Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012547.1 Kokia drynarioides strain JFW-HI SEQ_127556, 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: 170779
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 75 characters in sequence are not A, C, G, or T
Found at i:2658 original size:20 final size:19
Alignment explanation
Indices: 2635--2680 Score: 83
Period size: 20 Copynumber: 2.4 Consensus size: 19
2625 TTAATAGTTG
2635 TTATGTTAGTTTACATTAA
1 TTATGTTAGTTTACATTAA
2654 TTTATGTTAGTTTACATTAA
1 -TTATGTTAGTTTACATTAA
2674 TTATGTT
1 TTATGTT
2681 TTACTTGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.28, C:0.04, G:0.11, T:0.57
Consensus pattern (19 bp):
TTATGTTAGTTTACATTAA
Found at i:3580 original size:98 final size:98
Alignment explanation
Indices: 3322--3612 Score: 460
Period size: 98 Copynumber: 3.0 Consensus size: 98
3312 TTGAAAAAGG
* *
3322 GTATTCGATTATCCCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCAAAAC
1 GTATTCGATTATCCCGGTTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCAAAAC
*
3387 CCGAAATAAAAGAATATTGCCTTGA-TTTAAGA
66 CCGAAATAAAAGAATATTGCCTTGATTTTAAAA
*
3419 GTATTCGA-TATCCCGGTTTGAAGAAAAATCGCGCCTAGTAAGTTAAGACACAAATTTTCAAAAC
1 GTATTCGATTATCCCGGTTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCAAAAC
*
3483 CCGAAATAAAAGAATATTTCCTTGATTTTAAAA
66 CCGAAATAAAAGAATATTGCCTTGATTTTAAAA
* * * *
3516 GTATTCGATTATCCCGGTTTGAAGAAAAATCGTGCCAAGTAAGTTAAGGCTCAAATTTTTAAAAC
1 GTATTCGATTATCCCGGTTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCAAAAC
* **
3581 CCGAAATAAATGAATATTGCCTCAATTTTAAA
66 CCGAAATAAAAGAATATTGCCTTGATTTTAAA
3613 TATTTTGGAG
Statistics
Matches: 178, Mismatches: 14, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
96 77 0.43
97 22 0.12
98 79 0.44
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (98 bp):
GTATTCGATTATCCCGGTTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCAAAAC
CCGAAATAAAAGAATATTGCCTTGATTTTAAAA
Found at i:4005 original size:28 final size:29
Alignment explanation
Indices: 3919--4008 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 29
3909 TTTGAAATCG
* * **
3919 AAAAT-GTGACTTTTGGAAATTTGGGAGCA
1 AAAATGGTAACTTTTGGAAATTT-CGAGGT
*
3948 AAAATGGTAACTTTTGG--ATGTTCAGGGGT
1 AAAATGGTAACTTTTGGAAAT-TTC-GAGGT
3977 AAAATGGTAA-TTTTGGAAATTTCGAGGT
1 AAAATGGTAACTTTTGGAAATTTCGAGGT
4005 AAAA
1 AAAA
4009 ATGTGATTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
28 16 0.32
29 22 0.44
30 12 0.24
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.32
Consensus pattern (29 bp):
AAAATGGTAACTTTTGGAAATTTCGAGGT
Found at i:4023 original size:30 final size:29
Alignment explanation
Indices: 3947--4412 Score: 432
Period size: 30 Copynumber: 15.9 Consensus size: 29
3937 ATTTGGGAGC
* *
3947 AAAAATGGTAACTTTTGGATGTTC-AGGGGT
1 AAAAAT-GTAATTTTTGGAAGTTCGA-GGGT
*
3977 -AAAATGGTAA-TTTTGGAAATTTCGA-GGT
1 AAAAAT-GTAATTTTTGG-AAGTTCGAGGGT
*
4005 AAAAATGTGATTTTTTGGAAGTTCGAGGGCT
1 AAAAATGT-AATTTTTGGAAGTTCGAGGG-T
* * *
4036 -AAAATGTGATTTTTTGGAAGTTTGGGGGT
1 AAAAATGT-AATTTTTGGAAGTTCGAGGGT
* * *
4065 AAAATTATAATTTTTAGAAGTTCGAGGG-
1 AAAAATGTAATTTTTGGAAGTTCGAGGGT
* * * * *
4093 ACAAATGCAGTTTTTGAAAGTTTGAGGGT
1 AAAAATGTAATTTTTGGAAGTTCGAGGGT
*
4122 AAAAATGTAATTTTTAAGAAGTTCGAGGGT
1 AAAAATGTAATTTTT-GGAAGTTCGAGGGT
*
4152 AAAAATGTAATTTTTGGAAGTTTGAGGGT
1 AAAAATGTAATTTTTGGAAGTTCGAGGGT
4181 -AAAATGTAATTTTTGAGAAGTTCGAGGGT
1 AAAAATGTAATTTTTG-GAAGTTCGAGGGT
* * *
4210 AGAAATGTAATTTTTGCGAAGTTCGAGAGC
1 AAAAATGTAATTTTTG-GAAGTTCGAGGGT
*
4240 AAAAATGTAATTTTAGGAAGTTCGAGGGT
1 AAAAATGTAATTTTTGGAAGTTCGAGGGT
* * *
4269 AAAAATGTAATTTTTGAGAAGTTTGAAGGC
1 AAAAATGTAATTTTTG-GAAGTTCGAGGGT
* *
4299 GAAAATGTAATTTTTGAGAAGTT-TAGGG-
1 AAAAATGTAATTTTTG-GAAGTTCGAGGGT
* * *
4327 CAAAATGTGATTTTTGGATGTTCGAGGGT
1 AAAAATGTAATTTTTGGAAGTTCGAGGGT
* *
4356 -AAAACGTAATTTTTGAGAAGTTC-AGGAGC
1 AAAAATGTAATTTTTG-GAAGTTCGAGG-GT
*
4385 AAAAATATAATTTTTGAGAAGTTCGAGG
1 AAAAATGTAATTTTTG-GAAGTTCGAGG
4413 TTCAAAATAT
Statistics
Matches: 363, Mismatches: 54, Indels: 37
0.80 0.12 0.08
Matches are distributed among these distances:
27 5 0.01
28 80 0.22
29 116 0.32
30 158 0.44
31 4 0.01
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (29 bp):
AAAAATGTAATTTTTGGAAGTTCGAGGGT
Found at i:4085 original size:59 final size:57
Alignment explanation
Indices: 3948--4412 Score: 439
Period size: 59 Copynumber: 8.0 Consensus size: 57
3938 TTTGGGAGCA
* * *
3948 AAAATGGTAACTTTTG-GATGTTC-AGGGGTAAAATGGTAA-TTTTGGAAATTTCGA-GGT
1 AAAAT-GTAATTTTTGAGAAGTTCGA-GGGTAAAAT-GTAATTTTTGGAAGTTT-GAGGGT
* * *
4005 AAAAATGTGATTTTTTG-GAAGTTCGAGGGCTAAAATGTGATTTTTTGGAAGTTTGGGGGT
1 -AAAATGT-AATTTTTGAGAAGTTCGAGGG-TAAAATGT-AATTTTTGGAAGTTTGAGGGT
* * * *
4065 AAAATTATAATTTTT-AGAAGTTCGAGGG-ACAAATGCAGTTTTTGAAAGTTTGAGGGT
1 AAAA-TGTAATTTTTGAGAAGTTCGAGGGTA-AAATGTAATTTTTGGAAGTTTGAGGGT
*
4122 AAAAATGTAATTTTTAAGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTGAGGGT
1 -AAAATGTAATTTTTGAGAAGTTCGAGGGT-AAAATGTAATTTTTGGAAGTTTGAGGGT
* **
4181 AAAATGTAATTTTTGAGAAGTTCGAGGGTAGAAATGTAATTTTTGCGAAGTTCGAGAGCA
1 AAAATGTAATTTTTGAGAAGTTCGAGGGTA-AAATGTAATTTTTG-GAAGTTTGAG-GGT
*
4241 AAAATGTAATTTTAG-GAAGTTCGAGGGTAAAAATGTAATTTTTGAGAAGTTTGAAGGCG-
1 AAAATGTAATTTTTGAGAAGTTCGAGGGT-AAAATGTAATTTTTG-GAAGTTTG-AGG-GT
* * * * *
4300 AAAATGTAATTTTTGAGAAGTT-TAGGGCAAAATGTGATTTTTGGATGTTCGAGGGT
1 AAAATGTAATTTTTGAGAAGTTCGAGGGTAAAATGTAATTTTTGGAAGTTTGAGGGT
* * * *
4356 AAAACGTAATTTTTGAGAAGTTC-AGGAGCAAAAATATAATTTTTGAGAAGTTCGAGG
1 AAAATGTAATTTTTGAGAAGTTCGAGG-G-TAAAATGTAATTTTTG-GAAGTTTGAGG
4413 TTCAAAATAT
Statistics
Matches: 347, Mismatches: 35, Indels: 49
0.81 0.08 0.11
Matches are distributed among these distances:
55 1 0.00
56 27 0.08
57 38 0.11
58 113 0.33
59 127 0.37
60 41 0.12
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (57 bp):
AAAATGTAATTTTTGAGAAGTTCGAGGGTAAAATGTAATTTTTGGAAGTTTGAGGGT
Found at i:6704 original size:78 final size:78
Alignment explanation
Indices: 6648--7422 Score: 892
Period size: 78 Copynumber: 9.9 Consensus size: 78
6638 GCTGATAGTG
** * *
6648 ATCTGCCTTAGGCTCGAGGTAAGAGATTTCCTGATGATGATCTGCCCCAGGTTCGGGGTAAAAGA
1 ATCTGCCCCAGGCTCGAGGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCGGGGTAAAAGA
* *
6713 TCAAATGATTGTA
66 TCGAATGATTGCA
* * * * ** * *
6726 ATTTGCCTCAGGCTCGGGGTAAGAGATTTGCTGATTATGATATCTAG-CTGAGGCTCGTGGTAAG
1 ATCTGCCCCAGGCTCGAGGTAAGAGATTTGCTGATGATG--ATCT-GCCCCAGGCTCGGGGTAAA
* *
6790 AGATTGGATGATTGCA
63 AGATCGAATGATTGCA
* * * * *
6806 ATCTGCCCC-GATCTCAAGGTAAGAGATTTGCTGATGATGATCTGTCCTAGGCTTGGGGTAAAAG
1 ATCTGCCCCAG-GCTCGAGGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCGGGGTAAAAG
6870 ATC-AACTGATTGCA
65 ATCGAA-TGATTGCA
* * * *
6884 ATCTGCCCCAGGCTTGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAAGCTCGGGGTAAAAAA
1 ATCTGCCCCAGGCTCGAGGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCGGGGTAAAAGA
* * * *
6949 TCTAATGGTCGTA
66 TCGAATGATTGCA
* * * *
6962 ATCTGCCCCAGTCTCGAGGTAAGAGATTTGCTGATGATGATATGCCCCAAGCTCGAGGTAAAAGA
1 ATCTGCCCCAGGCTCGAGGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCGGGGTAAAAGA
* * *
7027 TCGAATGGTTACT
66 TCGAATGATTGCA
* *
7040 ATCTGCCCCAGGCTCAAGGTAAGAGATTTGCTGATGATGATCT-CCCCAAGCTCGGGGTAAAAGA
1 ATCTGCCCCAGGCTCGAGGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCGGGGTAAAAGA
* **
7104 TCTAATGGCTGCA
66 TCGAATGATTGCA
* * * * * * *
7117 ATCTTCCCCATGATCGAGGTAAGAGATTTACTGATGGTGATCTGCCTCAGGCTCGGGGTAAGAGA
1 ATCTGCCCCAGGCTCGAGGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCGGGGTAAAAGA
**
7182 TCGAATGGCTGCA
66 TCGAATGATTGCA
** * *
7195 ATCTGCCCCATTCTCGAGGTAAGAGATTTGCTGATGATGATCTACCCCAGGCTCAGGGTAAAAGA
1 ATCTGCCCCAGGCTCGAGGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCGGGGTAAAAGA
*
7260 TCGAATGGTTGCA
66 TCGAATGATTGCA
* * *
7273 ATCTGCCCCAGGTTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCGAGGTAAAAGA
1 ATCTGCCCCAGGCTCGAGGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCGGGGTAAAAGA
*
7338 TCGAATGGTTGCA
66 TCGAATGATTGCA
* * * * *
7351 ATCTGCCCCAGGCTCGGGGTAAGAGATTTGTTGATGATGATCTACCTCAGGCTCGGGGTAAAGGA
1 ATCTGCCCCAGGCTCGAGGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCGGGGTAAAAGA
7416 TCAGAAT
66 TC-GAAT
7423 CTTTAATCTG
Statistics
Matches: 596, Mismatches: 91, Indels: 19
0.84 0.13 0.03
Matches are distributed among these distances:
77 68 0.11
78 460 0.77
79 8 0.01
80 59 0.10
81 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (78 bp):
ATCTGCCCCAGGCTCGAGGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCGGGGTAAAAGA
TCGAATGATTGCA
Found at i:7402 original size:39 final size:39
Alignment explanation
Indices: 6609--7411 Score: 456
Period size: 39 Copynumber: 20.6 Consensus size: 39
6599 AATGGCTGCA
* * *
6609 ATCTGTCCCTGGCTCGGGGTAAGAGATTGGCTGAT-AGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGA-TG
** * *
6648 ATCTGCCTTAGGCTCGAGGTAAGAGATTTCCTGATGATG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGATG
* * **** *
6687 ATCTGCCCCAGGTTCGGGGTAAAAGATCAAATGATTG-TA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTGA-TGATG
* * *
6726 ATTTGCCTCAGGCTCGGGGTAAGAGATTTGCTGATTATG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGATG
** *
6765 ATATCTAG-CTGAGGCTCGTGGTAAGAGA-TTG--GATGATTG
1 --ATCT-GCCCCAGGCTCGGGGTAAGAGATTTGCTGATGA-TG
* **
6804 CAATCTGCCCC-GATCTCAAGGTAAGAGATTTGCTGATGATG
1 --ATCTGCCCCAG-GCTCGGGGTAAGAGATTTGCTGATGATG
* * * * ***
6845 ATCTGTCCTAGGCTTGGGGTAAAAGATCAACTGAT--TG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGATG
*
6882 CAATCTGCCCCAGGCTTGGGGTAAGAGATTTGCTGATGATG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGATG
* * * * ** * *
6923 ATCTGCCCCAAGCTCGGGGTAAAAAATCTAATGGTCG-TA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTGAT-GATG
* *
6962 ATCTGCCCCAGTCTCGAGGTAAGAGATTTGCTGATGATG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGATG
* * * * * * * *
7001 ATATGCCCCAAGCTCGAGGTAAAAGA-TCGAATGGTTACT-
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTTG-CTGATGA-TG
**
7040 ATCTGCCCCAGGCTCAAGGTAAGAGATTTGCTGATGATG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGATG
