Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 2 of 226
Found at i:346893 original size:48 final size:48
Alignment explanation
Indices: 346833--346949 Score: 164
Period size: 48 Copynumber: 2.4 Consensus size: 48
346823 TATTTAAAAG
* *
346833 AATTTCTATTATATTAAAAATTGCCTTATTTAAAACGTTATTGTAAAAA
1 AATTTCGATTATATTAAAAATTACCTTATTTAAAACGTTATTGT-AAAA
** *
346882 AATTT-GATTATAAAAAAAATTACCTTATTTAAAACGTTATTGTAAAG
1 AATTTCGATTATATTAAAAATTACCTTATTTAAAACGTTATTGTAAAA
*
346929 AATTTCGACTATATTAAAAAT
1 AATTTCGATTATATTAAAAAT
346950 ATTAAAGTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
47 8 0.14
48 46 0.78
49 5 0.08
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (48 bp):
AATTTCGATTATATTAAAAATTACCTTATTTAAAACGTTATTGTAAAA
Found at i:347542 original size:18 final size:18
Alignment explanation
Indices: 347516--347558 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
347506 GACTCGAAAA
* * *
347516 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
347534 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
347552 AGGATAC
1 AGGATAC
347559 GCACCTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:349402 original size:11 final size:11
Alignment explanation
Indices: 349386--349427 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
349376 AAATAAGGAT
349386 TTGAGAGAAAA
1 TTGAGAGAAAA
*
349397 TTGAGAGGAAA
1 TTGAGAGAAAA
*
349408 TTGAGAGGAAA
1 TTGAGAGAAAA
349419 TT-AGAGAAA
1 TTGAGAGAAA
349428 GGATTTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
10 6 0.21
11 23 0.79
ACGTcount: A:0.50, C:0.00, G:0.31, T:0.19
Consensus pattern (11 bp):
TTGAGAGAAAA
Found at i:350134 original size:28 final size:29
Alignment explanation
Indices: 350080--350135 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
350070 TTATTTAAAG
* * *
350080 TATTTCAAAAATTATAAAAACATTTAATT
1 TATTTAAAAAATTACAAAAACAATTAATT
*
350109 TATTTAAAAAATT-CAAAAATAATTAAT
1 TATTTAAAAAATTACAAAAACAATTAAT
350136 AGTTATTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (29 bp):
TATTTAAAAAATTACAAAAACAATTAATT
Found at i:366882 original size:11 final size:11
Alignment explanation
Indices: 366868--366904 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
366858 AAAAATAGGG
366868 ATTTAAGAGAA
1 ATTTAAGAGAA
366879 ATTTAAGAGAA
1 ATTTAAGAGAA
*
366890 ATTTGAGAGCAA
1 ATTTAAGAG-AA
366902 ATT
1 ATT
366905 GAGATTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 19 0.79
12 5 0.21
ACGTcount: A:0.49, C:0.03, G:0.19, T:0.30
Consensus pattern (11 bp):
ATTTAAGAGAA
Found at i:366921 original size:51 final size:50
Alignment explanation
Indices: 366860--366959 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 50
366850 AATTATTTAA
366860 AAATAGGGATTTAAGAGAAATTT-AAGAGAAATTTGAGAGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTGAAG-GAAA-TTGAGAGCAAATTGAGATT
* *
366911 AAATATGGATTTCAGAGAAATTTGGAAGGAAATTGAGAGCAAATTGAGA
1 AAATAGGGATTTAAGAGAAATTT-GAAGGAAATTGAGAGCAAATTGAGA
366960 GCAAATTTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
51 38 0.84
52 4 0.09
53 3 0.07
ACGTcount: A:0.46, C:0.03, G:0.25, T:0.26
Consensus pattern (50 bp):
AAATAGGGATTTAAGAGAAATTTGAAGGAAATTGAGAGCAAATTGAGATT
Found at i:366975 original size:33 final size:34
Alignment explanation
Indices: 366919--366995 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 34
366909 TTAAATATGG
* *
366919 ATTTCAGAGAAATTTGGAAGGAAATTGAGAGCAA
1 ATTTGAGAGAAATTTAGAAGGAAATTGAGAGCAA
* *
366953 A-TTGAGAGCAAATTTAG-AGGAAATTTAGAGGAA
1 ATTTGAGAG-AAATTTAGAAGGAAATTGAGAGCAA
366986 ATTTGAGAGA
1 ATTTGAGAGA
366996 GGATTAGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
33 22 0.59
34 15 0.41
ACGTcount: A:0.44, C:0.04, G:0.27, T:0.25
Consensus pattern (34 bp):
ATTTGAGAGAAATTTAGAAGGAAATTGAGAGCAA
Found at i:366998 original size:14 final size:11
Alignment explanation
Indices: 366927--366994 Score: 73
Period size: 11 Copynumber: 6.0 Consensus size: 11
366917 GGATTTCAGA
*
366927 GAAATTTGGAAG
1 GAAATTTAG-AG
*
366939 GAAATTGAGAG
1 GAAATTTAGAG
* *
366950 CAAATTGAGAG
1 GAAATTTAGAG
*
366961 CAAATTTAGAG
1 GAAATTTAGAG
366972 GAAATTTAGAG
1 GAAATTTAGAG
366983 GAAATTTGAGAG
1 GAAATTT-AGAG
366995 AGGATTAGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
11 39 0.78
12 11 0.22
ACGTcount: A:0.44, C:0.03, G:0.29, T:0.24
Consensus pattern (11 bp):
GAAATTTAGAG
Found at i:371968 original size:16 final size:15
Alignment explanation
Indices: 371949--371980 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
371939 AAATATTAAA
371949 TTTAAAATAACAAAAT
1 TTTAAAATAA-AAAAT
371965 TTTAAAATAAAAAAT
1 TTTAAAATAAAAAAT
371980 T
1 T
371981 AATATAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (15 bp):
TTTAAAATAAAAAAT
Found at i:382953 original size:7 final size:8
Alignment explanation
Indices: 382923--382952 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
382913 TTAGTCTTAT
382923 ATTTTTTA
1 ATTTTTTA
382931 ATTTTTTA
1 ATTTTTTA
382939 ATTTTTTA
1 ATTTTTTA
382947 ATTTTT
1 ATTTTT
382953 AGTCATCACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
ATTTTTTA
Found at i:385686 original size:31 final size:31
Alignment explanation
Indices: 385644--385716 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
385634 ATCAAATGCT
*
385644 CAAATC-AATTCGGTAATATATATCCATATA
1 CAAATCAAATTCGGCAATATATATCCATATA
* * * *
385674 CGAATCAAATTCGGCAGTGTATATCTATATA
1 CAAATCAAATTCGGCAATATATATCCATATA
*
385705 CAAATAAAATTC
1 CAAATCAAATTC
385717 TACAATGTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
30 5 0.14
31 30 0.86
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (31 bp):
CAAATCAAATTCGGCAATATATATCCATATA
Found at i:385726 original size:31 final size:31
Alignment explanation
Indices: 385662--385727 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
385652 TTCGGTAATA
* * * *
385662 TATATCCATATACGAATCAAATTCGGCAGTG
1 TATATCCATATACAAATAAAATTCGACAATG
* *
385693 TATATCTATATACAAATAAAATTCTACAATG
1 TATATCCATATACAAATAAAATTCGACAATG
385724 TATA
1 TATA
385728 AAACATATAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.33
Consensus pattern (31 bp):
TATATCCATATACAAATAAAATTCGACAATG
Found at i:388639 original size:11 final size:10
Alignment explanation
Indices: 388625--388669 Score: 54
Period size: 11 Copynumber: 4.3 Consensus size: 10
388615 TTTCTCCCTG
388625 TTTTGTTTCT
1 TTTTGTTTCT
388635 ATTTTGTTTCGT
1 -TTTTGTTTC-T
* *
388647 TTCTATTTCT
1 TTTTGTTTCT
388657 TTTTGTTTCT
1 TTTTGTTTCT
388667 TTT
1 TTT
388670 ATTTCTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
10 12 0.41
11 16 0.55
12 1 0.03
ACGTcount: A:0.04, C:0.11, G:0.09, T:0.76
Consensus pattern (10 bp):
TTTTGTTTCT
Found at i:388664 original size:16 final size:16
Alignment explanation
Indices: 388623--388666 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
388613 TTTTTCTCCC
388623 TGTTTTGTTTCTATTT
1 TGTTTTGTTTCTATTT
*
388639 TGTTTCGTTTCTATTT
1 TGTTTTGTTTCTATTT
388655 CT-TTTTGTTTCT
1 -TGTTTTGTTTCT
388667 TTTATTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 24 0.96
17 1 0.04
ACGTcount: A:0.05, C:0.11, G:0.11, T:0.73
Consensus pattern (16 bp):
TGTTTTGTTTCTATTT
Found at i:388759 original size:30 final size:30
Alignment explanation
Indices: 388677--388759 Score: 75
Period size: 30 Copynumber: 2.8 Consensus size: 30
388667 TTTATTTCTT
*
388677 ATATTTACTT-AT-TATAATATATAATATA
1 ATATATACTTAATATATAATATATAATATA
* *
388705 ATATATACTTAATA-ATTAAGATATAATATT
1 ATATATACTTAATATA-TAATATATAATATA
* *
388735 GTA-ATATTGTAATATATAATATATA
1 ATATATACT-TAATATATAATATATA
388760 TTTTCAGCTT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
28 9 0.20
29 7 0.16
30 27 0.61
31 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (30 bp):
ATATATACTTAATATATAATATATAATATA
Found at i:390280 original size:19 final size:19
