Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 2 of 438
Found at i:360071 original size:12 final size:12
Alignment explanation
Indices: 360054--360086 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
360044 GTAAAGTAAG
360054 ATATATATATAT
1 ATATATATATAT
360066 ATATATAT-TAT
1 ATATATATATAT
360077 ATAT-TATATA
1 ATATATATATA
360087 ATACAGACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 3 0.15
11 9 0.45
12 8 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
ATATATATATAT
Found at i:361447 original size:2 final size:2
Alignment explanation
Indices: 361442--361469 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
361432 TTTTCTATCA
361442 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
361470 CAGTTTTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:366033 original size:22 final size:20
Alignment explanation
Indices: 365998--366038 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
365988 TTATTTTAAA
*
365998 ATATTATATATATATAAAAAG
1 ATATTATACATATA-AAAAAG
366019 ATATTGATACATATAAAAAA
1 ATATT-ATACATATAAAAAA
366039 TTATTGGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (20 bp):
ATATTATACATATAAAAAAG
Found at i:366986 original size:9 final size:9
Alignment explanation
Indices: 366972--366998 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
366962 TTTAGTATTT
366972 ATATTTAAA
1 ATATTTAAA
366981 ATATTTAAA
1 ATATTTAAA
366990 ATATTTAAA
1 ATATTTAAA
366999 TTCTTTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
ATATTTAAA
Found at i:369144 original size:2 final size:2
Alignment explanation
Indices: 369137--369180 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
369127 AACAACAAAC
369137 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
369179 AT
1 AT
369181 CTTACAAATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:370833 original size:31 final size:30
Alignment explanation
Indices: 370779--370839 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
370769 ACCCGATGAT
* * *
370779 TTAAATAAATTTTTTGAATAGTTTAGTGAC
1 TTAAATAAAATTTTTAAAAAGTTTAGTGAC
370809 TTAAATGAAAATTTTTAAAAAGTTTAGTGAC
1 TTAAAT-AAAATTTTTAAAAAGTTTAGTGAC
370840 CATTTTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 6 0.22
31 21 0.78
ACGTcount: A:0.41, C:0.03, G:0.13, T:0.43
Consensus pattern (30 bp):
TTAAATAAAATTTTTAAAAAGTTTAGTGAC
Found at i:371710 original size:20 final size:20
Alignment explanation
Indices: 371685--371723 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
371675 AAATTAAAAC
371685 TTTCAAATAGTTCAATAACT
1 TTTCAAATAGTTCAATAACT
*
371705 TTTCAAATAGTTTAATAAC
1 TTTCAAATAGTTCAATAAC
371724 GATTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.41
Consensus pattern (20 bp):
TTTCAAATAGTTCAATAACT
Found at i:375193 original size:22 final size:22
Alignment explanation
Indices: 375167--375208 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
375157 AAAATTTGGG
375167 AAAATTATAATTAAACCCCTTA
1 AAAATTATAATTAAACCCCTTA
* *
375189 AAAATTTTAATTATACCCCT
1 AAAATTATAATTAAACCCCT
375209 CATAATTTTT
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:0.45, C:0.19, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAATTATAATTAAACCCCTTA
Found at i:375218 original size:22 final size:22
Alignment explanation
Indices: 375167--375220 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
375157 AAAATTTGGG
* *
375167 AAAATTATAATTAAACCCCTTA
1 AAAATTTTAATTAAACCCCTCA
*
375189 AAAATTTTAATTATACCCCTCA
1 AAAATTTTAATTAAACCCCTCA
* *
375211 TAATTTTTAA
1 AAAATTTTAA
375221 AAATTCTCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAATTTTAATTAAACCCCTCA
Found at i:375223 original size:31 final size:30
Alignment explanation
Indices: 375186--375342 Score: 100
Period size: 31 Copynumber: 5.1 Consensus size: 30
375176 ATTAAACCCC
375186 TTAAAAATTTTAATTATACCCCTCATAATTT
1 TTAAAAATTTTAATTATACCCCTCA-AATTT
* * * * *
375217 TTAAAAATTCTCATTAGACCACTCAAAATT
1 TTAAAAATTTTAATTATACCCCTCAAATTT
* ** * *
375247 TTAGAAAATTTGAATTACGCTCTCACAAAATTTT
1 TTA-AAAATTTTAATTATAC-CCCTC-AAA-TTT
* * * * *
375281 TTAGAAATTTTTATCATGCCCCT-TAATTAT
1 TTAAAAATTTTAATTATACCCCTCAAATT-T
* *
375311 TTAAAAACTTTAATTATACCCTTCAAATTT
1 TTAAAAATTTTAATTATACCCCTCAAATTT
375341 TT
1 TT
375343 TGAAAATTCA
Statistics
Matches: 92, Mismatches: 28, Indels: 13
0.69 0.21 0.10
Matches are distributed among these distances:
29 2 0.02
30 30 0.33
31 36 0.39
32 5 0.05
33 14 0.15
34 5 0.05
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.42
Consensus pattern (30 bp):
TTAAAAATTTTAATTATACCCCTCAAATTT
Found at i:377656 original size:84 final size:85
Alignment explanation
Indices: 377558--377723 Score: 219
Period size: 84 Copynumber: 2.0 Consensus size: 85
377548 ATACTTTTTG
* * * * * * *
377558 AGGGAGGTTAAAGTATAATCTT-ATCATTGTATTAACATATAATTTTATAATTTCTAAAGGGATT
1 AGGGAGGTTAAAGTACAA-CTTAATCATTGTAGTAACATAAAAATTCAAAATTTCTAAAGGGACT
*
377622 ATAAAGAAATTTTACCATCTT
65 AAAAAGAAATTTTACCATCTT
* *
377643 AGGG-GGTTAAAGTACAACTTAATCATTGTAGTAACTTAAAAATTCAAAATTTTTAAAGGGACTA
1 AGGGAGGTTAAAGTACAACTTAATCATTGTAGTAACATAAAAATTCAAAATTTCTAAAGGGACTA
377707 AAAAGAAATTTTACCAT
66 AAAAGAAATTTTACCAT
377724 TTGTCACCTT
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
83 3 0.04
84 63 0.90
85 4 0.06
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.36
Consensus pattern (85 bp):
AGGGAGGTTAAAGTACAACTTAATCATTGTAGTAACATAAAAATTCAAAATTTCTAAAGGGACTA
AAAAGAAATTTTACCATCTT
Found at i:380732 original size:27 final size:31
Alignment explanation
Indices: 380672--380737 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
380662 AAAATCTAAG
* *
380672 ATAGTTGGGTGACCAAAAAAGACAAAATTGA
1 ATAGTTGAGTGACCAAAAAAGACAAAACTGA
380703 ATAGTTGAGTGA-CAAAAAA-A-AAAACT-A
1 ATAGTTGAGTGACCAAAAAAGACAAAACTGA
*
380730 ATAATTGA
1 ATAGTTGA
380738 ATGATCATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 8 0.25
28 5 0.16
29 1 0.03
30 7 0.22
31 11 0.34
ACGTcount: A:0.53, C:0.08, G:0.18, T:0.21
Consensus pattern (31 bp):
ATAGTTGAGTGACCAAAAAAGACAAAACTGA
Found at i:383630 original size:22 final size:24
Alignment explanation
Indices: 383605--383658 Score: 58
Period size: 27 Copynumber: 2.2 Consensus size: 24
383595 CCTATTGATA
383605 TTCG-GAAG-TAAGAAAATTTGAC
1 TTCGTGAAGTTAAGAAAATTTGAC
*
383627 TTCGTTTAGAGGTTAAGAAAATTTGAC
1 TTCG--T-GAAGTTAAGAAAATTTGAC
383654 TTCGT
1 TTCGT
383659 TTAGAGGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
22 4 0.15
25 1 0.04
26 3 0.12
27 18 0.69
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.35
Consensus pattern (24 bp):
TTCGTGAAGTTAAGAAAATTTGAC
Found at i:383643 original size:27 final size:27
Alignment explanation
Indices: 383613--383668 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
383603 TATTCGGAAG
383613 TAAGAAAATTTGACTTCGTTTAGAGGT
1 TAAGAAAATTTGACTTCGTTTAGAGGT
383640 TAAGAAAATTTGACTTCGTTTAGAGGT
1 TAAGAAAATTTGACTTCGTTTAGAGGT
383667 TA
1 TA
383669 TTAGAAATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.38
Consensus pattern (27 bp):
TAAGAAAATTTGACTTCGTTTAGAGGT
Found at i:386180 original size:35 final size:35
Alignment explanation
Indices: 386134--386203 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
386124 GCGCTATTCA
386134 AATAGACATCATTGTCTTCCTTCTCTAGCCTTATT
1 AATAGACATCATTGTCTTCCTTCTCTAGCCTTATT
386169 AATAGACATCATTGTCTTCCTTCTCTAGCCTTATT
1 AATAGACATCATTGTCTTCCTTCTCTAGCCTTATT
386204 TGAATTTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.23, C:0.26, G:0.09, T:0.43
Consensus pattern (35 bp):
AATAGACATCATTGTCTTCCTTCTCTAGCCTTATT
Found at i:399211 original size:69 final size:71
Alignment explanation
Indices: 399072--399221 Score: 216
Period size: 69 Copynumber: 2.1 Consensus size: 71
399062 ATCAGTAAAA
*
399072 CTAGCTAAATCTTACATTAATTTACGAAACATTAATCGAAAAAACCCCGGAAAAAGTAGTAAATC
1 CTAGCTAAATATTACATTAATTTACGAAACATTAATCGAAAAAACCCCGGAAAAAGTAGTAAATC
399137 GAGCTC
66 GAGCTC
* * * **
399143 GTAGCTAAATATTCCATTAA-TTACCG-AACATTAGTCGATCAAACCCCGG-AAAAGTAGTAAAT
1 CTAGCTAAATATTACATTAATTTA-CGAAACATTAATCGAAAAAACCCCGGAAAAAGTAGTAAAT
399205 CGAGCTC
65 CGAGCTC
399212 CTAGCTAAAT
1 CTAGCTAAAT
399222 CTAGCTAAAT
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
69 29 0.41
70 23 0.32
71 19 0.27
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.25
Consensus pattern (71 bp):
CTAGCTAAATATTACATTAATTTACGAAACATTAATCGAAAAAACCCCGGAAAAAGTAGTAAATC
GAGCTC
Found at i:402883 original size:26 final size:25
Alignment explanation
Indices: 402842--402937 Score: 75
Period size: 26 Copynumber: 3.5 Consensus size: 25
402832 TTAAAACATA
402842 ATAAAAATATAATAAAAAAACTTTAT
1 ATAAAAATATAATAAAAAAA-TTTAT
* * *
402868 ATAAAAATCTATTAAACAAATTTAT
1 ATAAAAATATAATAAAAAAATTTAT
**
402893 ATAGAAATAAAATTATTAATATTAAAATTTAT
1 AT----A-AAAA-TA-TAATAAAAAAATTTAT
402925 ATAAAAATATAAT
1 ATAAAAATATAAT
402938 TTTAAATATA
Statistics
Matches: 55, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
25 11 0.20
26 19 0.35
27 4 0.07
28 1 0.02
29 1 0.02
30 4 0.07
31 1 0.02
32 14 0.25
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.35
Consensus pattern (25 bp):
ATAAAAATATAATAAAAAAATTTAT
Found at i:403097 original size:2 final size:2
Alignment explanation
Indices: 403090--403121 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
403080 AAAATTTGGT
403090 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
403122 GCTACTGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:404469 original size:14 final size:14
Alignment explanation
Indices: 404435--404469 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
404425 TTATCAGATC
404435 AATAAAAAAATTTA
1 AATAAAAAAATTTA
* *
404449 GAGAAAAAAATTTA
1 AATAAAAAAATTTA
404463 AATAAAA
1 AATAAAA
404470 TTTAATAGTT
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (14 bp):
AATAAAAAAATTTA
Found at i:408805 original size:2 final size:2
Alignment explanation
Indices: 408798--408831 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
408788 ATAATATTAG
408798 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
408832 AAAGAAGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:408891 original size:12 final size:11
Alignment explanation
Indices: 408858--408887 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
408848 AATGATATTT
408858 AAATATATATA
1 AAATATATATA
408869 ATAATATATATA
1 A-AATATATATA
408881 AAATATA
1 AAATATA
408888 ATATTAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AAATATATATA
Found at i:409104 original size:13 final size:14
Alignment explanation
Indices: 409086--409116 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
409076 ATGTACGAAT
409086 ATATACATATA-TA
1 ATATACATATATTA
409099 ATATACATATATTA
1 ATATACATATATTA
409113 ATAT
1 ATAT
409117 TAATAATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATACATATATTA
Found at i:413215 original size:31 final size:31
Alignment explanation
Indices: 413179--413237 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
413169 ATTTGGTCAT
*
413179 TGAACTATTCGAAAGTTTTCATTTAAGTTGC
1 TGAACTATTCAAAAGTTTTCATTTAAGTTGC
*
413210 TGAACTATTCAAAAGTTTTTATTTAAGT
1 TGAACTATTCAAAAGTTTTCATTTAAGT
413238 CATTGGGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.44
Consensus pattern (31 bp):
TGAACTATTCAAAAGTTTTCATTTAAGTTGC
Found at i:416182 original size:61 final size:61
Alignment explanation
