Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009330.1 Hibiscus syriacus cultivar Beakdansim tig00113096_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: 1820295
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:242676 original size:83 final size:83
Alignment explanation
Indices: 242382--243182 Score: 1325
Period size: 83 Copynumber: 9.6 Consensus size: 83
242372 CCTACCGAAT
* * *
242382 CAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATGAGTACATTGCATTTGTTCC-ATTT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT-CA--TCTTCCAATTT
* *
242446 TAAGGATTGGTTCTGCCAAAC
63 CAATGATTGGTTCTGCCAAAC
* *
242467 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGATCACATTCATCTTTCAATTTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATTTCAA
*
242532 TGATTTGATTCTGCCAAAC
66 TGA-TTGGTTCTGCCAAAC
* * *
242551 CAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCGTCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATTTCAA
*
242616 TGATTGGTTCTACCAAAC
66 TGATTGGTTCTGCCAAAC
* *
242634 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCGTCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATTTCAA
242699 TGATTGGTTCTGCCAAAC
66 TGATTGGTTCTGCCAAAC
* *
242717 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCGTCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATTTCAA
242782 TGATTGGTTCTGCCAAAC
66 TGATTGGTTCTGCCAAAC
*
242800 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAATTTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATTTCAA
* *
242865 TGATTTGATTTTGCCAAAC
66 TGA-TTGGTTCTGCCAAAC
*
242884 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAATTTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATTTCAA
*
242949 TGATTTGATTCTGCCAAAC
66 TGA-TTGGTTCTGCCAAAC
*
242968 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATTTCAA
243033 TGATTGGTTCTGCCAAAC
66 TGATTGGTTCTGCCAAAC
*
243051 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAATTTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATTTCAA
243116 TGATTGGTTCTGCCAAAC
66 TGATTGGTTCTGCCAAAC
*
243134 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGTACATT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
243183 GCATTTGTTC
Statistics
Matches: 683, Mismatches: 30, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
82 4 0.01
83 392 0.57
84 241 0.35
85 46 0.07
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATTTCAA
TGATTGGTTCTGCCAAAC
Found at i:244341 original size:6 final size:6
Alignment explanation
Indices: 244330--244398 Score: 78
Period size: 6 Copynumber: 12.5 Consensus size: 6
244320 TTGACCCCCC
244330 CTTTTT CTTTTT C-TTTT -TTTTT CTTTTT CTTTTT -TTTTT C--TTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
* *
244373 CTTTTT -TCTTT CTTCTT CTTTTT CTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTT
244399 CAAGCATAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
4 4 0.08
5 17 0.32
6 32 0.60
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
CTTTTT
Found at i:244346 original size:11 final size:11
Alignment explanation
Indices: 244330--244394 Score: 73
Period size: 11 Copynumber: 6.0 Consensus size: 11
244320 TTGACCCCCC
244330 CTTTTTCTTTTT
1 CTTTTTC-TTTT
244342 CTTTTT-TTTT
1 CTTTTTCTTTT
244352 CTTTTTCTTTT
1 CTTTTTCTTTT
*
244363 TTTTTTC-TTT
1 CTTTTTCTTTT
244373 CTTTTT-TCTTT
1 CTTTTTCT-TTT
*
244384 CTTCTTCTTTT
1 CTTTTTCTTTT
244395 TCTTCAAGCA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
10 18 0.39
11 21 0.46
12 7 0.15
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
CTTTTTCTTTT
Found at i:244352 original size:16 final size:16
Alignment explanation
Indices: 244331--244395 Score: 96
Period size: 16 Copynumber: 4.1 Consensus size: 16
244321 TGACCCCCCC
244331 TTTTTCTTTTTCTTTT
1 TTTTTCTTTTTCTTTT
244347 TTTTTCTTTTTCTTTT
1 TTTTTCTTTTTCTTTT
*
244363 TTTTT-TCTTTCTTTT
1 TTTTTCTTTTTCTTTT
*
244378 TTCTTTCTTCTTCTTTT
1 TT-TTTCTTTTTCTTTT
244395 T
1 T
244396 CTTCAAGCAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
15 11 0.25
16 24 0.55
17 9 0.20
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTTCTTTTTCTTTT
Found at i:248820 original size:167 final size:166
Alignment explanation
Indices: 248542--249342 Score: 1352
Period size: 167 Copynumber: 4.8 Consensus size: 166
248532 CCTACCGAAT
* * *
248542 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGGTACATTGCATTTGTTCC-ATTT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT-CA--TCTTCCAATTT
* *
248606 TAAGGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGC
63 CAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGC
* *
248671 ACATTCATCTTTCAATTTCAATGATTTGATTCTGCCAAAC
128 ACATTCATCTTCCAAATTCAATGA-TTGATTCTGCCAAAC
* * *
248711 CAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCGTCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATTTCAA
248776 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACA
66 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACA
* *
248841 TTCGTCTTCCAAATTCAATGATTGGTTCTGCCAAAC
131 TTCATCTTCCAAATTCAATGATTGATTCTGCCAAAC
* *
248877 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCGTCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATTTCAA
248942 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACA
66 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACA
* *
249007 TTCATCTTTCAATTTCAATGATTTGATTCTGCCAAAC
131 TTCATCTTCCAAATTCAATGA-TTGATTCTGCCAAAC
*
249044 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAATTTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATTTCAA
*
249109 TGATTTGATTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAC
66 TGA-TTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAC
*
249174 ATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAAC
130 ATTCATCTTCCAAATTCAATGATTGATTCTGCCAAAC
*
249211 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAATTTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATTTCAA
*
249276 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGTACA
66 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACA
249341 TT
131 TT
249343 GCATTTGTTC
Statistics
Matches: 601, Mismatches: 28, Indels: 9
0.94 0.04 0.01
Matches are distributed among these distances:
166 228 0.38
167 246 0.41
168 81 0.13
169 46 0.08
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (166 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATTTCAA
TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACA
TTCATCTTCCAAATTCAATGATTGATTCTGCCAAAC
Found at i:248835 original size:83 final size:83
Alignment explanation
Indices: 248542--249342 Score: 1352
Period size: 83 Copynumber: 9.6 Consensus size: 83
248532 CCTACCGAAT
* * *
248542 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGGTACATTGCATTTGTTCC-ATTT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT-CA--TCTTCCAATTT
* *
248606 TAAGGATTGGTTCTGCCAAAC
63 CAATGATTGGTTCTGCCAAAC
*
248627 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAATTTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATTTCAA
*
248692 TGATTTGATTCTGCCAAAC
66 TGA-TTGGTTCTGCCAAAC
* * *
248711 CAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCGTCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATTTCAA
248776 TGATTGGTTCTGCCAAAC
66 TGATTGGTTCTGCCAAAC
* *
248794 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCGTCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATTTCAA
248859 TGATTGGTTCTGCCAAAC
66 TGATTGGTTCTGCCAAAC
* *
248877 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCGTCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATTTCAA
248942 TGATTGGTTCTGCCAAAC
66 TGATTGGTTCTGCCAAAC
*
248960 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAATTTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATTTCAA
*
249025 TGATTTGATTCTGCCAAAC
66 TGA-TTGGTTCTGCCAAAC
*
249044 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAATTTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATTTCAA
*
249109 TGATTTGATTCTGCCAAAC
66 TGA-TTGGTTCTGCCAAAC
*
249128 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATTTCAA
249193 TGATTGGTTCTGCCAAAC
66 TGATTGGTTCTGCCAAAC
*
249211 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAATTTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATTTCAA
249276 TGATTGGTTCTGCCAAAC
66 TGATTGGTTCTGCCAAAC
*
249294 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGTACATT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
249343 GCATTTGTTC
Statistics
Matches: 689, Mismatches: 24, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
82 4 0.01
83 394 0.57
84 244 0.35
85 47 0.07
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATTTCAA
TGATTGGTTCTGCCAAAC
Found at i:250505 original size:11 final size:11
Alignment explanation
Indices: 250491--250544 Score: 56
Period size: 12 Copynumber: 4.7 Consensus size: 11
250481 TGACCCCCCC
250491 TTTTTC-TTTT
1 TTTTTCTTTTT
250501 TTTTTCTTTTTT
1 TTTTTC-TTTTT
250513 TTCTTTCTTTTT
1 TT-TTTCTTTTT
* *
250525 TCTTTCTTCTTC
1 TTTTTCTT-TTT
250537 TTTTTCTT
1 TTTTTCTT
250545 CAAGCATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
10 6 0.16
11 6 0.16
12 21 0.57
13 4 0.11
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:250506 original size:10 final size:10
Alignment explanation
Indices: 250491--250541 Score: 68
Period size: 10 Copynumber: 5.1 Consensus size: 10
250481 TGACCCCCCC
250491 TTTTTCTTTT
1 TTTTTCTTTT
250501 TTTTTC-TTT
1 TTTTTCTTTT
250510 TTTTTCTTTCT
1 TTTTTCTTT-T
*
250521 TTTTTCTTTC
1 TTTTTCTTTT
*
250531 TTCTTCTTTT
1 TTTTTCTTTT
250541 T
1 T
250542 CTTCAAGCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
9 9 0.25
10 17 0.47
11 10 0.28
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:261842 original size:17 final size:18
Alignment explanation
Indices: 261798--261842 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
261788 TTGATATTGA
*
261798 TAAAT-ATTAATTTAAAT
1 TAAATAATTATTTTAAAT
261815 TAAATAA-TATTTTAAA-
1 TAAATAATTATTTTAAAT
*
261831 TAATTAATTATT
1 TAAATAATTATT
261843 AAATTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 6 0.25
17 17 0.71
18 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAAATAATTATTTTAAAT
Found at i:263374 original size:21 final size:21
Alignment explanation
Indices: 263333--263376 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
263323 ATTGGGCTTG
* *
263333 TATATATTTTTTATTATTATT
1 TATATATTATTTAATATTATT
263354 TATATATGTATTTAATA-TATT
1 TATATAT-TATTTAATATTATT
263375 TA
1 TA
263377 ATAATAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TATATATTATTTAATATTATT
Found at i:263383 original size:3 final size:3
Alignment explanation
Indices: 263375--263458 Score: 159
Period size: 3 Copynumber: 28.0 Consensus size: 3
263365 TTAATATATT
*
263375 TAA TAA TAA TAA TAA TGA 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
263423 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
263459 ATCAATATGG
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:270018 original size:2 final size:2
