Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006094.1 Hibiscus syriacus cultivar Beakdansim tig00014445_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: 761529
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 4 of 5
Found at i:503640 original size:190 final size:191
Alignment explanation
Indices: 503297--503710 Score: 643
Period size: 190 Copynumber: 2.2 Consensus size: 191
503287 ATCAAATCAA
* * * * * *
503297 TCTGATATTCACTAAAGAATAGTGAAATTAGATTTTTGTCAAGTCAATCATTTTTAGTCTTCATG
1 TCTGATATTCACGAAAGAGTAGTGAAATTAGATTCTTGTCAAGCCAATCATTTTCAGTCTTCACG
*
503362 GAAGAGTAGTGAAGCAAAATTCAGAAGCAAGATCAAAATTCGCTCTCCACGGAAGAGTAGTGGAA
66 AAAGAGTAGTGAAGCAAAATTCAGAAGCAAGATCAAAATTCGCTCTCCACGGAAGAGTAGTGGAA
* *
503427 TGGATTTTACAGCAAAGTATGAAACCTTCACGGAAGAGTAGTGAAGCAATCAAATTGCGAG
131 TGAATTTTACAGCAAAGTATGAAACCTTCACGGAAGAATAGTGAAGCAATCAAATTGCGAG
* *
503488 TTTGATTTTCACGAAAGAGTAGTGAAATTAGATTCTTGTCAAGCCAATCATTTTCAGTCTTCACG
1 TCTGATATTCACGAAAGAGTAGTGAAATTAGATTCTTGTCAAGCCAATCATTTTCAGTCTTCACG
*
503553 AAAGAGTAGTGAAG-AAAATTCAGAAGTAAGATCAAAATTCGCTCTCCACGGAAGAGTAGTGGAA
66 AAAGAGTAGTGAAGCAAAATTCAGAAGCAAGATCAAAATTCGCTCTCCACGGAAGAGTAGTGGAA
* * * *
503617 TGAATTTTTCAGTAAAGTATGAAACCTTCACGGAAGAATAGTGAAGCAATCTAATTTCGAG
131 TGAATTTTACAGCAAAGTATGAAACCTTCACGGAAGAATAGTGAAGCAATCAAATTGCGAG
* * *
503678 TCTGATCTTCACGGAAGAGTAGTCAAA-TAGATT
1 TCTGATATTCACGAAAGAGTAGTGAAATTAGATT
503711 ATGTTCAAGT
Statistics
Matches: 203, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
189 6 0.03
190 127 0.63
191 70 0.34
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (191 bp):
TCTGATATTCACGAAAGAGTAGTGAAATTAGATTCTTGTCAAGCCAATCATTTTCAGTCTTCACG
AAAGAGTAGTGAAGCAAAATTCAGAAGCAAGATCAAAATTCGCTCTCCACGGAAGAGTAGTGGAA
TGAATTTTACAGCAAAGTATGAAACCTTCACGGAAGAATAGTGAAGCAATCAAATTGCGAG
Found at i:506635 original size:19 final size:19
Alignment explanation
Indices: 506608--506644 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
506598 CTAGAACCGG
506608 GAAAGGGTATCGATACCAA
1 GAAAGGGTATCGATACCAA
* *
506627 GAAATGGTATCGGTACCA
1 GAAAGGGTATCGATACCA
506645 CACTGAAGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.16, G:0.27, T:0.19
Consensus pattern (19 bp):
GAAAGGGTATCGATACCAA
Found at i:506843 original size:18 final size:18
Alignment explanation
Indices: 506816--506865 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
506806 AGCAAGTTCT
*
506816 GGAACAATCGAAGAGTTA
1 GGAACGATCGAAGAGTTA
506834 GGAACGATCGAAGAGTTA
1 GGAACGATCGAAGAGTTA
*
506852 AGAACGATC-AAGAG
1 GGAACGATCGAAGAG
506866 ATAAAGTCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 5 0.17
18 25 0.83
ACGTcount: A:0.44, C:0.12, G:0.30, T:0.14
Consensus pattern (18 bp):
GGAACGATCGAAGAGTTA
Found at i:508437 original size:13 final size:13
Alignment explanation
Indices: 508421--508445 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
508411 GTAAAATGGG
508421 AAAATAGCAAAGA
1 AAAATAGCAAAGA
508434 AAAATAGCAAAG
1 AAAATAGCAAAG
508446 TTTTGGTAAT
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:0.68, C:0.08, G:0.16, T:0.08
Consensus pattern (13 bp):
AAAATAGCAAAGA
Found at i:511550 original size:64 final size:63
Alignment explanation
Indices: 511453--511593 Score: 169
Period size: 64 Copynumber: 2.2 Consensus size: 63
511443 CATATTCAAT
* * *
511453 GTGCATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAA-TTGATGCATCGATGCATAAGGA
1 GTGCATCGATGCACCCCTTAAAGAAGAAACATCGAAGGCAATTTG-TGCATCGATGCATAAGGA
* * * * *
511516 GTGCATCGATGCATCCCCTTAAA-ATGAAAACATCGAAGGTAATTTGTGTATCGATGCATGAGTA
1 GTGCATCGATGCA-CCCCTTAAAGAAG-AAACATCGAAGGCAATTTGTGCATCGATGCATAAGGA
511580 GTGCATCGATGCAC
1 GTGCATCGATGCAC
511594 ATGTTAAAGA
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
63 16 0.24
64 48 0.72
65 3 0.04
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCACCCCTTAAAGAAGAAACATCGAAGGCAATTTGTGCATCGATGCATAAGGA
Found at i:511626 original size:20 final size:20
Alignment explanation
Indices: 511581--511638 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
511571 GCATGAGTAG
511581 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
511605 TGTATCGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
511625 TGCATCGATGCACT
1 TGCATCGATGCACT
511639 TCAAGGGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.53
22 1 0.03
23 2 0.06
24 12 0.38
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:516034 original size:64 final size:63
Alignment explanation
Indices: 515939--516078 Score: 185
Period size: 64 Copynumber: 2.2 Consensus size: 63
515929 ATATTCAATA
* * *
515939 TGCATCGATGCACTCTTTAAAGAAGAAACATCGAATGTAA-TTGATGCATCGATGCATAAGTAG
1 TGCATCGATGCACCCCTTAAAGAAGAAACATCGAAGGTAATTTG-TGCATCGATGCATAAGTAG
* * *
516002 TGCATCGATGCATCCCCTTAAA-ATGAAAACATCGAAGGTAATTTGTGTATCGATGCATGAGTAG
1 TGCATCGATGCA-CCCCTTAAAGAAG-AAACATCGAAGGTAATTTGTGCATCGATGCATAAGTAG
516066 TGCATCGATGCAC
1 TGCATCGATGCAC
516079 ATGTTAAAGA
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
63 15 0.22
64 50 0.74
65 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCACCCCTTAAAGAAGAAACATCGAAGGTAATTTGTGCATCGATGCATAAGTAG
Found at i:516111 original size:20 final size:20
Alignment explanation
Indices: 516066--516123 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
516056 GCATGAGTAG
516066 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
516090 TGTATCGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
516110 TGCATCGATGCACT
1 TGCATCGATGCACT
516124 TCAAGGGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.53
22 1 0.03
23 2 0.06
24 12 0.38
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:516660 original size:12 final size:12
Alignment explanation
Indices: 516643--516667 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
516633 GGAATATCAA
516643 ATAAGTTATGTG
1 ATAAGTTATGTG
516655 ATAAGTTATGTG
1 ATAAGTTATGTG
516667 A
1 A
516668 CATGATATAT
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:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (12 bp):
ATAAGTTATGTG
Found at i:517035 original size:31 final size:31
Alignment explanation
Indices: 516997--517073 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 31
516987 AGAGTTGAGG
*
516997 GTTTACCTATG-TCTTTCGAGA-CATATGGACA
1 GTTTACCTAGGTTC-TTCGAGATC-TATGGACA
517028 GTTTACCTAGGTTCTTCGAGATCTATGGACA
1 GTTTACCTAGGTTCTTCGAGATCTATGGACA
*
517059 -TTTACCGAGGTTCTT
1 GTTTACCTAGGTTCTT
517074 TGTGACCTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
30 14 0.33
31 25 0.60
32 3 0.07
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGAGATCTATGGACA
Found at i:517104 original size:29 final size:30
Alignment explanation
Indices: 517060--517118 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
517050 CTATGGACAT
*
517060 TTACCGAGGTTCTTTGTGACCTTTGGATAG
1 TTACCGAGGGTCTTTGTGACCTTTGGATAG
517090 TTACCG-GGGTCTTTGTGACCTTTGGATAG
1 TTACCGAGGGTCTTTGTGACCTTTGGATAG
517119 GTCCTTTGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 22 0.79
30 6 0.21
ACGTcount: A:0.15, C:0.17, G:0.29, T:0.39
Consensus pattern (30 bp):
TTACCGAGGGTCTTTGTGACCTTTGGATAG
Found at i:517393 original size:2 final size:2
Alignment explanation
Indices: 517388--517427 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
517378 ATATACGTGG
517388 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
517428 AAAGGTGCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:518907 original size:18 final size:18
Alignment explanation
Indices: 518886--518921 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
518876 AATAATATAA
518886 TAAATTATTATTA-TATTT
1 TAAATTATT-TTATTATTT
518904 TAAATTATTTTATTATTT
1 TAAATTATTTTATTATTT
518922 AATGGTTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.18
18 14 0.82
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TAAATTATTTTATTATTT
Found at i:519647 original size:15 final size:15
Alignment explanation
Indices: 519627--519662 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
519617 GCCGTTTAGG
519627 GAGGCTGCCGGAAGA
1 GAGGCTGCCGGAAGA
*
519642 GAGGCTGTCGGAAGA
1 GAGGCTGCCGGAAGA
519657 GAGGCT
1 GAGGCT
519663 CATCTCCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.47, T:0.11
Consensus pattern (15 bp):
GAGGCTGCCGGAAGA
Found at i:521282 original size:19 final size:19
Alignment explanation
Indices: 521255--521293 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
521245 TTTATTAAAA
521255 ATAAAAAAATATTTA-AATC
1 ATAAAAAAA-ATTTATAATC
*
521274 ATAATAAAAATTTATAATC
1 ATAAAAAAAATTTATAATC
521293 A
1 A
521294 CTACACTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAAAAAAAATTTATAATC
Found at i:523136 original size:9 final size:9
Alignment explanation
Indices: 523122--523413 Score: 100
Period size: 9 Copynumber: 32.9 Consensus size: 9
523112 AAAAGGTAAT
523122 GAAAATAAA
1 GAAAATAAA
523131 GAAAATAAA
1 GAAAATAAA
*
523140 AACAAATGAAA
1 GA-AAAT-AAA
*
523151 CAAAA-AAA
1 GAAAATAAA
*
523159 TG-AGATAAA
1 -GAAAATAAA
523168 GAAAA-AAA
1 GAAAATAAA
*
523176 -AAGATAAA
1 GAAAATAAA
523184 GAAAA-AAA
1 GAAAATAAA
*
523192 -AAGATAAA
1 GAAAATAAA
523200 GAAAATTAAA
1 GAAAA-TAAA
523210 G-AAATAAAA
1 GAAAAT-AAA
523219 GAAAA-AATA
1 GAAAATAA-A
*
523228 AAAAAT-AA
1 GAAAATAAA
523236 -AAAATAAA
1 GAAAATAAA
523244 GAAAATAATA
1 GAAAATAA-A
* *
523254 -ATAATATA
1 GAAAATAAA
* *
523262 TATAATAAA
1 GAAAATAAA
*
523271 -TAAATAAA
1 GAAAATAAA
*
523279 TAAAA-ACAA
1 GAAAATA-AA
* * *
523288 GAATAGAAT
1 GAAAATAAA
523297 GAAAATAAA
1 GAAAATAAA
*
523306 -TAAATAAAA
1 GAAAAT-AAA
*
523315 TAAATATAAA
1 GAAA-ATAAA
*
523325 GGAAATAAA
1 GAAAATAAA
523334 -AATAAGGTAAA
1 GAA-AA--TAAA
523345 GATAAAGTAAA
1 GA-AAA-TAAA
*
523356 -TAAATAAA
1 GAAAATAAA
* *
523364 -AAAAGAGA
1 GAAAATAAA
523372 GAAAATAAA
1 GAAAATAAA
*
523381 -TAAATAAA
1 GAAAATAAA
*
523389 -TAAATAAA
1 GAAAATAAA
*
523397 GAAAAAAAA
1 GAAAATAAA
523406 GAAAATAA
1 GAAAATAA
523414 TAGTATATAT
Statistics
Matches: 215, Mismatches: 37, Indels: 62
0.68 0.12 0.20
Matches are distributed among these distances:
7 11 0.05
8 61 0.28
9 100 0.47
10 24 0.11
11 15 0.07
12 3 0.01
13 1 0.00
ACGTcount: A:0.74, C:0.01, G:0.09, T:0.15
