTTATTGAGCTCTCCATGGATCATAGGATTGTTTTGAAAGTGCAGTAGTTGT
66 GCCGGTCTATGTTTTTATTGAGCTCTACATGGATCATAGGATTGTTTTGAAAGTGCAGAAGTTGT
* *
173049 GAACTTGCTGTGATTAGTGGTTGAGTATTAGTGTATTCGGGGGTTAGTATCGAGCTTGATTTAAT
131 GAACTTGCTGTGACTAGTGGTTGAGTATTAGTGTATTCCGGGGTTAGTATCGAGCTTGATTTAAT
173114 GTTGTGATGCTAAAGTTCATTCTTTT
196 GTTGTGATGCTAAAGTTCATTCTTTT
173140 AAATATGAAG
Statistics
Matches: 209, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
234 209 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.41
Consensus pattern (234 bp):
TTTCGAGACCGAAAACATGTATATATATTTGAAGTATGGGAATTTTGAGTTTAGAGATTAGATAT
GCCGGTCTATGTTTTTATTGAGCTCTACATGGATCATAGGATTGTTTTGAAAGTGCAGAAGTTGT
GAACTTGCTGTGACTAGTGGTTGAGTATTAGTGTATTCCGGGGTTAGTATCGAGCTTGATTTAAT
GTTGTGATGCTAAAGTTCATTCTTTTCTCTACAACTATA
Found at i:176017 original size:20 final size:20
Alignment explanation
Indices: 175994--176033 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
175984 TTTATTTGGT
175994 CACTTTAGTTAATATTGTTA
1 CACTTTAGTTAATATTGTTA
176014 CACTTTAGTTAATATTGTTA
1 CACTTTAGTTAATATTGTTA
176034 ATTATTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
CACTTTAGTTAATATTGTTA
Found at i:178342 original size:18 final size:17
Alignment explanation
Indices: 178305--178348 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
178295 GGTTTTATAT
* *
178305 ATTTTTTAAAATTTTGA
1 ATTTTTTATAATTTTAA
178322 ATTTTTTATAATTATTAA
1 ATTTTTTATAATT-TTAA
*
178340 ATTATTTAT
1 ATTTTTTAT
178349 CGTCGTGGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
ATTTTTTATAATTTTAA
Found at i:179316 original size:19 final size:21
Alignment explanation
Indices: 179276--179317 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
179266 CTGTATTAAT
*
179276 ATTAATATTCATATCAATCGA
1 ATTAATACTCATATCAATCGA
179297 ATTAATACTCA-ATC-ATCGA
1 ATTAATACTCATATCAATCGA
179316 AT
1 AT
179318 AAAATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 3 0.15
21 10 0.50
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.36
Consensus pattern (21 bp):
ATTAATACTCATATCAATCGA
Found at i:198309 original size:17 final size:17
Alignment explanation
Indices: 198287--198333 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
198277 TAAAGCAATT
198287 AAATAATAAATAAATAA
1 AAATAATAAATAAATAA
198304 AAATAATAAATAAATAA
1 AAATAATAAATAAATAA
198321 AAATAAT-AATAAA
1 AAATAATAAATAAA
198334 AATTTAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 6 0.20
17 24 0.80
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (17 bp):
AAATAATAAATAAATAA
Found at i:198558 original size:42 final size:43
Alignment explanation
Indices: 198476--198558 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 43
198466 TAGATTAAAT
* *
198476 AATAATAAAATAATTTAAGATTAATCAAAATTTGATTAAAACA
1 AATAATAAAATAATTTAAGATTAATCAAAATTTAACTAAAACA
198519 AATAATAAAATAATTT-AGATTAATCAAAATTTAACTAAAA
1 AATAATAAAATAATTTAAGATTAATCAAAATTTAACTAAAA
198559 AATTATTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 22 0.58
43 16 0.42
ACGTcount: A:0.59, C:0.05, G:0.04, T:0.33
Consensus pattern (43 bp):
AATAATAAAATAATTTAAGATTAATCAAAATTTAACTAAAACA
Found at i:200811 original size:14 final size:14
Alignment explanation
