Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold145
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1177157
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.31
Warning! 98840 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:378139 original size:39 final size:40
Alignment explanation
Indices: 378072--378160 Score: 135
Period size: 39 Copynumber: 2.2 Consensus size: 40
378062 TCGAAAACTA
* *
378072 TATAGTTAACGACGTTAATCTATATTTCACGTCTGTAAAC
1 TATAGTTAACGACGATAATCTATATTTCACATCTGTAAAC
* *
378112 TATAGTTAACG-CGATAATCTATGTTTCACATCTGTTAAC
1 TATAGTTAACGACGATAATCTATATTTCACATCTGTAAAC
378151 TATAGTTAAC
1 TATAGTTAAC
378161 ACTGAAAACA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
39 34 0.76
40 11 0.24
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (40 bp):
TATAGTTAACGACGATAATCTATATTTCACATCTGTAAAC
Found at i:378956 original size:20 final size:20
Alignment explanation
Indices: 378933--379009 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
378923 TGTTAAACAG
378933 ACGTAAACTATAGTTTACGA
1 ACGTAAACTATAGTTTACGA
* * *
378953 ACGTGAATTATAGTTTA-GG
1 ACGTAAACTATAGTTTACGA
* *
378972 ACGATAAACTAT-GATTAACAA
1 ACG-TAAACTATAG-TTTACGA
*
378993 ACGTAAATTATAGTTTA
1 ACGTAAACTATAGTTTA
379010 TCTCTCAAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
19 5 0.12
20 34 0.79
21 4 0.09
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (20 bp):
ACGTAAACTATAGTTTACGA
Found at i:379623 original size:20 final size:20
Alignment explanation
Indices: 379600--379661 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
379590 AGATGTGAAA
379600 TATAGATTAACGTCGGT-AAC
1 TATAG-TTAACGTCGGTAAAC
* *
379620 TATAGTTTACGATCCGTAAAC
1 TATAGTTAACG-TCGGTAAAC
*
379641 TATAGTTAACAGTCGATAAAC
1 TATAGTTAAC-GTCGGTAAAC
379662 CTAGTTTATC
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
19 5 0.15
20 9 0.26
21 19 0.56
22 1 0.03
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (20 bp):
TATAGTTAACGTCGGTAAAC
Found at i:379650 original size:40 final size:41
Alignment explanation
Indices: 379541--379655 Score: 116
Period size: 39 Copynumber: 2.9 Consensus size: 41
379531 CAGTGTTAAA
* * * * *
379541 TATAGTTTACAGATATGAAACATAGATT-A-TGGCGTTAAC
1 TATAGTTTACAGATGTGAAATATAGATTAACAGTCGGTAAC
379580 TATAGTTTACAGATGTGAAATATAGATTAAC-GTCGGTAAC
1 TATAGTTTACAGATGTGAAATATAGATTAACAGTCGGTAAC
379620 TATAGTTTAC-GATCCGT-AAACTATAG-TTAACAGTCG
1 TATAGTTTACAGAT--GTGAAA-TATAGATTAACAGTCG
379656 ATAAACCTAG
Statistics
Matches: 66, Mismatches: 4, Indels: 10
0.82 0.05 0.12
Matches are distributed among these distances:
39 29 0.44
40 26 0.39
41 11 0.17
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (41 bp):
TATAGTTTACAGATGTGAAATATAGATTAACAGTCGGTAAC
Found at i:381211 original size:14 final size:15
Alignment explanation
Indices: 381186--381215 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
381176 TGGTAGTTAC
381186 TGATTATTGTGTTGG
1 TGATTATTGTGTTGG
381201 TGATT-TTGTGTTGG
1 TGATTATTGTGTTGG
381215 T
1 T
381216 ATATGTGGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.10, C:0.00, G:0.33, T:0.57
Consensus pattern (15 bp):
TGATTATTGTGTTGG
Found at i:387623 original size:84 final size:86
Alignment explanation
Indices: 387526--387691 Score: 246
Period size: 89 Copynumber: 1.9 Consensus size: 86
387516 AGATTGCCAG
* * *
387526 AAAAAAATATTTTGTCTGTCC-TT-AAAAATGAATTATCAGAATGATTGATAGTTTTAATAATTG
1 AAAAAAATATTTTGCCTGTCCTTTAAAAAATGAATTATCAGAATGATTGAAAGTTTGAATAATTG
387589 GTCATACATATCAGTTAGAGA
66 GTCATACATATCAGTTAGAGA
* *
387610 AAAAAAATGTTTTGCCTGTCCTTATTAAAAAAATGAATTATCAGTATGATTGAAAGTTTGAATAA
1 AAAAAAATATTTTGCCTGTCC-T-TT-AAAAAATGAATTATCAGAATGATTGAAAGTTTGAATAA
387675 TTGGTCATACATATCAG
63 TTGGTCATACATATCAG
387692 CTTGAGTTAT
Statistics
Matches: 72, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
84 19 0.26
87 2 0.03
89 51 0.71
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.36
Consensus pattern (86 bp):
AAAAAAATATTTTGCCTGTCCTTTAAAAAATGAATTATCAGAATGATTGAAAGTTTGAATAATTG
GTCATACATATCAGTTAGAGA
Found at i:393121 original size:10 final size:10
Alignment explanation
Indices: 393106--393133 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
393096 TATATACATA
393106 AAAAAAAACC
1 AAAAAAAACC
393116 AAAAAAAACC
1 AAAAAAAACC
393126 AAAAAAAA
1 AAAAAAAA
393134 AACTCTCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAACC
Found at i:393691 original size:19 final size:19
Alignment explanation
Indices: 393667--393704 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
393657 TCCTAAATAT
393667 TGGCCCAGTTTAGTTTATG
1 TGGCCCAGTTTAGTTTATG
393686 TGGCCCAGTTTAGTTTATG
1 TGGCCCAGTTTAGTTTATG
393705 CCAAGTAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.26, T:0.42
Consensus pattern (19 bp):
TGGCCCAGTTTAGTTTATG
Found at i:397707 original size:21 final size:21
Alignment explanation
Indices: 397673--397841 Score: 257
Period size: 21 Copynumber: 8.0 Consensus size: 21
397663 AGGAATGTAA
397673 TCATCTCAAAGTACAGGTAGG
1 TCATCTCAAAGTACAGGTAGG
* * *
397694 TCAACTCAAGGTACAGGTAGT
1 TCATCTCAAAGTACAGGTAGG
397715 TCATCTCAAAGTACAGGTAGG
1 TCATCTCAAAGTACAGGTAGG
*
397736 TCAACTCAAAGTACAGGTAGG
1 TCATCTCAAAGTACAGGTAGG
* *
397757 TCATCTCAAAGTATAAGTAGG
1 TCATCTCAAAGTACAGGTAGG
* *
397778 TCATCTCAAAGTATAAGTAGG
1 TCATCTCAAAGTACAGGTAGG
397799 TCATCTCAAAGTACAGGTAGG
1 TCATCTCAAAGTACAGGTAGG
*
397820 TCATCTCAAAGTTCAGGTAGG
1 TCATCTCAAAGTACAGGTAGG
397841 T
1 T
397842 TTTAATTAGC
Statistics
Matches: 135, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 135 1.00
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.25
Consensus pattern (21 bp):
TCATCTCAAAGTACAGGTAGG
Found at i:404458 original size:161 final size:160
Alignment explanation
Indices: 403954--404442 Score: 753
Period size: 161 Copynumber: 3.0 Consensus size: 160
403944 GGTCCACCAA
* * *
403954 CAGTTTCTGTTCATTTTCTTCGCAGAGTATAAACATATTGAAATGAAATTTGGTATACAGGTTTA
1 CAGTTTCTGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA
* * * *
404019 TCAAGATAATATCTAGGTCAGGTTTGATACTGGGTACAATCGAGCAATTTTCGACAGAGTTATGG
66 TCATGATAATATCTAGGTCAAG-TTGATATTGGGTACAATCGAGCAATTTTCAACAGAGTTATGG
404084 CCCTTGGACATAGAAAAATTCCAGTTATTTG
130 CCCTTGGACATAGAAAAATTCCAGTTATTTG
* *
404115 CAGTTTCTGCTCATTTTCTTCGCAGAGGATGAACATATGGTAATGAAATTTGGTATACAGGTTTA
1 CAGTTTCTGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA
*
404180 TCATGATAATATCTAGGTCAAGTTCGATATTGGGTACAATCGAGCAATTTTCAAGAGAGTTATGG
66 TCATGATAATATCTAGGTCAAGTT-GATATTGGGTACAATCGAGCAATTTTCAACAGAGTTATGG
* *
404245 CCCTTGGACTTAGAAACATTCCAGTTATTTG
130 CCCTTGGACATAGAAAAATTCCAGTTATTTG
* * *
404276 CAGTTTCTGCTCATTTTCTTTGCAAAGGATGAACATATTGAAATAAAATTTGGTATACAGGTTTA
1 CAGTTTCTGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA
* * * *
404341 TCATGATAATATCTAGGTCAAGTATGATTTTGGTTACAATTGAGCAATTTTCAACAGAGTTATGT
66 TCATGATAATATCTAGGTCAAGT-TGATATTGGGTACAATCGAGCAATTTTCAACAGAGTTATGG
* * *
404406 CCCTTTGACGTAGAAAAATTGCAGTTATTTG
130 CCCTTGGACATAGAAAAATTCCAGTTATTTG
404437 CAGTTT
1 CAGTTT
404443 ACGTTAATTT
Statistics
Matches: 300, Mismatches: 26, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
160 2 0.01
161 297 0.99
162 1 0.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (160 bp):
CAGTTTCTGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA
TCATGATAATATCTAGGTCAAGTTGATATTGGGTACAATCGAGCAATTTTCAACAGAGTTATGGC
CCTTGGACATAGAAAAATTCCAGTTATTTG
Found at i:416772 original size:14 final size:14
Alignment explanation
Indices: 416725--416772 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
416715 CGGTCGAGGT
*
416725 GCGAAGTTGCGACG
1 GCGAAGTTGCGAAG
416739 GCGAAAG-TGCGAAG
1 GCG-AAGTTGCGAAG
416753 GCGAAGTTGCGAAG
1 GCGAAGTTGCGAAG
416767 GCGAAG
1 GCGAAG
416773 AAGCAATACT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 3 0.10
14 25 0.81
15 3 0.10
ACGTcount: A:0.29, C:0.17, G:0.44, T:0.10
Consensus pattern (14 bp):
GCGAAGTTGCGAAG
Found at i:420364 original size:49 final size:49
Alignment explanation
Indices: 420307--420502 Score: 326
Period size: 49 Copynumber: 4.1 Consensus size: 49
420297 TTGGTAAAAT
* *
420307 TAGACAACTAAACAATCAACAGAGAGGAATGAGTAAGGACTAGTGAAAG
1 TAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAAAG
420356 TAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAAAG
1 TAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAAAG
*
420405 TAGACAACTAAATAATCAACAGGGAGGAATGAGTAAGGATTAGTG--A-
1 TAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAAAG
* *
420451 TAGACAACTAAACAAACAACAGGGAGGAATGAGGAAGGATTAGTGAAAG
1 TAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAAAG
420500 TAG
1 TAG
420503 NNNNNNNNNN
Statistics
Matches: 138, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
46 42 0.30
47 1 0.01
48 1 0.01
49 94 0.68
ACGTcount: A:0.47, C:0.10, G:0.27, T:0.16
Consensus pattern (49 bp):
TAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAAAG
Found at i:420495 original size:95 final size:97
Alignment explanation
Indices: 420307--420502 Score: 324
Period size: 95 Copynumber: 2.0 Consensus size: 97
420297 TTGGTAAAAT
*
420307 TAGACAACTAAACAATCAACAGAGAGGAATGAGTAAGGACTAGTGAAAGTAGACAACTAAACAAT
1 TAGACAACTAAACAATCAACAGAGAGGAATGAGTAAGGACTAGTG-AAGTAGACAACTAAACAAA
*
420372 CAACAGGGAGGAATGAGTAAGGATTAGTGAAAG
65 CAACAGGGAGGAATGAGGAAGGATTAGTGAAAG
* * *
420405 TAGACAACTAAATAATCAACAGGGAGGAATGAGTAAGGATTAGTG-A-TAGACAACTAAACAAAC
1 TAGACAACTAAACAATCAACAGAGAGGAATGAGTAAGGACTAGTGAAGTAGACAACTAAACAAAC
420468 AACAGGGAGGAATGAGGAAGGATTAGTGAAAG
66 AACAGGGAGGAATGAGGAAGGATTAGTGAAAG
