Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3723_ERROPOS41587+
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 657619
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 2
Found at i:380066 original size:104 final size:104
Alignment explanation
Indices: 379886--380107 Score: 349
Period size: 104 Copynumber: 2.1 Consensus size: 104
379876 TGTATATAAA
** * * *
379886 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTAATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
379951 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
379990 AGGGGGTTG-TAAGTGCTAATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATC
1 A-GGGGTTGCTAAGTGCTAATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATC
380053 TTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
64 TTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
380094 AGGGGTTGCTAAGT
1 AGGGGTTGCTAAGT
380108 ACGATATCCA
Statistics
Matches: 108, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
103 7 0.06
104 93 0.86
105 8 0.07
ACGTcount: A:0.18, C:0.18, G:0.32, T:0.32
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTAATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:380160 original size:71 final size:72
Alignment explanation
Indices: 380028--380178 Score: 232
Period size: 71 Copynumber: 2.1 Consensus size: 72
380018 TCATTGGTGG
* * *
380028 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTACGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
*
380093 GAGGGGT
66 GAGAGGT
***
380100 TGCTAAGTACGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTACGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
380164 GAGAGGT
66 GAGAGGT
380171 TGCTAAGT
1 TGCTAAGT
380179 GATGATTCCC
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
71 43 0.60
72 29 0.40
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (72 bp):
TGCTAAGTACGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGAGGT
Found at i:383045 original size:28 final size:27
Alignment explanation
Indices: 382988--383139 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
382978 TAAATTGTGC
*
382988 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
383015 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
383043 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
383070 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* *
383098 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
383125 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
383140 GACTTAATAT
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:383052 original size:55 final size:55
Alignment explanation
Indices: 382988--383139 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
382978 TAAATTGTGC
*
382988 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
*
383043 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * *
383098 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
383140 GACTTAATAT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:391036 original size:28 final size:27
Alignment explanation
Indices: 390979--391130 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
390969 TAAATTGTGC
*
390979 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
391006 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
391034 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
391061 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* *
391089 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
391116 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
391131 GACTTAATAT
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:391043 original size:55 final size:55
Alignment explanation
Indices: 390979--391130 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
390969 TAAATTGTGC
*
390979 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
*
391034 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * *
391089 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
391131 GACTTAATAT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:394946 original size:37 final size:37
Alignment explanation
Indices: 394883--395061 Score: 288
Period size: 37 Copynumber: 4.9 Consensus size: 37
394873 AGCTCAGACG
* * * *
394883 AAATCTCCACATGAAGTTATCAGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
394920 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
394957 TAATCTCCACACGTAGTCATCGGGTCTTA-CCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
**
394993 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGATG
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
395030 AAATCTCCACACGTAGTCATCGGGTCTTACCC
1 AAATCTCCACACGTAGTCATCGGGTCTTACCC
395062 AGAATATATT
Statistics
Matches: 133, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
36 35 0.26
37 98 0.74
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:395004 original size:73 final size:73
Alignment explanation
Indices: 394883--395060 Score: 286
Period size: 73 Copynumber: 2.4 Consensus size: 73
394873 AGCTCAGACG
* * * *
394883 AAATCTCCACATGAAGTTATCAGGTCTTACCCGGACAAAATCTCCACACGTAGTCATCGGGTCTT
1 AAATCTCCACACGTAGTCATCGGGTCTTA-CCGGACAAAATCTCCACACGTAGTCATCGGGTCTT
394948 ACCCGGA-C
65 ACCCGGATC
394956 ATAATCTCCACACGTAGTCATCGGGTCTTACCGGACAAAATCTCCACACGTAGTCATCGGGTCTT
1 A-AATCTCCACACGTAGTCATCGGGTCTTACCGGACAAAATCTCCACACGTAGTCATCGGGTCTT
*
395021 ACCCGGATG
65 ACCCGGATC
395030 AAATCTCCACACGTAGTCATCGGGTCTTACC
1 AAATCTCCACACGTAGTCATCGGGTCTTACC
395061 CAGAATATAT
Statistics
Matches: 98, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
73 73 0.74
74 25 0.26
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (73 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCGGACAAAATCTCCACACGTAGTCATCGGGTCTTA
CCCGGATC
Found at i:395266 original size:48 final size:48
Alignment explanation
Indices: 395211--395345 Score: 225
Period size: 48 Copynumber: 2.8 Consensus size: 48
395201 GCACATCGCC
395211 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATACCTCA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATACCTCA
* *
395259 TACATATTTCGCACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATACCTCA
* * *
395307 TACATATTTCACATTAGCCATTCGGCCTTATCACATATA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATA
395346 TGCATGTTCA
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 81 1.00
ACGTcount: A:0.30, C:0.29, G:0.07, T:0.33
Consensus pattern (48 bp):
TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATACCTCA
Found at i:395380 original size:47 final size:47
Alignment explanation
Indices: 395315--395508 Score: 325
Period size: 47 Copynumber: 4.1 Consensus size: 47
395305 CATACATATT
* * * *
395315 TCACATTAGCCATTCGGCCTTATCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
*
395362 TCATATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
395409 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
* *
395456 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
395503 TCACAT
1 TCACAT
395509 AAAATCCTAA
Statistics
Matches: 139, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 139 1.00
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.33
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
Found at i:395412 original size:25 final size:25
Alignment explanation
Indices: 395383--395460 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 25
395373 ATTCGGCCTT
395383 ATCACACATATGCATGCTCACATTC
1 ATCACACATATGCATGCTCACATTC
* *
395408 AT--CACAT-TGGCCAT--TCGGCCTT-
1 ATCACACATAT-G-CATGCTC-ACATTC
395430 ATCACACATATGCATGCTCACATTC
1 ATCACACATATGCATGCTCACATTC
395455 ATCACA
1 ATCACA
395461 TTGGCCATTC
Statistics
Matches: 40, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 5 0.12
23 12 0.30
24 12 0.30
25 11 0.28
ACGTcount: A:0.29, C:0.32, G:0.10, T:0.28
Consensus pattern (25 bp):
ATCACACATATGCATGCTCACATTC
Found at i:395435 original size:22 final size:22
Alignment explanation
Indices: 395408--395483 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
395398 GCTCACATTC
395408 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* *
395430 ATCACACATAT-G-CATGCTC-ACATT
1 AT--CACAT-TGGCCAT--TCGGCCTT
395454 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