Consensus pattern (9 bp):
GAAAATAAA
Found at i:523167 original size:37 final size:34
Alignment explanation
Indices: 523126--523251 Score: 98
Period size: 34 Copynumber: 3.6 Consensus size: 34
523116 GGTAATGAAA
*
523126 ATAAAGAAAATAAAAACAAATGAAACAAAAAAATGAG
1 ATAAAGAAAATAAAAA-AAAT-AAACAAAAAAA-AAG
* *
523163 ATAAAG-AAA-AAAAAAGATAAAGAAAAAAAAAG
1 ATAAAGAAAATAAAAAAAATAAACAAAAAAAAAG
* *
523195 ATAAAGAAAATTAAAGAAATAAA-AGAAAAAATAA-
1 ATAAAGAAAATAAAAAAAATAAACA-AAAAAA-AAG
* * *
523229 AAAATAAAAAATAAAGAAAATAA
1 ATAA-AGAAAATAAAAAAAATAA
523252 TAATAATATA
Statistics
Matches: 73, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
32 8 0.11
33 14 0.19
34 21 0.29
35 21 0.29
36 3 0.04
37 6 0.08
ACGTcount: A:0.78, C:0.02, G:0.10, T:0.11
Consensus pattern (34 bp):
ATAAAGAAAATAAAAAAAATAAACAAAAAAAAAG
Found at i:523194 original size:10 final size:10
Alignment explanation
Indices: 523165--523248 Score: 53
Period size: 10 Copynumber: 7.8 Consensus size: 10
523155 AAAATGAGAT
523165 AAAGAAAAAA
1 AAAGAAAAAA
523175 AAAGATAAAGAA
1 AAAGA-AAA-AA
*
523187 AAA-AAAAGAT
1 AAAGAAAA-AA
**
523197 AAAGAAAATT
1 AAAGAAAAAA
523207 AAAGAAATAAA
1 AAAGAAA-AAA
*
523218 AGAAAAAATAAA
1 A-AAGAAA-AAA
*
523230 AAATAAAAAA
1 AAAGAAAAAA
523240 TAAAGAAAA
1 -AAAGAAAA
523249 TAATAATAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
10 24 0.39
11 22 0.36
12 15 0.25
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:523221 original size:19 final size:19
Alignment explanation
Indices: 523169--523237 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 19
523159 TGAGATAAAG
*
523169 AAAAA-AAAAGATAAAGAAAA
1 AAAAATAAAAGA-AAA-AATA
* *
523189 AAAAAGATAAAG-AAAATTA
1 AAAAATA-AAAGAAAAAATA
523208 AAGAAATAAAAGAAAAAATA
1 AA-AAATAAAAGAAAAAATA
523228 AAAAATAAAA
1 AAAAATAAAA
523238 AATAAAGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
19 16 0.39
20 20 0.49
21 1 0.02
22 4 0.10
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.10
Consensus pattern (19 bp):
AAAAATAAAAGAAAAAATA
Found at i:523230 original size:7 final size:7
Alignment explanation
Indices: 523215--523284 Score: 52
Period size: 7 Copynumber: 9.4 Consensus size: 7
523205 TTAAAGAAAT
*
523215 AAAAGAA
1 AAAATAA
523222 AAAATAA
1 AAAATAA
523229 AAAATAA
1 AAAATAA
523236 AAAATAAA
1 AAAAT-AA
523244 GAAAATAA
1 -AAAATAA
523252 TAATAAT-A
1 -AA-AATAA
* *
523260 TATATAA
1 AAAATAA
*
523267 TAAATAA
1 AAAATAA
523274 ATAAATAA
1 A-AAATAA
523282 AAA
1 AAA
523285 CAAGAATAGA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
6 2 0.04
7 28 0.54
8 14 0.27
9 8 0.15
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (7 bp):
AAAATAA
Found at i:523230 original size:26 final size:25
Alignment explanation
Indices: 523165--523415 Score: 74
Period size: 26 Copynumber: 9.5 Consensus size: 25
523155 AAAATGAGAT
523165 AAAGAAAAAA-AAAGATAAAGAAA-A
1 AAAGAAAAAATAAA-ATAAAGAAATA
*
523189 AAA-AAGATAAAGAAAATTAAAGAAATA
1 AAAGAA-A-AAATAAAA-TAAAGAAATA
523216 AAAGAAAAAATAAAAAATAAA-AAAT-
1 AAAGAAAAAAT--AAAATAAAGAAATA
* *
523241 AAAGAAAATAATAATAATATATATAATA
1 AAAGAAAA-AATAA-AATAAAGA-AATA
*
523269 AATA-AATAAATAAAA-ACAAG-AATA
1 AA-AGAAAAAATAAAATA-AAGAAATA
* *
523293 GAATGAAAATAA-ATAAATAAAATAAATA
1 -AAAGAAAA-AATA-AAAT-AAAGAAATA
* * * *
523321 TAAAGGAAATA-AAAATAAGGTAAAGA
1 -AAAGAAAAAATAAAATAAAG-AAATA
* *
523347 TAAAGTAAATAAATAAAA-AAAGAGAGA
1 -AAAG-AAA-AAATAAAATAAAGAAATA
* *
523374 AAATAAATAAATAAATAAATAAAGAAAAA
1 AAAGAAA-AAAT--A-AAATAAAGAAATA
523403 AAAGAAAATAATA
1 AAAGAAAA-AATA
523416 GTATATATGT
Statistics
Matches: 173, Mismatches: 23, Indels: 59
0.68 0.09 0.23
Matches are distributed among these distances:
23 2 0.01
24 10 0.06
25 34 0.20
26 46 0.27
27 29 0.17
28 31 0.18
29 21 0.12
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (25 bp):
AAAGAAAAAATAAAATAAAGAAATA
Found at i:523249 original size:16 final size:16
Alignment explanation
Indices: 523123--523405 Score: 101
Period size: 16 Copynumber: 17.1 Consensus size: 16
523113 AAAGGTAATG
523123 AAAATAAAGAAAATAAAA
1 AAAATAAAGAAAAT--AA
*
523141 ACAAATGAAACAAAA-AA
1 A-AAAT-AAAGAAAATAA
*
523158 ATGAGATAAAGAAAA-AA
1 A--AAATAAAGAAAATAA
523175 AAAGATAAAGAAAA-AA
1 AAA-ATAAAGAAAATAA
523191 AAAGATAAAGAAAAT--
1 AAA-ATAAAGAAAATAA
* * * *
523206 TAAAGAAATAAAAGAA
1 AAAATAAAGAAAATAA
523222 AAAAT-AA-AAAATAA
1 AAAATAAAGAAAATAA
523236 AAAATAAAGAAAATAA
1 AAAATAAAGAAAATAA
* * *
523252 TAATAATATATATAATAA
1 -AA-AATAAAGAAAATAA
*
523270 ATAAATAAATAAAA-ACA
1 A-AAATAAAGAAAATA-A
*
523287 AGAATAGAATGAAAAT--
1 AAAATA-AA-GAAAATAA
*
523303 -AAATAAATAAAAT-A
1 AAAATAAAGAAAATAA
* *
523317 AATATAAAGGAAATAAA
1 AAAATAAAGAAAAT-AA
523334 AATAAGGTAAAGATAAAGTAA
1 AA-AA--TAAAGA-AAA-TAA
*
523355 ATAAATAAA-AAAAGAGA
1 A-AAATAAAGAAAATA-A
*
523372 GAAAATAAA-TAAATAA
1 -AAAATAAAGAAAATAA
523388 ATAAATAAAGAAAA-AA
1 A-AAATAAAGAAAATAA
523404 AA
1 AA
523406 GAAAATAATA
Statistics
Matches: 205, Mismatches: 30, Indels: 63
0.69 0.10 0.21
Matches are distributed among these distances:
13 5 0.02
14 21 0.10
15 23 0.11
16 53 0.26
17 50 0.24
18 23 0.11
19 8 0.04
20 12 0.06
21 8 0.04
22 2 0.01
ACGTcount: A:0.75, C:0.01, G:0.09, T:0.16
Consensus pattern (16 bp):
AAAATAAAGAAAATAA
Found at i:523272 original size:4 final size:4
Alignment explanation
Indices: 523223--523396 Score: 75
Period size: 4 Copynumber: 42.8 Consensus size: 4
523213 ATAAAAGAAA
* *
523223 AAAT AAA- AAAT AAA- AAAT AAAG AAA- ATAAT -AAT -AAT ATAT ATAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT A-AAT
523268 AAAT AAAT AAAT AAA- AACA- AGAAT AGAAT GAAAAT AAAT AAAT AAAAT
1 AAAT AAAT AAAT AAAT AA-AT A-AAT A-AAT --AAAT AAAT AAAT -AAAT
* *
523316 AAAT --AT AAAGG AAAT -AA- AAAT AAGGT AAAGAT AAAGT AAAT AAAT
1 AAAT AAAT AAA-T AAAT AAAT AAAT AA-AT -AA-AT AAA-T AAAT AAAT
* *
523361 AAAA AAAG AGAGA- AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT A-A-AT AAAT AAAT AAAT AAAT AAAT AAA
523397 GAAAAAAAAG
Statistics
Matches: 138, Mismatches: 9, Indels: 46
0.72 0.05 0.24
Matches are distributed among these distances:
2 2 0.01
3 20 0.14
4 82 0.59
5 25 0.18
6 8 0.06
7 1 0.01
ACGTcount: A:0.72, C:0.01, G:0.07, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:523332 original size:75 final size:73
Alignment explanation
Indices: 523191--523394 Score: 190
Period size: 81 Copynumber: 2.7 Consensus size: 73
523181 AAAGAAAAAA
* * *
523191 AAAGATAAAGAAAATTAAAGAAATAAAAGA-A-AAAATAAA-AAAT-AA-AAA-ATAAAGAAAAT
1 AAAGATAAAGTAAA-TAAATAAA-AAAAGAGAGAAAATAAATAAATAAATAAATATAAAGGAAAT
*
523250 AATAATAA-T
64 AAAAATAAGT
*
523259 ATATATAATAAA-TAAATAAATAAAAACAAGAATAGAATGAAAATAAATAAATAAAATAAATATA
1 A-A-A-GATAAAGTAAATAAATAAAAA-AAG---AG-A-GAAAATAAATAAAT-AAATAAATATA
523323 AAGGAAATAAAAATAAGGT
56 AAGGAAATAAAAATAA-GT
523342 AAAGATAAAGTAAATAAATAAAAAAAGAGAGAAAATAAATAAATAAATAAATA
1 AAAGATAAAGTAAATAAATAAAAAAAGAGAGAAAATAAATAAATAAATAAATA
523395 AAGAAAAAAA
Statistics
Matches: 111, Mismatches: 6, Indels: 32
0.74 0.04 0.21
Matches are distributed among these distances:
68 3 0.03
69 11 0.10
70 4 0.04
71 5 0.05
72 1 0.01
74 10 0.09
75 14 0.13
76 9 0.08
77 6 0.05
79 2 0.02
80 11 0.10
81 32 0.29
82 1 0.01
83 2 0.02
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (73 bp):
AAAGATAAAGTAAATAAATAAAAAAAGAGAGAAAATAAATAAATAAATAAATATAAAGGAAATAA
AAATAAGT
Found at i:523412 original size:81 final size:79
Alignment explanation
Indices: 523215--523413 Score: 203
Period size: 81 Copynumber: 2.5 Consensus size: 79
523205 TTAAAGAAAT
* * * *
523215 AAAAGAAAAAATAAA-AAAT-AAAAAATAAAGAAAATAATAATAATATATATAATAAATAAATAA
1 AAAATAAAAAATAAATAAATAAAAAAAAAAAGAAAATAAAAATAAGATATATAATAAATAAATAA
*
523278 ATAAAAACAAGAAT
66 ATAAAAACAAGAAG
* * * *
523292 AGAAT-GAAAATAAATAAATAAAATAAATATAAAGGAAATAAAAATAAGGTA-A-AGATAAAGTA
1 AAAATAAAAAATAAATAAATAAAA-AAA-A-AAAGAAAATAAAAATAAGATATATA-ATAAA-TA
523354 AATAAATAAAAA-AAGAGAG
61 AATAAATAAAAACAAGA-AG
523373 AAAATAAATAAATAAATAAATAAAGAAAAAAAAGAAAATAA
1 AAAATAAA-AAATAAATAAATAAA-AAAAAAAAGAAAATAA
523414 TAGTATATAT
Statistics
Matches: 99, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
76 8 0.08
77 7 0.07
78 3 0.03
79 4 0.04
80 10 0.10
81 46 0.46
82 2 0.02
83 18 0.18
84 1 0.01
ACGTcount: A:0.74, C:0.01, G:0.08, T:0.18
Consensus pattern (79 bp):
AAAATAAAAAATAAATAAATAAAAAAAAAAAGAAAATAAAAATAAGATATATAATAAATAAATAA
ATAAAAACAAGAAG
Found at i:523413 original size:75 final size:72
Alignment explanation
Indices: 523163--523415 Score: 205
Period size: 75 Copynumber: 3.4 Consensus size: 72
523153 AAAAAATGAG
* * * * * *
523163 ATAAAGAAAAAAAAAGATAAAGAAAAAAAAAGATAAAGAAAATTAAAGAAATAAAAGA-A-AAAA
1 ATAAATAAAGAAAAA-ATAAA-AATAATAAAGATAAAGTAAA-TAAATAAA-AAAAGAGAGAAAA
523226 TAAA-AAATAA
62 TAAATAAATAA
* *
523236 A-AAATAAAGAAAATAATAATAATATATATA-ATAAA-TAAATAAATAAAAACAAGAATAGAATG
1 ATAAATAAAGAAAA-AATAAAAATA-ATAAAGATAAAGTAAATAAATAAAAA-AAG---AG-A-G
523298 AAAATAAATAAATAAA
58 AAAATAAATAAAT-AA
**
523314 ATAAATATAA-AGGAAATAAAAATAAGGTAAAGATAAAGTAAATAAATAAAAAAAGAGAGAAAAT
1 ATAAATA-AAGAAAAAATAAAAATAA--TAAAGATAAAGTAAATAAATAAAAAAAGAGAGAAAAT
523378 AAATAAATAA
63 AAATAAATAA
*
523388 ATAAATAAAGAAAAAAAAGAAAATAATA
1 ATAAATAAAGAAAAAATA-AAAATAATA
523416 GTATATATGT
Statistics
Matches: 145, Mismatches: 15, Indels: 40
0.73 0.08 0.20
Matches are distributed among these distances:
68 2 0.01
69 10 0.07
70 3 0.02
71 8 0.06
72 18 0.12
73 6 0.04
74 15 0.10
75 21 0.14
76 9 0.06
77 7 0.05
78 12 0.08
79 10 0.07
80 10 0.07
81 14 0.10
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (72 bp):
ATAAATAAAGAAAAAATAAAAATAATAAAGATAAAGTAAATAAATAAAAAAAGAGAGAAAATAAA
TAAATAA
Found at i:523422 original size:2 final size:2
Alignment explanation
Indices: 523417--523448 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
523407 AAAATAATAG
*
523417 TA TA TA TG 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
523449 AATGTTAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:523513 original size:22 final size:21
Alignment explanation
Indices: 523458--523514 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
523448 AAATGTTAGG
* *
523458 AAAACCAATAATATAGAAAACC
1 AAAACGAATAA-ATAGAAAAAC
* *