420500 TAG
1 TAG
420503 NNNNNNNNNN
Statistics
Matches: 93, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
95 50 0.54
96 1 0.01
98 42 0.45
ACGTcount: A:0.47, C:0.10, G:0.27, T:0.16
Consensus pattern (97 bp):
TAGACAACTAAACAATCAACAGAGAGGAATGAGTAAGGACTAGTGAAGTAGACAACTAAACAAAC
AACAGGGAGGAATGAGGAAGGATTAGTGAAAG
Found at i:420636 original size:49 final size:49
Alignment explanation
Indices: 420564--421077 Score: 866
Period size: 49 Copynumber: 10.5 Consensus size: 49
420554 NNNNNNNNNN
* **
420564 AGTAGACAACTAAATAATCAACAGAAAGGAATGAGTAAGGATTAGTGAA
1 AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAA
*
420613 AGTAGACAACTAAATAATCAACAGGGAGGAATGAGTAAGGATTAGTGAA
1 AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAA
** *
420662 AGTAGACAACTAAACAATCAACAGGGAATAATGAATAAGGATTAGTGAA
1 AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAA
*
420711 AGTAGACAACTAAACAATCAACAGGGAGGAGTGAGTAAGGATTAGTGAA
1 AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAA
420760 AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAA
1 AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAA
*
420809 AGTAGACAACTAAATAATCAACAGGGAGGAATGAGTAAGGATTAGTGAA
1 AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAA
* *
420858 AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAAGATTAGTAAA
1 AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAA
*
420907 AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTTAA
1 AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAA
* *
420956 GGTAGACAACTAAACAATCAACAGGGAGGAGTGAGTAAGGATTAGTGAA
1 AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAA
* *
421005 AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAAGATTAGTTAA
1 AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAA
* *
421054 GGTAGACAACTAAATAATCAACAG
1 AGTAGACAACTAAACAATCAACAG
421078 CCTTTCAATT
Statistics
Matches: 439, Mismatches: 26, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 439 1.00
ACGTcount: A:0.48, C:0.10, G:0.25, T:0.18
Consensus pattern (49 bp):
AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAA
Found at i:428540 original size:10 final size:10
Alignment explanation
Indices: 428527--428556 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
428517 AAAAATCGCC
428527 AGAGTTCTCT
1 AGAGTTCTCT
428537 AGAGTTCTCT
1 AGAGTTCTCT
*
428547 AGAATTCTCT
1 AGAGTTCTCT
428557 GTTTAGTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (10 bp):
AGAGTTCTCT
Found at i:437299 original size:2 final size:2
Alignment explanation
Indices: 437294--437338 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
437284 TATATATATA
437294 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
437336 TG T
1 TG T
437339 TGGTGTAGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:441178 original size:2 final size:2
Alignment explanation
Indices: 441171--441230 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
441161 TTATCTCCCT
441171 GA GA GA GA GA G- 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 GA GA GA
441212 GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA G
441231 NNNNNNNNNN
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 56 0.98
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:452258 original size:2 final size:2
Alignment explanation
Indices: 452251--452318 Score: 118
Period size: 2 Copynumber: 34.0 Consensus size: 2
452241 CTATCTCCCT
452251 GA GA GA 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 GA GA GA
* *
452293 GA GA GA GA GA GA GA GA AA TA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
452319 TTACAAGTAC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.47, T:0.01
Consensus pattern (2 bp):
GA
Found at i:453161 original size:2 final size:2
Alignment explanation
Indices: 453156--453216 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
453146 ATTAAAATCC
453156 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
453198 AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG A
453217 TTTTCTCAAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:454748 original size:3 final size:3
Alignment explanation
Indices: 454722--454770 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
454712 AATATGCATG
* * * *
454722 TAT TCT TAT TAT CAT TAAT CAT TAT TAT TAT TAT CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT
454768 TAT
1 TAT
454771 AAAGGAATAC
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
3 35 0.95
4 2 0.05
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:460033 original size:10 final size:10
Alignment explanation
Indices: 460018--460044 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
460008 GAGCGTCGAG
460018 TTGAACTATA
1 TTGAACTATA
460028 TTGAACTATA
1 TTGAACTATA
460038 TTGAACT
1 TTGAACT
460045 CTGGCGTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (10 bp):
TTGAACTATA
Found at i:461888 original size:15 final size:13
Alignment explanation
Indices: 461860--461894 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 13
461850 TATTCATTAT
461860 TTTATTTTATTTA
1 TTTATTTTATTTA
461873 TTTATTTGTAATTTA
1 TTTATTT-T-ATTTA
461888 TTTATTT
1 TTTATTT
461895 AGTGCCACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.35
14 1 0.05
15 12 0.60
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:461889 original size:19 final size:18
Alignment explanation
Indices: 461856--461895 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
461846 TGTTTATTCA
*
461856 TTATTTTATTTTATTTAT
1 TTATTTTAATTTATTTAT
461874 TTATTTGTAATTTATTTAT
1 TTATTT-TAATTTATTTAT
461893 TTA
1 TTA
461896 GTGCCACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (18 bp):
TTATTTTAATTTATTTAT
Found at i:464457 original size:4 final size:4
Alignment explanation
Indices: 464448--464502 Score: 110
Period size: 4 Copynumber: 13.8 Consensus size: 4
464438 TATTTGTAGT
464448 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
464496 TCTA TCT
1 TCTA TCT
464503 GTCTGTCTGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.24, C:0.25, G:0.00, T:0.51
Consensus pattern (4 bp):
TCTA
Found at i:467468 original size:64 final size:64
Alignment explanation
Indices: 467367--467498 Score: 255
Period size: 64 Copynumber: 2.1 Consensus size: 64
467357 TTTTTCTATA
*
467367 ATTAAGGTCTTCCGTTTCCAACGGAAGCCCTTATAGTGATTGTTAGGTTTTTTCTTTCTTTCTT
1 ATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTTAGGTTTTTTCTTTCTTTCTT
467431 ATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTTAGGTTTTTTCTTTCTTTCTT
1 ATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTTAGGTTTTTTCTTTCTTTCTT
467495 ATTA
1 ATTA
467499 TTATTATTTT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 67 1.00
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (64 bp):
ATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTTAGGTTTTTTCTTTCTTTCTT
Found at i:476638 original size:12 final size:12
Alignment explanation
Indices: 476621--476671 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
476611 AGTGCCCATA
*
476621 ATGGAACATTGC
1 ATGGAACATTAC
*
476633 ATGGAACATTGC
1 ATGGAACATTAC
*
476645 GTGGAACATTAC
1 ATGGAACATTAC
*
476657 AGGGAACATTAC
1 ATGGAACATTAC
476669 ATG
1 ATG
476672 CAAACCAAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (12 bp):
ATGGAACATTAC
Found at i:484340 original size:22 final size:22
Alignment explanation
Indices: 484315--484364 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
484305 TCGCTTCTTT
484315 GCCTTTGCAA-CTTCGCACTCTC
1 GCCTTTG-AATCTTCGCACTCTC
* * *
484337 GCCTTCGAATCTTCGCGCTTTC
1 GCCTTTGAATCTTCGCACTCTC
484359 GCCTTT
1 GCCTTT
484365 TTAGCTCATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.10, C:0.38, G:0.16, T:0.36
Consensus pattern (22 bp):
GCCTTTGAATCTTCGCACTCTC
Found at i:485791 original size:11 final size:11
Alignment explanation
Indices: 485761--485792 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
485751 TAAAGACGGT
*
485761 CTTTAAGCCAC
1 CTTTAAGCTAC
485772 CTTTAAGCTAC
1 CTTTAAGCTAC
485783 CTTTAAGCTA
1 CTTTAAGCTA
485793 TATGTATTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.34
Consensus pattern (11 bp):
CTTTAAGCTAC
Found at i:485851 original size:22 final size:22
Alignment explanation
Indices: 485801--485853 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
485791 TATATGTATT
*
485801 GCTTAAAGGTGGCTTAAAGAAA
1 GCTTAAAGATGGCTTAAAGAAA
* **
485823 GCGTAAAGATGGCTTAAAGGCA
1 GCTTAAAGATGGCTTAAAGAAA
485845 GCTTAAAGA
1 GCTTAAAGA
485854 CTATCTTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.40, C:0.11, G:0.28, T:0.21
Consensus pattern (22 bp):
GCTTAAAGATGGCTTAAAGAAA
Found at i:485874 original size:11 final size:11
Alignment explanation
Indices: 485858--485886 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
485848 TAAAGACTAT
485858 CTTTAAGCCAC
1 CTTTAAGCCAC
485869 CTTTAAGCCAC
1 CTTTAAGCCAC
485880 CTTTAAG
1 CTTTAAG
485887 GACAACTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:485934 original size:11 final size:11
Alignment explanation
Indices: 485918--485971 Score: 99
Period size: 11 Copynumber: 4.9 Consensus size: 11
485908 GTCCAAACTT
485918 CTTTAAGCCAC
1 CTTTAAGCCAC
485929 CTTTAAGCCAC
1 CTTTAAGCCAC
*
485940 CTTTAAGCTAC
1 CTTTAAGCCAC
485951 CTTTAAGCCAC
1 CTTTAAGCCAC
485962 CTTTAAGCCA
1 CTTTAAGCCA
485972 TTAAAAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 41 1.00
ACGTcount: A:0.28, C:0.33, G:0.09, T:0.30
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:487187 original size:112 final size:112
Alignment explanation