Indices: 416087--416276 Score: 247
Period size: 61 Copynumber: 3.0 Consensus size: 61
416077 TATCAAACAC
* **
416087 AAACCTTTATTAAAATCTTTGCGGGGCAACTACAACCACTTGTTTGCCCATGTTGCGACCA
1 AAACCTTTATTAAAATCATTGCGGGGCAACTACAACCACTTGTTTGCCCACATTGCGACCA
*
416148 AAACCTTTATTAAAATCATTGCGGGGCAACTACAACCAATAACCACTTGTTT-CCCTACATTGTG
1 AAACCTTTATTAAAATCATTGCGGGGCAACT---A-C---AACCACTTGTTTGCCC-ACATTGCG
416212 ACCA
58 ACCA
* *
416216 AAACCTTTATTAAAATCATTGCGAGGCAACTACAACCACTTGTTTGCCCACATTGCAACCA
1 AAACCTTTATTAAAATCATTGCGGGGCAACTACAACCACTTGTTTGCCCACATTGCGACCA
416277 TTGAAGAGTC
Statistics
Matches: 113, Mismatches: 7, Indels: 18
0.82 0.05 0.13
Matches are distributed among these distances:
61 52 0.46
62 3 0.03
64 2 0.02
65 2 0.02
67 3 0.03
68 51 0.45
ACGTcount: A:0.32, C:0.27, G:0.13, T:0.28
Consensus pattern (61 bp):
AAACCTTTATTAAAATCATTGCGGGGCAACTACAACCACTTGTTTGCCCACATTGCGACCA
Found at i:416229 original size:68 final size:68
Alignment explanation
Indices: 416120--416253 Score: 216
Period size: 68 Copynumber: 2.0 Consensus size: 68
416110 GGGCAACTAC
** *
416120 AACCACTTGTTTGCCCATGTTGCGACCAAAACCTTTATTAAAATCATTGCGGGGCAACTACAACC
1 AACCACTTGTTTGCCCACATTGCGACCAAAACCTTTATTAAAATCATTGCGAGGCAACTACAACC
416185 AAT
66 AAT
*
416188 AACCACTTGTTT-CCCTACATTGTGACCAAAACCTTTATTAAAATCATTGCGAGGCAACTACAAC
1 AACCACTTGTTTGCCC-ACATTGCGACCAAAACCTTTATTAAAATCATTGCGAGGCAACTACAAC
416252 CA
65 CA
416254 CTTGTTTGCC
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
67 3 0.05
68 58 0.95
ACGTcount: A:0.34, C:0.27, G:0.13, T:0.27
Consensus pattern (68 bp):
AACCACTTGTTTGCCCACATTGCGACCAAAACCTTTATTAAAATCATTGCGAGGCAACTACAACC
AAT
Found at i:422627 original size:93 final size:94
Alignment explanation
Indices: 422515--422685 Score: 281
Period size: 94 Copynumber: 1.8 Consensus size: 94
422505 GCCCATAAGT
* * *
422515 GAACTCGGACTCAACTCAACGAGCTCGGGCGTT-CGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCCACATCCATAAGTGAACTCGGACTCAACTCA
*
422579 ATGAGTTCGGATGCCTAGTTACATCTCAC
66 ACGAGTTCGGATGCCTAGTTACATCTCAC
* *
422608 GAACTCGGACTCAACTCAACGAGTTCGGACATTCCACATCCATAAGTGAACTCGGACTCAATTCA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCCACATCCATAAGTGAACTCGGACTCAACTCA
422673 ACGAGTTCGGATG
66 ACGAGTTCGGATG
422686 TTCAACCATC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
93 30 0.42
94 41 0.58
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (94 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCCACATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:422659 original size:47 final size:46
Alignment explanation
Indices: 422507--422683 Score: 200
Period size: 47 Copynumber: 3.8 Consensus size: 46
422497 TGTAACCCGC
* * * *
422507 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
*
422553 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCACAT
* *
422603 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATT-CACAT
*
422647 CCATAAGTGAACTCGGACTCAATTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
422684 TGTTCAACCA
Statistics
Matches: 110, Mismatches: 11, Indels: 19
0.79 0.08 0.14
Matches are distributed among these distances:
42 2 0.02
43 1 0.01
44 5 0.05
45 1 0.01
46 36 0.33
47 56 0.51
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
Found at i:423139 original size:30 final size:30
Alignment explanation
Indices: 423105--423164 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
423095 CCTTAATACG
423105 AACTTTGGCAAAATTAC-CATTTTGCCCCTA
1 AACTTTGGCAAAATTACAC-TTTTGCCCCTA
* *
423135 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
423165 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.28, C:0.27, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:435865 original size:21 final size:21
Alignment explanation
Indices: 435839--435879 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
435829 AGACGAGCGA
* *
435839 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
435860 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
435880 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:448302 original size:80 final size:80
Alignment explanation
Indices: 448148--448302 Score: 238
Period size: 80 Copynumber: 1.9 Consensus size: 80
448138 TCAATTCTGA
* ***
448148 TTTCAAATTTGATCATTTCAGGTTCATATAGAACGGTGTTGGATTATTTTTTAATCAAAACGGGT
1 TTTCAAATTTGATCATTTCAGGTTCATATAGAACGGTGTTGGATTATTTTTAAATCAAAACAAAT
*
448213 ATTAGAATTTCCAGG
66 ATTAAAATTTCCAGG
* *
448228 TTTCGAATTTGATCATTTCAGGTTCATATAGAACGGTGTTGGATTATTTTTAAATCAAATCAAAT
1 TTTCAAATTTGATCATTTCAGGTTCATATAGAACGGTGTTGGATTATTTTTAAATCAAAACAAAT
*
448293 TTTAAAATTT
66 ATTAAAATTT
448303 TTGGATCATT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 67 1.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (80 bp):
TTTCAAATTTGATCATTTCAGGTTCATATAGAACGGTGTTGGATTATTTTTAAATCAAAACAAAT
ATTAAAATTTCCAGG
Found at i:455838 original size:2 final size:2
Alignment explanation
Indices: 455831--455855 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
455821 TTAAATATTA
455831 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
455856 CGTATACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:456801 original size:2 final size:2
Alignment explanation
Indices: 456794--456835 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
456784 ATATTATAGC
*
456794 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
456836 TCCTCGCATG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:458737 original size:93 final size:93
Alignment explanation
Indices: 458625--458796 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
458615 GCCCATAAGT
* *
458625 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
458690 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
458718 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
458783 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
458797 CAAATATCCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:458792 original size:46 final size:46
Alignment explanation
Indices: 458617--458792 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
458607 TGTAACCCGC
* * *
458617 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
458663 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
458713 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
458756 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
458793 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:460417 original size:131 final size:131
Alignment explanation
Indices: 460084--460417 Score: 352
Period size: 131 Copynumber: 2.5 Consensus size: 131
460074 GGATATTACA
* * *
460084 CGTGCCCTAACGTGCTGGGTTGCAATTTCTCGTTTGCTT-AAAATAATCAAATATCCCTTCAAAA
1 CGTGCCCTATCGTGCTGGGTTGCGATTTCTCGTTTG-TTCAAAACAATCAAATATCCCTTCAAAA
* * * *
460148 TTTCACGCATGTCTTCTAAAAATCCTTTAAAATGAAGGCAATACTCGGTGTTTGACAATTCGGGA
65 TTTCACTCATGTCTTCTAAAAATCCTTTAAAACGAAGGCAATACTCGATGTTTGACAATTCGAGA
460213 AT
130 AT
* * * * * * **
460215 CATACCCTATCGTGTTGGGTTGTGATTTCTCGTTTGTTCAAAACAATCAAATATTCCTT-TAGGT
1 CGTGCCCTATCGTGCTGGGTTGCGATTTCTCGTTTGTTCAAAACAATCAAATATCCCTTCAAAAT
* ** * * *
460279 TTCCACTCATGT-TTATTAAAAA-CCTTTCAAAACGAAGGCAATGTTCGATGTTTGGCGATTTGA
66 TT-CACTCATGTCTT-CTAAAAATCCTTT-AAAACGAAGGCAATACTCGATGTTTGACAATTCGA
460342 GAAT
128 GAAT
* * * * * * *
460346 CGTGCCCTATCATGCTGGGTTGCGCTTTTTCATTTGTTCAAAACAATCGAAGATCCCTTCGAAAT
1 CGTGCCCTATCGTGCTGGGTTGCGATTTCTCGTTTGTTCAAAACAATCAAATATCCCTTCAAAAT
460411 TTCACTC
66 TTCACTC
460418 GTATTTTCTA
Statistics
Matches: 163, Mismatches: 35, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
130 13 0.08
131 146 0.90
132 4 0.02
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (131 bp):
CGTGCCCTATCGTGCTGGGTTGCGATTTCTCGTTTGTTCAAAACAATCAAATATCCCTTCAAAAT
TTCACTCATGTCTTCTAAAAATCCTTTAAAACGAAGGCAATACTCGATGTTTGACAATTCGAGAA
T
Found at i:461169 original size:18 final size:18
Alignment explanation
Indices: 461135--461242 Score: 101
Period size: 18 Copynumber: 6.1 Consensus size: 18
461125 TCATTAACTC
* *
461135 TCAG-AACAATTATTTAT
1 TCAGTAACAATCAGTTAT
*
461152 TCAGTAACAGTCAGTTAT
1 TCAGTAACAATCAGTTAT
* **
461170 TCGGTAACAATCAAATAT
1 TCAGTAACAATCAGTTAT
* *
461188 TCAGTAATAACCAGTTAT
1 TCAGTAACAATCAGTTAT
* * *
461206 TCAATAACAGTCAATTAT
1 TCAGTAACAATCAGTTAT
*
461224 TCAGTAATAATCAGTTAT
1 TCAGTAACAATCAGTTAT
461242 T
1 T
461243 TTATACCTTA
Statistics
Matches: 69, Mismatches: 21, Indels: 1
0.76 0.23 0.01
Matches are distributed among these distances:
17 4 0.06
18 65 0.94
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (18 bp):
TCAGTAACAATCAGTTAT
Found at i:461180 original size:36 final size:36
Alignment explanation
Indices: 461139--461242 Score: 127
Period size: 36 Copynumber: 2.9 Consensus size: 36
461129 TAACTCTCAG
* * * * **
461139 AACAATTATTTATTCAGTAACAGTCAGTTATTCGGT
1 AACAATCAATTATTCAGTAATAATCAGTTATTCAAT
* *
461175 AACAATCAAATATTCAGTAATAACCAGTTATTCAAT
1 AACAATCAATTATTCAGTAATAATCAGTTATTCAAT
*
461211 AACAGTCAATTATTCAGTAATAATCAGTTATT
1 AACAATCAATTATTCAGTAATAATCAGTTATT
461243 TTATACCTTA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (36 bp):
AACAATCAATTATTCAGTAATAATCAGTTATTCAAT
Found at i:461744 original size:23 final size:22
Alignment explanation
Indices: 461706--461766 Score: 90
Period size: 21 Copynumber: 2.8 Consensus size: 22
461696 GACACATAAA
*
461706 GTGCCT-AAAACGACACACGAG
1 GTGCCTGAATACGACACACGAG
461727 GTGCCTG-ATACGACACACGAG
1 GTGCCTGAATACGACACACGAG
461748 GTGCCTGAAATACGACACA
1 GTGCCTG-AATACGACACA
461767 TAAAGTGCCT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
21 26 0.72
23 10 0.28
ACGTcount: A:0.34, C:0.28, G:0.25, T:0.13
Consensus pattern (22 bp):
GTGCCTGAATACGACACACGAG
Found at i:461774 original size:23 final size:23
Alignment explanation
Indices: 461696--461778 Score: 84
Period size: 21 Copynumber: 3.8 Consensus size: 23
461686 ATCAGTATAT
*
461696 GACACATAAAGTGCCT-AAA-AC
1 GACACACAAAGTGCCTGAAATAC
* *
461717 GACACACGAGGTGCCTG--ATAC
1 GACACACAAAGTGCCTGAAATAC
* *
461738 GACACACGAGGTGCCTGAAATAC
1 GACACACAAAGTGCCTGAAATAC
*
461761 GACACATAAAGTGCCTGA
1 GACACACAAAGTGCCTGA
461779 TCAGTAAAGC
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
20 1 0.02
21 32 0.62
23 19 0.37
ACGTcount: A:0.37, C:0.25, G:0.23, T:0.14
Consensus pattern (23 bp):
GACACACAAAGTGCCTGAAATAC
Found at i:462174 original size:15 final size:15
Alignment explanation
Indices: 462149--462206 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
462139 TCATATATAT
462149 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
462165 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
462180 AATAATTTCAATCAA
1 TATAAATTCAATCAA
462195 TATAAATTCAAT
1 TATAAATTCAAT
462207 AAATTCATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:463477 original size:5 final size:5
Alignment explanation
Indices: 463462--463510 Score: 59
Period size: 5 Copynumber: 10.0 Consensus size: 5
463452 TTACTTATTT
463462 ATATA ATAT- ATA-A TATATA ATATA ATA-A TATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA -ATATA ATATA ATATA -ATATA ATATA ATATA ATATA
463511 TTTTAACACA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
4 4 0.10
5 33 0.85
6 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:463511 original size:7 final size:7
Alignment explanation
Indices: 463461--463500 Score: 71