Indices: 200792--200819 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
200782 AATCGATGAG
200792 ACACTAGGTGTCAC
1 ACACTAGGTGTCAC
200806 ACACTAGGTGTCAC
1 ACACTAGGTGTCAC
200820 CTTTATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (14 bp):
ACACTAGGTGTCAC
Found at i:201109 original size:2 final size:2
Alignment explanation
Indices: 201102--201144 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
201092 TTATATCATG
* *
201102 TA TA TA TA TA TA TA TA TA TA -A AA TT TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
201143 TA
1 TA
201145 ATTTAAAATC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:201130 original size:21 final size:21
Alignment explanation
Indices: 201106--201149 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
201096 ATCATGTATA
201106 TATATATATATATATAAAATT
1 TATATATATATATATAAAATT
*
201127 TATATATATATATATATAATT
1 TATATATATATATATAAAATT
201148 TA
1 TA
201150 AAATCTTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TATATATATATATATAAAATT
Found at i:222657 original size:61 final size:59
Alignment explanation
Indices: 222589--223071 Score: 425
Period size: 61 Copynumber: 8.1 Consensus size: 59
222579 CTTTTCATCT
* * *
222589 TTTTTATCTGATAAAAAATTCAATTTTTTTTTGTGTTGGTCATTCATTGGCCAACACCACC
1 TTTTTATCTGATAAAAAA-T-AATTTTTTTTGGTGTTGGTCATGCATTGGCCGACACCACC
* * * * *
222650 TTTTTATCAGAT-AAAAAT-ATATTTTTCTGGTGTTGGTCATTG-TTTGGTCGACACCACTT
1 TTTTTATCTGATAAAAAATAAT-TTTTTTTGGTGTTGGTCA-TGCATTGGCCGACACCAC-C
* * * * * *
222709 TTTTTATCTGGTAAAAAATTAAAATTTTTTT-GTGTTAGCCATGCTTTGAG-CGACAGCACC
1 TTTTTATCTGATAAAAAA-T-AATTTTTTTTGGTGTTGGTCATGCATTG-GCCGACACCACC
* * * **
222769 TTTTTATCTAAT-AAAAAT-ATTTTTTTTGGTGTTGGCCATTGC-TTGGCCGACATCATA
1 TTTTTATCTGATAAAAAATAATTTTTTTTGGTGTTGGTCA-TGCATTGGCCGACACCACC
* *
222826 TTTCTTATCTGATAAAAAAATAATTTTTTTTGGTGTTGGTCATGCATTGGCCGACGCCAACATT
1 TTT-TTATCTGAT-AAAAAATAATTTTTTTTGGTGTTGGTCATGCATTGGCCGACACC-AC--C
* * *
222890 TTTTTATCAGATAAAAAAT-A-TTTTTTTGGTGTTGGTCAATGC-TTGACCGACATCACC
1 TTTTTATCTGATAAAAAATAATTTTTTTTGGTGTTGGTC-ATGCATTGGCCGACACCACC
* *
222947 TTTTTATCTGATAAAAAACGAA-TTTTTTTGGTGTTGGTCATGCATTGGTCGACACCACC
1 TTTTTATCTGATAAAAAA-TAATTTTTTTTGGTGTTGGTCATGCATTGGCCGACACCACC
* * ** *
223006 TTTTTTAATCAGATAAAAAAACAATTTTTTTTGGTG-TGACCATGCATTGGCCGACACCAAC
1 -TTTTT-ATCTGAT-AAAAAATAATTTTTTTTGGTGTTGGTCATGCATTGGCCGACACCACC
223067 TTTTT
1 TTTTT
223072 CTCCTTTCTC
Statistics
Matches: 349, Mismatches: 45, Indels: 57
0.77 0.10 0.13
Matches are distributed among these distances:
56 9 0.03
57 41 0.12
58 44 0.13
59 49 0.14
60 67 0.19
61 95 0.27
62 32 0.09
63 9 0.03
64 3 0.01
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.42
Consensus pattern (59 bp):
TTTTTATCTGATAAAAAATAATTTTTTTTGGTGTTGGTCATGCATTGGCCGACACCACC
Found at i:222769 original size:119 final size:120
Alignment explanation
Indices: 222588--223042 Score: 498
Period size: 118 Copynumber: 3.8 Consensus size: 120
222578 CCTTTTCATC
* * * * *
222588 TTTTTTATCTGATAAAAAATTCAATTTTTTTTTGTGTTGGTCATTCATTGGCCAACACCACCTTT
1 TTTTTTATCTGATAAAAAATTAAAATTTTTTTGGTGTTGGTCATGCATTGGCCGACACCACCTTT
* * * *
222653 TTATCAGATAAAAATATATTTTTCTGGTGTTGGTCATTGTTTGGTCGACACCACT
66 TTATCAGATAAAAATATATTTTTTTGGTGTTGGTCATTGCTTGGCCGACATCACT