Alignment explanation
Indices: 270011--270048 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
270001 TTATTAAATC
270011 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
270049 GGGTTAGGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:273431 original size:3 final size:3
Alignment explanation
Indices: 273425--273464 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
273415 ATAATAATAA
273425 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
273465 TAAGATAGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:275583 original size:94 final size:93
Alignment explanation
Indices: 275415--275590 Score: 205
Period size: 94 Copynumber: 1.9 Consensus size: 93
275405 TTATTTATTT
* * * *
275415 ATTTAAAAATATCAGAAAAGAACTTCTAGGTGCCTTAAGACGCTCTTTTCTTTGATATTGATAAA
1 ATTTAAAAATATCAGAAAAGAACATCTAGGTGCATTAAGACGCTCTTTTCTTCGATATTGAAAAA
*
275480 TATTAATTTAAATAATTATTTACTTTTTA
66 TAATAATTTAAA-AATTATTTACTTTTTA
* * * * *
275509 ATTTTAAAATATCAGAATAGGACATCTAGTTGTATTAAGACTG-TCCTTTTCTTCGATATT-AAA
1 ATTTAAAAATATCAGAAAAGAACATCTAGGTGCATTAAGAC-GCT-CTTTTCTTCGATATTGAAA
275572 AATAA-ATATTTAAAAATTA
64 AATAATA-ATTTAAAAATTA
275591 CTATTTATTA
Statistics
Matches: 69, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
93 6 0.09
94 48 0.70
95 15 0.22
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (93 bp):
ATTTAAAAATATCAGAAAAGAACATCTAGGTGCATTAAGACGCTCTTTTCTTCGATATTGAAAAA
TAATAATTTAAAAATTATTTACTTTTTA
Found at i:277077 original size:3 final size:3
Alignment explanation
Indices: 277069--277178 Score: 195
Period size: 3 Copynumber: 36.7 Consensus size: 3
277059 TTTATATATT
277069 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
*
277117 TAA TAGA TAA TAG TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
277162 TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
277179 TGGATAAAAA
Statistics
Matches: 103, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
2 2 0.02
3 98 0.95
4 3 0.03
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:277744 original size:113 final size:113
Alignment explanation
Indices: 277497--277906 Score: 716
Period size: 113 Copynumber: 3.6 Consensus size: 113
277487 GAATTATGCC
* * *
277497 AAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
277561 TATGAAC-TTCTCCGGAAAAGATAATCCATCAATTGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
277608 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
277673 TATGAACTTTTTCTGGAAAAGGTGATCCATTAAGTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
277721 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
277786 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
277834 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
277899 TATGAACT
66 TATGAACT
277907 CGAACTGGAA
Statistics
Matches: 284, Mismatches: 13, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
111 4 0.01
112 64 0.23
113 216 0.76
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
Found at i:278706 original size:84 final size:84
Alignment explanation
Indices: 278608--279462 Score: 1622
Period size: 84 Copynumber: 10.2 Consensus size: 84
278598 TTCATCTTTT
* * *
278608 AATTCCAACGATTGGTTCTGTCC-AACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 AATT-CAATGATTGGTTCTG-CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
278672 ATTGAGCAAATTCATCTTCCA
64 ATTGAGCAAATTCATCTTCCA
278693 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
278758 TGAGCAAATTCATCTTCCA
66 TGAGCAAATTCATCTTCCA
278777 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
278842 TGAGCAAATTCATCTTCCA
66 TGAGCAAATTCATCTTCCA
278861 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
278926 TGAGCAAATTCATCTTCCA
66 TGAGCAAATTCATCTTCCA
* *
278945 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACACAAAGAACACTTCCAGAAGATGTTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
279010 TGAGCAAATTCATCTTCCA
66 TGAGCAAATTCATCTTCCA
279029 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
279094 TGAGCAAATTCATCTTCCA
66 TGAGCAAATTCATCTTCCA
*
279113 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACACAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
279178 TGAGCAAATTCATCTTCCA
66 TGAGCAAATTCATCTTCCA
279197 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
279262 TGAGCAAATTCATCTTCCA
66 TGAGCAAATTCATCTTCCA
*
279281 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
279346 TGAGCAAATTCATCTTCCA
66 TGAGCAAATTCATCTTCCA
279365 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
279430 TGAGCAAATTCATCTTCCA
66 TGAGCAAATTCATCTTCCA
279449 AATTCAATGATTGG
1 AATTCAATGATTGG
279463 ACTAAGATAT
Statistics
Matches: 758, Mismatches: 11, Indels: 3
0.98 0.01 0.00
Matches are distributed among these distances:
83 2 0.00
84 752 0.99
85 4 0.01
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.27
Consensus pattern (84 bp):
AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
TGAGCAAATTCATCTTCCA
Found at i:280626 original size:17 final size:18
Alignment explanation
Indices: 280588--280626 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
280578 TTTCTTTTTC
* *
280588 TTCTCTTTTTTTTTCATT
1 TTCTATTTTTTTTTCATA
280606 TTCTATTTTTTTTTC-TA
1 TTCTATTTTTTTTTCATA
280623 TTCT
1 TTCT
280627 CTTCAAGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (18 bp):
TTCTATTTTTTTTTCATA
Found at i:291250 original size:13 final size:15
Alignment explanation
Indices: 291228--291264 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
291218 TTTGACAGAA
291228 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
291240 AAATAAAATACTTGC
1 AAATAAAATACTTGC
291255 AAATAAAATA
1 AAATAAAATA
291265 AAACATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 2 0.09
15 10 0.45
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAAATACTTGC
Found at i:291303 original size:18 final size:17
Alignment explanation
Indices: 291255--291305 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
291245 AAATACTTGC
*
291255 AAATAAAATAAAACATAT
1 AAAT-AAATAAAAAATAT
*
291273 AAAT-ATTATAAAAATAAT
1 AAATAAATA-AAAAAT-AT
291291 AAATAAATAAAAAAT
1 AAATAAATAAAAAAT
291306 TTGAATAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 3 0.11
17 5 0.19
18 16 0.59
19 3 0.11
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATAAATAAAAAATAT
Found at i:293476 original size:20 final size:19
Alignment explanation
Indices: 293453--293497 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
293443 TATTTTTTAT
* *
293453 TATTTATTTATTTTTAATAA
1 TATTTATATATATTTAAT-A
*
293473 TATTTATATGTATTTAATA
1 TATTTATATATATTTAATA
293492 TATTTA
1 TATTTA
293498 ATAATAATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TATTTATATATATTTAATA
Found at i:293487 original size:26 final size:30
Alignment explanation
Indices: 293448--293503 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
293438 AATTATATTT
*
293448 TTTATTATTTATTT-AT-T-TTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
293475 TTTA-TATGTATTTAATATATTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
293504 ATAGTAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 8 0.32
27 6 0.24
28 1 0.04
29 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (30 bp):
TTTATTATGTATTTAATATATTTAATAATA
Found at i:293504 original size:3 final size:3
Alignment explanation
Indices: 293496--293622 Score: 220
Period size: 3 Copynumber: 42.7 Consensus size: 3
293486 TTAATATATT
*
293496 TAA TAA TAA TAG 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
*
293544 TAA TAA TAA TAA TAA TAA T-A TAA TAG TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
293591 TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
293623 TGGATAAAAA
Statistics
Matches: 117, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
2 2 0.02
3 115 0.98
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:296980 original size:22 final size:21
Alignment explanation
Indices: 296955--296995 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
296945 TAAAAAATAA
296955 AATAAAAATACCAAAAACATTT
1 AATAAAAA-ACCAAAAACATTT
*
296977 AATAAAAAACTAAAAACAT
1 AATAAAAAACCAAAAACAT
296996 CCCCACAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.20
Consensus pattern (21 bp):
AATAAAAAACCAAAAACATTT
Found at i:297203 original size:15 final size:15
Alignment explanation
Indices: 297153--297201 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
297143 TAAGAATAAA
* *
297153 GAAAACTAAAAAGCT
1 GAAAACGAAAAGGCT
297168 GAAAACGAAAAGGCT
1 GAAAACGAAAAGGCT
*
297183 GTAAACGAAAAGGC-
1 GAAAACGAAAAGGCT
297197 GAAAA
1 GAAAA
297202 ACAGTTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 4 0.13
15 26 0.87
ACGTcount: A:0.57, C:0.12, G:0.22, T:0.08
Consensus pattern (15 bp):
GAAAACGAAAAGGCT
Found at i:298812 original size:124 final size:126
Alignment explanation
Indices: 298496--298821 Score: 350
Period size: 124 Copynumber: 2.6 Consensus size: 126
298486 ATAATTCTAA
* * * *
298496 GAGAGAAAATGATAATATATAATTATTTCCGATCGAGAATAAATGACCTCTCATGCCTCAAAGCA
1 GAGAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACATCTCATGCCTTAAAGCA
* * * * * *
298561 ATCATTTATTACTTCAATCGAATTAAAGATATATTACTATTTCGTCTTAAAATTCAATATCAATT
66 ATC----ATTAC-TCAATCAAAATAAAGAGATATCACTATTTCGTCTTAAAAATCAATATCAACT
*
298626 T
126 C
* * * * * * *
298627 GAGTGAAAACGATAATATCTAATGATTTCCAATCGAGATTAAATGACATCTTATACCTTAAAACA
1 GAGAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACATCTCATGCCTTAAAGCA
* * * **
298692 ATCATT-C-CAATCAAAATGAAGAGATATCCCTATTTTGTCTTAAAAATCAATATTGACTC
66 ATCATTACTCAATCAAAATAAAGAGATATCACTATTTCGTCTTAAAAATCAATATCAACTC
* * *
298751 GAGAGAAAATGAAAATATCTAATTATTTCCAATCGAGAATAAATGACTTCTCATGCTTTAAAGCA
1 GAGAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACATCTCATGCCTTAAAGCA
*
298816 GTCATT
66 ATCATT
298822 TATTACCCCA
Statistics
Matches: 161, Mismatches: 34, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
124 100 0.62
126 1 0.01
127 3 0.02
131 57 0.35
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (126 bp):
GAGAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACATCTCATGCCTTAAAGCA
ATCATTACTCAATCAAAATAAAGAGATATCACTATTTCGTCTTAAAAATCAATATCAACTC
Found at i:302010 original size:130 final size:130
Alignment explanation
Indices: 301706--302072 Score: 407
Period size: 130 Copynumber: 2.8 Consensus size: 130
301696 ATAATTCTAA
* * * * * *
301706 GAGAGAAAATGATAATATCTAATTGTTTCCGATCAAGAATAAATAACATCTCATGCCTCAAAACA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCAAGAATAAATGACCTCTCATGCCTTAAAACA
* * * ** *
301771 ATCATTTACTACTCCAATTGAAATAAAGAGA-AACTACTATTTTGTCTTAAAATTCAATATCAAT
66 ATCATTTATTACTCCAATCGAAAT-AAGAGATATC-ACTATTCCGTCTTAAAATTCAATATCAAC
301835 TC
129 TC
* * ** ** *
301837 GAGTGAAAACGATAATATCTAATGATTTCCAATTGAGGTTAAATGACCTCTCATACCTTAAAGA-
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCAAGAATAAATGACCTCTCATGCCTTAAA-AC
* * * * *
301901 ATTCATTTATTGCTCTAATCGAAATGAAGAGATATCCCTATTCCGTCTTAAAA-TCAATATCGAC
65 AATCATTTATTACTCCAATCGAAAT-AAGAGATATCACTATTCCGTCTTAAAATTCAATATCAAC