Period size: 7 Copynumber: 5.6 Consensus size: 7
463451 TTTACTTATT
463461 TATATAA
1 TATATAA
463468 TATATAA
1 TATATAA
463475 TATATAA
1 TATATAA
463482 TATAATAA
1 TAT-ATAA
463490 TATATAA
1 TATATAA
463497 TATA
1 TATA
463501 ATATAATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 25 0.78
8 7 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TATATAA
Found at i:463511 original size:12 final size:12
Alignment explanation
Indices: 463462--463505 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
463452 TTACTTATTT
463462 ATATAATATATA
1 ATATAATATATA
463474 ATAT-ATA-AT-
1 ATATAATATATA
463483 ATAATAATATATA
1 AT-ATAATATATA
463496 ATATAATATA
1 ATATAATATA
463506 ATATATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 2 0.07
10 4 0.14
11 6 0.21
12 14 0.50
13 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATAATATATA
Found at i:465921 original size:3 final size:3
Alignment explanation
Indices: 465913--465987 Score: 86
Period size: 3 Copynumber: 26.0 Consensus size: 3
465903 CCTGGGCAAT
* *
465913 AGA AGA AGA A-T AGA AGA AGA AGA ATA AG- AGA AGA A-A CAG- AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA -AGA AGA
*
465955 AGA AGA AGA AGA AGA AAA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
465988 GGAGGAGGAG
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
2 6 0.10
3 55 0.90
ACGTcount: A:0.67, C:0.01, G:0.29, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:470491 original size:2 final size:2
Alignment explanation
Indices: 470484--470509 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
470474 ACAAGAAATA
470484 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
470510 GGCTGTAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:483392 original size:94 final size:96
Alignment explanation
Indices: 483294--483471 Score: 245
Period size: 96 Copynumber: 1.9 Consensus size: 96
483284 GATAATTTCA
* * * **
483294 GGCTCATATTGGACGGTGTTGGATAAT-TTTTTTAGTCAAATC-GAG-TTTAAAGTTTCCAAATC
1 GGCTCATATTGAACGGTGTTCGATAATCTTTTTTAATCAAATCAG-GTTTTAAAACTTCCAAATC
*
483356 ATTTTGGTTCAAGCTAGTTTTGATCATTTTGG
65 ATTTTGATTCAAGCTAGTTTTGATCATTTTGG
* *
483388 GGCTCATATTGAACGGTGTTCGATTATCTTTTTTAATCAAATCAGGTTTTAAAACTTCCAGATCA
1 GGCTCATATTGAACGGTGTTCGATAATCTTTTTTAATCAAATCAGGTTTTAAAACTTCCAAATCA
*
483453 TTTTGATTCAAGTTAGTTT
66 TTTTGATTCAAGCTAGTTT
483472 CAAGTTTAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
94 24 0.33
95 15 0.21
96 33 0.46
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.43
Consensus pattern (96 bp):
GGCTCATATTGAACGGTGTTCGATAATCTTTTTTAATCAAATCAGGTTTTAAAACTTCCAAATCA
TTTTGATTCAAGCTAGTTTTGATCATTTTGG
Found at i:483605 original size:122 final size:123
Alignment explanation
Indices: 483391--483616 Score: 269
Period size: 122 Copynumber: 1.8 Consensus size: 123
483381 ATTTTGGGGC
*
483391 TCATATTGAACGGTGTTCGATTATCTTTTTTAATCAAATCAGGTTTTAAAACTTCCAGATCATTT
1 TCATATAGAACGGTGTTCGATTA-CTTTTTTAATCAAATCAGGTTTTAAAACTTCCAGATCATTT
* * * *
483456 TGATTCAAGTTAGTTTCAAGTTTAAATCAATTTCAATTTCGGATTTGATTATTTCAAGT
65 TGATTCAAGTTAATTCCAAGTTCAAATCAAATTCAATTTCGGATTTGATTATTTCAAGT
* ** ***
483515 TCATATAGAACGGTGTTGGATTA-TTTTTTAATCAAATTGGGTTTTAAAA-TTTTTGAATCATTT
1 TCATATAGAACGGTGTTCGATTACTTTTTTAATCAAATCAGGTTTTAAAACTTCCAG-ATCATTT
* ** *
483578 TCG-TTCTAGTTAATTCCCGGTTCAAATCAAATTCGATTT
65 T-GATTCAAGTTAATTCCAAGTTCAAATCAAATTCAATTT
483617 TAGATCATTT
Statistics
Matches: 85, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
121 3 0.04
122 60 0.71
123 1 0.01
124 21 0.25
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (123 bp):
TCATATAGAACGGTGTTCGATTACTTTTTTAATCAAATCAGGTTTTAAAACTTCCAGATCATTTT
GATTCAAGTTAATTCCAAGTTCAAATCAAATTCAATTTCGGATTTGATTATTTCAAGT
Found at i:501511 original size:7 final size:7
Alignment explanation
Indices: 501501--501526 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
501491 ACAAAAACCC
501501 AAAACGT
1 AAAACGT
501508 AAAACGT
1 AAAACGT
501515 AAAACGT
1 AAAACGT
501522 AAAAC
1 AAAAC
501527 AAAGAGGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.15, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAACGT
Found at i:504015 original size:46 final size:46
Alignment explanation
Indices: 503948--504221 Score: 404
Period size: 46 Copynumber: 6.0 Consensus size: 46
503938 AGTGTGCTCT
*
503948 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
503994 CTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
504040 CTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
504086 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAAT
1 CTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * ***
504132 GTGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * * *
504178 ATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
504222 TCATGTCAAA
Statistics
Matches: 209, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 209 1.00
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.23
Consensus pattern (46 bp):
CTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:505272 original size:22 final size:21
Alignment explanation
Indices: 505225--505272 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
505215 GTTCAAATTT
505225 AAAAT-TTAAATTGATTAATA
1 AAAATATTAAATTGATTAATA
*
505245 AAAATATTAAAGTTGGTTAA-A
1 AAAATATTAAA-TTGATTAATA
505266 AATAATA
1 AA-AATA
505273 AATTTTATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 5 0.21
21 8 0.33
22 11 0.46
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.35
Consensus pattern (21 bp):
AAAATATTAAATTGATTAATA
Found at i:506460 original size:2 final size:2
Alignment explanation
Indices: 506453--506478 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
506443 GGTAGACTAT
506453 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
506479 AACAAATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:513804 original size:29 final size:29
Alignment explanation
Indices: 513758--513815 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
513748 TGGATTTTTT
*
513758 TTTAATAATATAGAGACTAAATTGATACA
1 TTTAATAATAGAGAGACTAAATTGATACA
* * *
513787 TTTAATAGTAGAGGGACTAATTTGATACA
1 TTTAATAATAGAGAGACTAAATTGATACA
513816 ATCTATATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (29 bp):
TTTAATAATAGAGAGACTAAATTGATACA
Found at i:515571 original size:25 final size:25
Alignment explanation
Indices: 515537--515584 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
515527 TACGTTAGAT
515537 TAAAGAGCAAACAGGTCCTTGTATG
1 TAAAGAGCAAACAGGTCCTTGTATG
515562 TAAAGAGCAAACAGGTCCTTGTA
1 TAAAGAGCAAACAGGTCCTTGTA
515585 CGTTAACATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.23
Consensus pattern (25 bp):
TAAAGAGCAAACAGGTCCTTGTATG
Found at i:519013 original size:28 final size:30
Alignment explanation
Indices: 518977--519042 Score: 82
Period size: 28 Copynumber: 2.2 Consensus size: 30
518967 CTATTTGAAT
* * *
518977 TAATCAATAACATTA-CAAAATATTAA-AC
1 TAATTAATAACATTATAAAAATATAAATAC
519005 TAATTAATAACATTATAAAAATATAAATAC
1 TAATTAATAACATTATAAAAATATAAATAC
519035 TAAATTAA
1 T-AATTAA
519043 GTTAGAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 14 0.44
29 9 0.28
30 3 0.09
31 6 0.19
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATTAATAACATTATAAAAATATAAATAC
Found at i:519668 original size:43 final size:43
Alignment explanation
Indices: 519607--519689 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
519597 TGATCACGTG
* *
519607 ACGAGAAACTAAGGTGTCAATAAGACATTGCTAAGAAGATGAA
1 ACGAGAAACTAAGGTGTCAACAAAACATTGCTAAGAAGATGAA
519650 ACGAGAAACTAAGGTGTCAACAAAACATTGCTAAGAAGAT
1 ACGAGAAACTAAGGTGTCAACAAAACATTGCTAAGAAGAT
519690 TTCAATGATG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.47, C:0.13, G:0.22, T:0.18
Consensus pattern (43 bp):
ACGAGAAACTAAGGTGTCAACAAAACATTGCTAAGAAGATGAA
Found at i:524657 original size:39 final size:39
Alignment explanation
Indices: 524603--524680 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
524593 TGTTGGTGTT
524603 CTTCATCAATTGCATCTCAACTCAGTGGTAAAGTTATAA
1 CTTCATCAATTGCATCTCAACTCAGTGGTAAAGTTATAA
524642 CTTCATCAATTGCATCTCAACTCAGTGGTAAAGTTATAA
1 CTTCATCAATTGCATCTCAACTCAGTGGTAAAGTTATAA
524681 AAGAATCTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (39 bp):
CTTCATCAATTGCATCTCAACTCAGTGGTAAAGTTATAA
Found at i:533239 original size:82 final size:83
Alignment explanation
Indices: 533130--533294 Score: 314
Period size: 82 Copynumber: 2.0 Consensus size: 83
533120 AAAGAAGGTT
533130 TTTTTTTTTTTTATTATTATGTATATTTCAGATTATTTAGAATGCCTAATAGGTCTGGGTTTATA
1 TTTTTTTTTTTTATTATTATGTATATTTCAGATTATTTAGAATGCCTAATAGGTCTGGGTTTATA
*
533195 AGATATTATTGAATTTGG
66 AGATACTATTGAATTTGG
533213 TTTTTTTTTTTT-TTATTATGTATATTTCAGATTATTTAGAATGCCTAATAGGTCTGGGTTTATA
1 TTTTTTTTTTTTATTATTATGTATATTTCAGATTATTTAGAATGCCTAATAGGTCTGGGTTTATA
533277 AGATACTATTGAATTTGG
66 AGATACTATTGAATTTGG
533295 ACTAGTTTGA
Statistics
Matches: 81, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
82 69 0.85
83 12 0.15
ACGTcount: A:0.26, C:0.05, G:0.16, T:0.53
Consensus pattern (83 bp):
TTTTTTTTTTTTATTATTATGTATATTTCAGATTATTTAGAATGCCTAATAGGTCTGGGTTTATA
AGATACTATTGAATTTGG
Found at i:533329 original size:82 final size:82
Alignment explanation
Indices: 533145--533318 Score: 231
Period size: 82 Copynumber: 2.1 Consensus size: 82
533135 TTTTTTTATT
*
533145 ATTATGTATATTTCAGATTATTTAGAATGCCTAATAGGTCTGGGTTTATAAGATATTATTGAATT
1 ATTATGTATATTTCAGATTATTTAGAATGCCTAATAGGTCTGGGTTTATAAGATACTATTGAATT
* **** **
533210 TGGTTTTTTTTTTTTTT
66 TGGTTTTATCCGGTTGA
533227 ATTATGTATATTTCAGATTATTTAGAATGCCTAATAGGTCTGGGTTTATAAGATACTATTGAATT
1 ATTATGTATATTTCAGATTATTTAGAATGCCTAATAGGTCTGGGTTTATAAGATACTATTGAATT
533292 TGGACTAGTTTGATCCGGTTGA
66 TGG--T--TTT-ATCCGGTTGA
533314 ATTAT
1 ATTAT
533319 TAATTAATTA
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
82 67 0.85
84 1 0.01
86 3 0.04
87 8 0.10
ACGTcount: A:0.28, C:0.07, G:0.18, T:0.48
Consensus pattern (82 bp):
ATTATGTATATTTCAGATTATTTAGAATGCCTAATAGGTCTGGGTTTATAAGATACTATTGAATT
TGGTTTTATCCGGTTGA
Found at i:547200 original size:2 final size:2
Alignment explanation
Indices: 547193--547218 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
547183 CCTCTAGGTG
547193 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
547219 GGCATTACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:550497 original size:65 final size:65
Alignment explanation
Indices: 550393--550524 Score: 264
Period size: 65 Copynumber: 2.0 Consensus size: 65
550383 ATACCGAGTG
550393 CTTATCTGAACTTCTCAAACTTTGGTTAATTAGACTCTTCGTGTTTATGTCTGCAACTTGCTCAT
1 CTTATCTGAACTTCTCAAACTTTGGTTAATTAGACTCTTCGTGTTTATGTCTGCAACTTGCTCAT
550458 CTTATCTGAACTTCTCAAACTTTGGTTAATTAGACTCTTCGTGTTTATGTCTGCAACTTGCTCAT
1 CTTATCTGAACTTCTCAAACTTTGGTTAATTAGACTCTTCGTGTTTATGTCTGCAACTTGCTCAT
550523 CT
1 CT
550525 GCCTTTGTTC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.43
Consensus pattern (65 bp):
CTTATCTGAACTTCTCAAACTTTGGTTAATTAGACTCTTCGTGTTTATGTCTGCAACTTGCTCAT
Found at i:552593 original size:18 final size:16
Alignment explanation
Indices: 552571--552603 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
552561 TAACATATTT
*
552571 AATAAT-ATCATTAAA
1 AATAATAATAATTAAA
552586 AATAATAATAATTAAA
1 AATAATAATAATTAAA
552602 AA
1 AA
552604 CTATTATTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