395477 ATCACAT
1 ATCACAT
395484 ATATGCATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 12 0.29
23 12 0.29
24 12 0.29
25 5 0.12
ACGTcount: A:0.25, C:0.32, G:0.13, T:0.30
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:406619 original size:51 final size:51
Alignment explanation
Indices: 406564--406684 Score: 138
Period size: 51 Copynumber: 2.4 Consensus size: 51
406554 ATCACATCTA
* * * * *
406564 TGGTAGTAAGTGCAGGGCACTATGTGTAA-AAGATAGCTTTG-GTCACAAGTG
1 TGGTACTATGTGCAGGCCACTATGTG-AAGAAGATAGCTTTGACT-ACAAGGG
* * *
406615 TGGTACTATGTGAAGGCCACTTTGTGAAGAAGGTAGCTTTGACTACAAGGG
1 TGGTACTATGTGCAGGCCACTATGTGAAGAAGATAGCTTTGACTACAAGGG
406666 TGGTACTATGTGCAGGCCA
1 TGGTACTATGTGCAGGCCA
406685 TCGGGCATCT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
50 2 0.03
51 56 0.95
52 1 0.02
ACGTcount: A:0.27, C:0.14, G:0.31, T:0.27
Consensus pattern (51 bp):
TGGTACTATGTGCAGGCCACTATGTGAAGAAGATAGCTTTGACTACAAGGG
Found at i:408488 original size:16 final size:15
Alignment explanation
Indices: 408463--408496 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
408453 AAGTTTGATA
*
408463 ATAATTAATATATATT
1 ATAATAAATATA-ATT
408479 ATAATAAATATAATT
1 ATAATAAATATAATT
408494 ATA
1 ATA
408497 TACTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:410472 original size:20 final size:18
Alignment explanation
Indices: 410447--410483 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
410437 ACCTAACACG
410447 AATTAAATTTAAACCATATT
1 AATTAAA-TTAAA-CATATT
410467 AATTAAATTAAACATAT
1 AATTAAATTAAACATAT
410484 CAACATCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 5 0.29
20 7 0.41
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTAAATTAAACATATT
Found at i:411354 original size:12 final size:12
Alignment explanation
Indices: 411332--411361 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
411322 AAATGATCAA
411332 AATTAATAAAATT
1 AATT-ATAAAATT
411345 AATTATAAAATT
1 AATTATAAAATT
411357 AATTA
1 AATTA
411362 AAATTTAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AATTATAAAATT
Found at i:413611 original size:50 final size:50
Alignment explanation
Indices: 413394--413729 Score: 345
Period size: 50 Copynumber: 6.7 Consensus size: 50
413384 CTAGTACGCA
*
413394 TAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTGGTACACG
* * * * *
413444 TAATAG-CTGCACTTAGTACTACACATGTGACTTATCCATCTGATACAGG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTGGTACACG
* * ** * * * *
413493 TAGTAGCCTGCACTTAGTACTACACACGTAATCGAAGTTAA-CGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGTGA-CCTA-TCAATCTGGTACACG
* *
413544 TAGTAGCCTAG-AATTAGTACTACACATGTGACCTATCAATCCGGTACACG
1 TAGTAGCCT-GCACTTAGTACTACACATGTGACCTATCAATCTGGTACACG
* ** * * * ** *
413594 TAGTAGCCTGCACTTAGTACTACACACGTGATCAAAACTATCGGGTATGCA
1 TAGTAGCCTGCACTTAGTACTACACATGTGA-CCTATCAATCTGGTACACG
* * *
413645 TAGTAGCCTTCACTTAGTACTACACATGCGACCTAACAATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTGGTACACG
* *
413695 TAGTAGGCTGCACTTAGTACTACACACGTGACCTA
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTA
413730 AAACTGTCTT
Statistics
Matches: 228, Mismatches: 51, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
49 47 0.21
50 106 0.46
51 72 0.32
52 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTGGTACACG
Found at i:413724 original size:101 final size:101
Alignment explanation
Indices: 413453--413734 Score: 393
Period size: 101 Copynumber: 2.8 Consensus size: 101
413443 GTAATAGCTG
* * * *
413453 CACTTAGTACTACACATGTGACTTATCCATCTGATACAGGTAGTAGCCTGCACTTAGTACTACAC
1 CACTTAGTACTACACATGTGACCTATCAATCTGGTACACGTAGTAGCCTGCACTTAGTACTACAC
* * **
413518 ACGTAATCGAAGTTAACGGGTACGCATAGTAGCCTA
66 ACGTGATCAAAACTAACGGGTACGCATAGTAGCCTA
* * *
413554 GAATTAGTACTACACATGTGACCTATCAATCCGGTACACGTAGTAGCCTGCACTTAGTACTACAC
1 CACTTAGTACTACACATGTGACCTATCAATCTGGTACACGTAGTAGCCTGCACTTAGTACTACAC
* * *
413619 ACGTGATCAAAACTATCGGGTATGCATAGTAGCCTT
66 ACGTGATCAAAACTAACGGGTACGCATAGTAGCCTA
* * *
413655 CACTTAGTACTACACATGCGACCTAACAATCTGGTACACGTAGTAGGCTGCACTTAGTACTACAC
1 CACTTAGTACTACACATGTGACCTATCAATCTGGTACACGTAGTAGCCTGCACTTAGTACTACAC
*
413720 ACGTGACCTAAAACT
66 ACGTGATC-AAAACT
413735 GTCTTAAACA
Statistics
Matches: 159, Mismatches: 21, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
101 153 0.96
102 6 0.04
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (101 bp):
CACTTAGTACTACACATGTGACCTATCAATCTGGTACACGTAGTAGCCTGCACTTAGTACTACAC
ACGTGATCAAAACTAACGGGTACGCATAGTAGCCTA
Found at i:413730 original size:50 final size:50
Alignment explanation
Indices: 413394--413776 Score: 344
Period size: 50 Copynumber: 7.6 Consensus size: 50
413384 CTAGTACGCA
* *
413394 TAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTGGTACACG
* * * * * *
413444 TAATAG-CTGCACTTAGTACTACACATGTGACTTATCCATCTGATACAGG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTGGTACACG
* * * * * * * *
413493 TAGTAGCCTGCACTTAGTACTACACACGTAATCGAAGTTAA-CGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAA--CAATCTGGTACACG
* * *
413544 TAGTAGCCTAG-AATTAGTACTACACATGTGACCTATCAATCCGGTACACG
1 TAGTAGCCT-GCACTTAGTACTACACATGTGACCTAACAATCTGGTACACG
* ** * * ** *
413594 TAGTAGCCTGCACTTAGTACTACACACGTGATCAAAACTATCGGGTATGCA
1 TAGTAGCCTGCACTTAGTACTACACATGTGA-CCTAACAATCTGGTACACG
* *
413645 TAGTAGCCTTCACTTAGTACTACACATGCGACCTAACAATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTGGTACACG
* * * *
413695 TAGTAGGCTGCACTTAGTACTACACACGTGACCTAA-AA-CTGTCTTAAACACA
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTG--GT--ACACG
* *
413747 AAGTAGCCTGCACATAGTACTACACATGTG
1 TAGTAGCCTGCACTTAGTACTACACATGTG
413777 TTCTCACAAC
Statistics
Matches: 262, Mismatches: 60, Indels: 20
0.77 0.18 0.06
Matches are distributed among these distances:
48 3 0.01
49 48 0.18
50 107 0.41
51 72 0.27
52 32 0.12
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTGGTACACG
Found at i:420620 original size:180 final size:178
Alignment explanation
Indices: 420314--420674 Score: 492
Period size: 180 Copynumber: 2.0 Consensus size: 178
420304 TAGCTTGAGC
* * *
420314 TACGGAACTCCAAATTAAGATCTATTAATTTTTCCAGAAACCAGACACATATATTATTACCATAA
1 TACGGAACTCCAAATTAAGAACCACTAATTTTTCCAGAAACCAGACACATATATTATTACCATAA
* * *
420379 AATTTTTAGAATTTTTGGTTTATCCAATTAGTACATTTTATTCATTAAATTTACCCCTATTTCAC
66 AATTTTCAGAATTTTTGGTTTAGCCAATTAGTACATTTTATTCATTAAATATACCCCTATTTCAC
* * *
420444 TGTCCAACAGTTCTC-ACCTCTCTTCAGTAAAAATTATTTATCTCATGG
131 TATCCAACAATTC-CAACCTCTCTTCACTAAAAATTATTTATCTCATGG
* * * *
420492 TACGGGACTCCAAATTAAGAACCACTAA-TTTTCCTAGAAACTATACTCATATATATTATTACCA
1 TACGGAACTCCAAATTAAGAACCACTAATTTTTCC-AGAAACCAGA--CACATATATTATTACCA
* *
420556 TAAAATTTTCAGAATTTTTGGTTTAGCCAGTTAGTATATTTTATTCATTAAATATACCCCTATTT
63 TAAAATTTTCAGAATTTTTGGTTTAGCCAATTAGTACATTTTATTCATTAAATATACCCCTATTT
** * * *
420621 CACTATCTGATAATTCCAATCTTTCTTCACTAAAAATTATTTATCTCATGG
128 CACTATCCAACAATTCCAACCTCTCTTCACTAAAAATTATTTATCTCATGG
420672 TAC
1 TAC
420675 AGATCTCGGA
Statistics
Matches: 159, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
177 6 0.04
178 32 0.20
179 1 0.01
180 120 0.75
ACGTcount: A:0.34, C:0.19, G:0.08, T:0.40
Consensus pattern (178 bp):
TACGGAACTCCAAATTAAGAACCACTAATTTTTCCAGAAACCAGACACATATATTATTACCATAA
AATTTTCAGAATTTTTGGTTTAGCCAATTAGTACATTTTATTCATTAAATATACCCCTATTTCAC
TATCCAACAATTCCAACCTCTCTTCACTAAAAATTATTTATCTCATGG
Found at i:421410 original size:101 final size:100
Alignment explanation
Indices: 421236--421521 Score: 315
Period size: 101 Copynumber: 2.9 Consensus size: 100
421226 TTGGTACGCA
* * * * * * **
421236 TAGTAGCCTGCAGTTAGTACTACACATGCAACCTATCAATTTGGTACACGTAGTAGCCTGCACTT
1 TAGTAGCCTGCACTTAATACTACACACGCGACCGAACAATCGGGTACACGTAGTAGCCTGCACTT
* * *
421301 AGTACTACACACGTGACTTATCCATCTGATACA-C
66 AGTACTACACACGTGACCTATCAATCCGATACATC
* * * * * *
421335 GTAGTAGCCTGTACTTAATACTACACACGTGATCGAAGTTAA-CGGGTACACATAGTGGCCTGCA
1 -TAGTAGCCTGCACTTAATACTACACACGCGACCGAA--CAATCGGGTACACGTAGTAGCCTGCA
* *
421399 CTTAGTACTACACATGTGACCTATCAATCCGGTACATC
63 CTTAGTACTACACACGTGACCTATCAATCCGATACATC
* * * * *
421437 TAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGTACATGTAGTAGCCTGCACTT
1 TAGTAGCCTGCACTTAATACTACACACGCGACCGAACAATCGGGTACACGTAGTAGCCTGCACTT
421502 AGTACTACACACGTGACCTA
