Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005844.1 Hibiscus syriacus cultivar Beakdansim tig00013712_pilon, 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: 151518
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4459 original size:32 final size:32
Alignment explanation
Indices: 4423--4499 Score: 127
Period size: 33 Copynumber: 2.4 Consensus size: 32
4413 ACAAAGTTTA
*
4423 CGATAATTGAAATACTTAAATACTTCCAAGTT
1 CGATAATTGAAATACTTAAAAACTTCCAAGTT
*
4455 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGAT-AATTGAAATACTTAAAAACTTCCAAGTT
4488 CGATAATTGAAA
1 CGATAATTGAAA
4500 CAAAGTTTAC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 11 0.27
33 30 0.73
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (32 bp):
CGATAATTGAAATACTTAAAAACTTCCAAGTT
Found at i:4513 original size:21 final size:21
Alignment explanation
Indices: 4488--4529 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
4478 CTTCCAAGTT
4488 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
4509 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
4530 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:12278 original size:40 final size:39
Alignment explanation
Indices: 12234--12363 Score: 100
Period size: 40 Copynumber: 3.4 Consensus size: 39
12224 CGGGGAAACA
12234 ATAGTGGCGTTTTTTGACAAACGCTGCAATAAGTCCATCT
1 ATAGTGGCGTTTTTTGACAAACGCTGCAATAA-TCCATCT
* *
12274 ATAGTAGCGTTTTTTCAATCAAAC-C-GC---AA--CA---
1 ATAGTGGCGTTTTTT-GA-CAAACGCTGCAATAATCCATCT
*
12305 ATAGTGGCGTTTTTTTTGAAAAACGCTGCAATAAATCCATCT
1 ATAGTGGCG--TTTTTTGACAAACGCTGCAAT-AATCCATCT
*
12347 ATAGTGGCGTTTATTGA
1 ATAGTGGCGTTTTTTGA
12364 AAAAACGCCA
Statistics
Matches: 69, Mismatches: 6, Indels: 30
0.66 0.06 0.29
Matches are distributed among these distances:
31 12 0.17
32 2 0.03
33 8 0.12
34 2 0.03
37 4 0.06
39 2 0.03
40 23 0.33
41 2 0.03
42 14 0.20
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (39 bp):
ATAGTGGCGTTTTTTGACAAACGCTGCAATAATCCATCT
Found at i:12392 original size:73 final size:72
Alignment explanation
Indices: 12230--12371 Score: 182
Period size: 73 Copynumber: 2.0 Consensus size: 72
12220 ATTTCGGGGA
* * * *
12230 AACAATAGTGGCG--TTTTTTGACAAACGCTGCAATAAGTCCATCTATAGTAGCGTTTTTTCAAT
1 AACAATAGTGACGTTTTTTTTGAAAAACGCTGCAATAAATCCATCTATAGTAGCGTTTATTCAA-
*
12293 CAAACCGC
65 CAAAACGC
* * *
12301 AACAATAGTGGCGTTTTTTTTGAAAAACGCTGCAATAAATCCATCTATAGTGGCGTTTATTGAA-
1 AACAATAGTGACGTTTTTTTTGAAAAACGCTGCAATAAATCCATCTATAGTAGCGTTTATTCAAC
12365 AAAACGC
66 AAAACGC
12372 CACTATAGAT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
71 19 0.30
73 44 0.70
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (72 bp):
AACAATAGTGACGTTTTTTTTGAAAAACGCTGCAATAAATCCATCTATAGTAGCGTTTATTCAAC
AAAACGC
Found at i:15446 original size:391 final size:391
Alignment explanation
Indices: 14720--15502 Score: 1467
Period size: 391 Copynumber: 2.0 Consensus size: 391
14710 TCTCCTAGAG
*
14720 AGCACACATCATAAAGAGAAGATCTCACGCAACTATACTCTAATTTAAAGATTCTGAGACTCTAC
1 AGCACACATCATAAAGAGAAGATCTCACGCAACTACACTCTAATTTAAAGATTCTGAGACTCTAC
**
14785 GTCTTGCACTCACTAACGTTTACCACCATTGAGCTATCTGATGACAACTAGCGCTAATTAATCGA
66 GTCTTGCACTCACTAACACTTACCACCATTGAGCTATCTGATGACAACTAGCGCTAATTAATCGA
14850 CCCTTAAGGTACTTAATCTCCTTTAGTCTCAGGTACTAAAATCCACGGTATTACACAATGTTGTA
131 CCCTTAAGGTACTTAATCTCCTTTAGTCTCAGGTACTAAAATCCACGGTATTACACAATGTTGTA
*
14915 AACTATTATGTGTTGTATATAGCTCGTTCTTATATATCAACACGAAAATAACAATGACGAAGTTT
196 AACTATTATGTGCTGTATATAGCTCGTTCTTATATATCAACACGAAAATAACAATGACGAAGTTT
14980 AGGGTCAAAAACTCAAACTCTTACTTAATCACATATACATAATTTATGGTGTAATCTGAAGTCAA
261 AGGGTCAAAAACTCAAACTCTTACTTAATCACATATACATAATTTATGGTGTAATCTGAAGTCAA
15045 ACAACATCCCAAGACTTACACCTTACAATTCTACTAATGAAGTTACCTTGGATGAGACCTAAACA
326 ACAACATCCCAAGACTTACACCTTACAATTCTACTAATGAAGTTACCTTGGATGAGACCTAAACA
15110 C
391 C
* *
15111 AGCACACATCATAAAGAGAATATCTCACGCAACTGCACTCTAATTTAAAGATTCTGAGACTCTAC
1 AGCACACATCATAAAGAGAAGATCTCACGCAACTACACTCTAATTTAAAGATTCTGAGACTCTAC
15176 GTCTTGCACTCACTAACACTTACCACCATTGAGCTATCTGATGACAACTAGCGCTAATTAATCGA
66 GTCTTGCACTCACTAACACTTACCACCATTGAGCTATCTGATGACAACTAGCGCTAATTAATCGA
*
15241 CCCTTAAGGTACTTAATCTCTTTTAGTCTCAGGTACTAAAATCCACGGTATTACACAATGTTGTA
131 CCCTTAAGGTACTTAATCTCCTTTAGTCTCAGGTACTAAAATCCACGGTATTACACAATGTTGTA
*
15306 AACTATTATGTGCTGTATATAGCTCGTTCTTATATATCAACACGAAAATAACAATGATGAAGTTT
196 AACTATTATGTGCTGTATATAGCTCGTTCTTATATATCAACACGAAAATAACAATGACGAAGTTT
*
15371 AGGGTCGAAAACTCAAACTCTTACTTAATCACATATACATAATTTATGGTGTAATCTGAAGTCAA
261 AGGGTCAAAAACTCAAACTCTTACTTAATCACATATACATAATTTATGGTGTAATCTGAAGTCAA
**
15436 ACGGCATCCCAAGACTTACACCTTACAATTCTACTAATGAAGTTACCTTGGATGAGACCTAAACA
326 ACAACATCCCAAGACTTACACCTTACAATTCTACTAATGAAGTTACCTTGGATGAGACCTAAACA
15501 C
391 C
15502 A
1 A
15503 CTCACTTTTG
Statistics
Matches: 381, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
391 381 1.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (391 bp):
AGCACACATCATAAAGAGAAGATCTCACGCAACTACACTCTAATTTAAAGATTCTGAGACTCTAC
GTCTTGCACTCACTAACACTTACCACCATTGAGCTATCTGATGACAACTAGCGCTAATTAATCGA
CCCTTAAGGTACTTAATCTCCTTTAGTCTCAGGTACTAAAATCCACGGTATTACACAATGTTGTA
AACTATTATGTGCTGTATATAGCTCGTTCTTATATATCAACACGAAAATAACAATGACGAAGTTT
AGGGTCAAAAACTCAAACTCTTACTTAATCACATATACATAATTTATGGTGTAATCTGAAGTCAA
ACAACATCCCAAGACTTACACCTTACAATTCTACTAATGAAGTTACCTTGGATGAGACCTAAACA
C
Found at i:17725 original size:46 final size:45
Alignment explanation
Indices: 17644--17731 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 45
17634 AACATATCTC
17644 AAATACCTCAGGCGAGGTCCAGGTCACACAACATCGACACCTCCT
1 AAATACCTCAGGCGAGGTCCAGGTCACACAACATCGACACCTCCT
* * * * *
17689 AAATACCTTTAGGCTAGGTCCAGGTCATATAGCATCGACACCT
1 AAATACC-TCAGGCGAGGTCCAGGTCACACAACATCGACACCT
17732 TACTTGGCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 7 0.19
46 30 0.81
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (45 bp):
AAATACCTCAGGCGAGGTCCAGGTCACACAACATCGACACCTCCT
Found at i:27206 original size:20 final size:20
Alignment explanation
