Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 2 of 168
Found at i:325857 original size:39 final size:39
Alignment explanation
Indices: 325811--325890 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
325801 GGGCTTAGGA
325811 TTTTTGGTTATTGGGCTGGGGTGTATTGGGTAATTCAGG
1 TTTTTGGTTATTGGGCTGGGGTGTATTGGGTAATTCAGG
*
325850 TTTTTGGTTATTGGGCTGGGGTGTATTGGGTAATTCGGG
1 TTTTTGGTTATTGGGCTGGGGTGTATTGGGTAATTCAGG
325889 TT
1 TT
325891 AGACTTTGGG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.11, C:0.05, G:0.39, T:0.45
Consensus pattern (39 bp):
TTTTTGGTTATTGGGCTGGGGTGTATTGGGTAATTCAGG
Found at i:326972 original size:216 final size:216
Alignment explanation
Indices: 326541--327106 Score: 861
Period size: 216 Copynumber: 2.6 Consensus size: 216
326531 TCTAGTCGGC
* * * *
326541 AAGACTTGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTC
1 AAGACCTGATGCGATCTACTCTACTGCAATTTCAGAGAGATAAGATCTATTACTTTAATCCGTTC
* * *
326606 CACTACAACTTT-AGGGAGATAGGATTATCGACTTCAACCTACTCCACTGCAACCTCAGGAAGAT
66 CACTACAA-TTTCAGGGAGATAGGATTATCGACTTCAATCTGCT-CACTGCAACCTCAGGGAGAT
* * *
326670 AAGATTTGCTTCTTCGGTCTGCCCCACTGTGACTTCAGGGGGATAAGACTTACTTTCTCAGTCTG
129 AAGATTTGCTTCTTCGGTCTGCCCCACTGTGACTTCAAGGGGATAAGACTTACTTTCTCAATCTA
*
326735 CTCTGCTACAACTTCAGGGAGAT
194 CTCCGCTACAACTTCAGGGAGAT
* *
326758 AAGACCTGATGTGATCTACTCTGCTGCAATTTCAGAGAGATAAGA-CTATTACTTTAATCCGTTC
1 AAGACCTGATGCGATCTACTCTACTGCAATTTCAGAGAGATAAGATCTATTACTTTAATCCGTTC
** *
326822 CACTACAATTTCAGGGAGATAGGATTATCGGTTTCAATCTGCTCTACTGCAACCTTAGGGAGATA
66 CACTACAATTTCAGGGAGATAGGATTATCGACTTCAATCTGCTC-ACTGCAACCTCAGGGAGATA
*
326887 AGATTTGCTTCTTCGTTCTGCCCCACTGTGACTTCAAGGGGATAAGACTTACTTTCTCAATCTAC
130 AGATTTGCTTCTTCGGTCTGCCCCACTGTGACTTCAAGGGGATAAGACTTACTTTCTCAATCTAC
*
326952 TCCGCTGCAACCTT-AGGGAGAT
195 TCCGCTACAA-CTTCAGGGAGAT
* *
326974 AAGACCTGATGCGATCCACTCTACTGCAACTTT-AGAGAGATAAGATCCATTACTTTAATCCGTT
1 AAGACCTGATGCGATCTACTCTACTGCAA-TTTCAGAGAGATAAGATCTATTACTTTAATCCGTT
* *
327038 CCACTACAACTTCAGGGAGATAGGATTATCGACTTCAATCTGCTCACTGCAACCTCAGAGAGATA
65 CCACTACAATTTCAGGGAGATAGGATTATCGACTTCAATCTGCTCACTGCAACCTCAGGGAGATA
327103 AGAT
130 AGAT
327107 CTGTAATTTC
Statistics
Matches: 317, Mismatches: 27, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
215 4 0.01
216 208 0.66
217 105 0.33
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (216 bp):
AAGACCTGATGCGATCTACTCTACTGCAATTTCAGAGAGATAAGATCTATTACTTTAATCCGTTC
CACTACAATTTCAGGGAGATAGGATTATCGACTTCAATCTGCTCACTGCAACCTCAGGGAGATAA
GATTTGCTTCTTCGGTCTGCCCCACTGTGACTTCAAGGGGATAAGACTTACTTTCTCAATCTACT
CCGCTACAACTTCAGGGAGAT
Found at i:327304 original size:129 final size:128
Alignment explanation
Indices: 327097--327400 Score: 466
Period size: 129 Copynumber: 2.4 Consensus size: 128
327087 CAACCTCAGA
* **
327097 GAGATAAGATCTGTAA-TTTCCAACCTATTCCACTGCTGACCAGGGAAATAGGACTTGTGGCTTA
1 GAGACAAGATCTGTAATTTTCCAACCTATTCCACTGCTG-TTAGGGAAATAGGACTTGTGGCTTA
* * *
327161 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCTTCTTCGATCTGCTCCACTACTGCTTAGG