AATAATAATAATTAAA
Found at i:555270 original size:2 final size:2
Alignment explanation
Indices: 555263--555293 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
555253 CTCGCAACTC
555263 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
555294 AACGCAGCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:562558 original size:20 final size:20
Alignment explanation
Indices: 562521--562561 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
562511 TATATATAAT
*
562521 TAAATTAACTAATAAAATTA
1 TAAATTAAATAATAAAATTA
* *
562541 TAAATTAAATGATTAAATTA
1 TAAATTAAATAATAAAATTA
562561 T
1 T
562562 TTGAATTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (20 bp):
TAAATTAAATAATAAAATTA
Found at i:569669 original size:16 final size:18
Alignment explanation
Indices: 569648--569684 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
569638 AAGAATTGTA
569648 TTAATGT-TGT-AATAAT
1 TTAATGTATGTCAATAAT
569664 TTAATGTCATGTCAATAAT
1 TTAATGT-ATGTCAATAAT
569683 TT
1 TT
569685 TATCCTGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.39
18 3 0.17
19 8 0.44
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.49
Consensus pattern (18 bp):
TTAATGTATGTCAATAAT
Found at i:573258 original size:12 final size:12
Alignment explanation
Indices: 573225--573259 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
573215 TAAGTATAAT
*
573225 TATATATATATA
1 TATATATATTTA
573237 TATATATATTTA
1 TATATATATTTA
*
573249 TATATTTATTT
1 TATATATATTT
573260 TTTTAAGTTC
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATATATATTTA
Found at i:589724 original size:2 final size:2
Alignment explanation
Indices: 589719--589746 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
589709 CACTTAGGCT
589719 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
589747 GGTTATTCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:600904 original size:195 final size:192
Alignment explanation
Indices: 600689--601193 Score: 518
Period size: 195 Copynumber: 2.6 Consensus size: 192
600679 CCCTTTTTTC
*
600689 TTTTAAAAATTTAAATATATT-AAT-CCTTT-TTTACCTATTAAAAAATATATTAAAATTTTAAA
1 TTTTAAAATTTTAAATATATTAAATACCTTTCTTTACCTATTAAAAAATATATTAAAATTTTAAA
* * **
600751 ATTTTAAAATTGATTATACTTAAAATTTTTTAATATGTTCAAAATTTTAATATACTTTAATATAT
66 ATTTTAAAATTGATTATACTTAACATTTTTTAATATATT-AAAATTTT-AT-TA--AAAATATAT
* *
600816 TGAGTATATTAAAAATTTT-AAATTAGTTATACTCAACATTTTCTTTAATATATTTAATTTTTTT
126 TAAATATATT-AAAATTTTAAAATTAGTTATACTCAACA-TTT-TTTAATATATTTAATTTTTTT
600880 AA-AT
188 AAGAT
**
600884 TTTTAAAATTTTAAATATATTAAAAAATAATTTTCTCTTTACCTATTAAAAAATATATTAAAATT
1 TTTTAAAATTTTAAATATATT---AAAT-ACCTT-TCTTTACCTATTAAAAAATATATTAAAATT
* * *
600949 TT--AATATT---A--G-TTACACTTAACATTTTTTAATATATT-TAATTTT-TTAAAAATATAT
61 TTAAAATTTTAAAATTGATTATACTTAACATTTTTTAATATATTAAAATTTTATTAAAAATATAT
* *
601004 TAAATATATTAAAATTTTAAAATTGGTTATACTTAACATTTTTTAATATATTTAATTTTTTTAAG
126 TAAATATATTAAAATTTTAAAATTAGTTATACTCAACATTTTTTAATATATTTAATTTTTTTAAG
*
601069 TT
191 AT
*
601071 TTTTAAAATTTTAAATATATTTAGAAAATCCCTTTTTTCTTTACCTATTAAAAATATATATTAAT
1 TTTTAAAATTTTAAATATA-TT---AAATACC---TTTCTTTACCTATTAAAAA-ATATATTAA-
* * * *
601136 TATATTAAAAATTTAAAATTAATTATACTTAACATTTTTTAATATATTTAAAATTTTA
57 AATTTTAAAATTTTAAAATTGATTATACTTAACATTTTTTAATATA-TTAAAATTTTA
601194 GAAAAATTGA
Statistics
Matches: 257, Mismatches: 26, Indels: 47
0.78 0.08 0.14
Matches are distributed among these distances:
186 23 0.09
187 31 0.12
188 40 0.16
189 17 0.07
190 13 0.05
191 5 0.02
193 10 0.04
195 43 0.17
196 2 0.01
198 1 0.00
199 26 0.10
200 2 0.01
201 13 0.05
202 1 0.00
203 30 0.12
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (192 bp):
TTTTAAAATTTTAAATATATTAAATACCTTTCTTTACCTATTAAAAAATATATTAAAATTTTAAA
ATTTTAAAATTGATTATACTTAACATTTTTTAATATATTAAAATTTTATTAAAAATATATTAAAT
ATATTAAAATTTTAAAATTAGTTATACTCAACATTTTTTAATATATTTAATTTTTTTAAGAT
Found at i:601015 original size:20 final size:20
Alignment explanation
Indices: 600977--601017 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
600967 AACATTTTTT
* * *
600977 AATATATTTAATTTTTTAAA
1 AATATATTAAATATATTAAA
600997 AATATATTAAATATATTAAA
1 AATATATTAAATATATTAAA
601017 A
1 A
601018 TTTTAAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATATATTAAATATATTAAA
Found at i:601141 original size:22 final size:23
Alignment explanation
Indices: 601116--601167 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
601106 TTTCTTTACC
*
601116 TATTAAAAATAT-ATATTAATTA
1 TATTAAAAATATAAAATTAATTA
*
601138 TATTAAAAATTTAAAATTAATTA
1 TATTAAAAATATAAAATTAATTA
601161 TACTTAA
1 TA-TTAA
601168 CATTTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 11 0.42
23 11 0.42
24 4 0.15
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TATTAAAAATATAAAATTAATTA
Found at i:601186 original size:19 final size:20
Alignment explanation
Indices: 601154--601192 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
601144 AAATTTAAAA
*
601154 TTAATTATACTTAACATTTT
1 TTAATTATACTTAAAATTTT
*
601174 TTAA-TATATTTAAAATTTT
1 TTAATTATACTTAAAATTTT
601193 AGAAAAATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAATTATACTTAAAATTTT
Found at i:606223 original size:210 final size:210
Alignment explanation
Indices: 605999--606651 Score: 990
Period size: 210 Copynumber: 3.1 Consensus size: 210
605989 CTCCTTGAGG
* * * * * *
605999 CAAGTGGCGGTAGACAACCCGTCTCCTATATTGCTTAATTTAGGACACCG-GGAAATGAGAAGCT
1 CAAGTGGAGGTAGACAACCAGTCTCCTATCTTGCTTAATTTTGGACA-CGAGGAAACGTGAAGCT
*
606063 TCTCAAGAGAT-ACACATCTTCCTCTTATCGGAACAGTTTCCAGTT-TGTGGCAGTCTGATATAT
65 TTTCAAGAGATGA-ACATCTTCCTCTTATCGGAACAGTTTCCAGTTCT-TGGCAGTCTGATATAT
* * * * *
606126 ATAAAATTCGAAGAGAGGAAACTCCTTTCAAATCTGGAATGAAACGTAAATTAGGACAATTGCTT
128 ATAAAATTCGAAGAGAGGAAAGTCCTTCCAAATTTGGAATGGAACTTAAATTAGGACAATTGCTT
606191 AACTTCAATTCTTTAAAA
193 AACTTCAATTCTTTAAAA
606209 CAAGTGGAGGTAGACAACCAGTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTT
1 CAAGTGGAGGTAGACAACCAGTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTT
* * *
606274 TTCAAGAGATGAACATATTCCTCTTATCGGAACGGTTTCCAGTTCTTGGCAGTCTGATATATCTA
66 TTCAAGAGATGAACATCTTCCTCTTATCGGAACAGTTTCCAGTTCTTGGCAGTCTGATATATATA
* * *
606339 AACTTCGAAGAGAGGAAAGTCC-TCGCAATTTTGGAATGGAACTTAAATCAGGACAATTGCTTAA
131 AAATTCGAAGAGAGGAAAGTCCTTC-CAAATTTGGAATGGAACTTAAATTAGGACAATTGCTTAA
*
606403 CTTCAATTCTTTAAGA
195 CTTCAATTCTTTAAAA
606419 CAAGTGGAGGTAGACAACCAGTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTT
1 CAAGTGGAGGTAGACAACCAGTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTT
* *
606484 TTCAAGAGATGAACATCTTCCTCTAATCGGAACAGTTTCCAGTTCTTGGCAGTCTGATATATTTA
66 TTCAAGAGATGAACATCTTCCTCTTATCGGAACAGTTTCCAGTTCTTGGCAGTCTGATATATATA
606549 AAATTCGAAGAGAGGAAAGTCCTTCCAAATTTGGAATGGAACTTAAATTAGGACAATTGCTTAAC
131 AAATTCGAAGAGAGGAAAGTCCTTCCAAATTTGGAATGGAACTTAAATTAGGACAATTGCTTAAC
* * *
606614 TTTAATTCTTCAAGA
196 TTCAATTCTTTAAAA
*** *
606629 TTCGTGGAGGTAAACAACCAGTC
1 CAAGTGGAGGTAGACAACCAGTC
606652 AATTTCCAGT
Statistics
Matches: 406, Mismatches: 32, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
209 3 0.01
210 399 0.98
211 4 0.01
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (210 bp):
CAAGTGGAGGTAGACAACCAGTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTT
TTCAAGAGATGAACATCTTCCTCTTATCGGAACAGTTTCCAGTTCTTGGCAGTCTGATATATATA
AAATTCGAAGAGAGGAAAGTCCTTCCAAATTTGGAATGGAACTTAAATTAGGACAATTGCTTAAC
TTCAATTCTTTAAAA
Found at i:606697 original size:135 final size:135
Alignment explanation
Indices: 606519--606763 Score: 409
Period size: 135 Copynumber: 1.8 Consensus size: 135
606509 ATCGGAACAG
* * * * *
606519 TTTCCAGTTCTTGGCAGTCTGATATATTTAAAATTCGAAGAGAGGAAAGTCCTTCCAAATTTGGA
1 TTTCCAGTTCGTGGCAGTCTGATATATCTAAAATTCGAAGAGAGGAAAATCCTTCCAAATCTAGA
* *
606584 ATGGAACTTAAATTAGGACAATTGCTTAACTTTAATTCTTCAAGATTCGTGGAGGTAAACAACCA
66 ATGGAACTCAAATTAGGACAATTGCTTAACTTCAATTCTTCAAGATTCGTGGAGGTAAACAACCA
606649 GTCAA
131 GTCAA
*
606654 TTTCCAGTTCGTGGCAGTCTGCTATATCTAAAATTCGAAGAGAGGAAAATCCTTCCAAATCTAGA
1 TTTCCAGTTCGTGGCAGTCTGATATATCTAAAATTCGAAGAGAGGAAAATCCTTCCAAATCTAGA
*
606719 ATGGAACTCAAATTAGGACAATTGTTTAACTTCAATTCTTCAAGA
66 ATGGAACTCAAATTAGGACAATTGCTTAACTTCAATTCTTCAAGA
606764 CAAGTGGCGG
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
135 101 1.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (135 bp):
TTTCCAGTTCGTGGCAGTCTGATATATCTAAAATTCGAAGAGAGGAAAATCCTTCCAAATCTAGA
ATGGAACTCAAATTAGGACAATTGCTTAACTTCAATTCTTCAAGATTCGTGGAGGTAAACAACCA
GTCAA
Found at i:606940 original size:345 final size:345
Alignment explanation
Indices: 606309--606996 Score: 1038
Period size: 345 Copynumber: 2.0 Consensus size: 345
606299 ATCGGAACGG
* * * * * *
606309 TTTCCAGTTCTTGGCAGTCTGATATATCTAAACTTCGAAGAGAGGAAAGTCCTCGCAATTTTGGA
1 TTTCCAGTTCGTGGCAGTCTGATATATCTAAAATTCGAAGAGAGGAAAATCCTCGCAAATCTAGA
* *
606374 ATGGAACTTAAATCAGGACAATTGCTTAACTTCAATTCTTTAAGACAAGTGGAGGTAGACAACCA
66 ATGGAACTCAAATCAGGACAATTGCTTAACTTCAATTCTTCAAGACAAGTGGAGGTAGACAACCA
* * *
606439 GTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATGAACATCTTC
131 GTCTCCTATCTTGATGAATTTTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATAAACATCTTC
* * * *
606504 CTCTAATCGGAACAGTTTCCAGTTCTTGGCAGTCTGATATATTTAAAATTCGAAGAGAGGAAAGT
196 CTCTAATCGGAACAGTTTCCAGTTCGTGGCAGTCTGATATATCTAAAACTCGAAGAGAGGAAAAT
* * *** * *
606569 CCTTCCAAATTTGGAATGGAACTTAAATTAGGACAATTGCTTAACTTTAATTCTTCAAGATTCGT
261 CCTTCCAAATCTGGAATGGAACTTAAATTAGCACAACCACTTAACTTTAATTCTTCAAGACTAGT
606634 GGAGGTAAACAACCAGTCAA
326 GGAGGTAAACAACCAGTCAA
*
606654 TTTCCAGTTCGTGGCAGTCTGCTATATCTAAAATTCGAAGAGAGGAAAATCCTTC-CAAATCTAG
1 TTTCCAGTTCGTGGCAGTCTGATATATCTAAAATTCGAAGAGAGGAAAATCC-TCGCAAATCTAG
* * * *
606718 AATGGAACTCAAATTAGGACAATTGTTTAACTTCAATTCTTCAAGACAAGTGGCGGTAGGCAACC
65 AATGGAACTCAAATCAGGACAATTGCTTAACTTCAATTCTTCAAGACAAGTGGAGGTAGACAACC
* * *
606783 AGTCTTCTATCTTGATGATATTTT-GACAGGAGGAAATGTGAAGCTTTTCAAGAGATAAACATCT
130 AGTCTCCTATCTTGATGA-ATTTTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATAAACATCT
* *
606847 TCCTCTTATCGGAACAGTTTCCAGTTCGTGGCAGTCTGATATATCTAAAACTCGGAGAGAGGAAA
194 TCCTCTAATCGGAACAGTTTCCAGTTCGTGGCAGTCTGATATATCTAAAACTCGAAGAGAGGAAA
*
606912 ATCCTTCCAAATCTGGAATGGAACTTAAATTAGCACAACCACTTAGCTTTAATTCTTCAAGACTA
259 ATCCTTCCAAATCTGGAATGGAACTTAAATTAGCACAACCACTTAACTTTAATTCTTCAAGACTA
*
606977 GTGGAGGTAGACAACCAGTC
324 GTGGAGGTAAACAACCAGTC
606997 TCCTATCTTG
Statistics
Matches: 307, Mismatches: 34, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
345 300 0.98
346 7 0.02
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (345 bp):
TTTCCAGTTCGTGGCAGTCTGATATATCTAAAATTCGAAGAGAGGAAAATCCTCGCAAATCTAGA
ATGGAACTCAAATCAGGACAATTGCTTAACTTCAATTCTTCAAGACAAGTGGAGGTAGACAACCA
GTCTCCTATCTTGATGAATTTTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATAAACATCTTC
CTCTAATCGGAACAGTTTCCAGTTCGTGGCAGTCTGATATATCTAAAACTCGAAGAGAGGAAAAT
CCTTCCAAATCTGGAATGGAACTTAAATTAGCACAACCACTTAACTTTAATTCTTCAAGACTAGT
GGAGGTAAACAACCAGTCAA
Found at i:607028 original size:210 final size:210
Alignment explanation
Indices: 606654--607852 Score: 1914
Period size: 210 Copynumber: 5.7 Consensus size: 210
606644 AACCAGTCAA
* * *
606654 TTTCCAGTTCGTGGCAGTCTGCTATATCTAAAATTCGAAGAGAGGAAAATCCTTCCAAATCTAGA
1 TTTCCAGTTCGTGGCAGTCTGATATATCTAAAATTCGGAGAGAGGAAAATCCTTCCAAATCTGGA
* * *** * * * * *
