Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 114 of 120
Found at i:34266044 original size:21 final size:21
Alignment explanation
Indices: 34266020--34266070 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
34266010 ATAATAGCAT
*
34266020 AATCTAAATATAAAATTTAGA
1 AATCCAAATATAAAATTTAGA
* * *
34266041 AATCCAAACATAAAGTTTATA
1 AATCCAAATATAAAATTTAGA
34266062 AATCCAAAT
1 AATCCAAAT
34266071 TACATCATTC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.55, C:0.12, G:0.04, T:0.29
Consensus pattern (21 bp):
AATCCAAATATAAAATTTAGA
Found at i:34267263 original size:2 final size:2
Alignment explanation
Indices: 34267256--34267284 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
34267246 CATCAATTGC
34267256 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34267285 TGTTCATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34279589 original size:16 final size:15
Alignment explanation
Indices: 34279568--34279611 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
34279558 GATTTAATTT
34279568 TATAAAATTATAAAAA
1 TATAAAA-TATAAAAA
*
34279584 TATAAAATATTAAAA
1 TATAAAATATAAAAA
34279599 TGATAAAAATATA
1 T-AT-AAAATATA
34279612 TAATTTAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 8 0.33
16 9 0.38
17 7 0.29
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (15 bp):
TATAAAATATAAAAA
Found at i:34279619 original size:23 final size:23
Alignment explanation
Indices: 34279570--34279642 Score: 92
Period size: 23 Copynumber: 3.1 Consensus size: 23
34279560 TTTAATTTTA
* *
34279570 TAAAATTATAAAAATATAAAATAT
1 TAAAATCATAAAAATATATAAT-T
*
34279594 TAAAATGATAAAAATATATAATT
1 TAAAATCATAAAAATATATAATT
**
34279617 TAATCTCATAAAAATATATAATT
1 TAAAATCATAAAAATATATAATT
34279640 TAA
1 TAA
34279643 TTTCGTTCCA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 24 0.55
24 20 0.45
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (23 bp):
TAAAATCATAAAAATATATAATT
Found at i:34285299 original size:12 final size:12
Alignment explanation
Indices: 34285282--34285307 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
34285272 GGGAGAATGA
34285282 AAAGAAAAATAG
1 AAAGAAAAATAG
34285294 AAAGAAAAATAG
1 AAAGAAAAATAG
34285306 AA
1 AA
34285308 TAAATTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAGAAAAATAG
Found at i:34285340 original size:19 final size:19
Alignment explanation
Indices: 34285298--34285339 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
34285288 AAATAGAAAG
* *
34285298 AAAAATAGAATAAATTATT
1 AAAAATAGAAAAAATTATA
34285317 AAAAATAGAAAAAA-TATA
1 AAAAATAGAAAAAATTATA
34285335 AAAAA
1 AAAAA
34285340 ACATATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (19 bp):
AAAAATAGAAAAAATTATA
Found at i:34288939 original size:3 final size:3
Alignment explanation
Indices: 34288931--34288962 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
34288921 TGGAATACCC
34288931 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
34288963 AGTAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:34291252 original size:7 final size:7
Alignment explanation
Indices: 34291240--34291273 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
34291230 TTGTAAGTAT
34291240 CTCTCTC
1 CTCTCTC
34291247 CTCTCTC
1 CTCTCTC
34291254 CTCTCTC
1 CTCTCTC
34291261 CTCTCTC
1 CTCTCTC
34291268 CTCTCT
1 CTCTCT
34291274 GCATTCTGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (7 bp):
CTCTCTC
Found at i:34293908 original size:2 final size:2
Alignment explanation
Indices: 34293903--34293927 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34293893 GTGTGTGCGT
34293903 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
34293928 GGAGTACCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:34297889 original size:23 final size:23
Alignment explanation
Indices: 34297859--34297913 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
34297849 TTATCTGTCT
34297859 TTGTGGCACGTTGTTTCTCTACC
1 TTGTGGCACGTTGTTTCTCTACC
34297882 TTGTGGCACGTTGTTTCTCTACC
1 TTGTGGCACGTTGTTTCTCTACC
34297905 TTGTGGCAC
1 TTGTGGCAC
34297914 ATCTTCGTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (23 bp):
TTGTGGCACGTTGTTTCTCTACC
Found at i:34297927 original size:22 final size:23
Alignment explanation
Indices: 34297859--34297928 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 23
34297849 TTATCTGTCT
* *
34297859 TTGTGGCACGTTGTTTCTCTACC
1 TTGTGGCACGATGCTTCTCTACC
* *
34297882 TTGTGGCACGTTGTTTCTCTACC
1 TTGTGGCACGATGCTTCTCTACC
34297905 TTGTGGCAC-AT-CTTCGTCTACC
1 TTGTGGCACGATGCTTC-TCTACC
34297927 TT
1 TT
34297929 TGTGATAGAT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
21 3 0.07
22 9 0.20
23 32 0.73
ACGTcount: A:0.10, C:0.27, G:0.20, T:0.43
Consensus pattern (23 bp):
TTGTGGCACGATGCTTCTCTACC
Found at i:34298387 original size:2 final size:2
Alignment explanation
Indices: 34298380--34298415 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
34298370 AGTTTCTTTT
34298380 TC TC TC TC TC TC TC T- TC TC TC T- TC TC TC T- TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
34298416 TTCCACTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.10
2 28 0.90
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (2 bp):
TC
Found at i:34298400 original size:7 final size:7
Alignment explanation
Indices: 34298379--34298416 Score: 67
Period size: 7 Copynumber: 5.3 Consensus size: 7
34298369 TAGTTTCTTT
34298379 TTCTCTC
1 TTCTCTC
34298386 TCTCTCTC
1 T-TCTCTC
34298394 TTCTCTC
1 TTCTCTC
34298401 TTCTCTC
1 TTCTCTC
34298408 TTCTCTC
1 TTCTCTC
34298415 TT
1 TT
34298417 TCCACTTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 23 0.77
8 7 0.23
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (7 bp):
TTCTCTC
Found at i:34298990 original size:13 final size:13
Alignment explanation
Indices: 34298964--34299026 Score: 51
Period size: 13 Copynumber: 4.8 Consensus size: 13
34298954 AGTTTAGTAT
**
34298964 TACTTTTATGAAG
1 TACTTTTAAAAAG
34298977 TACTTTTAAAAAG
1 TACTTTTAAAAAG
*
34298990 T-GTTTTGAAAAAG
1 TACTTTT-AAAAAG
34299003 TTA-TTTTAAAAA-
1 -TACTTTTAAAAAG
34299015 TACTTTTGAAAA
1 TACTTTT-AAAA
34299027 TATTGGTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
11 2 0.05
12 8 0.19
13 27 0.64
14 5 0.12
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (13 bp):
TACTTTTAAAAAG
Found at i:34299436 original size:34 final size:34
Alignment explanation
Indices: 34299398--34299464 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
34299388 AAAATTATTT
34299398 ATTTAACATTCCTTTGGATTCAAAAATATTTTTC
1 ATTTAACATTCCTTTGGATTCAAAAATATTTTTC
* * *
34299432 ATTTAGCATTCCTTTTGATTCAAAAATGTTTTT
1 ATTTAACATTCCTTTGGATTCAAAAATATTTTT
34299465 GAGGTAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.49
Consensus pattern (34 bp):
ATTTAACATTCCTTTGGATTCAAAAATATTTTTC
Found at i:34300746 original size:15 final size:15
Alignment explanation
Indices: 34300726--34300758 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
34300716 AGAATTTGAA
34300726 AGTTAGTTAAGAA-TT
1 AGTTAG-TAAGAAGTT
34300741 AGTTAGTAAGAAGTT
1 AGTTAGTAAGAAGTT
34300756 AGT
1 AGT
34300759 AAAATGGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.36
Consensus pattern (15 bp):
AGTTAGTAAGAAGTT
Found at i:34300823 original size:25 final size:25
Alignment explanation
Indices: 34300777--34300825 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
34300767 AGTTTTAAGG
*
34300777 AGATCAATAAAACTGTGAGTTTTGA
1 AGATCAATAAAACTGGGAGTTTTGA
*
34300802 AGATTAATAAAA-TGGGACGTTTTG
1 AGATCAATAAAACTGGGA-GTTTTG
34300826 TTGGGAGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33
Consensus pattern (25 bp):
AGATCAATAAAACTGGGAGTTTTGA
Found at i:34305761 original size:80 final size:81
Alignment explanation
Indices: 34305619--34305912 Score: 382
Period size: 80 Copynumber: 3.7 Consensus size: 81
34305609 AGTTTAGCAG
* * *
34305619 GAGTTAGTGGTTAAAAGTTTTATGTTCGCATTT-AAAGTTTAGGGTTCATATATCATTTGAATTT
1 GAGTTAGTGGTTAAAAGTTTTATGTTCGCATTTGAAAGTTTAGGATTCAAATATTATTTGAATTT
*
34305683 ACCCAACAATTCGGAA
66 ACCCAACAATTCGAAA
* * * *
34305699 GAGCTAGTTGTTAAAAATTTTATGTTCGCATTTGAAA-TTTAGGATTCAAAAATTATTTGAATTT
1 GAGTTAGTGGTTAAAAGTTTTATGTTCGCATTTGAAAGTTTAGGATTCAAATATTATTTGAATTT
**
34305763 ATTCAACAATTCGAAA
66 ACCCAACAATTCGAAA
* * * * *
34305779 GAGTTAGTGGTTAAAAGTTTTATGTTCTCA-TTCAAAGTTTAAGATTTAAATATTATTTCAATTT
1 GAGTTAGTGGTTAAAAGTTTTATGTTCGCATTTGAAAGTTTAGGATTCAAATATTATTTGAATTT
*
34305843 ACCCAACAATT-TAAGA
66 ACCCAACAATTCGAA-A
* *
34305859 GAGTTAGTGGTTAAAAGTTTTATGTTCTCATTTG-AAGTTTAGGGTTCAAATATT
1 GAGTTAGTGGTTAAAAGTTTTATGTTCGCATTTGAAAGTTTAGGATTCAAATATT
34305913 TGTAATGTCA
Statistics
Matches: 184, Mismatches: 26, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
79 7 0.04
80 172 0.93
81 5 0.03
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (81 bp):
GAGTTAGTGGTTAAAAGTTTTATGTTCGCATTTGAAAGTTTAGGATTCAAATATTATTTGAATTT
ACCCAACAATTCGAAA
Found at i:34307906 original size:21 final size:21
Alignment explanation
Indices: 34307882--34307921 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
34307872 TCGAGAATTG
34307882 AAAAATGAAAG-AAGAGAAATC
1 AAAAATG-AAGCAAGAGAAATC
*
34307903 AAAATTGAAGCAAGAGAAA
1 AAAAATGAAGCAAGAGAAA
