Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold102
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: 1727112
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 166202 characters in sequence are not A, C, G, or T
File 3 of 5
Found at i:382750 original size:27 final size:27
Alignment explanation
Indices: 382630--382765 Score: 114
Period size: 27 Copynumber: 5.0 Consensus size: 27
382620 ACAGAACACT
* **
382630 CACTCACTGAGTAAGTGGCCCAAAGGA
1 CACTCACTGAGTATGTGATCCAAAGGA
* *
382657 AACTCACTGAGTATGTGGTCCAAAAGGA
1 CACTCACTGAGTATGTGATCC-AAAGGA
* * *
382685 AACTCACTGAATATGTGAT-CAATAAGA
1 CACTCACTGAGTATGTGATCCAA-AGGA
* *
382712 CACCCA-TCGAGTATGTGATCCATAGGA
1 CACTCACT-GAGTATGTGATCCAAAGGA
* * *
382739 CACTCACTGAGTCTGTGACCCAGAGGA
1 CACTCACTGAGTATGTGATCCAAAGGA
382766 AACTTACTCA
Statistics
Matches: 89, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
26 3 0.03
27 60 0.67
28 26 0.29
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.21
Consensus pattern (27 bp):
CACTCACTGAGTATGTGATCCAAAGGA
Found at i:383499 original size:2 final size:2
Alignment explanation
Indices: 383492--383530 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
383482 TTGTTTTGCC
* *
383492 AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG AA AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
383531 AATGTGGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (2 bp):
AG
Found at i:384434 original size:1 final size:1
Alignment explanation
Indices: 384430--384462 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
384420 CCCCCCCCCC
*
384430 AAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
384463 CAATGCAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:384463 original size:13 final size:13
Alignment explanation
Indices: 384430--384465 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
384420 CCCCCCCCCC
384430 AAAAAAAA-AAAA
1 AAAAAAAACAAAA
384442 AAAAAAAACAAAA
1 AAAAAAAACAAAA
384455 AAAAAAAACAA
1 AAAAAAAACAA
384466 TGCAAGTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 8 0.35
13 15 0.65
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAACAAAA
Found at i:388846 original size:48 final size:48
Alignment explanation
Indices: 388766--389002 Score: 287
Period size: 48 Copynumber: 4.9 Consensus size: 48
388756 TCATGTCTGG
* *
388766 TCCTAGCAAGACTTACCTATGCCAATGCTTCCTTTGAGTTTATGAAGA
1 TCCTAGCATGACTTACCTATGCCAATGTTTCCTTTGAGTTTATGAAGA
** * * * * *
388814 TTGTTGCATGACTTGCCTGTGCCAATGTTTCCTTTGAGTTTATGGAGG
1 TCCTAGCATGACTTACCTATGCCAATGTTTCCTTTGAGTTTATGAAGA
* * *
388862 TCCTAGCATGACTTACCTATGCCAATATTTCCCTTGAGTTTATAAAGA
1 TCCTAGCATGACTTACCTATGCCAATGTTTCCTTTGAGTTTATGAAGA
* * * * *
388910 TTCTTGCATGACTTGCCTGTACCAATGTTTCCTTTGAGTTTTATGGAAG-
1 TCCTAGCATGACTTACCTATGCCAATGTTTCCTTTGAG-TTTAT-GAAGA
*
388959 TCCTAGCATGACTTACCTATGCCAATGTTTCCCTTGAGTTTATG
1 TCCTAGCATGACTTACCTATGCCAATGTTTCCTTTGAGTTTATG
389003 GAGGTCCTCC
Statistics
Matches: 154, Mismatches: 33, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
47 1 0.01
48 113 0.73
49 37 0.24
50 3 0.02
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (48 bp):
TCCTAGCATGACTTACCTATGCCAATGTTTCCTTTGAGTTTATGAAGA
Found at i:388928 original size:96 final size:97
Alignment explanation
Indices: 388764--389001 Score: 397
Period size: 96 Copynumber: 2.5 Consensus size: 97
388754 TCTCATGTCT
* * * * *
388764 GGTCCTAGCAAGACTTACCTATGCCAATGCTTCCTTTGAGTTTATGAAGATTGTTGCATGACTTG
1 GGTCCTAGCATGACTTACCTATGCCAATGTTTCCCTTGAGTTTATAAAGATTCTTGCATGACTTG
*
388829 CCTGTGCCAATGTTTCCTTTGAG-TTTATGGA
66 CCTGTACCAATGTTTCCTTTGAGTTTTATGGA
*
388860 GGTCCTAGCATGACTTACCTATGCCAATATTTCCCTTGAGTTTATAAAGATTCTTGCATGACTTG
1 GGTCCTAGCATGACTTACCTATGCCAATGTTTCCCTTGAGTTTATAAAGATTCTTGCATGACTTG
388925 CCTGTACCAATGTTTCCTTTGAGTTTTATGGA
66 CCTGTACCAATGTTTCCTTTGAGTTTTATGGA
*
388957 AGTCCTAGCATGACTTACCTATGCCAATGTTTCCCTTGAGTTTAT
1 GGTCCTAGCATGACTTACCTATGCCAATGTTTCCCTTGAGTTTAT
389002 GGAGGTCCTC
Statistics
Matches: 132, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
96 81 0.61
97 51 0.39
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (97 bp):
GGTCCTAGCATGACTTACCTATGCCAATGTTTCCCTTGAGTTTATAAAGATTCTTGCATGACTTG
CCTGTACCAATGTTTCCTTTGAGTTTTATGGA
Found at i:393796 original size:31 final size:31
Alignment explanation
Indices: 393761--393871 Score: 107
Period size: 31 Copynumber: 3.5 Consensus size: 31
393751 ATTATTCCTG
*
393761 GTACGACTTAACAAAATCCGAATGATTTTAA
1 GTACGACTTAACAAAATCCGAATGATTTCAA
* ***
393792 GTACGACTTAACAAAAACCTTTCTGATTTCAA
1 GTACGACTTAACAAAATCC-GAATGATTTCAA
* *
393824 GAACGACTTAACAAAAAAATCCGAATG-TGGTCAA
1 GTACGACTTAAC---AAAATCCGAATGAT-TTCAA
393858 GTACGACTTAACAA
1 GTACGACTTAACAA
393872 TTATTTTTGG
Statistics
Matches: 63, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
31 20 0.32
32 19 0.30
33 1 0.02
34 17 0.27
35 6 0.10
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (31 bp):
GTACGACTTAACAAAATCCGAATGATTTCAA
Found at i:395406 original size:31 final size:31
Alignment explanation
Indices: 395371--395481 Score: 109
Period size: 31 Copynumber: 3.5 Consensus size: 31
395361 ATTATTCCTG
*
395371 GTACGACTTAACAAAATCCGAATGATTTTAA
1 GTACGACTTAACAAAATCCGAATGATTTCAA
* **
395402 GTACGACTTAACAAAAACC-TTTCCGATTTCAA
1 GTACGACTTAACAAAATCCGAAT--GATTTCAA
*
395434 GAACGACTTAACAAAAAAATCCGAATG-TGTTCAA
1 GTACGACTTAAC---AAAATCCGAATGAT-TTCAA
395468 GTACGACTTAACAA
1 GTACGACTTAACAA
395482 TTATTTATGG
Statistics
Matches: 64, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
30 1 0.02
31 20 0.31
32 18 0.28
33 1 0.02
34 17 0.27
35 6 0.09
36 1 0.02
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.25
Consensus pattern (31 bp):
GTACGACTTAACAAAATCCGAATGATTTCAA
Found at i:396889 original size:212 final size:211
Alignment explanation
Indices: 396522--396944 Score: 837
Period size: 212 Copynumber: 2.0 Consensus size: 211
396512 GGGCCGATCC
396522 CATTTCTCCTTAAAGGGGCCCTTTAACGATATTTTAAAGGTTACATATTGTTAAGAACATCGTTC
1 CATTTCTCCTTAAAGGGGCCCTTTAACGATATTTTAAAGGTTACATATTGTTAAGAACATCGTTC
396587 TGAACAACTATTCTTCTGTACTGCATTTCAAAATATTTTTCCTTTCTGAGATATGGGTGTCCAAA
66 TGAACAACTATTCTTCTGTACTGCATTTCAAAATATTTTTCCTTTCTGAGATATGGGTGTCCAAA
396652 ATTTTGGAATTTTGGTCCCTAAAAACCCTTAATTACGTAACACATGAAAAAATCATTACATTGCT
131 ATTTTGGAATTTTGGTCCCTAAAAACCCTTAATTACGTAACACATGAAAAAATCATTACATTGCT
396717 TGGATATATTATAACT
196 TGGATATATTATAACT
396733 NCATTTCTCCTTAAAGGGGCCCTTTAACGATATTTTAAAGGTTACATATTGTTAAGAACATCGTT
1 -CATTTCTCCTTAAAGGGGCCCTTTAACGATATTTTAAAGGTTACATATTGTTAAGAACATCGTT
396798 CTGAACAACTATTCTTCTGTACTGCATTTCAAAATATTTTTCCTTTCTGAGATATGGGTGTCCAA
65 CTGAACAACTATTCTTCTGTACTGCATTTCAAAATATTTTTCCTTTCTGAGATATGGGTGTCCAA
396863 AATTTTGGAATTTTGGTCCCTAAAAACCCTTAATTACGTAACACATGAAAAAATCATTACATTGC
130 AATTTTGGAATTTTGGTCCCTAAAAACCCTTAATTACGTAACACATGAAAAAATCATTACATTGC
396928 TTGGATATATTATAACT
195 TTGGATATATTATAACT
396945 GTGGGATAAA
Statistics
Matches: 211, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
212 211 1.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.37
Consensus pattern (211 bp):
CATTTCTCCTTAAAGGGGCCCTTTAACGATATTTTAAAGGTTACATATTGTTAAGAACATCGTTC
TGAACAACTATTCTTCTGTACTGCATTTCAAAATATTTTTCCTTTCTGAGATATGGGTGTCCAAA
ATTTTGGAATTTTGGTCCCTAAAAACCCTTAATTACGTAACACATGAAAAAATCATTACATTGCT
TGGATATATTATAACT
Found at i:397953 original size:437 final size:436
Alignment explanation
Indices: 396953--397954 Score: 1493
Period size: 437 Copynumber: 2.3 Consensus size: 436
396943 CTGTGGGATA
* * * * *
396953 AACATATTTGCTTCTATAACCTTTCACAAAATATCTCTCAGTAAAAAGTTATCATTAAAAGACTT
1 AACATAATTGCTTCTATAACGTATCACAAAATATATCACAGTAAAAAGTTATCATTAAAAGACTT
* * * * * *
397018 GAG-GCCCCCTCAGCCCCTTATTTAAAGGGCCAGCCTCTGTTTCAAGATTTCAAATAAAAACTCT
66 TAGAGCCCCCTCAGCCCCTTATTTGAAGGGCCAGCCCCTTTTTCATGATTTCAAATAAAAGCTCT
** * *
397082 AATCAATTAAAACATTTTTTGTTCAATAAGTAATTACAAATTTTGTACCATTCTTGAGATATCTT
131 AATCAATTAAAACACATTTTGTTCAACAAGTAATTACAAATTTTGTACCATTCTCGAGATATCTT
*
397147 GAGAGGGTCATTTTAGAAGCCGATCCTTAACTCCCTTAAAGGACCACATAACAAAGAAATAATGG
196 GAGAGGGTCATTTTAGAAGCCGACCCTTAACTCCCTTAAAGGACCACATAACAAAGAAATAATGG
* *
397212 TTAATTATTGTTAAGCTCAGTATTTTGAGCATCTTTTGTTCAATATTGCTTTTCAAAATTTTCCT
261 TTAATTATTGTTAAGCTCAATATTTTGAGCATCTTTTGTTCAATATTGCTTTTCAAAATGTTCCT
*
397277 CCATTTTGAGATATTGAACATCAAAGTTTTGGACTTCTGGCCCCTTAGAATCCCTAATTACGTAA
326 CCATTTTGAGATATTGAACATCAAAGTTTTGGACTTCTGGCCCCTTAAAATCCCTAATTACGTAA
* * *
397342 CATAGGAGGGAATGATTACCATGTATATGTGGATAACGTTAGAATG
391 CATAGGAGGAAATAATTACCATGTATAGGTGGATAACGTTAGAATG
397388 AACATAATTGCTTCTATAACGTATCACAAAATATATCACAGTAAAAAGTTATCATTAAAAGACTT
1 AACATAATTGCTTCTATAACGTATCACAAAATATATCACAGTAAAAAGTTATCATTAAAAGACTT
* * *
397453 TAAAGCCCCCTCAGCCCCTTATTTGAAGGGCCAGCCCCTTTTTCATGATTTTAAATGAAAGCTCT
66 TAGAGCCCCCTCAGCCCCTTATTTGAAGGGCCAGCCCCTTTTTCATGATTTCAAATAAAAGCTCT
* * ** * *
397518 AATCAATTCAAACACATTTTGTTCAACATGTGTTTACAAATTTTGTACCGTTCTCGAGATATTTT
131 AATCAATTAAAACACATTTTGTTCAACAAGTAATTACAAATTTTGTACCATTCTCGAGATATCTT
* ** * * * *
397583 GAGAGGGTCGTTTTAGGGGCCGACCCTGTAACTCCTTTTAGGGACCGCATAACAAAGAAATAATG
196 GAGAGGGTCATTTTAGAAGCCGACCCT-TAACTCCCTTAAAGGACCACATAACAAAGAAATAATG
*
397648 GTTAATTATTGTTAAGCTTAATATTTTGAGCATCTTTTGTTCAATATTGCTTTTCAAAATGTTCC
260 GTTAATTATTGTTAAGCTCAATATTTTGAGCATCTTTTGTTCAATATTGCTTTTCAAAATGTTCC
* * * *
397713 TCCATTTTGAGATATTTAGCATGAAAGTTTTGGACTTTTGGCCCCTTAAAATCCCTAATTACGTA
325 TCCATTTTGAGATATTGAACATCAAAGTTTTGGACTTCTGGCCCCTTAAAATCCCTAATTACGTA
* * *
397778 ACATAGGAGTAAATAATTGCCATGTGTAGGTGGATAACGTTAGAATG
390 ACATAGGAGGAAATAATTACCATGTATAGGTGGATAACGTTAGAATG
* * * *
397825 AACATAATTGCTTCTATAACGTATCACAAAATATTTCACGGTAACAAGTTATCATTTAAAGACTT
1 AACATAATTGCTTCTATAACGTATCACAAAATATATCACAGTAAAAAGTTATCATTAAAAGACTT
* * * * *
397890 TAGAGCCCCCTCAGCCCCTTATTTGAAGGGTCAGCCCCTTTTTCTTGATGTCACATCAAAGCTCT
66 TAGAGCCCCCTCAGCCCCTTATTTGAAGGGCCAGCCCCTTTTTCATGATTTCAAATAAAAGCTCT
397955 TGACTTTATA
Statistics
Matches: 508, Mismatches: 57, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
435 61 0.12
436 132 0.26
437 315 0.62
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (436 bp):
AACATAATTGCTTCTATAACGTATCACAAAATATATCACAGTAAAAAGTTATCATTAAAAGACTT
TAGAGCCCCCTCAGCCCCTTATTTGAAGGGCCAGCCCCTTTTTCATGATTTCAAATAAAAGCTCT
AATCAATTAAAACACATTTTGTTCAACAAGTAATTACAAATTTTGTACCATTCTCGAGATATCTT
GAGAGGGTCATTTTAGAAGCCGACCCTTAACTCCCTTAAAGGACCACATAACAAAGAAATAATGG
TTAATTATTGTTAAGCTCAATATTTTGAGCATCTTTTGTTCAATATTGCTTTTCAAAATGTTCCT
CCATTTTGAGATATTGAACATCAAAGTTTTGGACTTCTGGCCCCTTAAAATCCCTAATTACGTAA
CATAGGAGGAAATAATTACCATGTATAGGTGGATAACGTTAGAATG
Found at i:398537 original size:53 final size:53
Alignment explanation
Indices: 398399--398620 Score: 266
Period size: 53 Copynumber: 4.0 Consensus size: 53
398389 AATAATAGGG
* * * *
398399 AAAAAGAAACCGAACG-AAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAAT
1 AAAAAGAAACCGAA-GAAAAACAAGAGGGTCTTCCGTTGAAAACGGAAGACC---CT
