Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004238.1 Hibiscus syriacus cultivar Beakdansim tig00009283_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: 88349
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:2236 original size:134 final size:136
Alignment explanation
Indices: 1897--2369 Score: 720
Period size: 135 Copynumber: 3.6 Consensus size: 136
1887 GACTTGAAAG
* * * * *
1897 GAACAAGTTCTTTTCATTATGAAC-T-TTCTCCAT-TA--AGATGGGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACT
* * ** **
1957 CTTC--TAGAAATGTCAATTTCTCAA--GAGGTGTCACTGATTCGAAATGTCGTGAATCGAGTGA
66 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGCATCACTGATTCGAAATGTCGTGAATCGAGTGA
2018 TAGGTC
131 TAGGTC
2024 GAACAAGCTCTTC-CATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACT
2088 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGCATCACTGATTCGAAATGTCGTGAATCGAGTGA
66 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGCATCACTGATTCGAAATGTCGTGAATCGAGTGA
2153 TAGGTC
131 TAGGTC
2159 GAACAAGCTCTTCTCATTATGAACTTC-T-TCCCTCTATCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACT
*
2222 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGCATCACTGATTCG-AATGCCGTGAATCGAGTGA
66 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGCATCACTGATTCGAAATGTCGTGAATCGAGTGA
2286 TAGGTC
131 TAGGTC
*
2292 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACT
* *
2357 CTCTATTGAAAAT
66 CTCCATTGGAAAT
2370 ATTGATGCAA
Statistics
Matches: 319, Mismatches: 15, Indels: 16
0.91 0.04 0.05
Matches are distributed among these distances:
126 10 0.03
127 12 0.04
128 7 0.02
129 2 0.01
131 26 0.08
133 68 0.21
134 81 0.25
135 100 0.31
136 13 0.04
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.34
Consensus pattern (136 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACT
CTCCATTGGAAATGTCAATCCCTCAAGCGAGGCATCACTGATTCGAAATGTCGTGAATCGAGTGA
TAGGTC
Found at i:2445 original size:88 final size:92
Alignment explanation
Indices: 2289--2455 Score: 261
Period size: 88 Copynumber: 1.9 Consensus size: 92
2279 CGAGTGATAG
*
2289 GTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGA
1 GTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAATTCTTCTCATTATGA
*
2354 ACTCTCTATTGAAAATATTGATGCAAA
66 ACTCTCCATTGAAAATATTGATGCAAA
* * *
2381 GTCGAACAAGTTCTTCTCATTGTGAACTT-TT-T-CTTCT-TCGGATGAATTCTTCTCATTATGA
1 GTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAATTCTTCTCATTATGA
2442 ACTCTCCATTGAAA
66 ACTCTCCATTGAAA
2456 TGTTGATCCA
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
88 36 0.51
89 4 0.06
90 1 0.01
91 2 0.03
92 27 0.39
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (92 bp):
GTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAATTCTTCTCATTATGA
ACTCTCCATTGAAAATATTGATGCAAA
Found at i:3455 original size:7 final size:8
Alignment explanation
Indices: 3443--3494 Score: 74
Period size: 7 Copynumber: 6.8 Consensus size: 8
3433 TCTCTTCGTT
3443 TTTTTTC-
1 TTTTTTCA
3450 TTTTTTCA
1 TTTTTTCA
3458 TTTTTTTCA
1 -TTTTTTCA
3467 -TTTTTCA
1 TTTTTTCA
3474 TTTTTTC-
1 TTTTTTCA
3481 TTTTTTCA
1 TTTTTTCA
3489 TTTTTT
1 TTTTTT
3495 TCTTCAAGCA
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
7 21 0.51
8 12 0.29
9 8 0.20
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTCA
Found at i:3461 original size:15 final size:15
Alignment explanation
Indices: 3443--3494 Score: 86
Period size: 15 Copynumber: 3.4 Consensus size: 15
3433 TCTCTTCGTT
3443 TTTTTTCTTTTTTCA
1 TTTTTTCTTTTTTCA
*
3458 TTTTTTTCATTTTTCA
1 -TTTTTTCTTTTTTCA
3474 TTTTTTCTTTTTTCA
1 TTTTTTCTTTTTTCA
3489 TTTTTT
1 TTTTTT
3495 TCTTCAAGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
15 20 0.59
16 14 0.41
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTTCTTTTTTCA
Found at i:3461 original size:16 final size:16
Alignment explanation
Indices: 3442--3498 Score: 98
Period size: 16 Copynumber: 3.6 Consensus size: 16
3432 TTCTCTTCGT
3442 TTTTTTTCTTTTTTCA
1 TTTTTTTCTTTTTTCA
*
3458 TTTTTTTCATTTTTCA
1 TTTTTTTCTTTTTTCA
3474 -TTTTTTCTTTTTTCA
1 TTTTTTTCTTTTTTCA
3489 TTTTTTTCTT
1 TTTTTTTCTT
3499 CAAGCATAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.37
16 24 0.63
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTTTCTTTTTTCA
Found at i:16267 original size:2 final size:2
Alignment explanation
Indices: 16245--16283 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
16235 AAAATAAAAA
16245 AT AT A- AT AT A- AT AT GAT 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 AT AT AT AT AT AT AT
