Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008514.1 Hibiscus syriacus cultivar Beakdansim tig00111377_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: 567339
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:339890 original size:25 final size:25
Alignment explanation
Indices: 339859--339907 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
339849 ATCCCCGCAG
*
339859 TTTTTAAACAGGG-ACGGGTACGAGT
1 TTTTTAAAC-GGGAACGGGGACGAGT
339884 TTTTTAAACGGGAACGGGGACGAG
1 TTTTTAAACGGGAACGGGGACGAG
339908 GGAACCAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 3 0.14
25 19 0.86
ACGTcount: A:0.29, C:0.12, G:0.35, T:0.24
Consensus pattern (25 bp):
TTTTTAAACGGGAACGGGGACGAGT
Found at i:341673 original size:46 final size:46
Alignment explanation
Indices: 341602--341723 Score: 163
Period size: 46 Copynumber: 2.7 Consensus size: 46
341592 ATTAAGTAAT
* * *
341602 CGAAAATCTAAAGGTTGATCCGAACCTAAACTAACCCGAATTGACC
1 CGAAAATTTAAAGGTTGATCCGAACCGAAACCAACCCGAATTGACC
* * *
341648 CGAAAATTTAAAGGTTGATCTGAACCGATACCAACCTGAATTGACC
1 CGAAAATTTAAAGGTTGATCCGAACCGAAACCAACCCGAATTGACC
* * *
341694 TGAAAATTTAAAGCTTGACCCGAACCGAAA
1 CGAAAATTTAAAGGTTGATCCGAACCGAAA
341724 TCAATCGATC
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 65 1.00
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.21
Consensus pattern (46 bp):
CGAAAATTTAAAGGTTGATCCGAACCGAAACCAACCCGAATTGACC
Found at i:344234 original size:13 final size:13
Alignment explanation
Indices: 344197--344236 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
344187 TCGATATTGA
344197 AAAATAAATA-TT
1 AAAATAAATATTT
*
344209 AAAATAATTTATTT
1 AAAATAA-ATATTT
344223 AAAATAAATATTT
1 AAAATAAATATTT
344236 A
1 A
344237 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:344250 original size:17 final size:17
Alignment explanation
Indices: 344210--344258 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
344200 ATAAATATTA
*
344210 AAATAATTTATTTAAAAT
1 AAAT-ATTTATTTATAAT
*
344228 AAATATTTATTTATTAT
1 AAATATTTATTTATAAT
* *
344245 ATATATATATTTAT
1 AAATATTTATTTAT
344259 GACTATAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 23 0.85
18 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AAATATTTATTTATAAT
Found at i:345713 original size:3 final size:3
Alignment explanation
Indices: 345705--345819 Score: 203
Period size: 3 Copynumber: 38.3 Consensus size: 3
345695 TTAATATATT
* *
345705 TAA TAA TAA GAA TAA TAA TGA TAA 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
345753 TAA TAA TAA TAA TAA TAA TAA TAA 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
*
345801 TAA TAA TAA TAA TGA TAA T
1 TAA TAA TAA TAA TAA TAA T
345820 GATATGGGTA
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 106 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:346389 original size:113 final size:113
Alignment explanation
Indices: 346143--346566 Score: 733
Period size: 113 Copynumber: 3.8 Consensus size: 113
346133 AGAATTATGC
* * * *
346143 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
346208 TATGAAC-TTCTCCGGAAAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
*
346255 AAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
346320 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
346368 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
346433 TATGAACTTTCTCTGGAAAAGCTGATCCCTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
*
346481 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
346546 TATGAACTTTCTCTGGAAAAG
66 TATGAACTTTCTCTGGAAAAG
346567 CTAATCTTTC
Statistics
Matches: 300, Mismatches: 11, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
112 69 0.23
113 231 0.77
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
Found at i:347373 original size:83 final size:83
Alignment explanation
Indices: 347234--347872 Score: 1016
Period size: 83 Copynumber: 7.7 Consensus size: 83
347224 AGTTCTTACC
* * * *
347234 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAAT
*
347299 TTAATGATTGGTTCTGCT
66 TCAATGATTGGTTCTGCT
*
347317 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATTAACAAATTCATCTTCTAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAAT
347382 TCAATGATTGGTTCTG-T
66 TCAATGATTGGTTCTGCT
* * * **
347399 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACCTTCATCTTCCT-A
1 -AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTT-CTAA
347463 ATTCAATGATTGGTTCTGCT
64 ATTCAATGATTGGTTCTGCT
*
347483 AAACCAGGTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAAT
347548 TCAATGATTGGTTCTGCT
66 TCAATGATTGGTTCTGCT
* * * **
347566 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCCAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAAT
347631 TCAATGATTGGTTCTGCT
66 TCAATGATTGGTTCTGCT
*
347649 AAACCAGGTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAAT
*
347714 TCAATGGTTGGTTCTGCT
66 TCAATGATTGGTTCTGCT
347732 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAAT
347797 TCAATGATT-GTTCTG-T
66 TCAATGATTGGTTCTGCT
* * **
347813 CCAACCAGATCAGATAACTCAAAGAACACTTCCGGAAGATGCTATTGGCAAATTCATCTT
1 -AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTT
347873 TCAGTTAATG
Statistics
Matches: 514, Mismatches: 37, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
81 1 0.00
82 64 0.12
83 446 0.87
84 3 0.01
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (83 bp):
AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAAT
TCAATGATTGGTTCTGCT
Found at i:349026 original size:10 final size:10
Alignment explanation
Indices: 349013--349065 Score: 70
Period size: 10 Copynumber: 4.9 Consensus size: 10
349003 TTGACCCCCC
349013 TTTTTTCTTTT
1 TTTTTTC-TTT
349024 TTTTTCTCTTT
1 TTTTT-TCTTT
349035 TTTTTTCTTT
1 TTTTTTCTTT
349045 TTTTTTCTTCAT
1 TTTTTTCTT--T
349057 TTTTTTCTT
1 TTTTTTCTT
349066 CAAGCATAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
10 14 0.36
11 13 0.33
12 12 0.31
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:349033 original size:12 final size:12
Alignment explanation
Indices: 349013--349050 Score: 62
Period size: 11 Copynumber: 3.3 Consensus size: 12
349003 TTGACCCCCC
349013 TTTTT-TCTTTT
1 TTTTTCTCTTTT
349024 TTTTTCTCTTTT
1 TTTTTCTCTTTT
349036 TTTTTCT-TTTT
1 TTTTTCTCTTTT
349047 TTTT
1 TTTT
349051 CTTCATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 13 0.50
12 13 0.50
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (12 bp):
TTTTTCTCTTTT
Found at i:349041 original size:22 final size:23
Alignment explanation
Indices: 349013--349062 Score: 84
Period size: 22 Copynumber: 2.2 Consensus size: 23
349003 TTGACCCCCC
*
349013 TTTTTTCTTTTTTTTTC-TCTTT
1 TTTTTTCTTTTTTTTTCTTCATT
349035 TTTTTTCTTTTTTTTTCTTCATT
1 TTTTTTCTTTTTTTTTCTTCATT
349058 TTTTT
1 TTTTT
349063 CTTCAAGCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 17 0.65
23 9 0.35
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (23 bp):
TTTTTTCTTTTTTTTTCTTCATT
Found at i:349067 original size:12 final size:11
Alignment explanation
Indices: 349013--349066 Score: 67
Period size: 12 Copynumber: 4.9 Consensus size: 11
349003 TTGACCCCCC
349013 TTTTTTCTT-T
1 TTTTTTCTTCT
*
349023 TTTTTTCTCTTT
1 TTTTTTCT-TCT
349035 TTTTTTCTT-T
1 TTTTTTCTTCT
349045 TTTTTTCTTCAT
1 TTTTTTCTTC-T
349057 TTTTTTCTTC
1 TTTTTTCTTC
349067 AAGCATAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
10 18 0.45
11 2 0.05
12 20 0.50
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTTCTTCT
Found at i:356344 original size:14 final size:15
Alignment explanation
Indices: 356325--356357 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
356315 ATTATTTTTC
356325 AAATTTTA-ATTAAT
1 AAATTTTATATTAAT
*
356339 AAATTTTATCTTAAT
1 AAATTTTATATTAAT
356354 AAAT
1 AAAT
356358 AAAATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATTTTATATTAAT
Found at i:360434 original size:13 final size:13
Alignment explanation
Indices: 360397--360436 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
360387 TCGATATTGA
360397 AAAATAAATA-TT
1 AAAATAAATATTT
*
360409 AAAATAATTTATTT
1 AAAATAA-ATATTT
360423 AAAATAAATATTT
1 AAAATAAATATTT
360436 A
1 A
360437 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:361377 original size:14 final size:14
Alignment explanation
Indices: 361360--361386 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
361350 TTAGTATATC
361360 TTTTTTTTTCTCTG
1 TTTTTTTTTCTCTG
361374 TTTTTTTTTCTCT
1 TTTTTTTTTCTCT
361387 CTCTCTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (14 bp):
TTTTTTTTTCTCTG
Found at i:361889 original size:3 final size:3
Alignment explanation
Indices: 361881--361986 Score: 176
Period size: 3 Copynumber: 35.3 Consensus size: 3
361871 TTAATATATT
* *
361881 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
361929 TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
361977 TAA TGA TAA T
1 TAA TAA TAA T
361987 GATATGGGTA
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 97 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:377100 original size:21 final size:21
Alignment explanation
Indices: 377075--377122 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 21
377065 GTGTCGGTAC
377075 TTACCTCTTAG-TATCGATACT
1 TTACC-CTTAGATATCGATACT
377096 TTA-CCTTAGATATCGATACT
1 TTACCCTTAGATATCGATACT
377116 TTACCCT
1 TTACCCT
377123 ATTATTTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.20
20 14 0.56
21 6 0.24
ACGTcount: A:0.25, C:0.25, G:0.08, T:0.42
Consensus pattern (21 bp):
TTACCCTTAGATATCGATACT