Alignment explanation
Indices: 390240--390282 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
390230 GTTTTTTTCC
* *
390240 ATTTTGAATAATTTTTATA
1 ATTTTCAATAATTTTTAAA
390259 ATTTTCAAT-ATTTTTAGAA
1 ATTTTCAATAATTTTTA-AA
390278 ATTTT
1 ATTTT
390283 TCGTACTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (19 bp):
ATTTTCAATAATTTTTAAA
Found at i:407539 original size:30 final size:30
Alignment explanation
Indices: 407503--407568 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
407493 GACAGCTAAA
407503 GCTATCCTTGCCT-AGTCACATGTTAGAATT
1 GCTATCCTTGCCTGA-TCACATGTTAGAATT
*
407533 GCTATCCTTGCCTGATCGCATGTTAGAATT
1 GCTATCCTTGCCTGATCACATGTTAGAATT
*
407563 GTTATC
1 GCTATC
407569 TTAAAGTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 32 0.97
31 1 0.03
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (30 bp):
GCTATCCTTGCCTGATCACATGTTAGAATT
Found at i:412278 original size:15 final size:15
Alignment explanation
Indices: 412258--412301 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
412248 GGTTAATAGG
*
412258 AAAGAAAAAAAGGGA
1 AAAGAAAAAAAGGAA
*
412273 AAAGAAAAGAAAAGAA
1 AAAGAAAA-AAAGGAA
412289 AAAGAAAGAAAAG
1 AAAGAAA-AAAAG
412302 AGACGAGACG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 8 0.33
16 15 0.62
17 1 0.04
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAAGGAA
Found at i:412302 original size:15 final size:15
Alignment explanation
Indices: 412258--412302 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
412248 GGTTAATAGG
*
412258 AAAGAAA-AAAAGGGA
1 AAAGAAAGAAAA-GAA
412273 AAAGAAAAGAAAAGAA
1 AAAG-AAAGAAAAGAA
412289 AAAGAAAGAAAAGA
1 AAAGAAAGAAAAGA
412303 GACGAGACGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 14 0.52
16 9 0.33
17 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAAAAGAA
Found at i:412554 original size:2 final size:2
Alignment explanation
Indices: 412547--412571 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
412537 CAGGTAGGTA
412547 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
412572 GGGTAGTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:414476 original size:45 final size:45
Alignment explanation
Indices: 414421--414506 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
414411 GCAGTAATAG
* *
414421 TAACAATATTCAACACACAAAGT-GCTGAATCTGTAACAGTAACGA
1 TAACAATATTCAACACACAAAGTATC-GAATCAGTAACAGTAACGA
* *
414466 TAACAGTATTCGACACACAAAGTATCGAATCAGTAACAGTA
1 TAACAATATTCAACACACAAAGTATCGAATCAGTAACAGTA
414507 GTCGGCACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
45 35 0.97
46 1 0.03
ACGTcount: A:0.44, C:0.20, G:0.14, T:0.22
Consensus pattern (45 bp):
TAACAATATTCAACACACAAAGTATCGAATCAGTAACAGTAACGA
Found at i:445247 original size:3 final size:3
Alignment explanation
Indices: 445239--445264 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
445229 TAAAGTGCAT
445239 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
445265 TGATGAAGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:451346 original size:19 final size:20
Alignment explanation
Indices: 451301--451353 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
451291 TAGGTACGAT
*
451301 AATTTTTATAGTTCTTTTAC
1 AATTTTTATATTTCTTTTAC
*
451321 AAATTTTATATTTC-TTTAC
1 AATTTTTATATTTCTTTTAC
*
451340 ATTTTTTATTATTT
1 AATTTTTA-TATTT
451354 TCTTACGACT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.26, C:0.08, G:0.02, T:0.64
Consensus pattern (20 bp):
AATTTTTATATTTCTTTTAC
Found at i:451466 original size:27 final size:26
Alignment explanation
Indices: 451428--451490 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 26
451418 TTTCTTTTTA
*
451428 ATTTTTAATAAAATTAAATATTTCTT
1 ATTTTTATTAAAATTAAATATTTCTT
* * *
451454 ATATTTTATTAAAATTTAATTTTTTTT
1 AT-TTTTATTAAAATTAAATATTTCTT
451481 ATTTTTATTA
1 ATTTTTATTA
451491 TTTTATTATC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 10 0.31
27 22 0.69
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (26 bp):
ATTTTTATTAAAATTAAATATTTCTT
Found at i:457164 original size:30 final size:30
Alignment explanation
Indices: 457130--457191 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
457120 AGATATGTTG
457130 CACAACATTCTTGAGTCTTATATAAACCTA
1 CACAACATTCTTGAGTCTTATATAAACCTA
*
457160 CACAACATTCTTGGGTCTTATATAAACCTA
1 CACAACATTCTTGAGTCTTATATAAACCTA
457190 CA
1 CA
457192 AATGTTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.32
Consensus pattern (30 bp):
CACAACATTCTTGAGTCTTATATAAACCTA
Found at i:457832 original size:57 final size:59
Alignment explanation
Indices: 457701--457834 Score: 161
Period size: 57 Copynumber: 2.3 Consensus size: 59
457691 GGACTGTTAT
*
457701 AATTATTCTCACATTGGGGCTTAAATTTTTTATTATACAAGTTAAGCCTTGAACTTGAC
1 AATTATTCTCACATTGGGGCTTAAATTTTTTATTATACAAGTTAAGCATTGAACTTGAC
* *
457760 AATTGTTCTCACATTGGGGCTTGAATTTTTT-TT-T-CTAAGTT-AGTCATTGAACTTTG-C
1 AATTATTCTCACATTGGGGCTTAAATTTTTTATTATAC-AAGTTAAG-CATTGAAC-TTGAC
* *
457817 AATTTTTCTCCCATTGGG
1 AATTATTCTCACATTGGG
457835 ATCTAAACTT
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
56 3 0.04
57 30 0.45
58 5 0.07
59 29 0.43
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.44
Consensus pattern (59 bp):
AATTATTCTCACATTGGGGCTTAAATTTTTTATTATACAAGTTAAGCATTGAACTTGAC
Found at i:458644 original size:20 final size:19
Alignment explanation
Indices: 458617--458661 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
458607 TTTTATAATT
458617 TTAA-AAAAATTCTATATTC
1 TTAATAAAAATTCTAT-TTC
*
458636 TTAATAAAATTTCTATTTC
1 TTAATAAAAATTCTATTTC
*
458655 TTTATAA
1 TTAATAA
458662 TTTTTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAATAAAAATTCTATTTC
Found at i:458988 original size:19 final size:19
Alignment explanation
Indices: 458931--458986 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 19
458921 AATAAACACC
458931 AAAAAA-ATTTTAGAAAATTA
1 AAAAAATATTTTA-AAAA-TA
458951 AAAAAATATTTTAAAAATA
1 AAAAAATATTTTAAAAATA
458970 AAAAAAGTATTTTAAAA
1 AAAAAA-TATTTTAAAA
458987 TATTTTTACA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.24
20 20 0.59
21 6 0.18
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (19 bp):
AAAAAATATTTTAAAAATA
Found at i:461188 original size:57 final size:55
Alignment explanation
Indices: 461091--461224 Score: 166
Period size: 57 Copynumber: 2.4 Consensus size: 55
461081 TTTACCTCGG
* * * *
461091 TAGTCATTCAATTATTATTA-TTTTTTATCATTTAACTATGAAAAA-TTATAAAA
1 TAGTCATTTAATTATTATAATTTTTTTATAATTTAACTATGAAAAAGTTACAAAA
*
461144 TAGTCCATTTAATTATTAATAATTTTTTTGATAATTTAATTATGAAAAAGTTACAAAA
1 TAGT-CATTTAATTATT-ATAATTTTTTT-ATAATTTAACTATGAAAAAGTTACAAAA
*
461202 TAGTCACTTAATTATT-TAATTTT
1 TAGTCATTTAATTATTATAATTTT
461225 ATTTTTTAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
53 4 0.06
54 11 0.16
55 10 0.14
56 6 0.09
57 28 0.40
58 11 0.16
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (55 bp):
TAGTCATTTAATTATTATAATTTTTTTATAATTTAACTATGAAAAAGTTACAAAA
Found at i:462142 original size:21 final size:21
Alignment explanation
Indices: 462116--462155 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
462106 AAATAATTAT
* *
462116 TTAATATACATTTTAAAATAA
1 TTAATATAAATTTAAAAATAA
462137 TTAATATAAATTTAAAAAT
1 TTAATATAAATTTAAAAAT
462156 TCAATTAGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAATATAAATTTAAAAATAA
Found at i:465481 original size:5 final size:5
Alignment explanation
Indices: 465471--465502 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
465461 TAGGTAACCC
465471 AACAA AACAA AACAA AACAA AACAA AACAA AA
1 AACAA AACAA AACAA AACAA AACAA AACAA AA
465503 GCTCCTGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (5 bp):
AACAA
Found at i:470099 original size:2 final size:2
Alignment explanation
Indices: 470092--470127 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