523480 AAAAAGAA-AAATAGTAAAAAT
1 AAAACGAATAAATAG-AAAAAC
523501 AAAACGAATAAATA
1 AAAACGAATAAATA
523515 AAATAAATAG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 4 0.14
21 13 0.46
22 11 0.39
ACGTcount: A:0.70, C:0.09, G:0.07, T:0.14
Consensus pattern (21 bp):
AAAACGAATAAATAGAAAAAC
Found at i:540602 original size:58 final size:58
Alignment explanation
Indices: 540537--540652 Score: 187
Period size: 58 Copynumber: 2.0 Consensus size: 58
540527 TGATCTGGCC
* *
540537 TCATGTCATTGACGTGTTTGTATTGTTCCAGAAACGACTTGGCTAAATCCTTCCAAGT
1 TCATGTCATTGACGTGTTTGTATTGTTCCAGAAAAGACATGGCTAAATCCTTCCAAGT
* * *
540595 TCATGTCATTGACGTGTTTGTATTGTTCTATAAAAGACATGGTTAAATCCTTCCAAGT
1 TCATGTCATTGACGTGTTTGTATTGTTCCAGAAAAGACATGGCTAAATCCTTCCAAGT
540653 CTTGATATGG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (58 bp):
TCATGTCATTGACGTGTTTGTATTGTTCCAGAAAAGACATGGCTAAATCCTTCCAAGT
Found at i:544721 original size:5 final size:5
Alignment explanation
Indices: 544694--544896 Score: 61
Period size: 5 Copynumber: 39.8 Consensus size: 5
544684 GTACCCTTAG
* * * * *
544694 AAAAT AAAA- AAAGAT -AAAG AAAAT AAAAG AAATT AAAGA- AAAAT TAAAG
1 AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AAAAT AAA-AT AAAAT AAAAT
* *
544743 AAAAT AAAGAAT ATAAT AATAAT ATAAT -AAAT -AAAT -AAAT -AAAT
1 AAAAT -AA-AAT AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT AAAAT
* *
544787 AAAAAC AAGAAT AAAAT GAAAAT -AAAT AACGAAT -AAAT ATAAAT GAAAT
1 -AAAAT AA-AAT AAAAT -AAAAT AAAAT AA--AAT AAAAT A-AAAT AAAAT
* *
544836 AAAAAT AAAGT AAAGAT AAAGA- AAAAT AAGAA- AAGAAG AAAAT -AAAT
1 -AAAAT AAAAT AAA-AT AAA-AT AAAAT AA-AAT AA-AAT AAAAT AAAAT
* *
544883 AAAAG AAAAG AAAA
1 AAAAT AAAAT AAAA
544897 AAAGAAAAGA
Statistics
Matches: 153, Mismatches: 22, Indels: 46
0.69 0.10 0.21
Matches are distributed among these distances:
4 32 0.21
5 77 0.50
6 38 0.25
7 6 0.04
ACGTcount: A:0.73, C:0.01, G:0.09, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:544742 original size:20 final size:20
Alignment explanation
Indices: 544694--544909 Score: 87
Period size: 20 Copynumber: 10.7 Consensus size: 20
544684 GTACCCTTAG
544694 AAAATAAAA-AAAGATAAAG-
1 AAAATAAAAGAAA-ATAAAGA
*
544713 AAAATAAAAGAAATTAAAGA
1 AAAATAAAAGAAAATAAAGA
*
544733 AAAATTAAAGAAAATAAAGA
1 AAAATAAAAGAAAATAAAGA
* *
544753 ATATAATAATAATATAAT-AA-A
1 A-A-AATAA-AAGAAAATAAAGA
* *
544774 TAAATAAATA-AATAA-AAACA
1 AAAATAAA-AGAA-AATAAAGA
* *
544794 AGAATAAAATGAAAATAAATA
1 AAAATAAAA-GAAAATAAAGA
* * *
544815 ACGAATAAATA-TAAATGAAATA
1 A-AAATAAA-AGAAAAT-AAAGA
544837 AAAAT-AAAGTAAAGATAAAGA
1 AAAATAAAAG-AAA-ATAAAGA
*
544858 AAAATAAGAA-AAGAAGAAA-A
1 AAAATAA-AAGAA-AATAAAGA
* *
544878 TAAATAAAAGAAAA-GAA-A
1 AAAATAAAAGAAAATAAAGA
*
544896 AAAAGAAAAGAAAA
1 AAAATAAAAGAAAA
544910 AAGAAGAAGA
Statistics
Matches: 155, Mismatches: 20, Indels: 45
0.70 0.09 0.20
Matches are distributed among these distances:
18 17 0.11
19 30 0.19
20 43 0.28
21 33 0.21
22 23 0.15
23 9 0.06
ACGTcount: A:0.74, C:0.01, G:0.09, T:0.16
Consensus pattern (20 bp):
AAAATAAAAGAAAATAAAGA
Found at i:544775 original size:12 final size:12
Alignment explanation
Indices: 544745--544788 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
544735 AATTAAAGAA
*
544745 AATAAAGAATAT
1 AATAAATAATAT
544757 AAT-AATAATAT
1 AATAAATAATAT
544768 AATAAATAA-AT
1 AATAAATAATAT
544779 AAATAAATAA
1 -AATAAATAA
544789 AAACAAGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 12 0.41
12 17 0.59
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (12 bp):
AATAAATAATAT
Found at i:544803 original size:21 final size:22
Alignment explanation
Indices: 544779--544840 Score: 63
Period size: 26 Copynumber: 2.6 Consensus size: 22
544769 ATAAATAAAT
544779 AAAT-AAATAAAAACAAGAATA
1 AAATGAAATAAAAACAAGAATA
*
544800 AAATGAAAATAAATAACGAATAAATA
1 AAATG-AAATAAA-AAC-AA-GAATA
544826 TAAATGAAATAAAAA
1 -AAATGAAATAAAAA
544841 TAAAGTAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
21 4 0.12
23 7 0.21
24 3 0.09
25 4 0.12
26 11 0.32
27 5 0.15
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.18
Consensus pattern (22 bp):
AAATGAAATAAAAACAAGAATA
Found at i:544849 original size:11 final size:10
Alignment explanation
Indices: 544744--544864 Score: 73
Period size: 11 Copynumber: 11.2 Consensus size: 10
544734 AAATTAAAGA
544744 AAATAAAGAAT
1 AAATAAA-AAT
*
544755 ATAATAATAAT
1 A-AATAAAAAT
544766 ATAATAAATAAAT
1 A-AAT-AA-AAAT
544779 AAATAAATAA-
1 AAATAAA-AAT
* *
544789 AAACAAGAAT
1 AAATAAAAAT
*
544799 AAAATGAAAAT
1 -AAATAAAAAT
*
544810 AAATAACGAAT
1 AAATAA-AAAT
*
544821 AAATATAAAT
1 AAATAAAAAT
544831 GAAATAAAAAT
1 -AAATAAAAAT
*
544842 AAAGTAAAGAT
1 AAA-TAAAAAT
*
544853 AAAGAAAAAT
1 AAATAAAAAT
544863 AA
1 AA
544865 GAAAAGAAGA
Statistics
Matches: 86, Mismatches: 15, Indels: 19
0.72 0.12 0.16
Matches are distributed among these distances:
9 2 0.02
10 24 0.28
11 46 0.53
12 10 0.12
13 4 0.05
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.21
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:544874 original size:8 final size:8
Alignment explanation
Indices: 544858--544917 Score: 51
Period size: 7 Copynumber: 8.2 Consensus size: 8
544848 AAGATAAAGA
*
544858 AAAATAAG
1 AAAAGAAG
544866 AAAAGAAG
1 AAAAGAAG
*
544874 AAAATAA-
1 AAAAGAAG
*
544881 ATAA-AAG
1 AAAAGAAG
544888 AAAAG-A-
1 AAAAGAAG
544894 AAAA-AAG
1 AAAAGAAG
544901 AAAAGAA-
1 AAAAGAAG
544908 AAAAGAAG
1 AAAAGAAG
544916 AA
1 AA
544918 GAAAATAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
6 7 0.17
7 18 0.43
8 17 0.40
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (8 bp):
AAAAGAAG
Found at i:544879 original size:37 final size:34
Alignment explanation
Indices: 544836--544911 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 34
544826 TAAATGAAAT
544836 AAAAATAAAGT-AAAGATAAAGAAAAATAAGAAAAGA
1 AAAAATAAA-TAAAAGA-AAAGAAAAA-AAGAAAAGA
544872 AGAAAATAAATAAAAGAAAAGAAAAAAAGAAAAGA
1 A-AAAATAAATAAAAGAAAAGAAAAAAAGAAAAGA
544907 AAAAA
1 AAAAA
544912 GAAGAAGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
34 4 0.11
35 10 0.26
36 11 0.29
37 13 0.34
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (34 bp):
AAAAATAAATAAAAGAAAAGAAAAAAAGAAAAGA
Found at i:544901 original size:13 final size:13
Alignment explanation
Indices: 544863--544922 Score: 77
Period size: 13 Copynumber: 4.5 Consensus size: 13
544853 AAAGAAAAAT
*
544863 AAGAAAAGAAGAA
1 AAGAAAAAAAGAA
*
544876 AATAAATAAAAGAA
1 AAGAAA-AAAAGAA
544890 AAGAAAAAAAGAA
1 AAGAAAAAAAGAA
544903 AAG-AAAAAAGAA
1 AAGAAAAAAAGAA
544915 GAAGAAAA
1 -AAGAAAA
544923 TAATAGTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
12 9 0.22
13 18 0.44
14 14 0.34
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (13 bp):
AAGAAAAAAAGAA
Found at i:544904 original size:5 final size:5
Alignment explanation
Indices: 544842--544909 Score: 52
Period size: 5 Copynumber: 13.6 Consensus size: 5
544832 AAATAAAAAT
* * * *
544842 AAAGT AAAGA TAAAGA AAA-A TAAGA AAAGA AGAAAA TAAATA AAAGA
1 AAAGA AAAGA -AAAGA AAAGA AAAGA AAAGA A-AAGA -AAAGA AAAGA
544889 AAAG- AAA-A AAAGA AAAGA AAA
1 AAAGA AAAGA AAAGA AAAGA AAA
544910 AAGAAGAAGA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
4 9 0.18
5 30 0.59
6 11 0.22
7 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (5 bp):
AAAGA
Found at i:547399 original size:18 final size:18
Alignment explanation
Indices: 547378--547414 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
547368 AGAGTGTAAG
*
547378 CAAGGTTTTGAGTATAAA
1 CAAGGTTTTAAGTATAAA
547396 CAAGGTTTTAAGTATAAA
1 CAAGGTTTTAAGTATAAA
547414 C
1 C
547415 TTTATGTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (18 bp):
CAAGGTTTTAAGTATAAA
Found at i:547640 original size:2 final size:2
Alignment explanation
Indices: 547635--547686 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
547625 TAAAAAATTA
547635 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
547677 AT AT AT AT AT
1 AT AT AT AT AT
547687 TTGTATTTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:548021 original size:35 final size:36
Alignment explanation
Indices: 547980--548056 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 36
547970 TTACATATTG
* *
547980 TCTTTAAAAATTAACAAGTCTAGTGGATTTAAGAAA
1 TCTTTAAAAATTAACAAATCTAGTAGATTTAAGAAA
** *
548016 T-TTTAAAGGTTAATAAATCTAGTAGATTTAAGAAA
1 TCTTTAAAAATTAACAAATCTAGTAGATTTAAGAAA
548051 TCTTTA
1 TCTTTA
548057 GTATGAATAC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 30 0.86
36 5 0.14
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.38
Consensus pattern (36 bp):
TCTTTAAAAATTAACAAATCTAGTAGATTTAAGAAA
Found at i:550759 original size:19 final size:21
Alignment explanation
Indices: 550732--550781 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
550722 CTTTCCTCTT
* *
550732 AGTACCGATACC-C-TACTTC
1 AGTATCGATACCACTTACATC
*
550751 AGTATCGATACCACTTGCATC
1 AGTATCGATACCACTTACATC
550772 AGTATCGATA
1 AGTATCGATA
550782 TTGTTCATCG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 11 0.42
20 1 0.04
21 14 0.54
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (21 bp):
AGTATCGATACCACTTACATC
Found at i:557419 original size:22 final size:22
Alignment explanation
Indices: 557393--557563 Score: 292
Period size: 22 Copynumber: 7.9 Consensus size: 22
557383 TTCTAAATGT
*
557393 TGAACGATTCAGCATTCAGCGC
1 TGAACGGTTCAGCATTCAGCGC
*
557415 TGAACGGTTCAGCTTTCAGCGC
1 TGAACGGTTCAGCATTCAGCGC
557437 TGAACGGTTCAGCATTCAGCGC
1 TGAACGGTTCAGCATTCAGCGC
557459 TGAACGGTTCAGCATTCAGCGC
1 TGAACGGTTCAGCATTCAGCGC
557481 TGAACGGTTCAGCATTCAGCGC
1 TGAACGGTTCAGCATTCAGCGC
557503 TGAACGGTTCAGCATTCAGCGC
1 TGAACGGTTCAGCATTCAGCGC
557525 TGAACGGTTCAGCATTCAGCGC
1 TGAACGGTTCAGCATTCAGCGC
* *
557547 TAAATGGTTC--CATTCAG
1 TGAACGGTTCAGCATTCAG
557564 AGCCAAGCAG
Statistics
Matches: 144, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
20 7 0.05
22 137 0.95
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.25
Consensus pattern (22 bp):
TGAACGGTTCAGCATTCAGCGC
Found at i:572363 original size:21 final size:21
Alignment explanation
Indices: 572337--572416 Score: 76
