Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold962
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: 1469792
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.31
Warning! 91164 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:371418 original size:2 final size:2
Alignment explanation
Indices: 371411--371472 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
371401 TAGAATTGAT
371411 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
371453 GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA
371473 TATGAAAGGG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:372570 original size:2 final size:2
Alignment explanation
Indices: 372563--372608 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
372553 TGAGTCTCAT
372563 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
372605 GA GA
1 GA GA
372609 TTTCACAAAA
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:390005 original size:17 final size:17
Alignment explanation
Indices: 389983--390016 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
389973 ACTTGGTGTG
389983 GATTGACTTCACCAGTT
1 GATTGACTTCACCAGTT
390000 GATTGACTTCACCAGTT
1 GATTGACTTCACCAGTT
390017 CACCTTGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.35
Consensus pattern (17 bp):
GATTGACTTCACCAGTT
Found at i:393867 original size:39 final size:40
Alignment explanation
Indices: 393796--393888 Score: 125
Period size: 39 Copynumber: 2.4 Consensus size: 40
393786 TACGGATCAA
* * *
393796 AAACTATAGTTTACGACGTTAATCTATATTTCACGTCTGT
1 AAACTATAGTTAACGACGATAATCTATATTTCACATCTGT
* *
393836 AAACTATAGTTAACG-CGATAATCTATGTTTCACATTTGT
1 AAACTATAGTTAACGACGATAATCTATATTTCACATCTGT
*
393875 TAACTATAGTTAAC
1 AAACTATAGTTAAC
393889 ACTGAAAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 33 0.70
40 14 0.30
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (40 bp):
AAACTATAGTTAACGACGATAATCTATATTTCACATCTGT
Found at i:394596 original size:20 final size:20
Alignment explanation
Indices: 394556--394647 Score: 66
Period size: 20 Copynumber: 4.6 Consensus size: 20
394546 TTTATACTTA
394556 TAAACTAT-GTTTAAC-AGACG
1 TAAACTATAGTTT-ACGA-ACG
394576 TAAACTATAGTTTACGAACG
1 TAAACTATAGTTTACGAACG
* * *
394596 TGAATTATAGTTTA-GGACG
1 TAAACTATAGTTTACGAACG
* *
394615 ATAAACTAT-GATTAACAAACG
1 -TAAACTATAG-TTTACGAACG
*
394636 TAAATTATAGTT
1 TAAACTATAGTT
394648 ATCTCTCAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
19 5 0.09
20 43 0.75
21 9 0.16
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (20 bp):
TAAACTATAGTTTACGAACG
Found at i:394620 original size:40 final size:39
Alignment explanation
Indices: 394572--394647 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 39
394562 ATGTTTAACA
* * *
394572 GACGTAAACTAT-AGTTTACGAACGTGAATTATAGTTTAG
1 GACGTAAACTATGA-TTAACAAACGTAAATTATAGTTTAG
394611 GACGATAAACTATGATTAACAAACGTAAATTATAGTT
1 GACG-TAAACTATGATTAACAAACGTAAATTATAGTT
394648 ATCTCTCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
39 4 0.12
40 27 0.84
41 1 0.03
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.32
Consensus pattern (39 bp):
GACGTAAACTATGATTAACAAACGTAAATTATAGTTTAG
Found at i:398599 original size:19 final size:19
Alignment explanation
Indices: 398552--398593 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
398542 ATCAAAGGGC
398552 ACCTGCTCCAAAAACTTTA
1 ACCTGCTCCAAAAACTTTA
398571 ACCTGCTCCAAAAACTTTA
1 ACCTGCTCCAAAAACTTTA
398590 ACCT
1 ACCT
398594 CTTCCAGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.33, G:0.05, T:0.26
Consensus pattern (19 bp):
ACCTGCTCCAAAAACTTTA
Found at i:405167 original size:13 final size:13
Alignment explanation
Indices: 405148--405181 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
405138 TGCATATTTA
*
405148 CAAATGTTTTATT
1 CAAATGTTTTAAT
*
405161 GAAATGTTTTAAT
1 CAAATGTTTTAAT
405174 CAAATGTT
1 CAAATGTT
405182 GTTTCCTTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (13 bp):
CAAATGTTTTAAT
Found at i:411984 original size:30 final size:31
Alignment explanation
Indices: 411937--412000 Score: 121
Period size: 30 Copynumber: 2.1 Consensus size: 31
411927 ATGTAATAAT
411937 AATCAATTATGAAAAACCTGTTTATACATGG
1 AATCAATTATGAAAAACCTGTTTATACATGG
411968 AATCAATTAT-AAAAACCTGTTTATACATGG
1 AATCAATTATGAAAAACCTGTTTATACATGG
411998 AAT
1 AAT
412001 TAAAATTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 23 0.70
31 10 0.30
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (31 bp):
AATCAATTATGAAAAACCTGTTTATACATGG
Found at i:417965 original size:19 final size:19
Alignment explanation
Indices: 417921--417959 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
417911 CAAGAGCACT
*
417921 TGCTCCAAAAACTTTAACC
1 TGCTCCAAAAACCTTAACC
417940 TGCTCCAAAAACCTTAACC
1 TGCTCCAAAAACCTTAACC
417959 T
1 T
417960 CTTCCAGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.36, C:0.33, G:0.05, T:0.26
Consensus pattern (19 bp):
TGCTCCAAAAACCTTAACC
Found at i:418209 original size:14 final size:14
Alignment explanation
Indices: 418182--418220 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
418172 TAAAATTGTT
* *
418182 AACGCATGAAGCAC
1 AACGCACGACGCAC
*
418196 ACCGCACGACGCAC
1 AACGCACGACGCAC
418210 AACGCACGACG
1 AACGCACGACG
418221 ACGGATGAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.38, G:0.23, T:0.03
Consensus pattern (14 bp):
AACGCACGACGCAC
Found at i:419172 original size:23 final size:23
Alignment explanation
Indices: 419136--419187 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
419126 TGTAAATTAA
* * * *
419136 AAAATAACATAGTTTGTTTATAT
1 AAAATAAAACAGTTAGTTTAAAT
419159 AAAATAAAACAGTTAGTTTAAAT
1 AAAATAAAACAGTTAGTTTAAAT
*
419182 GAAATA
1 AAAATA
419188 CTGGATTTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.52, C:0.04, G:0.10, T:0.35
Consensus pattern (23 bp):
AAAATAAAACAGTTAGTTTAAAT
Found at i:424065 original size:17 final size:18
Alignment explanation
Indices: 424038--424073 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
424028 GCGTTGTTAC
424038 AATTAACGCACTTTGAAA
1 AATTAACGCACTTTGAAA
424056 AATT-ACGCACTTTGAAA
1 AATTAACGCACTTTGAAA
424073 A
1 A
424074 CAATTTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (18 bp):
AATTAACGCACTTTGAAA
Found at i:424991 original size:7 final size:7
Alignment explanation
Indices: 424979--425045 Score: 73
Period size: 7 Copynumber: 9.6 Consensus size: 7
424969 GAGAAGGATC
424979 ATTCGAG
1 ATTCGAG
424986 ATTCGAG
1 ATTCGAG
* *
424993 ATTCAAA
1 ATTCGAG
*
425000 ATACGAG
1 ATTCGAG
*
425007 ATTCGAA
1 ATTCGAG
*
425014 ATACGAG
1 ATTCGAG
425021 ATTCGAG
1 ATTCGAG
425028 ATTCGA-
1 ATTCGAG
425034 ATTTCGAG
1 A-TTCGAG
425042 ATTC
1 ATTC
425046 AATATCTAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
6 1 0.02
7 46 0.96
8 1 0.02
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (7 bp):
ATTCGAG
Found at i:426138 original size:7 final size:7
Alignment explanation
Indices: 426123--426189 Score: 80
Period size: 7 Copynumber: 9.6 Consensus size: 7
426113 ATTAGATATT
426123 GAATCTC
1 GAATCTC
*
426130 GAATTTC
1 GAATCTC
426137 GAATCTC
1 GAATCTC
426144 GAATCTC
1 GAATCTC
* *
426151 GTATTTC
1 GAATCTC
426158 GAATCTC
1 GAATCTC
* * *
426165 GTATTTT
1 GAATCTC
426172 GAATCTC
1 GAATCTC
426179 GAATCTC
1 GAATCTC
426186 GAAT
1 GAAT
426190 GATCCTTCTC
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 48 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (7 bp):
GAATCTC
Found at i:426148 original size:21 final size:21
Alignment explanation
Indices: 426123--426189 Score: 89
Period size: 21 Copynumber: 3.2 Consensus size: 21
426113 ATTAGATATT
426123 GAATCTCGAATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
*
426144 GAATCTCGTATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
* * * *
426165 GTATTTTGAATCTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
426186 GAAT
1 GAAT
426190 GATCCTTCTC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (21 bp):
GAATCTCGAATTTCGAATCTC
Found at i:432418 original size:13 final size:13
Alignment explanation
Indices: 432400--432424 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
432390 TTCATGCTTA
432400 ATTTTGTTTTTAC
1 ATTTTGTTTTTAC
432413 ATTTTGTTTTTA
1 ATTTTGTTTTTA
432425 TGCATCGTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.04, G:0.08, T:0.72
Consensus pattern (13 bp):
ATTTTGTTTTTAC
Found at i:432636 original size:12 final size:12
Alignment explanation