*
398455 AATAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCT
1 -A-AAAAGAAACCGAAGAAAAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCT
* *
398510 AAAAAGAAACCGAAGAAAAACAAGAGGGGCTTCCGTTGGAAACGGAAGACCCTAAT
1 AAAAAGAAACCGAAGAAAAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCC---T
* * *
398566 AAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGCTGAAGACGGAAGACCCT
1 AAAAAGAAACCGAAGAAAAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCT
398619 AA
1 AA
398621 CAAATAATTG
Statistics
Matches: 147, Mismatches: 13, Indels: 14
0.84 0.07 0.08
Matches are distributed among these distances:
53 51 0.35
54 1 0.01
55 1 0.01
56 48 0.33
57 2 0.01
58 44 0.30
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (53 bp):
AAAAAGAAACCGAAGAAAAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCT
Found at i:398590 original size:56 final size:56
Alignment explanation
Indices: 398399--398620 Score: 310
Period size: 56 Copynumber: 4.0 Consensus size: 56
398389 AATAATAGGG
* * *
398399 AAAAAGAAACCGAACGAA-AACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAAT
1 AAAAAGAAACCGAA-GAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAAT
*
398455 AATAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCC---T
1 -A-AAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAAT
* *
398510 AAAAAGAAACCGAAGAAAAACAAGAGGGGCTTCCGTTGGAAACGGAAGACCCTAAT
1 AAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAAT
*
398566 AAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGCT-GAAGACGGAAGACCCTAA
1 AAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGGAA-ACGGAAGACCCTAA
398621 CAAATAATTG
Statistics
Matches: 149, Mismatches: 10, Indels: 13
0.87 0.06 0.08
Matches are distributed among these distances:
53 48 0.32
54 1 0.01
55 4 0.03
56 49 0.33
57 4 0.03
58 43 0.29
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (56 bp):
AAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAAT
Found at i:412442 original size:2 final size:2
Alignment explanation
Indices: 412435--412478 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
412425 ACTTGGAAAA
412435 TC TC TC TC TC TC 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
412477 TC
1 TC
412479 CTGTATTTTC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:419719 original size:13 final size:14
Alignment explanation
Indices: 419697--419725 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
419687 CATTGAAAAG
419697 AAAAATTAGTGCAT
1 AAAAATTAGTGCAT
419711 AAAAA-TAGTGCAT
1 AAAAATTAGTGCAT
419724 AA
1 AA
419726 TGTTACTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.24
Consensus pattern (14 bp):
AAAAATTAGTGCAT
Found at i:434567 original size:29 final size:30
Alignment explanation
Indices: 434525--434589 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
434515 ATTTAGGAAT
*
434525 TAAATAAGAAAACA-TTTTGAGGAAAGTTA
1 TAAAAAAGAAAACATTTTTGAGGAAAGTTA
434554 TAAAAAAGAAAACATTTTTGAGGAAAGTTA
1 TAAAAAAGAAAACATTTTTGAGGAAAGTTA
434584 TAAAAA
1 TAAAAA
434590 TTGGATTGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 13 0.38
30 21 0.62
ACGTcount: A:0.55, C:0.03, G:0.15, T:0.26
Consensus pattern (30 bp):
TAAAAAAGAAAACATTTTTGAGGAAAGTTA
Found at i:435385 original size:20 final size:20
Alignment explanation
Indices: 435356--435404 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
435346 GAAATGAAAC
435356 GAAACAAAATATACCAAAAT
1 GAAACAAAATATACCAAAAT
* * *
435376 GAAACGAAATCTACCGAAAT
1 GAAACAAAATATACCAAAAT
*
435396 GAAATAAAA
1 GAAACAAAA
435405 CAAAATAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.61, C:0.14, G:0.10, T:0.14
Consensus pattern (20 bp):
GAAACAAAATATACCAAAAT
Found at i:448578 original size:2 final size:2
Alignment explanation
Indices: 448571--448619 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
448561 TCTGTTTCCA
448571 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
448613 AG AG AG A
1 AG AG AG A
448620 ATTTTAATCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:450599 original size:15 final size:14
Alignment explanation
Indices: 450567--450595 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
450557 ATAAGATATA
450567 TTCT-TTAATTTCT
1 TTCTCTTAATTTCT
450580 TTCTCTTAATTTCT
1 TTCTCTTAATTTCT
450594 TT
1 TT
450596 TCTCCACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (14 bp):
TTCTCTTAATTTCT
Found at i:463194 original size:32 final size:32
Alignment explanation
Indices: 463158--463221 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
463148 TATGAAAACA
463158 TGAAGTTTGGTTTAGTATTTATATAACATTTT
1 TGAAGTTTGGTTTAGTATTTATATAACATTTT
463190 TGAAGTTTGGTTTAGTATTTATATAACATTTT
1 TGAAGTTTGGTTTAGTATTTATATAACATTTT
463222 GCTCAGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.03, G:0.16, T:0.53
Consensus pattern (32 bp):
TGAAGTTTGGTTTAGTATTTATATAACATTTT
Found at i:471482 original size:4 final size:4
Alignment explanation
Indices: 471465--471514 Score: 66
Period size: 4 Copynumber: 12.8 Consensus size: 4
471455 AAAGTTTACA
* * *
471465 GACG GACA GACG GACG GACG GACA GACG GACG GACA GACG GAC- GACG
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG
471512 GAC
1 GAC
471515 AAAATGTGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 3 0.08
4 36 0.92
ACGTcount: A:0.32, C:0.26, G:0.42, T:0.00
Consensus pattern (4 bp):
GACG
Found at i:471482 original size:12 final size:12
Alignment explanation
Indices: 471462--471508 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
471452 TAAAAAGTTT
*
471462 ACAGACGGACAG
1 ACAGACGGACGG
*
471474 ACGGACGGACGG
1 ACAGACGGACGG
471486 ACAGACGGACGG
1 ACAGACGGACGG
471498 ACAGACGGACG
1 ACAGACGGACG
471509 ACGGACAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.34, C:0.26, G:0.40, T:0.00
Consensus pattern (12 bp):
ACAGACGGACGG
Found at i:477968 original size:168 final size:167
Alignment explanation
Indices: 477561--478249 Score: 905
Period size: 166 Copynumber: 4.1 Consensus size: 167
477551 AGAAATTTTC
*
477561 AAAAATCTTCTTCTCATGAAAC--ATAAGACCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCA
1 AAAAATCTTCTTCTCA-GAAACTAATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA
* * * * * *
477624 GGTAGTGTGGATACAAAGTTGTGAAAATTATAACCCCTGGGGGTAGGGTGGGGCCACAAT-GGGG
65 GGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCC-AGGGGTAGGATGGGGCCACAATGGGGG
* *
477688 GTCGAAATTTTACATA-GGAATATATAGAGTAAATCTTT
129 GTCAAAATTTAACATATGGAATATATAGAGTAAATCTTT
* *
477726 AAAAATCTTTTTCTCATG-AAC-CATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA
1 AAAAATCTTCTTCTCA-GAAACTAATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA
* *
477789 GGTAATGTAGATTCAAAGTTGAGAAAATCATGACCTCCAGGGGTAGGATGGGGCCACAATGGGGG
65 GGTAGTGTAGATTCAAAGTTGTGAAAATCATGACC-CCAGGGGTAGGATGGGGCCACAATGGGGG
* *
477854 GTCAAAATTTAACATATGAATATATATAGAGTAAATATTT
129 GTCAAAATTTAACATATGGA-ATATATAGAGTAAATCTTT
* * * * *
477894 TAAAATTTTCTTCTCAGAAACTAATCAG-CCAGGAAAGCTGAAACTTGTGTGGAAGCATCTTCAA
1 AAAAATCTTCTTCTCAGAAACTAATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
* ** **
477958 GTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTA-GATTTTGGCCACAATTTGGG
66 GTAGTGTAGATTCAAAGTTGTGAAAATCATGA-CCCCAGGGGTAGGA-TGGGGCCACAATGGGGG
* *
478022 GTCAAAGTTTAACACAT-GAATATATAGAGTAAATCTTT
129 GTCAAAATTTAACATATGGAATATATAGAGTAAATCTTT
* * *
478060 AAAAATCTTCTTCTCAGAAAATAATCAG-CCAGGAAAGCTGAAACTTGTGTCGAAGCATCCTCAG
1 AAAAATCTTCTTCTCAGAAACTAATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
*
478124 GTAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCCAGGGGTAGGGTGGGGCCACAATGGGGGG
66 GTAGTGTAGATTCAAAGTTGTGAAAATCATGA-CCCCAGGGGTAGGATGGGGCCACAAT-GGGGG
* * * *
478189 GTCAAATTTTAACA-AAGGAATATATGGAGTAAATCTTA
129 GTCAAAATTTAACATATGGAATATATAGAGTAAATCTTT
478227 AAAAATCTTCTTCTCAGAAACTA
1 AAAAATCTTCTTCTCAGAAACTA
478250 TAATTGTTAA
Statistics
Matches: 462, Mismatches: 50, Indels: 22
0.87 0.09 0.04
Matches are distributed among these distances:
164 3 0.01
165 106 0.23
166 149 0.32
167 64 0.14
168 134 0.29
169 6 0.01
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (167 bp):
AAAAATCTTCTTCTCAGAAACTAATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
GTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCAGGGGTAGGATGGGGCCACAATGGGGGGT
CAAAATTTAACATATGGAATATATAGAGTAAATCTTT
Found at i:478177 original size:334 final size:333
Alignment explanation
Indices: 477561--478249 Score: 962
Period size: 334 Copynumber: 2.1 Consensus size: 333
477551 AGAAATTTTC
477561 AAAAATCTTCTTCTCATGAAAC--ATAAGACCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCA
1 AAAAATCTTCTTCTCA-GAAACTAATAAGACCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCA
* * * * *
477624 GGTAGTGTGGATACAAAGTTGTGAAAATTATAACCCCTGGGGGTAGGGTGGGGCCACAATGGGGG
65 AGTAGTGTAGATACAAAGTTGTGAAAATCATAACCCCCGGGGGTAGAGTGGGGCCACAATGGGGG
* * * * *
477689 TCGAAATTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTTTTCTCATGAACCATAAGA
130 TCGAAATTTAACACAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCATGAACAATAACA
*
477754 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAATGTAGATTCAAAGTTGAGAAAATCA
195 CCAGGAAAGCTGAAACTTGTGTCGAAGCATCCTCAGGTAATGTAGATTCAAAGTTGAGAAAATCA
*
477819 TGACCTCCAGGGGTAGGATGGGGCCACAAT-GGGGGGTCAAAATTTAACATATGAATATATATAG
260 TGACCTCCAGGGGTAGGATGGGGCCACAATGGGGGGGTCAAAATTTAACA-AAGAA-ATATATAG
*
477883 AGTAAATATTT
323 AGTAAATATTA
* * * * *
477894 TAAAATTTTCTTCTCAGAAACTAATCAG-CCAGGAAAGCTGAAACTTGTGTGGAAGCATCTTCAA
1 AAAAATCTTCTTCTCAGAAACTAATAAGACCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAA
* * * ** *
477958 GTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGATTTTGGCCACAATTTGGGG
66 GTAGTGTAGATACAAAGTTGTGAAAATCATAACCCCCGGGGGTAGAGTGGGGCCACAA-TGGGGG
*
478023 TC-AAAGTTTAACACATGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCA-GAA-AATAAT
130 TCGAAA-TTTAACACAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCATGAACAATAA-
* *
478085 CAGCCAGGAAAGCTGAAACTTGTGTCGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAA
193 CA-CCAGGAAAGCTGAAACTTGTGTCGAAGCATCCTCAGGTAATGTAGATTCAAAGTTGAGAAAA
* * *
478150 TCATGATCC-CCAGGGGTAGGGTGGGGCCACAATGGGGGGGTCAAATTTTAACAAAGGAATATAT
257 TCATGA-CCTCCAGGGGTAGGATGGGGCCACAATGGGGGGGTCAAAATTTAACAAAGAAATATAT
* *
478214 GGAGTAAATCTTA
321 AGAGTAAATATTA
478227 AAAAATCTTCTTCTCAGAAACTA
1 AAAAATCTTCTTCTCAGAAACTA
478250 TAATTGTTAA
Statistics
Matches: 314, Mismatches: 34, Indels: 16
0.86 0.09 0.04
Matches are distributed among these distances:
332 9 0.03
333 140 0.45
334 145 0.46
335 20 0.06
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (333 bp):
AAAAATCTTCTTCTCAGAAACTAATAAGACCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAA
GTAGTGTAGATACAAAGTTGTGAAAATCATAACCCCCGGGGGTAGAGTGGGGCCACAATGGGGGT
CGAAATTTAACACAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCATGAACAATAACAC
CAGGAAAGCTGAAACTTGTGTCGAAGCATCCTCAGGTAATGTAGATTCAAAGTTGAGAAAATCAT
GACCTCCAGGGGTAGGATGGGGCCACAATGGGGGGGTCAAAATTTAACAAAGAAATATATAGAGT
AAATATTA
Found at i:481542 original size:93 final size:93
Alignment explanation
Indices: 481379--481554 Score: 237
Period size: 93 Copynumber: 1.9 Consensus size: 93
481369 TGAAGTGGGT
* * * *
481379 CGTCTCCTGGGTGGGCGGGACCTCTGGCACCATGTTCCTCATCGTCAGGCGGTGATGGCAGCTCC
1 CGTCTCCTGGGTGGGAGGGACCTCTGGCACCAGGTTCCTCATCATCAGGCGGCGATGGCAGCTCC
481444 GCAGGGGGGCCAGCCATCAGGTTTCCTA
66 GCAGGGGGGCCAGCCATCAGGTTTCCTA
* * * * *
481472 CGTCTCC-GGGTTGGGAGGGACCTCTTGCACCCGGTTCCTCGTCATCAGGCTGCGATGGCGGCTC
1 CGTCTCCTGGG-TGGGAGGGACCTCTGGCACCAGGTTCCTCATCATCAGGCGGCGATGGCAGCTC
* *
481536 CTCAGGGGGGCCTGCCATC
65 CGCAGGGGGGCCAGCCATC
481555 GGCGCCCTTT
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
92 3 0.04
93 68 0.96
ACGTcount: A:0.11, C:0.32, G:0.35, T:0.22
Consensus pattern (93 bp):
CGTCTCCTGGGTGGGAGGGACCTCTGGCACCAGGTTCCTCATCATCAGGCGGCGATGGCAGCTCC
GCAGGGGGGCCAGCCATCAGGTTTCCTA
Found at i:488164 original size:166 final size:166
Alignment explanation
Indices: 487890--488315 Score: 689
Period size: 166 Copynumber: 2.6 Consensus size: 166
487880 NNNNNNNNNN
487890 ACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTCCCATTTTAATTTGAGCTTTT
1 ACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTCCCATTTTAATTTGAGCTTTT
487955 CTGGCCTGATAGTTTTTGAGAAGAAGATTCTTAAAGATTTTCTCTATATATTCCTATGTAAAACT
66 CTGGCCTGATAGTTTTTGAGAAGAAGATTCTTAAAGATTTTCTCTATATATTCCTATGTAAAACT
*
488020 TGATCCCCCAATTGTGGCCCCACCCTTCCCCCGGGA
131 TGATCCCCCAATTGTGGCCCCACCCTACCCCCGGGA
488056 ACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTCCCATTTTAATTTGAGCTTTT
1 ACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTCCCATTTTAATTTGAGCTTTT
*
488121 CTGGCCTGATAGTTTTTGAGAAGAAGATTCTTAAAGATTTTCTCTATGTATTCCTATGTAAAACT
66 CTGGCCTGATAGTTTTTGAGAAGAAGATTCTTAAAGATTTTCTCTATATATTCCTATGTAAAACT
** * *
488186 TGATCCCCCTCTTGTGGCCCCTCCCTACCCCCGGGG
131 TGATCCCCCAATTGTGGCCCCACCCTACCCCCGGGA
* * * *
488222 ACCATGATTTGAACAAACTTAAATCTACACTACCTGATGATGCCTCCACA---CAAGTTTAAGCT
1 ACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATG-CTCC-CATTTTAA-TTTGAGCT
*
488284 TTTCCGG-CTGAATAGTTTTTGAGAAGAAGATT
63 TTTCTGGCCTG-ATAGTTTTTGAGAAGAAGATT
488316 TTTGAAAAAT
Statistics
Matches: 245, Mismatches: 11, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
165 5 0.02
166 234 0.96
167 4 0.02
168 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.33
Consensus pattern (166 bp):
ACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTCCCATTTTAATTTGAGCTTTT
CTGGCCTGATAGTTTTTGAGAAGAAGATTCTTAAAGATTTTCTCTATATATTCCTATGTAAAACT
TGATCCCCCAATTGTGGCCCCACCCTACCCCCGGGA
Found at i:488500 original size:3 final size:3
Alignment explanation
Indices: 488494--488536 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
488484 GTTTACAACA
* * * *
488494 ACG ACG ACG ACA ACA ACG ACG ACG ACG ACG ACA ACG ACC ACG A
1 ACG ACG ACG ACG ACG ACG ACG ACG ACG ACG ACG ACG ACG ACG A
488537 GAGACAGCGG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.42, C:0.35, G:0.23, T:0.00
Consensus pattern (3 bp):
ACG
Found at i:488508 original size:15 final size:15
Alignment explanation
Indices: 488488--488519 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
488478 TGAAAAGTTT
488488 ACAACAACGACGACG
1 ACAACAACGACGACG
488503 ACAACAACGACGACG
1 ACAACAACGACGACG
488518 AC
1 AC
488520 GACGACAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.34, G:0.19, T:0.00
Consensus pattern (15 bp):
ACAACAACGACGACG
Found at i:488515 original size:18 final size:18
Alignment explanation
Indices: 488488--488536 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
488478 TGAAAAGTTT
*
488488 ACAACAACGACGACGACA
1 ACAACGACGACGACGACA
*
488506 ACAACGACGACGACGACG
1 ACAACGACGACGACGACA
*
488524 ACAACGACCACGA
1 ACAACGACGACGA
488537 GAGACAGCGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.45, C:0.35, G:0.20, T:0.00
Consensus pattern (18 bp):
ACAACGACGACGACGACA
Found at i:503745 original size:163 final size:165
Alignment explanation
Indices: 503466--504240 Score: 891
Period size: 156 Copynumber: 4.7 Consensus size: 165
503456 AAAATAAGCG
* * * * * *
503466 AAGTCGACATTTAACAGAAAGCTGGCATCCGATTGATACAGAAATATATCCCACAATATGGCATG
1 AAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCACAATATGGCATG
* * * ** * *
503531 -TTTAAACAAATAGTGTGTTCAAATTTCAAGCATCTGCGATAATTAGCTGCTGAGAAATCTTTGA
66 CCTT-AACAAACA-CGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAAATCTTTGA
* *
503595 GGAAAATTTGTTTGAAAATTTTGGCTAAATTTAA-AA
129 CGAAAATTTGTTTGAAAATTTTGGCTAAATATAAGAA
* * *
503631 AAGTAC-TCATTTAACAGGAAGTTGACGTACGATTGGTACAAAAATA-ATTCCCACGATATGGCA
1 AAGT-CGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATA-TCCCACAATATGGCA
* *
503694 TGCCTTAACAAACAC-TGTAAAAATTTCAAGCATCTGCGATTAATAGCTGCTGAGAAATCTTTGA
64 TGCCTTAACAAACACGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAAATCTTTGA
*
503758 CGAAAATTTGTTTGAAAATTTTGGCTAAAAATAA-ACA
129 CGAAAATTTGTTTGAAAATTTTGGCTAAATATAAGA-A
* ** * * *
503795 ATGTAATTATTTAACAGGAAGTTGATGTCCGATTGATACAAAAATATATCCCACAATATGTCATG
1 AAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCACAATATGGCATG
** * * **
503860 CCAAAAACAAATAGTGTGTTCAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAAATCTTTGA
66 CC-TTAACAAACA-CGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAAATCTTTGA
* * **
503925 TGGAAATTTGTTTGAAAATTTTGGCTAAAAATAATAATCA
129 CGAAAATTTGTTTGAAAATTTTGGCT--AAAT-ATAAGAA
* * *
503965 AAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATACATCCCACGATATAGCATG
1 AAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCACAATATGGCATG
* * *
504030 CC-TATACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCTGAGAATTCTTTGA
66 CCTTA-ACAAACAC-GTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAAATCTTTGA
* *
504094 CAAAAATTTGTTTGAAAA-------T--A-ATAAGCA
129 CGAAAATTTGTTTGAAAATTTTGGCTAAATATAAGAA
*
504121 AAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACAATATGGCATG
1 AAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCACAATATGGCATG
*
504186 CCTTAACAAACACTGTGTAAAAATTTCAAGCATCTGCGATGAATAGTTGCTGAGA
66 CCTTAACAAACAC-GTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
504241 TAAATGCGAC
Statistics
Matches: 529, Mismatches: 65, Indels: 41
0.83 0.10 0.06
Matches are distributed among these distances:
156 116 0.22
157 2 0.00
158 1 0.00
162 1 0.00
163 77 0.15
164 58 0.11
165 67 0.13
166 3 0.01
167 69 0.13
168 1 0.00
169 71 0.13
170 63 0.12
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (165 bp):
AAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCACAATATGGCATG
CCTTAACAAACACGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAAATCTTTGACG
AAAATTTGTTTGAAAATTTTGGCTAAATATAAGAA
Found at i:504273 original size:4 final size:4
Alignment explanation
Indices: 504271--504310 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
504261 GTTACGGACG
*
504271 GACA GACA GACA GACA GACG GACA GACA GACA GACA GACA
1 GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA
504311 CACAAGGGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.47, C:0.25, G:0.28, T:0.00
Consensus pattern (4 bp):
GACA
Found at i:510222 original size:31 final size:31
Alignment explanation
Indices: 510187--510254 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
510177 ACAATGGTAA
510187 CATTCTCAGCAGTTATCTCTCTTTGCCCATT
1 CATTCTCAGCAGTTATCTCTCTTTGCCCATT
510218 CATTCTCAGCAGTTATCTCTCTTTGCCCATT
1 CATTCTCAGCAGTTATCTCTCTTTGCCCATT
510249 CATTCT
1 CATTCT
510255 TATGCATAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.16, C:0.32, G:0.09, T:0.43
Consensus pattern (31 bp):
CATTCTCAGCAGTTATCTCTCTTTGCCCATT
Found at i:511627 original size:31 final size:31
Alignment explanation
Indices: 511588--511718 Score: 190
Period size: 31 Copynumber: 4.2 Consensus size: 31
511578 ATAGCTAGAG
* *
511588 CCAATCAGTGAATAGCACCAAAGACGCTGAC
1 CCAATCAGTGAATAGCACCACAGACCCTGAC
*
511619 TCAATCAGTGAATAGCACCACAGACCCTGAC
1 CCAATCAGTGAATAGCACCACAGACCCTGAC
* *
511650 CCATTCAGTGAAAAGCACCACAGACCCTGAC
1 CCAATCAGTGAATAGCACCACAGACCCTGAC
**
511681 CCAATCAAAGAATAGCACCACAGACCCTGAC
1 CCAATCAGTGAATAGCACCACAGACCCTGAC
*
511712 GCAATCA
1 CCAATCA
511719 AGGGAAAGCA
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 89 1.00
ACGTcount: A:0.38, C:0.33, G:0.16, T:0.13
Consensus pattern (31 bp):
CCAATCAGTGAATAGCACCACAGACCCTGAC
Found at i:512846 original size:2 final size:2
Alignment explanation
Indices: 512839--512865 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
512829 TGAAATATGC
512839 AG 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 AG A
512866 AATTTGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:517821 original size:12 final size:12
Alignment explanation
Indices: 517804--517828 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
517794 ATAGACTAAA
517804 TGTCTGATCTAC
1 TGTCTGATCTAC
517816 TGTCTGATCTAC
1 TGTCTGATCTAC
517828 T
1 T
517829 AAGATTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (12 bp):
TGTCTGATCTAC
Found at i:517859 original size:22 final size:22
Alignment explanation
Indices: 517819--517986 Score: 178
Period size: 22 Copynumber: 7.6 Consensus size: 22
517809 GATCTACTGT
*
517819 CTGATCTACTAAGATTTAATGC
1 CTGATCTACTAAGACTTAATGC
*
517841 CTGCTCTAC-AAGGACTTAATGC
1 CTGATCTACTAA-GACTTAATGC
* * *
517863 CTGATCTACTAAGATTTATTGT
1 CTGATCTACTAAGACTTAATGC
**
517885 CTGATCTACTTGGACTTAATGC
1 CTGATCTACTAAGACTTAATGC
* **
517907 CTGATCTACTAAGATTTAATAT
1 CTGATCTACTAAGACTTAATGC
* * *
517929 CTAATCTACTAAGACTAAATGT
1 CTGATCTACTAAGACTTAATGC
*
517951 CTGTTCTAC-AAGGACTTAATGC
1 CTGATCTACTAA-GACTTAATGC
517973 CTGATCTACTAAGA
1 CTGATCTACTAAGA
517987 TTTACTTGGA
Statistics
Matches: 117, Mismatches: 25, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
21 4 0.03
22 109 0.93
23 4 0.03
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (22 bp):
CTGATCTACTAAGACTTAATGC
Found at i:517893 original size:44 final size:44
Alignment explanation
Indices: 517819--518287 Score: 410
Period size: 44 Copynumber: 10.4 Consensus size: 44
517809 GATCTACTGT
* *
517819 CTGATCTACTAA-GATTTAATGCCTGCTCTAC-AAGGACTTAATGC
1 CTGATCTAC-AAGGACTTAATGCCTGATCTACTAA-GACTTAATGC
* * * **
517863 CTGATCTACTAA-GATTTATTGTCTGATCTACTTGGACTTAATGC
1 CTGATCTAC-AAGGACTTAATGCCTGATCTACTAAGACTTAATGC
* ** * * *
517907 CTGATCTACTAA-GATTTAATATCTAATCTACTAAGACTAAATGT
1 CTGATCTAC-AAGGACTTAATGCCTGATCTACTAAGACTTAATGC
*
517951 CTGTTCTACAAGGACTTAATGCCTGATCTACTAAGATTTACTTGGACTTAATGC
1 CTGATCTACAAGGACTTAATGCCTGATCTACT---A---A----GACTTAATGC
* * * * *
518005 CTGATCTACTAA-GA-TTAAAGTCTAATCTCCTAAGATTTAATGC
1 CTGATCTAC-AAGGACTTAATGCCTGATCTACTAAGACTTAATGC
* *
518048 CTGTTCTACAAGGACTTAATGCCTGATCTACTAAGATTTAATGC
1 CTGATCTACAAGGACTTAATGCCTGATCTACTAAGACTTAATGC
* * * * **
518092 CTGTTCTACAAGGACTTAATGCCTGATCAACTGAGACTAAATAT