66 AGTACTACACACGTGACCTA
421522 AAATTGTCTT
Statistics
Matches: 151, Mismatches: 31, Indels: 8
0.79 0.16 0.04
Matches are distributed among these distances:
99 2 0.01
100 67 0.44
101 79 0.52
102 3 0.02
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (100 bp):
TAGTAGCCTGCACTTAATACTACACACGCGACCGAACAATCGGGTACACGTAGTAGCCTGCACTT
AGTACTACACACGTGACCTATCAATCCGATACATC
Found at i:421491 original size:151 final size:151
Alignment explanation
Indices: 421228--421517 Score: 420
Period size: 151 Copynumber: 1.9 Consensus size: 151
421218 GAAGCTGTTT
* * **
421228 GGTACGCATAGTAGCCTGCAGTTAGTACTACACATGCAACCTATCAATTTGGTACACGTAGTAGC
1 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCAACCTATCAATCCGGTACACGTAGTAGC
* * * * *
421293 CTGCACTTAGTACTACACACGTGACTTATCCATCTGATACACGTAGTAGCCTGTACTTAATACTA
66 CTGCACTTAGTACTACACACGCGACCTAACAATCTGATACACGTAGTAGCCTGCACTTAATACTA
421358 CACACGTGATCGAAGTTAACG
131 CACACGTGATCGAAGTTAACG
* **
421379 GGTACACATAGTGGCCTGCACTTAGTACTACACATGTGACCTATCAATCCGGTACATC-TAGTAG
1 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCAACCTATCAATCCGGTACA-CGTAGTAG
* * * *
421443 CCTGCACTTAGTACTACACATGCGACCTAACAATCTGGTACATGTAGTAGCCTGCACTTAGTACT
65 CCTGCACTTAGTACTACACACGCGACCTAACAATCTGATACACGTAGTAGCCTGCACTTAATACT
421508 ACACACGTGA
130 ACACACGTGA
421518 CCTAAAATTG
Statistics
Matches: 122, Mismatches: 16, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
151 121 0.99
152 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.27
Consensus pattern (151 bp):
GGTACACATAGTAGCCTGCACTTAGTACTACACATGCAACCTATCAATCCGGTACACGTAGTAGC
CTGCACTTAGTACTACACACGCGACCTAACAATCTGATACACGTAGTAGCCTGCACTTAATACTA
CACACGTGATCGAAGTTAACG
Found at i:421522 original size:50 final size:50
Alignment explanation
Indices: 421227--421564 Score: 317
Period size: 50 Copynumber: 6.7 Consensus size: 50
421217 CGAAGCTGTT
* * * * ** * *
421227 TGGTACGCATAGTAGCCTGCAGTTAGTACTACACATGCAACCTATCAATT
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATC
* * *
421277 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACTTATCCATC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATC
* * * * * *
421327 TGATACACGTAGTAGCCTGTACTTAATACTACACACGTGATCGAAGTTAA-C
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA--CAATC
* * * * *
421378 GGGTACACATAGTGGCCTGCACTTAGTACTACACATGTGACCTATCAATC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATC
* * *
421428 CGGTACATC-TAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATC
1 TGGTACA-CGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATC
*
421478 TGGTACATGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA-AAT-
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATC
* *
421526 TGTCTTAAACACATAGTAGCCTGCA-TATAGTACTACACA
1 TG--GT--ACACGTAGTAGCCTGCACT-TAGTACTACACA
421565 TGTGTTCTCA
Statistics
Matches: 238, Mismatches: 40, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
48 2 0.01
49 5 0.02
50 165 0.69
51 38 0.16
52 28 0.12
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.27
Consensus pattern (50 bp):
TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATC
Found at i:427742 original size:42 final size:43
Alignment explanation
Indices: 427643--427805 Score: 149
Period size: 44 Copynumber: 3.8 Consensus size: 43
427633 AGCTCGTGCA
* * ** *
427643 ATGCCAACATCCTAGACGTTGTCTTACATGT-ACTCAAATATCG
1 ATGCCAACATCCCAGACGTGGTCTTACACATAAATCAAATA-CG
* *
427686 ATGCC-ACTGTCCCAGGCAG-GGTCTTACACGA-AAA-CAAATACG
1 ATGCCAAC-ATCCCAGAC-GTGGTCTTACAC-ATAAATCAAATACG
427728 ATGCCAACATCCCAGACGTGGTCTTACACATAAATCATAAGT-CG
1 ATGCCAACATCCCAGACGTGGTCTTACACATAAATCA-AA-TACG
*
427772 ATGCCAACATCCCAGACGTGGTCTGACACGATAA
1 ATGCCAACATCCCAGACGTGGTCTTACAC-ATAA
427806 CACATATCGG
Statistics
Matches: 99, Mismatches: 10, Indels: 20
0.77 0.08 0.16
Matches are distributed among these distances:
41 2 0.02
42 29 0.29
43 29 0.29
44 34 0.34
45 5 0.05
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.22
Consensus pattern (43 bp):
ATGCCAACATCCCAGACGTGGTCTTACACATAAATCAAATACG
Found at i:438192 original size:27 final size:27
Alignment explanation
Indices: 438134--438211 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
438124 ATGATGACCG
* *
438134 AAATACCCCTATAGGGTAAAATTACTA
1 AAATACCCCTATAGGGTAAAATGAATA
*
438161 AAATACCCCTATAGGGTAAAATGAATG
1 AAATACCCCTATAGGGTAAAATGAATA
* * * *
438188 TAATACCCTTGTAAGGTAAAATGA
1 AAATACCCCTATAGGGTAAAATGA
438212 CTGTTTGCCC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (27 bp):
AAATACCCCTATAGGGTAAAATGAATA
Found at i:447875 original size:27 final size:26
Alignment explanation
Indices: 447807--447981 Score: 165
Period size: 27 Copynumber: 6.5 Consensus size: 26
447797 TTAGATTACC
*
447807 AAATTACTGAAATACCCCCAG-TTGTA
1 AAATTACT-AAATACCCTCAGTTTGTA
* * *
447833 AAATTACCAAAGTACCCCCAGTTTATA
1 AAATTACTAAA-TACCCTCAGTTTGTA
* *
447860 AAATTACTACAATACCGTC-GATTGTA
1 AAATTACTA-AATACCCTCAGTTTGTA
* *
447886 AAATTACTGAAATACCCTGAATTTGTA
1 AAATTACT-AAATACCCTCAGTTTGTA
* * *
447913 AAATTATCGAAATACCTTCAGTTTGCA
1 AAATTA-CTAAATACCCTCAGTTTGTA
*
447940 AAATTACTAAAATACCCTCAATTTGTA
1 AAATTACT-AAATACCCTCAGTTTGTA
447967 AAATTACTGAAATAC
1 AAATTACT-AAATAC
447982 TCCTGTAAGA
Statistics
Matches: 121, Mismatches: 21, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
25 3 0.02
26 37 0.31
27 78 0.64
28 3 0.02
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.30
Consensus pattern (26 bp):
AAATTACTAAATACCCTCAGTTTGTA
Found at i:447902 original size:53 final size:53
Alignment explanation
Indices: 447807--447981 Score: 183
Period size: 53 Copynumber: 3.3 Consensus size: 53
447797 TTAGATTACC
** * * * * *
447807 AAATTACTGAAATACCCCCAG-TTGTAAAATTACCAAAGTACCCCCAGTTTATA
1 AAATTACT-AAATACCGTCAGATTGTAAAATTACTAAAATACCCTCAATTTGTA
* *
447860 AAATTACTACAATACCGTC-GATTGTAAAATTACTGAAATACCCTGAATTTGTA
1 AAATTACTA-AATACCGTCAGATTGTAAAATTACTAAAATACCCTCAATTTGTA
* * * *
447913 AAATTATCGAAATACCTTCAGTTTGCAAAATTACTAAAATACCCTCAATTTGTA
1 AAATTA-CTAAATACCGTCAGATTGTAAAATTACTAAAATACCCTCAATTTGTA
447967 AAATTACTGAAATAC
1 AAATTACT-AAATAC
447982 TCCTGTAAGA
Statistics
Matches: 101, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
52 2 0.02
53 55 0.54
54 44 0.44
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.30
Consensus pattern (53 bp):
AAATTACTAAATACCGTCAGATTGTAAAATTACTAAAATACCCTCAATTTGTA
Found at i:448021 original size:27 final size:27
Alignment explanation
Indices: 447991--448189 Score: 274
Period size: 27 Copynumber: 7.4 Consensus size: 27
447981 CTCCTGTAAG
447991 ATAGAATTACCATTTTACCCTCGATTT
1 ATAGAATTACCATTTTACCCTCGATTT
* *
448018 ATAGAATTATCGTTTTACCCTCGATTT
1 ATAGAATTACCATTTTACCCTCGATTT
*
448045 ATAGAATTACCATTTTACCTTCGATTT
1 ATAGAATTACCATTTTACCCTCGATTT
*
448072 ATAGAATTA-CATTTTTACCCTCAATTT
1 ATAGAATTACCA-TTTTACCCTCGATTT
* * *
448099 ACAGAATTACCGTCTTACCCTCGATTT
1 ATAGAATTACCATTTTACCCTCGATTT
* *
448126 ATAGAATTACCATTTTACCTTTGATTT
1 ATAGAATTACCATTTTACCCTCGATTT
*
448153 ACAGAATTACCATTTTACCCTCGATTT
1 ATAGAATTACCATTTTACCCTCGATTT
* *
448180 ACAAAATTAC
1 ATAGAATTAC
448190 TGAAATACCC
Statistics
Matches: 150, Mismatches: 20, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
26 2 0.01
27 147 0.98
28 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.41
Consensus pattern (27 bp):
ATAGAATTACCATTTTACCCTCGATTT
Found at i:448077 original size:81 final size:81
Alignment explanation
Indices: 447991--448189 Score: 319
Period size: 81 Copynumber: 2.5 Consensus size: 81
447981 CTCCTGTAAG
* * *
447991 ATAGAATTACCATTTTACCCTCGATTTATAGAATTATCGTTTTACCCTCGATTTATAGAATTACC
1 ATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTCTTACCCTCGATTTATAGAATTACC
448056 ATTTTACCTTCGATTT
66 ATTTTACCTTCGATTT
*
448072 ATAGAATTA-CATTTTTACCCTCAATTTACAGAATTACCGTCTTACCCTCGATTTATAGAATTAC
1 ATAGAATTACCA-TTTTACCCTCGATTTACAGAATTACCGTCTTACCCTCGATTTATAGAATTAC
*
448136 CATTTTACCTTTGATTT
65 CATTTTACCTTCGATTT
* *
448153 ACAGAATTACCATTTTACCCTCGATTTACAAAATTAC
1 ATAGAATTACCATTTTACCCTCGATTTACAGAATTAC
448190 TGAAATACCC
Statistics
Matches: 108, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
80 2 0.02
81 104 0.96
82 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.41
Consensus pattern (81 bp):
ATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTCTTACCCTCGATTTATAGAATTACC