Indices: 432619--432644 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
432609 CATGTGATAT
432619 CTGATTGTAGAC
1 CTGATTGTAGAC
432631 CTGATTGTAGAC
1 CTGATTGTAGAC
432643 CT
1 CT
432645 TAATAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (12 bp):
CTGATTGTAGAC
Found at i:441834 original size:26 final size:26
Alignment explanation
Indices: 441798--441900 Score: 152
Period size: 26 Copynumber: 4.0 Consensus size: 26
441788 TCACATTTAC
* ** *
441798 AAGTCAATGTTAGTATATATTCACAG
1 AAGTTAATGTTAAAATATATTCACTG
*
441824 AAGTTAATGTTAAAATATATTGACTG
1 AAGTTAATGTTAAAATATATTCACTG
*
441850 AAGTTAATGTTAAAATATATTTACTG
1 AAGTTAATGTTAAAATATATTCACTG
441876 AAGTTAATGTTAAAATATATTCACT
1 AAGTTAATGTTAAAATATATTCACT
441901 AAATTACTGA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 70 1.00
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.39
Consensus pattern (26 bp):
AAGTTAATGTTAAAATATATTCACTG
Found at i:445081 original size:32 final size:32
Alignment explanation
Indices: 445045--445110 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
445035 TGTATATGCC
*
445045 AACAAAAATACGTTCTTTTATCCTTGTCAATA
1 AACAAAAATACGTTCTTTTAGCCTTGTCAATA
445077 AACAAAAATACGTTCTTTTAGCCTTGTCAATA
1 AACAAAAATACGTTCTTTTAGCCTTGTCAATA
445109 AA
1 AA
445111 AATTTGTTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (32 bp):
AACAAAAATACGTTCTTTTAGCCTTGTCAATA
Found at i:452476 original size:15 final size:15
Alignment explanation
Indices: 452458--452492 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
452448 CGACGATGAA
452458 GATGACGAGGAAAGC
1 GATGACGAGGAAAGC
**
452473 GATGACGTTGAAAGC
1 GATGACGAGGAAAGC
452488 GATGA
1 GATGA
452493 TGACAAAAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.37, T:0.14
Consensus pattern (15 bp):
GATGACGAGGAAAGC
Found at i:454263 original size:2 final size:2
Alignment explanation
Indices: 454256--454294 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
454246 NNNNNNNNNN
454256 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
454295 GTTTGACAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:456277 original size:30 final size:30
Alignment explanation
Indices: 456241--456374 Score: 153
Period size: 30 Copynumber: 4.5 Consensus size: 30
456231 GTTTCAAAGT
*
456241 GATCTATTGAACTGCCGGTCAATAGACTGC
1 GATCTATTGAACCGCCGGTCAATAGACTGC
* * *
456271 GATCTATT-AGATCGCCGGTGAATAGACTGT
1 GATCTATTGA-ACCGCCGGTCAATAGACTGC
* * *
456301 GATCTATTGGACCGCCGGTCAATAGGCTGT
1 GATCTATTGAACCGCCGGTCAATAGACTGC
* *
456331 GATCTATTGGACCGCCGGTCAATATACTGC
1 GATCTATTGAACCGCCGGTCAATAGACTGC
* *
456361 GATTTATTGGACCG
1 GATCTATTGAACCG
456375 GCAACGCATT
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
29 1 0.01
30 89 0.99
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (30 bp):
GATCTATTGAACCGCCGGTCAATAGACTGC
Found at i:456318 original size:60 final size:60
Alignment explanation
Indices: 456239--456374 Score: 182
Period size: 60 Copynumber: 2.3 Consensus size: 60
456229 AGGTTTCAAA
* * * *
456239 GTGATCTATTGAACTGCCGGTCAATAGACTGCGATCTATTAGATCGCCGGTGAATAGACT
1 GTGATCTATTGGACCGCCGGTCAATAGACTGCGATCTATTAGACCGCCGGTCAATAGACT
* * * *
456299 GTGATCTATTGGACCGCCGGTCAATAGGCTGTGATCTATTGGACCGCCGGTCAATATACT
1 GTGATCTATTGGACCGCCGGTCAATAGACTGCGATCTATTAGACCGCCGGTCAATAGACT
* *
456359 GCGATTTATTGGACCG
1 GTGATCTATTGGACCG
456375 GCAACGCATT
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 66 1.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (60 bp):
GTGATCTATTGGACCGCCGGTCAATAGACTGCGATCTATTAGACCGCCGGTCAATAGACT
Found at i:458516 original size:15 final size:15
Alignment explanation
Indices: 458496--458588 Score: 82
Period size: 15 Copynumber: 5.8 Consensus size: 15
458486 CAAAAAAGTT
458496 ACAGGTAAACAACTG
1 ACAGGTAAACAACTG
*
458511 ACAGGTAAACACAATAG
1 ACAGGTAAACA-ACT-G
458528 TTACA-GTAAACAACTG
1 --ACAGGTAAACAACTG
*
458544 ACAGGTAAACACAATAG
1 ACAGGTAAACA-ACT-G
458561 TAACA-GTAAACAACTG
1 --ACAGGTAAACAACTG
458577 ACAGGTAAACAA
1 ACAGGTAAACAA
458589 AATAGTTACA
Statistics
Matches: 64, Mismatches: 4, Indels: 20
0.73 0.05 0.23
Matches are distributed among these distances:
14 6 0.09
15 26 0.41
16 6 0.09
17 6 0.09
18 14 0.22
19 6 0.09
ACGTcount: A:0.51, C:0.18, G:0.16, T:0.15
Consensus pattern (15 bp):
ACAGGTAAACAACTG
Found at i:458538 original size:18 final size:17
Alignment explanation
Indices: 458515--458572 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
458505 CAACTGACAG
458515 GTAAACACAATAGTTACA
1 GTAAACACAATAG-TACA
*
458533 GTAAACA-ACT-G-ACA
1 GTAAACACAATAGTACA
458547 GGTAAACACAATAGTAACA
1 -GTAAACACAATAGT-ACA
458566 GTAAACA
1 GTAAACA
458573 ACTGACAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 3 0.09
15 7 0.21
16 3 0.09
17 3 0.09
18 14 0.42
19 3 0.09
ACGTcount: A:0.52, C:0.17, G:0.14, T:0.17
Consensus pattern (17 bp):
GTAAACACAATAGTACA
Found at i:458623 original size:33 final size:33
Alignment explanation
Indices: 458477--458604 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
458467 AAGCCGACTT
*
458477 ACAGGTAAACAAAAAAGTTACAGGTAAACAACTG
1 ACAGGTAAACAAAATAGTTACA-GTAAACAACTG
*
458511 ACAGGTAAACACAATAGTTACAGTAAACAACTG
1 ACAGGTAAACAAAATAGTTACAGTAAACAACTG
* *
458544 ACAGGTAAACACAATAGTAACAGTAAACAACTG
1 ACAGGTAAACAAAATAGTTACAGTAAACAACTG
*
458577 ACAGGTAAACAAAATAGTTACAGCAAAC
1 ACAGGTAAACAAAATAGTTACAGTAAAC
458605 CAACGTACAG
Statistics
Matches: 88, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
33 68 0.77
34 20 0.23
ACGTcount: A:0.52, C:0.17, G:0.16, T:0.16
Consensus pattern (33 bp):
ACAGGTAAACAAAATAGTTACAGTAAACAACTG
Found at i:464219 original size:14 final size:14
Alignment explanation
Indices: 464200--464226 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
464190 AATTTTACTA
464200 AATCTCTCTCTCTT
1 AATCTCTCTCTCTT
464214 AATCTCTCTCTCT
1 AATCTCTCTCTCT
464227 CTCTCTCTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.37, G:0.00, T:0.48
Consensus pattern (14 bp):
AATCTCTCTCTCTT
Found at i:472593 original size:7 final size:7
Alignment explanation
Indices: 472579--472616 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
472569 CTTCGTCCGT
472579 CGTCGTG
1 CGTCGTG
*
472586 CGTTGTG
1 CGTCGTG
472593 CGTCGTG
1 CGTCGTG
472600 CGTCGTG
1 CGTCGTG
472607 CGTCGTG
1 CGTCGTG
472614 CGT
1 CGT
472617 TAACAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.00, C:0.26, G:0.42, T:0.32
Consensus pattern (7 bp):
CGTCGTG
Found at i:473039 original size:168 final size:168
Alignment explanation
Indices: 472821--473743 Score: 1429
Period size: 168 Copynumber: 5.5 Consensus size: 168
472811 CAAGTGAGGA
* * * * * *
472821 AAAAACTGAATGCATGGTTATGATGTCCATGAGGCCTTCTACCAAAATTGTGAAATTTATGGCCC
1 AAAAACTAAATGCATGGTTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAATTCATGACCC
*
472886 CTGGGTCAGGGGTTCTGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATC
66 CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATC
*
472951 TTAAAAAATCTTCTTCTCTACTCTCATATATATTTGTT
131 TTAAAAAATCTTCTTCTCTACTCCCATATATATTTGTT
472989 AAAAACTAAATGCATGGTTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAATTCATGACCC
1 AAAAACTAAATGCATGGTTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAATTCATGACCC
473054 CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATC
66 CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATC
*
473119 TTAAAAAATCTTCTTCTCTACTCTCATATATATTTGTT
131 TTAAAAAATCTTCTTCTCTACTCCCATATATATTTGTT
* * *
473157 AAATACTAAATGCATGATAATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAATTCATGACCC
1 AAAAACTAAATGCATGGTTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAATTCATGACCC
473222 CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATC
66 CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATC
*
473287 TTAGAAAATCTTCTTCTCTACTCCCATATATATTTGTT
131 TTAAAAAATCTTCTTCTCTACTCCCATATATATTTGTT
* *
473325 AAAAACTAAATGCATGGTTATGATGTCCATGAAGCCCTCTACTTTAATTGTGAAATTCATGACCC
1 AAAAACTAAATGCATGGTTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAATTCATGACCC
* *
473390 CTCGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCGATATGGCCAAATAGTAAAAATGTATTAAATC
66 CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATC
*
473455 TTAGAAAATCTTCTTCTCTACTCCCATATATATTTGTT
131 TTAAAAAATCTTCTTCTCTACTCCCATATATATTTGTT
* * *
473493 AAAAACTAAATGCATGATTATGATGTCCATGAGGCTCTCTA-CTAAAATTGTGAAATTCATGACC
1 AAAAACTAAATGCATGGTTATGATGTCCATGAAGCCCTCTACCT-AAATTGTGAAATTCATGACC