34307922 GAAGTGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.65, C:0.05, G:0.20, T:0.10
Consensus pattern (21 bp):
AAAAATGAAGCAAGAGAAATC
Found at i:34309627 original size:15 final size:15
Alignment explanation
Indices: 34309607--34309644 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
34309597 ATATAATGAT
34309607 ATATATGTGAGAAAA
1 ATATATGTGAGAAAA
* *
34309622 ATATATGTGTGAAAT
1 ATATATGTGAGAAAA
34309637 AT-TATGTG
1 ATATATGTG
34309645 GTTAATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (15 bp):
ATATATGTGAGAAAA
Found at i:34309779 original size:6 final size:6
Alignment explanation
Indices: 34309768--34309818 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
34309758 TGATCAAAAT
* * *
34309768 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG
34309816 TGA
1 TGA
34309819 TATGAATTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:34311062 original size:18 final size:18
Alignment explanation
Indices: 34311041--34311087 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
34311031 TAAAATCGAA
34311041 TTAA-TCGATTGAATCAAT
1 TTAATTCGATT-AATCAAT
*
34311059 TTAATTCGATTAATCGAT
1 TTAATTCGATTAATCAAT
*
34311077 CTAATTCGATT
1 TTAATTCGATT
34311088 TGAGGTCGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 20 0.77
19 6 0.23
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.43
Consensus pattern (18 bp):
TTAATTCGATTAATCAAT
Found at i:34315931 original size:19 final size:18
Alignment explanation
Indices: 34315890--34315933 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
34315880 GATTCGATTT
34315890 TAATTAAATAAATTATAA
1 TAATTAAATAAATTATAA
*
34315908 TAATTAGAATAATATTTTAA
1 TAATTA-AATAA-ATTATAA
34315928 -AATTAA
1 TAATTAA
34315934 TTTAATTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 7 0.30
19 10 0.43
20 6 0.26
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
TAATTAAATAAATTATAA
Found at i:34316792 original size:16 final size:16
Alignment explanation
Indices: 34316773--34316813 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
34316763 TTTAATTTTT
34316773 TAAAAATTATAAAATA
1 TAAAAATTATAAAATA
34316789 T--AAATTATTAAAATA
1 TAAAAATTA-TAAAATA
34316804 -AAAAATTATA
1 TAAAAATTATA
34316814 TTTTTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
14 6 0.27
15 9 0.41
16 7 0.32
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TAAAAATTATAAAATA
Found at i:34321523 original size:6 final size:6
Alignment explanation
Indices: 34321512--34321536 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
34321502 ATCTCACTCG
34321512 AATTTA AATTTA AATTTA AATTTA A
1 AATTTA AATTTA AATTTA AATTTA A
34321537 TTATAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTTA
Found at i:34324284 original size:24 final size:23
Alignment explanation
Indices: 34324257--34324301 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
34324247 GTTCTTGAAG
34324257 AAAAAAGAAAAAAGAAGAGGGTGT
1 AAAAAAGAAAAAAGAA-AGGGTGT
** *
34324281 AAAAGGGAAAAGAGAAAGGGT
1 AAAAAAGAAAAAAGAAAGGGT
34324302 ACACTGGGAG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 5 0.28
24 13 0.72
ACGTcount: A:0.60, C:0.00, G:0.33, T:0.07
Consensus pattern (23 bp):
AAAAAAGAAAAAAGAAAGGGTGT
Found at i:34327576 original size:26 final size:27
Alignment explanation
Indices: 34327540--34327603 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 27
34327530 TTATTTTATG
34327540 TTTATAT-TTTATAT-ACAT-AAATAA
1 TTTATATATTTATATAACATAAAATAA
* *
34327564 TTATATTTATTTA-ATAATATAAAATAA
1 TT-TATATATTTATATAACATAAAATAA
34327591 TTTATATATTTAT
1 TTTATATATTTAT
34327604 TTTTAAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 2 0.06
25 6 0.19
26 16 0.50
27 8 0.25
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (27 bp):
TTTATATATTTATATAACATAAAATAA
Found at i:34331254 original size:18 final size:18
Alignment explanation
Indices: 34331215--34331255 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
34331205 TGATGTCAAA
* * *
34331215 AAAATTTAAAATATATTT
1 AAAATTTAAAAAAAATTC
34331233 AAAATTTAAAAAAAATTC
1 AAAATTTAAAAAAAATTC
34331251 AAAAT
1 AAAAT
34331256 ATATAAAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAATTTAAAAAAAATTC
Found at i:34336244 original size:13 final size:13
Alignment explanation
Indices: 34336200--34336255 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
34336190 ACAAGTTTGT
* *
34336200 TTATTTTATAAAA
1 TTATTTAATTAAA
34336213 TT-TTTAATTTTAAA
1 TTATTTAA--TTAAA
*
34336227 ATATTTAATTAAA
1 TTATTTAATTAAA
*
34336240 TTATTAAATTAAA
1 TTATTTAATTAAA
34336253 TTA
1 TTA
34336256 AATTAATATA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 4 0.11
13 21 0.60
14 5 0.14
15 5 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTATTTAATTAAA
Found at i:34339759 original size:16 final size:16
Alignment explanation
Indices: 34339740--34339770 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34339730 AATTATATGA
34339740 TTATTTTATTACAGTT
1 TTATTTTATTACAGTT
*
34339756 TTATTTTATTCCAGT
1 TTATTTTATTACAGT
34339771 GAATTAAACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.10, G:0.06, T:0.61
Consensus pattern (16 bp):
TTATTTTATTACAGTT
Found at i:34349478 original size:30 final size:30
Alignment explanation
Indices: 34349437--34349501 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
34349427 TGTCCCTGTA
34349437 TTTTTTCACATTTAAAGTTTAGTCTCTCCG
1 TTTTTTCACATTTAAAGTTTAGTCTCTCCG
*
34349467 TTTTTTTACATTTAAAGTTTAGTCTCTCCG
1 TTTTTTCACATTTAAAGTTTAGTCTCTCCG
34349497 TTTTT
1 TTTTT
34349502 AATTTCAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.18, C:0.17, G:0.09, T:0.55
Consensus pattern (30 bp):
TTTTTTCACATTTAAAGTTTAGTCTCTCCG
Found at i:34349516 original size:29 final size:29
Alignment explanation
Indices: 34349437--34349522 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 29
34349427 TGTCCCTGTA
*
34349437 TTTTTTCACATTTAAAGTTTAGTCTCTCCG
1 TTTTTT-ACATTTAAAATTTAGTCTCTCCG
*
34349467 TTTTTTTACATTTAAAGTTTAGTCTCTCCG
1 -TTTTTTACATTTAAAATTTAGTCTCTCCG
*
34349497 -TTTTTA-ATTTCAAGAATTTAATCTCT
1 TTTTTTACATTT-AA-AATTTAGTCTCT
34349523 TTACTCTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
27 4 0.08
28 8 0.16
29 10 0.20
30 23 0.45
31 6 0.12
ACGTcount: A:0.23, C:0.16, G:0.08, T:0.52
Consensus pattern (29 bp):
TTTTTTACATTTAAAATTTAGTCTCTCCG
Found at i:34357262 original size:19 final size:19
Alignment explanation
Indices: 34357240--34357278 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
34357230 TTTTTAATTA
*
34357240 AATTTATAGTTAAAAATAT
1 AATTAATAGTTAAAAATAT
* *
34357259 AATTAATTGTTAAAATTAT
1 AATTAATAGTTAAAAATAT
34357278 A
1 A
34357279 TCATATAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (19 bp):
AATTAATAGTTAAAAATAT
Found at i:34357901 original size:18 final size:18
Alignment explanation
Indices: 34357878--34357920 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
34357868 GAATAAATTT
34357878 TTAATTAAATAATTTT-AA
1 TTAATTAAA-AATTTTAAA
34357896 TTAATTAAAAATTTTAAA
1 TTAATTAAAAATTTTAAA
34357914 TTAATTA
1 TTAATTA
34357921 CAACTGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTAATTAAAAATTTTAAA
Found at i:34358414 original size:20 final size:20
Alignment explanation
Indices: 34358391--34358429 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
34358381 TTACATCATT
34358391 AATTTT-ATATTAAATTTTAG
1 AATTTTCAT-TTAAATTTTAG
34358411 AATTTTCATTTAAATTTTA
1 AATTTTCATTTAAATTTTA
34358430 TTTTTTAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (20 bp):
AATTTTCATTTAAATTTTAG
Found at i:34359893 original size:13 final size:14
Alignment explanation
Indices: 34359866--34359896 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
34359856 AATTATTTCA
34359866 TATTTTTCATAATT
1 TATTTTTCATAATT
*
34359880 TATTTTTCATATTT
1 TATTTTTCATAATT
34359894 TAT
1 TAT
34359897 AATATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTTTTCATAATT
Found at i:34359911 original size:10 final size:11
Alignment explanation
Indices: 34359895--34359930 Score: 58
Period size: 10 Copynumber: 3.5 Consensus size: 11
34359885 TTCATATTTT
34359895 ATAATATATTA
1 ATAATATATTA
34359906 AT-ATATATTA
1 ATAATATATTA
34359916 ATAATATATT-
1 ATAATATATTA
34359926 ATAAT
1 ATAAT
34359931 TCTACTTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATAATATATTA
Found at i:34378347 original size:19 final size:19
Alignment explanation
Indices: 34378315--34378368 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
34378305 ATATTTACTT
*
34378315 TTTTAAATTTTTAAATTTAA
1 TTTT-AATTATTAAATTTAA
*
34378335 TTTTAATTGTT-AATTTAA
1 TTTTAATTATTAAATTTAA
34378353 TTTT--TTATTAAATTTA
1 TTTTAATTATTAAATTTA
34378369 TTTGTATGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 4 0.13
17 6 0.19
18 11 0.35
19 6 0.19
20 4 0.13
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTAATTATTAAATTTAA
Found at i:34378507 original size:20 final size:20
Alignment explanation
Indices: 34378465--34378532 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
34378455 TTAAGGAATA
*
34378465 AAAATAATAATAAATTT-CTT
1 AAAATAAAAATAAATTTAC-T
*
34378485 AAAATAAAAATCAATTTACT
1 AAAATAAAAATAAATTTACT
* *
34378505 AAATTAAAATATAAGAATTACT
1 AAAATAAAA-ATAA-ATTTACT
34378527 AAAATA
1 AAAATA