470082 TTATCCATAA
470092 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
470128 CCTCTATCTA
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:471311 original size:2 final size:2
Alignment explanation
Indices: 471304--471341 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
471294 TGACCAAAAT
471304 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
471342 AAAGTTGATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:477831 original size:5 final size:5
Alignment explanation
Indices: 477823--477865 Score: 70
Period size: 5 Copynumber: 8.6 Consensus size: 5
477813 AAGAAAGGCC
477823 GAAGA GAAGA GAAGA GAAGA GAAGA GAA-A GGAAGA GAAGA GAA
1 GAAGA GAAGA GAAGA GAAGA GAAGA GAAGA -GAAGA GAAGA GAA
477866 TTATAGAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 1 0.03
5 34 0.94
6 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (5 bp):
GAAGA
Found at i:478002 original size:6 final size:6
Alignment explanation
Indices: 477987--478019 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
477977 AAGGTAGAGT
477987 AAAAAG AAAAA- AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
478020 CCCACATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:478003 original size:11 final size:12
Alignment explanation
Indices: 477987--478019 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
477977 AAGGTAGAGT
477987 AAAAAGAAAAA-
1 AAAAAGAAAAAG
477998 AAAAAGAAAAAG
1 AAAAAGAAAAAG
478010 AAAAAGAAAA
1 AAAAAGAAAA
478020 CCCACATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:478740 original size:45 final size:46
Alignment explanation
Indices: 478629--478746 Score: 141
Period size: 45 Copynumber: 2.6 Consensus size: 46
478619 GTTTGTACAT
* * * * *
478629 AGTTTCAGCCTC-AACATTATTTAAAATGGGTTTTTGTTTATAATA
1 AGTTTCAGCTTCAAACATTCTTGAAAATGGGTTTATGTTTATAAGA
* **
478674 AGTTTTAGCTTCAAATGTTCTTGAAAAT-GGTTTATGTTTATAAGA
1 AGTTTCAGCTTCAAACATTCTTGAAAATGGGTTTATGTTTATAAGA
*
478719 AGTTTCAGCTTCAAACATTCTTGTAAAT
1 AGTTTCAGCTTCAAACATTCTTGAAAAT
478747 ACTTAATGAA
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
45 49 0.82
46 11 0.18
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.43
Consensus pattern (46 bp):
AGTTTCAGCTTCAAACATTCTTGAAAATGGGTTTATGTTTATAAGA
Found at i:481247 original size:26 final size:25
Alignment explanation
Indices: 481197--481248 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
481187 GCCGTTCGAA
481197 ATATATAAAAATTTAAAAATCTAAAT
1 ATATATAAAAATTTAAAAA-CTAAAT
*
481223 ATATATTAAAACTTTATAAAA-TAAAT
1 ATATA-TAAAAATTTA-AAAACTAAAT
481249 TTTCAAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 10 0.43
27 9 0.39
28 4 0.17
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (25 bp):
ATATATAAAAATTTAAAAACTAAAT
Found at i:481505 original size:16 final size:16
Alignment explanation
Indices: 481482--481515 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
481472 TTTCAATAAA
481482 TTTTAATTTTTT-ACT
1 TTTTAATTTTTTAACT
481497 TTTTGAATTTTTTAACT
1 TTTT-AATTTTTTAACT
481514 TT
1 TT
481516 ATATTTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 8 0.47
17 5 0.29
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTTAATTTTTTAACT
Found at i:483511 original size:23 final size:23
Alignment explanation
Indices: 483481--483526 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
483471 TTAAGTACTT
483481 AATTTTCACTTTTACAAATTGCC
1 AATTTTCACTTTTACAAATTGCC
*
483504 AATTTTCACTTTTGCAAATTGCC
1 AATTTTCACTTTTACAAATTGCC
483527 TCCATCGAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.28, C:0.22, G:0.07, T:0.43
Consensus pattern (23 bp):
AATTTTCACTTTTACAAATTGCC
Found at i:500312 original size:15 final size:15
Alignment explanation
Indices: 500292--500325 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
500282 TTAAAAATTT
* *
500292 AAAATAATTATTAAG
1 AAAATAATGATGAAG
500307 AAAATAATGATGAAG
1 AAAATAATGATGAAG
500322 AAAA
1 AAAA
500326 ATAAATAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.24
Consensus pattern (15 bp):
AAAATAATGATGAAG
Found at i:503710 original size:23 final size:26
Alignment explanation
Indices: 503684--503740 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 26
503674 TTTAATTTTA
503684 AAATTTAAAAA-ATAAA-A-AAAATC
1 AAATTTAAAAATATAAATATAAAATC
*
503707 AAATTTTTAAAAATATAAATATAAAATT
1 AAA--TTTAAAAATATAAATATAAAATC
503735 AAATTT
1 AAATTT
503741 CAATTTTATG
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 3 0.11
25 8 0.29
26 8 0.29
27 1 0.04
28 8 0.29
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
AAATTTAAAAATATAAATATAAAATC
Found at i:506299 original size:2 final size:2
Alignment explanation
Indices: 506292--506319 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
506282 GCATGAGTTT
506292 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
506320 AAATATCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:511884 original size:3 final size:3
Alignment explanation
Indices: 511876--511960 Score: 66
Period size: 3 Copynumber: 28.3 Consensus size: 3
511866 TGTTATTAAT
* * * *
511876 TTA TTA TTA TAA TTA TTA TAA TTA TAA TTA TTAA TTA TTA TTA TGTT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA T-TA
* * * *
511923 TTT TTA TT- TAA ATA TTA TTA TTA ATA TTA TTA -TA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
511961 GAAATAAAAT
Statistics
Matches: 64, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
2 3 0.05
3 56 0.88
4 5 0.08
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:512533 original size:17 final size:18
Alignment explanation
Indices: 512511--512544 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
512501 TAAATGAGTT
512511 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
512528 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
512545 AAAAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:512959 original size:19 final size:19
Alignment explanation
Indices: 512935--512973 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
512925 TAACCGGGCT
512935 TAGTCGGATATAGTTAGCA
1 TAGTCGGATATAGTTAGCA
512954 TAGTCGGATATAGTTAGCA
1 TAGTCGGATATAGTTAGCA
512973 T
1 T
512974 GCCATAGGAT
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:0.31, C:0.10, G:0.26, T:0.33
Consensus pattern (19 bp):
TAGTCGGATATAGTTAGCA
Found at i:513045 original size:21 final size:22
Alignment explanation
Indices: 513017--513080 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 22
513007 GCTTTGCCGA
513017 TCAGGCACTATATGTGTCGTAT
1 TCAGGCACTATATGTGTCGTAT
* **
513039 T-AGGCACCACGTGTGTCGT-T
1 TCAGGCACTATATGTGTCGTAT
* *
513059 TCAGGCACTTTATGTGTTGTAT
1 TCAGGCACTATATGTGTCGTAT
513081 ACTGCTTCTG
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 2 0.06
21 28 0.88
22 2 0.06
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (22 bp):
TCAGGCACTATATGTGTCGTAT
Found at i:513676 original size:21 final size:22
Alignment explanation
Indices: 513617--513680 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 22
513607 CAGAAGCAGT
* * *
513617 ATACAACACATAAAATGCCTGA
1 ATACGACACATATAGTGCCTGA
** *
513639 A-ACGACACACGTGGTGCCT-A
1 ATACGACACATATAGTGCCTGA
513659 ATACGACACATATAGTGCCTGA
1 ATACGACACATATAGTGCCTGA
513681 TCGGCAAAGC
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (22 bp):
ATACGACACATATAGTGCCTGA
Found at i:519778 original size:12 final size:12
Alignment explanation
Indices: 519752--519788 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
519742 TAAAAAATTT
519752 AAAATCATTTT-A
1 AAAAT-ATTTTAA
519764 AAAAT-TTTTAA
1 AAAATATTTTAA
519775 AAAATATTTTAA
1 AAAATATTTTAA
519787 AA
1 AA
519789 TGCATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.17
11 6 0.26
12 13 0.57
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (12 bp):
AAAATATTTTAA
Found at i:519788 original size:11 final size:11