* * * * *
222708 TTTTTTATCTGGTAAAAAATTAAAATTTTTTT-GTGTTAGCCATGCTTTGAG-CGACAGCACCTT
1 TTTTTTATCTGATAAAAAATTAAAATTTTTTTGGTGTTGGTCATGCATTG-GCCGACACCACCTT
*
222771 TTTATCTA-ATAAAAATAT-TTTTTTTGGTGTTGGCCATTGCTTGGCCGACATCA-T
65 TTTATC-AGATAAAAATATATTTTTTTGGTGTTGGTCATTGCTTGGCCGACATCACT
* * * *
222825 ATTTCTTATCTGATAAAAAAAT-AATTTTTTTTGGTGTTGGTCATGCATTGGCCGACGCCAACAT
1 -TTTTTTATCTGATAAAAAATTAAAATTTTTTTGGTGTTGGTCATGCATTGGCCGACACC-AC--
* * *
222889 TTTTTTATCAGATAAAAA-ATATTTTTTTGGTGTTGGTCAATGCTTGACCGACATCAC-
62 CTTTTTATCAGATAAAAATATATTTTTTTGGTGTTGGTCATTGCTTGGCCGACATCACT
* ** *
222946 CTTTTTATCTGATAAAAAA--CGAATTTTTTTGGTGTTGGTCATGCATTGGTCGACACCACCTTT
1 TTTTTTATCTGATAAAAAATTAAAATTTTTTTGGTGTTGGTCATGCATTGGCCGACACCACC-TT
* *
223009 TTTAATCAGATAAAAAAACAATTTTTTTTGGTGT
65 TTT-ATCAGATAAAAATA-TA-TTTTTTTGGTGT
223043 GACCATGCAT
Statistics
Matches: 283, Mismatches: 35, Indels: 33
0.81 0.10 0.09
Matches are distributed among these distances:
117 16 0.06
118 81 0.29
119 75 0.27
120 52 0.18
121 59 0.21
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.43
Consensus pattern (120 bp):
TTTTTTATCTGATAAAAAATTAAAATTTTTTTGGTGTTGGTCATGCATTGGCCGACACCACCTTT
TTATCAGATAAAAATATATTTTTTTGGTGTTGGTCATTGCTTGGCCGACATCACT
Found at i:226874 original size:17 final size:16
Alignment explanation
Indices: 226852--226886 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
226842 ATTTGTGTAA
*
226852 AAATTAATTTGAAAATT
1 AAATTAAGTTG-AAATT
226869 AAATTAAGTTGAAATT
1 AAATTAAGTTGAAATT
226885 AA
1 AA
226887 TTTCAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (16 bp):
AAATTAAGTTGAAATT
Found at i:226994 original size:12 final size:11
Alignment explanation
Indices: 226964--227016 Score: 63
Period size: 12 Copynumber: 4.7 Consensus size: 11
226954 TTCTACTTTA
226964 AATTTAAAATT
1 AATTTAAAATT
*
226975 GAAATTAAAATT
1 -AATTTAAAATT
*
226987 ACATTTAAAATA
1 A-ATTTAAAATT
226999 AATTTAAAATT
1 AATTTAAAATT
227010 -ATTTAAA
1 AATTTAAA
227017 TAAAAAAGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
10 7 0.19
11 10 0.28
12 19 0.53
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (11 bp):
AATTTAAAATT
Found at i:227111 original size:95 final size:95
Alignment explanation
Indices: 226998--227671 Score: 778
Period size: 95 Copynumber: 7.0 Consensus size: 95
226988 CATTTAAAAT
* * * *
226998 AAATTTAAAATTATTTAAATAAAAAAGATTATTATAATATTTCAATTTATATTAAATAATGTATT
1 AAATTTAAAATTATTTAAATAAAAAATATTATTATAATATTTCAATTTTTATCAAATAATGTGTT
*
227063 GATTTGACAATATATTATTTATCAAATTCA
66 GATTTGACAATACATTATTTATCAAATTCA
* * *
227093 AATTTTAAAATTATTTAAATAAAAAAGATTATTATAATATTTCAAATTTTATCAAATAATGTGTT
1 AAATTTAAAATTATTTAAATAAAAAATATTATTATAATATTTCAATTTTTATCAAATAATGTGTT
227158 GATTTGACAATACATTATTTTGATTTGACAACA-T-A
66 GATTTGACAATACATTA-TTT-A--T--CAA-ATTCA
** * * * * * *
227193 TTATTTACCAAATTCA---AAATTCAAAATTATTTAAATAAAAAATATT-ATATTATTAT-AATA
1 AAATTTA--AAATT-ATTTAAA-TAAAAAATA-TT-ATTATAATAT-TTCA-ATTTTTATCAA-A
*
227253 TTTTAAT-T-TTTATCTTGATTTGACAATACATTATTTATCAAATTCA
57 ---TAATGTGTTGA--TT----TGACAATACATTATTTATCAAATTCA
*
227299 AAATTTAAAATTATTTAAAT-AAAAA-ATTATTATAATATTTCAAATTTTATCAAATAATGTGTT