34378533 TTTTAACCTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 24 0.62
21 4 0.10
22 11 0.28
ACGTcount: A:0.60, C:0.06, G:0.01, T:0.32
Consensus pattern (20 bp):
AAAATAAAAATAAATTTACT
Found at i:34379002 original size:21 final size:20
Alignment explanation
Indices: 34378956--34379003 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
34378946 GAACAATAGA
34378956 AAAATATATTAAAATAACAT
1 AAAATATATTAAAATAACAT
* *
34378976 TAAATA-ATTAATAAGTAATAT
1 AAAATATATTAA-AA-TAACAT
34378997 AAAATAT
1 AAAATAT
34379004 CTAATCTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 5 0.23
20 7 0.32
21 10 0.45
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
AAAATATATTAAAATAACAT
Found at i:34384467 original size:4 final size:4
Alignment explanation
Indices: 34384458--34384483 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
34384448 GTTGGGTTAA
34384458 TGAG TGAG TGAG TGAG TGAG TGAG TG
1 TGAG TGAG TGAG TGAG TGAG TGAG TG
34384484 TATTTATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.50, T:0.27
Consensus pattern (4 bp):
TGAG
Found at i:34388372 original size:19 final size:16
Alignment explanation
Indices: 34388333--34388429 Score: 72
Period size: 16 Copynumber: 5.9 Consensus size: 16
34388323 TAAATTTAAA
*
34388333 TTTATTATTAATGCTAAT
1 TTTATTATTAA--ATAAT
34388351 TTTATTATTACAATAAAAT
1 TTTATTATTA-AAT--AAT
*
34388370 TTTAATATTAAATAAT
1 TTTATTATTAAATAAT
*
34388386 TTTATTA-T-ATTAAT
1 TTTATTATTAAATAAT
* * * *
34388400 TATATTAATAATTTAT
1 TTTATTATTAAATAAT
34388416 TTTATTATTAAATA
1 TTTATTATTAAATA
34388430 TAATTATGCA
Statistics
Matches: 64, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
14 11 0.17
15 2 0.03
16 24 0.38
17 1 0.02
18 13 0.20
19 13 0.20
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (16 bp):
TTTATTATTAAATAAT
Found at i:34388388 original size:16 final size:17
Alignment explanation
Indices: 34388347--34388389 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
34388337 TTATTAATGC
*
34388347 TAATTTTATTATTACAA
1 TAATTTTAATATTACAA
34388364 TAAAATTTTAATATTA-AA
1 T--AATTTTAATATTACAA
34388382 TAATTTTA
1 TAATTTTA
34388390 TTATATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 7 0.30
17 1 0.04
18 3 0.13
19 12 0.52
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
TAATTTTAATATTACAA
Found at i:34391864 original size:18 final size:18
Alignment explanation
Indices: 34391843--34391878 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
34391833 ATCATATCTG
* *
34391843 ATAAGTATAATTATATTA
1 ATAAATATAATTAAATTA
34391861 ATAAATATAATTAAATTA
1 ATAAATATAATTAAATTA
34391879 TTAATCTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
ATAAATATAATTAAATTA
Found at i:34402500 original size:20 final size:20
Alignment explanation
Indices: 34402477--34402514 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
34402467 GTAAACACTC
34402477 TAAAA-AAAACTTTTAAAAAA
1 TAAAATAAAA-TTTTAAAAAA
*
34402497 TAAAATAATATTTTAAAA
1 TAAAATAAAATTTTAAAA
34402515 TTTAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAAATAAAATTTTAAAAAA
Found at i:34423216 original size:58 final size:58
Alignment explanation
Indices: 34423128--34423273 Score: 174
Period size: 58 Copynumber: 2.5 Consensus size: 58
34423118 ATATATTATA
* **
34423128 ATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAA-AT-ATT-ATTAAATTACAT
1 ATTTTTATTAAATT-ATA-TTTAATAATAATTATATTAAAATATAATTAAAGAAATTA-AT
* *
34423185 ATTATTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAAGAAATTAAT
1 A-T-TTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAAGAAATTAAT
34423245 ATTTTTATTAAATTATATTTAATAATAAT
1 ATTTTTATTAAATTATATTTAATAATAAT
34423274 CATTAAAATT
Statistics
Matches: 77, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
57 1 0.01
58 48 0.62
59 11 0.14
60 10 0.13
61 7 0.09
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (58 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAAGAAATTAAT
Found at i:34423464 original size:16 final size:16
Alignment explanation
Indices: 34423443--34423498 Score: 94
Period size: 16 Copynumber: 3.5 Consensus size: 16
34423433 TGAATTACTG
34423443 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
34423459 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCC
*
34423475 ATTACACCTCTATTCC
1 ATTACAGCTCTATTCC
34423491 ATTACAGC
1 ATTACAGC
34423499 GAACCAAACG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.27, C:0.30, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:34429507 original size:17 final size:17
Alignment explanation
Indices: 34429485--34429528 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
34429475 TGGTTTAGTA
*
34429485 AAAAATATTTATGGGAT
1 AAAAATATTTATGAGAT
* *
34429502 AAAAATCGTTTTTGAGAT
1 AAAAAT-ATTTATGAGAT
34429520 AAAAATATT
1 AAAAATATT
34429529 CCTAAACAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.36
Consensus pattern (17 bp):
AAAAATATTTATGAGAT
Found at i:34433073 original size:19 final size:19
Alignment explanation
Indices: 34433035--34433070 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
34433025 CTTGAGTCCG
*
34433035 AGGTTTGAGTTTGAAGTTC
1 AGGTTTGAGTTTCAAGTTC
34433054 AGGTTTGAG-TTCAAGTT
1 AGGTTTGAGTTTCAAGTT
34433071 TCAAGATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.22, C:0.06, G:0.31, T:0.42
Consensus pattern (19 bp):
AGGTTTGAGTTTCAAGTTC
Found at i:34440307 original size:18 final size:18
Alignment explanation
Indices: 34440284--34440320 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
34440274 TTTGTGATCA
34440284 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
34440302 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
34440320 A
1 A
34440321 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:34445078 original size:16 final size:16
Alignment explanation
Indices: 34445038--34445084 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
34445028 TAGTTAAATT
*
34445038 CTAATTGATGACTAATTC
1 CTAATTGATGA-T-GTTC
*
34445056 TTAATTGATGATGTTC
1 CTAATTGATGATGTTC
34445072 CTAATTGATGATG
1 CTAATTGATGATG
34445085 GGCTGATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 15 0.58
17 1 0.04
18 10 0.38
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.43
Consensus pattern (16 bp):
CTAATTGATGATGTTC
Found at i:34447699 original size:17 final size:18
Alignment explanation
Indices: 34447669--34447710 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
34447659 TACAGAATCG
34447669 TTAAAAA-TAAAAAATTA
1 TTAAAAATTAAAAAATTA
*
34447686 -TAAAAATTACAAAATTA
1 TTAAAAATTAAAAAATTA
34447703 TTAAAAAT
1 TTAAAAAT
34447711 AGACAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 9 0.41
18 7 0.32
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
TTAAAAATTAAAAAATTA
Found at i:34450627 original size:19 final size:19
Alignment explanation
Indices: 34450600--34450650 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
34450590 ATTAGAAAAA
*
34450600 TTATGAAAATATTTT-TTT
1 TTATTAAAATATTTTATTT
*
34450618 GTTATTAAAATGTTTTATTT
1 -TTATTAAAATATTTTATTT
34450638 TT-TTAAAAGTATT
1 TTATTAAAA-TATT
34450651 ATAATTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 6 0.22
19 18 0.67
20 3 0.11
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (19 bp):
TTATTAAAATATTTTATTT
Found at i:34451586 original size:22 final size:22
Alignment explanation
Indices: 34451561--34451603 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
34451551 TATTCAAACA
34451561 ATAACAACAAAAT-AGTAGCAAT
1 ATAACAACAAAATGA-TAGCAAT
* *
34451583 ATAATAGCAAAATGATAGCAA
1 ATAACAACAAAATGATAGCAA
34451604 AACAATGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATGATAGCAAT
Found at i:34457013 original size:18 final size:16
Alignment explanation
Indices: 34456992--34457025 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
34456982 TAACCTTATA
34456992 AAATTCTTAATATAATTT
1 AAATTC-TAAT-TAATTT
34457010 AAATTCTAATTAATTT
1 AAATTCTAATTAATTT
34457026 TTTTTATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 4 0.25
18 6 0.38
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATTCTAATTAATTT
Found at i:34461474 original size:23 final size:23
Alignment explanation
Indices: 34461427--34461480 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
34461417 CATAAGGCAG
* * *
34461427 AAGCGTTCTACAAGGCAGAGGAA
1 AAGCGTGCTACAAGGCAAAGAAA
*
34461450 AAGCGTGCTACAAGGTAAAGAAA
1 AAGCGTGCTACAAGGCAAAGAAA
*
34461473 AAGTGTGC
1 AAGCGTGC
34461481 CGCAAAGGCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.15, G:0.30, T:0.15
Consensus pattern (23 bp):
AAGCGTGCTACAAGGCAAAGAAA
Found at i:34478001 original size:49 final size:49
Alignment explanation
Indices: 34477929--34478038 Score: 220
Period size: 49 Copynumber: 2.2 Consensus size: 49
34477919 AGAATTCCAA
34477929 CATGGTTCCAAGCACTATCATGCTCCCATATCGTGTAAATGTCCCATAT
1 CATGGTTCCAAGCACTATCATGCTCCCATATCGTGTAAATGTCCCATAT
34477978 CATGGTTCCAAGCACTATCATGCTCCCATATCGTGTAAATGTCCCATAT
1 CATGGTTCCAAGCACTATCATGCTCCCATATCGTGTAAATGTCCCATAT
34478027 CATGGTTCCAAG
1 CATGGTTCCAAG
34478039 TACAGCTCAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 61 1.00
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.30
Consensus pattern (49 bp):