16284 TAGATCCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 30 0.88
3 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:18420 original size:200 final size:200
Alignment explanation
Indices: 18072--18445 Score: 466
Period size: 200 Copynumber: 1.9 Consensus size: 200
18062 TCGAATTTGA
* * * ** *
18072 AAGCTTTGGTCGACATATAGCTCTTTTGGACTTAAGCTATGCAAGATCTGGGCTAAAAAGTAGTT
1 AAGCTTTGGTCGACAAATAACTCTTCTCCACTTAAGCTATGCAAAATCTGGGCTAAAAAGTAGTT
** * * *
18137 TGTTGTTGCTAAATAACATCCGATTTAGGCCTTCTTTTAGACTTGAAGACTTTGGTTTGAATTTT
66 CCTCGTTGCTAAATAACACCCGATTTAGGCCTTCTTATAGACTTGAAGACTTTGGTTTGAATTTT
* * * *
18202 AACCGGAAGGTAGTTCCTCGTTGCTACC-TGCGATTAATGTGCTCCTGAGTTGAATTAAATCAAA
131 AACCGAAAGGTAGTTCCTCATTGCCACCATGCGATCAATGTGCTCCTGAGTTGAATTAAATCAAA
18266 CTATG
196 CTATG
** *
18271 AAGCTTTGGTCGACAAATAACTCTTCTCCACTTAAGCTATGTCAAAATCTGGGCTGGGATA-TAG
1 AAGCTTTGGTCGACAAATAACTCTTCTCCACTTAAGCTATG-CAAAATCTGGGCT-AAAAAGTAG
** * *
18335 TTCCTCGTTGCTAAATCGCACCCGATTTGGGCCTTCTTATAGGCTTGAAGAAC-TTGGTTTGAAT
64 TTCCTCGTTGCTAAATAACACCCGATTTAGGCCTTCTTATAGACTTGAAG-ACTTTGGTTTGAAT
* * * *
18399 TTTAACCTAAATGTGGTTCCTCATTGCCACCATGGGATCAATGTGCT
128 TTTAACCGAAAGGTAGTTCCTCATTGCCACCATGCGATCAATGTGCT
18446 TTCAAGTTGA
Statistics
Matches: 145, Mismatches: 26, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
199 36 0.25
200 92 0.63
201 17 0.12
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (200 bp):
AAGCTTTGGTCGACAAATAACTCTTCTCCACTTAAGCTATGCAAAATCTGGGCTAAAAAGTAGTT
CCTCGTTGCTAAATAACACCCGATTTAGGCCTTCTTATAGACTTGAAGACTTTGGTTTGAATTTT
AACCGAAAGGTAGTTCCTCATTGCCACCATGCGATCAATGTGCTCCTGAGTTGAATTAAATCAAA
CTATG
Found at i:18635 original size:71 final size:71
Alignment explanation
Indices: 18529--18710 Score: 179
Period size: 71 Copynumber: 2.5 Consensus size: 71
18519 TGGATGAATC
* * * * * *
18529 CCCTTTGTGGGAAAGACAGGTGAGATGAATCCCCTTCACGGTTTAAGTAAGTCTTGATTAGTTGG
1 CCCTTCGTGAGAAAG-CAGGTGAGATGACTCCCCTTCAAGGTTTAACTAAGTCTTGATTAGTTGA
18594 ATGAC-A
65 ATGACTA
* * ** **
18600 CCCTTCGTGAGAAAGCTAGGTGAGATGACTTCCCTTTAAGGTTTAACTTGGTCTTGATTCTTTGA
1 CCCTTCGTGAGAAAGC-AGGTGAGATGACTCCCCTTCAAGGTTTAACTAAGTCTTGATTAGTTGA
18665 ATGACTA
65 ATGACTA
* *
18672 CCCTTCAT-AGGAAAGGCCAGGTGAGACGACTCCCCTTCA
1 CCCTTCGTGA-GAAA-G-CAGGTGAGATGACTCCCCTTCA
18711 TGAGTCTAAT
Statistics
Matches: 90, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
70 1 0.01
71 57 0.63
72 12 0.13
73 19 0.21
74 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (71 bp):
CCCTTCGTGAGAAAGCAGGTGAGATGACTCCCCTTCAAGGTTTAACTAAGTCTTGATTAGTTGAA
TGACTA
Found at i:21818 original size:54 final size:54
Alignment explanation
Indices: 21743--21897 Score: 159
Period size: 54 Copynumber: 2.9 Consensus size: 54
21733 AAAATCTATA
* * * *
21743 CAGAAACCACAGAAAATGATGAATGTGTTGTAAAATGCTTTACGAACATCTGAC
1 CAGAAGCCACAAAAAAAGATGAATGTGTTGTAAAATGCTTTACGAACATCCGAC
* * **
21797 CAGAAGCCACAAAAAAAGATGAATGTGTTATCAAAA-GCTTTACGAAAATCCGGG
1 CAGAAGCCACAAAAAAAGATGAATGTGTTGT-AAAATGCTTTACGAACATCCGAC
* * * * * * *
21851 CAGAAGCCACGAGAAAGGATGAATGTATTGTCACATGTTTTACGAAC
1 CAGAAGCCACAAAAAAAGATGAATGTGTTGTAAAATGCTTTACGAAC
21898 CAGTGATTAT
Statistics
Matches: 82, Mismatches: 17, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
53 2 0.02
54 76 0.93
55 4 0.05
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.22
Consensus pattern (54 bp):
CAGAAGCCACAAAAAAAGATGAATGTGTTGTAAAATGCTTTACGAACATCCGAC
Found at i:22282 original size:22 final size:22
Alignment explanation
Indices: 22257--22331 Score: 123
Period size: 22 Copynumber: 3.4 Consensus size: 22
22247 CTACATTCTC
22257 CAAAGATGATAGATTCTCTCTT
1 CAAAGATGATAGATTCTCTCTT
* *
22279 CAAAGATGATATATTCTCTCTC
1 CAAAGATGATAGATTCTCTCTT
*
22301 CAAAGATGATAGATTCTCTTTT
1 CAAAGATGATAGATTCTCTCTT
22323 CAAAGATGA
1 CAAAGATGA
22332 AAGCTTTATT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (22 bp):
CAAAGATGATAGATTCTCTCTT
Found at i:22700 original size:17 final size:17
Alignment explanation
Indices: 22678--22712 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
22668 TACATTTCAT
22678 TGCATTCAAACATGAAG
1 TGCATTCAAACATGAAG
22695 TGCATTCAAACATGAAG
1 TGCATTCAAACATGAAG
22712 T
1 T
22713 TTTACAGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (17 bp):
TGCATTCAAACATGAAG
Found at i:23060 original size:45 final size:45
Alignment explanation
Indices: 22995--23344 Score: 583
Period size: 45 Copynumber: 7.8 Consensus size: 45
22985 CTATTTCCCA
* *