* * * *
7079 ATCT-CCCCAAGCTCGGGGTAAAAGA--T-CTAATGGCTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTGAT-GATG
* * * * * *
7115 CAATCTTCCCCATGATCGAGGTAAGAGATTTACTGATGGTG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGATG
* *
7156 ATCTGCCTCAGGCTCGGGGTAAGAGA--T-C-GAATGGCTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTG-AT-GATG
** *
7193 CAATCTGCCCCATTCTCGAGGTAAGAGATTTGCTGATGATG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGATG
* * * *
7234 ATCTACCCCAGGCTCAGGGTAAAAGA--T-C-GAATGGTTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTG-AT-GATG
*
7271 CAATCTGCCCCAGGTTCGGGGTAAGAGATTTGCTGATGATG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGATG
* * *
7312 ATCTGCCCCAGGCTCGAGGTAAAAGA--T-C-GAATGGTTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTG-AT-GATG
*
7349 CAATCTGCCCCAGGCTCGGGGTAAGAGATTTGTTGATGATG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGATG
* *
7390 ATCTACCTCAGGCTCGGGGTAA
1 ATCTGCCCCAGGCTCGGGGTAA
7412 AGGATCAGAA
Statistics
Matches: 576, Mismatches: 134, Indels: 108
0.70 0.16 0.13
Matches are distributed among these distances:
35 7 0.01
36 13 0.02
37 14 0.02
38 32 0.06
39 434 0.75
40 14 0.02
41 41 0.07
42 18 0.03
43 3 0.01
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (39 bp):
ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGATG
Found at i:19187 original size:97 final size:96
Alignment explanation
Indices: 19018--19313 Score: 468
Period size: 97 Copynumber: 3.1 Consensus size: 96
19008 TTGAAAAAGG
19018 GTATTTGATTATCCCGGTTTGAAGAAAAATCACGCCTAGTAAGTTAAGGCACAAATTTTCAAAAC
1 GTATTTGATTATCCCGGTTTGAAGAAAAATCACGCCTAGTAAGTTAAGGCACAAATTTTCAAAAC
*
19083 CCGAAATAAAAGAATATTACCTCGATTTAAGA
66 CCGAAATAAAAGAATATTGCCTCGATTTAA-A
* *
19115 GTATTCGATTATCCCGGTTTGAAGAAAAATCATGCCTAGTAAGTTAAGGCACAAATTTTCAAAAC
1 GTATTTGATTATCCCGGTTTGAAGAAAAATCACGCCTAGTAAGTTAAGGCACAAATTTTCAAAAC
*
19180 CCAAAATAAAAGAATATTGCCTCGATTTTAAA
66 CCGAAATAAAAGAATATTGCCTCGA-TTTAAA
* * *
19212 GTGTTTGATTATCTCGGTTTGAAGAAAAATTACGCCTAGTAAGTTAAGGCACAAATTTTCAAAAC
1 GTATTTGATTATCCCGGTTTGAAGAAAAATCACGCCTAGTAAGTTAAGGCACAAATTTTCAAAAC
* **
19277 CTGAAATAATGGAATATTGCCTCGATTTTAAA
66 CCGAAATAAAAGAATATTGCCTCGA-TTTAAA
19309 -TATTT
1 GTATTT
19314 TTGAGAAAAA
Statistics
Matches: 184, Mismatches: 14, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
96 4 0.02
97 175 0.95
98 5 0.03
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (96 bp):
GTATTTGATTATCCCGGTTTGAAGAAAAATCACGCCTAGTAAGTTAAGGCACAAATTTTCAAAAC
CCGAAATAAAAGAATATTGCCTCGATTTAAA
Found at i:19599 original size:28 final size:29
Alignment explanation
Indices: 19550--19607 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
19540 AAAGGAAAAA
*
19550 TGGGGTCAAAAATGAAGTTTTGGAGAGTT
1 TGGGGTCAAAAATGAAGTTTTGGAAAGTT
*
19579 TGGGGTTAAAACAT-AA-TTTTGGAAAGTT
1 TGGGGTCAAAA-ATGAAGTTTTGGAAAGTT
19607 T
1 T
19608 ATGGTCGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 12 0.46
29 12 0.46
30 2 0.08
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.34
Consensus pattern (29 bp):
TGGGGTCAAAAATGAAGTTTTGGAAAGTT
Found at i:19734 original size:29 final size:28
Alignment explanation
Indices: 19700--20048 Score: 188
Period size: 29 Copynumber: 12.0 Consensus size: 28
19690 AATTCAAGGC
*
19700 TAAAAAGTGATTTTTTGGAAGTTTAGGGG
1 TAAAATGT-ATTTTTTGGAAGTTTAGGGG
**
19729 TTAAAATGTATCGTTTGGAAGTTTAGGGG
1 -TAAAATGTATTTTTTGGAAGTTTAGGGG
* *
19758 TAAAAATGTAATTTTTGGAAGTTTGAGGGC
1 T-AAAATGTATTTTTTGGAAGTTT-AGGGG
* * *
19788 AAAAATGT-TTTTTTAGAAG-TTCGAGGG
1 TAAAATGTATTTTTTGGAAGTTTAG-GGG
** **
19815 TAAAAATGTAATTTTTAAGAAGTACAGGGG
1 T-AAAATGT-ATTTTTTGGAAGTTTAGGGG
* * *
19845 TAAAAATGTAGTTTTTGAAAGTTCAGGAGG
1 T-AAAATGTATTTTTTGGAAGTTTAGG-GG
* * * * *
19875 -AAAACTATAATTTTTGAGAAGTTCGATGGC
1 TAAAA-TGTATTTTTTG-GAAGTT-TAGGGG
* *
19905 AAAAATGTAATTTTTGGAAGTTT-GGGG
1 TAAAATGTATTTTTTGGAAGTTTAGGGG
* * * *
19932 GAAAATGTAATTTTTAGAAGTTTGAGGGC
1 TAAAATGTATTTTTTGGAAGTTT-AGGGG
*
19961 AAAAATGTAATTTTTTGAGAAGTTTA-GGG
1 TAAAATGT-ATTTTTTG-GAAGTTTAGGGG
* **
19990 TAAAAATATAATTTTTAAGAAGTTTAGGGG
1 T-AAAATGT-ATTTTTTGGAAGTTTAGGGG
* *
20020 TCAAAATATGA-TTTTTGGACAATTTAGGG
1 T-AAAATGT-ATTTTTTGGA-AGTTTAGGG
20049 ACTTTCTAGG
Statistics
Matches: 252, Mismatches: 48, Indels: 38
0.75 0.14 0.11
Matches are distributed among these distances:
26 1 0.00
27 27 0.11
28 21 0.08
29 98 0.39
30 91 0.36
31 14 0.06
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.36
Consensus pattern (28 bp):
TAAAATGTATTTTTTGGAAGTTTAGGGG
Found at i:19774 original size:87 final size:86
Alignment explanation
Indices: 19673--20036 Score: 215
Period size: 86 Copynumber: 4.2 Consensus size: 86
19663 GTTCGAGGGC
* *
19673 AAAATGGTAA-TTTTGAAAATTCAAGGCTAAAAAGTGATTTTTTGGAAGTTTAG-GGGTTAAAAT
1 AAAAT-GTAATTTTTGAAAATTCAAGGC-AAAAA-TGATTTTTTAGAAG-TTAGAGGGTAAAAAT
* **
19736 GT-ATCGTTT-GGAAGTTTAGGGGTA
62 GTAAT-GTTTAAGAAGTACAGGGGTA
** * * * *
19760 AAAATGTAATTTTTGGAAGTTTGAGGGCAAAAATGTTTTTTTAGAAGTTCGAGGGTAAAAATGTA
1 AAAATGTAATTTTT-GAAAATTCAAGGCAAAAATGATTTTTTAGAAGTTAGAGGGTAAAAATGTA
*
19825 ATTTTTAAGAAGTACAGGGGTA
65 ATGTTTAAGAAGTACAGGGGTA
* * * * * * *
19847 AAAATGTAGTTTTTGAAAGTTCAGGAGG-AAAACTATAATTTTTGAGAAGTTCGATGGCAAAAAT
1 AAAATGTAATTTTTGAAAATTCA--AGGCAAAA--ATGATTTTTTAGAAGTTAGAGGGTAAAAAT
** ** *
19911 GTAAT-TTTTGGAAGT-TTGGGG-G
62 GTAATGTTTAAGAAGTACAGGGGTA
** * * *
19933 AAAATGTAATTTTTAGAAGTTTGAGGGCAAAAATGTAATTTTTTGAGAAGTT-TAGGGTAAAAAT
1 AAAATGTAATTTTT-GAAAATTCAAGGCAAAAATG--ATTTTTT-AGAAGTTAGAGGGTAAAAAT
* * ** *
19997 ATAATTTTTAAGAAGTTTAGGGGTC
62 GTAATGTTTAAGAAGTACAGGGGTA
* *
20022 AAAATATGATTTTTG
1 AAAATGTAATTTTTG
20037 GACAATTTAG
Statistics
Matches: 216, Mismatches: 44, Indels: 33
0.74 0.15 0.11
Matches are distributed among these distances:
84 2 0.01
85 5 0.02
86 72 0.33
87 70 0.32
88 25 0.12
89 42 0.19
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (86 bp):
AAAATGTAATTTTTGAAAATTCAAGGCAAAAATGATTTTTTAGAAGTTAGAGGGTAAAAATGTAA
TGTTTAAGAAGTACAGGGGTA
Found at i:19829 original size:116 final size:115
Alignment explanation
Indices: 19655--20018 Score: 325
Period size: 116 Copynumber: 3.1 Consensus size: 115
19645 AGATGGTAAC
* * * * * * * *
19655 TTTTGGATGTTCGAGGGC-AAAATGGTAATTTTGA-AAATTCAAGGCTAAAAA-GTGATTTTTTG
1 TTTTGGAAGTTTGAGGGCAAAAAT-GTAATTTTTAGAAGTTC-GGGGTAAAAATGTAATTTTTTA
* * *
19717 GAAGTTTAGGGGTTAAAATGTATCGTTTGGAAGTTTAGGGGTAAAAATGTAAT
64 GAAGTTTAGGGGTAAAAATGTAT-TTTTGGAAGTTTAGGGGTAAAAATATAAT
* *
19770 TTTTGGAAGTTTGAGGGCAAAAATGT-TTTTTTAGAAGTTCGAGGGTAAAAATGTAATTTTTAAG
1 TTTTGGAAGTTTGAGGGCAAAAATGTAATTTTTAGAAGTTCG-GGGTAAAAATGTAATTTTTTAG
** * * *
19834 AAGTACAGGGGTAAAAATGTAGTTTTTGAAAGTTCAGGAGG-AAAACTATAAT
65 AAGTTTAGGGGTAAAAATGTA-TTTTTGGAAGTTTAGG-GGTAAAAATATAAT
* * * * *
19886 TTTTGAGAAGTTCGATGGCAAAAATGTAATTTTTGGAAGTTTGGGG-GAAAATGTAA-TTTTTAG
1 TTTTG-GAAGTTTGAGGGCAAAAATGTAATTTTTAGAAGTTCGGGGTAAAAATGTAATTTTTTAG
*
19949 AAGTTT-GAGGGCAAAAATGTAATTTTTTGAGAAGTTTA-GGGTAAAAATATAAT
65 AAGTTTAG-GGGTAAAAATGT-A-TTTTTG-GAAGTTTAGGGGTAAAAATATAAT
*
20002 TTTTAAGAAGTTT-AGGG
1 TTTT-GGAAGTTTGAGGG
20019 GTCAAAATAT
Statistics
Matches: 201, Mismatches: 35, Indels: 26
0.77 0.13 0.10
Matches are distributed among these distances:
114 6 0.03
115 57 0.28
116 95 0.47
117 31 0.15
118 12 0.06
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (115 bp):
TTTTGGAAGTTTGAGGGCAAAAATGTAATTTTTAGAAGTTCGGGGTAAAAATGTAATTTTTTAGA
AGTTTAGGGGTAAAAATGTATTTTTGGAAGTTTAGGGGTAAAAATATAAT
Found at i:19887 original size:59 final size:57
Alignment explanation
Indices: 19742--20013 Score: 200
Period size: 59 Copynumber: 4.6 Consensus size: 57
19732 AAATGTATCG
* * * *
19742 TTTGGAAGTTTAGGGGTAAAAATGTAATTTTT-GGAAGTT-TGAGGGCAAAAATGT--TT
1 TTTGAAAG-TTAGGGG--AAAATATAATTTTTAAGAAGTTCAGAGGGCAAAAATGTAATT
* * * * * *
19798 TTTTAGAAGTTCGAGGGTAAAAATGTAATTTTTAAGAAGTACAG-GGGTAAAAATGTAGTT
1 TTTGA-AAGTT--AGGG-GAAAATATAATTTTTAAGAAGTTCAGAGGGCAAAAATGTAATT
* *
19858 TTTGAAAGTTCAGGAGGAAAACTATAATTTTTGAGAAGTTC-GATGGCAAAAATGTAATT
1 TTTGAAAGTT-AGG-GGAAAA-TATAATTTTTAAGAAGTTCAGAGGGCAAAAATGTAATT
* * * *
19917 TTTGGAAGTTTGGGGGAAAATGTAATTTTT-AGAAGTT-TGAGGGCAAAAATGTAATTT
1 TTTGAAAG-TTAGGGGAAAATATAATTTTTAAGAAGTTCAGAGGGCAAAAATGTAA-TT
*
19974 TTTGAGAAGTTTAGGGTAAAAATATAATTTTTAAGAAGTT
1 TTTGA-AAG-TTAGGG-GAAAATATAATTTTTAAGAAGTT
20014 TAGGGGTCAA
Statistics
Matches: 175, Mismatches: 24, Indels: 30
0.76 0.10 0.13
Matches are distributed among these distances:
56 27 0.15
57 32 0.18
58 43 0.25
59 58 0.33
60 15 0.09
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (57 bp):
TTTGAAAGTTAGGGGAAAATATAATTTTTAAGAAGTTCAGAGGGCAAAAATGTAATT
Found at i:20028 original size:30 final size:28
Alignment explanation
Indices: 19711--20019 Score: 248
Period size: 29 Copynumber: 10.6 Consensus size: 28
19701 AAAAAGTGAT
* *
19711 TTTTTGGAAGTTTAGGGGTTAAAATGT-A
1 TTTTTAGAAGTTTAGGGG-AAAAATGTAA
* *
19739 TCGTTTGGAAGTTTAGGGGTAAAAATGTAA
1 T-TTTTAGAAGTTTAGGGG-AAAAATGTAA
* * *
19769 TTTTTGGAAGTTTGAGGGCAAAAATGT-T
1 TTTTTAGAAGTTT-AGGGGAAAAATGTAA
* *
19797 TTTTTAGAAGTTCGAGGGTAAAAATGTAA
1 TTTTTAGAAGTT-TAGGGGAAAAATGTAA
** *
19826 TTTTTAAGAAGTACAGGGGTAAAAATGTAG
1 TTTTT-AGAAGTTTAGGGG-AAAAATGTAA
* * *
19856 TTTTT-GAAAGTTCAGGAGGAAAACTATAA
1 TTTTTAG-AAGTTTAGG-GGAAAAATGTAA
* * *
19885 TTTTTGAGAAGTTCGATGGCAAAAATGTAA
1 TTTTT-AGAAGTT-TAGGGGAAAAATGTAA
* *
19915 TTTTTGGAAGTTT-GGGGGAAAATGTAA
1 TTTTTAGAAGTTTAGGGGAAAAATGTAA
*
19942 TTTTTAGAAGTTTGAGGGCAAAAATGTAA
1 TTTTTAGAAGTTT-AGGGGAAAAATGTAA
* *
19971 TTTTTTGAGAAGTTTAGGGTAAAAATATAA
1 -TTTTT-AGAAGTTTAGGGGAAAAATGTAA
20001 TTTTTAAGAAGTTTAGGGG
1 TTTTT-AGAAGTTTAGGGG
20020 TCAAAATATG
Statistics
Matches: 231, Mismatches: 34, Indels: 31
0.78 0.11 0.10
Matches are distributed among these distances:
27 23 0.10
28 25 0.11
29 107 0.46
30 65 0.28
31 11 0.05
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (28 bp):
TTTTTAGAAGTTTAGGGGAAAAATGTAA
Found at i:20034 original size:30 final size:29
Alignment explanation
Indices: 19746--20035 Score: 189
Period size: 30 Copynumber: 9.9 Consensus size: 29
19736 GTATCGTTTG
* *
19746 GAAGTTTAGGGGTAAAAATGTAATTTTT-G