** * * * *
473557 CCTTTGTTAGGTGTTCATGCTCTAGGGTGGGGCCAATATGGCCATATAGTAAAAATG-ATTTAAA
65 CCTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTA-TTAAA
* * * ** **
473621 TCTTAAAAAATCTTCTTCTCTACTCCCACAAATGTGGGCA
129 TCTTAAAAAATCTTCTTCTCTACTCCCATATATATTTGTT
* * * * * * *
473661 AAAAACTGAATACATGGTTATGATATCCA-CAATCTCCTTTACCTAAATTGTGAAATTCATGGCC
1 AAAAACTAAATGCATGGTTATGATGTCCATGAAGC-CCTCTACCTAAATTGTGAAATTCATGACC
473725 CCTGGGTCAGGGGTTCAGG
65 CCTGGGTCAGGGGTTCAGG
473744 ACATGAGGGG
Statistics
Matches: 697, Mismatches: 54, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
167 4 0.01
168 691 0.99
169 2 0.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (168 bp):
AAAAACTAAATGCATGGTTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAATTCATGACCC
CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATC
TTAAAAAATCTTCTTCTCTACTCCCATATATATTTGTT
Found at i:484708 original size:4 final size:4
Alignment explanation
Indices: 484686--484727 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
484676 ATCACATTTT
* * *
484686 GTCC GT-C GTCC GTCT GTCC GTCC GTCC GTCT GTCT GTCC GTC
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTC
484728 TGTAAACTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.00, C:0.40, G:0.26, T:0.33
Consensus pattern (4 bp):
GTCC
Found at i:484709 original size:12 final size:12
Alignment explanation
Indices: 484686--484730 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
484676 ATCACATTTT
484686 GTCCGTC-GTCC
1 GTCCGTCTGTCC
* *
484697 GTCTGTCCGTCC
1 GTCCGTCTGTCC
*
484709 GTCCGTCTGTCT
1 GTCCGTCTGTCC
484721 GTCCGTCTGT
1 GTCCGTCTGT
484731 AAACTTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 6 0.21
12 23 0.79
ACGTcount: A:0.00, C:0.38, G:0.27, T:0.36
Consensus pattern (12 bp):
GTCCGTCTGTCC
Found at i:484713 original size:16 final size:16
Alignment explanation
Indices: 484685--484727 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
484675 GATCACATTT
484685 TGTCCGT-CGTCCGTC
1 TGTCCGTCCGTCCGTC
484700 TGTCCGTCCGTCCGTC
1 TGTCCGTCCGTCCGTC
*
484716 TGTCTGTCCGTC
1 TGTCCGTCCGTC
484728 TGTAAACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 7 0.27
16 19 0.73
ACGTcount: A:0.00, C:0.40, G:0.26, T:0.35
Consensus pattern (16 bp):
TGTCCGTCCGTCCGTC
Found at i:486850 original size:2 final size:2
Alignment explanation
Indices: 486843--486899 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
486833 TTTTATACAT
486843 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
486885 AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC A
486900 TATACATATA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:486910 original size:2 final size:2
Alignment explanation
Indices: 486899--486952 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
486889 ACACACACAC
* *
486899 AT AT AC AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
486941 AT AT AT AT AT AT
1 AT AT AT AT AT AT
486953 NNNNNNNNNN
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:494399 original size:2 final size:2
Alignment explanation
Indices: 494392--494509 Score: 227
Period size: 2 Copynumber: 59.0 Consensus size: 2
494382 TTAAAAGCAG
494392 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
*
494434 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GN 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
494476 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
494510 TTTCAGTCTT
Statistics
Matches: 114, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 114 1.00
ACGTcount: A:0.49, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:501682 original size:18 final size:19
Alignment explanation
Indices: 501659--501694 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
501649 AATTTATATA
501659 AAATAATTATA-AATAAAT
1 AAATAATTATATAATAAAT
501677 AAATAATTATATAATAAA
1 AAATAATTATATAATAAA
501695 ACCAGGACTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATAATTATATAATAAAT
Found at i:511948 original size:12 final size:12
Alignment explanation
Indices: 511931--511955 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
511921 TACGAAAAAC
511931 TAGTTTATTATA
1 TAGTTTATTATA
511943 TAGTTTATTATA
1 TAGTTTATTATA
511955 T
1 T
511956 CCTCAAAACA
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:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (12 bp):
TAGTTTATTATA
Found at i:512884 original size:8 final size:8
Alignment explanation
Indices: 512867--512901 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
512857 TTTCCTCTGC
512867 GTCCGTCT
1 GTCCGTCT
*
512875 GTCTGTCT
1 GTCCGTCT
*
512883 GTCCGTCC
1 GTCCGTCT
512891 GTCCGTCT
1 GTCCGTCT
512899 GTC
1 GTC
512902 TGTCCCACTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.00, C:0.37, G:0.26, T:0.37
Consensus pattern (8 bp):
GTCCGTCT
Found at i:512888 original size:16 final size:16
Alignment explanation
Indices: 512867--512906 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
512857 TTTCCTCTGC
* *
512867 GTCCGTCTGTCTGTCT
1 GTCCGTCCGTCCGTCT
512883 GTCCGTCCGTCCGTCT
1 GTCCGTCCGTCCGTCT
*
512899 GTCTGTCC
1 GTCCGTCC
512907 CACTTCAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.00, C:0.38, G:0.25, T:0.38
Consensus pattern (16 bp):
GTCCGTCCGTCCGTCT
Found at i:512891 original size:20 final size:20
Alignment explanation
Indices: 512866--512906 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
512856 CTTTCCTCTG
*
512866 CGTCCGTCTGTCTGTCTGTC
1 CGTCCGTCCGTCTGTCTGTC
512886 CGTCCGTCCGTCTGTCTGTC
1 CGTCCGTCCGTCTGTCTGTC
512906 C
1 C
512907 CACTTCAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.00, C:0.39, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTCCGTCCGTCTGTCTGTC
Found at i:519461 original size:1 final size:1
Alignment explanation
Indices: 519455--519496 Score: 84
Period size: 1 Copynumber: 42.0 Consensus size: 1
519445 TATTCCAAAA
519455 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
519497 ACAAATTTGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:521225 original size:2 final size:2
Alignment explanation
Indices: 521218--521257 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
521208 GAGGTTAGTT
521218 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
521258 CTGTATAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:525337 original size:18 final size:18
Alignment explanation
Indices: 525299--525335 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
525289 GCTTTAATTA
525299 TTTATGTTTTTATTTGAT
1 TTTATGTTTTTATTTGAT
525317 TTTAT-TTTTTATTT-AT
1 TTTATGTTTTTATTTGAT
525333 TTT
1 TTT
525336 TTCGTTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.26
17 9 0.47
18 5 0.26
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.78
Consensus pattern (18 bp):
TTTATGTTTTTATTTGAT
Found at i:526548 original size:22 final size:22
Alignment explanation
Indices: 526523--526594 Score: 126
Period size: 22 Copynumber: 3.3 Consensus size: 22
526513 ATTGCGGTCC
526523 CTTTTTGATTACAGACATAACT
1 CTTTTTGATTACAGACATAACT
526545 CTTTTTGATTACAGACATAACT
1 CTTTTTGATTACAGACATAACT
*
526567 TTTTTTGATTACAGACATAACT
1 CTTTTTGATTACAGACATAACT
*
526589 TTTTTT
1 CTTTTT
526595 TCAATCAACA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.47
Consensus pattern (22 bp):
CTTTTTGATTACAGACATAACT
Found at i:533112 original size:20 final size:20
Alignment explanation
Indices: 533087--533151 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
533077 TTTACTGACG
* *
533087 GTACTGAGAAACGTAGAAAA
1 GTACTGACAAACTTAGAAAA
*
533107 GTACTGACAAACTTAG-ACA
1 GTACTGACAAACTTAGAAAA
* *
533126 GTACTGATAAACTTAGAGAA
1 GTACTGACAAACTTAGAAAA
533146 GTACTG
1 GTACTG
533152 GCGGTACTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
19 17 0.45
20 21 0.55
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.22
Consensus pattern (20 bp):
GTACTGACAAACTTAGAAAA
Found at i:548222 original size:36 final size:36
Alignment explanation
Indices: 548175--548248 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
548165 AACTACGTTG
548175 AATTTGCCTCGGTAGTTCTTGAGAAGAAGATTTTTA
1 AATTTGCCTCGGTAGTTCTTGAGAAGAAGATTTTTA
548211 AATTTGCCTCGGTAGTTCTTGAGAAGAAGATTTTTA
1 AATTTGCCTCGGTAGTTCTTGAGAAGAAGATTTTTA
548247 AA
1 AA
548249 AATGCACCCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.38
Consensus pattern (36 bp):
AATTTGCCTCGGTAGTTCTTGAGAAGAAGATTTTTA
Found at i:548433 original size:12 final size:12