22995 CATCTGTAAGCCCTTTAGTGCATGATGTTATCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
23040 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTCCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
23085 CATCTGTAAGCCCTTCAGTGCATTATGTTTTCAAAACTTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
23130 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACTTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * **
23175 CATATGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGATT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
23220 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
23265 CATCTGTAAGCCCTTCAGTGCATGATATTTTCAAAACCCTTCGGAT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAA-CCTTCGGGT
23311 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
23345 CATTTTCATC
Statistics
Matches: 285, Mismatches: 19, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
45 244 0.86
46 41 0.14
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:23471 original size:3 final size:3
Alignment explanation
Indices: 23463--23551 Score: 117
Period size: 3 Copynumber: 29.0 Consensus size: 3
23453 CAATTTGCTT
*
23463 TTA TTA TTA TTA TTA TTA TTTA TT- TTA TTA TTG TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
23508 TACA TTA TTA TTA TTA TTA TTG TTA TTTA TTA TTA TTA TTA TTA
1 T-TA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
23552 AATAAATATT
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
2 2 0.03
3 66 0.87
4 8 0.11
ACGTcount: A:0.30, C:0.01, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:25070 original size:21 final size:22
Alignment explanation
Indices: 25024--25068 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
25014 TCATTGTTTA
25024 TTTATAT-TTTAATTTTATATG
1 TTTATATATTTAATTTTATATG
25045 TTTATATATTTAATTATTAT-TG
1 TTTATATATTTAATT-TTATATG
25067 TT
1 TT
25069 ATTATTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.32
22 11 0.50
23 4 0.18
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTATATATTTAATTTTATATG
Found at i:25336 original size:35 final size:32
Alignment explanation
Indices: 25293--25363 Score: 90
Period size: 32 Copynumber: 2.1 Consensus size: 32
25283 AATATCTTAT
25293 TTTTAGAGAAAT-TTTAATATTAATTTATTTAATTA
1 TTTTAGAGAAATGTTT--TATTAA--TATTTAATTA
*
25328 TTTTAGAGAAATGTTTTATTAATATTTATTTA
1 TTTTAGAGAAATGTTTTATTAATATTTAATTA
25360 TTTT
1 TTTT
25364 TAATATTAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
32 13 0.38
34 6 0.18
35 12 0.35
36 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (32 bp):
TTTTAGAGAAATGTTTTATTAATATTTAATTA
Found at i:25457 original size:9 final size:9
Alignment explanation
Indices: 25439--25467 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
25429 AATATCTTAT
25439 TTAT-AAAA
1 TTATAAAAA
25447 TTATAAAAA
1 TTATAAAAA
25456 TTATAAAAA
1 TTATAAAAA
25465 TTA
1 TTA
25468 ATATATTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.20
9 16 0.80
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
TTATAAAAA
Found at i:31360 original size:3 final size:3
Alignment explanation
Indices: 31354--31382 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
31344 TTTAATTTAT
31354 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
31383 TTAAAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:37936 original size:151 final size:148
Alignment explanation
Indices: 37744--38017 Score: 410
Period size: 151 Copynumber: 1.8 Consensus size: 148
37734 TTAATTTATA
*
37744 TATATAAATAAGATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGGTGCCTTAAGACAG
1 TATATAAATAAGATATTTACTTATTTAGAAATATCAGAAAAGGACTTCTAGGTGCCTTAAGACAG
37809 CTCTTTTCTTCGATATTGAAAAAATGAA-TAAATATA-AAAACATTTTTCTAAAAATAATAATAA
66 CTCTTTTCTTCGATATT-AAAAAAT-AAGTAAATA-ACAAAACA-TTTTCTAAAAA-AATAATAA
37872 AAAATAGATTGATACATATAATT
126 AAAATAGATTGATACATATAATT
* * *
37895 TATA-AAAGTAAGATATTTACTTATTTAGAAATATCATAAAAGGGCTTCTAGGTGCTTTAAGACA
1 TATATAAA-TAAGATATTTACTTATTTAGAAATATCAGAAAAGGACTTCTAGGTGCCTTAAGACA
* *
37959 GCTCTTTTCTTTGATATTAAAAAATAAGTAAATAACTAAAACATTTTCTTAAAAAATAA
65 GCTCTTTTCTTCGATATTAAAAAATAAGTAAATAAC-AAAACATTTTCTAAAAAAATAA
38018 AAATTTATTT
Statistics
Matches: 113, Mismatches: 6, Indels: 10
0.88 0.05 0.08
Matches are distributed among these distances:
149 8 0.07
150 26 0.23
151 79 0.70
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.35
Consensus pattern (148 bp):
TATATAAATAAGATATTTACTTATTTAGAAATATCAGAAAAGGACTTCTAGGTGCCTTAAGACAG