Indices: 486990--487213 Score: 421
Period size: 112 Copynumber: 2.0 Consensus size: 112
486980 AACCCTGACG
*
486990 TGCACCTGGGCAAACGACACACCTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT
1 TGCACCTGGGCAAACGACACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT
*
487055 TTCTTAAGTTGGACAAACAATAGACTTTAATTAGATATACACAAACA
66 TTCTTAAGTTGGACAAACAATAGACTCTAATTAGATATACACAAACA
*
487102 TGCACCTGGGCACACGACACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT
1 TGCACCTGGGCAAACGACACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT
487167 TTCTTAAGTTGGACAAACAATAGACTCTAATTAGATATACACAAACA
66 TTCTTAAGTTGGACAAACAATAGACTCTAATTAGATATACACAAACA
487214 AACAAAACTA
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
112 109 1.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (112 bp):
TGCACCTGGGCAAACGACACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT
TTCTTAAGTTGGACAAACAATAGACTCTAATTAGATATACACAAACA
Found at i:487434 original size:2 final size:2
Alignment explanation
Indices: 487427--487466 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
487417 CGGATGAACT
*
487427 GA GA GA GA GA GA AA 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 GA GA
487467 TTTTTTCACC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:487828 original size:22 final size:22
Alignment explanation
Indices: 487800--487860 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
487790 AATATTGACT
* *
487800 TAAAGGCCACTTAAAGACAGTG
1 TAAAGGCCAATTAAAGACAGCG
* *
487822 TAAAGG-CAGTGTAAAGAGAGCG
1 TAAAGGCCAAT-TAAAGACAGCG
*
487844 TAAATGCCAATTAAAGA
1 TAAAGGCCAATTAAAGA
487861 TGCTTAAAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 3 0.09
22 26 0.81
23 3 0.09
ACGTcount: A:0.44, C:0.13, G:0.25, T:0.18
Consensus pattern (22 bp):
TAAAGGCCAATTAAAGACAGCG
Found at i:487977 original size:11 final size:11
Alignment explanation
Indices: 487961--487990 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
487951 CGTTTAAGCT
*
487961 CCTTTAAGTCA
1 CCTTTAAGCCA
487972 CCTTTAAGCCA
1 CCTTTAAGCCA
487983 CCTTTAAG
1 CCTTTAAG
487991 GACTTGCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33
Consensus pattern (11 bp):
CCTTTAAGCCA
Found at i:490503 original size:53 final size:53
Alignment explanation
Indices: 490430--490596 Score: 183
Period size: 53 Copynumber: 3.2 Consensus size: 53
490420 AAAAAATATT
* * *
490430 TTATTTCAATAATGGTTGTAATGAAATGCAT-CTTTAACCACAATTGAAATAAA
1 TTATTTCAATAGTGGTTGTAATGAAATGCATAC-CTAACCACAATTGAAACAAA
* ** *
490483 TTATTTCAATAGTTGTTGTAATGAAATGCATACCTAACCACTTTTGAAACAAT
1 TTATTTCAATAGTGGTTGTAATGAAATGCATACCTAACCACAATTGAAACAAA
* * * * * * * *
490536 TTATTTCAATAGTGGTTATAATGAAACGGATACCCAACCACTAGTGAAATAAT
1 TTATTTCAATAGTGGTTGTAATGAAATGCATACCTAACCACAATTGAAACAAA
490589 TTATTTCA
1 TTATTTCA
490597 TTCAATATTG
Statistics
Matches: 98, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
53 97 0.99
54 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (53 bp):
TTATTTCAATAGTGGTTGTAATGAAATGCATACCTAACCACAATTGAAACAAA
Found at i:491497 original size:17 final size:17
Alignment explanation
Indices: 491475--491509 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
491465 ATTGAAATAA
491475 TTTATTTCAATAATGGT
1 TTTATTTCAATAATGGT
*
491492 TTTATTTCAATAGTGGT
1 TTTATTTCAATAATGGT
491509 T
1 T
491510 GCAACAGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.06, G:0.14, T:0.54
Consensus pattern (17 bp):
TTTATTTCAATAATGGT
Found at i:497357 original size:165 final size:166
Alignment explanation
Indices: 497160--497517 Score: 456
Period size: 168 Copynumber: 2.2 Consensus size: 166
497150 GGGGCCACGA
* * *
497160 ATTTCACAATTTTGGTAGAAGGCTTCATGGACATCATAATCA-TGCATTTATTTTTTAACAAATA
1 ATTTCACAATTTTGGTAGAGGGCTTAATGGACATCATAAT-ATTGCATTTAGTTTTTAACAAATA
* * * * * * *
497224 TATATGGAAGTAGAGAAG-ATTGTCTACGATTTAATATATTTTAACCT-TATGGCCAT-ATTGGT
65 TATATGGAAGCAGAGAAGAATTGTCTAAGATGTAATACATTTTAA-ATATATGACCATCA-TGGC
* *
497286 CCCA-CTGTAGAGCCAGAACCCCTGACAAAGGGGTCATAC
128 CCCATC-CTAGAGCCAGAACCCCTGACAAAGGGGCCATAC
*
497325 ATTTCACAATATTGGTAGAGGGCTTAATGGACATCATAATATTGCATTTAGTTTTTAACAAATAT
1 ATTTCACAATTTTGGTAGAGGGCTTAATGGACATCATAATATTGCATTTAGTTTTTAACAAATAT
* *
497390 ATATGGGAGCAGAGAAGAATATTTTCTAAGATGTAATACATTTTAAATATATGACCATCATGGCC
66 ATATGGAAGCAGAGAAG-A-ATTGTCTAAGATGTAATACATTTTAAATATATGACCATCATGGCC
* ** *
497455 CCATCCTAGATCCAGAACCCCTGACCTAGGGGCCATGC
129 CCATCCTAGAGCCAGAACCCCTGACAAAGGGGCCATAC
497493 ATTTCACAATTTTGGTAGAGGGCTT
1 ATTTCACAATTTTGGTAGAGGGCTT
497518 CCTGGTTATC
Statistics
Matches: 166, Mismatches: 20, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
164 1 0.01
165 74 0.45
167 1 0.01
168 88 0.53
169 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (166 bp):
ATTTCACAATTTTGGTAGAGGGCTTAATGGACATCATAATATTGCATTTAGTTTTTAACAAATAT
ATATGGAAGCAGAGAAGAATTGTCTAAGATGTAATACATTTTAAATATATGACCATCATGGCCCC
ATCCTAGAGCCAGAACCCCTGACAAAGGGGCCATAC
Found at i:498240 original size:2 final size:2
Alignment explanation
Indices: 498235--498280 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
498225 AAAACAGTTT
* *
498235 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GG GG GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
498277 GA GA
1 GA GA
498281 AAGATTCAGC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
GA
Found at i:504190 original size:13 final size:13
Alignment explanation
Indices: 504172--504200 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
504162 AAAATAGTGC
504172 AACTTCAAAAGTA
1 AACTTCAAAAGTA
504185 AACTTCAAAAGTA
1 AACTTCAAAAGTA
504198 AAC
1 AAC
504201 AAAAAACCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.17, G:0.07, T:0.21
Consensus pattern (13 bp):
AACTTCAAAAGTA
Found at i:505166 original size:2 final size:2
Alignment explanation
Indices: 505161--505203 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
505151 GTGTGTGTGT
505161 GA GA GA 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 GA GA GA
505203 G
1 G
505204 NNNNNNNNNN
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:512685 original size:14 final size:13
Alignment explanation
Indices: 512666--512710 Score: 56
Period size: 14 Copynumber: 3.4 Consensus size: 13
512656 AGTTAGTTAT
512666 ATTTTTTTCTAGAC
1 ATTTTTTTCTA-AC
512680 ATTTTTTTCTAA-
1 ATTTTTTTCTAAC
*
512692 ACTTTTTTCTACAC
1 ATTTTTTTCTA-AC
512706 ATTTT
1 ATTTT
512711 AAAAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 10 0.37
13 2 0.07
14 15 0.56
ACGTcount: A:0.22, C:0.16, G:0.02, T:0.60
Consensus pattern (13 bp):
ATTTTTTTCTAAC
Found at i:521653 original size:4 final size:4
Alignment explanation
Indices: 521635--521679 Score: 63
Period size: 4 Copynumber: 11.2 Consensus size: 4
521625 AATGAGTTTT
* * *
521635 TCTG TCCG TCCG TCTG TCTG TCTG TCTG TCTG TCTC TCTG TCTG T
1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG T
521680 AAACTTTTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.00, C:0.31, G:0.22, T:0.47
Consensus pattern (4 bp):
TCTG
Found at i:526764 original size:21 final size:21
Alignment explanation
Indices: 526738--526801 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
526728 TTGGGGTGTT
*
526738 AGATTTCAATGCTATGGTATG
1 AGATTTCAATGCTATGCTATG
*
526759 AGATTTCAATGCTATACTATG
1 AGATTTCAATGCTATGCTATG
* * *
526780 AAATGTCAATGATATGCTATG
1 AGATTTCAATGCTATGCTATG
526801 A
1 A
526802 TATGGTGTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (21 bp):
AGATTTCAATGCTATGCTATG
Found at i:534142 original size:28 final size:29
Alignment explanation
Indices: 534110--534177 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 29
534100 ATGCATGATA
* * *
534110 TACTTGTATTTTG-CCGTGTAGTTCGGTG
1 TACTTGTATATTGTCCGTGTAGTACGGAG
534138 TACTTGTATATTGTCCGTGTAGTACGGAG
1 TACTTGTATATTGTCCGTGTAGTACGGAG
*
534167 TATTTGTATAT
1 TACTTGTATAT
534178 CGTTTTGACG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
28 12 0.34
29 23 0.66
ACGTcount: A:0.18, C:0.12, G:0.25, T:0.46
Consensus pattern (29 bp):
TACTTGTATATTGTCCGTGTAGTACGGAG
Found at i:538318 original size:43 final size:43
Alignment explanation
Indices: 538270--538364 Score: 122
Period size: 43 Copynumber: 2.2 Consensus size: 43
538260 ATATGTTTTT
538270 TCGTAATAAAGAGATAATTAACTCGCT-ATAACGAGATCGTTTC
1 TCGTAATAAAGAGATAATTAACTCG-TAATAACGAGATCGTTTC
* ** *
538313 TCGTAA-ATATGAGATAATTAACTCGTAATTTCGAGATCTTTTC
1 TCGTAATA-AAGAGATAATTAACTCGTAATAACGAGATCGTTTC
538356 TCGTAATAA
1 TCGTAATAA
538365 CGATATTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
42 2 0.04
43 42 0.93
44 1 0.02
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (43 bp):
TCGTAATAAAGAGATAATTAACTCGTAATAACGAGATCGTTTC
Found at i:538360 original size:21 final size:21
Alignment explanation
Indices: 538300--538434 Score: 83
Period size: 21 Copynumber: 6.3 Consensus size: 21
538290 ACTCGCTATA
* *
538300 ACGAGATCGTTTCTCGTAAAT
1 ACGAGATCTTTTCTCGTAATT
* * **
538321 ATGAGATAATTAACTCGTAATT
1 ACGAGAT-CTTTTCTCGTAATT
* *
538343 TCGAGATCTTTTCTCGTAATA
1 ACGAGATCTTTTCTCGTAATT
* *
538364 ACGATATTTTTTCTCGTAATT
1 ACGAGATCTTTTCTCGTAATT
* ** ** *
538385 CCGAGAAAATTAACTCGTAATA
1 ACGAG-ATCTTTTCTCGTAATT
*
538407 ACGAGATCTGTTT-TGGTAATT
1 ACGAGATCT-TTTCTCGTAATT
538428 ACGAGAT
1 ACGAGAT
538435 AATCAACTCA
Statistics
Matches: 81, Mismatches: 30, Indels: 6
0.69 0.26 0.05
Matches are distributed among these distances:
21 51 0.63
22 30 0.37
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (21 bp):
ACGAGATCTTTTCTCGTAATT
Found at i:538426 original size:43 final size:43
Alignment explanation