Indices: 27181--27218 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
27171 ATTCATCCTA
*
27181 GTTCATCCAGTATCGATATT
1 GTTCATCCAATATCGATATT
27201 GTTCATCCAATATCGATA
1 GTTCATCCAATATCGATA
27219 CTAGAACCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (20 bp):
GTTCATCCAATATCGATATT
Found at i:27800 original size:19 final size:19
Alignment explanation
Indices: 27776--27827 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
27766 ATTGCATTTT
27776 ATGCATCGATGCACACACC
1 ATGCATCGATGCACACACC
27795 ATGCATCGATGCACACACC
1 ATGCATCGATGCACACACC
27814 ATGCATCGATGCAC
1 ATGCATCGATGCAC
27828 TTAGGCTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.31, C:0.35, G:0.17, T:0.17
Consensus pattern (19 bp):
ATGCATCGATGCACACACC
Found at i:27801 original size:84 final size:83
Alignment explanation
Indices: 27711--27872 Score: 243
Period size: 83 Copynumber: 1.9 Consensus size: 83
27701 AATGCAGTTT
* * * *
27711 ATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGTTTTAATGAAAACATCGATTGCATTTT
1 ATGCATCGATGCACACACCATGCATCGATGCACTCAGG-CTTAATGAAAACATCGAATGCATTTT
*
27776 ATGCATCGATGCACACACC
65 ATACATCGATGCACACACC
* * *
27795 ATGCATCGATGCACACACCATGCATCGATGCACTTAGGCTTATTTAAAACATCGAATGCATTTTA
1 ATGCATCGATGCACACACCATGCATCGATGCACTCAGGCTTAATGAAAACATCGAATGCATTTTA
27860 TACATCGATGCAC
66 TACATCGATGCAC
27873 TAAGTGTTCC
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
83 35 0.50
84 35 0.50
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.28
Consensus pattern (83 bp):
ATGCATCGATGCACACACCATGCATCGATGCACTCAGGCTTAATGAAAACATCGAATGCATTTTA
TACATCGATGCACACACC
Found at i:36570 original size:20 final size:20
Alignment explanation
Indices: 36533--36571 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
36523 AGATTGAGTA
* * *
36533 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
36553 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
36572 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:36757 original size:21 final size:21
Alignment explanation
Indices: 36731--36770 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
36721 CAGAACCCCA
*
36731 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
36752 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
36771 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:45256 original size:16 final size:16
Alignment explanation
Indices: 45235--45268 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
45225 ATTTAACAAA
*
45235 AAGGGGGAGAAGTTTT
1 AAGGGGGAGAAGTGTT
45251 AAGGGGGAGAAGTGTT
1 AAGGGGGAGAAGTGTT
45267 AA
1 AA
45269 AGTAAGGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.44, T:0.21
Consensus pattern (16 bp):
AAGGGGGAGAAGTGTT
Found at i:45627 original size:20 final size:20
Alignment explanation
Indices: 45598--45655 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
45588 TTTCAAGGGA
*
45598 ATGCACCGATGCACCAATCC
1 ATGCATCGATGCACCAATCC
45618 ATGCATCGATGCACCAATCC
1 ATGCATCGATGCACCAATCC
45638 ATGCATCGATGCACCAAT
1 ATGCATCGATGCACCAAT
45656 GAATAAATTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.31, C:0.34, G:0.16, T:0.19
Consensus pattern (20 bp):
ATGCATCGATGCACCAATCC
Found at i:53195 original size:31 final size:32
Alignment explanation
Indices: 53141--53220 Score: 112
Period size: 31 Copynumber: 2.6 Consensus size: 32
53131 TAGTTTATCC
*
53141 ATTAATA-TTTAACT-AAAGTTTAAGGATCAA
1 ATTAATATTTTACCTAAAAGTTTAAGGATCAA
*
53171 ATTGATATTTTACCTAAAAG-TTAAGGATCAA
1 ATTAATATTTTACCTAAAAGTTTAAGGATCAA
*
53202 ATTAATATTTTATCTAAAA
1 ATTAATATTTTACCTAAAA
53221 TATAATGTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
30 6 0.14
31 34 0.77
32 4 0.09
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (32 bp):
ATTAATATTTTACCTAAAAGTTTAAGGATCAA
Found at i:86778 original size:13 final size:12
Alignment explanation
Indices: 86746--86779 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
86736 AATTTCGTTA
*
86746 TATTTTTATTTT
1 TATTTTTTTTTT
*
86758 TATTTTTTCTTT
1 TATTTTTTTTTT
86770 TATTTTTTTT
1 TATTTTTTTT
86780 CCGATTAAGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (12 bp):
TATTTTTTTTTT
Found at i:91725 original size:31 final size:31
Alignment explanation
Indices: 91690--91751 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
91680 TAAAATCATT
91690 CCAGCACTGATTTTTGCACAAAAAAAAAAAC
1 CCAGCACTGATTTTTGCACAAAAAAAAAAAC
91721 CCAGCACTGATTTTTGCACAAAAAAAAAAAC
1 CCAGCACTGATTTTTGCACAAAAAAAAAAAC
91752 AGAAAAACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.48, C:0.23, G:0.10, T:0.19
Consensus pattern (31 bp):
CCAGCACTGATTTTTGCACAAAAAAAAAAAC
Found at i:92466 original size:22 final size:20
Alignment explanation
Indices: 92428--92467 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
92418 ATCACTACAA
92428 AAATTTGAAATTTTAATATT
1 AAATTTGAAATTTTAATATT
92448 AAATTTAGAAATGTTTAATA
1 AAATTT-GAAAT-TTTAATA
92468 AATTATGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 5 0.28
22 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
AAATTTGAAATTTTAATATT
Found at i:95163 original size:2 final size:2
Alignment explanation
Indices: 95156--95196 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
95146 ATCATTAAAG
95156 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
95197 GTTAGTATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:95720 original size:15 final size:16
Alignment explanation
Indices: 95700--95741 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
95690 TAATTATTTT
*
95700 TATTTTCTTTTTA-AA
1 TATTTTATTTTTATAA
*
95715 TATTTTAATTTTATAA
1 TATTTTATTTTTATAA
95731 TATTTTATTTT
1 TATTTTATTTT
95742 AAAGTAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (16 bp):
TATTTTATTTTTATAA
Found at i:95742 original size:15 final size:15
Alignment explanation
Indices: 95708--95744 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
95698 TTTATTTTCT
95708 TTTTAAATATTTTAA
1 TTTTAAATATTTTAA
95723 TTTTATAATATTTT-A
1 TTTTA-AATATTTTAA
95738 TTTTAAA
1 TTTTAAA