1 GAAGTTTA-GGGTAAAAATATAATTTTTAA
* * *
19775 GAAGTTTGAGGGCAAAAATGT--TTTTTTA
1 GAAGTTT-AGGGTAAAAATATAATTTTTAA
* *
19803 GAAGTTCGAGGGTAAAAATGTAATTTTTAA
1 GAAGTT-TAGGGTAAAAATATAATTTTTAA
** * * *
19833 GAAGTACAGGGGTAAAAATGTAGTTTTTGA
1 GAAGTTTA-GGGTAAAAATATAATTTTTAA
* * * *
19863 -AAGTTCAGGAGGAAAACTATAATTTTTGA
1 GAAGTTTAGG-GTAAAAATATAATTTTTAA
* * * * *
19892 GAAGTTCGATGGCAAAAATGTAATTTTT-G
1 GAAGTT-TAGGGTAAAAATATAATTTTTAA
** *
19921 GAAGTTT-GGGGGAAAATGTAATTTTT-A
1 GAAGTTTAGGGTAAAAATATAATTTTTAA
* * *
19948 GAAGTTTGAGGGCAAAAATGTAATTTTTTGA
1 GAAGTTT-AGGGTAAAAATATAA-TTTTTAA
19979 GAAGTTTAGGGTAAAAATATAATTTTTAA
1 GAAGTTTAGGGTAAAAATATAATTTTTAA
* *
20008 GAAGTTTAGGGGTCAAAATATGATTTTT
1 GAAGTTTA-GGGTAAAAATATAATTTTT
20036 GGACAATTTA
Statistics
Matches: 215, Mismatches: 32, Indels: 27
0.78 0.12 0.10
Matches are distributed among these distances:
27 28 0.13
28 20 0.09
29 72 0.33
30 85 0.40
31 10 0.05
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.36
Consensus pattern (29 bp):
GAAGTTTAGGGTAAAAATATAATTTTTAA
Found at i:21871 original size:6 final size:6
Alignment explanation
Indices: 21860--21962 Score: 74
Period size: 6 Copynumber: 18.0 Consensus size: 6
21850 ATTTATTTAT
* * * *
21860 TTTAAA TTTAAA TTCAAA --TAAA TTCAAA ATTAAA -TTAAT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * *
21905 TTTAAA -ATAACT TTTAAA TTTAAA -ATAAA TTTAAA CTTAAA -ATAAA
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
21951 TTTAAA TTTAAA
1 TTTAAA TTTAAA
21963 ACAAATTTTT
Statistics
Matches: 74, Mismatches: 16, Indels: 14
0.71 0.15 0.13
Matches are distributed among these distances:
4 3 0.04
5 15 0.20
6 53 0.72
7 3 0.04
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:21919 original size:18 final size:17
Alignment explanation
Indices: 21862--21970 Score: 130
Period size: 17 Copynumber: 6.4 Consensus size: 17
21852 TTATTTATTT
*
21862 TAAATTTAAA-TTCAAA
1 TAAATTTAAATTTAAAA
* * *
21878 TAAATTCAAAATTAAAT
1 TAAATTTAAATTTAAAA
*
21895 TAATTTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
21912 TAACTTTTAAATTTAAAA
1 TAA-ATTTAAATTTAAAA
*
21930 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
21947 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
21964 CAAATTT
1 TAAATTT
21971 TTAAAAAATG
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
16 9 0.11
17 54 0.68
18 17 0.21
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:21945 original size:52 final size:51
Alignment explanation
Indices: 21866--21963 Score: 142
Period size: 52 Copynumber: 1.9 Consensus size: 51
21856 TTATTTTAAA
* * *
21866 TTTAAATTCAAATAAATTCAAAATTAAATTAATTTTAAATTTAAAATAACT
1 TTTAAATTAAAATAAATTCAAAATTAAAATAAATTTAAATTTAAAATAACT
* *
21917 TTTAAATTTAAAATAAATTTAAACTTAAAATAAATTTAAATTTAAAA
1 TTTAAA-TTAAAATAAATTCAAAATTAAAATAAATTTAAATTTAAAA
21964 CAAATTTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
51 6 0.15
52 35 0.85
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (51 bp):
TTTAAATTAAAATAAATTCAAAATTAAAATAAATTTAAATTTAAAATAACT
Found at i:22041 original size:15 final size:15
Alignment explanation
Indices: 22021--22049 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
22011 TTCAATAGTT
22021 TTCTCTCATTTCCTC
1 TTCTCTCATTTCCTC
22036 TTCTCTCATTTCCT
1 TTCTCTCATTTCCT
22050 TGGATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.38, G:0.00, T:0.55
Consensus pattern (15 bp):
TTCTCTCATTTCCTC
Found at i:24915 original size:3 final size:3
Alignment explanation
Indices: 24907--24931 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
24897 ATTTATATTA
24907 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
24932 GCTAGTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:25832 original size:16 final size:16
Alignment explanation
Indices: 25781--25835 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 16
25771 AGAGAAAATA
25781 AAAATAGAAA-TGAGAG
1 AAAA-AGAAATTGAGAG
*
25797 AAAAAGAAATTAAAAGAG
1 AAAAAGAAATT--GAGAG
*
25815 AAAAAGAACTTGAGAG
1 AAAAAGAAATTGAGAG
25831 AAAAA
1 AAAAA
25836 AGAGAGAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 5 0.15
16 14 0.42
18 14 0.42
ACGTcount: A:0.67, C:0.02, G:0.20, T:0.11
Consensus pattern (16 bp):
AAAAAGAAATTGAGAG
Found at i:25836 original size:18 final size:18
Alignment explanation
Indices: 25792--25838 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
25782 AAATAGAAAT
25792 GAGAGAAAAAGAAATTAA
1 GAGAGAAAAAGAAATTAA
* * *
25810 AAGAGAAAAAGAACTTGA
1 GAGAGAAAAAGAAATTAA
25828 GAGA-AAAAAGA
1 GAGAGAAAAAGA
25839 GAGAAGAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.66, C:0.02, G:0.23, T:0.09
Consensus pattern (18 bp):
GAGAGAAAAAGAAATTAA
Found at i:27742 original size:44 final size:44
Alignment explanation
Indices: 27662--27745 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 44
27652 TTTTTCTTAC
*
27662 AACCATTCTATACATTCGACCACCAAGAATTTACCATTTGAAGT
1 AACCATTCTATACATTCGACCACCAAGAATTCACCATTTGAAGT
* * * *
27706 AACCGTTCTGTACATTCGGCCACCAAGCATTCACCATTTG
1 AACCATTCTATACATTCGACCACCAAGAATTCACCATTTG
27746 TAGTTGTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.29
Consensus pattern (44 bp):
AACCATTCTATACATTCGACCACCAAGAATTCACCATTTGAAGT
Found at i:30701 original size:15 final size:15
Alignment explanation
Indices: 30683--30730 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
30673 AAGATGAGAG
30683 CACTCATGTTGCGAA
1 CACTCATGTTGCGAA
* * *
30698 CACT-AGAGCTGTGAA
1 CACTCA-TGTTGCGAA
30713 CACTCATGTTGCGAA
1 CACTCATGTTGCGAA
30728 CAC
1 CAC
30731 ACACAACGCA
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
14 1 0.04
15 23 0.92
16 1 0.04
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (15 bp):
CACTCATGTTGCGAA
Found at i:32055 original size:18 final size:17
Alignment explanation
Indices: 32029--32077 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
32019 CTCGTAATTA
*
32029 TAAA-TAAAAAATATAT
1 TAAATTAAAAAATAAAT
*
32045 TAATTTAAAAAATAAAT
1 TAAATTAAAAAATAAAT
32062 TAAATTAAAAAATAAA
1 TAAATTAAAAAATAAA
32078 ATCCATTTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 3 0.10
17 26 0.90
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAATTAAAAAATAAAT
Found at i:36068 original size:21 final size:21
Alignment explanation
Indices: 36019--36070 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
36009 TGGAGTTTTT
* *
36019 TGTATCGGTAGAAGTATAACT
1 TGTATCAGTAGAAGTATAACA
*
36040 TGTTTCAGTAGAAGT-TATACA
1 TGTATCAGTAGAAGTATA-ACA
36061 TGTATCAGTA
1 TGTATCAGTA
36071 AAACTTTCCC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 2 0.08
21 24 0.92
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.37
Consensus pattern (21 bp):
TGTATCAGTAGAAGTATAACA
Found at i:41406 original size:26 final size:26
Alignment explanation
Indices: 41358--41409 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
41348 ACTATAATGA
41358 GTTAGAAAATATAAAAACTAAGTATG
1 GTTAGAAAATATAAAAACTAAGTATG
41384 GTTAGAAAATATAAAAACTAAGTATG
1 GTTAGAAAATATAAAAACTAAGTATG
41410 AAATGCTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.54, C:0.04, G:0.15, T:0.27
Consensus pattern (26 bp):
GTTAGAAAATATAAAAACTAAGTATG
Found at i:43876 original size:19 final size:19
Alignment explanation
Indices: 43849--43909 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
43839 GATTTATAAT
*
43849 TAATATTTATAATTTTATA
1 TAATTTTTATAATTTTATA
*
43868 TAATTTTTATAATTCTATA
1 TAATTTTTATAATTTTATA
*
43887 T--TTTTTTTACATTTT-TA
1 TAATTTTTATA-ATTTTATA
43904 TAATTT
1 TAATTT
43910 GTTTAATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
17 10 0.29
18 4 0.11
19 21 0.60
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (19 bp):
TAATTTTTATAATTTTATA
Found at i:43878 original size:9 final size:9
Alignment explanation
Indices: 43849--43909 Score: 61
Period size: 9 Copynumber: 6.7 Consensus size: 9
43839 GATTTATAAT
*
43849 TAATATTTA
1 TAATTTTTA
43858 TAATTTTATA
1 TAATTTT-TA
43868 TAATTTTTA
1 TAATTTTTA
*
43877 TAA-TTCTA
1 TAATTTTTA
* *
43885 TATTTTTTT
1 TAATTTTTA
43894 TACATTTTTA
1 TA-ATTTTTA
43904 TAATTT
1 TAATTT
43910 GTTTAATATT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
8 6 0.14
9 20 0.48
10 16 0.38
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (9 bp):
TAATTTTTA
Found at i:43891 original size:27 final size:27
Alignment explanation
Indices: 43856--43908 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
43846 AATTAATATT
43856 TATAATTTTATATA-ATTTTTATAATTC
1 TATAATTTT-TATACATTTTTATAATTC
* *
43883 TATATTTTTTTTACATTTTTATAATT
1 TATAATTTTTATACATTTTTATAATT
43909 TGTTTAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 3 0.13
27 20 0.87
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (27 bp):
TATAATTTTTATACATTTTTATAATTC
Found at i:43981 original size:45 final size:46
Alignment explanation
Indices: 43891--43981 Score: 125
Period size: 45 Copynumber: 2.0 Consensus size: 46
43881 TCTATATTTT
*
43891 TTTTACATTTTTATAATTTGTTTAATATTTTTTTACTTTTTTAAAA
1 TTTTACATTTTTATAATTTGTTTAATATTTTTTTACATTTTTAAAA
*
43937 TTTTACATTTTTAT-ATGTT-TTT-GTGATTTTTTTACATTTTTAAAA
1 TTTTACATTTTTATAAT-TTGTTTAAT-ATTTTTTTACATTTTTAAAA
43982 AAATTTAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
44 1 0.02
45 24 0.59
46 16 0.39
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.65
Consensus pattern (46 bp):
TTTTACATTTTTATAATTTGTTTAATATTTTTTTACATTTTTAAAA
Found at i:49531 original size:15 final size:15
Alignment explanation
Indices: 49513--49542 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
49503 AATTGAAAAT
*
49513 AATTCTACAAATATA
1 AATTCTAAAAATATA
49528 AATTCTAAAAATATA
1 AATTCTAAAAATATA
49543 GTAATAGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (15 bp):
AATTCTAAAAATATA
Found at i:49708 original size:17 final size:15
Alignment explanation
Indices: 49662--49708 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 15
49652 AATAATGTGC
49662 AAATATATATTTTTT
1 AAATATATATTTTTT
*
49677 AAATATTTAACTTTTTT
1 AAATATAT-A-TTTTTT
49694 AAAATATATATTTTT
1 -AAATATATATTTTT
49709 CAATTCTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 7 0.26
16 6 0.22
17 7 0.26
18 7 0.26