Alignment explanation
Indices: 519732--519788 Score: 59
Period size: 11 Copynumber: 5.3 Consensus size: 11
519722 AGCATAAAAT
519732 AAAATAGTTTTA
1 AAAATA-TTTTA
519744 AAAA-A-TTT-
1 AAAATATTTTA
519752 AAAATCATTTTA
1 AAAAT-ATTTTA
519764 AAAAT-TTTTAA
1 AAAATATTTT-A
519775 AAAATATTTTA
1 AAAATATTTTA
519786 AAA
1 AAA
519789 TGCATAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
8 4 0.10
9 3 0.08
10 5 0.13
11 14 0.36
12 13 0.33
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (11 bp):
AAAATATTTTA
Found at i:519796 original size:21 final size:20
Alignment explanation
Indices: 519772--519817 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
519762 TAAAAATTTT
519772 TAAAAAA-TATTTTAAAATGCA
1 TAAAAAATTATTTT-AAA-GCA
519793 TAAAAAAATTATTTTAAAGCA
1 T-AAAAAATTATTTTAAAGCA
519814 TAAA
1 TAAA
519818 CTCGAATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
20 3 0.13
21 5 0.22
22 9 0.39
23 6 0.26
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (20 bp):
TAAAAAATTATTTTAAAGCA
Found at i:519799 original size:23 final size:21
Alignment explanation
Indices: 519773--519817 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
519763 AAAAATTTTT
519773 AAAAAATATTTTAAAATGCATAA
1 AAAAAATATTTT-AAA-GCATAA
*
519796 AAAAATTATTTTAAAGCATAA
1 AAAAAATATTTTAAAGCATAA
519817 A
1 A
519818 CTCGAATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.33
22 3 0.14
23 11 0.52
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (21 bp):
AAAAAATATTTTAAAGCATAA
Found at i:527390 original size:2 final size:2
Alignment explanation
Indices: 527385--527423 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
527375 TATATATATA
527385 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
527424 TCTATTATTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:527668 original size:101 final size:101
Alignment explanation
Indices: 527535--527763 Score: 404
Period size: 101 Copynumber: 2.3 Consensus size: 101
527525 TGAATTGACG
*
527535 GATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTT
1 GATAAGACCATAACTGGGTTATGGCACGATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTT
527600 ATATATAAGATCATAGCTGGGCTATGACATTCTGAT
66 ATATATAAGATCATAGCTGGGCTATGACATTCTGAT
*
527636 GATAAGACCATAACTAGGTTATGGCACGATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTT
1 GATAAGACCATAACTGGGTTATGGCACGATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTT
* * * *
527701 ATATGTAAGATCATAGCTGGGCTATGGCATTTTGTT
66 ATATATAAGATCATAGCTGGGCTATGACATTCTGAT
527737 GATAAGACCATAACTGGGTTATGGCAC
1 GATAAGACCATAACTGGGTTATGGCAC
527764 TACGAATGTA
Statistics
Matches: 121, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
101 121 1.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (101 bp):
GATAAGACCATAACTGGGTTATGGCACGATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTT
ATATATAAGATCATAGCTGGGCTATGACATTCTGAT
Found at i:527804 original size:24 final size:24
Alignment explanation
Indices: 527768--527818 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
527758 TGGCACTACG
527768 AATGTAAAGGATGAATTGACGGAA
1 AATGTAAAGGATGAATTGACGGAA
* *
527792 AATGTAAATGATGAATTGACGGCA
1 AATGTAAAGGATGAATTGACGGAA
527816 AAT
1 AAT
527819 TACTCAAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.45, C:0.06, G:0.25, T:0.24
Consensus pattern (24 bp):
AATGTAAAGGATGAATTGACGGAA
Found at i:528389 original size:20 final size:20
Alignment explanation
Indices: 528350--528389 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
528340 GGTTGAATGA
*
528350 TATGCTTATGATTGATGTGT
1 TATGCTTATGAATGATGTGT
528370 TATGCTTATGGAATGA-GTGT
1 TATGCTTAT-GAATGATGTGT
528390 GCAAAGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.23, C:0.05, G:0.28, T:0.45
Consensus pattern (20 bp):
TATGCTTATGAATGATGTGT
Found at i:529333 original size:40 final size:42
Alignment explanation
Indices: 529289--529372 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
529279 CTTTTATATA
529289 TTTTTC-TT-TATATATAGTATTTATATGTCAAATATTTATT
1 TTTTTCTTTATATATATAGTATTTATATGTCAAATATTTATT
529329 TTTTTCTTTATATATATAGTATTTATATGTCAAATATTTATT
1 TTTTTCTTTATATATATAGTATTTATATGTCAAATATTTATT
529371 TT
1 TT
529373 CTCCACCTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 6 0.14
41 2 0.05
42 34 0.81
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.61
Consensus pattern (42 bp):
TTTTTCTTTATATATATAGTATTTATATGTCAAATATTTATT
Found at i:533784 original size:35 final size:35
Alignment explanation
Indices: 533745--533811 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
533735 TATGCTGATA
533745 AGCCACTTAAATAAATCTAAATCCCAATATCTATT
1 AGCCACTTAAATAAATCTAAATCCCAATATCTATT
*
533780 AGCCACTTAAATAAATTTAAATCCCAATATCT
1 AGCCACTTAAATAAATCTAAATCCCAATATCT
533812 TTTGAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.43, C:0.22, G:0.03, T:0.31
Consensus pattern (35 bp):
AGCCACTTAAATAAATCTAAATCCCAATATCTATT
Found at i:543613 original size:88 final size:89
Alignment explanation
Indices: 543476--543638 Score: 210
Period size: 89 Copynumber: 1.8 Consensus size: 89
543466 AAAAAATTTA
* * * *
543476 AAGGTTTTTTTATGCAATTTGAAAGTTCAAGTATTCAATTGAGTAGAAAAAATTAAGA-GCTTAA
1 AAGGTTTTTTTATACAATTTGAAAGTTAAAGTATTCAATTAAGTAGAAAAAA-AAAGAGGCTTAA
543540 TTACTT-TTTTCTTTAAGAAGTTTG
65 TTACTTATTTTCTTTAAGAAGTTTG
*
543564 AAGGTCTTTTTTATAC-ATTTGAAAAGTTAAAGTGCTT-AATTAAGT-GAAAAAAAAAGAGGCTT
1 AAGGT-TTTTTTATACAATTTG-AAAGTTAAAGT-ATTCAATTAAGTAGAAAAAAAAAGAGGCTT
543626 AATTACTTATTTT
63 AATTACTTATTTT
543639 AAAAATATTT
Statistics
Matches: 65, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
87 4 0.06
88 29 0.45
89 30 0.46
90 2 0.03
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.40
Consensus pattern (89 bp):
AAGGTTTTTTTATACAATTTGAAAGTTAAAGTATTCAATTAAGTAGAAAAAAAAAGAGGCTTAAT
TACTTATTTTCTTTAAGAAGTTTG
Found at i:543759 original size:23 final size:24
Alignment explanation
Indices: 543728--543776 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
543718 TACTATTTGT
*
543728 AAACAAAATTACACTTAAATCATA
1 AAACAAAATTACACTGAAATCATA
*
543752 AAAC-AAATTACACTGAAATCGTA
1 AAACAAAATTACACTGAAATCATA
543775 AA
1 AA
543777 TCAGAAGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.57, C:0.16, G:0.04, T:0.22
Consensus pattern (24 bp):
AAACAAAATTACACTGAAATCATA
Found at i:547465 original size:2 final size:2
Alignment explanation
Indices: 547458--547494 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
547448 NNNNNNNNTA
547458 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
547495 AACTTGACCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:575368 original size:19 final size:17
Alignment explanation
Indices: 575327--575369 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
575317 AGATTTTTAA
*
575327 AAAATATATTTAAATTT
1 AAAATATATTCAAATTT
*
575344 AAAATATATTCATATATT
1 AAAATATATTCAAAT-TT
575362 AATAATAT
1 AA-AATAT
575370 TAATAATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 13 0.59
18 4 0.18
19 5 0.23
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAATATATTCAAATTT
Found at i:586869 original size:6 final size:6
Alignment explanation
Indices: 586858--586885 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
586848 TATGATTTCA
586858 ATATCC ATATCC ATATCC ATATCC ATAT
1 ATATCC ATATCC ATATCC ATATCC ATAT
586886 TAATTATACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.29, G:0.00, T:0.36
Consensus pattern (6 bp):
ATATCC
Found at i:597493 original size:112 final size:112
Alignment explanation
Indices: 597220--597493 Score: 295
Period size: 112 Copynumber: 2.4 Consensus size: 112
597210 TTAACATCGT
* * *
597220 TTTGGTCTTGATGTATACTATAATTAGTGGCGAC-TATGATAAAACGCCGCTAAAGCAAGTATTA
1 TTTGGTCTTGATGTATATTAGAATTAGTGGCG-CTTATGAGAAAACGCCGCTAAAGCAAGTATTA
* * * **