Alignment explanation
Indices: 548416--548450 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
548406 TAAAAAGTTT
548416 ACAGACGGACGG
1 ACAGACGGACGG
*
548428 ACAGACAGACGG
1 ACAGACGGACGG
548440 ACAGACGGACG
1 ACAGACGGACG
548451 ACGGACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.37, C:0.26, G:0.37, T:0.00
Consensus pattern (12 bp):
ACAGACGGACGG
Found at i:548444 original size:8 final size:8
Alignment explanation
Indices: 548416--548457 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
548406 TAAAAAGTTT
548416 ACAGACGG
1 ACAGACGG
* *
548424 ACGGACAG
1 ACAGACGG
548432 ACAGACGG
1 ACAGACGG
548440 ACAGACGG
1 ACAGACGG
548448 AC-GACGG
1 ACAGACGG
548455 ACA
1 ACA
548458 AAATGTGATC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
7 7 0.24
8 22 0.76
ACGTcount: A:0.38, C:0.26, G:0.36, T:0.00
Consensus pattern (8 bp):
ACAGACGG
Found at i:551003 original size:16 final size:16
Alignment explanation
Indices: 550982--551016 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
550972 ACCTTCTTTT
550982 AAACAGGCGTATTTAC
1 AAACAGGCGTATTTAC
* *
550998 AAACAGTCGTATTTTC
1 AAACAGGCGTATTTAC
551014 AAA
1 AAA
551017 AGTTCTCTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (16 bp):
AAACAGGCGTATTTAC
Found at i:552741 original size:18 final size:19
Alignment explanation
Indices: 552718--552757 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
552708 ATTTTGACCC
552718 TTTCAT-ATTTTGCTACTT
1 TTTCATCATTTTGCTACTT
* *
552736 TTTCATCATTTTTCTGCTT
1 TTTCATCATTTTGCTACTT
552755 TTT
1 TTT
552758 AGACCTCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.12, C:0.17, G:0.05, T:0.65
Consensus pattern (19 bp):
TTTCATCATTTTGCTACTT
Found at i:555064 original size:14 final size:15
Alignment explanation
Indices: 555016--555066 Score: 50
Period size: 17 Copynumber: 3.3 Consensus size: 15
555006 ATGTTCACCA
**
555016 AAAATAAGATATATTT
1 AAAATAAG-TATAGAT
555032 AAGAATAAAGTATAGAT
1 AA-AAT-AAGTATAGAT
555049 AAAATAAGTA-AGAT
1 AAAATAAGTATAGAT
555063 AAAA
1 AAAA
555067 GATAAAGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 8 0.26
15 5 0.16
16 5 0.16
17 10 0.32
18 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.12, T:0.25
Consensus pattern (15 bp):
AAAATAAGTATAGAT
Found at i:556236 original size:18 final size:18
Alignment explanation
Indices: 556208--556256 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
556198 AAATCATATA
556208 GCGTAATTAACGCTAAACT
1 GCGT-ATTAACGCTAAACT
*
556227 GCGTATTAACGCTGAACT
1 GCGTATTAACGCTAAACT
*
556245 GCGTATTGACGC
1 GCGTATTAACGC
556257 ATTATTTTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (18 bp):
GCGTATTAACGCTAAACT
Found at i:562502 original size:4 final size:4
Alignment explanation
Indices: 562493--562549 Score: 87
Period size: 4 Copynumber: 14.2 Consensus size: 4
562483 GATAAAAGAT
* *
562493 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTT TCTT
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
*
562541 TCTT TCTA T
1 TCTA TCTA T
562550 AAGTTTGTTA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.19, C:0.25, G:0.00, T:0.56
Consensus pattern (4 bp):
TCTA
Found at i:563536 original size:4 final size:4
Alignment explanation
Indices: 563527--563559 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
563517 AGACAAAGTA
563527 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
563560 TCAAATAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:575132 original size:13 final size:13
Alignment explanation
Indices: 575107--575144 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
575097 GTTCATTTCC
575107 CTTT-TTTTATTTT
1 CTTTATTTT-TTTT
575120 CTTTATTTTTTTT
1 CTTTATTTTTTTT
*
575133 ATTTATTTTTTT
1 CTTTATTTTTTT
575145 GGGGGTAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.11, C:0.05, G:0.00, T:0.84
Consensus pattern (13 bp):
CTTTATTTTTTTT
Found at i:576540 original size:11 final size:11
Alignment explanation
Indices: 576524--576548 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
576514 CGTGCATGGT
576524 TCATATGGAGG
1 TCATATGGAGG
576535 TCATATGGAGG
1 TCATATGGAGG
576546 TCA
1 TCA
576549 GAAAAGTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.12, G:0.32, T:0.28
Consensus pattern (11 bp):
TCATATGGAGG
Found at i:578597 original size:17 final size:17
Alignment explanation
Indices: 578575--578607 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
578565 CTGGTACTGT
578575 ACCAGTTATCGGCTAAG
1 ACCAGTTATCGGCTAAG
578592 ACCAGTTATCGGCTAA
1 ACCAGTTATCGGCTAA
578608 ACTGAGAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (17 bp):
ACCAGTTATCGGCTAAG
Found at i:580470 original size:30 final size:29
Alignment explanation
Indices: 580433--580516 Score: 109
Period size: 27 Copynumber: 2.9 Consensus size: 29
580423 TATTTTTCAA
580433 ACAGTACACACGCACCATGTTCAGTTTTAG
1 ACAGTACACACGCACCA-GTTCAGTTTTAG
*
580463 TCAGTACACACGCA-C-GTTCAGTTTTAG
1 ACAGTACACACGCACCAGTTCAGTTTTAG
* *
580490 ACAATACACAAGCACCAAGTTCAGTTT
1 ACAGTACACACGCACC-AGTTCAGTTT
580517 CAGATATTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
27 23 0.49
28 1 0.02
29 1 0.02
30 22 0.47
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (29 bp):
ACAGTACACACGCACCAGTTCAGTTTTAG
Found at i:581757 original size:15 final size:15
Alignment explanation
Indices: 581739--581769 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
581729 AATACAAATC
581739 CATAATATACTTATA
1 CATAATATACTTATA
*
581754 CATAATATATTTATA
1 CATAATATACTTATA
581769 C
1 C
581770 TTACTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (15 bp):
CATAATATACTTATA
Found at i:583390 original size:23 final size:21
Alignment explanation
Indices: 583363--583404 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
583353 ATGTAGCGAG
583363 AGCATTATCAAGGAGATGTATGA
1 AGCATTA-C-AGGAGATGTATGA
*
583386 AGCATTACTGGAGATGTAT
1 AGCATTACAGGAGATGTAT
583405 ATGGTATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 1 0.06
23 7 0.39
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.29
Consensus pattern (21 bp):
AGCATTACAGGAGATGTATGA
Found at i:584166 original size:17 final size:18
Alignment explanation
Indices: 584144--584184 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
584134 AACTTAATCA
*
584144 AGTTTTAAATT-AATTTT
1 AGTTTTAAATTAAAGTTT
584161 AGTTTT-AATTAAAGTTT
1 AGTTTTAAATTAAAGTTT
584178 AGTTTTA
1 AGTTTTA
584185 GTTTTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (18 bp):
AGTTTTAAATTAAAGTTT
Found at i:586993 original size:2 final size:2
Alignment explanation
Indices: 586986--587034 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
586976 CGTCCGTATG
586986 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
587028 CT CT CT C
1 CT CT CT C
587035 CAAATTATAC
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:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:590394 original size:12 final size:12
Alignment explanation
Indices: 590377--590402 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
590367 TGAGGGATTT
590377 TTGCTAAAAATA
1 TTGCTAAAAATA
590389 TTGCTAAAAATA
1 TTGCTAAAAATA
590401 TT
1 TT
590403 ATTTCAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (12 bp):
TTGCTAAAAATA
Found at i:600689 original size:5 final size:5
Alignment explanation
Indices: 600679--600729 Score: 93
Period size: 5 Copynumber: 10.2 Consensus size: 5
600669 NNNNNNNNNN
*
600679 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATTTT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
600729 A
1 A
600730 CTCTGACCAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 44 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
ATATT
Found at i:601835 original size:12 final size:12
Alignment explanation
Indices: 601818--601851 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
601808 TAGGACATTA
601818 TTTTATATACAT
1 TTTTATATACAT
*
601830 TTTTATATGCAT
1 TTTTATATACAT
601842 TTTTAT-TACA
1 TTTTATATACA
601852 ACTATTTGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 3 0.15
12 17 0.85
ACGTcount: A:0.29, C:0.09, G:0.03, T:0.59
Consensus pattern (12 bp):
TTTTATATACAT
Found at i:607542 original size:41 final size:41
Alignment explanation
Indices: 607468--607653 Score: 205
Period size: 41 Copynumber: 4.5 Consensus size: 41
607458 CTCTACCTCA
* * *
607468 TCATCCACCTAAAAAAACACAAAACAATGGTTAAGTAACTCC
1 TCATCCACCTCAAATAA-ACAATACAATGGTTAAGTAACTCC
