Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 102 of 187
Found at i:30084584 original size:84 final size:84
Alignment explanation
Indices: 30084440--30084681 Score: 310
Period size: 84 Copynumber: 2.9 Consensus size: 84
30084430 AGAGTCTGCT
30084440 ACAAAGGCTTATTCTTTCATAGTTCGCCACAAAGGCTTATTCTTTCGTAGTT--TGCTACAAAGG
1 ACAAAGGCTTATTCTTTCATAGTTCGCCACAAAGGCTTATTCTTTCGTAGTTCAT-C-ACAAAGG
* * *
30084503 CTTATTTTTTCGTAGTTTGTC
64 CTTATTTTTTCATAGGTCGTC
* * *
30084524 ACAAAGGCTTATTCTTTCATAGTTCGCCACAAAGGCTTATTCTTTCATAGTTCATCACAAAAGTT
1 ACAAAGGCTTATTCTTTCATAGTTCGCCACAAAGGCTTATTCTTTCGTAGTTCATCACAAAGGCT
30084589 TATTCTTTT-ATAGGTCGTC
66 TATT-TTTTCATAGGTCGTC
* ** * * * *
30084608 ATAAAGGCTTATTCTTTTTTTGTTCGCCATAAAGGCTTATTCTTTCGTAGTTCATTAGAAAGGCT
1 ACAAAGGCTTATTCTTTCATAGTTCGCCACAAAGGCTTATTCTTTCGTAGTTCATCACAAAGGCT
*
30084673 TATTCTTTC
66 TATTTTTTC
30084682 CTGATGTGTT
Statistics
Matches: 137, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
83 3 0.02
84 128 0.93
85 5 0.04
86 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.42
Consensus pattern (84 bp):
ACAAAGGCTTATTCTTTCATAGTTCGCCACAAAGGCTTATTCTTTCGTAGTTCATCACAAAGGCT
TATTTTTTCATAGGTCGTC
Found at i:30088644 original size:18 final size:17
Alignment explanation
Indices: 30088621--30088654 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
30088611 AAATACATAC
30088621 ATTAATAAATAAATATGA
1 ATTAATAAA-AAATATGA
*
30088639 ATTAATATAAAATATG
1 ATTAATAAAAAATATG
30088655 TATGAAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (17 bp):
ATTAATAAAAAATATGA
Found at i:30095977 original size:27 final size:27
Alignment explanation
Indices: 30095944--30096010 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
30095934 GTAGGTATAT
30095944 GCCAGTAGGCCTGGCAAACTGGTGTAC
1 GCCAGTAGGCCTGGCAAACTGGTGTAC
* * * * *
30095971 GCTAGTAGGCCTAGCTAGCTGTTGTAC
1 GCCAGTAGGCCTGGCAAACTGGTGTAC
30095998 GCCAGTAGGCCTG
1 GCCAGTAGGCCTG
30096011 ATGAGTTAGT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.19, C:0.25, G:0.33, T:0.22
Consensus pattern (27 bp):
GCCAGTAGGCCTGGCAAACTGGTGTAC
Found at i:30097077 original size:19 final size:20
Alignment explanation
Indices: 30097035--30097077 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
30097025 TCATGCTTTC
*
30097035 TATTCACATTTTCATATTCA
1 TATTCACATTTTCAAATTCA
30097055 -ATTCACATTTTCAAATT-A
1 TATTCACATTTTCAAATTCA
30097073 TATTC
1 TATTC
30097078 CACAATCACG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTCACATTTTCAAATTCA
Found at i:30097272 original size:38 final size:38
Alignment explanation
Indices: 30097198--30097278 Score: 94
Period size: 38 Copynumber: 2.2 Consensus size: 38
30097188 CCAAACACAC
* *
30097198 CAAA-TTGGCACCCAGTGCCTCATCGGATAGTTCGAAG
1 CAAAGTTGACACCCAGTGCCTCATCGGATAGTCCGAAG
* *
30097235 CAAAGTTGACACCCAGTGTCTCATCGGCCTAG-CCGAAG
1 CAAAGTTGACACCCAGTGCCTCATCGG-ATAGTCCGAAG
*
30097273 TAAAGT
1 CAAAGT
30097279 GATACTCAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
37 4 0.11
38 30 0.81
39 3 0.08
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.21
Consensus pattern (38 bp):
CAAAGTTGACACCCAGTGCCTCATCGGATAGTCCGAAG
Found at i:30098722 original size:29 final size:29
Alignment explanation
Indices: 30098680--30098736 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
30098670 GTCTTTTCTT
* *
30098680 AATTTATTTCATAATATAATAATATAATC
1 AATTTATTTCATAATATAAGAAAATAATC
30098709 AATTTAATTT-ATAATATAAGAAAATAAT
1 AATTT-ATTTCATAATATAAGAAAATAAT
30098737 AACAATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (29 bp):
AATTTATTTCATAATATAAGAAAATAATC
Found at i:30105169 original size:2 final size:2
Alignment explanation
Indices: 30105162--30105216 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
30105152 TTCAAGGAGG
30105162 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
30105204 TC TC TC TC TC TC T
1 TC TC TC TC TC TC T
30105217 TTTCTTTTCT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:30106242 original size:12 final size:12
Alignment explanation
Indices: 30106221--30106253 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
30106211 CGTAAGTTTT
*
30106221 TCTCTCTCTCTC
1 TCTCTTTCTCTC
30106233 TCTCTTTCTCTC
1 TCTCTTTCTCTC
30106245 TCTCTTTCT
1 TCTCTTTCT
30106254 GAGCATGCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (12 bp):
TCTCTTTCTCTC
Found at i:30106772 original size:124 final size:124
Alignment explanation
Indices: 30106549--30106792 Score: 364
Period size: 124 Copynumber: 2.0 Consensus size: 124
30106539 TAAATGCTTC
* *
30106549 AGTTGGTTTTGAAGTCTGGACTTAGCTTTTTCTCCCTGCCTTGCACAATTAGACAGATCGGTGAT
1 AGTTGGTTTCGAAGTCTGGACTTAGCCTTTTCTCCCTGCCTTGCACAATTAGACAGATCGGTGAT
* * * *
30106614 TGTGGAGTTACTTTGGCAAAAATCTTTAGTATCCTCCTGGTGATATTTGATTAGCATCA
66 TGTGGAGTTACCTTAGCAAAAACCTTTAGCATCCTCCTGGTGATATTTGATTAGCATCA
* ** * *
30106673 AGTTGGTTTCGAAGTTTTTACTTAGCCTTTTCTCCTTGCCTTGCACAATTAGACATG-TTGGTGA
1 AGTTGGTTTCGAAGTCTGGACTTAGCCTTTTCTCCCTGCCTTGCACAATTAGACA-GATCGGTGA
*
30106737 TTGTGGAGTTACCTTAGCAAAAACCTTTAGCATCCTCTTGGTGATATTTGATTAGC
65 TTGTGGAGTTACCTTAGCAAAAACCTTTAGCATCCTCCTGGTGATATTTGATTAGC
30106793 TACAAGCAAC
Statistics
Matches: 107, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
124 106 0.99
125 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (124 bp):
AGTTGGTTTCGAAGTCTGGACTTAGCCTTTTCTCCCTGCCTTGCACAATTAGACAGATCGGTGAT
TGTGGAGTTACCTTAGCAAAAACCTTTAGCATCCTCCTGGTGATATTTGATTAGCATCA
Found at i:30108058 original size:17 final size:18
Alignment explanation
Indices: 30108033--30108078 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
30108023 ATTTATTAAA
*
30108033 TTAAATTAATTAATTTTC
1 TTAATTTAATTAATTTTC
*
30108051 -TAATTTAAATAATTTTC
1 TTAATTTAATTAATTTTC
30108068 TTAATTTAATT
1 TTAATTTAATT
30108079 TTAATTTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAATTTAATTAATTTTC
Found at i:30114571 original size:81 final size:82
Alignment explanation
Indices: 30114468--30114680 Score: 313
Period size: 84 Copynumber: 2.5 Consensus size: 82
30114458 GGCATGTTTG
* *
30114468 TGTTTGAGTATTGAGGAAGATGTTGATTTTATAGTCTCTTTAAGTTTCACTTCTATG-TC-TCTT
1 TGTTTGTGT-TTGAGGAAGATGTTGATTTTATGGTCT-TTTAAGTTTCACTTCTATGCTCTTCTT
30114531 ATTCTTTTAGATGATTGCA
64 ATTCTTTTAGATGATTGCA
30114550 TGTTTGTGTTTGAGGAAGATGTTGATTTTATGGTCTTTTTAAGTTTCACTTCTATGTCTCTTCTT
1 TGTTTGTGTTTGAGGAAGATGTTGATTTTATGGTC-TTTTAAGTTTCACTTCTATG-CTCTTCTT
*
30114615 ATTTTTTTAGATGATTGCA
64 ATTCTTTTAGATGATTGCA
* *
30114634 TATTTGTGTTTGAGGAAGATATTGATTTTTATGGTCTTTTAAAGTTT
1 TGTTTGTGTTTGAGGAAGATGTTGA-TTTTATGGTCTTTT-AAGTTT
30114681 TTTTTTTTTT
Statistics
Matches: 120, Mismatches: 5, Indels: 9
0.90 0.04 0.07
Matches are distributed among these distances:
81 44 0.37
82 9 0.08
83 2 0.02
84 49 0.41
85 16 0.13
ACGTcount: A:0.21, C:0.08, G:0.19, T:0.52
Consensus pattern (82 bp):
TGTTTGTGTTTGAGGAAGATGTTGATTTTATGGTCTTTTAAGTTTCACTTCTATGCTCTTCTTAT
TCTTTTAGATGATTGCA
Found at i:30114660 original size:84 final size:81
Alignment explanation
Indices: 30114478--30114680 Score: 316
Period size: 81 Copynumber: 2.5 Consensus size: 81
30114468 TGTTTGAGTA
* *
30114478 TTGAGGAAGATGTTGATTTTATAGTCTCTTTAAGTTTCACTTCTATGTCTCTTATTCTTTTAGAT
1 TTGAGGAAGATGTTGATTTTATGGTCTTTTTAAGTTTCACTTCTATGTCTCTTATTCTTTTAGAT
*
30114543 GATTGCATGTTTGTGT
66 GATTGCATATTTGTGT
*
30114559 TTGAGGAAGATGTTGATTTTATGGTCTTTTTAAGTTTCACTTCTATGTCTCTTCTTATTTTTTTA
1 TTGAGGAAGATGTTGATTTTATGGTCTTTTTAAGTTTCACTTCTATG--TC-TCTTATTCTTTTA
30114624 GATGATTGCATATTTGTGT
63 GATGATTGCATATTTGTGT
* *
30114643 TTGAGGAAGATATTGATTTTTATGGTCTTTTAAAGTTT
1 TTGAGGAAGATGTTGA-TTTTATGGTCTTTTTAAGTTT
30114681 TTTTTTTTTT
Statistics
Matches: 112, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
81 45 0.40
83 2 0.02
84 45 0.40
85 20 0.18
ACGTcount: A:0.21, C:0.09, G:0.19, T:0.52
Consensus pattern (81 bp):
TTGAGGAAGATGTTGATTTTATGGTCTTTTTAAGTTTCACTTCTATGTCTCTTATTCTTTTAGAT
GATTGCATATTTGTGT
Found at i:30117507 original size:16 final size:16
Alignment explanation
Indices: 30117486--30117516 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30117476 TTCTCTATTA
*
30117486 TGTCTTTTGTATTTTC
1 TGTCTTTTATATTTTC
30117502 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
30117517 GCATGCATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.71
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:30132345 original size:18 final size:18
Alignment explanation
Indices: 30132311--30132357 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 18
30132301 TTACATAGTT
*
30132311 ATATTAATATTTTTAAAA
1 ATATTAATATTTGTAAAA
30132329 ATATTAAT-TATTGTAAAA
1 ATATTAATAT-TTGTAAAA
30132347 AGTTATTAATA
1 A--TATTAATA
30132358 CAATAAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 1 0.04
18 16 0.67
20 7 0.29
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (18 bp):
ATATTAATATTTGTAAAA
Found at i:30134096 original size:16 final size:16
Alignment explanation
Indices: 30134075--30134107 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
30134065 TTCGCTGTAT
30134075 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
30134091 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
30134107 T
1 T
30134108 AGCAAATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.36, T:0.21
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:30134182 original size:44 final size:45
Alignment explanation
Indices: 30134089--30134183 Score: 131
Period size: 44 Copynumber: 2.1 Consensus size: 45
30134079 ATAGAGGCGT
*
30134089 AATGGAATAGAGGCGTAATAGCAAATCAATTGTTTGGTTGAATGT
1 AATGGAATAGAGGCGTAATAGCAAATCAATTGTTTGGTTGAATGG
* * *
30134134 AATGGAATAGAGGCGTAATAG-TATTC-TTGTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGCAAATCAAT-TGTTTGGTTGAATGG
30134178 AATGGA
1 AATGGA
30134184 GGTGTAATAG
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.51
45 21 0.47
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (45 bp):
AATGGAATAGAGGCGTAATAGCAAATCAATTGTTTGGTTGAATGG
Found at i:30134361 original size:18 final size:17
Alignment explanation
Indices: 30134340--30134374 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
30134330 TTATTATTAA
*
30134340 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
30134358 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
30134375 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:30134481 original size:18 final size:17
Alignment explanation
Indices: 30134458--30134494 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
30134448 AATTATTATT
30134458 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
30134474 AAATATATGATTTAATA
1 AAATATATGATTTAATA
30134491 AAAT
1 AAAT
30134495 TCTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:30134533 original size:120 final size:120
Alignment explanation
Indices: 30134326--30134739 Score: 742
Period size: 120 Copynumber: 3.5 Consensus size: 120
30134316 ATATTTTAAC
*
30134326 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATCAATAT
* *
30134391 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTT-AA
66 TCTTATATGAATTTACTAAAATCATAATATATGATAGTATAAAATATAATTTGAA
30134445 GATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATCAATA
1 -ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATCAATA
*
30134510 TTCTTATATGAATTTACTAAAATCATAATATATGATAGTATAAAATATATTTTGAA
65 TTCTTATATGAATTTACTAAAATCATAATATATGATAGTATAAAATATAATTTGAA
30134566 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATCAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATCAATAT
* * *
30134631 TCTTATATGAATTTACTAAAATTATAATATGTTATAGTATAAAATATAATTTGAA
66 TCTTATATGAATTTACTAAAATCATAATATATGATAGTATAAAATATAATTTGAA
30134686 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT-TTAA
1 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAA
30134740 AAAATTATTA
Statistics
Matches: 285, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
119 4 0.01
120 279 0.98
121 2 0.01
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (120 bp):
ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATCAATAT
TCTTATATGAATTTACTAAAATCATAATATATGATAGTATAAAATATAATTTGAA
Found at i:30134601 original size:18 final size:17
Alignment explanation
Indices: 30134578--30134614 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