Found at i:386364 original size:13 final size:13
Alignment explanation
Indices: 386346--386370 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
386336 TTAGTTTTAT
386346 TATTATATTATTA
1 TATTATATTATTA
386359 TATTATATTATT
1 TATTATATTATT
386371 TTACACCGAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTATATTATTA
Found at i:386900 original size:16 final size:17
Alignment explanation
Indices: 386879--386919 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
386869 AATCTACTTA
386879 TATATTATTGTTAA-AT
1 TATATTATTGTTAATAT
386895 TATATTA-TGTTAATAT
1 TATATTATTGTTAATAT
386911 TATTATTAT
1 TA-TATTAT
386920 ATATTAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 6 0.27
16 11 0.50
17 5 0.23
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (17 bp):
TATATTATTGTTAATAT
Found at i:390902 original size:18 final size:18
Alignment explanation
Indices: 390876--390911 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
390866 TTGACTCAGC
*
390876 TGAGTTGATCCAACCCGA
1 TGAGGTGATCCAACCCGA
*
390894 TGAGGTGATCCGACCCGA
1 TGAGGTGATCCAACCCGA
390912 CGGAGTCATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.19
Consensus pattern (18 bp):
TGAGGTGATCCAACCCGA
Found at i:393144 original size:22 final size:23
Alignment explanation
Indices: 393119--393164 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
393109 GTTTTTCCTA
393119 TATTT-TTTT-TTATAAACACTAT
1 TATTTATTTTATTA-AAACACTAT
*
393141 TATTTATTTTATTAAAAGACTAT
1 TATTTATTTTATTAAAACACTAT
393164 T
1 T
393165 CCAATTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 13 0.62
24 3 0.14
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.57
Consensus pattern (23 bp):
TATTTATTTTATTAAAACACTAT
Found at i:393419 original size:20 final size:20
Alignment explanation
Indices: 393377--393481 Score: 140
Period size: 20 Copynumber: 5.1 Consensus size: 20
393367 ATTTTTAATT
393377 TCGTAACGTGAATAGTAAAAA
1 TCGTAACGTGAATAGT-AAAA
393398 TCGTAACGTGAATAGTAAAA
1 TCGTAACGTGAATAGTAAAA
393418 TCGTAACGTGAATAGTAGAAA
1 TCGTAACGTGAATAGTA-AAA
* *
393439 TTAC-AAATGTGAATAGTAAAA
1 -T-CGTAACGTGAATAGTAAAA
*
393460 TCGCAACGTGAATAGTAAAA
1 TCGTAACGTGAATAGTAAAA
393480 TC
1 TC
393482 ATAAAATCGC
Statistics
Matches: 76, Mismatches: 4, Indels: 9
0.85 0.04 0.10
Matches are distributed among these distances:
19 1 0.01
20 39 0.51
21 22 0.29
22 13 0.17
23 1 0.01
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGTAACGTGAATAGTAAAA
Found at i:393861 original size:20 final size:20
Alignment explanation
Indices: 393836--393923 Score: 90
Period size: 20 Copynumber: 4.4 Consensus size: 20
393826 CATATAGATT
393836 CGTTGCGATTTTACTATTCA
1 CGTTGCGATTTTACTATTCA
*
393856 CGTTGCAATTTTACTATTCA
1 CGTTGCGATTTTACTATTCA
* **
393876 CGTTGCGAATTTGACT-TTTG
1 CGTTGCG-ATTTTACTATTCA
* *
393896 TGTTGCGA-TTTACAAATTCA
1 CGTTGCGATTTTAC-TATTCA
393916 CGTTGCGA
1 CGTTGCGA
393924 ATTTGGAAAA
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
18 4 0.07
19 1 0.02
20 42 0.78
21 7 0.13
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (20 bp):
CGTTGCGATTTTACTATTCA
Found at i:394021 original size:20 final size:21
Alignment explanation
Indices: 393972--394025 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
393962 CGATTTACAT
393972 ATTCGCGTTGCGAAATTAGAA
1 ATTCGCGTTGCGAAATTAGAA
* *
393993 ATT-GGGTTGCGAAATT-GGA
1 ATTCGCGTTGCGAAATTAGAA
*
394012 GTTCGCGTTGCGAA
1 ATTCGCGTTGCGAA
394026 TTTGTTGGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.14
20 21 0.75
21 3 0.11
ACGTcount: A:0.26, C:0.13, G:0.31, T:0.30
Consensus pattern (21 bp):
ATTCGCGTTGCGAAATTAGAA
Found at i:409948 original size:15 final size:15
Alignment explanation
Indices: 409928--409981 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
409918 TGCACTTTAA
*
409928 AAATAATTATATTAT
1 AAATAAATATATTAT
*
409943 AAATAAATCTAGTTAT
1 AAATAAATATA-TTAT
*
409959 ACTAAAAAATATATTAT
1 A--AATAAATATATTAT
409976 AAATAA
1 AAATAA
409982 GTATTTAAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 13 0.42
16 5 0.16
17 5 0.16
18 8 0.26
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (15 bp):
AAATAAATATATTAT
Found at i:410258 original size:13 final size:13
Alignment explanation
Indices: 410242--410274 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
410232 GATAAAAAAA
410242 TATTTTAAATATC
1 TATTTTAAATATC
*
410255 TA-TTTAAATATT
1 TATTTTAAATATC
410267 TATTTTAA
1 TATTTTAA
410275 TTAAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (13 bp):
TATTTTAAATATC
Found at i:410270 original size:41 final size:40
Alignment explanation
Indices: 410216--410293 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 40
410206 GATTAAAAGT
*
410216 TTTAAACACTTATTATGATAAAAAAATATTTTAAATATCTA
1 TTTAAACACTTATTATAAT-AAAAAATATTTTAAATATCTA
* * * * *
410257 TTTAAATATTTATTTTAATTAAAAATATTTTATATAT
1 TTTAAACACTTATTATAATAAAAAATATTTTAAATAT
410294 TTAAATAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
40 16 0.52
41 15 0.48
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (40 bp):
TTTAAACACTTATTATAATAAAAAATATTTTAAATATCTA
Found at i:411384 original size:32 final size:32
Alignment explanation
Indices: 411343--411411 Score: 138
Period size: 32 Copynumber: 2.2 Consensus size: 32
411333 AAAAATATAT
411343 ATATAGAGGGGTATTATTGTAATTATTCCTAA
1 ATATAGAGGGGTATTATTGTAATTATTCCTAA
411375 ATATAGAGGGGTATTATTGTAATTATTCCTAA
1 ATATAGAGGGGTATTATTGTAATTATTCCTAA
411407 ATATA
1 ATATA
411412 TAAGGTAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.41
Consensus pattern (32 bp):
ATATAGAGGGGTATTATTGTAATTATTCCTAA
Found at i:416033 original size:20 final size:19
Alignment explanation
Indices: 416008--416045 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
415998 ACATGCCATG
416008 ATTTTTTCAATAATAAAACA
1 ATTTTTTCAATAA-AAAACA
416028 ATTTTTTCAATAAAAAAC
1 ATTTTTTCAATAAAAAAC
416046 TTTAAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (19 bp):
ATTTTTTCAATAAAAAACA
Found at i:416391 original size:21 final size:20
Alignment explanation
Indices: 416306--416462 Score: 84
Period size: 21 Copynumber: 7.8 Consensus size: 20
416296 AATGACCAAT
** *
416306 AAAATCGCAACGCGA-AATA
1 AAAATCGCAACGCGATTTTC
***
416325 AAAATCGCAACGCGATCCCC
1 AAAATCGCAACGCGATTTTC
* ** *
416345 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGA-TTTTC
*
416365 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTC
* * *
416386 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGAT-TTTC
* **
416407 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTT-C
* * *
416428 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTC
416448 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
416463 ACACATAAAT
Statistics
Matches: 104, Mismatches: 28, Indels: 11
0.73 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTC
Found at i:416491 original size:20 final size:20
Alignment explanation
Indices: 416429--416621 Score: 228
Period size: 20 Copynumber: 9.7 Consensus size: 20
416419 CGATTTTCCA
* ** *
416429 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
416449 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
416469 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
416489 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
416509 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
416529 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
416549 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
416569 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* *
416589 AAATCGCAACGAGAATCCGT
1 AAATCGCAACGCGTATCCGT
416609 AAATCGCAACGCG
1 AAATCGCAACGCG
416622 ATATTTAAAG
Statistics
Matches: 148, Mismatches: 21, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
19 2 0.01
20 144 0.97
21 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:417145 original size:19 final size:19
Alignment explanation
Indices: 417121--417180 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
417111 TGCAGAAGAG
*
417121 TCGCAACGCGAAATGACAA
1 TCGCAACGCGAAATGAAAA
*
417140 TCGCAA--CG--A-GATAA
1 TCGCAACGCGAAATGAAAA
417154 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
417173 TCGCAACG
1 TCGCAACG
417181 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 18 0.53
ACGTcount: A:0.42, C:0.25, G:0.22, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:417157 original size:14 final size:14
Alignment explanation
Indices: 417138--417199 Score: 52
Period size: 14 Copynumber: 4.1 Consensus size: 14
417128 GCGAAATGAC
*
417138 AATCGCAACGAGAT
1 AATCGCAACGAGAA
417152 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAA
*
417171 AATCGCAACGAGAG
1 AATCGCAACGAGAA
*
417185 AATCGCAACGCGAA
1 AATCGCAACGAGAA
417199 A
1 A
417200 CCAAAATCGC
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
14 23 0.59
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.45, C:0.23, G:0.23, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAA
Found at i:417163 original size:33 final size:33
Alignment explanation
Indices: 417121--417210 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
417111 TGCAGAAGAG
* *
417121 TCGCAACGCGAAATGACAATCGCAACGAGATAA
1 TCGCAACGCGAAATGAAAATCGCAACGAGAGAA
417154 TCGCAACGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAATGAAAATCGCAACGAGAGAA
**
417187 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAATGAAAATCGCA
417211 TTGCGATTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.43, C:0.26, G:0.21, T:0.10
Consensus pattern (33 bp):
TCGCAACGCGAAATGAAAATCGCAACGAGAGAA
Found at i:417228 original size:19 final size:19
