Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015381.1 Kokia drynarioides strain JFW-HI SEQ_130428, 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: 2291099
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 587 characters in sequence are not A, C, G, or T
File 2 of 8
Found at i:375087 original size:126 final size:126
Alignment explanation
Indices: 374831--375062 Score: 281
Period size: 126 Copynumber: 1.9 Consensus size: 126
374821 TAGCCACACC
* *
374831 TTTAAATATATCATATTAGTCCCTACATGCAATTATTTCACATCAAATACATTTACTTTTATCAT
1 TTTAAATATATCATATCAGACCCTACATGCAATTATTTCACATCAAATACATTTACTTTTATCAT
*** ** * * ** ** **
374896 TTTAACAATCTAGTCCCTACATACAATCATTTTTTTAATAAAACCCATGATTAGCTGCACC
66 TTTAACAATCTAGTCCCTACATACAATCAAAATCATAAAAAAACACATGACAAAATGCAAA
374957 TTTAAATATATCATATCAGACCCTACATGCAATTATTTCACATCAAATACATTTACTTTTATCAT
1 TTTAAATATATCATATCAGACCCTACATGCAATTATTTCACATCAAATACATTTACTTTTATCAT
* * *
375022 TTTAACAATCTAGTCCTTA-A-AC-GTTAAAATCATAAAAAAAC
66 TTTAACAATCTAGTCCCTACATACAATCAAAATCATAAAAAAAC
375063 TACTTTACAA
Statistics
Matches: 95, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
123 11 0.12
124 2 0.02
125 1 0.01
126 81 0.85
ACGTcount: A:0.38, C:0.20, G:0.04, T:0.38
Consensus pattern (126 bp):
TTTAAATATATCATATCAGACCCTACATGCAATTATTTCACATCAAATACATTTACTTTTATCAT
TTTAACAATCTAGTCCCTACATACAATCAAAATCATAAAAAAACACATGACAAAATGCAAA
Found at i:377010 original size:62 final size:62
Alignment explanation
Indices: 376885--377011 Score: 209
Period size: 62 Copynumber: 2.0 Consensus size: 62
376875 TTCGAACAAA
* * * *
376885 TTGGTTTAATAATAACATCCGTTAATTACATTAATACCCTTTGTATATTATTTTTAATTTTT
1 TTGGTTTAATAATAACATCCATTAATTACATTAATACCCTTTGTATATTATCTTCAATGTTT
*
376947 TTGGTTTAATAATAACATCCATTAATTACATTAATACCCTTTGTATATTGTCTTCAATGTTT
1 TTGGTTTAATAATAACATCCATTAATTACATTAATACCCTTTGTATATTATCTTCAATGTTT
377009 TTG
1 TTG
377012 CATGCAAAGC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.50
Consensus pattern (62 bp):
TTGGTTTAATAATAACATCCATTAATTACATTAATACCCTTTGTATATTATCTTCAATGTTT
Found at i:380313 original size:47 final size:47
Alignment explanation
Indices: 380260--380476 Score: 224
Period size: 47 Copynumber: 4.6 Consensus size: 47
380250 CATAATGACA
* *
380260 CGGGCCTTGTACCTAACAGGCTTTAATGCTAGTGTATTGTACTGTAT
1 CGGGCCTTGTACCTAGCAGGCTTTAATGCTAGTGTACTGTACTGTAT
* * * **
380307 CGGGCCTAGTGCCTAGCAGGCTTTAATGCCAGTGTACTGTACCATAT
1 CGGGCCTTGTACCTAGCAGGCTTTAATGCTAGTGTACTGTACTGTAT
* * * *
380354 CAGGCCTTGTGCCTAGCAAGCTTTAATG-TCAGTTTACTGTACCT-TAT
1 CGGGCCTTGTACCTAGCAGGCTTTAATGCT-AGTGTACTGTA-CTGTAT
** * * * *
380401 CGAACCTTGTACCTAGCAGCCTTTAATGATGGTGTACCGTA-TCGTAT
1 CGGGCCTTGTACCTAGCAGGCTTTAATGCTAGTGTACTGTACT-GTAT
*
380448 CGGGCCTTGTACCTAGCAAGCTTTAATGC
1 CGGGCCTTGTACCTAGCAGGCTTTAATGC
380477 CAATGTATTG
Statistics
Matches: 138, Mismatches: 27, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
45 1 0.01
47 135 0.98
48 2 0.01
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.32
Consensus pattern (47 bp):
CGGGCCTTGTACCTAGCAGGCTTTAATGCTAGTGTACTGTACTGTAT
Found at i:380504 original size:94 final size:92
Alignment explanation
Indices: 380260--380512 Score: 245
Period size: 94 Copynumber: 2.7 Consensus size: 92
380250 CATAATGACA
* * * * *
380260 CGGGCCTTGTACCTAACAGGCTTTAATGCTAGTGTATTGTACTGTATCGGGCCTAGTGCCTAGCA
1 CGGGCCTTGTACCTAGCAAGCTTTAATGCCAGTGTATTGTAC-GTAT-AGGCCTTGTGCCTAGCA
* * *
380325 GGCTTTAATGCCAGTGTACTGTACCATAT
64 GCCTTTAATGACAGTGTACCGTACCATAT
* * * * * * * * *
380354 CAGGCCTTGTGCCTAGCAAGCTTTAATGTCAGTTTACTGTACCTTATCGAACCTTGTACCTAGCA
1 CGGGCCTTGTACCTAGCAAGCTTTAATGCCAGTGTATTGTA-CGTATAG-GCCTTGTGCCTAGCA
** * *
380419 GCCTTTAATGATGGTGTACCGTATCGTAT
64 GCCTTTAATGACAGTGTACCGTACCATAT
* *
380448 CGGGCCTTGTACCTAGCAAGCTTTAATGCCAATGTATTGTATCGTAATAGGTCTTGTGCCTAGCA
1 CGGGCCTTGTACCTAGCAAGCTTTAATGCCAGTGTATTGTA-CGT-ATAGGCCTTGTGCCTAGCA
380513 AGCTTCATTC
Statistics
Matches: 124, Mismatches: 32, Indels: 6
0.77 0.20 0.04
Matches are distributed among these distances:
93 1 0.01
94 119 0.96
95 4 0.03
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.33
Consensus pattern (92 bp):
CGGGCCTTGTACCTAGCAAGCTTTAATGCCAGTGTATTGTACGTATAGGCCTTGTGCCTAGCAGC
CTTTAATGACAGTGTACCGTACCATAT
Found at i:381502 original size:34 final size:34
Alignment explanation
Indices: 381459--381527 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
381449 TGTTTTAGGG
381459 CCTCGGAGGCCCGATTTAAAGCCGTAAATGTATA
1 CCTCGGAGGCCCGATTTAAAGCCGTAAATGTATA
*
381493 CCTCGGAGGCTCGATTTAAAGCCGTAAATGTATA
1 CCTCGGAGGCCCGATTTAAAGCCGTAAATGTATA
381527 C
1 C
381528 TCTAGTTCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (34 bp):
CCTCGGAGGCCCGATTTAAAGCCGTAAATGTATA
Found at i:388970 original size:23 final size:23
Alignment explanation
Indices: 388944--388991 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
388934 TGCACAGGTA
388944 TAATAGATTTCAAATAGTTTGAG
1 TAATAGATTTCAAATAGTTTGAG
388967 TAATAGATTTCAAATAGTTTGAG
1 TAATAGATTTCAAATAGTTTGAG
388990 TA
1 TA
388992 GTTGATCCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.17, T:0.40
Consensus pattern (23 bp):
TAATAGATTTCAAATAGTTTGAG
Found at i:390636 original size:258 final size:257
Alignment explanation
Indices: 390134--390641 Score: 775
Period size: 258 Copynumber: 2.0 Consensus size: 257
390124 ACTCCATTTA
*
390134 AAATCGATTCGAAATCTATCAAGCAATTCAAATTTTGCCATCCATAATTGTAACAACTATTTTGT
1 AAATCGATTCGAAATCTATCAAGCAATTCAAATTTTACCATCCATAATTGTAACAACTATTTTGT
* ** *
390199 GAAAAATTATTTTTAGGATAAAATCCCCTATAAATGTTTAATTTTTTATATTAAAATTTTTGAAA
66 GAAAAATGATTTTTAGGATAAAATCCCCTATAAACATTTAATTTTTTATATTAAAACTTTTGAAA
**
390264 TATGTCAAATTTTGCCATCCATAATTGTAGCAACATTAAATTTCATTAAAATTTATTTATATTTA
131 TATGTCAAATTTTGCCATCCATAATTGTAGCAACATTAAATAACATTAAAATTTATTTATATTTA
*
390329 TAAATAAATAATTTATATTATTTTTACTTAAAATTAAAATTTAATATATATCCCATTTAAAAC
196 TAAATAAATAATTTATATTATTTTTACTTAAAATT-AAATATAATATATATCCCATTTAAAAC
* *
390392 AAATCGATTCGAAATCTATCAAGCAATTCAAATTTTACCATTCATAATTGTAGCAACTATTTTGT
1 AAATCGATTCGAAATCTATCAAGCAATTCAAATTTTACCATCCATAATTGTAACAACTATTTTGT
* * * *
390457 GAAATATGATTTTTAGGATAAAATCGCCTATAAACATTTTATTTTTTATATTAAAGCTTTTGAAA
66 GAAAAATGATTTTTAGGATAAAATCCCCTATAAACATTTAATTTTTTATATTAAAACTTTTGAAA
* ***
390522 TATGTCAAATTTTGCCATCCATAATTGTAGGAACTATTTTGTGAAACATT-AAATTATATTTATA
131 TATGTCAAATTTTGCCATCCATAATTGTAGCAAC-ATTAAAT--AACATTAAAATT-TATTTATA
*
390586 TTTATAAATAAATAATTTATATTATTTTTACTTAAAATTGATATATATATATATAT
192 TTTATAAATAAATAATTTATATTATTTTTACTTAAAATT-AAATATA-ATATATAT
390642 ATATCCTGTT
Statistics
Matches: 225, Mismatches: 20, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
258 152 0.68
259 4 0.02
260 5 0.02
261 56 0.25
262 8 0.04
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (257 bp):
AAATCGATTCGAAATCTATCAAGCAATTCAAATTTTACCATCCATAATTGTAACAACTATTTTGT
GAAAAATGATTTTTAGGATAAAATCCCCTATAAACATTTAATTTTTTATATTAAAACTTTTGAAA
TATGTCAAATTTTGCCATCCATAATTGTAGCAACATTAAATAACATTAAAATTTATTTATATTTA
TAAATAAATAATTTATATTATTTTTACTTAAAATTAAATATAATATATATCCCATTTAAAAC
Found at i:394158 original size:17 final size:17
Alignment explanation
Indices: 394137--394168 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
394127 TATCATAAAT
394137 TTTTTTC-TTCTTTTTC
1 TTTTTTCTTTCTTTTTC
394153 TTTTTTCTTTCTTTTT
1 TTTTTTCTTTCTTTTT
394169 ATGTGATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTTTCTTTCTTTTTC
Found at i:394755 original size:17 final size:17
Alignment explanation
Indices: 394735--394773 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
394725 AACAATGTAG
394735 ATGCAACGACAATAAAA
1 ATGCAACGACAATAAAA
* * *
394752 ATGCAATGACATTAATA
1 ATGCAACGACAATAAAA
394769 ATGCA
1 ATGCA
394774 GGGACAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.15, G:0.13, T:0.21
Consensus pattern (17 bp):
ATGCAACGACAATAAAA
Found at i:401007 original size:36 final size:36
Alignment explanation
Indices: 400960--401032 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
400950 AGAAATGAGT
*
400960 TAACGAATACATCAAAATATACTATCTCTAGGCTAC
1 TAACGAATACATCAAAATATACTATCACTAGGCTAC
**
400996 TAACGAATACATCGGAATATACTATCACTAGGCTAC
1 TAACGAATACATCAAAATATACTATCACTAGGCTAC
401032 T
1 T
401033 CGGATTACCC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.40, C:0.22, G:0.11, T:0.27
Consensus pattern (36 bp):
TAACGAATACATCAAAATATACTATCACTAGGCTAC
Found at i:407722 original size:30 final size:30
Alignment explanation
Indices: 407686--407750 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
407676 TTCCAGTCAA
*
407686 TATAACATTGTAGTGTCACTACCAACTCAG
1 TATAACATTGCAGTGTCACTACCAACTCAG
407716 TATAACATTGCAGTGTCACTACCAACTCAG
1 TATAACATTGCAGTGTCACTACCAACTCAG
407746 TATAA
1 TATAA
407751 AACAGTTGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.29
Consensus pattern (30 bp):
TATAACATTGCAGTGTCACTACCAACTCAG
Found at i:407824 original size:39 final size:39
Alignment explanation
Indices: 407781--407890 Score: 166
Period size: 39 Copynumber: 2.8 Consensus size: 39
407771 ATGACCTGGT
*
407781 AGTGTTTACAGTATCACTGCCAGCTCAGTATAACATTGC
1 AGTGTTTACAGTGTCACTGCCAGCTCAGTATAACATTGC
* * *
407820 AGTGTCTACAGTGTCACTGCCAGTTCAGTATAACATTGT
1 AGTGTTTACAGTGTCACTGCCAGCTCAGTATAACATTGC
* *
407859 AGTATTTATAGTGTCACTGCCAGCTCAGTATA
1 AGTGTTTACAGTGTCACTGCCAGCTCAGTATA
407891 TTTTCGACGT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 63 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (39 bp):
AGTGTTTACAGTGTCACTGCCAGCTCAGTATAACATTGC
Found at i:413690 original size:20 final size:21
Alignment explanation
Indices: 413662--413701 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
413652 GAAAGCTCTA
*
413662 GATTGTTTGT-TTTCTTTTCT
1 GATTGTTTGTGTTTATTTTCT
*
413682 GATTTTTTGTGTTTATTTTC
1 GATTGTTTGTGTTTATTTTC
413702 ACACTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.07, C:0.07, G:0.15, T:0.70
Consensus pattern (21 bp):
GATTGTTTGTGTTTATTTTCT
Found at i:419588 original size:25 final size:23
Alignment explanation