30134568 AATTATTATT
30134578 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
30134594 AAATATATGATTTAATA
1 AAATATATGATTTAATA
30134611 AAAT
1 AAAT
30134615 TCTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:30134721 original size:18 final size:17
Alignment explanation
Indices: 30134698--30134734 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
30134688 AATTATTATT
30134698 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
30134714 AAATATATGATTTAATA
1 AAATATATGATTTAATA
30134731 AAAT
1 AAAT
30134735 TTTAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:30134732 original size:59 final size:60
Alignment explanation
Indices: 30134326--30134734 Score: 275
Period size: 59 Copynumber: 6.8 Consensus size: 60
30134316 ATATTTTAAC
* * *
30134326 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCA
1 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAA-TCATAATAATAA
* * * * ** * * * *
30134387 AT-ATTCTTATATGAATTTACTCAAATCATAATATATGATACT-ATAAAAT-ATAAT-TTAA
1 ATAATTATTAT-TAAATATATTTTAATTAAAATATATGAT-TTAATAAAATCATAATAATAA
* *
30134445 GATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATCA
1 -ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAA-TCATAATAATAA
* * * * ** * * * **
30134507 AT-ATTCTTATATGAATTTACTAAAATCATAATATATGATAGT-ATAAAAT-AT-ATTTTGAA
1 ATAATTATTAT-TAAATATATTTTAATTAAAATATATGAT-TTAATAAAATCATAATAAT-AA
* *
30134566 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATCA
1 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAA-TCATAATAATAA
* * * * ** * * * * *
30134627 AT-ATTCTTATATGAATTTACTAAAATTATAATATGTTATAGT-ATAAAAT-ATAAT-TTGAA
1 ATAATTATTAT-TAAATATATTTTAATTAAAATATATGAT-TTAATAAAATCATAATAAT-AA
30134686 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAAT
30134735 TTTAAAAAAT
Statistics
Matches: 253, Mismatches: 74, Indels: 44
0.68 0.20 0.12
Matches are distributed among these distances:
58 9 0.04
59 98 0.39
60 47 0.19
61 91 0.36
62 8 0.03
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.44
Consensus pattern (60 bp):
ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATCATAATAATAA
Found at i:30134825 original size:18 final size:17
Alignment explanation
Indices: 30134802--30134836 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
30134792 TATTATTAAA
30134802 TATAATTTAATAATAATT
1 TATAATTTAATAA-AATT
*
30134820 TATAATTTCATAAAATT
1 TATAATTTAATAAAATT
30134837 CTTGATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
TATAATTTAATAAAATT
Found at i:30134835 original size:91 final size:91
Alignment explanation
Indices: 30134751--30135139 Score: 697
Period size: 91 Copynumber: 4.3 Consensus size: 91
30134741 AAATTATTAG
* * *
30134751 TAATAAATTTTCTTATATGAATTTGTATAATTTAATATAATTATTATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
30134816 AATTTATAATTTCATAAAATTCTTGA
66 AATATATAATTTCATAAAATTCTTGA
30134842 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
* *
30134907 GATATATAATTTCATAAAATTTTTGA
66 AATATATAATTTCATAAAATTCTTGA
30134933 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
30134998 AATATATAATTTCATAAAATTCTTGA
66 AATATATAATTTCATAAAATTCTTGA
30135024 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
* *
30135089 GATATATAATTTCATAAAATTCTTAA
66 AATATATAATTTCATAAAATTCTTGA
*
30135115 TAATAAATATTCTTATATGAATTTA
1 TAATAAATTTTCTTATATGAATTTA
30135140 CTAAAATCAT
Statistics
Matches: 287, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 287 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (91 bp):
TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
AATATATAATTTCATAAAATTCTTGA
Found at i:30134990 original size:16 final size:16
Alignment explanation
Indices: 30134960--30135008 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
30134950 TGAATTTATA
30134960 TAAT-TTAAA-ATAAT
1 TAATATTAAATATAAT
30134974 TAATATTAAATATAATT
1 TAATATTAAATATAA-T
*
30134991 TAATAATAATATATAAT
1 TAATATTAA-ATATAAT
30135008 T
1 T
30135009 TCATAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 4 0.13
15 5 0.17
16 4 0.13
17 11 0.37
18 6 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATATTAAATATAAT
Found at i:30135006 original size:18 final size:17
Alignment explanation
Indices: 30134965--30135014 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 17
30134955 TTATATAATT
*
30134965 TAAA-ATAA-TTAATAT
1 TAAATATAATTTAATAA
30134980 TAAATATAATTTAATAA
1 TAAATATAATTTAATAA
*
30134997 TAATATATAATTTCATAA
1 TAA-ATATAATTTAATAA
30135015 AATTCTTGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 4 0.13
16 4 0.13
17 9 0.30
18 13 0.43
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATATAATTTAATAA
Found at i:30141736 original size:2 final size:2
Alignment explanation
Indices: 30141670--30141717 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
30141660 ACTGAAAATA
* *
30141670 AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
30141712 AG AG AG
1 AG AG AG
30141718 CTTACAGATC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:30144003 original size:22 final size:22
Alignment explanation
Indices: 30143978--30144020 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
30143968 AATTAAATTT
30143978 TTAAATT-CAAAAAATATAAAAA
1 TTAAATTCCAAAAAAT-TAAAAA
* *
30144000 TTAACTTCCTAAAAATTAAAA
1 TTAAATTCCAAAAAATTAAAA
30144021 TAAGAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
TTAAATTCCAAAAAATTAAAAA
Found at i:30145636 original size:120 final size:120
Alignment explanation
Indices: 30145423--30145663 Score: 446
Period size: 120 Copynumber: 2.0 Consensus size: 120
30145413 TTGAAGCTAT
* *
30145423 TGATGATGATGTAATTGAATCTTCTGCTATAGCATTCTCAGCGGTATGCAGTTCTTGTTCAATAG
1 TGATGATGATGTAATTGAATCTTCCGCTATAGCATTCGCAGCGGTATGCAGTTCTTGTTCAATAG
30145488 TATTTTGTTTTCACATTAACTGTACATTAAACCTGTCTTTATGGATTCATTTGCA
66 TATTTTGTTTTCACATTAACTGTACATTAAACCTGTCTTTATGGATTCATTTGCA
*
30145543 TGATGGTGATGTAATTGAATCTTCCGCTATAGCATTCGCAGCGGTATGCAGTTCTTGTTCAATAG
1 TGATGATGATGTAATTGAATCTTCCGCTATAGCATTCGCAGCGGTATGCAGTTCTTGTTCAATAG
*
30145608 TATTTTGTTTTCACATTAACTGTACATTAAACTTGTCTTTATGGATTCATTTGCA
66 TATTTTGTTTTCACATTAACTGTACATTAAACCTGTCTTTATGGATTCATTTGCA
30145663 T
1 T
30145664 TATGTAGACT
Statistics
Matches: 117, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 117 1.00
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.42
Consensus pattern (120 bp):
TGATGATGATGTAATTGAATCTTCCGCTATAGCATTCGCAGCGGTATGCAGTTCTTGTTCAATAG
TATTTTGTTTTCACATTAACTGTACATTAAACCTGTCTTTATGGATTCATTTGCA
Found at i:30154680 original size:69 final size:69
Alignment explanation
Indices: 30154569--30155107 Score: 648
Period size: 69 Copynumber: 7.8 Consensus size: 69
30154559 ACAACATTTA
* * *** * *
30154569 TGTCATACTAAGGTTCACAGGATAAAAGTTGCAGCCTCCAACACAGTTAGTGATAGCAAAGCTCC
1 TGTCATACTAAGGCTCGCAGGATAAAAACCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCC
*
30154634 CAGT
66 CAGC
* * * * *
30154638 TGTCATATTAAGGTTCACAGGATAAAAACCGCAGCCTGCAACACAGTTAGCAAGAGCAAAGCTCC
1 TGTCATACTAAGGCTCGCAGGATAAAAACCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCC
* *
30154703 TACC
66 CAGC
* * ** * *
30154707 TATTATACTAAGGCTCGCAGGATAAAAACCATAGCCTCCAACATAGTTAGCAAGAGCAAAGCTCC
1 TGTCATACTAAGGCTCGCAGGATAAAAACCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCC
30154772 CAGC
66 CAGC
* * * *
30154776 TATCATACTAAGGCTCGCAGGATAAAAACCGCAGCCTCCAACACAATTAGTGAGAGCAAAGTTCC
1 TGTCATACTAAGGCTCGCAGGATAAAAACCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCC
*
30154841 CAAC
66 CAGC
* * * * *
30154845 TGTCACACTAAAGCTCGCAGGATAAAAACCGCAGCCTCCAACATAATTTGCGAGAGCAAAGCTCC
1 TGTCATACTAAGGCTCGCAGGATAAAAACCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCC
*
30154910 TA-C
66 CAGC
* ** *
30154913 TTGTCATACTAAGGCTCGCAGGATAAAAATCATAGCCTCTAACACAGTTAGCGAGAGCAAAGCTC
1 -TGTCATACTAAGGCTCGCAGGATAAAAACCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTC
30154978 CCAGC
65 CCAGC
* * ** * *
30154983 TGTCATAGTAAGGCTTGCAGGATAAAAAGTGTAGCCTCCAACACAGTTAGCGAGAGCAAAACTCC
1 TGTCATACTAAGGCTCGCAGGATAAAAACCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCC
*
30155048 TAGC
66 CAGC
* * *
30155052 TGTCATACTAAGGCTCGCAGGATAAAGATCGCAGCCTCCAACATAGTTAGCGAGAG
1 TGTCATACTAAGGCTCGCAGGATAAAAACCGCAGCCTCCAACACAGTTAGCGAGAG
30155108 TTAAAAACTT
Statistics
Matches: 404, Mismatches: 64, Indels: 4
0.86 0.14 0.01
Matches are distributed among these distances:
68 1 0.00
69 402 1.00
70 1 0.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.19
Consensus pattern (69 bp):
TGTCATACTAAGGCTCGCAGGATAAAAACCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCC
CAGC
Found at i:30154926 original size:207 final size:207
Alignment explanation
Indices: 30154571--30155107 Score: 741
Period size: 207 Copynumber: 2.6 Consensus size: 207
30154561 AACATTTATG
* * ** *
30154571 TCATACTAAGGTTCACAGGATAAAAGTTGCAGCCTCCAACACAGTTAGTGATAGCAAAGCTCCCA
1 TCATACTAAGGCTCGCAGGATAAAAACTGCAGCCTCCAACACAGTTAGTGAGAGCAAAGCTCCCA
* * * * * * *
30154636 GTTGTCATATTAAGGTTCACAGGATAAAAACCGCAGCCTGCAACACAGTTAGCAAGAGCAAAGCT
66 GCTGTCATACTAAGGCTCGCAGGATAAAAACCGCAGCCTCCAACATAGTTAGCGAGAGCAAAGCT
* *
30154701 CCTACCTATTATACTAAGGCTCGCAGGATAAAAACCATAGCCTCCAACATAGTTAGCAAGAGCAA
131 CCTACCTATCATACTAAGGCTCGCAGGATAAAAACCATAGCCTCCAACACAGTTAGCAAGAGCAA
30154766 AGCTCCCAGCTA
196 AGCTCCCAGCTA
* * *
30154778 TCATACTAAGGCTCGCAGGATAAAAACCGCAGCCTCCAACACAATTAGTGAGAGCAAAGTTCCCA
1 TCATACTAAGGCTCGCAGGATAAAAACTGCAGCCTCCAACACAGTTAGTGAGAGCAAAGCTCCCA
* * * * *
30154843 ACTGTCACACTAAAGCTCGCAGGATAAAAACCGCAGCCTCCAACATAATTTGCGAGAGCAAAGCT
66 GCTGTCATACTAAGGCTCGCAGGATAAAAACCGCAGCCTCCAACATAGTTAGCGAGAGCAAAGCT
* * * * *
30154908 CCTACTTGTCATACTAAGGCTCGCAGGATAAAAATCATAGCCTCTAACACAGTTAGCGAGAGCAA
131 CCTACCTATCATACTAAGGCTCGCAGGATAAAAACCATAGCCTCCAACACAGTTAGCAAGAGCAA
*
30154973 AGCTCCCAGCTG
196 AGCTCCCAGCTA
* * * * * * *
30154985 TCATAGTAAGGCTTGCAGGATAAAAAGTGTAGCCTCCAACACAGTTAGCGAGAGCAAAACTCCTA
1 TCATACTAAGGCTCGCAGGATAAAAACTGCAGCCTCCAACACAGTTAGTGAGAGCAAAGCTCCCA
* *
30155050 GCTGTCATACTAAGGCTCGCAGGATAAAGATCGCAGCCTCCAACATAGTTAGCGAGAG
66 GCTGTCATACTAAGGCTCGCAGGATAAAAACCGCAGCCTCCAACATAGTTAGCGAGAG
30155108 TTAAAAACTT
Statistics
Matches: 285, Mismatches: 45, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
207 285 1.00
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (207 bp):
TCATACTAAGGCTCGCAGGATAAAAACTGCAGCCTCCAACACAGTTAGTGAGAGCAAAGCTCCCA
GCTGTCATACTAAGGCTCGCAGGATAAAAACCGCAGCCTCCAACATAGTTAGCGAGAGCAAAGCT
CCTACCTATCATACTAAGGCTCGCAGGATAAAAACCATAGCCTCCAACACAGTTAGCAAGAGCAA
AGCTCCCAGCTA
Found at i:30161079 original size:12 final size:12
Alignment explanation
Indices: 30161055--30161087 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
30161045 CATATTGATA
30161055 CAAAATA-TTTT
1 CAAAATATTTTT
30161066 CAAAATATTTTT
1 CAAAATATTTTT
30161078 C-AAATATTTT
1 CAAAATATTTT
30161088 CTTAATACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (12 bp):
CAAAATATTTTT
Found at i:30170069 original size:57 final size:57
Alignment explanation
Indices: 30169997--30170109 Score: 156
Period size: 57 Copynumber: 2.0 Consensus size: 57
30169987 AAAGCTTTTA
* * * *
30169997 TGGTGAACTTGCTAAAGGACAACGTTTGTGGAAAAACTTTAGAAAGGTAAGACTTTG
1 TGGTGAACTTGCTAAAGGACAACATTTCTAGAAAAACTCTAGAAAGGTAAGACTTTG
* *
30170054 TGGTGAATCTT-CTAAAGGACAATATTTCTAGCAAAACTCTAGAAAGGTAAGACTTT
1 TGGTGAA-CTTGCTAAAGGACAACATTTCTAGAAAAACTCTAGAAAGGTAAGACTTT
30170110 ATGGCTAACC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
57 46 0.94
58 3 0.06
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (57 bp):
TGGTGAACTTGCTAAAGGACAACATTTCTAGAAAAACTCTAGAAAGGTAAGACTTTG
Found at i:30178264 original size:50 final size:48
Alignment explanation
Indices: 30178198--30178373 Score: 203
Period size: 50 Copynumber: 3.6 Consensus size: 48
30178188 TTCTGTACTA
* *
30178198 CCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGAGA--TCTCATATCGGTG
* ** * *
30178248 CCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGAGA--TCTCATATCGGTG
* * *
30178298 CCAAAGCCATGTCCCAGACATGGTCTTACATGAGACCTCTTAT--GTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGAGATCTCATATCGGTG
*
30178344 CCAACGCCATGTCCCAGACATGGTCTTACA
1 CCAATGCCATGTCCCAGACATGGTCTTACA
30178374 CGGGACCTCT