1 AAATTTAAAATTATTTAAATAAAAAATATTATTATAATATTTCAATTTTTATCAAATAATGTGTT
*
227362 GATTTGA-AATACATTATTTACCAAATTCA
66 GATTTGACAATACATTATTTATCAAATTCA
*
227391 AAATTTAAAATTATTTAAATAAAAAAAATTATTATAATATTTCAATTTTTATCAAATAATGTGTT
1 AAATTTAAAATTATTTAAATAAAAAATATTATTATAATATTTCAATTTTTATCAAATAATGTGTT
*
227456 GATTTGACGATACATTATTTATCAAATTCA
66 GATTTGACAATACATTATTTATCAAATTCA
*
227486 AATTTTAAAATTATTTAAATAAAAAATATTATTATAATATTTCAATTTTTATCAAATAATGTGTT
1 AAATTTAAAATTATTTAAATAAAAAATATTATTATAATATTTCAATTTTTATCAAATAATGTGTT
* *
227551 GACTTGATAATACATTATTTATCAAATTCA
66 GATTTGACAATACATTATTTATCAAATTCA
* * *
227581 AAATTTAAAATTATTTAAATAAAAAATATTATTATATTATTTCAATTTTTATTAAATAATATGTT
1 AAATTTAAAATTATTTAAATAAAAAATATTATTATAATATTTCAATTTTTATCAAATAATGTGTT
* *
227646 GATTTGACAATATATTATGTATCAAA
66 GATTTGACAATACATTATTTATCAAA
227672 ATACCCTTAA
Statistics
Matches: 498, Mismatches: 44, Indels: 74
0.81 0.07 0.12
Matches are distributed among these distances:
92 41 0.08
93 8 0.02
94 44 0.09
95 269 0.54
96 3 0.01
97 7 0.01
98 1 0.00
99 4 0.01
100 17 0.03
101 20 0.04
102 10 0.02
103 13 0.03
104 19 0.04
105 8 0.02
106 10 0.02
107 7 0.01
109 1 0.00
110 3 0.01
111 13 0.03
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (95 bp):
AAATTTAAAATTATTTAAATAAAAAATATTATTATAATATTTCAATTTTTATCAAATAATGTGTT
GATTTGACAATACATTATTTATCAAATTCA
Found at i:227180 original size:21 final size:21
Alignment explanation
Indices: 227156--227198 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
227146 AAATAATGTG
*
227156 TTGATTTGACAATACATTATT
1 TTGATTTGACAACACATTATT
*
227177 TTGATTTGACAACATATTATT
1 TTGATTTGACAACACATTATT
227198 T
1 T
227199 ACCAAATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (21 bp):
TTGATTTGACAACACATTATT
Found at i:227318 original size:16 final size:17
Alignment explanation
Indices: 227299--227353 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 17
227289 ATCAAATTCA
227299 AAATTTAAAATTATT-T
1 AAATTTAAAATTATTAT
**
227315 AAATAAAAAATTATTAT
1 AAATTTAAAATTATTAT
*
227332 AATATTTCAAATT-TTAT
1 AA-ATTTAAAATTATTAT
227349 CAAAT
1 -AAAT
227354 AATGTGTTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 13 0.42
17 9 0.29
18 9 0.29
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATTTAAAATTATTAT
Found at i:228595 original size:18 final size:18
Alignment explanation
Indices: 228574--228614 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
228564 AGCTTGAGGA
228574 CGAGCCCGAGGACCAGTT
1 CGAGCCCGAGGACCAGTT
228592 CGAGCCCGAGGACCAGTT
1 CGAGCCCGAGGACCAGTT
228610 CGAGC
1 CGAGC
228615 AACAACTCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.22, C:0.34, G:0.34, T:0.10
Consensus pattern (18 bp):
CGAGCCCGAGGACCAGTT
Found at i:229168 original size:30 final size:30
Alignment explanation
Indices: 229051--229170 Score: 154
Period size: 30 Copynumber: 4.1 Consensus size: 30
229041 TTTTGATTTT
* * *
229051 TTTCGTTTATTTTTTAAATTGAATTTGTAA
1 TTTCGTTTATATTTTAAATTTAATTTCTAA
*
229081 TTTCG-TTATATTTT-AATTTAATTTATAA
1 TTTCGTTTATATTTTAAATTTAATTTCTAA
* *
229109 TTTCCTTTATATTTTAAATTTAATATCTAA
1 TTTCGTTTATATTTTAAATTTAATTTCTAA
**
229139 TTTCGTTTATATTTTAAATTTCTTTTCTAA
1 TTTCGTTTATATTTTAAATTTAATTTCTAA
229169 TT
1 TT
229171 ATTATTTTTT