Period size: 21 Copynumber: 3.7 Consensus size: 21
572327 TCGAGGGTTC
572337 TATGTGGTC-CTTCGGGACAAT
1 TATGTGG-CACTTCGGGACAAT
* *
572358 TATGTGGCACTTTGGTG-CAAACC
1 TATGTGGCACTTCGG-GAC-AA-T
572381 TATGTGGTC-CTTCGGGACAAT
1 TATGTGG-CACTTCGGGACAAT
572402 TATGTGGCACTTCGG
1 TATGTGGCACTTCGG
572417 TGCAAATTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
20 2 0.04
21 26 0.54
22 6 0.12
23 13 0.27
24 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.29, T:0.33
Consensus pattern (21 bp):
TATGTGGCACTTCGGGACAAT
Found at i:572399 original size:44 final size:44
Alignment explanation
Indices: 572336--572422 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
572326 GTCGAGGGTT
*
572336 CTATGTGGTCCTTCGGGACAATTATGTGGCACTTTGGTGCAAAC
1 CTATGTGGTCCTTCGGGACAATTATGTGGCACTTCGGTGCAAAC
572380 CTATGTGGTCCTTCGGGACAATTATGTGGCACTTCGGTGCAAA
1 CTATGTGGTCCTTCGGGACAATTATGTGGCACTTCGGTGCAAA
572423 TTATGAGCTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.31
Consensus pattern (44 bp):
CTATGTGGTCCTTCGGGACAATTATGTGGCACTTCGGTGCAAAC
Found at i:578195 original size:13 final size:13
Alignment explanation
Indices: 578163--578198 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
578153 AGTGAATTAG
*
578163 AAATGGATTTGTA
1 AAATGGGTTTGTA
578176 AAATGGGTTTGTA
1 AAATGGGTTTGTA
578189 AAATGGGTTT
1 AAATGGGTTT
578199 TGAAATGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.39
Consensus pattern (13 bp):
AAATGGGTTTGTA
Found at i:579272 original size:21 final size:21
Alignment explanation
Indices: 579246--579369 Score: 67
Period size: 21 Copynumber: 5.7 Consensus size: 21
579236 TCGAGGGTTC
579246 TATGTGGTC-CTTCGGAACAAT
1 TATGTGG-CACTTCGGAACAAT
** *
579267 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGCACTTCGGAAC-AA-T
*
579290 TATGTGGTC-CTTC-GAGATAAT
1 TATGTGG-CACTTCGGA-ACAAT
* * *
579311 TATGTGGCACTTTGGTACAAACC
1 TATGTGGCACTTCGGAAC-AA-T
* *
579334 TATGTGGTC-CTTCGGGATAAT
1 TATGTGG-CACTTCGGAACAAT
579355 TATGTGGCACTTCGG
1 TATGTGGCACTTCGG
579370 TGTAAATTAC
Statistics
Matches: 77, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
20 3 0.04
21 38 0.49
22 10 0.13
23 24 0.31
24 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (21 bp):
TATGTGGCACTTCGGAACAAT
Found at i:579295 original size:23 final size:22
Alignment explanation
Indices: 579267--579371 Score: 69
Period size: 21 Copynumber: 4.8 Consensus size: 22
579257 TCGGAACAAT
579267 TATGTGGCACTTCGGTGCA-AACC
1 TATGTGGCACTTCGGTG-ATAA-C
* *
579290 TATGTGGTC-CTTC-GAGATAAT
1 TATGTGG-CACTTCGGTGATAAC
* *
579311 TATGTGGCACTTTGGT-ACAAACC
1 TATGTGGCACTTCGGTGA-TAA-C
*
579334 TATGTGGTC-CTTCGG-GATAAT
1 TATGTGG-CACTTCGGTGATAAC
579355 TATGTGGCACTTCGGTG
1 TATGTGGCACTTCGGTG
579372 TAAATTACGA
Statistics
Matches: 63, Mismatches: 9, Indels: 21
0.68 0.10 0.23
Matches are distributed among these distances:
20 2 0.03
21 25 0.40
22 10 0.16
23 24 0.38
24 2 0.03
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (22 bp):
TATGTGGCACTTCGGTGATAAC
Found at i:579312 original size:44 final size:43
Alignment explanation
Indices: 579245--579371 Score: 200
Period size: 44 Copynumber: 2.9 Consensus size: 43
579235 GTCGAGGGTT
*
579245 CTATGTGGTCCTTCGGAACAATTATGTGGCACTTCGGTGCAAAC
1 CTATGTGGTCCTTCGG-ATAATTATGTGGCACTTCGGTGCAAAC
* *
579289 CTATGTGGTCCTTCGAGATAATTATGTGGCACTTTGGTACAAAC
1 CTATGTGGTCCTTCG-GATAATTATGTGGCACTTCGGTGCAAAC
579333 CTATGTGGTCCTTCGGGATAATTATGTGGCACTTCGGTG
1 CTATGTGGTCCTTC-GGATAATTATGTGGCACTTCGGTG
579372 TAAATTACGA
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
44 74 0.97
45 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (43 bp):
CTATGTGGTCCTTCGGATAATTATGTGGCACTTCGGTGCAAAC
Found at i:579837 original size:12 final size:14
Alignment explanation
Indices: 579822--579883 Score: 78
Period size: 12 Copynumber: 4.6 Consensus size: 14
579812 ATTTTACTTT
579822 TTATTAT-TAT-TA
1 TTATTATATATATA
579834 TTATTATATATATA
1 TTATTATATATATA
579848 TATATATATATATATA
1 T-TAT-TATATATATA
579864 TTATTA-A-ATATA
1 TTATTATATATATA
579876 TTATTATA
1 TTATTATA
579884 GGCCAGAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
12 18 0.40
13 5 0.11
14 5 0.11
15 6 0.13
16 11 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTATTATATATATA
Found at i:579845 original size:2 final size:2
Alignment explanation
Indices: 579838--579876 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
579828 TTATTATTAT
*
579838 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA T- TA AA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
579877 TATTATAGGC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:580977 original size:2 final size:2
Alignment explanation
Indices: 580970--581010 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
580960 TATTTAGTCT
580970 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
581011 TTTGGATAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:581317 original size:11 final size:11
Alignment explanation
Indices: 581289--581322 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
581279 ATATGTTTAA
*
581289 ATTATTACTTTA
1 ATTATTA-TTTT
581301 ATTATTATTTT
1 ATTATTATTTT
581312 ATTATTATTTT
1 ATTATTATTTT
581323 CATACTAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTATTATTTT
Found at i:581493 original size:36 final size:35
Alignment explanation
Indices: 581453--581524 Score: 85
Period size: 35 Copynumber: 2.0 Consensus size: 35
581443 TAAATAAATG
581453 TTATAAAAATTATATATATT-A-ATTTATTTTATTTTT
1 TTATAAAAA-TAT-TATATTAATATTTA-TTTATTTTT
* *
581489 TTATAGAAATATTTTATTAATATTTATTTATTTTT
1 TTATAAAAATATTATATTAATATTTATTTATTTTT
581524 T
1 T
581525 AATATTAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
34 5 0.16
35 14 0.44
36 13 0.41
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (35 bp):
TTATAAAAATATTATATTAATATTTATTTATTTTT
Found at i:581617 original size:2 final size:2
Alignment explanation
Indices: 581612--581643 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
581602 TAAAAACTTA
581612 AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
581644 TTTCTTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:586801 original size:125 final size:124
Alignment explanation
Indices: 586652--586898 Score: 406
Period size: 125 Copynumber: 2.0 Consensus size: 124
586642 CAAGTTCTCC
* *
586652 AATGAAAAAAAAAAGTCATATATTCAAAGCATGACCTTGATCGGGTATTTGGCAGTTCGGTGTTT
1 AATGAAAAAAAAAAATCATATATTCAAAGCATAACCTTGATCGGGTATTTGGCAGTTCGGTGTTT
* * *
586717 GCT-CACTATGATTGTCAAGTCAAAGACATTGTGATGAGTTGAACCTTTTAATTAGTTT
66 GCTCCACTATGATTATCAAATCAAAGACATTGTGATGAGTTGAACCCTTTAATTAGTTT
586775 AATGAAAAAAAAAGAAATCATATATTCAAAGCATAACCTTGATCGGGTATTTGGCAGTTCGGTGT
1 AATG-AAAAAAAA-AAATCATATATTCAAAGCATAACCTTGATCGGGTATTTGGCAGTTCGGTGT
* *
586840 TTGCTCCACTGTGATTATTAAATCAAAGACATTGTGATGAGTTGAACCCTTTAATTAGT
64 TTGCTCCACTATGATTATCAAATCAAAGACATTGTGATGAGTTGAACCCTTTAATTAGT
586899 CCGATGAAGG
Statistics
Matches: 114, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
123 4 0.04
124 8 0.07
125 54 0.47
126 48 0.42
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.33
Consensus pattern (124 bp):
AATGAAAAAAAAAAATCATATATTCAAAGCATAACCTTGATCGGGTATTTGGCAGTTCGGTGTTT
GCTCCACTATGATTATCAAATCAAAGACATTGTGATGAGTTGAACCCTTTAATTAGTTT
Found at i:590231 original size:22 final size:22
Alignment explanation
Indices: 590153--590215 Score: 108
Period size: 22 Copynumber: 2.9 Consensus size: 22
590143 ACATCTACAT
*
590153 TCTTCAAAGATAATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
590175 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
590197 TCTTCAAATATGATAGATT
1 TCTTCAAAGATGATAGATT
590216 ATCATTTCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:591020 original size:76 final size:75
Alignment explanation
Indices: 590894--591033 Score: 201
Period size: 76 Copynumber: 1.9 Consensus size: 75
590884 CTTCAGTGCA
* *
590894 TGATGTTATCAAAACCTTTGGGGCATCTATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATGTTATCAAAACCTTTGGGCCATCTATAAGACCTACAGTACAGGATGTTTTCAAAAA-CCTT
590959 TGGGAGTTTTT
65 TGGGAGTTTTT
* * * *
590970 TGATGTTTTCAAAACCTTCT-GGCCATCTGTAAGACCTTCAGTACATGATGTTTTCAAAAACCTT
1 TGATGTTATCAAAACCTT-TGGGCCATCTATAAGACCTACAGTACAGGATGTTTTCAAAAACCTT
591034 CAGGTTATCC
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
75 4 0.07
76 52 0.91
77 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (75 bp):
TGATGTTATCAAAACCTTTGGGCCATCTATAAGACCTACAGTACAGGATGTTTTCAAAAACCTTT
GGGAGTTTTT
Found at i:591049 original size:46 final size:46
Alignment explanation
Indices: 590970--591081 Score: 136
Period size: 46 Copynumber: 2.4 Consensus size: 46
590960 GGGAGTTTTT
* ** *
590970 TGATGTTTTC-AAAACCTTCTGGCCATCTGTAAGACCTTCAGTACA
1 TGATGTTTTCAAAAACCTTCAGGCCATCCATAAGACCTACAGTACA
** *
591015 TGATGTTTTCAAAAACCTTCAGGTTATCCATAAGACCTACAGTGCA
1 TGATGTTTTCAAAAACCTTCAGGCCATCCATAAGACCTACAGTACA
*
591061 GGATGTTTTCAAAAAGCCTTC
1 TGATGTTTTCAAAAA-CCTTC
591082 GGGAGATTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
45 10 0.18
46 42 0.74
47 5 0.09
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.32
Consensus pattern (46 bp):
TGATGTTTTCAAAAACCTTCAGGCCATCCATAAGACCTACAGTACA
Found at i:591145 original size:45 final size:45
Alignment explanation
Indices: 591094--591195 Score: 134
Period size: 45 Copynumber: 2.3 Consensus size: 45
591084 GAGATTTTTA
* * * *
591094 ATGTTTTCATAGCCTTC-GCGTCATCTCTAACACCTTCAGTGCATG
1 ATGTTTTCAAAACCTTCAG-GTCATCTCTAACACCTACAGTGCAGG
* *
591139 ATGTTTTCAAAACCTTCAGGTCATCTGTAAGACCTACAGTGCAGG
1 ATGTTTTCAAAACCTTCAGGTCATCTCTAACACCTACAGTGCAGG
591184 ATGTTTTCAAAA
1 ATGTTTTCAAAA
591196 AGCCTTCGGG
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
45 49 0.98
46 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (45 bp):
ATGTTTTCAAAACCTTCAGGTCATCTCTAACACCTACAGTGCAGG
Found at i:591206 original size:121 final size:120
Alignment explanation
Indices: 590884--591270 Score: 531
Period size: 121 Copynumber: 3.2 Consensus size: 120
590874 TAAGAAATCA
* ** *
590884 CTTCAGTGCATGATGTTATCAAAACCTTTGGGGCATCTATAAGACCTACAGTGCAGGATGTTTTC
1 CTTCAGTGCATGATGTTTTCAAAACCTTCAGGTCATCTATAAGACCTACAGTGCAGGATGTTTTC
