Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008337.1 Hibiscus syriacus cultivar Beakdansim tig00111057_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: 840327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:5515 original size:21 final size:21
Alignment explanation
Indices: 5491--5540 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
5481 CAAAGGTCAA
5491 TGATGATCATCAAAAGAAAAT
1 TGATGATCATCAAAAGAAAAT
5512 TGATGATCATCAAAAGAAAAT
1 TGATGATCATCAAAAGAAAAT
5533 TGATGATC
1 TGATGATC
5541 TTAAAACTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.26
Consensus pattern (21 bp):
TGATGATCATCAAAAGAAAAT
Found at i:10877 original size:12 final size:12
Alignment explanation
Indices: 10856--10885 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
10846 AGGTGAGCCT
*
10856 GAGCAGCCCGAG
1 GAGCAACCCGAG
10868 GAGCAACCCGAG
1 GAGCAACCCGAG
10880 GAGCAA
1 GAGCAA
10886 GCACAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.30, G:0.37, T:0.00
Consensus pattern (12 bp):
GAGCAACCCGAG
Found at i:20337 original size:21 final size:20
Alignment explanation
Indices: 20291--20451 Score: 175
Period size: 21 Copynumber: 8.0 Consensus size: 20
20281 TTTTGTTGCT
20291 GAAAGTATCGATACTCTT-G
1 GAAAGTATCGATACTCTTGG
*
20310 GAAAGTATCCATACTCTTGG
1 GAAAGTATCGATACTCTTGG
20330 GAAAAGTATCGATACTCTTGG
1 G-AAAGTATCGATACTCTTGG
* *
20351 GTAAAGTGTCAATACTCTT-G
1 G-AAAGTATCGATACTCTTGG
20371 GAAAGTATCGATACTCTTGG
1 GAAAGTATCGATACTCTTGG
* * *
20391 GTAAAGTATCCATTCT-TTTG
1 G-AAAGTATCGATACTCTTGG
*
20411 GAAAGTATAGATACTCTTGG
1 GAAAGTATCGATACTCTTGG
* * *
20431 GTAAGGTATCCATACTATTGG
1 G-AAAGTATCGATACTCTTGG
20452 AAGGTATCAA
Statistics
Matches: 118, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 43 0.36
20 14 0.12
21 61 0.52
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (20 bp):
GAAAGTATCGATACTCTTGG
Found at i:20347 original size:40 final size:41
Alignment explanation
Indices: 20291--20468 Score: 222
Period size: 40 Copynumber: 4.4 Consensus size: 41
20281 TTTTGTTGCT
20291 GAAAGTATCGATACTCTT-GG-AAAGTATCCATACTCTTGG
1 GAAAGTATCGATACTCTTGGGTAAAGTATCCATACTCTTGG
* *
20330 GAAAAGTATCGATACTCTTGGGTAAAGTGTCAATACTCTT-G
1 G-AAAGTATCGATACTCTTGGGTAAAGTATCCATACTCTTGG
* *
20371 GAAAGTATCGATACTCTTGGGTAAAGTATCCATTCT-TTTG
1 GAAAGTATCGATACTCTTGGGTAAAGTATCCATACTCTTGG
* * *
20411 GAAAGTATAGATACTCTTGGGTAAGGTATCCATACTATT-G
1 GAAAGTATCGATACTCTTGGGTAAAGTATCCATACTCTTGG
* * *
20451 GAAGGTATCAATGCTCTT
1 GAAAGTATCGATACTCTT
20469 TGTCTGAAAT
Statistics
Matches: 122, Mismatches: 12, Indels: 9
0.85 0.08 0.06
Matches are distributed among these distances:
39 3 0.02
40 98 0.80
41 6 0.05
42 15 0.12
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.33
Consensus pattern (41 bp):
GAAAGTATCGATACTCTTGGGTAAAGTATCCATACTCTTGG
Found at i:20440 original size:61 final size:60
Alignment explanation
Indices: 20291--20451 Score: 191
Period size: 61 Copynumber: 2.6 Consensus size: 60
20281 TTTTGTTGCT
* *
20291 GAAAGTATCGATACTCTTGGAAAGTATCCATACTCTTGGGAAAAGTATCGATACTCTTGG
1 GAAAGTATAGATACTCTTGGAAAGTATCCATACTCTTGGGAAAAGTATCCATACTCTTGG
* * * * *
20351 GTAAAGTGTCA-ATACTCTTGGAAAGTATCGATACTCTTGGGTAAAGTATCCATTCT-TTTG
1 G-AAAGTAT-AGATACTCTTGGAAAGTATCCATACTCTTGGGAAAAGTATCCATACTCTTGG
* *
20411 GAAAGTATAGATACTCTTGGGTAAGGTATCCATACTATTGG
1 GAAAGTATAGATACTCTT-GG-AAAGTATCCATACTCTTGG
20452 AAGGTATCAA
Statistics
Matches: 85, Mismatches: 11, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
58 1 0.01
59 14 0.16
60 7 0.08
61 63 0.74
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (60 bp):
GAAAGTATAGATACTCTTGGAAAGTATCCATACTCTTGGGAAAAGTATCCATACTCTTGG
Found at i:22026 original size:40 final size:41
Alignment explanation
Indices: 21964--22065 Score: 104
Period size: 40 Copynumber: 2.5 Consensus size: 41
21954 TTTAAACATA
21964 TAGTGGCATTTATATTT-C-AAACGCCACAAAATG-GTA-ACTT
1 TAGTGGCATTT-T-TTTACAAAACGCCACAAAA-GAGTAGACTT
* *
22004 TAGTGGCATTTTTTTACAAAACGTCACGAAAGAGTAGTACTT
1 TAGTGGCATTTTTTTACAAAACGCCACAAAAGAGTAG-ACTT
* *
22046 TAGTGGCGTTTTTATACAAA
1 TAGTGGCATTTTTTTACAAA
22066 TGCCGTTCAT
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
38 3 0.06
39 3 0.06
40 25 0.47
42 22 0.42
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (41 bp):
TAGTGGCATTTTTTTACAAAACGCCACAAAAGAGTAGACTT
Found at i:22225 original size:82 final size:82
Alignment explanation
Indices: 22078--22249 Score: 220
Period size: 82 Copynumber: 2.1 Consensus size: 82
22068 CCGTTCATTC
* * * ** *
22078 TATACAAATGTCGCAATAAGTTCATTCATAGTGGCTTTTTTTCAACAAACACCGTGACAGTGTAG
1 TATACAAATGCCGCAATAAGTTCATCCATAGTGGCTTTTTTTAAACAAACACCGCAACAGAGTAG
**
22143 TACTTTAGTGGTGTTTT
66 TACTTTAGCAGTGTTTT
* * *
22160 TATACAAATGCCTCAATAGGGTTCATCCATAGTGGC-TTTTTTAAACAAACGCCGCAACAGAGTA
1 TATACAAATGCCGCAATA-AGTTCATCCATAGTGGCTTTTTTTAAACAAACACCGCAACAGAGTA
*
22224 GTACTTTAGCAGTTTTTT
65 GTACTTTAGCAGTGTTTT
22242 TATACAAA
1 TATACAAA
22250 CGTCGTGGCG
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
82 62 0.81
83 15 0.19
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (82 bp):
TATACAAATGCCGCAATAAGTTCATCCATAGTGGCTTTTTTTAAACAAACACCGCAACAGAGTAG
TACTTTAGCAGTGTTTT
Found at i:26223 original size:18 final size:20
Alignment explanation
Indices: 26192--26234 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
26182 AGTATATAAT
*
26192 TTAAACACTTATTTT-TTTA
1 TTAAACACTTATTTTAATTA
26211 TTAAACA-TTATTTTAATTA
1 TTAAACACTTATTTTAATTA
26230 TTAAA
1 TTAAA
26235 GTAAAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAAACACTTATTTTAATTA
Found at i:33518 original size:20 final size:20
Alignment explanation
Indices: 33493--33535 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
33483 AAAGTTTTCC
*
33493 ACGGTGATCTGGTGTATTTG
1 ACGGTGATCTGGCGTATTTG
*
33513 ACGGTGGTCTGGCGTATTTG
1 ACGGTGATCTGGCGTATTTG
33533 ACG
1 ACG
33536 ATGACACAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.37, T:0.35
Consensus pattern (20 bp):
ACGGTGATCTGGCGTATTTG
Found at i:34218 original size:20 final size:20
Alignment explanation
Indices: 34190--34250 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 20
34180 AAATCTTACT
34190 TATGCATATAAAAAAGAATA
1 TATGCATATAAAAAAGAATA
* * * *
34210 TATGTATATAATATA-TATA
1 TATGCATATAAAAAAGAATA
34229 TATGCATATAAAAAAGAATA
1 TATGCATATAAAAAAGAATA
34249 TA
1 TA
34251 CGTATATATA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.56, C:0.03, G:0.08, T:0.33
Consensus pattern (20 bp):
TATGCATATAAAAAAGAATA
Found at i:34244 original size:39 final size:38
Alignment explanation
Indices: 34190--34263 Score: 130
Period size: 39 Copynumber: 1.9 Consensus size: 38
34180 AAATCTTACT
*
34190 TATGCATATAAAAAAGAATATATGTATATAATATATATA
1 TATGCATATAAAAAAGAATATACGTATAT-ATATATATA
34229 TATGCATATAAAAAAGAATATACGTATATATATAT
1 TATGCATATAAAAAAGAATATACGTATATATATAT
34264 GGTAAGGGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
38 6 0.18
39 28 0.82
ACGTcount: A:0.53, C:0.04, G:0.08, T:0.35
Consensus pattern (38 bp):
TATGCATATAAAAAAGAATATACGTATATATATATATA
Found at i:36548 original size:28 final size:28
Alignment explanation
Indices: 36511--36574 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 28
36501 CAGCATTTTA
36511 AATTT-CAGTA-TTTATTTCAGTCCTTT
1 AATTTCCAGTATTTTATTTCAGTCCTTT
36537 AATTTTCCAGTATTTTATTTCAGTCCTTT
1 AA-TTTCCAGTATTTTATTTCAGTCCTTT
36566 AATTTCCAG
1 AATTTCCAG
36575 CCTTTTAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
26 2 0.06
27 3 0.09
28 12 0.34
29 18 0.51
ACGTcount: A:0.23, C:0.17, G:0.08, T:0.52
Consensus pattern (28 bp):
AATTTCCAGTATTTTATTTCAGTCCTTT
Found at i:36585 original size:29 final size:29
Alignment explanation
Indices: 36521--36581 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
36511 AATTTCAGTA
*
36521 TTTATTTCAGTCCTTTAATTTTCCAGTAT
1 TTTATTTCAGTCCTTTAATTTTCCAGCAT
*
36550 TTTATTTCAGTCCTTTAA-TTTCCAGCCT
1 TTTATTTCAGTCCTTTAATTTTCCAGCAT
36578 TTTA
1 TTTA
36582 ATTTTCTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 12 0.40
29 18 0.60
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.54
Consensus pattern (29 bp):
TTTATTTCAGTCCTTTAATTTTCCAGCAT
Found at i:36813 original size:2 final size:2
Alignment explanation
Indices: 36806--36861 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
36796 ATGCTTTCTA
36806 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
36848 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
36862 GTAAATAAGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37044 original size:16 final size:16
Alignment explanation
Indices: 37023--37056 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
37013 CCTCTTTTGA
37023 TTATTTTATTTTATTT
1 TTATTTTATTTTATTT
* *
37039 TTATTTTGTTTTGTTT
1 TTATTTTATTTTATTT
37055 TT
1 TT
37057 TTAAATGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (16 bp):
TTATTTTATTTTATTT
Found at i:39587 original size:29 final size:30
Alignment explanation
Indices: 39551--39616 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 30
39541 GTATGATTTT
39551 GAAACAAATAAAAGTTTAAGTACTAAAA-A
1 GAAACAAATAAAAGTTTAAGTACTAAAACA
39580 GAAACAAATAAAAGTTTAAGTACTAAAACA
1 GAAACAAATAAAAGTTTAAGTACTAAAACA
39610 -AAACAAA
1 GAAACAAA
39617 ATTGATAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 35 0.97
30 1 0.03
ACGTcount: A:0.64, C:0.09, G:0.09, T:0.18
Consensus pattern (30 bp):
GAAACAAATAAAAGTTTAAGTACTAAAACA
Found at i:41632 original size:452 final size:452
Alignment explanation
Indices: 40788--41688 Score: 1437
Period size: 452 Copynumber: 2.0 Consensus size: 452
40778 CATTATTATG
* **
40788 GATGAATCAAGAATAGATTATAATTCCAAGTGAATTATTAAGGGACATGATATAGTTGGCATGCC
1 GATGAATCAAGAATAGACTATAAGCCCAAGTGAATTATTAAGGGACATGATATAGTTGGCATGCC
* *
40853 ATAGAGTCCAACAACAGGCTATATATTCGGCATTACACTAAAGTATAATTAGTGTATATAGTGGG
66 ATAGAGTCCAACAACAGACTACATATTCGGCATTACACTAAAGTATAATTAGTGTATATAGTGGG
* * * * * * *
40918 CATAATCTTATGTGTCATATTCGGGACTGTACTTAAGTATACCTAGTACAGATGGTGAACACCAC
131 AACAATCTTATGTGTCATATTCAGGACTGTACATAAGTATACCCAATACAGATAGTGAACACCAC
* *
40983 CTTATGTGTCATACTAGGGTTAGCACTTCGGTGTTTATTTATATTGACTCGTGTACCTAGGGTCC
196 CTTATGTGTCATACTAGGGTTAGAACTACGGTGTTTATTTATATTGACTCGTGTACCTAGGGTCC