Alignment explanation
Indices: 417206--417289 Score: 106
Period size: 19 Copynumber: 4.7 Consensus size: 19
417196 GAAACCAAAA
*
417206 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
417225 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
417239 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
417258 TCGCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
417277 TCGCGTTGCGATT
1 TCGCGTTGCGATT
417290 CTCTCGTTGC
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
14 10 0.18
16 3 0.05
17 3 0.05
19 40 0.71
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:417289 original size:52 final size:52
Alignment explanation
Indices: 417206--417311 Score: 194
Period size: 52 Copynumber: 2.0 Consensus size: 52
417196 GAAACCAAAA
*
417206 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTGTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
*
417258 TCGCGTTGCGATTGTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTGTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
417310 TC
1 TC
417312 AACCCAAAGA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTGTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:417440 original size:19 final size:19
Alignment explanation
Indices: 417416--417513 Score: 91
Period size: 19 Copynumber: 5.4 Consensus size: 19
417406 GCGATTCTTT
417416 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTGGTTTCG
*
417435 CGTTGCGA---T--TTT-A
1 CGTTGCGATTTTGGTTTCG
* **
417448 AGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTGGTTTCG
417467 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTGGTTTCG
*
417486 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTT-GGTTTCG
*
417506 TGTTGCGA
1 CGTTGCGA
417514 AAGTAAACTA
Statistics
Matches: 64, Mismatches: 8, Indels: 13
0.75 0.09 0.15
Matches are distributed among these distances:
13 7 0.11
14 3 0.05
16 2 0.03
18 3 0.05
19 36 0.56
20 13 0.20
ACGTcount: A:0.11, C:0.15, G:0.28, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTGGTTTCG
Found at i:417458 original size:32 final size:32
Alignment explanation
Indices: 417401--417478 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 32
417391 TATCTTCACA
** **
417401 GCGTTGCGATTCTTTCGTTGCGATTTTGGTTTC
1 GCGTTGCGATT-TTAAGTTGCGATTTTCATTTC
417434 GCGTTGCGATTTTAAGTTGCGATTTTCATTTC
1 GCGTTGCGATTTTAAGTTGCGATTTTCATTTC
417466 GCGTTGCGATTTT
1 GCGTTGCGATTTT
417479 GGTTTCGCGT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 30 0.73
33 11 0.27
ACGTcount: A:0.10, C:0.17, G:0.26, T:0.47
Consensus pattern (32 bp):
GCGTTGCGATTTTAAGTTGCGATTTTCATTTC
Found at i:419454 original size:14 final size:14
Alignment explanation
Indices: 419435--419470 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
419425 ATTGTTTAAT
419435 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
419449 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
419463 TGATTTGT
1 TGATTTGT
419471 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:419589 original size:19 final size:19
Alignment explanation
Indices: 419573--419670 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
419563 AAAAATGACT
419573 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
419592 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
419611 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
419625 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
419644 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
419664 ATCGCAA
1 ATCGCAA
419671 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:419702 original size:53 final size:53
Alignment explanation
Indices: 419573--419689 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
419563 AAAAATGACT
419573 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
419625 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
419678 ATCGCAATGCGA
1 ATCGCAATGCGA
419690 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:419707 original size:19 final size:19
Alignment explanation
Indices: 419679--419898 Score: 223
Period size: 19 Copynumber: 12.7 Consensus size: 19
419669 AACGAGAGAA
*
419679 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
419698 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
419717 TCGCATTGC-A-ATT-ATC
1 TCGCATTGCGATTTTCATT
419733 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
419750 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
419769 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
419785 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
419802 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
419821 TCGCATTGCGA---T--TT
1 TCGCATTGCGATTTTCATT
*
419835 TCG--TTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
419852 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
419870 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
419886 TCGCATTGCGATT
1 TCGCATTGCGATT
419899 CTCTCGTTGC
Statistics
Matches: 168, Mismatches: 10, Indels: 46
0.75 0.04 0.21
Matches are distributed among these distances:
12 6 0.04
14 26 0.15
15 2 0.01
16 17 0.10
17 18 0.11
18 4 0.02
19 84 0.50
20 11 0.07
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:419742 original size:52 final size:51
Alignment explanation
Indices: 419685--419870 Score: 320
Period size: 52 Copynumber: 3.6 Consensus size: 51
419675 AGAATCGCAA
*
419685 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCAATTATCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT-TCTCGT
419737 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT-TCTCGT
419789 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTT-TCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTCTCGT
*
419839 TGCGATTTTTATTTCCGCATTGCGATTTTCAT
1 TGCGATTTTCATTT-CGCATTGCGATTTTCAT
419871 GTTGGGATTT
Statistics
Matches: 130, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
50 17 0.13
51 18 0.14
52 95 0.73
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (51 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTCTCGT
Found at i:419765 original size:71 final size:69
Alignment explanation
Indices: 419679--419898 Score: 224
Period size: 71 Copynumber: 3.2 Consensus size: 69
419669 AACGAGAGAA
*
419679 TCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCAATTATCTCGTTGCGATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC-ATT-TCTCGTTGCGATT
419744 TTCATT
64 TTCATT
* * * * *
419750 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATT-T-TCATTTCGCA-TTGCATTTCTCGTTGCGAT
419814 TTTCATT
63 TTTCATT
* *
419821 TCGCATTGCGA---T--TTTCG--TTGCGATTTTTATTTCCGCATTGCGATTT-TCATGTTGGGA
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGC-ATTTCTC--GTTGCGA
419878 TTTTCATT
62 TTTTCATT
419886 TCGCATTGCGATT
1 TCGCATTGCGATT
419899 CTCTCGTTGC
Statistics
Matches: 126, Mismatches: 13, Indels: 24
0.77 0.08 0.15
Matches are distributed among these distances:
62 3 0.02
63 7 0.06
64 13 0.10
65 24 0.19
66 5 0.04
68 1 0.01
71 59 0.47
72 5 0.04
73 9 0.07
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.46
Consensus pattern (69 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCATTTCTCGTTGCGATTTT
CATT
Found at i:419920 original size:33 final size:32
Alignment explanation
Indices: 419703--419912 Score: 194
Period size: 33 Copynumber: 6.2 Consensus size: 32
419693 TCATTTCGCA
*
419703 TTGCGATTTTCATTTCGCATTGCAATTATCTCG
1 TTGCGATTTTCATTTCGCATTGCGATT-TCTCG
419736 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA-TTTC---TCG
* * * * *
419772 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATTTCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTTCTCG
419807 TTGCGATTTTCATTTCGCATTGCGATTT-TCG
1 TTGCGATTTTCATTTCGCATTGCGATTTCTCG
*
419838 TTGCGATTTTTATTTCCGCATTGCGATTT-TCATG
1 TTGCGATTTTCATTT-CGCATTGCGATTTCTC--G
*
419872 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATT-TCTCG
419905 TTGCGATT
1 TTGCGATT
419913 GTAATTTCCG
Statistics
Matches: 146, Mismatches: 15, Indels: 32
0.76 0.08 0.17
Matches are distributed among these distances:
31 24 0.16
32 21 0.14
33 54 0.37
34 17 0.12
35 3 0.02
36 3 0.02
38 12 0.08
39 3 0.02
40 9 0.06
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (32 bp):
TTGCGATTTTCATTTCGCATTGCGATTTCTCG
Found at i:422447 original size:24 final size:24
Alignment explanation
Indices: 422413--422459 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
422403 CTGAAACATC
422413 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
422437 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
422460 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:423365 original size:20 final size:20
Alignment explanation
Indices: 423187--423394 Score: 233
Period size: 20 Copynumber: 10.4 Consensus size: 20
423177 CAGATTCTCG
*
423187 TGCGATTTACGGATTA-TCGT
1 TGCGATTTACGGA-TACGCGT
*
423207 TGCGATTTACGGATTA-TCGT
1 TGCGATTTACGGA-TACGCGT
* *
423227 TGCGATTTACGGATTCTCGT
1 TGCGATTTACGGATACGCGT
423247 TGCGATTTACGGATACGCGT
1 TGCGATTTACGGATACGCGT
* *
423267 TGCGATATACGGATACGCAT
1 TGCGATTTACGGATACGCGT
**
423287 TGCGATTTACCCATACGCGT
1 TGCGATTTACGGATACGCGT
*
423307 TGCGATTTACGGATACACGT
1 TGCGATTTACGGATACGCGT
423327 TGCGATTTACGGATACGCGT
1 TGCGATTTACGGATACGCGT
* *
423347 TGCGATTTATGTG-TTCGCGT
1 TGCGATTTACG-GATACGCGT
* ** *
423367 TGCGATTTTCATATTCGCGT
1 TGCGATTTACGGATACGCGT
423387 TGCGATTT
1 TGCGATTT
423395 TGGAAAATCG
Statistics
Matches: 166, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
19 1 0.01
20 164 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.36