* * * *
590949 AAAAAGCCTTTGGGAGTTTTTTGATGTTTTCAAAACCTTCTGGCCATCTGTAAGAC
66 AAAAAGCCTTCGGGAGATTTTTGATGTTTTCAAAGCCTTC-GGTCATCTGTAAGAC
* * *
591005 CTTCAGTACATGATGTTTTCAAAAACCTTCAGGTTATCCATAAGACCTACAGTGCAGGATGTTTT
1 CTTCAGTGCATGATGTTTTC-AAAACCTTCAGGTCATCTATAAGACCTACAGTGCAGGATGTTTT
* * * *
591070 CAAAAAGCCTTCGGGAGATTTTTAATGTTTTCATAGCCTTCGCGTCATCTCTAACAC
65 CAAAAAGCCTTCGGGAGATTTTTGATGTTTTCAAAGCCTTCG-GTCATCTGTAAGAC
*
591127 CTTCAGTGCATGATGTTTTCAAAACCTTCAGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTC
1 CTTCAGTGCATGATGTTTTCAAAACCTTCAGGTCATCTATAAGACCTACAGTGCAGGATGTTTTC
** * * *
591192 AAAAAGCCTTCGGGATCTATTTGATATTTTCAAAGCCTTCGGGTCATTTGTAAGAC
66 AAAAAGCCTTCGGGAGATTTTTGATGTTTTCAAAGCCTTC-GGTCATCTGTAAGAC
* *
591248 CTACAGTGCAGGATGTTTTCAAA
1 CTTCAGTGCATGATGTTTTCAAA
591271 GAGCCTTTGG
Statistics
Matches: 233, Mismatches: 30, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
121 127 0.55
122 106 0.45
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (120 bp):
CTTCAGTGCATGATGTTTTCAAAACCTTCAGGTCATCTATAAGACCTACAGTGCAGGATGTTTTC
AAAAAGCCTTCGGGAGATTTTTGATGTTTTCAAAGCCTTCGGTCATCTGTAAGAC
Found at i:591222 original size:76 final size:76
Alignment explanation
Indices: 591137--591355 Score: 334
Period size: 76 Copynumber: 2.9 Consensus size: 76
591127 CTTCAGTGCA
* * *
591137 TGATGTTTTCAAAACCTTCAGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
*
591202 CGGGATCTATT
66 CGGGAGCTATT
* *
591213 TGATATTTTCAAAGCCTTCGGGTCATTTGTAAGACCTACAGTGCAGGATGTTTTCAAAGAGCCTT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
* *
591278 TGGGAGCTTTT
66 CGGGAGCTATT
* *
591289 TGATATTTTCAAAGCCTTCGGGTCATCTTTAAGACCTACAGTGCATGATGTTTTC-AAAA-CCTT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
591352 CGGG
66 CGGG
591356 TCATCCATAA
Statistics
Matches: 130, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
74 7 0.05
75 3 0.02
76 120 0.92
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (76 bp):
TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
CGGGAGCTATT
Found at i:591269 original size:197 final size:197
Alignment explanation
Indices: 591045--591659 Score: 745
Period size: 197 Copynumber: 3.0 Consensus size: 197
591035 AGGTTATCCA
*
591045 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGATTTTTAATGTTTTCATAGCCTT
1 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGATTTTTAATGTTTTCAAAGCCTT
* * * * **
591110 CGCGTCATCTCTAACACCTTCAGTGCATGATGTTTTCAAAACCTTCAGGTCATCTGTAAGACCTA
66 CGGGTCATCTCTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTA
* * *
591175 CAGTGCAGGATGTTTTCAAAAAGCCTTCGGGATCTATTTGATATTTTCAAAGCCTTCGGGTCATT
131 CAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATC
591240 TG
196 TG
* * * * *
591242 TAAGACCTACAGTGCAGGATGTTTTCAAAGAGCCTTTGGGAGCTTTTTGATATTTTCAAAGCCTT
1 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGATTTTTAATGTTTTCAAAGCCTT
*
591307 CGGGTCATCTTTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTA
66 CGGGTCATCTCTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTA
* * *
591372 TAGTGCAGGATGTTTTCAAAAATCCTTCAGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATC
131 CAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATC
591437 TG
196 TG
** * * * **
591439 TAAGACCTACAGTGCATAATGTTTTC-TAAA-CCTTCAGGTCATCCATAAGACCTACAATGCAGG
1 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTC-GG--------GAGA--T---TTTTA--
*
591502 ATGTTTTCAAAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCG
50 ATGTTTTC--AAAGCCTTCGGGTCATCTCTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCG
* *
591567 GGTCATCCATAAGACATACAGTGCAGGATGTGTTCAAACAAGCCTTCGGGAGCTTTTTGATA-TT
113 GGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAA-AAGCCTTCGGGAGCTTTTTGATATTT
*
591631 T-AAAACC-TCTGGGTCATCTG
177 TCAAAGCCTTC-GGGTCATCTG
591651 TAAGACCTA
1 TAAGACCTA
591660 TGCAAGATGA
Statistics
Matches: 360, Mismatches: 38, Indels: 25
0.85 0.09 0.06
Matches are distributed among these distances:
195 4 0.01
196 4 0.01
197 202 0.56
204 2 0.01
206 1 0.00
209 1 0.00
211 9 0.03
212 24 0.07
213 92 0.26
214 21 0.06
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (197 bp):
TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGATTTTTAATGTTTTCAAAGCCTT
CGGGTCATCTCTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTA
CAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATC
TG
Found at i:591358 original size:45 final size:45
Alignment explanation
Indices: 591289--591392 Score: 154
Period size: 45 Copynumber: 2.3 Consensus size: 45
591279 GGGAGCTTTT
* * **
591289 TGATATTTTCAAAGCCTTCGGGTCATCTTTAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCA
*
591334 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTATAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCA
*
591379 GGATGTTTTCAAAA
1 TGATGTTTTCAAAA
591393 ATCCTTCAGG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCA
Found at i:591377 original size:121 final size:121
Alignment explanation
Indices: 591213--591520 Score: 481
Period size: 121 Copynumber: 2.5 Consensus size: 121
591203 GGGATCTATT
* * *** *
591213 TGATATTTTCAAAGCCTTCGGGTCATTTGTAAGACCTACAGTGCAGGATGTTTTCAAAGAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
** *
591278 TGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATCTTTAAGACCTACAGTGCA
66 CAGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCA
* *
591334 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTATAGTGCAGGATGTTTTCAAAAATCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
591399 CAGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCA
66 CAGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCA
* * * *
591455 TAATGTTTTCTAAACCTTCAGGTCATCCATAAGACCTACAATGCAGGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
591520 C
66 C
591521 GGGTCATCTG
Statistics
Matches: 170, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
121 170 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (121 bp):
TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
CAGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCA
Found at i:591479 original size:45 final size:46
Alignment explanation
Indices: 591410--591616 Score: 249
Period size: 45 Copynumber: 4.5 Consensus size: 46
591400 AGGAGCTTTT
* **
591410 TGATATTTTC-AAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCA
1 TGATGTTTTCAAAAGCCTTCGGGTCATCCATAAGACCTACAGTGCA
* * * *
591455 TAATGTTTTCTAAA-CCTTCAGGTCATCCATAAGACCTACAATGCA
1 TGATGTTTTCAAAAGCCTTCGGGTCATCCATAAGACCTACAGTGCA
* **
591500 GGATGTTTTCAAAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCA
1 TGATGTTTTC-AAAAGCCTTCGGGTCATCCATAAGACCTACAGTGCA
*
591547 TGATGTTTTCAAAA-CCTTCGGGTCATCCATAAGACATACAGTGCA
1 TGATGTTTTCAAAAGCCTTCGGGTCATCCATAAGACCTACAGTGCA
* *
591592 GGATGTGTTCAAACAAGCCTTCGGG
1 TGATGTTTTC-AA-AAGCCTTCGGG
591617 AGCTTTTTGA
Statistics
Matches: 137, Mismatches: 19, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
45 79 0.58
46 12 0.09
47 38 0.28
48 8 0.06
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (46 bp):
TGATGTTTTCAAAAGCCTTCGGGTCATCCATAAGACCTACAGTGCA
Found at i:591533 original size:92 final size:92
Alignment explanation
Indices: 591420--591616 Score: 331
Period size: 92 Copynumber: 2.1 Consensus size: 92
591410 TGATATTTTC
*
591420 AAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATAATGTTTTCTAAACCTTCAGGTCATCCAT
1 AAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATAATGTTTTCAAAACCTTCAGGTCATCCAT
* *
591485 AAGACCTACAATGCAGGATGTTTTCAA
66 AAGACATACAATGCAGGATGTGTTCAA
* *
591512 AAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCAT
1 AAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATAATGTTTTCAAAACCTTCAGGTCATCCAT
*
591577 AAGACATACAGTGCAGGATGTGTTCAA
66 AAGACATACAATGCAGGATGTGTTCAA
591604 ACAAGCCTTCGGG
1 A-AAGCCTTCGGG
591617 AGCTTTTTGA
Statistics
Matches: 98, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
92 87 0.89
93 11 0.11
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.27
Consensus pattern (92 bp):
AAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATAATGTTTTCAAAACCTTCAGGTCATCCAT
AAGACATACAATGCAGGATGTGTTCAA
Found at i:592007 original size:12 final size:12
Alignment explanation
Indices: 591979--592020 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
591969 CTTTTTTTAT
591979 TATTATTATA-A
1 TATTATTATATA
591990 TA-TATTATATA
1 TATTATTATATA
*
592001 TATTATTAAATA
1 TATTATTATATA
592013 TATTATTA
1 TATTATTA
592021 CAGGCCAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 7 0.25
11 5 0.18
12 16 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TATTATTATATA
Found at i:593097 original size:2 final size:2
Alignment explanation
Indices: 593090--593118 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
593080 AGTCCTTATC
593090 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
593119 TAGGATAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:593682 original size:11 final size:11
Alignment explanation
Indices: 593654--593687 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
593644 ATATGTTTAA
*
593654 ATTATTACTTTA
1 ATTATTA-TTTT
593666 ATTATTATTTT
1 ATTATTATTTT
593677 ATTATTATTTT
1 ATTATTATTTT
593688 CATACTAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTATTATTTT
Found at i:593983 original size:2 final size:2
Alignment explanation
Indices: 593976--594024 Score: 68
Period size: 2 Copynumber: 26.0 Consensus size: 2
593966 TAAAAACTTA
*
593976 AT AT AT AT AT AT AT AT AT AT -T AA 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
594017 -T A- AT AT AT
1 AT AT AT AT AT
594025 TTTCTTAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 3 0.07
2 39 0.93
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:609694 original size:2 final size:2
Alignment explanation
Indices: 609689--609714 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
609679 ATTATATATA
609689 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
609715 GTGGAATACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:611649 original size:2 final size:2
Alignment explanation
Indices: 611644--612064 Score: 197