301965 TC
129 TC
* * *
301967 GAGAGAAAACAATAATATCTAATTATTTCCAATCAAGAATAAATGATCTCTCATGCTTTAAAACA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCAAGAATAAATGACCTCTCATGCCTTAAAACA
* *
302032 ATCATTTATTACCCCAACCGAAACTAAGAGATATCACTATT
66 ATCATTTATTACTCCAATCGAAA-TAAGAGATATCACTATT
302073 TTCAATATTT
Statistics
Matches: 191, Mismatches: 41, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
129 1 0.01
130 97 0.51
131 90 0.47
132 3 0.02
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (130 bp):
GAGAGAAAACGATAATATCTAATTATTTCCAATCAAGAATAAATGACCTCTCATGCCTTAAAACA
ATCATTTATTACTCCAATCGAAATAAGAGATATCACTATTCCGTCTTAAAATTCAATATCAACTC
Found at i:304356 original size:135 final size:136
Alignment explanation
Indices: 304099--304680 Score: 659
Period size: 135 Copynumber: 4.3 Consensus size: 136
304089 ATCATATCGA
* * * * * * *
304099 GAAACATTGATTCATTCCACTGTTCTACAAGGAAGATTGAATTGAGGCAGACTTGTTTCATTGTT
1 GAAACGTTGATTCATTCCATTGTTCTTCAGGGAAGATTGAATCGAGACAGACTTGTTTCACTGTT
* * * ** * *
304164 ACTCAGGGAAGATCCAATCTGGAAAAAAGAAGGAT-TCGTTCCACTACTTCTTGAGGAAAAATCA
66 CCTCAGGGAAGATCAAATCTGGAAAAAAGAGGGATCT-GTTCTGCTACTTTTTCAGGAAAAATCA
*
304228 TAT-TAG
130 GATCTAG
* * * * * *
304234 GAAATGTTGATTTATTCCACTGTTCTTCAGGGAAGATTGAATCAAGACATACTTGTTCCACTGTT
1 GAAACGTTGATTCATTCCATTGTTCTTCAGGGAAGATTGAATCGAGACAGACTTGTTTCACTGTT
*
304299 CCTCAGGGAAGATCAAATCT-GAAAAAAGAGGGATCTGTTCTGCTACTTCTTTAAGG-AAAATCA
66 CCTCAGGGAAGATCAAATCTGGAAAAAAGAGGGATCTGTTCTGCTACTT-TTTCAGGAAAAATCA
304362 GATCTA-
130 GATCTAG
* *
304368 GAAACGTTGATTCGTTCCATTGTTCTTCAGGGATGATTGAATCGAGACAGACTTGTTTCACTGTT
1 GAAACGTTGATTCATTCCATTGTTCTTCAGGGAAGATTGAATCGAGACAGACTTGTTTCACTGTT
* * * * * *
304433 CCTCAGGGAAGATCAAATCTAG-AAAAA-A-GGATCTATTATGCTGCTTATTCA-GAGAAAATTA
66 CCTCAGGGAAGATCAAATCTGGAAAAAAGAGGGATCTGTTCTGCTACTTTTTCAGGA-AAAATCA
304494 GATCT-G
130 GATCTAG
* * * *
304500 GAAACGTTGATTCATTCCATTATTCTTCAGGGAATATTGAATCGAGATAGACTTGTTTCATTGTT
1 GAAACGTTGATTCATTCCATTGTTCTTCAGGGAAGATTGAATCGAGACAGACTTGTTTCACTGTT
* * *
304565 CCTTAGGGAAGATTAAATCTGGAAAAAAGAGGGATCTGTTCTGCTGA-TTTTTCAGGGAAAATCA
66 CCTCAGGGAAGATCAAATCTGGAAAAAAGAGGGATCTGTTCTGCT-ACTTTTTCAGGAAAAATCA
304629 G-T-TATG
130 GATCTA-G
* * * *
304635 GAAACATTGATTCATTCCATTATTCTTCAGGAAATATTGAATCGAG
1 GAAACGTTGATTCATTCCATTGTTCTTCAGGGAAGATTGAATCGAG
304681 TTCAATTTGC
Statistics
Matches: 383, Mismatches: 50, Indels: 28
0.83 0.11 0.06
Matches are distributed among these distances:
130 1 0.00
131 3 0.01
132 104 0.27
133 7 0.02
134 116 0.30
135 151 0.39
136 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Consensus pattern (136 bp):
GAAACGTTGATTCATTCCATTGTTCTTCAGGGAAGATTGAATCGAGACAGACTTGTTTCACTGTT
CCTCAGGGAAGATCAAATCTGGAAAAAAGAGGGATCTGTTCTGCTACTTTTTCAGGAAAAATCAG
ATCTAG
Found at i:324603 original size:131 final size:131
Alignment explanation
Indices: 324256--324622 Score: 438
Period size: 131 Copynumber: 2.8 Consensus size: 131
324246 TAATTCTTGG
* * *
324256 AGAGAAAATAATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTCAAAGCAG
1 AGAGAAAATGATAATATCTAATTATTTTCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAG
* *
324321 TCATTTATTACTCTAATCG-AATGAAGAGATATTACTATTTCATCTTAAAATTCAATATCAATTC
66 TCATTTATTACTCTAATCGAAATGAAGAGATATCACTATTTCATCTTAAAATTCAATATCAACTC
*
324385 G
131 C
* * * * * * *
324386 AGTGAAAATGATAATATCTAATGA-TTTCTAATAGAGATTAAATGACCACTCATACCTTAAAGTA
1 AGAGAAAATGATAATATCTAATTATTTTC-AATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * * * * **
324450 GTCATTTATTGCTCCAATCGAAATGAAAAGATATCCCTATTAT-GTCTTAAAAATT-AATATTGA
65 GTCATTTATTACTCTAATCGAAATGAAGAGATATCACTATT-TCATCTT-AAAATTCAATATCAA
324513 CTCC
128 CTCC
* * *
324517 AGAGAAAACGATAATATCTAATTATTTTCAATCGAGAATAAATTACCTCTCATGCTTTAAAGCAG
1 AGAGAAAATGATAATATCTAATTATTTTCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAG
* *
324582 TCATTTATTAC-CATAACCGAAACGAAGAGATATCACTATTT
66 TCATTTATTACTC-TAATCGAAATGAAGAGATATCACTATTT
324623 TCAATATTTA
Statistics
Matches: 195, Mismatches: 36, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
129 3 0.02
130 70 0.36
131 111 0.57
132 11 0.06
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (131 bp):
AGAGAAAATGATAATATCTAATTATTTTCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAG
TCATTTATTACTCTAATCGAAATGAAGAGATATCACTATTTCATCTTAAAATTCAATATCAACTC
C
Found at i:337910 original size:15 final size:15
Alignment explanation
Indices: 337890--337920 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
337880 ATGGACCCTT
337890 TAATGGAGGCAGTGG
1 TAATGGAGGCAGTGG
337905 TAATGGAGGCAGTGG
1 TAATGGAGGCAGTGG
337920 T
1 T
337921 GGGTTGAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.45, T:0.23
Consensus pattern (15 bp):
TAATGGAGGCAGTGG
Found at i:338857 original size:112 final size:112
Alignment explanation
Indices: 338655--339079 Score: 688
Period size: 112 Copynumber: 3.8 Consensus size: 112
338645 ACTTTTTTAC
* ** * * *
338655 TACCGGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
1 TACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGA
*
338720 TACATTTTTATAAAGTATTGACACTTTCAATATATCCGGTAGCGCTT
66 TACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTT
* *
338767 TACATGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACTTGTTATATTGTTATGGATCGA
1 TACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGA
* *
338832 TACATTTTTATAAAATATCGACACTTTCAATATATCCGGTAGTGCTT
66 TACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTT
* *
338879 TACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATAGG
1 TACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGA
* *
338944 TACATTTTTATAAAGTATCGATACTTTCAATATATCCGATAGCGCTT
66 TACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTT
* *
338991 TACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACTTGTTATATTGTTATGGATCAA
1 TACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGA
*
339056 TATATTTTTATAAAGTATCGACAC
66 TACATTTTTATAAAGTATCGACAC
339080 AAACCGACAA
Statistics
Matches: 288, Mismatches: 25, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
112 288 1.00
ACGTcount: A:0.24, C:0.14, G:0.15, T:0.47
Consensus pattern (112 bp):
TACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGA
TACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTT
Found at i:339511 original size:21 final size:21
Alignment explanation
Indices: 339468--339632 Score: 112
Period size: 21 Copynumber: 7.9 Consensus size: 21
339458 ACTTCGACTA
*
339468 TCGCATTGCGAT-TTCCATA-T
1 TCGCATTGCGATAGTCCA-AGT
339488 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
339509 TCGCGTTGCGATTTATTCCAAGT
1 TCGCATTGCGA--TAGTCCAAGT
*
339532 TCG--TTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
* * *
339551 TCGCGTTGCGATTTATTCCAAAT
1 TCGCATTGCGA--TAGTCCAAGT
* *
339574 T--CACTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
339593 TCGCGTTGCGATTTATTCCAAGT
1 TCGCATTGCGA--TAGTCCAAGT
339616 TCG--TTGCGATAGTCCAA
1 TCGCATTGCGATAGTCCAA
339633 AATCGCAACG
Statistics
Matches: 115, Mismatches: 18, Indels: 25
0.73 0.11 0.16
Matches are distributed among these distances:
19 26 0.23
20 13 0.11
21 45 0.39
23 31 0.27
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:339543 original size:42 final size:42
Alignment explanation
Indices: 339493--339632 Score: 235
Period size: 42 Copynumber: 3.3 Consensus size: 42
339483 CATATTCGCA
339493 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
* * *
339535 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCA
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
* *
339577 CTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
339619 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
339633 AATCGCAACG
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 90 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
Found at i:339729 original size:6 final size:6
Alignment explanation
Indices: 339718--339750 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
339708 GACACGTATT
339718 ACCACG ACCACG ACCACG ACCACG ACC-CG ACCA
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCA
339751 GAGACGAGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:340250 original size:6 final size:6
Alignment explanation
Indices: 340241--340280 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
340231 GTCCGTCTCG
340241 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
340281 ATACATGTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:340408 original size:20 final size:20
Alignment explanation
Indices: 340377--340531 Score: 147
Period size: 20 Copynumber: 7.6 Consensus size: 20
340367 TTTTGGACTA
*
340377 TCGCAATGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
* *
340397 TCTCATTGCGATAGT-CGACTA-
1 TCGCATTGCGAT-TTAC-A-TAT
*
340418 TCGTATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
340438 TCGCATTGCGATAGT-CGACTA-
1 TCGCATTGCGAT-TTAC-A-TAT
340459 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
* * *
340479 TCGCATTGCGATAGTCCAAAT
1 TCGCATTGCGAT-TTACATAT
340500 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
340520 TCGCATTGCGAT
1 TCGCATTGCGAT
340532 AGTCCAAGTT
Statistics
Matches: 109, Mismatches: 15, Indels: 22
0.75 0.10 0.15
Matches are distributed among these distances:
19 4 0.04
20 56 0.51
21 45 0.41
22 4 0.04
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.35
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:340417 original size:41 final size:41
Alignment explanation
Indices: 340372--340535 Score: 267
Period size: 41 Copynumber: 4.0 Consensus size: 41
340362 TGTGATTTTG
* *
340372 GACTATCGCAATGCGATTTACATATTCTCATTGCGATAGTC
1 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTC
*
340413 GACTATCGTATTGCGATTTACATATTCGCATTGCGATAGTC
1 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTC
340454 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTC
1 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTC
* *
340495 CA-AATTCGCATTGCGATTTACATATTCGCATTGCGATAGTC
1 GACTA-TCGCATTGCGATTTACATATTCGCATTGCGATAGTC
340536 CAAGTTCGCA
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
40 1 0.01
41 115 0.99
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (41 bp):
GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTC
Found at i:340503 original size:62 final size:65
Alignment explanation
Indices: 340391--340577 Score: 185
Period size: 62 Copynumber: 3.0 Consensus size: 65
340381 AATGCGATTT
* * * * * * *
340391 ACATATTCTCATTGCGATAGT-CGACTATCGTATTGCGAT-TTACATATTCGCATTGCGATAGTC
1 ACATATTCGCATTGCGATAGTACAAGT-TCGCATTGCGATAGTCCAAATTCGCATTGCGATAGTC
340454 G
65 G
*
340455 AC-TA-TCGCATTGCGAT-TTACATA-TTCGCATTGCGATAGTCCAAATTCGCATTGCGAT--T-
1 ACATATTCGCATTGCGATAGTACA-AGTTCGCATTGCGATAGTCCAAATTCGCATTGCGATAGTC
*
340513 T
65 G
* * *
340514 ACATATTCGCATTGCGATAGTCCAAGTTCGCATTGTGATAGTCCAAGTTCGCATTGCGATAGTC
1 ACATATTCGCATTGCGATAGTACAAGTTCGCATTGCGATAGTCCAAATTCGCATTGCGATAGTC
340578 AAAGTTCGTG
Statistics
Matches: 101, Mismatches: 12, Indels: 19
0.77 0.09 0.14