Statistics
Matches: 108, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
46 32 0.30
48 5 0.05
50 71 0.66
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (48 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGAGATCTCATATCGGTG
Found at i:30178371 original size:96 final size:98
Alignment explanation
Indices: 30178198--30178383 Score: 259
Period size: 96 Copynumber: 1.9 Consensus size: 98
30178188 TTCTGTACTA
* * * * *
30178198 CCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATCGGTGCCCATGCCATGTCCC
1 CCAAAGCCATATCCCAGACATGGTCTTACATGAGAG-CCTCATATC-GTGCCAACGCCATGTCCC
**
30178263 AGACATGGTCTTACGGGGGACCTCTCATCTCGGTG
64 AGACATGGTCTTACACGGGACCTCTCATCTCGGTG
* *
30178298 CCAAAGCCATGTCCCAGACATGGTCTTACATGAGA-CCTCTTAT-GTGCCAACGCCATGTCCCAG
1 CCAAAGCCATATCCCAGACATGGTCTTACATGAGAGCCTCATATCGTGCCAACGCCATGTCCCAG
30178361 ACATGGTCTTACACGGGACCTCT
66 ACATGGTCTTACACGGGACCTCT
30178384 TTACCCAAAT
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
96 39 0.51
98 6 0.08
100 32 0.42
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.25
Consensus pattern (98 bp):
CCAAAGCCATATCCCAGACATGGTCTTACATGAGAGCCTCATATCGTGCCAACGCCATGTCCCAG
ACATGGTCTTACACGGGACCTCTCATCTCGGTG
Found at i:30178569 original size:23 final size:23
Alignment explanation
Indices: 30178543--30178613 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
30178533 TAATAATTAT
30178543 TAAAATATTGCATTTATTTACCG
1 TAAAATATTGCATTTATTTACCG
* ** * * *
30178566 TAAACT-TTTAATAATAATTA--T
1 TAAAATATTGCAT-TTATTTACCG
30178587 TAAAATATTGCATTTATTTACCG
1 TAAAATATTGCATTTATTTACCG
30178610 TAAA
1 TAAA
30178614 CTTACCTCGA
Statistics
Matches: 32, Mismatches: 12, Indels: 8
0.62 0.23 0.15
Matches are distributed among these distances:
21 10 0.31
22 8 0.25
23 14 0.44
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.44
Consensus pattern (23 bp):
TAAAATATTGCATTTATTTACCG
Found at i:30178580 original size:44 final size:44
Alignment explanation
Indices: 30178529--30178616 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
30178519 AATAACAACA
30178529 TTAATAATAATTATTAAAATATTGCATTTATTTACCGTAAACTT
1 TTAATAATAATTATTAAAATATTGCATTTATTTACCGTAAACTT
30178573 TTAATAATAATTATTAAAATATTGCATTTATTTACCGTAAACTT
1 TTAATAATAATTATTAAAATATTGCATTTATTTACCGTAAACTT
30178617 ACCTCGATAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (44 bp):
TTAATAATAATTATTAAAATATTGCATTTATTTACCGTAAACTT
Found at i:30185477 original size:43 final size:43
Alignment explanation
Indices: 30185429--30185515 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
30185419 TAAAATCATC
*
30185429 TCTATTCTGCTGTCTAACAGTTCCGACCCTTCTTCACTAAAAA
1 TCTATTCTGCCGTCTAACAGTTCCGACCCTTCTTCACTAAAAA
30185472 TCTATTCTGCCGTCTAACAGTTCCGACCCTTCTTCACTAAAAA
1 TCTATTCTGCCGTCTAACAGTTCCGACCCTTCTTCACTAAAAA
30185515 T
1 T
30185516 TAATTATCTC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.25, C:0.31, G:0.09, T:0.34
Consensus pattern (43 bp):
TCTATTCTGCCGTCTAACAGTTCCGACCCTTCTTCACTAAAAA
Found at i:30186370 original size:8 final size:8
Alignment explanation
Indices: 30186357--30186381 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
30186347 TATACTAAAC
30186357 AATAAAAT
1 AATAAAAT
30186365 AATAAAAT
1 AATAAAAT
30186373 AATAAAAT
1 AATAAAAT
30186381 A
1 A
30186382 TTATTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:30187888 original size:49 final size:49
Alignment explanation
Indices: 30187798--30187898 Score: 127
Period size: 49 Copynumber: 2.1 Consensus size: 49
30187788 CTCGTTTTCT
* *
30187798 CGATGCCATAGTCCAACTATGGTCTTACATGTAATCGCATATCA-TATAC
1 CGATGCCATAGCCCAACTATGGTCTTACATGTAATCACATATCACT-TAC
*
30187847 CGATGCCATAGCCCAGCTATGGTCCTATACA-G-AATCACATATCACTTAC
1 CGATGCCATAGCCCAACTATGGT-CT-TACATGTAATCACATATCACTTAC
30187896 CGA
1 CGA
30187899 AAGTATTCAT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
49 38 0.83
50 4 0.09
51 4 0.09
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.27
Consensus pattern (49 bp):
CGATGCCATAGCCCAACTATGGTCTTACATGTAATCACATATCACTTAC
Found at i:30188718 original size:33 final size:33
Alignment explanation
Indices: 30188676--30188798 Score: 111
Period size: 33 Copynumber: 3.4 Consensus size: 33
30188666 TGGTGGATTT
*
30188676 AGCACTTAGCAACCACCAGTGATTCGGGGAATC
1 AGCACTTAGCAACCACCAATGATTCGGGGAATC
*
30188709 AGCACTTAGCAACCCCTTTCACATTCAATGATACGGTGGAATC
1 AGCACTTAGCAA---C---CAC---CAATGATTCGG-GGAATC
* *
30188752 AGCACTTAGCAACCACCAATGAATCGGAGAATC
1 AGCACTTAGCAACCACCAATGATTCGGGGAATC
*
30188785 AACACTTAGCAACC
1 AGCACTTAGCAACC
30188799 CCTTGGGGGA
Statistics
Matches: 74, Mismatches: 6, Indels: 20
0.74 0.06 0.20
Matches are distributed among these distances:
33 30 0.41
34 9 0.12
36 1 0.01
37 3 0.04
39 3 0.04
40 1 0.01
42 9 0.12
43 18 0.24
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.20
Consensus pattern (33 bp):
AGCACTTAGCAACCACCAATGATTCGGGGAATC
Found at i:30189099 original size:101 final size:102
Alignment explanation
Indices: 30188922--30189107 Score: 286
Period size: 101 Copynumber: 1.8 Consensus size: 102
30188912 ACCGGTTCAT
* * *
30188922 ATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATAGGATACACGTAATAGCCTACAC
1 ATAGTAGCCTGCACATAATACCACACATGCGACCATCACTATAGGATACACGTAATAGCCTACAC
30188987 ATAGTACTACACACGTGATCGAAGCTATCCGGTACGC
66 ATAGTACTACACACGTGATCGAAGCTATCCGGTACGC
* * * *
30189024 ATAGTAGCCTGCACATAATACCACACATGCGACCTATCATTCT-GG-TACACGTAGTAGCCTGCA
1 ATAGTAGCCTGCACATAATACCACACATGCGACC-ATCACTATAGGATACACGTAATAGCCTACA
30189087 CATAGTACTACACACGTGATC
65 CATAGTACTACACACGTGATC
30189108 ATCACTTTCA
Statistics
Matches: 76, Mismatches: 7, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
101 37 0.49
102 33 0.43
103 6 0.08
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.23
Consensus pattern (102 bp):
ATAGTAGCCTGCACATAATACCACACATGCGACCATCACTATAGGATACACGTAATAGCCTACAC
ATAGTACTACACACGTGATCGAAGCTATCCGGTACGC
Found at i:30191513 original size:8 final size:8
Alignment explanation
Indices: 30191500--30191524 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
30191490 TATACTAAAC
30191500 AATAAAAT
1 AATAAAAT
30191508 AATAAAAT
1 AATAAAAT
30191516 AATAAAAT
1 AATAAAAT
30191524 A
1 A
30191525 TTATTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:30193488 original size:50 final size:50
Alignment explanation
Indices: 30193426--30193647 Score: 273
Period size: 50 Copynumber: 4.4 Consensus size: 50
30193416 CAATGACATA
* * ** * * * * *
30193426 TCCCAGATATGGTCTTACATGAGAGTTCTCATATTTGTGCCCATGCTATA
1 TCCCAGACATGGTCTTACATGGGACCTCTCATATTGGTGCCAACGCCATG
** *
30193476 TCCCAGACATGGTCTTACGGGGGACCTCTCATCTTGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATATTGGTGCCAACGCCATG
* * *
30193526 TCCCAGACATGGTCTTACATGGAACCTCTTATGTTGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATATTGGTGCCAACGCCATG
* * **
30193576 TCCCAGACATGGTCTTACATGGGACCTCTTATCTTGGTGCCAATTCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATATTGGTGCCAACGCCATG
30193626 TCCCAGACATGGTCTTACATGG
1 TCCCAGACATGGTCTTACATGG
30193648 TCTTTACCCA
Statistics
Matches: 151, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 151 1.00
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.30
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACATGGGACCTCTCATATTGGTGCCAACGCCATG
Found at i:30196784 original size:203 final size:203
Alignment explanation
Indices: 30196500--30196910 Score: 531
Period size: 203 Copynumber: 2.0 Consensus size: 203
30196490 GAAGCTCTCT
* * * *
30196500 AATTGAGTCATAATAACTAAAATTTATAGTAATATTTTTAAATGAACAAATTAGCTCAATTATAG
1 AATTCAGTCATAAGAACTAAAACTTATAGTAATATTTTTAAATGAACAAATTAGCTCAATTATAC
* * * * * *
30196565 GCAGCTAAACATGTTAATTAAGGCAGTGTGGATGAAAAACATCCTTAGTTTATAATTGGGCCATG
66 ACAGCTAAACATGTTAACTAAGGCAGTGTGGATGAAAAACACCCTCAGCTAATAATTGGGCCATG
* * * * *
30196630 TCGGATGAGTGTT-GCGACACCCTATATTTTTGTGTCA-CGACATTGAACATCAAATACTCTCAT
131 TCAGACGAGT-TTCACAACACCCTATAGTTTTGTGT-AGCGACATTGAACATCAAATACTCTCAT
30196693 TATTGGTTCA
194 TATTGGTTCA
* * * *
30196703 GATTCAGTCCTAAGAACTAATACTTATAGTAGTATTTTTAAATG-ACAAAATTAGCTCAATTATA
1 AATTCAGTCATAAGAACTAAAACTTATAGTAATATTTTTAAATGAAC-AAATTAGCTCAATTATA
* ** * *
30196767 CACTGCTAAACATGTTAACTAAGGTTGTGTGGATGAAAAGCACCCTCAGCTAATAATTGGGCCTT
65 CACAGCTAAACATGTTAACTAAGGCAGTGTGGATGAAAAACACCCTCAGCTAATAATTGGGCCAT
*
30196832 GTTAGACGAGTTTCACAACACCCTATAGTTTTGTGTAGCGACATTGAACATCAAATACTCTCATT
130 GTCAGACGAGTTTCACAACACCCTATAGTTTTGTGTAGCGACATTGAACATCAAATACTCTCATT
* *
30196897 TTTTGTTCA
195 ATTGGTTCA
30196906 AATTC
1 AATTC
30196911 GATTTTCGTG
Statistics
Matches: 177, Mismatches: 28, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
202 5 0.03
203 172 0.97
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (203 bp):
AATTCAGTCATAAGAACTAAAACTTATAGTAATATTTTTAAATGAACAAATTAGCTCAATTATAC
ACAGCTAAACATGTTAACTAAGGCAGTGTGGATGAAAAACACCCTCAGCTAATAATTGGGCCATG
TCAGACGAGTTTCACAACACCCTATAGTTTTGTGTAGCGACATTGAACATCAAATACTCTCATTA
TTGGTTCA
Found at i:30204812 original size:36 final size:36
Alignment explanation
Indices: 30204765--30204840 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
30204755 ACCAATTTGG
* *
30204765 TATGAAAGCTACCGATTTGAGGTTTCAATGTTGACT
1 TATGAAAGCTACCGATTTGAGGTTTCAATATCGACT
30204801 TATGAAAGCTACCGATTTGAGGTTTCAATATCGACT
1 TATGAAAGCTACCGATTTGAGGTTTCAATATCGACT
30204837 TATG
1 TATG
30204841 GTTCAATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (36 bp):
TATGAAAGCTACCGATTTGAGGTTTCAATATCGACT
Found at i:30205517 original size:15 final size:15
Alignment explanation
Indices: 30205499--30205545 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
30205489 AAATATTTTT
*
30205499 TATAAAATTCTAAAA
1 TATAAAATTTTAAAA
*
30205514 TATATAATTTTAAAA
1 TATAAAATTTTAAAA
*
30205529 TTTAAAATTTTAAAA
1 TATAAAATTTTAAAA
30205544 TA
1 TA
30205546 ATATAAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
TATAAAATTTTAAAA
Found at i:30205534 original size:22 final size:23
Alignment explanation
Indices: 30205484--30205536 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
30205474 ATATAATATT
**
30205484 TTTAAAA-ATATTTTTTATAAAA
1 TTTAAAATATATAATTTATAAAA
30205506 TTCTAAAATATATAATTT-TAAAA
1 TT-TAAAATATATAATTTATAAAA
30205529 TTTAAAAT
1 TTTAAAAT
30205537 TTTAAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 8 0.30
23 12 0.44
24 7 0.26
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTAAAATATATAATTTATAAAA
Found at i:30205805 original size:21 final size:23
Alignment explanation
Indices: 30205779--30205824 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
30205769 CTATTATAAA
*
30205779 TTTTTTTATA-ATT-TATATGTT
1 TTTTTTTATAGATTATATATATT
*
30205800 TTTTTTTCTAGATTATATATATT
1 TTTTTTTATAGATTATATATATT
30205823 TT
1 TT
30205825 GAATTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.43
22 3 0.14
23 9 0.43
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTTTTTATAGATTATATATATT
Found at i:30223212 original size:40 final size:39
Alignment explanation
Indices: 30223161--30223289 Score: 127
Period size: 40 Copynumber: 3.3 Consensus size: 39
30223151 TGTTTGAACA
* * *
30223161 AAAAATGCCGCTATAGATCGAGAATTAGCAGCGCTTTTTG
1 AAAAACGCCGCTATA-ATCGAGCATTAGCGGCGCTTTTTG
* * * * *
30223201 AAAATCGCCGCTATAAATCAAGCATTAGCGGTGCTTTCTA
1 AAAAACGCCGCTAT-AATCGAGCATTAGCGGCGCTTTTTG
* *
30223241 AAAAACACCGCTAT-ATGCG-CCATTAGCGGCGCTTTTTG
1 AAAAACGCCGCTATAAT-CGAGCATTAGCGGCGCTTTTTG
30223279 AAAAACGCCGC
1 AAAAACGCCGC
30223290 AAAAAAAGAA
Statistics
Matches: 71, Mismatches: 16, Indels: 6
0.76 0.17 0.06
Matches are distributed among these distances:
38 27 0.38
39 1 0.01
40 42 0.59
41 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (39 bp):
AAAAACGCCGCTATAATCGAGCATTAGCGGCGCTTTTTG
Found at i:30223424 original size:39 final size:40
Alignment explanation
Indices: 30223325--30223618 Score: 152
Period size: 40 Copynumber: 7.7 Consensus size: 40
30223315 GCTTTAGTGG
* *
30223325 CATTAGCGGCGCCTTTTGAAAAACGCCGCTATAGATCGAG
1 CATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATCGAC
* * * * * *
30223365 CATTAGTGTCGCTTTCTGAAAAACGCCGTTATAGGTTG-C
1 CATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATCGAC
* * ** *
30223404 CATTAGCGGCGCTTTTTGAAAAACGCTGCAAAATAG-TTAAG