CTCTTTTCTTCGATATTAAAAAATAAGTAAATAACAAAACATTTTCTAAAAAAATAATAAAAAAT
AGATTGATACATATAATT
Found at i:39628 original size:3 final size:3
Alignment explanation
Indices: 39620--39684 Score: 69
Period size: 3 Copynumber: 21.7 Consensus size: 3
39610 ACTGTTTGTA
* *
39620 AAT AAT AAT TAT AAT -AT AAT AAT AAT ATTT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
** *
39665 AAT TTT AAT CAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
39685 AAACAAAAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
2 2 0.04
3 46 0.92
4 2 0.04
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:39654 original size:13 final size:13
Alignment explanation
Indices: 39621--39667 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
39611 CTGTTTGTAA
*
39621 ATAATAATTATAAT
1 ATAATAATAAT-AT
39635 ATAATAATAATAT
1 ATAATAATAATAT
*
39648 TTAATAATAATA-
1 ATAATAATAATAT
39660 ATAATAAT
1 ATAATAAT
39668 TTTAATCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
12 7 0.23
13 13 0.43
14 10 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATAATAATAATAT
Found at i:40506 original size:76 final size:76
Alignment explanation
Indices: 39842--40478 Score: 1148
Period size: 76 Copynumber: 8.4 Consensus size: 76
39832 GAGGTCTTAA
*
39842 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
39907 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
39918 AAACATCATGCACTGCAGGACTTACAGATGATCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
39983 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
39994 AAACATCATGTACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAATCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
40059 AGGCTTTTTGG
66 AGGCTTTTTGG
40070 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
40135 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
40146 AAACATCGTGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
40211 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
40222 AAACATCATGCACTGAAGGACTTACAGGTGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
40287 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
40298 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGTTCCTGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
40363 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
40374 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
40439 AGGCTTTTTGG
66 AGGCTTTTTGG
40450 AAACATCATGCACTGCAGGACTTACAGAT
1 AAACATCATGCACTGCAGGACTTACAGAT
40479 ATGGGAAATA
Statistics
Matches: 541, Mismatches: 20, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 541 1.00
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (76 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:40756 original size:165 final size:168
Alignment explanation
Indices: 40482--40811 Score: 558
Period size: 168 Copynumber: 2.0 Consensus size: 168
40472 TACAGATATG
* *
40482 GGAAATAGTTTACTAAGTAAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTT
1 GGAAATAGTTTACTAAGTAAAAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTT
** *
40547 TTAGAAAAGATTGAATGAGAAACTATGGAAATCGTTTTCTCATTA-TTTTTCAAAATAACATGTT
66 TTAGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTTCAAAATAACATGTT
40611 GATTGGGTAACATGCCCCAATCTCAAGATAATGTTGTT
131 GATTGGGTAACATGCCCCAATCTCAAGATAATGTTGTT
40649 GGAAATAGTTTACTAAGT-AAAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCA-TT
1 GGAAATAGTTTACTAAGTAAAAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTT
**
40712 TTAGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATGTTTTTTTGAAATAACATG
66 TTAGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTA--TTTTTTCAAAATAACATG
40777 TTGATTGGGTAACATGCCCCAATCTCAAGATAATG
129 TTGATTGGGTAACATGCCCCAATCTCAAGATAATG
40812 CTCATTTTTG
Statistics
Matches: 153, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
165 44 0.29
166 41 0.27
167 18 0.12
168 50 0.33
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (168 bp):
GGAAATAGTTTACTAAGTAAAAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTT
TTAGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTTCAAAATAACATGTT
GATTGGGTAACATGCCCCAATCTCAAGATAATGTTGTT
Found at i:41349 original size:22 final size:22
Alignment explanation
Indices: 41324--41378 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
41314 CATAAAGCTT
*
41324 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATATA
*
41346 TCATCTTTAAAAAGAGAATATA
1 TCATCTTTGAAAAGAGAATATA
41368 TCATCTTTGAA
1 TCATCTTTGAA