* *
41048 TCAAGGTCTATATATTAGGCTATGATTTATTGAAAATATTTTATAATGCACCATTATCATGTTTA
261 TCAAGGTCTACATATTAGGCTAAGATTTATTGAAAATATTTTATAATGCACCATTATCATGTTTA
41113 CTATAGTAATTAAATGGTTATACAGGTAAGTGATCATGCTACATTGATTATGACATATGGTTGTA
326 CTATAGTAATTAAATGGTTATACAGGTAAGTGATCATGCTACATTGATTATGACATATGGTTGTA
*
41178 TATTAATGATGTATTGCACTGTTTATTACTATTGATTACCTCACTAAGTATATACTTAGCAT
391 TATTAATGATGTATTGCACGGTTTATTACTATTGATTACCTCACTAAGTATATACTTAGCAT
* *
41240 GATGAATCAAGAATAGACTATAAGCCCAAGTGAATTATTGAGGGACATGGTATAGTTGGCATGCC
1 GATGAATCAAGAATAGACTATAAGCCCAAGTGAATTATTAAGGGACATGATATAGTTGGCATGCC
* ** * *
41305 ATAGAGTCCAGCAGTAGACTGCATATTCGGGATTACACTAAAGTATAATTAGTGTATATAGTGGG
66 ATAGAGTCCAACAACAGACTACATATTCGGCATTACACTAAAGTATAATTAGTGTATATAGTGGG
* ** *
41370 AACAATCTTATGTGTCATATTTAGGACTGTACATAAGTATACCCAATACAGATAGTGGGCACGAC
131 AACAATCTTATGTGTCATATTCAGGACTGTACATAAGTATACCCAATACAGATAGTGAACACCAC
* *
41435 CTTATGTGTCATACTCGGGTTAGAACTACGGTGTTTGTTTATATTGACTCGTGTACCTAGGGTCC
196 CTTATGTGTCATACTAGGGTTAGAACTACGGTGTTTATTTATATTGACTCGTGTACCTAGGGTCC
* * *
41500 TGAAGGTTTACATATTGGGCTACAG-TTTATTGAAAATATTTTATAATGCACCATTATCATGTTT
261 TCAAGGTCTACATATTAGGCTA-AGATTTATTGAAAATATTTTATAATGCACCATTATCATGTTT
*
41564 ATTATAGTAATTAAATGGTTATA-ATGGTAAGTGATCATGCTACATTGATTATGACATATGGTTG
325 ACTATAGTAATTAAATGGTTATACA-GGTAAGTGATCATGCTACATTGATTATGACATATGGTTG
* * *
41628 TATATTAATGATGTATTGCACGGTTTATTACTGTTGATTGCCTCACTAAGTATGTACTTAG
389 TATATTAATGATGTATTGCACGGTTTATTACTATTGATTACCTCACTAAGTATATACTTAG
41689 TGTGATGCTT
Statistics
Matches: 410, Mismatches: 37, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
451 1 0.00
452 408 1.00
453 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (452 bp):
GATGAATCAAGAATAGACTATAAGCCCAAGTGAATTATTAAGGGACATGATATAGTTGGCATGCC
ATAGAGTCCAACAACAGACTACATATTCGGCATTACACTAAAGTATAATTAGTGTATATAGTGGG
AACAATCTTATGTGTCATATTCAGGACTGTACATAAGTATACCCAATACAGATAGTGAACACCAC
CTTATGTGTCATACTAGGGTTAGAACTACGGTGTTTATTTATATTGACTCGTGTACCTAGGGTCC
TCAAGGTCTACATATTAGGCTAAGATTTATTGAAAATATTTTATAATGCACCATTATCATGTTTA
CTATAGTAATTAAATGGTTATACAGGTAAGTGATCATGCTACATTGATTATGACATATGGTTGTA
TATTAATGATGTATTGCACGGTTTATTACTATTGATTACCTCACTAAGTATATACTTAGCAT
Found at i:45870 original size:42 final size:41
Alignment explanation
Indices: 45772--45879 Score: 112
Period size: 41 Copynumber: 2.6 Consensus size: 41
45762 TTTTTACTTG
** *
45772 ACTCGAATTAATTTCAAGTTGTAATTTCATAACTCAACTCT
1 ACTCGAAAAAATTTCAAGTTGAAATTTCATAACTCAACTCT
** *
45813 ACTCGAATTAATTTCAAGTTGAAATTTCATAAACTCGACT-T
1 ACTCGAAAAAATTTCAAGTTGAAATTTCAT-AACTCAACTCT
*
45854 GACTC-AAAAAGATTTCAAGTTCAAAT
1 -ACTCGAAAAA-ATTTCAAGTTGAAAT
45880 CGAGTTGTGA
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
41 33 0.56
42 26 0.44
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (41 bp):
ACTCGAAAAAATTTCAAGTTGAAATTTCATAACTCAACTCT
Found at i:47322 original size:28 final size:28
Alignment explanation
Indices: 47290--47348 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
47280 TGTATCTTTC
* *
47290 CTTGCTAGTATATATGTTTTATTGTTTA
1 CTTGCTACTATATATGTTTTATTGATTA
*
47318 CTTGCTACTATATTTGTTTTATTGATTA
1 CTTGCTACTATATATGTTTTATTGATTA
47346 CTT
1 CTT
47349 TTAAATATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.20, C:0.10, G:0.12, T:0.58
Consensus pattern (28 bp):
CTTGCTACTATATATGTTTTATTGATTA
Found at i:47538 original size:42 final size:42
Alignment explanation
Indices: 47474--47598 Score: 189
Period size: 42 Copynumber: 3.0 Consensus size: 42
47464 CCAGTTAAAC
*
47474 CTTCTAATAATCCGATTGGAAA-TTCTAATGATTCACCTAATA
1 CTTCTAATAATCCTATTGGAAATTTC-AATGATTCACCTAATA
* *
47516 CTTCTAATAATCCTATTAGAAATTTCAATGATTCACCTAATT
1 CTTCTAATAATCCTATTGGAAATTTCAATGATTCACCTAATA
* *
47558 CTTCTAATAATCCTATTGGGAATTTCAATAATTCACCTAAT
1 CTTCTAATAATCCTATTGGAAATTTCAATGATTCACCTAAT
47599 GATTCAGTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
42 73 0.96
43 3 0.04
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.38
Consensus pattern (42 bp):
CTTCTAATAATCCTATTGGAAATTTCAATGATTCACCTAATA
Found at i:63402 original size:41 final size:41
Alignment explanation
Indices: 63342--63419 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
63332 GGGTCGGGTC
* *
63342 GGGCAGTCGGGTCGGACCGGATCGGGTCGGTCAAAAGTGTT
1 GGGCAGTCAGGTCGAACCGGATCGGGTCGGTCAAAAGTGTT
*
63383 GGGCAGTCAGGTCGAACCGGGTCGGGTCGGTCAAAAG
1 GGGCAGTCAGGTCGAACCGGATCGGGTCGGTCAAAAG
63420 GGTCAAAACT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.19, C:0.21, G:0.44, T:0.17
Consensus pattern (41 bp):
GGGCAGTCAGGTCGAACCGGATCGGGTCGGTCAAAAGTGTT
Found at i:63474 original size:13 final size:13
Alignment explanation
Indices: 63455--63492 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
63445 GACTTCCCCA
63455 CGCGTAGGGGCGG
1 CGCGTAGGGGCGG
*
63468 TGCGTAGGGGCGG
1 CGCGTAGGGGCGG
63481 CGCGTAGGGGCG
1 CGCGTAGGGGCG
63493 TGTGAACCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.08, C:0.21, G:0.61, T:0.11
Consensus pattern (13 bp):
CGCGTAGGGGCGG
Found at i:64585 original size:16 final size:17
Alignment explanation
Indices: 64555--64587 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
64545 AGAAAACATG
64555 TATTATAAAGATAAAAT
1 TATTATAAAGATAAAAT
*
64572 TATTA-AAAGTTAAAAT
1 TATTATAAAGATAAAAT
64588 AATAAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (17 bp):
TATTATAAAGATAAAAT
Found at i:64886 original size:21 final size:21
Alignment explanation
Indices: 64860--64912 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
64850 TTTCCAGAAA
**
64860 CGCAATGCGATTTTGGACTAT
1 CGCAATGCGAACTTGGACTAT
64881 CGCAATGCGAACTTGGACTAT
1 CGCAATGCGAACTTGGACTAT
64902 CGCAATGCGAA
1 CGCAATGCGAA
64913 TATGTAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (21 bp):
CGCAATGCGAACTTGGACTAT
Found at i:65192 original size:39 final size:39
Alignment explanation
Indices: 65138--65232 Score: 165
Period size: 38 Copynumber: 2.5 Consensus size: 39
65128 TTCACAATAG
65138 TGTTTCCAATACTATGTGGGATTGAGCATTACCAACACT
1 TGTTTCCAATACTATGTGGGATTGAGCATTACCAACACT
*
65177 TGTTTCCAATACTATGT-GGATTGAGCATTACCAACATT
1 TGTTTCCAATACTATGTGGGATTGAGCATTACCAACACT
*
65215 TGTTTCCAATACAATGTG
1 TGTTTCCAATACTATGTG
65233 ATTATTCAGG
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
38 36 0.68
39 17 0.32
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (39 bp):
TGTTTCCAATACTATGTGGGATTGAGCATTACCAACACT
Found at i:65591 original size:6 final size:6
Alignment explanation
Indices: 65570--65618 Score: 84
Period size: 6 Copynumber: 8.5 Consensus size: 6
65560 CGTCGTCTCG
65570 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
65616 GGT
1 GGT
65619 AATACGTGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.23
6 33 0.77
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:65727 original size:21 final size:21
Alignment explanation
Indices: 65701--65784 Score: 79
Period size: 21 Copynumber: 4.2 Consensus size: 21
65691 CACCAGTCGT
*
65701 TGCGATTTTGGACTATCGCAA
1 TGCGATTTTCGACTATCGCAA
*
65722 TGCGATTTTGGAC--T---AA
1 TGCGATTTTCGACTATCGCAA
**
65738 TGCGATAGTCGACTATCGCAA
1 TGCGATTTTCGACTATCGCAA
**
65759 TGCGAACTTCGACTATCGCAA
1 TGCGATTTTCGACTATCGCAA
65780 TGCGA
1 TGCGA
65785 ATATGTAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
16 12 0.23
18 1 0.02
19 1 0.02
21 38 0.73
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (21 bp):
TGCGATTTTCGACTATCGCAA
Found at i:65785 original size:21 final size:21
Alignment explanation
Indices: 65746--65785 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
65736 AATGCGATAG
65746 TCGACTATCGCAATGCGAACT
1 TCGACTATCGCAATGCGAACT
65767 TCGACTATCGCAATGCGAA
1 TCGACTATCGCAATGCGAA
65786 TATGTAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.23
Consensus pattern (21 bp):
TCGACTATCGCAATGCGAACT
Found at i:65824 original size:21 final size:21
Alignment explanation
Indices: 65791--65846 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
65781 GCGAATATGT
* *
65791 AAATCGCAATGCGATAGTCGA
1 AAATCGCATTGCGATAGTCCA
**
65812 AGTTCGCATTGCGATAGTCCA
1 AAATCGCATTGCGATAGTCCA
65833 AAATCGCATTGCGA
1 AAATCGCATTGCGA
65847 ATCTGGAAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.23
Consensus pattern (21 bp):
AAATCGCATTGCGATAGTCCA
Found at i:67298 original size:20 final size:20
Alignment explanation
Indices: 67273--67327 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
67263 TTTGGTTCAC
*
67273 GGAATGTAAGATTATCAGTG
1 GGAATGTAAGATTACCAGTG
67293 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
67313 GGAATGTAAGATTAC
1 GGAATGTAAGATTAC
67328 TAGGGAATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.36, C:0.07, G:0.29, T:0.27
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:67557 original size:35 final size:37
Alignment explanation
Indices: 67486--67558 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 37
67476 GTTGGAAAAT
* *
67486 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
67523 ATTTATAT-TTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
67558 A
1 A
67559 GGTTTAATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 6 0.19
36 18 0.56
37 8 0.25
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:70087 original size:13 final size:13
Alignment explanation
Indices: 70069--70095 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
70059 TATAGTTGAA
70069 CAGTCTTCATATG
1 CAGTCTTCATATG
70082 CAGTCTTCATATG
1 CAGTCTTCATATG
70095 C
1 C
70096 GTGTCTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:72575 original size:21 final size:23
Alignment explanation
Indices: 72549--72596 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
72539 ATTGATATAG
*
72549 TTTACCTTT-TATTTT-AAATAA
1 TTTACCTTTAAATTTTCAAATAA
*
72570 TTTACCTTTAAATTTTCAACTAA
1 TTTACCTTTAAATTTTCAAATAA
72593 TTTA
1 TTTA
72597 TAATTATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 9 0.39
22 5 0.22
23 9 0.39
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTACCTTTAAATTTTCAAATAA
Found at i:72857 original size:111 final size:113
Alignment explanation
Indices: 72695--72924 Score: 331
Period size: 111 Copynumber: 2.1 Consensus size: 113
72685 AGAGTTGTAG
* *
72695 AATTTTCCAAGTATAAAATAATTAGAACTAATATAAATGCAATCAAATTGATTTTTCTTACATAA