1 CATTAGCGGCGCTTTTTGAAAAACGCCGC--TATAGATCGAC
* * ** * *
30223445 CA-TAACGCCG-TCGTTG---AA-----CTTTAG-T-GGC
1 CATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATCGAC
* * * * *
30223473 -ATTAGCGGCGCTTTTTGAAAAACACTGCTATAAATTGAG
1 CATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATCGAC
* * ** *
30223512 TATTAGAGGCGCTTTTTGAAAAACGCCGCTATAGATTAAG
1 CATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATCGAC
* * *
30223552 CATTAGTGGCACTTTTTGAAAAATGCCGCTATAAGA-CGAC
1 CATTAGCGGCGCTTTTTGAAAAACGCCGCTAT-AGATCGAC
*
30223592 CATTAGCGGCACTTTTTGAAAAACGCC
1 CATTAGCGGCGCTTTTTGAAAAACGCC
30223619 ACAAAAAAAT
Statistics
Matches: 190, Mismatches: 47, Indels: 34
0.70 0.17 0.13
Matches are distributed among these distances:
27 1 0.01
28 6 0.03
29 8 0.04
31 1 0.01
32 2 0.01
36 2 0.01
37 4 0.02
38 1 0.01
39 29 0.15
40 127 0.67
41 9 0.05
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (40 bp):
CATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATCGAC
Found at i:30223517 original size:147 final size:143
Alignment explanation
Indices: 30223184--30223580 Score: 426
Period size: 147 Copynumber: 2.7 Consensus size: 143
30223174 TAGATCGAGA
* * * * * *
30223184 ATTAGCAGCGCTTTTTGAAAATCGCCGCTATAAATCAAGCATTAGCGGT-GCTTTCTAAAAAACA
1 ATTAGCGGCGCTTTTTGAAAAACGCCGCTATAAATCGAGCATTAG-AGTCGCTTTCTGAAAAACG
* *
30223248 CCGCTATATG-CGCCATTAGCGGCGCTTTTTGAAAAACGCCGCAAAAAAAGAAGAAGCACAATGC
65 CCGCTATAGGTTGCCATTAGCGGCGCTTTTTGAAAAACGCCGCAAAAAAAGAAGAAGCACAATGC
*
30223312 TGAGCTTTAGTGGC
130 TGAACTTTAGTGGC
* * *
30223326 ATTAGCGGCGCCTTTTGAAAAACGCCGCTATAGATCGAGCATTAGTGTCGCTTTCTGAAAAACGC
1 ATTAGCGGCGCTTTTTGAAAAACGCCGCTATAAATCGAGCATTAGAGTCGCTTTCTGAAAAACGC
* * * *
30223391 CGTTATAGGTTGCCATTAGCGGCGCTTTTTGAAAAACGCTGCAAAATAGTTAAGCATAACGC-C-
66 CGCTATAGGTTGCCATTAGCGGCGCTTTTTGAAAAACGCCGCAAAA-A---AAGAAGAA-GCACA
* *
30223454 GTCGTTGAACTTTAGTGGC
126 AT-GCTGAACTTTAGTGGC
* * * * * *
30223473 ATTAGCGGCGCTTTTTGAAAAACACTGCTATAAATTGAGTATTAGAGGCGCTTTTTGAAAAACGC
1 ATTAGCGGCGCTTTTTGAAAAACGCCGCTATAAATCGAGCATTAGAGTCGCTTTCTGAAAAACGC
* * * *
30223538 CGCTATAGATTAAG-CATTAGTGGCACTTTTTGAAAAATGCCGC
66 CGCTATAGGTT--GCCATTAGCGGCGCTTTTTGAAAAACGCCGC
30223581 TATAAGACGA
Statistics
Matches: 213, Mismatches: 32, Indels: 14
0.82 0.12 0.05
Matches are distributed among these distances:
141 2 0.01
142 61 0.29
143 34 0.16
144 1 0.00
146 1 0.00
147 86 0.40
148 27 0.13
149 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (143 bp):
ATTAGCGGCGCTTTTTGAAAAACGCCGCTATAAATCGAGCATTAGAGTCGCTTTCTGAAAAACGC
CGCTATAGGTTGCCATTAGCGGCGCTTTTTGAAAAACGCCGCAAAAAAAGAAGAAGCACAATGCT
GAACTTTAGTGGC
Found at i:30228445 original size:9 final size:9
Alignment explanation
Indices: 30228431--30228512 Score: 67
Period size: 9 Copynumber: 9.1 Consensus size: 9
30228421 ATAAAATATA
30228431 TACATAACT
1 TACATAACT
* *
30228440 TGCATAATT
1 TACATAACT
30228449 TACATAACT
1 TACATAACT
* *
30228458 TACTTAA-A
1 TACATAACT
* * *
30228466 TATATATCA
1 TACATAACT
*
30228475 TATCAAAACT
1 TA-CATAACT
30228485 TACATAACT
1 TACATAACT
*
30228494 TACATAATT
1 TACATAACT
30228503 TACATAACT
1 TACATAACT
30228512 T
1 T
30228513 TAAAGAATTA
Statistics
Matches: 55, Mismatches: 16, Indels: 4
0.73 0.21 0.05
Matches are distributed among these distances:
8 4 0.07
9 46 0.84
10 5 0.09
ACGTcount: A:0.44, C:0.17, G:0.01, T:0.38
Consensus pattern (9 bp):
TACATAACT
Found at i:30228476 original size:22 final size:21
Alignment explanation
Indices: 30228416--30228476 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 21
30228406 ATATTTTTAA
*
30228416 AACTTA-TAAAATATATACAT
1 AACTTACTTAAATATATACAT
* *
30228436 AACTTGCAT-AAT-T-TACAT
1 AACTTACTTAAATATATACAT
30228454 AACTTACTTAAATATATATCAT
1 AACTTACTTAAATATATA-CAT
30228476 A
1 A
30228477 TCAAAACTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
18 12 0.39
19 4 0.13
20 9 0.29
21 2 0.06
22 4 0.13
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.38
Consensus pattern (21 bp):
AACTTACTTAAATATATACAT
Found at i:30228597 original size:47 final size:47
Alignment explanation
Indices: 30228544--30228687 Score: 195
Period size: 47 Copynumber: 3.1 Consensus size: 47
30228534 CTTTGGATCT
*
30228544 TAACTTAATAACTTATATATATCATATCATAACATACATAACTCACA
1 TAACTTAATAACTTATATATATTATATCATAACATACATAACTCACA
**
30228591 TAACTTAATAACTTATATATATTATATCATAATTTACATAACTCACA
1 TAACTTAATAACTTATATATATTATATCATAACATACATAACTCACA
* *
30228638 TAACTTACATAACTTA-ATA-ACTTATAT-ATATCATATCATAACTTACA
1 TAACTTA-ATAACTTATATATA-TTATATCATAACATA-CATAACTCACA
30228685 TAA
1 TAA
30228688 ATAAATTATA
Statistics
Matches: 87, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
46 6 0.07
47 73 0.84
48 8 0.09
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.38
Consensus pattern (47 bp):
TAACTTAATAACTTATATATATTATATCATAACATACATAACTCACA
Found at i:30228639 original size:56 final size:56
Alignment explanation
Indices: 30228571--30228687 Score: 191
Period size: 56 Copynumber: 2.1 Consensus size: 56
30228561 TATATCATAT
* *
30228571 CATAACATACATAACTCACATAACTTAATAACTTATATATATTATATCATAATTTA
1 CATAACATACATAACTCACATAACTTAATAACTTATATATATCATATCATAACTTA
*
30228627 CATAAC-TCACATAACTTACATAACTTAATAACTTATATATATCATATCATAACTTA
1 CATAACAT-ACATAACTCACATAACTTAATAACTTATATATATCATATCATAACTTA
30228683 CATAA
1 CATAA
30228688 ATAAATTATA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
55 1 0.02
56 56 0.98
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (56 bp):
CATAACATACATAACTCACATAACTTAATAACTTATATATATCATATCATAACTTA
Found at i:30234527 original size:43 final size:42
Alignment explanation
Indices: 30234480--30234698 Score: 190
Period size: 43 Copynumber: 5.1 Consensus size: 42
30234470 GAACGGTACT
*
30234480 TTTAGCGGCGTTTGTGAAAAAAGCATCGCTAAAGGTCATATTC
1 TTTAGCGGCGTTTGTGAAAAAAGCA-CGCTAAAGGTCATGTTC
* * * *
30234523 TTTAGCGACGTTTGTGAAAAAGGCGCCACTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGAAAAAAGC-ACGCTAAAGGTCATGTTC
* * * * *
30234566 TGTAGCGACATTTGTGACAAAAGCACTGCGAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGAAAAAAGCAC-GCTAAAGGTCATGTTC
* * * **** *
30234609 TTTAGCCGCGCTTCTCTTTAAAGC-CGCTAAAGGTCATGATC
1 TTTAGCGGCGTTTGTGAAAAAAGCACGCTAAAGGTCATGTTC
* *
30234650 TTTAGCGGCGTTTGTGGTAAAAA-CACCTCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGT-GAAAAAAGCA-CGCTAAAGGTCATGTTC
*
30234693 TCTAGC
1 TTTAGC
30234699 ACCGTTTATG
Statistics
Matches: 138, Mismatches: 33, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
41 27 0.20
42 6 0.04
43 105 0.76
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (42 bp):
TTTAGCGGCGTTTGTGAAAAAAGCACGCTAAAGGTCATGTTC
Found at i:30236280 original size:92 final size:93
Alignment explanation
Indices: 30236115--30236382 Score: 305
Period size: 92 Copynumber: 2.9 Consensus size: 93
30236105 GCTACATGTT
* * *
30236115 GTGTAGGTTCAACCCTGACGGGTGACCAGGCACTATTATTTGATTCATGTTGGTTCAA-CTATAA
1 GTGTAGGTTCAACCCTAACGGGTGACTAGGCACTATTATTTGATTCATGTAGGTTCAACCTATAA
*
30236179 CGAGTGACCA-AGCACTATTATCCGATTC
66 CGAGAGACCAGA-CACTATTATCCGATTC
* * *
30236207 GTGTGGGTTCAACCCTAATGGGTGACTAGCCACTATTATTTGATTCATGTAGGTTCAACCT-TAA
1 GTGTAGGTTCAACCCTAACGGGTGACTAGGCACTATTATTTGATTCATGTAGGTTCAACCTATAA
* * *
30236271 CGGGAGACCAGACACTATTATCTGATTT
66 CGAGAGACCAGACACTATTATCCGATTC
* * * * * * *
30236299 GTGTAGGTTTAACCCAAACGGGT-AATCAGGCACTATTATTCGATTCGTGTAGGTTTAACCCA-A
1 GTGTAGGTTCAACCCTAACGGGTGACT-AGGCACTATTATTTGATTCATGTAGGTTCAACCTATA
*
30236362 ATGAGTA-ACCAGACACTATTA
65 ACGAG-AGACCAGACACTATTA
30236383 CTTTCATCTT
Statistics
Matches: 149, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
91 2 0.01
92 143 0.96
93 4 0.03
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (93 bp):
GTGTAGGTTCAACCCTAACGGGTGACTAGGCACTATTATTTGATTCATGTAGGTTCAACCTATAA
CGAGAGACCAGACACTATTATCCGATTC
Found at i:30236354 original size:46 final size:46
Alignment explanation
Indices: 30236115--30236382 Score: 227
Period size: 46 Copynumber: 5.8 Consensus size: 46
30236105 GCTACATGTT
** * *
30236115 GTGTAGGTTCAACCCTGACGGGTGACCAGGCACTATTATTTGATTC
1 GTGTAGGTTCAACCCAAACGGGTAACCAGGCACTATTATTCGATTC
* * * * * * *
30236161 ATGTTGGTTCAA-CTATAACGAGTGACCAAGCACTATTATCCGATTC
1 GTGTAGGTTCAACCCA-AACGGGTAACCAGGCACTATTATTCGATTC
* * * * * * *
30236207 GTGTGGGTTCAACCCTAATGGGTGACTAGCCACTATTATTTGATTC
1 GTGTAGGTTCAACCCAAACGGGTAACCAGGCACTATTATTCGATTC
* ** * *
30236253 ATGTAGGTTCAACCTTAACGGG-AGACCAGACACTATTA-TCTGATTT
1 GTGTAGGTTCAACCCAAACGGGTA-ACCAGGCACTATTATTC-GATTC
* *
30236299 GTGTAGGTTTAACCCAAACGGGTAATCAGGCACTATTATTCGATTC
1 GTGTAGGTTCAACCCAAACGGGTAACCAGGCACTATTATTCGATTC
* * * *
30236345 GTGTAGGTTTAACCCAAATGAGTAACCAGACACTATTA
1 GTGTAGGTTCAACCCAAACGGGTAACCAGGCACTATTA
30236383 CTTTCATCTT
Statistics
Matches: 176, Mismatches: 40, Indels: 12
0.77 0.18 0.05
Matches are distributed among these distances:
45 2 0.01
46 170 0.97
47 4 0.02
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (46 bp):
GTGTAGGTTCAACCCAAACGGGTAACCAGGCACTATTATTCGATTC
Found at i:30236379 original size:138 final size:138
Alignment explanation
Indices: 30236116--30236382 Score: 320
Period size: 138 Copynumber: 1.9 Consensus size: 138
30236106 CTACATGTTG
* * * * * *
30236116 TGTAGGTTCAACCCTGACGGGTGACCAGGCACTATTATTTGATTCATGTTGGTTCAACTATAACG
1 TGTAGGTTCAACCCTAACGGGAGACCAGACACTATTATCTGATTCATGTAGGTTCAACCATAACG
* * * * * * *
30236181 AGTGACCAAGCACTATTATCCGATTCGTGTGGGTTCAACCCTAATGGGTGACTAGCCACTATTAT
66 AGTAACCAAGCACTATTATCCGATTCGTGTAGGTTCAACCCAAATGAGTAACCAGACACTATTAT
30236246 TTGATTCA
131 TTGATTCA
* ** *
30236254 TGTAGGTTCAACCTTAACGGGAGACCAGACACTATTATCTGATTTGTGTAGGTTTAACCCA-AAC
1 TGTAGGTTCAACCCTAACGGGAGACCAGACACTATTATCTGATTCATGTAGGTTCAA-CCATAAC
* * * * *
30236318 GGGTAATCAGGCACTATTATTCGATTCGTGTAGGTTTAACCCAAATGAGTAACCAGACACTATTA
65 GAGTAACCAAGCACTATTATCCGATTCGTGTAGGTTCAACCCAAATGAGTAACCAGACACTATTA
30236383 CTTTCATCTT
Statistics
Matches: 106, Mismatches: 22, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
138 104 0.98
139 2 0.02
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (138 bp):
TGTAGGTTCAACCCTAACGGGAGACCAGACACTATTATCTGATTCATGTAGGTTCAACCATAACG
AGTAACCAAGCACTATTATCCGATTCGTGTAGGTTCAACCCAAATGAGTAACCAGACACTATTAT
TTGATTCA
Found at i:30238853 original size:33 final size:33
Alignment explanation
Indices: 30238809--30238877 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
30238799 ATCAGTAACC
*
30238809 AAAAACCCCATTCTAACTTTAAAGCAATCGGAA
1 AAAAACACCATTCTAACTTTAAAGCAATCGGAA
* *
30238842 AAAAACACCATTCTGACTTTAAAGCAATCGGCA
1 AAAAACACCATTCTAACTTTAAAGCAATCGGAA
30238875 AAA
1 AAA
30238878 GCAAAAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.46, C:0.23, G:0.10, T:0.20
Consensus pattern (33 bp):
AAAAACACCATTCTAACTTTAAAGCAATCGGAA
Found at i:30246991 original size:20 final size:20
Alignment explanation
Indices: 30246958--30246997 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
30246948 CCAACCTTCA
*
30246958 AAACTTTTTATTTTCCCCCT
1 AAACTTTTTATTTTCACCCT
30246978 AAAC-TTTTACTTTTCACCCT
1 AAACTTTTTA-TTTTCACCCT
30246998 TTACCCCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (20 bp):
AAACTTTTTATTTTCACCCT
Found at i:30254423 original size:24 final size:24
Alignment explanation
Indices: 30254391--30254439 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
30254381 GGATGAGATA
*
30254391 TCGACCTTTGCATTGCTATCCTTT
1 TCGACCTTTGCATTGATATCCTTT
*
30254415 TCGACCTTTTCATTGATATCCTTT
1 TCGACCTTTGCATTGATATCCTTT
30254439 T
1 T
30254440 TGGATAGCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.14, C:0.27, G:0.10, T:0.49
Consensus pattern (24 bp):
TCGACCTTTGCATTGATATCCTTT
Found at i:30254453 original size:40 final size:40
Alignment explanation
Indices: 30254408--30254512 Score: 165
Period size: 41 Copynumber: 2.6 Consensus size: 40
30254398 TTGCATTGCT
* * *
30254408 ATCCTTTTCGACCTTTTCATTGATATCCTTTTTGGATAGC
1 ATCCTTTTCAACCTTTTCATTGATATCCTTTTCGGATAAC
30254448 ATCCTTTTCAACCTTTTCATTTGATATCCTTTTCGGATAAC
1 ATCCTTTTCAACCTTTTCA-TTGATATCCTTTTCGGATAAC
*
30254489 ATCCTTTTCAAGCTTTTCATTGAT
1 ATCCTTTTCAACCTTTTCATTGAT
30254513 TTGGAAATAC
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
40 23 0.38
41 37 0.62
ACGTcount: A:0.20, C:0.23, G:0.10, T:0.48
Consensus pattern (40 bp):