Indices: 419560--419617 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 23
419550 AGTGCTGGGC
419560 AACAGAGAGCAC-ACACAGTGCTAA
1 AACAGAGAGCACGACAC-GTGCT-A
* *
419584 TAACAAAGAGCACGAGACGTGCTA
1 -AACAGAGAGCACGACACGTGCTA
419608 AACAGAGAGC
1 AACAGAGAGC
419618 GCACTAGTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 9 0.31
24 1 0.03
25 16 0.55
26 3 0.10
ACGTcount: A:0.45, C:0.22, G:0.24, T:0.09
Consensus pattern (23 bp):
AACAGAGAGCACGACACGTGCTA
Found at i:424370 original size:3 final size:3
Alignment explanation
Indices: 424364--424410 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
424354 ATTAACCTAA
424364 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
424411 AAAGTTGGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:426551 original size:2 final size:2
Alignment explanation
Indices: 426544--426574 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
426534 CCGACATAAT
*
426544 AC AC AC AC AC AC AC AC AC AC AC AA AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
426575 TTATATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.45, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:427357 original size:16 final size:18
Alignment explanation
Indices: 427325--427367 Score: 56
Period size: 16 Copynumber: 2.5 Consensus size: 18
427315 TTTCATAATT
427325 TTCTCTCATTTTCTTCT-C
1 TTCTCTC-TTTTCTTCTGC
427343 TTCTCTCTTTT-TTCTGC
1 TTCTCTCTTTTCTTCTGC
427360 TT-TCTCTT
1 TTCTCTCTT
427368 CAACAACGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 10 0.42
17 7 0.29
18 7 0.29
ACGTcount: A:0.02, C:0.30, G:0.02, T:0.65
Consensus pattern (18 bp):
TTCTCTCTTTTCTTCTGC
Found at i:429517 original size:21 final size:21
Alignment explanation
Indices: 429493--429541 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
429483 GGTTGGGAAG
429493 ATGATCCACCTTGGTAAAACA
1 ATGATCCACCTTGGTAAAACA
*
429514 ATGATCTACCTTGGTAAAACA
1 ATGATCCACCTTGGTAAAACA
429535 ATGATCC
1 ATGATCC
429542 CAGATGTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (21 bp):
ATGATCCACCTTGGTAAAACA
Found at i:430248 original size:18 final size:17
Alignment explanation
Indices: 430200--430249 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
430190 CAAATGATAT
*
430200 TTTTATTAATAGTAATA
1 TTTTATTAATAATAATA
* *
430217 TTATAATAAGTAATAATA
1 TTTTATTAA-TAATAATA
430235 TTTTATTAATTAATA
1 TTTTATTAA-TAATA
430250 TTATATAGCA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 7 0.27
18 19 0.73
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
TTTTATTAATAATAATA
Found at i:431254 original size:59 final size:59
Alignment explanation
Indices: 431181--431342 Score: 245
Period size: 59 Copynumber: 2.7 Consensus size: 59
431171 CTAGAACCAA
* *
431181 AAGCAAGGCTGTTAAGCTACTTTCTTTCCCTAGATGCATATATTGAA-TCAGAAGTAAGG
1 AAGCAAGGCTGTTAAGCTACTTGCTTTCCCTAGATGCATATACTGAACT-AGAAGTAAGG
* ** *
431240 AAGCAAGGTTGTTAAGCTACTTGCTTTCCCTAGATGTGTATACTGAACTGGAAGTAAGG
1 AAGCAAGGCTGTTAAGCTACTTGCTTTCCCTAGATGCATATACTGAACTAGAAGTAAGG
*
431299 AAGCAAGGCTGCTAAGCTACTTGCTTTCCCTAGATGCATATACT
1 AAGCAAGGCTGTTAAGCTACTTGCTTTCCCTAGATGCATATACT
431343 AAGCTCGCTA
Statistics
Matches: 92, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
59 91 0.99
60 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (59 bp):
AAGCAAGGCTGTTAAGCTACTTGCTTTCCCTAGATGCATATACTGAACTAGAAGTAAGG
Found at i:432190 original size:16 final size:16
Alignment explanation
Indices: 432169--432199 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
432159 CTATGAGTAG
432169 TTATATTAATTTTATT
1 TTATATTAATTTTATT
*
432185 TTATATTATTTTTAT
1 TTATATTAATTTTAT
432200 GAGTTTTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATATTAATTTTATT
Found at i:449861 original size:23 final size:24
Alignment explanation
Indices: 449828--449876 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
449818 ACAATTAATT
* *
449828 CATTTTCTATTA-ATTTGCTCTGA
1 CATTTTATATTATATTTGCACTGA
449851 CATTTTATATTATATTTGCACTGA
1 CATTTTATATTATATTTGCACTGA
449875 CA
1 CA
449877 AATTTAACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.27, C:0.16, G:0.08, T:0.49
Consensus pattern (24 bp):
CATTTTATATTATATTTGCACTGA
Found at i:459197 original size:23 final size:24
Alignment explanation
Indices: 459164--459212 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
459154 ACAATCAATT
* *
459164 CATTTTCTATTA-ATTTGCTCTGA
1 CATTTTATATTATATTTGCACTGA
459187 CATTTTATATTATATTTGCACTGA
1 CATTTTATATTATATTTGCACTGA
459211 CA
1 CA
459213 GATTTAACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.27, C:0.16, G:0.08, T:0.49
Consensus pattern (24 bp):
CATTTTATATTATATTTGCACTGA
Found at i:460796 original size:22 final size:22
Alignment explanation
Indices: 460758--460801 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
460748 ACTTTTATCA
*
460758 TTAAGCCTTAATTAACCCATTT
1 TTAAGCCTTAATAAACCCATTT
*
460780 TTAA-CCTTAATCAAACCTATTT
1 TTAAGCCTTAAT-AAACCCATTT
460802 ATACTTAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (22 bp):
TTAAGCCTTAATAAACCCATTT
Found at i:465271 original size:18 final size:17
Alignment explanation
Indices: 465223--465272 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
465213 CAAATTATAT
*
465223 TTTTATTAATAATAATA
1 TTTTATTAATAATAACA
* *
465240 TTATAATAAGTAATAACA
1 TTTTATTAA-TAATAACA
465258 TTTTATTAATTAATA
1 TTTTATTAA-TAATA
465273 TTATAAAGCA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 7 0.27
18 19 0.73
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (17 bp):
TTTTATTAATAATAACA
Found at i:469274 original size:4 final size:4
Alignment explanation
Indices: 469248--469294 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
469238 TAACTAATAA
* * * *
469248 ATAT ATGT ATGT ATGT ATGT ATAT ATAT ATAT ATAT ATAT ATAT ATA
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATA
469295 ATACGACAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (4 bp):
ATAT
Found at i:470338 original size:81 final size:83
Alignment explanation
Indices: 470234--470403 Score: 236
Period size: 81 Copynumber: 2.1 Consensus size: 83
470224 CTTGTAAAAT
* ** *
470234 ATTGGATGACGTCTTCAATCTGCCTCATGATCGGGGTAAAAGATTGGATG-G-CTTCAATTTGCC
1 ATTGGATGACGTCTTCAATCTGCCCCATGATCAAGGTAAAAGATTGGATGAGTCTTCAATCTGCC
470297 CCATAATCGAGGTAAGAG
66 CCATAATCGAGGTAAGAG
* *
470315 ATTGGATGACGTCTTCAATCTGCCCCATGATCAAGGTAAGAGATTGGATGATGTCTTTAATCTGC
1 ATTGGATGACGTCTTCAATCTGCCCCATGATCAAGGTAAAAGATTGGATGA-GTCTTCAATCTGC
* * *
470380 CCTATGATCGGGGTAAGAG
65 CCCATAATCGAGGTAAGAG
470399 ATTGG
1 ATTGG
470404 TGTGTAGCTT
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
81 46 0.60
83 1 0.01
84 30 0.39
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (83 bp):
ATTGGATGACGTCTTCAATCTGCCCCATGATCAAGGTAAAAGATTGGATGAGTCTTCAATCTGCC
CCATAATCGAGGTAAGAG
Found at i:470342 original size:42 final size:42
Alignment explanation
Indices: 470234--470403 Score: 229
Period size: 42 Copynumber: 4.1 Consensus size: 42
470224 CTTGTAAAAT
* * *
470234 ATTGGATGACGTCTTCAATCTGCCTCATGATCGGGGTAAAAG
1 ATTGGATGACGTCTTCAATCTGCCCCATGATCGAGGTAAGAG
* *
470276 ATTGGATG--G-CTTCAATTTGCCCCATAATCGAGGTAAGAG
1 ATTGGATGACGTCTTCAATCTGCCCCATGATCGAGGTAAGAG
*
470315 ATTGGATGACGTCTTCAATCTGCCCCATGATCAAGGTAAGAG
1 ATTGGATGACGTCTTCAATCTGCCCCATGATCGAGGTAAGAG
* * * *
470357 ATTGGATGATGTCTTTAATCTGCCCTATGATCGGGGTAAGAG
1 ATTGGATGACGTCTTCAATCTGCCCCATGATCGAGGTAAGAG
470399 ATTGG
1 ATTGG
470404 TGTGTAGCTT
Statistics
Matches: 112, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
39 33 0.29
40 1 0.01
41 1 0.01
42 77 0.69
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (42 bp):
ATTGGATGACGTCTTCAATCTGCCCCATGATCGAGGTAAGAG
Found at i:470811 original size:49 final size:49
Alignment explanation
Indices: 470708--470931 Score: 200
Period size: 49 Copynumber: 4.5 Consensus size: 49
470698 CTCCATTATG
* * * *** **
470708 GCCTCAATCCTTCCCATTACATCTTCTAAGGTACCGGGTTCGCCGTTGTG
1 GCCTCAATCCTTCCCATCACATCTTC-ATGGTACCGGATTTATCGTTGCA
* * *
470758 GCCTCAA-CCTTTCCCTTCATATCTTCATGGTACCGGATTTACCGTTGCA
1 GCCTCAATCC-TTCCCATCACATCTTCATGGTACCGGATTTATCGTTGCA
* * * *
470807 GCCTCAATCCTTCCCATCACATCTTCTAAGGTACCGGGTTTTTCGTTGTA
1 GCCTCAATCCTTCCCATCACATCTTC-ATGGTACCGGATTTATCGTTGCA
* * * * * * *
470857 GTCT-TAGCCTTTCCCTTCATATCTTCATGGAACCGGATTTATCGTTGCG
1 GCCTCAATCC-TTCCCATCACATCTTCATGGTACCGGATTTATCGTTGCA
470906 GCCTCAATCCTTCCCATCACATCTTC
1 GCCTCAATCCTTCCCATCACATCTTC
470932 TAAGGTAATG
Statistics
Matches: 137, Mismatches: 32, Indels: 11
0.76 0.18 0.06
Matches are distributed among these distances:
49 77 0.56
50 60 0.44
ACGTcount: A:0.17, C:0.32, G:0.16, T:0.35
Consensus pattern (49 bp):
GCCTCAATCCTTCCCATCACATCTTCATGGTACCGGATTTATCGTTGCA
Found at i:470818 original size:99 final size:99
Alignment explanation
Indices: 470707--471073 Score: 443
Period size: 99 Copynumber: 3.7 Consensus size: 99
470697 TCTCCATTAT
*
470707 GGCCTCAATCCTTCCCATTACATCTTCTAAGGTACCGGGTTCGCCGTTGTGGCCTCAACCTTTCC
1 GGCCTCAATCCTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCGTTGTGGCCTCAACCTTTCC
470772 CTTCATATCTTCATGGTACCGGATTTACCGTTGC
66 CTTCATATCTTCATGGTACCGGATTTACCGTTGC
* *** * * * *
470806 AGCCTCAATCCTTCCCATCACATCTTCTAAGGTACCGGGTTTTTCGTTGTAGTCTTAGCCTTTCC
1 GGCCTCAATCCTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCGTTGTGGCCTCAACCTTTCC
* *
470871 CTTCATATCTTCATGGAACCGGATTTATCGTTGC
66 CTTCATATCTTCATGGTACCGGATTTACCGTTGC
** * * *
470905 GGCCTCAATCCTTCCCATCACATCTTCTAAGGTAATGGGTTCGTCATTGCGGCCTCAACCTTTCC
1 GGCCTCAATCCTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCGTTGTGGCCTCAACCTTTCC
** *** *
470970 CTT--TAT-TTCCATGGTACTAGATCCGCCGTTAC
66 CTTCATATCTT-CATGGTACCGGATTTACCGTTGC
* * ** * * *
471002 GGCCTCGATCTTTCCCATCATGTCTTCTAAGGTATCGAGTTCACCGTTGTGGCCTCAACCTTTCC
1 GGCCTCAATCCTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCGTTGTGGCCTCAACCTTTCC
471067 CTTCATA
66 CTTCATA
471074 CCTCTATGTT
Statistics
Matches: 224, Mismatches: 41, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
96 2 0.01