CATGGTTCCAAGCACTATCATGCTCCCATATCGTGTAAATGTCCCATAT
Found at i:34482554 original size:13 final size:13
Alignment explanation
Indices: 34482536--34482560 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34482526 ACACATCAAT
34482536 GTTAAATTTTTTG
1 GTTAAATTTTTTG
34482549 GTTAAATTTTTT
1 GTTAAATTTTTT
34482561 ATTTGGTCAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (13 bp):
GTTAAATTTTTTG
Found at i:34486167 original size:22 final size:22
Alignment explanation
Indices: 34486141--34486194 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
34486131 GATTTAAAAA
34486141 TTTAAATTTAATGAT-TAATAT
1 TTTAAATTTAATGATGTAATAT
*
34486162 TATT-AATTTATTGATGTAATAT
1 T-TTAAATTTAATGATGTAATAT
*
34486184 TTTAAAATTAA
1 TTTAAATTTAA
34486195 AAAAATTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.52
Consensus pattern (22 bp):
TTTAAATTTAATGATGTAATAT
Found at i:34486169 original size:21 final size:21
Alignment explanation
Indices: 34486140--34486188 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
34486130 GGATTTAAAA
*
34486140 ATTTAAATTTAATGAT-TAAT
1 ATTTTAATTTAATGATGTAAT
*
34486160 ATTATTAATTTATTGATGTAAT
1 ATT-TTAATTTAATGATGTAAT
34486182 ATTTTAA
1 ATTTTAA
34486189 AATTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 3 0.12
21 15 0.60
22 7 0.28
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (21 bp):
ATTTTAATTTAATGATGTAAT
Found at i:34488205 original size:75 final size:79
Alignment explanation
Indices: 34488062--34488371 Score: 488
Period size: 78 Copynumber: 4.0 Consensus size: 79
34488052 ACATTGTCAT
* * * *
34488062 CATCCTTGGACTTGGTAGACTTGGGTGTGTCACCAGCGTCCTCATTTTTGGATTTGTTGCCTAGT
1 CATCCTTGGATTTGGTAGACTTGGGTGTATCACCAGTGTCCTCATTTTTGGATTTGTTGCCTATT
34488127 TTTGAAGCGACATC
66 TTTGAAGCGACATC
*
34488141 C-TCCTTGGATTTGGTAGACTTGGGTGTGTCACCAGTGT-C-C-TTTTTGGATTTGTTGCCTATT
1 CATCCTTGGATTTGGTAGACTTGGGTGTATCACCAGTGTCCTCATTTTTGGATTTGTTGCCTATT
*
34488202 TTTGAAGCGGCA-C
66 TTTGAAGCGACATC
*
34488215 CATCCTTGGATTTGGTAGACTTGGGTGTATCACCAGTGTCCTCATTTTTGGATTTGTTTCCTATT
1 CATCCTTGGATTTGGTAGACTTGGGTGTATCACCAGTGTCCTCATTTTTGGATTTGTTGCCTATT
34488280 TTTGAAGCGACA-C
66 TTTGAAGCGACATC
* *
34488293 CATCCTTGGATTTGATAGACTTGGGTGTATCACCAGTGTCCTCATTTTTGGATTTGTTGCCTACT
1 CATCCTTGGATTTGGTAGACTTGGGTGTATCACCAGTGTCCTCATTTTTGGATTTGTTGCCTATT
*
34488358 TTTGAAGCGCCATC
66 TTTGAAGCGACATC
34488372 AACTGATCTA
Statistics
Matches: 215, Mismatches: 11, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
74 2 0.01
75 67 0.31
76 2 0.01
77 2 0.01
78 140 0.65
79 2 0.01
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.39
Consensus pattern (79 bp):
CATCCTTGGATTTGGTAGACTTGGGTGTATCACCAGTGTCCTCATTTTTGGATTTGTTGCCTATT
TTTGAAGCGACATC
Found at i:34488371 original size:153 final size:152
Alignment explanation
Indices: 34488062--34488366 Score: 486
Period size: 153 Copynumber: 2.0 Consensus size: 152
34488052 ACATTGTCAT
*
34488062 CATCCTTGGACTTGGTAGACTTGGGTGTGTCACCAGCGTCCTCATTTTTGGATTTGTTGCCTAGT
1 CATCCTTGGACTTGGTAGACTTGGGTGTATCACCAGCGTCCTCATTTTTGGATTTGTTGCCTAGT
* *
34488127 TTTGAAGCGACATCCTCCTTGGATTTGGTAGACTTGGGTGTGTCACCAGTGTCCTTTTTGGATTT
66 TTTGAAGCGACATCCTCCTTGGATTTGATAGACTTGGGTGTATCACCAGTGTCCTTTTTGGATTT
*
34488192 GTTGCCTATTTTTGAAGCGGCAC
131 GTTGCCTACTTTTGAAGCGG-AC
* * * *
34488215 CATCCTTGGATTTGGTAGACTTGGGTGTATCACCAGTGTCCTCATTTTTGGATTTGTTTCCTATT
1 CATCCTTGGACTTGGTAGACTTGGGTGTATCACCAGCGTCCTCATTTTTGGATTTGTTGCCTAGT
34488280 TTTGAAGCGACA-CCATCCTTGGATTTGATAGACTTGGGTGTATCACCAGTGTCCTCATTTTTGG
66 TTTGAAGCGACATCC-TCCTTGGATTTGATAGACTTGGGTGTATCACCAGTGT-C-C-TTTTTGG
34488344 ATTTGTTGCCTACTTTTGAAGCG
127 ATTTGTTGCCTACTTTTGAAGCG
34488367 CCATCAACTG
Statistics
Matches: 140, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
152 2 0.01
153 107 0.76
154 1 0.01
155 1 0.01
156 29 0.21
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (152 bp):
CATCCTTGGACTTGGTAGACTTGGGTGTATCACCAGCGTCCTCATTTTTGGATTTGTTGCCTAGT
TTTGAAGCGACATCCTCCTTGGATTTGATAGACTTGGGTGTATCACCAGTGTCCTTTTTGGATTT
GTTGCCTACTTTTGAAGCGGAC
Found at i:34494805 original size:112 final size:112
Alignment explanation
Indices: 34494600--34495043 Score: 601
Period size: 112 Copynumber: 4.0 Consensus size: 112
34494590 CACCGCATAT
** * ** ** *
34494600 AGAC-AAAAAACTCGTGCACGTTTAGATAGACACTCACTTAAATGCAGCTCACATAATTCCCTTT
1 AGACAAAAAAACTCACGCACGTGTAGATAGACACTCACTTAAATGCAAATCATGTGATTCCCTTT
* * *
34494664 AGGAGGAATCAAGACTGTTACGCCACAATTCCCTTTAGAAGGAATCA
66 AGGAGGAATCAAGACCGTTACGCCGCAATTCCCTTTAGGAGGAATCA
* ** *
34494711 AGACAAAAAAACTCACACACGTGTAGATAGA-AGCTCACTTAAATATAAATCATGTGATTCACTT
1 AGACAAAAAAACTCACGCACGTGTAGATAGACA-CTCACTTAAATGCAAATCATGTGATTCCCTT
* *
34494775 TAGGAGGAATCGAGACCATTACGCCGCAATTCCCTTTAGGAGGAATCA
65 TAGGAGGAATCAAGACCGTTACGCCGCAATTCCCTTTAGGAGGAATCA
* *
34494823 AGACAAAAAAACTCACGCACGTGAAGATAGACACTCACTTAAATGCAAGTCATGTGATTCCCTTT
1 AGACAAAAAAACTCACGCACGTGTAGATAGACACTCACTTAAATGCAAATCATGTGATTCCCTTT
* *
34494888 AGGAGGAATCAAGATCGTT-TGCCGCAATTCCCTTTAGGAGGAATCA
66 AGGAGGAATCAAGACCGTTACGCCGCAATTCCCTTTAGGAGGAATCA
*
34494934 AGAC--AAAAACTCGCGCACGTGTAGATAGACACTCACTTAAATGCAAATCATGTGATTCCCTTT
1 AGACAAAAAAACTCACGCACGTGTAGATAGACACTCACTTAAATGCAAATCATGTGATTCCCTTT
** * * *
34494997 AGGAGGAATCAAGATTGTTTCGCTGCAATTCCCTTTAGGATGAATCA
66 AGGAGGAATCAAGACCGTTACGCCGCAATTCCCTTTAGGAGGAATCA
34495044 TGACCGTTGC
Statistics
Matches: 295, Mismatches: 34, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
109 74 0.25
110 24 0.08
111 35 0.12
112 161 0.55
113 1 0.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.25
Consensus pattern (112 bp):
AGACAAAAAAACTCACGCACGTGTAGATAGACACTCACTTAAATGCAAATCATGTGATTCCCTTT
AGGAGGAATCAAGACCGTTACGCCGCAATTCCCTTTAGGAGGAATCA
Found at i:34495000 original size:221 final size:222
Alignment explanation
Indices: 34494600--34495043 Score: 610
Period size: 221 Copynumber: 2.0 Consensus size: 222
34494590 CACCGCATAT
** **
34494600 AGACAAAAAACTCGTGCACGTTTAGATAGACACTCACTTAAATGCAGCTCACATAATTCCCTTTA
1 AGACAAAAAACTCACGCACGTGAAGATAGACACTCACTTAAATGCAGCTCACATAATTCCCTTTA
34494665 GGAGGAATCAAGACTGTTACGCCACAATTCCCTTTAGAAGGAATCAAGACAAAAAAACTCACACA
66 GGAGGAATCAAGACTGTTACGCCACAATTCCCTTTAGAAGGAATCAAGAC-AAAAAACTCACACA
* *
34494730 CGTGTAGATAGAAGCTCACTTAAATATAAATCATGTGATTCACTTTAGGAGGAATCGAGACCATT
130 CGTGTAGATAGAAGCTCACTTAAATACAAATCATGTGATTCACTTTAGGAGGAATCAAGACCATT
34494795 ACGCCGCAATTCCCTTTAGGAGGAATCA
195 ACGCCGCAATTCCCTTTAGGAGGAATCA
** *
34494823 AGACAAAAAAACTCACGCACGTGAAGATAGACACTCACTTAAATGCAAG-TCATGTGATTCCCTT
1 AGAC-AAAAAACTCACGCACGTGAAGATAGACACTCACTTAAATGC-AGCTCACATAATTCCCTT
* * * * *
34494887 TAGGAGGAATCAAGA-TCGTT-TGCCGCAATTCCCTTTAGGAGGAATCAAGAC-AAAAACTCGCG
64 TAGGAGGAATCAAGACT-GTTACGCCACAATTCCCTTTAGAAGGAATCAAGACAAAAAACTCACA
* * **
34494949 CACGTGTAGATAGACA-CTCACTTAAATGCAAATCATGTGATTCCCTTTAGGAGGAATCAAGATT
128 CACGTGTAGATAGA-AGCTCACTTAAATACAAATCATGTGATTCACTTTAGGAGGAATCAAGACC
* * * *
34495013 GTTTCGCTGCAATTCCCTTTAGGATGAATCA
192 ATTACGCCGCAATTCCCTTTAGGAGGAATCA
34495044 TGACCGTTGC
Statistics
Matches: 195, Mismatches: 22, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
221 92 0.47
222 1 0.01
223 33 0.17
224 67 0.34
225 2 0.01
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.25
Consensus pattern (222 bp):
AGACAAAAAACTCACGCACGTGAAGATAGACACTCACTTAAATGCAGCTCACATAATTCCCTTTA
GGAGGAATCAAGACTGTTACGCCACAATTCCCTTTAGAAGGAATCAAGACAAAAAACTCACACAC
GTGTAGATAGAAGCTCACTTAAATACAAATCATGTGATTCACTTTAGGAGGAATCAAGACCATTA
CGCCGCAATTCCCTTTAGGAGGAATCA
Found at i:34495085 original size:35 final size:36
Alignment explanation
Indices: 34494988--34495086 Score: 137
Period size: 36 Copynumber: 2.8 Consensus size: 36
34494978 AAATCATGTG
** *
34494988 ATTCCCTTTAGGAGGAATCAAGATTGTTTCGCTGCA
1 ATTCCCTTTAGGAGGAATCAAGACCGTTGCGCTGCA
* *
34495024 ATTCCCTTTAGGATGAATCATGACCGTTGCGCTGCA
1 ATTCCCTTTAGGAGGAATCAAGACCGTTGCGCTGCA
*
34495060 ATTCCCTTTA-GAGGAATCAAAACCGTT
1 ATTCCCTTTAGGAGGAATCAAGACCGTT
34495087 ACACCACATA
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 14 0.25
36 41 0.75
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.31
Consensus pattern (36 bp):
ATTCCCTTTAGGAGGAATCAAGACCGTTGCGCTGCA
Found at i:34495201 original size:36 final size:36
Alignment explanation
Indices: 34495153--34495245 Score: 116
Period size: 36 Copynumber: 2.6 Consensus size: 36
34495143 TGCAGCTCAC
* * ** *
34495153 GCGA-TCCTCTTTAAGAGGAATCAAGATCGTTATGCG
1 GCGATTCC-CTTTAGGAGGAATCAAGACCGTTACACA
34495189 GCGATTCCCTTTAGGAGGAATCAAGACCGTTACACA
1 GCGATTCCCTTTAGGAGGAATCAAGACCGTTACACA
*
34495225 GTGATTCCCTTTAGGAGGAAT
1 GCGATTCCCTTTAGGAGGAAT
34495246 TAGGACTGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
36 47 0.94
37 3 0.06
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (36 bp):
GCGATTCCCTTTAGGAGGAATCAAGACCGTTACACA
Found at i:34504528 original size:2 final size:2
Alignment explanation
Indices: 34504509--34504552 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
34504499 AAGAATTTAT
34504509 TA TA T- TA TA T- TA -A 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 TA TA TA TA TA TA
34504548 TA TA T
1 TA TA T
34504553 TAAAATAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 3 0.08
2 36 0.92