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (15 bp):
AAATATATATTTTTT
Found at i:51455 original size:14 final size:15
Alignment explanation
Indices: 51426--51467 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
51416 ATACACAGAG
51426 TTTTTTAAAA-TATA
1 TTTTTTAAAACTATA
51440 TTTTTTAAAACT-TA
1 TTTTTTAAAACTATA
*
51454 TTGTATTAAAACTA
1 TT-TTTTAAAACTA
51468 CTTATAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 14 0.58
15 10 0.42
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.52
Consensus pattern (15 bp):
TTTTTTAAAACTATA
Found at i:52166 original size:15 final size:16
Alignment explanation
Indices: 52146--52187 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
52136 GACTTACATG
52146 TTAAATTAAAATATA-
1 TTAAATTAAAATATAT
*
52161 TTAAATTATAATATAT
1 TTAAATTAAAATATAT
52177 TTAAAGTTAAA
1 TTAAA-TTAAA
52188 TTGACATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 14 0.61
16 5 0.22
17 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
TTAAATTAAAATATAT
Found at i:52440 original size:59 final size:58
Alignment explanation
Indices: 52346--52492 Score: 188
Period size: 58 Copynumber: 2.5 Consensus size: 58
52336 ATTTGGTATA
** **
52346 TGAACTTGACACTTTTTCTTAATTTGGTATTTAAACTTTTTTTGACCCAATTTAGTACT
1 TGAACTTGACACTTTTTCTTAATTTGGTACCTAAAC-TTTTTAAACCCAATTTAGTACT
* * *
52405 TGAACTTGACACTTTTTTTTAGTTTGGTACCTAAACTTTTTAAACCCAATTTGGTACT
1 TGAACTTGACACTTTTTCTTAATTTGGTACCTAAACTTTTTAAACCCAATTTAGTACT
* *
52463 TGAACTTTG-CATTTTTTCCTAATTTGGTAC
1 TGAAC-TTGACACTTTTTCTTAATTTGGTAC
52493 TGAAGTTTTT
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
58 41 0.54
59 35 0.46
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (58 bp):
TGAACTTGACACTTTTTCTTAATTTGGTACCTAAACTTTTTAAACCCAATTTAGTACT
Found at i:52479 original size:58 final size:59
Alignment explanation
Indices: 52336--52492 Score: 194
Period size: 59 Copynumber: 2.7 Consensus size: 59
52326 TTAATATAAT
** **
52336 ATTTGGTA-TATGAACTTGACACTTTTTCTTAATTTGGTATTTAAACTTTTTTTGACCCA
1 ATTTGGTACT-TGAACTTGACACTTTTTCTTAATTTGGTACCTAAACTTTTTTAAACCCA
* * *
52395 ATTTAGTACTTGAACTTGACACTTTTTTTTAGTTTGGTACCTAAAC-TTTTTAAACCCA
1 ATTTGGTACTTGAACTTGACACTTTTTCTTAATTTGGTACCTAAACTTTTTTAAACCCA
* *
52453 ATTTGGTACTTGAACTTTG-CATTTTTTCCTAATTTGGTAC
1 ATTTGGTACTTGAAC-TTGACACTTTTTCTTAATTTGGTAC
52493 TGAAGTTTTT
Statistics
Matches: 84, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
58 41 0.49
59 42 0.50
60 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.48
Consensus pattern (59 bp):
ATTTGGTACTTGAACTTGACACTTTTTCTTAATTTGGTACCTAAACTTTTTTAAACCCA
Found at i:52767 original size:30 final size:31
Alignment explanation
Indices: 52731--52867 Score: 133
Period size: 31 Copynumber: 4.5 Consensus size: 31
52721 GGATCTCAAA
*
52731 AAGTTTAAGTACCAACTTAA-AAAAAGTGTC
1 AAGTTTAAGTACCAAATTAAGAAAAAGTGTC
*
52761 AAGTTTAGGTACCAAATTAAGAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAAGAAAAAGTGTC
* * * *
52792 AAGTTTGAGTATCAAATT-GGACCAAAA----A
1 AAGTTTAAGTACCAAATTAAGA--AAAAGTGTC
*
52820 AAGTTCAAGTACCAAATTAAGAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAAGAAAAAGTGTC
* *
52851 AAGTTCAGGTACCAAAT
1 AAGTTTAAGTACCAAAT
52868 ATTATATTAA
Statistics
Matches: 86, Mismatches: 13, Indels: 15
0.75 0.11 0.13
Matches are distributed among these distances:
27 4 0.05
28 15 0.17
29 2 0.02
30 20 0.23
31 41 0.48
32 4 0.05
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAAGAAAAAGTGTC
Found at i:52809 original size:89 final size:90
Alignment explanation
Indices: 52675--52867 Score: 257
Period size: 89 Copynumber: 2.2 Consensus size: 90
52665 AAAAAAAAAA
* * ** *
52675 TTTATGTACCAAATTAGAAAGAAGAGTCAAGTTCATGTACCAAATTGGATCTCAAAAAGTTTAAG
1 TTTAGGTACCAAATTAGAAAGAAGAGTCAAGTTCATGTACCAAATTGGACCAAAAAAAGTTCAAG
*
52740 TACCAACTTAA-AAAAAGTGTCAAG
66 TACCAAATTAAGAAAAAGTGTCAAG
* * *
52764 TTTAGGTACCAAATTAAGAAA-AAGTGTCAAGTTTGA-GTATCAAATTGGACCAAAAAAAGTTCA
1 TTTAGGTACCAAATT-AGAAAGAAGAGTCAAG-TTCATGTACCAAATTGGACCAAAAAAAGTTCA
52827 AGTACCAAATTAAGAAAAAGTGTCAAG
64 AGTACCAAATTAAGAAAAAGTGTCAAG
*
52854 TTCAGGTACCAAAT
1 TTTAGGTACCAAAT
52868 ATTATATTAA
Statistics
Matches: 91, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
89 57 0.63
90 34 0.37
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.26
Consensus pattern (90 bp):
TTTAGGTACCAAATTAGAAAGAAGAGTCAAGTTCATGTACCAAATTGGACCAAAAAAAGTTCAAG
TACCAAATTAAGAAAAAGTGTCAAG
Found at i:53973 original size:14 final size:14
Alignment explanation
Indices: 53954--53983 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
53944 TATGTTACTT
53954 TTATATATTATATA
1 TTATATATTATATA
53968 TTATATATTATATA
1 TTATATATTATATA
53982 TT
1 TT
53984 TTAAAACACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTATATATTATATA
Found at i:54089 original size:17 final size:16
Alignment explanation
Indices: 54067--54123 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
54057 AGATGATTAT
54067 ATAAAAATTTTCAATAA
1 ATAAAAATTTT-AATAA
* *
54084 ATAAAAATTATAAATTA
1 ATAAAAATT-TTAATAA
* *
54101 TTAAATATTTTAATAAA
1 ATAAAAATTTTAAT-AA
54118 ATAAAA
1 ATAAAA
54124 TAAATATTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
16 4 0.13
17 25 0.83
18 1 0.03
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
ATAAAAATTTTAATAA
Found at i:54130 original size:22 final size:23
Alignment explanation
Indices: 54102--54151 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
54092 TATAAATTAT
*
54102 TAAATA-TTTTAATAAAATAAAA
1 TAAATATTTTTAAAAAAATAAAA
*
54124 TAAATATTTTTAAAAAAATTAAA
1 TAAATATTTTTAAAAAAATAAAA
54147 -AAATA
1 TAAATA
54152 ATATGGGCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 11 0.44
23 14 0.56
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
TAAATATTTTTAAAAAAATAAAA
Found at i:54902 original size:18 final size:18
Alignment explanation
Indices: 54879--54920 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
54869 TAATAGGTTT
54879 TTAATTGAATAAATTT-AA
1 TTAATTGAA-AAATTTAAA
*
54897 TTAATTGAAAATTTTAAA
1 TTAATTGAAAAATTTAAA
54915 TTAATT
1 TTAATT
54921 ACACCTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (18 bp):
TTAATTGAAAAATTTAAA
Found at i:61495 original size:69 final size:69
Alignment explanation
Indices: 61379--61536 Score: 226
Period size: 69 Copynumber: 2.3 Consensus size: 69
61369 CTTATATCTT
* * *
61379 TGATTAAATATTAATATGATTTACGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGA
1 TGATCAAATATTAATGTGATTTACGCTTAAATATTAATGTGATTTGTGCTTAAATATTAAAATGA
* *
61444 TTTG
66 TATA
* * * *
61448 TGCTCAAATATCAATGTGATTTATGTTTAAATATTAATGTGATTTGTGCTTAAATATTAAAATGA
1 TGATCAAATATTAATGTGATTTACGCTTAAATATTAATGTGATTTGTGCTTAAATATTAAAATGA
61513 TATA
66 TATA
*
61517 TGATTAAATATTAATGTGAT
1 TGATCAAATATTAATGTGAT
61537 ATTGTGAACA
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 77 1.00
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.45
Consensus pattern (69 bp):
TGATCAAATATTAATGTGATTTACGCTTAAATATTAATGTGATTTGTGCTTAAATATTAAAATGA
TATA
Found at i:61538 original size:23 final size:23
Alignment explanation
Indices: 61382--61536 Score: 193
Period size: 23 Copynumber: 6.7 Consensus size: 23
61372 ATATCTTTGA
* *
61382 TTAAATATTAATATGATTTACGC
1 TTAAATATTAATGTGATTTATGC
*
61405 TTAAATATTAATGTGATTTGTGC
1 TTAAATATTAATGTGATTTATGC
* *
61428 TTAAATATTAATATGATTTGTGC
1 TTAAATATTAATGTGATTTATGC
* * *
61451 TCAAATATCAATGTGATTTATGT
1 TTAAATATTAATGTGATTTATGC
*
61474 TTAAATATTAATGTGATTTGTGC
1 TTAAATATTAATGTGATTTATGC
** * *
61497 TTAAATATTAAAATGATATATGA
1 TTAAATATTAATGTGATTTATGC
61520 TTAAATATTAATGTGAT
1 TTAAATATTAATGTGAT
61537 ATTGTGAACA
Statistics
Matches: 112, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 112 1.00
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (23 bp):
TTAAATATTAATGTGATTTATGC
Found at i:61641 original size:36 final size:36
Alignment explanation
Indices: 61601--61701 Score: 157
Period size: 36 Copynumber: 2.8 Consensus size: 36
61591 TGTCAAAGTG
* *
61601 AATATGTGGGTAAGTTCTTCATGCCATGTGATAAAA
1 AATATGTGGGTATGTTCTTCATGCCATGTGACAAAA
*
61637 AATATGTGGGTATGTTCTTCATGCCATGAGACAAAA
1 AATATGTGGGTATGTTCTTCATGCCATGTGACAAAA
**
61673 AATATGTTAGTATGTTCTTCATGCCATGT
1 AATATGTGGGTATGTTCTTCATGCCATGT
61702 AATTGATTAT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.36
Consensus pattern (36 bp):
AATATGTGGGTATGTTCTTCATGCCATGTGACAAAA
Found at i:64133 original size:418 final size:418
Alignment explanation
Indices: 63328--64164 Score: 1541
Period size: 419 Copynumber: 2.0 Consensus size: 418
63318 AAAGCAAACC
* *
63328 TAGGTTAGGAGTCCAAGGAAGAGCTAAACACCAATGAAGTTTATTGCACGGATGAAGGAATGTGC
1 TAGGTTAGGAGTCCAAGGAAGAGCTAAACACCAATGAAGTTTATTGCACAGATGAAAGAATGTGC
63393 TATTTTGTCAACCCTAATAACACAAGAAAAAAAAAGTGTTATAAAGAGTAAAAGAACAATAAAAA
66 TATTTTGTCAACCCTAATAACACAAGAAAAAAAAAGTGTTATAAAGAGTAAAAGAACAATAAAAA
*
63458 GCTAAAAAAACAAAGGAAATCCTACTGTTAAGAGTCAAAGAAATCACATAAAACTCAAAAAATCC
131 GCTAAAAAAACAAAGGAAATCCTACTGTTAAGAGTCAAAGAAATCACATAAAACCCAAAAAATCC
*
63523 AAAATTGCTGTGCAACTTGAAAGACTTCGTTTGCTAGGTTCCCAAAGTGTAAAAATCACAAAATT
196 AAAATTGCTGTGCAACTTGAAAGACTTCGTTCGCTAGGTTCCCAAAGTGTAAAAATCACAAAATT
*
63588 TAATGAGGTGTCTCCTCTAATATAATAGGTCTGATCTGGAAAGTTTGGGCCATGACTTCCTTCAA
261 TAATGAGGTGTCTCCTCTAATATAATAGGACTGATCTGGAAAGTTTGGGCCATGACTTCCTTCAA
*
63653 ATAAATTTTTTTTTTCATTTTTTTGAAGGAAAACTAAAAAACATGAGAAAAATCAATTGGGGTTG
326 ATAAATTTTTTTTTTCAATTTTTTGAAGGAAAACTAAAAAACATGAGAAAAATCAATTGGGGTTG
63718 AAATTGGATTAAGAAAATTCCAAATAAA
391 AAATTGGATTAAGAAAATTCCAAATAAA
63746 TAGGTTAGGAGTCCAAGGAAGAGCTAAACACCAATGAAGTTTATTGCACAGATGAAAGAATGTGC
1 TAGGTTAGGAGTCCAAGGAAGAGCTAAACACCAATGAAGTTTATTGCACAGATGAAAGAATGTGC
*
63811 TATTTTGTCAATCCTAATAACACAAGAAAATAAAAAGTGTTATAAAGAGTAAAAGAACAATAAAA
66 TATTTTGTCAACCCTAATAACACAAGAAAA-AAAAAGTGTTATAAAGAGTAAAAGAACAATAAAA
63876 AGCTAAAAAAACAAAGGAAATCCTACTGTTAAGAGTCAAAGAAATCACATAAAACCCAAAAAATC
130 AGCTAAAAAAACAAAGGAAATCCTACTGTTAAGAGTCAAAGAAATCACATAAAACCCAAAAAATC
* *
63941 CAAAATTGCTGTGCAACTTGAAAGACTTCGTTCGCTAGGTTCCCATAGTGTAAAAATCACAATAT
195 CAAAATTGCTGTGCAACTTGAAAGACTTCGTTCGCTAGGTTCCCAAAGTGTAAAAATCACAAAAT
*