65 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATATGCTCCACTACTACTTAGG
* *
327225 GAGACAAGATCTGTAATTTTCCAACCTATTCCACTGCTAGTTAGGGATATAGGGCTTGTGGCTTA
1 GAGACAAGATCTGTAATTTTCCAACCTATTCCACTGCT-GTTAGGGAAATAGGACTTGTGGCTTA
**
327290 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATATGCTCTGCTACTACTTAGG
65 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATATGCTCCACTACTACTTAGG
* *
327354 GAGACAAGATCTGTAATTTCCCAACCTATTCCACTTCTGGTTAGGGA
1 GAGACAAGATCTGTAATTTTCCAACCTATTCCACTGCT-GTTAGGGA
327401 GCTAGGTTTT
Statistics
Matches: 161, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
128 15 0.09
129 145 0.90
130 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (128 bp):
GAGACAAGATCTGTAATTTTCCAACCTATTCCACTGCTGTTAGGGAAATAGGACTTGTGGCTTAA
ATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATATGCTCCACTACTACTTAGG
Found at i:328733 original size:17 final size:17
Alignment explanation
Indices: 328711--328744 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
328701 TTAGCCTCTC
328711 CATTTTT-ACTTTTTCAT
1 CATTTTTCA-TTTTTCAT
328728 CATTTTTCATTTTTCAT
1 CATTTTTCATTTTTCAT
328745 TTTCATTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.94
18 1 0.06
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.65
Consensus pattern (17 bp):
CATTTTTCATTTTTCAT
Found at i:328737 original size:7 final size:7
Alignment explanation
Indices: 328727--328761 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
328717 TACTTTTTCA
328727 TCATTTT
1 TCATTTT
328734 TCATTTT
1 TCATTTT
328741 TCA-TTT
1 TCATTTT
328747 TCATTTT
1 TCATTTT
*
328754 CCATTTT
1 TCATTTT
328761 T
1 T
328762 TTTGACTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (7 bp):
TCATTTT
Found at i:328749 original size:13 final size:13
Alignment explanation
Indices: 328731--328760 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
328721 TTTTCATCAT
*
328731 TTTTCATTTTTCA
1 TTTTCATTTTCCA
328744 TTTTCATTTTCCA
1 TTTTCATTTTCCA
328757 TTTT
1 TTTT
328761 TTTTGACTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTCATTTTCCA
Found at i:338179 original size:69 final size:69
Alignment explanation
Indices: 338058--338320 Score: 274
Period size: 69 Copynumber: 3.8 Consensus size: 69
338048 GGGTATTACA
* * *** * * * * * *
338058 TTTGCTCTTGCTAACTGTTTTGGAGGTTATGGCTCTTCCCCTGCGAATCTTAACATTACAGTTGG
1 TTTGCTCTCGCTAACTGTTTTAGAGGTTGCAGCTCTTCGCTTGCGAACCTTAATATAACAGCTGG
338123 GAGC
66 GAGC
* * * ** * *
338127 TTTACTCTCGCTAACTGTTTTGGAGGTTGCGGCTCTTAACTTGTGAACCTTAATATAACAGCTAG
1 TTTGCTCTCGCTAACTGTTTTAGAGGTTGCAGCTCTTCGCTTGCGAACCTTAATATAACAGCTGG
*
338192 GAGT
66 GAGC
* * * * *
338196 TTTGCTCTCACTAACTATTTTAGAGGTTGCAGCTCTTCGCTTGCAAACCTTAATGTGACAGCTGG
1 TTTGCTCTCGCTAACTGTTTTAGAGGTTGCAGCTCTTCGCTTGCGAACCTTAATATAACAGCTGG
338261 GAGC
66 GAGC
* * * *
338265 TTTGCTCTCGCTAACTGTTTTAGAGGTTGCAACTTTTTGCTTGTGAACCTTAATAT
1 TTTGCTCTCGCTAACTGTTTTAGAGGTTGCAGCTCTTCGCTTGCGAACCTTAATAT
338321 CATAAGAATG
Statistics