* * *
607510 TCATCCACCTTAAATAAACAATACAATTGTTAAGTACCTCC
1 TCATCCACCTCAAATAAACAATACAATGGTTAAGTAACTCC
* *
607551 TCATCCACCTCAAATATACAATACAATGGTT-AGATACCTCC
1 TCATCCACCTCAAATAAACAATACAATGGTTAAG-TAACTCC
* * * * *
607592 TAATCCACCTCAAATATACAATACAATGGTAAAG-CACATTC
1 TCATCCACCTCAAATAAACAATACAATGGTTAAGTAAC-TCC
*
607633 TCATCCACCTCAAACAAACAA
1 TCATCCACCTCAAATAAACAA
607654 AGGTTAAGTA
Statistics
Matches: 125, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
40 3 0.02
41 105 0.84
42 17 0.14
ACGTcount: A:0.42, C:0.28, G:0.06, T:0.24
Consensus pattern (41 bp):
TCATCCACCTCAAATAAACAATACAATGGTTAAGTAACTCC
Found at i:618617 original size:40 final size:40
Alignment explanation
Indices: 618562--618642 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
618552 ATGTCTTCCC
618562 GCTTGTCATATACATGTATGAATAATTCCTCAGTAGTTTT
1 GCTTGTCATATACATGTATGAATAATTCCTCAGTAGTTTT
*
618602 GCTTGTCATCTACATGTATGAATAATTCCTCAGTAGTTTT
1 GCTTGTCATATACATGTATGAATAATTCCTCAGTAGTTTT
618642 G
1 G
618643 AAAATAAAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (40 bp):
GCTTGTCATATACATGTATGAATAATTCCTCAGTAGTTTT
Found at i:620075 original size:15 final size:17
Alignment explanation
Indices: 620055--620087 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
620045 GATATTTATG
620055 ATTTTAT-TT-ATATAA
1 ATTTTATGTTAATATAA
620070 ATTTTATGTTAATATAA
1 ATTTTATGTTAATATAA
620087 A
1 A
620088 GCAGTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 2 0.12
17 7 0.44
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
ATTTTATGTTAATATAA
Found at i:622178 original size:167 final size:166
Alignment explanation
Indices: 621802--622290 Score: 827
Period size: 167 Copynumber: 2.9 Consensus size: 166
621792 TTGGTTGAAG
* *
621802 TTTCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGATATTTAAAGATTTACT
1 TTTCACACAAGTTTCAGCTTTGCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACT
* *
621867 CTATATATTCATATGTTAAACTTCGACCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGA
66 CTATATATTCCTATGTTAAACTTCGACCCCCCATTGTGGCCCCACCCTACCCCAGGGGGTCATGA
*
621932 TTTTCACAACTTTAAATCTACACTACCTGAGGATGC
131 TTTTCACAACTTTGAATCTACACTACCTGAGGATGC
* *
621968 TTCCACACAAGTTTCAGCTTTGCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTTAAGATTTACT
1 TTTCACACAAGTTTCAGCTTTGCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACT
* * *
622033 CTATATATTCCTGTGTAAAACTTCGACCCCCCATTGTGGCCCCACCCTACCCCATGGGGGTCATA
66 CTATATATTCCTATGTTAAACTTCGACCCCCCATTGTGGCCCCACCCTACCCCA-GGGGGTCATG
*
622098 ATTTTCACAATTTTGAATCTACACTACCTGAGGATGC
130 ATTTTCACAACTTTGAATCTACACTACCTGAGGATGC
622135 TTTCACACAAGTTTCAGCTTTGCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACT
1 TTTCACACAAGTTTCAGCTTTGCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACT
**
622200 CTATATATTCCTATGTTAAACTTCGACCCATCATTGTGGCCCCACCCTACCCTCA-GGGGTCATG
66 CTATATATTCCTATGTTAAACTTCGACCCCCCATTGTGGCCCCACCCTACCC-CAGGGGGTCATG
*
622264 ATTTTCACAACTTTGTATCTACACTAC
130 ATTTTCACAACTTTGAATCTACACTAC
622291 GCTTGACTGA
Statistics
Matches: 301, Mismatches: 20, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
166 144 0.48
167 155 0.51
168 2 0.01
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.34
Consensus pattern (166 bp):
TTTCACACAAGTTTCAGCTTTGCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACT
CTATATATTCCTATGTTAAACTTCGACCCCCCATTGTGGCCCCACCCTACCCCAGGGGGTCATGA
TTTTCACAACTTTGAATCTACACTACCTGAGGATGC
Found at i:624070 original size:17 final size:17
Alignment explanation
Indices: 624044--624083 Score: 71
Period size: 18 Copynumber: 2.3 Consensus size: 17
624034 ATCCTTGAAG
624044 TTTTTAAAAATAAAATAT
1 TTTTTAAAAATAAAAT-T
624062 TTTTTAAAAATAAAATT
1 TTTTTAAAAATAAAATT
624079 TTTTT
1 TTTTT
624084 CCTACCTACC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTTTAAAAATAAAATT
Found at i:628187 original size:22 final size:22
Alignment explanation
Indices: 628146--628187 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
628136 ACTCACGACA
*
628146 CTGTATCTATATGTACATGTGT
1 CTGTATCTATATGAACATGTGT
*
628168 CTGTATCTATATGAATATGT
1 CTGTATCTATATGAACATGT
628188 ATCAATATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (22 bp):
CTGTATCTATATGAACATGTGT
Found at i:629693 original size:9 final size:9
Alignment explanation
Indices: 629681--629706 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
629671 TGGGGTTTCT
629681 GGGTTTTGG
1 GGGTTTTGG
629690 GGGTTTTGG
1 GGGTTTTGG
629699 GGGTTTTG
1 GGGTTTTG
629707 TTTTGTTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.54, T:0.46
Consensus pattern (9 bp):
GGGTTTTGG
Found at i:631905 original size:14 final size:13
Alignment explanation
Indices: 631862--631906 Score: 51
Period size: 12 Copynumber: 3.6 Consensus size: 13
631852 ATCTTGGTAG
631862 TAAAAAATAT--A
1 TAAAAAATATCGA
*
631873 TAAAAGAT-TCGA
1 TAAAAAATATCGA
631885 TAAAAAATATCGA
1 TAAAAAATATCGA
631898 TAAGAAAAT
1 TAA-AAAAT
631907 CTTTACGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
10 1 0.04
11 7 0.25
12 8 0.29
13 7 0.25
14 5 0.18
ACGTcount: A:0.62, C:0.04, G:0.09, T:0.24
Consensus pattern (13 bp):
TAAAAAATATCGA
Found at i:632308 original size:2 final size:2
Alignment explanation
Indices: 632301--632352 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
632291 TGACCTCCTG
632301 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
632343 CT CT CT CT CT
1 CT CT CT CT CT
632353 TCATATTACA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:634058 original size:15 final size:15
Alignment explanation
Indices: 634040--634077 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
634030 GTACTTTTTA
634040 AAATT-AATTCAAATT
1 AAATTGAATT-AAATT
634055 AAATTGAATTAAATT
1 AAATTGAATTAAATT
634070 AAATTGAA
1 AAATTGAA
634078 ATTGGACACT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (15 bp):
AAATTGAATTAAATT
Found at i:645778 original size:1 final size:1
Alignment explanation
Indices: 645772--645801 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
645762 ACGGTTGGAA
645772 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
645802 TAATTAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:647597 original size:3 final size:3
Alignment explanation
Indices: 647582--647629 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
647572 AAACAAGTGG
*
647582 TGA TGA TGG TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
647630 AAGACTTGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:652410 original size:31 final size:31
Alignment explanation
Indices: 652372--652439 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
652362 ACTATGCATA
652372 AGAATGAATGGGCAAAGAGAGATAACTGCTG
1 AGAATGAATGGGCAAAGAGAGATAACTGCTG
652403 AGAATGAATGGGCAAAGAGAGATAACTGCTG
1 AGAATGAATGGGCAAAGAGAGATAACTGCTG
652434 AGAATG
1 AGAATG
652440 TTACCATCGT
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:0.43, C:0.09, G:0.32, T:0.16
Consensus pattern (31 bp):
AGAATGAATGGGCAAAGAGAGATAACTGCTG
Found at i:659777 original size:2 final size:2
Alignment explanation
Indices: 659770--659825 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
659760 TATCAAAGCA
659770 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
659812 TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC
659826 ATTTTATCTC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:665088 original size:42 final size:42
Alignment explanation
Indices: 665029--665115 Score: 147
Period size: 42 Copynumber: 2.1 Consensus size: 42
665019 TGATTTTCTG
665029 GAATCCATAATATGGGTTTTTGATTCCATATCACCACTTAAT
1 GAATCCATAATATGGGTTTTTGATTCCATATCACCACTTAAT
* * *
665071 GAATCGATAATATGGGTTTTTGATTCCATATTACCACTTTAT
1 GAATCCATAATATGGGTTTTTGATTCCATATCACCACTTAAT
665113 GAA
1 GAA
665116 ACTGATGATG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (42 bp):
GAATCCATAATATGGGTTTTTGATTCCATATCACCACTTAAT
Found at i:670305 original size:40 final size:42
Alignment explanation
Indices: 670237--670344 Score: 121
Period size: 40 Copynumber: 2.5 Consensus size: 42
670227 TAGTAATTTA
* * * *
670237 TAAATCTGGTAAACTGTTATTCTTGAAAGATGATA-T-GCTG
1 TAAACCTGGTAAACTGTAAATCTGGAAAGATGATAGTAGCTG
* *
670277 TAAACCTGGTAAACTATAAATCTGGAAAGATTATATGGTAAGCTG
1 TAAACCTGGTAAACTGTAAATCTGGAAAGATGATA--GT-AGCTG
670322 TAAACCTGGTAAACTGTAAATCT
1 TAAACCTGGTAAACTGTAAATCT
670345 ACAGGCAAGA
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
40 29 0.52
43 1 0.02
45 26 0.46