606719 ATGGAACTCAAATTAGGACAATTGTTTAACTTCAATTCTTCAAGACAAGTGGCGGTAGGCAACCA
66 ATGGAACTTAAATTAGCACAATCACTTAGCTTTAATTCTTCAAGACTAGTGGAGGTAGACAACCA
* * * * * *
606784 GTCTTCTATCTTGATGATATTTT-GACAGGAGGAAATGTGAAGCTTTTCAAGAGATAAACATCTT
131 GTCTCCTATCTTGCTTA-ATTTTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATGAACATCTT
*
606848 CCTCTTATCGGAACAG
195 CCTCTTATCGGAATAG
*
606864 TTTCCAGTTCGTGGCAGTCTGATATATCTAAAACTCGGAGAGAGGAAAATCCTTCCAAATCTGGA
1 TTTCCAGTTCGTGGCAGTCTGATATATCTAAAATTCGGAGAGAGGAAAATCCTTCCAAATCTGGA
*
606929 ATGGAACTTAAATTAGCACAACCACTTAGCTTTAATTCTTCAAGACTAGTGGAGGTAGACAACCA
66 ATGGAACTTAAATTAGCACAATCACTTAGCTTTAATTCTTCAAGACTAGTGGAGGTAGACAACCA
*
606994 GTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATGAACATCTTT
131 GTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATGAACATCTTC
*
607059 CTCTTATCGGAATGG
196 CTCTTATCGGAATAG
* *
607074 TTTCCAGTTCGTGGCAGTCTAATATATCTAAAATTCGGAGAGAGGAAAATCCTTCCAAATCTGAA
1 TTTCCAGTTCGTGGCAGTCTGATATATCTAAAATTCGGAGAGAGGAAAATCCTTCCAAATCTGGA
607139 ATGGAACTTAAATTAGCACAATCACTTAGCTTTAATTCTTCAAGACTAGTGGAGGTAGACAACCA
66 ATGGAACTTAAATTAGCACAATCACTTAGCTTTAATTCTTCAAGACTAGTGGAGGTAGACAACCA
*
607204 GTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATAAACATCTTC
131 GTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATGAACATCTTC
*
607269 CTCTTATCGGAATGG
196 CTCTTATCGGAATAG
* * *
607284 TTTCCAGTTCGTGACAGCCTAATATATCTAAAATTCGGAGAGAGGAAAATCCTTCCAAATCTGGA
1 TTTCCAGTTCGTGGCAGTCTGATATATCTAAAATTCGGAGAGAGGAAAATCCTTCCAAATCTGGA
* *
607349 ATGGAACTTAAATCAGCACAATCATTTAGCTTTAATTCTTCAAGACTAGTGGAGGTAGACAACCA
66 ATGGAACTTAAATTAGCACAATCACTTAGCTTTAATTCTTCAAGACTAGTGGAGGTAGACAACCA
* * * *
607414 GTCTCCAATCTTGCTTAATTTTGGACACGAGGAAATGCGAAGCTTTTGAAGAGATGAACATCTTC
131 GTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATGAACATCTTC
*
607479 CTCTTATCGGAACAG
196 CTCTTATCGGAATAG
*
607494 TTTCCAGTTCGTTGCAGTCTGATATATCTAAAATTCGGAGAGAGGAAAATCCTTCCAAATCTGGA
1 TTTCCAGTTCGTGGCAGTCTGATATATCTAAAATTCGGAGAGAGGAAAATCCTTCCAAATCTGGA
* *
607559 ATGGAACTTAACTTAGCACAATCACTTAGCTTTAATGCTTCAAGACTAGTGGAGGTAGACAACCA
66 ATGGAACTTAAATTAGCACAATCACTTAGCTTTAATTCTTCAAGACTAGTGGAGGTAGACAACCA
*
607624 GTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATGAACATCTTT
131 GTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATGAACATCTTC
607689 CTCTTATCGGAATAG
196 CTCTTATCGGAATAG
*
607704 TTTCCAGTTCGTGGCAGTCTGATATATCTAAAATTCGGAGAGAGGAAAATTCTTCCAAATCTGGA
1 TTTCCAGTTCGTGGCAGTCTGATATATCTAAAATTCGGAGAGAGGAAAATCCTTCCAAATCTGGA
* * * * * * *
607769 ATGAAACTTAATTTAGCACAACCACTTAGCTTTAATTCTTTAAGACAAATGGAGGTAGACAACCC
66 ATGGAACTTAAATTAGCACAATCACTTAGCTTTAATTCTTCAAGACTAGTGGAGGTAGACAACCA
* *
607834 CTCTCCAATCTTGCTTAAT
131 GTCTCCTATCTTGCTTAAT
607853 CTATTGCACT
Statistics
Matches: 920, Mismatches: 68, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
209 5 0.01
210 915 0.99
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (210 bp):
TTTCCAGTTCGTGGCAGTCTGATATATCTAAAATTCGGAGAGAGGAAAATCCTTCCAAATCTGGA
ATGGAACTTAAATTAGCACAATCACTTAGCTTTAATTCTTCAAGACTAGTGGAGGTAGACAACCA
GTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATGAACATCTTC
CTCTTATCGGAATAG
Found at i:607149 original size:555 final size:555
Alignment explanation
Indices: 606099--607206 Score: 1684
Period size: 555 Copynumber: 2.0 Consensus size: 555
606089 ATCGGAACAG
* * * *
606099 TTTCCAGTTTGTGGCAGTCTGATATATATAAAATTCGAAGAGAGGAAACTCCTTTCAAATCTGGA
1 TTTCCAGTTCGTGGCAGTCTGATATATATAAAATTCGAAGAGAGGAAAATCCTTCCAAATCTAGA
*
606164 ATGAAACGTAAATTAGGACAATTGCTTAACTTCAATTCTTTAAAACAAGTGGAGGTAGACAACCA
66 ATGAAACGTAAATTAGGACAATTGCTTAACTTCAATTCTTCAAAACAAGTGGAGGTAGACAACCA
* * *
606229 GTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATGAACATATTC
131 GTCTCCTATCTTGATGAATTTTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATAAACATATTC
* * *
606294 CTCTTATCGGAACGGTTTCCAGTTCTTGGCAGTCTGATATATCTAAACTTCGAAGAGAGGAAAGT
196 CTCTTATCGGAACAGTTTCCAGTTCGTGGCAGTCTGATATATCTAAACTTCGAAGAGAGGAAAAT
* * * *** *
606359 CCTCGCAATTTTGGAATGGAACTTAAATCAGGACAATTGCTTAACTTCAATTCTTTAAGACAAGT
261 CCTCGCAAATCTGGAATGGAACTTAAATCAGCACAACCACTTAACTTCAATTCTTCAAGACAAGT
606424 GGAGGTAGACAACCAGTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTTTTCAA
326 GGAGGTAGACAACCAGTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTTTTCAA
* * *
606489 GAGATGAACATCTTCCTCTAATCGGAACAGTTTCCAGTTCTTGGCAGTCTGATATATTTAAAATT
391 GAGATGAACATCTTCCTCTAATCGGAACAGTTTCCAGTTCGTGGCAGTCTAATATATCTAAAATT
* * * * **
606554 CGAAGAGAGGAAAGTCCTTCCAAATTTGGAATGGAACTTAAATTAGGACAATTGCTTAACTTTAA
456 CGAAGAGAGGAAAATCCTTCCAAATCTGAAATGGAACTTAAATTAGCACAATCACTTAACTTTAA
* *
606619 TTCTTCAAGATTCGTGGAGGTAAACAACCAGTCAA
521 TTCTTCAAGACTAGTGGAGGTAAACAACCAGTCAA
* *
606654 TTTCCAGTTCGTGGCAGTCTGCTATATCTAAAATTCGAAGAGAGGAAAATCCTTCCAAATCTAGA
1 TTTCCAGTTCGTGGCAGTCTGATATATATAAAATTCGAAGAGAGGAAAATCCTTCCAAATCTAGA
* * * * *
606719 ATGGAAC-TCAAATTAGGACAATTGTTTAACTTCAATTCTTCAAGACAAGTGGCGGTAGGCAACC
66 ATGAAACGT-AAATTAGGACAATTGCTTAACTTCAATTCTTCAAAACAAGTGGAGGTAGACAACC
* * * *
606783 AGTCTTCTATCTTGATGATATTTT-GACAGGAGGAAATGTGAAGCTTTTCAAGAGATAAACATCT
130 AGTCTCCTATCTTGATGA-ATTTTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATAAACATAT
*
606847 TCCTCTTATCGGAACAGTTTCCAGTTCGTGGCAGTCTGATATATCTAAAAC-TCGGAGAGAGGAA
194 TCCTCTTATCGGAACAGTTTCCAGTTCGTGGCAGTCTGATATATCT-AAACTTCGAAGAGAGGAA
* * *
606911 AATCCTTC-CAAATCTGGAATGGAACTTAAATTAGCACAACCACTTAGCTTTAATTCTTCAAGAC
258 AATCC-TCGCAAATCTGGAATGGAACTTAAATCAGCACAACCACTTAACTTCAATTCTTCAAGAC
*
606975 TAGTGGAGGTAGACAACCAGTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTTT
322 AAGTGGAGGTAGACAACCAGTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTTT
* * **
607040 TCAAGAGATGAACATCTTTCTCTTATCGGAATGGTTTCCAGTTCGTGGCAGTCTAATATATCTAA
387 TCAAGAGATGAACATCTTCCTCTAATCGGAACAGTTTCCAGTTCGTGGCAGTCTAATATATCTAA
* *
607105 AATTCGGAGAGAGGAAAATCCTTCCAAATCTGAAATGGAACTTAAATTAGCACAATCACTTAGCT
452 AATTCGAAGAGAGGAAAATCCTTCCAAATCTGAAATGGAACTTAAATTAGCACAATCACTTAACT
*
607170 TTAATTCTTCAAGACTAGTGGAGGTAGACAACCAGTC
517 TTAATTCTTCAAGACTAGTGGAGGTAAACAACCAGTC
607207 TCCTATCTTG
Statistics
Matches: 497, Mismatches: 52, Indels: 8
0.89 0.09 0.01
Matches are distributed among these distances:
554 1 0.00
555 485 0.98
556 11 0.02
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (555 bp):
TTTCCAGTTCGTGGCAGTCTGATATATATAAAATTCGAAGAGAGGAAAATCCTTCCAAATCTAGA
ATGAAACGTAAATTAGGACAATTGCTTAACTTCAATTCTTCAAAACAAGTGGAGGTAGACAACCA
GTCTCCTATCTTGATGAATTTTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATAAACATATTC
CTCTTATCGGAACAGTTTCCAGTTCGTGGCAGTCTGATATATCTAAACTTCGAAGAGAGGAAAAT
CCTCGCAAATCTGGAATGGAACTTAAATCAGCACAACCACTTAACTTCAATTCTTCAAGACAAGT
GGAGGTAGACAACCAGTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTTTTCAA
GAGATGAACATCTTCCTCTAATCGGAACAGTTTCCAGTTCGTGGCAGTCTAATATATCTAAAATT
CGAAGAGAGGAAAATCCTTCCAAATCTGAAATGGAACTTAAATTAGCACAATCACTTAACTTTAA
TTCTTCAAGACTAGTGGAGGTAAACAACCAGTCAA
Found at i:622460 original size:35 final size:35
Alignment explanation
Indices: 622369--622535 Score: 183
Period size: 35 Copynumber: 4.6 Consensus size: 35
622359 CATGGCAAAG
*
622369 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGT
* *
622404 TGTGAAATGTGGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGT
622439 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTA-T-T---ATCCATACTGAGT
*** * *
622479 TAAAAAATGTAGGTATGGCATT-TCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATTAT-CCATACTGAGT
**
622514 TGAAAAATGTAGGTATGGTATT
1 TGTGAAATGTAGGTATGGTATT
622536 TCAATGAGGA
Statistics
Matches: 114, Mismatches: 12, Indels: 12
0.83 0.09 0.09
Matches are distributed among these distances:
34 1 0.01
35 81 0.71
36 1 0.01
37 1 0.01
38 1 0.01
39 1 0.01
40 28 0.25
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.34
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATTATCCATACTGAGT
Found at i:622495 original size:75 final size:75
Alignment explanation
Indices: 622369--622539 Score: 203
Period size: 75 Copynumber: 2.4 Consensus size: 75
622359 CATGGCAAAG
*** * *
622369 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTGGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAAAAATGTAGGTATGGCATT-TC
*
622428 CCATACTGAGC
65 CCATACCGAGC
622439 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAAAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAAAAATGTAGGTATGGCATTTCC
*
622504 CATACCGAGT
66 CATACCGAGC
**
622514 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
622540 TGAGGAAAAC
Statistics
Matches: 86, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
70 18 0.21
73 4 0.05
74 5 0.06
75 59 0.69
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAAAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:628173 original size:210 final size:205
Alignment explanation
Indices: 627670--628432 Score: 822
Period size: 210 Copynumber: 3.7 Consensus size: 205
627660 TCTGTTATTC
* * * *
627670 GAACAATTTCCAGATTGTTGCAGTTTGATATATTTAAAATAT-GAAGAGAGGAAAAT-CGTCCTA
1 GAACAATTTCCAG-TTGTTGCAG-TAGATATATCTAAAAT-TCGAAAAGAGGAAAATCCTTCC-A
* * * * ** * * * ** * * *
627733 AATCTGGAATGGAATTTAAGTTACCACAATGGGATAGCTTTAACTCTTTGAGGCAAGGGGCGGTA
62 AATCTGGAATGGAACTTAAATTAGCACAATTGCTTAACTTCAATTCTTCAAGACAAGTGGAGGTA
* * * * * * *
627798 GACAACCCGTCTCCTATCTTGCTTAATTTAGGACACCAGGAAATGAGAAGCTTCTCAATAGGTGA
127 GACAA-CCATCTCCTATCTTGCTTAATTTTGGACACGAGGAAATGTGAAGCTTTTCAAGAGATGA
*
627863 ACATCTT--ACTATCG
191 ACAT-TTCCTCTATCG
* * * *
627877 GAACAGTTTCCAGTTCGTGGCAGTATGATATATCTAAAATTTGGAGAAAGA--AAAATCGTTCCA
1 GAACAATTTCCAGTT-GTTGCAGTA-GATATATCTAAAA-TTCGA-AAAGAGGAAAATCCTTCCA
** * * *
627940 AATCTGGAATGGAACTTAAATTAGCACAATCACTTAGCTTTAATTCTTCAAGACTAGTGGAGGTA
62 AATCTGGAATGGAACTTAAATTAGCACAATTGCTTAACTTCAATTCTTCAAGACAAGTGGAGGTA
* *
628005 GACAACACATCTCCTATCTTGCTTAATTTTTGACATGAGGAAATGTGAAGCTTTTCAAGAGATGA
127 GACAAC-CATCTCCTATCTTGCTTAATTTTGGACACGAGGAAATGTGAAGCTTTTCAAGAGATGA
628070 ACATTGTCCTCCTATCG
191 ACATT-TCCT-CTATCG
628087 GAACAATTTCCAGATTGTTGCAGATAGATATATCTAAAATTCGAAAAGAGGAAAATCCTTCCAAA
1 GAACAATTTCCAG-TTGTTGCAG-TAGATATATCTAAAATTCGAAAAGAGGAAAATCCTTCCAAA
* * * *
628152 TCTGGAATGAAACTTAAATTAGGAAAATTGCTTAACTTCAATTCTTTAAGACAAGTGGAGGTAGA
64 TCTGGAATGGAACTTAAATTAGCACAATTGCTTAACTTCAATTCTTCAAGACAAGTGGAGGTAGA
*
628217 CAACCAGTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATGAAC
129 CAACCA-TCTCCTATCTTGCTTAATTTTGGACACGAGGAAATGTGAAGCTTTTCAAGAGATGAAC
628282 ATCTTCCTCTAATCG
193 AT-TTCCTCT-ATCG
* * * *
628297 GAACAGTTTCCAGTTCTTGGCAGTCTGATATATCTAAAATTC-AAAGAGAGGAAAGTCCTTCCAA
1 GAACAATTTCCAGTTGTT-GCAGT-AGATATATCTAAAATTCGAAA-AGAGGAAAATCCTTCCAA
* * *
628361 ATTTGGAATGGAACTTAAATTAGGACAATTGCTTAACTTCAATTCTTCAAGATTAA-TGGAGGTA
63 ATCTGGAATGGAACTTAAATTAGCACAATTGCTTAACTTCAATTCTTCAAGA-CAAGTGGAGGTA
*
628425 AACAACCA
127 GACAACCA
628433 GTCAATTTCC
Statistics
Matches: 477, Mismatches: 57, Indels: 41
0.83 0.10 0.07
Matches are distributed among these distances:
206 5 0.01
207 147 0.31
208 11 0.02
209 20 0.04
210 287 0.60
211 7 0.01
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.30
Consensus pattern (205 bp):
GAACAATTTCCAGTTGTTGCAGTAGATATATCTAAAATTCGAAAAGAGGAAAATCCTTCCAAATC
TGGAATGGAACTTAAATTAGCACAATTGCTTAACTTCAATTCTTCAAGACAAGTGGAGGTAGACA
ACCATCTCCTATCTTGCTTAATTTTGGACACGAGGAAATGTGAAGCTTTTCAAGAGATGAACATT