Matches are distributed among these distances:
59 2 0.02
60 3 0.03
61 25 0.25
62 65 0.64
63 3 0.03
64 3 0.03
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.34
Consensus pattern (65 bp):
ACATATTCGCATTGCGATAGTACAAGTTCGCATTGCGATAGTCCAAATTCGCATTGCGATAGTCG
Found at i:340536 original size:41 final size:40
Alignment explanation
Indices: 340377--340585 Score: 249
Period size: 41 Copynumber: 5.1 Consensus size: 40
340367 TTTTGGACTA
* * * *
340377 TCGCAATGCGATTTACATATTCTCATTGCGATAGTCGACT
1 TCGCATTGCGATTTACATATTCGCATTGCGATAGTCAAAT
* * *
340417 ATCGTATTGCGATTTACATATTCGCATTGCGATAGTCGACT
1 -TCGCATTGCGATTTACATATTCGCATTGCGATAGTCAAAT
340458 ATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAAT
1 -TCGCATTGCGATTTACATATTCGCATTGCGATAGT-CAAAT
*
340500 TCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATTTACATATTCGCATTGCGATAGT-CAAAT
* * *
340541 TCGCATTGTGATAGTCCA-AGTTCGCATTGCGATAGTCAAAGT
1 TCGCATTGCGAT-TTACATA-TTCGCATTGCGATAGTCAAA-T
340583 TCG
1 TCG
340586 TGTTGCGAAT
Statistics
Matches: 153, Mismatches: 11, Indels: 7
0.89 0.06 0.04
Matches are distributed among these distances:
41 127 0.83
42 26 0.17
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (40 bp):
TCGCATTGCGATTTACATATTCGCATTGCGATAGTCAAAT
Found at i:340582 original size:21 final size:20
Alignment explanation
Indices: 340395--340585 Score: 145
Period size: 21 Copynumber: 9.2 Consensus size: 20
340385 CGATTTACAT
* *
340395 ATTCTCATTGCGATAGTCGA
1 ATTCGCATTGCGATAGTCAA
* * * *
340415 CTATCGTATTGCGAT-TTACAT
1 AT-TCGCATTGCGATAGT-CAA
*
340436 ATTCGCATTGCGATAGTCGA
1 ATTCGCATTGCGATAGTCAA
* * *
340456 CTATCGCATTGCGAT-TTACAT
1 AT-TCGCATTGCGATAGT-CAA
340477 ATTCGCATTGCGATAGTCCAA
1 ATTCGCATTGCGATAGT-CAA
* *
340498 ATTCGCATTGCGAT-TTACAT
1 ATTCGCATTGCGATAGT-CAA
340518 ATTCGCATTGCGATAGTCCAA
1 ATTCGCATTGCGATAGT-CAA
* *
340539 GTTCGCATTGTGATAGTCCAA
1 ATTCGCATTGCGATAGT-CAA
*
340560 GTTCGCATTGCGATAGTCAA
1 ATTCGCATTGCGATAGTCAA
340580 AGTTCG
1 A-TTCG
340586 TGTTGCGAAT
Statistics
Matches: 134, Mismatches: 29, Indels: 15
0.75 0.16 0.08
Matches are distributed among these distances:
20 48 0.36
21 86 0.64
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (20 bp):
ATTCGCATTGCGATAGTCAA
Found at i:340593 original size:21 final size:21
Alignment explanation
Indices: 340437--340585 Score: 155
Period size: 21 Copynumber: 7.2 Consensus size: 21
340427 GATTTACATA
* *
340437 TTCGCATTGCGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
* *
340457 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
*
340478 TTCGCATTGCGATAGTCCAAA
1 TTCGCATTGCGATAGTCCAAG
* *
340499 TTCGCATTGCGAT-TTACATA-
1 TTCGCATTGCGATAGTCCA-AG
340519 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
340540 TTCGCATTGTGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
340561 TTCGCATTGCGATAGTCAAAG
1 TTCGCATTGCGATAGTCCAAG
340582 TTCG
1 TTCG
340586 TGTTGCGAAT
Statistics
Matches: 110, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
20 32 0.29
21 77 0.70
22 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:343494 original size:6 final size:6
Alignment explanation
Indices: 343485--343523 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
343475 GGAAAAATGT
*
343485 AAATAA AAATAA AAATAA AAATAA ATAGAGAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA A-A-ATAA AAATAA A
343524 TAAATAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 23 0.79
7 2 0.07
8 4 0.14
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:343520 original size:14 final size:13
Alignment explanation
Indices: 343489--343549 Score: 56
Period size: 13 Copynumber: 4.7 Consensus size: 13
343479 AAATGTAAAT
*
343489 AAAAATAAA-AAT
1 AAAAATAAATAAG
343501 AAAAATAAATAGAG
1 AAAAATAAATA-AG
343515 AAAAATAAATAA-
1 AAAAATAAATAAG
*
343527 ATAAAATAGATAA-
1 A-AAAATAAATAAG
343540 AATAAATAAA
1 AA-AAATAAA
343550 ACAAATGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
12 11 0.26
13 19 0.45
14 12 0.29
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (13 bp):
AAAAATAAATAAG
Found at i:343539 original size:9 final size:9
Alignment explanation
Indices: 343485--343555 Score: 60
Period size: 9 Copynumber: 7.9 Consensus size: 9
343475 GGAAAAATGT
343485 AAATAAA-A
1 AAATAAATA
343493 ATAA-AAATAA
1 A-AATAAAT-A
343503 AAATAAATA
1 AAATAAATA
343512 GAGAA-AAAT-
1 -A-AATAAATA
343521 AAATAAATA
1 AAATAAATA
*
343530 AAATAGATA
1 AAATAAATA
343539 AAATAAATA
1 AAATAAATA
*
343548 AAACAAAT
1 AAATAAAT
343556 GAAAGTAATA
Statistics
Matches: 52, Mismatches: 3, Indels: 15
0.74 0.04 0.21
Matches are distributed among these distances:
7 2 0.04
8 9 0.17
9 28 0.54
10 11 0.21
11 2 0.04
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.18
Consensus pattern (9 bp):
AAATAAATA
Found at i:343541 original size:22 final size:23
Alignment explanation
Indices: 343497--343555 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
343487 ATAAAAATAA
343497 AAATAAAAATAAATAGAGAAAAAT
1 AAAT-AAAATAAATAGAGAAAAAT
*
343521 AAAT-AAATAAAATAGA-TAAAAT
1 AAATAAAAT-AAATAGAGAAAAAT
*
343543 AAATAAAACAAAT
1 AAATAAAATAAAT
343556 GAAAGTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
22 17 0.55
23 10 0.32
24 4 0.13
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.19
Consensus pattern (23 bp):
AAATAAAATAAATAGAGAAAAAT
Found at i:343656 original size:9 final size:9
Alignment explanation
Indices: 343599--343814 Score: 71
Period size: 9 Copynumber: 23.8 Consensus size: 9
343589 ACAACAAGAA
343599 AATAAAAAT
1 AATAAAAAT
343608 AAGT--AAAT
1 AA-TAAAAAT
*
343616 AA-ATAAAT
1 AATAAAAAT
343624 AA-AGAAAAT
1 AATA-AAAAT
343633 -ATAAAGAA-
1 AATAAA-AAT
343641 AAT-AAAAT
1 AATAAAAAT
343649 AATAAAAAT
1 AATAAAAAT
* *
343658 AATATATAT
1 AATAAAAAT
343667 ATATACAAAAT
1 A-ATA-AAAAT
343678 AA-AAGAAAT
1 AATAA-AAAT
343687 GAA-AAAAAT
1 -AATAAAAAT
343696 -ATCAAAACAT
1 AAT-AAAA-AT
*
343706 -ATAAAGAT
1 AATAAAAAT
* ** *
343714 GATGTTATAT
1 AAT-AAAAAT
*
343724 AAAAACAAAT
1 AATAA-AAAT
343734 AATATACCAAAT
1 AATA-A--AAAT
*
343746 AATAATAAT
1 AATAAAAAT
*
343755 AATAATAAT
1 AATAAAAAT
*
343764 -ATAATAAT
1 AATAAAAAT
*
343772 AATAATAAT
1 AATAAAAAT
343781 -ATAATAAAT
1 AATAA-AAAT
*
343790 AATAATAAT
1 AATAAAAAT
*
343799 AATAATAAT
1 AATAAAAAT
343808 AATAAAA
1 AATAAAA
343815 CAAAAAAATC
Statistics
Matches: 164, Mismatches: 19, Indels: 48
0.71 0.08 0.21
Matches are distributed among these distances:
7 3 0.02
8 36 0.22
9 83 0.51
10 27 0.16
11 6 0.04
12 9 0.05
ACGTcount: A:0.68, C:0.03, G:0.04, T:0.26
Consensus pattern (9 bp):
AATAAAAAT
Found at i:343749 original size:3 final size:3
Alignment explanation
Indices: 343743--343812 Score: 117
Period size: 3 Copynumber: 23.7 Consensus size: 3
343733 TAATATACCA
343743 AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT -AT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
343790 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
343813 AACAAAAAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.06
3 57 0.89
4 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:344040 original size:22 final size:22
Alignment explanation
Indices: 344012--344056 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
344002 AAGATATATA
344012 AAAAAGATTAAAATAAAAAAAT
1 AAAAAGATTAAAATAAAAAAAT
*
344034 AAAAAGATTAAAATAAAATAAT
1 AAAAAGATTAAAATAAAAAAAT
344056 A
1 A
344057 TATATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (22 bp):
AAAAAGATTAAAATAAAAAAAT
Found at i:344061 original size:2 final size:2
Alignment explanation
Indices: 344054--344084 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
344044 AAATAAAATA
344054 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 A
344085 ATGTATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:344574 original size:20 final size:21
Alignment explanation
Indices: 344551--344592 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
344541 CGAAAGCTTT
*
344551 TCAAAAC-ACTTTTTTAAAAA
1 TCAAAACGAATTTTTTAAAAA
*
344571 TCAAAGCGAATTTTTTAAAAA
1 TCAAAACGAATTTTTTAAAAA
344592 T
1 T
344593 ATAAACCTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.36
Consensus pattern (21 bp):
TCAAAACGAATTTTTTAAAAA
Found at i:345101 original size:2 final size:2
Alignment explanation
Indices: 345094--345122 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
345084 TGAAATAATG
345094 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 A
345123 ATTATAATTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:346065 original size:110 final size:110
Alignment explanation
Indices: 345910--346113 Score: 318
Period size: 110 Copynumber: 1.9 Consensus size: 110
345900 TGTGAAATTA
* * * *
345910 TTTGTTGACAGCCAGCCGCCCCTTCGCTGTGAAGTTGAGTTTGTGTTGTCTCGAGTCCAATATCC
1 TTTGTTGACAACCAGCCGCCCATTCACTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCC
345975 TTCGTTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTG
66 TTCGTTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTG
* * * * *
346020 TTTGTTGACAATCAGTCGCCCATTCATTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATCT
1 TTTGTTGACAACCAGCCGCCCATTCACTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCC
*
346085 TTCGTTGTGAAGTTGAAATTGACTCTGAA
66 TTCGTTGTGAAGTTAAAATTGACTCTGAA
346114 ATTGGGAAGC
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
110 84 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (110 bp):
TTTGTTGACAACCAGCCGCCCATTCACTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCC
TTCGTTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTG
Found at i:347229 original size:11 final size:11
Alignment explanation
Indices: 347210--347265 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
347200 CTTTAACCCA
347210 TCTTATTTTTATT
1 TCTT-TTTTT-TT
347223 T-TTTTTTCTTT
1 TCTTTTTT-TTT
* *
347234 TGTTCTTTTTT
1 TCTTTTTTTTT
347245 TCTTTTTTTTT
1 TCTTTTTTTTT
347256 TCTTTTTTTT
1 TCTTTTTTTT
347266 CCAATTTAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
11 29 0.76
12 8 0.21
13 1 0.03
ACGTcount: A:0.04, C:0.09, G:0.02, T:0.86
Consensus pattern (11 bp):
TCTTTTTTTTT
Found at i:347234 original size:8 final size:8
Alignment explanation
Indices: 347223--347265 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
347213 TATTTTTATT
347223 TTTTTTTC
1 TTTTTTTC
*
347231 TTTTGTTC
1 TTTTTTTC
347239 TTTTTTTC
1 TTTTTTTC
347247 TTTTTTT-
1 TTTTTTTC
*
347254 TTTCTTT-
1 TTTTTTTC
347261 TTTTT
1 TTTTT
347266 CCAATTTAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
7 10 0.32
8 21 0.68
ACGTcount: A:0.00, C:0.09, G:0.02, T:0.88
Consensus pattern (8 bp):
TTTTTTTC
Found at i:347245 original size:27 final size:27
Alignment explanation
Indices: 347210--347261 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
347200 CTTTAACCCA
347210 TCTTATTTT-TATTTTTTTTTCTTTTGT
1 TCTTATTTTCT-TTTTTTTTTCTTTTGT
*
347237 TCTTTTTTTCTTTTTTTTTTCTTTT
1 TCTTATTTTCTTTTTTTTTTCTTTT
347262 TTTTCCAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.04, C:0.10, G:0.02, T:0.85
Consensus pattern (27 bp):
TCTTATTTTCTTTTTTTTTTCTTTTGT