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
28 16 0.21
29 17 0.22
30 45 0.58
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (30 bp):
TTTCGTTTATATTTTAAATTTAATTTCTAA
Found at i:230108 original size:57 final size:56
Alignment explanation
Indices: 230046--230182 Score: 150
Period size: 57 Copynumber: 2.3 Consensus size: 56
230036 ACAAATTTTT
* *
230046 TTTTTTATCAGATAAATAAAGTTG-TGTCGGTCAAAAAATGGTCAACACCAAAAAAATA
1 TTTTTTATCAGATAAA-AAA-ATGATGTCGGTCAAAAAATGATCAACA-CAAAAAAATA
* ***
230104 TTTTTTATCTGATAAAAAAATGATGTCGGTCAATGCATGATCAACACAAAAAAATTTAAA
1 TTTTTTATCAGATAAAAAAATGATGTCGGTCAAAAAATGATCAACACAAAAAAA--T--A
230164 TTTTTTATCAGATAAAAAA
1 TTTTTTATCAGATAAAAAA
230183 TGTGGTGTCA
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
56 10 0.15
57 22 0.33
58 16 0.24
60 19 0.28
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (56 bp):
TTTTTTATCAGATAAAAAAATGATGTCGGTCAAAAAATGATCAACACAAAAAAATA
Found at i:230191 original size:118 final size:118
Alignment explanation
Indices: 230046--230740 Score: 623
Period size: 118 Copynumber: 5.9 Consensus size: 118
230036 ACAAATTTTT
* * * * **
230046 TTTTTTATCAGATAAATAAAGTTGTGTCGGTCAAAAAATGGTCAACACCAAAAAAATATTTTTTA
1 TTTTTTATCAGATAAAAAAAGTGGTGTCGGCCAAACAATGACCAACACCAAAAAAATATTTTTTA
* * *
230111 TCTGATAAAAAAATGATGTCGGTCAATGCATGATCAACACAAAAAAATTTAAA
66 TCTGATAAAAAAGTGGTGTCGGCCAATGCATGATCAACACAAAAAAATTTAAA
* ** *
230164 TTTTTTATCAGATAAAAAATGTGGTGTC-AACAAAGCAATGACCAACACC---AAAATTTTTTTT
1 TTTTTTATCAGATAAAAAAAGTGGTGTCGGCCAAA-CAATGACCAACACCAAAAAAATATTTTTT
* * * * * * *
230225 ATTTGATAAAAATGTGGTGTAGACCAATGCATG-GCTAACACTAAAAGAATTTGAA
65 ATCTGATAAAAAAGTGGTGTCGGCCAATGCATGATC-AACAC-AAAAAAATTTAAA
* * * * **
230280 TTTTTTATCAGATAAAAAAAAATGGTGTCGACCAAGCAATGATCAACATTAAAAAAATATTTTTT
1 TTTTTTATCAGAT-AAAAAAAGTGGTGTCGGCCAAACAATGACCAACACCAAAAAAATATTTTTT
* * * *
230345 ATCTGATAAAAAGGTAGTGTCGGCCAAAGCATGACCAACACAAAAAAATTTAAA
65 ATCTGATAAAAAAGTGGTGTCGGCCAATGCATGATCAACACAAAAAAATTTAAA
* * * * * ***
230399 ATTTTTATCAGATAAAAAAAGTGATGTCGGCCAAATAATTG-CCAATACCAAAAAAAAAAAAATT
1 TTTTTTATCAGATAAAAAAAGTGGTGTCGGCCAAACAA-TGACCAACACC-AAAAAAATATTTTT
* * * *
230463 TATCTAATAAAAAATGCTGGTGTCGGCCAATGCATGACCAACTCTAAAAAAATTTGAA
64 TATCTGATAAAAAA-G-TGGTGTCGGCCAATGCATGATCAACAC-AAAAAAATTTAAA
* * * * * ** *
230521 TTTTTTATTAGA-CAAAAAGGTGGTGTTGGCTAAGTAATGACCAACATCAAAAAAATATTTTTTA
1 TTTTTTATCAGATAAAAAAAGTGGTGTCGGCCAAACAATGACCAACACCAAAAAAATATTTTTTA
* *
230585 TCTGATAAAAATA-TGGTGTCGGCCAATGCATGGTCAACACAAAAAAA--T-CA
66 TCTGATAAAAA-AGTGGTGTCGGCCAATGCATGATCAACACAAAAAAATTTAAA
* * * * * *
230635 TTTTTT-TCAGATAAAAAAGGTGGTGTCGGCCAATGC-ACGGCCAACA-C--TAAAATTTTTTTT
1 TTTTTTATCAGATAAAAAAAGTGGTGTCGGCCAA-ACAATGACCAACACCAAAAAAATATTTTTT
* *
230695 ATCTGATAAAAAAGTGGTGTCGGCCAA-GGATTGATCAACACCAAAA
65 ATCTGATAAAAAAGTGGTGTCGGCCAATGCA-TGATCAACACAAAAA
230741 TTTTTTTTAT
Statistics
Matches: 470, Mismatches: 87, Indels: 47
0.78 0.14 0.08
Matches are distributed among these distances:
110 3 0.01
111 49 0.10
113 5 0.01
114 34 0.07
115 44 0.09
116 24 0.05
117 35 0.07
118 88 0.19
119 47 0.10
120 68 0.14
121 51 0.11
122 22 0.05
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (118 bp):