ATTTTACCTTCGATTT
Found at i:448198 original size:27 final size:27
Alignment explanation
Indices: 448087--448308 Score: 131
Period size: 27 Copynumber: 8.2 Consensus size: 27
448077 ATTACATTTT
* * ****
448087 TACCCTCAATTTACAGAATTACCGTCT
1 TACCCTCGATTTACAAAATTACCAAAA
* * ***
448114 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAAAATTACCAAAA
* * * ***
448141 TACCTTTGATTTACAGAATTACCATTT
1 TACCCTCGATTTACAAAATTACCAAAA
**
448168 TACCCTCGATTTACAAAATTACTGAAA
1 TACCCTCGATTTACAAAATTACCAAAA
* *
448195 TACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACCAAAA
** *
448222 TACCCTCGATCAATAAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACCAAAA
* * * **
448249 TATCCTTGGTTTGTAAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACCAAAA
*** *
448276 TACCCGT-GATTTGTGAAATTACCGAAA
1 TACCC-TCGATTTACAAAATTACCAAAA
448303 TACCCT
1 TACCCT
448309 TGTAGGGTAG
Statistics
Matches: 160, Mismatches: 34, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
26 1 0.01
27 158 0.99
28 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.33
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACCAAAA
Found at i:448199 original size:81 final size:81
Alignment explanation
Indices: 447993--448218 Score: 294
Period size: 81 Copynumber: 2.8 Consensus size: 81
447983 CCTGTAAGAT
* *
447993 AGAATTACCATTTTACCCTCGATTTATAGAATTA-TCGTTTTACCCTCGATTTATAGAATTACCA
1 AGAATTACCATTTTACCCTCGATTTACAGAATTACT-GTATTACCCTCGATTTATAGAATTACCA
*
448057 TTTTACCTTCGATTTAT
65 TTTTACCTTCGATTTAC
* * *
448074 AGAATTA-CATTTTTACCCTCAATTTACAGAATTACCGTCTTACCCTCGATTTATAGAATTACCA
1 AGAATTACCA-TTTTACCCTCGATTTACAGAATTACTGTATTACCCTCGATTTATAGAATTACCA
*
448138 TTTTACCTTTGATTTAC
65 TTTTACCTTCGATTTAC
* * * * * * *
448155 AGAATTACCATTTTACCCTCGATTTACAAAATTACTGAAATACCCTTGGTTTACAAAATTACCA
1 AGAATTACCATTTTACCCTCGATTTACAGAATTACTGTATTACCCTCGATTTATAGAATTACCA
448219 AAATACCCTC
Statistics
Matches: 126, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
80 2 0.02
81 122 0.97
82 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.39
Consensus pattern (81 bp):
AGAATTACCATTTTACCCTCGATTTACAGAATTACTGTATTACCCTCGATTTATAGAATTACCAT
TTTACCTTCGATTTAC
Found at i:448208 original size:54 final size:54
Alignment explanation
Indices: 447993--448218 Score: 251
Period size: 54 Copynumber: 4.2 Consensus size: 54
447983 CCTGTAAGAT
* * *
447993 AGAATTACCATTTTACCCTCGATTTATAGAATTA-TCGTTTTACCCTCGATTTAT
1 AGAATTACCATTTTACCCTCGATTTATAGAATTACT-GATTTACCCTTGATTTAC
* * **
448047 AGAATTACCATTTTACCTTCGATTTATAGAATTACAT-TTTTACCCTCAATTTAC
1 AGAATTACCATTTTACCCTCGATTTATAGAATTAC-TGATTTACCCTTGATTTAC
* * * *
448101 AGAATTACCGTCTTACCCTCGATTTATAGAATTAC-CATTTTACCTTTGATTTAC
1 AGAATTACCATTTTACCCTCGATTTATAGAATTACTGA-TTTACCCTTGATTTAC
* * ** *
448155 AGAATTACCATTTTACCCTCGATTTACAAAATTACTGAAATACCCTTGGTTTAC
1 AGAATTACCATTTTACCCTCGATTTATAGAATTACTGATTTACCCTTGATTTAC
*
448209 AAAATTACCA
1 AGAATTACCA
448219 AAATACCCTC
Statistics
Matches: 147, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
54 145 0.99
55 1 0.01
56 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.39
Consensus pattern (54 bp):
AGAATTACCATTTTACCCTCGATTTATAGAATTACTGATTTACCCTTGATTTAC
Found at i:448226 original size:54 final size:54
Alignment explanation
Indices: 447885--448310 Score: 191
Period size: 54 Copynumber: 7.9 Consensus size: 54
447875 CGTCGATTGT
** * * * *
447885 AAAATTACTGAAATACCCT-GAATTTGTAAAATTATCGAAATA-CCTTCAGTTTGC
1 AAAATTACCAAAATACCCTCG-ATTTATAAAATTACCGAAATACCCTT-GGTTTAC
* * * * * *
447939 AAAATTACTAAAATACCCTCAATTTGTAAAATTACTGAAATACTCC-T-G-TAAG
1 AAAATTACCAAAATACCCTCGATTTATAAAATTACCGAAATAC-CCTTGGTTTAC
*** * * *** * * *
447991 ATAGAATTACCATTTTACCCTCGATTTATAGAATTATCGTTTTACCCTCGATTTAT
1 A-A-AATTACCAAAATACCCTCGATTTATAAAATTACCGAAATACCCTTGGTTTAC
* *** * * ***** ***
448047 AGAATTACCATTTTACCTTCGATTTATAGAATTACATTTTTACCCTCAATTTAC
1 AAAATTACCAAAATACCCTCGATTTATAAAATTACCGAAATACCCTTGGTTTAC
* **** * ** * *
448101 AGAATTACCGTCTTACCCTCGATTTATAGAATTACC-ATTTTACCTTTGATTTAC
1 AAAATTACCAAAATACCCTCGATTTATAAAATTACCGA-AATACCCTTGGTTTAC
* *** * *
448155 AGAATTACCATTTTACCCTCGATTTACAAAATTACTGAAATACCCTTGGTTTAC
1 AAAATTACCAAAATACCCTCGATTTATAAAATTACCGAAATACCCTTGGTTTAC
** * * **
448209 AAAATTACCAAAATACCCTCGATCAATAAAATTACCAAAATATCCTTGGTTTGT
1 AAAATTACCAAAATACCCTCGATTTATAAAATTACCGAAATACCCTTGGTTTAC
* *
448263 AAAATTACCAAAATACCCGT-GATTTGTGAAATTACCGAAATACCCTTG
1 AAAATTACCAAAATACCC-TCGATTTATAAAATTACCGAAATACCCTTG
448311 TAGGGTAGAA
Statistics
Matches: 296, Mismatches: 65, Indels: 22
0.77 0.17 0.06
Matches are distributed among these distances:
52 2 0.01
53 4 0.01
54 282 0.95
55 3 0.01
56 5 0.02
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (54 bp):
AAAATTACCAAAATACCCTCGATTTATAAAATTACCGAAATACCCTTGGTTTAC
Found at i:448322 original size:27 final size:27
Alignment explanation
Indices: 448292--448666 Score: 475
Period size: 27 Copynumber: 14.3 Consensus size: 27
448282 TGATTTGTGA
*
448292 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
448319 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
448346 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
448373 AATTACCG-AA-A------TA-GGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
448391 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
448418 AATTACC-AGAATACCCCTATAGGGTAG
1 AATTACCGA-AATACCCCTGTAGGGTAG
*
448445 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
448472 ACTTATCGCAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
448499 AATTATCGAAATGCCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
448526 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
448553 AATTACCAAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
448580 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
448607 AATTACTAAAATACCCCTGTAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
448634 AATTACCGAGATA-CCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
448660 AATTACC
1 AATTACC
448667 ATTTTTCCCC
Statistics
Matches: 306, Mismatches: 31, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
18 13 0.04
19 4 0.01
20 1 0.00
25 1 0.00
26 21 0.07
27 265 0.87
28 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:448391 original size:18 final size:18
Alignment explanation
Indices: 448368--448403 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
448358 ACCCCTGTAG
448368 GGTAGAATTACCGAAATA
1 GGTAGAATTACCGAAATA
448386 GGTAGAATTACCGAAATA
1 GGTAGAATTACCGAAATA
448404 CCCCTGTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.22
Consensus pattern (18 bp):
GGTAGAATTACCGAAATA
Found at i:450936 original size:40 final size:40
Alignment explanation
Indices: 450713--450969 Score: 324
Period size: 40 Copynumber: 6.5 Consensus size: 40
450703 CGGATGATAA
* * * *
450713 CCGGGCTAACTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
*
450753 TCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
450793 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
450833 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
450873 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
450913 CCGGGCTATGTCCCGAAGGCA-TTGAGTGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
450952 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
450970 TACTTGGCTT
Statistics
Matches: 191, Mismatches: 24, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
38 15 0.08
39 14 0.07
40 162 0.85
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:458909 original size:40 final size:40
Alignment explanation
Indices: 458854--459110 Score: 342
Period size: 40 Copynumber: 6.5 Consensus size: 40
458844 CGGATGATAA
* * * *
458854 CCGGGCTAACTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
458894 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
458934 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
458974 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
459014 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
459054 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
459093 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
459111 TACTTGGCTT
Statistics
Matches: 196, Mismatches: 19, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