95745 GTAAAATGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.10
15 11 0.52
16 8 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTAAATATTTTAA
Found at i:98624 original size:25 final size:26
Alignment explanation
Indices: 98572--98624 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
98562 ATTAAGGTTG
* * **
98572 TTTTTAAAATATAATAATTTTTTTAA
1 TTTTTAAAAAATAATAATTCTTAAAA
98598 TTTTTAAAAAATAA-AATTCTTAAAA
1 TTTTTAAAAAATAATAATTCTTAAAA
98623 TT
1 TT
98625 ATCAAAACGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (26 bp):
TTTTTAAAAAATAATAATTCTTAAAA
Found at i:100283 original size:5 final size:5
Alignment explanation
Indices: 100260--100368 Score: 186
Period size: 5 Copynumber: 21.8 Consensus size: 5
100250 TAATATAAAT
100260 ATATG -TATG ATGAATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
1 ATATG ATATG AT--ATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
100311 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
100361 ATAT- ATAT
1 ATATG ATAT
100369 ATAAGTAATT
Statistics
Matches: 101, Mismatches: 0, Indels: 7
0.94 0.00 0.06
Matches are distributed among these distances:
4 8 0.08
5 88 0.87
7 5 0.05
ACGTcount: A:0.40, C:0.00, G:0.19, T:0.40
Consensus pattern (5 bp):
ATATG
Found at i:100503 original size:19 final size:20
Alignment explanation
Indices: 100469--100506 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
100459 ACATATAAAT
100469 ATATATATGCATGCATGTAC
1 ATATATATGCATGCATGTAC
*
100489 ATATGTATG-ATGCATGTA
1 ATATATATGCATGCATGTA
100507 TATACATACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (20 bp):
ATATATATGCATGCATGTAC
Found at i:100512 original size:23 final size:22
Alignment explanation
Indices: 100446--100522 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
100436 AACATAAGTG
* * *
100446 TATATATAAGCATACATATAAA
1 TATATATATGCATGCATATACA
*
100468 TATATATATGCATGCATGTACA
1 TATATATATGCATGCATATACA
* *
100490 TATGTATGATGCATGTATATACA
1 TATATAT-ATGCATGCATATACA
100513 TACT-TATATG
1 TA-TATATATG
100523 TATATATATG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
22 27 0.59
23 18 0.39
24 1 0.02
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (22 bp):
TATATATATGCATGCATATACA
Found at i:101801 original size:16 final size:16
Alignment explanation
Indices: 101777--101807 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
101767 TTAATTATAG
*
101777 GTCATGTTCATAACAT
1 GTCAGGTTCATAACAT
101793 GTCAGGTTCATAACA
1 GTCAGGTTCATAACA
101808 GGTCGGGTAA
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:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (16 bp):
GTCAGGTTCATAACAT
Found at i:104702 original size:24 final size:24
Alignment explanation
Indices: 104624--104712 Score: 96
Period size: 23 Copynumber: 3.8 Consensus size: 24
104614 ACATATTATA
*
104624 TGGCACTACGGTGC-AATTCTACG
1 TGGCACTTCGGTGCAAATTCTACG
* *
104647 TGGCACTTTGGTGC-ATTTCTACG
1 TGGCACTTCGGTGCAAATTCTACG
*
104670 CGGTC-CTTCGG-GACAAATTCTACG
1 TGG-CACTTCGGTG-CAAATTCTACG
104694 TGGCACTTCGGTGCAAATT
1 TGGCACTTCGGTGCAAATT
104713 TATATGAGCT
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
22 1 0.02
23 29 0.54
24 23 0.43
25 1 0.02
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.30
Consensus pattern (24 bp):
TGGCACTTCGGTGCAAATTCTACG
Found at i:105094 original size:12 final size:12
Alignment explanation
Indices: 105077--105101 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
105067 ATCAGATCAG
105077 AAGTAATTGATA
1 AAGTAATTGATA
105089 AAGTAATTGATA
1 AAGTAATTGATA
105101 A
1 A
105102 GAACCAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (12 bp):
AAGTAATTGATA
Found at i:105290 original size:22 final size:22
Alignment explanation
Indices: 105256--105323 Score: 100
Period size: 22 Copynumber: 3.1 Consensus size: 22
105246 TACGGAAGTA
105256 CTGTAGCAGGGGAATCGGTTCC
1 CTGTAGCAGGGGAATCGGTTCC
* *
105278 CTGTTGCATGGGAATCGGTTCC
1 CTGTAGCAGGGGAATCGGTTCC
* *
105300 CTATAGCAGGGGAATCGATTCC
1 CTGTAGCAGGGGAATCGGTTCC
105322 CT
1 CT
105324 TTTTGCAATC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.19, C:0.24, G:0.31, T:0.26
Consensus pattern (22 bp):
CTGTAGCAGGGGAATCGGTTCC
Found at i:105394 original size:25 final size:25
Alignment explanation
Indices: 105366--105414 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
105356 AATGTAGCAA
105366 GGTACTGTAGCAGGTTACTGTTCAC
1 GGTACTGTAGCAGGTTACTGTTCAC
*
105391 GGTATTGTAGCAGGTTACTGTTCA
1 GGTACTGTAGCAGGTTACTGTTCA
105415 TACATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.20, C:0.16, G:0.29, T:0.35
Consensus pattern (25 bp):
GGTACTGTAGCAGGTTACTGTTCAC
Found at i:107132 original size:21 final size:21
Alignment explanation
Indices: 107096--107153 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
107086 ATTTTGTGAA
**
107096 AGGGATCGATTATTTT-CATCG
1 AGGGATCGATCCTTTTAC-TCG
107117 AGGGATCGATCCTTTTACTCG
1 AGGGATCGATCCTTTTACTCG
107138 ATGGG-TCGATCCTTTT
1 A-GGGATCGATCCTTTT
107154 TGTAAAGAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 29 0.88
22 4 0.12
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (21 bp):
AGGGATCGATCCTTTTACTCG
Found at i:107247 original size:41 final size:41
Alignment explanation
Indices: 107188--107265 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
107178 ACTGGAATCC
* * * *
107188 AAGGGATTGATTCTTTTTC-AAGTGGATCGATCTTTTGGTCA
1 AAGGGATCGATTCGTTTTCTAAG-GGATCAATCCTTTGGTCA
107229 AAGGGATCGATTCGTTTTCTAAGGGATCAATCCTTTG
1 AAGGGATCGATTCGTTTTCTAAGGGATCAATCCTTTG
107266 AGCCAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
41 29 0.91
42 3 0.09
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.38
Consensus pattern (41 bp):
AAGGGATCGATTCGTTTTCTAAGGGATCAATCCTTTGGTCA
Found at i:107254 original size:20 final size:19
Alignment explanation
Indices: 107187--107256 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 19
107177 TACTGGAATC
*
107187 CAAGGGATTGATTCTTTTT
1 CAAGGGATCGATTCTTTTT
107206 CAAGTGGATCGA-TCTTTTGGT
1 CAAG-GGATCGATTCTTTT--T
*