TTTTTTATCAGATAAAAAAAGTGGTGTCGGCCAAACAATGACCAACACCAAAAAAATATTTTTTA
TCTGATAAAAAAGTGGTGTCGGCCAATGCATGATCAACACAAAAAAATTTAAA
Found at i:230314 original size:63 final size:60
Alignment explanation
Indices: 230103--230418 Score: 151
Period size: 61 Copynumber: 5.3 Consensus size: 60
230093 CCAAAAAAAT
* * ** * *
230103 ATTTTTTATCTGAT--AAAAAAATGATGTCGGTCAATGCAT-GATCAACACAAAAAAATTTAA
1 ATTTTTTATCAGATAAAAAAAAATGGTGTCGACCAA-GCATGGCT-AACACTAAAAAATTT-A
** * * * * *
230163 ATTTTTTATCAGAT-AAAAAATGTGGTGTCAACAAAGCAATGACCAACAC--CAAAA-TT-
1 ATTTTTTATCAGATAAAAAAAAATGGTGTCGACCAAGC-ATGGCTAACACTAAAAAATTTA
** ** *
230219 -TTTTTTATTTGAT--AAAAATGTGGTGTAGACCAATGCATGGCTAACACTAAAAGAATTTGA
1 ATTTTTTATCAGATAAAAAAAAATGGTGTCGACCAA-GCATGGCTAACACTAAAA-AATTT-A
* * *
230279 ATTTTTTATCAGATAAAAAAAAATGGTGTCGACCAAGCAAT-GATCAACATTAAAAAA-AT-
1 ATTTTTTATCAGATAAAAAAAAATGGTGTCGACCAAGC-ATGGCT-AACACTAAAAAATTTA
* ** * * * * *
230338 ATTTTTTATCTGAT--AAAAAGGTAGTGTCGGCCAAAGCATGACCAACACAAAAAAATTTAA
1 ATTTTTTATCAGATAAAAAAAAATGGTGTCGACC-AAGCATGGCTAACACTAAAAAATTT-A
*
230398 AATTTTTATCAGATAAAAAAA
1 ATTTTTTATCAGATAAAAAAA
230419 GTGATGTCGG
Statistics
Matches: 193, Mismatches: 41, Indels: 42
0.70 0.15 0.15
Matches are distributed among these distances:
54 26 0.13
55 13 0.07
56 2 0.01
57 28 0.15
58 9 0.05
59 17 0.09
60 27 0.14
61 32 0.17
62 11 0.06
63 28 0.15
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.30
Consensus pattern (60 bp):
ATTTTTTATCAGATAAAAAAAAATGGTGTCGACCAAGCATGGCTAACACTAAAAAATTTA
Found at i:230348 original size:235 final size:235
Alignment explanation
Indices: 230046--230714 Score: 719
Period size: 235 Copynumber: 2.9 Consensus size: 235
230036 ACAAATTTTT
* * * * * *
230046 TTTTTTATCAGAT-AAATAAAGTTGTGTCGGTCAAAAAATGGTCAACACCAAAAAAATATTTTTT
1 TTTTTTATCAGATAAAAAAAAGTGGTGTCGGCCAAGAAATGATCAACATCAAAAAAATATTTTTT
*
230110 ATCTGATAAAAAAATGATGTCGGTCAATGCATGATCAACACAAAAAAATTTAAATTTTTTATCAG
66 ATCTGATAAAAAAATGATGTCGGCCAATGCATGATCAACACAAAAAAATTTAAATTTTTTATCAG
* ** *
230175 ATAAAAAATGTGGTGTC-AACAAAGCAATGACCAACACCAAAATTTTTTTTATTTGATAAAAATG
131 ATAAAAAAAGTGGTGTCGGCCAAAGCAATG-CCAACACCAAAATTTTTTTTATCTGATAAAAATG
* * *
230239 TGGTGTAGACCAATGCATGGCTAACACTAAAAGAATTTGAA
195 TGGTGTAGACCAATGCATGACCAACACTAAAAAAATTTGAA
* * * *
230280 TTTTTTATCAGATAAAAAAAAATGGTGTCGACCAAGCAATGATCAACATTAAAAAAATATTTTTT
1 TTTTTTATCAGATAAAAAAAAGTGGTGTCGGCCAAGAAATGATCAACATCAAAAAAATATTTTTT
** * * *
230345 ATCTGATAAAAAGGT-AGTGTCGGCCAAAGCATGACCAACACAAAAAAATTTAAAATTTTTATCA
66 ATCTGATAAAAAAATGA-TGTCGGCCAATGCATGATCAACACAAAAAAATTTAAATTTTTTATCA
* * * ***** *
230409 GATAAAAAAAGTGATGTCGGCCAAA-TAATTGCCAATACCAAAAAAAAAAAAATTTATCTAATAA
130 GATAAAAAAAGTGGTGTCGGCCAAAGCAA-TGCCAACACC----AAAATTTTTTTTATCTGAT-A
* * *
230473 AAAATGCTGGTGTCGGCCAATGCATGACCAACTCTAAAAAAATTTGAA
189 AAAATG-TGGTGTAGACCAATGCATGACCAACACTAAAAAAATTTGAA
* * * * * * *
230521 TTTTTTATTAG--ACAAAAAGGTGGTGTTGGCTAAGTAATGACCAACATCAAAAAAATATTTTTT
1 TTTTTTATCAGATAAAAAAAAGTGGTGTCGGCCAAGAAATGATCAACATCAAAAAAATATTTTTT
* * * *
230584 ATCTGATAAAAATATGGTGTCGGCCAATGCATGGTCAACACAAAAAAA--T-CATTTTTT-TCAG
66 ATCTGATAAAAAAATGATGTCGGCCAATGCATGATCAACACAAAAAAATTTAAATTTTTTATCAG
* * ** * *