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34516853 original size:31 final size:30
Alignment explanation
Indices: 34516803--34516890 Score: 97
Period size: 30 Copynumber: 2.9 Consensus size: 30
34516793 GGAATATGGG
*
34516803 AACTTTGA-TTTGATGCAATTGTACACATCA
1 AACTTTGATTTTGATTCAATTGTACACAT-A
* * *
34516833 AACTTTGATTTTGATTCAATTCTAAAGATA
1 AACTTTGATTTTGATTCAATTGTACACATA
** *
34516863 AACTTCAATTTTGGTTCAATTGTACACA
1 AACTTTGATTTTGATTCAATTGTACACA
34516891 ATAGAAAATC
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
30 31 0.66
31 16 0.34
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (30 bp):
AACTTTGATTTTGATTCAATTGTACACATA
Found at i:34518381 original size:235 final size:238
Alignment explanation
Indices: 34517954--34518430 Score: 834
Period size: 235 Copynumber: 2.0 Consensus size: 238
34517944 GCATTTAAAA
*
34517954 TTACATCTTTTTGGAAGAAAGAATAGAGAATTTTCATCTGTGTGCATCCCTAATATATTGATTTT
1 TTACATCTTTTTGCAAGAAAGAATAGAGAATTTTCATCTGTGTGCATCCCTAATATATTGATTTT
34518019 GTTTTTGGAGTGCCCAAATTTAGTAATTGTGCAGTCTGCCTTTTATAGTGTTTTATTTAGCATAA
66 GTTTTTGGAGTGCCCAAATTTAGTAATTGTGCAGTCTGCCTTTTATAGTGTTTTATTTAGCATAA
* * *
34518084 TATCTTAACTAATAGAACATTCAGAGCAATGATAGTAGACTGCTCTCTTGAAGGTTTCAGTGTTG
131 TATCTCAACTAATAGAACATTCAGAACAATGATAGTAGACTGCGCTCTTGAAGGTTTCAGTGTTG
34518149 GATTTGAGTGGTTAGATTGGTCAATTAATTGTCTT-AGGTATT
196 GATTTGAGTGGTTAGATTGGTCAATTAATTGTCTTAAGGTATT
* *
34518191 TTACATTTTTTTGCAAGAAAGAATAGAGAATTTTCATCTGTGTGCATCCTTAATATATTGA-TTT
1 TTACATCTTTTTGCAAGAAAGAATAGAGAATTTTCATCTGTGTGCATCCCTAATATATTGATTTT
* *
34518255 -TTTTTGGAGTGCCCAAATTTAGTAATTGTGGAGTCTGCCTTTTATAGTGTTTTATTTATCATAA
66 GTTTTTGGAGTGCCCAAATTTAGTAATTGTGCAGTCTGCCTTTTATAGTGTTTTATTTAGCATAA
* * *
34518319 TATCTCGACTAATAGAACATTGAGAACAATGATAGTAGACTTCGCTCTTGAAGGTTTCAGTGTTG
131 TATCTCAACTAATAGAACATTCAGAACAATGATAGTAGACTGCGCTCTTGAAGGTTTCAGTGTTG
34518384 GATTTGAGTGGTTAGATTGGTCAATTAATTGTCTTAAGGTATT
196 GATTTGAGTGGTTAGATTGGTCAATTAATTGTCTTAAGGTATT
34518427 TTAC
1 TTAC
34518431 TTTGATGAGA
Statistics
Matches: 228, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
235 156 0.68
236 14 0.06
237 58 0.25
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (238 bp):
TTACATCTTTTTGCAAGAAAGAATAGAGAATTTTCATCTGTGTGCATCCCTAATATATTGATTTT
GTTTTTGGAGTGCCCAAATTTAGTAATTGTGCAGTCTGCCTTTTATAGTGTTTTATTTAGCATAA
TATCTCAACTAATAGAACATTCAGAACAATGATAGTAGACTGCGCTCTTGAAGGTTTCAGTGTTG
GATTTGAGTGGTTAGATTGGTCAATTAATTGTCTTAAGGTATT
Found at i:34528151 original size:15 final size:16
Alignment explanation
Indices: 34528131--34528165 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
34528121 GATTGGGGTA
*
34528131 AAAAAAT-TAAAAAGT
1 AAAAAATATAAAAACT
34528146 AAAAAATATAAAAACT
1 AAAAAATATAAAAACT
34528162 AAAA
1 AAAA
34528166 TAATGCATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (16 bp):
AAAAAATATAAAAACT
Found at i:34536548 original size:34 final size:33
Alignment explanation
Indices: 34536479--34536548 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 33
34536469 AATGTCCTAT
*
34536479 AAAAATATATTAAAATATTAAAAAGATATTTTA
1 AAAAATATATTAAAATATTAAAAAGATATTATA
*
34536512 AAAAATATA-TAATTAATTTTAAAAA-ATAATTATA
1 AAAAATATATTAA--AATATTAAAAAGAT-ATTATA
34536546 AAA
1 AAA
34536549 TAAAAAATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
32 3 0.09
33 11 0.34
34 18 0.56
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (33 bp):
AAAAATATATTAAAATATTAAAAAGATATTATA
Found at i:34536568 original size:18 final size:18
Alignment explanation
Indices: 34536531--34536566 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
34536521 TAATTAATTT
*
34536531 TAAAAAATAATTATAAAA
1 TAAAAAATAACTATAAAA
34536549 TAAAAAATACACTATAAA
1 TAAAAAATA-ACTATAAA
34536567 TATACCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (18 bp):
TAAAAAATAACTATAAAA
Found at i:34537607 original size:30 final size:31
Alignment explanation
Indices: 34537568--34537638 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 31
34537558 AGTCCCAGTC
*
34537568 CTTTTTATTTGC-ACATTTTTTA-AATTTAGT
1 CTTTTTATTTGCTAC-TTTTTAAGAATTTAGT
34537598 -TTTTCTATTT-CTACTTTTTAAGAATTTAGT
1 CTTTT-TATTTGCTACTTTTTAAGAATTTAGT
34537628 CTTTTTATTTG
1 CTTTTTATTTG
34537639 TTTAATTTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
29 11 0.31
30 20 0.57
31 4 0.11
ACGTcount: A:0.21, C:0.10, G:0.07, T:0.62
Consensus pattern (31 bp):
CTTTTTATTTGCTACTTTTTAAGAATTTAGT
Found at i:34547239 original size:22 final size:22
Alignment explanation
Indices: 34547197--34547242 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
34547187 AATATTTTAG
*
34547197 TTTATATTTTTATTTAAAATAA
1 TTTATATTTTTAATTAAAATAA
*
34547219 TTTAT-TTTTTAATTATTAATAA
1 TTTATATTTTTAATTA-AAATAA
34547241 TT
1 TT
34547243 AAATTTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTATATTTTTAATTAAAATAA
Found at i:34547388 original size:31 final size:32
Alignment explanation
Indices: 34547335--34547394 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
34547325 TTTTTTTGAG
34547335 TTAAACTTGATTCTCAAACTTTT-AAAAACAA
1 TTAAACTTGATTCTCAAACTTTTGAAAAACAA
* *
34547366 TTAAATTTGACTT-TCAATCTTTTGAAAAA
1 TTAAACTTGA-TTCTCAAACTTTTGAAAAA
34547395 AAGTCGTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.40
Consensus pattern (32 bp):
TTAAACTTGATTCTCAAACTTTTGAAAAACAA
Found at i:34548442 original size:41 final size:41
Alignment explanation
Indices: 34548389--34548479 Score: 155
Period size: 41 Copynumber: 2.2 Consensus size: 41
34548379 TGTACATAAT
* *
34548389 TTATTTATGTGTCCATGCTATGTATCATAAAAATAATATAC
1 TTATTTACGTGTCCATGCTATGTATCATAAAAACAATATAC
34548430 TTATTTACGTGTCCATGCTATGTATCATAAAAACAATATAC
1 TTATTTACGTGTCCATGCTATGTATCATAAAAACAATATAC
34548471 TTAATTTAC
1 TT-ATTTAC
34548480 TTATTATAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 41 0.87
42 6 0.13
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (41 bp):
TTATTTACGTGTCCATGCTATGTATCATAAAAACAATATAC
Found at i:34556345 original size:8 final size:8
Alignment explanation
Indices: 34556332--34556361 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
34556322 TATATAACTA
34556332 ATTAAATG
1 ATTAAATG
34556340 ATTAAATG
1 ATTAAATG
34556348 ATTAAATG
1 ATTAAATG
34556356 ATTAAA
1 ATTAAA
34556362 AGAGTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (8 bp):
ATTAAATG
Found at i:34556369 original size:16 final size:16
Alignment explanation
Indices: 34556334--34556369 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
34556324 TATAACTAAT
* *
34556334 TAAATGATTAAATGAT
1 TAAATGATTAAAAGAG
34556350 TAAATGATTAAAAGAG
1 TAAATGATTAAAAGAG
34556366 TAAA
1 TAAA
34556370 AATATCTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.14, T:0.31
Consensus pattern (16 bp):
TAAATGATTAAAAGAG
Found at i:34569515 original size:80 final size:80
Alignment explanation
Indices: 34569374--34569523 Score: 228
Period size: 80 Copynumber: 1.9 Consensus size: 80
34569364 ATAAACCGAC
* * *
34569374 AATCCTGACACCCAGTGCCTAGCAGATAAACCGCGAAAGTGAGCCCAACTCTAGTCGGTTAAACT
1 AATCCTGACACCCAGTGCCTAGCAGATAAACCGCAAAAATGAGCCCAACTCTAGTCAGTTAAACT
34569439 GACAAATATTCGTTA
66 GACAAATATTCGTTA
* ** * *
34569454 AATCTTGACACCCAGTGCCTAGTGGATAAACCGTAAAAATGAGCCCAGCTCTAGTCAGTTAAACT
1 AATCCTGACACCCAGTGCCTAGCAGATAAACCGCAAAAATGAGCCCAACTCTAGTCAGTTAAACT
34569519 GACAA
66 GACAA
34569524 CATGAATAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 62 1.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (80 bp):
AATCCTGACACCCAGTGCCTAGCAGATAAACCGCAAAAATGAGCCCAACTCTAGTCAGTTAAACT
GACAAATATTCGTTA
Found at i:34574617 original size:30 final size:30
Alignment explanation
Indices: 34574577--34574680 Score: 86
Period size: 30 Copynumber: 3.4 Consensus size: 30
34574567 AAACAATGAA
* *
34574577 TTTAATTTAATTTAATATTA-AAATAATCAT
1 TTTAAATTAATTTAATATTATAAA-AATAAT
** *
34574607 TTTAAATTAATAAAATATTATTAAAATAAT
1 TTTAAATTAATTTAATATTATAAAAATAAT
* *
34574637 TATTAAATTAAATTTAATGTTAT-TAAATAAT
1 T-TTAAATT-AATTTAATATTATAAAAATAAT
*
34574668 TATTAAATAAATT
1 T-TTAAATTAATT
34574681 ATTTAAAATT
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
30 27 0.44
31 24 0.39
32 10 0.16
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (30 bp):
TTTAAATTAATTTAATATTATAAAAATAAT
Found at i:34574644 original size:11 final size:11
Alignment explanation
Indices: 34574619--34574683 Score: 57
Period size: 11 Copynumber: 6.0 Consensus size: 11
34574609 TAAATTAATA
34574619 AAAT-ATTATT
1 AAATAATTATT
34574629 AAAATAATTATT
1 -AAATAATTATT
34574641 AAATTAA--ATT
1 AAA-TAATTATT
* *
34574651 TAAT-GTTATT
1 AAATAATTATT
34574661 AAATAATTATT
1 AAATAATTATT
34574672 AAATAAATTATT
1 AAAT-AATTATT
34574684 TAAAATTTGC
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
9 1 0.02
10 11 0.25
11 16 0.36
12 16 0.36
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (11 bp):
AAATAATTATT
Found at i:34574646 original size:31 final size:32
Alignment explanation
Indices: 34574592--34574679 Score: 101
Period size: 31 Copynumber: 2.8 Consensus size: 32
34574582 TTTAATTTAA
*
34574592 TATTAAAATAATCATTTTAAATT-AATAAAATAT
1 TATTAAAATAAT--TATTAAATTAAATAAAATAT
** *
34574625 TATTAAAATAATTATTAAATTAAATTTAATGT
1 TATTAAAATAATTATTAAATTAAATAAAATAT
34574657 TATT-AAATAATTATTAAA-TAAAT