Found at i:355927 original size:19 final size:20
Alignment explanation
Indices: 355900--355938 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
355890 GAACGCTGGA
355900 AACCAGTTTTG-ACCGGTTT
1 AACCAGTTTTGAACCGGTTT
*
355919 AACCGGTTTTGAACCGGTTT
1 AACCAGTTTTGAACCGGTTT
355939 TGACCGGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.36
Consensus pattern (20 bp):
AACCAGTTTTGAACCGGTTT
Found at i:355935 original size:11 final size:11
Alignment explanation
Indices: 355900--355946 Score: 57
Period size: 10 Copynumber: 4.6 Consensus size: 11
355890 GAACGCTGGA
*
355900 AACCAGTTTTG
1 AACCGGTTTTG
355911 -ACCGG-TTT-
1 AACCGGTTTTG
355919 AACCGGTTTTG
1 AACCGGTTTTG
355930 AACCGGTTTTG
1 AACCGGTTTTG
355941 -ACCGGT
1 AACCGGT
355947 CACGACCCGT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
9 8 0.25
10 13 0.41
11 11 0.34
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:355946 original size:10 final size:10
Alignment explanation
Indices: 355905--355946 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
355895 CTGGAAACCA
355905 GTTTTGACCG
1 GTTTTGACCG
*
355915 G-TTTAACCG
1 GTTTTGACCG
355924 GTTTTGAACCG
1 GTTTTG-ACCG
355935 GTTTTGACCG
1 GTTTTGACCG
355945 GT
1 GT
355947 CACGACCCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 8 0.29
10 10 0.36
11 10 0.36
ACGTcount: A:0.14, C:0.19, G:0.29, T:0.38
Consensus pattern (10 bp):
GTTTTGACCG
Found at i:356005 original size:13 final size:13
Alignment explanation
Indices: 355959--356005 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
355949 CGACCCGTTT
*
355959 ACCCGTTTACCCG
1 ACCCGTTGACCCG
355972 ACCCGTTGACCCG
1 ACCCGTTGACCCG
355985 ACCC---GACCCG
1 ACCCGTTGACCCG
355995 ACCCGTTGACC
1 ACCCGTTGACC
356006 GTTGACCGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
10 10 0.33
13 20 0.67
ACGTcount: A:0.17, C:0.49, G:0.19, T:0.15
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:356074 original size:29 final size:29
Alignment explanation
Indices: 356013--356088 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
356003 ACCGTTGACC
*** *
356013 GGTGCTATTCTGGGAATTAATTCGGGTTT
1 GGTGCTATTCTGGGAATTAATTCGAAATG
356042 GGTGCTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTCTGGGAATTAATTCGAAATG
* *
356071 GGTGCTATTTTGGTAATT
1 GGTGCTATTCTGGGAATT
356089 TTTTTAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.21, C:0.09, G:0.29, T:0.41
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAATG
Found at i:363188 original size:9 final size:10
Alignment explanation
Indices: 363157--363192 Score: 56
Period size: 11 Copynumber: 3.6 Consensus size: 10
363147 AACGCTGGAA
363157 ACCGGTTTTG
1 ACCGGTTTTG
363167 AACCGGTTTTG
1 -ACCGGTTTTG
363178 ACCGG-TTTG
1 ACCGGTTTTG
363187 ACCGGT
1 ACCGGT
363193 CACGACCCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.38
10 5 0.21
11 10 0.42
ACGTcount: A:0.14, C:0.22, G:0.31, T:0.33
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:363251 original size:13 final size:13
Alignment explanation
Indices: 363205--363251 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
363195 CGACCCGTTT
*
363205 ACCCGTTTACCCG
1 ACCCGTTGACCCG
363218 ACCCGTTGACCCG
1 ACCCGTTGACCCG
363231 ACCC---GACCCG
1 ACCCGTTGACCCG
363241 ACCCGTTGACC
1 ACCCGTTGACC
363252 GTTGACCGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
10 10 0.33
13 20 0.67
ACGTcount: A:0.17, C:0.49, G:0.19, T:0.15
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:363320 original size:29 final size:29
Alignment explanation
Indices: 363259--363334 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
363249 ACCGTTGACC
*** *
363259 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGAAATG
363288 GGTGCTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTCTGGGAATTAATTCGAAATG
* *
363317 GGTGCTATTTTGGTAATT
1 GGTGCTATTCTGGGAATT
363335 TTTTTTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.21, C:0.09, G:0.28, T:0.42
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAATG
Found at i:367445 original size:2 final size:2
Alignment explanation
Indices: 367438--367462 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
367428 AAGGAAAATA
367438 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 A
367463 ATAAAAGAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:367537 original size:3 final size:3
Alignment explanation
Indices: 367531--367555 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
367521 TAATATACCA
367531 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
367556 CAAAACAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:368209 original size:27 final size:26
Alignment explanation
Indices: 368171--368226 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 26
368161 TGGGTCCTGA
368171 AATAATGATATATATATTATAATTTAT
1 AATAATGATATATATA-TATAATTTAT
368198 AATAAT-ATTATATATATATAATTTAT
1 AATAATGA-TATATATATATAATTTAT
368224 AAT
1 AAT
368227 TTAGACGGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 14 0.50
27 14 0.50
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
AATAATGATATATATATATAATTTAT
Found at i:369749 original size:11 final size:11
Alignment explanation
Indices: 369730--369771 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
369720 TTTTCGAATT
*
369730 TTCTCTTTTTC
1 TTCTATTTTTC
*
369741 TTCTGTTTTT-
1 TTCTATTTTTC
*
369751 TTCTTTTTTTC
1 TTCTATTTTTC
369762 TTCTATTTTT
1 TTCTATTTTT
369772 TTCCGAACTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTATTTTTC
Found at i:369754 original size:21 final size:21
Alignment explanation
Indices: 369728--369774 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
369718 TTTTTTCGAA
*
369728 TTTTCTCTTTTTCTTCTGTTT
1 TTTTCTCTTTTTCTTCTATTT
*
369749 TTTTCTTTTTTTCTTCTATTT
1 TTTTCTCTTTTTCTTCTATTT
369770 TTTTC
1 TTTTC
369775 CGAACTGAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTTCTCTTTTTCTTCTATTT
Found at i:370365 original size:3 final size:3
Alignment explanation
Indices: 370337--370388 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
370327 ATTGGGCCTT
* * * *
370337 ATA ATA AAA ATA AAA ATA ATTA ATA ATA ATA CTA ATA ATG ATA ATA
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA
370383 ATA ATA
1 ATA ATA
370389 GTAGTAGTAG
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:374326 original size:73 final size:72
Alignment explanation
Indices: 374237--374459 Score: 324
Period size: 73 Copynumber: 3.1 Consensus size: 72
374227 GCGCATTTAA
* * *
374237 TTTTAGTCCTAAATGTTAATTTCTTTGA-TCTT-TGTTGTTTAGACATTATGATTCTATATTTTT
1 TTTTAGTCCTACATGTTGATTTATTT-ACT-TTCTGTTGTTTAGACATTATGATTCTATATTTTT
374300 GCATGATTCT
64 GCATG-TTCT
374310 TTTTAGTCCTACATGTTGATTTATTTACTTTCTGTTGTTTAGACATTATGATTCTATATTTTTGC
1 TTTTAGTCCTACATGTTGATTTATTTACTTTCTGTTGTTTAGACATTATGATTCTATATTTTTGC
374375 ATGTTTCT
66 ATG-TTCT
* * * *
374383 TTTTAGTCCTACATGTTGATTTATTTACTTTCTGCTGTTTAGATATTAGGATTCTATATTTTTGT
1 TTTTAGTCCTACATGTTGATTTATTTACTTTCTGTTGTTTAGACATTATGATTCTATATTTTTGC
374448 ATGTCTCT
66 ATGT-TCT
374456 TTTT
1 TTTT
374460 GGTCTTGTGT
Statistics
Matches: 139, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
72 4 0.03
73 135 0.97
ACGTcount: A:0.20, C:0.12, G:0.13, T:0.56
Consensus pattern (72 bp):
TTTTAGTCCTACATGTTGATTTATTTACTTTCTGTTGTTTAGACATTATGATTCTATATTTTTGC
ATGTTCT
Found at i:374330 original size:41 final size:40
Alignment explanation
Indices: 374285--374403 Score: 107
Period size: 41 Copynumber: 3.1 Consensus size: 40
374275 TTAGACATTA
374285 TGATTCTATATTTTTGCATGATTCTTTTTAGTCCTACATGT
1 TGATTCTATATTTTTGCATG-TTCTTTTTAGTCCTACATGT
*
374326 TGATT-TAT-TTACTTT-C-TG-T-TGTTTAG----ACAT-T
1 TGATTCTATATT--TTTGCATGTTCTTTTTAGTCCTACATGT
374357 ATGATTCTATATTTTTGCATGTTTCTTTTTAGTCCTACATGT
1 -TGATTCTATATTTTTGCATG-TTCTTTTTAGTCCTACATGT
374399 TGATT
1 TGATT
374404 TATTTACTTT
Statistics
Matches: 61, Mismatches: 2, Indels: 30
0.66 0.02 0.32
Matches are distributed among these distances:
31 1 0.02
32 12 0.20
33 4 0.07
34 4 0.07
36 7 0.11
37 7 0.11
39 4 0.07
40 4 0.07
41 17 0.28
42 1 0.02
ACGTcount: A:0.19, C:0.13, G:0.13, T:0.55
Consensus pattern (40 bp):
TGATTCTATATTTTTGCATGTTCTTTTTAGTCCTACATGT
Found at i:374335 original size:38 final size:37
Alignment explanation
Indices: 374293--374408 Score: 89
Period size: 38 Copynumber: 3.1 Consensus size: 37
374283 TATGATTCTA
374293 TATTTTTGCATGATTCTTTTTAGTCCTACATGTTGATT
1 TATTTTTGCATG-TTCTTTTTAGTCCTACATGTTGATT
* * * * * * *
374331 TATTTACTTTC-TG-T-TGTTTAGACAT-TATGATT-CTA
1 TATTT--TTGCATGTTCTTTTTAGTCCTACATG-TTGATT
374366 TATTTTTGCATGTTTCTTTTTAGTCCTACATGTTGATT
1 TATTTTTGCATG-TTCTTTTTAGTCCTACATGTTGATT
374404 TATTT
1 TATTT
374409 ACTTTCTGCT
Statistics
Matches: 55, Mismatches: 14, Indels: 18
0.63 0.16 0.21
Matches are distributed among these distances:
33 3 0.05
34 2 0.04
35 9 0.16
36 11 0.20
37 11 0.20
38 14 0.25
39 2 0.04
40 3 0.05
ACGTcount: A:0.19, C:0.12, G:0.12, T:0.57
Consensus pattern (37 bp):
TATTTTTGCATGTTCTTTTTAGTCCTACATGTTGATT
Found at i:374351 original size:36 final size:36
Alignment explanation
Indices: 374311--374424 Score: 92
Period size: 36 Copynumber: 3.1 Consensus size: 36
374301 CATGATTCTT
374311 TTTAGTCCTACATGTTGATTTATTTACTTTCTGTTG
1 TTTAGTCCTACATGTTGATTTATTTACTTTCTGTTG
* * * * * *
374347 TTTAGACAT-TATGATTCTATATT-TTTGCATGTT-TCTT-
1 TTTAGTCCTACATG-TT-GAT-TTATTTAC-T-TTCTGTTG
*
374384 TTTAGTCCTACATGTTGATTTATTTACTTTCTGCTG
1 TTTAGTCCTACATGTTGATTTATTTACTTTCTGTTG
374420 TTTAG
1 TTTAG
374425 ATATTAGGAT
Statistics
Matches: 56, Mismatches: 13, Indels: 18
0.64 0.15 0.21
Matches are distributed among these distances:
34 2 0.04
35 8 0.14
36 20 0.36
37 15 0.27
38 9 0.16
39 2 0.04
ACGTcount: A:0.18, C:0.13, G:0.13, T:0.55
Consensus pattern (36 bp):
TTTAGTCCTACATGTTGATTTATTTACTTTCTGTTG
Found at i:377039 original size:23 final size:24
Alignment explanation
Indices: 377013--377074 Score: 81
Period size: 23 Copynumber: 2.6 Consensus size: 24
377003 AAATGAACGC
* *
377013 TAAATGAACATGTTCGTAAACAT-
1 TAAACGAACACGTTCGTAAACATA
* *
377036 TAAACGAACACGTTTGTGAACATA
1 TAAACGAACACGTTCGTAAACATA
377060 TAAACGAACACGTTC
1 TAAACGAACACGTTC
377075 ACGAACATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
23 19 0.58
24 14 0.42
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.26
Consensus pattern (24 bp):
TAAACGAACACGTTCGTAAACATA
Found at i:377080 original size:24 final size:23
Alignment explanation
Indices: 377031--377082 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
377021 CATGTTCGTA
***
377031 AACATTAAACGAACACGTTTGTG
1 AACATTAAACGAACACGTTCACG
377054 AACATATAAACGAACACGTTCACG
1 AACAT-TAAACGAACACGTTCACG
377078 AACAT
1 AACAT
377083 GTCCATGAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.44, C:0.21, G:0.13, T:0.21
Consensus pattern (23 bp):
AACATTAAACGAACACGTTCACG
Found at i:378137 original size:28 final size:29
Alignment explanation
Indices: 378106--378161 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
378096 TTCCAGCAGC
*
378106 TTCACCCA-CAAAAGCAGCCCCTCCACGT