97 75 0.33
99 147 0.66
ACGTcount: A:0.17, C:0.31, G:0.17, T:0.35
Consensus pattern (99 bp):
GGCCTCAATCCTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCGTTGTGGCCTCAACCTTTCC
CTTCATATCTTCATGGTACCGGATTTACCGTTGC
Found at i:470881 original size:149 final size:150
Alignment explanation
Indices: 470568--470882 Score: 350
Period size: 149 Copynumber: 2.1 Consensus size: 150
470558 CAGCCTCACT
** * *
470568 CTTTCCCTTCATATC-TCTAAGGTTTAAGGTTCGTCGTTGCGGCTTCAACCTTTCCCTCCATATC
1 CTTTCCCTTCATATCTTCTAAGGTACAAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTCCATATC
** * * *
470632 TCCATGGTACAAGATTTTTCACTGCGGCCTCAATCTTTCCTATCACATCTTCTAAGGTACCGGGT
66 TCCATGGTACAAGATTTACCACTGCAGCCTCAATCCTTCCCATCACATCTTCTAAGGTACCGGGT
* *
470697 TCTCCATTATGGCCTCAATC
131 TCTCCATTATAGCCTCAAGC
* ** * *
470717 C-TTCCCATT-ACATCTTCTAAGGTACCGGGTTCGCCGTTGTGGCCTCAACCTTTCCCTTCATAT
1 CTTTCCC-TTCATATCTTCTAAGGTACAAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTCCATAT
* ** **
470780 CTTCATGGTACCGGATTTACCGTTGCAGCCTCAATCCTTCCCATCACATCTTCTAAGGTACCGGG
65 CTCCATGGTACAAGATTTACCACTGCAGCCTCAATCCTTCCCATCACATCTTCTAAGGTACCGGG
* * * * * *
470845 TTTTTCGTTGTAGTCT-TAGC
130 TTCTCCATTATAGCCTCAAGC
470865 CTTTCCCTTCATATCTTC
1 CTTTCCCTTCATATCTTC
470883 ATGGAACCGG
Statistics
Matches: 134, Mismatches: 28, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
148 14 0.10
149 120 0.90
ACGTcount: A:0.17, C:0.31, G:0.15, T:0.37
Consensus pattern (150 bp):
CTTTCCCTTCATATCTTCTAAGGTACAAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTCCATATC
TCCATGGTACAAGATTTACCACTGCAGCCTCAATCCTTCCCATCACATCTTCTAAGGTACCGGGT
TCTCCATTATAGCCTCAAGC
Found at i:470970 original size:50 final size:50
Alignment explanation
Indices: 470654--471067 Score: 261
Period size: 50 Copynumber: 8.4 Consensus size: 50
470644 GATTTTTCAC
* * *
470654 TGCGGCCTCAATCTTTCCTATCACATCTTCTAAGGTACCGGGTTC-TCCAT
1 TGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCAT-CGT
** * **
470704 TATGGCCTCAATCC-TTCCCATTACATCTTCTAAGGTACCGGGTTCGCCGT
1 TGCGGCCTCAA-CCTTTCCCATCACATCTTCTAAGGTACCGGGTTCATCGT
* * * * * * *
470754 TGTGGCCTCAACCTTTCCCTTCATATCTTC-ATGGTACCGGATTTACCGT
1 TGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCATCGT
* **
470803 TGCAGCCTCAATCC-TTCCCATCACATCTTCTAAGGTACCGGGTTTTTCGT
1 TGCGGCCTCAA-CCTTTCCCATCACATCTTCTAAGGTACCGGGTTCATCGT
** * * * * * * * * *
470853 TGTAGTCTTAGCCTTTCCCTTCATATCTTC-ATGGAACCGGATTTATCGT
1 TGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCATCGT
** * *
470902 TGCGGCCTCAATCC-TTCCCATCACATCTTCTAAGGTAATGGGTTCGTCAT
1 TGCGGCCTCAA-CCTTTCCCATCACATCTTCTAAGGTACCGGGTTCATCGT
** * * ** * * **
470952 TGCGGCCTCAACCTTTCCC-T-TTAT-TTCCATGGTACTAGATCCGCCGT
1 TGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCATCGT
* * * ** * * *
470999 TACGGCCTCGATCTTTCCCATCATGTCTTCTAAGGTATCGAGTTCACCGT
1 TGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCATCGT
*
471049 TGTGGCCTCAACCTTTCCC
1 TGCGGCCTCAACCTTTCCC
471068 TTCATACCTC
Statistics
Matches: 276, Mismatches: 76, Indels: 24
0.73 0.20 0.06
Matches are distributed among these distances:
47 31 0.11
48 3 0.01
49 82 0.30
50 159 0.58
51 1 0.00
ACGTcount: A:0.17, C:0.31, G:0.17, T:0.35
Consensus pattern (50 bp):
TGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCATCGT
Found at i:471936 original size:6 final size:6
Alignment explanation
Indices: 471925--471966 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
471915 TCGATCTCTC
*
471925 CTTTTT C-TTTT -TTCTT CTCTTTT CTTTTT CTTTTT CTTTTT C
1 CTTTTT CTTTTT CTTTTT CT-TTTT CTTTTT CTTTTT CTTTTT C
471967 CTTTCTTTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
5 7 0.23
6 19 0.61
7 5 0.16
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (6 bp):
CTTTTT
Found at i:471962 original size:17 final size:17
Alignment explanation
Indices: 471925--471974 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
471915 TCGATCTCTC
*
471925 CTTTTTCTTTT-TTCTT
1 CTTTTTCTTTTCTTTTT
471941 CTCTTTTCTTTTTCTTTTT
1 CT-TTTTC-TTTTCTTTTT
*
471960 CTTTTTCCTTTCTTT
1 CTTTTTCTTTTCTTT
471975 CCCTTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 2 0.07
17 12 0.41
18 9 0.31
19 6 0.21
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (17 bp):
CTTTTTCTTTTCTTTTT
Found at i:471971 original size:23 final size:23
Alignment explanation
Indices: 471925--471983 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
471915 TCGATCTCTC
*
471925 CTTTTTCTTTTTTCTTCTCTTTT
1 CTTTTTCTTTTTTCTTCTCCTTT
*
471948 CTTTTTC-TTTTTCTTTTTCCTTT
1 CTTTTTCTTTTTTC-TTCTCCTTT
**
471971 CTTTCCCTTTTTT
1 CTTTTTCTTTTTT
471984 ATTTTTTGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 6 0.20
23 19 0.63
24 5 0.17
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (23 bp):
CTTTTTCTTTTTTCTTCTCCTTT
Found at i:472860 original size:7 final size:7
Alignment explanation
Indices: 472843--472875 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
472833 TTTTCTTTGA
472843 TTTTTTC
1 TTTTTTC
472850 -TTTTTC
1 TTTTTTC
472856 TTTTTTC
1 TTTTTTC
472863 TTTTTTC
1 TTTTTTC
472870 TTTTTT
1 TTTTTT
472876 TTTCTTGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:476829 original size:21 final size:21
Alignment explanation
Indices: 476805--476849 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
476795 GAACAATACA
476805 TAAAACAAATAAA-ATAATATT
1 TAAAACAAATAAATAT-ATATT
* *
476826 TAAAATAAATACATATATATT
1 TAAAACAAATAAATATATATT
476847 TAA
1 TAA
476850 TTGTATTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAAACAAATAAATATATATT
Found at i:477089 original size:27 final size:28
Alignment explanation
Indices: 477059--477114 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
477049 GGATTTAAAA
477059 AATTT-AAAGAAACAAAAATGAA-AGGGT
1 AATTTAAAAGAAACAAAAAT-AAGAGGGT
*
477086 AATTTCAAAAGGAACAAAAATAAGAGGGT
1 AATTT-AAAAGAAACAAAAATAAGAGGGT
477115 TGAATTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 5 0.20
28 2 0.08
29 18 0.72
ACGTcount: A:0.57, C:0.05, G:0.20, T:0.18
Consensus pattern (28 bp):
AATTTAAAAGAAACAAAAATAAGAGGGT
Found at i:478039 original size:21 final size:20
Alignment explanation
Indices: 478011--478050 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
478001 TTTTAATCTG
478011 TTTTTTTTT-TCATTTTTTA
1 TTTTTTTTTCTCATTTTTTA
*
478030 TTTTTATTTTCTCCTTTTTTA
1 TTTTT-TTTTCTCATTTTTTA
478051 ATCGATAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 4 0.22
21 9 0.50
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTTTTTTCTCATTTTTTA
Found at i:481688 original size:37 final size:38
Alignment explanation
Indices: 481551--481705 Score: 208
Period size: 38 Copynumber: 4.1 Consensus size: 38
481541 AAAGTGAAAC
* *
481551 CATTTT-TTTCTTATTTTGCACATTAAAAATGTCAAAT
1 CATTTTCTTTCCTATTTTGCACATTAAAAATTTCAAAT
*
481588 CATTTTCTTTCCTATTTTGCTCATTAAAAATATT-AAAT
1 CATTTTCTTTCCTATTTTGCACATTAAAAAT-TTCAAAT
* *
481626 CATTGTTTTTTCCTATTTTACACATTAAAAATTTCAAAT
1 CATT-TTCTTTCCTATTTTGCACATTAAAAATTTCAAAT
* *
481665 CATTTTCTTT-CTATTTTTCACATTAAAAATCTCAAAT
1 CATTTTCTTTCCTATTTTGCACATTAAAAATTTCAAAT
481702 CATT
1 CATT
481706 AAATGGAACA
Statistics
Matches: 105, Mismatches: 9, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
37 35 0.33
38 37 0.35
39 33 0.31
ACGTcount: A:0.32, C:0.16, G:0.03, T:0.49
Consensus pattern (38 bp):
CATTTTCTTTCCTATTTTGCACATTAAAAATTTCAAAT
Found at i:481943 original size:22 final size:22
Alignment explanation
Indices: 481900--481943 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
481890 TTGAAAATAG
* *
481900 TTTTCGAAAATTTATTTATTTT
1 TTTTAGAAAATTGATTTATTTT
481922 TTTTAGAAAATTGA--TATTTT
1 TTTTAGAAAATTGATTTATTTT
481942 TT
1 TT
481944 AGTGTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
22 12 0.60
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTTAGAAAATTGATTTATTTT
Found at i:484785 original size:11 final size:11
Alignment explanation
Indices: 484750--484789 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
484740 ATAACATTTC
484750 AAATAT-AAAT
1 AAATATAAAAT
484760 -AAT-TAAAAT
1 AAATATAAAAT
484769 ATAATATAAAAT
1 A-AATATAAAAT
484781 AAATATAAA
1 AAATATAAA
484790 TAATTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
8 1 0.04
9 7 0.27
11 11 0.42
12 7 0.27
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AAATATAAAAT
Found at i:484793 original size:20 final size:20
Alignment explanation
Indices: 484751--484791 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
484741 TAACATTTCA
*
484751 AATATAAATAATTAAAATAT
1 AATATAAATAAATAAAATAT
484771 AATATAAAATAAATATAAATA
1 AATAT-AAATAAATA-AAATA
484792 ATTATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 8 0.44
22 5 0.28
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AATATAAATAAATAAAATAT
Found at i:486681 original size:18 final size:17
Alignment explanation
Indices: 486658--486691 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
486648 ATCCCCCAAA
486658 AAAATAATATTAATTTTT
1 AAAATAATATT-ATTTTT
486676 AAAATAATATTATTTT
1 AAAATAATATTATTTT
486692 ATTTTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAAATAATATTATTTTT
Found at i:491747 original size:21 final size:21
Alignment explanation
Indices: 491713--491752 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
491703 TAAAATTTCA
*
491713 TTAATGACGCCAAAACACAAGT
1 TTAATGAC-CCCAAACACAAGT
491735 TTAAT-ACCCCAAACACAA
1 TTAATGACCCCAAACACAA
491753 CCAATATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 2 0.12
22 5 0.29
ACGTcount: A:0.47, C:0.28, G:0.07, T:0.17
Consensus pattern (21 bp):
TTAATGACCCCAAACACAAGT
Found at i:500970 original size:20 final size:22
Alignment explanation
Indices: 500931--500977 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 22
500921 AATTAGTATT
500931 AACAT-TATTAGAAGGTTTCTA
1 AACATATATTAGAAGGTTTCTA
500952 AACATATATTA-AA-GTTTCTA
1 AACATATATTAGAAGGTTTCTA
500972 AACATA
1 AACATA
500978 CCTTGAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.52
21 7 0.28
22 5 0.20