1 AATTTTCCAAGTATAAAATAATTAGAACTAATATAAATACAATCAAATTGATTTTTCTTACAAAA
** * *
72760 -TTTATATATAGTCATTATTTAATAAATGCTTAAATTATATCTTCTATT
66 CTTTATATATAACCATTA-TTAATAAATGCTTAAATTATATCCTCAATT
* * * *
72808 AATTTTTCAAGTAT-AAATAATTA-AAGTAATATAAATACAATCAAGTTGATTTTTGTTACAAAA
1 AATTTTCCAAGTATAAAATAATTAGAACTAATATAAATACAATCAAATTGATTTTTCTTACAAAA
*
72871 CTTTATATATAACCATTATTAATAAGTGCTTAAATTATATCCTCAATT
66 CTTTATATATAACCATTATTAATAAATGCTTAAATTATATCCTCAATT
72919 AATTTT
1 AATTTT
72925 AAGAGGTTAA
Statistics
Matches: 105, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
111 68 0.65
112 24 0.23
113 13 0.12
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.43
Consensus pattern (113 bp):
AATTTTCCAAGTATAAAATAATTAGAACTAATATAAATACAATCAAATTGATTTTTCTTACAAAA
CTTTATATATAACCATTATTAATAAATGCTTAAATTATATCCTCAATT
Found at i:76616 original size:35 final size:34
Alignment explanation
Indices: 76531--76617 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
76521 ATTTGGTATT
*
76531 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
76565 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
76603 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
76618 ACTGAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:79005 original size:105 final size:110
Alignment explanation
Indices: 78725--79050 Score: 524
Period size: 110 Copynumber: 3.0 Consensus size: 110
78715 ATTACAAAAA
*
78725 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAAT-ATGCATTAAATAAATCAATTAATTATTACTAATAATTTAAATTA
*
78790 AATTAAAACGTTAAAATGTTACCGTATCAGC-AAGTGTAGAGATAT
65 AATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTGTAGAGATAT
78835 TTAATTCTTAATCTAATAATTATGCATTAAATAAATC-ATCTAATTATTACTAATAATTTAAATT
1 TTAATTCTTAATCTAATAA-TATGCATTAAATAAATCAAT-TAATTATTACTAATAATTTAAATT
*
78899 AAATTAAAACGCTAAAATG-TACTGTATCAGCAAAGTGTCA-AGATAT
64 AAATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTGT-AGAGATAT
*
78945 TTAATTCTTAATCTAAT-A-AT-CATT-AATAAATCAATTAAATATTACTAATAATTTAAATTAA
1 TTAATTCTTAATCTAATAATATGCATTAAATAAATCAATTAATTATTACTAATAATTTAAATTAA
79006 ATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTGTAGAGATAT
66 ATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTGTAGAGATAT
79051 ATGATTTCCA
Statistics
Matches: 204, Mismatches: 5, Indels: 18
0.90 0.02 0.08
Matches are distributed among these distances:
105 50 0.25
106 31 0.15
107 2 0.01
109 13 0.06
110 106 0.52
111 2 0.01
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (110 bp):
TTAATTCTTAATCTAATAATATGCATTAAATAAATCAATTAATTATTACTAATAATTTAAATTAA
ATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTGTAGAGATAT
Found at i:79149 original size:17 final size:17
Alignment explanation
Indices: 79109--79142 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
79099 GAATTATATT
79109 AGTAAAT-ATTAAATAA
1 AGTAAATAATTAAATAA
79125 AGTAAATAATTAAATAA
1 AGTAAATAATTAAATAA
79142 A
1 A
79143 TTCAATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
AGTAAATAATTAAATAA
Found at i:79261 original size:19 final size:20
Alignment explanation
Indices: 79237--79278 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
79227 AATGATTGAT
79237 GATGGGGTA-TTATAGGGAG
1 GATGGGGTATTTATAGGGAG
79256 GATGGGGTATTTATAGGGAG
1 GATGGGGTATTTATAGGGAG
79276 GAT
1 GAT
79279 TGGGATGTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.26, C:0.00, G:0.45, T:0.29
Consensus pattern (20 bp):
GATGGGGTATTTATAGGGAG
Found at i:84422 original size:12 final size:12
Alignment explanation
Indices: 84405--84439 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
84395 GAACAAAGCG
84405 TCTTTTTTTTTT
1 TCTTTTTTTTTT
*
84417 TCTTTTCTTTTT
1 TCTTTTTTTTTT
84429 TCTTCTTTTTT
1 TCTT-TTTTTT
84440 ATGTTGTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (12 bp):
TCTTTTTTTTTT
Found at i:85419 original size:110 final size:108
Alignment explanation
Indices: 85292--85506 Score: 403
Period size: 110 Copynumber: 2.0 Consensus size: 108
85282 ATGACACTAT
85292 GGAATGCTCGGCGTCTTCAAGCAATTGGACTGTGGGATATCTCGGCGTCTTCTGCATGCTACAAG
1 GGAATGCTCGGCGTCTTCAAGCAATTGGACTGTGGGATATCTCGGCGTCTTCTGCATGCTACAAG
85357 GAATGCCAAGGTGGATCTCTCGGCGTCTTCACCTGTCGTCTGATG
66 GAATGCCAAGGTGGA--TCTCGGCGTCTTCACCTGTCGTCTGATG
*
85402 GGAATGCTCGGCGTCTTCAAGCAATTGGACTGTGGGATCTCTCGGCGTCTTCTGCATGCTACAAG
1 GGAATGCTCGGCGTCTTCAAGCAATTGGACTGTGGGATATCTCGGCGTCTTCTGCATGCTACAAG
85467 GAATGCCAAGGTGGATCTCGGCGTCTTCACCTGTCGTCTG
66 GAATGCCAAGGTGGATCTCGGCGTCTTCACCTGTCGTCTG
85507 GCGGGAATCT
Statistics
Matches: 104, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
108 25 0.24
110 79 0.76
ACGTcount: A:0.18, C:0.25, G:0.29, T:0.28
Consensus pattern (108 bp):
GGAATGCTCGGCGTCTTCAAGCAATTGGACTGTGGGATATCTCGGCGTCTTCTGCATGCTACAAG
GAATGCCAAGGTGGATCTCGGCGTCTTCACCTGTCGTCTGATG
Found at i:85770 original size:18 final size:18
Alignment explanation
Indices: 85749--85813 Score: 121
Period size: 18 Copynumber: 3.6 Consensus size: 18
85739 TTCTTCTTCC
85749 GAAGCGTGAGATTCGTCT
1 GAAGCGTGAGATTCGTCT
85767 GAAGCGTGAGATTCGTCT
1 GAAGCGTGAGATTCGTCT
*
85785 GAAGCGTGAGATTCATCT
1 GAAGCGTGAGATTCGTCT
85803 GAAGCGTGAGA
1 GAAGCGTGAGA
85814 CTAATAATTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.26, C:0.15, G:0.34, T:0.25
Consensus pattern (18 bp):
GAAGCGTGAGATTCGTCT
Found at i:88279 original size:14 final size:14
Alignment explanation
Indices: 88260--88689 Score: 148
Period size: 14 Copynumber: 29.1 Consensus size: 14
88250 CTCGAGTACA
*
88260 TATTTAATAATAAT
1 TATTTAATATTAAT
88274 TATTTAA-ATTTAAT
1 TATTTAATA-TTAAT
88288 TATTTAACT-TTAAT
1 TATTTAA-TATTAAT
* *
88302 GATTTAATAATAAT
1 TATTTAATATTAAT
88316 TATTTAACT-TTAAT
1 TATTTAA-TATTAAT
* *
88330 GATTTAATAATAAT
1 TATTTAATATTAAT
88344 TACTTTAATGATTTAA-
1 TA-TTTAAT-A-TTAAT
*
88360 -CTTTAATGATTTAAT
1 TATTTAAT-A-TTAAT
* *
88375 AATAATTACT-TTAAT
1 --TATTTAATATTAAT
* *
88390 GATTTAATTTTAAT
1 TATTTAATATTAAT
* *
88404 GATTTAATAATAAT
1 TATTTAATATTAAT
88418 TACTTTAATGATT--T
1 TA-TTTAAT-ATTAAT
*
88432 AATTTAATGATTTAAT
1 TATTTAAT-A-TTAAT
*
88448 GATTTAACT-TTAAT
1 TATTTAA-TATTAAT
* *
88462 GATTTAATAATAAT
1 TATTTAATATTAAT
*
88476 TACTTTGAT-TTAAT
1 TA-TTTAATATTAAT
* *
88490 GATTTAATAATAAT
1 TATTTAATATTAAT
88504 TATTTTAATGATTTAAT
1 TA-TTTAAT-A-TTAAT
*
88521 GATTTAATGATTTAA-
1 TATTTAAT-A-TTAAT
*
88536 TA-ATAATACTTTAAT
1 TATTTAATA--TTAAT
*
88551 GATTTAACT-TTAAT
1 TATTTAA-TATTAAT
** *
88565 GCTTTAATAATAAT
1 TATTTAATATTAAT
88579 TACTTTAATGATTTAAT
1 TA-TTTAAT-A-TTAAT
* *
88596 GATTTAATAATAAT
1 TATTTAATATTAAT
88610 TACTTTAATGATTTAATTT
1 TA-TTTAAT-A-TTAA--T
*
88629 TAATAATTAATAATAAT
1 T-AT--TTAATATTAAT
* *
88646 TACTTAATTTTAAT
1 TATTTAATATTAAT
* *
88660 GATTTAATTTTAAT
1 TATTTAATATTAAT
* *
88674 GATTTAATAATAAT
1 TATTTAATATTAAT
88688 TA
1 TA
88690 CTTGACTTTA
Statistics
Matches: 320, Mismatches: 54, Indels: 84
0.70 0.12 0.18
Matches are distributed among these distances:
13 24 0.08
14 179 0.56
15 44 0.14
16 36 0.11
17 20 0.06
18 4 0.01
19 6 0.02
20 2 0.01
21 5 0.02
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.50
Consensus pattern (14 bp):
TATTTAATATTAAT
Found at i:88359 original size:37 final size:37
Alignment explanation
Indices: 88312--88692 Score: 323
Period size: 37 Copynumber: 10.0 Consensus size: 37
88302 GATTTAATAA
* *
88312 TAATTATTTAACTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAATTTTAATGATTTAATAATAATTACTT
*
88349 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAATTTTAATGATTTAATAATAATTACTT
88386 TAATGATTTAATTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAATTTTAATGATTTAATAATAATTACTT
*
88423 TAATGATTTAA-TTTAATGATTTAATGAT--TTAACTT
1 TAATGATTTAATTTTAATGATTTAATAATAATT-ACTT
** * * * *
88458 TAATGATTTAATAATAATTACTTTGAT-TTAATGA-TT
1 TAATGATTTAATTTTAATGA-TTTAATAATAATTACTT
* * *
88494 TAATAATAATT-ATTTTAATGATTTAATGATTTAATGA-TT
1 TAATGAT--TTAATTTTAATGATTTAAT-A-ATAATTACTT
* ** * *
88533 TAAT-A-ATAATACTTTAATGATTTAACTTTAATGCTTTAATAA
1 TAATGATTTAAT--TTTAATGATTTAA---TAAT-AATTACT-T
*
88575 TAATTACTTTAATGATTTAATGATTTAATAATAATTACTT
1 TAATGA-TTTAAT--TTTAATGATTTAATAATAATTACTT
*
88615 TAATGATTTAATTTTAAT-AATTAATAATAATTACTTAATTT
1 TAATGATTTAATTTTAATGATTTAATAATAATTAC-----TT
88656 TAATGATTTAATTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAATTTTAATGATTTAATAATAATTACTT
88693 GACTTTATGA
Statistics
Matches: 286, Mismatches: 30, Indels: 56
0.77 0.08 0.15
Matches are distributed among these distances:
34 2 0.01
35 16 0.06
36 52 0.18
37 104 0.36
38 17 0.06
39 20 0.07
40 8 0.03
41 26 0.09
42 23 0.08
43 1 0.00
45 17 0.06
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.50
Consensus pattern (37 bp):
TAATGATTTAATTTTAATGATTTAATAATAATTACTT
Found at i:88426 original size:9 final size:8
Alignment explanation
Indices: 88270--88681 Score: 65
Period size: 8 Copynumber: 54.5 Consensus size: 8
88260 TATTTAATAA
88270 TAATTATT
1 TAATTATT
88278 TAA--ATT
1 TAATTATT
88284 TAATTATT
1 TAATTATT
*
88292 TAA--CTT
1 TAATTATT
*
88298 TAATGATT
1 TAATTATT
*
88306 TAA-TA-A
1 TAATTATT
88312 TAATTATT
1 TAATTATT
*
88320 TAA--CTT
1 TAATTATT
*
88326 TAATGATT
1 TAATTATT
*
88334 TAA-TA-A
1 TAATTATT
88340 TAATTACTT
1 TAATTA-TT
*
88349 TAATGATT
1 TAATTATT
*
88357 TAA--CTT
1 TAATTATT
*
88363 TAATGATT
1 TAATTATT
*
88371 TAA-TA-A
1 TAATTATT
88377 TAATTACTT
1 TAATTA-TT
*
88386 TAATGATT
1 TAATTATT
88394 TAA-T-TT
1 TAATTATT
*
88400 TAATGATT
1 TAATTATT
*
88408 TAA-TA-A
1 TAATTATT
88414 TAATTACTT
1 TAATTA-TT
*
88423 TAATGATT
1 TAATTATT
88431 T-A--ATT
1 TAATTATT
*
88436 TAATGATT
1 TAATTATT
*
88444 TAATGATT
1 TAATTATT
*
88452 TAA--CTT
1 TAATTATT
*
88458 TAATGATT
1 TAATTATT
*
88466 TAATAATAAT
1 TAAT--TATT
*
88476 TACTTTGATT
1 TA-ATT-ATT
*
88486 TAATGATT
1 TAATTATT
*
88494 TAA-TA-A
1 TAATTATT
88500 TAATTATTT
1 TAATTA-TT
*
88509 TAATGATT
1 TAATTATT
*
88517 TAATGATT
1 TAATTATT
*
88525 TAATGATT
1 TAATTATT
*
88533 TAA-TA-A
1 TAATTATT
88539 TAA-TACTT
1 TAATTA-TT
*
88547 TAATGATT
1 TAATTATT
*
88555 TAA--CTT
1 TAATTATT
**
88561 TAATGCTT
1 TAATTATT
*
88569 TAA-TA-A
1 TAATTATT
88575 TAATTACTT
1 TAATTA-TT
*
88584 TAATGATT
1 TAATTATT
*
88592 TAATGATT
1 TAATTATT
*
88600 TAA-TA-A
1 TAATTATT
88606 TAATTACTT
1 TAATTA-TT