64006 TTAATGAGGTGTCTCCTCTAATATAATATGACTGATCTGGAAAGTTTGGGCCATGACTTCCTTCA
260 TTAATGAGGTGTCTCCTCTAATATAATAGGACTGATCTGGAAAGTTTGGGCCATGACTTCCTTCA
*
64071 AAT-AATTTTTTTTTTCAATTTTTTGAAGTAAAACTAAAAAACATGAGAAAAATCAATTGGGGTT
325 AATAAATTTTTTTTTTCAATTTTTTGAAGGAAAACTAAAAAACATGAGAAAAATCAATTGGGGTT
* *
64135 GTAATTGGATTAAGAGAATTCCAAATAAA
390 GAAATTGGATTAAGAAAATTCCAAATAAA
64164 T
1 T
64165 CAAAATAGCC
Statistics
Matches: 405, Mismatches: 13, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
418 179 0.44
419 226 0.56
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (418 bp):
TAGGTTAGGAGTCCAAGGAAGAGCTAAACACCAATGAAGTTTATTGCACAGATGAAAGAATGTGC
TATTTTGTCAACCCTAATAACACAAGAAAAAAAAAGTGTTATAAAGAGTAAAAGAACAATAAAAA
GCTAAAAAAACAAAGGAAATCCTACTGTTAAGAGTCAAAGAAATCACATAAAACCCAAAAAATCC
AAAATTGCTGTGCAACTTGAAAGACTTCGTTCGCTAGGTTCCCAAAGTGTAAAAATCACAAAATT
TAATGAGGTGTCTCCTCTAATATAATAGGACTGATCTGGAAAGTTTGGGCCATGACTTCCTTCAA
ATAAATTTTTTTTTTCAATTTTTTGAAGGAAAACTAAAAAACATGAGAAAAATCAATTGGGGTTG
AAATTGGATTAAGAAAATTCCAAATAAA
Found at i:67626 original size:18 final size:19
Alignment explanation
Indices: 67600--67637 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
67590 TTAGCACAAC
*
67600 TTTTGTTTACACCAA-AAT
1 TTTTGTTTAAACCAATAAT
*
67618 TTTTTTTTAAACCAATAAT
1 TTTTGTTTAAACCAATAAT
67637 T
1 T
67638 GCAAATTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.34, C:0.13, G:0.03, T:0.50
Consensus pattern (19 bp):
TTTTGTTTAAACCAATAAT
Found at i:67788 original size:44 final size:44
Alignment explanation
Indices: 67725--67814 Score: 119
Period size: 44 Copynumber: 2.0 Consensus size: 44
67715 TAATTATAGT
* * *
67725 TTAAATTCTAATAAGTTTTAAAAT-TGTAATTATCCCAACTTCTA
1 TTAAATTATAATAAGTTTT-AAATGTATAATTATCACAACTTCTA
* *
67769 TTAAATTATAATTATTTTTAAATGTATAATTATCACAACTTCTA
1 TTAAATTATAATAAGTTTTAAATGTATAATTATCACAACTTCTA
67813 TT
1 TT
67815 TTATTTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 4 0.10
44 36 0.90
ACGTcount: A:0.39, C:0.11, G:0.03, T:0.47
Consensus pattern (44 bp):
TTAAATTATAATAAGTTTTAAATGTATAATTATCACAACTTCTA
Found at i:73875 original size:13 final size:13
Alignment explanation
Indices: 73857--73887 Score: 53
Period size: 13 Copynumber: 2.3 Consensus size: 13
73847 AATATTTAGA
73857 TAAAAATATAAATT
1 TAAAAA-ATAAATT
73871 TAAAAAATAAATT
1 TAAAAAATAAATT
73884 TAAA
1 TAAA
73888 TAAAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAAAAATAAATT
Found at i:74878 original size:26 final size:28
Alignment explanation
Indices: 74825--74882 Score: 75
Period size: 26 Copynumber: 2.1 Consensus size: 28
74815 ATCAACTATA
74825 ATTAATATATTAATAAATAAAATATTAG
1 ATTAATATATTAATAAATAAAATATTAG
* * *
74853 ATTAA-ATA-TAATAATTATAATTTTAG
1 ATTAATATATTAATAAATAAAATATTAG
74879 ATTA
1 ATTA
74883 TGATAACTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 19 0.70
27 3 0.11
28 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (28 bp):
ATTAATATATTAATAAATAAAATATTAG
Found at i:76600 original size:39 final size:40
Alignment explanation
Indices: 76546--76632 Score: 142
Period size: 39 Copynumber: 2.2 Consensus size: 40
76536 TGAAACACAT
*
76546 AAATATTTGAAAATGTTCCAATAATC-TCTCCCCATTTTC-
1 AAATATTTGAAAATGTTCCAACAATCTTC-CCCCATTTTCA
76585 AAATATTTGAAAATGTTCCAACAATCTTCCCCCATTTTCA
1 AAATATTTGAAAATGTTCCAACAATCTTCCCCCATTTTCA
76625 AAATATTT
1 AAATATTT
76633 TAGATTTTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
39 35 0.78
40 10 0.22
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.38
Consensus pattern (40 bp):
AAATATTTGAAAATGTTCCAACAATCTTCCCCCATTTTCA
Found at i:81122 original size:18 final size:19
Alignment explanation
Indices: 81088--81123 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
81078 TGAGGAAAAT
81088 CTCGAACACAAAAATGAAA
1 CTCGAACACAAAAATGAAA
*
81107 CTCGAACA-AGAAATGAA
1 CTCGAACACAAAAATGAA
81124 GAAATAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.56, C:0.19, G:0.14, T:0.11
Consensus pattern (19 bp):
CTCGAACACAAAAATGAAA
Found at i:85244 original size:17 final size:17
Alignment explanation
Indices: 85211--85244 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
85201 CACTAACACT
*
85211 AAAATGCAATGACAATG
1 AAAATGCAACGACAATG
*
85228 AAAATGCAACGATAATG
1 AAAATGCAACGACAATG
85245 CTTACTAACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.12, G:0.18, T:0.18
Consensus pattern (17 bp):
AAAATGCAACGACAATG
Found at i:90098 original size:17 final size:17
Alignment explanation
Indices: 90076--90108 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
90066 ACTAACACTG
90076 AAATGCAACGACAATGA
1 AAATGCAACGACAATGA
90093 AAATGCAACGACAATG
1 AAATGCAACGACAATG
90109 CTTACTAACA
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:0.52, C:0.18, G:0.18, T:0.12
Consensus pattern (17 bp):
AAATGCAACGACAATGA
Found at i:95466 original size:158 final size:158
Alignment explanation
Indices: 95178--95508 Score: 477
Period size: 158 Copynumber: 2.1 Consensus size: 158
95168 GTAATCATAT
* * *
95178 ATGCTCACACGAGCTGTGAAATGGGCCTGCTCACACGAGTTGTGGGTCGAGATGTGGGGCTACAC
1 ATGCTCACACGAGCTATGAAATGGGCCTACTCACACGAGTTATGGGTCGAGATGTGGGGCTACAC
* * * * **
95243 AATGCTACTCACACGAGCTGTGGAGAATTTGCAATATATGTCGGACCTCAGCTATTGGTAAGACA
66 AATGCTACTCACACGAGCTGTGGAGAATCTACAACATATGTAGGACCTCAGCTATCAGTAAGACA
95308 TCTAAGACCAACACCCATATAACCTGTA
131 TCTAAGACCAACACCCATATAACCTGTA
* ** *
95336 ATGCTCACAGGAGCTATGAAATGGGCCTACTCACACGAGTTATGGGTCGAGATGTTTGGCTACGC
1 ATGCTCACACGAGCTATGAAATGGGCCTACTCACACGAGTTATGGGTCGAGATGTGGGGCTACAC
* * *
95401 GATGCTGCTCACACGAGCTGTGGAGAATCTACAACCA-ATGTAGGACCTCAG-TCATCAGTAGGA
66 AATGCTACTCACACGAGCTGTGGAGAATCTACAA-CATATGTAGGACCTCAGCT-ATCAGTAAGA
*
95464 CATCTAAGACCAACACCCATATAACTTGTA
129 CATCTAAGACCAACACCCATATAACCTGTA
95494 ATGCTCACACGAGCT
1 ATGCTCACACGAGCT
95509 GTGGGTTGAG
Statistics
Matches: 153, Mismatches: 18, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
157 1 0.01
158 151 0.99
159 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (158 bp):
ATGCTCACACGAGCTATGAAATGGGCCTACTCACACGAGTTATGGGTCGAGATGTGGGGCTACAC
AATGCTACTCACACGAGCTGTGGAGAATCTACAACATATGTAGGACCTCAGCTATCAGTAAGACA
TCTAAGACCAACACCCATATAACCTGTA
Found at i:95602 original size:132 final size:132
Alignment explanation
Indices: 95365--95792 Score: 415
Period size: 132 Copynumber: 3.1 Consensus size: 132
95355 AATGGGCCTA
* *
95365 CTCACACGAGTTATGGGTCGAGATGTTTGGCTACGCGATGCTGCTCACACGAGCTGTGGAGAATC
1 CTCACACGAGCTATGGGTCGAGATGTTAGGCTACGCGATGCTGCTCACACGAGCTGTGGAGAATC
* * * * *
95430 TACAACCAATGTAGGACCTCAGTCATCAGTAGGACATCTAAGACCAACACCCATATAACTTGTAA
66 CACAACCAATGTAGGACCTCAGCCATCAGTAGAACATCTAAGACCAACACCCATATAACCTATAA
95495 TG
131 TG
* * *
95497 CTCACACGAGCTGTGGGTTGAGATGTTAGGCTACGCGATGCTGCTCACATGAGCTGTGGAGAATC
1 CTCACACGAGCTATGGGTCGAGATGTTAGGCTACGCGATGCTGCTCACACGAGCTGTGGAGAATC
* * * *
95562 CGCAACCAATGTAGGACCTCAGCCATCGGTAGAACATCTAAGACCAGCACCTATATAACCTATAA
66 CACAACCAATGTAGGACCTCAGCCATCAGTAGAACATCTAAGACCAACACCCATATAACCTATAA
95627 TG
131 TG
* * * * *
95629 TTCACATGAGCTAATGGGCCTGCTCACACGAGCTGTGGGTCGAGATGTTAGGCTACGCAATGCTA
1 CTCACACGAGCT-AT-GG---G-T----CGAGATGT---T--AG--G-----CTACGCGATGCTG
* * * * * *
95694 CTCACACGAACTGTGGAGAATCCACAACCAATGAAGGACCTCAACCATCGGTAGGACATTTAAGA
44 CTCACACGAGCTGTGGAGAATCCACAACCAATGTAGGACCTCAGCCATCAGTAGAACATCTAAGA
*
95759 CCAACACGCATATAACCTATAATG
109 CCAACACCCATATAACCTATAATG
*
95783 CTCATACGAG
1 CTCACACGAG
95793 TTGTAACTGT
Statistics
Matches: 240, Mismatches: 34, Indels: 22
0.81 0.11 0.07
Matches are distributed among these distances:
132 128 0.53
133 1 0.00
134 2 0.01
137 1 0.00
138 1 0.00
142 6 0.03
145 1 0.00
147 2 0.01
149 1 0.00
154 97 0.40
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (132 bp):
CTCACACGAGCTATGGGTCGAGATGTTAGGCTACGCGATGCTGCTCACACGAGCTGTGGAGAATC
CACAACCAATGTAGGACCTCAGCCATCAGTAGAACATCTAAGACCAACACCCATATAACCTATAA
TG
Found at i:95726 original size:286 final size:288
Alignment explanation
Indices: 95205--95792 Score: 788
Period size: 286 Copynumber: 2.0 Consensus size: 288
95195 GAAATGGGCC
* *
95205 TGCTCACACGAGTTGTGGGTCGAGATGTGGGGCTACACAATGCTACTCACACGAGCTGTGGAGAA
1 TGCTCACACGAGCTGTGGGTCGAGATGTGAGGCTACACAATGCTACTCACACGAGCTGTGGAGAA
** * * * * *
95270 TTTGCAATATATGTCGGACCTCAGCTATTGGTAAGACATCTAAGACCAACACCCATATAACCTGT
66 TCCGCAACATATGTAGGACCTCAGCCATCGGTAAGACATCTAAGACCAACACCCATATAACCTAT
* *
95335 AATGCTCACAGGAGCTATGAAATGGGCCTACTCACACGAGTTATGGGTCGAGATGTTTGGCTACG
131 AATGCTCACAGGAGC-AT-AAATGGGCCTACTCACACGAGCTATGGGTCGAGATGTTAGGCTACG
* * * * * **
95400 CGATGCTGCTCACACGAGCTGTGGAGAATCTACAACCAATGTAGGACCTCAGTCATCAGTAGGAC
194 CAATGCTACTCACACGAACTGTGGAGAATCCACAACCAATGAAGGACCTCAACCATCAGTAGGAC
* *
95465 ATCTAAGACCAACACCCATATAACTTGTAA
259 ATCTAAGACCAACACCCATATAACCTATAA
* * * * * *
95495 TGCTCACACGAGCTGTGGGTTGAGATGTTAGGCTACGCGATGCTGCTCACATGAGCTGTGGAGAA
1 TGCTCACACGAGCTGTGGGTCGAGATGTGAGGCTACACAATGCTACTCACACGAGCTGTGGAGAA
* *
95560 TCCGCAACCA-ATGTAGGACCTCAGCCATCGGT-AGAACATCTAAGACCAGCACCTATATAACCT
66 TCCGCAA-CATATGTAGGACCTCAGCCATCGGTAAG-ACATCTAAGACCAACACCCATATAACCT
* * * *
95623 ATAATGTTCACATGAGC-T-AATGGGCCTGCTCACACGAGCTGTGGGTCGAGATGTTAGGCTACG
129 ATAATGCTCACAGGAGCATAAATGGGCCTACTCACACGAGCTATGGGTCGAGATGTTAGGCTACG
*
95686 CAATGCTACTCACACGAACTGTGGAGAATCCACAACCAATGAAGGACCTCAACCATCGGTAGGAC
194 CAATGCTACTCACACGAACTGTGGAGAATCCACAACCAATGAAGGACCTCAACCATCAGTAGGAC
* *
95751 ATTTAAGACCAACACGCATATAACCTATAA
259 ATCTAAGACCAACACCCATATAACCTATAA
*
95781 TGCTCATACGAG
1 TGCTCACACGAG
95793 TTGTAACTGT
Statistics
Matches: 260, Mismatches: 36, Indels: 8
0.86 0.12 0.03
Matches are distributed among these distances:
286 135 0.52
288 1 0.00
289 2 0.01
290 121 0.47
291 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.22
Consensus pattern (288 bp):
TGCTCACACGAGCTGTGGGTCGAGATGTGAGGCTACACAATGCTACTCACACGAGCTGTGGAGAA
TCCGCAACATATGTAGGACCTCAGCCATCGGTAAGACATCTAAGACCAACACCCATATAACCTAT
AATGCTCACAGGAGCATAAATGGGCCTACTCACACGAGCTATGGGTCGAGATGTTAGGCTACGCA
ATGCTACTCACACGAACTGTGGAGAATCCACAACCAATGAAGGACCTCAACCATCAGTAGGACAT
CTAAGACCAACACCCATATAACCTATAA
Found at i:95775 original size:154 final size:154
Alignment explanation
Indices: 95495--95782 Score: 461