ATCCTTTTCAACCTTTTCATTGATATCCTTTTCGGATAAC
Found at i:30256400 original size:37 final size:36
Alignment explanation
Indices: 30256352--30256470 Score: 123
Period size: 37 Copynumber: 3.2 Consensus size: 36
30256342 AAACACTCAT
*
30256352 AAGAGCTAATCCAACTGATAACACGCAAAGAGCTCCG
1 AAGAGCTAATCCAACTGATAACACGCAAA-AGCTCCA
* *** * *
30256389 AAGAGCTAATCCAA-TCAATAATGTGAAAAATACTCCA
1 AAGAGCTAATCCAACT-GATAACACGCAAAA-GCTCCA
*
30256426 AAGAGCTAATCCAACTGATAACACGCCAAATGCTCCA
1 AAGAGCTAATCCAACTGATAACACG-CAAAAGCTCCA
30256463 AAGAGCTA
1 AAGAGCTA
30256471 TACATTCGCC
Statistics
Matches: 64, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
36 2 0.03
37 58 0.91
38 4 0.06
ACGTcount: A:0.44, C:0.24, G:0.15, T:0.17
Consensus pattern (36 bp):
AAGAGCTAATCCAACTGATAACACGCAAAAGCTCCA
Found at i:30273797 original size:2 final size:2
Alignment explanation
Indices: 30273790--30273814 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30273780 ACTTTGATTA
30273790 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
30273815 TCTTATGCTT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:30275420 original size:6 final size:6
Alignment explanation
Indices: 30275411--30275454 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
30275401 ATATATATGA
* * * *
30275411 TTTGAT TTTGAT TTTGAT TTTGAC TTTAAT TTTAAT TTTAAT TT
1 TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TT
30275455 ATGCTACTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.23, C:0.02, G:0.09, T:0.66
Consensus pattern (6 bp):
TTTGAT
Found at i:30276079 original size:25 final size:25
Alignment explanation
Indices: 30276051--30276119 Score: 72
Period size: 24 Copynumber: 2.8 Consensus size: 25
30276041 AAATTTTAAT
30276051 TATATTTTTATTTTACAAATTTATA
1 TATATTTTTATTTTACAAATTTATA
*
30276076 TATA-TTTAATTTTTA-AAATTTATA
1 TATATTTTTA-TTTTACAAATTTATA
*
30276100 AAGTAATTTTTATTTT-CAAA
1 TA-T-ATTTTTATTTTACAAA
30276120 ACATATGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
24 14 0.39
25 10 0.28
26 8 0.22
27 4 0.11
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (25 bp):
TATATTTTTATTTTACAAATTTATA
Found at i:30276094 original size:24 final size:25
Alignment explanation
Indices: 30276031--30276099 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 25
30276021 AGTCAAATAG
30276031 TAATTTTCTAAAATTT-TAATTATATT
1 TAATTTT-TAAAATTTAT-ATTATATT
*
30276057 T-TTATTTTACAAATTTATA-TATATT
1 TAAT-TTTTA-AAATTTATATTATATT
30276082 TAATTTTTAAAATTTATA
1 TAATTTTTAAAATTTATA
30276100 AAGTAATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
24 9 0.24
25 15 0.41
26 12 0.32
27 1 0.03
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (25 bp):
TAATTTTTAAAATTTATATTATATT
Found at i:30276318 original size:2 final size:2
Alignment explanation
Indices: 30276311--30276360 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
30276301 AAGCCATTCA
30276311 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
30276353 AT AT AT AT
1 AT AT AT AT
30276361 TTACTTTTCT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30279106 original size:25 final size:25
Alignment explanation
Indices: 30279077--30279137 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
30279067 ATTTTATTTT
*
30279077 TTAATATAAAAATAAATTTAAAAATA
1 TTAATATAAAAATAAA-CTAAAAATA
30279103 -TAATA-AATCAAATAAACTAAAAATA
1 TTAATATAA--AAATAAACTAAAAATA
*
30279128 TTAAAATAAA
1 TTAATATAAA
30279138 TATTTCCAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
24 2 0.07
25 14 0.48
26 11 0.38
27 2 0.07
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (25 bp):
TTAATATAAAAATAAACTAAAAATA
Found at i:30279305 original size:21 final size:21
Alignment explanation
Indices: 30279268--30279330 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
30279258 ATATAATATT
* *
30279268 AAAATAGCAGCGAAACAACATC
1 AAAATAGTAG-GAAACAACAGC
*
30279290 AAAATAGTAGGAAACAATAGC
1 AAAATAGTAGGAAACAACAGC
**
30279311 AAAATAGTAATAAACAACAG
1 AAAATAGTAGGAAACAACAG
30279331 TGAAAAAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 26 0.74
22 9 0.26
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.13
Consensus pattern (21 bp):
AAAATAGTAGGAAACAACAGC
Found at i:30279523 original size:2 final size:2
Alignment explanation
Indices: 30279516--30279548 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
30279506 TCATGTTTAC
30279516 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30279549 AAAAAATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30280383 original size:8 final size:8
Alignment explanation
Indices: 30280370--30280400 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
30280360 AATAAATCTA
30280370 ATTTAATT
1 ATTTAATT
30280378 ATTTAATT
1 ATTTAATT
30280386 ATTTAATT
1 ATTTAATT
30280394 ATTTAAT
1 ATTTAAT
30280401 ACACATTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
ATTTAATT
Found at i:30293088 original size:100 final size:99
Alignment explanation
Indices: 30292930--30294047 Score: 1300
Period size: 100 Copynumber: 11.2 Consensus size: 99
30292920 CTGGCAGTGT
* *
30292930 AGTGGAGCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGCAATTTAAAAGATTGA
1 AGTGGAGCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTGA
* * *
30292995 AGCCGCAATGGCGAATCCTACTTCCATGGCGATCC
66 AGCCGCAACGGCGAATCTTACTTCC-TGGCGATGC
* *
30293030 AGTGGAGCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCAGACATTGCAATTTAAAAGATTGA
1 AGTGGAGCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTGA
* * * * *
30293095 GGCCGCAACGGCGAATCTTACTTCCCTAGTGGTGT
66 AGCCGCAACGGCGAATCTTACTT-CCTGGCGATGC
* *
30293130 AATGG-GACAGATTAAAGCTACAACGGCGAATTTTG-TTCCCCGACATTGCAATTAAAAAGATTG
1 AGTGGAG-CAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTG
* * *
30293193 AAGCCACAACAGTGAATCTTACTTTCCTGGCGATGC
65 AAGCCGCAACGGCGAATCTTAC-TTCCTGGCGATGC
* * *
30293229 AGTGAAGTAGATTAAAGCTACGACGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTGA
1 AGTGGAGCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTGA
* * * *
30293294 AGCTGCAACAGCGAATCTTACTTTCTTGGCGGTGC
66 AGCCGCAACGGCGAATCTTAC-TTCCTGGCGATGC
** * * *
30293329 AGTGGAGCAGATTAAAGCTATGACGGTGAATCTTGCTTCCCCGACATTTCAATT-ACAAGATTGA
1 AGTGGAGCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTGA
* * *
30293393 AGCCACAACGGCAAATCTTACTTCCCTGGTGATGC
66 AGCCGCAACGGCGAATCTTACTT-CCTGGCGATGC
* * * *
30293428 AGTGAAGCAGATTAAAGCTACGACGGCTAATCTTGCTTCCCCGACATTGCAATTGAAAAGATTGA
1 AGTGGAGCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTGA
* * * *
30293493 AGCCGAAACGGTGAATCTTACTTCCCTAGCGATGT
66 AGCCGCAACGGCGAATCTTACTT-CCTGGCGATGC
* * * *
30293528 AGTGGATCAGATTGAAGCTACAACGACGAATCTTG-TTCCCCAACATTGCAATTAAAAAGATTGA
1 AGTGGAGCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTGA
* *
30293592 AGCCACAATGGCGAATCTTACTTCTCTGGCGATGC
66 AGCCGCAACGGCGAATCTTACTTC-CTGGCGATGC
* *
30293627 AGTGAAGCAGATTAAAGCTACGACGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTGA
1 AGTGGAGCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTGA
* * *
30293692 AGTCGCAACGGTGAATCTTACTTTCCTGG-TAGTGC
66 AGCCGCAACGGCGAATCTTAC-TTCCTGGCGA-TGC
* * **
30293727 AGTGGAGCAGATTAAAGCTACAACGGTGAATTTTGCTTCCCCGACATCACAATT-AAAAGATTGA
1 AGTGGAGCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTGA
* * * *
30293791 AGCCGCAATGGTGAATCTTACTTCCTTGGTGGTGC
66 AGCCGCAACGGCGAATCTTACTTCC-TGGCGATGC
* * * * * * *
30293826 ATTGGAACAGATTGAAGCTACAACAGTGAATCTT-ATTCCCTGACATTGCAATTTAAAAA-ATTT
1 AGTGGAGCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAA-TTAAAAAGA-TT
* *
30293889 GAAGCCGCAACGGCGAATCTTACTTCTCTGG-TAGTGT
64 GAAGCCGCAACGGCGAATCTTACTTC-CTGGCGA-TGC
* * * * *
30293926 AGTAGAACAGATTGAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGCAATTAAAAATATTGA
1 AGTGGAGCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTGA
* * * ** *
30293991 AGCCGCAACGGCAAATCCTATCTCCCTGAAGTTGC
66 AGCCGCAACGGCGAATCTTA-CTTCCTGGCGATGC
* *
30294026 AGTGGAGCGGATTAAAACTACA
1 AGTGGAGCAGATTAAAGCTACA
30294048 GATCGTATCT
Statistics
Matches: 872, Mismatches: 124, Indels: 44
0.84 0.12 0.04
Matches are distributed among these distances:
98 20 0.02
99 315 0.36
100 512 0.59
101 25 0.03
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (99 bp):
AGTGGAGCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTGA
AGCCGCAACGGCGAATCTTACTTCCTGGCGATGC
Found at i:30293257 original size:199 final size:199
Alignment explanation
Indices: 30292915--30294007 Score: 1401
Period size: 199 Copynumber: 5.5 Consensus size: 199
30292905 ATGAAGTTAC
**
30292915 CTTCCCTGGCAGTGTAGTGGAGCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGC
1 CTTCCCTGGTGGTGTAGTGGAGCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGC
* * * * * *
30292980 AATTTAAAAGATTGAAGCCGCAATGGCGAATCCTACTTCCATGGCGATCCAGTGGAGCAGATTAA
66 AATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCC-TGGCGATGCAGTGAAGCAGATTAA
* * * *
30293045 AGCTACAACGGCGAATCTTGCTTCCCAGACATTGCAATTTAAAAGATTGAGGCCGCAACGGCGAA
130 AGCTACGACGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTGAAGCCGCAACGGCGAA
30293110 TCTTA
195 TCTTA
* * * *
30293115 CTTCCCTAGTGGTGTAATGG-GACAGATTAAAGCTACAACGGCGAATTTTG-TTCCCCGACATTG
1 CTTCCCTGGTGGTGTAGTGGAG-CAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTG
* * *
30293178 CAATTAAAAAGATTGAAGCCACAACAGTGAATCTTACTTTCCTGGCGATGCAGTGAAGTAGATTA
65 CAATTAAAAAGATTGAAGCCACAACGGCGAATCTTAC-TTCCTGGCGATGCAGTGAAGCAGATTA
* *
30293243 AAGCTACGACGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTGAAGCTGCAACAGCGA
129 AAGCTACGACGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTGAAGCCGCAACGGCGA
30293308 ATCTTA
194 ATCTTA
* * * * ** *
30293314 CTTTCTTGGCGGTGCAGTGGAGCAGATTAAAGCTATGACGGTGAATCTTGCTTCCCCGACATTTC
1 CTTCCCTGGTGGTGTAGTGGAGCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGC
* * *
30293379 AATT-ACAAGATTGAAGCCACAACGGCAAATCTTACTTCCCTGGTGATGCAGTGAAGCAGATTAA
66 AATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTT-CCTGGCGATGCAGTGAAGCAGATTAA
* * * *
30293443 AGCTACGACGGCTAATCTTGCTTCCCCGACATTGCAATTGAAAAGATTGAAGCCGAAACGGTGAA
130 AGCTACGACGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTGAAGCCGCAACGGCGAA
30293508 TCTTA
195 TCTTA
* * * * * ** *
30293513 CTTCCCTAGCGATGTAGTGGATCAGATTGAAGCTACAACGACGAATCTTG-TTCCCCAACATTGC
1 CTTCCCTGGTGGTGTAGTGGAGCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGC
*
30293577 AATTAAAAAGATTGAAGCCACAATGGCGAATCTTACTTCTCTGGCGATGCAGTGAAGCAGATTAA
66 AATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTC-CTGGCGATGCAGTGAAGCAGATTAA
* *
30293642 AGCTACGACGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTGAAGTCGCAACGGTGAA
130 AGCTACGACGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTGAAGCCGCAACGGCGAA
30293707 TCTTA
195 TCTTA
* * * * **
30293712 CTTTCCTGGTAGTGCAGTGGAGCAGATTAAAGCTACAACGGTGAATTTTGCTTCCCCGACATCAC
1 CTTCCCTGGTGGTGTAGTGGAGCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGC
* * * * * * *
30293777 AATT-AAAAGATTGAAGCCGCAATGGTGAATCTTACTTCCTTGGTGGTGCATTGGAA-CAGATTG
66 AATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCC-TGGCGATGCAGT-GAAGCAGATTA
* * * * *
30293840 AAGCTACAACAGTGAATCTT-ATTCCCTGACATTGCAATTTAAAAA-ATTTGAAGCCGCAACGGC
129 AAGCTACGACGGCGAATCTTGCTTCCCCGACATTGCAA-TTAAAAAGA-TTGAAGCCGCAACGGC
30293903 GAATCTTA
192 GAATCTTA
* * * * *
30293911 CTTCTCTGGTAGTGTAGTAGAACAGATTGAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGC
1 CTTCCCTGGTGGTGTAGTGGAGCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGC
* * *
30293976 AATTAAAAATATTGAAGCCGCAACGGCAAATC
66 AATTAAAAAGATTGAAGCCACAACGGCGAATC
30294008 CTATCTCCCT
Statistics
Matches: 775, Mismatches: 105, Indels: 26
0.86 0.12 0.03
Matches are distributed among these distances:
198 36 0.05
199 634 0.82
200 105 0.14
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (199 bp):
CTTCCCTGGTGGTGTAGTGGAGCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGC
AATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCTGGCGATGCAGTGAAGCAGATTAAA
GCTACGACGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTGAAGCCGCAACGGCGAAT
CTTA
Found at i:30294150 original size:44 final size:44
Alignment explanation
Indices: 30294009--30294165 Score: 144
Period size: 44 Copynumber: 3.6 Consensus size: 44
30293999 CGGCAAATCC