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (42 bp):
TAAACCTGGTAAACTGTAAATCTGGAAAGATGATAGTAGCTG
Found at i:671885 original size:59 final size:58
Alignment explanation
Indices: 671789--671913 Score: 223
Period size: 59 Copynumber: 2.1 Consensus size: 58
671779 GAAATCTCTA
*
671789 TTCTTCATATTACTTTGATAATTATAACAGATATATGTATCAGTTAATATGGTTGGGAT
1 TTCTTCATATTACTTTGATAATTATAACAGATATATGTATCAGTAAATATGG-TGGGAT
*
671848 TTCTTCATATTACTTTGATAATTATAACAGATGTATGTATCAGTAAATATGGTGGGAT
1 TTCTTCATATTACTTTGATAATTATAACAGATATATGTATCAGTAAATATGGTGGGAT
671906 TTCTTCAT
1 TTCTTCAT
671914 CAACTCAGTG
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
58 14 0.22
59 50 0.78
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (58 bp):
TTCTTCATATTACTTTGATAATTATAACAGATATATGTATCAGTAAATATGGTGGGAT
Found at i:672195 original size:13 final size:13
Alignment explanation
Indices: 672177--672207 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
672167 TTCTTTTTCC
672177 TTTTGGTGGTGGT
1 TTTTGGTGGTGGT
672190 TTTTGGTGGTGGT
1 TTTTGGTGGTGGT
672203 TTTTG
1 TTTTG
672208 CGATGTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.42, T:0.58
Consensus pattern (13 bp):
TTTTGGTGGTGGT
Found at i:676231 original size:44 final size:46
Alignment explanation
Indices: 676155--676244 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 46
676145 TCTTATATAA
676155 ATTATTAAATCAATGTTTCGTTTTAAATATGAC-TTAAAATTTTTG
1 ATTATTAAATCAATGTTTCGTTTTAAATATGACTTTAAAATTTTTG
676200 ATTATTAAATCAATG-TTCGTTTTAAATATGACTTTAAAATTTTTG
1 ATTATTAAATCAATGTTTCGTTTTAAATATGACTTTAAAATTTTTG
676245 TCACTCGACA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
44 17 0.39
45 27 0.61
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.49
Consensus pattern (46 bp):
ATTATTAAATCAATGTTTCGTTTTAAATATGACTTTAAAATTTTTG
Found at i:677337 original size:33 final size:33
Alignment explanation
Indices: 677295--677361 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 33
677285 TGTTTTTTGT
*
677295 AGAATCATGTTATGATGACCCATTT-GATTTAGC
1 AGAATCATGTGATGATGACCC-TTTCGATTTAGC
677328 AGAATCATGTGATGATGACCCTTTCGATTTAGC
1 AGAATCATGTGATGATGACCCTTTCGATTTAGC
677361 A
1 A
677362 CCTGGAAGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 3 0.09
33 29 0.91
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Consensus pattern (33 bp):
AGAATCATGTGATGATGACCCTTTCGATTTAGC
Found at i:679168 original size:2 final size:2
Alignment explanation
Indices: 679161--679219 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
679151 NNNNNNNNNN
*
679161 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA 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
679203 AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG A
679220 ATGAGACCTT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:681500 original size:21 final size:21
Alignment explanation
Indices: 681463--681627 Score: 215
Period size: 21 Copynumber: 7.9 Consensus size: 21
681453 TTTAGCAAAG
*
681463 CGTACCGTGCA-AGAAGCGAAC
1 CGTACCGTTCACA-AAGCGAAC
* * *
681484 TGTTCCGTTCACAAAGCGTAC
1 CGTACCGTTCACAAAGCGAAC
* *
681505 CGTACCGTTCGCGAAGCGAAC
1 CGTACCGTTCACAAAGCGAAC
*
681526 CGTACCGTTCACAAAACGAAC
1 CGTACCGTTCACAAAGCGAAC
* *
681547 CATACCGTTCACAAAGCGTAC
1 CGTACCGTTCACAAAGCGAAC
681568 CGTACCGTTCACAAAGCGAAC
1 CGTACCGTTCACAAAGCGAAC
681589 CGTACCGTTCACAAAGCGAAC
1 CGTACCGTTCACAAAGCGAAC
* *
681610 CGTACTGTTCAAAAAGCG
1 CGTACCGTTCACAAAGCG
681628 TAACGAACCG
Statistics
Matches: 124, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
21 123 0.99
22 1 0.01
ACGTcount: A:0.32, C:0.31, G:0.21, T:0.17
Consensus pattern (21 bp):
CGTACCGTTCACAAAGCGAAC
Found at i:687624 original size:158 final size:158
Alignment explanation
Indices: 687280--687629 Score: 451
Period size: 161 Copynumber: 2.2 Consensus size: 158
687270 GGGCTGTCCT
* ** *
687280 ATAGATGTGCAATACGGTTTTAAAACTTTAAATTTCATCCAGGGAGTCAAATAGTAGCAGAAAAT
1 ATAGATGTGCATTA-GGTTTTAAAAAATTAAAATTCATCCAGGGAGTCAAATAG-AGCAGAAAAT
*
687345 TGACGTTTATCACTAAAAACAACATAGATCCAAGAGCTCCTCTTATGATTTAATGGATAGACACA
64 TGACGTTTATCACTAAAAACAACATAGATCCAAGAACTCCTCTTATGATTTAATGGATAGA-ACA
*
687410 TCATATATTGGGATATGATAGGGAATGTTCT
128 TCATATATTGGGATATGATAGGGAATGTTCC
* * *
687441 ATAGATGTGCAGTAAGGTTTTAAAAAATTAAAATTCATCCAGGGGGTCAAA-A-AGTAGAAAATT
1 ATAGATGTGCA-TTAGGTTTTAAAAAATTAAAATTCATCCAGGGAGTCAAATAGAGCAGAAAATT
* *
687504 GACGTTTATCACTTAAAAA-AACCCCATAGATCCTAGAACTCCTTTTATGATTTAATGGATAG-A
65 GACGTTTATCAC-TAAAAACAA---CATAGATCCAAGAACTCCTCTTATGATTTAATGGATAGAA
* *
687567 CA-CATATCTTGGGATATGATA-TGAACTGTTCC
126 CATCATATATTGGGATATGATAGGGAA-TGTTCC
*
687599 ATAGATGTGCATTAGGTTTTGAAAAATTAAA
1 ATAGATGTGCATTAGGTTTTAAAAAATTAAA
687630 TTTAACCCTG
Statistics
Matches: 168, Mismatches: 15, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
157 21 0.12
158 58 0.35
159 9 0.05
160 1 0.01
161 78 0.46
162 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (158 bp):
ATAGATGTGCATTAGGTTTTAAAAAATTAAAATTCATCCAGGGAGTCAAATAGAGCAGAAAATTG
ACGTTTATCACTAAAAACAACATAGATCCAAGAACTCCTCTTATGATTTAATGGATAGAACATCA
TATATTGGGATATGATAGGGAATGTTCC
Found at i:687956 original size:134 final size:135
Alignment explanation
Indices: 687680--687972 Score: 328
Period size: 134 Copynumber: 2.2 Consensus size: 135
687670 CTTTAAGGAT
* *
687680 CAAGAATATATATGG-TTAAGGGGTGGGAATCTCAACCGTTTTCTAGATATTCGTGCACTTCCTG
1 CAAGAATATATATGGTTTAA-GGGTGGGAATCTCAACCGTTTTCAAGATATTAGTGCACTTCCTG
* * * *
687744 TTCGAGGGGTGTCATGACCACCGCCAGGGCTCATGACCTACATACTGTTTGATGCCCCTTGACAC
65 TTCGAGGGGTGTCAGGACCACCGCCAAGGCCCATGACCTACATACTATTTGATGCCCCTTGACAC
687809 AAGAAA
130 AAGAAA
* * ** * * *
687815 CAAGAATAAATATGGTTTAAGGGTGGGGATCTCAATTGTTTTGAAGATATTAAG-GGACTTGCTG
1 CAAGAATATATATGGTTTAAGGGTGGGAATCTCAACCGTTTTCAAGATATT-AGTGCACTTCCTG
* *
687879 TTTGAGTGG-GTCAGGACCACC-CACAAGGCCCATGACCTACATAAC-ATTTGATGCCCCTTGAC
65 TTCGAGGGGTGTCAGGACCACCGC-CAAGGCCCATGACCTACAT-ACTATTTGATGCCCCTTGAC
687941 ATC-AGAAA
128 A-CAAGAAA
* * * *
687949 TATGAATATATATGATTTAGGGGT
1 CAAGAATATATATGGTTTAAGGGT
687973 CATGATTATA
Statistics
Matches: 133, Mismatches: 20, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
133 1 0.01
134 69 0.52
135 58 0.44
136 5 0.04
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (135 bp):
CAAGAATATATATGGTTTAAGGGTGGGAATCTCAACCGTTTTCAAGATATTAGTGCACTTCCTGT
TCGAGGGGTGTCAGGACCACCGCCAAGGCCCATGACCTACATACTATTTGATGCCCCTTGACACA
AGAAA
Found at i:712034 original size:2 final size:2
Alignment explanation
Indices: 712027--712056 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
712017 ATGATAAAAA
712027 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
712057 CCTCCCTCCC
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:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:714699 original size:115 final size:116
Alignment explanation
Indices: 714506--714728 Score: 387
Period size: 115 Copynumber: 1.9 Consensus size: 116
714496 TGTTTCTGCA
*
714506 GCTGCAAAAACCAGCAATTATTGTGAATTGATGTAAGGATTAACTTCTGCCAGGGGAAACGTCCT
1 GCTGCAAAAACCAGCAATTACTGTGAATTGATGTAAGGATTAACTTCTGCCAGGGGAAACGTCCT
*
714571 AGAATGTTGA-TTTTTTAGGGCAAAGATCATT-AATGGGGTAAGTTTCTGTG
66 AGAATGTTGATTTTTTTAAGGCAAAGATCATTGAA-GGGGTAAGTTTCTGTG
* *
714621 GCTGCAATAACCAGCAATTACTGTGAATTGATGTAAGGATTAACTTCTGGCAGGGGAAACGTCCT
1 GCTGCAAAAACCAGCAATTACTGTGAATTGATGTAAGGATTAACTTCTGCCAGGGGAAACGTCCT
714686 AGAATGTTGATTTTTTTAAGGCAAAGATCATTGAAGGGGTAAG
66 AGAATGTTGATTTTTTTAAGGCAAAGATCATTGAAGGGGTAAG
714729 AAATGTTACA
Statistics
Matches: 102, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
115 72 0.71
116 28 0.27
117 2 0.02
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (116 bp):
GCTGCAAAAACCAGCAATTACTGTGAATTGATGTAAGGATTAACTTCTGCCAGGGGAAACGTCCT
AGAATGTTGATTTTTTTAAGGCAAAGATCATTGAAGGGGTAAGTTTCTGTG
Found at i:723227 original size:22 final size:23
Alignment explanation
Indices: 723202--723244 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
723192 GATCCTTTTG
723202 TGTTTT-GTTTTGTTTGTTTGCT
1 TGTTTTGGTTTTGTTTGTTTGCT
* *
723224 TGTTTTGGTTTTTTTTTTTTG
1 TGTTTTGGTTTTGTTTGTTTG
723245 GTTTTGGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.00, C:0.02, G:0.21, T:0.77
Consensus pattern (23 bp):
TGTTTTGGTTTTGTTTGTTTGCT
Found at i:723365 original size:2 final size:2
Alignment explanation
Indices: 723358--723408 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
723348 TAATACATGC