41379 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATATA
Found at i:43798 original size:114 final size:114
Alignment explanation
Indices: 43598--43819 Score: 372
Period size: 114 Copynumber: 1.9 Consensus size: 114
43588 ATCATGCAGC
* * *
43598 TCATCTTTTAATTCCAATGATTGGTTCTGTGGTTCCTACCAAACCAGATCAGATAACTCAAAGAA
1 TCATCTTTTAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
*
43663 TACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGATCAAAT
66 CACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGATCAAAT
*
43712 TCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
1 TCATCTTTTAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
* * *
43777 CACTTCCAGAAGATGCTATTGGGTCTCTTTATTTCTACTATGA
66 CACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGA
43820 GAACATGGCA
Statistics
Matches: 100, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 100 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (114 bp):
TCATCTTTTAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
CACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGATCAAAT
Found at i:51568 original size:133 final size:132
Alignment explanation
Indices: 51321--51562 Score: 350
Period size: 133 Copynumber: 1.8 Consensus size: 132
51311 TTTATAAAAG
* * *
51321 TAAGATATTTACTTATTTATAAATATCAGAAAAGGGCTTCTAGGTGCTTTAAGACAGCTCTTTTC
1 TAAGATATTTACTTATTTATAAATATCAGAAAAGGGCTTCTAGGTGCCTTAAGACAGCTATTCTC
*
51386 TTTGATATTAAAAAATAAGTAAATAACTAAAACATTTTCTTAAAAAATAAAAATTTATTTTAATA
66 TTCGATATTAAAAAATAAGTAAATAAC-AAAACATTTTCTTAAAAAATAAAAATTTATTTTAATA
51451 TAA
130 TAA
*
51454 TAAGATATTTATTTATTTGA-AAATATCAGAAAAGGGCTTCTAGGTGCCTTAAGACAGCTATTCT
1 TAAGATATTTACTTATTT-ATAAATATCAGAAAAGGGCTTCTAGGTGCCTTAAGACAGCTATTCT
*
51518 CTTCGATATT-GAAAATGAA-TAAATATA-AAAACATTTT-TATAAAAA
65 CTTCGATATTAAAAAAT-AAGTAAATA-ACAAAACATTTTCT-TAAAAA
51563 TAATAATAAT
Statistics
Matches: 99, Mismatches: 6, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
130 1 0.01
131 16 0.16
132 11 0.11
133 70 0.71
134 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.37
Consensus pattern (132 bp):
TAAGATATTTACTTATTTATAAATATCAGAAAAGGGCTTCTAGGTGCCTTAAGACAGCTATTCTC
TTCGATATTAAAAAATAAGTAAATAACAAAACATTTTCTTAAAAAATAAAAATTTATTTTAATAT
AA
Found at i:51761 original size:21 final size:20
Alignment explanation
Indices: 51727--51779 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
51717 AACAAATAAA
51727 ATTAAAAT--AATAAAT-TG
1 ATTAAAATAAAATAAATATG
51744 AATTAAAATATAAATAAATAGTG
1 -ATTAAAATA-AAATAAATA-TG
51767 ATTAAAATAAAAT
1 ATTAAAATAAAAT
51780 TAAAACTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
18 8 0.27
21 11 0.37
22 9 0.30
23 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (20 bp):
ATTAAAATAAAATAAATATG
Found at i:53078 original size:3 final size:3
Alignment explanation
Indices: 53070--53134 Score: 78
Period size: 3 Copynumber: 21.7 Consensus size: 3
53060 ACTGTTTGTA
* *
53070 AAT AAT AAT TAT AAT -AT AAT AAT AAT ATTT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
**
53115 AAT TTT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
53135 AAACAAAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
2 2 0.04
3 48 0.92
4 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:54175 original size:16 final size:16
Alignment explanation
Indices: 54154--54193 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
54144 AATTGAGAAA
*
54154 ACATACATCAATGCAT
1 ACATACATCAACGCAT
54170 ACATACATCAACGCAT
1 ACATACATCAACGCAT
54186 ACATACAT
1 ACATACAT
54194 ATTACATGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.45, C:0.28, G:0.05, T:0.23
Consensus pattern (16 bp):
ACATACATCAACGCAT
Found at i:54895 original size:109 final size:105
Alignment explanation
Indices: 54583--54897 Score: 370
Period size: 109 Copynumber: 3.0 Consensus size: 105
54573 CTTGAGACAA
* *
54583 TTTC-TTTCAAAACAAAATTTCGTCTCACTTGAGGCATTTTTCCTTTGAGATACAAAATTTGAAT
1 TTTCTTTTCAAAAC-AAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAAATTTGAAT
* *
54647 TTGTTTCACATTAAACAAAGTTGATCTCATTTGAGA-TCAC
65 TTGTTTCACATTAAACAAAGTTAATCTCACTTGAGATTCAC
* * * *
54687 TTTCTCTT-AAAACAAACTTCGTCTTGCTTGAGACATTTTTTCCTTTGATATAC-AAATTTCGAA
1 TTTCTTTTCAAAACAAATTTCGTCTCGCTTGAGACA-TTTTTCCTTTGAGATACAAAATTT-GAA
* * * *
54750 TTTGATTCAC-TTGAAACAAAAATTAATCTCACTTGAGATTGTTATT
64 TTTGTTTCACATT-AAAC-AAAGTTAATCTCACTTGAGA-T-TCA-C
* * * *
54796 TTTTTTTTCAAAACAAATTTCATCTCGTTTGAGACATTTTTCCTTTGAGATACAAAATTTGGATT
1 TTTCTTTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAAATTTGAATT
54861 TGTTTTCACATTAAACAAAGTTAATCTCACTTGAGAT
66 TG-TTTCACATTAAACAAAGTTAATCTCACTTGAGAT
54898 CGTTTTCTCA
Statistics
Matches: 176, Mismatches: 22, Indels: 22
0.80 0.10 0.10
Matches are distributed among these distances:
103 26 0.15
104 41 0.23
105 19 0.11
108 3 0.02
109 47 0.27
110 38 0.22
111 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (105 bp):
TTTCTTTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAAATTTGAATT
TGTTTCACATTAAACAAAGTTAATCTCACTTGAGATTCAC
Found at i:55048 original size:30 final size:31
Alignment explanation
Indices: 55012--55070 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
55002 AACAAACATT
*
55012 ATCTTTGAGT-TGTTTCTTTTGAAACAAAGG
1 ATCTTTGAGTCTATTTCTTTTGAAACAAAGG
55042 ATCTTTGAGTCTATTTCTTTTGAAACAAA
1 ATCTTTGAGTCTATTTCTTTTGAAACAAA
55071 ACTTTGTCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (31 bp):
ATCTTTGAGTCTATTTCTTTTGAAACAAAGG
Found at i:55202 original size:100 final size:101
Alignment explanation
Indices: 55042--55222 Score: 235
Period size: 100 Copynumber: 1.8 Consensus size: 101
55032 GAAACAAAGG
* *
55042 ATCTTTGAGTCTATTTCTTTTGAAACAAAACTTTGTCTCTCTTGAGACATATTTTATTGAAA-AA
1 ATCTTTGAGTATATTTCTTTTGAAACAAAACTTTGTCTCTCTTGAGACAAATTTTATTGAAAGAA
*
55106 TATTTGAGTCTGTTTCATCTAAAACAAAATGAAAAA
66 TATTTGAGTATGTTTCATCTAAAACAAAATGAAAAA
* * * *
55142 ATCTTTGAGTATGTTTC-TTTGACAACAAAATTTTGTCTCTTTTGA-A-AAAGTTTCTTTTGAAA
1 ATCTTTGAGTATATTTCTTTTGA-AACAAAACTTTGTCTCTCTTGAGACAAA-TTT-TATTGAAA
*
55204 GAATCTTTGAGTATGTTTC
63 GAATATTTGAGTATGTTTC
55223 TTTGGAAACA
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
98 2 0.03
99 9 0.13
100 42 0.61
101 16 0.23
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (101 bp):
ATCTTTGAGTATATTTCTTTTGAAACAAAACTTTGTCTCTCTTGAGACAAATTTTATTGAAAGAA
TATTTGAGTATGTTTCATCTAAAACAAAATGAAAAA
Found at i:55419 original size:28 final size:29
Alignment explanation
Indices: 55260--55424 Score: 145
Period size: 29 Copynumber: 5.6 Consensus size: 29
55250 AGAAATACAA
* * * *
55260 TTTCTCTTAAAACAAATATCTTTGTGATTG
1 TTTCTTTTGAAACAAAAATCTTTGAG-TTG
** *
55290 TTTCCCTTGAAACAAAACCTATCTTTAAGTTTG
1 TTTCTTTTGAAACAAAA---ATCTTTGAG-TTG
* * *
55323 TTTCTCTTGAAACAAAAGTCTGTGAGTTG
1 TTTCTTTTGAAACAAAAATCTTTGAGTTG
*
55352 TTTCTTTTGAAATAAAAATCTTTGAGTTG
1 TTTCTTTTGAAACAAAAATCTTTGAGTTG
*
55381 TTTCTTTTG-AA-AAAATTCTTTGAGTCTG
1 TTTCTTTTGAAACAAAAATCTTTGAGT-TG
*
55409 TTTCTTTTGAACCAAA
1 TTTCTTTTGAAACAAA
55425 GTTTTGTTTC
Statistics
Matches: 113, Mismatches: 16, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
27 13 0.12
28 13 0.12
29 38 0.34
30 23 0.20
33 26 0.23
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (29 bp):
TTTCTTTTGAAACAAAAATCTTTGAGTTG
Found at i:55515 original size:29 final size:29
Alignment explanation
Indices: 55260--55515 Score: 134
Period size: 29 Copynumber: 8.6 Consensus size: 29
55250 AGAAATACAA
* * * *
55260 TTTCTCTTAAAACAAATATCTTTGTGATTG
1 TTTCTTTTGAAACAAA-ATCTTTGAGTTTG
** *
55290 TTTCCCTTGAAACAAAACCTATCTTTAAGTTTG
1 TTTCTTTTGAAAC-AAA---ATCTTTGAGTTTG
* *
55323 TTTCTCTTGAAACAAAAGTCTGTGAG-TTG
1 TTTCTTTTGAAACAAAA-TCTTTGAGTTTG
*
55352 TTTCTTTTGAAATAAAAATCTTTGAG-TTG
1 TTTCTTTTGAAA-CAAAATCTTTGAGTTTG
* *
55381 TTTCTTTTGAAA-AAATTCTTTGAGTCTG
1 TTTCTTTTGAAACAAAATCTTTGAGTTTG
* * *
55409 TTTCTTTTGAACCAAAGT-TTT--GTTTC
1 TTTCTTTTGAAACAAAATCTTTGAGTTTG
***
55435 TCTTAAGGCAATTTCGTG-AA-AAAATCTTTGAG-ACA
1 T-TT----C--TTT--TGAAACAAAATCTTTGAGTTTG
55470 TTTCTTTTGAAACCAAAATCTTTGAGTTTG
1 TTTCTTTTGAAA-CAAAATCTTTGAGTTTG
55500 TTTCTTTTGAAACAAA
1 TTTCTTTTGAAACAAA
55516 GTTTTGTCTC
Statistics
Matches: 178, Mismatches: 25, Indels: 47
0.71 0.10 0.19
Matches are distributed among these distances:
26 6 0.03
27 15 0.08
28 19 0.11
29 57 0.32
30 34 0.19
31 4 0.02
32 3 0.02
33 30 0.17
34 6 0.03
35 3 0.02
36 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (29 bp):
TTTCTTTTGAAACAAAATCTTTGAGTTTG
Found at i:55516 original size:91 final size:89
Alignment explanation
Indices: 55365--55586 Score: 252
Period size: 91 Copynumber: 2.4 Consensus size: 89
55355 CTTTTGAAAT
*** * *
55365 AAAAATCTTTGAGTTGTTTCTTTTGAAAAAATTCTTTGAGTCTGTTTCTTTTGAACCAAAGTTTT
1 AAAAATCTTTGAGACATTTCTTTTGAAAAAAATCTTTGAGTCTGTTTCTTTTGAAACAAAGTTTT
*
55430 GTTTCTCTTAAGGCAATTTCGTGA
66 GTCTCTCTTAAGGCAATTTCGTGA
*
55454 AAAAATCTTTGAGACATTTCTTTTGAAACCAAAATCTTTGAGTTTGTTTCTTTTGAAACAAAGTT
1 AAAAATCTTTGAGACATTTCTTTTGAAA--AAAATCTTTGAGTCTGTTTCTTTTGAAACAAAGTT
* * * *