* * * * *
30294009 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACTACAGATCG
1 TATCTCCCTGAAGATGCAGTGGAGCAGATTAAAACAATAGATCA
* * *
30294053 TATCTCCCT-AAGAAGTAGTGGAGCAGA-CAGAAGA-AATCA-ATCA
1 TATCTCCCTGAAGATGCAGTGGAGCAGATTA-AA-ACAAT-AGATCA
*
30294096 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACAATAGATC-
1 TATCTCCCTGAAGATGCAGTGGAGCAGATTAAAACAATAGATCA
* *
30294139 TCATCTTCCTGAAAATGCAGTGGAGCA
1 T-ATCTCCCTGAAGATGCAGTGGAGCA
30294166 AACCAATCCT
Statistics
Matches: 90, Mismatches: 15, Indels: 16
0.74 0.12 0.13
Matches are distributed among these distances:
42 1 0.01
43 32 0.36
44 56 0.62
45 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (44 bp):
TATCTCCCTGAAGATGCAGTGGAGCAGATTAAAACAATAGATCA
Found at i:30294561 original size:289 final size:289
Alignment explanation
Indices: 30294188--30294767 Score: 1142
Period size: 289 Copynumber: 2.0 Consensus size: 289
30294178 CTCCCTGAAG
30294188 TGGCAGTGGAGCGGATTAAAATCATAAATCCTATACCTCTGAAGTTGCAGTAGGTCGGATTAAAT
1 TGGCAGTGGAGCGGATTAAAATCATAAATCCTATACCTCTGAAGTTGCAGTAGGTCGGATTAAAT
*
30294253 TTACCATGACAAGTCTTATCTCATTGAAGTTGCAGTGGAGCAGGCTAAAACCACAAATCTCATCC
66 TTACCATGACAAGTCTTATCTCATTGAAGTTGCAGTGGAGCAGACTAAAACCACAAATCTCATCC
30294318 CCATAGAGTTGCAGCAGAGTAGATTGAACTCATACCTCTCTAAAGATGCCGAGAAGTGGATCAAA
131 CCATAGAGTTGCAGCAGAGTAGATTGAACTCATACCTCTCTAAAGATGCCGAGAAGTGGATCAAA
30294383 GCAACAGGACACATTGGATTGAAATGAGACTACTTGAAGAAGAAAGGCACCAAAAAGTCAAGACT
196 GCAACAGGACACATTGGATTGAAATGAGACTACTTGAAGAAGAAAGGCACCAAAAAGTCAAGACT
30294448 CGGCGACACCAGTCAAAATTGGTCCCTTT
261 CGGCGACACCAGTCAAAATTGGTCCCTTT
30294477 TGGCAGTGGAGCGGATTAAAATCATAAATCCTATACCTCTGAAGTTGCAGTAGGTCGGATTAAAT
1 TGGCAGTGGAGCGGATTAAAATCATAAATCCTATACCTCTGAAGTTGCAGTAGGTCGGATTAAAT
30294542 TTACCATGACAAGTCTTATCTCATTGAAGTTGCAGTGGAGCAGACTAAAACCACAAATCTCATCC
66 TTACCATGACAAGTCTTATCTCATTGAAGTTGCAGTGGAGCAGACTAAAACCACAAATCTCATCC
*
30294607 CCATAGAGTTGCAGCAGAGTAGATTGAACTCGTACCTCTCTAAAGATGCCGAGAAGTGGATCAAA
131 CCATAGAGTTGCAGCAGAGTAGATTGAACTCATACCTCTCTAAAGATGCCGAGAAGTGGATCAAA
30294672 GCAACAGGACACATTGGATTGAAATGAGACTACTTGAAGAAGAAAGGCACCAAAAAGTCAAGACT
196 GCAACAGGACACATTGGATTGAAATGAGACTACTTGAAGAAGAAAGGCACCAAAAAGTCAAGACT
30294737 CGGCGACACCAGTCAAAATTGGTCCCTTT
261 CGGCGACACCAGTCAAAATTGGTCCCTTT
30294766 TG
1 TG
30294768 ATGTCTTTGC
Statistics
Matches: 289, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
289 289 1.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (289 bp):
TGGCAGTGGAGCGGATTAAAATCATAAATCCTATACCTCTGAAGTTGCAGTAGGTCGGATTAAAT
TTACCATGACAAGTCTTATCTCATTGAAGTTGCAGTGGAGCAGACTAAAACCACAAATCTCATCC
CCATAGAGTTGCAGCAGAGTAGATTGAACTCATACCTCTCTAAAGATGCCGAGAAGTGGATCAAA
GCAACAGGACACATTGGATTGAAATGAGACTACTTGAAGAAGAAAGGCACCAAAAAGTCAAGACT
CGGCGACACCAGTCAAAATTGGTCCCTTT
Found at i:30302891 original size:12 final size:12
Alignment explanation
Indices: 30302850--30302890 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
30302840 TTTAAAGACT
30302850 TTTTTAAAATAA
1 TTTTTAAAATAA
30302862 TTTTTAAAAT-A
1 TTTTTAAAATAA
*
30302873 TTTTTATAATAA
1 TTTTTAAAATAA
30302885 TTTTTA
1 TTTTTA
30302891 TGTATTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTTTAAAATAA
Found at i:30302899 original size:23 final size:22
Alignment explanation
Indices: 30302839--30302890 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 22
30302829 ACATTTTGCA
30302839 TTTTAAAGACTTTTTTAAAATAAT
1 TTTTAAA-A-TTTTTTAAAATAAT
*
30302863 TTTTAAAATATTTTTATAATAAT
1 TTTTAAAAT-TTTTTAAAATAAT
30302886 TTTTA
1 TTTTA
30302891 TGTATTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 1 0.04
23 18 0.69
24 7 0.27
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTTAAAATTTTTTAAAATAAT
Found at i:30303383 original size:30 final size:30
Alignment explanation
Indices: 30303347--30303406 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
30303337 TTGTTAAGGG
30303347 TGTGTCAGTTGTTTAAAAAAAATTAGTATC
1 TGTGTCAGTTGTTTAAAAAAAATTAGTATC
30303377 TGTGTCAGTTGTTTAAAAAAAATTAGTATC
1 TGTGTCAGTTGTTTAAAAAAAATTAGTATC
30303407 ATACTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.40
Consensus pattern (30 bp):
TGTGTCAGTTGTTTAAAAAAAATTAGTATC
Found at i:30303614 original size:2 final size:2
Alignment explanation
Indices: 30303602--30303634 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
30303592 TGTAAAATCT
*
30303602 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30303635 TGAAACTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:30310561 original size:61 final size:59
Alignment explanation
Indices: 30310479--30310612 Score: 182
Period size: 61 Copynumber: 2.2 Consensus size: 59
30310469 TTATTTAATT
* *
30310479 TTAATA-AGATTATTATTAAATATAATTTAATAAAAATAAAAATAAATAATTTAATCATATT-
1 TTAATATA-ATTATTATTAAATATAATTTAATAAAAAT---AATAAATAATTTAATAACATTC
* *
30310540 TTACTATAATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAATAACATTC
1 TTAATATAATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAACATTC
30310599 TTAATATAATTATT
1 TTAATATAATTATT
30310613 TTTATATTAA
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
58 18 0.27
59 13 0.20
61 34 0.52
62 1 0.02
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (59 bp):
TTAATATAATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAACATTC
Found at i:30310630 original size:16 final size:16
Alignment explanation
Indices: 30310609--30310639 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
30310599 TTAATATAAT
30310609 TATTTTTATATTAAAA
1 TATTTTTATATTAAAA
30310625 TATTTTTATATTAAA
1 TATTTTTATATTAAA
30310640 TTATATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTTTTATATTAAAA
Found at i:30314424 original size:2 final size:2
Alignment explanation
Indices: 30314417--30314456 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
30314407 CCTTGAATTA
30314417 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
30314457 CTCATTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30314838 original size:15 final size:16
Alignment explanation
Indices: 30314818--30314848 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
30314808 ATGGTAATTT
30314818 CTCTTA-TTTTCTTTC
1 CTCTTATTTTTCTTTC
30314833 CTCTTATTTTTCTTTC
1 CTCTTATTTTTCTTTC
30314849 TAACCAAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.06, C:0.26, G:0.00, T:0.68
Consensus pattern (16 bp):
CTCTTATTTTTCTTTC
Found at i:30315679 original size:22 final size:22
Alignment explanation
Indices: 30315654--30315704 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
30315644 TAACAGAATG
*
30315654 TATCATAGCATATCAAATTTCA
1 TATCATAGCATATCAAATATCA
** *
30315676 TATCGGAGCATATCATATATCA
1 TATCATAGCATATCAAATATCA
30315698 TATCATA
1 TATCATA
30315705 TTTATTTTCA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (22 bp):
TATCATAGCATATCAAATATCA
Found at i:30316874 original size:10 final size:11
Alignment explanation
Indices: 30316838--30316876 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
30316828 AAAAGTACTT
*
30316838 AAAGAAAAGTG
1 AAAGAAAAGAG
30316849 AAAGAAAAAGAG
1 AAAG-AAAAGAG
30316861 AAAGAAAA-AG
1 AAAGAAAAGAG
30316871 AAAGAA
1 AAAGAA
30316877 CAAAAGGAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 8 0.31
11 8 0.31
12 10 0.38
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (11 bp):
AAAGAAAAGAG
Found at i:30322937 original size:22 final size:22
Alignment explanation
Indices: 30322912--30322962 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
30322902 ATACAGAATG
*
30322912 TATCATAGCATATCAGATTTCA
1 TATCATAGCATATCAGATATCA
* *
30322934 TATCGA-AGCTTATCATATATCA
1 TATC-ATAGCATATCAGATATCA
30322956 TATCATA
1 TATCATA
30322963 TCTGTTTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 1 0.04
22 22 0.92
23 1 0.04
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (22 bp):
TATCATAGCATATCAGATATCA
Found at i:30322998 original size:44 final size:44
Alignment explanation
Indices: 30322970--30323064 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 44
30322960 ATATCTGTTT
* * * * *
30322970 TCATATCATGTTGTAGCATGTTTCATATCTTGTCATATCATAAC
1 TCATATCATGTTATAGCATATATCATATCATATCATATCATAAC
* *
30323014 TCATGTCATGTTATATCATATATCATATCATATCATATCAT-A-
1 TCATATCATGTTATAGCATATATCATATCATATCATATCATAAC
30323056 TCATATCAT
1 TCATATCAT
30323065 ATCCTACCCC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 8 0.19
43 1 0.02
44 34 0.79
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (44 bp):
TCATATCATGTTATAGCATATATCATATCATATCATATCATAAC
Found at i:30323017 original size:22 final size:21
Alignment explanation
Indices: 30322992--30323064 Score: 85
Period size: 22 Copynumber: 3.4 Consensus size: 21
30322982 GTAGCATGTT
*
30322992 TCATATCTTGTCATATCATAA
1 TCATATCATGTCATATCATAA
* *
30323013 CTCATGTCATGTTATATCATATA
1 -TCATATCATGTCATATCATA-A
*
30323036 TCATATCATATCATATCAT-A
1 TCATATCATGTCATATCATAA
30323056 TCATATCAT
1 TCATATCAT
30323065 ATCCTACCCC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
20 10 0.23
22 33 0.75
23 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.42
Consensus pattern (21 bp):
TCATATCATGTCATATCATAA
Found at i:30323034 original size:5 final size:5
Alignment explanation
Indices: 30322992--30323067 Score: 71
Period size: 5 Copynumber: 14.4 Consensus size: 5
30322982 GTAGCATGTT
* * * * *
30322992 TCATA TCTTG TCATA TCATAA CTCATG TCATG TTATA TCATATA TCATA
1 TCATA TCATA TCATA TCAT-A -TCATA TCATA TCATA TC--ATA TCATA
30323041 TCATA TCATA TCATA TCATA TCATA TC
1 TCATA TCATA TCATA TCATA TCATA TC
30323068 CTACCCCAAC
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
5 49 0.83
6 1 0.02
7 9 0.15
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (5 bp):
TCATA
Found at i:30324155 original size:6 final size:6
Alignment explanation
Indices: 30324146--30324182 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
30324136 AAGAAAAGTG
*
30324146 AAAGAA AAAGAA AAAGAA AAAGAA AGAACAA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA A-AAGAA AAAGAA
30324183 GATGAAGCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:30324872 original size:15 final size:15
Alignment explanation
Indices: 30324852--30324882 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
30324842 TTATCTCACC
30324852 ATTCCAATTTAGAAG
1 ATTCCAATTTAGAAG
30324867 ATTCCAATTTAGAAG
1 ATTCCAATTTAGAAG
30324882 A
1 A
30324883 ATTAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (15 bp):
ATTCCAATTTAGAAG
Found at i:30326211 original size:19 final size:20
Alignment explanation
Indices: 30326187--30326231 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
30326177 TTGAGATGGA
30326187 ATGATATTCAACTTTGTGG-
1 ATGATATTCAACTTTGTGGT
* *
30326206 ATGATATTTAACTTTTTGGT
1 ATGATATTCAACTTTGTGGT
30326226 ATGATA
1 ATGATA
30326232 GGGACATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.29, C:0.07, G:0.18, T:0.47
Consensus pattern (20 bp):
ATGATATTCAACTTTGTGGT
Found at i:30327872 original size:25 final size:25
Alignment explanation
Indices: 30327821--30327872 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
30327811 AACCTACACT
* **
30327821 AATCAAAGTTTAAGTGGGAAACTAA
1 AATCAAAGTTTAACTGGGAAAAGAA
30327846 AATCAAAGTTTAACTGGGAAAAGAA
1 AATCAAAGTTTAACTGGGAAAAGAA
30327871 AA
1 AA
30327873 GCCGAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.52, C:0.08, G:0.19, T:0.21
Consensus pattern (25 bp):
AATCAAAGTTTAACTGGGAAAAGAA
Found at i:30334383 original size:179 final size:179
Alignment explanation
Indices: 30334104--30334759 Score: 952
Period size: 179 Copynumber: 3.7 Consensus size: 179
30334094 TTTGATTCGT
* * * * * *
30334104 TCCAGTGTAATTTCAGGGTGAAGAGACTTGTAGCTTTGATCTACTCCGCTGCAACATCAAGGAGA
1 TCCAATGTAATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTGGAACTTCAAGGAGA
* * * * * *
30334169 TAGGAATTGGTAATTTCAACCCGCTCAATTGCAACTTCAAGGAGATAAGGTTTGTATATTTTTAT
66 TAAGAATTGGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTATATTTTTAT
* * *
30334234 CCTTCTCCACTGCAACTTTAGGGAGATAATGATTGTAGCTTCGATCTGC
131 CCTGCTCCACTGCAACTTTAGGGAGATAAGGATTGTGGCTTCGATCTGC
** * *
30334283 TTTAATGTAATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTAGTCCGTTGGAACTTCAAGGAGA
1 TCCAATGTAATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTGGAACTTCAAGGAGA
* * ** *
30334348 TAAGAATTGGTAACTTCAACTTGCTCCACTGCAACTTTAGGGAGGGAAGGTTTATATATTTTTAT
66 TAAGAATTGGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTATATTTTTAT
* * *
30334413 CCTGCTCCACTACAACTTTAGGGAGATAAGGGTTGTGGCTTCAATCTGC
131 CCTGCTCCACTGCAACTTTAGGGAGATAAGGATTGTGGCTTCGATCTGC
* * *
30334462 TCCAATGTAATTTCAGGGAGAAGAGATTTGTAGCTTTGATCTACTACGCTGGAACTTTAAGGAGA
1 TCCAATGTAATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTGGAACTTCAAGGAGA
* *
30334527 TAGGAATTGGTAACTTCAACCTGCTCCACTGTAACTTCAGGGAGATAAGGTTTGTATATTTTTAT
66 TAAGAATTGGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTATATTTTTAT
* * *
30334592 CCTGCTCTACTGCAACTTCAGGGAGATAAGGATTTTGGCTTCGATCTGC
131 CCTGCTCCACTGCAACTTTAGGGAGATAAGGATTGTGGCTTCGATCTGC
* *
30334641 TCCAATGTAATTTCAGGGAGAAGAGATTTGTAGTTTCGATCTACTCTGCTGGAACTTCAAGGAGA
1 TCCAATGTAATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTGGAACTTCAAGGAGA
* * *
30334706 TAAGAATTGGTAACTTCAACCTGTTCCATTGTAACTTCAGGGAGATAAGGTTTG
66 TAAGAATTGGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTG
30334760 CAACTTGTAG
Statistics
Matches: 422, Mismatches: 55, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
179 422 1.00
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.33
Consensus pattern (179 bp):
TCCAATGTAATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTGGAACTTCAAGGAGA
TAAGAATTGGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTATATTTTTAT
CCTGCTCCACTGCAACTTTAGGGAGATAAGGATTGTGGCTTCGATCTGC
Found at i:30334480 original size:44 final size:44
Alignment explanation
Indices: 30334238--30334755 Score: 189
Period size: 44 Copynumber: 11.6 Consensus size: 44
30334228 TTTTATCCTT
* * *
30334238 CTCCACTGCAACTTT-AGGGAGATAATGATTGTAGCTTCGATCTG
1 CTCCACTGTAA-TTTCAGGGAGATAAGGATTGTAGCTTCAATCTG
** * *
30334282 CTTTAATGTAATTTCAGGGAG--AAGAGATTTGTAGCTTCGATCTAG
1 CTCCACTGTAATTTCAGGGAGATAAG-GA-TTGTAGCTTCAATCT-G
** * * * * *
30334327 -TCCGTTGGAACTTCAAGGAGATAAGAATTGGTAACTTCAA-CTTG
1 CTCCACTGTAATTTCAGGGAGATAAGGATT-GTAGCTTCAATC-TG
* ** * * ** **
30334371 CTCCACTGCAACTTT-AGGGAGGGAAGGTTTATATATTTTTATCCTG
1 CTCCACTGTAA-TTTCAGGGAGATAAGGATTGTA-GCTTCAAT-CTG
** * *
30334417 CTCCACTACAACTTT-AGGGAGATAAGGGTTGTGGCTTCAATCTG
1 CTCCACTGTAA-TTTCAGGGAGATAAGGATTGTAGCTTCAATCTG
* ** *
30334461 CTCCAATGTAATTTCAGGGAG--AAGAGATTTGTAGCTTTGATCTA
1 CTCCACTGTAATTTCAGGGAGATAAG-GA-TTGTAGCTTCAATCTG
* * * * * *
30334505 CTACGCTGGAACTTT-AAGGAGAT-AGGAATTGGTAACTTCAACCTG
1 CTCCACTGTAA-TTTCAGGGAGATAAGG-ATT-GTAGCTTCAATCTG
* * ** **
30334550 CTCCACTGTAACTTCAGGGAGATAAGGTTTGTATATTTTTATCCTG
1 CTCCACTGTAATTTCAGGGAGATAAGGATTGTA-GCTTCAAT-CTG
* * * * * *
30334596 CTCTACTGCAACTTCAGGGAGATAAGGATTTTGGCTTCGATCTG
1 CTCCACTGTAATTTCAGGGAGATAAGGATTGTAGCTTCAATCTG
* * * *
30334640 CTCCAATGTAATTTCAGGGAG--AAGAGATTTGTAGTTTCGATCTA
1 CTCCACTGTAATTTCAGGGAGATAAG-GA-TTGTAGCTTCAATCTG
** * * * * * *
30334684 CTCTGCTGGAACTTCAAGGAGATAAGAATTGGTAACTTCAACCTG
1 CTCCACTGTAATTTCAGGGAGATAAGGATT-GTAGCTTCAATCTG
* * *
30334729 TTCCATTGTAACTTCAGGGAGATAAGG
1 CTCCACTGTAATTTCAGGGAGATAAGG
30334756 TTTGCAACTT
Statistics
Matches: 342, Mismatches: 102, Indels: 59
0.68 0.20 0.12
Matches are distributed among these distances:
42 8 0.02
43 11 0.03
44 145 0.42
45 106 0.31
46 71 0.21
47 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (44 bp):
CTCCACTGTAATTTCAGGGAGATAAGGATTGTAGCTTCAATCTG
Found at i:30334878 original size:44 final size:45
Alignment explanation
Indices: 30334788--30334895 Score: 137
Period size: 44 Copynumber: 2.4 Consensus size: 45
30334778 TGTTCTGTTA
* * * * * *
30334788 CAACTTCAGGGAAATAAGATTCATTGTCTTCAGTCTACTCCGCTG
1 CAACTTCAGGGAGATAAGACTCAGTGGCTTCAATCTACTCCACTG
*
30334833 CAACTTCAGGGAGATAAGGCT-AGTGGCTTCAATCTACTCCACTG
1 CAACTTCAGGGAGATAAGACTCAGTGGCTTCAATCTACTCCACTG
*
30334877 CAACTTCAGGAAGATAAGA
1 CAACTTCAGGGAGATAAGA
30334896 TCCGCCATAA
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 36 0.67
45 18 0.33
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (45 bp):
CAACTTCAGGGAGATAAGACTCAGTGGCTTCAATCTACTCCACTG
Found at i:30335240 original size:143 final size:143
Alignment explanation
Indices: 30334798--30335237 Score: 664
Period size: 143 Copynumber: 3.1 Consensus size: 143
30334788 CAACTTCAGG
** *
30334798 GAAATAAGATTCATTGTCTTCAGTCTACTCCGCTGCAACTTCAGGGAGATAAGGCTAGTGGCTTC
1 GAAATAAGATTCGCTGTCTTCAGTCTACTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTC
* *
30334863 AATCTACTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCA
66 AATCTGCTCCACTGCAACTTCAGAAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCA
* *
30334928 CTATAATGCCAGA
131 CTACAATGCTAGA
* **
30334941 GAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTATAACTTCAGGGAGATAAGGCTGGTGGCTTC
1 GAAATAAGATTCGCTGTCTTCAGTCTACTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTC
* * * *
30335006 AATTTGCTCCACTACAACTTCAGAAAGATAAGATCCGCCATAATTTGTAGCTTAAATCTATTCCA
66 AATCTGCTCCACTGCAACTTCAGAAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCA
30335071 CTACAATGCTAGA
131 CTACAATGCTAGA
* * *
30335084 GAAATAAGATTTGCCGTCTTCAGTCTACTCCGTTGCAACTTCAGGGAGATAAGGCTGGTGGCTTC
1 GAAATAAGATTCGCTGTCTTCAGTCTACTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTC
* * *
30335149 AATCTGCTCCACTGCAACTTCAGAAAGATAAGGTTCGCTATAATTTGTAGCTTTAATCTGTTCCA
66 AATCTGCTCCACTGCAACTTCAGAAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCA
* * * *
30335214 TTGCAACGCTAGG
131 CTACAATGCTAGA
30335227 GAAATAAGATT
1 GAAATAAGATT
30335238 TGCGGTTTCG
Statistics
Matches: 266, Mismatches: 31, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
143 266 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (143 bp):
GAAATAAGATTCGCTGTCTTCAGTCTACTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTC
AATCTGCTCCACTGCAACTTCAGAAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCA
CTACAATGCTAGA
Found at i:30336096 original size:15 final size:14
Alignment explanation
Indices: 30336067--30336116 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
30336057 CACCTTGGCC
* *
30336067 TCTCCTTTTTCTTT
1 TCTCTTTTTTTTTT
30336081 TCTCTTTTTTGTTTT
1 TCTCTTTTTT-TTTT
30336096 TCT-TTTCTTTTTTT
1 TCTCTTT-TTTTTTT
30336110 T-TCTTTT
1 TCTCTTTT
30336117 CGTTTTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
13 2 0.06
14 20 0.65
15 9 0.29
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (14 bp):
TCTCTTTTTTTTTT
Found at i:30336117 original size:15 final size:15
Alignment explanation
Indices: 30336071--30336124 Score: 65
Period size: 15 Copynumber: 3.5 Consensus size: 15
30336061 TTGGCCTCTC
30336071 CTTTTTCTTTTCTCTTT
1 CTTTTT-TTTTCT-TTT
*
30336088 -TTTGTTTTTCTTTT
1 CTTTTTTTTTCTTTT
30336102 CTTTTTTTTTCTTTT
1 CTTTTTTTTTCTTTT
30336117 CGTTTTTT
1 C-TTTTTT
30336125 AAGGTCTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
14 3 0.09
15 20 0.61
16 10 0.30
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (15 bp):
CTTTTTTTTTCTTTT
Found at i:30336117 original size:20 final size:20
Alignment explanation
Indices: 30336072--30336109 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
30336062 TGGCCTCTCC
30336072 TTTTTCTTTTCTCTTTTTTG
1 TTTTTCTTTTCTCTTTTTTG
30336092 TTTTTCTTTTCT-TTTTTT
1 TTTTTCTTTTCTCTTTTTT
30336110 TTCTTTTCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.84
Consensus pattern (20 bp):
TTTTTCTTTTCTCTTTTTTG
Found at i:30336122 original size:6 final size:5
Alignment explanation
Indices: 30336073--30336122 Score: 50
Period size: 5 Copynumber: 9.8 Consensus size: 5
30336063 GGCCTCTCCT
*
30336073 TTTTC TTTTC TCTTT- TTTGT- TTTTC TTTTC TTTTT TTTTC TTTTC GTTTT
1 TTTTC TTTTC T-TTTC TTT-TC TTTTC TTTTC TTTTC TTTTC TTTTC -TTTT
30336123 TTAAGGTCTC
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
4 3 0.08
5 29 0.74
6 7 0.18
ACGTcount: A:0.00, C:0.14, G:0.04, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:30336581 original size:16 final size:15
Alignment explanation
Indices: 30336560--30336597 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
30336550 AGGTTTTTAT
30336560 TTTTTTTGTTCTTTGG
1 TTTTTTTGTT-TTTGG
*
30336576 TTTTTTTGTTTTTTG
1 TTTTTTTGTTTTTGG
30336591 TTTTTTT
1 TTTTTTT
30336598 CCTCCACTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.00, C:0.03, G:0.13, T:0.84
Consensus pattern (15 bp):
TTTTTTTGTTTTTGG
Found at i:30336588 original size:8 final size:8
Alignment explanation
Indices: 30336560--30336597 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
30336550 AGGTTTTTAT
30336560 TTTTTTTG
1 TTTTTTTG
* *
30336568 TTCTTTGG
1 TTTTTTTG
30336576 TTTTTTTG
1 TTTTTTTG
30336584 -TTTTTTG
1 TTTTTTTG
30336591 TTTTTTT
1 TTTTTTT
30336598 CCTCCACTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
7 7 0.28
8 18 0.72
ACGTcount: A:0.00, C:0.03, G:0.13, T:0.84
Consensus pattern (8 bp):
TTTTTTTG
Found at i:30354009 original size:129 final size:129
Alignment explanation
Indices: 30353779--30354035 Score: 408
Period size: 129 Copynumber: 2.0 Consensus size: 129
30353769 GGAGAACGTT
* * * * * * *
30353779 AAACTGATTAGTGATAGACTGAAAGTCGCTTCTAATAGGCAGAAGTTTTATGTAGATTTGAAATG
1 AAACTGATTAATGATAGACTAAAAGCCACTTCTAATAGGCAGAAGTCTTACGTAGATTTGAAACG
*
30353844 TTGTGACATCAAGTTTCAGATTGGGGATCGAGTGTTCCTTAAGGTTTCACCTTGGAAGAAAGTG
66 TTATGACATCAAGTTTCAGATTGGGGATCGAGTGTTCCTTAAGGTTTCACCTTGGAAGAAAGTG
*
30353908 AAACTGATTAATGATAGACTAAAAGCCACTTCTGATAGGCAGAAGTCTTACGTAGATTTGAAACG
1 AAACTGATTAATGATAGACTAAAAGCCACTTCTAATAGGCAGAAGTCTTACGTAGATTTGAAACG
*
30353973 TTATGACATCAAGTTTCA-AGTTGGGGATCGAGTGTTCCTTAAGGTTTCACCTTGGAAGGAAGT
66 TTATGACATCAAGTTTCAGA-TTGGGGATCGAGTGTTCCTTAAGGTTTCACCTTGGAAGAAAGT
30354036 TCTAAGATTC
Statistics
Matches: 117, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
128 1 0.01
129 116 0.99
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (129 bp):
AAACTGATTAATGATAGACTAAAAGCCACTTCTAATAGGCAGAAGTCTTACGTAGATTTGAAACG
TTATGACATCAAGTTTCAGATTGGGGATCGAGTGTTCCTTAAGGTTTCACCTTGGAAGAAAGTG
Found at i:30355788 original size:11 final size:11
Alignment explanation
Indices: 30355774--30355798 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
30355764 ATCATTAAAG
30355774 AATAATCAATC
1 AATAATCAATC
30355785 AATAATCAATC
1 AATAATCAATC
30355796 AAT
1 AAT
30355799 TTACCTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (11 bp):
AATAATCAATC
Found at i:30358576 original size:20 final size:21
Alignment explanation
Indices: 30358543--30358582 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
30358533 AAATACCTAA
30358543 ATTTAAAGTGTCTC-TAAGGT
1 ATTTAAAGTGTCTCTTAAGGT
30358563 ATTTAAAGAT-TCTCTTAAGG
1 ATTTAAAG-TGTCTCTTAAGG
30358583 GCTTGTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (21 bp):
ATTTAAAGTGTCTCTTAAGGT
Found at i:30360044 original size:334 final size:334
Alignment explanation
Indices: 30359435--30360103 Score: 1338
Period size: 334 Copynumber: 2.0 Consensus size: 334
30359425 ATTTAGTACC
30359435 TATAGTAGATTTATCACTAGGTGTAGGGTCCAAACTTTACTTCTCTCACATTGATTTAACTCTTC
1 TATAGTAGATTTATCACTAGGTGTAGGGTCCAAACTTTACTTCTCTCACATTGATTTAACTCTTC
30359500 TTGTATGGCCAATATCCAATATTCAACATTTAATGCTTCTTTGATATTTTTAGGCTCAATGCATG
66 TTGTATGGCCAATATCCAATATTCAACATTTAATGCTTCTTTGATATTTTTAGGCTCAATGCATG
30359565 AGATAAATGCAACATACTTACAAGTATTTCTAAGAGAAGATCTAGTAATTACCTCTTGAGATGGA
131 AGATAAATGCAACATACTTACAAGTATTTCTAAGAGAAGATCTAGTAATTACCTCTTGAGATGGA
30359630 TCTCCCAAAATCATACCATCCTTCACATAGTTGAAATCTCTTGGATGAGTGACTTCCCTTTCCTC
196 TCTCCCAAAATCATACCATCCTTCACATAGTTGAAATCTCTTGGATGAGTGACTTCCCTTTCCTC
30359695 AATTGAAAGTTCTTCTAGAGCATCATGTGTTTGTTCTTGAATTTTTTTCATTTGATGATTGATCC
261 AATTGAAAGTTCTTCTAGAGCATCATGTGTTTGTTCTTGAATTTTTTTCATTTGATGATTGATCC
30359760 TCTTTATCA
326 TCTTTATCA
30359769 TATAGTAGATTTATCACTAGGTGTAGGGTCCAAACTTTACTTCTCTCACATTGATTTAACTCTTC
1 TATAGTAGATTTATCACTAGGTGTAGGGTCCAAACTTTACTTCTCTCACATTGATTTAACTCTTC
30359834 TTGTATGGCCAATATCCAATATTCAACATTTAATGCTTCTTTGATATTTTTAGGCTCAATGCATG
66 TTGTATGGCCAATATCCAATATTCAACATTTAATGCTTCTTTGATATTTTTAGGCTCAATGCATG
30359899 AGATAAATGCAACATACTTACAAGTATTTCTAAGAGAAGATCTAGTAATTACCTCTTGAGATGGA
131 AGATAAATGCAACATACTTACAAGTATTTCTAAGAGAAGATCTAGTAATTACCTCTTGAGATGGA
30359964 TCTCCCAAAATCATACCATCCTTCACATAGTTGAAATCTCTTGGATGAGTGACTTCCCTTTCCTC