230645 ATAAAAAAGGTGGTGTCGGCCAATGCACGGCCAACACTAAAATTTTTTTTATCTGATAAAAAAGT
131 ATAAAAAAAGTGGTGTCGGCCAAAGCAATGCCAACACCAAAATTTTTTTTATCTGATAAAAATGT
230710 GGTGT
196 GGTGT
230715 CGGCCAAGGA
Statistics
Matches: 355, Mismatches: 68, Indels: 29
0.79 0.15 0.06
Matches are distributed among these distances:
229 6 0.02
230 6 0.02
231 13 0.04
234 14 0.04
235 154 0.43
236 13 0.04
237 1 0.00
239 96 0.27
240 7 0.02
241 45 0.13
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.29
Consensus pattern (235 bp):
TTTTTTATCAGATAAAAAAAAGTGGTGTCGGCCAAGAAATGATCAACATCAAAAAAATATTTTTT
ATCTGATAAAAAAATGATGTCGGCCAATGCATGATCAACACAAAAAAATTTAAATTTTTTATCAG
ATAAAAAAAGTGGTGTCGGCCAAAGCAATGCCAACACCAAAATTTTTTTTATCTGATAAAAATGT
GGTGTAGACCAATGCATGACCAACACTAAAAAAATTTGAA
Found at i:230523 original size:121 final size:116
Alignment explanation
Indices: 230230--230667 Score: 344
Period size: 120 Copynumber: 3.7 Consensus size: 116
230220 TTTTTATTTG
* * * * * *
230230 ATAAAAATGTGGTGTAGACCAATGCATGGCTAACACTAAAAGAATTTGAATTTTTTATCAGATAA
1 ATAAAAATATGGTGTCGGCCAATGCATGACCAACAC-AAAAAAATTT-AA-TTTTTATCAGAT-A
** * ** * ** * *** *
230295 AAAAAAATGGTGTCGACCAAGCAATGATCAACATTAAAAAAATATTTTTTATCTG
62 AAAAAGGTGGTGTCGGCCAAATAATGACCAACACCAAAAAAAAAAAATTTATCTA
** * *
230350 ATAAAAAGGTAGTGTCGGCCAAAGCATGACCAACACAAAAAAATTTAAAATTTTTATCAGATAAA
1 ATAAAAATATGGTGTCGGCCAATGCATGACCAACACAAAAAAATTT--AATTTTTATCAGATAAA
* * *
230415 AAAAGTGATGTCGGCCAAATAATTG-CCAATACCAAAAAAAAAAAAATTTATCTA
64 AAAGGTGGTGTCGGCCAAATAA-TGACCAACACC-AAAAAAAAAAAATTTATCTA
* * *
230469 ATAAAAAATGCTGGTGTCGGCCAATGCATGACCAACTCTAAAAAAATTTGAATTTTTTATTAGA-
1 AT-AAAAAT-ATGGTGTCGGCCAATGCATGACCAACAC-AAAAAAATTT-AA-TTTTTATCAGAT
* * * * * * *** *
230533 CAAAAAGGTGGTGTTGGCTAAGTAATGACCAACATCAAAAAAATATTTTTTATCTG
61 AAAAAAGGTGGTGTCGGCCAAATAATGACCAACACCAAAAAAAAAAAATTTATCTA
** * *
230589 ATAAAAATATGGTGTCGGCCAATGCATGGTCAACACAAAAAAA--TCATTTTTTTCAGATAAAAA
1 ATAAAAATATGGTGTCGGCCAATGCATGACCAACACAAAAAAATTTAATTTTTATCAGATAAAAA
230652 AGGTGGTGTCGGCCAA
66 AGGTGGTGTCGGCCAA
230668 TGCACGGCCA
Statistics
Matches: 256, Mismatches: 53, Indels: 24
0.77 0.16 0.07
Matches are distributed among these distances:
113 9 0.04
114 19 0.07
115 1 0.00
117 7 0.03
118 48 0.19
119 46 0.18
120 55 0.21
121 51 0.20
122 20 0.08
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.27
Consensus pattern (116 bp):
ATAAAAATATGGTGTCGGCCAATGCATGACCAACACAAAAAAATTTAATTTTTATCAGATAAAAA
AGGTGGTGTCGGCCAAATAATGACCAACACCAAAAAAAAAAAATTTATCTA
Found at i:230623 original size:57 final size:56
Alignment explanation
Indices: 230088--230760 Score: 352
Period size: 57 Copynumber: 11.6 Consensus size: 56
230078 AAAAAATGGT
* * * *
230088 CAACACCAAAAAAATATTTTTTATCTGATAAAAAAATGATGTCGGTCAATGCATGAT
1 CAACA-CAAAAAAATATTTTTTATCTGATAAAAATATGGTGTCGGCCAATGCATGAC
* * ** *
230145 CAACACAAAAAAATTTAAATTTTTTATCAGATAAAAAATGTGGTGTC-AACAAAGCAATGAC
1 CAACACAAAAAAA--T--ATTTTTTATCTGAT-AAAAATATGGTGTCGGCCAATGC-ATGAC
* * * * * * *
230206 CAACAC--CAAAATTTTTTTTATTTGATAAAAATGTGGTGTAGACCAATGCATGGC
1 CAACACAAAAAAATATTTTTTATCTGATAAAAATATGGTGTCGGCCAATGCATGAC
* * * * * *
230260 TAACACTAAAAGAATTTGAATTTTTTATCAGATAAAAAAAAATGGTGTCGACCAA-GCAATGAT