107227 CAAAGGGATCGATTCGTTTT
1 C-AAGGGATCGATTCTTTTT
107247 CTAAGGGATC
1 C-AAGGGATC
107257 AATCCTTTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
19 10 0.23
20 16 0.37
21 9 0.21
22 8 0.19
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.37
Consensus pattern (19 bp):
CAAGGGATCGATTCTTTTT
Found at i:117216 original size:21 final size:22
Alignment explanation
Indices: 117149--117217 Score: 95
Period size: 23 Copynumber: 3.1 Consensus size: 22
117139 GGTTCTATAC
*
117149 GGTCCTTCGGGACAAACCTATGT
1 GGTCCTTCGAGACAAA-CTATGT
117172 GGTCCTTCGAGACAAAACTATGT
1 GGTCCTTCGAGAC-AAACTATGT
*
117195 GGTCATTCGAGACAAA-TATGT
1 GGTCCTTCGAGACAAACTATGT
117216 GG
1 GG
117218 CACTTCAGTG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.16
22 3 0.07
23 30 0.70
24 3 0.07
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (22 bp):
GGTCCTTCGAGACAAACTATGT
Found at i:122071 original size:12 final size:12
Alignment explanation
Indices: 122056--122080 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
122046 CGTGGCTTCC
122056 GACGAGGATCGT
1 GACGAGGATCGT
122068 GACGAGGATCGT
1 GACGAGGATCGT
122080 G
1 G
122081 TCGTGCATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.44, T:0.16
Consensus pattern (12 bp):
GACGAGGATCGT
Found at i:122172 original size:29 final size:29
Alignment explanation
Indices: 122110--122244 Score: 99
Period size: 29 Copynumber: 4.5 Consensus size: 29
122100 AACCCAACCA
* * * **
122110 TAGGTCGCCAAGCACTCCAAGCAACCTAC
1 TAGGTCGCCATGCACTCCCAGCGACCTTG
* *
122139 AAGGTCGCCATGCACTCCCAACGACCTTG
1 TAGGTCGCCATGCACTCCCAGCGACCTTG
* * * *
122168 TAGGTCGCCAAGCAATCCCGGCGACCAAGATGG
1 TAGGTCGCCATGCACTCCCAGCGACC----TTG
* * * *
122201 TAGGTCGTCATGTACGCCCAGCGACCTTA
1 TAGGTCGCCATGCACTCCCAGCGACCTTG
122230 TAGGTCGCCATGCAC
1 TAGGTCGCCATGCAC
122245 GCCGGCGTCC
Statistics
Matches: 79, Mismatches: 23, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
29 57 0.72
33 22 0.28
ACGTcount: A:0.25, C:0.34, G:0.24, T:0.17
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCTTG
Found at i:122854 original size:23 final size:23
Alignment explanation
Indices: 122826--122875 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
122816 TATAAAGTAA
122826 TTTAGTTTAGTATAAATTA-TTAG
1 TTTAGTTTAGT-TAAATTAGTTAG
*
122849 TTTAGTTTAGTTATATTAGTTAG
1 TTTAGTTTAGTTAAATTAGTTAG
122872 TTTA
1 TTTA
122876 AGTATATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56
Consensus pattern (23 bp):
TTTAGTTTAGTTAAATTAGTTAG
Found at i:122916 original size:44 final size:41
Alignment explanation
Indices: 122825--122917 Score: 109
Period size: 44 Copynumber: 2.2 Consensus size: 41
122815 ATATAAAGTA
122825 ATTTAGTTTAGTATAAATTATTAGTTTAGTTTAGTTATATT
1 ATTTAGTTTAGTATAAATTATTAGTTTAGTTTAGTTATATT
* *
122866 AGTTAGTTTAAGTATATATATTA-TATTTGTAGTTTAAGTTAT-TT
1 ATTTAGTTT-AGTATA-A-ATTATTAGTT-TAGTTT-AGTTATATT
122910 ATTTAGTT
1 ATTTAGTT
122918 AGTTAAGTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
41 8 0.18
42 6 0.14
43 5 0.11
44 19 0.43
45 6 0.14
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (41 bp):
ATTTAGTTTAGTATAAATTATTAGTTTAGTTTAGTTATATT
Found at i:125960 original size:60 final size:59
Alignment explanation
Indices: 125889--126703 Score: 705
Period size: 60 Copynumber: 14.9 Consensus size: 59
125879 TTATAAGATT
*
125889 TAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAGTAATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAA-TTGA
*
125949 TAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTT--T-A----AT-G-ATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATTGA
*
125998 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAA-TGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATTGA
*
126056 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAA-TGA
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATTGA
* * *
126116 TTTAGTAATGATTGGTAATAATAAAATTATTATTAATTTTTAATGATTTGATAGTAA-TG-
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATTGA
126175 -A-T--T-A--A-TAATAATGAAATTATTATTAAT-TTTAATGATTTGATAGTAA-TGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATTGA
126224 TTAGTAATGATTAG---TAATGAAATTATTA-TAAT-TTT-A--A--TG--A-T--TTGA
1 -TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATTGA
*
126269 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAA-TGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATTGA
* *
126327 TTTAATAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAA-TGA
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATTGA
* *
126387 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGAAAGTAA-TGA
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATTGA
* *
126447 TTTTGTAATGATTAGTAATAATGAAATTATTATT-AT-TTT--T-A----AT-G-ATTTGA
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATTGA
126497 TAGTAATGATTAGTAATAATGAAATTATTA-TAATATTT-A--ATTTGATA-TAA-TGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATTGA
* * * * * * *
126550 TTAGTAAT-AAT-GAAATCAT--TATTAATTTTTAATGATTTGAT-A--T-A-A-TGATT--
1 -TAGTAATGATTAGTAATAATGAAATT-ATTATTAAT-ATTTAATGATTTGATAGTAATTGA
* *
126600 TAGTAATGATTAGTAATAATGAAATTATTA-T--TA-TT--T--TTT-ATAATTATT--
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATTGA
*
126648 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
126704 GATTTGAAAT
Statistics
Matches: 646, Mismatches: 35, Indels: 151
0.78 0.04 0.18
Matches are distributed among these distances:
44 13 0.02
45 4 0.01
46 3 0.00
47 19 0.03
48 91 0.14
49 79 0.12
50 14 0.02
51 18 0.03
52 23 0.04
53 18 0.03
54 20 0.03
55 18 0.03
56 7 0.01
57 11 0.02
58 9 0.01
59 6 0.01
60 293 0.45
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (59 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATTGA
Found at i:126001 original size:49 final size:49
Alignment explanation
Indices: 125943--126337 Score: 431
Period size: 49 Copynumber: 7.6 Consensus size: 49
125933 TTTGATAGTA
125943 ATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATG
1 ATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATG
*
125992 ATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTG
1 ATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTT--T-A-ATG
*
126046 ATATTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTG
1 --ATT--TGA--TAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTT--T-A-ATG
* *
126106 ATATTAATGATTTAGTAATGATTGGTAATAATAAAATTATTATTAATTTTTAATG
1 --ATT--TGA--TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATG
*
126161 ATTTGATAGTAATGATTAATAATAATGAAATTATTATTAA-TTTTAATG
1 ATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATG
126209 ATTTGATAGTAATGATTAGTAATGATTAGTAATGAAATTATTA-TAA-TTTTAATG
1 ATTTGATAGTAATGATTAG---T-A--A-TAATGAAATTATTATTAATTTTTAATG
*
126263 ATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATG
1 ATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATG
*
126312 ATTTGATATTAATGATT--TAATAATGA
1 ATTTGATAGTAATGATTAGTAATAATGA
126338 TTAGTAATAA
Statistics
Matches: 316, Mismatches: 10, Indels: 42
0.86 0.03 0.11
Matches are distributed among these distances:
47 23 0.07
48 30 0.09
49 95 0.30
50 4 0.01
51 5 0.02
52 2 0.01
53 4 0.01
54 33 0.10
55 16 0.05
56 4 0.01
57 1 0.00
58 3 0.01
59 3 0.01
60 93 0.29
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (49 bp):
ATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATG
Found at i:126050 original size:21 final size:20
Alignment explanation
Indices: 126026--126119 Score: 61
Period size: 21 Copynumber: 4.6 Consensus size: 20
126016 ATGAAATTAT
126026 TATTAATATTTAATGATTTGA
1 TATTAATATTTAAT-ATTTGA
* *
126047 TATTAATGATTTAGTA-ATGA
1 TATTAAT-ATTTAATATTTGA
* * *
126067 TTAGTAATAATGAA-A-TT-A
1 -TATTAATATTTAATATTTGA
126085 TTATTAATATTTAATGATTTGA
1 -TATTAATATTTAAT-ATTTGA
126107 TATTAATGATTTA
1 TATTAAT-ATTTA
126120 GTAATGATTG
Statistics
Matches: 56, Mismatches: 10, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
18 12 0.21
19 2 0.04
20 7 0.12
21 23 0.41
22 12 0.21
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (20 bp):
TATTAATATTTAATATTTGA
Found at i:126224 original size:48 final size:48
Alignment explanation
Indices: 126118--126707 Score: 458
Period size: 48 Copynumber: 12.2 Consensus size: 48
126108 ATTAATGATT
* *
126118 TAGTAATGATTGGTAATAATAAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAA-TTTTAATGATTTGA
*
126167 TAGTAATGATTAATAATAATGAAATTATTATTAATTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTAATGATTTGA
126215 TAGTAATGATTAGTAATGATTAGTAATGAAATTATTA-TAATTTTAATGATTTGA
1 TAGTAATGATTAG---T-A--A-TAATGAAATTATTATTAATTTTAATGATTTGA
126269 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTTAATGATTTGA
* * * ** *
126318 TATTAATGATT--TAATAATG--ATTAGTAATAA-TGAAATTA-TT-A
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTAATGATTTGA
* *** * * *
126359 T--TAAT-ATT--TAATGATTTGA-TATTAATGATTTAGTAATGATTAG-
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTT--TAATGATTTGA
* * * ** * * **
126402 TAATAATGAAATTATTATTAATTTTTAATGATT-TGAA-AGTAATGATTT--
1 TAGTAATG--ATTAGTAATAA--TGAAATTATTATTAATTTTAATGATTTGA
*
126450 T-GTAATGATTAGTAATAATGAAATTATTATTATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTAATGATTTGA
126497 TAGTAATGATTAGTAATAATGAAATTATTA-TAATATTT-A--ATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTTAATGATTTGA
*
126542 TA-TAATGATTAGTAATAATGAAATCATTATTAATTTTTAATGATTTGATATAATGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAA-TTTT-A--A--TGAT-T--TGA
* * * *
126598 TTTAGTAATGATTAGTAATAATGAAATTATTATTATTTTTTATAATTAT-T
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTAATGATT-TGA
126648 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAA-TTTTAATGATTTGA
126697 TAGTAATGATT
1 TAGTAATGATT
126708 TGAAATTATT
Statistics
Matches: 442, Mismatches: 49, Indels: 100
0.75 0.08 0.17
Matches are distributed among these distances:
38 9 0.02
39 11 0.02
40 2 0.00
41 2 0.00
42 6 0.01
43 14 0.03
44 28 0.06
45 45 0.10
46 1 0.00
47 32 0.07
48 100 0.23
49 83 0.19
50 5 0.01
51 4 0.01
52 7 0.02
53 8 0.02
54 32 0.07
55 15 0.03
56 3 0.01
58 6 0.01
59 29 0.07
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (48 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTAATGATTTGA
Found at i:126230 original size:10 final size:10
Alignment explanation
Indices: 126215--126243 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
126205 AATGATTTGA
126215 TAGTAATGAT
1 TAGTAATGAT
126225 TAGTAATGAT
1 TAGTAATGAT
126235 TAGTAATGA
1 TAGTAATGA
126244 AATTATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:126302 original size:151 final size:151
Alignment explanation
Indices: 126118--126707 Score: 615
Period size: 151 Copynumber: 3.7 Consensus size: 151
126108 ATTAATGATT
* * *
126118 TAGTAATGATTGGTAATAATAAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAATAA
1 TAGTAATGATTAGTAATAATGAAATTATTATT-ATTTTTAATGATTTGATAGTAATGATTAGTAA
126183 TAATGAAATTATTATTAAT-TTTAATGATTTGATAGTAATGATTAGTAATGATTAGTAATGAAAT
65 TAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATGATTAGTAATGAAAT
126247 TATTATAATTTTAATGATTTGA
130 TATTATAATTTTAATGATTTGA
*
126269 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAATA
1 TAGTAATGATTAGTAATAATGAAATTATTATT-ATTTTTAATGATTTG--A-T-A-G------TA
*
126334 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGAT
54 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA-TTAGTAATGAT
126399 TAGTAATAATGAAATTATTATTAATTTTTAATGATTTGAAAGTAA
118 TAG---TAATGAAATTATTA-TAA-TTTTAATGATTT----G--A
126444 TGATTTTGTAATGATTAGTAATAATGAAATTATTATTATTTTTAATGATTTGATAGTAATGATTA
1 T-A----GTAATGATTAGTAATAATGAAATTATTATTATTTTTAATGATTTGATAGTAATGATTA
* * *
126509 GTAATAATGAAATTATTA-TAATATTT-A--ATTTGATA-TAATGATTAGTAAT-AAT-GAAATC
61 GTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATGATTAGTAATG
* * * *
126567 ATTATTAATTTTTAATGATTTGAT-ATAATGA
126 A-AATT-A-TTATAAT--TTTAATGAT-TTGA
* * *
126598 TTTAGTAATGATTAGTAATAATGAAATTATTATTATTTTTTATAATTAT-TTAGTAATGATTAGT
1 --TAGTAATGATTAGTAATAATGAAATTATTATTATTTTTAATGATT-TGATAGTAATGATTAGT