1 CTGATCTACAAGGACTTAATGCCTGATCTACTAAGACTTAATGC
* * * *
518136 CTGATCTACTAGCTAGGATTTAATGTCTAATCTACTAAGATTTAATGC
1 CTGATCTAC-A---AGGACTTAATGCCTGATCTACTAAGACTTAATGC
* *
518184 CTGTTCTACAAGGACTTAATGCCTGATCTACTAAGATTTAATGC
1 CTGATCTACAAGGACTTAATGCCTGATCTACTAAGACTTAATGC
* *
518228 CTGTTCTACAAGGACTTAATGCCTGATCTACTAGGACTTAATGC
1 CTGATCTACAAGGACTTAATGCCTGATCTACTAAGACTTAATGC
518272 CTGATCTACAAGGACT
1 CTGATCTACAAGGACT
518288 CATTAAAAGG
Statistics
Matches: 353, Mismatches: 53, Indels: 38
0.80 0.12 0.09
Matches are distributed among these distances:
42 2 0.01
43 21 0.06
44 258 0.73
45 1 0.00
47 3 0.01
48 33 0.09
50 2 0.01
53 13 0.04
54 18 0.05
55 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (44 bp):
CTGATCTACAAGGACTTAATGCCTGATCTACTAAGACTTAATGC
Found at i:517926 original size:66 final size:66
Alignment explanation
Indices: 517816--518280 Score: 434
Period size: 66 Copynumber: 6.8 Consensus size: 66
517806 TCTGATCTAC
* * *
517816 TGTCTGATCTACTAAGATTTAATGCCTGCTCTAC-AAGGACTTAATGCCTGATCTACTAAGATTT
1 TGTCTGATCTACTAGGACTTAATGCCTGATCTACTAA-GACTTAATGCCTGATCTACTAAGATTT
*
517880 AT
65 AA
* * ** * * *
517882 TGTCTGATCTACTTGGACTTAATGCCTGATCTACTAAGATTTAATATCTAATCTACTAAGACTAA
1 TGTCTGATCTACTAGGACTTAATGCCTGATCTACTAAGACTTAATGCCTGATCTACTAAGATTTA
517947 A
66 A
* *
517948 TGTCTGTTCTACAAGGACTTAATGCCTGATCTACTAAGATTTACTTGGACTTAATGCCTGATCTA
1 TGTCTGATCTACTAGGACTTAATGCCTGATCTACT---A---A----GACTTAATGCCTGATCTA
518013 CTAAGA-TTAA
56 CTAAGATTTAA
* * * * * *
518023 AGTCTAATCTCCTAAGATTTAATGCCTGTTCTAC-AAGGACTTAATGCCTGATCTACTAAGATTT
1 TGTCTGATCTACTAGGACTTAATGCCTGATCTACTAA-GACTTAATGCCTGATCTACTAAGATTT
518087 AA
65 AA
* * * * * * **
518089 TGCCTGTTCTACAAGGACTTAATGCCTGATCAACTGAGACTAAATATCTGATCTACTAGCTAGGA
1 TGTCTGATCTACTAGGACTTAATGCCTGATCTACTAAGACTTAATGCCTGATCTACTA---A-GA
518154 TTTAA
62 TTTAA
* * * *
518159 TGTCTAATCTACTAAGATTTAATGCCTGTTCTAC-AAGGACTTAATGCCTGATCTACTAAGATTT
1 TGTCTGATCTACTAGGACTTAATGCCTGATCTACTAA-GACTTAATGCCTGATCTACTAAGATTT
518223 AA
65 AA
* * * *
518225 TGCCTGTTCTACAAGGACTTAATGCCTGATCTACTAGGACTTAATGCCTGATCTAC
1 TGTCTGATCTACTAGGACTTAATGCCTGATCTACTAAGACTTAATGCCTGATCTAC
518281 AAGGACTCAT
Statistics
Matches: 319, Mismatches: 61, Indels: 38
0.76 0.15 0.09
Matches are distributed among these distances:
65 25 0.08
66 183 0.57
67 5 0.02
68 1 0.00
69 3 0.01
70 51 0.16
71 1 0.00
72 1 0.00
75 29 0.09
76 20 0.06
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (66 bp):
TGTCTGATCTACTAGGACTTAATGCCTGATCTACTAAGACTTAATGCCTGATCTACTAAGATTTA
A
Found at i:518065 original size:97 final size:98
Alignment explanation
Indices: 517891--518087 Score: 335
Period size: 97 Copynumber: 2.0 Consensus size: 98
517881 TTGTCTGATC
*
517891 TACTTGGACTTAATGCCTGATCTACTAAGATTTAATATCTAATCTACTAAGACTAAATGTCTGTT
1 TACTTGGACTTAATGCCTGATCTACTAAGATTTAATATCTAATCTACTAAGACTAAATGCCTGTT
517956 CTACAAGGACTTAATGCCTGATCTACTAAGATT
66 CTACAAGGACTTAATGCCTGATCTACTAAGATT
* * *
517989 TACTTGGACTTAATGCCTGATCTACTAAGA-TTAA-AGTCTAATCTCCTAAGATTTAATGCCTGT
1 TACTTGGACTTAATGCCTGATCTACTAAGATTTAATA-TCTAATCTACTAAGACTAAATGCCTGT
518052 TCTACAAGGACTTAATGCCTGATCTACTAAGATT
65 TCTACAAGGACTTAATGCCTGATCTACTAAGATT
518086 TA
1 TA
518088 ATGCCTGTTC
Statistics
Matches: 94, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
96 1 0.01
97 63 0.67
98 30 0.32
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (98 bp):
TACTTGGACTTAATGCCTGATCTACTAAGATTTAATATCTAATCTACTAAGACTAAATGCCTGTT
CTACAAGGACTTAATGCCTGATCTACTAAGATT
Found at i:518069 original size:22 final size:22
Alignment explanation
Indices: 517994--518287 Score: 260
Period size: 22 Copynumber: 13.2 Consensus size: 22
517984 AGATTTACTT
517994 GGACTTAATGCCTGATCTACTAA
1 GGACTTAATGCCTGATCTAC-AA
* * * *
518017 -GA-TTAAAGTCTAATCTCCTAA
1 GGACTTAATGCCTGATCTAC-AA
* *
518038 -GATTTAATGCCTGTTCTACAA
1 GGACTTAATGCCTGATCTACAA
518059 GGACTTAATGCCTGATCTACTAA
1 GGACTTAATGCCTGATCTAC-AA
* *
518082 -GATTTAATGCCTGTTCTACAA
1 GGACTTAATGCCTGATCTACAA
* *
518103 GGACTTAATGCCTGATCAAC-T
1 GGACTTAATGCCTGATCTACAA
* **
518124 GAGACTAAATATCTGATCTACTAGCTA
1 G-GACTTAATGCCTGATCTAC-A---A
* * *
518151 GGATTTAATGTCTAATCTACTAA
1 GGACTTAATGCCTGATCTAC-AA
* *
518174 -GATTTAATGCCTGTTCTACAA
1 GGACTTAATGCCTGATCTACAA
518195 GGACTTAATGCCTGATCTACTAA
1 GGACTTAATGCCTGATCTAC-AA
* *
518218 -GATTTAATGCCTGTTCTACAA
1 GGACTTAATGCCTGATCTACAA
*
518239 GGACTTAATGCCTGATCTACTA
1 GGACTTAATGCCTGATCTACAA
518261 GGACTTAATGCCTGATCTACAA
1 GGACTTAATGCCTGATCTACAA
518283 GGACT
1 GGACT
518288 CATTAAAAGG
Statistics
Matches: 221, Mismatches: 37, Indels: 27
0.78 0.13 0.09
Matches are distributed among these distances:
21 26 0.12
22 172 0.78
23 5 0.02
26 17 0.08
27 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (22 bp):
GGACTTAATGCCTGATCTACAA
Found at i:518276 original size:136 final size:130
Alignment explanation
Indices: 517993--518280 Score: 459
Period size: 136 Copynumber: 2.2 Consensus size: 130
517983 AAGATTTACT
*
517993 TGGACTTAATGCCTGATCTACTAAGATTAAAGTCTAATCTCCTAAGATTTAATGCCTGTTCTACA
1 TGGACTTAATGCCTGATCTACTAAGATTAAAGTCTAATCTACTAAGATTTAATGCCTGTTCTACA
*
518058 AGGACTTAATGCCTGATCTACTAAGATTTAATGCCTGTTCTACAAGGACTTAATGCCTGATCAAC
66 AGGACTTAATGCCTGATCTACTAAGATTTAATGCCTGTTCTACAAGGACTTAATGCCTGATCTAC
* ** *
518123 TGAGACTAAATATCTGATCTACTAGCTAGGATTTAATGTCTAATCTACTAAGATTTAATGCCTGT
1 TG-GACTTAATGCCTGATCTACTA---A-GA-TTAAAGTCTAATCTACTAAGATTTAATGCCTGT
518188 TCTACAAGGACTTAATGCCTGATCTACTAAGATTTAATGCCTGTTCTACAAGGACTTAATGCCTG
60 TCTACAAGGACTTAATGCCTGATCTACTAAGATTTAATGCCTGTTCTACAAGGACTTAATGCCTG
518253 ATCTAC
125 ATCTAC
518259 TAGGACTTAATGCCTGATCTAC
1 T-GGACTTAATGCCTGATCTAC
518281 AAGGACTCAT
Statistics
Matches: 142, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
130 2 0.01
131 18 0.13
134 1 0.01
135 2 0.01
136 118 0.83
137 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.34
Consensus pattern (130 bp):
TGGACTTAATGCCTGATCTACTAAGATTAAAGTCTAATCTACTAAGATTTAATGCCTGTTCTACA
AGGACTTAATGCCTGATCTACTAAGATTTAATGCCTGTTCTACAAGGACTTAATGCCTGATCTAC
Found at i:518815 original size:23 final size:24
Alignment explanation
Indices: 518785--518833 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
518775 TTAGTGTCTG
518785 ATCTAC-TAGAAATCAATGCCTTT
1 ATCTACTTAGAAATCAATGCCTTT
*
518808 ATCTACTATTAGGAATCAATGCCTTT
1 ATCTAC--TTAGAAATCAATGCCTTT
518834 TGTATTAGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 6 0.27
26 16 0.73
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (24 bp):
ATCTACTTAGAAATCAATGCCTTT
Found at i:522618 original size:2 final size:2
Alignment explanation
Indices: 522611--522640 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
522601 GTATAAAACA
522611 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
522641 CCTGTCATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:524524 original size:2 final size:2
Alignment explanation
Indices: 524517--524600 Score: 96
Period size: 2 Copynumber: 41.5 Consensus size: 2
524507 TTAATATACA
* * * *
524517 AG AG AG AG AG AT AG AG AG AG AG TCG AC AG AC 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
* * *
524560 AG AG AG AG AG AG AG AG AG AG AG AC AG GG AG AA AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
524601 AAATAAGTAA
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
2 66 0.99
3 1 0.01
ACGTcount: A:0.49, C:0.05, G:0.44, T:0.02
Consensus pattern (2 bp):
AG
Found at i:526107 original size:31 final size:31
Alignment explanation
Indices: 526067--526131 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
526057 ACAATGGTAA
526067 CATTATCAGCAGTTATCTCTCTTTGCCCATT
1 CATTATCAGCAGTTATCTCTCTTTGCCCATT
*
526098 CATTCTCAGCAGTTATCTCTCTTTGCCCATT
1 CATTATCAGCAGTTATCTCTCTTTGCCCATT
526129 CAT
1 CAT
526132 CCTTATGCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.18, C:0.31, G:0.09, T:0.42
Consensus pattern (31 bp):
CATTATCAGCAGTTATCTCTCTTTGCCCATT
Found at i:526914 original size:166 final size:166
Alignment explanation
Indices: 526639--527168 Score: 733
Period size: 166 Copynumber: 3.2 Consensus size: 166
526629 TTAATTTCTG
* * * *
526639 AGAAGATTTTTAAAAATTTACCCTATATATTCCTTTG-ATAAACTTTGA-CTCCCCATTGTGGCC
1 AGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTA-AAACTTCGACCT-CCCATTGTGGCC
* ** * * * *
526702 CCATCCTACCCCTTGGGATCATGATTTTCACAACTTTGAGTCTACACTACCTGAGGATGCTTTCA
64 CCAACCTACCCCCAGGGGTCATGATTTTCACAAATTTGAATCTACACTACCTGAGGATGCTTCCA
526767 CACAAGTTTCAGCTTTCCTGGCTAATTAGTTTCTGAGA
129 CACAAGTTTCAGCTTTCCTGGCTAATTAGTTTCTGAGA
* * * *
526805 AGAAGATTTTTAAAGATTTACTCTGTTTATTCCTATGTAAAACATCGACCTCCCATTGTGGCCCA
1 AGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCTCCCATTGTGGCCCC
526870 AACCTACCCCCAGGGGTCATGATTTTCACAAATTTGAATCTACACTACCTGAGGATAG-TTCCAC
66 AACCTACCCCCAGGGGTCATGATTTTCACAAATTTGAATCTACACTACCTGAGGAT-GCTTCCAC
*
526934 ACAAGTTTCAGCTTTCCTGGCTAATTAGTTTCGGAGA
130 ACAAGTTTCAGCTTTCCTGGCTAATTAGTTTCTGAGA
* * * * * *
526971 AGTAGATTTTTAAAGATTTACTCTATATAATCATATGTTAAATTTCGACCCCCCATTGTGGCCCC
1 AGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCTCCCATTGTGGCCCC
* ** * * * *
527036 CACCTACCTACAGGGGTAATTATTTTCACAAATTTGAATCTACACTATCTGAGGATGCATCCACA
66 AACCTACCCCCAGGGGTCATGATTTTCACAAATTTGAATCTACACTACCTGAGGATGCTTCCACA
* *
527101 CAAGTGTCAGCTTTCCTGGCTAATTAATTTCTGAGA
131 CAAGTTTCAGCTTTCCTGGCTAATTAGTTTCTGAGA
527137 AGAAGATTTTTAAAGATTTACTCTATATATTC
1 AGAAGATTTTTAAAGATTTACTCTATATATTC
527169 ATTTGTTAAA
Statistics
Matches: 322, Mismatches: 38, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
165 1 0.00
166 317 0.98
167 4 0.01
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.34
Consensus pattern (166 bp):
AGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCTCCCATTGTGGCCCC
AACCTACCCCCAGGGGTCATGATTTTCACAAATTTGAATCTACACTACCTGAGGATGCTTCCACA
CAAGTTTCAGCTTTCCTGGCTAATTAGTTTCTGAGA
Found at i:528657 original size:8 final size:8
Alignment explanation
Indices: 528646--528685 Score: 64
Period size: 8 Copynumber: 5.1 Consensus size: 8
528636 TAAAAAGTTT
528646 ACAGACGG
1 ACAGACGG
528654 ACAGACGG
1 ACAGACGG
*
528662 ACGGACGG
1 ACAGACGG
528670 ACAGACGG
1 ACAGACGG
528678 A-AGACGG
1 ACAGACGG
528685 A
1 A
528686 AAAAATGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
7 7 0.23
8 23 0.77
ACGTcount: A:0.38, C:0.23, G:0.40, T:0.00
Consensus pattern (8 bp):
ACAGACGG
Found at i:533443 original size:2 final size:2
Alignment explanation
Indices: 533438--533463 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
533428 AGAATGTGTG
533438 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
533464 GTGAACAATA
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):
TA
Found at i:535114 original size:53 final size:53
Alignment explanation
Indices: 535008--535114 Score: 142
Period size: 53 Copynumber: 2.0 Consensus size: 53
534998 TTTTTCATGG
* * * * ***
535008 AAACTAAGAACTTGTTGTATTAAATATAAAGATTTTTATTATTGGATCCAAAA