1 TATTAAAATAATTATTAAATTAAAT
34574680 TATTTAAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
30 5 0.10
31 22 0.44
32 11 0.22
33 12 0.24
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (32 bp):
TATTAAAATAATTATTAAATTAAATAAAATAT
Found at i:34574790 original size:222 final size:222
Alignment explanation
Indices: 34574472--34574896 Score: 751
Period size: 222 Copynumber: 1.9 Consensus size: 222
34574462 ATTAAATTTA
*
34574472 ATATTAAATTAATAAAATATTTATCTTGTAGATAAATATTAAATTAAATCTAATATTAAATGTTA
1 ATATTAAATTAATAAAACATTTATCTTGTAGATAAATATTAAATTAAATCTAATATTAAATGTTA
* *
34574537 TTAAATTAATAGAATATTTATCTAGAAGATAAACAATGAATTTAATTTAATTTAATATTAAAATA
66 TTAAATTAATAGAATATTTATCTACAAGATAAACAATGAATTAAATTTAATTTAATATTAAAATA
34574602 ATCATTTTAAATTAATAAAATATTATTAAAATAATTATTAAATTAAATTTAATGTTATTAAATAA
131 ATCATTTTAAATTAATAAAATATTATTAAAATAATTATTAAATTAAATTTAATGTTATTAAATAA
34574667 TTATTAAATAAATTATTTAAAATTTGC
196 TTATTAAATAAATTATTTAAAATTTGC
* * *
34574694 ATATTAAATTAATAGAACATTTATCTTGTAGATAAATATTAGATTAAATTTAATATTAAATGTTA
1 ATATTAAATTAATAAAACATTTATCTTGTAGATAAATATTAAATTAAATCTAATATTAAATGTTA
* *
34574759 TTAAATTAATAGAATATTTATCTACAAGATAAATATTGAATTAAATTTAATTTAATATTAAAATA
66 TTAAATTAATAGAATATTTATCTACAAGATAAACAATGAATTAAATTTAATTTAATATTAAAATA
* * *
34574824 ATCATTTTAAATTAATAAAATATTATTAAGATAATTATTAAATTTAATTTAATTTTATTAAATAA
131 ATCATTTTAAATTAATAAAATATTATTAAAATAATTATTAAATTAAATTTAATGTTATTAAATAA
34574889 TTATTAAA
196 TTATTAAA
34574897 ATTTGCATAT
Statistics
Matches: 192, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
222 192 1.00
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (222 bp):
ATATTAAATTAATAAAACATTTATCTTGTAGATAAATATTAAATTAAATCTAATATTAAATGTTA
TTAAATTAATAGAATATTTATCTACAAGATAAACAATGAATTAAATTTAATTTAATATTAAAATA
ATCATTTTAAATTAATAAAATATTATTAAAATAATTATTAAATTAAATTTAATGTTATTAAATAA
TTATTAAATAAATTATTTAAAATTTGC
Found at i:34574857 original size:67 final size:67
Alignment explanation
Indices: 34574697--34574889 Score: 179
Period size: 62 Copynumber: 2.9 Consensus size: 67
34574687 AATTTGCATA
* * ** * *
34574697 TTAAATTAATAGAACATTTATCTTGTAGATAAATATTAGATTAAATTTAA---TATTAAAT-GT-
1 TTAAATTAATAAAATATTTATC-TAAAGATAAATATTAAATTAAATTTAATTTTATTAAATAATC
*
34574757 -TA
65 ATT
* *
34574759 TTAAATTAATAGAATATTTATCTACAAGATAAATATTGAATTAAATTTAATTTAATATTAAAATA
1 TTAAATTAATAAAATATTTATCTA-AAGATAAATATTAAATTAAATTTAATTT--TATT-AAATA
34574824 ATCATT
62 ATCATT
* *
34574830 TTAAATTAATAAAATA-TTAT-T-AAGATAATTATTAAATTTAATTTAATTTTATTAAATAAT
1 TTAAATTAATAAAATATTTATCTAAAGATAAATATTAAATTAAATTTAATTTTATTAAATAAT
34574890 TATTAAAATT
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
61 1 0.01
62 43 0.39
64 7 0.06
65 4 0.04
67 29 0.26
68 4 0.04
69 2 0.02
70 4 0.04
71 16 0.15
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.45
Consensus pattern (67 bp):
TTAAATTAATAAAATATTTATCTAAAGATAAATATTAAATTAAATTTAATTTTATTAAATAATCA
TT
Found at i:34575572 original size:237 final size:237
Alignment explanation
Indices: 34575157--34576347 Score: 1999
Period size: 237 Copynumber: 5.0 Consensus size: 237
34575147 ACAAGGGAAC
34575157 AGTAAGAAGCATTCTCCCAACACCTCCCCTCCTTCTCAGCCCACCGTCGATCGCCCTAAAGCTCC
1 AGTAAGAAGCATTCTCCCAACACCTCCCCTCCTTCTCAGCCCACCGTCGATCGCCCTAAAGCTCC
* *
34575222 GGCCAAGAATCTCGTCATTGGTCAATTCAAGATCGCCATACGCGGCGAAGAGAAGCATGTGAGGT
66 GGCCGAGAATCTCGCCATTGGTCAATTCAAGATCGCCATACGCGGCGAAGAGAAGCATGTGAGGT
34575287 TCGGAAAGGAAAACGTTGATGTAAATGTACGTCCCACCGACAGCTTGAGTCCAAATCTCGTGTCT
131 TCGGAAAGGAAAACGTTGATGTAAATGTACGTCCCACCGACAGCTTGAGTCCAAATCTCGTGTCT
34575352 GTTCCGACCCAGCTCCAACCCACCGAGTCAGAAAACAGCGGA
196 GTTCCGACCCAGCTCCAACCCACCGAGTCAGAAAACAGCGGA
*
34575394 AGTAAGAAGCATTCTCCCAACACCTCCCCTCCTTCTCAGCCCACCGTCGTTCGCCCTAAAGCTCC
1 AGTAAGAAGCATTCTCCCAACACCTCCCCTCCTTCTCAGCCCACCGTCGATCGCCCTAAAGCTCC
* *
34575459 GGCCAAGAATCTCGTCATTGGTCAATTCAAGATCGCCATACGCGGCGAAGAGAAGCATGTGAGGT
66 GGCCGAGAATCTCGCCATTGGTCAATTCAAGATCGCCATACGCGGCGAAGAGAAGCATGTGAGGT
34575524 TCGGAAAGGAAAACGTTGATGTAAATGTACGTCCCACCGACAGCTTGAGTCCAAATCTCGTGTCT
131 TCGGAAAGGAAAACGTTGATGTAAATGTACGTCCCACCGACAGCTTGAGTCCAAATCTCGTGTCT
34575589 GTTCCGACCCAGCTCCAACCCACCGAGTCAGAAAACAGCGGA
196 GTTCCGACCCAGCTCCAACCCACCGAGTCAGAAAACAGCGGA
34575631 AGTAAGAAGCATTCTCCCAACACCTCCCCTCCTTCTCAGCCCACCGTCGATCGCCCTAAAGCTCC
1 AGTAAGAAGCATTCTCCCAACACCTCCCCTCCTTCTCAGCCCACCGTCGATCGCCCTAAAGCTCC
*
34575696 GGCCGAGAATCTCGCCTTTGGTCAATTCAAGATCGCCATACGCGGCGAAGAGAAGCATGTGAGGT
66 GGCCGAGAATCTCGCCATTGGTCAATTCAAGATCGCCATACGCGGCGAAGAGAAGCATGTGAGGT
34575761 TCGGAAAGGAAAACGTTGATGTAAATGTACGTCCCACCGACAGCTTGAGTCCAAATCTCGTGTCT
131 TCGGAAAGGAAAACGTTGATGTAAATGTACGTCCCACCGACAGCTTGAGTCCAAATCTCGTGTCT
34575826 GTTCCGACCCAGCTCCAACCCACCGAGTCAGAAAACAGCGGA
196 GTTCCGACCCAGCTCCAACCCACCGAGTCAGAAAACAGCGGA
* *
34575868 AGTAAGAAGCATTCTCCCAACACCTCCCCTCCTTCTCGGCCCACCGTCGATCGCCCTGAAGCTCC
1 AGTAAGAAGCATTCTCCCAACACCTCCCCTCCTTCTCAGCCCACCGTCGATCGCCCTAAAGCTCC
* * * * * * * *
34575933 GACCGAGAATCTCGCCATTGGTCAAATCAAGGTTGTCATA-GACGGCGAAGAGAAGTATTTCAGG
66 GGCCGAGAATCTCGCCATTGGTCAATTCAAGATCGCCATACG-CGGCGAAGAGAAGCATGTGAGG
* * * * ** *
34575997 TTCGAAAAGGAAAACGCTGATGTGAATGTAGGTCCCATTGACAGTTTGAGTCCAAATCTCGTGTC
130 TTCGGAAAGGAAAACGTTGATGTAAATGTACGTCCCACCGACAGCTTGAGTCCAAATCTCGTGTC
*
34576062 TGTTCCGACCCAGCTCCAACCCACCGAGTCAGAAAACAGCAGA
195 TGTTCCGACCCAGCTCCAACCCACCGAGTCAGAAAACAGCGGA
* *
34576105 AGTAAGAAGCATTCTCCCAACACCTCCCCTCCTTCTCGGCCCACCGTCGATCGCCCTGAAGCTCC
1 AGTAAGAAGCATTCTCCCAACACCTCCCCTCCTTCTCAGCCCACCGTCGATCGCCCTAAAGCTCC
* * * * * *
34576170 GGCCGAGAATCTCGCCATTGGTCAAATCAAGGTCGTCATA-GACGGCGAAGAGAAGTATTTCAGG
66 GGCCGAGAATCTCGCCATTGGTCAATTCAAGATCGCCATACG-CGGCGAAGAGAAGCATGTGAGG
* * * * ** *
34576234 TTCGAAAAGGAAAACGCTGATGTGAATGTAGGTCCCATTGACAGTTTGAGTCCAAATCTCGTGTC
130 TTCGGAAAGGAAAACGTTGATGTAAATGTACGTCCCACCGACAGCTTGAGTCCAAATCTCGTGTC
34576299 TGTTCCGACCCAGCTCCAACCCACCGAGTCAGAAAACAGCGGA
195 TGTTCCGACCCAGCTCCAACCCACCGAGTCAGAAAACAGCGGA
34576342 AGTAAG
1 AGTAAG
34576348 GTTGTGCCGG
Statistics
Matches: 926, Mismatches: 27, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
236 1 0.00
237 925 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (237 bp):
AGTAAGAAGCATTCTCCCAACACCTCCCCTCCTTCTCAGCCCACCGTCGATCGCCCTAAAGCTCC
GGCCGAGAATCTCGCCATTGGTCAATTCAAGATCGCCATACGCGGCGAAGAGAAGCATGTGAGGT
TCGGAAAGGAAAACGTTGATGTAAATGTACGTCCCACCGACAGCTTGAGTCCAAATCTCGTGTCT
GTTCCGACCCAGCTCCAACCCACCGAGTCAGAAAACAGCGGA
Found at i:34584722 original size:2 final size:2
Alignment explanation
Indices: 34584715--34584744 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
34584705 GTCCAAGTGT
34584715 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
34584745 AATATAGGTT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:34586533 original size:2 final size:2
Alignment explanation
Indices: 34586528--34586553 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
34586518 ATAAAAAAAG
34586528 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
34586554 TTTTTATTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34588533 original size:57 final size:58
Alignment explanation
Indices: 34588454--34588614 Score: 209
Period size: 58 Copynumber: 2.8 Consensus size: 58
34588444 TAAATGAGTA
* * * * *
34588454 ATTTACCTAAAGT-AAAAGTAAGTGTTTTAAACAGGGAGTGCCATTTGT-AGAAAAACT
1 ATTTACCCAAAATCAAAA-TAAGTGTTTTAAACAAGGAGTGCCACTTGTAAAAAAAACT
*
34588511 ATTTACCCAAAATCAAAATAAGTGTTTTAAACAAGGAGTGCCACTTGTAAAAAAAATT
1 ATTTACCCAAAATCAAAATAAGTGTTTTAAACAAGGAGTGCCACTTGTAAAAAAAACT
* * * *
34588569 ATTTATCCAAAATCAAAATAAGTGTTTTAAAAAAGAAGTGTCACTT
1 ATTTACCCAAAATCAAAATAAGTGTTTTAAACAAGGAGTGCCACTT
34588615 ATGATTAAAT
Statistics
Matches: 92, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
57 39 0.42
58 53 0.58
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (58 bp):
ATTTACCCAAAATCAAAATAAGTGTTTTAAACAAGGAGTGCCACTTGTAAAAAAAACT
Found at i:34589770 original size:71 final size:71
Alignment explanation
Indices: 34589659--34589813 Score: 215
Period size: 71 Copynumber: 2.2 Consensus size: 71
34589649 TTGACCGTCT
*
34589659 AATGGCCGACACCACCTGTCCAATGATTGATGTCAAACATAAAAAATTGTATTTTTTTGTGTTGA
1 AATGGCCGACACCACCTGTCCAATGATTGATGTCAAACATAAAAAATTGTATTTTTTGGTGTTGA
34589724 CCATGC
66 CCATGC
* * *
34589730 AATGGCCGACACCA-CT-TACTCAATGATTGGTGTCAGACATAAAAATTTGTATTTTTTGGTGTT
1 AATGGCCGACACCACCTGT-C-CAATGATTGATGTCAAACATAAAAAATTGTATTTTTTGGTGTT
**
34589793 GGTCATGC
64 GACCATGC
*
34589801 AATGGCCAACACC
1 AATGGCCGACACC
34589814 TATGTATTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
69 1 0.01
70 3 0.04
71 71 0.95
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Consensus pattern (71 bp):
AATGGCCGACACCACCTGTCCAATGATTGATGTCAAACATAAAAAATTGTATTTTTTGGTGTTGA
CCATGC
Found at i:34590061 original size:60 final size:59
Alignment explanation
Indices: 34589949--34590156 Score: 260
Period size: 59 Copynumber: 3.5 Consensus size: 59
34589939 CTTTTTGTCA
* *
34589949 AATAAAAAATTCAATTTTTTTGGTGTTGACCATGCCATGGCCGACACT-CCTTTTTATCTG
1 AATAAAAAA-TCAA-ATTTTTGGTGTTGGCCATGCCATGGCCGACACTCCCTTTTTATCTG
* *
34590009 AATAAAAATTCAAATTTTTGGATGTTGGCTATGCCATGGCCGACACTCCCTTTTTTATCTG
1 AATAAAAAATCAAATTTTTGG-TGTTGGCCATGCCATGGCCGACACTCCC-TTTTTATCTG
* * * * * *