597284 GCGGCGCATTGTCGAAAGCGCCGCAAAAATCTTAACGAAAACATATCG
65 GCGGCGCATTGACGAAAGCGCCGCAAAAATCTTAACCAAAACACAGAG
* * * * * *
597332 TTTTGTCTTGCTGTATATTAGCATTAGTGGCACTTACGA-AAACCTGCCGCTAAAGCAAGTATTA
1 TTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTATGAGAAAAC-GCCGCTAAAGCAAGTATTA
* * *
597396 GCGGCGC-TT-ACGAAAAGCGCCGCAATATATGTTAACCAAAACGCAGAG
65 GCGGCGCATTGACG-AAAGCGCCGCAA-AAATCTTAACCAAAACACAGAG
* * * *
597444 TTTGGTCTAGAGGTATATTAGAATTTGTGGCGCTTATGGGAAAACGCCGC
1 TTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTATGAGAAAACGCCGC
597494 AAAATATCCT
Statistics
Matches: 131, Mismatches: 26, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
110 2 0.02
111 19 0.15
112 106 0.81
113 4 0.03
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (112 bp):
TTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTATGAGAAAACGCCGCTAAAGCAAGTATTAG
CGGCGCATTGACGAAAGCGCCGCAAAAATCTTAACCAAAACACAGAG
Found at i:597836 original size:115 final size:114
Alignment explanation
Indices: 597488--598100 Score: 637
Period size: 115 Copynumber: 5.4 Consensus size: 114
597478 TATGGGAAAA
* * ** * ** * *
597488 CGCCGCAAAATATCCTAACCAAAGCGCACCGTTTTGGTCTTGGTGTATGTTACAGTTAGTGGCGC
1 CGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGC
* * * *
597553 TTAAGGGAAAACACCGCTAAAGCATAATATTAGCGGCG-TTTCGTGAGAAG
66 ATACGGGAAAACGCCGCTAAAGCATACTATTAGCGGCGCTTTC--GAGAAG
* *
597603 CGCCGCAAAATATTTTAACCAAAACGCAGAG-TTTGGTCTTGAGGTATACTAGAATTAGTGGCGC
1 CGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGC
* * * * *
597667 A-AAGGGAACACGCCGCTAAGGCATACTATTAGCGGCGCGTCTGGAGAAG
66 ATACGGGAAAACGCCGCTAAAGCATACTATTAGCGGCGC-TTTCGAGAAG
* * * *
597716 CGCCGCAAAATTTCTTAACCAAAACGCA-ACGTTTTTGTCTTGATGTATACAACAATTAGTGGCG
1 CGCCGCAAAATATCTTAACCAAAACGCAGA-GTTTTGGTCTTGATGTATACTAGAATTAGTGGCG
* * * * *
597780 CATACTGGAAAACGCTGCTAAAGCATAGTATTAGCGGCGCTTTACAAAAAG
65 CATACGGGAAAACGCCGCTAAAGCATACTATTAGCGGCGCTTT-CGAGAAG
* * *
597831 CGCCGCAAAATATGC-TCACCAAAACGCAGAGTTTT-GTCTTGAGGTATATTAGAATTAGTGGCG
1 CGCCGCAAAATAT-CTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATACTAGAATTAGTGGCG
* * *
597894 CTTACGGGAGAACGCCGCTAAAGCATACTATTAGCGGCGCGTTTTGAGAAG
65 CATACGGGAAAACGCCGCTAAAGCATACTATTAGCGGCGC-TTTCGAGAAG
* ** * ** ** *
597945 CACCATAAAATATATTAACCAAAACGCATCGTTTAAGTCTTGATGTATACTGGAATTAGTGGCGT
1 CGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATACTAGAATTAGTGGCG-
* * * * * *
598010 C-CACGAGAAATCACCGCTAAAGCATAGTATTAGCGGCGCTTTTTGAGAAG
65 CATACGGGAAAACGCCGCTAAAGCATACTATTAGCGGCGC-TTTCGAGAAG
*
598060 CGCCGGAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTT
1 CGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTT
598101 AACCATGCAT
Statistics
Matches: 412, Mismatches: 74, Indels: 24
0.81 0.15 0.05
Matches are distributed among these distances:
112 1 0.00
113 65 0.16
114 148 0.36
115 195 0.47
116 3 0.01
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.25
Consensus pattern (114 bp):
CGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGC
ATACGGGAAAACGCCGCTAAAGCATACTATTAGCGGCGCTTTCGAGAAG
Found at i:597886 original size:228 final size:225
Alignment explanation
Indices: 597488--598100 Score: 728
Period size: 229 Copynumber: 2.7 Consensus size: 225
597478 TATGGGAAAA
* * * * * ** *
597488 CGCCGCAAAATATCCTAACCAAAGCGCACCGTTTTGGTCTTGGTGTATGTTACAGTTAGTGGCGC
1 CGCCGCAAAATATCTTAACCAAAACGCAACGTTTTAGTCTTGATGTATACTACAATTAGTGGCGC
* *
597553 TTAAGGGAAAACACCGCTAAAGCATAATATTAGCGGCG-TTTCGTGAGAAGCGCCGCAAAATATT
66 -T-ACGGAAAACACCGCTAAAGCATAGTATTAGCGGCGCTTTC--GAGAAGCGCCGCAAAATA-T
* *
597617 TTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTGGCGC-AAAGGGA-ACACGC
126 CTAACCAAAACGCAGAGTTTTGTCTTGAGGTATACTAGAATTAGTGGCGCTAAAGGGAGA-ACGC
*
597680 CGCTAAGGCATACTATTAGCGGCGCGTCTGGAGAAG
190 CGCTAAAGCATACTATTAGCGGCGCGTCTGGAGAAG
* * *
597716 CGCCGCAAAATTTCTTAACCAAAACGCAACGTTTTTGTCTTGATGTATACAACAATTAGTGGCGC
1 CGCCGCAAAATATCTTAACCAAAACGCAACGTTTTAGTCTTGATGTATACTACAATTAGTGGCGC
* * * *
597781 ATACTGGAAAACGCTGCTAAAGCATAGTATTAGCGGCGCTTTACAAAAAGCGCCGCAAAATATGC
66 -TAC-GGAAAACACCGCTAAAGCATAGTATTAGCGGCGCTTT-CGAGAAGCGCCGCAAAATAT-C
* * * *
597846 TCACCAAAACGCAGAGTTTTGTCTTGAGGTATATTAGAATTAGTGGCGCTTACGGGAGAACGCCG
127 TAACCAAAACGCAGAGTTTTGTCTTGAGGTATACTAGAATTAGTGGCGCTAAAGGGAGAACGCCG
* *
597911 CTAAAGCATACTATTAGCGGCGCGTTTTGAGAAG
192 CTAAAGCATACTATTAGCGGCGCGTCTGGAGAAG
* ** * * * **
597945 CACCATAAAATATATTAACCAAAACGCATCGTTTAAGTCTTGATGTATACTGGAATTAGTGGCGT
1 CGCCGCAAAATATCTTAACCAAAACGCAACGTTTTAGTCTTGATGTATACTACAATTAGTGGCG-
* * * *
598010 CCACGAGAAATCACCGCTAAAGCATAGTATTAGCGGCGCTTTTTGAGAAGCGCCGGAAAATATCT
65 CTACG-GAAAACACCGCTAAAGCATAGTATTAGCGGCGC-TTTCGAGAAGCGCCGCAAAATATC-
598075 TAACCAAAACGCAGAGTTTTGGTCTT
127 TAACCAAAACGCAGAGTTTT-GTCTT
598101 AACCATGCAT
Statistics
Matches: 328, Mismatches: 46, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
227 2 0.01
228 150 0.46
229 165 0.50
230 11 0.03
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.25
Consensus pattern (225 bp):
CGCCGCAAAATATCTTAACCAAAACGCAACGTTTTAGTCTTGATGTATACTACAATTAGTGGCGC
TACGGAAAACACCGCTAAAGCATAGTATTAGCGGCGCTTTCGAGAAGCGCCGCAAAATATCTAAC
CAAAACGCAGAGTTTTGTCTTGAGGTATACTAGAATTAGTGGCGCTAAAGGGAGAACGCCGCTAA
AGCATACTATTAGCGGCGCGTCTGGAGAAG
Found at i:601836 original size:43 final size:43
Alignment explanation
Indices: 601749--601927 Score: 157
Period size: 42 Copynumber: 4.2 Consensus size: 43
601739 CAAAAATAGT
* * * ** * *
601749 GGCGTTTTTGTACAAAAGCGCCTCGAAAGATTATGATCTCTAGC
1 GGCGTTTTTATACAAAA-CGCCGCTAAAGAACATGTTCTTTAGC
* *
601793 GGCGTTTTTATACAAAGCGCCGTTAAAGAACATGTTCTTTAGC
1 GGCGTTTTTATACAAAACGCCGCTAAAGAACATGTTCTTTAGC
* * * * * *
601836 GGCG-CTTAATA-AAAAAGCCACTAAAGATCATTTTCTTTAGC
1 GGCGTTTTTATACAAAACGCCGCTAAAGAACATGTTCTTTAGC
* * * *
601877 GGCGCTTATA-AAAAAACGCCGCTAAAGAACATGGTCTTTAGC
1 GGCGTTTTTATACAAAACGCCGCTAAAGAACATGTTCTTTAGC
601919 GGCGTTTTT
1 GGCGTTTTT
601928 GTTTGTAAAC
Statistics
Matches: 106, Mismatches: 27, Indels: 6
0.76 0.19 0.04
Matches are distributed among these distances:
41 29 0.27
42 39 0.37
43 23 0.22
44 15 0.14
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (43 bp):
GGCGTTTTTATACAAAACGCCGCTAAAGAACATGTTCTTTAGC
Found at i:601915 original size:42 final size:42
Alignment explanation
Indices: 601810--601922 Score: 158
Period size: 41 Copynumber: 2.7 Consensus size: 42
601800 TTATACAAAG
*
601810 CGCCGTTAAAGAACATGTTCTTTAGCGGCGCTTAATAAAAAA
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAATAAAAAA
* * *
601852 -GCCACTAAAGATCATTTTCTTTAGCGGCGCTT-ATAAAAAAA
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAAT-AAAAAA
*
601893 CGCCGCTAAAGAACATGGTCTTTAGCGGCG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCG
601923 TTTTTGTTTG
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
40 2 0.03
41 34 0.56
42 25 0.41
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAATAAAAAA
Found at i:603450 original size:5 final size:5
Alignment explanation
Indices: 603436--603488 Score: 99
Period size: 5 Copynumber: 10.8 Consensus size: 5
603426 AATTATTAAG
603436 TATA- TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
603485 TATA
1 TATA
603489 ATGATGAAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 4 0.08
5 44 0.92
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:603508 original size:4 final size:4
Alignment explanation
Indices: 603494--603545 Score: 63
Period size: 4 Copynumber: 13.2 Consensus size: 4
603484 TTATAATGAT
* *
603494 GAAA TAAA GAAA GAAA GAAA -AAA GAAA GAAA GAAAA GAAA -AAG GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA GAAA GAAA GAAA
603541 GAAA G
1 GAAA G
603546 GAAGGAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 5 0.12
4 32 0.78
5 4 0.10
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:603519 original size:15 final size:15