1 TTCACCAAGCAAAAGCAGCCCCTCCACGT
*
378134 TTCAGCAAGCAAAAGCAGCCCCTCCACG
1 TTCACCAAGCAAAAGCAGCCCCTCCACG
378162 CGCATCAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.30, C:0.43, G:0.14, T:0.12
Consensus pattern (29 bp):
TTCACCAAGCAAAAGCAGCCCCTCCACGT
Found at i:378727 original size:20 final size:21
Alignment explanation
Indices: 378683--378727 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 21
378673 CTATATTTTT
378683 ATTTTCTTTTATTTTGATATC
1 ATTTTCTTTTATTTTGATATC
378704 -TTTTC-TTTATTTT-ATTATC
1 ATTTTCTTTTATTTTGA-TATC
378723 ATTTT
1 ATTTT
378728 AGTCATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 1 0.05
19 12 0.55
20 9 0.41
ACGTcount: A:0.18, C:0.09, G:0.02, T:0.71
Consensus pattern (21 bp):
ATTTTCTTTTATTTTGATATC
Found at i:379476 original size:265 final size:268
Alignment explanation
Indices: 379128--379657 Score: 989
Period size: 270 Copynumber: 2.0 Consensus size: 268
379118 TTGATCAATT
379128 TCATAATTTGATTAAATATAATATTTATTTTTAAATATTAAGAAATGATTGTCTTAACATAACTA
1 TCATAATTTGATTAAATATAATATTTATTTTTAAATATTAAGAAATGATTGTCTTAACATAACTA
379193 GATGTCATATTTTAATA-TTAAAAATAAATAAATGTTTTG-T-TAAAAACCTAAAAAATAAAATA
66 GATGTCATATTTTAATATTTAAAAATAAATAAATGTTTTGTTATAAAAACCTAAAAAATAAAATA
379255 TGTTTAACTTAATTATATTTATTTTGATATTTAA-TTTTATAATTTTCTTATAATTTTCTTTAAA
131 TGTTTAACTTAATTATATTTATTTTGATATTTAATTTTTATAATTTTCTTATAATTTTCTTTAAA
*
379319 TAAAATTATGCGGTTAAATATGGAATAACGTGATTATAAATTGGAAA-TAAATATAAATTTGTTA
196 TAAAATTATGCGGTTAAATATGGAATAACGGGATTATAAATT-GAAATTAAATATAAATTTGTTA
379383 AATTTGCAA
260 AATTTGCAA
379392 TCATAATTTGATTAAATTATAATATTTATTTTTAAATATTAAGAAATGATTGTCTTAACATAACT
1 TCATAATTTGATTAAA-TATAATATTTATTTTTAAATATTAAGAAATGATTGTCTTAACATAACT
379457 AGATGTCATATTTTAATATTTAAAAATAAATAAATGTTTTGTTTATAAAAACCTAAAAAATAAAA
65 AGATGTCATATTTTAATATTTAAAAATAAATAAATGTTTTG-TTATAAAAACCTAAAAAATAAAA
379522 TATGTTTAACTTAATTATATTTATTTTGATATTTAATTTTTATAATTTTCTTATAATTTTCTTTA
129 TATGTTTAACTTAATTATATTTATTTTGATATTTAATTTTTATAATTTTCTTATAATTTTCTTTA
379587 AATAAAATTATGCGGTTAAATATGGAATAACGGGATTATAAATTGAAATTAAATATAAATTTGTT
194 AATAAAATTATGCGGTTAAATATGGAATAACGGGATTATAAATTGAAATTAAATATAAATTTGTT
379652 AAATTT
259 AAATTT
379658 ATTGCAAAGA
Statistics
Matches: 258, Mismatches: 1, Indels: 8
0.97 0.00 0.03
Matches are distributed among these distances:
264 16 0.06
265 66 0.26
266 22 0.09
268 1 0.00
269 60 0.23
270 93 0.36
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.45
Consensus pattern (268 bp):
TCATAATTTGATTAAATATAATATTTATTTTTAAATATTAAGAAATGATTGTCTTAACATAACTA
GATGTCATATTTTAATATTTAAAAATAAATAAATGTTTTGTTATAAAAACCTAAAAAATAAAATA
TGTTTAACTTAATTATATTTATTTTGATATTTAATTTTTATAATTTTCTTATAATTTTCTTTAAA
TAAAATTATGCGGTTAAATATGGAATAACGGGATTATAAATTGAAATTAAATATAAATTTGTTAA
ATTTGCAA
Found at i:386579 original size:51 final size:51
Alignment explanation
Indices: 386444--386578 Score: 171
Period size: 51 Copynumber: 2.6 Consensus size: 51
386434 TATCTATCTG
* * * * *
386444 GGGCATATTGAAGGCTCACATCAGCATAAAAAAGATATAAGTTATCCATGT
1 GGGCATCTTGAAGGCTCACACCAGCATAAAAAAGATAGAAGTAATCCATAT
* * * *
386495 GGGTATCTTAAAGGCTCATACCAGCATGAAAAAGATAGAAGTAATCCATAT
1 GGGCATCTTGAAGGCTCACACCAGCATAAAAAAGATAGAAGTAATCCATAT
*
386546 GAGGCATCTTGAAGGCTCACACCAGAATAAAAA
1 G-GGCATCTTGAAGGCTCACACCAGCATAAAAA
386579 GGTTGGGATA
Statistics
Matches: 69, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
51 43 0.62
52 26 0.38
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (51 bp):
GGGCATCTTGAAGGCTCACACCAGCATAAAAAAGATAGAAGTAATCCATAT
Found at i:388070 original size:42 final size:42
Alignment explanation
Indices: 388002--388083 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
387992 CACAAATTTG
* * * * *
388002 TAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCT
1 TAAAACCTTCAGGTCATCTGTCAGTCTTTCAAGCAAGATGCT
388044 TAAAACCTTCAGGTCATCTGTCAGTCTTTCAAGCAAGATG
1 TAAAACCTTCAGGTCATCTGTCAGTCTTTCAAGCAAGATG
388084 ATAAGTCCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (42 bp):
TAAAACCTTCAGGTCATCTGTCAGTCTTTCAAGCAAGATGCT
Found at i:388136 original size:249 final size:249
Alignment explanation
Indices: 387667--388692 Score: 1694
Period size: 249 Copynumber: 4.1 Consensus size: 249
387657 CCCAACCAAC
* * *
387667 AAGTTTCTCATTTAATCTTTTTTAGAAAATGAAATTCTTGAAAAGTAAGAAGTTTCTTACCCAGT
1 AAGTTTCTCATTTAA--TGTTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCCAGT
* * * *
387732 AAAGTGTTTCCCCCAAATTTATAAATCCTTCGGGTCATCTGTTAATCTTTCGAGCATGATGCTTA
64 AAAGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTA
* * * *
387797 AAACCTTCGGGTCATCTGTCAGTTTTTCGAGTAAGATGATAAGTCTTTAGGGCCATCCGTAAAGC
129 AAACCTTCGGGTCATCTGTCAGTCTTTCAAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGC
**
387862 CTTTGGGTAGGATGTTCACATATGATTTAGGCATGAAAATGAGATAGCGATTTTCA
194 CTTTGGGTAGGATGTTCACATATGATTTTCGCATGAAAATGAGATAGCGATTTTCA
* * *
387918 AAGTTTCTCATTTAATGTTCTATAAAATCAAATTCTTGAAAAATAAGAATTTTCTTACCCAGTAA
1 AAGTTTCTCATTTAATGTTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCCAGTAA
387983 AGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTAAA
66 AGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTAAA
*
388048 ACCTTCAGGTCATCTGTCAGTCTTTCAAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGCCT
131 ACCTTCGGGTCATCTGTCAGTCTTTCAAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGCCT
* * *
388113 TTGGGTAGGATGTTCATATATGATTTTCGCATGAAATTGAGATAGCGATTTTTA
196 TTGGGTAGGATGTTCACATATGATTTTCGCATGAAAATGAGATAGCGATTTTCA
*
388167 AAGTTTCTCATTTAATGTTCTAGAAAATCAAATTCTTGAAAAGTAATAAGTTTCTTACCCAGTAA
1 AAGTTTCTCATTTAATGTTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCCAGTAA
*
388232 AGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATTTGTTAGTCTTTCGAGCATGATGCTTAAA
66 AGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTAAA
*
388297 ACCTTCGAGTCATCTGTCAGTCTTTCAAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGCCT
131 ACCTTCGGGTCATCTGTCAGTCTTTCAAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGCCT
*
388362 TTGGGTATGATGTTCACATATGATTTTCGCATGAAAATGAGATAGCGATTTTCA
196 TTGGGTAGGATGTTCACATATGATTTTCGCATGAAAATGAGATAGCGATTTTCA
*
388416 AAGTTTCTCATTTAATGTTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCTAGTAA
1 AAGTTTCTCATTTAATGTTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCCAGTAA
388481 AGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTAAA
66 AGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTAAA
* * * *
388546 ACCTCCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCTTTAGGGCCATTCGTAAAGCCT
131 ACCTTCGGGTCATCTGTCAGTCTTTCAAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGCCT
* * * **
388611 TTGGGTA-GATGTTCACATATGATTTTTGCATGAAAAATGAGAAAACGATTACCA
196 TTGGGTAGGATGTTCACATATGATTTTCGCATG-AAAATGAGATAGCGATTTTCA
* *
388665 AAGTTTCTCATTTAATATTCGAGAAAAT
1 AAGTTTCTCATTTAATGTTCTAGAAAAT
388693 TAAAACCTCC
Statistics
Matches: 728, Mismatches: 46, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
248 24 0.03
249 689 0.95
251 15 0.02
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (249 bp):
AAGTTTCTCATTTAATGTTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCCAGTAA
AGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTAAA
ACCTTCGGGTCATCTGTCAGTCTTTCAAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGCCT
TTGGGTAGGATGTTCACATATGATTTTCGCATGAAAATGAGATAGCGATTTTCA
Found at i:388319 original size:42 final size:42
Alignment explanation
Indices: 388251--388332 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
388241 CACAAATTTG
* * * * * *
388251 TAAATCCTTCGGGTCATTTGTTAGTCTTTCGAGCATGATGCT
1 TAAAACCTTCGAGTCATCTGTCAGTCTTTCAAGCAAGATGCT
388293 TAAAACCTTCGAGTCATCTGTCAGTCTTTCAAGCAAGATG
1 TAAAACCTTCGAGTCATCTGTCAGTCTTTCAAGCAAGATG
388333 ATAAGTCCTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (42 bp):
TAAAACCTTCGAGTCATCTGTCAGTCTTTCAAGCAAGATGCT
Found at i:388568 original size:42 final size:42
Alignment explanation
Indices: 388500--388581 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
388490 CACAAATTTG
* * * *
388500 TAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCT
1 TAAAACCTCCGGGTCATCTGTCAGTCTTTCGAGCAAGATGCT
388542 TAAAACCTCCGGGTCATCTGTCAGTCTTTCGAGCAAGATG
1 TAAAACCTCCGGGTCATCTGTCAGTCTTTCGAGCAAGATG
388582 ATAAGTCTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.33
Consensus pattern (42 bp):
TAAAACCTCCGGGTCATCTGTCAGTCTTTCGAGCAAGATGCT
Found at i:388776 original size:46 final size:47
Alignment explanation
Indices: 388709--388807 Score: 164
Period size: 47 Copynumber: 2.1 Consensus size: 47
388699 CTCCGGGTAA
* *
388709 TTCAAAAAGCCTTCGGGTCATCC-TAAGACCTTCAGTGCAGGATGTT
1 TTCAAAAAACCTTCAGGTCATCCATAAGACCTTCAGTGCAGGATGTT
*
388755 TTCAAAAAACCTTCAGGTCATCCATAAGACCTTTAGTGCAGGATGTT
1 TTCAAAAAACCTTCAGGTCATCCATAAGACCTTCAGTGCAGGATGTT
388802 TTCAAA
1 TTCAAA
388808 TGAGATTTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
46 21 0.43
47 28 0.57
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.29
Consensus pattern (47 bp):
TTCAAAAAACCTTCAGGTCATCCATAAGACCTTCAGTGCAGGATGTT
Found at i:389386 original size:28 final size:29
Alignment explanation
Indices: 389355--389413 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
389345 AATTCCAGCA
*
389355 GTTTCACCCA-CAAAAGCAGCCCCTCCAC
1 GTTTCACCAAGCAAAAGCAGCCCCTCCAC
*
389383 GTTTCAGCAAGCAAAAGCAGCCCCTCCAC
1 GTTTCACCAAGCAAAAGCAGCCCCTCCAC
389412 GT
1 GT
389414 GCATCAACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 8 0.29
29 20 0.71
ACGTcount: A:0.29, C:0.41, G:0.15, T:0.15
Consensus pattern (29 bp):
GTTTCACCAAGCAAAAGCAGCCCCTCCAC
Found at i:389675 original size:18 final size:18
Alignment explanation
Indices: 389652--389695 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
389642 TTTATTTTTG
389652 AAAAAAATTAAGTTAAAT
1 AAAAAAATTAAGTTAAAT
389670 AAAAAAATTAAGTTAAAT
1 AAAAAAATTAAGTTAAAT
389688 AAATAAAA
1 AAA-AAAA
389696 AAATAGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (18 bp):
AAAAAAATTAAGTTAAAT
Found at i:389994 original size:20 final size:21
Alignment explanation
Indices: 389950--389994 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
389940 CTATATTTTT
*
389950 ATTTTCTTTCATTTTGATCTC
1 ATTTTCTTTCATTTTGATATC
389971 -TTTTCTTT-ATTTT-ATTATC
1 ATTTTCTTTCATTTTGA-TATC
389990 ATTTT
1 ATTTT
389995 AGTCATCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
18 1 0.05
19 8 0.38
20 12 0.57
ACGTcount: A:0.16, C:0.13, G:0.02, T:0.69
Consensus pattern (21 bp):
ATTTTCTTTCATTTTGATATC
Found at i:391101 original size:4 final size:4
Alignment explanation
Indices: 391094--391122 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
391084 GAACACACAC
391094 AAAT AAAT AAAT AAAT -AAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
391123 TGATTTAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:391115 original size:11 final size:11
Alignment explanation
Indices: 391094--391123 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
391084 GAACACACAC
391094 AAATAAATAAAT
1 AAAT-AATAAAT
391106 AAATAATAAAT
1 AAATAATAAAT