1 AAACTAAAAAATTGTTGTATTAAATATAAAGATCTTTATTATTAGAAAAAAAA
*
535061 AAACTAAAAAATTGTTGTCTTAAATATAAAGATCTTTATTATTAGAAAAAAAA
1 AAACTAAAAAATTGTTGTATTAAATATAAAGATCTTTATTATTAGAAAAAAAA
535114 A
1 A
535115 CATGCTGATA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.36
Consensus pattern (53 bp):
AAACTAAAAAATTGTTGTATTAAATATAAAGATCTTTATTATTAGAAAAAAAA
Found at i:547317 original size:22 final size:22
Alignment explanation
Indices: 547287--547334 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
547277 TTATAAAAAG
*
547287 GCGATGGCGAAAGTGCGAAGAT
1 GCGAAGGCGAAAGTGCGAAGAT
* *
547309 GCGAAGGCGAGAGTGCGAAGTT
1 GCGAAGGCGAAAGTGCGAAGAT
547331 GCGA
1 GCGA
547335 TAGTAGTATC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.15, G:0.44, T:0.12
Consensus pattern (22 bp):
GCGAAGGCGAAAGTGCGAAGAT
Found at i:547368 original size:8 final size:7
Alignment explanation
Indices: 547357--547465 Score: 82
Period size: 8 Copynumber: 14.9 Consensus size: 7
547347 TTCTTCGCCC
547357 TCGCAACT
1 TCGC-ACT
547365 TCGCACTT
1 TCGCAC-T
547373 TCGC-CT
1 TCGCACT
547379 TCGCATCT
1 TCGCA-CT
*
547387 TCGCGCT
1 TCGCACT
*
547394 TCGC-CG
1 TCGCACT
547400 TCGCATCT
1 TCGCA-CT
547408 TCGCACTT
1 TCGCAC-T
*
547416 TCGCCCCT
1 TCG-CACT
547424 TCGC-CT
1 TCGCACT
547430 TCGCACTT
1 TCGCAC-T
547438 TCGC-CT
1 TCGCACT
547444 TCGCAACT
1 TCGC-ACT
547452 TCGCACT
1 TCGCACT
547459 CTCGCAC
1 -TCGCAC
547466 CTCGACCTAA
Statistics
Matches: 85, Mismatches: 4, Indels: 24
0.75 0.04 0.21
Matches are distributed among these distances:
6 21 0.25
7 16 0.19
8 46 0.54
9 2 0.02
ACGTcount: A:0.10, C:0.44, G:0.16, T:0.30
Consensus pattern (7 bp):
TCGCACT
Found at i:547375 original size:22 final size:22
Alignment explanation
Indices: 547350--547469 Score: 129
Period size: 22 Copynumber: 5.5 Consensus size: 22
547340 GTATCGCTTC
547350 TTCGCCCTCGCAACTTCGCACT
1 TTCGCCCTCGCAACTTCGCACT
* * *
547372 TTCGCCTTCGCATCTTCGCGC-
1 TTCGCCCTCGCAACTTCGCACT
* *
547393 TTCGCCGTCGCATCTTCGCACT
1 TTCGCCCTCGCAACTTCGCACT
547415 TTCGCCCCTTCGC--CTTCGCACT
1 TTCG-CCC-TCGCAACTTCGCACT
*
547437 TTCGCCTTCGCAACTTCGCACT
1 TTCGCCCTCGCAACTTCGCACT
*
547459 CTCGCACCTCG
1 TTCGC-CCTCG
547470 ACCTAAAGGC
Statistics
Matches: 83, Mismatches: 9, Indels: 11
0.81 0.09 0.11
Matches are distributed among these distances:
20 4 0.05
21 21 0.25
22 48 0.58
23 6 0.07
24 4 0.05
ACGTcount: A:0.09, C:0.45, G:0.16, T:0.30
Consensus pattern (22 bp):
TTCGCCCTCGCAACTTCGCACT
Found at i:547454 original size:14 final size:13
Alignment explanation
Indices: 547349--547465 Score: 74
Period size: 14 Copynumber: 8.1 Consensus size: 13
547339 AGTATCGCTT
*
547349 CTTCGCCCTCGCAA
1 CTTCGCCTTCGC-A
547363 CTTCGCACTTTCGC-
1 CTTCGC-C-TTCGCA
*
547377 CTTCGCATCTTCGCG
1 CTTCGC--CTTCGCA
*
547392 CTTCGCCGTCGCA
1 CTTCGCCTTCGCA
*
547405 TCTTCGCACTTTCGCCC
1 -CTTCGC-C-TTCG-CA
547422 CTTCGCCTTCGCA
1 CTTCGCCTTCGCA
547435 CTTTCGCCTTCGCAA
1 C-TTCGCCTTCGC-A
547450 CTTCGCACTCTCGCA
1 CTTCGC-CT-TCGCA
547465 C
1 C
547466 CTCGACCTAA
Statistics
Matches: 84, Mismatches: 7, Indels: 23
0.74 0.06 0.20
Matches are distributed among these distances:
13 7 0.08
14 43 0.51
15 16 0.19
16 17 0.20
17 1 0.01
ACGTcount: A:0.09, C:0.45, G:0.15, T:0.30
Consensus pattern (13 bp):
CTTCGCCTTCGCA
Found at i:549037 original size:30 final size:30
Alignment explanation
Indices: 549002--549122 Score: 188
Period size: 30 Copynumber: 4.0 Consensus size: 30
548992 ATTTTGAACT
* *
549002 GCCGGTCAATAGACTGCAATCTATTAGACC
1 GCCGGTCAATAGACTGCGATCTATTGGACC
**
549032 GCCGGTCAATAGACTTTGATCTATTGGACC
1 GCCGGTCAATAGACTGCGATCTATTGGACC
* *
549062 GCCGGTCAATAGACTTCGATCTTTTGGACC
1 GCCGGTCAATAGACTGCGATCTATTGGACC
549092 GCCGGTCAATAGACTGCGATCTATTGGACC
1 GCCGGTCAATAGACTGCGATCTATTGGACC
549122 G
1 G
549123 GCAACGTATT
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 83 1.00
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (30 bp):
GCCGGTCAATAGACTGCGATCTATTGGACC
Found at i:560174 original size:39 final size:39
Alignment explanation
Indices: 560131--560337 Score: 274
Period size: 39 Copynumber: 5.3 Consensus size: 39
560121 CTCCTCTACC
* * * *
560131 ACAGCCACTGACAAAGGTAAGTCGGCTGGGAAAATATTT
1 ACAGCCACTGACAAAGGTAAGTCAGCTTGGAGAATGTTT
* *
560170 ACAGCCACTGACAAAGGTAATCTCAGCGTGGAGAATGTTT
1 ACAGCCACTGACAAAGGTAA-GTCAGCTTGGAGAATGTTT
*
560210 AAAGCCACTGACAAAGGTAAGTC-GACTTGGAGAATGTTT
1 ACAGCCACTGACAAAGGTAAGTCAG-CTTGGAGAATGTTT
** * *
560249 ACAG-CAAGGGCAAAGGTAAGTCAGCTTTGAGAATGTTT
1 ACAGCCACTGACAAAGGTAAGTCAGCTTGGAGAATGTTT
*
560287 ACAGCCACTGACAAAAGTAAGTCAGCTTGGAGAATGTTT
1 ACAGCCACTGACAAAGGTAAGTCAGCTTGGAGAATGTTT
560326 ACAGCCACTGAC
1 ACAGCCACTGAC
560338 TAATGGAAGT
Statistics
Matches: 145, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
38 33 0.23
39 80 0.55
40 32 0.22
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (39 bp):
ACAGCCACTGACAAAGGTAAGTCAGCTTGGAGAATGTTT
Found at i:560307 original size:77 final size:78
Alignment explanation
Indices: 560131--560330 Score: 260
Period size: 77 Copynumber: 2.6 Consensus size: 78
560121 CTCCTCTACC
* * * * **
560131 ACAGCCACTGACAAAGGTAAGTCGGCTGGGAAAATATTTACAGCCACTGACAAAGGTAATCTCAG
1 ACAGCCACTGACAAAGGTAAGTCGACTTGGAGAATGTTTACAG-CAAGGACAAAGGTAATCTCAG
560196 CGTGGAGAATGTTT
65 CGTGGAGAATGTTT
* * *
560210 AAAGCCACTGACAAAGGTAAGTCGACTTGGAGAATGTTTACAGCAAGGGCAAAGGTAA-GTCAGC
1 ACAGCCACTGACAAAGGTAAGTCGACTTGGAGAATGTTTACAGCAAGGACAAAGGTAATCTCAGC
* *
560274 TTTGAGAATGTTT
66 GTGGAGAATGTTT
*
560287 ACAGCCACTGACAAAAGTAAGTC-AGCTTGGAGAATGTTTACAGC
1 ACAGCCACTGACAAAGGTAAGTCGA-CTTGGAGAATGTTTACAGC
560331 CACTGACTAA
Statistics
Matches: 107, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
76 1 0.01
77 56 0.52
78 12 0.11
79 38 0.36
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (78 bp):
ACAGCCACTGACAAAGGTAAGTCGACTTGGAGAATGTTTACAGCAAGGACAAAGGTAATCTCAGC
GTGGAGAATGTTT
Found at i:561902 original size:12 final size:12
Alignment explanation
Indices: 561885--561909 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
561875 ATACAGTGTG
561885 TTTTTTTTTTTA
1 TTTTTTTTTTTA
561897 TTTTTTTTTTTA
1 TTTTTTTTTTTA
561909 T
1 T
561910 ATAAATTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTTTTTTTTA
Found at i:568830 original size:31 final size:31
Alignment explanation
Indices: 568795--568860 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
568785 TATGCATAAA
568795 AATGAATGGGCAAAGAGAGATAACTGCTGAG
1 AATGAATGGGCAAAGAGAGATAACTGCTGAG
*
568826 AATGACTGGGCAAAGAGAGATAACTGCTGAG
1 AATGAATGGGCAAAGAGAGATAACTGCTGAG
568857 AATG
1 AATG
568861 TTAGCATTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.41, C:0.11, G:0.32, T:0.17
Consensus pattern (31 bp):
AATGAATGGGCAAAGAGAGATAACTGCTGAG
Found at i:569507 original size:167 final size:166
Alignment explanation
Indices: 569224--569564 Score: 648
Period size: 167 Copynumber: 2.0 Consensus size: 166
569214 ATTAAATTCA
569224 ATAAAGAGATTTTTATCCAACTTGTGTGTTTTATCCCCTCACTAAGGCTCAAGAAAAAACACTTT
1 ATAAAGAGATTTTTATCCAACTTGTGTGTTTTATCCCCTCACTAAGGCTCAAGAAAAAACACTTT
569289 AATTGTTGGATGAAAATCATATCCAACTACAAATCACGAGATCCTATATATTCCAGTTCTTTACA
66 AATTGTTGGATGAAAATCATATCCAACTACAAATCACGAGATCCTATATATTCCAGTTCTTTACA
*
569354 TCTTCTGCCGGGCATTTATTTTTCATCATTGTTAAT
131 TCTTCTGCCAGGCATTTATTTTTCATCATTGTTAAT
569390 ATAAAGAGATTTTTATCCAACTTGTGTGTTTTATCCCCTCACTAAGGCTCAAGAAAAAAACACTT
1 ATAAAGAGATTTTTATCCAACTTGTGTGTTTTATCCCCTCACTAAGGCTCAAG-AAAAAACACTT
569455 TAATTGTTGGAT-AAAAGTCATATCCAACTACAAATCACGAGATCCTATATATTCCAGTTCTTTA
65 TAATTGTTGGATGAAAA-TCATATCCAACTACAAATCACGAGATCCTATATATTCCAGTTCTTTA
569519 CATCTTCTGCCAGGCATTTATTTTTCATCATTGTTAAT
129 CATCTTCTGCCAGGCATTTATTTTTCATCATTGTTAAT
569557 ATAAAGAG
1 ATAAAGAG
569565 GATGGAATTC
Statistics
Matches: 172, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
166 57 0.33
167 115 0.67
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (166 bp):
ATAAAGAGATTTTTATCCAACTTGTGTGTTTTATCCCCTCACTAAGGCTCAAGAAAAAACACTTT
AATTGTTGGATGAAAATCATATCCAACTACAAATCACGAGATCCTATATATTCCAGTTCTTTACA
TCTTCTGCCAGGCATTTATTTTTCATCATTGTTAAT
Found at i:570856 original size:24 final size:24
Alignment explanation
Indices: 570819--570867 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
570809 ATAAAAATTA
570819 AAATCCATTATAATATATATTTTT
1 AAATCCATTATAATATATATTTTT
* * * *
570843 AAATCTATTTTAATATTTCTTTTT
1 AAATCCATTATAATATATATTTTT
570867 A
1 A
570868 TTTATTAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (24 bp):
AAATCCATTATAATATATATTTTT
Found at i:579113 original size:11 final size:13
Alignment explanation
Indices: 579085--579116 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
579075 ACTAAACCCT
579085 GGGTTTACTTTCC
1 GGGTTTACTTTCC
579098 GGGTTTAC-TT-C
1 GGGTTTACTTTCC
579109 GGGTTTAC
1 GGGTTTAC
579117 CAGAGTGGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 9 0.47
12 2 0.11
13 8 0.42
ACGTcount: A:0.09, C:0.19, G:0.28, T:0.44
Consensus pattern (13 bp):
GGGTTTACTTTCC
Found at i:579130 original size:11 final size:11
Alignment explanation
Indices: 579125--579155 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
579115 ACCAGAGTGG
579125 ACCCAGAGTAA
1 ACCCAGAGTAA
*
579136 ACCCAAAGTAA
1 ACCCAGAGTAA
579147 ACCCAGAGT
1 ACCCAGAGT
579156 GGACACAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.45, C:0.29, G:0.16, T:0.10
Consensus pattern (11 bp):
ACCCAGAGTAA
Found at i:579332 original size:11 final size:11
Alignment explanation
Indices: 579318--579357 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
579308 AAAGCAATTT
579318 CAAAGTAAACC
1 CAAAGTAAACC
579329 CAAAGTAAACC
1 CAAAGTAAACC
**
579340 CCGAGTAAACC
1 CAAAGTAAACC
*
579351 CAGAGTA
1 CAAAGTA
579358 TATCCCGAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.47, C:0.28, G:0.15, T:0.10
Consensus pattern (11 bp):
CAAAGTAAACC
Found at i:579346 original size:22 final size:22
Alignment explanation
Indices: 579321--579367 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
579311 GCAATTTCAA
579321 AGTAAACCCAAAGTAAACCCCG
1 AGTAAACCCAAAGTAAACCCCG
* * *
579343 AGTAAACCCAGAGTATATCCCG
1 AGTAAACCCAAAGTAAACCCCG
579365 AGT
1 AGT
579368 GGACCAACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.28, G:0.17, T:0.15
Consensus pattern (22 bp):
AGTAAACCCAAAGTAAACCCCG
Found at i:581953 original size:37 final size:37
Alignment explanation
Indices: 581907--582017 Score: 124
Period size: 37 Copynumber: 3.1 Consensus size: 37
581897 TTAATTCTTA
* * *
581907 ATTTTGCGAAAATTAGAAATACTTATTTTTCATACTT
1 ATTTAGCGAATATTAAAAATACTTATTTTTCATACTT
581944 ATTTAGCGAATATTAAAAATAC-TA-TTTT--TA-TT
1 ATTTAGCGAATATTAAAAATACTTATTTTTCATACTT
* * * *
581976 ATTTTGGGAATATTAAAAATACTTATTTTACATACGT
1 ATTTAGCGAATATTAAAAATACTTATTTTTCATACTT
582013 ATTTA
1 ATTTA
582018 TATACATTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
32 22 0.36
33 4 0.07
34 3 0.05
35 4 0.07
36 4 0.07
37 24 0.39