*
88615 TAATGATT
1 TAATTATT
88623 TAATT-TT
1 TAATTATT
*
88630 AATAATTAATAA
1 --TAATT-AT-T
*
88642 TAATTACT
1 TAATTATT
88650 TAA-T-TT
1 TAATTATT
*
88656 TAATGATT
1 TAATTATT
88664 TAA-T-TT
1 TAATTATT
*
88670 TAATGATT
1 TAATTATT
88678 TAAT
1 TAAT
88682 AATAATTACT
Statistics
Matches: 294, Mismatches: 57, Indels: 106
0.64 0.12 0.23
Matches are distributed among these distances:
5 4 0.01
6 72 0.24
7 25 0.09
8 139 0.47
9 39 0.13
10 13 0.04
11 2 0.01
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.50
Consensus pattern (8 bp):
TAATTATT
Found at i:88579 original size:75 final size:75
Alignment explanation
Indices: 88484--88692 Score: 265
Period size: 75 Copynumber: 2.8 Consensus size: 75
88474 ATTACTTTGA
88484 TTTAATGATTTAATAATAATTATTTTAATGATTTAATGATTTAATGATTTAATAATAATACTTTA
1 TTTAATGATTTAATAATAATTATTTTAATGATTTAATGATTTAATGATTTAATAATAATACTTTA
88549 ATGATTTAAC
66 ATGATTTAAC
* *
88559 TTTAATGCTTTAATAATAATTACTTTAATGATTTAATGATTT-A--A--TAATAAT--TACTTTA
1 TTTAATGATTTAATAATAATTATTTTAATGATTTAATGATTTAATGATTTAATAATAATACTTTA
*
88617 ATGATTTAAT
66 ATGATTTAAC
* *
88627 TTTAATAATTAATAATAATTACTTAATTTTAATGATTTAAT--TTTAATGATTTAATAATAATTA
1 TTTAATGATT--TAATAA-TAATT-ATTTTAATGATTTAATGATTTAATGATTTAATAATAA-TA
88690 CTT
61 CTT
88693 GACTTTATGA
Statistics
Matches: 115, Mismatches: 7, Indels: 21
0.80 0.05 0.15
Matches are distributed among these distances:
68 24 0.21
70 16 0.14
71 5 0.04
72 16 0.14
73 1 0.01
74 1 0.01
75 47 0.41
78 5 0.04
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.50
Consensus pattern (75 bp):
TTTAATGATTTAATAATAATTATTTTAATGATTTAATGATTTAATGATTTAATAATAATACTTTA
ATGATTTAAC
Found at i:88680 original size:28 final size:28
Alignment explanation
Indices: 88261--88681 Score: 193
Period size: 28 Copynumber: 15.2 Consensus size: 28
88251 TCGAGTACAT
** * * *
88261 ATTTAATAATAATTATTTAAATTTAATT
1 ATTTAATTTTAATGATTTAATTTTAATG
* ** *
88289 ATTTAACTTTAATGATTTAATAATAATT
1 ATTTAATTTTAATGATTTAATTTTAATG
*
88317 ATTTAACTTTAATGATTTAA---TAAT-
1 ATTTAATTTTAATGATTTAATTTTAATG
* * *
88341 AATT-ACTTTAATGATTTAACTTTAATG
1 ATTTAATTTTAATGATTTAATTTTAATG
* *
88368 ATTTAA---TAAT-AATT-ACTTTAATG
1 ATTTAATTTTAATGATTTAATTTTAATG
** *
88391 ATTTAATTTTAATGATTTAATAATAATT
1 ATTTAATTTTAATGATTTAATTTTAATG
88419 ACTTTAATGATTT-A--ATTTAATGATTTAATG
1 A-TTTAAT--TTTAATGATTTAAT--TTTAATG
* ** *
88449 ATTTAACTTTAATGATTTAATAATAATT
1 ATTTAATTTTAATGATTTAATTTTAATG
* ** *
88477 ACTTTGA-TTTAATGATTTAATAATAATT
1 A-TTTAATTTTAATGATTTAATTTTAATG
88505 ATTTTAATGATTTAATGATTTAATGATTTAAT-
1 A-TTTAAT--TTTAATGATTTAAT--TTTAATG
* *
88537 A-ATAATACTTTAATGATTTAACTTTAATG
1 ATTTAAT--TTTAATGATTTAATTTTAATG
* ** *
88566 CTTTAATAATAATTACTTTAATGATTTAATG
1 ATTTAATTTTAATGA-TTTAAT--TTTAATG
* *
88597 ATTTAA---TAAT-AATT-ACTTTAATG
1 ATTTAATTTTAATGATTTAATTTTAATG
* ** *
88620 ATTTAATTTTAAT-AATTAATAATAATT
1 ATTTAATTTTAATGATTTAATTTTAATG
*
88647 ACTTAATTTTAATGATTTAATTTTAATG
1 ATTTAATTTTAATGATTTAATTTTAATG
88675 ATTTAAT
1 ATTTAAT
88682 AATAATTACT
Statistics
Matches: 309, Mismatches: 50, Indels: 68
0.72 0.12 0.16
Matches are distributed among these distances:
23 43 0.14
24 6 0.02
25 9 0.03
26 18 0.06
27 27 0.09
28 118 0.38
29 20 0.06
30 34 0.11
31 29 0.09
32 1 0.00
33 4 0.01
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.50
Consensus pattern (28 bp):
ATTTAATTTTAATGATTTAATTTTAATG
Found at i:88723 original size:41 final size:41
Alignment explanation
Indices: 88590--88711 Score: 155
Period size: 41 Copynumber: 3.0 Consensus size: 41
88580 ACTTTAATGA
*
88590 TTTAATGATT--TAATAA-TAATT-ACTTTAATGATTTAAT
1 TTTAATGATTAATAATAATTACTTAACTTTAATGATTTAAT
* *
88627 TTTAATAATTAATAATAATTACTTAATTTTAATGATTTAAT
1 TTTAATGATTAATAATAATTACTTAACTTTAATGATTTAAT
*
88668 TTTAATGATTTAATAATAATTACTTGACTTT-ATGATTTATAT
1 TTTAATGA-TTAATAATAATTACTTAACTTTAATGATTTA-AT
88710 TT
1 TT
88712 ACTGATATAA
Statistics
Matches: 73, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
37 9 0.12
39 6 0.08
40 4 0.05
41 30 0.41
42 24 0.33
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.52
Consensus pattern (41 bp):
TTTAATGATTAATAATAATTACTTAACTTTAATGATTTAAT
Found at i:89707 original size:16 final size:15
Alignment explanation
Indices: 89674--89717 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
89664 TTAATTAATA
89674 ATTATAAA-AACAAC
1 ATTATAAATAACAAC
*
89688 ATTAATAAATAACAAT
1 ATT-ATAAATAACAAC
89704 ATTATAATATAACA
1 ATTATAA-ATAACA
89718 CATAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 3 0.12
15 9 0.35
16 14 0.54
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (15 bp):
ATTATAAATAACAAC
Found at i:91149 original size:168 final size:169
Alignment explanation
Indices: 90888--91230 Score: 491
Period size: 168 Copynumber: 2.0 Consensus size: 169
90878 CATCAAATAT
* *
90888 AAAATGATCCTAATTACTATTTGCTCTCAACATTTTCAAACTTTGCAATTTAATCACTAAATTTA
1 AAAACGATCCTAATTACTATTTGCTCTCAACATTTTCAAACTTAGCAATTTAATCACTAAATTTA
*
90953 TAAATTCTTTCAAATTTAACCAATTAAGCATATTAATACTAAATTCAAGCATAGTATACCAACTT
66 TAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACT-AATTCAAGCATAGTATACCAACTT
* *
91018 TT-ATAA-TTACTCTAATTTCTTAAATTCCTCAAATTTTGC
130 TTAATAATTTACTCTAATTCCTTAAATTCCTCAAA-TTTAC
* *
91057 AAAACGATCTCTAATTACTATTTGGTTCTCAACATTTTC-AAGTTAGC-ATTTAATC-CATAAAT
1 AAAACGATC-CTAATTACTATTT-GCTCTCAACATTTTCAAACTTAGCAATTTAATCAC-TAAAT
* * *
91119 TT-TAAATTCTTTCTAATTTAACCAATTAAGCATACTAATACTAATTCCAGCATAGTATAGCAAC
63 TTATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAATTCAAGCATAGTATACCAAC
* *
91183 TTTTAATAATTTACTCTTATTCCTTAAATTCCTTAAATTTAC
128 TTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTAC
91225 AAAACG
1 AAAACG
91231 GTCCCTAAAA
Statistics
Matches: 157, Mismatches: 12, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
167 24 0.15
168 53 0.34
169 47 0.30
170 19 0.12
171 14 0.09
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (169 bp):
AAAACGATCCTAATTACTATTTGCTCTCAACATTTTCAAACTTAGCAATTTAATCACTAAATTTA
TAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAATTCAAGCATAGTATACCAACTTT
TAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTAC
Found at i:91706 original size:23 final size:23
Alignment explanation
Indices: 91680--91723 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
91670 AGTTGCATGC
91680 CCCCCACATGCAGACGTGCAGGA
1 CCCCCACATGCAGACGTGCAGGA
91703 CCCCCACATGCAGACGTGCAG
1 CCCCCACATGCAGACGTGCAG
91724 CCCTGCAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.25, C:0.41, G:0.25, T:0.09
Consensus pattern (23 bp):
CCCCCACATGCAGACGTGCAGGA
Found at i:91805 original size:21 final size:23
Alignment explanation
Indices: 91753--91805 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
91743 CGTGATTTCT
91753 GTGC-TTTCTCCTTGCAGAACCC
1 GTGCATTTCTCCTTGCAGAACCC
*
91775 GTGCA-CTCTCCTTGCA-AACCC
1 GTGCATTTCTCCTTGCAGAACCC
91796 GTG-ATTTCTC
1 GTGCATTTCTC
91806 ACGTCCAGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 1 0.04
21 12 0.44
22 14 0.52
ACGTcount: A:0.15, C:0.36, G:0.17, T:0.32
Consensus pattern (23 bp):
GTGCATTTCTCCTTGCAGAACCC
Found at i:91881 original size:34 final size:34
Alignment explanation
Indices: 91827--91910 Score: 134
Period size: 34 Copynumber: 2.5 Consensus size: 34
91817 CATGCACAGC
*
91827 ACTGAAGAC-CCGAGATTTCCTACGAAGAATCCA
1 ACTGAAGACGCCGAGAGTTCCTACGAAGAATCCA
* *
91860 ACTGAAGACGCCGAGAGTTCCTATGAAGAGTCCA
1 ACTGAAGACGCCGAGAGTTCCTACGAAGAATCCA
91894 ACTGAAGACGCCGAGAG
1 ACTGAAGACGCCGAGAG
91911 ATCAATCATA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 9 0.19
34 38 0.81
ACGTcount: A:0.35, C:0.25, G:0.25, T:0.15
Consensus pattern (34 bp):
ACTGAAGACGCCGAGAGTTCCTACGAAGAATCCA
Found at i:97742 original size:2 final size:2
Alignment explanation
Indices: 97735--97772 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
97725 GTCATTGTTT
97735 TA TA TA TA 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
97773 GAATTATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:101674 original size:35 final size:35
Alignment explanation
Indices: 101607--101678 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
101597 CCACCGAAAG
*
101607 TGGCCTCCAAATCCACCAAAAATTGCCCCCAATTT
1 TGGCCTCCAAATCCACCAAAAATTGCCACCAATTT
* *
101642 TGGCTTCCAAATCCA-CTAAAATTGCCTACCAATTT
1 TGGCCTCCAAATCCACCAAAAATTGCC-ACCAATTT
101677 TG
1 TG
101679 ACTTTTCCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 10 0.30
35 23 0.70
ACGTcount: A:0.31, C:0.32, G:0.10, T:0.28
Consensus pattern (35 bp):
TGGCCTCCAAATCCACCAAAAATTGCCACCAATTT
Found at i:104075 original size:37 final size:37
Alignment explanation
Indices: 104034--104115 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 37
104024 TTTGTTGTTT
104034 CCACCGAA-AATGGCCTCCAAAATCCACCGAAAATTAC
1 CCACC-AATAATGGCCTCCAAAATCCACCGAAAATTAC
** * *
104071 CCACCAATTTTGGCTTCCAAAATCCACCGAAAATTAT
1 CCACCAATAATGGCCTCCAAAATCCACCGAAAATTAC
*
104108 CCATCAAT
1 CCACCAAT
104116 TTTGACTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
36 2 0.05
37 37 0.95
ACGTcount: A:0.38, C:0.33, G:0.09, T:0.21
Consensus pattern (37 bp):
CCACCAATAATGGCCTCCAAAATCCACCGAAAATTAC
Found at i:104116 original size:37 final size:37
Alignment explanation
Indices: 104044--104119 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
104034 CCACCGAAAA
104044 TGGCCTCCAAAATCCACCGAAAATTACCCACCAATTT
1 TGGCCTCCAAAATCCACCGAAAATTACCCACCAATTT
* * *
104081 TGGCTTCCAAAATCCACCGAAAATTATCCATCAATTT
1 TGGCCTCCAAAATCCACCGAAAATTACCCACCAATTT
104118 TG
1 TG
104120 ACTTTTCCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.34, C:0.30, G:0.09, T:0.26
Consensus pattern (37 bp):
TGGCCTCCAAAATCCACCGAAAATTACCCACCAATTT
Found at i:107070 original size:13 final size:13
Alignment explanation
Indices: 107052--107078 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
107042 ATAGTTGAAG
107052 AGTCTTCATATGC
1 AGTCTTCATATGC
107065 AGTCTTCATATGC
1 AGTCTTCATATGC
107078 A
1 A
107079 CGTGTGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (13 bp):
AGTCTTCATATGC
Found at i:113084 original size:17 final size:17
Alignment explanation
Indices: 113062--113094 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
113052 AACATTCAAT
*