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.36
Consensus pattern (22 bp):
AACATATATTAGAAGGTTTCTA
Found at i:500986 original size:20 final size:20
Alignment explanation
Indices: 500945--500989 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
500935 TTATTAGAAG
*
500945 GTTTCTAAACATATATTAAA
1 GTTTCTAAACATACATTAAA
* *
500965 GTTTCTAAACATACCTTGAA
1 GTTTCTAAACATACATTAAA
500985 GTTTC
1 GTTTC
500990 GTTAAGGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.40
Consensus pattern (20 bp):
GTTTCTAAACATACATTAAA
Found at i:504790 original size:26 final size:26
Alignment explanation
Indices: 504750--504809 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
504740 AATTTTCTTG
504750 AAATTTTACTAGGGGGAAAATAGTCA
1 AAATTTTACTAGGGGGAAAATAGTCA
* *
504776 AAATTTTGCT-GGGGGTAAAATCGTCA
1 AAATTTTACTAGGGGG-AAAATAGTCA
504802 AAATTTTA
1 AAATTTTA
504810 TTAAGGTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 5 0.17
26 25 0.83
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (26 bp):
AAATTTTACTAGGGGGAAAATAGTCA
Found at i:505684 original size:35 final size:35
Alignment explanation
Indices: 505638--505712 Score: 150
Period size: 35 Copynumber: 2.1 Consensus size: 35
505628 TTTCCTACTC
505638 AATACCTCTCATCTTTTACAATTCTAATATAAGTA
1 AATACCTCTCATCTTTTACAATTCTAATATAAGTA
505673 AATACCTCTCATCTTTTACAATTCTAATATAAGTA
1 AATACCTCTCATCTTTTACAATTCTAATATAAGTA
505708 AATAC
1 AATAC
505713 TTTATCAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.39, C:0.20, G:0.03, T:0.39
Consensus pattern (35 bp):
AATACCTCTCATCTTTTACAATTCTAATATAAGTA
Found at i:513218 original size:58 final size:58
Alignment explanation
Indices: 513062--513422 Score: 192
Period size: 59 Copynumber: 6.1 Consensus size: 58
513052 GATACTCGGG
* ** **
513062 GGGTAAAATGGTAATTTTGGGAAAATTCGGGGTTAAAAAATGGAATTTTTAAACATTCTA
1 GGGTAAAATGGTAATTTTTGGAAGTTTCGGGGTT--AAAATGGAATTTTTGGACATTCTA
* * * *
513122 GGGTAAAAAGGTAA-TTTT-GAGAGTTTCGAGGTCGAAAATGGAGTTTTTGGACA-TCTAA
1 GGGTAAAATGGTAATTTTTGGA-AGTTTCGGGGT-TAAAATGGAATTTTTGGACATTCT-A
* *
513180 GGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAATGGAATTTTTGGA-AGTTTTA
1 GGGTAAAATGGTAATTTTTGGAAGTTTCGGGGTTAAAATGGAATTTTTGGACA-TTCTA
* * ** * *
513238 GGGTCAAAAAT-G-AGATTTTTGGGA-CTTCAAAGGTAAAAATGGAATTTTTGGA-AGTTTTAA
1 GGGT--AAAATGGTA-ATTTTTGGAAGTTTC-GGGGTTAAAATGGAATTTTTGGACA-TTCT-A
* * * * * *
513298 GGTTAAAAATGG-GATTTTTGGAAG-TTCGGGGGTAAAAAGGGAATTTTTGGA-AGTTTTG
1 GGGT-AAAATGGTAATTTTTGGAAGTTTC-GGGGTTAAAATGGAATTTTTGGACA-TTCTA
* * ** * *
513356 GGGTAAAAAATGG-GATTCTTAAAAGTTT-GAGGGTAAAAATGGAATTTTTGGA-AGTTCAA
1 GGGT--AAAATGGTAATTTTTGGAAGTTTCG-GGGTTAAAATGGAATTTTTGGACA-TTCTA
513415 GGGTAAAA
1 GGGTAAAA
513423 ACAAAATTTT
Statistics
Matches: 247, Mismatches: 37, Indels: 37
0.77 0.12 0.12
Matches are distributed among these distances:
57 8 0.03
58 60 0.24
59 152 0.62
60 27 0.11
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.34
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTTGGAAGTTTCGGGGTTAAAATGGAATTTTTGGACATTCTA
Found at i:513282 original size:59 final size:59
Alignment explanation
Indices: 513184--513423 Score: 275
Period size: 59 Copynumber: 4.1 Consensus size: 59
513174 ATCTAAGGGT
* * * *
513184 AAAATGGTAATTTTTGGAAGTTTTG-GGGTTAAAATGGAATTTTTGGAAGTTTTAGGGTCA
1 AAAATGG-GATTTTTGGAAG-TTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTAA
* * * * * * *
513244 AAAATGAGATTTTTGGGACTTCAAAGGTAAAAATGGAATTTTTGGAAGTTTTAAGGTTA
1 AAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTAA
* * *
513303 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAAAGGGAATTTTTGGAAGTTTTGGGGTAA
1 AAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTAA
* ** * **
513362 AAAATGGGATTCTTAAAAGTTTGAGGGTAAAAATGGAATTTTTGGAAGTTCAAGGGTAA
1 AAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTAA
513421 AAA
1 AAA
513424 CAAAATTTTA
Statistics
Matches: 150, Mismatches: 29, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
58 2 0.01
59 142 0.95
60 6 0.04
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (59 bp):
AAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTAA
Found at i:513417 original size:29 final size:29
Alignment explanation
Indices: 513156--513423 Score: 245
Period size: 29 Copynumber: 9.1 Consensus size: 29
513146 TTCGAGGTCG
* *
513156 AAAATGGAGTTTTTGGACA-TCTAAGGGT-
1 AAAATGGAATTTTTGGA-AGTTTAAGGGTA
** *
513184 AAAATGGTAATTTTTGGAAGTTTTGGGGTT
1 AAAATGG-AATTTTTGGAAGTTTAAGGGTA
*
513214 AAAATGGAATTTTTGGAAGTTTTAGGGTCA
1 AAAATGGAATTTTTGGAAGTTTAAGGGT-A
* * * *
513244 AAAAT-GAGATTTTTGGGACTTCAAAGGTA
1 AAAATGGA-ATTTTTGGAAGTTTAAGGGTA
*
513273 AAAATGGAATTTTTGGAAGTTTTAAGGTTA
1 AAAATGGAATTTTTGGAAG-TTTAAGGGTA
* ***
513303 AAAATGGGATTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTAAGGGTA
* **
513332 AAAAGGGAATTTTTGGAAGTTTTGGGGTAA
1 AAAATGGAATTTTTGGAAGTTTAAGGGT-A
* * ** *
513362 AAAATGGGATTCTTAAAAGTTTGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTAAGGGTA
*
513391 AAAATGGAATTTTTGGAAGTTCAAGGGTA
1 AAAATGGAATTTTTGGAAGTTTAAGGGTA
513420 AAAA
1 AAAA
513424 CAAAATTTTA
Statistics
Matches: 194, Mismatches: 38, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
28 8 0.04
29 110 0.57
30 76 0.39
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTAAGGGTA
Found at i:514566 original size:3 final size:3
Alignment explanation
Indices: 514558--514642 Score: 170
Period size: 3 Copynumber: 28.3 Consensus size: 3
514548 TCATTTTCCT
514558 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
514606 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
514643 CAAAAGCTTG
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 82 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:515344 original size:17 final size:16
Alignment explanation
Indices: 515307--515371 Score: 67
Period size: 17 Copynumber: 3.9 Consensus size: 16
515297 AAATAAATTT
*
515307 TAAATTTAAATTTCAAC
1 TAAATTTAAATTT-AAA
515324 TAAATTTAAATTTAGAA
1 TAAATTTAAATTTA-AA
* *
515341 TAAACTTAATTTTAAAA
1 TAAATTTAAATTT-AAA
*
515358 TAAATTTAAGTTTA
1 TAAATTTAAATTTA
515372 TTGGGCCCAG
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
16 2 0.05
17 38 0.93
18 1 0.02
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:515354 original size:23 final size:22
Alignment explanation
Indices: 515302--515356 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
515292 ATTTAAAATA
*
515302 AATTTTAAATTTAAATTTCAACT
1 AATTTTAAATTTAAA-TTAAACT
*
515325 AAATTTAAATTTAGAA-TAAACTT
1 AATTTTAAATTTA-AATTAAAC-T
515348 AATTTTAAA
1 AATTTTAAA
515357 ATAAATTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 4 0.15
23 21 0.78
24 2 0.07
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (22 bp):
AATTTTAAATTTAAATTAAACT
Found at i:516749 original size:18 final size:18
Alignment explanation
Indices: 516726--516827 Score: 123
Period size: 18 Copynumber: 5.7 Consensus size: 18
516716 AAGGAATAGT
516726 ATACTGGCTCATTTGAGC
1 ATACTGGCTCATTTGAGC
** *
516744 ATACTGGCTNGTTCGAGC
1 ATACTGGCTCATTTGAGC
* * *
516762 ATACTAGCTCGTTAGAGC
1 ATACTGGCTCATTTGAGC
*
516780 ATACTAGCTCATTTGAGC
1 ATACTGGCTCATTTGAGC
* *
516798 ATACTGGCTCGTTTTAGC
1 ATACTGGCTCATTTGAGC
516816 ATACTGGCTCAT
1 ATACTGGCTCAT
516828 GAGAGTGATA
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 72 1.00
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32
Consensus pattern (18 bp):
ATACTGGCTCATTTGAGC
Found at i:516780 original size:36 final size:36
Alignment explanation
Indices: 516726--516845 Score: 132
Period size: 36 Copynumber: 3.3 Consensus size: 36
516716 AAGGAATAGT
* **
516726 ATACTGGCTCATTTGAGCATACTGGCTNGTTCGAGC
1 ATACTGGCTCGTTTGAGCATACTGGCTCATTCGAGC
* * * *
516762 ATACTAGCTCGTTAGAGCATACTAGCTCATTTGAGC
1 ATACTGGCTCGTTTGAGCATACTGGCTCATTCGAGC
* ** *
516798 ATACTGGCTCGTTTTAGCATACTGGCTCATGAGAGTG
1 ATACTGGCTCGTTTGAGCATACTGGCTCATTCGAG-C
516835 ATACTGGCTCG
1 ATACTGGCTCG
516846 AAAGAGCGAC
Statistics
Matches: 69, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
36 58 0.84
37 11 0.16
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (36 bp):
ATACTGGCTCGTTTGAGCATACTGGCTCATTCGAGC
Found at i:519117 original size:26 final size:26
Alignment explanation
Indices: 519055--519117 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
519045 TGAGTTATCG
*
519055 ACTCGCCTTGCGAGTAGGACTCACAA
1 ACTCGCCTTGCGAGCAGGACTCACAA
* * * *
519081 ACCCGCGTTGCGAGCAGGACTCGCGA
1 ACTCGCCTTGCGAGCAGGACTCACAA
519107 ACTCGCCTTGC
1 ACTCGCCTTGC
519118 ATCTAGTCTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.21, C:0.35, G:0.27, T:0.17
Consensus pattern (26 bp):
ACTCGCCTTGCGAGCAGGACTCACAA
Found at i:523058 original size:22 final size:22
Alignment explanation
Indices: 523017--523059 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
523007 GTTTTAAATT
*
523017 ACATAATATATATATATATATA
1 ACATAATATAAATATATATATA
523039 ACATAATATAAA-ATAT-TATA
1 ACATAATATAAATATATATATA
523059 A
1 A
523060 ACTTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 4 0.20
22 11 0.55
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (22 bp):
ACATAATATAAATATATATATA
Found at i:524773 original size:73 final size:75
Alignment explanation
Indices: 524644--524791 Score: 237
Period size: 73 Copynumber: 2.0 Consensus size: 75
524634 AAATACACGA
* * *
524644 GATTATAGGACACCAATGATATAAGTGTTAAAAAAAAAACTTATGAAAAGAGTTTGATATTAAAA
1 GATTATAGCACACCAATGATATAAGTGATAAAAAAAAAACTTATGAAAAGAATTTGATATTAAAA
524709 CCAAATAAGG
66 CCAAATAAGG
* *
524719 GATTATAGCACACC-ATGATGTAAGTGAT-AAAAAAAAACTTATGTAAAGAATTTGATATTAAAA
1 GATTATAGCACACCAATGATATAAGTGATAAAAAAAAAACTTATGAAAAGAATTTGATATTAAAA
524782 CCAAATAAGG
66 CCAAATAAGG
524792 CTTTTATTGA
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
73 43 0.63
74 12 0.18
75 13 0.19
ACGTcount: A:0.50, C:0.09, G:0.16, T:0.26
Consensus pattern (75 bp):
GATTATAGCACACCAATGATATAAGTGATAAAAAAAAAACTTATGAAAAGAATTTGATATTAAAA
CCAAATAAGG
Found at i:529633 original size:20 final size:20
Alignment explanation