34590070 -GTAAAAAATCAAATTTTTTTGTGTTGGCCATGCAATAGTCGACAC-CCCTTTTTATCTA
1 AATAAAAAATCAAA-TTTTTGGTGTTGGCCATGCCATGGCCGACACTCCCTTTTTATCTG
34590128 AATAAAAAATCAAATTTTTGGTGTTGGCC
1 AATAAAAAATCAAATTTTTGGTGTTGGCC
34590157 CTTTTTGTCA
Statistics
Matches: 129, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
58 30 0.23
59 42 0.33
60 41 0.32
61 16 0.12
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (59 bp):
AATAAAAAATCAAATTTTTGGTGTTGGCCATGCCATGGCCGACACTCCCTTTTTATCTG
Found at i:34591096 original size:17 final size:17
Alignment explanation
Indices: 34591076--34591130 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
34591066 AAAAAATAAT
*
34591076 AATTAGAATATACAGGA
1 AATTAGAATATATAGGA
34591093 AATTAGAA-AT-TA--A
1 AATTAGAATATATAGGA
*
34591106 AATTAAAATATATAGGA
1 AATTAGAATATATAGGA
34591123 AATTAGAA
1 AATTAGAA
34591131 ATTAAATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
13 8 0.26
14 2 0.06
15 3 0.10
16 2 0.06
17 16 0.52
ACGTcount: A:0.58, C:0.02, G:0.13, T:0.27
Consensus pattern (17 bp):
AATTAGAATATATAGGA
Found at i:34591110 original size:30 final size:30
Alignment explanation
Indices: 34591076--34591143 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
34591066 AAAAAATAAT
*
34591076 AATTAGAATATACAGGAAATTAGAAATTAA
1 AATTAAAATATACAGGAAATTAGAAATTAA
*
34591106 AATTAAAATATATAGGAAATTAGAAATTAA
1 AATTAAAATATACAGGAAATTAGAAATTAA
*
34591136 ATTTAAAA
1 AATTAAAA
34591144 AGGAAACGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.59, C:0.01, G:0.10, T:0.29
Consensus pattern (30 bp):
AATTAAAATATACAGGAAATTAGAAATTAA
Found at i:34591687 original size:36 final size:36
Alignment explanation
Indices: 34591647--34591729 Score: 139
Period size: 36 Copynumber: 2.3 Consensus size: 36
34591637 CGCAGGTTCG
34591647 TCCGCGGGCTCGTACTAGAGCTCGTCATTAGGCTCA
1 TCCGCGGGCTCGTACTAGAGCTCGTCATTAGGCTCA
* *
34591683 TCCGCGGGCTCGTACTCGGGCTCGTCATTAGGCTCA
1 TCCGCGGGCTCGTACTAGAGCTCGTCATTAGGCTCA
*
34591719 TCCTCGGGCTC
1 TCCGCGGGCTC
34591730 TGAATCTGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.12, C:0.34, G:0.29, T:0.25
Consensus pattern (36 bp):
TCCGCGGGCTCGTACTAGAGCTCGTCATTAGGCTCA
Found at i:34593456 original size:22 final size:22
Alignment explanation
Indices: 34593431--34593480 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
34593421 GGGGTGTTGG
* *
34593431 TGAGCTGCAATTTCAGTTTTGA
1 TGAGCTGAAATTTCAGTTTAGA
* **
34593453 TGAGTTGAAATTTTGGTTTAGA
1 TGAGCTGAAATTTCAGTTTAGA
34593475 TGAGCT
1 TGAGCT
34593481 TGAATTTGGG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.08, G:0.26, T:0.42
Consensus pattern (22 bp):
TGAGCTGAAATTTCAGTTTAGA
Found at i:34593811 original size:84 final size:84
Alignment explanation
Indices: 34593580--34593954 Score: 584
Period size: 80 Copynumber: 4.5 Consensus size: 84
34593570 TAAATTTAAA
* * *
34593580 ATTTGATAAAAATTGTAATATAATAATAATTTTTAATTTAAATATTCAAATTTGGTAAATAATAT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTCAAATTTGATAAATAATGT
34593645 ATTGTCAAATCAACACATT
66 ATTGTCAAATCAACACATT
*
34593664 A-TTGATAAAAATTGTAATATAATAAT-ATTTTTAATTTAAATATT-AAATTTGATAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTCAAATTTGATAAATAATGT
34593726 ATTGTCAAATCAACACATT
66 ATTGTCAAATCAACACATT
*
34593745 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTGATAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTCAAATTTGATAAATAATGT
34593810 ATTGTCAAATCAACACATT
66 ATTGTCAAATCAACACATT
*
34593829 ATTTGATAAAAATTATAATATAATAAT-A--TTTT-TTTAAATATTCAAATTTGATAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTCAAATTTGATAAATAATGT
*
34593890 ATTATCAAATCAACACATT
66 ATTGTCAAATCAACACATT
* * * *
34593909 ACTTGATATAAATCGAAATATAATAATAATCTTTTTTATTTAAATA
1 ATTTGATAAAAATTGTAATATAATAATAA--TTTTTTATTTAAATA
34593955 ATGTTAAATT
Statistics
Matches: 271, Mismatches: 11, Indels: 16
0.91 0.04 0.05
Matches are distributed among these distances:
80 68 0.25
81 41 0.15
82 43 0.16
83 43 0.16
84 64 0.24
85 4 0.01
86 8 0.03
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (84 bp):
ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTCAAATTTGATAAATAATGT
ATTGTCAAATCAACACATT
Found at i:34593915 original size:80 final size:83
Alignment explanation
Indices: 34593580--34593954 Score: 573
Period size: 84 Copynumber: 4.5 Consensus size: 83
34593570 TAAATTTAAA
* *
34593580 ATTTGATAAAAATTGTAATATAATAATAATTTTTAATTTAAATATTCAAATTTGGTAAATAATAT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTT-ATTTAAATATTCAAATTTGATAAATAATGT
34593645 ATTGTCAAATCAACACATT
65 ATTGTCAAATCAACACATT
34593664 A-TTGATAAAAATTGTAATATAATAAT-ATTTTTAATTTAAATATT-AAATTTGATAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTT-ATTTAAATATTCAAATTTGATAAATAATGT
34593726 ATTGTCAAATCAACACATT
65 ATTGTCAAATCAACACATT
*
34593745 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTGATAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAA-TTTTTATTTAAATATTCAAATTTGATAAATAATGT
34593810 ATTGTCAAATCAACACATT
65 ATTGTCAAATCAACACATT
*
34593829 ATTTGATAAAAATTATAATATAATAAT-A-TTTT-TTTAAATATTCAAATTTGATAAATAATGTA
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTATTTAAATATTCAAATTTGATAAATAATGTA
*
34593891 TTATCAAATCAACACATT
66 TTGTCAAATCAACACATT
* * * *
34593909 ACTTGATATAAATCGAAATATAATAATAATCTTTTTTATTTAAATA
1 ATTTGATAAAAATTGTAATATAATAATAA---TTTTTATTTAAATA
34593955 ATGTTAAATT
Statistics
Matches: 271, Mismatches: 10, Indels: 18
0.91 0.03 0.06
Matches are distributed among these distances:
80 68 0.25
81 41 0.15
82 43 0.16
83 38 0.14
84 69 0.25
85 4 0.01
86 8 0.03
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (83 bp):
ATTTGATAAAAATTGTAATATAATAATAATTTTTATTTAAATATTCAAATTTGATAAATAATGTA
TTGTCAAATCAACACATT
Found at i:34594126 original size:28 final size:28
Alignment explanation
Indices: 34594070--34594134 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 28
34594060 AACATGTACC
**
34594070 TTAATTTTCAAATTAATTTCAACTTAAA
1 TTAATTTTCAAATTAATTTCAACACAAA
* **
34594098 TTAATTTTCAAATTATTTTTTACACAAA
1 TTAATTTTCAAATTAATTTCAACACAAA
*
34594126 -TATTTTTCA
1 TTAATTTTCA
34594135 TGTATACTAG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
27 8 0.26
28 23 0.74
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (28 bp):
TTAATTTTCAAATTAATTTCAACACAAA
Found at i:34596044 original size:13 final size:13
Alignment explanation
Indices: 34596026--34596053 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
34596016 ACAACTAACT
34596026 TTAAGTTGTATTG
1 TTAAGTTGTATTG
34596039 TTAAGTTGTATTG
1 TTAAGTTGTATTG
34596052 TT
1 TT
34596054 TTATTGCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.57
Consensus pattern (13 bp):
TTAAGTTGTATTG
Found at i:34597125 original size:11 final size:12
Alignment explanation
Indices: 34597082--34597129 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 12
34597072 TTATTTTCGT
*
34597082 TTATTTCTTAAAA
1 TTATTT-TTAATA
*
34597095 TTAATTTTAATTA
1 TTATTTTTAA-TA
34597108 TTATTTTTAATA
1 TTATTTTTAATA
34597120 -TATTTTTAAT
1 TTATTTTTAAT
34597130 TTGTCGATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
11 10 0.32
12 6 0.19
13 15 0.48
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATTTTTAATA
Found at i:34598156 original size:58 final size:58
Alignment explanation
Indices: 34597857--34598184 Score: 229
Period size: 59 Copynumber: 5.6 Consensus size: 58
34597847 AGGGAAAGTT
* *
34597857 GGTGTCGACCATTGCATGGCCAACACAAAAAAATTGA-TTTTTTACCAGATAAAAAAG
1 GGTGTCGACCATTGCATGGCCAACACAAAAAATTTGATTTTTTTATCAGATAAAAAAG
* * * * * * *
34597914 TGAGTGTCGGCCA-TGCAATGACCAATACCAAAAA-TTCATTTTTTTATCTGACAAAAAGAG
1 -G-GTGTCGACCATTGC-ATGGCCAACACAAAAAATTTGATTTTTTTATCAGATAAAAA-AG
* * * * * * *
34597974 GGTGTCGATCATGGCATGACCAACACCCATAAATTTGA-ATTTTTATTCAGATAAAAAAA
1 GGTGTCGACCATTGCATGGCCAACA-CAAAAAATTTGATTTTTTTA-TCAGATAAAAAAG
* * * * ***
34598033 GGTGTCGGCCA-TGCAATGGTCAATACCAAAAAAATTTGAAATTTTTTTATCTGA-AAATGGG
1 GGTGTCGACCATTGC-ATGGCCAACA-C-AAAAAATTTG--ATTTTTTTATCAGATAAAAAAG
* *
34598094 GGTGTCGACCATTACATGGCCAACACAAAATAATTTGATTTTTTTATCAG-TAAATAAG
1 GGTGTCGACCATTGCATGGCCAACACAAAA-AATTTGATTTTTTTATCAGATAAAAAAG
** * *
34598152 GGTGTCGGTCATGGCATGACCAACACCAAAAAA
1 GGTGTCGACCATTGCATGGCCAACA-CAAAAAA
34598185 ATTAAACTTT
Statistics
Matches: 209, Mismatches: 44, Indels: 34
0.73 0.15 0.12
Matches are distributed among these distances:
58 65 0.31
59 81 0.39
60 29 0.14
61 21 0.10
62 7 0.03
63 6 0.03
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (58 bp):
GGTGTCGACCATTGCATGGCCAACACAAAAAATTTGATTTTTTTATCAGATAAAAAAG
Found at i:34598196 original size:58 final size:58
Alignment explanation
Indices: 34597857--34598199 Score: 189
Period size: 58 Copynumber: 5.8 Consensus size: 58
34597847 AGGGAAAGTT
* * * * *
34597857 GGTGTCGACCATTGCATGGCCAACA-CAAAAAAATT-GATTTTTTACCAGATAAAAAAG
1 GGTGTCGACCATGGCATGACCAACACCAAAAAAATTAAATTTTTTATCAG-TAAATAAG
* * * * * * *
34597914 TGAGTGTCGGCCAT-GCAATGACCAATACC--AAAAATTCATTTTTTTATCTGACAAAAAGAG
1 -G-GTGTCGACCATGGC-ATGACCAACACCAAAAAAATTAAATTTTTTATCAG-TAAATA-AG
* * * * * * *
34597974 GGTGTCGATCATGGCATGACCAACACCCATAAATTTGAA-TTTTTATTCAGATAAAAAAA
1 GGTGTCGACCATGGCATGACCAACACCAAAAAAATTAAATTTTTTA-TCAG-TAAATAAG
* ** * * * **