Indices: 538355--538443 Score: 108
Period size: 43 Copynumber: 2.1 Consensus size: 43
538345 GAGATCTTTT
* * * *
538355 CTCGTAATAACGATATTTTTTCTCGTAATTCCGAGAAAATTAA
1 CTCGTAATAACGAGATTGTTTCTCGTAATTACGAGAAAATCAA
* *
538398 CTCGTAATAACGAGATCTGTTT-TGGTAATTACGAGATAATCAA
1 CTCGTAATAACGAGAT-TGTTTCTCGTAATTACGAGAAAATCAA
538441 CTC
1 CTC
538444 ATTCGTAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 35 0.90
44 4 0.10
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (43 bp):
CTCGTAATAACGAGATTGTTTCTCGTAATTACGAGAAAATCAA
Found at i:538434 original size:107 final size:106
Alignment explanation
Indices: 538238--538443 Score: 258
Period size: 107 Copynumber: 1.9 Consensus size: 106
538228 CTTATGATAA
* *
538238 CGAGATCTTTTCTTAAATTACGATATGTTTTTTCGTAATAAAGAGATAATTAACTCGCTATAACG
1 CGAGATCTTTTCTTAAATAACGATATGTTTTTTCGTAATAAAGAGAAAATTAACTCGCTATAACG
* *
538303 AGATCGTTTCTCGTAAATATGAGATAATTAACTCGTAATTT
66 AGATCGTTTCTCGTAAATACGAGATAATCAACTCGTAATTT
***
538344 CGAGATCTTTTCTCGT-AATAACGATAT-TTTTTCTCGTAATTCCGAGAAAATTAACTCG-TAAT
1 CGAGATCTTTTCT--TAAATAACGATATGTTTTT-TCGTAATAAAGAGAAAATTAACTCGCT-AT
* *
538406 AACGAGATCTGTTT-TGGTAATTACGAGATAATCAACTC
62 AACGAGATC-GTTTCTCGTAAATACGAGATAATCAACTC
538444 ATTCGTAATT
Statistics
Matches: 86, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
106 19 0.22
107 62 0.72
108 5 0.06
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (106 bp):
CGAGATCTTTTCTTAAATAACGATATGTTTTTTCGTAATAAAGAGAAAATTAACTCGCTATAACG
AGATCGTTTCTCGTAAATACGAGATAATCAACTCGTAATTT
Found at i:539307 original size:21 final size:21
Alignment explanation
Indices: 539283--539340 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
539273 GTCATTGGGA
539283 TATCATTTGGTATCATAAGGG
1 TATCATTTGGTATCATAAGGG
* * **
539304 TATCAGTAGGTATCATTGGGG
1 TATCATTTGGTATCATAAGGG
539325 T-TCATTTGGGTATCAT
1 TATCATTT-GGTATCAT
539341 TGGAGTATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 4 0.13
21 26 0.87
ACGTcount: A:0.24, C:0.10, G:0.26, T:0.40
Consensus pattern (21 bp):
TATCATTTGGTATCATAAGGG
Found at i:539341 original size:21 final size:21
Alignment explanation
Indices: 539312--539378 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
539302 GGTATCAGTA
*
539312 GGTATCATTGGGGTTCATTTG
1 GGTATCATTGGGGTTCATTGG
* *
539333 GGTATCATTGGAGTATTATTGG
1 GGTATCATTGGGGT-TCATTGG
* *
539355 GGT-TCATCGCGGTTCATTGG
1 GGTATCATTGGGGTTCATTGG
539375 GGTA
1 GGTA
539379 AAATGACGCA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 9 0.24
21 20 0.54
22 8 0.22
ACGTcount: A:0.16, C:0.10, G:0.34, T:0.39
Consensus pattern (21 bp):
GGTATCATTGGGGTTCATTGG
Found at i:539348 original size:11 final size:10
Alignment explanation
Indices: 539261--539355 Score: 70
Period size: 11 Copynumber: 9.2 Consensus size: 10
539251 TGCTCATTAT
539261 GGTATCATTG
1 GGTATCATTG
539271 TGG--TCATTG
1 -GGTATCATTG
*
539280 GGATATCATTT
1 GG-TATCATTG
*
539291 GGTATCATAAG
1 GGTATCAT-TG
* *
539302 GGTATCAGTA
1 GGTATCATTG
539312 GGTATCATTGG
1 GGTATCATT-G
539323 GGT-TCATTTG
1 GGTATCA-TTG
539333 GGTATCATTG
1 GGTATCATTG
*
539343 GAGTATTATTG
1 G-GTATCATTG
539354 GG
1 GG
539356 GTTCATCGCG
Statistics
Matches: 67, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
8 2 0.03
9 6 0.09
10 26 0.39
11 33 0.49
ACGTcount: A:0.22, C:0.08, G:0.31, T:0.39
Consensus pattern (10 bp):
GGTATCATTG
Found at i:545777 original size:10 final size:10
Alignment explanation
Indices: 545764--545949 Score: 152
Period size: 10 Copynumber: 18.2 Consensus size: 10
545754 CCCCCCCCCC
545764 AAAAAAAAC-
1 AAAAAAAACA
545773 AAAAAAAACA
1 AAAAAAAACA
545783 AAAACAAAA-A
1 AAAA-AAAACA
*
545793 CAAAAACAA-A
1 -AAAAAAAACA
*
545803 AACAAAAACA
1 AAAAAAAACA
545813 AAAAAAAGA-A
1 AAAAAAA-ACA
545823 CAAAAAAAACA
1 -AAAAAAAACA
*
545834 AAACAAAACA
1 AAAAAAAACA
545844 AAAAAAAACA
1 AAAAAAAACA
*
545854 AAACAAAACA
1 AAAAAAAACA
545864 AAACAAAAA-A
1 AAA-AAAAACA
545874 AAAAAAAACA
1 AAAAAAAACA
545884 AAAAAAAA-A
1 AAAAAAAACA
545893 AAAAAAAA-A
1 AAAAAAAACA
545902 AATGTAAAAAACCCA
1 AA---AAAAAA--CA
*
545917 AAACAAAACA
1 AAAAAAAACA
* *
545927 AAGTAAAACCA
1 AA-AAAAAACA
*
545938 AAAAAAATCA
1 AAAAAAAACA
545948 AA
1 AA
545950 GTACTGATGT
Statistics
Matches: 147, Mismatches: 14, Indels: 31
0.77 0.07 0.16
Matches are distributed among these distances:
9 32 0.22
10 73 0.50
11 28 0.19
12 11 0.07
15 3 0.02
ACGTcount: A:0.83, C:0.13, G:0.02, T:0.02
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:545787 original size:15 final size:15
Alignment explanation
Indices: 545767--545903 Score: 149
Period size: 15 Copynumber: 8.9 Consensus size: 15
545757 CCCCCCCAAA
545767 AAAAACAAAAAAAAC
1 AAAAACAAAAAAAAC
545782 AAAAACAAAAACAAAAAC
1 AAAAAC--AAA-AAAAAC
*
545800 AAAAACAAAAACAAAAA
1 AAAAAC-AAAA-AAAAC
545817 AAAGAACAAAAAAAAC
1 AAA-AACAAAAAAAAC
545833 -AAAACAAAACAAAA-
1 AAAAACAAAA-AAAAC
545847 AAAAACAAAACAAAAC
1 AAAAACAAAA-AAAAC
*
545863 -AAAACAAAAAAAAA
1 AAAAACAAAAAAAAC
545877 AAAAACAAAAAAAA-
1 AAAAACAAAAAAAAC
545891 AAAAA-AAAAAAAA
1 AAAAACAAAAAAAA
545904 TGTAAAAAAC
Statistics
Matches: 110, Mismatches: 3, Indels: 20
0.83 0.02 0.15
Matches are distributed among these distances:
13 8 0.07
14 16 0.15
15 48 0.44
16 5 0.05
17 18 0.16
18 15 0.14
ACGTcount: A:0.88, C:0.12, G:0.01, T:0.00
Consensus pattern (15 bp):
AAAAACAAAAAAAAC
Found at i:545912 original size:1 final size:1
Alignment explanation
Indices: 545764--545903 Score: 127
Period size: 1 Copynumber: 140.0 Consensus size: 1
545754 CCCCCCCCCC
* * * * * * * * *
545764 AAAAAAAACAAAAAAAACAAAAACAAAAACAAAAACAAAAACAAAAACAAAAAAAAGAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * *
545829 AAACAAAACAAAACAAAAAAAAACAAAACAAAACAAAACAAAAAAAAAAAAAACAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
545894 AAAAAAAAAA
1 AAAAAAAAAA
545904 TGTAAAAAAC
Statistics
Matches: 105, Mismatches: 34, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 105 1.00
ACGTcount: A:0.88, C:0.11, G:0.01, T:0.00
Consensus pattern (1 bp):
A
Found at i:545912 original size:22 final size:22
Alignment explanation
Indices: 545763--545903 Score: 158
Period size: 24 Copynumber: 6.0 Consensus size: 22
545753 CCCCCCCCCC
545763 CAAAAAAAACAAAAAAAACAAAAA
1 CAAAAAAAA-AAAAAAAA-AAAAA
*
545787 CAAAAACAAAAACAAAAACAAAAA
1 CAAAAA-AAAAA-AAAAAAAAAAA
* *
545811 C-AAAAAAAAGAACAAAAAAAA
1 CAAAAAAAAAAAAAAAAAAAAA
545832 CAAAACAAAACAAAAAAAAACAAAA
1 CAAAA-AAAA-AAAAAAAAA-AAAA
545857 CAAAACAAAACAAAAAAAAAAAAAA
1 C-AAA-AAAA-AAAAAAAAAAAAAA
545882 CAAAAAAAAAAAAAAAAAAAAA
1 CAAAAAAAAAAAAAAAAAAAAA
545904 TGTAAAAAAC
Statistics
Matches: 102, Mismatches: 6, Indels: 20
0.80 0.05 0.16
Matches are distributed among these distances:
21 10 0.10
22 21 0.21
23 12 0.12
24 24 0.24
25 18 0.18
26 15 0.15
27 2 0.02
ACGTcount: A:0.87, C:0.12, G:0.01, T:0.00
Consensus pattern (22 bp):
CAAAAAAAAAAAAAAAAAAAAA
Found at i:546591 original size:8 final size:8
Alignment explanation
Indices: 546578--546648 Score: 78
Period size: 8 Copynumber: 9.4 Consensus size: 8
546568 TTGCCAGAGT
*
546578 AAACAAAC
1 AAACAAAA
*
546586 AAACAAAC
1 AAACAAAA
546594 AAA-AAAA
1 AAACAAAA
546601 AAA-AAAA
1 AAACAAAA
546608 AAACAAAA
1 AAACAAAA
546616 AAA-AAAA
1 AAACAAAA
*
546623 AAAAAAAA
1 AAACAAAA
546631 AAACAAAA
1 AAACAAAA
*
546639 CAA-AAAA
1 AAACAAAA
546646 AAA
1 AAA
546649 TCTAACAAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
7 26 0.46
8 31 0.54
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (8 bp):
AAACAAAA
Found at i:546614 original size:22 final size:23
Alignment explanation
Indices: 546586--546648 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
546576 GTAAACAAAC
546586 AAAC-AAACAAAAAAAAAAAAAA
1 AAACAAAACAAAAAAAAAAAAAA
*
546608 AAACAAAAAAAAAAAAAAAAAAA
1 AAACAAAACAAAAAAAAAAAAAA
546631 AAACAAAACAAAAAAAAA
1 AAACAAAACAAAAAAAAA
546649 TCTAACAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 4 0.11
23 34 0.89
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (23 bp):
AAACAAAACAAAAAAAAAAAAAA
Found at i:546655 original size:20 final size:19
Alignment explanation
Indices: 546590--546659 Score: 79
Period size: 20 Copynumber: 3.6 Consensus size: 19
546580 ACAAACAAAC
546590 AAACAA-AAAAAAAAAAAA
1 AAACAACAAAAAAAAAAAA
*
546608 AAACAAAAAAAAAAAAAAAA
1 AAAC-AACAAAAAAAAAAAA
* *
546628 AAAAAACAAAACAAAAAAA
1 AAACAACAAAAAAAAAAAA
*
546647 AATCTAACAAAAA
1 AAAC-AACAAAAA
546660 TTATTTTTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
18 4 0.09
19 17 0.40
20 22 0.51
ACGTcount: A:0.89, C:0.09, G:0.00, T:0.03
Consensus pattern (19 bp):
AAACAACAAAAAAAAAAAA
Found at i:546659 original size:1 final size:1
Alignment explanation
Indices: 546594--546648 Score: 83
Period size: 1 Copynumber: 55.0 Consensus size: 1
546584 ACAAACAAAC
* * *
546594 AAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAACAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
546649 TCTAACAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.95, C:0.05, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:560792 original size:3 final size:3
Alignment explanation
Indices: 560433--560777 Score: 268
Period size: 3 Copynumber: 114.0 Consensus size: 3
560423 GATTTGACCG
* * *
560433 TAC TAC TAC TAC TTC TAC TAC TAC GAAT TAC TAC TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC -TAC TAC TAC TAC TAC TAC TAC
** *
560479 TAC TAC TAC TAC TTT TAC TAC TAT TAC TAC TAC TAC TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
* * * * *
560527 TAC TAC TGC TAC TAC TAC TTC TAC TAC TAC TTC TAC TAC TAC AAC AAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