Consensus pattern (20 bp):
TGCGATTTACGGATACGCGT
Found at i:423411 original size:21 final size:21
Alignment explanation
Indices: 423381--423463 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
423371 ATTTTCATAT
*
423381 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
423402 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
423423 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
423444 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
423464 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:423454 original size:42 final size:43
Alignment explanation
Indices: 423361--423459 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
423351 ATTTATGTGT
* *
423361 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
423402 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
423444 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
423460 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:423790 original size:59 final size:58
Alignment explanation
Indices: 423670--423791 Score: 136
Period size: 59 Copynumber: 2.1 Consensus size: 58
423660 TTGTCCCTCA
* * * * ***
423670 ACTATAGTGTATTGTTTTATTAATCCCTCGACTATTAAAAGTTATAAAATGATCTTTG
1 ACTATAGAGTATTGTTTCATTAATCCATCGACTATTAAAAGTTACAAAATGATCACCG
* * * *
423728 ACTATAGAGTGTTGTTTCGTTAAGTCCATCGACTATTAAAAGTTACACAATGGTCACCG
1 ACTATAGAGTATTGTTTCATTAA-TCCATCGACTATTAAAAGTTACAAAATGATCACCG
423787 ACTAT
1 ACTAT
423792 TCGTTATGTT
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
58 19 0.37
59 33 0.63
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.38
Consensus pattern (58 bp):
ACTATAGAGTATTGTTTCATTAATCCATCGACTATTAAAAGTTACAAAATGATCACCG
Found at i:426989 original size:16 final size:16
Alignment explanation
Indices: 426951--426994 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 16
426941 TGAGTTCTAA
426951 TTAATT-TTTTAAATT
1 TTAATTATTTTAAATT
*
426966 TT-ATTATTCTAAATT
1 TTAATTATTTTAAATT
426981 TTAATTATTTTAAA
1 TTAATTATTTTAAA
426995 AATATTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 3 0.12
15 12 0.48
16 10 0.40
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
TTAATTATTTTAAATT
Found at i:427074 original size:17 final size:17
Alignment explanation
Indices: 427041--427074 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
427031 AACATATAAT
*
427041 TAAAAATATTTTAAAAA
1 TAAAAATATTTAAAAAA
*
427058 TAAAATTATTTAAAAAA
1 TAAAAATATTTAAAAAA
427075 GATTTAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAAATATTTAAAAAA
Found at i:433522 original size:36 final size:36
Alignment explanation
Indices: 433480--433556 Score: 136
Period size: 36 Copynumber: 2.1 Consensus size: 36
433470 CCTAATGAAG
* *
433480 ATAACCTGATTGTGCCTCTCGAGGCATTTGCTTCCT
1 ATAACCTGATCGTGCCTCTCGAGGCATTTGCTTCAT
433516 ATAACCTGATCGTGCCTCTCGAGGCATTTGCTTCAT
1 ATAACCTGATCGTGCCTCTCGAGGCATTTGCTTCAT
433552 ATAAC
1 ATAAC
433557 TACATTCCCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.34
Consensus pattern (36 bp):
ATAACCTGATCGTGCCTCTCGAGGCATTTGCTTCAT
Found at i:436861 original size:14 final size:14
Alignment explanation
Indices: 436838--436875 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
436828 TCGTACTAAC
*
436838 ATAATCTAAACTTA
1 ATAATATAAACTTA
436852 ATAATATAAACTTA
1 ATAATATAAACTTA
436866 ATAATATAAA
1 ATAATATAAA
436876 AGTCTATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAATATAAACTTA
Found at i:438571 original size:18 final size:16
Alignment explanation
Indices: 438548--438581 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
438538 TTTAAGGGGG
438548 CTAAAATATATAACTTTT
1 CTAAAAT-TATAA-TTTT
438566 CTAAAATTATAATTTT
1 CTAAAATTATAATTTT
438582 AGTCCTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 5 0.31
18 7 0.44
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (16 bp):
CTAAAATTATAATTTT
Found at i:439483 original size:30 final size:30
Alignment explanation
Indices: 439447--439530 Score: 109
Period size: 32 Copynumber: 2.8 Consensus size: 30
439437 TATATTTTAA
* *
439447 AAATATATTTTATTTATGTTTTAACTTGTT
1 AAATATATTTTATTTATATTTTAACTTATT
*
439477 AAATATATTTTATTTTATTTTCTTAACTTATT
1 AAATATATTTTA-TTTATATT-TTAACTTATT
439509 AAATATA-TTTATTT-TATTTTAA
1 AAATATATTTTATTTATATTTTAA
439531 TATAAAAATA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
28 4 0.08
29 3 0.06
30 15 0.31
31 11 0.22
32 16 0.33
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (30 bp):
AAATATATTTTATTTATATTTTAACTTATT
Found at i:439503 original size:32 final size:31
Alignment explanation
Indices: 439447--439528 Score: 123
Period size: 31 Copynumber: 2.7 Consensus size: 31
439437 TATATTTTAA
* *
439447 AAATATATTTTA-TTTATGTTTTAACTTGTT
1 AAATATATTTTATTTTATTTTTTAACTTATT
439477 AAATATATTTTATTTTATTTTCTTAACTTATT
1 AAATATATTTTATTTTATTTT-TTAACTTATT
439509 AAATATA-TTTATTTTATTTT
1 AAATATATTTTATTTTATTTT
439529 AATATAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
30 12 0.25
31 20 0.42
32 16 0.33
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (31 bp):
AAATATATTTTATTTTATTTTTTAACTTATT
Found at i:439789 original size:19 final size:20
Alignment explanation
Indices: 439748--439789 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
439738 GTTTTAGGCT
*
439748 TTTTCAATTTAAAAATGTGC
1 TTTTCAATTTAAAAAAGTGC
439768 TTTT-AATTTAAAATAAGT-C
1 TTTTCAATTTAAAA-AAGTGC
439787 TTT
1 TTT
439790 ATTATCTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (20 bp):
TTTTCAATTTAAAAAAGTGC
Found at i:439852 original size:18 final size:17
Alignment explanation
Indices: 439820--439920 Score: 54
Period size: 17 Copynumber: 6.0 Consensus size: 17
439810 AAGATAAAAT
*
439820 ATAAAAATATTTTTTAA
1 ATAAAAATATATTTTAA
439837 ATAAAATATATATTTTATA
1 ATAAAA-ATATATTTTA-A
* *
439856 TTAAATGAATA-A--TAAA
1 ATAAA--AATATATTTTAA
*
439872 ATATTTAAATATATTTTAA
1 ATA--AAAATATATTTTAA
*
439891 ATTAAAATAT-TTTT-A
1 ATAAAAATATATTTTAA
439906 A-AAAAATAT-TTTTAA
1 ATAAAAATATATTTTAA
439921 GTGATTATAA
Statistics
Matches: 65, Mismatches: 9, Indels: 22
0.68 0.09 0.23
Matches are distributed among these distances:
14 11 0.17
15 3 0.05
16 11 0.17
17 15 0.23
18 10 0.15
19 11 0.17
20 3 0.05
21 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (17 bp):
ATAAAAATATATTTTAA
Found at i:439913 original size:14 final size:15
Alignment explanation
Indices: 439878--439920 Score: 61
Period size: 14 Copynumber: 2.8 Consensus size: 15
439868 TAAAATATTT
439878 AAATATATTTTAAATTA
1 AAATAT-TTTTAAA-TA
439895 AAATATTTTTAAA-A
1 AAATATTTTTAAATA
439909 AAATATTTTTAA
1 AAATATTTTTAA
439921 GTGATTATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.50
16 7 0.27
17 6 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AAATATTTTTAAATA
Found at i:439918 original size:15 final size:16
Alignment explanation
Indices: 439823--439918 Score: 52
Period size: 16 Copynumber: 5.7 Consensus size: 16
439813 ATAAAATATA
439823 AAAATATTTTTTAAAT
1 AAAATATTTTTTAAAT
*
439839 AAAATATATATTTTATAT
1 AAAATAT-T-TTTTAAAT
* * ** *
439857 TAAATGAATAATAAAAT
1 AAAAT-ATTTTTTAAAT
*
439874 ATTTAAATATATTTTAAATT
1 A---AAATATTTTTTAAA-T
439894 AAAATA-TTTTTAAA-
1 AAAATATTTTTTAAAT
439908 AAAATATTTTT
1 AAAATATTTTT
439919 AAGTGATTAT
Statistics
Matches: 58, Mismatches: 14, Indels: 17
0.65 0.16 0.19
Matches are distributed among these distances:
14 6 0.10
15 4 0.07
16 14 0.24
17 10 0.17
18 12 0.21
19 6 0.10
20 6 0.10
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (16 bp):
AAAATATTTTTTAAAT
Found at i:441320 original size:11 final size:11
Alignment explanation
Indices: 441304--441332 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
441294 TCGTATTTAT
441304 TAATTTTAAAA
1 TAATTTTAAAA
441315 TAATTTTAAAA
1 TAATTTTAAAA
441326 TAATTTT
1 TAATTTT
441333 TTATTTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TAATTTTAAAA
Found at i:442079 original size:24 final size:24
Alignment explanation
Indices: 442047--442102 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
442037 GTTAAAATGA
* *
442047 TAAACGAACACAAATGAACGAACG
1 TAAACGAACACAAACGAACAAACG
* *
442071 TAAATGAACATAAACGAACAAACG
1 TAAACGAACACAAACGAACAAACG
442095 TAAACGAA
1 TAAACGAA
442103 AGAACATAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.57, C:0.18, G:0.14, T:0.11
Consensus pattern (24 bp):
TAAACGAACACAAACGAACAAACG
Found at i:442112 original size:14 final size:15
Alignment explanation
Indices: 442076--442112 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
442066 GAACGTAAAT
442076 GAACATAAACGAACA
1 GAACATAAACGAACA
*
442091 -AACGTAAACGAA-A
1 GAACATAAACGAACA
442104 GAACATAAA
1 GAACATAAA
442113 ATTAATTGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.95
ACGTcount: A:0.62, C:0.16, G:0.14, T:0.08
Consensus pattern (15 bp):
GAACATAAACGAACA
Found at i:442847 original size:32 final size:33
Alignment explanation
Indices: 442810--442874 Score: 123
Period size: 32 Copynumber: 2.0 Consensus size: 33
442800 AAAAATATAA
442810 AAAATCAAATTAAACAGGG-ACGGGAAAAATCG
1 AAAATCAAATTAAACAGGGAACGGGAAAAATCG
442842 AAAATCAAATTAAACAGGGAACGGGAAAAATCG
1 AAAATCAAATTAAACAGGGAACGGGAAAAATCG
442875 TTTATGCTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 19 0.59
33 13 0.41
ACGTcount: A:0.54, C:0.12, G:0.22, T:0.12
Consensus pattern (33 bp):
AAAATCAAATTAAACAGGGAACGGGAAAAATCG
Found at i:443033 original size:15 final size:15
Alignment explanation
Indices: 442973--443052 Score: 50
Period size: 13 Copynumber: 5.8 Consensus size: 15
442963 AATTATTATA
442973 TATATATATATAATAT