TCCTCTATCG
Found at i:628433 original size:210 final size:207
Alignment explanation
Indices: 627794--628435 Score: 828
Period size: 210 Copynumber: 3.1 Consensus size: 207
627784 GGCAAGGGGC
* * * * * *
627794 GGTAGACAACCCGTCTCCTATCTTGCTTAATTTAGGACACCAGGAAATGAGAAGCTTCTCAATAG
1 GGTAGACAACCAGTCTCCTATCTTGCTTAATTTTGGACACGAGGAAATGTGAAGCTTTTCAAGAG
* * * ***
627859 GTGAACATCTT--ACTATCGGAACAGTTTCCAGTTCGTGGCAGTATGATATATCTAAAATTTGGA
66 ATGAACATCTTCCTCTATCGGAACAGTTTCCAGTTCTTGGCAGT-TGATATATCTAAAATTCAAA
* * * * ** * *
627922 GAAAGAAAAATCGTTCCAAATCTGGAATGGAACTTAAATTAGCACAATCACTTAGCTTTAATTCT
130 GAGAGGAAAATCCTTCCAAATCTGGAATGGAACTTAAATTAGGACAATTGCTTAACTTCAATTCT
*
627987 TCAAGACTAGTGGA
195 TCAAGA-TAATGGA
* *
628001 GGTAGACAACACA-TCTCCTATCTTGCTTAATTTTTGACATGAGGAAATGTGAAGCTTTTCAAGA
1 GGTAGACAAC-CAGTCTCCTATCTTGCTTAATTTTGGACACGAGGAAATGTGAAGCTTTTCAAGA
* * *
628065 GATGAACAT-TGTCCTCCTATCGGAACAATTTCCAGATTGTT-GCAGATAGATATATCTAAAATT
65 GATGAACATCT-TCCT-CTATCGGAACAGTTTCCAG-TTCTTGGCAG-TTGATATATCTAAAATT
* *
628128 CGAAA-AGAGGAAAATCCTTCCAAATCTGGAATGAAACTTAAATTAGGAAAATTGCTTAACTTCA
126 C-AAAGAGAGGAAAATCCTTCCAAATCTGGAATGGAACTTAAATTAGGACAATTGCTTAACTTCA
* *
628192 ATTCTTTAAGACAAGTGGA
190 ATTCTTCAAGATAA-TGGA
*
628211 GGTAGACAACCAGTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTTTTCAAGAG
1 GGTAGACAACCAGTCTCCTATCTTGCTTAATTTTGGACACGAGGAAATGTGAAGCTTTTCAAGAG
628276 ATGAACATCTTCCTCTAATCGGAACAGTTTCCAGTTCTTGGCAGTCTGATATATCTAAAATTCAA
66 ATGAACATCTTCCTCT-ATCGGAACAGTTTCCAGTTCTTGGCAGT-TGATATATCTAAAATTCAA
* *
628341 AGAGAGGAAAGTCCTTCCAAATTTGGAATGGAACTTAAATTAGGACAATTGCTTAACTTCAATTC
129 AGAGAGGAAAATCCTTCCAAATCTGGAATGGAACTTAAATTAGGACAATTGCTTAACTTCAATTC
628406 TTCAAGATTAATGGA
194 TTCAAGA-TAATGGA
*
628421 GGTAAACAACCAGTC
1 GGTAGACAACCAGTC
628436 AATTTCCAGT
Statistics
Matches: 376, Mismatches: 43, Indels: 29
0.84 0.10 0.06
Matches are distributed among these distances:
206 1 0.00
207 63 0.17
208 1 0.00
209 13 0.03
210 290 0.77
211 8 0.02
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (207 bp):
GGTAGACAACCAGTCTCCTATCTTGCTTAATTTTGGACACGAGGAAATGTGAAGCTTTTCAAGAG
ATGAACATCTTCCTCTATCGGAACAGTTTCCAGTTCTTGGCAGTTGATATATCTAAAATTCAAAG
AGAGGAAAATCCTTCCAAATCTGGAATGGAACTTAAATTAGGACAATTGCTTAACTTCAATTCTT
CAAGATAATGGA
Found at i:628481 original size:135 final size:135
Alignment explanation
Indices: 628303--628547 Score: 427
Period size: 135 Copynumber: 1.8 Consensus size: 135
628293 ATCGGAACAG
* * * * *
628303 TTTCCAGTTCTTGGCAGTCTGATATATCTAAAATTCAAAGAGAGGAAAGTCCTTCCAAATTTGGA
1 TTTCCAGTTCGTGGCAGTCTGATATATCTAAAATTCAAAGAGAGGAAAATCCTTCAAAATATAGA
*
628368 ATGGAACTTAAATTAGGACAATTGCTTAACTTCAATTCTTCAAGATTAATGGAGGTAAACAACCA
66 ATGGAACTTAAATTAGGAAAATTGCTTAACTTCAATTCTTCAAGATTAATGGAGGTAAACAACCA
628433 GTCAA
131 GTCAA
*
628438 TTTCCAGTTCGTGGCAGTCTGATATATCTAAAATTCGAAGAGAGGAAAATCCTTCAAAATATAGA
1 TTTCCAGTTCGTGGCAGTCTGATATATCTAAAATTCAAAGAGAGGAAAATCCTTCAAAATATAGA
628503 ATGGAACTTAAATTAGGAAAATTGCTTAACTTCAATTCTTCAAGA
66 ATGGAACTTAAATTAGGAAAATTGCTTAACTTCAATTCTTCAAGA
628548 CAAGTGGCGG
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
135 103 1.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.31
Consensus pattern (135 bp):
TTTCCAGTTCGTGGCAGTCTGATATATCTAAAATTCAAAGAGAGGAAAATCCTTCAAAATATAGA
ATGGAACTTAAATTAGGAAAATTGCTTAACTTCAATTCTTCAAGATTAATGGAGGTAAACAACCA
GTCAA
Found at i:628723 original size:345 final size:345
Alignment explanation
Indices: 628113--628780 Score: 1034
Period size: 345 Copynumber: 1.9 Consensus size: 345
628103 GTTGCAGATA
* * *
628113 GATATATCTAAAATTCGAAAAGAGGAAAATCCTTCCAAATCTGGAATGAAACTTAAATTAGGAAA
1 GATATATCTAAAATTCGAAAAGAGGAAAATCCTTCAAAATATAGAATGAAACTTAAATTAGGAAA
* * * *
628178 ATTGCTTAACTTCAATTCTTTAAGACAAGTGGAGGTAGACAACCAGTCTCCTATCTTGCTTAATT
66 ATTGCTTAACTTCAATTCTTCAAGACAAGTGGAGGTAGACAACCAGACTCCTATCTTGATGAATT
*
628243 TTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATGAACATCTTCCTCTAATCGGAACAGTTTCC
131 TTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATAAACATCTTCCTCTAATCGGAACAGTTTCC
* * * *
628308 AGTTCTTGGCAGTCTGATATATCTAAAATTCAAAGAGAGGAAAGTCCTTCCAAATTTGGAATGGA
196 AGTTCGTGGCAGTCTGATATATCTAAAATTCAAAGAGAGGAAAATCCTTCCAAATCTGGAATGAA
* *** * *
628373 ACTTAAATTAGGACAATTGCTTAACT-TCAATTCTTCAAGATTAATGGAGGTAAACAACCAGTCA
261 ACTTAAATTAGCACAACCACTTAACTCT-AATTCTTCAAGACTAATGGACGTAAACAACCAGTCA
628437 ATTTCCAGTTCGTGGCAGTCT
325 ATTTCCAGTTCGTGGCAGTCT
* *
628458 GATATATCTAAAATTCGAAGAGAGGAAAATCCTTCAAAATATAGAATGGAACTTAAATTAGGAAA
1 GATATATCTAAAATTCGAAAAGAGGAAAATCCTTCAAAATATAGAATGAAACTTAAATTAGGAAA
* *
628523 ATTGCTTAACTTCAATTCTTCAAGACAAGTGGCGGTAGACAACCAGACTTCTATCTTGATGATAT
66 ATTGCTTAACTTCAATTCTTCAAGACAAGTGGAGGTAGACAACCAGACTCCTATCTTGATGA-AT
* * *
628588 TTT-GACAGGAGGAAATGTGAAGCTTTTCAAGAGATAAACATCTTCCTCTTATCGGAACAGTTTC
130 TTTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATAAACATCTTCCTCTAATCGGAACAGTTTC
**
628652 CAGTTCGTGGCAGTCTGATATATCTAAAATTCGGAGAGAGGAAAATCCTTCCAAATCTGGAATGA
195 CAGTTCGTGGCAGTCTGATATATCTAAAATTCAAAGAGAGGAAAATCCTTCCAAATCTGGAATGA
* * *
628717 AACTTAAATTAGCACAACCACTTAGCTCTAATTCTTCAAGACTAGTGGACGTAGACAACCAGTC
260 AACTTAAATTAGCACAACCACTTAACTCTAATTCTTCAAGACTAATGGACGTAAACAACCAGTC
628781 TCCTATCTTG
Statistics
Matches: 291, Mismatches: 30, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
345 285 0.98
346 6 0.02
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (345 bp):
GATATATCTAAAATTCGAAAAGAGGAAAATCCTTCAAAATATAGAATGAAACTTAAATTAGGAAA
ATTGCTTAACTTCAATTCTTCAAGACAAGTGGAGGTAGACAACCAGACTCCTATCTTGATGAATT
TTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATAAACATCTTCCTCTAATCGGAACAGTTTCC
AGTTCGTGGCAGTCTGATATATCTAAAATTCAAAGAGAGGAAAATCCTTCCAAATCTGGAATGAA
ACTTAAATTAGCACAACCACTTAACTCTAATTCTTCAAGACTAATGGACGTAAACAACCAGTCAA
TTTCCAGTTCGTGGCAGTCT
Found at i:628812 original size:210 final size:210
Alignment explanation
Indices: 628438--629636 Score: 1880
Period size: 210 Copynumber: 5.7 Consensus size: 210
628428 AACCAGTCAA
* * * *
628438 TTTCCAGTTCGTGGCAGTCTGATATATCTAAAATTCGAAGAGAGGAAAATCCTTCAAAATATAGA
1 TTTCCAGTTCGTGGCAGTCTGATATATCTAAAATTCGGAGAGAGGAAAATCCTTCCAAATCTGGA
* * ** * * * *
628503 ATGGAACTTAAATTAGGAAAATTGCTTAACTTCAATTCTTCAAGACAAGTGGCGGTAGACAACCA
66 ATGGAACTTAAATTAGCACAATCACTTAGCTTTAATTCTTCAAGACTAGTGGAGGTAGACAACCA
* * * * * * *
628568 GACTTCTATCTTGATGATATTTT-GACAGGAGGAAATGTGAAGCTTTTCAAGAGATAAACATCTT
131 GTCTCCTATCTTGCTTA-ATTTTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATGAACATCTT
*
628632 CCTCTTATCGGAACAG
195 CCTCTTATCGGAATAG
628648 TTTCCAGTTCGTGGCAGTCTGATATATCTAAAATTCGGAGAGAGGAAAATCCTTCCAAATCTGGA
1 TTTCCAGTTCGTGGCAGTCTGATATATCTAAAATTCGGAGAGAGGAAAATCCTTCCAAATCTGGA
* * * *
628713 ATGAAACTTAAATTAGCACAACCACTTAGCTCTAATTCTTCAAGACTAGTGGACGTAGACAACCA
66 ATGGAACTTAAATTAGCACAATCACTTAGCTTTAATTCTTCAAGACTAGTGGAGGTAGACAACCA
628778 GTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATGAACATCTTC
131 GTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATGAACATCTTC
* * *
628843 CTCTTATTGAAATGG
196 CTCTTATCGGAATAG
*
628858 TTTCCAGTTCGCGGCAGTCTGATATATCTAAAATTCGGAGAGAGGAAAATCCTTCCAAATCTGGA
1 TTTCCAGTTCGTGGCAGTCTGATATATCTAAAATTCGGAGAGAGGAAAATCCTTCCAAATCTGGA
* * *
628923 ATGGAACTTAAATCAGCACAATCATTTAGCTTTAATTCTTCAAGACTAGTGGAGGTAGACAACCC
66 ATGGAACTTAAATTAGCACAATCACTTAGCTTTAATTCTTCAAGACTAGTGGAGGTAGACAACCA
*
628988 GTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCCTTTCAAGAGATGAACATCTTC
131 GTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATGAACATCTTC
*
629053 CTCTTATCGGAACAG
196 CTCTTATCGGAATAG
*
629068 TTTCCAGTTCGTGGCAGTCTGATATATCTAAAATTCGGAGGGAGGAAAATCCTTCCAAATCTGGA
1 TTTCCAGTTCGTGGCAGTCTGATATATCTAAAATTCGGAGAGAGGAAAATCCTTCCAAATCTGGA
* * * * *
629133 ATGGCACTTAAATAAGCACAATCATTTAGCTTTAATTCTTCAAGACTAGTGCAGGTAGACAAACA
66 ATGGAACTTAAATTAGCACAATCACTTAGCTTTAATTCTTCAAGACTAGTGGAGGTAGACAACCA
629198 GTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATGAACATCTTT
131 GTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATGAACATC-TT
629263 CC-CTTATCGGAATAG
195 CCTCTTATCGGAATAG
* ** *
629278 TTTCCAGTTTGTAACAGTTTGATATATCTAAAATTCGGAGAGAGGAAAATCCTTCCAAATCTGGA
1 TTTCCAGTTCGTGGCAGTCTGATATATCTAAAATTCGGAGAGAGGAAAATCCTTCCAAATCTGGA
*
629343 ATGGAACTTAAATTAGCACAAGCACTTAGCTTTAATTCTTCAAGACTAGTGGAGGTAGACAACCA
66 ATGGAACTTAAATTAGCACAATCACTTAGCTTTAATTCTTCAAGACTAGTGGAGGTAGACAACCA
* *
629408 GTCTCCTATCTTGCATAATTTTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATGAACATCTTT
131 GTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATGAACATCTTC
629473 CTCTTATCGGAATAG
196 CTCTTATCGGAATAG
* * *
629488 TTTCCAGTTCCTGGCAGTCCGATATATCTAAAATTCGGAGAGAGGAAAATTCTTCCAAATCTGGA
1 TTTCCAGTTCGTGGCAGTCTGATATATCTAAAATTCGGAGAGAGGAAAATCCTTCCAAATCTGGA
* * *
629553 ATGGAACTTAATTTAGCACAACCACTTAGCTTTAATTCTTCAAGACTAGTGGAGGTAGACAACCC
66 ATGGAACTTAAATTAGCACAATCACTTAGCTTTAATTCTTCAAGACTAGTGGAGGTAGACAACCA
* *
629618 CTCTCCAATCTTGCTTAAT
131 GTCTCCTATCTTGCTTAAT
629637 CTATTGCACT
Statistics
Matches: 911, Mismatches: 75, Indels: 6
0.92 0.08 0.01
Matches are distributed among these distances:
209 8 0.01
210 899 0.99
211 4 0.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (210 bp):
TTTCCAGTTCGTGGCAGTCTGATATATCTAAAATTCGGAGAGAGGAAAATCCTTCCAAATCTGGA
ATGGAACTTAAATTAGCACAATCACTTAGCTTTAATTCTTCAAGACTAGTGGAGGTAGACAACCA
GTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTTTTCAAGAGATGAACATCTTC
CTCTTATCGGAATAG
Found at i:628876 original size:555 final size:555
Alignment explanation
Indices: 627883--628986 Score: 1581
Period size: 555 Copynumber: 2.0 Consensus size: 555
627873 ATCGGAACAG
* * * * * *
627883 TTTCCAGTTCGTGGCAGTATGATATATCTAAAATTTGGAGAAAGAAAAATCGTTCCAAATCTGGA
1 TTTCCAGTTCGTGGCAGTATGATATATCTAAAATTCGAAGAAAGAAAAATCCTTCAAAATATAGA
* * * *
627948 ATGGAACTTAAATTAGCACAATCACTTAGCTTTAATTCTTCAAGACTAGTGGAGGTAGACAACAC
66 ATGGAACTTAAATTAGCAAAATCACTTAACTTCAATTCTTCAAGACAAGTGGAGGTAGACAACAC
* * * * *
628013 ATCTCCTATCTTGCTTAATTTTTGACATGAGGAAATGTGAAGCTTTTCAAGAGATGAACATTGTC
131 AACTCCTATCTTGATGAATTTTTGACAGGAGGAAATGTGAAGCTTTTCAAGAGATAAACATTGTC
*
628078 CTCCTATCGGAACAATTTCCAGATTGTTGCAGATAGATATATCTAAAATTCGAAAAGAGGAAAAT
196 CTCCTATCGGAACAATTTCCAGATTGTGGCAGATAGATATATCTAAAATTCGAAAAGAGGAAAAT
* *** *
628143 CCTTCCAAATCTGGAATGAAACTTAAATTAGGAAAATTGCTTAACTTCAATTCTTTAAGACAAGT
261 CCTTCCAAATCTGGAATGAAACTTAAATTAGCAAAACCACTTAACTTCAATTCTTCAAGACAAGT
*
628208 GGAGGTAGACAACCAGTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTTTTCAA
326 GGACGTAGACAACCAGTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTTTTCAA
* **
628273 GAGATGAACATCTTCCTCTAATCGGAACAGTTTCCAGTTCTTGGCAGTCTGATATATCTAAAATT
391 GAGATGAACATCTTCCTCTAATCGAAACAGTTTCCAGTTCGCGGCAGTCTGATATATCTAAAATT
* * * * **
628338 CAAAGAGAGGAAAGTCCTTCCAAATTTGGAATGGAACTTAAATTAGGACAATTGCTTAACTTCAA
456 CAAAGAGAGGAAAATCCTTCCAAATCTGGAATGGAACTTAAATCAGCACAATCACTTAACTTCAA
*
628403 TTCTTCAAGATTAATGGAGGTAAACAACCAGTCAA
521 TTCTTCAAGACTAATGGAGGTAAACAACCAGTCAA
* * *
628438 TTTCCAGTTCGTGGCAGTCTGATATATCTAAAATTCGAAGAGAGGAAAATCCTTCAAAATATAGA
1 TTTCCAGTTCGTGGCAGTATGATATATCTAAAATTCGAAGAAAGAAAAATCCTTCAAAATATAGA
* ** *
628503 ATGGAACTTAAATTAGGAAAATTGCTTAACTTCAATTCTTCAAGACAAGTGGCGGTAGACAAC-C
66 ATGGAACTTAAATTAGCAAAATCACTTAACTTCAATTCTTCAAGACAAGTGGAGGTAGACAACAC
*