Period size: 2 Copynumber: 213.5 Consensus size: 2
611634 ATTGAACAAT
** * * * *
611644 TA TA TA TA TA TA TA TA TA TA TA T- TA CG TA AA AA CTA GA GTT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA
* * *
611687 TA TA TA AA GTA TA TA TA T- TA TA TA TA AA T- TA TA TA TA TA AA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
611728 CTA TA TA GTT TA TA TT TA TA T- TA T- TA TA TA CTA TA TA TA T-
1 -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * * *
611768 TA TG TA TA AA CTA TA TA GTT TA T- TA -A TA TA AA CTA TA TA TA
1 TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA
* * * * * *
611809 TA T- TG TA TA TA TA CA CTA TG TA CA TA AA CTA TA TA GTT TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA -TA TA TA
* *
611851 TT TA TA T- TA T- TA TA TA T- TA TA TA TA AA TA -A TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
611888 TA TG TA TA -A AA TA TA TA GTC CA T- TA -A TA TA AA CTT TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA
* * * *
611929 -A AA TA TA TA GTG TA TA TA TA -A TG TA TA TA TA -A TG TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
611969 GTT TA 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 TA TA
*
612012 TA TA TA TA TA TA TA TA TA CTA TA TA GA T- TA TA T- TA TA T- TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
612052 T- TA TA TA CTA TA T
1 TA TA TA TA -TA TA T
612065 TTAAACTGTA
Statistics
Matches: 312, Mismatches: 65, Indels: 84
0.68 0.14 0.18
Matches are distributed among these distances:
1 24 0.08
2 269 0.86
3 19 0.06
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:611701 original size:11 final size:11
Alignment explanation
Indices: 611684--612058 Score: 98
Period size: 11 Copynumber: 34.8 Consensus size: 11
611674 AAACTAGAGT
611684 TTATATATAAA
1 TTATATATAAA
*
611695 GTATATAT--A
1 TTATATATAAA
611704 TTATATATAAA
1 TTATATATAAA
611715 TTATATATATAA
1 TTATATATA-AA
**
611727 --ACTATATAGT
1 TTA-TATATAAA
* *
611737 TTATATTTATA
1 TTATATATAAA
*
611748 TTAT-TATATA
1 TTATATATAAA
*
611758 CTATATAT--A
1 TTATATATAAA
*
611767 TTATGTATAAA
1 TTATATATAAA
* **
611778 CTATATAGTTTA
1 TTATATA-TAAA
611790 TTA-ATATAAA
1 TTATATATAAA
* *
611800 CTATATATATAT
1 TTATATATA-AA
*
611812 TGTATATATACAC
1 T-TATATATA-AA
* *
611825 TATGTACATAAA
1 T-TATATATAAA
*
611837 CTATATAGT---
1 TTATATA-TAAA
* *
611846 TTATATTTATA
1 TTATATATAAA
*
611857 TTAT-TATATA
1 TTATATATAAA
611867 TTATATATAAA
1 TTATATATAAA
*
611878 -TA-ATATATA
1 TTATATATAAA
*
611887 TTATGTATAAA
1 TTATATATAAA
* **
611898 ATATATAGTCCA
1 TTATATA-TAAA
611910 TTA-ATATAAA
1 TTATATATAAA
611920 CTT-TATATAAA
1 -TTATATATAAA
*
611931 --ATATAT-AG
1 TTATATATAAA
611939 TGTATATAT-AA
1 T-TATATATAAA
611950 TGTATATAT-AA
1 T-TATATATAAA
* **
611961 -TGTATATAGT
1 TTATATATAAA
*
611971 TTATATATATA
1 TTATATATAAA
*
611982 -TATATATATA
1 TTATATATAAA
*
611992 -TATATATATA
1 TTATATATAAA
*
612002 TATATATATATA
1 T-TATATATAAA
*
612014 TATATATATATA
1 T-TATATATAAA
*
612026 TATACTATATAGA
1 T-TA-TATATAAA
*
612039 TTATAT-TATA
1 TTATATATAAA
612049 TTATTATATA
1 TTA-TATATA
612059 CTATATTTAA
Statistics
Matches: 276, Mismatches: 54, Indels: 67
0.70 0.14 0.17
Matches are distributed among these distances:
8 2 0.01
9 37 0.13
10 54 0.20
11 115 0.42
12 44 0.16
13 24 0.09
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.47
Consensus pattern (11 bp):
TTATATATAAA
Found at i:611837 original size:109 final size:100
Alignment explanation
Indices: 611643--612064 Score: 297
Period size: 109 Copynumber: 4.2 Consensus size: 100
611633 AATTGAACAA
*
611643 TTATA-TATATATATATATATATATTACGTAAAAACTAGAGTTTATATATAAAGTATATATATTA
1 TTATATTAT-TATATATATATATATTACGTAAAAACTAGAGTTTATATATAAAATATATATATTA
* *
611707 TATATAAATTATATATATAAACTATATAGTTTATAT
65 TATATAAACTATATACATAAACTATATAGTTTATAT
* * *
611743 TTATATTATTATATACTATATATATTATGTATAAACTATATAGTTTATTAATATAAACTATATAT
1 TTATATTATTATATA-TATATATATTACGTAAAAAC--TAGAGTTTA-T-ATATAAA--ATATAT
* *
611808 ATATTGTATATATACACTATGTACATAAACTATATAGTTTATAT
59 ATA-T-TATATATAAACTATATACATAAACTATATAGTTTATAT
* * *
611852 TTATATTATTATATAT-TATATA-TA---AATAA-TATA-TATTATGTATAAAATATATAGTCCA
1 TTATATTATTATATATATATATATTACGTAAAAACTAGAGT-TTATATATAAAATATATA-T--A
* * *
611910 TTA-ATATAAACT-T-TATATAAAATATATAGTGTATAT
62 TTATATATAAACTATATACATAAACTATATAGTTTATAT
* * * * * * *
611946 ATA-ATGTA-TATATAATGTATATAGTTTA--TATATA-TATA-TATATATATATATATATATAT
1 TTATAT-TATTATAT-ATATATATA--TTACGTAAAAACTAGAGTTTATATATA-AAATATATAT
* * * *
612005 ATATATATATATA-TATATATATATACTATATAGATTATA-
61 AT-TATATATAAACTATATACATAAACTATATAGTTTATAT
612044 TTATATTATTATATACTATAT
1 TTATATTATTATATA-TATAT
612065 TTAAACTGTA
Statistics
Matches: 264, Mismatches: 29, Indels: 59
0.75 0.08 0.17
Matches are distributed among these distances:
93 7 0.03
94 26 0.10
95 7 0.03
96 17 0.06
97 6 0.02
98 29 0.11
99 47 0.18
100 18 0.07
101 21 0.08
103 11 0.04
104 1 0.00
105 7 0.03
106 2 0.01
107 14 0.05
108 2 0.01
109 49 0.19
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (100 bp):
TTATATTATTATATATATATATATTACGTAAAAACTAGAGTTTATATATAAAATATATATATTAT
ATATAAACTATATACATAAACTATATAGTTTATAT
Found at i:612080 original size:4 final size:4
Alignment explanation
Indices: 612071--612406 Score: 663
Period size: 4 Copynumber: 84.0 Consensus size: 4
612061 ATATTTAAAC
612071 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
612119 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
612167 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
612215 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
612263 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
612311 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
612359 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGCA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
612407 ACGGTTGTCA
Statistics
Matches: 330, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 330 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:618566 original size:30 final size:31
Alignment explanation
Indices: 618480--618575 Score: 108
Period size: 32 Copynumber: 3.1 Consensus size: 31
618470 AAGAGTCGAG
* *
618480 GGTTACCTATGTCCTTCAGGACATATGAACA
1 GGTTACCTATGTTCTTCAGGACATATGGACA
*
618511 GGATTACCTATG-TCATTCGGGACATATGGACA
1 GG-TTACCTATGTTC-TTCAGGACATATGGACA
*
618543 -GTTACCTATGTTC-TCAGGAACATATGGATA
1 GGTTACCTATGTTCTTCAGG-ACATATGGACA
618573 GGT
1 GGT
618576 CCTTCGGGAC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
29 4 0.07
30 19 0.35
31 8 0.15
32 24 0.44
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (31 bp):
GGTTACCTATGTTCTTCAGGACATATGGACA
Found at i:621875 original size:42 final size:46
Alignment explanation
Indices: 621829--621948 Score: 135
Period size: 42 Copynumber: 2.7 Consensus size: 46
621819 TTTTATAAAA
*
621829 TATTTATTTTAATTAATAATTTATATATTATTA-TATT-TTA-A-T
1 TATTTATTATAATTAATAATTTATATATTATTATTATTGTTATATT
* *
621871 TATTTATTATATTTAATAATTAATATTATTAGTTATTATTGTTATATT
1 TATTTATTATAATTAATAATTTATA-TATTA-TTATTATTGTTATATT
* *
621919 TATTTATTATAA-T-ATAATTTTTTTATTATT
1 TATTTATTATAATTAATAATTTATATATTATT
621949 TCAAAATTTG
Statistics
Matches: 65, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
42 22 0.34
43 5 0.08
44 5 0.08
45 9 0.14
46 10 0.15
47 2 0.03
48 12 0.18
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (46 bp):
TATTTATTATAATTAATAATTTATATATTATTATTATTGTTATATT
Found at i:622018 original size:25 final size:24
Alignment explanation
Indices: 621986--622046 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 24
621976 TTTTTATAAA
*
621986 ATAT-TTATTTTATTTACTATATTT
1 ATATATTATTTTATTTAAT-TATTT
*
622010 ATATATTATTATATTTTAATTATTT
1 ATATATTATTTTA-TTTAATTATTT
622035 AT-TA-TATTTTAT
1 ATATATTATTTTAT
622047 AATTAATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
22 1 0.03
23 6 0.19
24 6 0.19
25 14 0.44
26 5 0.16
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (24 bp):
ATATATTATTTTATTTAATTATTT
Found at i:622024 original size:16 final size:16
Alignment explanation
Indices: 621963--622079 Score: 69
Period size: 16 Copynumber: 7.9 Consensus size: 16
621953 AATTTGCAAA
*
621963 ATATATTATAATATTTTT
1 ATATATTAT--TATATTT
* *
621981 ATAAAATATT-TATTT
1 ATATATTATTATATTT
*
621996 -TAT-TTACTATATTT
1 ATATATTATTATATTT
622010 ATATATTATTATATTT
1 ATATATTATTATATTT
622026 -TA-ATTATT-TA--T
1 ATATATTATTATATTT
*
622037 -TATATT-TTATAATT
1 ATATATTATTATATTT
622051 A-ATATTATTATATTT
1 ATATATTATTATATTT
*
622066 ACT-TATTATAATAT
1 A-TATATTATTATAT
622080 AATTTTATTT
Statistics
Matches: 79, Mismatches: 9, Indels: 24
0.71 0.08 0.21
Matches are distributed among these distances:
11 5 0.06
12 5 0.06
13 5 0.06
14 19 0.24
15 17 0.22
16 21 0.27
18 7 0.09
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (16 bp):
ATATATTATTATATTT
Found at i:622024 original size:47 final size:43
Alignment explanation
Indices: 621963--622065 Score: 113
Period size: 43 Copynumber: 2.4 Consensus size: 43
621953 AATTTGCAAA
* * *
621963 ATATATTATAATATTTTTATAAAATATTTATTTTATTTACTATATTT
1 ATATATTATTATATTTTT-T-AAATATTTATTATATTT--TATAATT
*
622010 ATATATTATTATA--TTTTAATTATTTATTATATTTTATAATT
1 ATATATTATTATATTTTTTAAATATTTATTATATTTTATAATT
622051 A-ATATTATTATATTT
1 ATATATTATTATATTT
622066 ACTTATTATA
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
40 11 0.22
41 7 0.14
42 1 0.02
43 15 0.30
44 1 0.02
45 3 0.06
47 12 0.24
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (43 bp):
ATATATTATTATATTTTTTAAATATTTATTATATTTTATAATT
Found at i:622051 original size:13 final size:14
Alignment explanation
Indices: 622011--622077 Score: 56
Period size: 13 Copynumber: 5.0 Consensus size: 14
622001 ACTATATTTA
622011 TATATTATTAT-AT
1 TATATTATTATAAT
*
622024 TTTAATTATT-T-AT
1 TAT-ATTATTATAAT
622037 TATATT-TTATAAT
1 TATATTATTATAAT
622050 TAATATTATTAT-AT
1 T-ATATTATTATAAT
622064 T-TACTTATTATAAT
1 TATA-TTATTATAAT
622078 ATAATTTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 2 0.04
12 6 0.13
13 17 0.38
14 16 0.36
15 4 0.09
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (14 bp):
TATATTATTATAAT
Found at i:622072 original size:35 final size:34