Indices: 529608--529650 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
529598 GCATGATTTG
529608 AATTAAGAGTAAAA-AGACTT
1 AATTAAGAGTAAAACAGA-TT
*
529628 AATTAAGATTAAAACAGATT
1 AATTAAGAGTAAAACAGATT
529648 AAT
1 AAT
529651 AAAAGCTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.56, C:0.05, G:0.12, T:0.28
Consensus pattern (20 bp):
AATTAAGAGTAAAACAGATT
Found at i:531461 original size:78 final size:78
Alignment explanation
Indices: 531371--531527 Score: 314
Period size: 78 Copynumber: 2.0 Consensus size: 78
531361 GAATAACAAG
531371 TATTGATAGTCTTGTGTTTAGAAATATCAGTAGTTTGCATACTTGTATCGGTAGAAGTAGTAGGG
1 TATTGATAGTCTTGTGTTTAGAAATATCAGTAGTTTGCATACTTGTATCGGTAGAAGTAGTAGGG
531436 TAAGATTTTTAGC
66 TAAGATTTTTAGC
531449 TATTGATAGTCTTGTGTTTAGAAATATCAGTAGTTTGCATACTTGTATCGGTAGAAGTAGTAGGG
1 TATTGATAGTCTTGTGTTTAGAAATATCAGTAGTTTGCATACTTGTATCGGTAGAAGTAGTAGGG
531514 TAAGATTTTTAGC
66 TAAGATTTTTAGC
531527 T
1 T
531528 CTCTAGAGTT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (78 bp):
TATTGATAGTCTTGTGTTTAGAAATATCAGTAGTTTGCATACTTGTATCGGTAGAAGTAGTAGGG
TAAGATTTTTAGC
Found at i:535039 original size:21 final size:21
Alignment explanation
Indices: 535015--535064 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
535005 TATAAGTAAG
* *
535015 ACTTATATGGGTAGAAGAGTC
1 ACTTATATCGGTAGAACAGTC
** *
535036 ACTTGCATCGGTAGAACTGTC
1 ACTTATATCGGTAGAACAGTC
535057 ACTTATAT
1 ACTTATAT
535065 TAGTAAGAGT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (21 bp):
ACTTATATCGGTAGAACAGTC
Found at i:537628 original size:41 final size:41
Alignment explanation
Indices: 537583--537736 Score: 227
Period size: 41 Copynumber: 3.7 Consensus size: 41
537573 ATAATTCGTA
*
537583 ATGAGCATGAGATTATGAATAAGGAAGACTCATGTCTCGAG
1 ATGAGAATGAGATTATGAATAAGGAAGACTCATGTCTCGAG
* *
537624 ATGAGAATGAGATTATGATTAAGGGAGACTCATGTCTCGAG
1 ATGAGAATGAGATTATGAATAAGGAAGACTCATGTCTCGAG
* *
537665 ATGAGAACGAGATTATGATTAAGGAAGACTCATGTCTCGAG
1 ATGAGAATGAGATTATGAATAAGGAAGACTCATGTCTCGAG
* **
537706 ATGAGAATGAGAATATGGTTAAAGGAAGACT
1 ATGAGAATGAGATTATGAAT-AAGGAAGACT
537737 TATGACTCAA
Statistics
Matches: 104, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
41 94 0.90
42 10 0.10
ACGTcount: A:0.38, C:0.10, G:0.28, T:0.25
Consensus pattern (41 bp):
ATGAGAATGAGATTATGAATAAGGAAGACTCATGTCTCGAG
Found at i:537753 original size:82 final size:82
Alignment explanation
Indices: 537513--537744 Score: 247
Period size: 82 Copynumber: 2.8 Consensus size: 82
537503 ATATTTGGTG
* * * **
537513 TATGAA-AAGGAAGACTCATGTCTC-AGGTTGAGCATGAGAA-ATCAAAAAAATGGAAGACTCAT
1 TATGAATAAGGAAGACTCATGTCTCGA-GATGAGAATGAGAATAT--GATTAA-GGAAGACTCAT
* * * *
537575 AATTCGTA-ATGAGCATGAGAT
62 GACTCG-AGATGAGAACGAGAT
* * *
537596 TATGAATAAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGATTAAGGGAGACTCATGTCT
1 TATGAATAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATTAAGGAAGACTCATGACT
537661 CGAGATGAGAACGAGAT
66 CGAGATGAGAACGAGAT
* * *
537678 TATGATTAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGGTTAAAGGAAGACTTATGAC
1 TATGAATAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT-AAGGAAGACTCATGAC
537743 TC
65 TC
537745 AATAGAGAAT
Statistics
Matches: 126, Mismatches: 18, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
81 1 0.01
82 69 0.55
83 24 0.19
84 29 0.23
85 3 0.02
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (82 bp):
TATGAATAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATTAAGGAAGACTCATGACT
CGAGATGAGAACGAGAT
Found at i:541464 original size:24 final size:24
Alignment explanation
Indices: 541426--541486 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
541416 TAAGAATTAA
*
541426 TTTTTAATAATAAAAATAAATAAAT
1 TTTTTAAT-ACAAAAATAAATAAAT
* **
541451 TTTTTAATACAAAAATCAATTCAT
1 TTTTTAATACAAAAATAAATAAAT
541475 TTTTTAAT-CAAA
1 TTTTTAATACAAA
541487 CGTACATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 4 0.12
24 20 0.62
25 8 0.25
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTTTAATACAAAAATAAATAAAT
Found at i:543446 original size:23 final size:23
Alignment explanation
Indices: 543403--543446 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
543393 AGAATTAAAT
* *
543403 TGTAATTTTTACATTAGTAAAAA
1 TGTAATTTTTAAAGTAGTAAAAA
*
543426 TGTAATTTTTAAAGTATTAAA
1 TGTAATTTTTAAAGTAGTAAA
543447 TCAAAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (23 bp):
TGTAATTTTTAAAGTAGTAAAAA
Found at i:545098 original size:31 final size:31
Alignment explanation
Indices: 545058--545120 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
545048 TATAAAATGG
* *
545058 TTATTAAATTATTTAAAAATTTTCATTTAAA
1 TTATGAAATTATTCAAAAATTTTCATTTAAA
* * *
545089 TTATGAAATTATTCGAAAGTTTTTATTTAAA
1 TTATGAAATTATTCAAAAATTTTCATTTAAA
545120 T
1 T
545121 CACTAAGCTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (31 bp):
TTATGAAATTATTCAAAAATTTTCATTTAAA
Found at i:567138 original size:26 final size:27
Alignment explanation
Indices: 567108--567158 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
567098 ATATTTAATA
567108 AAAG-ATATAT-TTGTAAAATTTGAAAG
1 AAAGAATATATGTT-TAAAATTTGAAAG
*
567134 AAAGAATATATGTTTAAATTTTGAA
1 AAAGAATATATGTTTAAAATTTGAA
567159 GATGTTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 4 0.18
27 16 0.73
28 2 0.09
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (27 bp):
AAAGAATATATGTTTAAAATTTGAAAG
Found at i:571646 original size:40 final size:40
Alignment explanation
Indices: 571591--571708 Score: 164
Period size: 40 Copynumber: 3.0 Consensus size: 40
571581 GTGGAAAGAA
* * *
571591 TCAAGCTACAACTTAGTAGGCTATGAGCCGATGTTAAAGT
1 TCAAGCTACAGCTTAGCAGGCTATGAGCCGGTGTTAAAGT
* *
571631 TCAAGCTACTGCTTAGCAGGCTATGAGTCGGTGTTAAAGT
1 TCAAGCTACAGCTTAGCAGGCTATGAGCCGGTGTTAAAGT
* * *
571671 TCAAGCTACGGCTTTGCAAGCTATGAGCCGGTGTTAAA
1 TCAAGCTACAGCTTAGCAGGCTATGAGCCGGTGTTAAA
571709 ATTTAAGCCA
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 69 1.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (40 bp):
TCAAGCTACAGCTTAGCAGGCTATGAGCCGGTGTTAAAGT
Found at i:575320 original size:24 final size:24
Alignment explanation
Indices: 575302--575376 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
575292 AGTTTGACTC
*
575302 AAACAAATAAACATAGTTTAATTG
1 AAACAAATAAACAAAGTTTAATTG
575326 AAACAAATAAACAAAGTTTAATTG
1 AAACAAATAAACAAAGTTTAATTG
* *
575350 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAAAGTTTAATTG
575374 AAA
1 AAA
575377 GATTATTTCT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAAAGTTTAATTG
Found at i:577256 original size:27 final size:27
Alignment explanation
Indices: 577219--577308 Score: 117
Period size: 27 Copynumber: 3.3 Consensus size: 27
577209 ACACGCTAAA
*
577219 AAATGAAAGCCTTTATGGCGATCAATG
1 AAATGGAAGCCTTTATGGCGATCAATG
* *
577246 AAGTGGAAGCCTTTATGGTGATCAATG
1 AAATGGAAGCCTTTATGGCGATCAATG
* * * *
577273 AAACGGAAGCCTTTGTGCCGATCTATG
1 AAATGGAAGCCTTTATGGCGATCAATG
577300 AAATGGAAG
1 AAATGGAAG
577309 ATGAAGGAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.33, C:0.14, G:0.27, T:0.26
Consensus pattern (27 bp):
AAATGGAAGCCTTTATGGCGATCAATG
Found at i:579045 original size:12 final size:12
Alignment explanation
Indices: 579024--579053 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
579014 TCATATTAAT
*
579024 TATATAATATAA
1 TATATTATATAA
579036 TATATTATATAA
1 TATATTATATAA
579048 TATATT
1 TATATT
579054 CCTAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TATATTATATAA
Found at i:581528 original size:2 final size:2
Alignment explanation
Indices: 581521--581556 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
581511 TTCAGAGGAG
581521 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
581557 AAAGAGGGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:582274 original size:20 final size:20
Alignment explanation
Indices: 582249--582287 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
582239 TAACCGATCA
**
582249 AATTAAAAATTATTAAAAAC
1 AATTAAAAAAGATTAAAAAC
582269 AATTAAAAAAGATTAAAAA
1 AATTAAAAAAGATTAAAAA
582288 TTTGGTTCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (20 bp):
AATTAAAAAAGATTAAAAAC
Found at i:584470 original size:27 final size:27
Alignment explanation
Indices: 584416--584476 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
584406 CAGATACGAC
*
584416 AACAT-AGATAGTCTGTCGGGACAATA
1 AACATGAGATAGTCCGTCGGGACAATA
*
584442 AACATGAGATAGTCCGTCAGGG-CATTA
1 AACATGAGATAGTCCGTC-GGGACAATA
*
584469 AAAATGAG
1 AACATGAG
584477 GTGGAATGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 5 0.17
27 22 0.73
28 3 0.10
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (27 bp):
AACATGAGATAGTCCGTCGGGACAATA
Found at i:590050 original size:20 final size:21
Alignment explanation
Indices: 590020--590077 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
590010 ATTTAAAATC
*
590020 AAGTTAAAATGATTTTAAACA
1 AAGTAAAAATGATTTTAAACA
*
590041 AAG-AAAAATGA-TTTAAACC
1 AAGTAAAAATGATTTTAAACA
* *
590060 AAGTCAAAATAATTTTAA
1 AAGTAAAAATGATTTTAA
590078 CACTTCAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 10 0.32
20 13 0.42
21 8 0.26
ACGTcount: A:0.55, C:0.07, G:0.09, T:0.29
Consensus pattern (21 bp):
AAGTAAAAATGATTTTAAACA
Found at i:590076 original size:21 final size:20
Alignment explanation
Indices: 590009--590110 Score: 66
Period size: 21 Copynumber: 5.0 Consensus size: 20
589999 ATTTTGAAAC
* *
590009 AATTTAAAATCAAGTTAAAAT
1 AATTTTAAA-CAAGTCAAAAT
* *
590030 GATTTTAAACAAAG-AAAAAT
1 AATTTTAAAC-AAGTCAAAAT
*
590050 GA-TTTAAACCAAGTCAAAAT
1 AATTTTAAA-CAAGTCAAAAT
**
590070 AATTTT-AACACTTCAAAAT
1 AATTTTAAACAAGTCAAAAT
**
590089 GTTTTTCAAACAAGTCAAAAT
1 AATTTT-AAACAAGTCAAAAT
590110 A
1 A
590111 GCTTCAGACC
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
19 22 0.35
20 17 0.27
21 24 0.38
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (20 bp):
AATTTTAAACAAGTCAAAAT
Found at i:598453 original size:20 final size:20
Alignment explanation