Period size: 154 Copynumber: 1.9 Consensus size: 154
95485 TAACTTGTAA
* * * * *
95495 TGCTCACACGAGCTGTGGGTTGAGATGTTAGGCTACGCGATGCTGCTCACATGAGCTGTGGAGAA
1 TGCTCACACGAGCTGTGGGTCGAGATGTTAGGCTACGCAATGCTACTCACACGAACTGTGGAGAA
* * * *
95560 TCCGCAACCAATGTAGGACCTCAGCCATCGGTAGAACATCTAAGACCAGCACCTATATAACCTAT
66 TCCACAACCAATGAAGGACCTCAACCATCGGTAGAACATCTAAGACCAACACCTATATAACCTAT
95625 AATGTTCACATGAGCTAATGGGCC
131 AATGTTCACATGAGCTAATGGGCC
95649 TGCTCACACGAGCTGTGGGTCGAGATGTTAGGCTACGCAATGCTACTCACACGAACTGTGGAGAA
1 TGCTCACACGAGCTGTGGGTCGAGATGTTAGGCTACGCAATGCTACTCACACGAACTGTGGAGAA
* *
95714 TCCACAACCAATGAAGGACCTCAACCATCGGTAGGACATTTAAGACCAACACGC-ATATAACCTA
66 TCCACAACCAATGAAGGACCTCAACCATCGGTAGAACATCTAAGACCAACAC-CTATATAACCTA
95778 TAATG
130 TAATG
95783 CTCATACGAG
Statistics
Matches: 122, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
154 121 0.99
155 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (154 bp):
TGCTCACACGAGCTGTGGGTCGAGATGTTAGGCTACGCAATGCTACTCACACGAACTGTGGAGAA
TCCACAACCAATGAAGGACCTCAACCATCGGTAGAACATCTAAGACCAACACCTATATAACCTAT
AATGTTCACATGAGCTAATGGGCC
Found at i:115841 original size:194 final size:194
Alignment explanation
Indices: 115512--115956 Score: 613
Period size: 194 Copynumber: 2.3 Consensus size: 194
115502 GACCGACGCT
* * * *
115512 ATGGCTGGGTTACCGTATATGTTGTGAGTCCTCGACAGCTCGTGTGAGAAGTATCGTGGGTCGAG
1 ATGGCTGGGGTACCGCATATGTTATGAGTCCTCGACAGCTCGTGTGAGAAGCATCGTGGGTCGAG
* *
115577 AAAATGTGAAATGAATCCAAAAATGGATTATAGGCCCTATGATGGTTGGGATTTATGCAAGTGCA
66 AAAATGTGAAATGAATCCAAAAATGGATTATAGGCCCTACGATGGCTGGGATTTATGCAAGTGCA
* * *
115642 TATTCTCAACAGCTCATGTAAGCAGCATCGTTAGGGGACAGTTATATGCATAGCGGCCATATCG
131 TATTCTCAACAGCTCATGTAAGCAACATCGTTAAGGGACAGTTATATGCATAGCGACCATATCG
* * *
115706 ATGGCTGGGGTACCGCATATGTTATGAGTCCTCGACAACTCGTGTGAGTAGCATTGTGGGTC-AG
1 ATGGCTGGGGTACCGCATATGTTATGAGTCCTCGACAGCTCGTGTGAGAAGCATCGTGGGTCGA-
*
115770 GAAAATGTGAAATGAATCCAAGAATGGATTATAGGCCCTACGATGGCTGGGATTTATGCAAGTGC
65 GAAAATGTGAAATGAATCCAAAAATGGATTATAGGCCCTACGATGGCTGGGATTTATGCAAGTGC
* * * * * ** * * *
115835 ATATTCTCGACAGCTCGTGTGAGCAACTTCGTTAAGGGACAGTTATATGCCTAGTTATCGTATTG
130 ATATTCTCAACAGCTCATGTAAGCAACATCGTTAAGGGACAGTTATATGCATAGCGACCATATCG
* * * * * *
115900 ATGGCTGAGGTACCACATATGTTACGAGTCCTCGACAGCTCATGTGAGCAGTATCGT
1 ATGGCTGGGGTACCGCATATGTTATGAGTCCTCGACAGCTCGTGTGAGAAGCATCGT
115957 ATACTAGTAA
Statistics
Matches: 219, Mismatches: 31, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
193 1 0.00
194 218 1.00
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.28
Consensus pattern (194 bp):
ATGGCTGGGGTACCGCATATGTTATGAGTCCTCGACAGCTCGTGTGAGAAGCATCGTGGGTCGAG
AAAATGTGAAATGAATCCAAAAATGGATTATAGGCCCTACGATGGCTGGGATTTATGCAAGTGCA
TATTCTCAACAGCTCATGTAAGCAACATCGTTAAGGGACAGTTATATGCATAGCGACCATATCG
Found at i:118464 original size:102 final size:99
Alignment explanation
Indices: 118161--118482 Score: 405
Period size: 100 Copynumber: 3.2 Consensus size: 99
118151 ACAGAATGAT
* * *
118161 AAATCCTATACCCTTAAAGTTGTAGAAGGACAGATTAAAACAAGTAACGAACCTCAATCTCCCTG
1 AAATCCTATACCCCTAAAGTTGTAGAGGGGCAGATTAAAACAAGTAACGAACCTCAATCTCCCTG
* * *
118226 AAGTTACGGTGGAATGGAGCAAAGTTACAACCCC
66 AAGTTACAGTGGAATGAAGCGAAGTTACAACCCC
* * * *
118260 AAATCCTATACCCCTAAAGTTGTAAAGAGGCGGATTTAAAACAAGTAACGAACCTTAATCTCCCT
1 AAATCCTATACCCCTAAAGTTGTAGAGGGGCAGA-TTAAAACAAGTAACGAACCTCAATCTCCCT
118325 GAAGTTACAGTGGAAT-AGAGCGAAGTTACAACCCC
65 GAAGTTACAGTGGAATGA-AGCGAAGTTACAACCCC
* * *
118360 AAATCCTATACCCCTAGAGTTGTAGAGGGGCAGATTAAAACTTATAGTATCGAATCTCAATCTCC
1 AAATCCTATACCCCTAAAGTTGTAGAGGGGCAGATTAAAAC--A-AGTAACGAACCTCAATCTCC
* ** *
118425 CTAAAGTTACAGTGGAATGAAATGAAGTTACGAA-ACC
63 CTGAAGTTACAGTGGAATGAAGCGAAGTTAC-AACCCC
* *
118462 AAATCATATATCCCTAAAGTT
1 AAATCCTATACCCCTAAAGTT
118483 ACAGTGGATT
Statistics
Matches: 192, Mismatches: 24, Indels: 11
0.85 0.11 0.05
Matches are distributed among these distances:
99 35 0.18
100 90 0.47
101 1 0.01
102 63 0.33
103 3 0.02
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (99 bp):
AAATCCTATACCCCTAAAGTTGTAGAGGGGCAGATTAAAACAAGTAACGAACCTCAATCTCCCTG
AAGTTACAGTGGAATGAAGCGAAGTTACAACCCC
Found at i:118501 original size:50 final size:50
Alignment explanation
Indices: 118422--118642 Score: 160
Period size: 50 Copynumber: 4.4 Consensus size: 50
118412 AATCTCAATC
* * * * *
118422 TCCCTAAAGTTACAGTGGAATGAAATGAAGTTACGAAACCAAATCATATA
1 TCCCTAAAGTTGCAGTGGATTGGATTGAAGTTACGAAACCAAATCCTATA
* * * *
118472 TCCCTAAAGTTACAGTGGATTGGATTGAAGATATGAAAGCAAATCCT-TA
1 TCCCTAAAGTTGCAGTGGATTGGATTGAAGTTACGAAACCAAATCCTATA
* ** ** * *
118521 TCTCTCTAAAATTGCAGTAAAGCAGGA-TGAAGCTACAAAACCAAATCCTATA
1 TC-C-CTAAAGTTGCAGTGGA-TTGGATTGAAGTTACGAAACCAAATCCTATA
* * * * * * * *
118573 TCCTTAAAGTTGCAGTCGG-TCGGATTAAAGTCATGAAAGCAAATCTTTATC
1 TCCCTAAAGTTGCAGT-GGATTGGATTGAAGTTACGAAACCAAATC-CTATA
118624 TCCCTAAAGTTGCAGTGGA
1 TCCCTAAAGTTGCAGTGGA
118643 AAAAAGATGA
Statistics
Matches: 131, Mismatches: 32, Indels: 15
0.74 0.18 0.08
Matches are distributed among these distances:
49 7 0.05
50 68 0.52
51 49 0.37
52 7 0.05
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.27
Consensus pattern (50 bp):
TCCCTAAAGTTGCAGTGGATTGGATTGAAGTTACGAAACCAAATCCTATA
Found at i:118552 original size:51 final size:50
Alignment explanation
Indices: 118497--118639 Score: 123
Period size: 51 Copynumber: 2.8 Consensus size: 50
118487 TGGATTGGAT
*
118497 TGAAGATATGAAAGCAAATCCTTATCTCTCTAAAATTGCAGTAAAG-CAGGA
1 TGAAGATATGAAAGCAAATCCTTATCTCTCTAAAGTTGCAGT-AAGTC-GGA
* ** * **
118548 TGAAGCTACAAAACCAAATCCTATATC-CT-TAAAGTTGCAGTCGGTCGGA
1 TGAAGATATGAAAGCAAATCCT-TATCTCTCTAAAGTTGCAGTAAGTCGGA
* * *
118597 TTAA-AGTCATGAAAGCAAATCTTTATCTCCCTAAAGTTGCAGT
1 TGAAGA-T-ATGAAAGCAAATCCTTATCTCTCTAAAGTTGCAGT
118640 GGAAAAAAGA
Statistics
Matches: 72, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
49 12 0.17
50 24 0.33
51 32 0.44
52 4 0.06
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (50 bp):
TGAAGATATGAAAGCAAATCCTTATCTCTCTAAAGTTGCAGTAAGTCGGA
Found at i:118562 original size:101 final size:101
Alignment explanation
Indices: 118446--118639 Score: 266
Period size: 101 Copynumber: 1.9 Consensus size: 101
118436 GTGGAATGAA
* * * *
118446 ATGAAGTTACGAAACCAAATCATATATCCCTAAAGTTACAGT-GGATTGGATTGAAGAT-ATGAA
1 ATGAAGCTACAAAACCAAATCATATATCCCTAAAGTTACAGTCGG-TCGGATTAAAG-TCATGAA
*
118509 AGCAAATCCTTATCTCTCTAAAATTGCAGTAAAGCAGG
64 AGCAAATCCTTATCTCCCTAAAATTGCAGTAAAGCAGG
* * *
118547 ATGAAGCTACAAAACCAAATCCTATATCCTTAAAGTTGCAGTCGGTCGGATTAAAGTCATGAAAG
1 ATGAAGCTACAAAACCAAATCATATATCCCTAAAGTTACAGTCGGTCGGATTAAAGTCATGAAAG
* *
118612 CAAATCTTTATCTCCCTAAAGTTGCAGT
66 CAAATCCTTATCTCCCTAAAATTGCAGT
118640 GGAAAAAAGA
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
100 1 0.01
101 78 0.96
102 2 0.02
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (101 bp):
ATGAAGCTACAAAACCAAATCATATATCCCTAAAGTTACAGTCGGTCGGATTAAAGTCATGAAAG
CAAATCCTTATCTCCCTAAAATTGCAGTAAAGCAGG
Found at i:119754 original size:30 final size:29
Alignment explanation
Indices: 119707--119763 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
119697 ATTTGAGAGA
*
119707 AAAAAGAAAAAGAAAATGATTTTTTTTTT
1 AAAAACAAAAAGAAAATGATTTTTTTTTT
*
119736 AAAAACAAAGAAGCAAATGATTTTTTTT
1 AAAAACAAA-AAGAAAATGATTTTTTTT
119764 AAAAAATCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.35
Consensus pattern (29 bp):
AAAAACAAAAAGAAAATGATTTTTTTTTT
Found at i:119759 original size:29 final size:29
Alignment explanation
Indices: 119706--119769 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
119696 CATTTGAGAG
*
119706 AAAAAAGAAAAAGAAAATGATTTTTTTTT
1 AAAAAACAAAAAGAAAATGATTTTTTTTT
* *
119735 TAAAAACAAAGAAGCAAATGA-TTTTTTTT
1 AAAAAACAAA-AAGAAAATGATTTTTTTTT
119764 AAAAAA
1 AAAAAA
119770 TCACTTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 21 0.70
30 9 0.30
ACGTcount: A:0.56, C:0.03, G:0.09, T:0.31
Consensus pattern (29 bp):
AAAAAACAAAAAGAAAATGATTTTTTTTT
Found at i:121929 original size:30 final size:30
Alignment explanation
Indices: 121891--122021 Score: 122
Period size: 30 Copynumber: 4.4 Consensus size: 30
121881 TCTAAAAAGT
121891 CCCTAAACTTTCCAAAAATCACATTTTAAC
1 CCCTAAACTTTCCAAAAATCACATTTTAAC
* * ***
121921 CTCTAAACTTTCCAAAAATTCA-AATTTGGT
1 CCCTAAACTTTCCAAAAA-TCACATTTTAAC
** * *
121951 CCCTAAACTTTTTAGAAATTACATTTTAAC
1 CCCTAAACTTTCCAAAAATCACATTTTAAC
* * *
121981 CCCTAAAATTCTCC-AAAATTACATTTTGAC
1 CCCTAAACTT-TCCAAAAATCACATTTTAAC
122011 CCCTAAACTTT
1 CCCTAAACTTT
122022 TCCTAAATTA
Statistics
Matches: 78, Mismatches: 20, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
29 3 0.04
30 71 0.91
31 4 0.05
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (30 bp):
CCCTAAACTTTCCAAAAATCACATTTTAAC
Found at i:121999 original size:60 final size:60
Alignment explanation
Indices: 121889--122023 Score: 157
Period size: 60 Copynumber: 2.2 Consensus size: 60
121879 TTTCTAAAAA
* * *
121889 GTCCCTAAACTTTCCAAAAATCACATTTTAACCTCTAAACTTTCCAAAAATT-CAAATTTG
1 GTCCCTAAACTTTTCAAAAATCACATTTTAACCCCTAAAATTTCCAAAAATTAC-AATTTG
* * * *
121949 GTCCCTAAACTTTTTAGAAATTACATTTTAACCCCTAAAATTCTCC-AAAATTACATTTTG
1 GTCCCTAAACTTTTCAAAAATCACATTTTAACCCCTAAAATT-TCCAAAAATTACAATTTG
**
122009 ACCCCTAAACTTTTC
1 GTCCCTAAACTTTTC
122024 CTAAATTATG
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
60 59 0.94
61 4 0.06
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.36
Consensus pattern (60 bp):
GTCCCTAAACTTTTCAAAAATCACATTTTAACCCCTAAAATTTCCAAAAATTACAATTTG
Found at i:122030 original size:60 final size:61
Alignment explanation
Indices: 121891--122052 Score: 149
Period size: 60 Copynumber: 2.7 Consensus size: 61
121881 TCTAAAAAGT
* * * **
121891 CCCTAAAC-TTTCCAAAAATCACATTTTAACCTCTAAACTT-TCCAAAAATTCAAATTTGGT
1 CCCTAAACTTTTCC-AAAATTACATTTTAACCCCTAAAATTCTCCAAAAATTCAAATTTGAC
* *
121951 CCCTAAACTTTT-TAGAAATTACATTTTAACCCCTAAAATTCTCC-AAAATT-ACATTTTGAC
1 CCCTAAACTTTTCCA-AAATTACATTTTAACCCCTAAAATTCTCCAAAAATTCA-AATTTGAC
* ** *
122011 CCCTAAACTTTTCCTAAATTATGTTTTAGCCCC--AAATTCTCC
1 CCCTAAACTTTTCCAAAATTACATTTTAACCCCTAAAATTCTCC
122053 GAAACTTCCT
Statistics