* * * * * ** *
560575 AAC AAC AAC TTC TAC TAC TAC TAC GAC TTT TAC TAC TAT TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
* * *
560623 TAC TAC TAC -AC GTTATG TAC TAC TAC TAC TAA TAC TAC TAC TGC TAC
1 TAC TAC TAC TAC --TA-C TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
* * * * * **
560670 TAC TAAC -AT TGC TAC TAC TAT TA- TCAC CAC TTC TTT TAC TAC TAC
1 TAC T-AC TAC TAC TAC TAC TAC TAC T-AC TAC TAC TAC TAC TAC TAC
* * * * *
560715 TTC TAC TAC TAC ATAC T-C TAC CAA TAGC -AC CAC TAC TAC TAC TAT
1 TAC TAC TAC TAC -TAC TAC TAC TAC TA-C TAC TAC TAC TAC TAC TAC
*
560760 TAC TAC AAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC
560778 ATCCATTACT
Statistics
Matches: 271, Mismatches: 58, Indels: 26
0.76 0.16 0.07
Matches are distributed among these distances:
2 7 0.03
3 255 0.94
4 8 0.03
5 1 0.00
ACGTcount: A:0.32, C:0.30, G:0.02, T:0.35
Consensus pattern (3 bp):
TAC
Found at i:565308 original size:21 final size:21
Alignment explanation
Indices: 565284--565324 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
565274 TATTCAGTGC
565284 GTGACGGTTGGTTTTGCATCT
1 GTGACGGTTGGTTTTGCATCT
** *
565305 GTGATTGTTTGTTTTGCATC
1 GTGACGGTTGGTTTTGCATC
565325 AATGTCTGCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.12, G:0.29, T:0.49
Consensus pattern (21 bp):
GTGACGGTTGGTTTTGCATCT
Found at i:568874 original size:22 final size:22
Alignment explanation
Indices: 568806--568875 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
568796 GTCTTAGAGT
568806 TTTTTCTCAGTGTCACTCAGGC
1 TTTTTCTCAGTGTCACTCAGGC
* * * *
568828 TTTTTTTTA-TAGT--CTAAGAGT
1 TTTTTCTCAGT-GTCACTCAG-GC
568849 TTTTTCTCAGTGTCACTCAGGC
1 TTTTTCTCAGTGTCACTCAGGC
568871 TTTTT
1 TTTTT
568876 TTATAGTCTC
Statistics
Matches: 35, Mismatches: 8, Indels: 10
0.66 0.15 0.19
Matches are distributed among these distances:
20 4 0.11
21 11 0.31
22 16 0.46
23 4 0.11
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.50
Consensus pattern (22 bp):
TTTTTCTCAGTGTCACTCAGGC
Found at i:568893 original size:19 final size:19
Alignment explanation
Indices: 568829--568896 Score: 59
Period size: 19 Copynumber: 3.4 Consensus size: 19
568819 CACTCAGGCT
*
568829 TTTTTTTATAGTCTAAGAG
1 TTTTTTTATAGTCTCAGAG
568848 TTTTTTCTCAGT-GTCACTCAG-G
1 TTTTTT-T-A-TAGT--CTCAGAG
568870 CTTTTTTTATAGTCTCAGAG
1 -TTTTTTTATAGTCTCAGAG
568890 TTTTTTT
1 TTTTTTT
568897 CATTACAGCA
Statistics
Matches: 40, Mismatches: 1, Indels: 16
0.70 0.02 0.28
Matches are distributed among these distances:
19 18 0.45
20 3 0.08
21 6 0.15
22 3 0.08
23 10 0.25
ACGTcount: A:0.18, C:0.13, G:0.15, T:0.54
Consensus pattern (19 bp):
TTTTTTTATAGTCTCAGAG
Found at i:568897 original size:43 final size:42
Alignment explanation
Indices: 568766--568895 Score: 208
Period size: 43 Copynumber: 3.1 Consensus size: 42
568756 TCTCTCAGGG
* * *
568766 TTTTCTCAGTGCCACTGAGGC-TTTTTTATAGTCTTAGAGTT
1 TTTTCTCAGTGTCACTCAGGCTTTTTTTATAGTCTAAGAGTT
568807 TTTTCTCAGTGTCACTCAGGCTTTTTTTTATAGTCTAAGAGTT
1 TTTTCTCAGTGTCACTCAGGC-TTTTTTTATAGTCTAAGAGTT
*
568850 TTTTCTCAGTGTCACTCAGGCTTTTTTTATAGTCTCAGAGTT
1 TTTTCTCAGTGTCACTCAGGCTTTTTTTATAGTCTAAGAGTT
568892 TTTT
1 TTTT
568896 TCATTACAGC
Statistics
Matches: 83, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
41 19 0.23
42 24 0.29
43 40 0.48
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.49
Consensus pattern (42 bp):
TTTTCTCAGTGTCACTCAGGCTTTTTTTATAGTCTAAGAGTT
Found at i:578449 original size:21 final size:21
Alignment explanation
Indices: 578423--578470 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
578413 ACCATAGCAA
* *
578423 AGCATAGCATTGAAATCGCAT
1 AGCATAGCACTGAAATCACAT
*
578444 AGCATAGCACTGGAATCACAT
1 AGCATAGCACTGAAATCACAT
*
578465 ACCATA
1 AGCATA
578471 CCATATAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.21
Consensus pattern (21 bp):
AGCATAGCACTGAAATCACAT
Found at i:578690 original size:10 final size:10
Alignment explanation
Indices: 578675--578705 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
578665 CAAATCTCAC
578675 AGCATACCAT
1 AGCATACCAT
*
578685 AGCATAGCAT
1 AGCATACCAT
578695 AGCATACCAT
1 AGCATACCAT
578705 A
1 A
578706 TCATTAAGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.26, G:0.13, T:0.19
Consensus pattern (10 bp):
AGCATACCAT
Found at i:578755 original size:21 final size:21
Alignment explanation
Indices: 578729--578808 Score: 108
Period size: 21 Copynumber: 3.8 Consensus size: 21
578719 AATTTCAATT
578729 TCTCATAGCATAGCATACAAA
1 TCTCATAGCATAGCATACAAA
578750 TCTCATAGCATAGCATACAAA
1 TCTCATAGCATAGCATACAAA
* *
578771 TATCATAGCATATCATTA-AAA
1 TCTCATAGCATAGCA-TACAAA
* *
578792 TCGCATATCATAGCATA
1 TCTCATAGCATAGCATA
578809 GCATACATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
20 2 0.04
21 48 0.92
22 2 0.04
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (21 bp):
TCTCATAGCATAGCATACAAA
Found at i:578782 original size:26 final size:25
Alignment explanation
Indices: 578732--578813 Score: 66
Period size: 26 Copynumber: 3.4 Consensus size: 25
578722 TTCAATTTCT
578732 CATAGCATAGCATACAA-ATC-T--
1 CATAGCATAGCATACAATATCATAG
578753 CATAGCATAGCATACAAATATCATAG
1 CATAGCATAGCATAC-AATATCATAG
* ** *
578779 CATATCATTAAAAT-CGCATATCATAG
1 CATAGCA-TAGCATAC-AATATCATAG
578805 CATAGCATA
1 CATAGCATA
578814 CATTTGTAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
21 15 0.31
22 2 0.04
23 3 0.06
24 1 0.02
25 2 0.04
26 22 0.45
27 4 0.08
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.26
Consensus pattern (25 bp):
CATAGCATAGCATACAATATCATAG
Found at i:583173 original size:27 final size:27
Alignment explanation
Indices: 583142--583194 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
583132 AAAAACCAAA
583142 ATTCCCCTTCTTTATACAATCAAATAT
1 ATTCCCCTTCTTTATACAATCAAATAT
*
583169 ATTCCTCTTCTTTATACAATCAAATA
1 ATTCCCCTTCTTTATACAATCAAATA
583195 GTTTGGCGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.34, C:0.25, G:0.00, T:0.42
Consensus pattern (27 bp):
ATTCCCCTTCTTTATACAATCAAATAT
Found at i:583364 original size:14 final size:14
Alignment explanation
Indices: 583345--583386 Score: 84
Period size: 14 Copynumber: 3.0 Consensus size: 14
583335 ATATCAACTG
583345 ATATAGATACAAAC
1 ATATAGATACAAAC
583359 ATATAGATACAAAC
1 ATATAGATACAAAC
583373 ATATAGATACAAAC
1 ATATAGATACAAAC
583387 TTCTATACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.57, C:0.14, G:0.07, T:0.21
Consensus pattern (14 bp):
ATATAGATACAAAC
Found at i:586320 original size:14 final size:14
Alignment explanation
Indices: 586301--586328 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
586291 AATCTGGTAG
586301 TACATTACTGCCAC
1 TACATTACTGCCAC
586315 TACATTACTGCCAC
1 TACATTACTGCCAC
586329 AGTGGTGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.36, G:0.07, T:0.29
Consensus pattern (14 bp):
TACATTACTGCCAC
Found at i:600022 original size:20 final size:21
Alignment explanation
Indices: 599997--600047 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
599987 TGAAAATGTC
*
599997 ATTTTTGCTGATAAT-TCCTG
1 ATTTTTGCTGATAATATACTG
* *
600017 ATTTTTACTGATATTATACTG
1 ATTTTTGCTGATAATATACTG
600038 -TTTTTGCTGA
1 ATTTTTGCTGA
600048 AGATTGCTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.22, C:0.12, G:0.14, T:0.53
Consensus pattern (21 bp):
ATTTTTGCTGATAATATACTG
Found at i:600119 original size:10 final size:10
Alignment explanation
Indices: 600104--600128 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
600094 GTTGTTGTTT
600104 CTGATATTTA
1 CTGATATTTA
600114 CTGATATTTA
1 CTGATATTTA
600124 CTGAT
1 CTGAT
600129 GCTTTTGCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (10 bp):
CTGATATTTA
Found at i:602279 original size:4 final size:4
Alignment explanation
Indices: 602270--602442 Score: 253
Period size: 4 Copynumber: 44.0 Consensus size: 4
602260 CTGTTCATAT
* * * *
602270 ATAG ATAG ATTG ATAG ATAG ATAA ATAC AT-G -TAG ATAG ATAG ATAA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
* * *
602316 AAAG AT-G ATAG ATAG ATAG TTAG ATAG ATAG ATAG ATAG ATAG ATGG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
602363 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
*
602411 ATAG ATAG ATAG ATAA ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
602443 GGTACACTTT
Statistics
Matches: 151, Mismatches: 15, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
2 1 0.01
3 4 0.03
4 146 0.97
ACGTcount: A:0.50, C:0.01, G:0.24, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:602925 original size:14 final size:14
Alignment explanation
Indices: 602906--602942 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
602896 ATCACTCATT
602906 AAAAAAACAGACAG
1 AAAAAAACAGACAG
* *
602920 AAAAAAAAAGAGAG
1 AAAAAAACAGACAG
602934 AAAAAAACA
1 AAAAAAACA
602943 AACATAGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.78, C:0.08, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAAACAGACAG
Found at i:605846 original size:13 final size:12
Alignment explanation
Indices: 605814--605861 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
605804 TGTTGAACTG
*
605814 TTTTTTTTTTTG
1 TTTTTTTTTTTA
* *
605826 GTGTTTTTTTTA
1 TTTTTTTTTTTA
*
605838 TTTTATTTTATTA
1 TTTT-TTTTTTTA
605851 TTTTTTTTTTT
1 TTTTTTTTTTT
605862 GGGGGGGGGG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
12 17 0.61
13 11 0.39
ACGTcount: A:0.08, C:0.00, G:0.06, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTTTA
Found at i:624512 original size:1 final size:1