*
126662 AATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
63 AATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATT
126708 TGAAATTATT
Statistics
Matches: 379, Mismatches: 17, Indels: 81
0.79 0.04 0.17
Matches are distributed among these distances:
151 116 0.31
152 8 0.02
153 2 0.01
154 2 0.01
155 10 0.03
156 11 0.03
157 4 0.01
158 4 0.01
159 6 0.02
160 9 0.02
161 2 0.01
162 39 0.10
163 27 0.07
164 22 0.06
166 1 0.00
167 22 0.06
168 30 0.08
169 12 0.03
173 1 0.00
174 1 0.00
175 3 0.01
176 2 0.01
177 1 0.00
179 14 0.04
180 30 0.08
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (151 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTATTTTTAATGATTTGATAGTAATGATTAGTAAT
AATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATGATTAGTAATGAAATT
ATTATAATTTTAATGATTTGA
Found at i:126321 original size:21 final size:21
Alignment explanation
Indices: 126297--126390 Score: 74
Period size: 21 Copynumber: 4.6 Consensus size: 21
126287 ATGAAATTAT
126297 TATTAATATTTAATGATTTGA
1 TATTAATATTTAATGATTTGA
*
126318 TATTAATGATTTAAT-A-ATG-
1 TATTAAT-ATTTAATGATTTGA
* * *
126337 -ATTAGTA-ATAATGAAATT-A
1 TATTAATATTTAATG-ATTTGA
126356 TTATTAATATTTAATGATTTGA
1 -TATTAATATTTAATGATTTGA
126378 TATTAATGATTTA
1 TATTAAT-ATTTA
126391 GTAATGATTA
Statistics
Matches: 56, Mismatches: 7, Indels: 19
0.68 0.09 0.23
Matches are distributed among these distances:
16 4 0.07
17 1 0.02
18 6 0.11
19 1 0.02
20 2 0.04
21 24 0.43
22 18 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (21 bp):
TATTAATATTTAATGATTTGA
Found at i:126322 original size:271 final size:271
Alignment explanation
Indices: 125889--126707 Score: 1202
Period size: 271 Copynumber: 3.0 Consensus size: 271
125879 TTATAAGATT
*
125889 TAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAGTAATTTGA-TAGT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTTAATGATTTGATAGTAA--TGATTAGT
125953 AATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAAT
63 AATGATTAG---TAATGAAATTATTA-TAA-TTTTAATGATTTGATAGTAATGATTAGTAATAAT
126018 GAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTAGTAATAATGAAAT
123 GAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTAGTAATAATGAAAT
* *
126083 TATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTGGTAATAATAAAATTATTA
188 TATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTAGTAATAATGAAATTATTA
126148 TTAATTTTTAATGATTTGA
253 TTAATTTTTAATGATTTGA
*
126167 TAGTAATGATTAATAATAATGAAATTATTATTAATTTTAATGATTTGATAGTAATGATTAGTAAT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTAATGATTTGATAGTAATGATTAGTAAT
126232 GATTAGTAATGAAATTATTATAATTTTAATGATTTGATAGTAATGATTAGTAATAATGAAATTAT
66 GATTAGTAATGAAATTATTATAATTTTAATGATTTGATAGTAATGATTAGTAATAATGAAATTAT
*
126297 TATTAATATTTAATGATTTGATATTAATGATTTAATAATGATTAGTAATAATGAAATTATTATTA
131 TATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTA
126362 ATATTTAATGATTTGATATTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTT
196 ATATTTAATGATTTGATATTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTT
126427 TAATGATTTGAAAGTAA
261 TAATGATTT----G--A
*
126444 TGATTTTGTAATGATTAGTAATAATGAAATTATTATTATTTTTAATGATTTGATAGTAATGATTA
1 T-A----GTAATGATTAGTAATAATGAAATTATTATTAATTTTAATGATTTGATAGTAATGATTA
126509 G---T-A--A-TAATGAAATTATTATAATATTT-A--ATTTGATA-TAATGATTAGTAATAATGA
61 GTAATGATTAGTAATGAAATTATTATAAT-TTTAATGATTTGATAGTAATGATTAGTAATAATGA
* *
126563 AATCATTATTAATTTTTAATGATTTGATA-TAATGATTTAGTAATGATTAGTAATAATGAAATTA
125 AATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTAGTAATAATGAAATTA
*
126627 TTA-T--TA--T--T--TTT--TA-TAATTATTTAGTAATGATTAGTAATAATGAAATTATTATT
190 TTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATT
126680 AATTTTTAATGATTTGA
255 AATTTTTAATGATTTGA
126697 TAGTAATGATT
1 TAGTAATGATT
126708 TGAAATTATT
Statistics
Matches: 517, Mismatches: 11, Indels: 56
0.89 0.02 0.10
Matches are distributed among these distances:
248 9 0.02
252 1 0.00
253 2 0.00
255 1 0.00
259 54 0.10
260 2 0.00
262 3 0.01
264 1 0.00
266 1 0.00
268 2 0.00
270 1 0.00
271 215 0.42
272 49 0.09
273 22 0.04
275 23 0.04
276 17 0.03
277 21 0.04
278 35 0.07
279 1 0.00
282 57 0.11
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (271 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTAATGATTTGATAGTAATGATTAGTAAT
GATTAGTAATGAAATTATTATAATTTTAATGATTTGATAGTAATGATTAGTAATAATGAAATTAT
TATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTA
ATATTTAATGATTTGATATTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTT
TAATGATTTGA
Found at i:126468 original size:24 final size:24
Alignment explanation
Indices: 126422--126470 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
126412 ATTATTATTA
*
126422 ATTTTTAATGATTTGAAAGTAATG
1 ATTTTTAATGATTAGAAAGTAATG
*
126446 ATTTTGTAATGATTAGTAA-TAATG
1 ATTTT-TAATGATTAGAAAGTAATG
126470 A
1 A
126471 AATTATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (24 bp):
ATTTTTAATGATTAGAAAGTAATG
Found at i:126606 original size:24 final size:23
Alignment explanation
Indices: 126579--126669 Score: 67
Period size: 24 Copynumber: 3.8 Consensus size: 23
126569 TATTAATTTT
126579 TAATGATTTGATATAATGATTTAG
1 TAATGATTTG-TATAATGATTTAG
* *
126603 TAATGATTAGTAATAATGAAATTA-
1 TAATGATTTGT-ATAATG-ATTTAG
* * * *
126627 TTATTATTTTTTATAATTATTTAG
1 TAATGA-TTTGTATAATGATTTAG
*
126651 TAATGATTAGTAATAATGA
1 TAATGATTTGT-ATAATGA
126670 AATTATTATT
Statistics
Matches: 49, Mismatches: 13, Indels: 10
0.68 0.18 0.14
Matches are distributed among these distances:
23 8 0.16
24 34 0.69
25 7 0.14
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (23 bp):
TAATGATTTGTATAATGATTTAG
Found at i:126606 original size:331 final size:318
Alignment explanation
Indices: 125943--126708 Score: 1050
Period size: 331 Copynumber: 2.4 Consensus size: 318
125933 TTTGATAGTA
*
125943 ATTTGATAGTAATGATTAGTAATAATGAAATTATTATTA--ATTT-TTAATGATTTGATAGTAAT
1 ATTT-ATAGTAATGATTAGTAATAATGAAATTATTATTATTTTTTATTAATGATTT-A-A-TAAT