391117 AAATAAT
1 AAATAAT
391124 GATTTAGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAATAATAAAT
Found at i:392536 original size:20 final size:20
Alignment explanation
Indices: 392475--392703 Score: 230
Period size: 20 Copynumber: 11.4 Consensus size: 20
392465 GATTTTCAAG
* ** *
392475 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
392495 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
392515 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
392535 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
392555 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
392575 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
392595 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
392615 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
392635 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
392655 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
392675 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
392695 AATCACAAC
1 AATCGCAAC
392704 ACTGAAATTT
Statistics
Matches: 175, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 171 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:393433 original size:24 final size:24
Alignment explanation
Indices: 393394--393440 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
393384 AAATTTGGTC
393394 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
393418 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
393441 GATGTTTCAG
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:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:393632 original size:12 final size:12
Alignment explanation
Indices: 393615--393639 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
393605 ATATAATCCT
393615 GAAGAAGAAAAA
1 GAAGAAGAAAAA
393627 GAAGAAGAAAAA
1 GAAGAAGAAAAA
393639 G
1 G
393640 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:396690 original size:20 final size:20
Alignment explanation
Indices: 396656--396752 Score: 91
Period size: 20 Copynumber: 5.2 Consensus size: 20
396646 TTTTGGTTGA
*
396656 AATGAAAATCCCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
396676 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
396696 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
396715 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
396730 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
396750 AAT
1 AAT
396753 CGCAACGCGA
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.07
17 2 0.03
19 15 0.25
20 19 0.31
21 12 0.20
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:396708 original size:21 final size:21
Alignment explanation
Indices: 396654--396718 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
396644 TCTTTTGGTT
*
396654 GAAATGAAAATCCCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
396675 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
396695 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
396716 GAA
1 GAA
396719 TCGCAACGCG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.44
21 20 0.56
ACGTcount: A:0.48, C:0.17, G:0.25, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:396722 original size:14 final size:14
Alignment explanation
Indices: 396703--396759 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
396693 GAGAAATGAA
396703 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
396717 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
396736 AATCGCAACGAGAG
1 AATCGCAACGAGAG
396750 AATCGCAACG
1 AATCGCAACG
396760 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:396735 original size:33 final size:33
Alignment explanation
Indices: 396695--396776 Score: 164
Period size: 33 Copynumber: 2.5 Consensus size: 33
396685 CGCAACGAGA
396695 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
396728 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
396761 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
396777 TGCGATTTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.48, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:396813 original size:14 final size:14
Alignment explanation
Indices: 396794--396849 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
396784 TTGGTTTCGT
396794 GTTGCGATTCTCTC
1 GTTGCGATTCTCTC
*
396808 GTTGCGATTTTCATTTCGC
1 GTTGCGA--TTC---TCTC
396827 GTTGCGATTCTCTC
1 GTTGCGATTCTCTC
396841 GTTGCGATT
1 GTTGCGATT
396850 TTCATTTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.45
Consensus pattern (14 bp):
GTTGCGATTCTCTC
Found at i:396825 original size:33 final size:33
Alignment explanation
Indices: 396777--396856 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
396767 AAAATCGCAA
** *
396777 TGCGATTTTGGTTTCGTGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
396810 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
396843 TGCGATTTTCATTT
1 TGCGATTTTCATTT
396857 TTCTCGTTGC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.09, C:0.20, G:0.23, T:0.49
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:396862 original size:21 final size:21
Alignment explanation
Indices: 396837--396910 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
396827 GTTGCGATTC
396837 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
396858 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
396879 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
396900 TCTCGTTGCGA
1 TCTCGTTGCGA
396911 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:397032 original size:33 final size:33
Alignment explanation
Indices: 396990--397060 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
396980 AATACTAACT
*
396990 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCAAAA
* *
397023 TGAAAATCGCAACGAGAGAATCGTAACGCAAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCAAAA
397056 TGAAA
1 TGAAA
397061 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.49, C:0.17, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCAAAA
Found at i:397465 original size:20 final size:20
Alignment explanation
Indices: 397440--397591 Score: 207
Period size: 20 Copynumber: 7.6 Consensus size: 20
397430 CTTTAAAAAT
397440 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
397460 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
397480 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
397500 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
397520 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
397540 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
397560 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
397580 CGCGTTGCGATT
1 CGCGTTGCGATT
397592 CTGGAAAATC
Statistics
Matches: 118, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
20 117 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.28, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:397876 original size:56 final size:53
Alignment explanation
Indices: 397815--397930 Score: 126
Period size: 56 Copynumber: 2.1 Consensus size: 53
397805 AAAATACTCA
** *
397815 ATTAAT-CATAATAATATAGGATATTATATTTTAAATTTATTAATATATAATAAATT
1 ATTAATACA-AATAATATAGGATATTAT-TTTTAAA-AAAATAATAT-TAATAAATT
* ** *
397871 ATTAATACAATTAATATAGTTTATTATTTTTAAAAAAATAATATTATTAAATT
1 ATTAATACAAATAATATAGGATATTATTTTTAAAAAAATAATATTAATAAATT
397924 ATTAATA
1 ATTAATA
397931 ATGAGTAATA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
53 15 0.29
54 7 0.13
55 7 0.13
56 21 0.40
57 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.47
Consensus pattern (53 bp):
ATTAATACAAATAATATAGGATATTATTTTTAAAAAAATAATATTAATAAATT
Found at i:398217 original size:18 final size:19
Alignment explanation
Indices: 398191--398228 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
398181 AATAATATTT
* *
398191 ATTATATATTTATT-TTAA
1 ATTACATATTAATTATTAA
398209 ATTACATATTAATTATTAA
1 ATTACATATTAATTATTAA
398228 A
1 A
398229 ATAGTTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTACATATTAATTATTAA
Found at i:398488 original size:14 final size:15
Alignment explanation
Indices: 398436--398496 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
398426 ATTGTTTTTC
*
398436 AATTCATTTTACATA
1 AATTCATTTTACGTA
*
398451 AA-TCAATTTTCAGGT-
1 AATTC-ATTTT-ACGTA
398466 AATTCATTTTACGTA
1 AATTCATTTTACGTA
*
398481 AATT-ATTTTTCGTA
1 AATTCATTTTACGTA
398495 AA
1 AA
398497 ATTAATTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
14 16 0.42
15 18 0.47
16 4 0.11
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (15 bp):
AATTCATTTTACGTA
Found at i:400516 original size:20 final size:20
Alignment explanation
Indices: 400493--400530 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
400483 GTTTCCAGAT
400493 TCGCAACGCGATTCTGACAA
1 TCGCAACGCGATTCTGACAA
400513 TCGCAACGCGATTCTGAC
1 TCGCAACGCGATTCTGAC
400531 TATCCAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.32, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACAA
Found at i:401120 original size:20 final size:20
Alignment explanation
Indices: 401095--401183 Score: 99
Period size: 20 Copynumber: 4.4 Consensus size: 20
401085 GAAATTCAGT
*
401095 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
401115 GTTGCGATAGTCAGAATCGA
1 GTTGCGATAGTCAGAATCGC
* ** *
401135 GTTGTGATTATGT-ATTATGGC
1 GTTGCGA-TA-GTCAGAATCGC
401156 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
401176 GTTGCGAT
1 GTTGCGAT
401184 TATGTATTAT
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
19 2 0.04
20 39 0.71
21 12 0.22
22 2 0.04
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:401158 original size:41 final size:41
Alignment explanation
Indices: 401110--401204 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
401100 GACAGTCAGA
*
401110 ATCGCGTTGCGATAGTCAGAATCGAGTTGTGATTATGTATT
1 ATCGCGTTGCGATAGTCAGAATCGAGTTGCGATTATGTATT
* *
401151 ATGGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATAGTCAGAATCGAGTTGCGATTATGTATT
401192 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
401205 TATGTATTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.35
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGAATCGAGTTGCGATTATGTATT
Found at i:401197 original size:21 final size:21
Alignment explanation
Indices: 401130--401226 Score: 126
Period size: 21 Copynumber: 4.7 Consensus size: 21
401120 GATAGTCAGA
* *
401130 ATCGAGTTGTGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
* **
401151 ATGGCGTTGCGA-TA-GTCAGA
1 ATCGCGTTGCGATTATGT-ATT
401171 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
401192 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
401213 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
401227 TACATATTCG
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.03
20 14 0.22
21 47 0.72
22 2 0.03
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.39
Consensus pattern (21 bp):
ATCGCGTTGCGATTATGTATT
Found at i:401246 original size:62 final size:62
Alignment explanation
Indices: 401095--401225 Score: 167
Period size: 62 Copynumber: 2.1 Consensus size: 62
401085 GAAATTCAGT