723358 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
723400 AG AG AG AG A
1 AG AG AG AG A
723409 TTGTCAATCT
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:724732 original size:17 final size:17
Alignment explanation
Indices: 724710--724745 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
724700 TATAACGTGT
724710 GAGTACCCATTATTGCC
1 GAGTACCCATTATTGCC
724727 GAGTACCCATTATTGCC
1 GAGTACCCATTATTGCC
724744 GA
1 GA
724746 TTGTTATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (17 bp):
GAGTACCCATTATTGCC
Found at i:727195 original size:25 final size:25
Alignment explanation
Indices: 727167--727216 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
727157 AGACGTATTA
727167 TTATTAATTAACAATTGTTATTTCC
1 TTATTAATTAACAATTGTTATTTCC
* *
727192 TTATTTATTTACAATTGTTATTTCC
1 TTATTAATTAACAATTGTTATTTCC
727217 ATACTTTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.28, C:0.12, G:0.04, T:0.56
Consensus pattern (25 bp):
TTATTAATTAACAATTGTTATTTCC
Found at i:747951 original size:13 final size:13
Alignment explanation
Indices: 747933--747958 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
747923 AATATCTAAC
747933 TAAAATTTTACCA
1 TAAAATTTTACCA
747946 TAAAATTTTACCA
1 TAAAATTTTACCA
747959 AGCACTCGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATTTTACCA
Found at i:753553 original size:22 final size:22
Alignment explanation
Indices: 753523--753643 Score: 228
Period size: 22 Copynumber: 5.6 Consensus size: 22
753513 GGTTGAACTA
753523 ACTT-GTATAAAAAGTACACTT
1 ACTTGGTATAAAAAGTACACTT
753544 ACTTGGTATAAAAA-TACACTT
1 ACTTGGTATAAAAAGTACACTT
753565 ACTTGGTATAAAAAGTACACTT
1 ACTTGGTATAAAAAGTACACTT
753587 ACTTGGTATAAAAAGTACACTT
1 ACTTGGTATAAAAAGTACACTT
753609 ACTTGGTATAAAAAGTACACTT
1 ACTTGGTATAAAAAGTACACTT
753631 ACTTGGTATAAAA
1 ACTTGGTATAAAA
753644 GCACTGAGGT
Statistics
Matches: 98, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
21 25 0.26
22 73 0.74
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.32
Consensus pattern (22 bp):
ACTTGGTATAAAAAGTACACTT
Found at i:759841 original size:20 final size:20
Alignment explanation
Indices: 759789--759847 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
759779 TTTACCTTTC
759789 AAAAACAA-ATTCCTATAGG
1 AAAAACAATATTCCTATAGG
* * *
759808 AAAATA-ATTTTTCCCATAGG
1 AAAA-ACAATATTCCTATAGG
759828 AAAAACAATATTCCTATAGG
1 AAAAACAATATTCCTATAGG
759848 TAATTTGAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.27
Consensus pattern (20 bp):
AAAAACAATATTCCTATAGG
Found at i:760087 original size:21 final size:21
Alignment explanation
Indices: 760067--760105 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
760057 AGGAGAATCA
760067 ATTCTCCGATGGGA-ATTATC
1 ATTCTCCGATGGGATATTATC
* *
760087 ATTTTCCTATGGGATATTA
1 ATTCTCCGATGGGATATTA
760106 ATTTTTAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (21 bp):
ATTCTCCGATGGGATATTATC
Found at i:769306 original size:2 final size:2
Alignment explanation
Indices: 769299--769350 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
769289 GTAAGCATAT
769299 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
769341 GA GA GA GA GA
1 GA GA GA GA GA
769351 AATATTGAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:770417 original size:26 final size:26
Alignment explanation
Indices: 770384--770436 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
770374 CCTGTTTTGT
770384 ATTTTTCCTACTTTTCCTAATGACAA
1 ATTTTTCCTACTTTTCCTAATGACAA
770410 ATTTTTCCTACTTTTCCTAATGACAA
1 ATTTTTCCTACTTTTCCTAATGACAA
770436 A
1 A
770437 GAGCGACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.28, C:0.23, G:0.04, T:0.45
Consensus pattern (26 bp):
ATTTTTCCTACTTTTCCTAATGACAA
Found at i:778903 original size:11 final size:12
Alignment explanation
Indices: 778887--778916 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
778877 CTGTTAATTT
778887 ACAATAAC-ATG
1 ACAATAACAATG
778898 ACAATAACAATG
1 ACAATAACAATG
778910 ACAATAA
1 ACAATAA
778917 AACCTGACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.60, C:0.17, G:0.07, T:0.17
Consensus pattern (12 bp):
ACAATAACAATG
Found at i:795756 original size:207 final size:205
Alignment explanation
Indices: 795390--796179 Score: 1119
Period size: 207 Copynumber: 3.8 Consensus size: 205
795380 TCGCTATAAT
* * *
795390 CCGATTTTGTTTCACCTGCTATTTTACTTTTGGTATTTCCTCTACTCTGGTCGCAGGCTGTCGCG
1 CCGATTCTGTGTCACCTGCTATTTTACTTTTGGTATTTCCTCTATTCTGGTCGCAGGCTGTCGCG
795455 GCTAACTCTTCGGCATTTGCATATAGTTCCTTTCCGGTTTTCGTTTTCGTAAAATTAGTTTCGGT
66 GCTAACTCTTCGGCATTTGCATATAGTTCCTTTCCGGTTTTCGTTTTCGTAAAATTAGTTTCGGT
* *
795520 AACTGGCGACTCATTAGTTTTAGCCCAATGAAGCGTTTCTAACGTTGAATTTTTTGCTTTCTTTT
131 AAATGGCGACTCATTAGTTTTAGCCCAAT-AAGCGTTTCTAACGTTGAATTTTTTGTTTTCTTTT
795585 TTCCAGACTTTC
195 TTCCAGA-TTTC
* *
795597 CCGATTCTGTGTCACCTGCTATTTTACTTTTGGTATTTTCTCTATTCTGGTCGCAGGCTGTTGCG
1 CCGATTCTGTGTCACCTGCTATTTTACTTTTGGTATTTCCTCTATTCTGGTCGCAGGCTGTCGCG
*
795662 GCTAACTCTTCGGCGTTTGCATATAGTTCCTTTCCGGTTTTCGTTTTCGTAAAATTAGTTTCGGT
66 GCTAACTCTTCGGCATTTGCATATAGTTCCTTTCCGGTTTTCGTTTTCGTAAAATTAGTTTCGGT
795727 AAATGGCGACTCATTAGTTTTAGCCCAATGAAGCGTTTCTAACGTTG-ATTTTATTGTTTTCTTT
131 AAATGGCGACTCATTAGTTTTAGCCCAAT-AAGCGTTTCTAACGTTGAATTTT-TTGTTTTCTTT
*
795791 TTTCCATAATTTC
194 TTTCCA-GATTTC
* *
795804 CCGATTCTGTGTCACCTACTATTTTACTTTTGGTATTTTCTCTATTCTGGTCGCAGGCTGTCGCG
1 CCGATTCTGTGTCACCTGCTATTTTACTTTTGGTATTTCCTCTATTCTGGTCGCAGGCTGTCGCG
* * * * *
795869 GCCAACTCTTCGGCGTTTGCATATAGTTCCTTTCCAGTTTTCGTTTTTGTAAAATAAGTTTCGGT
66 GCTAACTCTTCGGCATTTGCATATAGTTCCTTTCCGGTTTTCGTTTTCGTAAAATTAGTTTCGGT
* * * * * *
795934 AAATGGCGACTTATTAGTTTTAGCCCACTTAGCCGTTTCTAACGTCGAATATTTTGTTTTCTTCT
131 AAATGGCGACTCATTAGTTTTAGCCCAATAAG-CGTTTCTAACGTTGAATTTTTTGTTTTCTTTT
795999 TTCC-GATATTCC
195 TTCCAGAT-TT-C
* * * * *
796011 CCGATTCTGTGTCACTTGCTTTTTTACTTTTGGTATTCCCTCTATTCTGGTCGCAAGTTGTCGCG
1 CCGATTCTGTGTCACCTGCTATTTTACTTTTGGTATTTCCTCTATTCTGGTCGCAGGCTGTCGCG
* * * * *
796076 GCAAACTCATCGGTATTTGCATATAGTTCTTTTCC-----T-GTTTTCGTAAAATTAGTTTCTGT
66 GCTAACTCTTCGGCATTTGCATATAGTTCCTTTCCGGTTTTCGTTTTCGTAAAATTAGTTTCGGT
* * * *
796135 AACTGGCGACTCATTAATTTGAACCCAATAAGGCGTTTCTAACGT
131 AAATGGCGACTCATTAGTTTTAGCCCAATAA-GCGTTTCTAACGT
796180 CGGATAATTT
Statistics
Matches: 532, Mismatches: 44, Indels: 20
0.89 0.07 0.03
Matches are distributed among these distances:
201 56 0.11
202 2 0.00
205 2 0.00
206 9 0.02
207 458 0.86
208 5 0.01
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.43
Consensus pattern (205 bp):
CCGATTCTGTGTCACCTGCTATTTTACTTTTGGTATTTCCTCTATTCTGGTCGCAGGCTGTCGCG
GCTAACTCTTCGGCATTTGCATATAGTTCCTTTCCGGTTTTCGTTTTCGTAAAATTAGTTTCGGT
AAATGGCGACTCATTAGTTTTAGCCCAATAAGCGTTTCTAACGTTGAATTTTTTGTTTTCTTTTT
TCCAGATTTC
Found at i:800089 original size:17 final size:17
Alignment explanation
Indices: 800069--800102 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
800059 TAGGGGAAAT
*
800069 TGGGGTAAATGGGACAC
1 TGGGGCAAATGGGACAC
*
800086 TGGGGCAAGTGGGACAC
1 TGGGGCAAATGGGACAC
800103 ATAAACATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.15, G:0.44, T:0.15
Consensus pattern (17 bp):
TGGGGCAAATGGGACAC
Found at i:806564 original size:21 final size:21
Alignment explanation
Indices: 806534--806574 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
806524 CCCCCCCCCC
*
806534 AAAAAAAAAAGAAAAGAAAAG
1 AAAAAAAAAACAAAAGAAAAG
* *
806555 AAAAACAAAACCAAAGAAAA
1 AAAAAAAAAACAAAAGAAAA
806575 AACAACGAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAACAAAAGAAAAG
Found at i:806575 original size:17 final size:17
Alignment explanation
Indices: 806532--806579 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
806522 ACCCCCCCCC
* *
806532 CCAAAAAAAAAAGAAAA
1 CCAAAGAAAAAACAAAA
**
806549 GAAAAG-AAAAACAAAA
1 CCAAAGAAAAAACAAAA
806565 CCAAAGAAAAAACAA
1 CCAAAGAAAAAACAA
806580 CGAAAAAAAG
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.79, C:0.12, G:0.08, T:0.00
Consensus pattern (17 bp):
CCAAAGAAAAAACAAAA
Found at i:807083 original size:4 final size:4
Alignment explanation
Indices: 807046--807128 Score: 112
Period size: 4 Copynumber: 20.8 Consensus size: 4
807036 ACCCGCGTTA
* * * * * *
807046 TCTC TGTC TGTC TGTC TCTC TGTC TGTC TGTC TCTC TCTC TCTC TCTC
1 TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC
807094 TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCT
1 TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCT
807129 GTGCAATACA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 75 1.00
ACGTcount: A:0.00, C:0.42, G:0.07, T:0.51
Consensus pattern (4 bp):
TCTC
Found at i:807189 original size:21 final size:20
Alignment explanation
Indices: 807165--807204 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
807155 CAAAAAACCT
*
807165 TCATCATTTTACTATTTAAAC
1 TCATCATTATA-TATTTAAAC
*
807186 TCATGATTATATATTTAAA
1 TCATCATTATATATTTAAA
807205 TATATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (20 bp):
TCATCATTATATATTTAAAC
Found at i:811605 original size:13 final size:14
Alignment explanation
Indices: 811587--811615 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
811577 CTGCCCTAGA
811587 TTTTTTA-ATGAAT
1 TTTTTTACATGAAT
811600 TTTTTTACATGAAT
1 TTTTTTACATGAAT
811614 TT
1 TT
811616 CTACTGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.28, C:0.03, G:0.07, T:0.62
Consensus pattern (14 bp):
TTTTTTACATGAAT
Found at i:813260 original size:13 final size:13
Alignment explanation
Indices: 813242--813266 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
813232 TATCATGCAG
813242 TGTATGTAAAACA
1 TGTATGTAAAACA
813255 TGTATGTAAAAC
1 TGTATGTAAAAC
813267 CTTCAAAAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATGTAAAACA
Found at i:814196 original size:14 final size:16
Alignment explanation
Indices: 814169--814204 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
814159 TGTCATTCTG
814169 TTTTGTTTTGTTGTTT
1 TTTTGTTTTGTTGTTT
814185 TTTTGTTTTTGTT-TTT
1 TTTTG-TTTTGTTGTTT
814201 TTTT
1 TTTT
814205 AAAAGACATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (16 bp):
TTTTGTTTTGTTGTTT
Found at i:818065 original size:195 final size:194
Alignment explanation
Indices: 817732--818120 Score: 769
Period size: 195 Copynumber: 2.0 Consensus size: 194
817722 GCGCTTCTGG
817732 GTTAAAATGTGCACTTTACTATATATTTCATTGAAATGGCGTTGCTTGATTTTATTAATGACACT
1 GTTAAAATGTGCACTTTACTATATATTTCATTGAAATGGCGTTGCTTGATTTTATTAATGACACT
817797 GTATTTGAAACACAATAACATTATTACCGCGCAGACGAATCTTAAATAAATTTTAGAAATAAAAC
66 GTATTTGAAACACAATAACATTATTACCGCGCAGACGAATCTTAAATAAATTTTAGAAATAAAAC
817862 TATAAAACCTATGGATCATGTGGACAAATTTTCAAGGTAGGTTTTCTCACAAGCAGGTAAACCC
131 TATAAAACCTATGGATCATGTGGACAAATTTTCAAGGTAGGTTTTCTCACAAGCAGGTAAACCC
817926 GNTTAAAATGTGCACTTTACTATATATTTCATTGAAATGGCGTTGCTTGATTTTATTAATGACAC
1 G-TTAAAATGTGCACTTTACTATATATTTCATTGAAATGGCGTTGCTTGATTTTATTAATGACAC
817991 TGTATTTGAAACACAATAACATTATTACCGCGCAGACGAATCTTAAATAAATTTTAGAAATAAAA
65 TGTATTTGAAACACAATAACATTATTACCGCGCAGACGAATCTTAAATAAATTTTAGAAATAAAA
818056 CTATAAAACCTATGGATCATGTGGACAAATTTTCAAGGTAGGTTTTCTCACAAGCAGGTAAACCC
130 CTATAAAACCTATGGATCATGTGGACAAATTTTCAAGGTAGGTTTTCTCACAAGCAGGTAAACCC
818121 ATGAGCTACC
Statistics
Matches: 194, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
194 1 0.01
195 193 0.99
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (194 bp):
GTTAAAATGTGCACTTTACTATATATTTCATTGAAATGGCGTTGCTTGATTTTATTAATGACACT
GTATTTGAAACACAATAACATTATTACCGCGCAGACGAATCTTAAATAAATTTTAGAAATAAAAC
TATAAAACCTATGGATCATGTGGACAAATTTTCAAGGTAGGTTTTCTCACAAGCAGGTAAACCC
Found at i:841437 original size:53 final size:53
Alignment explanation
Indices: 841379--841490 Score: 215
Period size: 53 Copynumber: 2.1 Consensus size: 53
841369 TCCGCTTTAA
841379 ATTTGTATTTTGTTTAATGGATTTTTTTAATTGGTTGGCGATTTGTCATTTGC
1 ATTTGTATTTTGTTTAATGGATTTTTTTAATTGGTTGGCGATTTGTCATTTGC
*
841432 ATTTGTATTTTGTTTTATGGATTTTTTTAATTGGTTGGCGATTTGTCATTTGC
1 ATTTGTATTTTGTTTAATGGATTTTTTTAATTGGTTGGCGATTTGTCATTTGC
841485 ATTTGT
1 ATTTGT
841491 CATTGAAATT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 58 1.00
ACGTcount: A:0.16, C:0.05, G:0.21, T:0.58
Consensus pattern (53 bp):
ATTTGTATTTTGTTTAATGGATTTTTTTAATTGGTTGGCGATTTGTCATTTGC
Found at i:844359 original size:21 final size:21
Alignment explanation
Indices: 844333--844473 Score: 122
Period size: 21 Copynumber: 6.7 Consensus size: 21
844323 TACAAGATAA
844333 ACGATAGGATAGGATTCACGC
1 ACGATAGGATAGGATTCACGC
* *
844354 ACGATAGGATAGCATTAACGC
1 ACGATAGGATAGGATTCACGC
* * * *
844375 ACGATAGAACAGTATACACGC
1 ACGATAGGATAGGATTCACGC
* *
844396 ACGAAAGGATAGGATTAACGC
1 ACGATAGGATAGGATTCACGC
* * *
844417 ACGATAGAACT-GTATACACGC
1 ACGATAGGA-TAGGATTCACGC
* * **
844438 ACGATATGATAGGATTGATAC
1 ACGATAGGATAGGATTCACGC
*
844459 ACGATAGGAAAGGAT
1 ACGATAGGATAGGAT
844474 AAACGATGTT
Statistics
Matches: 91, Mismatches: 27, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
20 1 0.01
21 89 0.98
22 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (21 bp):
ACGATAGGATAGGATTCACGC
Found at i:844465 original size:42 final size:42
Alignment explanation
Indices: 844349--844453 Score: 174
Period size: 42 Copynumber: 2.5 Consensus size: 42
844339 GGATAGGATT
*
844349 CACGCACGATAGGATAGCATTAACGCACGATAGAACAGTATA
1 CACGCACGATAGGATAGGATTAACGCACGATAGAACAGTATA
* *
844391 CACGCACGAAAGGATAGGATTAACGCACGATAGAACTGTATA
1 CACGCACGATAGGATAGGATTAACGCACGATAGAACAGTATA
*
844433 CACGCACGATATGATAGGATT
1 CACGCACGATAGGATAGGATT
844454 GATACACGAT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (42 bp):
CACGCACGATAGGATAGGATTAACGCACGATAGAACAGTATA
Found at i:866693 original size:12 final size:12
Alignment explanation
Indices: 866676--866700 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
866666 GATGATTTGC
866676 AAAGGTGAGATG
1 AAAGGTGAGATG
866688 AAAGGTGAGATG
1 AAAGGTGAGATG
866700 A
1 A
866701 TAATCTTGAA
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:0.44, C:0.00, G:0.40, T:0.16
Consensus pattern (12 bp):
AAAGGTGAGATG
Found at i:872686 original size:2 final size:2
Alignment explanation
Indices: 872681--872727 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
872671 CATGCATAAT
872681 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
872723 TC TC T
1 TC TC T
872728 TCAGTACATG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:880992 original size:2 final size:2
Alignment explanation
Indices: 880985--881139 Score: 199
Period size: 2 Copynumber: 77.5 Consensus size: 2
880975 TCAATATAAA
880985 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
* *
881027 AG AG AG AG AG AG CG CG CA- 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
* * * *
881069 CG AG CG CA- AG AG AG AG AG AG AG AG AG AG AG CG AG CG CA- AG AG
1 AG AG AG -AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -AG AG AG
*
881111 AG AG AG AG AG CG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
881140 TCAGGGATTT
Statistics
Matches: 135, Mismatches: 12, Indels: 12
0.85 0.08 0.08
Matches are distributed among these distances:
1 3 0.02
2 132 0.98
ACGTcount: A:0.46, C:0.06, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:885583 original size:61 final size:61
Alignment explanation
Indices: 885507--885997 Score: 685
Period size: 61 Copynumber: 7.7 Consensus size: 61
885497 TTGCGTTCCT
* * * * *
885507 TGTACCTTACAACCACTGTAAACTATTCAAATCGTAACTAACATTATCACATACCTTCACA
1 TGTACCTTACAACCACTGTAAACTATTCACATCGTCACTTACATTGTCACATACCTTAACA
*
885568 TGTACCTTACAACCACTGTAAACTATTCACATCGTCACTTATATACATTGTCATATACCTTAACA
1 TGTACCTTACAACCACTGTAAACTATTCACATCGTCAC---T-TACATTGTCACATACCTTAACA
*
885633 TGTACCTTACAACCACTGTAAACTATTCACATCGTCACTTATATTGTCACATACCTTAACA
1 TGTACCTTACAACCACTGTAAACTATTCACATCGTCACTTACATTGTCACATACCTTAACA
885694 TGTACCTTACAACCACTGTAAACTATTCACATCGTCACTTACATTGTCACATACCTTAACA
1 TGTACCTTACAACCACTGTAAACTATTCACATCGTCACTTACATTGTCACATACCTTAACA
**
885755 TGTACAATACAACCACTGTAAACTATTCACATCGTCACTTATATACATTGTCACATACCTTAACA
1 TGTACCTTACAACCACTGTAAACTATTCACATCGTCAC---T-TACATTGTCACATACCTTAACA
* *
885820 TGTACCTTACAACCACTGTAAACTATTCACATCGTCAATTACATTATCACACACCTTAACATGTA
1 TGTACCTTACAACCACTGTAAACTATTCACATCGTCACTTACATTGT-------C---ACA--TA
885885 CCTTAACA
54 CCTTAACA
885893 TGTACCTTACAACCACTGTAAACTATTCACATCGTCACTTACATTGTCACATACCTTAACA
1 TGTACCTTACAACCACTGTAAACTATTCACATCGTCACTTACATTGTCACATACCTTAACA
* *
885954 TGTACCTTACGACCACTGTAAACTATTCAAATCGTCACTTACAT
1 TGTACCTTACAACCACTGTAAACTATTCACATCGTCACTTACAT
885998 CCATTGTCAC
Statistics
Matches: 391, Mismatches: 19, Indels: 40
0.87 0.04 0.09
Matches are distributed among these distances:
61 211 0.54
62 2 0.01
63 3 0.01
64 2 0.01
65 113 0.29
66 1 0.00
68 1 0.00
71 3 0.01
73 55 0.14
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.31
Consensus pattern (61 bp):
TGTACCTTACAACCACTGTAAACTATTCACATCGTCACTTACATTGTCACATACCTTAACA
Done.