113062 AAATAATTAGTTATAAA
1 AAATAATTAGGTATAAA
113079 AAATAATTAGGTATAA
1 AAATAATTAGGTATAA
113095 TTGAGGGGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (17 bp):
AAATAATTAGGTATAAA
Found at i:114351 original size:3 final size:3
Alignment explanation
Indices: 114343--114391 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
114333 TTCTTCACTT
* * *
114343 TAA TAA TAA TAC TAA TAC TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
114391 T
1 T
114392 TAAGGAGACG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:121894 original size:33 final size:33
Alignment explanation
Indices: 121847--121940 Score: 81
Period size: 33 Copynumber: 2.9 Consensus size: 33
121837 GAAATTGAAA
* * *
121847 TTAACCTGAACCGAAAGA-AACTTGAACCA-AAT
1 TTAACCCGATCCGAAAGACAACTCGAA-CATAAT
121879 TGTAACCCGATCCGAAA-ACAACTCGAACATAAT
1 T-TAACCCGATCCGAAAGACAACTCGAACATAAT
* * *
121912 TTATCCCGATCC-AAAG-CAACCCGAGCATA
1 TTAACCCGATCCGAAAGACAACTCGAACATA
121941 TTGAAATTGA
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
31 14 0.27
32 14 0.27
33 24 0.46
ACGTcount: A:0.41, C:0.28, G:0.13, T:0.18
Consensus pattern (33 bp):
TTAACCCGATCCGAAAGACAACTCGAACATAAT
Found at i:126817 original size:31 final size:30
Alignment explanation
Indices: 126782--126861 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 30
126772 TAAATTTAAA
126782 ATAAATATTTAATTTAACCTCT-ACACATTAG
1 ATAAATA-TTAATTTAACCTCTGA-ACATTAG
* * * * *
126813 ATAAAACATCAATTTAACATTTGAACTTTAG
1 AT-AAATATTAATTTAACCTCTGAACATTAG
126844 ATAAATATTAATTTAACC
1 ATAAATATTAATTTAACC
126862 ATTCAATTCG
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
30 13 0.33
31 21 0.54
32 5 0.13
ACGTcount: A:0.45, C:0.14, G:0.04, T:0.38
Consensus pattern (30 bp):
ATAAATATTAATTTAACCTCTGAACATTAG
Found at i:128560 original size:31 final size:31
Alignment explanation
Indices: 128522--128592 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
128512 TAAAATATTT
128522 AATTTAACCTCT-ACACATTAGATAAAACATC
1 AATTTAACCTCTGA-ACATTAGATAAAACATC
* * * * *
128553 AATTTAACATTTGAACTTTAGATAAAATATT
1 AATTTAACCTCTGAACATTAGATAAAACATC
128584 AATTTAACC
1 AATTTAACC
128593 ATTCAATTCG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.35
Consensus pattern (31 bp):
AATTTAACCTCTGAACATTAGATAAAACATC
Found at i:131464 original size:18 final size:19
Alignment explanation
Indices: 131425--131465 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
131415 ATTTAAAAAT
* *
131425 TAAATTAATATGAATGAGA
1 TAAAATAATATGAATGAAA
131444 TAAAATAATAT-AATGAAA
1 TAAAATAATATGAATGAAA
131462 TAAA
1 TAAA
131466 CAATATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (19 bp):
TAAAATAATATGAATGAAA
Found at i:131472 original size:17 final size:18
Alignment explanation
Indices: 131431--131472 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
131421 AAATTAAATT
* *
131431 AATATGAATGAGATAAAAT
1 AATAT-AATGAAATAAAAC
131450 AATATAATGAAAT-AAAC
1 AATATAATGAAATAAAAC
131467 AATATA
1 AATATA
131473 TAAACATACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 9 0.43
18 7 0.33
19 5 0.24
ACGTcount: A:0.62, C:0.02, G:0.10, T:0.26
Consensus pattern (18 bp):
AATATAATGAAATAAAAC
Found at i:131633 original size:16 final size:16
Alignment explanation
Indices: 131589--131646 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
131579 TTGAACTAGG
*
131589 ATAATAAAATGACATAAA
1 ATAATAAAAGGAC--AAA
* * *
131607 AAAACAAAAGGACTAA
1 ATAATAAAAGGACAAA
*
131623 ATTATAAAAGGACAAA
1 ATAATAAAAGGACAAA
131639 ATAATAAA
1 ATAATAAA
131647 GCATAAATAT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
16 21 0.68
18 10 0.32
ACGTcount: A:0.67, C:0.07, G:0.09, T:0.17
Consensus pattern (16 bp):
ATAATAAAAGGACAAA
Found at i:133115 original size:3 final size:3
Alignment explanation
Indices: 133107--133175 Score: 77
Period size: 3 Copynumber: 22.7 Consensus size: 3
133097 TTTGTATATC
* * * *
133107 AAT AAT AAT AAT AAA AAT AAT ATT AAT AAT AAT TAT AAT TAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
133155 AATT AA- AAT AAAT AAT AAT AA
1 AA-T AAT AAT -AAT AAT AAT AA
133176 AAAAGATCCG
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
2 2 0.04
3 47 0.85
4 6 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:133656 original size:42 final size:40
Alignment explanation
Indices: 133607--133701 Score: 104
Period size: 40 Copynumber: 2.3 Consensus size: 40
133597 AATCGGTTCT
133607 TACGTGATGAGGACGG-CAGGTTATCAAGGG-TGACACGGCTCC
1 TACGTGATGAGGA-GGTCAGG-T-T-AAGGGATGACACGGCTCC
* * *
133649 TACGTGATGAAGAGGTCTGGTTAAGGGATGACACGGTTCC
1 TACGTGATGAGGAGGTCAGGTTAAGGGATGACACGGCTCC
*
133689 TACGCGATGAGGA
1 TACGTGATGAGGA
133702 TGGTAGGCCA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
39 5 0.11
40 23 0.50
41 3 0.07
42 15 0.33
ACGTcount: A:0.25, C:0.18, G:0.36, T:0.21
Consensus pattern (40 bp):
TACGTGATGAGGAGGTCAGGTTAAGGGATGACACGGCTCC
Found at i:133711 original size:132 final size:133
Alignment explanation
Indices: 133365--133719 Score: 455
Period size: 132 Copynumber: 2.7 Consensus size: 133
133355 CTGGTCGTCT
* * * *
133365 AAGGGTGTATACGGCTCCTACGTGATGAGGAGATCTAGTCAGGGGATGACACTGCTCATACGTGA
1 AAGGGTG-ACACGGCTCCTACGTGATGAGGAGGTCTGGTCAGGGGATGACACGGCTCATACGTGA
* *
133430 TGAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACCCGGTTCTTACGTGATGAGGACGGCTGG
65 TGAAGA-TGCTTGGCCATCTTTAGGAAGGGTGATAACCCGGTTCTTACGTGATGAGGACGGCAGG
133495 TTATC
129 TTATC
* * * *
133500 AAGGGTGACACGACTCTTATGTGATGAGGAGGTCTGG-CCGGTGGATGACACGGCTCATACGTGA
1 AAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAGG-GGATGACACGGCTCATACGTGA
* * *
133564 TAAAGA-GTTCTGGCCATCTTTAGGAAGGGTGATAA-TCGGTTCTTACGTGATGAGGACGGCAGG
65 TGAAGATGCT-TGGCCATCTTTAGGAAGGGTGATAACCCGGTTCTTACGTGATGAGGACGGCAGG
133627 TTATC
129 TTATC
* * * * * *
133632 AAGGGTGACACGGCTCCTACGTGATGAAGAGGTCTGGTTAAGGGATGACACGGTTCCTACGCGAT
1 AAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAGGGGATGACACGGCTCATACGTGAT
* * *
133697 GAGGATGGTAGGCCATCTTTAGG
66 GAAGATGCTTGGCCATCTTTAGG
133720 GATAATGGTT
Statistics
Matches: 189, Mismatches: 27, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
132 101 0.53
133 31 0.16
134 50 0.26
135 7 0.04
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.25
Consensus pattern (133 bp):
AAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAGGGGATGACACGGCTCATACGTGAT
GAAGATGCTTGGCCATCTTTAGGAAGGGTGATAACCCGGTTCTTACGTGATGAGGACGGCAGGTT
ATC
Found at i:133851 original size:24 final size:28
Alignment explanation
Indices: 133822--133872 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
133812 TGGCAAATTT
133822 TGTTTC-C-AAAGAAAC-A-CTCAAAGA
1 TGTTTCTCAAAAGAAACAATCTCAAAGA
133846 TGTTTCTCAAAAGAAACAATCTCAAAG
1 TGTTTCTCAAAAGAAACAATCTCAAAG
133873 GTTGGGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 6 0.26
25 1 0.04
26 8 0.35
27 1 0.04
28 7 0.30
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.24
Consensus pattern (28 bp):
TGTTTCTCAAAAGAAACAATCTCAAAGA
Found at i:134044 original size:29 final size:30
Alignment explanation
Indices: 133971--134275 Score: 216
Period size: 29 Copynumber: 9.8 Consensus size: 30
133961 CTTAAATATT
133971 TTTCAAAA-AGAACAGACTCAAAGA--TTT-
1 TTTCAAAAGA-AACAGACTCAAAGATTTTTG
* *
133998 TCTCAAAAGAAACA-ACTCAAAGATTTTTA
1 TTTCAAAAGAAACAGACTCAAAGATTTTTG
*
134027 TTTCAAAAGAAAC-GACTCAAAGACTTTTG
1 TTTCAAAAGAAACAGACTCAAAGATTTTTG
* *
134056 TTTCAAGAGAAATAGACTCAAAGATGGGTTTTG
1 TTTCAAAAGAAACAGACTCAAAGAT---TTTTG
**
134089 TTTCAAGGGAAACA-ATCTCAAAGGTATTAAATTTTG
1 TTTCAAAAGAAACAGA-CTCAAA-G-A-T---TTTTG
* *
134125 TTTCCAAAGAAACAAACTCAAAGA-TTTT-
1 TTTCAAAAGAAACAGACTCAAAGATTTTTG
* * * * *
134153 TCTCAAAAGAAACTGTCTTAAGAGAGACAAAATTTTG
1 TTTCAAAAGAAACAGAC-TCA-A-AG----ATTTTTG
*
134190 TTTCAAAAGAAACAAACTCAAAGATTTTTG
1 TTTCAAAAGAAACAGACTCAAAGATTTTTG
*
134220 TTTAAAAAGAAACAGACTCAAAGATTTTTTTG
1 TTTCAAAAGAAACAGACTCAAAGA--TTTTTG
134252 TTTCAAAAGAAAC-GACTCAAAGAT
1 TTTCAAAAGAAACAGACTCAAAGAT
134276 GAAGTTTAAA
Statistics
Matches: 223, Mismatches: 30, Indels: 48
0.74 0.10 0.16
Matches are distributed among these distances:
26 9 0.04
27 11 0.05
28 16 0.07
29 43 0.19
30 39 0.17
31 12 0.05
32 19 0.09
33 23 0.10
34 4 0.02
35 4 0.02
36 29 0.13
37 14 0.06
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (30 bp):
TTTCAAAAGAAACAGACTCAAAGATTTTTG
Found at i:134219 original size:30 final size:30
Alignment explanation
Indices: 134185--134275 Score: 139
Period size: 30 Copynumber: 3.0 Consensus size: 30
134175 AGAGACAAAA
*
134185 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAGACTCAAAGAT
*
134215 TTTTGTTTAAAAAGAAACAGACTCAAAGATTT
1 TTTTGTTTCAAAAGAAACAGACTCAAAGA--T
134247 TTTTGTTTCAAAAGAAAC-GACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAGACTCAAAGAT
134276 GAAGTTTAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
29 1 0.02
30 27 0.48
31 10 0.18
32 18 0.32
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACAGACTCAAAGAT
Found at i:134583 original size:65 final size:64
Alignment explanation
Indices: 134447--134572 Score: 159
Period size: 62 Copynumber: 2.0 Consensus size: 64
134437 AGATGGTAAA
*
134447 TTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTCTTAAAAGAAACTGTCTCAAAAGAGACAAAT
1 TTTTTTTTCCAAAGAAACAGACTCAAAGATTTTTC-TAAAAGAAACTGTCTCAAAAGAGACAAAT
* * * **
134512 TTTTTTTTCCAAAGAAACATA-TTAAATGA-TTTTC-AAAAGAAATTGTCTCATGAGAGACAAA
1 TTTTTTTTCCAAAGAAACAGACTCAAA-GATTTTTCTAAAAGAAACTGTCTCAAAAGAGACAAA
134573 ACTTTGTTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
62 24 0.44
64 9 0.17
65 21 0.39
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (64 bp):
TTTTTTTTCCAAAGAAACAGACTCAAAGATTTTTCTAAAAGAAACTGTCTCAAAAGAGACAAAT
Found at i:134623 original size:100 final size:101
Alignment explanation
Indices: 134503--134685 Score: 246
Period size: 100 Copynumber: 1.8 Consensus size: 101
134493 TGTCTCAAAA
* * * * *
134503 GAGACAAATTTTTTTTTCCAAAGAAACATATT-AAATGA-TT-TTCAAAAGAAATTGTCTCATGA
1 GAGACAAAATTTTGTTTCCAAAGAAACAAATTCAAA-GATTTCTTCAAAAGAAACTGTCTCAAGA
*
134565 GAGACAAAACTTTGTTTTTCAGAAAATTTTATCTAAGT
65 GAAACAAAA-TTTGTTTTTCAGAAAATTTTATCTAAGT
134603 GAGACAAAATTTTGTTTCCAAAGAAACAAATTCAAAGATTTTTCTTCAAAAGAAACTGTCTCAAG