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (37 bp):
ATTTAGCGAATATTAAAAATACTTATTTTTCATACTT
Found at i:582908 original size:6 final size:6
Alignment explanation
Indices: 582897--582925 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
582887 TTCTGTCAAT
582897 TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
582926 TTTATACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (6 bp):
TTTTTG
Found at i:591636 original size:17 final size:17
Alignment explanation
Indices: 591594--591642 Score: 66
Period size: 15 Copynumber: 3.0 Consensus size: 17
591584 TTTGCAAAAT
*
591594 TTTACGGTTATAACGAA
1 TTTACGGATATAACGAA
591611 TTT--GGATATAACGAA
1 TTTACGGATATAACGAA
*
591626 TTTACGGATATAGCGAA
1 TTTACGGATATAACGAA
591643 CTGTTTTGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 14 0.50
17 14 0.50
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (17 bp):
TTTACGGATATAACGAA
Found at i:597189 original size:2 final size:2
Alignment explanation
Indices: 597182--597214 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
597172 CAATTAGAAG
597182 TA TA TA TA TA NTA 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
597215 GTGAAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:602525 original size:8 final size:8
Alignment explanation
Indices: 602514--602578 Score: 60
Period size: 8 Copynumber: 8.1 Consensus size: 8
602504 CGTGCGTGCG
*
602514 TGCATGCA
1 TGCATCCA
602522 TGCATCCA
1 TGCATCCA
602530 TGCATCCA
1 TGCATCCA
*
602538 TCCATCCA
1 TGCATCCA
* *
602546 TCCATACAA
1 TGCAT-CCA
602555 T-CATCCA
1 TGCATCCA
*
602562 TCCATCCA
1 TGCATCCA
*
602570 TCCATCCA
1 TGCATCCA
602578 T
1 T
602579 CCATACAATC
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
7 3 0.06
8 45 0.88
9 3 0.06
ACGTcount: A:0.28, C:0.40, G:0.06, T:0.26
Consensus pattern (8 bp):
TGCATCCA
Found at i:602539 original size:4 final size:4
Alignment explanation
Indices: 602524--602598 Score: 91
Period size: 4 Copynumber: 18.8 Consensus size: 4
602514 TGCATGCATG
* *
602524 CATC CATG CATC CATC CATC CATC CATAC AAT- CATC CATC CATC CATC
1 CATC CATC CATC CATC CATC CATC CAT-C CATC CATC CATC CATC CATC
*
602572 CATC CATC CATAC AAT- CATC CATC CAT
1 CATC CATC CAT-C CATC CATC CATC CAT
602599 ACATACATGC
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
3 4 0.07
4 51 0.84
5 6 0.10
ACGTcount: A:0.31, C:0.43, G:0.01, T:0.25
Consensus pattern (4 bp):
CATC
Found at i:602568 original size:32 final size:32
Alignment explanation
Indices: 602524--602598 Score: 141
Period size: 32 Copynumber: 2.3 Consensus size: 32
602514 TGCATGCATG
*
602524 CATCCATGCATCCATCCATCCATCCATACAAT
1 CATCCATCCATCCATCCATCCATCCATACAAT
602556 CATCCATCCATCCATCCATCCATCCATACAAT
1 CATCCATCCATCCATCCATCCATCCATACAAT
602588 CATCCATCCAT
1 CATCCATCCAT
602599 ACATACATGC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.31, C:0.43, G:0.01, T:0.25
Consensus pattern (32 bp):
CATCCATCCATCCATCCATCCATCCATACAAT
Found at i:602603 original size:20 final size:20
Alignment explanation
Indices: 602568--602605 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
602558 TCCATCCATC
*
602568 CATCCATCCATCCATACAAT
1 CATCCATCCATACATACAAT
602588 CATCCATCCATACATACA
1 CATCCATCCATACATACA
602606 TGCACACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.39, G:0.00, T:0.24
Consensus pattern (20 bp):
CATCCATCCATACATACAAT
Found at i:607117 original size:33 final size:32
Alignment explanation
Indices: 607078--607142 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 32
607068 TTTTAAGTTT
*
607078 TATACAGTGACATAATTATTCAATCATATATTA
1 TATACAGTCACATAATTATTCAATCATA-ATTA
607111 TATACAGTCACATAATTATTCAATCATAATTA
1 TATACAGTCACATAATTATTCAATCATAATTA
607143 AATGCTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 4 0.13
33 27 0.87
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.38
Consensus pattern (32 bp):
TATACAGTCACATAATTATTCAATCATAATTA
Found at i:607140 original size:14 final size:14
Alignment explanation
Indices: 607088--607142 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
607078 TATACAGTGA
607088 CATAATTATTCAAT
1 CATAATTATTCAAT
*
607102 CATATATTATATACAGT
1 CATA-ATTAT-T-CAAT
607119 CACATAATTATTCAAT
1 --CATAATTATTCAAT
607135 CATAATTA
1 CATAATTA
607143 AATGCTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 12 0.35
15 5 0.15
16 4 0.12
17 4 0.12
18 5 0.15
19 4 0.12
ACGTcount: A:0.44, C:0.15, G:0.02, T:0.40
Consensus pattern (14 bp):
CATAATTATTCAAT
Found at i:619181 original size:9 final size:9
Alignment explanation
Indices: 619167--619202 Score: 63
Period size: 9 Copynumber: 3.9 Consensus size: 9
619157 CCCCCCCCAA
619167 AAAAAAAAG
1 AAAAAAAAG
619176 AAAAAAAAG
1 AAAAAAAAG
619185 AAAGAAAAAG
1 AAA-AAAAAG
619195 AAAAAAAA
1 AAAAAAAA
619203 AAGAAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 17 0.65
10 9 0.35
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:619181 original size:10 final size:10
Alignment explanation
Indices: 619166--619208 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
619156 CCCCCCCCCA
619166 AAAAAAAAAG
1 AAAAAAAAAG
619176 -AAAAAAAAG
1 AAAAAAAAAG
*
619185 AAAGAAAAAG
1 AAAAAAAAAG
619195 AAAAAAAAAAG
1 -AAAAAAAAAG
619206 AAA
1 AAA
619209 TAATATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 9 0.31
10 11 0.38
11 9 0.31
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:619420 original size:21 final size:21
Alignment explanation
Indices: 619394--619490 Score: 108
Period size: 21 Copynumber: 4.7 Consensus size: 21
619384 TACACCATAG
619394 CATAGCATAGCATTGAAATCT
1 CATAGCATAGCATTGAAATCT
* *
619415 CATAGCATAGCATTGGAGTCT
1 CATAGCATAGCATTGAAATCT
* *
619436 CATAGCATAGCATTGGAATTT
1 CATAGCATAGCATTGAAATCT
*
619457 CATACCATAGCA-T-ACAATCT
1 CATAGCATAGCATTGA-AATCT
* *
619477 CATAGAATCGCATT
1 CATAGCATAGCATT
619491 CGTCATATCA
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
20 14 0.22
21 50 0.78
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (21 bp):
CATAGCATAGCATTGAAATCT
Found at i:619678 original size:5 final size:5
Alignment explanation
Indices: 619665--619708 Score: 70
Period size: 5 Copynumber: 8.8 Consensus size: 5
619655 GTTCAAATCT
* *
619665 CATAG CATAC CATAG CATAG CATAG CATAG CATAG CATAC CATA
1 CATAG CATAG CATAG CATAG CATAG CATAG CATAG CATAG CATA
619709 TCATTAAGCC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.41, C:0.25, G:0.14, T:0.20
Consensus pattern (5 bp):
CATAG
Found at i:619685 original size:15 final size:15
Alignment explanation
Indices: 619665--619708 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
619655 GTTCAAATCT
619665 CATAGCATACCATAG
1 CATAGCATACCATAG
*
619680 CATAGCATAGCATAG
1 CATAGCATACCATAG
619695 CATAGCATACCATA
1 CATAGCATACCATA
619709 TCATTAAGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.41, C:0.25, G:0.14, T:0.20
Consensus pattern (15 bp):
CATAGCATACCATAG
Found at i:619758 original size:21 final size:21
Alignment explanation
Indices: 619732--619811 Score: 108
Period size: 21 Copynumber: 3.8 Consensus size: 21
619722 CATTTCAATT
619732 TCTCATAGCATACCATACAAA
1 TCTCATAGCATACCATACAAA
619753 TCTCATAGCATACCATACAAA
1 TCTCATAGCATACCATACAAA
*
619774 TCTCATAGCATATCATTA-AAA
1 TCTCATAGCATACCA-TACAAA
* * *
619795 TCGCATACCATAGCATA
1 TCTCATAGCATACCATA
619812 GCATTAAATT
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
20 2 0.04
21 50 0.93
22 2 0.04
ACGTcount: A:0.41, C:0.26, G:0.06, T:0.26
Consensus pattern (21 bp):
TCTCATAGCATACCATACAAA
Found at i:622679 original size:20 final size:20
Alignment explanation
Indices: 622650--622692 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
622640 TAGTAATAGT
* *
622650 ATTAGTATTTCTTTGGACGA
1 ATTAGGATTTCTTCGGACGA
*
622670 ATTAGGATTTGTTCGGACGA
1 ATTAGGATTTCTTCGGACGA
622690 ATT
1 ATT
622693 TGTTCGGACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.42
Consensus pattern (20 bp):
ATTAGGATTTCTTCGGACGA
Found at i:622910 original size:62 final size:62
Alignment explanation
Indices: 622834--622950 Score: 164
Period size: 62 Copynumber: 1.9 Consensus size: 62
622824 CTGTATTTAA
* * * * *
622834 ACAAATACCAATTCGTCCGAACAAATAGCTTATTTGTCTGAAGAAATTGCTTATTTGTCCAC
1 ACAAATACCAATTCGTCCGAACAAATAACTTATTAGTCCGAACAAATAGCTTATTTGTCCAC
*
622896 ACAAAT-CCTAATTCGTCCGAACAAATAATTTATTAGTCCGAACAAATAGCTTATT
1 ACAAATACC-AATTCGTCCGAACAAATAACTTATTAGTCCGAACAAATAGCTTATT
622951 CGCCTGAACA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
61 2 0.04
62 46 0.96
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.32
Consensus pattern (62 bp):
ACAAATACCAATTCGTCCGAACAAATAACTTATTAGTCCGAACAAATAGCTTATTTGTCCAC
Found at i:622946 original size:83 final size:83
Alignment explanation
Indices: 622848--623002 Score: 222
Period size: 83 Copynumber: 1.9 Consensus size: 83
622838 ATACCAATTC
* * * * * *
622848 GTCCGAACAAATAGCTTATTTGTCTGAAGAAATTGCTTATTTGT-CCACACAAATCCTAATTCGT
1 GTCCGAACAAATAGCTTATTCGCCTGAACAAATAGCTTATTCGTACCA-ACAAATCCTAAATCGT
622912 CCGAACAAATAATTTATTA
65 CCGAACAAATAATTTATTA
* *
622931 GTCCGAACAAATAGCTTATTCGCCTGAACAAATAGTTTATTCGTACGAACAAATCCTAAATCGTC
1 GTCCGAACAAATAGCTTATTCGCCTGAACAAATAGCTTATTCGTACCAACAAATCCTAAATCGTC
622996 CGAACAA
66 CGAACAA
623003 TTAGATAATT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
83 61 0.97
84 2 0.03
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (83 bp):
GTCCGAACAAATAGCTTATTCGCCTGAACAAATAGCTTATTCGTACCAACAAATCCTAAATCGTC
CGAACAAATAATTTATTA
Found at i:622961 original size:42 final size:42
Alignment explanation
Indices: 622848--622984 Score: 136
Period size: 42 Copynumber: 3.3 Consensus size: 42
622838 ATACCAATTC
* * * * * *
622848 GTCCGAACAAATAGCTTATTTGTCTGAAGAAATTGCTTATTT
1 GTCCGAACAAATAGCTTATTCGCCTGAACAAATAGTTTATTA
* * *
622890 GTCC-ACACAAAT-CCTAATTCGTCC-GAACAAATAATTTATTA
1 GTCCGA-ACAAATAGCTTATTCG-CCTGAACAAATAGTTTATTA
*
622931 GTCCGAACAAATAGCTTATTCGCCTGAACAAATAGTTTATTC
1 GTCCGAACAAATAGCTTATTCGCCTGAACAAATAGTTTATTA
*
622973 GTACGAACAAAT
1 GTCCGAACAAAT
622985 CCTAAATCGT
Statistics
Matches: 76, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
41 31 0.41
42 45 0.59
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (42 bp):
GTCCGAACAAATAGCTTATTCGCCTGAACAAATAGTTTATTA
Found at i:622972 original size:21 final size:21
Alignment explanation
Indices: 622844--622984 Score: 117
Period size: 21 Copynumber: 6.8 Consensus size: 21
622834 ACAAATACCA
*
622844 ATTCGTCCGAACAAATAGCTT
1 ATTCGTCCGAACAAATAGTTT
* * * * *
622865 ATTTGTCTGAAGAAATTGCTT
1 ATTCGTCCGAACAAATAGTTT
* ** *
622886 ATTTGTCC-ACACAAAT-CCTA
1 ATTCGTCCGA-ACAAATAGTTT
*
622906 ATTCGTCCGAACAAATAATTT
1 ATTCGTCCGAACAAATAGTTT
* *
622927 ATTAGTCCGAACAAATAGCTT
1 ATTCGTCCGAACAAATAGTTT
622948 ATTCG-CCTGAACAAATAGTTT
1 ATTCGTCC-GAACAAATAGTTT
*
622969 ATTCGTACGAACAAAT
1 ATTCGTCCGAACAAAT
622985 CCTAAATCGT
Statistics
Matches: 97, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
20 18 0.19
21 78 0.80