1 TATATATATATAAT-T
* *
442989 TA-ATAAATTTAATT
1 TATATATATATAATT
* *
443003 TA-A-A-ATAAAATA
1 TATATATATATAATT
443015 TATATATA-AT-ATT
1 TATATATATATAATT
443028 TATATAT-T-TAATT
1 TATATATATATAATT
*
443041 TAAATATATATA
1 TATATATATATA
443053 TACCCGGCCC
Statistics
Matches: 49, Mismatches: 8, Indels: 15
0.68 0.11 0.21
Matches are distributed among these distances:
12 8 0.16
13 20 0.41
14 7 0.14
15 12 0.24
16 2 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATATATATATAATT
Found at i:443054 original size:38 final size:38
Alignment explanation
Indices: 442969--443054 Score: 129
Period size: 38 Copynumber: 2.3 Consensus size: 38
442959 AAATAATTAT
442969 TATATATATATATATAATATTAATAAATTTAATTTAAA
1 TATATATATATATATAATATTAATAAATTTAATTTAAA
* * *
443007 -ATAAAATATATATATAATATTTATATATTTAATTTAAA
1 TAT-ATATATATATATAATATTAATAAATTTAATTTAAA
443045 TATATATATA
1 TATATATATA
443055 CCCGGCCCGA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
37 2 0.05
38 38 0.90
39 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (38 bp):
TATATATATATATATAATATTAATAAATTTAATTTAAA
Found at i:446945 original size:17 final size:17
Alignment explanation
Indices: 446923--446962 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
446913 CTTACTCTTT
*
446923 TAAAATTT-TAAAGTATA
1 TAAAATTTATAAAAT-TA
446940 TAAAATTTATAAAATTA
1 TAAAATTTATAAAATTA
446957 TAAAAT
1 TAAAAT
446963 AAATTATAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (17 bp):
TAAAATTTATAAAATTA
Found at i:446967 original size:21 final size:21
Alignment explanation
Indices: 446942--446988 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
446932 AAAGTATATA
446942 AAATTTATA-A-AATTATAAAAT
1 AAATTTATAGAGAA-TA-AAAAT
446963 AAA-TTATAGAGAATAAAAAT
1 AAATTTATAGAGAATAAAAAT
446983 AAATTT
1 AAATTT
446989 TTAATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 13 0.57
21 8 0.35
22 2 0.09
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (21 bp):
AAATTTATAGAGAATAAAAAT
Found at i:454617 original size:31 final size:31
Alignment explanation
Indices: 454582--454667 Score: 145
Period size: 31 Copynumber: 2.8 Consensus size: 31
454572 AAATTACATG
*
454582 TTTAGTACCTAAACTATCAGTTTTGATCCTT
1 TTTAGTACCTAAACTATCAATTTTGATCCTT
*
454613 TTTAGTACCTAAACTATCAATTTTGGTCCTT
1 TTTAGTACCTAAACTATCAATTTTGATCCTT
*
454644 TTTAGTACCTAAACTTTCAATTTT
1 TTTAGTACCTAAACTATCAATTTT
454668 TTAAAATCAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.27, C:0.19, G:0.08, T:0.47
Consensus pattern (31 bp):
TTTAGTACCTAAACTATCAATTTTGATCCTT
Found at i:460035 original size:3 final size:3
Alignment explanation
Indices: 460027--460056 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
460017 GACATAGTAG
460027 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
460057 AATGAAAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:466679 original size:34 final size:34
Alignment explanation
Indices: 466635--466719 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
466625 TGTATGATTG
466635 ATCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
1 ATCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
* *
466669 CTCTCGGCGTCTTCAGTTGGATTCTTCGTAGGAA
1 ATCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
466703 ATCTCGGCGTCTTCAGT
1 ATCTCGGCGTCTTCAGT
466720 GCTGTGCATG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.16, C:0.24, G:0.25, T:0.35
Consensus pattern (34 bp):
ATCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
Found at i:466825 original size:23 final size:23
Alignment explanation
Indices: 466795--466838 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
466785 TTGAGCAGGG
466795 CTGCACGTCTGCATGTGGGGGTC
1 CTGCACGTCTGCATGTGGGGGTC
466818 CTGCACGTCTGCATGTGGGGG
1 CTGCACGTCTGCATGTGGGGG
466839 GCATGCAACT
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:0.09, C:0.25, G:0.41, T:0.25
Consensus pattern (23 bp):
CTGCACGTCTGCATGTGGGGGTC
Found at i:466845 original size:23 final size:22
Alignment explanation
Indices: 466792--466845 Score: 81
Period size: 23 Copynumber: 2.4 Consensus size: 22
466782 GGGTTGAGCA
466792 GGGCTGCACGTCTGCATGTGGG
1 GGGCTGCACGTCTGCATGTGGG
*
466814 GGTCCTGCACGTCTGCATGTGGG
1 GG-GCTGCACGTCTGCATGTGGG
466837 GGGCATGCA
1 GGGC-TGCA
466846 ACTGTTGGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 3 0.11
23 25 0.89
ACGTcount: A:0.11, C:0.24, G:0.43, T:0.22
Consensus pattern (22 bp):
GGGCTGCACGTCTGCATGTGGG
Found at i:467050 original size:41 final size:41
Alignment explanation
Indices: 466993--467070 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
466983 GAGACTGCTC
*
466993 GGGCTGAGGCAATTCACAATTATAGAAGCAGTGAGAGTTTG
1 GGGCTGAGGCAATTCACAATTACAGAAGCAGTGAGAGTTTG
467034 GGGCTGAGGCAATTCACAATTACAGAAGCAGTGAGAG
1 GGGCTGAGGCAATTCACAATTACAGAAGCAGTGAGAG
467071 CCTGAGAGGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.33, C:0.14, G:0.32, T:0.21
Consensus pattern (41 bp):
GGGCTGAGGCAATTCACAATTACAGAAGCAGTGAGAGTTTG
Found at i:469414 original size:6 final size:6
Alignment explanation
Indices: 469403--469433 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
469393 CAAGAAGGAC
*
469403 TGGGAG TGGGAG TGGGAG TGGGAG TAGGAG T
1 TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG T
469434 TCTTCTCACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.61, T:0.19
Consensus pattern (6 bp):
TGGGAG
Found at i:469933 original size:42 final size:41
Alignment explanation
Indices: 469884--470309 Score: 298
Period size: 37 Copynumber: 10.8 Consensus size: 41
469874 ATATATTTAC
* *
469884 TATTATTATATCAGTAAATATAAATCATTAAAGTCAAGTAAT
1 TATTATTAAATCATTAAATATAAATCATTAAA-TCAAGTAAT
*
469926 TATTATTAAATCATTAAA-ATTAAATCATTAAAATTAAGTAAT
1 TATTATTAAATCATTAAATA-TAAATCATT-AAATCAAGTAAT
*
469968 TATTATTAAATTATTAAAT-T-AATCATT--A--AAGTAAT
1 TATTATTAAATCATTAAATATAAATCATTAAATCAAGTAAT
470003 TATTATTAAATCATT-AATCATTAAATCATTAAATCATTAAAGTAAT
1 TATTATTAAATCATTAAAT-A-TAAATCATTAAATC----AAGTAAT
*
470049 TATTATTAAAGCATTAAAGT-TAAATCATT--A--AAGTAAT
1 TATTATTAAATCATTAAA-TATAAATCATTAAATCAAGTAAT
470086 TATTATTAAATC-----AT-TAAATCATTAAATCATAAGTAAT
1 TATTATTAAATCATTAAATATAAATCATTAAATC--AAGTAAT
*
470123 TATTATTAAAGCATTAAAGT-TAAATCATT--A--AAGTAAT
1 TATTATTAAATCATTAAA-TATAAATCATTAAATCAAGTAAT
* * *
470160 TATTATTAAATCATTAAAGTA-ATTATTATTAAATC-ATTAAAGT
1 TATTATTAAATCATTAAA-TATA-AATCATTAAATCAAGT-AA-T
*
470203 TAAATCATTAAATCATTAAA-ATTAAATCATT--A--AAGTAAT
1 T--ATTATTAAATCATTAAATA-TAAATCATTAAATCAAGTAAT
470242 TATTA-TAAATCATTAAA-ATTAAATCATT--A--AAGTAAT
1 TATTATTAAATCATTAAATA-TAAATCATTAAATCAAGTAAT
470278 TATTATTAAATCATTAAAGT-TAAATCATTAAA
1 TATTATTAAATCATTAAA-TATAAATCATTAAA
470310 GTTAAATCAT
Statistics
Matches: 320, Mismatches: 17, Indels: 97
0.74 0.04 0.22
Matches are distributed among these distances:
31 10 0.03
32 1 0.00
33 1 0.00
34 3 0.01
35 21 0.07
36 36 0.11
37 89 0.28
38 12 0.04
39 3 0.01
40 11 0.03
41 7 0.02
42 54 0.17
43 17 0.05
44 5 0.02
45 26 0.08
46 21 0.07
47 2 0.01
48 1 0.00
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (41 bp):
TATTATTAAATCATTAAATATAAATCATTAAATCAAGTAAT
Found at i:469943 original size:8 final size:8
Alignment explanation
Indices: 469930--470362 Score: 209
Period size: 8 Copynumber: 58.8 Consensus size: 8
469920 AGTAATTATT
469930 ATTAAATC
1 ATTAAATC
469938 ATTAAA--
1 ATTAAATC
469944 ATTAAATC
1 ATTAAATC
469952 ATTAAA--
1 ATTAAATC
* *
469958 ATTAAGTA
1 ATTAAATC
*
469966 ATT--ATT
1 ATTAAATC
*
469972 ATTAAATT
1 ATTAAATC
469980 ATT-AA--
1 ATTAAATC
469985 ATT-AATC
1 ATTAAATC
*
469992 ATTAAAGTA
1 ATTAAA-TC
*
470001 ATT--ATT
1 ATTAAATC
470007 ATTAAATC
1 ATTAAATC
470015 ATT-AATC
1 ATTAAATC
470022 ATTAAATC
1 ATTAAATC
470030 ATTAAATC
1 ATTAAATC
*
470038 ATTAAAGTA
1 ATTAAA-TC
*
470047 ATT--ATT
1 ATTAAATC
*
470053 ATTAAAGC
1 ATTAAATC
470061 ATTAAA--
1 ATTAAATC
*
470067 GTTAAATC
1 ATTAAATC
*
470075 ATTAAAGTA
1 ATTAAA-TC
*
470084 ATT--ATT
1 ATTAAATC
470090 ATTAAATC
1 ATTAAATC
470098 ATTAAATC
1 ATTAAATC
470106 ATTAAATC
1 ATTAAATC
* *
470114 A-TAAGTA
1 ATTAAATC
*
470121 ATT--ATT
1 ATTAAATC
*
470127 ATTAAAGC
1 ATTAAATC
470135 ATTAAA--
1 ATTAAATC
*
470141 GTTAAATC
1 ATTAAATC
*
470149 ATTAAAGTA
1 ATTAAA-TC
*
470158 ATT--ATT
1 ATTAAATC
470164 ATTAAATC
1 ATTAAATC
*
470172 ATTAAAGTA
1 ATTAAA-TC
*
470181 ATT--ATT
1 ATTAAATC
470187 ATTAAATC
1 ATTAAATC
470195 ATTAAA--
1 ATTAAATC
*
470201 GTTAAATC
1 ATTAAATC
470209 ATTAAATC
1 ATTAAATC
470217 ATTAAA--
1 ATTAAATC
470223 ATTAAATC
1 ATTAAATC
*
470231 ATTAAAGTA
1 ATTAAA-TC
*
470240 ATT--ATT
1 ATTAAATC
470246 A-TAAATC
1 ATTAAATC
470253 ATTAAA--
1 ATTAAATC
470259 ATTAAATC
1 ATTAAATC
*
470267 ATTAAAGTA
1 ATTAAA-TC
*
470276 ATT--ATT
1 ATTAAATC
470282 ATTAAATC
1 ATTAAATC
470290 ATTAAA--
1 ATTAAATC
*
470296 GTTAAATC
1 ATTAAATC
470304 ATTAAA--
1 ATTAAATC
*
470310 GTTAAATC
1 ATTAAATC
*
470318 ATTAAAGTA
1 ATTAAA-TC
*
470327 ATT--ATT
1 ATTAAATC
470333 ATTAAATC
1 ATTAAATC
470341 ATTAAATC
1 ATTAAATC
470349 ATTAAATC
1 ATTAAATC
470357 ATTAAA
1 ATTAAA
470363 GTTAAATCTT
Statistics
Matches: 329, Mismatches: 44, Indels: 104
0.69 0.09 0.22
Matches are distributed among these distances:
5 6 0.02
6 86 0.26
7 28 0.09
8 177 0.54
9 32 0.10
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (8 bp):
ATTAAATC
Found at i:470014 original size:23 final size:23
Alignment explanation
Indices: 469988--470068 Score: 103
Period size: 23 Copynumber: 3.5 Consensus size: 23
469978 TTATTAAATT
469988 AATCATTAAAGTAATTATTATTA
1 AATCATTAAAGTAATTATTATTA
* *