Alignment explanation
Indices: 603494--603544 Score: 68
Period size: 15 Copynumber: 3.3 Consensus size: 15
603484 TTATAATGAT
603494 GAAATAAAGAAAGAAA
1 GAAA-AAAGAAAGAAA
603510 GAAAAAAGAAAGAAA
1 GAAAAAAGAAAGAAA
603525 GAAAAGAA-AAAGGAAA
1 GAAAA-AAGAAA-GAAA
603541 GAAA
1 GAAA
603545 GGAAGGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
15 19 0.58
16 14 0.42
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (15 bp):
GAAAAAAGAAAGAAA
Found at i:603532 original size:20 final size:19
Alignment explanation
Indices: 603499--603556 Score: 80
Period size: 20 Copynumber: 3.0 Consensus size: 19
603489 ATGATGAAAT
603499 AAAGAAAGAAAGAAAAAAG
1 AAAGAAAGAAAGAAAAAAG
*
603518 AAAGAAAGAAAAGAAAAAGG
1 AAAGAAAG-AAAGAAAAAAG
* *
603538 AAAGAAAGGAAGGAAAAAG
1 AAAGAAAGAAAGAAAAAAG
603557 TCATTGTTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (19 bp):
AAAGAAAGAAAGAAAAAAG
Found at i:603556 original size:15 final size:13
Alignment explanation
Indices: 603503--603554 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 13
603493 TGAAATAAAG
603503 AAAGAAAGAA--A
1 AAAGAAAGAAGGA
*
603514 AAAGAAAGAAAGA
1 AAAGAAAGAAGGA
603527 AAAGAAA-AAGG-
1 AAAGAAAGAAGGA
603538 AAAGAAAGGAAGGA
1 AAAGAAA-GAAGGA
603552 AAA
1 AAA
603555 AGTCATTGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
11 17 0.49
12 3 0.09
13 12 0.34
14 3 0.09
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAGGA
Found at i:612415 original size:21 final size:21
Alignment explanation
Indices: 612391--612462 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
612381 GACACCGTCC
*
612391 GTGAAGGCGATGACTCACCTT
1 GTGACGGCGATGACTCACCTT
612412 GTGACGGCGATGACTCACCTT
1 GTGACGGCGATGACTCACCTT
* *
612433 GCGACGTCGATGACTCACCTT
1 GTGACGGCGATGACTCACCTT
**
612454 CCGACGGCG
1 GTGACGGCG
612463 GAGAATCCAT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.19, C:0.31, G:0.29, T:0.21
Consensus pattern (21 bp):
GTGACGGCGATGACTCACCTT
Found at i:614440 original size:25 final size:26
Alignment explanation
Indices: 614386--614449 Score: 76
Period size: 25 Copynumber: 2.4 Consensus size: 26
614376 TAAGTTTTTT
* *
614386 ATATATTAAAACTATGCAATTAAGAATA
1 ATATA-TAAAA-TATGCAAATAAAAATA
614414 ATATATAAAATAT-CAAATAAAAATA
1 ATATATAAAATATGCAAATAAAAATA
*
614439 ATAAATAAAAT
1 ATATATAAAAT
614450 CATAAGAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 20 0.61
26 3 0.09
27 5 0.15
28 5 0.15
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (26 bp):
ATATATAAAATATGCAAATAAAAATA
Found at i:614826 original size:23 final size:24
Alignment explanation
Indices: 614778--614824 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
614768 TAAAATATTT
*
614778 TTAATATTAACATTAATTTTTAAA
1 TTAATATTAACATTAATTTATAAA
*
614802 TTAAT-TTAATATTAATTTGATAA
1 TTAATATTAACATTAATTT-ATAA
614825 TTTTAATACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (24 bp):
TTAATATTAACATTAATTTATAAA
Found at i:620017 original size:8 final size:8
Alignment explanation
Indices: 620004--620028 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
619994 AAATAGCGGA
620004 AGAAATTG
1 AGAAATTG
620012 AGAAATTG
1 AGAAATTG
620020 AGAAATTG
1 AGAAATTG
620028 A
1 A
620029 ACACATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (8 bp):
AGAAATTG
Found at i:623605 original size:2 final size:2
Alignment explanation
Indices: 623598--623637 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
623588 ATTTTAGAAT
623598 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
623638 AAACAAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:633583 original size:2 final size:2
Alignment explanation
Indices: 633576--633601 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
633566 CTTACAAGTA
633576 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
633602 TTCAAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:640213 original size:59 final size:59
Alignment explanation
Indices: 640077--640197 Score: 242
Period size: 59 Copynumber: 2.1 Consensus size: 59
640067 TGTTAACAGC
640077 GATAACAATTGGATAAAAAAATTAAAGTAAAAAAAAGTAAATTCCTAAAAATAAAAAGA
1 GATAACAATTGGATAAAAAAATTAAAGTAAAAAAAAGTAAATTCCTAAAAATAAAAAGA
640136 GATAACAATTGGATAAAAAAATTAAAGTAAAAAAAAGTAAATTCCTAAAAATAAAAAGA
1 GATAACAATTGGATAAAAAAATTAAAGTAAAAAAAAGTAAATTCCTAAAAATAAAAAGA
640195 GAT
1 GAT
640198 GTGTAAATTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.64, C:0.05, G:0.11, T:0.21
Consensus pattern (59 bp):
GATAACAATTGGATAAAAAAATTAAAGTAAAAAAAAGTAAATTCCTAAAAATAAAAAGA
Found at i:653152 original size:16 final size:17
Alignment explanation
Indices: 653131--653167 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
653121 ACATTTAGTC
653131 ATATAATAAATTA-TTA
1 ATATAATAAATTATTTA
653147 ATATAATAAATTATTTA
1 ATATAATAAATTATTTA
653164 ATAT
1 ATAT
653168 TTAAATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATAAATTATTTA
Found at i:657995 original size:14 final size:14
Alignment explanation
Indices: 657976--658006 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
657966 TACTATTTTC
657976 AAAATCTGATTCCA
1 AAAATCTGATTCCA
657990 AAAATCTGATTCCA
1 AAAATCTGATTCCA
658004 AAA
1 AAA
658007 TCAAACATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.19, G:0.06, T:0.26
Consensus pattern (14 bp):
AAAATCTGATTCCA
Found at i:673187 original size:21 final size:19
Alignment explanation
Indices: 673157--673209 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
673147 CCGACCCATT
*
673157 TTTTAATAAATACCAAAAATTA
1 TTTT-ATAAATA--AAAAAATA
673179 TTTTATAAATTAAAAAAATA
1 TTTTATAAA-TAAAAAAATA
*
673199 TTTTAAAAATA
1 TTTTATAAATA
673210 TTTTAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 2 0.07
20 15 0.54
21 5 0.18
22 6 0.21
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.40
Consensus pattern (19 bp):
TTTTATAAATAAAAAAATA
Found at i:673200 original size:20 final size:20
Alignment explanation
Indices: 673171--673208 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
673161 AATAAATACC
* *
673171 AAAAATTATTTTATAAATTA
1 AAAAAATATTTTAAAAATTA
673191 AAAAAATATTTTAAAAAT
1 AAAAAATATTTTAAAAAT
673209 ATTTTAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAAATATTTTAAAAATTA
Found at i:673208 original size:11 final size:11
Alignment explanation
Indices: 673192--673255 Score: 86
Period size: 11 Copynumber: 6.4 Consensus size: 11
673182 TATAAATTAA
673192 AAAAATATTTT
1 AAAAATATTTT
673203 AAAAATATTTT
1 AAAAATATTTT
673214 --AAA-A--TT
1 AAAAATATTTT
673220 AAAAATA-TTT
1 AAAAATATTTT
673230 AAAAATATTTT
1 AAAAATATTTT
673241 AAAAATATTTT
1 AAAAATATTTT
673252 AAAA
1 AAAA
673256 TTAAAAAATA
Statistics
Matches: 48, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
6 2 0.04
8 4 0.08
9 4 0.08
10 9 0.19
11 29 0.60
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:673231 original size:27 final size:29
Alignment explanation
Indices: 673171--673244 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 29
673161 AATAAATACC
673171 AAAAATTATTTTATAAATTAAAAAAATATTTT
1 AAAAA-TATTTTA-AAATT-AAAAAATATTTT
673203 AAAAATATTTTAAAATT-AAAAATA-TTT
1 AAAAATATTTTAAAATTAAAAAATATTTT
673230 AAAAATATTTTAAAA
1 AAAAATATTTTAAAA
673245 ATATTTTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
27 18 0.43
28 7 0.17
30 5 0.12
31 7 0.17
32 5 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
AAAAATATTTTAAAATTAAAAAATATTTT
Found at i:673242 original size:38 final size:40
Alignment explanation
Indices: 673189--673289 Score: 152
Period size: 38 Copynumber: 2.5 Consensus size: 40
673179 TTTTATAAAT
673189 TAAAAAAATATTTTAAAAATATTTTAAAATT-AAAAAT-A
1 TAAAAAAATATTTTAAAAATATTTTAAAATTAAAAAATAA
**
673227 TTTAAAAATATTTTAAAAATATTTTAAAATTAAAAAATAA
1 TAAAAAAATATTTTAAAAATATTTTAAAATTAAAAAATAA
673267 TAAAAAAAGTATTTTTAAAAATA