Alignment explanation
Indices: 621968--622075 Score: 98
Period size: 34 Copynumber: 3.2 Consensus size: 34
621958 GCAAAATATA
* * *
621968 TTATAATATTTTTATA-AAATAT-TTAT-TTTAT
1 TTATTATATTTATATATTAATATATTATATTTAT
* * * *
621999 TTACTATATTTATATATTATTATATTTTAATTAT
1 TTATTATATTTATATATTAATATATTATATTTAT
*
622033 TTATTATATTT-TATAATTAATATTATTATATTTAC
1 TTATTATATTTATAT-ATTAATA-TATTATATTTAT
622068 TTATTATA
1 TTATTATA
622076 ATATAATTTT
Statistics
Matches: 60, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
31 13 0.22
32 4 0.07
33 6 0.10
34 20 0.33
35 17 0.28
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (34 bp):
TTATTATATTTATATATTAATATATTATATTTAT
Found at i:622571 original size:19 final size:19
Alignment explanation
Indices: 622547--622583 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
622537 ATGACCAACA
*
622547 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
622566 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
622584 CAGTATCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:622634 original size:20 final size:20
Alignment explanation
Indices: 622609--622696 Score: 63
Period size: 20 Copynumber: 4.3 Consensus size: 20
622599 GTTTCCAGAT
* *
622609 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTATGACAA
* *
622629 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTATG-ACAA
* *
622649 TCGTAACGCGATAAT-ACAAAA
1 TCGCAACGCGATTATGAC--AA
* *
622670 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTATGACAA
622690 TCGCAAC
1 TCGCAAC
622697 ACTGAATTTC
Statistics
Matches: 51, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
18 1 0.02
20 33 0.65
21 15 0.29
22 2 0.04
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGATTATGACAA
Found at i:623790 original size:14 final size:13
Alignment explanation
Indices: 623762--623799 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
623752 AAAAAAAGAA
*
623762 GAAG-AAATCCCC
1 GAAGAAAATACCC
623774 GAAGAAAAGTACCC
1 GAAGAAAA-TACCC
623788 GAAGAAAATACC
1 GAAGAAAATACC
623800 ACGGGAGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 4 0.17
13 7 0.30
14 12 0.52
ACGTcount: A:0.50, C:0.24, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAGAAAATACCC
Found at i:625853 original size:18 final size:18
Alignment explanation
Indices: 625830--625864 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
625820 AGCAAAAGGC
*
625830 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
625848 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
625865 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:626060 original size:20 final size:20
Alignment explanation
Indices: 626035--626111 Score: 120
Period size: 20 Copynumber: 3.9 Consensus size: 20
626025 TTACACATTC
*
626035 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
626055 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
626075 ATTTGATTATCGCAACAG-GA
1 ATTTGACTATCGCAAC-GCGA
626095 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
626112 AGAAAATCGT
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
19 1 0.02
20 51 0.96
21 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.27
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:626212 original size:20 final size:20
Alignment explanation
Indices: 626183--626240 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
626173 CCAACGCGAA
626183 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCGTTGCGATT
* *
626203 TTGTCTTTCGCATTGCGATT
1 TTGACTTTCGCGTTGCGATT
* *
626223 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCGTTGCGA
626241 AAGTGTACCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.12, C:0.17, G:0.26, T:0.45
Consensus pattern (20 bp):
TTGACTTTCGCGTTGCGATT
Found at i:626934 original size:20 final size:20
Alignment explanation
Indices: 626897--626934 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
626887 AAAATCAAAC
*
626897 AAAATATTAGATGGTAAAAT
1 AAAATATTAGATGCTAAAAT
626917 AAAATATT-GAATGCTAAA
1 AAAATATTAG-ATGCTAAA
626935 CAAAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.55, C:0.03, G:0.13, T:0.29
Consensus pattern (20 bp):
AAAATATTAGATGCTAAAAT
Found at i:626966 original size:26 final size:25
Alignment explanation
Indices: 626911--626972 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
626901 TATTAGATGG
*
626911 TAAAATAAAATATTGAATGCTAAAC
1 TAAAATAAAATATTGAATACTAAAC
* * * *
626936 AAAAATAAAATTTTAGAATATTAAAT
1 TAAAATAAAATATT-GAATACTAAAC
626962 TAAAAATAAAA
1 T-AAAATAAAA
626973 AAATTTTAAG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
25 12 0.41
26 8 0.28
27 9 0.31
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (25 bp):
TAAAATAAAATATTGAATACTAAAC
Found at i:627048 original size:20 final size:20
Alignment explanation
Indices: 627020--627066 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
627010 AAAATGTCAC
* *
627020 AAGAGAAATAA-ATAAAAATT
1 AAGAAAAATAATA-AAAAAGT
627040 AAGAAAAATAATAAAAAAGT
1 AAGAAAAATAATAAAAAAGT
627060 AAGAAAA
1 AAGAAAA
627067 TATTAATTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (20 bp):
AAGAAAAATAATAAAAAAGT
Found at i:628356 original size:85 final size:85
Alignment explanation
Indices: 628251--628454 Score: 336
Period size: 85 Copynumber: 2.4 Consensus size: 85
628241 TTTTTTGTTA
* * **
628251 ACAAATAACTCTTCTTGCCTTGAGCTATGTTGTAAATTTGATATGTCTTTGAGCTGAATGTAATC
1 ACAAATAACTCTTCTCGCCTTGAGTTATGTTGTAAATAGGATATGTCTTTGAGCTGAATGTAATC
628316 GAACTCGAAGGTCTTGGTTG
66 GAACTCGAAGGTCTTGGTTG
* *
628336 ACAAATAACCCTTCTCGCCTTGAGTTATGATGTAAATAGGATATGTCTTTGAGCTGAATGTAATC
1 ACAAATAACTCTTCTCGCCTTGAGTTATGTTGTAAATAGGATATGTCTTTGAGCTGAATGTAATC
*
628401 GAACTCGAAGGTCTTTGTTG
66 GAACTCGAAGGTCTTGGTTG
*
628421 ACAGATAACTCTTCTCGCCTTGAGTTATGTTGTA
1 ACAAATAACTCTTCTCGCCTTGAGTTATGTTGTA
628455 CTAAGCTGAG
Statistics
Matches: 109, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 109 1.00
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (85 bp):
ACAAATAACTCTTCTCGCCTTGAGTTATGTTGTAAATAGGATATGTCTTTGAGCTGAATGTAATC
GAACTCGAAGGTCTTGGTTG
Found at i:628750 original size:85 final size:85
Alignment explanation
Indices: 628555--628793 Score: 285
Period size: 84 Copynumber: 2.8 Consensus size: 85
628545 ATGTATCGTC
* * * *
628555 GAGCTGAATGGAATCAAACTC-ATCA-GTT-TTTGCTGATAGATAGCCCTTCTCGCCTTGAGCTA
1 GAGCTGAATGTAATCAAACTCGA--AGGTTCTTTGATGACAGATAACCCTTCTCGCCTTGAGCTA
* * *
628617 TGCTGTAAATTTTATATGCCTT
64 TGTTGTAAATTTGACATGCCTT
*
628639 GAGCTGAATGTAATCAAACTCGAAGG-TCTTTGATGACAGATAACCCTTCTCGCCTTGAGTTATG
1 GAGCTGAATGTAATCAAACTCGAAGGTTCTTTGATGACAGATAACCCTTCTCGCCTTGAGCTATG
628703 TTGTAAATTTGACATGTCCTT
66 TTGTAAATTTGACATG-CCTT
* * *
628724 GAGCTGAATGTAATCGAACTCGAAGGTTTCATTGTTGAC--ATAGA-CCTTCTCGCCTTGAGCTA
1 GAGCTGAATGTAATCAAACTCGAAGG-TTCTTTGATGACAGATA-ACCCTTCTCGCCTTGAGCTA
628786 TGTTGTAA
64 TGTTGTAA
628794 TAGGATGGGG
Statistics
Matches: 136, Mismatches: 12, Indels: 13
0.84 0.07 0.08
Matches are distributed among these distances:
83 2 0.01
84 66 0.49
85 58 0.43
86 1 0.01
87 9 0.07
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (85 bp):
GAGCTGAATGTAATCAAACTCGAAGGTTCTTTGATGACAGATAACCCTTCTCGCCTTGAGCTATG
TTGTAAATTTGACATGCCTT
Found at i:629190 original size:65 final size:67
Alignment explanation
Indices: 629049--629223 Score: 224
Period size: 65 Copynumber: 2.7 Consensus size: 67
629039 TGAAGTTGAG
* *
629049 CTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATTCAA--T-G-GT--TTCTTCACCAAATTG
1 CTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTCGAGTAAGTCTTCACCAAATTG
629108 GT
66 GT
* * *
629110 -TTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTCGAGTAAGT-TTCACTAAATT-
1 CTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTCGAGTAAGTCTTCACCAAATTG
629172 GT
66 GT
* *
629174 CTTTAAATTGGATATCCTTCGTTGTGAAGTTGAAATCTAATCTCGAGTAA
1 CTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTCGAGTAA
629224 ATTGTATCGC
Statistics
Matches: 98, Mismatches: 9, Indels: 10
0.84 0.08 0.09
Matches are distributed among these distances:
60 36 0.37
62 1 0.01
63 1 0.01
64 4 0.04
65 55 0.56
66 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (67 bp):
CTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTCGAGTAAGTCTTCACCAAATTG
GT
Found at i:634606 original size:20 final size:20
Alignment explanation
Indices: 634581--634618 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
634571 AAAATCAAAC
634581 AAAATATT-AGATGGTAAAAT
1 AAAATATTGA-ATGGTAAAAT
634601 AAAATATTGAATGGTAAA
1 AAAATATTGAATGGTAAA
634619 CAAAAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.55, C:0.00, G:0.16, T:0.29
Consensus pattern (20 bp):
AAAATATTGAATGGTAAAAT
Found at i:634624 original size:20 final size:20
Alignment explanation
Indices: 634577--634624 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
634567 TGAAAAAATC
634577 AAAC-AAAATATTAGATGGT
1 AAACAAAAATATTAGATGGT
634596 AAA-ATAAAATATT-GAATGGT
1 AAACA-AAAATATTAG-ATGGT
634616 AAACAAAAA
1 AAACAAAAA
634625 GAAATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
19 4 0.16
20 20 0.80
21 1 0.04
ACGTcount: A:0.60, C:0.04, G:0.12, T:0.23
Consensus pattern (20 bp):
AAACAAAAATATTAGATGGT
Found at i:634682 original size:27 final size:28
Alignment explanation
Indices: 634620--634683 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
634610 AATGGTAAAC
* *
634620 AAAAAGAAATTTTTTTAGAAGATTAAATT
1 AAAAATAAATTTTTTTA-AAGATTAAAAT
634649 AAAAATAAATTTTTTT-AAGA-TAATAAT
1 AAAAATAAATTTTTTTAAAGATTAA-AAT
*
634676 AATAATAA
1 AAAAATAA
634684 TGTGAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 3 0.10
27 13 0.42
29 15 0.48
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (28 bp):
AAAAATAAATTTTTTTAAAGATTAAAAT
Found at i:634728 original size:20 final size:20
Alignment explanation
Indices: 634700--634746 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
634690 AAAATGTCAC
* *
634700 AAGAGAAATAAATAAA-AATT
1 AAGAAAAAT-AATAAACAAAT
634720 AAGAAAAATAATAAACAAAT
1 AAGAAAAATAATAAACAAAT
634740 AAGAAAA
1 AAGAAAA
634747 TATTAATTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.15
Consensus pattern (20 bp):