34598033 GGTGTCGGCCAT-GCAATGGTCAATACCAAAAAAATTTGAAATTTTTTTATCTGAAAATGGG
1 GGTGTCGACCATGGC-ATGACCAACACCAAAAAAA-TT-AAA-TTTTTTATCAGTAAATAAG
** * * * *
34598094 GGTGTCGACCATTACATGGCCAACA-CAAAATAATTTGATTTTTTTATCAGTAAATAAG
1 GGTGTCGACCATGGCATGACCAACACCAAAA-AAATTAAATTTTTTATCAGTAAATAAG
** *
34598152 GGTGTCGGTCATGGCATGACCAACACCAAAAAAATTAAACTTTTTATC
1 GGTGTCGACCATGGCATGACCAACACCAAAAAAATTAAATTTTTTATC
34598200 TGACAAATTT
Statistics
Matches: 215, Mismatches: 53, Indels: 34
0.71 0.18 0.11
Matches are distributed among these distances:
58 80 0.37
59 72 0.33
60 27 0.13
61 26 0.12
62 4 0.02
63 6 0.03
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (58 bp):
GGTGTCGACCATGGCATGACCAACACCAAAAAAATTAAATTTTTTATCAGTAAATAAG
Found at i:34605949 original size:30 final size:29
Alignment explanation
Indices: 34605913--34605977 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
34605903 ATAATTTATA
*
34605913 AAAATTGGATC-AAATTAAAATTTCATGTAT
1 AAAATTGGA-CAAAATCAAAA-TTCATGTAT
*
34605943 AAAATTGTACAAAATCAAAATTCATGTAT
1 AAAATTGGACAAAATCAAAATTCATGTAT
*
34605972 ACAATT
1 AAAATT
34605978 ACACATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 15 0.48
30 16 0.52
ACGTcount: A:0.49, C:0.09, G:0.08, T:0.34
Consensus pattern (29 bp):
AAAATTGGACAAAATCAAAATTCATGTAT
Found at i:34621794 original size:16 final size:16
Alignment explanation
Indices: 34621764--34621793 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
34621754 TTTCATTAGT
34621764 TATGATATAATTTTTG
1 TATGATATAATTTTTG
34621780 TATGA-ATAATTTTT
1 TATGATATAATTTTT
34621794 TTTTACATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (16 bp):
TATGATATAATTTTTG
Found at i:34626995 original size:3 final size:3
Alignment explanation
Indices: 34626987--34627032 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
34626977 ATTCCAACCC
34626987 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
34627033 GGTCCCCCAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:34628955 original size:12 final size:12
Alignment explanation
Indices: 34628938--34628963 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
34628928 GCGTGTAAGG
34628938 CATGAACTCAAA
1 CATGAACTCAAA
34628950 CATGAACTCAAA
1 CATGAACTCAAA
34628962 CA
1 CA
34628964 GGGTTACAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.27, G:0.08, T:0.15
Consensus pattern (12 bp):
CATGAACTCAAA
Found at i:34630323 original size:31 final size:31
Alignment explanation
Indices: 34630287--34630349 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
34630277 ATCACTAAAT
34630287 TATTCAAAGATTTTCATTTAAATCATTCAAC
1 TATTCAAAGATTTTCATTTAAATCATTCAAC
* * * *
34630318 TATTCAATGATTTTTATTTAAGTCATTGAAC
1 TATTCAAAGATTTTCATTTAAATCATTCAAC
34630349 T
1 T
34630350 GTTAAGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (31 bp):
TATTCAAAGATTTTCATTTAAATCATTCAAC
Found at i:34638605 original size:28 final size:28
Alignment explanation
Indices: 34638559--34638613 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
34638549 AAGGTGAATT
* *
34638559 ATTTTTATTAATAAAATATTTATATTTA
1 ATTTTAATTAATAAAATATTTAAATTTA
34638587 ATTTTAATT-ATAAATATATTTAAATTT
1 ATTTTAATTAATAAA-ATATTTAAATTT
34638614 TAAATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
ATTTTAATTAATAAAATATTTAAATTTA
Found at i:34638621 original size:28 final size:27
Alignment explanation
Indices: 34638569--34638621 Score: 63
Period size: 28 Copynumber: 1.9 Consensus size: 27
34638559 ATTTTTATTA
* *
34638569 ATAAAATATTTATATTTAATTTTAATT
1 ATAAAATATTTAAATTTAATATTAATT
34638596 ATAAATATATTTAAATTTTAA-ATTAA
1 ATAAA-ATATTTAAA-TTTAATATTAA
34638622 AAAAATTGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 5 0.23
28 12 0.55
29 5 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
ATAAAATATTTAAATTTAATATTAATT
Found at i:34638622 original size:22 final size:22
Alignment explanation
Indices: 34638579--34638622 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
34638569 ATAAAATATT
*
34638579 TATATTTAATTTTAATTATAAA
1 TATATTTAATTTTAAATATAAA
34638601 TATATTTAAATTTTAAAT-TAAA
1 TATATTT-AATTTTAAATATAAA
34638623 AAAATTGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TATATTTAATTTTAAATATAAA
Found at i:34655911 original size:15 final size:15
Alignment explanation
Indices: 34655886--34655920 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
34655876 TAACATTTTT
34655886 TTAAA-AAAATATTA
1 TTAAACAAAATATTA
*
34655900 TTAAACAAAATATTT
1 TTAAACAAAATATTA
34655915 TTAAAC
1 TTAAAC
34655921 TTTTTCAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (15 bp):
TTAAACAAAATATTA
Found at i:34660254 original size:24 final size:24
Alignment explanation
Indices: 34660227--34660285 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 24
34660217 ATGACAATGA
34660227 TGATGAGGAAGATGAAGCA-GCAGG
1 TGATGAGGAAGATGAAG-ATGCAGG
*
34660251 TGAT---CAAGATGAAGATGCAGG
1 TGATGAGGAAGATGAAGATGCAGG
*
34660272 TGAGGAGGAAGATG
1 TGATGAGGAAGATG
34660286 GATCAGGTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
20 1 0.04
21 17 0.61
24 10 0.36
ACGTcount: A:0.37, C:0.07, G:0.41, T:0.15
Consensus pattern (24 bp):
TGATGAGGAAGATGAAGATGCAGG
Found at i:34660259 original size:21 final size:21
Alignment explanation
Indices: 34660235--34660274 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
34660225 GATGATGAGG
34660235 AAGATGAAGCA-GCAGGTGATC
1 AAGATGAAG-ATGCAGGTGATC
34660256 AAGATGAAGATGCAGGTGA
1 AAGATGAAGATGCAGGTGA
34660275 GGAGGAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.40, C:0.10, G:0.35, T:0.15
Consensus pattern (21 bp):
AAGATGAAGATGCAGGTGATC
Found at i:34660396 original size:3 final size:3
Alignment explanation
Indices: 34660390--34660423 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
34660380 CGACAACGAA
*
34660390 GAT GAT GAT GAC GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
34660424 GGGAGGAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.35, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:34660449 original size:18 final size:18
Alignment explanation
Indices: 34660426--34660469 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
34660416 TGATGATGGG
34660426 GAGGAAG-GTGAAGAAGAA
1 GAGGAAGAG-GAAGAAGAA
*
34660444 GAGGAAGAGGAGGAAGAA
1 GAGGAAGAGGAAGAAGAA
*
34660462 GATGAAGA
1 GAGGAAGA
34660470 AGAGGAAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.45, T:0.05
Consensus pattern (18 bp):
GAGGAAGAGGAAGAAGAA
Found at i:34660450 original size:9 final size:9
Alignment explanation
Indices: 34660438--34660478 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
34660428 GGAAGGTGAA
34660438 GAAGAAGAG
1 GAAGAAGAG
*
34660447 GAAGAGGAG
1 GAAGAAGAG
*
34660456 GAAGAAGAT
1 GAAGAAGAG
34660465 GAAGAAGAG
1 GAAGAAGAG
34660474 GAAGA
1 GAAGA
34660479 GCTTCAGCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.54, C:0.00, G:0.44, T:0.02
Consensus pattern (9 bp):
GAAGAAGAG
Found at i:34662208 original size:9 final size:9
Alignment explanation
Indices: 34662196--34662238 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
34662186 TTCCTAGATT
34662196 TTTTTATAA
1 TTTTTATAA
*
34662205 TTTTTAAAA
1 TTTTTATAA
34662214 TTTTTAATGAA
1 TTTTT-AT-AA
*
34662225 ATTTTATAA
1 TTTTTATAA
34662234 TTTTT
1 TTTTT
34662239 TTTATAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
9 19 0.68
10 3 0.11
11 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:34662216 original size:20 final size:21
Alignment explanation
Indices: 34662193--34662246 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
34662183 AATTTCCTAG
34662193 ATTTTTTTATAATTTTTA-AA
1 ATTTTTTTATAATTTTTATAA
* *
34662213 A-TTTTTAATGAAATTTTATAA
1 ATTTTTTTAT-AATTTTTATAA
*
34662234 TTTTTTTTATAAT
1 ATTTTTTTATAAT
34662247 ATACTCATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
19 7 0.27
20 8 0.31
21 4 0.15
22 7 0.27
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
ATTTTTTTATAATTTTTATAA
Found at i:34670445 original size:33 final size:33
Alignment explanation
Indices: 34670408--34670472 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
34670398 TTAACAATCA
34670408 ATATGAAAACATACGATGGGTTAATGAAATTAT
1 ATATGAAAACATACGATGGGTTAATGAAATTAT
*
34670441 ATATGAAAACATACGATTGGTTAATGAAATTA
1 ATATGAAAACATACGATGGGTTAATGAAATTA
34670473 AATCGAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.46, C:0.06, G:0.17, T:0.31
Consensus pattern (33 bp):
ATATGAAAACATACGATGGGTTAATGAAATTAT
Found at i:34675424 original size:21 final size:21
Alignment explanation
Indices: 34675378--34675428 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
34675368 TATCAACTCC
*
34675378 TTAACTTTATCCGTAATTGAA
1 TTAAATTTATCCGTAATTGAA
* *
34675399 ATAAATTTA-CCGTAATTAGTA
1 TTAAATTTATCCGTAATT-GAA
34675420 TTAAATTTA
1 TTAAATTTA
34675429 AATTTTTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (21 bp):
TTAAATTTATCCGTAATTGAA
Found at i:34676948 original size:25 final size:23
Alignment explanation
Indices: 34676919--34676964 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
34676909 GTTGGATCCA
34676919 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
34676944 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
34676965 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Done.