1 TAAAAAAA-TA-TTTTAAAAATA
673290 AATATATTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
38 29 0.53
39 6 0.11
40 7 0.13
41 2 0.04
42 11 0.20
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (40 bp):
TAAAAAAATATTTTAAAAATATTTTAAAATTAAAAAATAA
Found at i:682282 original size:28 final size:28
Alignment explanation
Indices: 682200--682294 Score: 75
Period size: 31 Copynumber: 3.2 Consensus size: 28
682190 CTTTTTTATT
*
682200 AAATTATAAAATAGTGATTCAATTATTAA
1 AAATTATAAAATA-TCATTCAATTATTAA
**** * *
682229 TAAATTTATCTTTTCATTATTTAATTATTAA
1 -AAA-TTATAAAAT-ATCATTCAATTATTAA
682260 AAATTATAAAATATCATTCAATTAATT-A
1 AAATTATAAAATATCATTCAATT-ATTAA
682288 AAATTAT
1 AAATTAT
682295 TTTTTACCAC
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
28 17 0.34
29 8 0.16
30 6 0.12
31 18 0.36
32 1 0.02
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.45
Consensus pattern (28 bp):
AAATTATAAAATATCATTCAATTATTAA
Found at i:688179 original size:2 final size:2
Alignment explanation
Indices: 688172--688196 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
688162 CCTTTTCGAT
688172 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
688197 ACCCAGGCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:692015 original size:6 final size:6
Alignment explanation
Indices: 692004--692034 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
691994 AATGAAGGAG
692004 CCATAC CCATAC CCATAC CCATAC CCATAC C
1 CCATAC CCATAC CCATAC CCATAC CCATAC C
692035 AGATCCTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (6 bp):
CCATAC
Found at i:702846 original size:3 final size:3
Alignment explanation
Indices: 702840--702875 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
702830 TTTTTTAAAT
702840 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
702876 GTCCATTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:720860 original size:3 final size:3
Alignment explanation
Indices: 720852--720890 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
720842 ATTTTGAATA
720852 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAGG AA- AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-G AAG AAG AAG
720891 TTGAAACTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:721052 original size:16 final size:17
Alignment explanation
Indices: 721022--721055 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
721012 GGAAGTTGGA
721022 GGAGAGGGGAAGGGATG
1 GGAGAGGGGAAGGGATG
*
721039 GGAG-GGGGAGGGGATG
1 GGAGAGGGGAAGGGATG
721055 G
1 G
721056 CTTTTGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.71, T:0.06
Consensus pattern (17 bp):
GGAGAGGGGAAGGGATG
Found at i:744255 original size:19 final size:19
Alignment explanation
Indices: 744212--744255 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
744202 ATTATTTTCG
744212 ATATAAGTATATATATAAA
1 ATATAAGTATATATATAAA
* * * *
744231 AAATAATTATATTTATCAA
1 ATATAAGTATATATATAAA
744250 ATATAA
1 ATATAA
744256 AATAAATTAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (19 bp):
ATATAAGTATATATATAAA
Found at i:750572 original size:4 final size:4
Alignment explanation
Indices: 750563--750617 Score: 110
Period size: 4 Copynumber: 13.8 Consensus size: 4
750553 AATGAGAAGG
750563 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
750611 CATA CAT
1 CATA CAT
750618 GTGGTGTTCC
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:0.49, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:756032 original size:18 final size:18
Alignment explanation
Indices: 756009--756048 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
755999 TATAATTTTA
*
756009 AAAAATA-TATAATACATC
1 AAAAATATTA-AAAACATC
756027 AAAAATATTAAAAACATC
1 AAAAATATTAAAAACATC
756045 AAAA
1 AAAA
756049 TAAATATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAATATTAAAAACATC
Found at i:762210 original size:21 final size:20
Alignment explanation
Indices: 762186--762228 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
762176 TATTAATATA
*
762186 AATAATATAATTTATTATTTC
1 AATAAT-TAATTTAATATTTC
*
762207 AATAATTTATTTAATATTTC
1 AATAATTAATTTAATATTTC
762227 AA
1 AA
762229 CTTTATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
AATAATTAATTTAATATTTC
Found at i:762251 original size:13 final size:14
Alignment explanation
Indices: 762233--762273 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
762223 TTTCAACTTT
762233 ATTTTAATAATA-A
1 ATTTTAATAATATA
762246 ATTTTAA-AATGATA
1 ATTTTAATAAT-ATA
762260 ATTTTAAATAATAT
1 ATTTT-AATAATAT
762274 TATTCACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.12
13 8 0.33
14 6 0.25
15 4 0.17
16 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:763477 original size:29 final size:30
Alignment explanation
Indices: 763407--763478 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
763397 AATAAGGCTT
* *
763407 ATAGGTCGGTTTTAAAATTTATTTAGGCAT
1 ATAGGTCGATTTTAAAATTTATTTAGGCAA
* * *
763437 TTAGG-CTAATTTTAAAA-TTATTTAGGGAA
1 ATAGGTC-GATTTTAAAATTTATTTAGGCAA
763466 ATAGGTCGATTTT
1 ATAGGTCGATTTT
763479 GAGGAAAAGC
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
29 20 0.61
30 13 0.39
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (30 bp):
ATAGGTCGATTTTAAAATTTATTTAGGCAA
Found at i:770701 original size:20 final size:20
Alignment explanation
Indices: 770676--770716 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
770666 ATCCAGCAAA
770676 GGAACCAAGGAAGGATTATT
1 GGAACCAAGGAAGGATTATT
*
770696 GGAACCAAGGCAGGATTATT
1 GGAACCAAGGAAGGATTATT
770716 G
1 G
770717 CCAAGGTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.12, G:0.32, T:0.20
Consensus pattern (20 bp):
GGAACCAAGGAAGGATTATT
Found at i:786280 original size:4 final size:4
Alignment explanation
Indices: 786271--786296 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
786261 TGAAAGGAGG
786271 GAAT GAAT GAAT GAAT GAAT GAAT GA
1 GAAT GAAT GAAT GAAT GAAT GAAT GA
786297 GGAACAATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.27, T:0.23
Consensus pattern (4 bp):
GAAT
Found at i:791769 original size:42 final size:42
Alignment explanation
Indices: 791722--791820 Score: 162
Period size: 42 Copynumber: 2.4 Consensus size: 42
791712 TATACGAACA
* * *
791722 GCACTAAGTGCGCGAAACTAAAATGACAATGTTGAATAACGG
1 GCACTAAGTGTGCGAAACAAAAATGACAATGTCGAATAACGG
*
791764 GCACTAAGTGTGCGAAACAAAAATGACGATGTCGAATAACGG
1 GCACTAAGTGTGCGAAACAAAAATGACAATGTCGAATAACGG
791806 GCACTAAGTGTGCGA
1 GCACTAAGTGTGCGA
791821 TATCAATATC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.18
Consensus pattern (42 bp):
GCACTAAGTGTGCGAAACAAAAATGACAATGTCGAATAACGG
Found at i:796551 original size:16 final size:16
Alignment explanation
Indices: 796530--796565 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
796520 ATATCGACTC
796530 AAAAAAGAA-AAAAGA
1 AAAAAAGAAGAAAAGA
796545 GAAAAAAGAAGAAAAGA
1 -AAAAAAGAAGAAAAGA
796562 AAAA
1 AAAA
796566 CCCTTTCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAGAAAAGA
Found at i:807127 original size:40 final size:37
Alignment explanation
Indices: 807083--807190 Score: 119
Period size: 40 Copynumber: 2.8 Consensus size: 37
807073 TGTTTGATTA
*
807083 AAAATATATATATTTAATATATAATTCGAATTAAAAGTCT
1 AAAATATATATATTTAATATATAATTCG-ATTAAAA--AT
* *
807123 AAAATATATATATTTAATAAAAAGTATATTTGATTAAAAAT
1 AAAATATATATATTTAAT--ATA-TA-ATTCGATTAAAAAT
807164 -AAATATATATATTTAATATATAATTCG
1 AAAATATATATATTTAATATATAATTCG
807191 GGCCGAGCCC
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
36 4 0.07
37 2 0.03
38 2 0.03
40 35 0.59
41 1 0.02
42 2 0.03
43 9 0.15
44 4 0.07
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.41
Consensus pattern (37 bp):
AAAATATATATATTTAATATATAATTCGATTAAAAAT
Found at i:807179 original size:20 final size:20
Alignment explanation