Indices: 598394--598454 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
598384 TTTTGAAACA
*
598394 ATTTTAAAATCAAGTTAAAATG
1 ATTTT-AAACCAAG-TAAAATG
*
598416 ATTTTAAACAAAGTAAAATG
1 ATTTTAAACCAAGTAAAATG
*
598436 A-TTTCAACCAAGTCAAAAT
1 ATTTTAAACCAAGT-AAAAT
598455 CAATTTAGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 10 0.29
20 13 0.38
21 6 0.18
22 5 0.15
ACGTcount: A:0.51, C:0.10, G:0.08, T:0.31
Consensus pattern (20 bp):
ATTTTAAACCAAGTAAAATG
Found at i:609869 original size:52 final size:52
Alignment explanation
Indices: 609712--609995 Score: 312
Period size: 52 Copynumber: 5.6 Consensus size: 52
609702 ATTCACATTT
* * * * * *
609712 TATACTCACAATG--ACATAGTCATCAGACCTC-TAATCC-CAATGGATTTA
1 TATACTCACGATGACACATAGTCATCGGACCACTTAATCCGTAAAGGATTCA
* * ** *
609760 TATACTCACGATGACAC-TAAGTCATTGGA-CTCTTAATCCGCT-GTGGAATCA
1 TATACTCACGATGACACAT-AGTCATCGGACCACTTAATCCG-TAAAGGATTCA
* *
609811 TATACTCACAATGACACATAGTCATCGGACCACTTAATCCATAAAGGATTCA
1 TATACTCACGATGACACATAGTCATCGGACCACTTAATCCGTAAAGGATTCA
**
609863 TATACTCACGATGACATGTAGTCATCGGACCACTTAATCCGTAAAGGATTCA
1 TATACTCACGATGACACATAGTCATCGGACCACTTAATCCGTAAAGGATTCA
* * * *
609915 TATACTGATGATGACATATAGTCATCGGACCACTTAATCTGTAAAGGATTCA
1 TATACTCACGATGACACATAGTCATCGGACCACTTAATCCGTAAAGGATTCA
* *
609967 TATACTCATGATGACACGTAGTCATCGGA
1 TATACTCACGATGACACATAGTCATCGGA
609996 TTACTTCTAT
Statistics
Matches: 202, Mismatches: 25, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
48 12 0.06
49 4 0.02
50 16 0.08
51 32 0.16
52 138 0.68
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (52 bp):
TATACTCACGATGACACATAGTCATCGGACCACTTAATCCGTAAAGGATTCA
Found at i:616938 original size:51 final size:52
Alignment explanation
Indices: 616851--617142 Score: 258
Period size: 52 Copynumber: 5.7 Consensus size: 52
616841 TTCGTGTTTG
* * * * *
616851 ATACTCACAATGACAC-AGAGTCATCAGG-CCTC-TAATTTGCAATGGATTTAT
1 ATACTCACGATGACACTA-AGTCATC-GGACCACTTAATTCGCAAAGGATTCAT
* * *
616902 ATACTCACGATGACACTAAGTCATCGGA-CTCTTAATTCGCAATGGAATCAT
1 ATACTCACGATGACACTAAGTCATCGGACCACTTAATTCGCAAAGGATTCAT
* * * *
616953 ATACTCACGATGACA-TGTAGTCATCGAACCACTTAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACT-AAGTCATCGGACCACTTAATTCGCAAAGGATTCAT
* **
617005 ATACTCACGATAACACGT-AGTCATCGGACCACTTAATTCATAAAGGATTCAT
1 ATACTCACGATGACAC-TAAGTCATCGGACCACTTAATTCGCAAAGGATTCAT
* * * * * **
617057 ATACTCACGATGACA-TGTAGTGATTGAACCACTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACT-AAGTCATCGGACCACTTAATTCGCAAAGGATTCAT
* *
617109 ATACTCACGATGACACATAA-TCATTGGACGACTT
1 ATACTCACGATGACAC-TAAGTCATCGGACCACTT
617143 CCATTTACGA
Statistics
Matches: 206, Mismatches: 24, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
50 7 0.03
51 62 0.30
52 134 0.65
53 1 0.00
54 2 0.01
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (52 bp):
ATACTCACGATGACACTAAGTCATCGGACCACTTAATTCGCAAAGGATTCAT
Found at i:617010 original size:52 final size:52
Alignment explanation
Indices: 616894--617123 Score: 293
Period size: 52 Copynumber: 4.4 Consensus size: 52
616884 AATTTGCAAT
* * * * * ** *
616894 GGATTTATATACTCACGATGACACT-AAGTCATCGGA-CTCTTAATTCGCAAT
1 GGATTCATATACTCACGATGACA-TGTAGTCATCGAACCACTTAATCCATAAA
* *
616945 GGAATCATATACTCACGATGACATGTAGTCATCGAACCACTTAATCCGTAAA
1 GGATTCATATACTCACGATGACATGTAGTCATCGAACCACTTAATCCATAAA
* * * *
616997 GGATTCATATACTCACGATAACACGTAGTCATCGGACCACTTAATTCATAAA
1 GGATTCATATACTCACGATGACATGTAGTCATCGAACCACTTAATCCATAAA
* *
617049 GGATTCATATACTCACGATGACATGTAGTGATTGAACCACTTAATCCATAAA
1 GGATTCATATACTCACGATGACATGTAGTCATCGAACCACTTAATCCATAAA
617101 GGATTCATATACTCACGATGACA
1 GGATTCATATACTCACGATGACA
617124 CATAATCATT
Statistics
Matches: 157, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
50 1 0.01
51 30 0.19
52 126 0.80
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (52 bp):
GGATTCATATACTCACGATGACATGTAGTCATCGAACCACTTAATCCATAAA
Found at i:617029 original size:103 final size:104
Alignment explanation
Indices: 616894--617142 Score: 351
Period size: 104 Copynumber: 2.4 Consensus size: 104
616884 AATTTGCAAT
* * * *
616894 GGATTTATATACTCACGATGACACTAAGTCATCGGA-CTCTTAATTCGCAATGGAATCATATACT
1 GGATTCATATACTCACGATGACACTAAGTCATCGGACCACTTAATTCACAAAGGAATCATATACT
*
616958 CACGATGACATGTAGTCATCGAACCACTTAATCCGTAAA
66 CACGATGACATGTAGTCATCGAACCACTTAATCCATAAA
* * *
616997 GGATTCATATACTCACGATAACACGT-AGTCATCGGACCACTTAATTCATAAAGGATTCATATAC
1 GGATTCATATACTCACGATGACAC-TAAGTCATCGGACCACTTAATTCACAAAGGAATCATATAC
* *
617061 TCACGATGACATGTAGTGATTGAACCACTTAATCCATAAA
65 TCACGATGACATGTAGTCATCGAACCACTTAATCCATAAA
* *
617101 GGATTCATATACTCACGATGACACATAA-TCATTGGACGACTT
1 GGATTCATATACTCACGATGACAC-TAAGTCATCGGACCACTT
617143 CCATTTACGA
Statistics
Matches: 129, Mismatches: 14, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
103 32 0.25
104 96 0.74
105 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (104 bp):
GGATTCATATACTCACGATGACACTAAGTCATCGGACCACTTAATTCACAAAGGAATCATATACT
CACGATGACATGTAGTCATCGAACCACTTAATCCATAAA
Found at i:629811 original size:20 final size:20
Alignment explanation
Indices: 629786--629829 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
629776 ATTTTATCAT
629786 TTTTTAACTTAGTAACTGCA
1 TTTTTAACTTAGTAACTGCA
629806 TTTTTAACTTAGTAACTGCA
1 TTTTTAACTTAGTAACTGCA
629826 TTTT
1 TTTT
629830 CTAATTCAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.14, G:0.09, T:0.50
Consensus pattern (20 bp):
TTTTTAACTTAGTAACTGCA
Found at i:642426 original size:13 final size:14
Alignment explanation
Indices: 642408--642437 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
642398 GTCAATGCAA
642408 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
642421 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
642435 TCA
1 TCA
642438 ATGTATTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:645077 original size:21 final size:21
Alignment explanation
Indices: 645053--645101 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
645043 CTTGGTAGGG
645053 TCCTTCTCTTCATTC-TCCTCT
1 TCCTTCTCTTC-TTCTTCCTCT
*
645074 TCCTTCTCTTCTTCTTCCTTT
1 TCCTTCTCTTCTTCTTCCTCT
645095 TCCTTCT
1 TCCTTCT
645102 GTTAGCCATC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.02, C:0.41, G:0.00, T:0.57
Consensus pattern (21 bp):
TCCTTCTCTTCTTCTTCCTCT
Found at i:646076 original size:35 final size:35
Alignment explanation
Indices: 646030--646099 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
646020 CCTTCTATGC
646030 ATGGTATAGTTGTGGAACCCGTTACCAATCCATGT
1 ATGGTATAGTTGTGGAACCCGTTACCAATCCATGT
646065 ATGGTATAGTTGTGGAACCCGTTACCAATCCATGT
1 ATGGTATAGTTGTGGAACCCGTTACCAATCCATGT
646100 GGCTCCATCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (35 bp):
ATGGTATAGTTGTGGAACCCGTTACCAATCCATGT
Found at i:646994 original size:20 final size:21
Alignment explanation
Indices: 646969--647007 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
646959 ACAAGGAATT
646969 TGAAAC-AACAAAAGTAAAAG
1 TGAAACAAACAAAAGTAAAAG
*
646989 TGAAACAAATAAAAGTAAA
1 TGAAACAAACAAAAGTAAA
647008 TAGAAAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.67, C:0.08, G:0.13, T:0.13
Consensus pattern (21 bp):
TGAAACAAACAAAAGTAAAAG
Found at i:652837 original size:13 final size:14
Alignment explanation
Indices: 652819--652848 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
652809 GCCAATGCAA
652819 TCAGAG-TTAAATG
1 TCAGAGTTTAAATG
652832 TCAGAGTTTAAATG
1 TCAGAGTTTAAATG
652846 TCA
1 TCA
652849 ATGTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (14 bp):
TCAGAGTTTAAATG
Found at i:656256 original size:17 final size:16
Alignment explanation
Indices: 656223--656256 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
656213 TTTGAAACCC
*
656223 TAAATATTAAGCATTA
1 TAAATATTAAACATTA
656239 TAAATATATAAACATTA
1 TAAATAT-TAAACATTA
656256 T
1 T
656257 TCTAACTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (16 bp):
TAAATATTAAACATTA
Found at i:658018 original size:4 final size:4
Alignment explanation
Indices: 658009--658039 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
657999 TTGTATAATA
658009 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
658040 TATATATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:668931 original size:30 final size:30
Alignment explanation
Indices: 668897--669259 Score: 220
Period size: 30 Copynumber: 12.3 Consensus size: 30
668887 CATAAAAAAG
*
668897 CCCTCAAACTTTTCAAAAATTACATTTTGA
1 CCCTCAAACTTTTCCAAAATTACATTTTGA
* *
668927 CCCTCAAACTTCTT-TAAAATTAAATTTT-A
1 CCCTCAAACTT-TTCCAAAATTACATTTTGA
* * * * *
668956 GCCCTCGAGCTCTTT-CAATATTGCATTTCGA
1 -CCCTCAAACT-TTTCCAAAATTACATTTTGA
* * *
668987 CCCTCGAACTTCTCCAAAATTATATTTT-A
1 CCCTCAAACTTTTCCAAAATTACATTTTGA
* * *
669016 GCCTCCAAACTCTTCCATAATTACATTTTGA
1 CCCT-CAAACTTTTCCAAAATTACATTTTGA
**
669047 -CCTTGAACTTCTT-CAAAATTACA-TTTGA
1 CCCTCAAACTT-TTCCAAAATTACATTTTGA
* * *
669075 GCCCTTAAACTCTTT--AAAATTTCATTTTAA
1 -CCCTCAAACT-TTTCCAAAATTACATTTTGA
669105 CCC-CTAAACTTTTCCAAAATTACATTTT-A
1 CCCTC-AAACTTTTCCAAAATTACATTTTGA
* ** *
669134 ACCTCAAAACTTTT-TGAAATTGCATTTTGA
1 CCCTC-AAACTTTTCCAAAATTACATTTTGA
* * * *
669164 CCCCTCAAA--TTCCCAAAATCATATTTTAA
1 -CCCTCAAACTTTTCCAAAATTACATTTTGA
* *
669193 CCCTCAAACTTTCCCAAAATCT-CATCTTGA
1 CCCTCAAACTTTTCCAAAAT-TACATTTTGA
*
669223 -CCTCTAAATTTTTCCAAAATTACATTTT-A
1 CCCTC-AAACTTTTCCAAAATTACATTTTGA
*
669252 ACCTCAAA
1 CCCTCAAA
669260 TTCTCCGAAA
Statistics
Matches: 258, Mismatches: 50, Indels: 51
0.72 0.14 0.14
Matches are distributed among these distances:
28 18 0.07
29 69 0.27
30 161 0.62
31 10 0.04
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (30 bp):
CCCTCAAACTTTTCCAAAATTACATTTTGA
Found at i:669085 original size:59 final size:60
Alignment explanation
Indices: 668895--669259 Score: 254
Period size: 59 Copynumber: 6.2 Consensus size: 60
668885 TGCATAAAAA
* * * *
668895 AGCCCTCAAACTTTTCAAAAATTACATTTTGACCCTCAAACTTCTTTAAAATTAAATTTT
1 AGCCCTCAAACTCTTCCAAAATTACATTTTGACCCTCAAACTTCTTCAAAATTACATTTT
* * * * * * * * *