22 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (21 bp):
ATTCGTCCGAACAAATAGTTT
Found at i:623563 original size:2 final size:2
Alignment explanation
Indices: 623556--623584 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
623546 ACCAAAGGTA
623556 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
623585 NNNNNNNNNN
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:629113 original size:11 final size:11
Alignment explanation
Indices: 629097--629123 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
629087 GAAATTTTGT
629097 AAAAAAAACAA
1 AAAAAAAACAA
629108 AAAAAAAACAA
1 AAAAAAAACAA
629119 AAAAA
1 AAAAA
629124 CTTTTGGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:636057 original size:10 final size:10
Alignment explanation
Indices: 636056--636114 Score: 63
Period size: 10 Copynumber: 6.2 Consensus size: 10
636046 CTTAAGCTTT
636056 CTTTCTTAAG
1 CTTTCTTAAG
*
636066 CTTTCTT--T
1 CTTTCTTAAG
*
636074 CTTTCTT--T
1 CTTTCTTAAG
636082 CTTTCTTAAG
1 CTTTCTTAAG
636092 CTTTTCTTAAG
1 C-TTTCTTAAG
636103 CTTTCTTAAG
1 CTTTCTTAAG
636113 CT
1 CT
636115 GACTTTCTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
8 15 0.34
10 19 0.43
11 10 0.23
ACGTcount: A:0.14, C:0.22, G:0.07, T:0.58
Consensus pattern (10 bp):
CTTTCTTAAG
Found at i:636061 original size:14 final size:14
Alignment explanation
Indices: 636042--636109 Score: 92
Period size: 14 Copynumber: 5.2 Consensus size: 14
636032 CACTGGCTGA
636042 CTTTCTTAAGCTTT
1 CTTTCTTAAGCTTT
636056 CTTTCTTAAGCTTT
1 CTTTCTTAAGCTTT
*
636070 CTTTCTT--TCTTT
1 CTTTCTTAAGCTTT
636082 CTTTCTTAAGC--T
1 CTTTCTTAAGCTTT
636094 -TTTCTTAAGCTTT
1 CTTTCTTAAGCTTT
636107 CTT
1 CTT
636110 AAGCTGACTT
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
11 10 0.21
12 12 0.26
13 1 0.02
14 24 0.51
ACGTcount: A:0.12, C:0.22, G:0.06, T:0.60
Consensus pattern (14 bp):
CTTTCTTAAGCTTT
Found at i:636122 original size:14 final size:14
Alignment explanation
Indices: 636037--636124 Score: 59
Period size: 14 Copynumber: 6.9 Consensus size: 14
636027 TATTCCACTG
*
636037 GCTGACTTTCTTAA
1 GCTGTCTTTCTTAA
*
636051 GCTTTCTTTCTTAA
1 GCTGTCTTTCTTAA
*
636065 GCTTTCTTTCTT--
1 GCTGTCTTTCTTAA
* *
636077 TCTTTCTTTCTTAA
1 GCTGTCTTTCTTAA
636091 GC--T-TTTCTTAA
1 GCTGTCTTTCTTAA
636102 ---G-CTTTCTTAA
1 GCTGTCTTTCTTAA
*
636112 GCTGACTTTCTTA
1 GCTGTCTTTCTTA
636125 GCTTTCAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 16
0.76 0.05 0.20
Matches are distributed among these distances:
10 8 0.13
11 8 0.13
12 12 0.19
13 1 0.02
14 33 0.53
ACGTcount: A:0.15, C:0.22, G:0.09, T:0.55
Consensus pattern (14 bp):
GCTGTCTTTCTTAA
Found at i:637887 original size:29 final size:28
Alignment explanation
Indices: 637855--637932 Score: 77
Period size: 29 Copynumber: 2.8 Consensus size: 28
637845 AGTCGATGAC
*
637855 GATGCGATGTTCATGTTGATGACGACGAT
1 GATG-GATGGTCATGTTGATGACGACGAT
* * * *
637884 GATGTTATGGTGATGATGACGACGACGAT
1 GATG-GATGGTCATGTTGATGACGACGAT
*
637913 GAT-GATGGTCATGTCGATGA
1 GATGGATGGTCATGTTGATGA
637933 AGATGATGTA
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
27 12 0.32
29 26 0.68
ACGTcount: A:0.26, C:0.12, G:0.33, T:0.29
Consensus pattern (28 bp):
GATGGATGGTCATGTTGATGACGACGAT
Found at i:637897 original size:23 final size:24
Alignment explanation
Indices: 637860--637905 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
637850 ATGACGATGC
*
637860 GATGTTCATGTTGATGACGACGAT
1 GATGTTCATGGTGATGACGACGAT
*
637884 GATGTT-ATGGTGATGATGACGA
1 GATGTTCATGGTGATGACGACGA
637906 CGACGATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.26, C:0.09, G:0.33, T:0.33
Consensus pattern (24 bp):
GATGTTCATGGTGATGACGACGAT
Found at i:637908 original size:118 final size:119
Alignment explanation
Indices: 637742--637967 Score: 357
Period size: 118 Copynumber: 1.9 Consensus size: 119
637732 AGTGTCATAT
* * *
637742 TGTTGATGTTGAGAAGATGATGATGTTATGGTGATGTCGATGACGACGATGATGATGATGGTCAT
1 TGTTCATGTTGAGAAGACGATGATGTTATGGTGA-GTCGATGACGACGACGATGATGATGGTCAT
* *
637807 GTCGATGATGATGGTGTAGATGATGTCGTTCATGGTGAAGTCGATGACGATGCGA
65 GTCGATGAAGATGATGTAGATGATGTCGTTCATGGTGAAGTCGATGACGATGCGA
*
637862 TGTTCATGTTGATGACGACGATGATGTTATGGTGA-T-GATGACGACGACGATGATGATGGTCAT
1 TGTTCATGTTGA-GAAGACGATGATGTTATGGTGAGTCGATGACGACGACGATGATGATGGTCAT
*
637925 GTCGATGAAGATGATGTAGATGATGTCGTTCATGGTGACGTCG
65 GTCGATGAAGATGATGTAGATGATGTCGTTCATGGTGAAGTCG
637968 GTGATGATTA
Statistics
Matches: 98, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
118 66 0.67
119 1 0.01
120 11 0.11
121 20 0.20
ACGTcount: A:0.25, C:0.10, G:0.34, T:0.31
Consensus pattern (119 bp):
TGTTCATGTTGAGAAGACGATGATGTTATGGTGAGTCGATGACGACGACGATGATGATGGTCATG
TCGATGAAGATGATGTAGATGATGTCGTTCATGGTGAAGTCGATGACGATGCGA
Found at i:643155 original size:23 final size:23
Alignment explanation
Indices: 643128--643189 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
643118 TGGTGAAGTC
* *
643128 GATGACGATG-CGATGTTCATGTT
1 GATGACGACGACGATGTT-ATGGT
*
643151 GATGACGACGATGATGTTATGGT
1 GATGACGACGACGATGTTATGGT
*
643174 GATGACGACGATGATG
1 GATGACGACGACGATG
643190 ATGGTCATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
23 29 0.83
24 6 0.17
ACGTcount: A:0.26, C:0.11, G:0.34, T:0.29
Consensus pattern (23 bp):
GATGACGACGACGATGTTATGGT
Found at i:643207 original size:21 final size:21
Alignment explanation
Indices: 643157--643213 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
643147 TGTTGATGAC
* *
643157 GACGATGATG-TTATGGTGAT
1 GACGATGATGATGATGGTCAT
*
643177 GACGACGATGATGATGGTCAT
1 GACGATGATGATGATGGTCAT
*
643198 GTCGATGATGATGATG
1 GACGATGATGATGATG
643214 TAGATGATGT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 9 0.29
21 22 0.71
ACGTcount: A:0.26, C:0.09, G:0.35, T:0.30
Consensus pattern (21 bp):
GACGATGATGATGATGGTCAT
Found at i:653097 original size:2 final size:2
Alignment explanation
Indices: 653090--653115 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
653080 TAATCGATAA
653090 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
653116 GGGAAATAGG
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:661026 original size:4 final size:4
Alignment explanation
Indices: 661017--661070 Score: 72
Period size: 4 Copynumber: 13.5 Consensus size: 4
661007 TATTTTATTC
* * * *
661017 CTGT CTGT CTGT CTTT CTGT CTGT CTGT CTGT ATGT CTGT CTCT CTCT
1 CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT
661065 CTGT CT
1 CTGT CT
661071 CTCTCTCTCT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.02, C:0.28, G:0.19, T:0.52
Consensus pattern (4 bp):
CTGT
Found at i:661063 original size:2 final size:2
Alignment explanation
Indices: 661056--661120 Score: 103
Period size: 2 Copynumber: 32.5 Consensus size: 2
661046 TGTATGTCTG
* * *
661056 TC TC TC TC TC TG TC TC TC TC TC TC TC TC TG TC TC TG 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
661098 TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC T
661121 ATTTCTGCAT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.45, G:0.05, T:0.51
Consensus pattern (2 bp):
TC
Found at i:661071 original size:8 final size:8
Alignment explanation
Indices: 661017--661120 Score: 91
Period size: 8 Copynumber: 13.0 Consensus size: 8
661007 TATTTTATTC
*
661017 CTGTCTGT
1 CTGTCTCT
*
661025 CTGTCTTT
1 CTGTCTCT
*
661033 CTGTCTGT
1 CTGTCTCT
*
661041 CTGTCTGT
1 CTGTCTCT
* *
661049 ATGTCTGT
1 CTGTCTCT
*
661057 CTCTCTCT
1 CTGTCTCT
661065 CTGTCTCT
1 CTGTCTCT
*
661073 CTCTCTCT
1 CTGTCTCT
* *
661081 CTCTGTCT
1 CTGTCTCT
661089 CTGTCTCT
1 CTGTCTCT
*
661097 CTCTCTCT
1 CTGTCTCT
*
661105 CTCTCTCT
1 CTGTCTCT
*
661113 CTCTCTCT
1 CTGTCTCT
661121 ATTTCTGCAT
Statistics
Matches: 84, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 84 1.00
ACGTcount: A:0.01, C:0.37, G:0.12, T:0.51
Consensus pattern (8 bp):
CTGTCTCT
Found at i:674495 original size:10 final size:10
Alignment explanation
Indices: 674479--674591 Score: 52
Period size: 10 Copynumber: 10.9 Consensus size: 10
674469 CCGTATGAAA
674479 ATCCCCTGTC
1 ATCCCCTGTC
*
674489 TTCCCCTGTC
1 ATCCCCTGTC
*
674499 ATCCCCTGTGT
1 ATCCCCTGT-C
* * *
674510 TTTCACTGTC
1 ATCCCCTGTC
*
674520 ATCCCCTATAC
1 ATCCCCTGT-C
674531 ATCCCCTGT-
1 ATCCCCTGTC
* *
674540 GTGCCACTGTAC
1 AT-CCCCTGT-C
*
674552 AGAGCCCCTGT-
1 --ATCCCCTGTC
*
674563 ATACCCTGTC
1 ATCCCCTGTC
674573 ATCCCCTGTGC
1 ATCCCCTGT-C
674584 A-CCCCTGT
1 ATCCCCTGT
674592 ACACAACCCC
Statistics
Matches: 74, Mismatches: 20, Indels: 18
0.66 0.18 0.16
Matches are distributed among these distances:
9 8 0.11
10 43 0.58
11 17 0.23
13 6 0.08
ACGTcount: A:0.13, C:0.42, G:0.14, T:0.31
Consensus pattern (10 bp):
ATCCCCTGTC
Found at i:674504 original size:20 final size:21
Alignment explanation
Indices: 674479--674526 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
674469 CCGTATGAAA
*
674479 ATCCCCTGT-CTTCCCCTGTC
1 ATCCCCTGTGCTTCCACTGTC
* *
674499 ATCCCCTGTGTTTTCACTGTC
1 ATCCCCTGTGCTTCCACTGTC
674520 ATCCCCT
1 ATCCCCT
674527 ATACATCCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.08, C:0.44, G:0.10, T:0.38
Consensus pattern (21 bp):
ATCCCCTGTGCTTCCACTGTC
Found at i:674635 original size:20 final size:20
Alignment explanation
Indices: 674612--674658 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
674602 TGTGTGCCAT
674612 TGTAAGCCCCTGTCACCCCC
1 TGTAAGCCCCTGTCACCCCC
* * *
674632 TGTACGCCCTTGTCATCCCC
1 TGTAAGCCCCTGTCACCCCC
674652 TGTAAGC
1 TGTAAGC
674659 AACTGTCTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.43, G:0.17, T:0.26
Consensus pattern (20 bp):
TGTAAGCCCCTGTCACCCCC
Found at i:675222 original size:2 final size:2
Alignment explanation
Indices: 675217--675267 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
675207 TATAAATCAT
675217 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
675259 GA GA GA GA G
1 GA GA GA GA G
675268 TTGATTTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:676307 original size:2 final size:2
Alignment explanation
Indices: 676300--676345 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
676290 ATCAATTCAA
676300 TC TC TC TC TC TC 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
676342 TC TC
1 TC TC
676346 ATGACTAATC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:677361 original size:20 final size:20
Alignment explanation
Indices: 677336--677401 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
677326 AGGGGCATGC
* *
677336 ACAGGGGTATACAGTGGCTT
1 ACAGGGGTAAACAGGGGCTT
* *
677356 ACAGGGGAAAACAGGGGCGT
1 ACAGGGGTAAACAGGGGCTT
*
677376 ACAGGGGGT-GACAGGGGCTT
1 ACA-GGGGTAAACAGGGGCTT
677396 ACAGGG
1 ACAGGG
677402 ACACACAGGG
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
19 3 0.08
20 31 0.82
21 4 0.11
ACGTcount: A:0.27, C:0.15, G:0.44, T:0.14
Consensus pattern (20 bp):
ACAGGGGTAAACAGGGGCTT
Found at i:677409 original size:20 final size:19
Alignment explanation
Indices: 677346--677412 Score: 53