55519 TTGTCTCTCTTGAGACAGTTTTTCTTGA
64 TTGTCTCTCTTAAGGCA--ATTTCGTGA
*
55547 GAAAAATCTTTGAGTC-TGTTCCTTTTG--AAAAATCTTTGAG
1 -AAAAATCTTTGAGACAT-TT-CTTTTGAAAAAAATCTTTGAG
55587 ATTGTGCCTC
Statistics
Matches: 114, Mismatches: 12, Indels: 12
0.83 0.09 0.09
Matches are distributed among these distances:
89 25 0.22
91 58 0.51
93 9 0.08
94 16 0.14
95 6 0.05
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.44
Consensus pattern (89 bp):
AAAAATCTTTGAGACATTTCTTTTGAAAAAAATCTTTGAGTCTGTTTCTTTTGAAACAAAGTTTT
GTCTCTCTTAAGGCAATTTCGTGA
Found at i:56041 original size:134 final size:134
Alignment explanation
Indices: 55799--56152 Score: 492
Period size: 134 Copynumber: 2.6 Consensus size: 134
55789 AATCATTATC
* * * * * * *
55799 CCTAAAGATGGCCAGAACTCTTTATCATGTGTGAGTTGTGTCATCTCCTGACCAGATCTCTTCAT
1 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCCCGACCAGATCTCCTCAT
* * * * *
55864 CACGTAGGAGTCGTGTCACCCCTAGATAACCAGACGTCGTCATCATGTAGGAACCGTGTTATCGC
66 CACGTAGGAGCCGTGTCACCCCTAGATAACCAGACGTCCTCATCACGTAGGAACCGAGTTATCAC
*
55929 CCTT
131 CATT
*
55933 CCTAAAGATGGCCAAAACTCTTCATCACGTATGAGTCGTGTCATCCCCCGACCAGATCTCCTCAT
1 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCCCGACCAGATCTCCTCAT
* * * * *
55998 CGCGTAGGAGCCGTGTTACCCCTAGATATCCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCAC
66 CACGTAGGAGCCGTGTCACCCCTAGATAACCAGACGTCCTCATCACGTAGGAACCGAGTTATCAC
56063 CATT
131 CATT
* * *
56067 CCTAAAGATGACCAGAACTCTTCATCACGTATGAGACGTGTCATCCCCCGACCAGATTTCCTCAT
1 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCCCGACCAGATCTCCTCAT
* *
56132 CACGTAGAAACCGTGTCACCC
66 CACGTAGGAGCCGTGTCACCC
56153 TTAAACGACC
Statistics
Matches: 193, Mismatches: 27, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
134 193 1.00
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (134 bp):
CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCCCGACCAGATCTCCTCAT
CACGTAGGAGCCGTGTCACCCCTAGATAACCAGACGTCCTCATCACGTAGGAACCGAGTTATCAC
CATT
Found at i:56176 original size:43 final size:40
Alignment explanation
Indices: 56076--56183 Score: 103
Period size: 40 Copynumber: 2.6 Consensus size: 40
56066 TCCTAAAGAT
* *
56076 GACCAGAACTCTTCATCACGTATGAGACGTGTCATCCCCC
1 GACCAGAACTCTTCATCACGTATGAAACGTGTCATCCCAC
** *
56116 GACCAGATTTCCTCATCACGTA-GAAACCGTGTCA-CCCTTAAAC
1 GACCAGAACTCTTCATCACGTATGAAA-CGTGTCATCCC----AC
*
56159 GACCAGAACTCTTCATCATGTATGA
1 GACCAGAACTCTTCATCACGTATGA
56184 GCAGTGTCGT
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
39 6 0.11
40 26 0.49
43 19 0.36
44 2 0.04
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24
Consensus pattern (40 bp):
GACCAGAACTCTTCATCACGTATGAAACGTGTCATCCCAC
Found at i:63204 original size:26 final size:26
Alignment explanation
Indices: 63174--63229 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
63164 TTTACAAATT
63174 CTTTCTTATTATCAATTCCTCAACTC
1 CTTTCTTATTATCAATTCCTCAACTC
63200 CTTTCTTATTATCAATTCCTCAACTC
1 CTTTCTTATTATCAATTCCTCAACTC
63226 CTTT
1 CTTT
63230 ATATTCTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.21, C:0.30, G:0.00, T:0.48
Consensus pattern (26 bp):
CTTTCTTATTATCAATTCCTCAACTC
Found at i:68027 original size:55 final size:55
Alignment explanation
Indices: 67980--68259 Score: 368
Period size: 55 Copynumber: 5.1 Consensus size: 55
67970 TTTACGTGGG
* * * *
67980 TTGCACACCCACTGTCAATACGAAAATTCATAAACTTATTATGAATTTTTTAGTT
1 TTGCACACACAGTGTCCATACGAAAATTCATAAACTTATTATGAATTTCTTAGTT
* * *
68035 TTGTACACACAGTGTCTATACGGAAATTCATAAACTTATTATGAATTTCTTAGTT
1 TTGCACACACAGTGTCCATACGAAAATTCATAAACTTATTATGAATTTCTTAGTT
*
68090 TTGCACACACAGTG-CCTATAC-AGAAATTCATAAATTTATTATGAATTTCTTAGTT
1 TTGCACACACAGTGTCC-ATACGA-AAATTCATAAACTTATTATGAATTTCTTAGTT
* * ** * *
68145 TTACACATACAGTACCCATATGAAAATTTATAAACTTATTATGAATTTCTTAGTT
1 TTGCACACACAGTGTCCATACGAAAATTCATAAACTTATTATGAATTTCTTAGTT
* * *
68200 TTACACACACAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAG-T
1 TTGCACACACAGTGTCCATACGAAAATTCATAAACTTATTATGAATTTCTTAGTT
68254 TTGCAC
1 TTGCAC
68260 GCATAGTGCC
Statistics
Matches: 199, Mismatches: 22, Indels: 9
0.87 0.10 0.04
Matches are distributed among these distances:
54 7 0.04
55 189 0.95
56 3 0.02
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (55 bp):
TTGCACACACAGTGTCCATACGAAAATTCATAAACTTATTATGAATTTCTTAGTT
Found at i:74407 original size:2 final size:2
Alignment explanation
Indices: 74374--74439 Score: 75
Period size: 2 Copynumber: 33.5 Consensus size: 2
74364 TGTATGATAA
* *