628567 AGACTTCTATCTTGATG-ATATTTTGACAGGAGGAAATGTGAAGCTTTTCAAGAGATAAACATCT
131 A-ACTCCTATCTTGATGAAT-TTTTGACAGGAGGAAATGTGAAGCTTTTCAAGAGATAAACAT-T
* * * * *
628631 -TCCTCTTATCGGAACAGTTTCCAG-TTCGTGGCAG-TCTGATATATCTAAAATTCGGAGAGAGG
193 GTCCTCCTATCGGAACAATTTCCAGATT-GTGGCAGAT-AGATATATCTAAAATTCGAAAAGAGG
* *
628693 AAAATCCTTCCAAATCTGGAATGAAACTTAAATTAGCACAACCACTTAGC-TCTAATTCTTCAAG
256 AAAATCCTTCCAAATCTGGAATGAAACTTAAATTAGCAAAACCACTTAACTTC-AATTCTTCAAG
*
628757 ACTAGTGGACGTAGACAACCAGTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCT
320 ACAAGTGGACGTAGACAACCAGTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCT
* * **
628822 TTTCAAGAGATGAACATCTTCCTCTTATTGAAATGGTTTCCAGTTCGCGGCAGTCTGATATATCT
385 TTTCAAGAGATGAACATCTTCCTCTAATCGAAACAGTTTCCAGTTCGCGGCAGTCTGATATATCT
** * *
628887 AAAATTCGGAGAGAGGAAAATCCTTCCAAATCTGGAATGGAACTTAAATCAGCACAATCATTTAG
450 AAAATTCAAAGAGAGGAAAATCCTTCCAAATCTGGAATGGAACTTAAATCAGCACAATCACTTAA
* * *
628952 CTTTAATTCTTCAAGACTAGTGGAGGTAGACAACC
515 CTTCAATTCTTCAAGACTAATGGAGGTAAACAACC
628987 CGTCTCCTAT
Statistics
Matches: 484, Mismatches: 59, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
554 9 0.02
555 474 0.98
556 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (555 bp):
TTTCCAGTTCGTGGCAGTATGATATATCTAAAATTCGAAGAAAGAAAAATCCTTCAAAATATAGA
ATGGAACTTAAATTAGCAAAATCACTTAACTTCAATTCTTCAAGACAAGTGGAGGTAGACAACAC
AACTCCTATCTTGATGAATTTTTGACAGGAGGAAATGTGAAGCTTTTCAAGAGATAAACATTGTC
CTCCTATCGGAACAATTTCCAGATTGTGGCAGATAGATATATCTAAAATTCGAAAAGAGGAAAAT
CCTTCCAAATCTGGAATGAAACTTAAATTAGCAAAACCACTTAACTTCAATTCTTCAAGACAAGT
GGACGTAGACAACCAGTCTCCTATCTTGCTTAATTTTGGACACGAGGAAACGTGAAGCTTTTCAA
GAGATGAACATCTTCCTCTAATCGAAACAGTTTCCAGTTCGCGGCAGTCTGATATATCTAAAATT
CAAAGAGAGGAAAATCCTTCCAAATCTGGAATGGAACTTAAATCAGCACAATCACTTAACTTCAA
TTCTTCAAGACTAATGGAGGTAAACAACCAGTCAA
Found at i:632884 original size:31 final size:31
Alignment explanation
Indices: 632849--632909 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
632839 GACCATGAAA
* *
632849 CTATTTGAAAGTTTTCGTTTAAGTCATTAAT
1 CTATTTAAAAGTTTTCATTTAAGTCATTAAT
*
632880 CTATTTAAAAGTTTTTATTTAAGTCATTAA
1 CTATTTAAAAGTTTTCATTTAAGTCATTAA
632910 GTTATGTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.49
Consensus pattern (31 bp):
CTATTTAAAAGTTTTCATTTAAGTCATTAAT
Found at i:636151 original size:20 final size:20
Alignment explanation
Indices: 636126--636169 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
636116 ATTTTCCAGG
636126 TTAGAATTGGTGTATTGCTT
1 TTAGAATTGGTGTATTGCTT
636146 TTAGAATTGGTGTATTGCTT
1 TTAGAATTGGTGTATTGCTT
636166 TTAG
1 TTAG
636170 TATCACCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.05, G:0.25, T:0.50
Consensus pattern (20 bp):
TTAGAATTGGTGTATTGCTT
Found at i:641457 original size:19 final size:19
Alignment explanation
Indices: 641411--641458 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
641401 GTATATATTT
*
641411 TAAA-TTTATTTAGTTAGA
1 TAAATTTTATTTAGGTAGA
*
641429 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
641448 TAAGTTTTATT
1 TAAATTTTATT
641459 CATATTCTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.50
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:641534 original size:42 final size:42
Alignment explanation
Indices: 641475--641563 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
641465 CTAGGAATAT
* * *
641475 TTTTATTTTATCTTTTAGTAGTTTATTAGGACAAGGGAACTA
1 TTTTCTTTTATATTTTAGTAGTTTATTAGAACAAGGGAACTA
*
641517 TTTTCTTTTATATTTTAGTAGTTTATTAGAATAAGGGAACTA
1 TTTTCTTTTATATTTTAGTAGTTTATTAGAACAAGGGAACTA
641559 TTTTC
1 TTTTC
641564 CCAATTAGGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.51
Consensus pattern (42 bp):
TTTTCTTTTATATTTTAGTAGTTTATTAGAACAAGGGAACTA
Found at i:645408 original size:19 final size:19
Alignment explanation
Indices: 645362--645409 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
645352 TATATTATTT
645362 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
645380 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
645399 TAAGTTTTATT
1 TAAATTTTATT
645410 CATATTCTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:645485 original size:42 final size:42
Alignment explanation
Indices: 645426--645514 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
645416 CTAGGAATAT
* * *
645426 TTTTATTTTATCTTTTAGTAGTTTATTAGGACAAGGGAACTA
1 TTTTCTTTTATATTTTAGTAGTTTATTAGAACAAGGGAACTA
*
645468 TTTTCTTTTATATTTTAGTAGTTTATTAGAAGAAGGGAACTA
1 TTTTCTTTTATATTTTAGTAGTTTATTAGAACAAGGGAACTA
645510 TTTTC
1 TTTTC
645515 CCAATTAGGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.28, C:0.07, G:0.16, T:0.49
Consensus pattern (42 bp):
TTTTCTTTTATATTTTAGTAGTTTATTAGAACAAGGGAACTA
Found at i:654643 original size:22 final size:23
Alignment explanation
Indices: 654612--654660 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
654602 TTTTTTTTAA
654612 ATTTATTTTTAATAATATT-T-ATT
1 ATTTATTTTT-ATAA-ATTATAATT
654635 ATTTA-TTTTATAAATTATAATT
1 ATTTATTTTTATAAATTATAATT
654657 ATTT
1 ATTT
654661 CTAAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 3 0.12
21 5 0.21
22 11 0.46
23 5 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
ATTTATTTTTATAAATTATAATT
Found at i:658580 original size:27 final size:28
Alignment explanation
Indices: 658548--658602 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
658538 AATAAGATTA
658548 TTATATTATT-TATA-TAGTTAAATAATC
1 TTATATT-TTGTATACTAGTTAAATAATC
*
658575 TTATATTTTGTCTACTAGTTAAATAATC
1 TTATATTTTGTATACTAGTTAAATAATC
658603 AGTCTATGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 2 0.08
27 10 0.40
28 13 0.52
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.51
Consensus pattern (28 bp):
TTATATTTTGTATACTAGTTAAATAATC
Found at i:661006 original size:33 final size:34
Alignment explanation
Indices: 660965--661029 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 34
660955 TGATTCCGAA
*
660965 GATGATGAAACT-ACTGCAACTCATCTT-TTCAGT
1 GATGATGAAA-TAAATGCAACTCATCTTATTCAGT
*
660998 GATGATGAAATAAATGCAACTCGTCTTATTCA
1 GATGATGAAATAAATGCAACTCATCTTATTCA
661030 AGGAATTTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 1 0.04
33 23 0.82
34 4 0.14
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32
Consensus pattern (34 bp):
GATGATGAAATAAATGCAACTCATCTTATTCAGT
Found at i:667502 original size:67 final size:67
Alignment explanation
Indices: 667280--667550 Score: 262
Period size: 67 Copynumber: 4.1 Consensus size: 67
667270 GACTTACATA
*
667280 AAATAGTACCAAAAAGCCCCTCTACTATAATATAACATGGACAAGAGGCTGAAGATTCCTGTCAA
1 AAATTGTACCAAAAAGCCCCTCTACTATAATATAACATGGACAAGAGGCTGAAGATTCCTGTCAA
667345 GC
66 GC
* * * * * * ** **
667347 AAATTGTACTCTAATA--CGCTC--CTATAATATTCACAAT--ACATA-ATGACAGAATTTTTTT
1 AAATTGTAC-CAAAAAGCCCCTCTACTATAATA-TAAC-ATGGACA-AGA-GGCTGAAGATTCCT
667405 GGT--AG-
61 -GTCAAGC
* * *
667410 -AA--GTACCATGAAAGTCTCTCTACTATAATATAACATGGACAAGAGGCTGAAGATTCCTGTCA
1 AAATTGTACCA-AAAAGCCCCTCTACTATAATATAACATGGACAAGAGGCTGAAGATTCCTGTCA
667472 AGC
65 AGC
667475 AAATTGTACCAAAAAGCCCCTCTACTATAATATAACATGGACAAGAGGCTGAAGATTCCTGTCAA
1 AAATTGTACCAAAAAGCCCCTCTACTATAATATAACATGGACAAGAGGCTGAAGATTCCTGTCAA
667540 GC
66 GC
667542 AAATTGTAC
1 AAATTGTAC
667551 TCTAATACGC
Statistics
Matches: 159, Mismatches: 25, Indels: 40
0.71 0.11 0.18
Matches are distributed among these distances:
59 1 0.01
60 6 0.04
62 10 0.06
63 12 0.08
64 28 0.18
65 12 0.08
66 10 0.06
67 70 0.44
68 10 0.06
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.26
Consensus pattern (67 bp):
AAATTGTACCAAAAAGCCCCTCTACTATAATATAACATGGACAAGAGGCTGAAGATTCCTGTCAA
GC
Found at i:669431 original size:21 final size:21
Alignment explanation
Indices: 669407--669470 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
669397 AAATCTAACT
669407 GAAGCACAAAAGTGCTAAACG
1 GAAGCACAAAAGTGCTAAACG
** *
669428 GAAGC-CCGAAG-GCT-AACT
1 GAAGCACAAAAGTGCTAAACG
*
669446 GAAGCACATAAGTGCTAAACG
1 GAAGCACAAAAGTGCTAAACG
669467 GAAG
1 GAAG
669471 GCCGAAGGCT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 8 0.24
19 7 0.21
20 7 0.21
21 12 0.35
ACGTcount: A:0.42, C:0.20, G:0.27, T:0.11
Consensus pattern (21 bp):
GAAGCACAAAAGTGCTAAACG
Found at i:669447 original size:39 final size:39
Alignment explanation
Indices: 669401--669489 Score: 160
Period size: 39 Copynumber: 2.3 Consensus size: 39
669391 AACCCGAAAT
669401 CTAACTGAAGCACAAAAGTGCTAAACGGAAGCCCGAAGG
1 CTAACTGAAGCACAAAAGTGCTAAACGGAAGCCCGAAGG
* *
669440 CTAACTGAAGCACATAAGTGCTAAACGGAAGGCCGAAGG
1 CTAACTGAAGCACAAAAGTGCTAAACGGAAGCCCGAAGG
669479 CTAACTGAAGC
1 CTAACTGAAGC
669490 TCATCAGAGC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.39, C:0.22, G:0.26, T:0.12
Consensus pattern (39 bp):
CTAACTGAAGCACAAAAGTGCTAAACGGAAGCCCGAAGG
Found at i:672376 original size:59 final size:59
Alignment explanation
Indices: 672312--672456 Score: 149
Period size: 59 Copynumber: 2.5 Consensus size: 59
672302 CATGATAAAA
* *
672312 AAAAAAGATTAGGTGCCAAATT-AGAAAAAAGAGTCAAGTTCAGG-TACTAAATTAAATCC
1 AAAAAAGA-TAAGTACCAAATTAAGAAAAAAGAGTCAAGTT-AGGATACTAAATTAAATCC
* * * **
672371 AAAAAATATAAGTACCAATTTAAGAAAAAAGAGTCAAGTTTGGATACTAAATTGGA--C
1 AAAAAAGATAAGTACCAAATTAAGAAAAAAGAGTCAAGTTAGGATACTAAATTAAATCC
*
672428 AAAAAA-AT-AGATATCAAATTAAGAAAAAA
1 AAAAAAGATAAG-TACCAAATTAAGAAAAAA
672457 TATGAAGTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
55 2 0.03
56 18 0.24
57 7 0.09
58 12 0.16
59 35 0.47
ACGTcount: A:0.54, C:0.09, G:0.14, T:0.22
Consensus pattern (59 bp):
AAAAAAGATAAGTACCAAATTAAGAAAAAAGAGTCAAGTTAGGATACTAAATTAAATCC
Found at i:677080 original size:15 final size:15
Alignment explanation
Indices: 677060--677090 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
677050 TGATTTTCCT
677060 TTTAACATCATATAA
1 TTTAACATCATATAA
*
677075 TTTAACATTATATAA
1 TTTAACATCATATAA
677090 T
1 T
677091 AGCTTCAAGT
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:0.10, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTAACATCATATAA
Found at i:678597 original size:13 final size:13
Alignment explanation
Indices: 678579--678604 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
678569 CACTTAATTT
678579 CAAAAAATCACAA
1 CAAAAAATCACAA
678592 CAAAAAATCACAA
1 CAAAAAATCACAA
678605 AATGATCGTT
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:0.69, C:0.23, G:0.00, T:0.08
Consensus pattern (13 bp):
CAAAAAATCACAA
Found at i:679915 original size:22 final size:23
Alignment explanation
Indices: 679889--679933 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
679879 CTAAAACCCG
*
679889 TATTAATT-TTTTTATAT-TATAT
1 TATT-ATTATTTTTAAATATATAT
679911 TATTATTATTTTTAAATATATAT
1 TATTATTATTTTTAAATATATAT
679934 AATACATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 3 0.15
22 12 0.60
23 5 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TATTATTATTTTTAAATATATAT
Found at i:686209 original size:5 final size:5
Alignment explanation
Indices: 686190--686281 Score: 69
Period size: 5 Copynumber: 16.8 Consensus size: 5
686180 CAACCCAATC
**
686190 TTTATT TTTATT TTTATT TTTATT TTTATT TATTAT TTTCC TTTAT TTTAT
1 TTTA-T TTTA-T TTTA-T TTTA-T TTTA-T T-TTAT TTTAT TTTAT TTTAT
*
686241 TTTATT ATTTAT TATT-T ATTAT TTTAT TTTAT TTTAT TTTA
1 TTTA-T -TTTAT T-TTAT TTTAT TTTAT TTTAT TTTAT TTTA
686282 GTTAAATATT
Statistics
Matches: 75, Mismatches: 6, Indels: 11
0.82 0.07 0.12