38 15 0.08
39 16 0.08
40 165 0.84
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:460594 original size:6 final size:6
Alignment explanation
Indices: 460579--460666 Score: 72
Period size: 6 Copynumber: 14.3 Consensus size: 6
460569 ATTCAGTTAC
* * *
460579 CTGATA CTGATT CTGATT TTGATT CTG-TT ACCTGATA CTGATT CTGATT
1 CTGATT CTGATT CTGATT CTGATT CTGATT --CTGATT CTGATT CTGATT
* * *
460628 CTGATT CTG-TCAC CTAATT CTGATT TTGATT CTGATT CT
1 CTGATT CTGAT--T CTGATT CTGATT CTGATT CTGATT CT
460667 AGTTTTGATA
Statistics
Matches: 65, Mismatches: 11, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
5 3 0.05
6 55 0.85
7 5 0.08
8 2 0.03
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.48
Consensus pattern (6 bp):
CTGATT
Found at i:460651 original size:37 final size:31
Alignment explanation
Indices: 460556--460666 Score: 150
Period size: 31 Copynumber: 3.5 Consensus size: 31
460546 TTGCATTCAT
* *
460556 ATTCTGATTTTTGATTCAGTTACCTGATACTG
1 ATTCTGA-TTCTGATTCTGTTACCTGATACTG
*
460588 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTCTGATTCTGTTACCTGATACTG
* * *
460619 ATTCTGATTCTGATTCTGTCACCTAATTCTG
1 ATTCTGATTCTGATTCTGTTACCTGATACTG
*
460650 ATTTTGATTCTGATTCT
1 ATTCTGATTCTGATTCT
460667 AGTTTTGATA
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
31 66 0.90
32 7 0.10
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.49
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTTACCTGATACTG
Found at i:466297 original size:17 final size:18
Alignment explanation
Indices: 466270--466303 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
466260 CTTTGCTCTG
*
466270 TTTTTGATGATTTTTACA
1 TTTTTGATGATTATTACA
466288 TTTTTG-TGATTATTAC
1 TTTTTGATGATTATTAC
466304 TTTGAGTACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.21, C:0.06, G:0.12, T:0.62
Consensus pattern (18 bp):
TTTTTGATGATTATTACA
Found at i:474705 original size:42 final size:42
Alignment explanation
Indices: 474609--474739 Score: 122
Period size: 43 Copynumber: 3.1 Consensus size: 42
474599 CATGCATGTT
* * *
474609 CATGTCTGGGACATTGGCATTGTATTGAGATTACGTGTAAGAC
1 CATGTCTGGGACATTGGCATCGTAAT-AGATTACATGTAAGAC
* *
474652 CATGTCTGGGACATTGGCATCGTTAAT-GATTTCATTTAAGAC
1 CATGTCTGGGACATTGGCATCG-TAATAGATTACATGTAAGAC
* * * * *
474694 CCTGTCTGGGACAGTGGCATTG-ATATGTGATAACATGTAAGAC
1 CATGTCTGGGACATTGGCATCGTA-AT-AGATTACATGTAAGAC
474737 CAT
1 CAT
474740 ATCTAGGATA
Statistics
Matches: 72, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
40 1 0.01
41 2 0.03
42 31 0.43
43 35 0.49
44 3 0.04
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (42 bp):
CATGTCTGGGACATTGGCATCGTAATAGATTACATGTAAGAC
Found at i:479014 original size:42 final size:43
Alignment explanation
Indices: 478921--479069 Score: 151
Period size: 43 Copynumber: 3.5 Consensus size: 43
478911 TAATGTCGTC
* ** *
478921 GTCCCAGACGTGGTCTTACATGTAATCAAATATCGATGCCACT
1 GTCCCAGACATGGTCTTACATAAAATCAAATATCGATGCCAAT
* * *
478964 GTCCCAGACAAGGTCTTACATAAAATTAGATAT-GATGCCAAT
1 GTCCCAGACATGGTCTTACATAAAATCAAATATCGATGCCAAT
* *
479006 GTCCCAGACATGGTCTTACGCATAAAA-CAAA-AGTCGGTGCCAAC
1 GTCCCAGACATGGTCTTA--CATAAAATCAAATA-TCGATGCCAAT
* *
479050 ATCCCAGACGTGGTCTTACA
1 GTCCCAGACATGGTCTTACA
479070 CGAAATCACA
Statistics
Matches: 88, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
42 28 0.32
43 30 0.34
44 30 0.34
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACATAAAATCAAATATCGATGCCAAT
Found at i:479276 original size:32 final size:32
Alignment explanation
Indices: 479238--479331 Score: 188
Period size: 32 Copynumber: 2.9 Consensus size: 32
479228 ACAATAATAA
479238 TTCAATTCAACCAAGCTTATTTGTATACCGAC
1 TTCAATTCAACCAAGCTTATTTGTATACCGAC
479270 TTCAATTCAACCAAGCTTATTTGTATACCGAC
1 TTCAATTCAACCAAGCTTATTTGTATACCGAC
479302 TTCAATTCAACCAAGCTTATTTGTATACCG
1 TTCAATTCAACCAAGCTTATTTGTATACCG
479332 GCTTACCTTG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (32 bp):
TTCAATTCAACCAAGCTTATTTGTATACCGAC
Found at i:488309 original size:44 final size:45
Alignment explanation
Indices: 488207--488376 Score: 272
Period size: 45 Copynumber: 3.8 Consensus size: 45
488197 TATCGTACAG
*
488207 TACTATTCGGGCCTTTGAGCCTAGTAGGCTATAATGCCGGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
*
488252 TACTATTAGGGCCTTTGAGCCTAGCAGGCTATAATGCC-GTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
*
488296 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATACCGGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
* *
488341 TACTATTCAGG-CTTTCGAGCCTGGCAGGCTATAATG
1 TACTATTCGGGCCTTT-GAGCCTAGCAGGCTATAATG
488377 TCAGTGAAAT
Statistics
Matches: 116, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
44 46 0.40
45 70 0.60
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (45 bp):
TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
Found at i:488361 original size:89 final size:89
Alignment explanation
Indices: 488207--488376 Score: 281
Period size: 89 Copynumber: 1.9 Consensus size: 89
488197 TATCGTACAG
* *
488207 TACTATTCGGGCCTTTGAGCCTAGTAGGCTATAATGCCGGTGAGATACTATTAGGGCCTTTGAGC
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATACCGGTGAGATACTATTAGGGCCTTTGAGC
488272 CTAGCAGGCTATAATGCCGTGAGA
66 CTAGCAGGCTATAATGCCGTGAGA
488296 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATACCGGTGAGATACTATTCA-GG-CTTTCGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATACCGGTGAGATACTATT-AGGGCCTTT-GA
*
488359 GCCTGGCAGGCTATAATG
64 GCCTAGCAGGCTATAATG
488377 TCAGTGAAAT
Statistics
Matches: 76, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
88 4 0.05
89 71 0.93
90 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (89 bp):
TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATACCGGTGAGATACTATTAGGGCCTTTGAGC
CTAGCAGGCTATAATGCCGTGAGA
Found at i:490843 original size:34 final size:34
Alignment explanation
Indices: 490789--490857 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
490779 CCAAATGCCT
*
490789 AGTATGCCAGCAAGTGAAGGCTGAGCACCAAGTA
1 AGTATGCCAGCAAGTGAAGGCCGAGCACCAAGTA
* * *
490823 AGTATGTCAGCGAGTTAAGGCCGAGCACCAAGTA
1 AGTATGCCAGCAAGTGAAGGCCGAGCACCAAGTA
490857 A
1 A
490858 CTTTGGGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.35, C:0.20, G:0.29, T:0.16
Consensus pattern (34 bp):
AGTATGCCAGCAAGTGAAGGCCGAGCACCAAGTA
Found at i:492735 original size:46 final size:45
Alignment explanation
Indices: 492682--492854 Score: 163
Period size: 46 Copynumber: 3.8 Consensus size: 45
492672 TTGGGCATCT
492682 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAACGTCC
* * *
492728 GAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAAC---G--TCC
* * * *
492775 GAGCTCTTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGCCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAACGTCC
* * * *
492821 GAGCTCATTGAGTTGAGTCTGAGTTCGCTTATGG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
492855 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
45 3 0.03
46 59 0.56
47 27 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (45 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAACGTCC
Found at i:492786 original size:93 final size:93
Alignment explanation
Indices: 492675--492847 Score: 265
Period size: 93 Copynumber: 1.9 Consensus size: 93
492665 CGGATGTTTG
* * *
492675 GGCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAG
492740 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* * * * *
492768 GGCATCCGAGCTCTTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGCCCGAGCTCATTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAG
*
492833 TTGAGTCTGAGTTCG
66 TTGAGTCCGAGTTCG
492848 CTTATGGGCG
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:509300 original size:23 final size:24
Alignment explanation
Indices: 509256--509300 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
509246 ATATGCTCAA
* *
509256 AGAATATTATGTACATATATATCT
1 AGAATATTATGCACATAAATATCT
*
509280 AGAA-ATTATGCACTTAAATAT
1 AGAATATTATGCACATAAATAT
509301 ATATATGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (24 bp):
AGAATATTATGCACATAAATATCT
Found at i:518228 original size:41 final size:41
Alignment explanation
Indices: 518128--518231 Score: 111
Period size: 41 Copynumber: 2.5 Consensus size: 41