Alignment explanation
Indices: 624506--624530 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
624496 CCGCGCATGG
624506 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
624531 ACCACCACAN
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:631356 original size:7 final size:7
Alignment explanation
Indices: 631341--631407 Score: 82
Period size: 7 Copynumber: 9.6 Consensus size: 7
631331 TTTAGATATT
631341 GAATCTC
1 GAATCTC
*
631348 GAATTTC
1 GAATCTC
631355 GAATCTC
1 GAATCTC
631362 GAATCTC
1 GAATCTC
* *
631369 GTATTTC
1 GAATCTC
631376 GAATCTC
1 GAATCTC
*
631383 GTAAT-TT
1 G-AATCTC
631390 GAATCTC
1 GAATCTC
631397 GAATCTC
1 GAATCTC
631404 GAAT
1 GAAT
631408 GATCCTTCTC
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
6 3 0.06
7 44 0.88
8 3 0.06
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (7 bp):
GAATCTC
Found at i:631366 original size:21 final size:21
Alignment explanation
Indices: 631341--631407 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
631331 TTTAGATATT
631341 GAATCTCGAATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
*
631362 GAATCTCGTATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
* *
631383 GTAAT-TTGAATCTCGAATCTC
1 G-AATCTCGAATTTCGAATCTC
631404 GAAT
1 GAAT
631408 GATCCTTCTC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
20 3 0.07
21 35 0.85
22 3 0.07
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (21 bp):
GAATCTCGAATTTCGAATCTC
Found at i:631441 original size:16 final size:16
Alignment explanation
Indices: 631412--631448 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
631402 TCGAATGATC
*
631412 CTTCTCGGCTTTCGTA
1 CTTCTCGGCCTTCGTA
*
631428 CTTCTTGGCCTTCGTA
1 CTTCTCGGCCTTCGTA
631444 CTTCT
1 CTTCT
631449 GAATTTTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.05, C:0.32, G:0.16, T:0.46
Consensus pattern (16 bp):
CTTCTCGGCCTTCGTA
Found at i:633771 original size:2 final size:2
Alignment explanation
Indices: 633766--633813 Score: 69
Period size: 2 Copynumber: 23.5 Consensus size: 2
633756 AAATCACACA
**
633766 AT AT AT AT AT CC ACT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
633809 AT AT A
1 AT AT A
633814 ACACACAAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 40 0.98
3 1 0.02
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:635064 original size:8 final size:8
Alignment explanation
Indices: 635051--635104 Score: 72
Period size: 8 Copynumber: 6.8 Consensus size: 8
635041 AATGCCGGGC
635051 GTCCGTGG
1 GTCCGTGG
635059 GTCCGTGG
1 GTCCGTGG
*
635067 GTCCGTGT
1 GTCCGTGG
*
635075 GTCTGTGG
1 GTCCGTGG
*
635083 GTCCGTGC
1 GTCCGTGG
*
635091 GTCCGTGT
1 GTCCGTGG
635099 GTCCGT
1 GTCCGT
635105 CCGTCACACT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 40 1.00
ACGTcount: A:0.00, C:0.26, G:0.43, T:0.31
Consensus pattern (8 bp):
GTCCGTGG
Found at i:635087 original size:24 final size:24
Alignment explanation
Indices: 635055--635101 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
635045 CCGGGCGTCC
*
635055 GTGGGTCCGTGGGTCCGTGTGTCT
1 GTGGGTCCGTGCGTCCGTGTGTCT
635079 GTGGGTCCGTGCGTCCGTGTGTC
1 GTGGGTCCGTGCGTCCGTGTGTC
635102 CGTCCGTCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.45, T:0.32
Consensus pattern (24 bp):
GTGGGTCCGTGCGTCCGTGTGTCT
Found at i:638229 original size:21 final size:21
Alignment explanation
Indices: 638203--638276 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
638193 TAATTATTTC
*
638203 GACATGCAAGATAAAGATGTT
1 GACATGCAAGATAAATATGTT
* *
638224 GACATGCAAGATAATTATGTC
1 GACATGCAAGATAAATATGTT
* * *
638245 AACATGCAACATAACTATGTT
1 GACATGCAAGATAAATATGTT
638266 GACATGCAAGA
1 GACATGCAAGA
638277 AAACTGCAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (21 bp):
GACATGCAAGATAAATATGTT
Found at i:638252 original size:42 final size:42
Alignment explanation
Indices: 638193--638276 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
638183 ATTTTTCTAT
* * *
638193 TAATTATTTCGACATGCAAGATAAAGATGTTGACATGCAAGA
1 TAATTATGTCAACATGCAACATAAAGATGTTGACATGCAAGA
**
638235 TAATTATGTCAACATGCAACATAACTATGTTGACATGCAAGA
1 TAATTATGTCAACATGCAACATAAAGATGTTGACATGCAAGA
638277 AAACTGCAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (42 bp):
TAATTATGTCAACATGCAACATAAAGATGTTGACATGCAAGA
Found at i:639223 original size:21 final size:21
Alignment explanation
Indices: 639166--639225 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
639156 CATAGCTATG
* * *
639166 TTGCATGTTGACATAATTATT
1 TTGCATGTCGACATATTTATC
*
639187 TTGCATGTCAACATATTTATC
1 TTGCATGTCGACATATTTATC
639208 TTGCATGTCGACATATTT
1 TTGCATGTCGACATATTT
639226 CATAGAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (21 bp):
TTGCATGTCGACATATTTATC
Found at i:648263 original size:183 final size:176
Alignment explanation
Indices: 647833--648284 Score: 440
Period size: 167 Copynumber: 2.6 Consensus size: 176
647823 ATTGTGAAAT
* * * **
647833 TCATGGCCCCTGGGTCTA-GGGTTCAGGCTCTAGGGTGTTGCCAATATGGCCATATAGTAAAAAT
1 TCATGACCCCTGTGTC-AGGGGTTCAGGCTCAAGGGTGCAGCCAATATGGCCATATAGTAAAAAT
* * * * ** * * * *
647897 ATTTTAAATATTAGAAAATCTTCACCTCTACTCCCATATCTATCTGT--------TAAA-AAGTA
65 GTATTAAATCTTGGAAAATCTTCTTCTCTACTCCCATATATATTTGTAAAAAAAAAAAACAACTA
* * *
647953 AATGGATGGTTATGATGTCCATGAAGTCCTCTACCAAAATAGTGAAC
130 AATGCATGATTATGATGTCCATGAAGCCCTCTACCAAAATAGTGAAC
* *
648000 TCATGACCCCTGTGTCAGGGGTTCAGGCTCAAGGTTGCAGCCAATTTGGCCATATAGTAAAAATG
1 TCATGACCCCTGTGTCAGGGGTTCAGGCTCAAGGGTGCAGCCAATATGGCCATATAGTAAAAATG
* *
648065 TTTTAAATCTTGGAAAATCTTCTTCTCTTCTCCCATATATATTTGTAAAAAAAAAAAACAACTAA
66 TATTAAATCTTGGAAAATCTTCTTCTCTACTCCCATATATATTTGTAAAAAAAAAAAACAACTAA
* * *
648130 ATGCATGATTATGATGTCCATGAGGCCCTCTATCAAAAGT-GTGAAAT
131 ATGCATGATTATGATGTCCATGAAGCCCTCTACCAAAA-TAGTG-AAC
* * * ** *
648177 TCATTACCCCTGTGTCACTTTTGAGGGTTCATGCTCTAGGGTGGGGCCAATATGGCCATTTAGTA
1 TCATGACCCCTGTGTCA-----G-GGGTTCAGGCTCAAGGGTGCAGCCAATATGGCCATATAGTA
* * *
648242 AAAATGTATTATATCTTGGAAAGTCTTCTTTTCTACTCCCATA
60 AAAATGTATTAAATCTTGGAAAATCTTCTTCTCTACTCCCATA
648285 CATGTCGGCA
Statistics
Matches: 231, Mismatches: 36, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
166 1 0.00
167 94 0.41
175 3 0.01
176 41 0.18
177 19 0.08
182 1 0.00
183 72 0.31
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (176 bp):
TCATGACCCCTGTGTCAGGGGTTCAGGCTCAAGGGTGCAGCCAATATGGCCATATAGTAAAAATG
TATTAAATCTTGGAAAATCTTCTTCTCTACTCCCATATATATTTGTAAAAAAAAAAAACAACTAA
ATGCATGATTATGATGTCCATGAAGCCCTCTACCAAAATAGTGAAC
Found at i:649349 original size:266 final size:266
Alignment explanation
Indices: 648875--649406 Score: 1028
Period size: 266 Copynumber: 2.0 Consensus size: 266
648865 CGCGGGCGCA
648875 ATGACTGAATCAAAAGTGATAAAATTAAAAAATGGGAAACCGTCTGACATGCGGTGGCGCCAACT
1 ATGACTGAATCAAAAGTGATAAAATTAAAAAATGGGAAACCGTCTGACATGCGGTGGCGCCAACT
*
648940 TAAGGCCCGACACGACACATTTTCGCTAAGGTCTCCAGAAGCAACCGCATCCGCGTGTCACGAAG
66 TAAGGCCCGACACGACACATTTTCGCTAAGGTCTCCAGAAGCAACCGCATCCGCGCGTCACGAAG
649005 CCATGACAAGACAACGCATGACACGCTATATCCATGAGCTAGAAAACATCATCCAGTCCCCGAAC
131 CCATGACAAGACAACGCATGACACGCTATATCCATGAGCTAGAAAACATCATCCAGTCCCCGAAC
*
649070 TTTAAAGATCACCGCGCATCTGGAACATGGATGAAACAGGGATCACAATGTCCCACAAATCCAAT
196 TTTAAAGATCACCGCGCATCTGGAACATGGATGAAACAGGGATAACAATGTCCCACAAATCCAAT
649135 AAAGTT
261 AAAGTT
*
649141 ATGACTGAATCAAAAGTGATAAAATTAAAAAATGGGAAACCTTCTGACATGCGGTGGCGCCAACT
1 ATGACTGAATCAAAAGTGATAAAATTAAAAAATGGGAAACCGTCTGACATGCGGTGGCGCCAACT
649206 TAAGGCCCGACACGACACATTTTCGCTAAGGTCTCCAGAAGCAACCGCATCCGCGCGTCACGAAG
66 TAAGGCCCGACACGACACATTTTCGCTAAGGTCTCCAGAAGCAACCGCATCCGCGCGTCACGAAG
649271 CCATGACAAGACAACGCATGACACGCTATATCCATGAGCTAGAAAACATCATCCAGTCCCCGAAC
131 CCATGACAAGACAACGCATGACACGCTATATCCATGAGCTAGAAAACATCATCCAGTCCCCGAAC
*
649336 TTTAAAGATCACCGCGCATTTGGAACATGGATGAAACAGGGATAACAATGTCCCACAAATCCAAT
196 TTTAAAGATCACCGCGCATCTGGAACATGGATGAAACAGGGATAACAATGTCCCACAAATCCAAT
649401 AAAGTT
261 AAAGTT
649407 CTGGCCAGAA
Statistics
Matches: 262, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
266 262 1.00
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (266 bp):
ATGACTGAATCAAAAGTGATAAAATTAAAAAATGGGAAACCGTCTGACATGCGGTGGCGCCAACT
TAAGGCCCGACACGACACATTTTCGCTAAGGTCTCCAGAAGCAACCGCATCCGCGCGTCACGAAG
CCATGACAAGACAACGCATGACACGCTATATCCATGAGCTAGAAAACATCATCCAGTCCCCGAAC
TTTAAAGATCACCGCGCATCTGGAACATGGATGAAACAGGGATAACAATGTCCCACAAATCCAAT
AAAGTT
Found at i:661871 original size:12 final size:12
Alignment explanation
Indices: 661850--661884 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
661840 GTCATAGTAG
661850 TTTTCCGTTCCA
1 TTTTCCGTTCCA
*
661862 TTTTCTGTTCCA
1 TTTTCCGTTCCA
*
661874 TTTTTCGTTCC
1 TTTTCCGTTCC
661885 GCGTTTTAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.29, G:0.09, T:0.57
Consensus pattern (12 bp):
TTTTCCGTTCCA
Found at i:669482 original size:19 final size:19
Alignment explanation
Indices: 669458--669496 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
669448 TATTCGCCAT
669458 AATTTTATTAAGGTTAAAC
1 AATTTTATTAAGGTTAAAC
669477 AATTTTATTAAGGTTAAAC
1 AATTTTATTAAGGTTAAAC
669496 A
1 A
669497 GCATCTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (19 bp):
AATTTTATTAAGGTTAAAC
Found at i:670787 original size:4 final size:4
Alignment explanation
Indices: 670778--670824 Score: 67
Period size: 4 Copynumber: 11.8 Consensus size: 4
670768 TTCATACCTT
* * *
670778 GATA GATA GATA GATA GATA GATA GATA GATA AAGA GAGA GATA GAT
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GAT
670825 GAATGCATGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.28, T:0.21