Matches are distributed among these distances:
4 2 0.03
5 35 0.47
6 31 0.41
7 7 0.09
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:686265 original size:37 final size:36
Alignment explanation
Indices: 686196--686281 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 36
686186 AATCTTTATT
*
686196 TTTATTTT-TATTT-TTATTTTTATTTATTATTTTCC
1 TTTATTTTAT-TTTATTATTTTTATTTATTATTTTAC
*
686231 TTTATTTTATTTTATTATTTATTATTTATTATTTTAT
1 TTTATTTTATTTTATTATTT-TTATTTATTATTTTAC
686268 TTTATTTTATTTTA
1 TTTATTTTATTTTA
686282 GTTAAATATT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
35 11 0.24
36 7 0.15
37 28 0.61
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (36 bp):
TTTATTTTATTTTATTATTTTTATTTATTATTTTAC
Found at i:687437 original size:117 final size:117
Alignment explanation
Indices: 687231--687460 Score: 388
Period size: 117 Copynumber: 2.0 Consensus size: 117
687221 TGTTTTCCAT
* *
687231 GGTTATGAGTACAGCTTAGATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
687296 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCGA
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCGA
**
687348 GGTTATGAGTATGGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
****
687413 CTACTTCGCGTCAAAAGGTTGTGTGACGTGTTGGGTAAAACTCCGCTA
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTA
687461 ACCGGAAATA
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
117 105 1.00
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (117 bp):
GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCGA
Found at i:692824 original size:15 final size:16
Alignment explanation
Indices: 692804--692834 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
692794 ATAGTCTTTG
692804 CTTTGTCTTTT-TTTC
1 CTTTGTCTTTTGTTTC
692819 CTTTGTCTTTTGTTTC
1 CTTTGTCTTTTGTTTC
692835 AGTTTTGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.00, C:0.19, G:0.10, T:0.71
Consensus pattern (16 bp):
CTTTGTCTTTTGTTTC
Found at i:699700 original size:12 final size:12
Alignment explanation
Indices: 699683--699708 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
699673 ACTTTATACG
699683 AGATTGATAATA
1 AGATTGATAATA
699695 AGATTGATAATA
1 AGATTGATAATA
699707 AG
1 AG
699709 TGTCTTCAGA
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:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (12 bp):
AGATTGATAATA
Found at i:713381 original size:23 final size:22
Alignment explanation
Indices: 713350--713393 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
713340 AAAACTAAGT
713350 TGACTGACGGAATAACCAGATG
1 TGACTGACGGAATAACCAGATG
*
713372 TGACTTGACGGAATAATCAGAT
1 TGAC-TGACGGAATAACCAGAT
713394 ATAGACATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (22 bp):
TGACTGACGGAATAACCAGATG
Found at i:716891 original size:4 final size:4
Alignment explanation
Indices: 716882--716907 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
716872 CACTCAATAC
716882 ACAT ACAT ACAT ACAT ACAT ACAT AC
1 ACAT ACAT ACAT ACAT ACAT ACAT AC
716908 CATTAAGTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:716943 original size:120 final size:116
Alignment explanation
Indices: 716726--716956 Score: 381
Period size: 120 Copynumber: 2.0 Consensus size: 116
716716 AAACGTCAAC
* *
716726 CATAAGACAATATAAACTCGGACATACGAACACTCAATACACATACACACATACATGCATACCAT
1 CATAAGACAATATAAACTCAGACATACGAACACTCAATACACATACACACATACATACATACCAT
* *
716791 TAAGTCTTCAGACAGGACCTCATCAGCTTGTTGAGCTCTTCTTTTTCTTAT
66 TAAGTCTTCAGACAAGACCTCATCAGCTTGTTGAGCTCTTATTTTTCTTAT
*
716842 CATAAGACAATATAAACTCAGACTTACGAACACTCAATACACATACATACATACATACATACATA
1 CATAAGACAATATAAACTCAGACATACGAACACTCAATACACATAC--AC--ACATACATACATA
716907 CCATTAAGTCTTCAGACAAGACCTCATCAGCTTGTTGAGCTCTTATTTTT
62 CCATTAAGTCTTCAGACAAGACCTCATCAGCTTGTTGAGCTCTTATTTTT
716957 TGTTGATTTG
Statistics
Matches: 106, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
116 44 0.42
118 2 0.02
120 60 0.57
ACGTcount: A:0.36, C:0.25, G:0.10, T:0.29
Consensus pattern (116 bp):
CATAAGACAATATAAACTCAGACATACGAACACTCAATACACATACACACATACATACATACCAT
TAAGTCTTCAGACAAGACCTCATCAGCTTGTTGAGCTCTTATTTTTCTTAT
Found at i:718319 original size:3 final size:3
Alignment explanation
Indices: 718311--718350 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
718301 CCACACAAGG
718311 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
718351 TGAAATTGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:718502 original size:24 final size:24
Alignment explanation
Indices: 718470--718517 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
718460 CCATACACCA
*
718470 CTTAATCAGAAAATATATATTTCG
1 CTTAATCAGAAAATATACATTTCG
718494 CTTAATCAGAAAATATACATTTCG
1 CTTAATCAGAAAATATACATTTCG
718518 TTCCCTAGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (24 bp):
CTTAATCAGAAAATATACATTTCG
Found at i:718728 original size:31 final size:31
Alignment explanation
Indices: 718685--718764 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
718675 AGACTATCCT
* *
718685 AGTGACTAAAATGAAAACAAATAGTAAGA-GG
1 AGTGTCTAAAATGAAAACAAAAAGTAA-ATGG
*
718716 AGTGTCTAAAATGATAAA-AAAAAGTAAATTG
1 AGTGTCTAAAATGA-AAACAAAAAGTAAATGG
718747 AGTGTCTAAAATGAAAAC
1 AGTGTCTAAAATGAAAAC
718765 TTATAAATTG
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
30 4 0.09
31 36 0.84
32 3 0.07
ACGTcount: A:0.54, C:0.06, G:0.19, T:0.21
Consensus pattern (31 bp):
AGTGTCTAAAATGAAAACAAAAAGTAAATGG
Found at i:733281 original size:50 final size:50
Alignment explanation
Indices: 733202--733382 Score: 192
Period size: 50 Copynumber: 3.6 Consensus size: 50
733192 ATTGTGAATA
* *
733202 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCATACTGTTAAGT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCATACTGTCAAGT
* * * *
733252 CGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCAATGACT-TCGA-T
1 CACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTAC-C-AT-ACTGTCAAGT
* * * * *
733303 CACGTGTGTAGTACTAAGTGTAGGCTACTATGTGTATCAGA-TGGTGAGGT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCATACT-GTCAAGT
733353 CACGTGTGTA--ACTAAGTGCAGGCTACTATG
1 CACGTGTGTAGTACTAAGTGCAGGCTACTATG
733383 CATCTCAGAT
Statistics
Matches: 109, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
47 1 0.01
48 20 0.18
49 2 0.02
50 45 0.41
51 34 0.31
52 4 0.04
53 3 0.03
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (50 bp):
CACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCATACTGTCAAGT
Found at i:733391 original size:48 final size:50
Alignment explanation
Indices: 733256--733392 Score: 154
Period size: 51 Copynumber: 2.7 Consensus size: 50
733246 TTAAGTCGCA
**
733256 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCA-ATGACTTCGATCACG
1 TGTGTAG-ACTAAGTGCAGGCTACTATGCGT-CTCAGATGACTGAGATCACG
* * * * *
733307 TGTGTAGTACTAAGTGTAGGCTACTATGTGTATCAGATG-GTGAGGTCACG
1 TGTGTAG-ACTAAGTGCAGGCTACTATGCGTCTCAGATGACTGAGATCACG
*
733357 TGTGTA-ACTAAGTGCAGGCTACTATGCATCTCAGAT
1 TGTGTAGACTAAGTGCAGGCTACTATGCGTCTCAGAT
733393 ATCTTCGACT
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
48 26 0.35
50 16 0.22
51 32 0.43
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (50 bp):
TGTGTAGACTAAGTGCAGGCTACTATGCGTCTCAGATGACTGAGATCACG
Found at i:733411 original size:101 final size:100
Alignment explanation
Indices: 733205--733389 Score: 241
Period size: 101 Copynumber: 1.9 Consensus size: 100
733195 GTGAATACAC
* * *
733205 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCATACTGTTAAGTCGCATGTGTAGTACTAAG
1 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTGAAGTCACATGTGTAG-ACTAAG
* *
733270 TGCAGGCTACTATGCGTACTCAATGACTTCGATCAC
65 TGCAGGCTACTATGCATACTCAATGACTTCGATCAA
* * * * *
733306 GTGTGTAGTACTAAGTGTAGGCTACTATGTGTATCAGA-TGGTGAGGTCACGTGTGTA-ACTAAG
1 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACT-GTGAAGTCACATGTGTAGACTAAG
733369 TGCAGGCTACTATGCAT-CTCA
65 TGCAGGCTACTATGCATACTCA
733390 GATATCTTCG
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
98 4 0.05
99 22 0.30
100 1 0.01
101 47 0.64
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (100 bp):
GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTGAAGTCACATGTGTAGACTAAGT
GCAGGCTACTATGCATACTCAATGACTTCGATCAA
Found at i:733510 original size:27 final size:26
Alignment explanation
Indices: 733480--733531 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
733470 GGGAAAATCG
733480 ATAAAGTGGTAATATGTG-AAAGTTATT
1 ATAAAGTGG--ATATGTGCAAAGTTATT
* *
733507 ATAAGGTGGATATGTGCAAATTTAT
1 ATAAAGTGGATATGTGCAAAGTTAT
733532 GTTTATGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 7 0.32
26 7 0.32
27 8 0.36
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (26 bp):
ATAAAGTGGATATGTGCAAAGTTATT
Found at i:735906 original size:21 final size:20
Alignment explanation
Indices: 735882--735923 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
735872 AAAATTTGTG
735882 TATTCTTTATTTTTATTTTTT
1 TATTCTTTA-TTTTATTTTTT
*
735903 TATTTTTTATTTTATTTTTT
1 TATTCTTTATTTTATTTTTT
735923 T
1 T
735924 CACAAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.83
Consensus pattern (20 bp):
TATTCTTTATTTTATTTTTT
Found at i:735923 original size:15 final size:15
Alignment explanation
Indices: 735887--735915 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
735877 TTGTGTATTC
735887 TTTA-TTTTTATTTT
1 TTTATTTTTTATTTT
735901 TTTATTTTTTATTTT
1 TTTATTTTTTATTTT
735916 ATTTTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTATTTTTTATTTT
Found at i:739143 original size:46 final size:44
Alignment explanation
Indices: 739037--739144 Score: 135
Period size: 44 Copynumber: 2.4 Consensus size: 44
739027 TGTCTTTGAC
** * * *
739037 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
* *
739081 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTCAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
739127 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
739145 TTTCGTTCTG
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 33 0.60
46 22 0.40
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:742893 original size:15 final size:15
Alignment explanation
Indices: 742857--742885 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
742847 TTGTGTGTTC
742857 TTTA-TTTTTATTTT
1 TTTATTTTTTATTTT
742871 TTTATTTTTTATTTT
1 TTTATTTTTTATTTT
742886 ATTTTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTATTTTTTATTTT
Found at i:749204 original size:19 final size:20
Alignment explanation
Indices: 749162--749213 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
749152 TTTCCATTAG
*
749162 GTTTTTTTAGATTCATTTCAT
1 GTTTTTTTA-TTTCATTTCAT
*
749183 GTTTTTTTATTTCA-TTCGT
1 GTTTTTTTATTTCATTTCAT
*
749202 GTTTATTTATTT
1 GTTTTTTTATTT
749214 GTATTAATCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 15 0.54
20 4 0.14
21 9 0.32
ACGTcount: A:0.15, C:0.08, G:0.10, T:0.67
Consensus pattern (20 bp):
GTTTTTTTATTTCATTTCAT
Found at i:752040 original size:13 final size:13
Alignment explanation
Indices: 752024--752048 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
752014 TGAAAAATAA
752024 AATTAACTAATGT
1 AATTAACTAATGT
752037 AATTAACTAATG
1 AATTAACTAATG
752049 AATGCCACAA
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:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (13 bp):
AATTAACTAATGT
Done.