518118 CCGGCACAAG
* * * * * * *
518128 GCCTGCTAGACTCAAAGTCTGATTTTATTCATCGGCATTAA
1 GCCTGCTAGGCTCAAAGCCCGATTATATTCACCAGCATAAA
*
518169 GCCTGCTAGGCAGC-AAGCCCGATTATATTCACCAGCATAAA
1 GCCTGCTAGGC-TCAAAGCCCGATTATATTCACCAGCATAAA
*
518210 GCTTGCTAGGCTCAAAGCCCGA
1 GCCTGCTAGGCTCAAAGCCCGA
518232 ATATCACTAT
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
40 1 0.02
41 49 0.96
42 1 0.02
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (41 bp):
GCCTGCTAGGCTCAAAGCCCGATTATATTCACCAGCATAAA
Found at i:521332 original size:53 final size:51
Alignment explanation
Indices: 521237--521391 Score: 167
Period size: 47 Copynumber: 3.0 Consensus size: 51
521227 CCATAGCAAC
* *
521237 ATGTGATATGTGATTTCCGTATAAGACCATAGT-TAGGCTATGGCATCAGAGAG
1 ATGTGATATGTG-CTTCCGTATAAGACCATA-TCTAGGATATGGCATCAG-GAG
*
521290 ATGTGATTATGTGCTTCCGTATAAGACCATATCTGGGATATGGCATC--G-G
1 ATGTGA-TATGTGCTTCCGTATAAGACCATATCTAGGATATGGCATCAGGAG
* * * *
521339 -TGTGATATATGCTACTGTATAAGACCATATCTAGGATATGGCACCAGTGAG
1 ATGTGATATGTGCTTCCGTATAAGACCATATCTAGGATATGGCATCAG-GAG
521390 AT
1 AT
521392 ATTTGATTCG
Statistics
Matches: 87, Mismatches: 8, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
47 35 0.40
48 5 0.06
49 1 0.01
50 2 0.02
51 1 0.01
52 2 0.02
53 35 0.40
54 6 0.07
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (51 bp):
ATGTGATATGTGCTTCCGTATAAGACCATATCTAGGATATGGCATCAGGAG
Found at i:521519 original size:49 final size:48
Alignment explanation
Indices: 521237--521526 Score: 228
Period size: 48 Copynumber: 5.9 Consensus size: 48
521227 CCATAGCAAC
* * * * *
521237 ATGTGATATGTGATTTCCGTATAAGACCATAGTTAGGCTATGGCATCAGAGAG
1 ATGTGATATGTGA--TACGTGTAAGACCATAGCTGGGCTATGGCATC---GAT
* * * * *
521290 ATGTGATTATGTGCTTCCGTATAAGACCATATCTGGGATATGGCATCG--
1 ATGTGA-TATGTG-ATACGTGTAAGACCATAGCTGGGCTATGGCATCGAT
* * * * * * * *
521338 GTGTGATATATGCTACTGTATAAGACCATATCTAGGATATGGCA-CCA-
1 ATGTGATATGTGATAC-GTGTAAGACCATAGCTGGGCTATGGCATCGAT
* * * * * *
521385 GTGAGATATTTGATTCGTGTAAGACCATAGATGGGCTATAGCATCGAT
1 ATGTGATATGTGATACGTGTAAGACCATAGCTGGGCTATGGCATCGAT
* *
521433 ATGTGATATGTGATCCGTGTAAGACCATAGCTGGGCTATGGCATTGAT
1 ATGTGATATGTGATACGTGTAAGACCATAGCTGGGCTATGGCATCGAT
*
521481 ATGTGATATGTGAATACGTGTAAGACAATAGCTGGGCTATGGCATC
1 ATGTGATATGTG-ATACGTGTAAGACCATAGCTGGGCTATGGCATC
521527 ATTGTGTGAA
Statistics
Matches: 198, Mismatches: 32, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
46 24 0.12
47 45 0.23
48 58 0.29
49 30 0.15
50 1 0.01
53 34 0.17
54 6 0.03
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (48 bp):
ATGTGATATGTGATACGTGTAAGACCATAGCTGGGCTATGGCATCGAT
Found at i:522295 original size:22 final size:26
Alignment explanation
Indices: 522251--522302 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
522241 AAATTGATTC
522251 ATAAATGTATTAAAATGTTGGTGA-AA
1 ATAAATGTATTAAAATG-TGGTGAGAA
522277 ATAAATG-ATT-AAATG-GGTGAGAA
1 ATAAATGTATTAAAATGTGGTGAGAA
522300 ATA
1 ATA
522303 TGGCTTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 5 0.20
23 5 0.20
24 5 0.20
25 3 0.12
26 7 0.28
ACGTcount: A:0.48, C:0.00, G:0.21, T:0.31
Consensus pattern (26 bp):
ATAAATGTATTAAAATGTGGTGAGAA
Found at i:523159 original size:24 final size:24
Alignment explanation
Indices: 523121--523191 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 24
523111 CTGTCAGGAG
*
523121 AGGATTTAGGCGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
*
523145 AGGATTTAAGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
**
523169 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGTTGATAAGGGA
523192 GGAAATCTAG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.35, C:0.03, G:0.37, T:0.25
Consensus pattern (24 bp):
AGGATTTAGGAGTTGATAAGGGAT
Found at i:524618 original size:27 final size:27
Alignment explanation
Indices: 524578--524689 Score: 138
Period size: 27 Copynumber: 4.1 Consensus size: 27
524568 AGGATGTGTC
*
524578 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
524605 CTGGTGGCTCTGCCACATATT-TCTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
*
524632 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * *
524660 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
524686 CTGG
1 CTGG
524690 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
26 8 0.11
27 49 0.65
28 18 0.24
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:524684 original size:54 final size:54
Alignment explanation
Indices: 524578--524689 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
524568 AGGATGTGTC
* *
524578 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * *
524632 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
524686 CTGG
1 CTGG
524690 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:531617 original size:47 final size:47
Alignment explanation
Indices: 531530--532122 Score: 992
Period size: 47 Copynumber: 12.6 Consensus size: 47
531520 CCCTTCGGGA
* * * * *
531530 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCA-GC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCA-TTAGGC
* *
531577 CCTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
531624 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
531671 CTTATCACATATATACACTTTCACATTCATCACATCGGCCA-TAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
531717 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
531764 CTTATCACATATAATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATAT-ATACACTTTCACATTCATCACATCGGCCATTAGGC
*
531812 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* **
531859 CTTATTACATATATACACTTTCACATTCATCACATCGGCTGTTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
531906 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
531953 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
532000 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
532049 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
532096 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
532123 TATTCAAATA
Statistics
Matches: 518, Mismatches: 23, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
46 48 0.09
47 380 0.73
48 45 0.09
49 45 0.09
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:536176 original size:40 final size:40
Alignment explanation
Indices: 536144--536452 Score: 444
Period size: 40 Copynumber: 7.8 Consensus size: 40
536134 CCAGCATGAT
* * * *
536144 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCA--AA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
** * * *
536182 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* **
536222 TGCTCTTCGGAACTTAGTTCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
536262 TGCTCTTTGAGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
536302 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
536342 TGCTCTTTGGGACTTAGCCCGGATACATCACTAGTACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
536382 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
536422 TGCTCTTC-GGACTTAGCCCGGATACATCACT
1 TGCTCTTCGGGACTTAGCCCGGATACATCACT
536453 CTCAATTCTC
Statistics
Matches: 243, Mismatches: 26, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
38 30 0.12
39 22 0.09
40 191 0.79
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:537930 original size:47 final size:47
Alignment explanation
Indices: 537859--538448 Score: 1001
Period size: 47 Copynumber: 12.6 Consensus size: 47
537849 TCCTTCGGGA
* * * * * *
537859 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
537906 CCTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
537953 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
538000 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
538047 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
538094 CTTATCACATATATATACACTTTCACATTCATCACAT-GGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
538142 CTTATCACATATATACACTTTCACATTCAT-ACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
538188 CTTATCACATATATACACTTTCACATTCAT-ACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
538234 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
538281 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
538328 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