1 GAGACAAAATTTTGTTTCCAAAGAAACAAATTCAAAGA--TTTCTTCAAAAGAAACTGTCTCAAG
*
134668 GGAAACAAAATTTGTTTT
64 AGAAACAAAATTTGTTTT
134686 AATAGAAACG
Statistics
Matches: 71, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
100 31 0.44
101 3 0.04
103 10 0.14
104 27 0.38
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (101 bp):
GAGACAAAATTTTGTTTCCAAAGAAACAAATTCAAAGATTTCTTCAAAAGAAACTGTCTCAAGAG
AAACAAAATTTGTTTTTCAGAAAATTTTATCTAAGT
Found at i:135008 original size:132 final size:125
Alignment explanation
Indices: 134710--135030 Score: 306
Period size: 132 Copynumber: 2.4 Consensus size: 125
134700 CAAAGGTAGG
* * *
134710 TGTTTCAAGAGAAACTA-ACTCAAAGATATATGTTTCTAAAGAAATGACTCAAAGATTTTTTTCA
1 TGTTTCAAGAGAAAC-AGACTCAAAGATATTTGTTTCAAAAGAAACGACTCAAAGA--TTTTTCA
* ** * *
134774 CGAAAAACTATCTCAAGCGAGACAAAATTTTGTTTCAAAAGAAAAATACTCAAAGATGAGTTT
63 CAAAAAACTATCTCAAAAGAGACAAAATTTTGTTTCAAAAGAAAAATACTAAAAGATCAGTTT
* * *
134837 TGTTTCAAGGGAAACAGACACACATATGATAAATGTTGTTTCCAAAGAAACAGACTCAAAGATTT
1 TGTTTCAAGAGAAACAGACTCA-A-A-GAT--AT-TTGTTTCAAAAGAAAC-GACTCAAAGATTT
* * **
134902 TTCA-AAAGAAACTTTCTCAAAAGAGACAAAATTTTGTTATC-AAAGACACTTACTAAAAGATTT
59 TTCACAAA-AAACTATCTCAAAAGAGACAAAATTTTGTT-TCAAAAGAAAAATACTAAAAGA---
*
134965 TTTCATTTT
119 --TCAGTTT
*
134974 TGTTTCAAGTGAAACAGACTCAAAGATCATTTGTTTCAAAAGAAACGACTCAAAGAT
1 TGTTTCAAGAGAAACAGACTCAAAGAT-ATTTGTTTCAAAAGAAACGACTCAAAGAT
135031 GATGTTTGTT
Statistics
Matches: 160, Mismatches: 19, Indels: 26
0.78 0.09 0.13
Matches are distributed among these distances:
126 1 0.01
127 18 0.11
128 1 0.01
129 1 0.01
130 3 0.02
131 13 0.08
132 66 0.41
133 17 0.11
134 13 0.08
135 1 0.01
136 1 0.01
137 25 0.16
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.30
Consensus pattern (125 bp):
TGTTTCAAGAGAAACAGACTCAAAGATATTTGTTTCAAAAGAAACGACTCAAAGATTTTTCACAA
AAAACTATCTCAAAAGAGACAAAATTTTGTTTCAAAAGAAAAATACTAAAAGATCAGTTT
Found at i:135051 original size:32 final size:31
Alignment explanation
Indices: 134972--135030 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
134962 TTTTTTCATT
*
134972 TTTGTTTCAAGTGAAACAGACTCAAAGATCA
1 TTTGTTTCAAATGAAACAGACTCAAAGATCA
*
135003 TTTGTTTCAAAAGAAAC-GACTCAAAGAT
1 TTTGTTTCAAATGAAACAGACTCAAAGAT
135031 GATGTTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (31 bp):
TTTGTTTCAAATGAAACAGACTCAAAGATCA
Found at i:135115 original size:36 final size:35
Alignment explanation
Indices: 135068--135177 Score: 159
Period size: 36 Copynumber: 3.1 Consensus size: 35
135058 ATAATTTGGA
*
135068 AAATTGTCTCAAGTGAGACAACATTTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAA-ATTTGTTTTTAGAG
* *
135104 AAATTGTCTCAAACGAGACAAAAATTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGAC-AAATTTGTTTTTAGAG
135140 AAATTGTCTCAAGCGAGACAAAGTTTGTTTTT-GAG
1 AAATTGTCTCAAGCGAGACAAA-TTTGTTTTTAGAG
135175 AAA
1 AAA
135178 ACAATATCAA
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
35 9 0.13
36 56 0.84
37 2 0.03
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (35 bp):
AAATTGTCTCAAGCGAGACAAATTTGTTTTTAGAG
Found at i:135911 original size:4 final size:4
Alignment explanation
Indices: 135902--135954 Score: 58
Period size: 4 Copynumber: 13.8 Consensus size: 4
135892 TAAATGTTTG
* *
135902 ATGT ATGT ATGT A--T ATAT ATGT ATGT ATGT ATGC ATGT ATGT AT-T
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
135947 GATGT ATG
1 -ATGT ATG
135955 CTTTTCTTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
2 2 0.05
3 1 0.02
4 38 0.90
5 1 0.02
ACGTcount: A:0.28, C:0.02, G:0.23, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:135939 original size:12 final size:11
Alignment explanation
Indices: 135895--135954 Score: 59
Period size: 12 Copynumber: 5.3 Consensus size: 11
135885 ACGATGATAA
*
135895 ATGTTTGATGT
1 ATGTATGATGT
*
135906 ATGTATG-TAT
1 ATGTATGATGT
*
135916 ATATATGTATGT
1 ATGTATG-ATGT
135928 ATGTATGCATGT
1 ATGTATG-ATGT
135940 ATGTATTGATGT
1 ATGTA-TGATGT
135952 ATG
1 ATG
135955 CTTTTCTTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
10 8 0.20
11 6 0.15
12 24 0.60
13 2 0.05
ACGTcount: A:0.27, C:0.02, G:0.23, T:0.48
Consensus pattern (11 bp):
ATGTATGATGT
Found at i:138334 original size:13 final size:13
Alignment explanation
Indices: 138318--138368 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
138308 CTTTTTGGTG
* *
138318 TTTGTTTTTTTCT
1 TTTGTTCTTTGCT
138331 TTTGTTCTTTGC-
1 TTTGTTCTTTGCT
138343 TTT-TTCTTTGCT
1 TTTGTTCTTTGCT
*
138355 TTTTTCTCTTTGCT
1 TTTGT-TCTTTGCT
138369 CTTTATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
11 8 0.24
12 6 0.18
13 11 0.33
14 8 0.24
ACGTcount: A:0.00, C:0.16, G:0.10, T:0.75
Consensus pattern (13 bp):
TTTGTTCTTTGCT
Found at i:138364 original size:14 final size:14
Alignment explanation
Indices: 138343--138418 Score: 50
Period size: 17 Copynumber: 5.1 Consensus size: 14
138333 TGTTCTTTGC
138343 TTTTTCTTTGCT-T
1 TTTTTCTTTGCTCT
138356 TTTTCTCTTTGCTCTT
1 TTTT-TCTTTGCTC-T
* *
138372 TATTTTACTTTGTTGTTT
1 T-TTTT-CTTTG--CTCT
138390 TTCTTTCTTTG-T-T
1 TT-TTTCTTTGCTCT
138403 TTTTTCTTTGCTCT
1 TTTTTCTTTGCTCT
138417 TT
1 TT
138419 GTTTTTCTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 19
0.71 0.03 0.26
Matches are distributed among these distances:
12 8 0.16
13 8 0.16
14 12 0.24
16 3 0.06
17 14 0.27
18 5 0.10
19 1 0.02
ACGTcount: A:0.03, C:0.16, G:0.08, T:0.74
Consensus pattern (14 bp):
TTTTTCTTTGCTCT
Found at i:138391 original size:32 final size:31
Alignment explanation
Indices: 138318--138395 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
138308 CTTTTTGGTG
* * *
138318 TTTGTTTTTTTCTTTTGTTCTTTGCTTTTTC
1 TTTGTTTTTTTCTTTTGCTCTTTGATTTTAC
*
138349 TTTGCTTTTTTCTCTTTGCTCTTT-ATTTTAC
1 TTTGTTTTTTTCT-TTTGCTCTTTGATTTTAC
138380 TTTGTTGTTTTTCTTT
1 TTTGTT-TTTTTCTTT
138396 CTTTGTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 24 0.60
32 16 0.40
ACGTcount: A:0.03, C:0.14, G:0.09, T:0.74
Consensus pattern (31 bp):
TTTGTTTTTTTCTTTTGCTCTTTGATTTTAC
Found at i:138399 original size:17 final size:18
Alignment explanation
Indices: 138379--138432 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 18
138369 CTTTATTTTA
138379 CTTTGTTGTTTTTCTTT-
1 CTTTGTTGTTTTTCTTTG
138396 CTTTGTT-TTTTTCTTTG
1 CTTTGTTGTTTTTCTTTG
* *
138413 CTCT-TTGTTTTTCTTCG
1 CTTTGTTGTTTTTCTTTG
138430 CTT
1 CTT
138433 CTTTAATTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 11 0.34
17 21 0.66
ACGTcount: A:0.00, C:0.17, G:0.11, T:0.72
Consensus pattern (18 bp):
CTTTGTTGTTTTTCTTTG
Found at i:138424 original size:19 final size:16
Alignment explanation
Indices: 138318--138411 Score: 63
Period size: 16 Copynumber: 5.9 Consensus size: 16
138308 CTTTTTGGTG
138318 TTTGTTTTTTTCTTT-
1 TTTGTTTTTTTCTTTC
* **
138333 TGTTCTTTGCTT-TTTC
1 T-TTGTTTTTTTCTTTC
*
138349 TTTGCTTTTTTC--TC
1 TTTGTTTTTTTCTTTC
* *
138363 TTTGCTCTTTATT-TTAC
1 TTTG-T-TTTTTTCTTTC
138380 TTTGTTGTTTTTCTTTC
1 TTTGTT-TTTTTCTTTC
138397 TTTGTTTTTTTCTTT
1 TTTGTTTTTTTCTTT
138412 GCTCTTTGTT
Statistics
Matches: 58, Mismatches: 12, Indels: 17
0.67 0.14 0.20
Matches are distributed among these distances:
14 6 0.10
15 11 0.19
16 27 0.47
17 14 0.24
ACGTcount: A:0.02, C:0.14, G:0.09, T:0.76
Consensus pattern (16 bp):
TTTGTTTTTTTCTTTC
Found at i:138435 original size:18 final size:17
Alignment explanation
Indices: 138403--138436 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
138393 TTTCTTTGTT
*
138403 TTTTTCTTTGCTCTTTG
1 TTTTTCTTCGCTCTTTG
138420 TTTTTCTTCGCTTCTTT
1 TTTTTCTTCGC-TCTTT
138437 AATTTCTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.00, C:0.21, G:0.09, T:0.71
Consensus pattern (17 bp):
TTTTTCTTCGCTCTTTG
Found at i:138443 original size:46 final size:48
Alignment explanation
Indices: 138344--138452 Score: 118
Period size: 46 Copynumber: 2.3 Consensus size: 48
138334 GTTCTTTGCT
* *
138344 TTTTCTTTGCTTTTTTCTCTTTGCTCTTTATTTTACTTTGTTG-TTT-T
1 TTTTCTTTG-TTTTTTCTCTTTGCTCTTTATTTTACTTCGTTGCTTTAA
* *
138391 TCTTTCTTTGTTTTTT-TCTTTGCTCTTTGTTTTTCTTCGCTT-CTTTAA
1 T-TTTCTTTGTTTTTTCTCTTTGCTCTTTATTTTACTTCG-TTGCTTTAA
138439 TTTCTCTTTGTTTT
1 TTT-TCTTTGTTTT
138453 GATTTGATCT
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
46 20 0.38
47 14 0.26
48 19 0.36
ACGTcount: A:0.04, C:0.17, G:0.08, T:0.72
Consensus pattern (48 bp):
TTTTCTTTGTTTTTTCTCTTTGCTCTTTATTTTACTTCGTTGCTTTAA
Found at i:142263 original size:18 final size:19
Alignment explanation
Indices: 142224--142264 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
142214 ATTTAAAAAT
* *
142224 TAAATTAATATGAATGAGA
1 TAAAATAATATGAATGAAA
142243 TAAAATAATAT-AATGAAA
1 TAAAATAATATGAATGAAA
142261 TAAA
1 TAAA
142265 CAATATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (19 bp):
TAAAATAATATGAATGAAA
Found at i:142271 original size:17 final size:18
Alignment explanation
Indices: 142230--142271 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
142220 AAATTAAATT
* *
142230 AATATGAATGAGATAAAAT
1 AATAT-AATGAAATAAAAC
142249 AATATAATGAAAT-AAAC
1 AATATAATGAAATAAAAC
142266 AATATA
1 AATATA
142272 TAAACATACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 9 0.43
18 7 0.33
19 5 0.24
ACGTcount: A:0.62, C:0.02, G:0.10, T:0.26
Consensus pattern (18 bp):
AATATAATGAAATAAAAC
Found at i:142351 original size:26 final size:26
Alignment explanation
Indices: 142292--142351 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 26
142282 AGGATTAAGA
*
142292 AAAAATAATTAAACACATATACACAT
1 AAAAATAATAAAACACATATACACAT
* *
142318 ATATATAATAAAACATC-TAATA-ACAT
1 AAAAATAATAAAACA-CAT-ATACACAT
142344 AAAAATAA
1 AAAAATAA
142352 ACATATTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
26 23 0.85
27 4 0.15
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.25
Consensus pattern (26 bp):
AAAAATAATAAAACACATATACACAT
Found at i:142424 original size:16 final size:16
Alignment explanation
Indices: 142380--142437 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
142370 TTGAACTAGG
*
142380 ATAATAAAATGACATAAA
1 ATAATAAAAGGAC--AAA
* * *
142398 AAAACAAAAGGACTAA
1 ATAATAAAAGGACAAA
*
142414 ATTATAAAAGGACAAA
1 ATAATAAAAGGACAAA
142430 ATAATAAA
1 ATAATAAA
142438 GCATAAATAT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