668955 AGCCCTCGAGCTCTTTCAATATTGCATTTCGACCCTCGAACTTCTCCAAAATTATATTTT
1 AGCCCTCAAACTCTTCCAAAATTACATTTTGACCCTCAAACTTCTTCAAAATTACATTTT
* ** *
669015 AG-CCTCCAAACTCTTCCATAATTACATTTTGA-CCTTGAACTTCTTCAAAATTACATTTG
1 AGCCCT-CAAACTCTTCCAAAATTACATTTTGACCCTCAAACTTCTTCAAAATTACATTTT
* * * *
669074 AGCCCTTAAACTCTT-TAAAATTTCATTTTAACCC-CTAAACTT-TTCCAAAATTACATTTT
1 AGCCCTCAAACTCTTCCAAAATTACATTTTGACCCTC-AAACTTCTT-CAAAATTACATTTT
* *** * * * *
669133 A-ACCTCAAAACT-TTTTGAAATTGCATTTTGACCCCTCAAA-TTC-CCAAAATCATATTTT
1 AGCCCTC-AAACTCTTCCAAAATTACATTTTGA-CCCTCAAACTTCTTCAAAATTACATTTT
* * *
669191 AACCCTCAAACT-TTCCCAAAATCT-CATCTTGA-CCTCTAAA-TTTTTCCAAAATTACATTTT
1 AGCCCTCAAACTCTT-CCAAAAT-TACATTTTGACCCTC-AAACTTCTT-CAAAATTACATTTT
*
669251 A-ACCTCAAA
1 AGCCCTCAAA
669260 TTCTCCGAAA
Statistics
Matches: 240, Mismatches: 49, Indels: 33
0.75 0.15 0.10
Matches are distributed among these distances:
57 4 0.02
58 44 0.18
59 99 0.41
60 92 0.38
61 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (60 bp):
AGCCCTCAAACTCTTCCAAAATTACATTTTGACCCTCAAACTTCTTCAAAATTACATTTT
Found at i:669144 original size:118 final size:118
Alignment explanation
Indices: 668913--669259 Score: 326
Period size: 118 Copynumber: 2.9 Consensus size: 118
668903 AACTTTTCAA
* * * * *
668913 AAATTACATTTTGACCCTCAAACTTCTTTAAAATTAAATTTTAGCCCTCGAGCTCTTTCAATATT
1 AAATTACATTTTGACCCTTAAACTTCTTCAAAATTAAATTTTAGCCCTCAAACTCTTT-AAAATT
* * * * * * *
668978 GCATTTCGA-CCCTCGAACTTCTCCAAAATTATATTTTAGCCTCCAAACTCTTCC
65 TCATTTTGACCCCT-AAACTTTTCCAAAATTACATTTTAACCTCAAAACTCTTCC
* * * *
669032 ATAATTACATTTTGA-CCTTGAACTTCTTCAAAATTACATTTGAGCCCTTAAACTCTTTAAAATT
1 A-AATTACATTTTGACCCTTAAACTTCTTCAAAATTAAATTTTAGCCCTCAAACTCTTTAAAATT
* * **
669096 TCATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCTCAAAACTTTTTG
65 TCATTTTGACCCCTAAACTTTTCCAAAATTACATTTTAACCTCAAAACTCTTCC
* * * * * * *
669150 AAATTGCATTTTGACCCCTCAAA-TTC-CCAAAATCATATTTTAACCCTCAAACT-TTCCCAAAA
1 AAATTACATTTTGA-CCCTTAAACTTCTTCAAAATTAAATTTTAGCCCTCAAACTCTT--TAAAA
* * * *
669212 TCTCATCTTGACCTCTAAATTTTTCCAAAATTACATTTTAACCTCAAA
63 TTTCATTTTGACCCCTAAACTTTTCCAAAATTACATTTTAACCTCAAA
669260 TTCTCCGAAA
Statistics
Matches: 187, Mismatches: 35, Indels: 13
0.80 0.15 0.06
Matches are distributed among these distances:
116 2 0.01
117 33 0.18
118 94 0.50
119 45 0.24
120 13 0.07
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (118 bp):
AAATTACATTTTGACCCTTAAACTTCTTCAAAATTAAATTTTAGCCCTCAAACTCTTTAAAATTT
CATTTTGACCCCTAAACTTTTCCAAAATTACATTTTAACCTCAAAACTCTTCC
Found at i:669182 original size:29 final size:29
Alignment explanation
Indices: 669150--669287 Score: 88
Period size: 30 Copynumber: 4.6 Consensus size: 29
669140 AAACTTTTTG
669150 AAATTGCATTTTGACCCCTCAAA-TTCCCA
1 AAATT-CATTTTGACCCCTCAAATTTCCCA
* *
669179 AAA-TCATATTTTAACCCTCAAACTTTCCCA
1 AAATTCAT-TTTGACCCCTCAAA-TTTCCCA
* * *
669209 AAATCTCATCTTGACCTCT-AAATTTTTCCA
1 AAAT-TCATTTTGACCCCTCAAA-TTTCCCA
* *
669239 AAATTACATTTT-A-ACCTCAAATTCTCCGA
1 AAATT-CATTTTGACCCCTCAAATT-TCCCA
*
669268 AACTTCATTTTTCGACCCCT
1 AAATTCA-TTTT-GACCCCT
669288 TTTTTATTTT
Statistics
Matches: 82, Mismatches: 15, Indels: 21
0.69 0.13 0.18
Matches are distributed among these distances:
27 3 0.04
28 19 0.23
29 19 0.23
30 27 0.33
31 7 0.09
32 7 0.09
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.36
Consensus pattern (29 bp):
AAATTCATTTTGACCCCTCAAATTTCCCA
Found at i:677254 original size:19 final size:19
Alignment explanation
Indices: 677232--677269 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
677222 CATTGTCAAC
677232 CACCATAATCAAATTTGTT
1 CACCATAATCAAATTTGTT
*
677251 CACCGTAATCAAATTTGTT
1 CACCATAATCAAATTTGTT
677270 ATTAACTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.37
Consensus pattern (19 bp):
CACCATAATCAAATTTGTT
Found at i:677773 original size:27 final size:28
Alignment explanation
Indices: 677719--677773 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
677709 AGGGTTTTAG
*
677719 GGAGTAAAATTTTGAGGAAGAGTAAATAGA
1 GGAGTAAAATTTT--GGAAGAGAAAATAGA
677749 GGAGTAAAATTTT-GAAGAGAAAATA
1 GGAGTAAAATTTTGGAAGAGAAAATA
677774 TTTAAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 11 0.46
30 13 0.54
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (28 bp):
GGAGTAAAATTTTGGAAGAGAAAATAGA
Found at i:677960 original size:21 final size:20
Alignment explanation
Indices: 677943--677979 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
677933 AGGGGGAAGG
*
677943 AGTAAAAGT-TTTGGGGGAA
1 AGTAAAAATGTTTGGGGGAA
677962 AGTAAAAATGTTTGGGGG
1 AGTAAAAATGTTTGGGGG
677980 TTTGGGGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.35, C:0.00, G:0.38, T:0.27
Consensus pattern (20 bp):
AGTAAAAATGTTTGGGGGAA
Found at i:679333 original size:17 final size:17
Alignment explanation
Indices: 679300--679351 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
679290 ACTCACTATG
*
679300 GTTTCAGATAC-AGAATA
1 GTTT-AGATACAAAAATA
679317 GTTTAGATACAAAAATA
1 GTTTAGATACAAAAATA
*
679334 GATTAGATA-AAAACATA
1 GTTTAGATACAAAA-ATA
679351 G
1 G
679352 ATACAAACGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 10 0.32
17 21 0.68
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (17 bp):
GTTTAGATACAAAAATA
Found at i:679352 original size:17 final size:17
Alignment explanation
Indices: 679313--679353 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
679303 TCAGATACAG
*
679313 AATAGTTTAGATACAAA
1 AATAGATTAGATACAAA
679330 AATAGATTAGATA-AAA
1 AATAGATTAGATACAAA
679346 ACATAGAT
1 A-ATAGAT
679354 ACAAACGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.56, C:0.05, G:0.12, T:0.27
Consensus pattern (17 bp):
AATAGATTAGATACAAA
Found at i:680688 original size:12 final size:13
Alignment explanation
Indices: 680671--680699 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
680661 ATGAAAGAAG
680671 AAAGAA-AACAAA
1 AAAGAAGAACAAA
680683 AAAGAAGAACAAA
1 AAAGAAGAACAAA
680696 AAAG
1 AAAG
680700 GAATTAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAGAAGAACAAA
Found at i:688870 original size:28 final size:29
Alignment explanation
Indices: 688839--688894 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
688829 AAAAAGGATA
**
688839 AATTATT-AAAATTACATTTTAATCACTT
1 AATTATTAAAAATTACATAATAATCACTT
*
688867 AATTTTTAAAAATTACATAATAATCACT
1 AATTATTAAAAATTACATAATAATCACT
688895 AACATTACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (29 bp):
AATTATTAAAAATTACATAATAATCACTT
Found at i:689338 original size:2 final size:2
Alignment explanation
Indices: 689331--689366 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
689321 ATTAAAAATA
689331 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
689367 TTGAAAGTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:689919 original size:21 final size:21
Alignment explanation
Indices: 689893--689947 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
689883 TACCCTGTAC
689893 TTCTACCGAAACATACATGGG
1 TTCTACCGAAACATACATGGG
*
689914 TTCTACCAAAACATACATGGG
1 TTCTACCGAAACATACATGGG
689935 TTCTACCGAAACA
1 TTCTACCGAAACA
689948 AGTATGCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (21 bp):
TTCTACCGAAACATACATGGG
Found at i:690571 original size:52 final size:51
Alignment explanation
Indices: 690481--690693 Score: 268
Period size: 52 Copynumber: 4.1 Consensus size: 51
690471 CATAGCTACT
* * *
690481 GGACCTTATAATCTGT-AAGGATTCGTATACTCACGATGACACAGAGTCATC
1 GGACCTT-TAATCTGTAAAGGATCCATATACTCACGATGACACTGAGTCATC
* *
690532 GGACCTCTTAATCTGTAAAGGATCCATATACTCATGATGACACTTAGTCATC
1 GGACCT-TTAATCTGTAAAGGATCCATATACTCACGATGACACTGAGTCATC
* * *
690584 GGACTGTTTAATCCGTAAAGGATTCATATACTCACGATGACAC-GTAGTCATC
1 GGAC-CTTTAATCTGTAAAGGATCCATATACTCACGATGACACTG-AGTCATC
* * *
690636 GGACCGTTTAATCAGTAAAGTATCCATATACTCACGATGACACTTAGTCATC
1 GGACC-TTTAATCTGTAAAGGATCCATATACTCACGATGACACTGAGTCATC
690688 GGACCT
1 GGACCT
690694 CTTCGTTTAT
Statistics
Matches: 141, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
51 15 0.11
52 125 0.89
53 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.29
Consensus pattern (51 bp):
GGACCTTTAATCTGTAAAGGATCCATATACTCACGATGACACTGAGTCATC
Found at i:690677 original size:104 final size:103
Alignment explanation
Indices: 690489--690691 Score: 320
Period size: 104 Copynumber: 2.0 Consensus size: 103
690479 CTGGACCTTA
* * *
690489 TAATCTGTAAGGATTCGTATACTCACGATGACACAGAGTCATCGGACCTCTTAATCTGTAAAGGA
1 TAATCCGTAAGGATTCATATACTCACGATGACACAGAGTCATCGGACCTCTTAATCAGTAAAGGA
*
690554 TCCATATACTCATGATGACACTTAGTCATCGGACTGTT
66 TCCATATACTCACGATGACACTTAGTCATCGGACTGTT
690592 TAATCCGTAAAGGATTCATATACTCACGATGACAC-GTAGTCATCGGACCGT-TTAATCAGTAAA
1 TAATCCGT-AAGGATTCATATACTCACGATGACACAG-AGTCATCGGACC-TCTTAATCAGTAAA
*
690655 GTATCCATATACTCACGATGACACTTAGTCATCGGAC
63 GGATCCATATACTCACGATGACACTTAGTCATCGGAC
690692 CTCTTCGTTT
Statistics
Matches: 92, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
103 8 0.09
104 83 0.90
105 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.29
Consensus pattern (103 bp):
TAATCCGTAAGGATTCATATACTCACGATGACACAGAGTCATCGGACCTCTTAATCAGTAAAGGA
TCCATATACTCACGATGACACTTAGTCATCGGACTGTT
Found at i:692447 original size:78 final size:78
Alignment explanation
Indices: 692382--692599 Score: 276
Period size: 78 Copynumber: 2.8 Consensus size: 78
692372 CAGCATTACG
* * * * *
692382 GTGTTTAAAGTGTCACCACCAGTTCAGTACGATATTATTATGTTTACAGTGTCACCGTCAATTCA
1 GTGTTTAAAGTGTCACTACCAGTTCAGTATGGTATTATCATGTTTACAGTGTCACCGTCAGTTCA
*
692447 GTGTTGTATTGTA
66 GTGTTGTATTGCA
* * * * * * *
692460 GTGTTTACAGCGTCACTACCAATTCAGTATGGTATTA-CAGTATTTATAGTATCACCATCAGTTC
1 GTGTTTAAAGTGTCACTACCAGTTCAGTATGGTATTATCA-TGTTTACAGTGTCACCGTCAGTTC
692524 AGTGTTGTATTGCA
65 AGTGTTGTATTGCA
* **
692538 GTGTTTATAGTGTCACTACCAGTTCAGTATGGTATTATGGTGTTTACAGTGTCACCGTCAGT
1 GTGTTTAAAGTGTCACTACCAGTTCAGTATGGTATTATCATGTTTACAGTGTCACCGTCAGT
692600 AATTTGATAA
Statistics
Matches: 116, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
77 1 0.01
78 115 0.99