126005 GATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTA
62 GATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTA
* * *
126070 GTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTGGTAAT
127 GTAATAATGAAATTATTATTAATATTTAATGATTTGAAAGTAATGATTTAGTAATGATTAGTAAT
126135 AATAAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAATAATAATGAAATTATTATTA
192 AATAAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAATAATAATGAAATTATTATTA
* * *
126200 ATTTTAATGATTTGATAGTAATGATTAGTAATGATTAGTAATGAAATTATTATAATTTTAATG
257 ATTTTAA-GATTTGATAGTAATGATTAGTAATAATAAATAATGAAATTATTATAATTTTAATG
126263 ATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGAT
1 ATTT-ATAGTAATGATTAGTAATAATGAAATTATTA-T--TA--T--T--TTT--TATTAATGAT
126328 TTAATAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGT
54 TTAATAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGT
* *
126393 AATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGAAAGTAATGATTTTGTAATGA
119 AATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGAAAGTAATGATTTAGTAATGA
* *
126458 TTAGTAATAATGAAATTATTATT-ATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
184 TTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAATAATAATGAAAT
* * *
126522 TATTA-TAATATTT-A-ATTTGATA-TAATGATTAGTAATAATGAAATCATTATTAATTTTTAAT
249 TATTATTAAT-TTTAAGATTTGATAGTAATGATTAGTAATAAT-AAATAATGA--AATTATT-AT
*
126583 GATTTGATATAATG
309 -AATT--T-TAATG
* *
126597 A-TT-TAGTAATGATTAGTAATAATGAAATTATTATTATTTTTTA-TAATTATTTAGTAATGATT
1 ATTTATAGTAATGATTAGTAATAATGAAATTATTATTATTTTTTATTAATGATTTAATAATGATT
* *
126659 AGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTT
66 AGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTT
126709 GAAATTATTA
Statistics
Matches: 404, Mismatches: 19, Indels: 47
0.86 0.04 0.10
Matches are distributed among these distances:
319 65 0.16
320 38 0.09
321 1 0.00
322 3 0.01
323 2 0.00
324 1 0.00
326 17 0.04
327 13 0.03
328 2 0.00
329 11 0.03
330 51 0.13
331 178 0.44
332 1 0.00
333 5 0.01
334 16 0.04
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (318 bp):
ATTTATAGTAATGATTAGTAATAATGAAATTATTATTATTTTTTATTAATGATTTAATAATGATT
AGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTAGTAA
TAATGAAATTATTATTAATATTTAATGATTTGAAAGTAATGATTTAGTAATGATTAGTAATAATA
AAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAATAATAATGAAATTATTATTAATTT
TAAGATTTGATAGTAATGATTAGTAATAATAAATAATGAAATTATTATAATTTTAATG
Found at i:127117 original size:138 final size:136
Alignment explanation
Indices: 126853--127128 Score: 518
Period size: 138 Copynumber: 2.0 Consensus size: 136
126843 CTGATGCGTT
126853 GTGGCCGTTGCGTTGCTCAGGAGTATGGTACCCATCCTCCTCATTCGTTGGGGGGCATTTGAACT
1 GTGGCCGTTGCGTTGCTCAGGAGTATGGTACCCATCCTCCTCATTCGTTGGGGGGCATTTGAACT
126918 GACATGTGTTCAAAGTCTTATCGACGAAAACATGGGAGAGTAGATGGATGCATCAGGCTGCACAA
66 GACATGTGTTCAAAGTCTTATCGACGAAAACATGGGAGAGTAGATGGATGCATCAGGCTGCACAA
126983 ACTCTG
131 ACTCTG
126989 GTGGCCGTTGCGGTTGCTCAGGAGTATGGTACCCATCCTCCTCATTCGTT-GGGGGCATTTGAAC
1 GTGGCCGTTGC-GTTGCTCAGGAGTATGGTACCCATCCTCCTCATTCGTTGGGGGGCATTTGAAC
127053 TGACATGTGTTCAAAGTCATATATCGACGAAAACATGGGAGAGTAGATGGATGCATCAGGCTGCA
65 TGACATGTGTTCAAAGTC-T-TATCGACGAAAACATGGGAGAGTAGATGGATGCATCAGGCTGCA
127118 CAAACTCTG
128 CAAACTCTG
127127 GT
1 GT
127129 ATGTATGCAT
Statistics
Matches: 137, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
136 43 0.31
137 39 0.28
138 55 0.40
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (136 bp):
GTGGCCGTTGCGTTGCTCAGGAGTATGGTACCCATCCTCCTCATTCGTTGGGGGGCATTTGAACT
GACATGTGTTCAAAGTCTTATCGACGAAAACATGGGAGAGTAGATGGATGCATCAGGCTGCACAA
ACTCTG
Found at i:129051 original size:24 final size:24
Alignment explanation
Indices: 129027--129078 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 24
129017 CTTAAACAAC
129027 TAATAAACTATTCTTTAATATAACT
1 TAAT-AACTATTCTTTAATATAACT
*
129052 TAATAACTATTCTTTAATATAAAT
1 TAATAACTATTCTTTAATATAACT
129076 TAA
1 TAA
129079 ACTAAAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (24 bp):
TAATAACTATTCTTTAATATAACT
Found at i:129545 original size:27 final size:28
Alignment explanation
Indices: 129515--129578 Score: 80
Period size: 27 Copynumber: 2.3 Consensus size: 28
129505 CAAATATAAC
129515 TTAACTATTTA-ACTAACT-ACAAACTAA
1 TTAA-TATTTAGACTAACTAACAAACTAA
*
129542 TTAATA-TTAGACTAACTAACACACTAA
1 TTAATATTTAGACTAACTAACAAACTAA
129569 TTAATTATTT
1 TTAA-TATTT
129579 TTTAATATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 3 0.09
26 9 0.28
27 16 0.50
28 2 0.06
29 2 0.06
ACGTcount: A:0.45, C:0.16, G:0.02, T:0.38
Consensus pattern (28 bp):
TTAATATTTAGACTAACTAACAAACTAA
Found at i:129691 original size:9 final size:9
Alignment explanation
Indices: 129659--129696 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
129649 CTAACAAACT
129659 AATAATTTAA
1 AATAA-TTAA
129669 AATAA-TAA
1 AATAATTAA
*
129677 ACTAATTAA
1 AATAATTAA
129686 AATAATTAA
1 AATAATTAA
129695 AA
1 AA
129697 AAAAAACTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 13 0.52
10 5 0.20
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (9 bp):
AATAATTAA
Found at i:129895 original size:12 final size:11
Alignment explanation
Indices: 129868--129903 Score: 63
Period size: 11 Copynumber: 3.2 Consensus size: 11
129858 ACGTTCACGG
129868 GCTGCAATAAT
1 GCTGCAATAAT
129879 GCTGCAATAAGT
1 GCTGCAATAA-T
129891 GCTGCAATAAT
1 GCTGCAATAAT
129902 GC
1 GC
129904 AGTTGATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (11 bp):
GCTGCAATAAT
Found at i:130047 original size:29 final size:28
Alignment explanation
Indices: 130000--130083 Score: 132
Period size: 29 Copynumber: 2.9 Consensus size: 28
129990 AAAGGCATAG
*
130000 GTCGTTGGGATCCCTTGGCGACCTACAAT
1 GTCGCTGGGATCCC-TGGCGACCTACAAT
130029 GTCGCTGGGATGCCCTGGCGACCTACAAT
1 GTCGCTGGGAT-CCCTGGCGACCTACAAT
130058 GTCGCTGGGATTCCCTGGCGACCTAC
1 GTCGCTGGGA-TCCCTGGCGACCTAC
130084 CCACGTTGCA
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
29 48 0.92
30 4 0.08
ACGTcount: A:0.15, C:0.31, G:0.30, T:0.24