Indices: 807123--807181 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
807113 TTAAAAGTCT
807123 AAAATATATATATTTAATAA
1 AAAATATATATATTTAATAA
* *
807143 AAAGTATATTTGA-TTAA-AA
1 AAAATATATAT-ATTTAATAA
807162 ATAAATATATATATTTAATA
1 A-AAATATATATATTTAATA
807182 TATAATTCGG
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
19 4 0.13
20 25 0.81
21 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (20 bp):
AAAATATATATATTTAATAA
Found at i:808435 original size:3 final size:3
Alignment explanation
Indices: 808427--808460 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
808417 TTAAGGGTTC
808427 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
808461 TGCATTTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:814100 original size:2 final size:2
Alignment explanation
Indices: 814093--814125 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
814083 TTTGAACCAA
814093 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
814126 ATTTTAACTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:819150 original size:20 final size:20
Alignment explanation
Indices: 819125--819162 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
819115 ATTTAACCAA
819125 AAAATT-AAGTATGAAAAAAC
1 AAAATTCAAG-ATGAAAAAAC
819145 AAAATTCAAGATGAAAAA
1 AAAATTCAAGATGAAAAA
819163 TATAAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.66, C:0.05, G:0.11, T:0.18
Consensus pattern (20 bp):
AAAATTCAAGATGAAAAAAC
Found at i:839901 original size:72 final size:72
Alignment explanation
Indices: 839797--839944 Score: 233
Period size: 72 Copynumber: 2.1 Consensus size: 72
839787 CAATTTCTTC
* * * *
839797 CAAATTTGACATACTCCCCATCCACCTTGGTATGTCCCCAGAAAGCTCGTTATTGCTTAAATCCA
1 CAAACTTGACATACTCCCCATCCACATTGGTATCTCCCCAGAAAGCACGTTATTGCTTAAATCCA
839862 ATGTTGA
66 ATGTTGA
* * *
839869 CAAACTTGACATATTCTCCATCGACATTGGTATCTCCCCAGAAAGCACGTTATTGCTTAAATCCA
1 CAAACTTGACATACTCCCCATCCACATTGGTATCTCCCCAGAAAGCACGTTATTGCTTAAATCCA
839934 ATGTTGA
66 ATGTTGA
839941 CAAA
1 CAAA
839945 AAGGAGCAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (72 bp):
CAAACTTGACATACTCCCCATCCACATTGGTATCTCCCCAGAAAGCACGTTATTGCTTAAATCCA
ATGTTGA
Found at i:839981 original size:72 final size:72
Alignment explanation
Indices: 839831--839982 Score: 173
Period size: 72 Copynumber: 2.1 Consensus size: 72
839821 CCTTGGTATG
* *** *** *
839831 TCCCCAGAAAGCTCGTTATTGCTTAAATCCAATGTTGACAAACTTGACATATTCTCCATCGACAT
1 TCCCCAGAAAGCACGTTATTGCTTAAATCCAATGTTGACAAAAAGGACATATTAGACAACGACAT
*
839896 TGGTATC
66 TGGGATC
*
839903 TCCCCAGAAAGCACGTTATTGCTTAAATCCAATGTTGACAAAAAGGAGCA-ATTAGACAAGGA-A
1 TCCCCAGAAAGCACGTTATTGCTTAAATCCAATGTTGACAAAAAGGA-CATATTAGACAACGACA
839966 TCTGGGATC
65 T-TGGGATC
*
839975 TTCCCAGA
1 TCCCCAGA
839983 GAAATGATTC
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
71 2 0.03
72 63 0.94
73 2 0.03
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (72 bp):
TCCCCAGAAAGCACGTTATTGCTTAAATCCAATGTTGACAAAAAGGACATATTAGACAACGACAT
TGGGATC
Found at i:846931 original size:15 final size:16
Alignment explanation
Indices: 846911--846940 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
846901 GTACTACAAG
846911 ATTATTTT-TTTAAAA
1 ATTATTTTATTTAAAA
846926 ATTATTTTATTTAAA
1 ATTATTTTATTTAAA
846941 TGCCTATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTATTTTATTTAAAA
Found at i:847367 original size:25 final size:25
Alignment explanation
Indices: 847285--847354 Score: 115
Period size: 25 Copynumber: 2.8 Consensus size: 25
847275 GAATTTTAGC
847285 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGATTATTAGCACGTTGGT
*
847310 GCTCTCTGATTATTAGCACATTGGT
1 GCTCTCTGATTATTAGCACGTTGGT
847335 GCTCTCTGA-TATTTAGCACG
1 GCTCTCTGATTA-TTAGCACG
847355 CCAGTGCTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
24 2 0.05
25 40 0.95
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACGTTGGT
Found at i:847374 original size:22 final size:22
Alignment explanation
Indices: 847308--847413 Score: 77
Period size: 22 Copynumber: 4.5 Consensus size: 22
847298 TAGCACGTTG
**
847308 GTGCTCTCTGATTATTAGCACATTG
1 GTGCTCTCTG--T-TTAGCACATCA
**
847333 GTGCTCTCTGATATTTAGCACGCCA
1 GTGCTCTCTG---TTTAGCACATCA
*
847358 GTGCTCTCTGTTTAGCACATCT
1 GTGCTCTCTGTTTAGCACATCA
* * * *
847380 GTGCTTTCTGTATAGCACTTTA
1 GTGCTCTCTGTTTAGCACATCA
847402 GTGCTCTCTGTT
1 GTGCTCTCTGTT
847414 CATTGGTGCA
Statistics
Matches: 64, Mismatches: 16, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
22 36 0.56
25 27 0.42
26 1 0.02
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.41
Consensus pattern (22 bp):
GTGCTCTCTGTTTAGCACATCA
Found at i:853681 original size:13 final size:13
Alignment explanation
Indices: 853663--853687 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
853653 GTTTTATTTT
853663 TTATTTAAAATTG
1 TTATTTAAAATTG
853676 TTATTTAAAATT
1 TTATTTAAAATT
853688 ATGTTACATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
TTATTTAAAATTG
Found at i:861898 original size:15 final size:15
Alignment explanation
Indices: 861880--861911 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
861870 AGATGACTAT
861880 ATAAAAAATGAATAA
1 ATAAAAAATGAATAA
*
861895 ATAAAAAATGTATAA
1 ATAAAAAATGAATAA
861910 AT
1 AT
861912 TATTAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (15 bp):
ATAAAAAATGAATAA
Found at i:866235 original size:13 final size:13
Alignment explanation
Indices: 866217--866246 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
866207 TCACTCTATC
866217 ATATAAGTAAAGA
1 ATATAAGTAAAGA
866230 ATATAAGTAAAGA
1 ATATAAGTAAAGA
866243 ATAT
1 ATAT
866247 TTGTTGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.27
Consensus pattern (13 bp):
ATATAAGTAAAGA
Found at i:871648 original size:2 final size:2
Alignment explanation
Indices: 871641--871665 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
871631 CCAAAAATGA
871641 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
871666 CTTTGGGCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:875688 original size:21 final size:21
Alignment explanation
Indices: 875651--875723 Score: 94
Period size: 21 Copynumber: 3.4 Consensus size: 21
875641 TGATCAGTAT
*
875651 ACGACACAT-AAGTGCCTGAA
1 ACGACACATGAGGTGCCTGAA
*
875671 ACGACACATGAGGTGCCTGAT
1 ACGACACATGAGGTGCCTGAA
*
875692 ACGACACACGAGGTGCCTGAGA
1 ACGACACATGAGGTGCCTGA-A
875714 TACGACACAT
1 -ACGACACAT
875724 AAAGTGCTTG
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 9 0.20
21 28 0.62
23 8 0.18
ACGTcount: A:0.34, C:0.26, G:0.25, T:0.15
Consensus pattern (21 bp):
ACGACACATGAGGTGCCTGAA
Found at i:875730 original size:23 final size:23
Alignment explanation
Indices: 875649--875757 Score: 104
Period size: 23 Copynumber: 5.0 Consensus size: 23
875639 CCTGATCAGT
875649 ATACGACACAT-AAGTGCCTGA-
1 ATACGACACATAAAGTGCCTGAG
* *
875670 A-ACGACACATGAGGTGCCT--G
1 ATACGACACATAAAGTGCCTGAG
** *
875690 ATACGACACACGAGGTGCCTGAG
1 ATACGACACATAAAGTGCCTGAG
*
875713 ATACGACACATAAAGTGCTTGATG
1 ATACGACACATAAAGTGCCTGA-G
*
875737 -TACAACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
875758 TCGGCAAAGC
Statistics
Matches: 74, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
20 10 0.14
21 25 0.34
23 38 0.51
24 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAG
Found at i:876892 original size:18 final size:18
Alignment explanation
Indices: 876869--876920 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
876859 TTTTAAGCTA
876869 TTTTGTTTCTATTTCTTC
1 TTTTGTTTCTATTTCTTC
*
876887 TTTTGTTTCT-TTTATTC
1 TTTTGTTTCTATTTCTTC
*
876904 TTTTATTT-TATTCTCTT
1 TTTTGTTTCTATT-TCTT
876921 TTATGCATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 1 0.03
17 15 0.52
18 13 0.45
ACGTcount: A:0.08, C:0.13, G:0.04, T:0.75
Consensus pattern (18 bp):
TTTTGTTTCTATTTCTTC
Done.