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (78 bp):
GTGTTTAAAGTGTCACTACCAGTTCAGTATGGTATTATCATGTTTACAGTGTCACCGTCAGTTCA
GTGTTGTATTGCA
Found at i:692465 original size:39 final size:39
Alignment explanation
Indices: 692376--692593 Score: 168
Period size: 39 Copynumber: 5.6 Consensus size: 39
692366 TCAGTACAGC
* * * * * *
692376 ATTACGGTGTTTAAAGTGTCACCACCAGTTCAGTACGAT
1 ATTACAGTGTTTACAGTGTCACCATCAATTCAGTATGGT
* * * *
692415 ATTATTA-TGTTTACAGTGTCACCGTCAATTCAGTGTTGT
1 ATTA-CAGTGTTTACAGTGTCACCATCAATTCAGTATGGT
** * * *
692454 ATTGTAGTGTTTACAGCGTCACTACCAATTCAGTATGGT
1 ATTACAGTGTTTACAGTGTCACCATCAATTCAGTATGGT
* * * * * *
692493 ATTACAGTATTTATAGTATCACCATCAGTTCAGTGTTGT
1 ATTACAGTGTTTACAGTGTCACCATCAATTCAGTATGGT
* * * * *
692532 ATTGCAGTGTTTATAGTGTCACTACCAGTTCAGTATGGT
1 ATTACAGTGTTTACAGTGTCACCATCAATTCAGTATGGT
**
692571 ATTATGGTGTTTACAGTGTCACC
1 ATTACAGTGTTTACAGTGTCACC
692594 GTCAGTAATT
Statistics
Matches: 137, Mismatches: 40, Indels: 4
0.76 0.22 0.02
Matches are distributed among these distances:
38 2 0.01
39 135 0.99
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (39 bp):
ATTACAGTGTTTACAGTGTCACCATCAATTCAGTATGGT
Found at i:695403 original size:12 final size:12
Alignment explanation
Indices: 695372--695404 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
695362 CATCACTATT
*
695372 CAGACTAAATTC
1 CAGACTTAATTC
695384 CA-ACTTAATTC
1 CAGACTTAATTC
695395 CAGACTTAAT
1 CAGACTTAAT
695405 CGTACTTAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.30
Consensus pattern (12 bp):
CAGACTTAATTC
Found at i:695574 original size:13 final size:13
Alignment explanation
Indices: 695556--695586 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
695546 AGTCATCACT
695556 CATCGACTTAAAG
1 CATCGACTTAAAG
695569 CATCGACTTAAAG
1 CATCGACTTAAAG
695582 CATCG
1 CATCG
695587 GCTACAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (13 bp):
CATCGACTTAAAG
Found at i:700115 original size:2 final size:2
Alignment explanation
Indices: 700108--700136 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
700098 TCCCGTACTT
700108 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
700137 TCTACCTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:704531 original size:52 final size:52
Alignment explanation
Indices: 704462--704702 Score: 267
Period size: 52 Copynumber: 4.6 Consensus size: 52
704452 GCTATAAACG
* * *
704462 AAAGGGTTCGATAACTAAGTGTCATCGTGAGTAAACGAATCCTTTACGAATT
1 AAAGGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATT
*
704514 AAAGGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATTCTTTACGAATT
1 AAAGGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATT
* * * * * *
704566 AAAGGGTCTGATGACTAAGTGTTATCGTGAGTAAATGAATCCATGATGGATT
1 AAAGGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATT
* * * *
704618 AAA-GGTTCGATGACTCCA-TGTCATCGTGAGTATATGAATTCTTATACGGAA--
1 AAAGGGTCCGATGACT-AAGTGTCATCGTGAGTAAATGAATCCTT-TAC-GAATT
*
704669 CAAGAGGTCCGATGACTATA-TGTCATCGTGAGTA
1 AAAG-GGTCCGATGACTA-AGTGTCATCGTGAGTA
704703 TTAAATGAAA
Statistics
Matches: 159, Mismatches: 24, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
51 33 0.21
52 98 0.62
53 28 0.18
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (52 bp):
AAAGGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATT
Found at i:705445 original size:21 final size:22
Alignment explanation
Indices: 705421--705480 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
705411 TAGTTGCATG
705421 ACTTGTATCGGTAGAAATTA-T
1 ACTTGTATCGGTAGAAATTAGT
* *
705442 ACTTATATCGATAG-AATTAGT
1 ACTTGTATCGGTAGAAATTAGT
***
705463 AAAAGTATCGGTAGAAAT
1 ACTTGTATCGGTAGAAAT
705481 ATGCACAGTT
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 5 0.17
21 22 0.73
22 3 0.10
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.33
Consensus pattern (22 bp):
ACTTGTATCGGTAGAAATTAGT
Found at i:711749 original size:52 final size:50
Alignment explanation
Indices: 711671--711865 Score: 241
Period size: 52 Copynumber: 3.8 Consensus size: 50
711661 GCTATAAACG
* *
711671 AAAGGGTCCGATGACTAAGTGTCATCGTAAGTAAACGAATCTTTTACGGATT
1 AAAGGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATC-TTTA-GGATT
711723 AAAGGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTAGGAATT
1 AAAGGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAAT-CTTTAGG-ATT
* * * * *
711775 AAAGGGTGCAATGACTAAGTGACATCGTGAGTAAATGAATACATGATGGATT
1 AAAGGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAAT-CTTTA-GGATT
*
711827 AAA-GGTCCGATGAC-ATAGTGTCATCGTGAGTATATGAAT
1 AAAGGGTCCGATGACTA-AGTGTCATCGTGAGTAAATGAAT
711866 TCCTATACAG
Statistics
Matches: 127, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
50 1 0.01
51 32 0.25
52 91 0.72
53 3 0.02
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (50 bp):
AAAGGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCTTTAGGATT
Found at i:711893 original size:104 final size:103
Alignment explanation
Indices: 711679--711911 Score: 235
Period size: 104 Copynumber: 2.2 Consensus size: 103
711669 CGAAAGGGTC
* * *
711679 CGATGACTAAGTGTCATCGTAAGTAAACGAATCTTTTACGGATTAAAGGGTCCGATGACTAAGTG
1 CGATGACTAAGTGTCATCGTGAGTAAACGAATCTATGACGGATTAAAGGGTCCGATGACTAAGTG
* * *
711744 TCATCGTGAGTAAATGAATCCTTTAGGAATTAAAGGGTG
66 TCATCGTGAGTAAATGAATCCTATA-GAAGTAAAGGATG
* * * *
711783 CAATGACTAAGTGACATCGTGAGTAAATGAATAC-ATGATGGATTAAA-GGTCCGATGAC-ATAG
1 CGATGACTAAGTGTCATCGTGAGTAAACGAAT-CTATGACGGATTAAAGGGTCCGATGACTA-AG
* *
711845 TGTCATCGTGAGTATATGAATTCCTATA-CAGTACAAGAGAT-
64 TGTCATCGTGAGTAAATGAA-TCCTATAGAAGTA-AAG-GATG
*
711886 CTGATGACCATA-TGTCATCGTGAGTA
1 C-GATGACTA-AGTGTCATCGTGAGTA
711912 TTAACTGAAA
Statistics
Matches: 107, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
102 4 0.04
103 36 0.34
104 65 0.61
105 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (103 bp):
CGATGACTAAGTGTCATCGTGAGTAAACGAATCTATGACGGATTAAAGGGTCCGATGACTAAGTG
TCATCGTGAGTAAATGAATCCTATAGAAGTAAAGGATG
Found at i:716989 original size:6 final size:6
Alignment explanation
Indices: 716976--717023 Score: 60
Period size: 6 Copynumber: 7.7 Consensus size: 6
716966 TAAAAAATAA
* *
716976 AAAAAG AAAGAG AAAAAG AAAAAAG AAAAAG AACAAGG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG -AAAAAG AAAAAG AA-AAAG AAAAAG AAAA
717024 TGAGAGGTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
6 25 0.69
7 11 0.31
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:716997 original size:19 final size:19
Alignment explanation
Indices: 716975--717023 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
716965 ATAAAAAATA
*
716975 AAAAAAGAAAGAGAAAAAG
1 AAAAAAGAAAAAGAAAAAG
*
716994 AAAAAAGAAAAAGAACAAG
1 AAAAAAGAAAAAGAAAAAG
*
717013 GAAAAAGAAAA
1 AAAAAAGAAAA
717024 TGAGAGGTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (19 bp):
AAAAAAGAAAAAGAAAAAG
Found at i:718034 original size:49 final size:49
Alignment explanation
Indices: 717970--718293 Score: 303
Period size: 49 Copynumber: 6.6 Consensus size: 49
717960 GGAAACATTG
* * * * * *
717970 AATCCTATACTCTAAAGATGTGAAGGGAAATATTGAAGCCGCAATGGCT
1 AATCTTATACCCTAGAGATGTGAAGGGAAAGATTGAAGCCACAACGGCT
* * * * * *
718019 AATCTTATACCCTAAAGACGT-AGAGGGAAAGGTTGAAGTCGCAACAGCT
1 AATCTTATACCCTAGAGATGTGA-AGGGAAAGATTGAAGCCACAACGGCT
* * * * ** *
718068 AACCTTATACCCTAG-GAATTTGAAGGGAAAGATTGAAACCAAAACAACG
1 AATCTTATACCCTAGAG-ATGTGAAGGGAAAGATTGAAGCCACAACGGCT
* * *
718117 AATCTTATACCCTAGAGATGTGGAGGGAAAGGTTGAAGCCACAACGGTT
1 AATCTTATACCCTAGAGATGTGAAGGGAAAGATTGAAGCCACAACGGCT
* * * * * *
718166 AACCTTATACCTTAGAGATGTGAAAGGAAAGATTGAAGCCAAAATGGCG
1 AATCTTATACCCTAGAGATGTGAAGGGAAAGATTGAAGCCACAACGGCT
* * *
718215 AATCTTATACCCTAGAGATGT-AGAGGGAAAGGTTGAAGCCGCAACGGCA
1 AATCTTATACCCTAGAGATGTGA-AGGGAAAGATTGAAGCCACAACGGCT
* *
718264 AACCTTATACCTTAGAGATGTGAAGGGAAA
1 AATCTTATACCCTAGAGATGTGAAGGGAAA
718294 TGGAAAATCT
Statistics
Matches: 221, Mismatches: 48, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
48 3 0.01
49 215 0.97
50 3 0.01
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.21
Consensus pattern (49 bp):
AATCTTATACCCTAGAGATGTGAAGGGAAAGATTGAAGCCACAACGGCT
Found at i:718144 original size:98 final size:98
Alignment explanation
Indices: 718019--718293 Score: 399
Period size: 98 Copynumber: 2.8 Consensus size: 98
718009 CGCAATGGCT
* * * * *
718019 AATCTTATACCCTAAAGACGTAGAGGGAAAGGTTGAAGTCGCAACAGCTAACCTTATACCCTAG-
1 AATCTTATACCCTAGAGATGTAGAGGGAAAGGTTGAAGCCGCAACGGCTAACCTTATACCTTAGA
*
718083 GAATTTGAAGGGAAAGATTGAAACCAAAACAACG
66 G-ATGTGAAGGGAAAGATTGAAACCAAAACAACG
* * *
718117 AATCTTATACCCTAGAGATGTGGAGGGAAAGGTTGAAGCCACAACGGTTAACCTTATACCTTAGA
1 AATCTTATACCCTAGAGATGTAGAGGGAAAGGTTGAAGCCGCAACGGCTAACCTTATACCTTAGA
* * ***
718182 GATGTGAAAGGAAAGATTGAAGCCAAAATGGCG
66 GATGTGAAGGGAAAGATTGAAACCAAAACAACG
*
718215 AATCTTATACCCTAGAGATGTAGAGGGAAAGGTTGAAGCCGCAACGGCAAACCTTATACCTTAGA
1 AATCTTATACCCTAGAGATGTAGAGGGAAAGGTTGAAGCCGCAACGGCTAACCTTATACCTTAGA
718280 GATGTGAAGGGAAA
66 GATGTGAAGGGAAA
718294 TGGAAAATCT
Statistics
Matches: 157, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
98 156 0.99
99 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (98 bp):
AATCTTATACCCTAGAGATGTAGAGGGAAAGGTTGAAGCCGCAACGGCTAACCTTATACCTTAGA
GATGTGAAGGGAAAGATTGAAACCAAAACAACG
Found at i:718407 original size:42 final size:42
Alignment explanation
Indices: 718322--718436 Score: 135
Period size: 42 Copynumber: 2.7 Consensus size: 42
718312 AAAGATGAGG
* * *
718322 AGAAGCATATTGAAGCCGCAAAGGCAAATCTCAAGACTATAA
1 AGAAGCAGATTGAAGTCGCAAAGGCGAATCTCAAGACTATAA
*
718364 AGAAGCAGATTGAAGTCGCAAAGGCGAATCTCGAAG-CTGTAA
1 AGAAGCAGATTGAAGTCGCAAAGGCGAATCTC-AAGACTATAA
* * *
718406 AG-GGCTAGATTGAAGTTGCAAAGGTGAATCT
1 AGAAGC-AGATTGAAGTCGCAAAGGCGAATCT
718437 TATGTCCTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
41 2 0.03
42 59 0.92
43 3 0.05
ACGTcount: A:0.39, C:0.16, G:0.26, T:0.19
Consensus pattern (42 bp):
AGAAGCAGATTGAAGTCGCAAAGGCGAATCTCAAGACTATAA
Done.