AAGAAAAATAATAAACAAAT
Found at i:636508 original size:2 final size:2
Alignment explanation
Indices: 636501--636541 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
636491 TTGTCCTTTA
636501 AT AT AT AT 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 AT AT AT AT A
636542 ACTATTATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:637850 original size:12 final size:13
Alignment explanation
Indices: 637833--637864 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
637823 GCCTTTCGTC
637833 ATTTATTTAT-TT
1 ATTTATTTATATT
637845 ATTTATTTATATT
1 ATTTATTTATATT
637858 -TTTATTT
1 ATTTATTT
637865 TACTAACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 17 0.89
13 2 0.11
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (13 bp):
ATTTATTTATATT
Found at i:649184 original size:29 final size:32
Alignment explanation
Indices: 649118--649194 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 32
649108 TTTATATAAC
649118 TATTATTATTACTATTTATTAACGTATGTATG
1 TATTATTATTACTATTTATTAACGTATGTATG
* *
649150 TA-TATT-TTA-TTTTTATTAACATTATG-AT-
1 TATTATTATTACTATTTATTAAC-GTATGTATG
649178 TATTATTATTACTATTT
1 TATTATTATTACTATTT
649195 TACTTTTAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
28 2 0.05
29 16 0.42
30 10 0.26
31 8 0.21
32 2 0.05
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.58
Consensus pattern (32 bp):
TATTATTATTACTATTTATTAACGTATGTATG
Found at i:649911 original size:23 final size:23
Alignment explanation
Indices: 649859--649917 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
649849 ACAATATGAA
* *
649859 AATAAATTAAAATAGCTTGTACC
1 AATAAATTAAAATAGCATGCACC
* *
649882 AAAAAATTAAAATAGCATGCACT
1 AATAAATTAAAATAGCATGCACC
*
649905 ATTAAATTTAAAA
1 AATAAA-TTAAAA
649918 AAATTTAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
23 23 0.79
24 6 0.21
ACGTcount: A:0.54, C:0.10, G:0.07, T:0.29
Consensus pattern (23 bp):
AATAAATTAAAATAGCATGCACC
Found at i:649927 original size:16 final size:17
Alignment explanation
Indices: 649906--649938 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
649896 GCATGCACTA
*
649906 TTAAATTTAA-AAAAAT
1 TTAAATTAAATAAAAAT
649922 TTAAATTAAATAAAAAT
1 TTAAATTAAATAAAAAT
649939 ATTCTTCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAATTAAATAAAAAT
Found at i:653665 original size:5 final size:5
Alignment explanation
Indices: 653655--653704 Score: 100
Period size: 5 Copynumber: 10.0 Consensus size: 5
653645 CTAATATCAT
653655 TAACC TAACC TAACC TAACC TAACC TAACC TAACC TAACC TAACC TAACC
1 TAACC TAACC TAACC TAACC TAACC TAACC TAACC TAACC TAACC TAACC
653705 CCAACTGCTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 45 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (5 bp):
TAACC
Found at i:657489 original size:21 final size:18
Alignment explanation
Indices: 657477--657514 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
657467 CCGGTTTCGG
657477 TTTGAAAAAAACCGGTTT
1 TTTGAAAAAAACCGGTTT
*
657495 TTTTAAAAAAACCGGTTT
1 TTTGAAAAAAACCGGTTT
657513 TT
1 TT
657515 AATCCGGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (18 bp):
TTTGAAAAAAACCGGTTT
Found at i:661342 original size:40 final size:39
Alignment explanation
Indices: 661283--661369 Score: 131
Period size: 40 Copynumber: 2.2 Consensus size: 39
661273 AAGAGAGAGC
661283 ATTTC-ATTTGTGTTGCGAAAGTGAAATTCGCAACGCGA
1 ATTTCAATTTGTGTTGCGAAAGTGAAATTCGCAACGCGA
* *
661321 ATTTCAATTGTGTGTTGCGAAATTGAAATTCGCAATGCGA
1 ATTTCAATT-TGTGTTGCGAAAGTGAAATTCGCAACGCGA
*
661361 ATTTTAATT
1 ATTTCAATT
661370 ATATGTTGTG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
38 5 0.11
39 3 0.07
40 36 0.82
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.37
Consensus pattern (39 bp):
ATTTCAATTTGTGTTGCGAAAGTGAAATTCGCAACGCGA
Found at i:662410 original size:20 final size:20
Alignment explanation
Indices: 662385--662502 Score: 148
Period size: 20 Copynumber: 5.8 Consensus size: 20
662375 CGCTACACAA
*
662385 ATTCGCGTTGCGAATTTCAT
1 ATTCGCGTTGCGAATTTCAG
**
662405 ATTCGCGTTGCGAAAATCAG
1 ATTCGCGTTGCGAATTTCAG
*
662425 ATCCGCGTTGCGAATTTCAG
1 ATTCGCGTTGCGAATTTCAG
*
662445 ATCCGCGTTGCGAATTTCAG
1 ATTCGCGTTGCGAATTTCAG
* *
662465 A-TCTGCGTTGTGAATTTACAT
1 ATTC-GCGTTGCGAATTT-CAG
662486 ATTCGCGTTGCGAATTT
1 ATTCGCGTTGCGAATTT
662503 GGAAAATCGC
Statistics
Matches: 85, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
19 1 0.01
20 67 0.79
21 15 0.18
22 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
ATTCGCGTTGCGAATTTCAG
Found at i:662512 original size:21 final size:21
Alignment explanation
Indices: 662488--662528 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
662478 ATTTACATAT
*
662488 TCGCGTTGCGAATTTGGAAAA
1 TCGCATTGCGAATTTGGAAAA
*
662509 TCGCATTGTGAATTTGGAAA
1 TCGCATTGCGAATTTGGAAA
662529 CTTTGTTGCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (21 bp):
TCGCATTGCGAATTTGGAAAA
Found at i:663099 original size:3 final size:3
Alignment explanation
Indices: 663091--663117 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
663081 CTATTGAGTT
663091 CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA
663118 AACCCAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:664540 original size:7 final size:7
Alignment explanation
Indices: 664528--664560 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
664518 AGTATCGTAT
664528 CATATAA
1 CATATAA
664535 CATATAA
1 CATATAA
664542 CATATAA
1 CATATAA
664549 CATATAA
1 CATATAA
*
664556 AATAT
1 CATAT
664561 CCAGTAGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (7 bp):
CATATAA
Found at i:669733 original size:45 final size:46
Alignment explanation
Indices: 669655--669742 Score: 133
Period size: 45 Copynumber: 1.9 Consensus size: 46
669645 AAAAAAACTG
* * *
669655 AGTGCATCGATGCATAGTCTTGTGCATCGATGCATCAAATGCACTA
1 AGTGCATCAATGCATAGTCATGTGCATCGATGCATAAAATGCACTA
*
669701 AGTGCATCAATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 AGTGCATCAATGCATAGTCATGTGCATCGATGCATAAAATGCA
669743 TTCGATGTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
45 22 0.58
46 16 0.42
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (46 bp):
AGTGCATCAATGCATAGTCATGTGCATCGATGCATAAAATGCACTA
Found at i:690608 original size:7 final size:7
Alignment explanation
Indices: 690598--690623 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
690588 AAGAAAAAGA
690598 AAAATGT
1 AAAATGT
690605 AAAATGT
1 AAAATGT
690612 AAAATGT
1 AAAATGT
690619 AAAAT
1 AAAAT
690624 ATACAGGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.27
Consensus pattern (7 bp):
AAAATGT
Found at i:695219 original size:20 final size:21
Alignment explanation
Indices: 695173--695233 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
695163 TTCCCCTGTG
695173 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
695196 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
695216 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
695234 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:702808 original size:19 final size:19
Alignment explanation
Indices: 702784--702841 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
702774 AAAAACAAAC
702784 AAACAAAAAAATATTAAAT
1 AAACAAAAAAATATTAAAT
702803 AAACAAAAGATAAT-TTAAAAT
1 AAACAAAA-A-AATATT-AAAT
* * *
702824 AAATAAGAAATTATTAAA
1 AAACAAAAAAATATTAAA
702842 ATAGGGGCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
19 13 0.41
20 6 0.19
21 13 0.41
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.24
Consensus pattern (19 bp):
AAACAAAAAAATATTAAAT
Found at i:704138 original size:22 final size:22
Alignment explanation
Indices: 704112--704166 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
704102 ATTATATAAC
704112 ATATATTATATTTTCAAAAACT
1 ATATATTATATTTTCAAAAACT
* * *
704134 ATATAATATGTTTTCAAAAATT
1 ATATATTATATTTTCAAAAACT
704156 ATATATTATAT
1 ATATATTATAT
704167 ATGTTTTCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.47
Consensus pattern (22 bp):
ATATATTATATTTTCAAAAACT
Found at i:704142 original size:27 final size:27
Alignment explanation
Indices: 704085--704139 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 27
704075 AATACGTACT
*
704085 ATATATTTATTTAAAAAATTATATAAC
1 ATATATTTATTTAAAAAACTATATAAC
*
704112 ATATATTATATTTTCAAAAACTATATAA
1 ATATATT-TA-TTTAAAAAACTATATAA
704140 TATGTTTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 7 0.29
28 2 0.08
29 15 0.62
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (27 bp):
ATATATTTATTTAAAAAACTATATAAC
Found at i:704200 original size:2 final size:2
Alignment explanation
Indices: 704193--704217 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
704183 TTTAAAACAC
704193 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
704218 TCAAAATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:704240 original size:45 final size:43
Alignment explanation
Indices: 704138--704249 Score: 112
Period size: 45 Copynumber: 2.7 Consensus size: 43
704128 AAAACTATAT
*
704138 AATATGTTTTCAAAA--AT-TATATAT-TATATATGTTTTCAA
1 AATATGTTTTCAAAACTATATATATATATATATATATTTTCAA
* *
704177 AA-ACCG-TTTAAAACACTATATATATATATATATATATATATTCAA
1 AATA-TGTTTTCAAA-ACTATATATATATATATATATAT-T-TTCAA
704222 AATATGTTTTCAAAACTATAT-TATATAT
1 AATATGTTTTCAAAACTATATATATATAT
704250 GTTTTCGAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
38 7 0.12
39 4 0.07
41 2 0.03
42 7 0.12
43 8 0.14
44 8 0.14
45 15 0.26
46 7 0.12
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.44
Consensus pattern (43 bp):
AATATGTTTTCAAAACTATATATATATATATATATATTTTCAA
Found at i:704305 original size:36 final size:36
Alignment explanation
Indices: 704234--704308 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
704224 TATGTTTTCA
** ** *
704234 AAACTATATTATATATGTTTTCGAAAACCCTTTTTT
1 AAACTATATTATATATGTTTTAAAAAAAACGTTTTT
704270 AAACTATA-TACTATATGTTTTAAAAAAAACGTTTTT
1 AAACTATATTA-TATATGTTTTAAAAAAAACGTTTTT
704306 AAA
1 AAA
704309 AAAACTATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
35 2 0.06
36 31 0.94
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (36 bp):
AAACTATATTATATATGTTTTAAAAAAAACGTTTTT
Done.