Period size: 20 Copynumber: 3.4 Consensus size: 19
677336 ACAGGGGTAT
*
677346 ACAGTGGCTTACAGGGGAAA
1 ACAGGGGCTTACA-GGGAAA
* ***
677366 ACAGGGGCGTACAGGGGGTG
1 ACAGGGGCTTACA-GGGAAA
*
677386 ACAGGGGCTTACAGGGACAC
1 ACAGGGGCTTACAGGGA-AA
677406 ACAGGGG
1 ACAGGGG
677413 GATGTGTACA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
19 3 0.08
20 34 0.92
ACGTcount: A:0.28, C:0.18, G:0.43, T:0.10
Consensus pattern (19 bp):
ACAGGGGCTTACAGGGAAA
Found at i:677488 original size:11 final size:10
Alignment explanation
Indices: 677472--677532 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
677462 ACAGTGGCAC
677472 ACAGGGGATG
1 ACAGGGGATG
677482 TACAGGGGATG
1 -ACAGGGGATG
** **
677493 ACAGTGAAAAC
1 ACAG-GGGATG
*
677504 ACAGGGGGTG
1 ACAGGGGATG
*
677514 ACAGGGGAAG
1 ACAGGGGATG
677524 ACAGGGGAT
1 ACAGGGGAT
677533 TTTCATACGG
Statistics
Matches: 37, Mismatches: 12, Indels: 3
0.71 0.23 0.06
Matches are distributed among these distances:
10 21 0.57
11 16 0.43
ACGTcount: A:0.34, C:0.11, G:0.44, T:0.10
Consensus pattern (10 bp):
ACAGGGGATG
Found at i:681019 original size:7 final size:7
Alignment explanation
Indices: 681007--681073 Score: 89
Period size: 7 Copynumber: 9.6 Consensus size: 7
680997 GAGAAGGATC
681007 ATTCGAG
1 ATTCGAG
681014 ATTCGAG
1 ATTCGAG
*
681021 ATTCGAA
1 ATTCGAG
*
681028 ATACGAG
1 ATTCGAG
*
681035 ATTCGAA
1 ATTCGAG
*
681042 ATACGAG
1 ATTCGAG
681049 ATTCGAG
1 ATTCGAG
*
681056 ATTCGAA
1 ATTCGAG
681063 ATTCGAG
1 ATTCGAG
681070 ATTC
1 ATTC
681074 AATATCTAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (7 bp):
ATTCGAG
Found at i:681575 original size:2 final size:2
Alignment explanation
Indices: 681568--681599 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
681558 TTGTCGATAT
681568 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
681600 NNNNNNNNNN
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:689535 original size:14 final size:12
Alignment explanation
Indices: 689507--689548 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
689497 TACTGAATAA
* *
689507 TCTCTCTCTCCC
1 TCTCTCTGTCTC
*
689519 TCTCTTTGTCTC
1 TCTCTCTGTCTC
689531 TCTCTCTGTCTC
1 TCTCTCTGTCTC
689543 TCTCTC
1 TCTCTC
689549 ACACACACAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.00, C:0.45, G:0.05, T:0.50
Consensus pattern (12 bp):
TCTCTCTGTCTC
Found at i:699670 original size:2 final size:2
Alignment explanation
Indices: 699663--699707 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
699653 CAAATGTACT
699663 TC TC TC TC TC TC 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
699705 TC T
1 TC T
699708 GTGCATGTTT
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:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:700421 original size:46 final size:46
Alignment explanation
Indices: 700336--700428 Score: 123
Period size: 46 Copynumber: 2.0 Consensus size: 46
700326 TTTTTCGTAT
* * * * *
700336 TTCCCTTTAAATATTACATATTTTTTCTGACACATTTGTAGCTTGA
1 TTCCCTTTAAATACTACATATTCTTCCCGACACAATTGTAGCTTGA
* *
700382 TTCCTTTTAAATACTACATATTCTTCCCGATACAATTGTAGCTTGA
1 TTCCCTTTAAATACTACATATTCTTCCCGACACAATTGTAGCTTGA
700428 T
1 T
700429 CATATAACTT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.27, C:0.19, G:0.09, T:0.45
Consensus pattern (46 bp):
TTCCCTTTAAATACTACATATTCTTCCCGACACAATTGTAGCTTGA
Found at i:700666 original size:2 final size:2
Alignment explanation
Indices: 700653--700773 Score: 80
Period size: 2 Copynumber: 60.5 Consensus size: 2
700643 AGATTAAGAT
* * *
700653 TC TC TG TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TG
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * * * * * * * *
700695 TG TG TG TG TC TC TC TC TC TA TC TC TC TT TC TG TG TG TG TG TG
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * *
700737 TG TG TG TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
700774 GAAATATTTA
Statistics
Matches: 108, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 108 1.00
ACGTcount: A:0.01, C:0.35, G:0.12, T:0.52
Consensus pattern (2 bp):
TC
Found at i:705979 original size:16 final size:16
Alignment explanation
Indices: 705958--705992 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
705948 TTGCTAAAAA
705958 TACTAGTTTCACAAAT
1 TACTAGTTTCACAAAT
705974 TACTAGTTTCACAAAT
1 TACTAGTTTCACAAAT
705990 TAC
1 TAC
705993 CGGGTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (16 bp):
TACTAGTTTCACAAAT
Found at i:706515 original size:12 final size:12
Alignment explanation
Indices: 706498--706522 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
706488 ATATTTTCCA
706498 TTCCGTTCCGCT
1 TTCCGTTCCGCT
706510 TTCCGTTCCGCT
1 TTCCGTTCCGCT
706522 T
1 T
706523 ATTATCGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.40, G:0.16, T:0.44
Consensus pattern (12 bp):
TTCCGTTCCGCT
Found at i:708894 original size:140 final size:135
Alignment explanation
Indices: 708606--708909 Score: 348
Period size: 134 Copynumber: 2.2 Consensus size: 135
708596 TATAATCATG
* * * * *
708606 ACCCCTAAACCATATATATTCATGTTTC-TGATGTCAAGGGGCATCAAATGTTATGTAGGTCATG
1 ACCCCTTAACCATATATATTCTTGTTCCTTGATGTCAAGGGGCATCAAACGGTATGTAGGTCATG
* * * * *
708670 CGCCCTGTGGGTGGTCCTGACCCCCTCAAACAGCAAGTCCCTTAATATCTTCAAAACAGTTGAGA
66 CGCCCCGGGGGTGGTCATGACCCCCTCAAACAGCAAGTCACTGAATATCTTCAAAACAGTTGAGA
708735 TCCCC
131 TCCCC
708740 A-CCCTTAAACCATATATATTCTTGTTCCTTG-TGTCAAGGGGCATCAAACGGTATGTAGGTCAT
1 ACCCCTT-AACCATATATATTCTTGTTCCTTGATGTCAAGGGGCATCAAACGGTATGTAGGTCAT
* ** *
708803 GGGCCCCGGGGGTGGTCATGACCCCCCCCCCCTTGAACAGGAAGTGCAC-GAATATC-TCGAAAA
65 GCGCCCCGGGGGTGGTCATGA------CCCCCTCAAACAGCAAGT-CACTGAATATCTTC-AAAA
*
708866 CGGTTGAGATCCCC
122 CAGTTGAGATCCCC
*
708880 ACCCCTTAACCATATATATTCTTGATCCTT
1 ACCCCTTAACCATATATATTCTTGTTCCTT
708910 AAAGGGCATC
Statistics
Matches: 143, Mismatches: 16, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
133 4 0.03
134 67 0.47
135 2 0.01
139 2 0.01
140 61 0.43
141 7 0.05
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.27
Consensus pattern (135 bp):
ACCCCTTAACCATATATATTCTTGTTCCTTGATGTCAAGGGGCATCAAACGGTATGTAGGTCATG
CGCCCCGGGGGTGGTCATGACCCCCTCAAACAGCAAGTCACTGAATATCTTCAAAACAGTTGAGA
TCCCC
Found at i:709283 original size:163 final size:162
Alignment explanation
Indices: 708966--709348 Score: 493
Period size: 163 Copynumber: 2.4 Consensus size: 162
708956 TAAATTTAAT
* * * *
708966 TTTTCAAAACCGTAATGCACATCTATGGAACAGTTCCTATCATATCCCAATATATGA-TGCGTCT
1 TTTTCAAAACCTTAATGCACATCTATAGAACAGTCCCTATCATATCCCAAGATATGACT-CGTCT
* * * *
709030 TTCCATTAAATCATAAAAGGAGTTCTAGGATCTATGTTTTTTTGAAGTGATAAACGTCAATTTTC
65 GTCCATTAAATCATAAAAGGAGCTCTAGGATCAATGTTTTTTTGAAGTAATAAACGTCAATTTTC
709095 TGCTACTTTTTGACTCCCTGGATGAAATTAAAA
130 TGCTACTTTTTGACTCCCTGGATGAAATTAAAA
* *
709128 TTTTGAAAACCTTACTGCACATCTATAGAACAGTCCCTATCATATCCCAAGATATGACT-GTCTG
1 TTTTCAAAACCTTAATGCACATCTATAGAACAGTCCCTATCATATCCCAAGATATGACTCGTCTG
* * **
709192 TCCATTAAATCATAAGAGGAGCTCTTGGATCAATGTTTGTCTTTTTAGTAATAAACGTCAATTTT
66 TCCATTAAATCATAAAAGGAGCTCTAGGATCAATGTTT-T-TTTGAAGTAATAAACGTCAATTTT
* * *
709257 CTGCTA-TTATTTGAGTCCCTGGATGAAATTTACA
129 CTGCTACTT-TTTGACTCCCTGGATGAAATTAAAA
* * * * * * *
709291 TTTTTAAAACCTTATTGCACATCTATAGGACAGCCCCAATTATATCCCAAGAGATGAC
1 TTTTCAAAACCTTAATGCACATCTATAGAACAGTCCCTATCATATCCCAAGATATGAC
709349 ATAGCTACTC
Statistics
Matches: 193, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
161 38 0.20
162 54 0.28
163 101 0.52
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.35
Consensus pattern (162 bp):
TTTTCAAAACCTTAATGCACATCTATAGAACAGTCCCTATCATATCCCAAGATATGACTCGTCTG
TCCATTAAATCATAAAAGGAGCTCTAGGATCAATGTTTTTTTGAAGTAATAAACGTCAATTTTCT
GCTACTTTTTGACTCCCTGGATGAAATTAAAA
Found at i:718385 original size:32 final size:32
Alignment explanation
Indices: 718337--718407 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
718327 CAAATTAATA
*
718337 GTACAGTG-CC-GTACAGTGGGGTACAGTGATG
1 GTACAGTGCCCGGTACAGTGGCGTACAGTGA-G
718368 GT-CAGTGCCCGGTACAGTGGCGTACAGTGAG
1 GTACAGTGCCCGGTACAGTGGCGTACAGTGAG
718399 GTACAGTGC
1 GTACAGTGC
718408 TGGTCAGTGC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
30 5 0.14
31 7 0.19
32 24 0.67
ACGTcount: A:0.21, C:0.20, G:0.38, T:0.21
Consensus pattern (32 bp):
GTACAGTGCCCGGTACAGTGGCGTACAGTGAG
Found at i:718396 original size:42 final size:43
Alignment explanation
Indices: 718337--718534 Score: 231
Period size: 42 Copynumber: 4.7 Consensus size: 43
718327 CAAATTAATA
* * *
718337 GTACAGTGCCGTACAGTGGGGTACAGTGATGGTCAGT-GCCCG
1 GTACAGTGGCGTACAGTGGGGTACAGTGATGGTCAGTAGCACT
* * *
718379 GTACAGTGGCGTACAGTGAGGTACAGTGCTGGTCAGT-GCCCT
1 GTACAGTGGCGTACAGTGGGGTACAGTGATGGTCAGTAGCACT
* *
718421 GTACAGTGGCGTACAGTGGGGTACAGTGGA-AGTCAGTAGGACT
1 GTACAGTGGCGTACAGTGGGGTACAGT-GATGGTCAGTAGCACT
* * * * * *
718464 GTACAGTGGTGTACAGTGGGATACAGTGCTGTTCAGTAGAAAT
1 GTACAGTGGCGTACAGTGGGGTACAGTGATGGTCAGTAGCACT
*
718507 GTACAGTGGGGTACAGTGGGGTACAGTG
1 GTACAGTGGCGTACAGTGGGGTACAGTG
718535 GAAGTCAGTG
Statistics
Matches: 135, Mismatches: 18, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
42 71 0.53
43 64 0.47
ACGTcount: A:0.23, C:0.16, G:0.38, T:0.23
Consensus pattern (43 bp):
GTACAGTGGCGTACAGTGGGGTACAGTGATGGTCAGTAGCACT
Found at i:718449 original size:10 final size:10
Alignment explanation
Indices: 718337--718535 Score: 89
Period size: 10 Copynumber: 18.9 Consensus size: 10
718327 CAAATTAATA
**
718337 GTACAGTGCC
1 GTACAGTGGG
718347 GTACAGTGGG
1 GTACAGTGGG
*
718357 GTACAGTGATG
1 GTACAGTG-GG
*
718368 GT-CAGTGCCCG
1 GTACAGTG--GG
*
718379 GTACAGTGGC
1 GTACAGTGGG
*
718389 GTACAGTGAG
1 GTACAGTGGG
*
718399 GTACAGTGCTG
1 GTACAGTG-GG
**
718410 GT-CAGTGCCCT
1 GTACAGTG--GG
*
718421 GTACAGTGGC
1 GTACAGTGGG
718431 GTACAGTGGG
1 GTACAGTGGG
*
718441 GTACAGTGGAA
1 GTACAGTGG-G
*
718452 GT-CAGTAGGACT
1 GTACAGT-GG--G
*
718464 GTACAGTGGT
1 GTACAGTGGG
718474 GTACAGTGGG
1 GTACAGTGGG
* **
718484 ATACAGTGCT
1 GTACAGTGGG
* **
718494 GTTCAGTAGAAAT
1 GTACAGT-G--GG
718507 GTACAGTGGG
1 GTACAGTGGG
718517 GTACAGTGGG
1 GTACAGTGGG
718527 GTACAGTGG
1 GTACAGTGG
718536 AAGTCAGTGA
Statistics
Matches: 148, Mismatches: 28, Indels: 26
0.73 0.14 0.13
Matches are distributed among these distances:
10 105 0.71
11 17 0.11
12 15 0.10
13 11 0.07
ACGTcount: A:0.23, C:0.16, G:0.38, T:0.23
Consensus pattern (10 bp):
GTACAGTGGG
Found at i:718566 original size:33 final size:31
Alignment explanation
Indices: 718527--718590 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 31
718517 GTACAGTGGG
718527 GTACAGTGGAAGTCAGTGA-AATGTACAGTCAAT
1 GTACAGTGGAAGTCA--GACAATGT-CAGTCAAT
*
718560 GTACAGTGGATGTCAGACAATGTCAGTCAAT
1 GTACAGTGGAAGTCAGACAATGTCAGTCAAT
718591 ATTTGGGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 10 0.34
32 5 0.17
33 14 0.48
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.25
Consensus pattern (31 bp):
GTACAGTGGAAGTCAGACAATGTCAGTCAAT
Done.