* * ** * *
401095 GTTGCGACAGTCAGAATCGCGTTGCGA-TA-GTCAGAATCGAGTTGTGATTATGTATTATGGC
1 GTTGCGATAGTCAGAATCGCATTGCGATTATGT-ATTATCGAGTTGCGATTATGTATTATCGC
* *
401156 GTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGCGTTGCGATTATGTATTATCGC
1 GTTGCGATAGTCAGAATCGCATTGCGATTATGTATTATCGAGTTGCGATTATGTATTATCGC
401218 GTTGCGAT
1 GTTGCGAT
401226 TTACATATTC
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
61 26 0.42
62 34 0.55
63 2 0.03
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.34
Consensus pattern (62 bp):
GTTGCGATAGTCAGAATCGCATTGCGATTATGTATTATCGAGTTGCGATTATGTATTATCGC
Found at i:401356 original size:19 final size:19
Alignment explanation
Indices: 401321--401369 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
401311 GGAAACTGAT
* *
401321 TTGCGATATTGGAGATCGCG
1 TTGCGAT-TTAGAGATCGCA
401341 TTGCGATTTAGAGATCGCA
1 TTGCGATTTAGAGATCGCA
401360 TTGCGATTTA
1 TTGCGATTTA
401370 TCTAAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.22, C:0.14, G:0.29, T:0.35
Consensus pattern (19 bp):
TTGCGATTTAGAGATCGCA
Found at i:406388 original size:31 final size:31
Alignment explanation
Indices: 406318--406395 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
406308 CTTTTAAAAC
** *
406318 TTGCAATACAATCCCCCAATATTTAGTCTGT
1 TTGCAATATGATCCCCCAACATTTAGTCTGT
406349 TTGCAATATGATCCCCCAACATTTAGTCTGT
1 TTGCAATATGATCCCCCAACATTTAGTCTGT
406380 TTGCAATATGATCCCC
1 TTGCAATATGATCCCC
406396 GACCGTTTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (31 bp):
TTGCAATATGATCCCCCAACATTTAGTCTGT
Found at i:414137 original size:20 final size:20
Alignment explanation
Indices: 414097--414138 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
414087 ATTCCACCAC
*
414097 ATGCAACTATATGCTCATAA
1 ATGCAACTATATGATCATAA
* *
414117 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCATAA
414137 AT
1 AT
414139 AGGCTCTTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCATAA
Found at i:419142 original size:59 final size:59
Alignment explanation
Indices: 419094--419367 Score: 408
Period size: 59 Copynumber: 4.6 Consensus size: 59
419084 TAAGTGTGTA
* *
419094 AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCTTATGGGGCACTTCGTATGCT
1 AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCTTATTGGGCACTTCGTGTGCT
*
419153 AAAATGTTAAGAAATTCATACTACGTGTATGAATTT-CTGTATTGGGCACTTCGTGTGCT
1 AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCT-TATTGGGCACTTCGTGTGCT
* * * * *
419212 AAAATGTTAAGAAATTTATACTAAGTGTATGAATTT-ATATATTAGACACTTTGTGTGCT
1 AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCT-TATTGGGCACTTCGTGTGCT
** *
419271 AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCAGTATTGGGCACTTTGTGTGCT
1 AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCTTATTGGGCACTTCGTGTGCT
*
419330 AAAATGATAAGAAATTCATACTAAGTGTATGAATTTCC
1 AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCC
419368 GTATGGGAAA
Statistics
Matches: 197, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
58 2 0.01
59 194 0.98
60 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (59 bp):
AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCTTATTGGGCACTTCGTGTGCT
Found at i:419428 original size:177 final size:177
Alignment explanation
Indices: 419094--419429 Score: 446
Period size: 177 Copynumber: 1.9 Consensus size: 177
419084 TAAGTGTGTA
**
419094 AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCTTATGGGGCACTTCGTATGCTAAAATG
1 AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCAGTATGGGGCACTTCGTATGCTAAAATG
* * * * * * **
419159 TTAAGAAATTCATACTACGTGTATGAATTTCTGTATTGGGCACTTCGTGTGCTAAAATGTTAAGA
66 ATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGAAATTCATGTGCTAAAATCATAAGA
* * ***
419224 AATTTATACTAAGTGTATGAATTTATATATTAGACACTTTGTGTGCT
131 AATTCATAATAAGAAAATGAATTTATATATTAGACACTTTGTGTGCT
* * *
419271 AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCAGTATTGGGCACTTTGTGTGCTAAAATG
1 AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCAGTATGGGGCACTTCGTATGCTAAAATG
419336 ATAAGAAATTCATACTAAGTGTATGAATTTCCGTA-TGGGAAATAT-ATGTG-TATAAA-CATAA
66 ATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGAAAT-TCATGTGCTA-AAATCATAA
* *
419397 GAAATTCATAATAAGAAAATGGATTTTTATATT
129 GAAATTCATAATAAGAAAATGAATTTATATATT
419430 GGTAATGGGT
Statistics
Matches: 137, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
175 31 0.23
176 13 0.09
177 93 0.68
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.37
Consensus pattern (177 bp):
AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCAGTATGGGGCACTTCGTATGCTAAAATG
ATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGAAATTCATGTGCTAAAATCATAAGA
AATTCATAATAAGAAAATGAATTTATATATTAGACACTTTGTGTGCT
Found at i:419974 original size:68 final size:68
Alignment explanation
Indices: 419806--420011 Score: 243
Period size: 68 Copynumber: 3.0 Consensus size: 68
419796 AAAGATCAAT
* *
419806 GGCCTAACTGTGCATTTGACAGAAAGGTATCAATTATGCCAGTTAGATGAAAGGCTAAGTAAGTG
1 GGCCTAACTGTGCATTTGACAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGC----TAAGTG
* *
419871 GCTTTTA
62 CCTTTGA
* * * *
419878 GGCCTAACTATGCATTT-AAAAGAAAGGTGTCAATTATTCCAGTTAGACGAAAGGCTAAGTGCCT
1 GGCCTAACTGTGCATTTGACAA-AAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
419942 TTGA
65 TTGA
* * * * *
419946 GGCCTAGCTGTGCATTTGACAAAAAGGTGTCAATCATGCCGGTTAGATGAAAGGTTAAATGCCTT
1 GGCCTAACTGTGCATTTGACAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
420011 T
66 T
420012 AGTAAAAGAC
Statistics
Matches: 115, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
68 64 0.56
69 3 0.03
71 2 0.02
72 46 0.40
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Consensus pattern (68 bp):
GGCCTAACTGTGCATTTGACAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
TGA
Found at i:420102 original size:45 final size:45
Alignment explanation
Indices: 420029--420153 Score: 178
Period size: 45 Copynumber: 2.7 Consensus size: 45
420019 GACTAGATGT
*
420029 ATAACAATGTATAATGGTATATAAAAGGCATGAAAGGATGCCCTAA
1 ATAA-AATGTATAATAGTATATAAAAGGCATGAAAGGATGCCCTAA
* * *
420075 ATAAAATATATAATAGTGTATAAAAGGCATGAAATGATGCCCTAA
1 ATAAAATGTATAATAGTATATAAAAGGCATGAAAGGATGCCCTAA
**
420120 ATGGAATGTATAATAGTATATAAGAAGGCATGAA
1 ATAAAATGTATAATAGTATATAA-AAGGCATGAA
420154 CGATTGTTAT
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
45 56 0.80
46 14 0.20
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.26
Consensus pattern (45 bp):
ATAAAATGTATAATAGTATATAAAAGGCATGAAAGGATGCCCTAA
Found at i:424362 original size:59 final size:59
Alignment explanation
Indices: 424307--424591 Score: 410
Period size: 59 Copynumber: 4.8 Consensus size: 59
424297 ATGGCACTAA
* *
424307 GTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATGGGGCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTC
* * **
424366 GTGTACTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTTGTATTGGATACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTC
* * * * *
424425 GTGTGCTAAAATGTTAAGAAATTCATACTAATTGTAAGAATTT-TCGTATTTGACACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCT-GTATTGGGCACTTC
* *
424484 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTC
* * *
424543 TTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTATGTAT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTAT
424592 GGGAAATATA
Statistics
Matches: 203, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
58 1 0.00
59 202 1.00
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (59 bp):
GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTC
Found at i:424453 original size:31 final size:31
Alignment explanation
Indices: 424418--424518 Score: 75
Period size: 31 Copynumber: 3.4 Consensus size: 31
424408 TTTGTATTGG
*
424418 ATACTTCGTGTGCTAAAATGTTAAGAAATTC
1 ATACTTAGTGTGCTAAAATGTTAAGAAATTC
* ** * * *
424449 ATAC-TAAT-TG-TAAGAAT-TTTCGTATTTG
1 ATACTTAGTGTGCTAA-AATGTTAAGAAATTC
* *
424477 ACACTTTGTGTGCTAAAATGTTAAGAAATTC
1 ATACTTAGTGTGCTAAAATGTTAAGAAATTC
*
424508 ATACTAAGTGT
1 ATACTTAGTGT
424519 ATGAATTTCC
Statistics
Matches: 47, Mismatches: 18, Indels: 10
0.63 0.24 0.13
Matches are distributed among these distances:
28 12 0.26
29 7 0.15
30 7 0.15
31 21 0.45
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.39
Consensus pattern (31 bp):
ATACTTAGTGTGCTAAAATGTTAAGAAATTC
Found at i:425112 original size:68 final size:68
Alignment explanation
Indices: 425027--425272 Score: 325
Period size: 68 Copynumber: 3.6 Consensus size: 68
425017 AAAGATCAAT
* * * * *
425027 GGCCTAAATGTGCATTTGACAAAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTTCATT
1 GGCCTAACTGTGCATTTGACAAAAAGGTGTCAATTATGACAGTTAGATGAAAGGCTAAGTGCCTT
425092 TGA
66 TGA
* * *
425095 GGCCTAACTGTGCATTTGACATAAAGGTGCCAATTATGTCAGTTAGATGAAAGGCTAAGTGCCTT
1 GGCCTAACTGTGCATTTGACAAAAAGGTGTCAATTATGACAGTTAGATGAAAGGCTAAGTGCCTT
425160 TGA
66 TGA
* * * *
425163 GGCCTAACTGTGTATTTGACAGAAAGGTGTAAATTATGACAGTTAGATGAAAGTCTAAGTGCCTT
1 GGCCTAACTGTGCATTTGACAAAAAGGTGTCAATTATGACAGTTAGATGAAAGGCTAAGTGCCTT
*
425228 TAA
66 TGA
* * * *
425231 GACCT-ATTGTTCATTTGAC-AGAAGGTGTCAATTATGACAGTT
1 GGCCTAACTGTGCATTTGACAAAAAGGTGTCAATTATGACAGTT
425273 CATTTGAGGC
Statistics
Matches: 157, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
66 20 0.13
67 11 0.07
68 126 0.80
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (68 bp):
GGCCTAACTGTGCATTTGACAAAAAGGTGTCAATTATGACAGTTAGATGAAAGGCTAAGTGCCTT
TGA
Found at i:425384 original size:68 final size:68
Alignment explanation
Indices: 425275--425687 Score: 560
Period size: 68 Copynumber: 6.1 Consensus size: 68
425265 TGACAGTTCA
* *
425275 TTTGAGGCCTAACTGTGCATTTGACATAAAGGTGCCAATTATGTCAGTTAGATGAAAGGCTAAGT
1 TTTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGGCTAAGT
425340 GCC
66 GCC
* * * *
425343 TTTGAGGCCTAACTGTGTATTTGACAGAAAGGTGTAAATTATGACAGTTAGATGAAAGTCTAAGT
1 TTTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGGCTAAGT
425408 GCC
66 GCC
* * * * * * *
425411 TTTAAGACCTTATTGTTCATTTGACAGAAAGGTGTCAATTATGACAGTTAGATGAAAGGCTTAGT
1 TTTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGGCTAAGT
425476 GCC
66 GCC
* *
425479 TTTGAGGCCTAACTGTGCATTTGACAAAAAGGTGTCAATTATGTCAGTTAGATGAAAGGCTAAAT
1 TTTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGGCTAAGT
425544 GCC
66 GCC
* * *
425547 TTTGAGGCCTAATTGTGCATTT-AGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTATG
1 TTTGAGGCCTAACTGTGCATTTGA-CAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGGCTAAG
425611 TGCC
65 TGCC
*** * * * * * *
425615 TTTGAGATTTAGCTGTGCATTTGACAGAAATGTGTCAATCATGTCGGTTAGATG-AAGGTTAAAT
1 TTTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGGCTAAGT
425679 GCC
66 GCC
425682 TTTGAG
1 TTTGAG
425688 TAAAAGACTT
Statistics
Matches: 302, Mismatches: 41, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
67 17 0.06
68 284 0.94
69 1 0.00
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.32
Consensus pattern (68 bp):
TTTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGGCTAAGT
GCC
Done.