538377 CTTATCAC--ATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
538422 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
538449 TATTCAAATA
Statistics
Matches: 517, Mismatches: 18, Indels: 16
0.94 0.03 0.03
Matches are distributed among these distances:
45 47 0.09
46 108 0.21
47 272 0.53
48 18 0.03
49 72 0.14
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:542016 original size:45 final size:45
Alignment explanation
Indices: 541948--542044 Score: 131
Period size: 45 Copynumber: 2.2 Consensus size: 45
541938 TGGTCTTACT
* * **
541948 CACATATATCGATGCCAATGTCCCAGACGTGGTCTTACACGAAAA
1 CACATATATCGATGCCAACGTCCCAAAAATGGTCTTACACGAAAA
* *
541993 CACATATATCGATGCCAACGTCCCAAAAATGGTCTTACTCGGAAA
1 CACATATATCGATGCCAACGTCCCAAAAATGGTCTTACACGAAAA
*
542038 TACATAT
1 CACATAT
542045 CAAAATCATA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (45 bp):
CACATATATCGATGCCAACGTCCCAAAAATGGTCTTACACGAAAA
Found at i:561763 original size:47 final size:47
Alignment explanation
Indices: 561712--561903 Score: 271
Period size: 47 Copynumber: 4.1 Consensus size: 47
561702 TTAGGATTTT
561712 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
561759 ATGTGATAAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * *
561806 GTGCGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * *
561853 ATGTGGTGAATATGAACATGC--ATATGTGGTAAAGCCGAATGGTCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
561898 ATGTGA
1 ATGTGA
561904 AATATATATA
Statistics
Matches: 129, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
45 25 0.19
47 104 0.81
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:561935 original size:50 final size:50
Alignment explanation
Indices: 561862--562008 Score: 244
Period size: 50 Copynumber: 3.0 Consensus size: 50
561852 AATGTGGTGA
*
561862 ATATGA-ACATGCATATGTGGTAAAGCCGAATGGTCAATGTGAAATATAT
1 ATATGAGATATGCATATGTGGTAAAGCCGAATGGTCAATGTGAAATATAT
561911 ATATGAGATATGCATATGTGGTAAAGCCGAATGGTCAATGTGAAATATAT
1 ATATGAGATATGCATATGTGGTAAAGCCGAATGGTCAATGTGAAATATAT
* *
561961 ATATGAGATATGTATATGTGGTAAAGCCGAATGG-CTAGTGTGAAATAT
1 ATATGAGATATGCATATGTGGTAAAGCCGAATGGTC-AATGTGAAATAT
562009 GTAGGTGATG
Statistics
Matches: 93, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
49 7 0.08
50 86 0.92
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.30
Consensus pattern (50 bp):
ATATGAGATATGCATATGTGGTAAAGCCGAATGGTCAATGTGAAATATAT
Found at i:562026 original size:50 final size:50
Alignment explanation
Indices: 561874--562032 Score: 173
Period size: 50 Copynumber: 3.2 Consensus size: 50
561864 ATGAACATGC
* *
561874 ATATGTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGC--
1 ATATGTGGTAAAGCCGAATGGTCAATGTG-AA-ATATATATGTGATGTGCGT
* **
561924 ATATGTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGA-GATATGT
1 ATATGTGGTAAAGCCGAATGGTCAATGTGAAATATATATGTGATG-TGCGT
* * *
561974 ATATGTGGTAAAGCCGAATGG-CTAGTGTGAAATATGTAGGTGATGTGCGT
1 ATATGTGGTAAAGCCGAATGGTC-AATGTGAAATATATATGTGATGTGCGT
562024 ATATTGTGG
1 ATA-TGTGG
562033 CCGAACGACC
Statistics
Matches: 92, Mismatches: 11, Indels: 11
0.81 0.10 0.10
Matches are distributed among these distances:
48 11 0.12
49 3 0.03
50 72 0.78
51 6 0.07
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.31
Consensus pattern (50 bp):
ATATGTGGTAAAGCCGAATGGTCAATGTGAAATATATATGTGATGTGCGT
Found at i:562221 original size:37 final size:37
Alignment explanation
Indices: 562158--562229 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
562148 GGAAATATAT
*
562158 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATAACTACGTGTGGAGATTTTG
* *
562195 TCCGGGTAAGACCTGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATAACTACGTGTGGAGATTT
562230 CGTCTGAGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATAACTACGTGTGGAGATTTTG
Found at i:574631 original size:13 final size:13
Alignment explanation
Indices: 574613--574641 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
574603 AGGCCACTTA
574613 AATTTTT-GATTT
1 AATTTTTGGATTT
574625 AATTTTTGGATTT
1 AATTTTTGGATTT
574638 AATT
1 AATT
574642 ACTCTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
AATTTTTGGATTT
Found at i:584398 original size:37 final size:37
Alignment explanation
Indices: 584345--584447 Score: 179
Period size: 37 Copynumber: 2.8 Consensus size: 37
584335 CGAATAGTCC
*
584345 CCACACGTAGTTATCGGGTCTTACCCGGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
*
584382 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
*
584419 CCACATGTAGTCATCGGGTCTTACCCGGA
1 CCACACGTAGTCATCGGGTCTTACCCGGA
584448 ATATATTTCC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.24
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
Found at i:588258 original size:29 final size:29
Alignment explanation
Indices: 588199--588331 Score: 146
Period size: 29 Copynumber: 4.7 Consensus size: 29
588189 CTGACTGATT
* * *
588199 TCGCACACATAGCG-CTCGATTATAGAAC
1 TCGCACACATAGTGCCTCAATTAAAGAAC
588227 TCGCACACATAGTGCCTCAATTAAAGAAC
1 TCGCACACATAGTGCCTCAATTAAAGAAC
* *
588256 TCGCACACATAGTGCCTCAATTACCA-ATC
1 TCGCACACATAGTGCCTCAATTA-AAGAAC
* * *
588285 TCGCACACATAGCG-CTCGATTGAAGAAC
1 TCGCACACATAGTGCCTCAATTAAAGAAC
**
588313 TTTCACACATAGTGCCTCA
1 TCGCACACATAGTGCCTCA
588332 TAATTCCAGC
Statistics
Matches: 87, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
27 1 0.01
28 32 0.37
29 53 0.61
30 1 0.01
ACGTcount: A:0.32, C:0.30, G:0.15, T:0.23
Consensus pattern (29 bp):
TCGCACACATAGTGCCTCAATTAAAGAAC
Found at i:588266 original size:57 final size:57
Alignment explanation
Indices: 588199--588331 Score: 144
Period size: 57 Copynumber: 2.3 Consensus size: 57
588189 CTGACTGATT
* * *
588199 TCGCACACATAGCG-CTCGATTA-TAGAACTCGCACACATAGTGCCTCAATTAAAGAAC
1 TCGCACACATAGCGCCTCAATTACCA-AACTCGCACACATAGCG-CTCAATTAAAGAAC
* * * *
588256 TCGCACACATAGTGCCTCAATTACCAATCTCGCACACATAGCGCTCGATTGAAGAAC
1 TCGCACACATAGCGCCTCAATTACCAAACTCGCACACATAGCGCTCAATTAAAGAAC
** *
588313 TTTCACACATAGTGCCTCA
1 TCGCACACATAGCGCCTCA
588332 TAATTCCAGC
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
57 42 0.65
58 22 0.34
59 1 0.02
ACGTcount: A:0.32, C:0.30, G:0.15, T:0.23
Consensus pattern (57 bp):
TCGCACACATAGCGCCTCAATTACCAAACTCGCACACATAGCGCTCAATTAAAGAAC
Found at i:588404 original size:40 final size:40
Alignment explanation
Indices: 588337--588567 Score: 340
Period size: 40 Copynumber: 5.8 Consensus size: 40
588327 CCTCATAATT
* * *
588337 CCAGCACGAATGC-CTTCGAGG-TTTAGCCCGGATATATCA
1 CCAGCACGAATGCTCTTCG-GGACTTAGCCCGGACATAACA
* * *
588376 CTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCA
1 CCAGCACGAATGCTCTTCGGGACTTAGCCCGGACATAACA
* * *
588416 CTAGCACAAATGCTCTTCGAGACTTAGCCCGGACATAACA
1 CCAGCACGAATGCTCTTCGGGACTTAGCCCGGACATAACA
*
588456 CCAGCATGAATGCTCTTCGGGACTTAGCCCGGACATAACA
1 CCAGCACGAATGCTCTTCGGGACTTAGCCCGGACATAACA
*
588496 CCAGCACGAATGCTCTTCGGGACTTAGCTCGGACATAACA
1 CCAGCACGAATGCTCTTCGGGACTTAGCCCGGACATAACA
588536 CCAGCACGAATGCTCTTCGGGACTTAGCCCGG
1 CCAGCACGAATGCTCTTCGGGACTTAGCCCGG
588568 CTATATAACT
Statistics
Matches: 177, Mismatches: 13, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
39 14 0.08
40 163 0.92
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.21
Consensus pattern (40 bp):
CCAGCACGAATGCTCTTCGGGACTTAGCCCGGACATAACA
Found at i:595006 original size:22 final size:21
Alignment explanation
Indices: 594980--595024 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
594970 ATTATATGTA
594980 TTAATTCATAATATAATTAATT
1 TTAATTCAT-ATATAATTAATT
* * *
595002 TTAATTTATATCTAATTTATT
1 TTAATTCATATATAATTAATT
595023 TT
1 TT
595025 GGGTTAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (21 bp):
TTAATTCATATATAATTAATT
Found at i:597345 original size:24 final size:24
Alignment explanation
Indices: 597318--597363 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
597308 GTTAGATTAG
597318 AAAGATAAATCTTAGAATATAACA
1 AAAGATAAATCTTAGAATATAACA
597342 AAAGATAAATCTTAGAATATAA
1 AAAGATAAATCTTAGAATATAA
597364 GATCAAGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.59, C:0.07, G:0.09, T:0.26
Consensus pattern (24 bp):
AAAGATAAATCTTAGAATATAACA
Found at i:599119 original size:49 final size:48
Alignment explanation
Indices: 599046--599240 Score: 237