Consensus pattern (4 bp):
GATA
Found at i:688516 original size:482 final size:479
Alignment explanation
Indices: 687613--688574 Score: 1879
Period size: 482 Copynumber: 2.0 Consensus size: 479
687603 CGTCACTCTC
*
687613 CGTATGCCCAGAGATTGTGCTTAGGTTGGGTGGTTGTAGGAGAAACATGTCTCAGCCAGTTTCAT
1 CGTATGCCCAGAGATTGCGCTTAGGTTGGGTGGTTGTAGGAGAAACATGTCTCAGCCAGTTTCAT
687678 CGACCAGATAGTCACTGTAAATAAGACCTACCTGTTACGTAATGGCAGATCATCAATATGCAAGC
66 CGACCAGATAGTCACTGTAAATAAGACCTACCTGTTACGTAATGGCAGATCATCAATATGCAAGC
*
687743 CATGTCCTAACCACTTTGAGATTAAGGAAGAGTTCACAACAGACTCATTTGACACAGATTCTAAT
131 CATGTCCTAACAACTTTGAGATTAAGGAAGAGTTCACAACAGACTCATTTGACACAGATTCTAAT
687808 ACACCCAAGTGTGATTCAGACATTTTTGCTAGAAGAAATGATGATGACACTGTCGGACTGTCCGT
196 ACACCCAAGTGTGATTCAGACATTTTTGCTAGAAGAAATGATGATGACACTGTCGGACTGTCCGT
687873 CGAAGATGAAGAGTTTCTTTGTATTATGGATCAGACGGTTTCTAAAAATGCTGAAGGGTTTTGGG
261 CGAAGATGAAGAGTTTCTTTGTATTATGGATCAGACGGTTTCTAAAAATGCTGAAGGGTTTTGGG
687938 AAGCCCCTCTACCTTTCCGTTCTCCAAGGAGAAGACTTCCGGATAATCGAACCCAAGCCCTTCAG
326 AAGCCCCTCTACCTTTCCGTTCTCCAAGGAGAAGACTTCCGGATAATCGAACCCAAGCCCTTCAG
688003 AGAGCTAAATCCCTGGATTTCTCCCTTCGAAAAGATGATGCGAAGAAAAATCATTTCCTGGAGTT
391 AGAGCTAAATCCCTGGATTTCTCCCTTCGAAAAGATGATGCGAAGAAAAATCATTTCCTGGAGTT
688068 CATGCGAAAAATCTTTGAGAACAA
456 CATGCGAAAAATCTTTGAGAACAA
688092 NCGTATGCCCAGAGATTGCGCTTAGGTTGGGTGGTTGTAGGAGAAACATGTCTCAGCCAGTTTCA
1 -CGTATGCCCAGAGATTGCGCTTAGGTTGGGTGGTTGTAGGAGAAACATGTCTCAGCCAGTTTCA
688157 TCGACCAGATACAGTCACTGTAAATAAGACCTACCTGTTACGTAATGGCAGATCATCAATATGCA
65 TCGACCAGAT--AGTCACTGTAAATAAGACCTACCTGTTACGTAATGGCAGATCATCAATATGCA
688222 AGCCATGTCCTAACAACTTTGAGATTAAGGAAGAGTTCACAACAGACTCATTTGACACAGATTCT
128 AGCCATGTCCTAACAACTTTGAGATTAAGGAAGAGTTCACAACAGACTCATTTGACACAGATTCT
688287 AATACACCCAAGTGTGATTCAGACATTTTTGCTAGAAGAAATGATGATGACACTGTCGGACTGTC
193 AATACACCCAAGTGTGATTCAGACATTTTTGCTAGAAGAAATGATGATGACACTGTCGGACTGTC
688352 CGTCGAAGATGAAGAGTTTCTTTGTATTATGGATCAGACGGTTTCTAAAAATGCTGAAGGGTTTT
258 CGTCGAAGATGAAGAGTTTCTTTGTATTATGGATCAGACGGTTTCTAAAAATGCTGAAGGGTTTT
688417 GGGAAGCCCCTCTACCTTTCCGTTCTCCAAGGAGAAGACTTCCGGATAATCGAACCCAAGCCCTT
323 GGGAAGCCCCTCTACCTTTCCGTTCTCCAAGGAGAAGACTTCCGGATAATCGAACCCAAGCCCTT
688482 CAGAGAGCTAAATCCCTGGATTTCTCCCTTCGAAAAGATGATGCGAAGAAAAATCATTTCCTGGA
388 CAGAGAGCTAAATCCCTGGATTTCTCCCTTCGAAAAGATGATGCGAAGAAAAATCATTTCCTGGA
688547 GTTCATGCGAAAAATCTTTGAGAACAA
453 GTTCATGCGAAAAATCTTTGAGAACAA
688574 C
1 C
688575 CATGCTGAGA
Statistics
Matches: 478, Mismatches: 2, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
480 73 0.15
481 1 0.00
482 404 0.85
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (479 bp):
CGTATGCCCAGAGATTGCGCTTAGGTTGGGTGGTTGTAGGAGAAACATGTCTCAGCCAGTTTCAT
CGACCAGATAGTCACTGTAAATAAGACCTACCTGTTACGTAATGGCAGATCATCAATATGCAAGC
CATGTCCTAACAACTTTGAGATTAAGGAAGAGTTCACAACAGACTCATTTGACACAGATTCTAAT
ACACCCAAGTGTGATTCAGACATTTTTGCTAGAAGAAATGATGATGACACTGTCGGACTGTCCGT
CGAAGATGAAGAGTTTCTTTGTATTATGGATCAGACGGTTTCTAAAAATGCTGAAGGGTTTTGGG
AAGCCCCTCTACCTTTCCGTTCTCCAAGGAGAAGACTTCCGGATAATCGAACCCAAGCCCTTCAG
AGAGCTAAATCCCTGGATTTCTCCCTTCGAAAAGATGATGCGAAGAAAAATCATTTCCTGGAGTT
CATGCGAAAAATCTTTGAGAACAA
Found at i:688841 original size:76 final size:75
Alignment explanation
Indices: 688715--688865 Score: 293
Period size: 76 Copynumber: 2.0 Consensus size: 75
688705 TTTCATTGAA
688715 CGATGTTCTCATGACTGGACCCGATTTGATCAATAGCCTTCTTGGCGTGTTATTGCGTTTCCGTA
1 CGATGTTCTCATGACTGGACCCGATTTGATCAATAGCCTTCTTGGCGTGTTATTGCGTTTCCGTA
688780 AAGACCTTGT
66 AAGACCTTGT
688790 NCGATGTTCTCATGACTGGACCCGATTTGATCAATAGCCTTCTTGGCGTGTTATTGCGTTTCCGT
1 -CGATGTTCTCATGACTGGACCCGATTTGATCAATAGCCTTCTTGGCGTGTTATTGCGTTTCCGT
688855 AAAGACCTTGT
65 AAAGACCTTGT
688866 TGCTATCACT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.36
Consensus pattern (75 bp):
CGATGTTCTCATGACTGGACCCGATTTGATCAATAGCCTTCTTGGCGTGTTATTGCGTTTCCGTA
AAGACCTTGT
Found at i:689066 original size:52 final size:55
Alignment explanation
Indices: 688939--689066 Score: 163
Period size: 56 Copynumber: 2.4 Consensus size: 55
688929 CTTTTTNTGA
* * *
688939 TAAGTGGTGCCAGGCTTTTGTGATTAAAGCTTATGTTAGTGTATGTACACAACAAT
1 TAAGTGGTGTCAGGCTGTGGTGATTAAAGCTTATGTTAGTGTA-GTACACAACAAT
* * *
688995 TAAGTGGTGTCAGGCTGTGGTGGTTCAAGCTTATGTTAGTGTA-TA-A-AACAGT
1 TAAGTGGTGTCAGGCTGTGGTGATTAAAGCTTATGTTAGTGTAGTACACAACAAT
*
689047 TGAGTGGTGTCAGGCTGTGG
1 TAAGTGGTGTCAGGCTGTGG
689067 AGGCACAATA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
52 24 0.37
53 1 0.02
54 2 0.03
56 38 0.58
ACGTcount: A:0.24, C:0.11, G:0.30, T:0.34
Consensus pattern (55 bp):
TAAGTGGTGTCAGGCTGTGGTGATTAAAGCTTATGTTAGTGTAGTACACAACAAT
Found at i:689741 original size:53 final size:52
Alignment explanation
Indices: 689594--689760 Score: 203
Period size: 52 Copynumber: 3.2 Consensus size: 52
689584 TAGATTTTCC
* * * *
689594 GTGGTGTTAGACTGTGATGACAC-AGGACTGTTTTATAGTGTGTCG-AAATTTA
1 GTGGTGTCAGACTGTGGTAACACAAGG-CTGTTTTATAGTGT-ACGAAAATTTA
* * * *
689646 GTGGTGTCAGATTGTGGTGACAAAAGGCTGTTTAATAGTGTACGAAAATTTA
1 GTGGTGTCAGACTGTGGTAACACAAGGCTGTTTTATAGTGTACGAAAATTTA
* *
689698 GTGGTGTCAGGACTGTGGTAACACAAGGCTGTTTTATAATGTACCAAAATTTA
1 GTGGTGTCA-GACTGTGGTAACACAAGGCTGTTTTATAGTGTACGAAAATTTA
689751 GTGGTGTCAG
1 GTGGTGTCAG
689761 GATTTTAGTA
Statistics
Matches: 100, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
51 2 0.02
52 49 0.49
53 49 0.49
ACGTcount: A:0.28, C:0.10, G:0.29, T:0.34
Consensus pattern (52 bp):
GTGGTGTCAGACTGTGGTAACACAAGGCTGTTTTATAGTGTACGAAAATTTA
Found at i:689772 original size:53 final size:53
Alignment explanation
Indices: 689639--689777 Score: 199
Period size: 53 Copynumber: 2.6 Consensus size: 53
689629 TAGTGTGTCG
* * * *
689639 AAATTTAGTGGTGTCA-GATTGTGGTGACAAAAGGCTGTTTAATAGTGTACGA
1 AAATTTAGTGGTGTCAGGATTGTGGTAACACAAGGCTGTTTAATAATGTACCA
* *
689691 AAATTTAGTGGTGTCAGGACTGTGGTAACACAAGGCTGTTTTATAATGTACCA
1 AAATTTAGTGGTGTCAGGATTGTGGTAACACAAGGCTGTTTAATAATGTACCA
* *
689744 AAATTTAGTGGTGTCAGGATTTTAGTAACACAAG
1 AAATTTAGTGGTGTCAGGATTGTGGTAACACAAG
689778 TTTATCATTT
Statistics
Matches: 77, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
52 16 0.21
53 61 0.79
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.32
Consensus pattern (53 bp):
AAATTTAGTGGTGTCAGGATTGTGGTAACACAAGGCTGTTTAATAATGTACCA
Found at i:698211 original size:2 final size:2
Alignment explanation
Indices: 698204--698257 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
698194 TACAAATTAA
*
698204 TC TC TC TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
698246 TC TC TC TC TC TC
1 TC TC TC TC TC TC
698258 NNNNNNNNNN
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:699195 original size:2 final size:2
Alignment explanation
Indices: 699188--699231 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
699178 NNNNNNNNNN
699188 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
699230 AG
1 AG
699232 TCAAGTGCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:700872 original size:2 final size:2
Alignment explanation
Indices: 700865--700911 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
700855 ATTCTTCAAA
700865 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
700907 CT CT C
1 CT CT C
700912 AGGAAATGCG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:708032 original size:26 final size:26
Alignment explanation
Indices: 707979--708042 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
707969 TCGAAAATAG
* * *
707979 ATAAATATTTATATAATATAAGAGAA
1 ATAATTATTTATATAATACAAGAAAA
* *
708005 ATAATTATTTCTATAATACAATAAAA
1 ATAATTATTTATATAATACAAGAAAA
708031 ATATATTATTTA
1 ATA-ATTATTTA
708043 GTGTTGGTTC
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
26 24 0.77
27 7 0.23
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (26 bp):
ATAATTATTTATATAATACAAGAAAA
Found at i:714987 original size:8 final size:9
Alignment explanation
Indices: 714968--715004 Score: 65
Period size: 9 Copynumber: 4.0 Consensus size: 9
714958 CATTAACACT
714968 TATAGAATA
1 TATAGAATA
714977 TATAGATATA
1 TATAGA-ATA
714987 TATAGAATA
1 TATAGAATA
714996 TATAGAATA
1 TATAGAATA
715005 GCACATAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 18 0.67
10 9 0.33
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.35
Consensus pattern (9 bp):
TATAGAATA
Found at i:720110 original size:13 final size:14
Alignment explanation
Indices: 720092--720121 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
720082 GGTAATGTGA
720092 GTTTTC-TTGTGTT
1 GTTTTCTTTGTGTT
720105 GTTTTCTTTGTGTT
1 GTTTTCTTTGTGTT
720119 GTT
1 GTT
720122 ACTTGTTGCT
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:0.00, C:0.07, G:0.23, T:0.70
Consensus pattern (14 bp):
GTTTTCTTTGTGTT
Found at i:720318 original size:27 final size:27
Alignment explanation
Indices: 720149--720306 Score: 289
Period size: 27 Copynumber: 5.9 Consensus size: 27
720139 TTATCGCTTC
720149 TGGATTGCTGAATATTGTTGTTGTTGG
1 TGGATTGCTGAATATTGTTGTTGTTGG
*
720176 TGGATTGCTGAATATTGTTGTTGTTGT
1 TGGATTGCTGAATATTGTTGTTGTTGG
*
720203 TGGATTGCTGAATATTGTTGTTGTTGT
1 TGGATTGCTGAATATTGTTGTTGTTGG
*
720230 TGGATTGCTGAATATTATTGTTGTTGG
1 TGGATTGCTGAATATTGTTGTTGTTGG
720257 TGGATTGCTGAATATTGTTGTTGTTGG
1 TGGATTGCTGAATATTGTTGTTGTTGG
720284 TGGATTGCTGAATATTGTTGTTG
1 TGGATTGCTGAATATTGTTGTTG
720307 CTTCAGTGTT
Statistics
Matches: 127, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 127 1.00
ACGTcount: A:0.16, C:0.04, G:0.31, T:0.49
Consensus pattern (27 bp):
TGGATTGCTGAATATTGTTGTTGTTGG
Found at i:720610 original size:24 final size:24