196 TCTCCCAAAATCATACCATCCTTCACATAGTTGAAATCTCTTGGATGAGTGACTTCCCTTTCCTC
30360029 AATTGAAAGTTCTTCTAGAGCATCATGTGTTTGTTCTTGAATTTTTTTCATTTGATGATTGATCC
261 AATTGAAAGTTCTTCTAGAGCATCATGTGTTTGTTCTTGAATTTTTTTCATTTGATGATTGATCC
30360094 TCTTTATCA
326 TCTTTATCA
30360103 T
1 T
30360104 TGTTAAAAAT
Statistics
Matches: 335, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
334 335 1.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (334 bp):
TATAGTAGATTTATCACTAGGTGTAGGGTCCAAACTTTACTTCTCTCACATTGATTTAACTCTTC
TTGTATGGCCAATATCCAATATTCAACATTTAATGCTTCTTTGATATTTTTAGGCTCAATGCATG
AGATAAATGCAACATACTTACAAGTATTTCTAAGAGAAGATCTAGTAATTACCTCTTGAGATGGA
TCTCCCAAAATCATACCATCCTTCACATAGTTGAAATCTCTTGGATGAGTGACTTCCCTTTCCTC
AATTGAAAGTTCTTCTAGAGCATCATGTGTTTGTTCTTGAATTTTTTTCATTTGATGATTGATCC
TCTTTATCA
Found at i:30365920 original size:157 final size:157
Alignment explanation
Indices: 30365634--30365947 Score: 538
Period size: 157 Copynumber: 2.0 Consensus size: 157
30365624 GAGAGATTAG
* *
30365634 GGAATGTCGAACATAACTACATTCACCGTAAATAGCGTGGTGTGTTTGGAGAGTGTGAGCCATCG
1 GGAATGTCAAACATAACTACATTCACCGTAAATAGCGTGGTGTGTTTGGAGAGTGTGAGCAATCG
* * * * * *
30365699 TGCTACACTTACATGGAGATAGTGTACGACTTTGTGAGTCATGAGGAGTGTTTGGAGATTTGTTT
66 TGCTACACTTACATAGAGATAGTGTACGACTTTATAAATCATGAAGAGTGTTTCGAGATTTGTTT
30365764 ATCTAGTGTATTATTGATTATATATAT
131 ATCTAGTGTATTATTGATTATATATAT
* *
30365791 GGAATGTCAAACATAGCTACATTCACCGTAGATAGCGTGGTGTGTTTGGAGAGTGTGAGCAATCG
1 GGAATGTCAAACATAACTACATTCACCGTAAATAGCGTGGTGTGTTTGGAGAGTGTGAGCAATCG
30365856 TGCTACACTTACATAGAGATAGTGTACGACTTTATAAATCATGAAGAGTGTTTCGAGATTTGTTT
66 TGCTACACTTACATAGAGATAGTGTACGACTTTATAAATCATGAAGAGTGTTTCGAGATTTGTTT
30365921 ATCTAGTGTATTATTGATTATATATAT
131 ATCTAGTGTATTATTGATTATATATAT
30365948 ATTCCATGTC
Statistics
Matches: 147, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
157 147 1.00
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.35
Consensus pattern (157 bp):
GGAATGTCAAACATAACTACATTCACCGTAAATAGCGTGGTGTGTTTGGAGAGTGTGAGCAATCG
TGCTACACTTACATAGAGATAGTGTACGACTTTATAAATCATGAAGAGTGTTTCGAGATTTGTTT
ATCTAGTGTATTATTGATTATATATAT
Found at i:30368041 original size:493 final size:492
Alignment explanation
Indices: 30367116--30368098 Score: 1750
Period size: 493 Copynumber: 2.0 Consensus size: 492
30367106 ATTTTTGCGG
*
30367116 GTACTTCCTCAACACCAATATATATTATGACATAGTTGAATTGGTAATTTTAATGTACTCGTGCT
1 GTACTTCCTCAACACCAATATATATTATGACATAGTTGAATTGCTAATTTTAATGTACTCGTGCT
* *
30367181 GTTGCAGGTATTTCACGGGATCATCTGAAATTGGGTTTGGAGATGATGGCGAACATAAACTACCT
66 GTTGCAGGTATTTCACGGAATCATCTGAAATTGGGTTTGGACATGATGGCGAACATAAACTACCT
* *
30367246 ATTGTTAAAGCGAGTCCCAATATTGCTGTGTCGATTGTAATTGCAAATATTCGTAGCTAGTTCGA
131 ATTGTTAAAGCGAGTCCCAATATTGCTGTGCCGATTGTAATTGCAAATATTCATAGCTAGTTCGA
*
30367311 TTACATGCCTTTGTACCGCAAGGTGTGGATTGTAAAGCATAAGGCATTGGAGAAGATGCATAGTG
196 TTACATGCCTTTGTACCGCAAGGTGTGGATTGTAAAGCATAAGGCATTAGAGAAGATGCATAGTG
* * *
30367376 AGTGGGACGCGTCTTACAACGAGGTATGGCAGTGGTGTCGGATGCTGGACCGATACGTCTCAAGT
261 AGTGGGACGCGTCGTACAACGAGGTATGGCAGTGGTGTCGGATGCTGGACAGATACATCTCAAGT
* *
30367441 TGCATACCCGATCTAGAAATGGGGCCTGTGTACTACAACGATCGGTTGCTCCATGGATGTCAAGT
326 TGCATAACCGATCTAGAAATGGGGCATGTGTACTACAACGATCGGTTGCTCCATGGATGTCAAGT
* *
30367506 GTTCCTCCGTTTGTTCTAGACTTTCAAGCAATGCCGATAAGCATTCTAGTTGCAAGCCATTGGTA
391 GTTCCTCCGTTTGTTCTAGAATTTCAAGCAATGCCGATAAGCATTCTAGTTGCAAGCCACTGGTA
*
30367571 CAAATCAACAAGTCTTTTGTGTACGAGAGATATACAT
456 CAAATCAACAAGTCCTTTGTGTACGAGAGATATACAT
*
30367608 GTACTTCCTCAACACCAATATATATTATGGCATAGTTGAATTGCTAATTTTAATGTACTCGTGCT
1 GTACTTCCTCAACACCAATATATATTATGACATAGTTGAATTGCTAATTTTAATGTACTCGTGCT
30367673 GTTGCAGGTATTTCACGGAATCATCTGAAATTGGGTTTGGACATGATGGCGAACATAATACTACC
66 GTTGCAGGTATTTCACGGAATCATCTGAAATTGGGTTTGGACATGATGGCGAACATAA-ACTACC
* *
30367738 TATTGTTAAAGCGAGTCCCAATATTGTTGTGCCGGTTGTAATTGCAAATATTCATAGCTAGTTCG
130 TATTGTTAAAGCGAGTCCCAATATTGCTGTGCCGATTGTAATTGCAAATATTCATAGCTAGTTCG
* *
30367803 ATTACATGCCTTTGTACCGCAATGTGTGGATTGTAAAGCGTAAGGCATTAGAGAAGATGCATAGT
195 ATTACATGCCTTTGTACCGCAAGGTGTGGATTGTAAAGCATAAGGCATTAGAGAAGATGCATAGT
*
30367868 GAGTGGGACGTGTCGTACAACGAGGTATGGCAGTGGTGTCGGATGCTGGACAGATACATCTCAAG
260 GAGTGGGACGCGTCGTACAACGAGGTATGGCAGTGGTGTCGGATGCTGGACAGATACATCTCAAG
* *
30367933 TTGCGTAACTGATCTAGAAATGGGGCATGTGTACTACAACGATCGGTTGCTCCATGGATGTCAAG
325 TTGCATAACCGATCTAGAAATGGGGCATGTGTACTACAACGATCGGTTGCTCCATGGATGTCAAG
30367998 TGTTCCTCCGTTTGTTCTAGAATTTCAAGCAATGCCGATAAGCATTCTAGTTGCAAGCCACTGGT
390 TGTTCCTCCGTTTGTTCTAGAATTTCAAGCAATGCCGATAAGCATTCTAGTTGCAAGCCACTGGT
*
30368063 ACAAATCATCAAGTCCTTTGTGTACGAGAGATATAC
455 ACAAATCAACAAGTCCTTTGTGTACGAGAGATATAC
30368099 CTATCGGTTG
Statistics
Matches: 467, Mismatches: 23, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
492 119 0.25
493 348 0.75
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (492 bp):
GTACTTCCTCAACACCAATATATATTATGACATAGTTGAATTGCTAATTTTAATGTACTCGTGCT
GTTGCAGGTATTTCACGGAATCATCTGAAATTGGGTTTGGACATGATGGCGAACATAAACTACCT
ATTGTTAAAGCGAGTCCCAATATTGCTGTGCCGATTGTAATTGCAAATATTCATAGCTAGTTCGA
TTACATGCCTTTGTACCGCAAGGTGTGGATTGTAAAGCATAAGGCATTAGAGAAGATGCATAGTG
AGTGGGACGCGTCGTACAACGAGGTATGGCAGTGGTGTCGGATGCTGGACAGATACATCTCAAGT
TGCATAACCGATCTAGAAATGGGGCATGTGTACTACAACGATCGGTTGCTCCATGGATGTCAAGT
GTTCCTCCGTTTGTTCTAGAATTTCAAGCAATGCCGATAAGCATTCTAGTTGCAAGCCACTGGTA
CAAATCAACAAGTCCTTTGTGTACGAGAGATATACAT
Found at i:30371734 original size:17 final size:18
Alignment explanation
Indices: 30371714--30371752 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
30371704 TTTAATAAAA
*
30371714 AAATAAAAATT-AGTGAG
1 AAATAAAAATTAAGTAAG
*
30371731 AAATAAAATTTAAGTAAG
1 AAATAAAAATTAAGTAAG
30371749 AAAT
1 AAAT
30371753 TAAGAAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.26
Consensus pattern (18 bp):
AAATAAAAATTAAGTAAG
Found at i:30371900 original size:16 final size:16
Alignment explanation
Indices: 30371879--30371909 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30371869 GCAGCTATTT
30371879 AAGTAGTCATTGGAGA
1 AAGTAGTCATTGGAGA
*
30371895 AAGTAGTCGTTGGAG
1 AAGTAGTCATTGGAG
30371910 GTTCCTGTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.35, T:0.26
Consensus pattern (16 bp):
AAGTAGTCATTGGAGA
Found at i:30373245 original size:11 final size:10
Alignment explanation
Indices: 30373229--30373262 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
30373219 TTAAAAATAA
30373229 TTAATTATTAT
1 TTAATTA-TAT
30373240 TTAATTACTAT
1 TTAATTA-TAT
30373251 TTAATTATAT
1 TTAATTATAT
30373261 TT
1 TT
30373263 TTATATTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 5 0.23
11 17 0.77
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (10 bp):
TTAATTATAT
Found at i:30375666 original size:23 final size:23
Alignment explanation
Indices: 30375622--30375709 Score: 72
Period size: 23 Copynumber: 3.8 Consensus size: 23
30375612 TTAATGTTCA
**
30375622 CGAACATGTTCATTTAAC-TTAAT
1 CGAACATGTTCA-CGAACATTAAT
*
30375645 CGAACATGTTCACGAACATTAAA
1 CGAACATGTTCACGAACATTAAT
* * *
30375668 CTAGCATGTTCATGAACATATAATT
1 CGAACATGTTCACGAACAT-TAA-T
*
30375693 C-AACATGTTCACAAACA
1 CGAACATGTTCACGAACA
30375710 ATGTTAATAA
Statistics
Matches: 52, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
22 3 0.06
23 32 0.62
24 16 0.31
25 1 0.02
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (23 bp):
CGAACATGTTCACGAACATTAAT
Found at i:30376191 original size:2 final size:2
Alignment explanation
Indices: 30376184--30376235 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
30376174 GAACCATTTG
30376184 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
*
30376226 AT AT AA AT AT
1 AT AT AT AT AT
30376236 GTTTTGGTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30378732 original size:281 final size:286
Alignment explanation
Indices: 30377914--30379018 Score: 1447
Period size: 281 Copynumber: 3.8 Consensus size: 286
30377904 GATTCTCAAT
* * *
30377914 AATCAAAGTAATGTTGCAAGCTTAGATTTCGTTTCTTGAAAATTCAAGCAGCAATAATTGGTTTA
1 AATCAAAGTAATGTTGCAAGCTTAGATTTTGTTTCTTGAAAATTCAAGCAACAACAATTGGTTTA
* * * * * *
30377979 ATGGTGAAATACAGACCTTTCATTGAGATGCATTTTGCTAGAGCTATAAAGGCTTTGCGAAAAAA
66 ATAGTGAAATACAAACCTTACATTGAGATGCATTTTGCTAGAGCTTTTAAGGCTTTGAGAAAAAA
*
30378044 AAAGTTGTAAAACAATTTGTGAGTAAAACAATATGAAGTAGTTGATGTCATTGAAGGTGCTCATC
131 AAAGTTGTAAAACAATTTGTGAGTAAAACAATATGAAGTAGTTGATGTGATTGAAGGTGCTCATC
* * *
30378109 AATAGTGGAAAACAAATAGAAATTTTTTTCTATTATTTTTTCATAATTATCAAGAAAATCATGTA
196 AATAGTGGAAAACAAATAG-AATTTTTTTCTTTTTTTTTTTCATAATTATCAGGAAAATCATGTA
*
30378174 GATA-GGCTGTTGATGGTAGAAGTTTTTATGATTCTCAA
260 GATAGGGC-GTTGATGGT---AG----TA--AGTCT--A
*
30378212 GAATCAAAGTAATGTTGCAAGCATAGATTTTGTTTCTTGAAAATTCAAG-AAGCAACAATTGGTT
1 -AATCAAAGTAATGTTGCAAGCTTAGATTTTGTTTCTTGAAAATTCAAGCAA-CAACAATTGGTT
* * *
30378276 TAATAATCAAATACAAACCTTACATTGAGACGCATTTTGCTAGAGCTTTTAAGGCTTTGAGAAAA
64 TAATAGTGAAATACAAACCTTACATTGAGATGCATTTTGCTAGAGCTTTTAAGGCTTTGAGAAAA
* * * * *
30378341 AAAAA-CTGTAAAACTATTTGTGAGTAAAACAATATAAAGTAGTTGATGTGATTGAAGGTTCTCT
129 AAAAAGTTGTAAAACAATTTGTGAGTAAAACAATATGAAGTAGTTGATGTGATTGAAGGTGCTCA
* *
30378405 TCAATAGTGGAAAACAAATAGAAGTTTTTCTT-TTTGTTTTTTTCATAATTAACAGGAAAATCAT
194 TCAATAGTGGAAAACAAATAGAA-TTTTT-TTCTTTTTTTTTTTCATAATTATCAGGAAAATCAT
*
30378469 GTAGGTAGGGCGTTGATGGTAG-AAGT-T-
257 GTAGATAGGGCGTTGATGGTAGTAAGTCTA
* * *
30378496 AATCAAAGTAATGTTGCAAGCTTAGA-TTTGCTTCTTGAAACTTCAAGCAACAACAATTGGTTAA
1 AATCAAAGTAATGTTGCAAGCTTAGATTTTGTTTCTTGAAAATTCAAGCAACAACAATTGGTTTA
30378560 ATAGTGAAATACAAACCTTACATTGAGATGCATTTTGCTAGAGCTTTTAAGGCTTTGAG-AAAAA
66 ATAGTGAAATACAAACCTTACATTGAGATGCATTTTGCTAGAGCTTTTAAGGCTTTGAGAAAAAA
* *
30378624 AAA-TTGTAAAATAATTTGTGAGTAAAACAATATGAAGTAGTTGATGTGATTGAATGTGCTCATC
131 AAAGTTGTAAAACAATTTGTGAGTAAAACAATATGAAGTAGTTGATGTGATTGAAGGTGCTCATC
*
30378688 AATAGTGGAAAGCAAATAGAATTTTTTTCTCTTTTTTTTTTCATAATTATCAGGAAAATCATGTA
196 AATAGTGGAAAACAAATAGAATTTTTTTCT-TTTTTTTTTTCATAATTATCAGGAAAATCATGTA
* *
30378753 GATAGGCCGTTGATGGTAAAAGTTTTTATAATTCTCAA
260 GATAGGGCGTTGATGGT---AG------TAAGTCT--A
*
30378791 GAATCAAAGTAATGTTGCAAGCTTAGATTTTGTTTCTTGAAAATTTAAGCAACAACAATTGGTTT
1 -AATCAAAGTAATGTTGCAAGCTTAGATTTTGTTTCTTGAAAATTCAAGCAACAACAATTGGTTT
* * *
30378856 AATAGTGAAATAGAGACCTTACATTGAGATGCATTTTGCTAGAGCTTTTAAGGTTTTGAGAAAAA
65 AATAGTGAAATACAAACCTTACATTGAGATGCATTTTGCTAGAGCTTTTAAGGCTTTGAG-----
*
30378921 AATAAAATAAAATTTGTAAAACAATTTGTGAGTAAAACAATATGAAGTAGTTGATGTGATTGAAG
125 -A-AAAA-AAAAGTTGTAAAACAATTTGTGAGTAAAACAATATGAAGTAGTTGATGTGATTGAAG
30378986 GTGCTCATCAATAGTGGAAAACAAATAGAATTT
187 GTGCTCATCAATAGTGGAAAACAAATAGAATTT
30379019 AGTTTGAAAA
Statistics
Matches: 717, Mismatches: 56, Indels: 58
0.86 0.07 0.07
Matches are distributed among these distances:
279 2 0.00
280 6 0.01
281 129 0.18
282 88 0.12
283 27 0.04
284 2 0.00
287 1 0.00
288 2 0.00
290 1 0.00
291 3 0.00
292 1 0.00
295 2 0.00
296 26 0.04
297 92 0.13
298 122 0.17
299 123 0.17
305 4 0.01
306 4 0.01
307 82 0.11
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.34
Consensus pattern (286 bp):
AATCAAAGTAATGTTGCAAGCTTAGATTTTGTTTCTTGAAAATTCAAGCAACAACAATTGGTTTA
ATAGTGAAATACAAACCTTACATTGAGATGCATTTTGCTAGAGCTTTTAAGGCTTTGAGAAAAAA
AAAGTTGTAAAACAATTTGTGAGTAAAACAATATGAAGTAGTTGATGTGATTGAAGGTGCTCATC
AATAGTGGAAAACAAATAGAATTTTTTTCTTTTTTTTTTTCATAATTATCAGGAAAATCATGTAG
ATAGGGCGTTGATGGTAGTAAGTCTA
Found at i:30379144 original size:21 final size:19
Alignment explanation
Indices: 30379120--30379169 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
30379110 TTGCTGCAAC
*
30379120 TGATTTTCTATATGAAATTTT
1 TGATTTT-T-TATAAAATTTT
*
30379141 TGATTTATTTTTAAAATTTT
1 TGATTT-TTTATAAAATTTT
30379161 TGATTTTTT
1 TGATTTTTT
30379170 TACAATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 3 0.12
20 15 0.58
21 7 0.27
22 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.08, T:0.64
Consensus pattern (19 bp):
TGATTTTTTATAAAATTTT
Found at i:30379176 original size:18 final size:20
Alignment explanation
Indices: 30379134--30379170 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
30379124 TTTCTATATG
30379134 AAATTTTTGATTTATTTTTA
1 AAATTTTTGATTTATTTTTA
30379154 AAATTTTTGATTT-TTTT
1 AAATTTTTGATTTATTTT
30379171 ACAATTATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (20 bp):
AAATTTTTGATTTATTTTTA
Done.