Period size: 49 Copynumber: 4.0 Consensus size: 48
599036 TAGCCGAAGC
*
599046 TATCTGGTACGCGTAGTAGCCTGCACTTAGTACTACACATGCGACCAA
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCAA
* * * *
599094 TAATCTGGTACACGTAGTAGCCTGCACTTGGTACTACACACGTGATCACAG
1 T-ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAA
* * * * *
599145 TTTTTGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCAACCAA
1 TATCT-GGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCAA
* *
599194 TTATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACC
1 -TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACC
599241 TCACAATAGT
Statistics
Matches: 121, Mismatches: 21, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
48 1 0.01
49 78 0.64
50 6 0.05
51 36 0.30
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (48 bp):
TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCAA
Found at i:599172 original size:100 final size:100
Alignment explanation
Indices: 599051--599238 Score: 322
Period size: 100 Copynumber: 1.9 Consensus size: 100
599041 GAAGCTATCT
* * *
599051 GGTACGCGTAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCTGGTACACGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCAACCAATAATCCGGTACACGTAGTAGCC
*
599116 TGCACTTGGTACTACACACGTGATCACAGTTTTTG
66 TGCACTTAGTACTACACACGTGATCACAGTTTTTG
*
599151 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCAACCAATTATCCGGTACACGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCAACCAATAATCCGGTACACGTAGTAGCC
*
599216 TGCACTTAGTACTACACATGTGA
66 TGCACTTAGTACTACACACGTGA
599239 CCTCACAATA
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
100 82 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (100 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCAACCAATAATCCGGTACACGTAGTAGCC
TGCACTTAGTACTACACACGTGATCACAGTTTTTG
Found at i:611774 original size:27 final size:27
Alignment explanation
Indices: 611703--611777 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 27
611693 CAACAGTTCG
* *
611703 CAAACCAACTGGCGAACACCCAGCTCGC
1 CAAACCAACTGGCAAAC-CCCAACTCGC
** *** *
611731 CAAACCTGCTTTTAAACCCCAACTTGC
1 CAAACCAACTGGCAAACCCCAACTCGC
611758 CAAACCAACTGGCAAACCCC
1 CAAACCAACTGGCAAACCCC
611778 TAGTTTGCAA
Statistics
Matches: 34, Mismatches: 13, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
27 23 0.68
28 11 0.32
ACGTcount: A:0.33, C:0.41, G:0.12, T:0.13
Consensus pattern (27 bp):
CAAACCAACTGGCAAACCCCAACTCGC
Found at i:612372 original size:25 final size:24
Alignment explanation
Indices: 612319--612365 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
612309 AGCTTCTAGT
*
612319 TATTTGATGATCCATTAATATGAC
1 TATTTAATGATCCATTAATATGAC
*
612343 CATTTAATGATACCATTAATATG
1 TATTTAATGAT-CCATTAATATG
612366 GGTATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (24 bp):
TATTTAATGATCCATTAATATGAC
Found at i:613559 original size:4 final size:4
Alignment explanation
Indices: 613550--613580 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
613540 AGTTTATGCA
*
613550 TACC TACC TACC TAGC TACC TACC TACC TAC
1 TACC TACC TACC TACC TACC TACC TACC TAC
613581 ATACATACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.45, G:0.03, T:0.26
Consensus pattern (4 bp):
TACC
Found at i:613585 original size:4 final size:4
Alignment explanation
Indices: 613578--613615 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
613568 CCTACCTACC
613578 TACA TACA TACA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TA
613616 GCTTTTCATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:624536 original size:22 final size:22
Alignment explanation
Indices: 624511--624560 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
624501 TTTTTTTCCT
*
624511 TATTTTCATTGATTTTCTAATC
1 TATTTTCATTGATTTACTAATC
*
624533 TATTTTCGTTGATTTACTAATC
1 TATTTTCATTGATTTACTAATC
*
624555 TGTTTT
1 TATTTT
624561 GGTCTCTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.20, C:0.12, G:0.08, T:0.60
Consensus pattern (22 bp):
TATTTTCATTGATTTACTAATC
Found at i:628441 original size:40 final size:39
Alignment explanation
Indices: 628359--628442 Score: 100
Period size: 41 Copynumber: 2.1 Consensus size: 39
628349 ATTTTAAAAA
*
628359 TTAAAATTTCTAAAATTATAAAAAATATAAATATAAACT
1 TTAAAAATTCTAAAATTATAAAAAATATAAATATAAACT
* *
628398 TTAAAAATTC-AAAATAATATAGAAAAATTTAAATATATA-T
1 TTAAAAATTCTAAAAT--TATA-AAAAATATAAATATAAACT
628438 TTAAA
1 TTAAA
628443 TTTTAAAAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
38 5 0.13
39 9 0.23
40 10 0.26
41 15 0.38
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.36
Consensus pattern (39 bp):
TTAAAAATTCTAAAATTATAAAAAATATAAATATAAACT
Found at i:628725 original size:34 final size:35
Alignment explanation
Indices: 628648--628729 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 35
628638 TTAAACTCCT
* * *
628648 TTTTTAAAAAATTTAATTTTTAAATATTATTTTGA
1 TTTTTAAAAAATTTAATATTTAAATATTATTATAA
* *
628683 CTTTTAAAAAATTT-ATATTTACATATT-TTATAA
1 TTTTTAAAAAATTTAATATTTAAATATTATTATAA
628716 TTTTATAAAAAATT
1 TTTT-TAAAAAATT
628730 AAATTAATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
33 7 0.17
34 20 0.50
35 13 0.32
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (35 bp):
TTTTTAAAAAATTTAATATTTAAATATTATTATAA
Found at i:631612 original size:46 final size:46
Alignment explanation
Indices: 631466--631631 Score: 155
Period size: 46 Copynumber: 3.7 Consensus size: 46
631456 TGTAACCCGC
* * * * * *
631466 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTTGGACATTTGCAT
* * * * *
631512 CCATGAGTGAACTCGGACTCAACTCAACGAG--T-GCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTTGGAC-ATTTGCAT
*
631556 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTTGGACATTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTTGGACATTTGCAT
* *
631599 CCATAAGTGAACTCGAACTCAACTCAACGAGTT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTT
631632 CGGATGCTCA
Statistics
Matches: 96, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
41 23 0.24
42 2 0.02
43 10 0.10
44 6 0.06
45 2 0.02
46 53 0.55
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTTGGACATTTGCAT
Found at i:634397 original size:29 final size:28
Alignment explanation
Indices: 634352--634406 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
634342 GCGAGTTATA
634352 CTAATTTGGCTTCGGGCCATGAATATCGG
1 CTAATTTGGCTTCGGGCCATG-ATATCGG
* *
634381 CTAATTTTGCTTTGGGCCATGATATC
1 CTAATTTGGCTTCGGGCCATGATATC
634407 AATAGTTCGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (28 bp):
CTAATTTGGCTTCGGGCCATGATATCGG
Found at i:640378 original size:39 final size:39
Alignment explanation
Indices: 640325--640448 Score: 203
Period size: 39 Copynumber: 3.2 Consensus size: 39
640315 GGACTTTAGC
* * *
640325 CCGGACATATTTCCAGCACGTAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
*
640364 CCAGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
*
640403 TCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
640442 CCGGATA
1 CCGGATA
640449 CACATCAAAT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.27, C:0.31, G:0.21, T:0.21
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
Found at i:650519 original size:28 final size:28
Alignment explanation
Indices: 650456--650606 Score: 214
Period size: 28 Copynumber: 5.4 Consensus size: 28
650446 ATATTAAGTC
*
650456 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
650483 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
650511 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTATATAATCAAACT
*
650539 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
650567 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
650596 CGCACACTTAG
1 CGCACACTTAG
650607 CGCCAATCTC
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.19
28 75 0.66
29 16 0.14
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:657114 original size:12 final size:12
Alignment explanation
Indices: 657097--657122 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
657087 TACCTATATG
657097 GTAGAATTTTTT
1 GTAGAATTTTTT
657109 GTAGAATTTTTT
1 GTAGAATTTTTT
657121 GT
1 GT
657123 CGGGCCAATT
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:0.00, G:0.19, T:0.58
Consensus pattern (12 bp):
GTAGAATTTTTT
Done.