1 CAACAC-AAAA-AA-AT--ATTTTTTATCTGAT--AAAAATATGGTGTCGGCCAATGC-ATGAC
* ** * *
230323 CAACATTAAAAAAATATTTTTTATCTGATAAAAAGGTAGTGTCGGCCAAAGCATGAC
1 CAACA-CAAAAAAATATTTTTTATCTGATAAAAATATGGTGTCGGCCAATGCATGAC
* * * * *
230380 CAACACAAAAAAATTTAAAATTTTTATCAGATAAAAAAAGTGATGTCGGCCAAAT-AATTG-C
1 CAACACAAAAAAA--T--ATTTTTTATCTGATAAAAATA-TGGTGTCGGCC-AATGCA-TGAC
* * *** * *
230441 CAATACCAAAAAAAAAAAAATTTATCTAATAAAAAATGCTGGTGTCGGCCAATGCATGAC
1 CAACA-C-AAAAAAATATTTTTTATCTGAT-AAAAAT-ATGGTGTCGGCCAATGCATGAC
* * ** * * *
230501 CAACTCTAAAAAAATTTGAATTTTTTAT-TAGACAAAAAGGTGGTGTTGGCTAA-GTAATGAC
1 CAACAC-AAAAAAA--T--ATTTTTTATCT-GATAAAAATATGGTGTCGGCCAATG-CATGAC
**
230562 CAACATCAAAAAAATATTTTTTATCTGATAAAAATATGGTGTCGGCCAATGCATGGT
1 CAACA-CAAAAAAATATTTTTTATCTGATAAAAATATGGTGTCGGCCAATGCATGAC
* * *
230619 CAACACAAAAAAATCATTTTTT-TCAGATAAAAA-AGGTGGTGTCGGCCAATGCACGGC
1 CAACACAAAAAAAT-ATTTTTTATCTGATAAAAATA--TGGTGTCGGCCAATGCATGAC
* * * *
230676 CAACAC--TAAAATTTTTTTTATCTGATAAAAA-AGTGGTGTCGGCCAA-GGATTGAT
1 CAACACAAAAAAATATTTTTTATCTGATAAAAATA-TGGTGTCGGCCAATGCA-TGAC
* * *
230730 CAACAC--CAAAATTTTTTTTATCTGACAAAAA
1 CAACACAAAAAAATATTTTTTATCTGATAAAAA
230761 AGGTGATGTC
Statistics
Matches: 480, Mismatches: 90, Indels: 95
0.72 0.14 0.14
Matches are distributed among these distances:
53 2 0.00
54 72 0.15
55 34 0.07
56 34 0.07
57 99 0.21
58 8 0.02
59 42 0.09
60 56 0.12
61 75 0.16
62 16 0.03
63 42 0.09
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.29
Consensus pattern (56 bp):
CAACACAAAAAAATATTTTTTATCTGATAAAAATATGGTGTCGGCCAATGCATGAC
Found at i:230717 original size:54 final size:54
Alignment explanation
Indices: 230571--230762 Score: 219
Period size: 54 Copynumber: 3.5 Consensus size: 54
230561 CCAACATCAA
230571 AAAAATATTTTTTATCTGATAAAAATA-TGGTGTCGGCCAATGCATGGTCAACAC
1 AAAAATATTTTTTATCTGATAAAAA-AGTGGTGTCGGCCAATGCATGGTCAACAC
* * *
230625 AAAAAAATCATTTTTT-TCAGATAAAAAAGGTGGTGTCGGCCAATGCACGGCCAACAC
1 --AAAAAT-ATTTTTTATCTGATAAAAAA-GTGGTGTCGGCCAATGCATGGTCAACAC
* * * *
230682 TAAAATTTTTTTTATCTGATAAAAAAGTGGTGTCGGCCAA-GGATTGATCAACAC
1 AAAAATATTTTTTATCTGATAAAAAAGTGGTGTCGGCCAATGCA-TGGTCAACAC
* * *
230736 CAAAATTTTTTTTATCTGACAAAAAAG
1 AAAAATATTTTTTATCTGATAAAAAAG
230763 GTGATGTCTG
Statistics
Matches: 119, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
53 2 0.02
54 52 0.44
55 17 0.14
56 16 0.13
57 32 0.27
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (54 bp):
AAAAATATTTTTTATCTGATAAAAAAGTGGTGTCGGCCAATGCATGGTCAACAC
Found at i:230795 original size:55 final size:54
Alignment explanation
Indices: 230675--230804 Score: 145
Period size: 54 Copynumber: 2.4 Consensus size: 54
230665 CAATGCACGG
* *
230675 CCAAC-ACTAAAATTTTTTTTATCTGATAAAAAAGTGGTGTCGGCCAAGGATTGA
1 CCAACAAC-AAAATTTTTTTTATCTGACAAAAAAGTGATGTCGGCCAAGGATTGA
* * * * * *
230729 TCAACACCAAAATTTTTTTTATCTGACAAAAAAGGTGATGTCTGCCATGTATTGG
1 CCAACAACAAAATTTTTTTTATCTGACAAAAAA-GTGATGTCGGCCAAGGATTGA
*
230784 CCAGCAACAAAATATTTTTTT
1 CCAACAACAAAAT-TTTTTTT
230805 TCAAAATCTC
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
54 28 0.45
55 27 0.44
56 7 0.11
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (54 bp):
CCAACAACAAAATTTTTTTTATCTGACAAAAAAGTGATGTCGGCCAAGGATTGA
Done.