Matches: 85, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
58 9 0.11
59 2 0.02
60 68 0.80
61 6 0.07
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.36
Consensus pattern (61 bp):
CCCTAAACTTTTCCAAAATTACATTTTAACCCCTAAAATTCTCCAAAAATTCAAATTTGAC
Found at i:122394 original size:56 final size:56
Alignment explanation
Indices: 122333--122446 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
122323 ATACAAATGA
122333 TTTTAAAATCGGGGCAATATTACTTTATTTCGGATTTTGAAAAATTGTGCCCTAAC
1 TTTTAAAATCGGGGCAATATTACTTTATTTCGGATTTTGAAAAATTGTGCCCTAAC
122389 TTTTAAAATCGGGGCAATATTACTTTATTTCGGATTTTGAAAAATTGTGCCCTAAC
1 TTTTAAAATCGGGGCAATATTACTTTATTTCGGATTTTGAAAAATTGTGCCCTAAC
122445 TT
1 TT
122447 ACTAGGCGTG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (56 bp):
TTTTAAAATCGGGGCAATATTACTTTATTTCGGATTTTGAAAAATTGTGCCCTAAC
Found at i:124042 original size:30 final size:33
Alignment explanation
Indices: 124007--124067 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
123997 TTGATGGGAC
124007 TTTAAA-AAATA-A-ATT-ATTAAAGAATAAATA
1 TTTAAATAAATAGATATTAATTAAA-AATAAATA
124037 TTTAAATAAATAGATATTAATTAAAAATAAA
1 TTTAAATAAATAGATATTAATTAAAAATAAA
124068 AAAAATTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 6 0.22
31 5 0.19
32 1 0.04
33 9 0.33
34 6 0.22
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (33 bp):
TTTAAATAAATAGATATTAATTAAAAATAAATA
Found at i:124050 original size:77 final size:75
Alignment explanation
Indices: 123968--124215 Score: 302
Period size: 77 Copynumber: 3.3 Consensus size: 75
123958 ATTTTAAAGG
* *
123968 AATAGATTTTAATTGAAAAAAAAAAGACATTGATGGGACTTTAAAAAATAAATTATTAAAGAATA
1 AATAGATTTTAATT-AAAAAAAAAAGACATTGATGGGACTTGAAAAAA-AAATAATTAAAGAATA
124033 AATATTTAAATA
64 AATATTTAAATA
* * * *
124045 AATAGATATTAATTAAAAATAAAAA-AAATTGATGGGACTTGACAGAAAAAATAATTAAAGGATA
1 AATAGATTTTAATTAAAAA-AAAAAGACATTGATGGGACTTGA-AAAAAAAATAATTAAAGAATA
*
124109 AATATTTAAATT
64 AATATTTAAATA
* * * * *
124121 ACTAAATTTTAATTAAAAAAAAAAGAACATTTATGGAACTTGAAAGAAGAAATAATTAAAGAATA
1 AATAGATTTTAATTAAAAAAAAAAG-ACATTGATGGGACTTGAAA-AAAAAATAATTAAAGAATA
* *
124186 AATTTTTAAATG
64 AATATTTAAATA
124198 AATAGATTTT-ATTAAAAA
1 AATAGATTTTAATTAAAAA
124216 GAGTGAAAAG
Statistics
Matches: 146, Mismatches: 20, Indels: 11
0.82 0.11 0.06
Matches are distributed among these distances:
75 5 0.03
76 70 0.48
77 71 0.49
ACGTcount: A:0.56, C:0.03, G:0.10, T:0.31
Consensus pattern (75 bp):
AATAGATTTTAATTAAAAAAAAAAGACATTGATGGGACTTGAAAAAAAAATAATTAAAGAATAAA
TATTTAAATA
Found at i:124056 original size:15 final size:14
Alignment explanation
Indices: 124008--124056 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
123998 TGATGGGACT
124008 TTAAAAAATAAATTA
1 TTAAAAAATAAA-TA
*
124023 TTAAAGAATAAATA
1 TTAAAAAATAAATA
*
124037 TTTAAATAAATAGATA
1 -TTAAA-AAATAAATA
124053 TTAA
1 TTAA
124057 TTAAAAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 2 0.07
15 20 0.69
16 7 0.24
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (14 bp):
TTAAAAAATAAATA
Found at i:124103 original size:76 final size:75
Alignment explanation
Indices: 123968--124215 Score: 302
Period size: 76 Copynumber: 3.3 Consensus size: 75
123958 ATTTTAAAGG
* * * *
123968 AATAGATTTTAATTGAAAAAAAAAAGACATTGATGGGACTTTAAAAAATAAATTATTAAAGAATA
1 AATAGATTTTAATT-AAAAAAAAAAGAAATTGATGGGACTTGAAGAAA-AAATAATTAAAGAATA
124033 AATATTTAAATA
64 AATATTTAAATA
* *
124045 AATAGATATTAATTAAAAATAAAAA-AAATTGATGGGACTTGACAGAAAAAATAATTAAAGGATA
1 AATAGATTTTAATTAAAAA-AAAAAGAAATTGATGGGACTTGA-AGAAAAAATAATTAAAGAATA
*
124109 AATATTTAAATT
64 AATATTTAAATA
* * * * *
124121 ACTAAATTTTAATTAAAAAAAAAAGAACATTTATGGAACTTGAAAGAAGAAATAATTAAAGAATA
1 AATAGATTTTAATTAAAAAAAAAAGAA-ATTGATGGGACTTG-AAGAAAAAATAATTAAAGAATA
* *
124186 AATTTTTAAATG
64 AATATTTAAATA
124198 AATAGATTTT-ATTAAAAA
1 AATAGATTTTAATTAAAAA
124216 GAGTGAAAAG
Statistics
Matches: 148, Mismatches: 18, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
75 5 0.03
76 71 0.48
77 71 0.48
78 1 0.01
ACGTcount: A:0.56, C:0.03, G:0.10, T:0.31
Consensus pattern (75 bp):
AATAGATTTTAATTAAAAAAAAAAGAAATTGATGGGACTTGAAGAAAAAATAATTAAAGAATAAA
TATTTAAATA
Found at i:126924 original size:20 final size:18
Alignment explanation
Indices: 126881--126917 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
126871 TTAAAGCTTT
126881 ATTTTAATATTTTTATAC
1 ATTTTAATATTTTTATAC
126899 ATTTTAAT-TTTATTATAC
1 ATTTTAATATTT-TTATAC
126917 A
1 A
126918 CATTTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTTAATATTTTTATAC
Found at i:127740 original size:15 final size:15
Alignment explanation
Indices: 127720--127771 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
127710 TTACTTAATC
127720 AATCTTTATAAACCT
1 AATCTTTATAAACCT
*
127735 AATCTTT-TACTAATC-
1 AATCTTTATA--AACCT
127750 AATCTTTATAAACCT
1 AATCTTTATAAACCT
127765 AATCTTT
1 AATCTTT
127772 TACTTTCTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 5 0.16
15 21 0.68
16 5 0.16
ACGTcount: A:0.37, C:0.19, G:0.00, T:0.44
Consensus pattern (15 bp):
AATCTTTATAAACCT
Found at i:127749 original size:30 final size:30
Alignment explanation
Indices: 127710--127775 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
127700 AATATCCAAA
127710 TTACTTAATCAATCTTTATAAACCTAATCTT
1 TTAC-TAATCAATCTTTATAAACCTAATCTT
127741 TTACTAATCAATCTTTATAAACCTAATCTT
1 TTACTAATCAATCTTTATAAACCTAATCTT
127771 TTACT
1 TTACT
127776 TTCTATAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 31 0.89
31 4 0.11
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.45
Consensus pattern (30 bp):
TTACTAATCAATCTTTATAAACCTAATCTT
Found at i:129516 original size:20 final size:20
Alignment explanation
Indices: 129491--129531 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
129481 AACTCCAAAC
129491 AAATTAAAAGTTACATAAAA
1 AAATTAAAAGTTACATAAAA
129511 AAATTAAAAGTTACATAAAA
1 AAATTAAAAGTTACATAAAA
129531 A
1 A
129532 TATACAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (20 bp):
AAATTAAAAGTTACATAAAA
Found at i:136188 original size:52 final size:52
Alignment explanation
Indices: 136105--136280 Score: 298
Period size: 52 Copynumber: 3.4 Consensus size: 52
136095 AAATGAAAAG
*
136105 GGTCCGATGACTATATGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
*
136157 GGTCAGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* *
136209 GGTCCGATGACTATGTGTCATCATGAGTATATGAATCTTTTACGGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* *
136261 GGTCTGGTGACTATGTGTCA
1 GGTCCGATGACTATGTGTCA
136281 CCATAAGTAT
Statistics
Matches: 117, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 117 1.00
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (52 bp):
GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
Found at i:136853 original size:21 final size:21
Alignment explanation
Indices: 136823--136862 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
136813 TGAGATTCTG
*
136823 CATACTTGTTTCAATAGAACC
1 CATACATGTTTCAATAGAACC
136844 CATACATGTTTCAATAGAA
1 CATACATGTTTCAATAGAA
136863 GTACAGGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.33
Consensus pattern (21 bp):
CATACATGTTTCAATAGAACC
Found at i:140022 original size:31 final size:31
Alignment explanation
Indices: 139971--140030 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 31
139961 AGATTTAAGG
139971 TAATAAAGTATTAGAGAATATATTTT-TTTTTTC
1 TAATAAAG-ATTAGA-AA-ATATTTTATTTTTTC
140004 TAATAAAG-TTAGAAAATATTTTATTTT
1 TAATAAAGATTAGAAAATATTTTATTTT
140031 GTTTTATGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 7 0.27
30 6 0.23
31 5 0.19
33 8 0.31
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (31 bp):
TAATAAAGATTAGAAAATATTTTATTTTTTC
Found at i:141337 original size:28 final size:27
Alignment explanation
Indices: 141284--141345 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
141274 TATGTTTTTT
*
141284 TATATATTATATCATATGAAAATTAAA
1 TATATATTATATAATATGAAAATTAAA
*
141311 TATATTTTATTATAATAT-AAATATTAAA
1 TATATATTA-TATAATATGAAA-ATTAAA
*
141339 AATATAT
1 TATATAT
141346 ATTAAGTTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 11 0.38
28 18 0.62
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (27 bp):
TATATATTATATAATATGAAAATTAAA
Found at i:145483 original size:3 final size:3
Alignment explanation
Indices: 145464--145496 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
145454 TTTAGGGTTT
145464 AAG AAG AA- AAG AA- AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
145497 TAAAATTGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:146311 original size:27 final size:27
Alignment explanation
Indices: 146258--146317 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
146248 GGTCAAAGGC
* * * *
146258 CAAAATGTTTACAAAAGATAGGGATGG
1 CAAACTGTTTACAAAAGAAAAGAATGG
*
146285 CAAACTGTTTACAAAATAAAAGAATGG
1 CAAACTGTTTACAAAAGAAAAGAATGG
146312 CAAACT
1 CAAACT
146318 ATTGTCAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.22
Consensus pattern (27 bp):
CAAACTGTTTACAAAAGAAAAGAATGG
Found at i:146684 original size:22 final size:21
Alignment explanation
Indices: 146606--146686 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
146596 CCATTTGCAA
* * *
146606 CTGAGTTGTGCTGCTCGCTTG
1 CTGAGTTGGGATGCTCACTTG
*
146627 CTGAGTTGGGGTGCTCACTTG
1 CTGAGTTGGGATGCTCACTTG
* * *
146648 CTAAGTTGTGTTGCTCACTTTG
1 CTGAGTTGGGATGCTCAC-TTG
*
146670 TTGAGTTGGGATGCTCA
1 CTGAGTTGGGATGCTCA
146687 AATGATAGTG
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
21 33 0.67
22 16 0.33
ACGTcount: A:0.11, C:0.19, G:0.32, T:0.38
Consensus pattern (21 bp):
CTGAGTTGGGATGCTCACTTG
Found at i:149250 original size:33 final size:33
Alignment explanation
Indices: 149213--149277 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
149203 CAAATTACTC
* * *
149213 ATCACTATTAGACCAGAAACAAACTTTTAATAT
1 ATCACTATCAGACCAAAAACAAACATTTAATAT
149246 ATCACTATCAGACCAAAAACAAACATTTAATA
1 ATCACTATCAGACCAAAAACAAACATTTAATA
149278 CAACACATGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.49, C:0.20, G:0.05, T:0.26
Consensus pattern (33 bp):
ATCACTATCAGACCAAAAACAAACATTTAATAT
Found at i:149365 original size:18 final size:17