74374 AT AT AT A- AT CT AT AC AT AT A- AT GAT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT
74414 AT AT AT AT AT AT AT AT AT AT ACT AT A
1 AT AT AT AT AT AT AT AT AT AT A-T AT A
74440 ACATAAATGT
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
1 3 0.05
2 48 0.87
3 4 0.07
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:77116 original size:54 final size:53
Alignment explanation
Indices: 76932--77343 Score: 469
Period size: 55 Copynumber: 7.6 Consensus size: 53
76922 ACCAATATAG
* * * * *
76932 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAATGCCTATATGG
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTT--TCACACAGTGCCCATACGA
* * *
76987 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGTACACATAGTGGCCATA-TA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTT-T-CACACAGTGCCCATACGA
*
77041 GAAATTCATAAACTTATTATGAATTT-TATAGTTTTTCACATATGTGCCCATACGA
1 -AAATTCATAAACTTATTATGAATTTCT-TAGTTTTTCACACA-GTGCCCATACGA
* *
77096 AAATTCATCAACTTATTATGAATTTCTTAGTTTGTACACACAGTGCCCATACGA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTT-TTCACACAGTGCCCATACGA
*
77150 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATAC-A
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTT--TCACACAGTGCCCATACGA
* *
77204 GAAA-TCATAAACTTATTATGAATTT-TATAGTTTTCCACACACAATGCCCATACGA
1 -AAATTCATAAACTTATTATGAATTTCT-TAGTTTT--TCACACAGTGCCCATACGA
* *
77259 AAATT-ATTCAACTTATTATGAATTTCTTTA-TTTTGTACACACAGTGCCCATACGG
1 AAATTCA-TAAACTTATTATGAATTTC-TTAGTTTT-T-CACACAGTGCCCATACGA
77314 AAATTCATAAACTTATTATGAATTTCTTAG
1 AAATTCATAAACTTATTATGAATTTCTTAG
77344 ATTGCACGCA
Statistics
Matches: 316, Mismatches: 22, Indels: 38
0.84 0.06 0.10
Matches are distributed among these distances:
53 8 0.03
54 137 0.43
55 167 0.53
56 3 0.01
57 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (53 bp):
AAATTCATAAACTTATTATGAATTTCTTAGTTTTTCACACAGTGCCCATACGA
Found at i:77277 original size:109 final size:108
Alignment explanation
Indices: 76932--77343 Score: 550
Period size: 109 Copynumber: 3.8 Consensus size: 108
76922 ACCAATATAG
* * *
76932 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAATGCCTATATGGAAATTCATAA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGGAAATTCATAA
* * *
76997 ACTTATTATGAATTTCTTAGTTTTGTACACATAGTGGCCATA-TA
66 ACTTATTATGAATTTCTTAG-TTT-TACACACAGTGCCCATACGA
* * * *
77041 GAAATTCATAAACTTATTATGAATTT-TATAGTTTTTCACATA-TGTGCCCATACGAAAATTCAT
1 -AAATTCATAAACTTATTATGAATTTCT-TAGTTTTGCACACACAGTGCCCATACGGAAATTCAT
*
77104 CAACTTATTATGAATTTCTTAGTTTGTACACACAGTGCCCATACGA
64 AAACTTATTATGAATTTCTTAGTTT-TACACACAGTGCCCATACGA
*
77150 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACAGAAA-TCATAA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGGAAATTCATAA
*
77214 ACTTATTATGAATTT-TATAGTTTTCCACACACAATGCCCATACGA
66 ACTTATTATGAATTTCT-TAGTTTT--ACACACAGTGCCCATACGA
* *
77259 AAATT-ATTCAACTTATTATGAATTTCTTTA-TTTTGTACACACAGTGCCCATACGGAAATTCAT
1 AAATTCA-TAAACTTATTATGAATTTC-TTAGTTTTGCACACACAGTGCCCATACGGAAATTCAT
77322 AAACTTATTATGAATTTCTTAG
64 AAACTTATTATGAATTTCTTAG
77344 ATTGCACGCA
Statistics
Matches: 270, Mismatches: 21, Indels: 22
0.86 0.07 0.07
Matches are distributed among these distances:
107 2 0.01
108 83 0.31
109 120 0.44
110 64 0.24
111 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (108 bp):
AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGGAAATTCATAA
ACTTATTATGAATTTCTTAGTTTTACACACAGTGCCCATACGA
Found at i:79207 original size:30 final size:29
Alignment explanation
Indices: 79173--79243 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
79163 TTTATATTTA
79173 TATTTTAGTCCTTTAAATGTCTAT-TTTTGC
1 TATTTTAGTCCTTT-AA-GTCTATGTTTTGC
* *
79203 TATTTTAGTTCC-TTAAGTTTTTGTTTTGC
1 TATTTTAG-TCCTTTAAGTCTATGTTTTGC
79232 TATTTTAGTCCT
1 TATTTTAGTCCT
79244 CAAGTTTATG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
28 7 0.19
29 16 0.44
30 10 0.28
31 3 0.08
ACGTcount: A:0.17, C:0.13, G:0.11, T:0.59
Consensus pattern (29 bp):
TATTTTAGTCCTTTAAGTCTATGTTTTGC
Found at i:79255 original size:28 final size:29
Alignment explanation
Indices: 79197--79255 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 29
79187 AAATGTCTAT
* *
79197 TTTTGCTATTTTAGTTCCTTAAGTTTTTG
1 TTTTGCTATTTTAGTTCCTCAAGTTTATG
79226 TTTTGCTATTTTAG-TCCTCAAGTTTATG
1 TTTTGCTATTTTAGTTCCTCAAGTTTATG
79254 TT
1 TT
79256 AATCATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.15, C:0.12, G:0.14, T:0.59
Consensus pattern (29 bp):
TTTTGCTATTTTAGTTCCTCAAGTTTATG
Done.