470011 AATCATT-AA-TCATTAAATCATTA
1 AATCATTAAAGTAATT--ATTATTA
470034 AATCATTAAAGTAATTATTATTA
1 AATCATTAAAGTAATTATTATTA
*
470057 AAGCATTAAAGT
1 AATCATTAAAGT
470069 TAAATCATTA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
21 4 0.08
22 2 0.04
23 37 0.76
24 2 0.04
25 4 0.08
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (23 bp):
AATCATTAAAGTAATTATTATTA
Found at i:470074 original size:37 final size:37
Alignment explanation
Indices: 470031--470311 Score: 365
Period size: 37 Copynumber: 7.4 Consensus size: 37
470021 CATTAAATCA
*
470031 TTAAATCATTAAAGTAATTATTATTAAAGCATTAAAG
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
*
470068 TTAAATCATTAAAGTAATTATTATTAAATCATTAAATCA
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAA--G
*
470107 TTAAATCA-T-AAGTAATTATTATTAAAGCATTAAAG
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
470142 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
* *
470179 TAATTATTATTAAATCATTAAAGTTAA--ATCATTAAATCATTAAAA
1 ---------TTAAATCATTAAAG-TAATTATTATTAAATCATTAAAG
*
470224 TTAAATCATTAAAGTAATTATTA-TAAATCATTAAAA
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
470260 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
470297 TTAAATCATTAAAGT
1 TTAAATCATTAAAGT
470312 TAAATCATTA
Statistics
Matches: 218, Mismatches: 9, Indels: 34
0.84 0.03 0.13
Matches are distributed among these distances:
35 11 0.05
36 51 0.23
37 114 0.52
38 1 0.00
39 8 0.04
45 16 0.07
46 14 0.06
47 3 0.01
ACGTcount: A:0.49, C:0.06, G:0.05, T:0.40
Consensus pattern (37 bp):
TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
Found at i:470087 original size:23 final size:22
Alignment explanation
Indices: 470022--470355 Score: 160
Period size: 23 Copynumber: 14.1 Consensus size: 22
470012 ATCATTAATC
*
470022 ATTAAATCATTAAA-TCATTAA
1 ATTAAATCATTAAAGTAATTAA
* * *
470043 AGTAATTATTATTAAAG-CATTAA
1 ATTAA--ATCATTAAAGTAATTAA
*
470066 AGTTAAATCATTAAAGTAATTATT
1 A-TTAAATCATTAAAGTAATTA-A
*
470090 ATTAAATCATTAAA-TCATTAA
1 ATTAAATCATTAAAGTAATTAA
* *
470111 ATCATAAGTAATTATTATTAAAG-CATTAA
1 AT--T-A--AA-T--CATTAAAGTAATTAA
*
470140 AGTTAAATCATTAAAGTAATTATT
1 A-TTAAATCATTAAAGTAATTA-A
*
470164 ATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAAGTAATTA-A
* *
470187 ATTAAATCATTAAAGTTAAAT-C
1 ATTAAATCATTAAAG-TAATTAA
*
470209 ATTAAATCATTAAAATTAAATCATTAA
1 ATTAAATCATT-AAAGT--A--ATTAA
* * * *
470236 AGT-AATTATTATAAATCATTAAA
1 ATTAAATCATTA-AAGTAATT-AA
*
470259 ATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAAGTAATTA-A
470282 ATTAAATCATTAAAGTTAAATCATTAA
1 ATTAAATCATTAAAG-T--A--ATTAA
*
470309 AGTTAAATCATTAAAGTAATTATT
1 A-TTAAATCATTAAAGTAATTA-A
*
470333 ATTAAATCATTAAA-TCATTAA
1 ATTAAATCATTAAAGTAATTAA
470354 AT
1 AT
470356 CATTAAAGTT
Statistics
Matches: 247, Mismatches: 30, Indels: 72
0.71 0.09 0.21
Matches are distributed among these distances:
21 8 0.03
22 42 0.17
23 119 0.48
24 21 0.09
25 4 0.02
26 14 0.06
27 6 0.02
28 19 0.08
29 13 0.05
30 1 0.00
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (22 bp):
ATTAAATCATTAAAGTAATTAA
Found at i:470369 original size:14 final size:13
Alignment explanation
Indices: 469888--470370 Score: 224
Period size: 14 Copynumber: 36.6 Consensus size: 13
469878 ATTTACTATT
* *
469888 ATTATATCAGTAA
1 ATTAAATCATTAA
469901 ATATAAATCATTAA
1 AT-TAAATCATTAA
* * * *
469915 AGTCAAGTAATTATT
1 A-TTAAATCATTA-A
469930 ATTAAATCATTAAA
1 ATTAAATCATT-AA
469944 ATTAAATCATTAAA
1 ATTAAATCATT-AA
* * *
469958 ATTAAGTAATTATT
1 ATTAAATCATTA-A
*
469972 ATTAAATTATTAA
1 ATTAAATCATTAA
469985 ATT-AATCATTAA
1 ATTAAATCATTAA
* *
469997 AGT-AATTATT--
1 ATTAAATCATTAA
470007 ATTAAATCATTAA
1 ATTAAATCATTAA
470020 TCATTAAATCATTAAA
1 --ATTAAATCATT-AA
* *
470036 TCATTAAAGTAATTATT
1 --ATTAAA-TCATTA-A
*
470053 ATTAAAGCATTAA
1 ATTAAATCATTAA
470066 AGTTAAATCATTAA
1 A-TTAAATCATTAA
* *
470080 AGTAATTATTATTAAA
1 ATTAA--ATCATT-AA
470096 TCATTAAATCATTAA
1 --ATTAAATCATTAA
* * *
470111 ATCATAAGTAATTATT
1 AT--TAAATCATTA-A
*
470127 ATTAAAGCATTAA
1 ATTAAATCATTAA
470140 AGTTAAATCATTAA
1 A-TTAAATCATTAA
* *
470154 AGT-AATTATT--
1 ATTAAATCATTAA
470164 ATTAAATCATTAA
1 ATTAAATCATTAA
* *
470177 AGT-AATTATT--
1 ATTAAATCATTAA
470187 ATTAAATCATTAA
1 ATTAAATCATTAA
470200 AGTTAAATC-----
1 A-TTAAATCATTAA
470209 ATTAAATCATTAAA
1 ATTAAATCATT-AA
470223 ATTAAATCATTAA
1 ATTAAATCATTAA
* *
470236 AGT-AATTATT--
1 ATTAAATCATTAA
470246 A-TAAATCATTAAA
1 ATTAAATCATT-AA
470259 ATTAAATCATTAA
1 ATTAAATCATTAA
* *
470272 AGT-AATTATT--
1 ATTAAATCATTAA
470282 ATTAAATCATTAA
1 ATTAAATCATTAA
470295 AGTTAAATCATTAA
1 A-TTAAATCATTAA
470309 AGTTAAATCATTAA
1 A-TTAAATCATTAA
* *
470323 AGT-AATTATT--
1 ATTAAATCATTAA
470333 ATTAAATCATTAAA
1 ATTAAATCATT-AA
470347 TCATTAAATCATTAA
1 --ATTAAATCATTAA
470362 AGTTAAATC
1 A-TTAAATC
470371 TTTTTTTCCT
Statistics
Matches: 360, Mismatches: 58, Indels: 103
0.69 0.11 0.20
Matches are distributed among these distances:
8 7 0.02
9 2 0.01
10 17 0.05
11 30 0.08
12 46 0.13
13 29 0.08
14 153 0.43
15 37 0.10
16 31 0.09
17 4 0.01
18 4 0.01
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.40
Consensus pattern (13 bp):
ATTAAATCATTAA
Found at i:473950 original size:19 final size:20
Alignment explanation
Indices: 473910--473960 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
473900 AACGCGATCC
473910 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
473930 CCAGAATCGCAAATC-GTTT
1 CCAGAATCGCAAATCAGTTT
*
473949 CCAAAATCGCAA
1 CCAGAATCGCAA
473961 CGTGATTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.37, C:0.27, G:0.14, T:0.22
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:474088 original size:20 final size:20
Alignment explanation
Indices: 474014--474204 Score: 201
Period size: 20 Copynumber: 9.6 Consensus size: 20
474004 GATTTTCCAT
* ** *
474014 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
474034 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
474054 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
474074 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
474094 AATCGCAATGCGTAT-GGTA
1 AATCGCAACGCGTATCCGTA
*
474113 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
474133 TATCGCAACGCGTATCCGT-
1 AATCGCAACGCGTATCCGTA
* * *
474152 AATCGCAACG-ATAATACATAA
1 AATCGCAACGCGT-ATCCGT-A
474173 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
474193 AATCGCAACGCG
1 AATCGCAACGCG
474205 ATATTTAAAG
Statistics
Matches: 143, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
18 1 0.01
19 32 0.22
20 93 0.65
21 16 0.11
22 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:474226 original size:60 final size:59
Alignment explanation
Indices: 474049--474204 Score: 169
Period size: 59 Copynumber: 2.6 Consensus size: 59
474039 CAACGCGAAC
* *
474049 ACAT-AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTAAATCGCAATGCG-T-AT
1 ACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGTAT-CGT-AAGCGCAA--CGATAAT
** * * *
474109 -GGT-AAATCGCAATGCGTATCCGTATATCGCAACGCGTATCCGTAATCGCAACGATAAT
1 ACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGTAT-CGTAAGCGCAACGATAAT
474167 ACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCG
1 ACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCG
474205 ATATTTAAAG
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
56 2 0.02
57 1 0.01
58 10 0.12
59 39 0.47
60 31 0.37
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (59 bp):
ACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCGTAAGCGCAACGATAAT
Found at i:474615 original size:32 final size:34
Alignment explanation
Indices: 474577--474644 Score: 104
Period size: 32 Copynumber: 2.1 Consensus size: 34
474567 TTCACTTAGA
474577 TTTCATTTCGCGTTACGA-T-TCTCGTTGCGATT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGATT
* *
474609 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGATT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGATT
474643 TT
1 TT
474645 CAAGTTAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 16 0.50
33 1 0.03
34 15 0.47
ACGTcount: A:0.10, C:0.22, G:0.18, T:0.50
Consensus pattern (34 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGATT
Found at i:474818 original size:19 final size:18
Alignment explanation
Indices: 474779--474821 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
474769 GCAACGAGAG
**
474779 ATCGCAACGCGAATGAAA
1 ATCGCAACGCGAACCAAA
474797 ATCGCAACGCGAAACCAAA
1 ATCGCAACGCG-AACCAAA
474816 ATCGCA
1 ATCGCA
474822 TTGCGATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.44, C:0.28, G:0.19, T:0.09
Consensus pattern (18 bp):
ATCGCAACGCGAACCAAA
Found at i:474839 original size:19 final size:19
Alignment explanation
Indices: 474817--474913 Score: 79
Period size: 19 Copynumber: 5.6 Consensus size: 19
474807 GAAACCAAAA
*
474817 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
474836 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
474850 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
474869 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
474883 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
474902 TCGCGTTGCGAT
1 TCGCGTTGCGAT
474914 CTCTCGTTGC
Statistics
Matches: 62, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 31 0.50
ACGTcount: A:0.10, C:0.25, G:0.23, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:474858 original size:14 final size:14
Alignment explanation
Indices: 474839--474927 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
474829 TTTCATTTCG