Alignment explanation
Indices: 149342--149390 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 17
149332 AATATTATAT
149342 AAACAAACAATGCCAAAA
1 AAACAAACAATG-CAAAA
149360 AAACAAAAACAATGCAAAA
1 AAAC--AAACAATGCAAAA
*
149379 ACAATAAACAAT
1 A-AACAAACAAT
149391 AAACACAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 11 0.41
19 6 0.22
20 10 0.37
ACGTcount: A:0.69, C:0.18, G:0.04, T:0.08
Consensus pattern (17 bp):
AAACAAACAATGCAAAA
Found at i:149903 original size:47 final size:47
Alignment explanation
Indices: 149841--149931 Score: 130
Period size: 47 Copynumber: 1.9 Consensus size: 47
149831 AAATAGTAGC
* *
149841 AATCAAAATCCAAATCCAAATAAAAAAAAACC-TAAATCGAAAATAAA
1 AATCAAAATCAAAATCAAAAT-AAAAAAAACCTTAAATCGAAAATAAA
* *
149888 AATCAAAATCAAAATCAAAATAAAATAAACCTTAAATTGAAAAT
1 AATCAAAATCAAAATCAAAATAAAAAAAACCTTAAATCGAAAAT
149932 CACAATTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
46 9 0.23
47 30 0.77
ACGTcount: A:0.65, C:0.14, G:0.02, T:0.19
Consensus pattern (47 bp):
AATCAAAATCAAAATCAAAATAAAAAAAACCTTAAATCGAAAATAAA
Found at i:149916 original size:5 final size:6
Alignment explanation
Indices: 149841--149913 Score: 62
Period size: 6 Copynumber: 12.5 Consensus size: 6
149831 AAATAGTAGC
* * * * * *
149841 AATCAA AATCCA AATCCA AAT-AA AA-AAA AACCTA AATCGAA AATAAA
1 AATCAA AATCAA AATCAA AATCAA AATCAA AATCAA AATC-AA AATCAA
149888 AATCAA AATCAA AATCAA AAT-AA AAT
1 AATCAA AATCAA AATCAA AATCAA AAT
149914 AAACCTTAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
5 12 0.21
6 40 0.71
7 4 0.07
ACGTcount: A:0.67, C:0.15, G:0.01, T:0.16
Consensus pattern (6 bp):
AATCAA
Found at i:154366 original size:11 final size:11
Alignment explanation
Indices: 154349--154425 Score: 66
Period size: 11 Copynumber: 6.9 Consensus size: 11
154339 CGGGGCCTTT
*
154349 TTTAATTT-AT
1 TTTAATTTAAA
*
154359 TTTAAATTTAGA
1 TTT-AATTTAAA
*
154371 TTTATTTTAAA
1 TTTAATTTAAA
* **
154382 TTTAAATTATC
1 TTTAATTTAAA
*
154393 TTAAATTTAAA
1 TTTAATTTAAA
154404 TTTAATTTAAA
1 TTTAATTTAAA
154415 TTTAAATTTAA
1 TTT-AATTTAA
154426 TTTCAAAGTT
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
10 3 0.06
11 38 0.75
12 10 0.20
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:154373 original size:6 final size:6
Alignment explanation
Indices: 154359--154438 Score: 73
Period size: 6 Copynumber: 14.0 Consensus size: 6
154349 TTTAATTTAT
* *
154359 TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA -TT--A TCTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
*
154404 TTT-AA TTTAAA TTTAAA TTT-AA TTTCAAA GTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
154439 AAGTCCAAAG
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
3 1 0.02
5 17 0.28
6 37 0.61
7 6 0.10
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:154386 original size:33 final size:33
Alignment explanation
Indices: 154349--154424 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
154339 CGGGGCCTTT
* * *
154349 TTTAATTTATTTTAAATTTAGATTTATTTTAAA
1 TTTAATTTATCTTAAATTTAAATTTAATTTAAA
*
154382 TTTAAATTATCTTAAATTTAAATTTAATTTAAA
1 TTTAATTTATCTTAAATTTAAATTTAATTTAAA
154415 TTTAAATTTA
1 TTT-AATTTA
154425 ATTTCAAAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 32 0.86
34 5 0.14
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (33 bp):
TTTAATTTATCTTAAATTTAAATTTAATTTAAA
Found at i:154425 original size:17 final size:17
Alignment explanation
Indices: 154352--154438 Score: 106
Period size: 17 Copynumber: 5.1 Consensus size: 17
154342 GGCCTTTTTT
*
154352 AATTTATTTTAAATTTA
1 AATTTAATTTAAATTTA
* *
154369 GATTTATTTTAAATTTA
1 AATTTAATTTAAATTTA
154386 AA-TT-ATCTTAAATTTA
1 AATTTAAT-TTAAATTTA
154402 AATTTAATTTAAATTTA
1 AATTTAATTTAAATTTA
*
154419 AATTTAATTTCAAAGTTA
1 AATTTAATTT-AAATTTA
154437 AA
1 AA
154439 AAGTCCAAAG
Statistics
Matches: 62, Mismatches: 4, Indels: 7
0.85 0.05 0.10
Matches are distributed among these distances:
15 1 0.02
16 13 0.21
17 38 0.61
18 10 0.16
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
AATTTAATTTAAATTTA
Found at i:156252 original size:59 final size:59
Alignment explanation
Indices: 156158--156598 Score: 558
Period size: 59 Copynumber: 7.4 Consensus size: 59
156148 GGAGGTCCCT
*
156158 AAACTATCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCT
1 AAACT-TCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCG
* * * ** *
156218 AATCTTCCTAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTCAACCTCG
1 AAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCG
* * * * *
156277 AACCTTCCTAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCTCG
1 AAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCG
* *
156336 AACCTTCCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTTACCCCG
1 AAACTT-CCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCG
* * * * * * **
156396 AAACTTCCTAAAATTACTATTTTACTCTCGAACTTCTAAAAATCCCATTTTTGACCCAA
1 AAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCG
* * * * *
156455 AAACTTCCTAAAATTACCATTTTACCCCTAAACTTTCAAAAGTCCCATTTTTTACCCCG
1 AAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCG
* * * **
156514 AAACTTCAAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCTCATTTTTGACCTTG
1 AAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCG
*
156573 ACACTTCCAAAAAATTACCATTTTAC
1 AAACTTCC-AAAAATTACCATTTTAC
156599 TCCCGGATGT
Statistics
Matches: 330, Mismatches: 49, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
59 256 0.78
60 74 0.22
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32
Consensus pattern (59 bp):
AAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCG
Found at i:156464 original size:178 final size:177
Alignment explanation
Indices: 156158--156603 Score: 615
Period size: 178 Copynumber: 2.5 Consensus size: 177
156148 GGAGGTCCCT
* *
156158 AAACTATCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCTAATCT
1 AAACT-TCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAAACT
* * *
156223 TCCTAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTCAACCTCGAACCTTCCTAA
65 TCCTAAAATTACCATTTTACTCCCGAACTTCCAAAAATCCCATTTTCAACCTCAAAACTTCCTAA
* * *
156288 AATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCTCG
130 AATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCG
* *
156336 AACCTTCCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTTACCCCGAAACT
1 AAACTT-CCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAAACT
* * * **
156401 TCCTAAAATTACTATTTTACTCTCGAACTTCTAAAAATCCCATTTTTGACC-CAAAAACTTCCTA
65 TCCTAAAATTACCATTTTACTCCCGAACTTCCAAAAATCCCATTTTCAACCTC-AAAACTTCCTA
* * * *
156465 AAATTACCATTTTACCCCTAAACTTTCAAAAGTCCCATTTTTTACCCCG
129 AAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCG
* * * ** *
156514 AAACTTCAAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCTCATTTTTGACCTTGACACTT
1 AAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTT
*
156579 CCAAAAAATTACCATTTTACTCCCG
66 CC-TAAAATTACCATTTTACTCCCG
156604 GATGTTCAAA
Statistics
Matches: 235, Mismatches: 30, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
177 56 0.24
178 179 0.76
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32
Consensus pattern (177 bp):
AAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTT
CCTAAAATTACCATTTTACTCCCGAACTTCCAAAAATCCCATTTTCAACCTCAAAACTTCCTAAA
ATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCG
Found at i:156658 original size:178 final size:171
Alignment explanation
Indices: 156158--156692 Score: 538
Period size: 178 Copynumber: 3.0 Consensus size: 171
156148 GGAGGTCCCT
156158 AAACTATCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCT-AATC
1 AAACT-TCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGA-CCCTGAA-C
* * * * *
156222 TTCCTAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTCAACCTCGAACCTTCCTA
63 TTCCTAAAATTACCATTTTACTCCCGGA-TTTCAAAAATCCCA-TTTCGACCTCGAA--ATCCTA
* * * * *
156287 AAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCTCG
124 AAATTACCATTTTACCCCCAAACTTTC-AAAATCCCATTTTTAACCCCG
* * *
156336 AACCTTCCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTTACCCCGAAACT
1 AAACTT-CCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCTG-AACT
* * * * * *
156401 TCCTAAAATTACTATTTTACTCTCGAACTTCTAAAAATCCCATTTTTGACC-CAAAAACTTCCTA
64 TCCTAAAATTACCATTTTACTCCCGGATTTC-AAAAATCCCA-TTTCGACCTC-GAAA--TCCTA
* *
156465 AAATTACCATTTTACCCCTAAACTTTCAAAAGTCCCATTTTTTACCCCG
124 AAATTACCATTTTACCCCCAAACTTTCAAAA-TCCCATTTTTAACCCCG
* * * *
156514 AAACTTCAAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCTCATTTTTGACCTTGACACTT
1 AAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCTGA-ACTT
* *
156579 CCAAAAAATTACCATTTTACTCCCGGATGTTCAAAGACTCCGC-TTTCGACCTCGAAATCCTCAA
65 CC-TAAAATTACCATTTTACTCCCGGAT-TTCAAA-AATCC-CATTTCGACCTCGAAATCCT-AA
* ** * *
156643 AGTTACTTTTTTTACCCCCAAA-TGTCTAAAATTCCATTTTTAACCCCG
125 AATTAC-CATTTTACCCCCAAACTTTC-AAAATCCCATTTTTAACCCCG
156691 AA
1 AA
156693 TTTTCTCGAA
Statistics
Matches: 300, Mismatches: 40, Indels: 35
0.80 0.11 0.09
Matches are distributed among these distances:
176 5 0.02
177 91 0.30
178 193 0.64
179 10 0.03
180 1 0.00
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (171 bp):
AAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCTGAACTTC
CTAAAATTACCATTTTACTCCCGGATTTCAAAAATCCCATTTCGACCTCGAAATCCTAAAATTAC
CATTTTACCCCCAAACTTTCAAAATCCCATTTTTAACCCCG
Found at i:158501 original size:3 final size:3
Alignment explanation
Indices: 158493--158520 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
158483 ATTCAGTTGC
158493 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
158521 TGTTTTCTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:158763 original size:21 final size:21
Alignment explanation
Indices: 158723--158763 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
158713 CTTTTCTTTT
*
158723 CATAGTTTTTATTTTTTAATG
1 CATAGTTTTTATTTTATAATG
158744 CATATGTTTTTA-TTTATAAT
1 CATA-GTTTTTATTTTATAAT
158764 ATTTAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.61
Consensus pattern (21 bp):
CATAGTTTTTATTTTATAATG
Done.