16 21 0.68
18 10 0.32
ACGTcount: A:0.67, C:0.07, G:0.09, T:0.17
Consensus pattern (16 bp):
ATAATAAAAGGACAAA
Found at i:145205 original size:24 final size:20
Alignment explanation
Indices: 145150--145207 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
145140 TTCCCATTGA
*
145150 AGTGCATCGGTGCATTCTTC
1 AGTGCATCGATGCATTCTTC
*
145170 AGTGCATAGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TT--C
145193 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
145208 CTACCATGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 15 0.48
21 2 0.06
23 2 0.06
24 12 0.39
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTTC
Found at i:145286 original size:19 final size:19
Alignment explanation
Indices: 145262--145328 Score: 125
Period size: 19 Copynumber: 3.5 Consensus size: 19
145252 AAGGGGATGT
145262 ATCGATGCACTCCTCATGC
1 ATCGATGCACTCCTCATGC
*
145281 ATCGATGCACTCCTCATGT
1 ATCGATGCACTCCTCATGC
145300 ATCGATGCACTCCTCATGC
1 ATCGATGCACTCCTCATGC
145319 ATCGATGCAC
1 ATCGATGCAC
145329 CAACTGTACT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 46 1.00
ACGTcount: A:0.22, C:0.34, G:0.16, T:0.27
Consensus pattern (19 bp):
ATCGATGCACTCCTCATGC
Found at i:146590 original size:3 final size:3
Alignment explanation
Indices: 146569--146637 Score: 77
Period size: 3 Copynumber: 22.7 Consensus size: 3
146559 TTTGTATATC
* * * *
146569 AAT AAA AAT AAT AAA AAT AAT AGT AAT AAT AAT TAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
146617 AATT AA- AAT AAAT AAT AAT AA
1 AA-T AAT AAT -AAT AAT AAT AA
146638 AAAAGACACA
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
2 2 0.04
3 47 0.85
4 6 0.11
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:149756 original size:24 final size:24
Alignment explanation
Indices: 149719--149770 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
149709 AGAAAACTTC
* *
149719 AATGACAATCGTAAGGACAATGAT
1 AATGACAATCGTAAAGACAATGAA
*
149743 AATGACAA-CGGTAAAGATAATGAA
1 AATGACAATC-GTAAAGACAATGAA
149767 AATG
1 AATG
149771 GTTATATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.50, C:0.10, G:0.21, T:0.19
Consensus pattern (24 bp):
AATGACAATCGTAAAGACAATGAA
Found at i:152342 original size:57 final size:57
Alignment explanation
Indices: 152248--152366 Score: 163
Period size: 57 Copynumber: 2.1 Consensus size: 57
152238 AGACATGACA
*
152248 GGGATATAAATCCCATACAGAAATAGGACGGGATATAATCCCATAT-AGAAA-CAGGAC
1 GGGATATAAATCCCATACAGAAACAGGACGGGATATAATCCCAT-TCA-AAATCAGGAC
* *
152305 GGGATAT-AATCCCATATAGAAACAGGACGGGGATATAATCTCATTCAAAATCAGGAC
1 GGGATATAAATCCCATACAGAAACAGGAC-GGGATATAATCCCATTCAAAATCAGGAC
152362 GGGAT
1 GGGAT
152367 GTTGCCCTCC
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
56 23 0.41
57 33 0.59
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.19
Consensus pattern (57 bp):
GGGATATAAATCCCATACAGAAACAGGACGGGATATAATCCCATTCAAAATCAGGAC
Found at i:152359 original size:29 final size:28
Alignment explanation
Indices: 152248--152366 Score: 161
Period size: 28 Copynumber: 4.2 Consensus size: 28
152238 AGACATGACA
* *
152248 GGGATATAAATCCCATACAGAAATAGGAC
1 GGGATAT-AATCCCATATAGAAACAGGAC
152277 GGGATATAATCCCATATAGAAACAGGAC
1 GGGATATAATCCCATATAGAAACAGGAC
152305 GGGATATAATCCCATATAGAAACAGGAC
1 GGGATATAATCCCATATAGAAACAGGAC
*
152333 GGGGATATAATCTCAT-TCA-AAATCAGGAC
1 -GGGATATAATCCCATAT-AGAAA-CAGGAC
152362 GGGAT
1 GGGAT
152367 GTTGCCCTCC
Statistics
Matches: 84, Mismatches: 3, Indels: 7
0.89 0.03 0.07
Matches are distributed among these distances:
28 56 0.67
29 28 0.33
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.19
Consensus pattern (28 bp):
GGGATATAATCCCATATAGAAACAGGAC
Found at i:152432 original size:71 final size:71
Alignment explanation
Indices: 152313--152499 Score: 198
Period size: 71 Copynumber: 2.6 Consensus size: 71
152303 ACGGGATATA
** * * *
152313 ATCCCATATAGAAACAGGACGGGGATATAATCTCATTCAAAATCAGGAC-GGGATGTTGCCCTCC
1 ATCCCATGCAGAAACAGGAC-GGGATATAATCTCATGCAAAATCAGGACAGAGATGTTACCC-CC
152377 -ATAAAGG
64 TATAAAGG
* * *
152384 ATCCCATGCAGAAACAGGACGGGAATATAATCTCATGCATAATTAGGACATAGATGTTACCCCCT
1 ATCCCATGCAGAAACAGGACGGG-ATATAATCTCATGCAAAATCAGGACAGAGATGTTACCCCCT
* *
152449 GTAAGGG
65 ATAAAGG
* * ** *
152456 ATCCCATGCAAAAACATGACAAGATATAATCCCATGCAAAATCA
1 ATCCCATGCAGAAACAGGACGGGATATAATCTCATGCAAAATCA
152500 ACCATGCAGA
Statistics
Matches: 96, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
70 3 0.03
71 60 0.62
72 33 0.34
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (71 bp):
ATCCCATGCAGAAACAGGACGGGATATAATCTCATGCAAAATCAGGACAGAGATGTTACCCCCTA
TAAAGG
Found at i:152506 original size:42 final size:42
Alignment explanation
Indices: 152459--152539 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
152449 GTAAGGGATC
*
152459 CCATGCAAAAACATGACAAGATATAATCCCATGCAAAATCAA
1 CCATGCAAAAACATGACAAGATATAATCACATGCAAAATCAA
* *
152501 CCATGCAGAAACATGACGAGATATAATCACATGCAAAAT
1 CCATGCAAAAACATGACAAGATATAATCACATGCAAAAT
152540 TAGGACGGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.48, C:0.22, G:0.12, T:0.17
Consensus pattern (42 bp):
CCATGCAAAAACATGACAAGATATAATCACATGCAAAATCAA
Found at i:152704 original size:41 final size:40
Alignment explanation
Indices: 152659--152786 Score: 148
Period size: 40 Copynumber: 3.1 Consensus size: 40
152649 ATAGCAGCAT
* *
152659 TTTAGCAGCATTTTTAGAACAAACGCCGCTAAAGACTATAC
1 TTTAGCAGCGTTTTTAG-ACAAACGCCGCTAAAGACTGTAC
** * *
152700 TTTAGTGGCGTTTTTACACAAACGCTGCTAAAGACTGTAC
1 TTTAGCAGCGTTTTTAGACAAACGCCGCTAAAGACTGTAC
* * *
152740 TTTAGCAACGTTTTTAGACAAAATGCCGCTAAATACTCGTAC
1 TTTAGCAGCGTTTTTAGAC-AAACGCCGCTAAAGACT-GTAC
152782 TTTAG
1 TTTAG
152787 TGGTGTTTTT
Statistics
Matches: 72, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
40 36 0.50
41 27 0.38
42 9 0.12
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Consensus pattern (40 bp):
TTTAGCAGCGTTTTTAGACAAACGCCGCTAAAGACTGTAC
Found at i:153800 original size:43 final size:43
Alignment explanation
Indices: 153732--154145 Score: 408
Period size: 43 Copynumber: 9.7 Consensus size: 43
153722 ATGGTAATTA
** *
153732 GCGGCGTTTGTATTAAAAAACGCCGCTATAGATTTGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
* * * *
153775 GTGGCGTTTATATCCAAAAATGCCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
* * *
153818 GCGGCATTTGTATCCAAAAACGCCGCAATAGATATGAACTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
* *
153861 ACGGCGTTTGTATCCTAAAACGCCGCTATAGATATGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
* * * * *
153904 GCGGCGTTTGTAT-CAAAAATGCCACTATAGATCTTACCTATT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
* * *
153946 ACGACGTTTGTATCCAAAAACGCCGCTATTGATATGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
* * * *
153989 GCGGCGTTTATATCCAAAAATGCCGTTATAGATATGATCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
* *** * *
154032 GCGGCATTTGTGAAATAAAAACGCCGCTATAGATCTCAACC---T
1 GCGGCGTTTGT-ATCCAAAAACGCCGCTATAGATAT-GACCTTTT
** * *
154074 GCGGTATTTGT-TTCAAAAACGCCGCTATAGA-ACTTGACTTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATA--TGACCTTTT
* * *
154117 GCGGCGTTTTTATTTCACAAACGCCGCTA
1 GCGGCGTTTGTA-TCCAAAAACGCCGCTA
154146 ACATTAGCGA
Statistics
Matches: 300, Mismatches: 61, Indels: 18
0.79 0.16 0.05
Matches are distributed among these distances:
40 19 0.06
41 1 0.00
42 45 0.15
43 200 0.67
44 18 0.06
45 17 0.06
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (43 bp):
GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
Found at i:153981 original size:128 final size:129
Alignment explanation
Indices: 153733--154042 Score: 424
Period size: 128 Copynumber: 2.4 Consensus size: 129
153723 TGGTAATTAG
** * * *
153733 CGGCGTTTGTATTAAAAAACGCCGCTATAGATTTGACCTTTTGTGGCGTTTATATCCAAAAATGC
1 CGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTATCCAAAAATGC
* * * *
153798 CGCTATAGATCTGACCTTTTGCGGCATTTGTATCCAAAAACGCCGCAATAGATATGAACTTTTA
66 CACTATAGATCTGACCTATTACGACATTTGTATCCAAAAACGCCGCAATAGATATGAACTTTTA
*
153862 CGGCGTTTGTATCCTAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTAT-CAAAAATGC
1 CGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTATCCAAAAATGC
* * * * * *
153926 CACTATAGATCTTACCTATTACGACGTTTGTATCCAAAAACGCCGCTATTGATATGACCTTTTG
66 CACTATAGATCTGACCTATTACGACATTTGTATCCAAAAACGCCGCAATAGATATGAACTTTTA
* * * * *
153990 CGGCGTTTATATCCAAAAATGCCGTTATAGATATGATCTTTTGCGGCATTTGT
1 CGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGT
154043 GAAATAAAAA
Statistics
Matches: 159, Mismatches: 22, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
128 110 0.69
129 49 0.31
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.34
Consensus pattern (129 bp):
CGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTATCCAAAAATGC
CACTATAGATCTGACCTATTACGACATTTGTATCCAAAAACGCCGCAATAGATATGAACTTTTA
Found at i:154084 original size:128 final size:126
Alignment explanation
Indices: 153732--154145 Score: 422
Period size: 128 Copynumber: 3.2 Consensus size: 126
153722 ATGGTAATTA
* ** * * * *
153732 GCGGCGTTTGTATTAAAAAACGCCGCTATAGATTTGACCTTTTGTGGCGTTTATATCCAAAAATG
1 GCGGCGTTTATATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCATTTGTAT-CAAAAATG
* * *
153797 CCGCTATAGATCTGACCTTTTGCGGCATTTGTATCCAAAAACGCCGCAATAGATATGAACTTTT
65 CCGCTATAGATCTAACC--TTGCGGCATTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
* * * *
153861 ACGGCGTTTGTATCCTAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTATCAAAAATGC
1 GCGGCGTTTATATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCATTTGTATCAAAAATGC
* * * * * *
153926 CACTATAGATCTTACCTATTACGACGTTTGTATCCAAAAACGCCGCTATTGATATGACCTTTT
66 CGCTATAGATCTAACC--TTGCGGCATTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
* * *
153989 GCGGCGTTTATATCCAAAAATGCCGTTATAGATATGATCTTTTGCGGCATTTGTGAAAT-AAAAA
1 GCGGCGTTTATATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCATTTGT---ATCAAAAA
* * * *
154053 CGCCGCTATAGATCTCAACC-TGCGGTATTTGT-TTCAAAAACGCCGCTATAGA-ACTTGACTTT
63 TGCCGCTATAGATCT-AACCTTGCGGCATTTGTATCCAAAAACGCCGCTATAGATA--TGACCTT
154115 TT
125 TT
* * *
154117 GCGGCGTTTTTATTTCACAAACGCCGCTA
1 GCGGCGTTTATA-TCCAAAAACGCCGCTA
154146 ACATTAGCGA
Statistics