474839 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
474853 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
474872 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
474886 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
474903 CGCGTTGCGA-TCTCT
1 --CGTTGCGATTCTCT
474918 CGTTGCGATT
1 CGTTGCGATT
474928 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 2, Indels: 22
0.72 0.02 0.26
Matches are distributed among these distances:
13 8 0.13
14 19 0.31
15 4 0.06
16 7 0.11
17 6 0.10
19 18 0.29
ACGTcount: A:0.09, C:0.26, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:474864 original size:33 final size:33
Alignment explanation
Indices: 474822--474935 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
474812 CAAAATCGCA
474822 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
474855 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
474888 TTGCGATTGTCATCTCGCGTTGCGA-TCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
474920 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
474936 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 21 0.27
33 56 0.73
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:478363 original size:12 final size:12
Alignment explanation
Indices: 478346--478370 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
478336 TCTTCGGGGA
478346 CTTTTTCTTCTT
1 CTTTTTCTTCTT
478358 CTTTTTCTTCTT
1 CTTTTTCTTCTT
478370 C
1 C
478371 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:478583 original size:24 final size:23
Alignment explanation
Indices: 478544--478589 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
478534 CTGAAACATC
478544 ATCAAATCCGTGTATTGACCAAT
1 ATCAAATCCGTGTATTGACCAAT
478567 ATCAAAGTCCG-GATATTGACCAA
1 ATCAAA-TCCGTG-TATTGACCAA
478590 GACCAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (23 bp):
ATCAAATCCGTGTATTGACCAAT
Found at i:479295 original size:20 final size:20
Alignment explanation
Indices: 479267--479597 Score: 452
Period size: 20 Copynumber: 16.6 Consensus size: 20
479257 AAATTTCAGT
* * * *
479267 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
479287 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
479307 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
479327 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
479347 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
479367 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
479387 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
479407 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
479427 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
479447 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
479467 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
479487 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
479507 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
479527 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
479547 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
479567 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
479587 GTTGCGATTTA
1 GTTGCGATTTA
479598 TATGTTCGCG
Statistics
Matches: 279, Mismatches: 26, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.02
20 270 0.97
21 4 0.01
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:479607 original size:20 final size:20
Alignment explanation
Indices: 479584--479635 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
479574 TTTACGGATA
*
479584 CGCGTTGCGATTTAT-ATGTT
1 CGCGTTGCGATTT-TCATATT
479604 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTTCATATT
479624 CGCGTTGCGATT
1 CGCGTTGCGATT
479636 ATGGAAAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.42
Consensus pattern (20 bp):
CGCGTTGCGATTTTCATATT
Found at i:482352 original size:33 final size:34
Alignment explanation
Indices: 482263--482363 Score: 107
Period size: 37 Copynumber: 2.9 Consensus size: 34
482253 GGGTTGGATT
* *
482263 TAAAAAAAATCGGGTTCGGGTCGGGTCGGTTATTTTA
1 TAAAAAAAATCGGGTTCGGGTCGGAT---TTTTTTTA
* *
482300 TAAAAAAAATTGGGATCGGGTCGGATTTTTTTTA
1 TAAAAAAAATCGGGTTCGGGTCGGATTTTTTTTA
* *
482334 -AAAAAAAATCGGCTTCGGGTC-GAGTTTTTT
1 TAAAAAAAATCGGGTTCGGGTCGGATTTTTTT
482364 AAAGTTTGAT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
32 8 0.14
33 18 0.32
34 7 0.12
37 23 0.41
ACGTcount: A:0.30, C:0.10, G:0.26, T:0.35
Consensus pattern (34 bp):
TAAAAAAAATCGGGTTCGGGTCGGATTTTTTTTA
Found at i:482362 original size:32 final size:33
Alignment explanation
Indices: 482283--482363 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 33
482273 CGGGTTCGGG
* * *
482283 TCGGGTCG-GTTATTTTATAAAAAAAATTGGGA
1 TCGGGTCGAGTTTTTTTATAAAAAAAATCGGCA
* *
482315 TCGGGTCGGATTTTTTTTA-AAAAAAAATCGGCT
1 TCGGGTC-GAGTTTTTTTATAAAAAAAATCGGCA
482348 TCGGGTCGAGTTTTTT
1 TCGGGTCGAGTTTTTT
482364 AAAGTTTGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
32 15 0.37
33 19 0.46
34 7 0.17
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.38
Consensus pattern (33 bp):
TCGGGTCGAGTTTTTTTATAAAAAAAATCGGCA
Found at i:482385 original size:33 final size:33
Alignment explanation
Indices: 482348--482419 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
482338 AAAATCGGCT
*
482348 TCGGGTC-GAGTTTTTTAAAGTTTGATATTCGGG
1 TCGGGTCAG-GTTTTTTAAAGTGTGATATTCGGG
*
482381 TCGGGTCAGGTTTTTTTAAGTGTGATATTCGGG
1 TCGGGTCAGGTTTTTTAAAGTGTGATATTCGGG
482414 TCGGGT
1 TCGGGT
482420 TCGGGTTTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 35 0.97
34 1 0.03
ACGTcount: A:0.15, C:0.10, G:0.33, T:0.42
Consensus pattern (33 bp):
TCGGGTCAGGTTTTTTAAAGTGTGATATTCGGG
Found at i:484972 original size:23 final size:24
Alignment explanation
Indices: 484941--484995 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 24
484931 GGGTCCCACT
*
484941 AGGAGCTATGA-AATTTGTCCCGA
1 AGGACCTATGATAATTTGTCCCGA
*
484964 AGGACCTATGATTGTATTTGTCCCGA
1 AGGACCTATGA-T-AATTTGTCCCGA
484990 AGGACC
1 AGGACC
484996 ACTCCTTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 10 0.37
26 17 0.63
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (24 bp):
AGGACCTATGATAATTTGTCCCGA
Found at i:485742 original size:63 final size:64
Alignment explanation
Indices: 485609--485770 Score: 274
Period size: 63 Copynumber: 2.5 Consensus size: 64
485599 CATCCCTTGA
*
485609 CAGGTGCATCGATGCACT-ATTCATGCATCGGTGCATAAATCCTATTCGATGTTTGTATTTTAAG
1 CAGGTGCATCGATGCACTCCTT-ATGCATCGGTGCATAAATCCTATTCGATGTTTGTATTTTAAG
*
485673 TAGGTGCATCGATGCACTCCTTATGCATCGGTGCAT-AATCCTATTCGATGTTTGTATTTTAAG
1 CAGGTGCATCGATGCACTCCTTATGCATCGGTGCATAAATCCTATTCGATGTTTGTATTTTAAG
*
485736 CAGGTGCATCGATGCACTCCTTATGCATCGATGCA
1 CAGGTGCATCGATGCACTCCTTATGCATCGGTGCA
485771 CTGATTGCAT
Statistics
Matches: 93, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
63 60 0.65
64 31 0.33
65 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (64 bp):
CAGGTGCATCGATGCACTCCTTATGCATCGGTGCATAAATCCTATTCGATGTTTGTATTTTAAG
Found at i:486635 original size:13 final size:13
Alignment explanation
Indices: 486617--486642 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
486607 CCTAACTTTT
486617 TTTAAAAAAATTA
1 TTTAAAAAAATTA
486630 TTTAAAAAAATTA
1 TTTAAAAAAATTA
486643 AAATTAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TTTAAAAAAATTA
Found at i:491405 original size:26 final size:26
Alignment explanation
Indices: 491368--491421 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
491358 TTCATGCTGC
*
491368 CTACAAATCTGGACACATCCAAATTG
1 CTACAAAGCTGGACACATCCAAATTG
491394 CTACAAAGCTGGACACATCCAAATTG
1 CTACAAAGCTGGACACATCCAAATTG
491420 CT
1 CT
491422 GACCACATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.37, C:0.28, G:0.13, T:0.22
Consensus pattern (26 bp):
CTACAAAGCTGGACACATCCAAATTG
Found at i:492378 original size:23 final size:23
Alignment explanation
Indices: 492348--492393 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
492338 TGTCATCTCT
492348 CTTTTTTTCTTGGTTTCTATTGG
1 CTTTTTTTCTTGGTTTCTATTGG
*
492371 CTTTTTTTCTTGGTTTCTGTTGG
1 CTTTTTTTCTTGGTTTCTATTGG
492394 TCATCTCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.02, C:0.13, G:0.20, T:0.65
Consensus pattern (23 bp):
CTTTTTTTCTTGGTTTCTATTGG
Found at i:493358 original size:16 final size:16
Alignment explanation
Indices: 493339--493374 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
493329 TTTCCCTGCT
493339 GATTTGGTTCCTACTA
1 GATTTGGTTCCTACTA
*
493355 GATTTGGTTCCTACTT
1 GATTTGGTTCCTACTA
493371 GATT
1 GATT
493375 CGGAAGTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.17, C:0.17, G:0.19, T:0.47
Consensus pattern (16 bp):
GATTTGGTTCCTACTA
Found at i:497018 original size:18 final size:20
Alignment explanation
Indices: 496985--497021 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
496975 AAAATTTAAG
496985 AATATTATTATTTTAAAAAA
1 AATATTATTATTTTAAAAAA
497005 AATATT-TT-TTTTAAAAA
1 AATATTATTATTTTAAAAA
497022 TTATAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 2 0.12
20 6 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATATTATTATTTTAAAAAA
Found at i:498829 original size:21 final size:21
Alignment explanation
Indices: 498803--498850 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
498793 GTTTGCCGCA
*
498803 ATTGCGAATATAACA-AGCGCT
1 ATTGCGAATATAA-AGAGCACT
498824 ATTGCGAATATAAAGAGCACT
1 ATTGCGAATATAAAGAGCACT
498845 ATTGCG
1 ATTGCG
498851 GGTATCGCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.25
Consensus pattern (21 bp):
ATTGCGAATATAAAGAGCACT