Alignment explanation
Indices: 720582--720672 Score: 155
Period size: 24 Copynumber: 3.8 Consensus size: 24
720572 TGCTACTGCT
* *
720582 ATATAGTGTACTAAGGTTGTACTG
1 ATATAGTGTACTAATGTTGTACTA
720606 ATATAGTGTACTAATGTTGTACTA
1 ATATAGTGTACTAATGTTGTACTA
*
720630 ATATAGTGTACTTATGTTGTACTA
1 ATATAGTGTACTAATGTTGTACTA
720654 ATATAGTGTACTAATGTTG
1 ATATAGTGTACTAATGTTG
720673 ATCTTTGTTT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.42
Consensus pattern (24 bp):
ATATAGTGTACTAATGTTGTACTA
Found at i:720617 original size:13 final size:12
Alignment explanation
Indices: 720580--720666 Score: 69
Period size: 11 Copynumber: 7.2 Consensus size: 12
720570 GTTGCTACTG
720580 CTATATAGTGTA
1 CTATATAGTGTA
*
720592 CTA-A-GGTTGTA
1 CTATATAG-TGTA
720603 CTGATATAGTGTA
1 CT-ATATAGTGTA
720616 CTA-AT-GTTGTA
1 CTATATAG-TGTA
720627 CTAATATAGTGTA
1 CT-ATATAGTGTA
720640 CT-TAT-GTTGTA
1 CTATATAG-TGTA
720651 CTAATATAGTGTA
1 CT-ATATAGTGTA
720664 CTA
1 CTA
720667 ATGTTGATCT
Statistics
Matches: 61, Mismatches: 2, Indels: 24
0.70 0.02 0.28
Matches are distributed among these distances:
10 3 0.05
11 24 0.39
12 7 0.11
13 24 0.39
14 3 0.05
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.41
Consensus pattern (12 bp):
CTATATAGTGTA
Found at i:720667 original size:13 final size:13
Alignment explanation
Indices: 720582--720668 Score: 80
Period size: 13 Copynumber: 7.2 Consensus size: 13
720572 TGCTACTGCT
720582 ATATAGTGTACTA
1 ATATAGTGTACTA
** *
720595 AGGT--TGTACTG
1 ATATAGTGTACTA
720606 ATATAGTGTACTA
1 ATATAGTGTACTA
*
720619 ATGT--TGTACTA
1 ATATAGTGTACTA
720630 ATATAGTGTACT-
1 ATATAGTGTACTA
720642 -TAT-GTTGTACTA
1 ATATAG-TGTACTA
720654 ATATAGTGTACTA
1 ATATAGTGTACTA
720667 AT
1 AT
720669 GTTGATCTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
10 1 0.02
11 27 0.47
13 29 0.50
14 1 0.02
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.41
Consensus pattern (13 bp):
ATATAGTGTACTA
Found at i:721294 original size:60 final size:60
Alignment explanation
Indices: 721225--721858 Score: 1124
Period size: 60 Copynumber: 10.6 Consensus size: 60
721215 AGATGGTATA
*
721225 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATAGTTCTATG
1 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATAGGTCTATG
*
721285 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATTGGTCTATG
1 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATAGGTCTATG
* * *
721345 GGTCTTATAGATACAAATGAATGAAGTAACGTCATGCTTTAGAGATGGTATAGGTTTATG
1 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATAGGTCTATG
*
721405 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATTGGTCTATG
1 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATAGGTCTATG
* * *
721465 GGTCTTATAGATACAAATGAATGAAGTAACGTCATGCTTTAGAGATGGTATAGGTTTATG
1 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATAGGTCTATG
*
721525 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATTGGTCTATG
1 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATAGGTCTATG
* * *
721585 GGTCTTATAGATACAAATGAATGAAGTAACGTCATGCTTTAGAGATGGTATAGGTTTATG
1 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATAGGTCTATG
*
721645 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGCTATAGGTCTATG
1 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATAGGTCTATG
721705 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATAGGTCTATG
1 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATAGGTCTATG
*
721765 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATTGGTCTATG
1 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATAGGTCTATG
*
721825 GGTCTTATAGATACAAATGTATGAAGTAACGTCA
1 GGTCTTATAGATACAAATGTATGTAGTAACGTCA
721859 CCACAGTAAA
Statistics
Matches: 545, Mismatches: 29, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 545 1.00
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.35
Consensus pattern (60 bp):
GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATAGGTCTATG
Found at i:723250 original size:15 final size:15
Alignment explanation
Indices: 723230--723263 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
723220 TTCCTAGTGC
723230 ATAATGGTTAGTTTT
1 ATAATGGTTAGTTTT
723245 ATAATGGTTAGTTTT
1 ATAATGGTTAGTTTT
723260 ATAA
1 ATAA
723264 GCGTGATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (15 bp):
ATAATGGTTAGTTTT
Found at i:724782 original size:53 final size:53
Alignment explanation
Indices: 724702--724809 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
724692 TAAGCATGCG
724702 CTCAGGTACAGCTGAGACGTACTACGCTAACATAGGAATAAAATAATATACCC
1 CTCAGGTACAGCTGAGACGTACTACGCTAACATAGGAATAAAATAATATACCC
724755 CTCAGGTACAGCTGAGACGTACTACGCTAACATAGGAATAAAATAATATACCC
1 CTCAGGTACAGCTGAGACGTACTACGCTAACATAGGAATAAAATAATATACCC
724808 CT
1 CT
724810 AAAGACACTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.21
Consensus pattern (53 bp):
CTCAGGTACAGCTGAGACGTACTACGCTAACATAGGAATAAAATAATATACCC
Found at i:726708 original size:2 final size:2
Alignment explanation
Indices: 726701--726735 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
726691 GGACTGCCGC
726701 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
726736 CGACCACACC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:729751 original size:20 final size:20
Alignment explanation
Indices: 729728--729773 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
729718 ATAACATTTA
729728 AAATTAAATACATGCATTAT
1 AAATTAAATACATGCATTAT
*
729748 AAATTGAATACATGCATTAT
1 AAATTAAATACATGCATTAT
729768 -AATTAA
1 AAATTAA
729774 GATTATTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.35
Consensus pattern (20 bp):
AAATTAAATACATGCATTAT
Found at i:731242 original size:14 final size:14
Alignment explanation
Indices: 731206--731236 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
731196 CTGTTTCTTG
*
731206 ATTGCTTTTTTATA
1 ATTGCTTTTTTAAA
731220 ATTGCTTTTTTAAA
1 ATTGCTTTTTTAAA
731234 ATT
1 ATT
731237 TGTTTTGCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.61
Consensus pattern (14 bp):
ATTGCTTTTTTAAA
Found at i:738624 original size:25 final size:25
Alignment explanation
Indices: 738596--738646 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
738586 GTAAACTGCC
738596 CCAAACCATTTTATATCGTATAAAA
1 CCAAACCATTTTATATCGTATAAAA
738621 CCAAACCATTTTATATCGTATAAAA
1 CCAAACCATTTTATATCGTATAAAA
738646 C
1 C
738647 TAAAAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.22, G:0.04, T:0.31
Consensus pattern (25 bp):
CCAAACCATTTTATATCGTATAAAA
Found at i:745485 original size:15 final size:15
Alignment explanation
Indices: 745465--745494 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
745455 TTCGAACGAT
745465 TTTCAAACAAAATTA
1 TTTCAAACAAAATTA
745480 TTTCAAACAAAATTA
1 TTTCAAACAAAATTA
745495 AATATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (15 bp):
TTTCAAACAAAATTA
Found at i:747027 original size:41 final size:41
Alignment explanation
Indices: 746970--747092 Score: 201
Period size: 41 Copynumber: 3.0 Consensus size: 41
746960 CGCTTCATTT
* **
746970 TAGCAAATATGACGCTATATCGAGCTACAACATATATCTAA
1 TAGCAAATATGTCGCTATATCGAGCTACAATTTATATCTAA
*
747011 TAGCAAATATGTCGCTATATCGTGCTACAATTTATATCTAA
1 TAGCAAATATGTCGCTATATCGAGCTACAATTTATATCTAA
*
747052 TAGCAAATATGTCGCTATATTGAGCTACAATTTATATCTAA
1 TAGCAAATATGTCGCTATATCGAGCTACAATTTATATCTAA
747093 GAGCGTAGTC
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 76 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.33
Consensus pattern (41 bp):
TAGCAAATATGTCGCTATATCGAGCTACAATTTATATCTAA
Found at i:747411 original size:2 final size:2
Alignment explanation
Indices: 747404--747448 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
747394 TTGTGAAAAC
747404 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
747446 AG A
1 AG A
747449 TTTTATTGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:749836 original size:4 final size:4
Alignment explanation
Indices: 749827--749904 Score: 66
Period size: 4 Copynumber: 19.5 Consensus size: 4
749817 GATCAGCTGA
* * * * * *
749827 CTCT CTCT CTCT GTCT CTGT CTGT CTGT CTCT CTCT CTCT TTCT GTCT
1 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT
* * * *
749875 CTGT CTGT CTGT CTGT CTCT CTCT CTCT CT
1 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CT
749905 AAAAAAAAAC
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 65 1.00
ACGTcount: A:0.00, C:0.37, G:0.12, T:0.51
Consensus pattern (4 bp):
CTCT
Found at i:749853 original size:14 final size:14
Alignment explanation
Indices: 749827--749904 Score: 84
Period size: 14 Copynumber: 5.6 Consensus size: 14
749817 GATCAGCTGA
749827 CTCTCTCTCTCTGT
1 CTCTCTCTCTCTGT
* *
749841 CTCTGTCTGTCTGT
1 CTCTCTCTCTCTGT
*
749855 CTCTCTCTCTCTTT
1 CTCTCTCTCTCTGT
* *
749869 CTGTCTCTGTCTGT
1 CTCTCTCTCTCTGT
* * *
749883 CTGTCTGTCTCTCT
1 CTCTCTCTCTCTGT
749897 CTCTCTCT
1 CTCTCTCT
749905 AAAAAAAAAC
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 51 1.00
ACGTcount: A:0.00, C:0.37, G:0.12, T:0.51
Consensus pattern (14 bp):
CTCTCTCTCTCTGT
Found at i:749871 original size:18 final size:18
Alignment explanation
Indices: 749840--749902 Score: 90
Period size: 18 Copynumber: 3.5 Consensus size: 18
749830 TCTCTCTCTG
*
749840 TCTCTGTCTGTCTGTCTC
1 TCTCTCTCTGTCTGTCTC
*
749858 TCTCTCTCTTTCTGTCTC
1 TCTCTCTCTGTCTGTCTC
* *
749876 TGTCTGTCTGTCTGTCTC
1 TCTCTCTCTGTCTGTCTC
749894 TCTCTCTCT
1 TCTCTCTCT
749903 CTAAAAAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.00, C:0.35, G:0.13, T:0.52
Consensus pattern (18 bp):
TCTCTCTCTGTCTGTCTC
Done.