Consensus pattern (28 bp):
GTCGCTGGGATCCCTGGCGACCTACAAT
Found at i:132560 original size:27 final size:28
Alignment explanation
Indices: 132508--132565 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
132498 TTATATTTTG
* * *
132508 AAAATAAACCTAATTTCTCTTAAATTAT
1 AAAAAAAACCCAATTTCTCTAAAATTAT
*
132536 AAAAAAAACCCAA-TTCTCTAAAATTCT
1 AAAAAAAACCCAATTTCTCTAAAATTAT
132563 AAA
1 AAA
132566 CCATAACCCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 15 0.58
28 11 0.42
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (28 bp):
AAAAAAAACCCAATTTCTCTAAAATTAT
Found at i:132853 original size:17 final size:17
Alignment explanation
Indices: 132827--132860 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
132817 ATGGTTGAAA
*
132827 TTAGGGTTTTTAAAGTT
1 TTAGGATTTTTAAAGTT
*
132844 TTAGGATTTTTTAAGTT
1 TTAGGATTTTTAAAGTT
132861 CTTTAATTTT
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:0.24, C:0.00, G:0.21, T:0.56
Consensus pattern (17 bp):
TTAGGATTTTTAAAGTT
Found at i:133759 original size:24 final size:25
Alignment explanation
Indices: 133719--133766 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
133709 CATCTCTAAA
*
133719 TCTTTCTTTTCTCCC-TTTCCCTCC
1 TCTTTCTTCTCTCCCTTTTCCCTCC
133743 TCTTTC-TCTCTCTCCTTTTCCCTC
1 TCTTTCTTCTCTC-CCTTTTCCCTC
133767 AAACCAAACG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.24
24 8 0.38
25 8 0.38
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (25 bp):
TCTTTCTTCTCTCCCTTTTCCCTCC
Found at i:133762 original size:25 final size:24
Alignment explanation
Indices: 133719--133766 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
133709 CATCTCTAAA
*
133719 TCTTTCTTTTCTCCCTTTCCCTCC
1 TCTTTCTTCTCTCCCTTTCCCTCC
*
133743 TCTTTCTCTCTCTCCTTTTCCCTC
1 TCTTTCT-TCTCTCCCTTTCCCTC
133767 AAACCAAACG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (24 bp):
TCTTTCTTCTCTCCCTTTCCCTCC
Found at i:138393 original size:22 final size:21
Alignment explanation
Indices: 138349--138389 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
138339 ATATAAGTTC
138349 ATTTTCTATTTTTAACAATTA
1 ATTTTCTATTTTTAACAATTA
*
138370 ATTTTCT-TTCTTTTACAATT
1 ATTTTCTATT-TTTAACAATT
138390 TAATCCTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTTTCTATTTTTAACAATTA
Found at i:139341 original size:39 final size:40
Alignment explanation
Indices: 139283--139364 Score: 107
Period size: 39 Copynumber: 2.1 Consensus size: 40
139273 TCTAAAAGAC
*
139283 ATTCTTATTTTCATTAAATT-TTGACAC-TATAACGTTCTAA
1 ATTCTTAATTTCATTAAATTATT-ACACAT-TAACGTTCTAA
*
139323 ATTCTTAATTTC-TTAAATTATTTCACATTAACGTTCTAA
1 ATTCTTAATTTCATTAAATTATTACACATTAACGTTCTAA
139362 ATT
1 ATT
139365 ATTTTTTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
39 24 0.63
40 14 0.37
ACGTcount: A:0.33, C:0.15, G:0.04, T:0.49
Consensus pattern (40 bp):
ATTCTTAATTTCATTAAATTATTACACATTAACGTTCTAA
Found at i:141415 original size:411 final size:412
Alignment explanation
Indices: 140629--141444 Score: 1382
Period size: 411 Copynumber: 2.0 Consensus size: 412
140619 GTGAAAACAA
* *
140629 AGAAAAGAGTAAAGACAAAAAAATTGGTTCACTAATGGATAAAAATGAAACGGGTAGGTAATTTG
1 AGAAAAGAGTAAAGACAAAAAAATTGGTTCACTAATGGATAAAAATGAAACAGGTAGGCAATTTG
140694 GGTAGAGAAGTGGGTTAATCCTAAGTGCCCTAATCATATTAAAGCATCAAGTTCGATGTGTGGTC
66 GGTAGAGAAGTGGGTTAATCCTAAGTGCCCTAATCATATTAAAGCATCAAGTTCGATGTGTGGTC
* * *
140759 TCGATATGCATTTATTACAAGTTCTAGAATATCAAAATTAATCTAGTGCACTCAATCAAATAAAT
131 TCAATATGCATTTATTACAAGTTCTAGAATATCAAAATTAATCCAGTGCACTCAATCAAACAAAT
* *
140824 GAGCAAGAATGAAAAAATATGCTCGCTTAGGCTCAAATCTCACAAGAAAGTGTATTTTGTATCGA
196 GAGCAAGAATGAAAAAATATGCTCACTTAGGCTCAAATCTCACAAGAAAGTGTATTGTGTATCGA
** * *
140889 GTTAAGAAACATATAAACTAATGGATTCTTCGAACATCAAGCAAAAAATTTAAGGGAAAATACTA
261 GACAAGAAACATATAAACTAATGGATTCTTCGAACATCAAACAAAAAATTTAAGGAAAAATACTA
* * * *
140954 ATCATGTCATTTTTACTATCATGAACTCTAAATCTGATAGAAGCATGATCACAAACTCATAAGGT
326 ATAATGTCATTTTTACTATCAGGAACTCTAAATCTGATAAAAGAATGATCACAAACTCATAAGGT
141019 AATCAATGGAACAAAAAACTAT
391 AATCAATGGAACAAAAAACTAT
*
141041 AGAAAGGAGTAAAGAC-AAAAAATTGGTTCACTAATGGATAAAAATGAAACAGGTAGGCAATTTG
1 AGAAAAGAGTAAAGACAAAAAAATTGGTTCACTAATGGATAAAAATGAAACAGGTAGGCAATTTG
* *
141105 GGTAGAGAAGTTGGTTAATCCTAAGTGCCCTAATCATATTAAAGCCTCAAGTTCGATGTGTGGTC
66 GGTAGAGAAGTGGGTTAATCCTAAGTGCCCTAATCATATTAAAGCATCAAGTTCGATGTGTGGTC
* *
141170 TTAATATGCATTTATTACAAGTTCTAGAATGTCAAAATTAATCCAGTGCACTCAATCAAACAAAT
131 TCAATATGCATTTATTACAAGTTCTAGAATATCAAAATTAATCCAGTGCACTCAATCAAACAAAT
* * *
141235 GAGCAAGAGTGAAAAAATATGCTCATTTAGGCTCAAATCTCACAAGAAAGTTTATTGTGTATCGA
196 GAGCAAGAATGAAAAAATATGCTCACTTAGGCTCAAATCTCACAAGAAAGTGTATTGTGTATCGA
*
141300 GACAAGAAACATATCAACTAATGGATTCTTCGAACATCAAACAAAAAATTTAAGGAAAAATACTA
261 GACAAGAAACATATAAACTAATGGATTCTTCGAACATCAAACAAAAAATTTAAGGAAAAATACTA
* **
141365 ATAATGTCATTTTTACTATCAGGCACTCTAAATCTGATAAAAGAATGATCACAAACTCATAATTT
326 ATAATGTCATTTTTACTATCAGGAACTCTAAATCTGATAAAAGAATGATCACAAACTCATAAGGT
141430 AATCAATGGAACAAA
391 AATCAATGGAACAAA
141445 GCAAGATTCA
Statistics
Matches: 377, Mismatches: 27, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
411 362 0.96
412 15 0.04
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (412 bp):
AGAAAAGAGTAAAGACAAAAAAATTGGTTCACTAATGGATAAAAATGAAACAGGTAGGCAATTTG
GGTAGAGAAGTGGGTTAATCCTAAGTGCCCTAATCATATTAAAGCATCAAGTTCGATGTGTGGTC
TCAATATGCATTTATTACAAGTTCTAGAATATCAAAATTAATCCAGTGCACTCAATCAAACAAAT
GAGCAAGAATGAAAAAATATGCTCACTTAGGCTCAAATCTCACAAGAAAGTGTATTGTGTATCGA
GACAAGAAACATATAAACTAATGGATTCTTCGAACATCAAACAAAAAATTTAAGGAAAAATACTA
ATAATGTCATTTTTACTATCAGGAACTCTAAATCTGATAAAAGAATGATCACAAACTCATAAGGT
AATCAATGGAACAAAAAACTAT
Found at i:151369 original size:2 final size:2
Alignment explanation
Indices: 151305--151360 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
151295 GTTTGTTTTG
151305 TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
151346 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
151361 TTTTATATAC
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.