Matches: 240, Mismatches: 38, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
126 1 0.00
127 18 0.08
128 137 0.57
129 61 0.25
130 18 0.08
131 5 0.02
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (126 bp):
GCGGCGTTTATATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCATTTGTATCAAAAATGC
CGCTATAGATCTAACCTTGCGGCATTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
Found at i:164078 original size:6 final size:6
Alignment explanation
Indices: 164067--164092 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
164057 AAAAGAATCA
164067 TTGATT TTGATT TTGATT TTGATT TT
1 TTGATT TTGATT TTGATT TTGATT TT
164093 TCATCCATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (6 bp):
TTGATT
Found at i:166744 original size:19 final size:19
Alignment explanation
Indices: 166720--166763 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
166710 AACATATTTT
166720 TGTAAAAAACTTGTAGTGG
1 TGTAAAAAACTTGTAGTGG
*
166739 TGTAAATAACTTGTAGTGG
1 TGTAAAAAACTTGTAGTGG
*
166758 AGTAAA
1 TGTAAA
166764 CATCCAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.32
Consensus pattern (19 bp):
TGTAAAAAACTTGTAGTGG
Found at i:172383 original size:29 final size:29
Alignment explanation
Indices: 172350--172424 Score: 114
Period size: 29 Copynumber: 2.6 Consensus size: 29
172340 TTTCTGATTC
* ** *
172350 TGCATGAGATTAATTCTTTGTCCTTATTT
1 TGCATGGGATTAATTCCATGTCCTAATTT
172379 TGCATGGGATTAATTCCATGTCCTAATTT
1 TGCATGGGATTAATTCCATGTCCTAATTT
172408 TGCATGGGATTAATTCC
1 TGCATGGGATTAATTCC
172425 CCGTCATGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.23, C:0.16, G:0.17, T:0.44
Consensus pattern (29 bp):
TGCATGGGATTAATTCCATGTCCTAATTT
Found at i:172437 original size:29 final size:29
Alignment explanation
Indices: 172350--172471 Score: 104
Period size: 29 Copynumber: 4.2 Consensus size: 29
172340 TTTCTGATTC
* ***
172350 TGCATGAGATTAATTCTTTGTCCT-TATTT
1 TGCATGGGATTAATTCCCCGTCCTGT-TTT
** **
172379 TGCATGGGATTAATTCCATGTCCTAATTT
1 TGCATGGGATTAATTCCCCGTCCTGTTTT
*
172408 TGCATGGGATTAATTCCCCGTCATGTTTT
1 TGCATGGGATTAATTCCCCGTCCTGTTTT
* * *
172437 TGCATAGGA-TCATATCCCCGTCCTGTTTC
1 TGCATGGGATTAAT-TCCCCGTCCTGTTTT
172466 TGCATG
1 TGCATG
172472 AGATCATATC
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
28 3 0.04
29 74 0.96
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (29 bp):
TGCATGGGATTAATTCCCCGTCCTGTTTT
Found at i:172476 original size:29 final size:29
Alignment explanation
Indices: 172422--172496 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
172412 TGGGATTAAT
* *
172422 TCCCCGTCATGTTTTTGCATAGGATCATA
1 TCCCCGTCCTGTTTCTGCATAGGATCATA
172451 TCCCCGTCCTGTTTCTGCAT-GAGATCATA
1 TCCCCGTCCTGTTTCTGCATAG-GATCATA
* * *
172480 TCTCTGTCCTATTTCTG
1 TCCCCGTCCTGTTTCTG
172497 TTTGGGATCC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
28 1 0.03
29 39 0.98
ACGTcount: A:0.16, C:0.28, G:0.16, T:0.40
Consensus pattern (29 bp):
TCCCCGTCCTGTTTCTGCATAGGATCATA
Found at i:172505 original size:29 final size:29
Alignment explanation
Indices: 172398--172505 Score: 85
Period size: 29 Copynumber: 3.7 Consensus size: 29
172388 TTAATTCCAT
*
172398 GTCCTAATTT-TGCATGGGATTA-ATTCCCC
1 GTCCT-ATTTCTGCATGGGATCATA-TCCCC
* * * *
172427 GTCATGTTTTTGCATAGGATCATATCCCC
1 GTCCTATTTCTGCATGGGATCATATCCCC
* * * *
172456 GTCCTGTTTCTGCATGAGATCATATCTCT
1 GTCCTATTTCTGCATGGGATCATATCCCC
**
172485 GTCCTATTTCTGTTTGGGATC
1 GTCCTATTTCTGCATGGGATC
172506 CTCTTCGGAT
Statistics
Matches: 63, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
28 3 0.05
29 59 0.94
30 1 0.02
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.41
Consensus pattern (29 bp):
GTCCTATTTCTGCATGGGATCATATCCCC
Found at i:174868 original size:19 final size:19
Alignment explanation
Indices: 174829--174873 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
174819 TTATAATTAA
*
174829 TTTATATGAATATTTGGAT
1 TTTATATGAATATTTGCAT
* *
174848 TTTATATGATTATTTTCAT
1 TTTATATGAATATTTGCAT
174867 TTCTATA
1 TT-TATA
174874 ATTTTGATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.29, C:0.04, G:0.09, T:0.58
Consensus pattern (19 bp):
TTTATATGAATATTTGCAT
Found at i:176477 original size:20 final size:20
Alignment explanation
Indices: 176452--176501 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
176442 CCTTTCTTCT
176452 GATCTGACCTTTGGTAAGGA
1 GATCTGACCTTTGGTAAGGA
*
176472 GATCTGACTTTTGGTAAGGA
1 GATCTGACCTTTGGTAAGGA
*
176492 GAACTGACCT
1 GATCTGACCT
176502 GTCTTGCTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (20 bp):
GATCTGACCTTTGGTAAGGA
Found at i:177051 original size:23 final size:23
Alignment explanation
Indices: 177017--177108 Score: 94
Period size: 23 Copynumber: 4.0 Consensus size: 23
177007 CACCACAGCT
* *
177017 CGTATAAATGCATCAAAGTGCCA
1 CGTAGAAATGCACCAAAGTGCCA
* * *
177040 CGTAGAATTGCACCATAGTGCCG
1 CGTAGAAATGCACCAAAGTGCCA
** * *
177063 CGTAGAAATGCACTGAAGTCCCG
1 CGTAGAAATGCACCAAAGTGCCA
*
177086 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCAAAGTGCCA
177109 TATAAGATTG
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.33, C:0.25, G:0.24, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCAAAGTGCCA
Found at i:177508 original size:2 final size:2
Alignment explanation
Indices: 177501--177545 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
177491 TGTCTTATCC
*
177501 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
177543 TA T
1 TA T
177546 TCACATGTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:177617 original size:2 final size:2
Alignment explanation
Indices: 177610--177681 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
177600 CATTTTTCCC
177610 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
177652 AT AT 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 AT AT
177682 CATTTTTTCC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:178823 original size:24 final size:20
Alignment explanation
Indices: 178766--178828 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 20
178756 TTTCCCTTGA
*
178766 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATCCTAC
*
178786 AGTGTATCGATGCATCCCTTAAC
1 AGTGCATCGATGCAT-CC-T-AC
178809 ATGTGCATCGATGCACTCCT
1 A-GTGCATCGATGCA-TCCT
178829 TATGCATTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
20 14 0.40
21 1 0.03
22 1 0.03
23 4 0.11
24 14 0.40
25 1 0.03
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (20 bp):
AGTGCATCGATGCATCCTAC
Found at i:178829 original size:24 final size:22
Alignment explanation
Indices: 178766--178830 Score: 71
Period size: 24 Copynumber: 2.9 Consensus size: 22
178756 TTTCCCTTGA
*
178766 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATCCTTAAC
*
178786 AGTGTATCGATGCATCCCTTAAC
1 AGTGCATCGATGCAT-CCTTAAC
178809 ATGTGCATCGATGCACTCCTTA
1 A-GTGCATCGATGCA-TCCTTA
178831 TGCATTGATA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 14 0.38
21 1 0.03
22 1 0.03
23 3 0.08
24 17 0.46
25 1 0.03
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATCCTTAAC
Found at i:182332 original size:23 final size:23
Alignment explanation
Indices: 182298--182366 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
182288 CACCATAGCT
*
182298 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* ** * *
182321 CGTAGAATTGCA-TTATAGTGTCG
1 CGTAGAAATGCACCGA-AGTGCCA
182344 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
182367 TATAAGATTG
Statistics
Matches: 33, Mismatches: 11, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
22 1 0.03
23 31 0.94
24 1 0.03
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:183992 original size:24 final size:23
Alignment explanation
Indices: 183927--183992 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 23
183917 TAATTCTATT
183927 TCCCTTAA-AGTGCATCGATGCA
1 TCCCTTAACAGTGCATCGATGCA
* *
183949 -CTC-T-ACAGTGTATCGATGCA
1 TCCCTTAACAGTGCATCGATGCA
183969 TCCCTTAACATGTGCATCGATGCA
1 TCCCTTAACA-GTGCATCGATGCA
183993 CTCCTTATGC
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
19 1 0.03
20 14 0.40
21 4 0.11
22 1 0.03
23 3 0.09
24 12 0.34
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (23 bp):
TCCCTTAACAGTGCATCGATGCA
Found at i:183998 original size:24 final size:23
Alignment explanation
Indices: 183929--183999 Score: 80
Period size: 24 Copynumber: 3.2 Consensus size: 23
183919 ATTCTATTTC
183929 CCTTAA-AGTGCATCGATGCACT
1 CCTTAACAGTGCATCGATGCACT
*
183951 -C-T-ACAGTGTATCGATGCA-T
1 CCTTAACAGTGCATCGATGCACT
183970 CCCTTAACATGTGCATCGATGCACT
1 -CCTTAACA-GTGCATCGATGCACT
183995 CCTTA
1 CCTTA
184000 TGCATCGATG
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
19 2 0.05
20 14 0.35
21 2 0.05
22 1 0.03
23 3 0.08
24 17 0.43
25 1 0.03
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (23 bp):
CCTTAACAGTGCATCGATGCACT
Found at i:190508 original size:13 final size:14
Alignment explanation
Indices: 190486--190523 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
190476 CAAAGTCAAA
* *
190486 GAGTTAACTCAG-T
1 GAGTTGACTCAGCC
190499 GAGTTGACTCAGCC
1 GAGTTGACTCAGCC
190513 GAGTTGACTCA
1 GAGTTGACTCA
190524 ATGACTGGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (14 bp):
GAGTTGACTCAGCC
Found at i:193558 original size:18 final size:18
Alignment explanation
Indices: 193535--193607 Score: 83
Period size: 18 Copynumber: 3.8 Consensus size: 18
193525 GTTCTTAAGG
*
193535 AGTGGTCATTCGGGACAT
1 AGTGGTCCTTCGGGACAT
193553 AGTGGTCCTTCGGGACATAT
1 AGTGGTCCTTCGGGAC--AT
*
193573 ACAGTGGTCCTTCGGGATAT
1 --AGTGGTCCTTCGGGACAT
*
193593 AGTGGTTCTTCGGGA
1 AGTGGTCCTTCGGGA
193608 AAAATATTCA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
18 29 0.60
20 4 0.08
22 15 0.31
ACGTcount: A:0.19, C:0.18, G:0.33, T:0.30
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:199315 original size:23 final size:23
Alignment explanation
Indices: 199282--199325 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
199272 GAGTCGAGGG
*
199282 TCTACGCGGTCCTTCGGGACAAT
1 TCTACGCGGTCCTTCGAGACAAT
*
199305 TCTACGTGGTCCTTCGAGACA
1 TCTACGCGGTCCTTCGAGACA
199326 TATATGTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.30, G:0.25, T:0.27
Consensus pattern (23 bp):
TCTACGCGGTCCTTCGAGACAAT
Done.