Found at i:499386 original size:12 final size:12
Alignment explanation
Indices: 499369--499393 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
499359 GGCCTGAGCT
499369 CTTTCAGTTAAA
1 CTTTCAGTTAAA
499381 CTTTCAGTTAAA
1 CTTTCAGTTAAA
499393 C
1 C
499394 AGCAGTCCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (12 bp):
CTTTCAGTTAAA
Found at i:503607 original size:14 final size:14
Alignment explanation
Indices: 503585--503631 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
503575 CGCTGGGCAT
*
503585 CCGATGCCATCCGA
1 CCGAGGCCATCCGA
*
503599 CCGAGGCCATTCGA
1 CCGAGGCCATCCGA
503613 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
503627 ACGAG
1 CCGAG
503632 CTATGCAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.23, C:0.38, G:0.28, T:0.11
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:503672 original size:23 final size:24
Alignment explanation
Indices: 503621--503677 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 24
503611 GACCGAGGCC
*
503621 ATCCGAACGAGCTATGCAAGGGCA
1 ATCCGAGCGAGCTATGCAAGGGCA
*
503645 A-CCGAGCGAGCTATGCGAGGG-A
1 ATCCGAGCGAGCTATGCAAGGGCA
503667 ATCCGAGCGAG
1 ATCCGAGCGAG
503678 GGTAGGTCGC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 2 0.07
23 27 0.90
24 1 0.03
ACGTcount: A:0.30, C:0.25, G:0.35, T:0.11
Consensus pattern (24 bp):
ATCCGAGCGAGCTATGCAAGGGCA
Found at i:503727 original size:29 final size:29
Alignment explanation
Indices: 503681--503736 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
503671 GAGCGAGGGT
* *
503681 AGGTCGCCCGGAGTGCATGGTGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
503710 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
503737 TGTTTTGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.20, C:0.29, G:0.38, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:503837 original size:29 final size:29
Alignment explanation
Indices: 503795--503851 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
503785 TAGCAAGGGT
*
503795 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCACCCGGAGTGCATGGCGACCTACA
503824 AGGTCACCCGGAGTGCATGGCGACCTAC
1 AGGTCACCCGGAGTGCATGGCGACCTAC
503852 GGCCAACACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.21, C:0.32, G:0.33, T:0.14
Consensus pattern (29 bp):
AGGTCACCCGGAGTGCATGGCGACCTACA
Found at i:508292 original size:45 final size:45
Alignment explanation
Indices: 508237--508324 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 45
508227 TTTTTTATTA
*
508237 TTAATCTGGGATAAGTATAAGGTAGTA-CATCTTCAAAGATAACTC
1 TTAATCTGGGATAAGTATAAGGTAGTATC-TATTCAAAGATAACTC
* * *
508282 TTAATTTGGGATCAGTATAAGGTATTATCTATTCAAAGATAAC
1 TTAATCTGGGATAAGTATAAGGTAGTATCTATTCAAAGATAAC
508325 CTCAACCATT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 37 0.97
46 1 0.03
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (45 bp):
TTAATCTGGGATAAGTATAAGGTAGTATCTATTCAAAGATAACTC
Found at i:508393 original size:52 final size:52
Alignment explanation
Indices: 508307--508456 Score: 250
Period size: 52 Copynumber: 2.9 Consensus size: 52
508297 TATAAGGTAT
*
508307 TATCTATTCAAAGATAAC-CTCAACCATTTGACATTGAACACTCACA-AGTAG
1 TATCTGTTCAAAGATAACTCTCAACCATTTGACATTGAACACTCACACA-TAG
508358 TATCTGTTCAAAGATAACTCTCAACCATTTGACATTGAACACTCACACATAG
1 TATCTGTTCAAAGATAACTCTCAACCATTTGACATTGAACACTCACACATAG
* *
508410 TATCTGTTCAAAAATAACTCTCAACTATTTGACATTGAACACTCACA
1 TATCTGTTCAAAGATAACTCTCAACCATTTGACATTGAACACTCACA
508457 TCCGTAGAAT
Statistics
Matches: 94, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
51 17 0.18
52 76 0.81
53 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.09, T:0.29
Consensus pattern (52 bp):
TATCTGTTCAAAGATAACTCTCAACCATTTGACATTGAACACTCACACATAG
Found at i:509105 original size:35 final size:35
Alignment explanation
Indices: 509059--509134 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
509049 AAAACAGTCC
* * *
509059 TCAATTTCATTCTAAACCCCAATTTTCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
509094 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
509129 TCAATT
1 TCAATT
509135 AAATTCAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:509672 original size:130 final size:130
Alignment explanation
Indices: 509531--509778 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
509521 TATTTATATA
* ** *
509531 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGAATCTGACATGTG
*
509596 TTAGCACATGATCATGACACGTGTCATTAGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTAGTGACACATGTCACCACCTAATTATTTATATATGCT
509661 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGAATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGAATCTGACATGTG
* * * *
509726 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACGTGTCATTAGTGACACATGTCACCACCTAATTA
509779 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGAATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTAGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:509809 original size:130 final size:129
Alignment explanation
Indices: 509545--509809 Score: 300
Period size: 130 Copynumber: 2.0 Consensus size: 129
509535 ATTTGGTCCT
* ** * *
509545 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGAATCTGACATGTGTTAACACATGATCA
*** * * **** *
509610 TGACACGTGTCATTAGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACGTGTCATTAGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
509675 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGAATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGAATCTGACATGTGTTAACACATGATCA
* * * * *
509740 TGATATGTGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACGTGTCATTAGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
509804 -A
128 CA
509805 AAATT
1 AAATT
509810 TGGGTCTTGG
Statistics
Matches: 112, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
130 99 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGAATCTGACATGTGTTAACACATGATCA
TGACACGTGTCATTAGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:510265 original size:16 final size:18
Alignment explanation
Indices: 510244--510277 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
510234 ATTTCTTATT
510244 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
510260 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
510278 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:510762 original size:141 final size:140
Alignment explanation
Indices: 510508--510762 Score: 315
Period size: 141 Copynumber: 1.8 Consensus size: 140
510498 AATAAAATTA
* **
510508 TTGGGGGACTGTTTTGCAAGTTTTAAAAGTTGGGGACCTAAATTCAAGTGTCTAAAAAGTTCAAT
1 TTGGGGGACTGTATTGCAAGTTTTAAAAGTTGGGGACCTAAATGAAAGTGTCTAAAAAGTTCAAT
* * * *
510573 GACCGTTTATATAATTTACCCTAATTTTCTAACAGTGATTTAAGTTGGGGGACCATATTGCAAAC
66 GACCGATTATATAATTTACCCTAATTTTATAACACTGATTGAAGTTGGGGGACCATATTGCAAAC
510638 GGAATAAATG
131 GGAATAAATG
*
510648 TTGGGGGACTGTATTGCAAGTTTTAAAAGTTGGGGGACCTAAATGAAAGCT-TC-AGAAATGTTC
1 TTGGGGGACTGTATTGCAAGTTTTAAAAGTT-GGGGACCTAAATGAAAG-TGTCTA-AAAAGTTC
* *
510711 AGTGACC-ATTACTATACTTTACCCTATATATTATATAA-ACT-ATTGAA-TTGGG
63 AATGACCGATTA-TATAATTTACCCTA-AT-TT-TATAACACTGATTGAAGTTGGG
510763 TGATGGTCAT
Statistics
Matches: 98, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
140 34 0.35
141 48 0.49
142 8 0.08
143 4 0.04
144 4 0.04
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (140 bp):
TTGGGGGACTGTATTGCAAGTTTTAAAAGTTGGGGACCTAAATGAAAGTGTCTAAAAAGTTCAAT
GACCGATTATATAATTTACCCTAATTTTATAACACTGATTGAAGTTGGGGGACCATATTGCAAAC
GGAATAAATG
Found at i:513225 original size:26 final size:25
Alignment explanation
Indices: 513179--513230 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
513169 GTTGGATCTT
513179 TATTGGACCTGGAATTGGATTTGGAC
1 TATTGGACCTGGAATTGGA-TTGGAC
*
513205 TATTGGACTTTGGAATT-GATTGGAC
1 TATTGGAC-CTGGAATTGGATTGGAC
513230 T
1 T
513231 TGACATGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 7 0.29
26 10 0.42
27 7 0.29
ACGTcount: A:0.23, C:0.10, G:0.29, T:0.38
Consensus pattern (25 bp):
TATTGGACCTGGAATTGGATTGGAC
Found at i:513468 original size:27 final size:25
Alignment explanation
Indices: 513404--513469 Score: 60
Period size: 27 Copynumber: 2.4 Consensus size: 25
513394 TCAAAAATTA
* *
513404 TATAATATATATATTTTATAAAAAAC
1 TATAA-ATATATATATAATAAAAAAC
*
513430 TATTAAACTATATAATATAATAAAATAC
1 TA-TAAA-TATAT-ATATAATAAAAAAC
513458 TATAACATATAT
1 TATAA-ATATAT
513470 TACATATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
26 3 0.09
27 16 0.48
28 14 0.42
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (25 bp):
TATAAATATATATATAATAAAAAAC
Found at i:514304 original size:41 final size:40
Alignment explanation
Indices: 514233--514313 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 40
514223 CCTGGCCTGG
*
514233 CCTATTTAACTAAACAGGCCAGGCCCAGGCCTTTTTAAAAA
1 CCTATTTAACTAAACAGGCCAGGCCCAGGCC-TATTAAAAA
* **
514274 CCTATTTAACTAAACAGGCTAGGCTTAGGCCTATTAAAAA
1 CCTATTTAACTAAACAGGCCAGGCCCAGGCCTATTAAAAA
514314 GCCTTATAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 8 0.22
41 28 0.78
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (40 bp):
CCTATTTAACTAAACAGGCCAGGCCCAGGCCTATTAAAAA
Found at i:517142 original size:2 final size:2
Alignment explanation
Indices: 517137--517211 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
517127 AAATTAAGAA
517137 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
517179 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
517212 GGTAAATCAG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.