Matches: 159, Mismatches: 35, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
69 159 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (69 bp):
TTTGCTCTCGCTAACTGTTTTAGAGGTTGCAGCTCTTCGCTTGCGAACCTTAATATAACAGCTGG
GAGC
Found at i:341656 original size:22 final size:23
Alignment explanation
Indices: 341626--341685 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 23
341616 TTTATTTGTA
*
341626 TTAATAATTTATTATATTATT-ATT
1 TTAA-AATTTATTATA-CATTAATT
*
341650 TT-AAATTTATCATACATTAATT
1 TTAAAATTTATTATACATTAATT
*
341672 TTAAAATTCATTAT
1 TTAAAATTTATTAT
341686 GTATTGCCAC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
21 3 0.10
22 15 0.50
23 10 0.33
24 2 0.07
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (23 bp):
TTAAAATTTATTATACATTAATT
Found at i:351613 original size:22 final size:22
Alignment explanation
Indices: 351587--351644 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
351577 ATATTTTCTG
351587 AAAAATTATAAAAAAAATACAA
1 AAAAATTATAAAAAAAATACAA
*
351609 AAAAATCTA-AAAAAAAATATAA
1 AAAAAT-TATAAAAAAAATACAA
* *
351631 AGAAAGT-TAAAAAA
1 AAAAATTATAAAAAA
351645 CTAAAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 7 0.23
22 22 0.71
23 2 0.06
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.17
Consensus pattern (22 bp):
AAAAATTATAAAAAAAATACAA
Found at i:357353 original size:41 final size:41
Alignment explanation
Indices: 357307--357413 Score: 180
Period size: 41 Copynumber: 2.6 Consensus size: 41
357297 CATTGAATGT
357307 AAGGGGTTGCTAAGTGCAGATTCCTCGAAC-CACTGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCTCG-ACTCACTGATCAAA
* *
357348 AAGGGGTTGCTAAGTGTAGATTCCCCGACTCACTGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCTCGACTCACTGATCAAA
357389 AAGGGGTTGCTAAGTGCAGATTCCT
1 AAGGGGTTGCTAAGTGCAGATTCCT
357414 TGAGGGGTTG
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
40 2 0.03
41 59 0.97
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (41 bp):
AAGGGGTTGCTAAGTGCAGATTCCTCGACTCACTGATCAAA
Found at i:357508 original size:43 final size:42
Alignment explanation
Indices: 357419--357556 Score: 127
Period size: 42 Copynumber: 3.3 Consensus size: 42
357409 TTCCTTGAGG
* * *** *
357419 GGTTGCTAAGTGCTGATTTCCTAAATTATTGATTCTAAAGGT
1 GGTTGCTAAGTGCTAATTCCCCGTATCATTGATTCTAAAGGT
*
357461 GGTTGCTAAGTGCTAATTCCACCGTATCATTGATTGTGAAAGG-
1 GGTTGCTAAGTGCTAATTCC-CCGTATCATTGATTCT-AAAGGT
* * * * * *
357504 GGTTGCTATGTGCTGATTCCCCGTATCACTGAATAT-AAGTT
1 GGTTGCTAAGTGCTAATTCCCCGTATCATTGATTCTAAAGGT
357545 GGTTGCTAAGTG
1 GGTTGCTAAGTG
357557 TTGATTCCAC
Statistics
Matches: 79, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
40 3 0.04
41 11 0.14
42 31 0.39
43 29 0.37
44 5 0.06
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (42 bp):
GGTTGCTAAGTGCTAATTCCCCGTATCATTGATTCTAAAGGT
Found at i:357562 original size:41 final size:42
Alignment explanation
Indices: 357454--357568 Score: 126
Period size: 43 Copynumber: 2.7 Consensus size: 42
357444 TTATTGATTC
* * * *
357454 TAAAGGTGGTTGCTAAGTGCTAATTCCACCGTATCATTGATTG
1 TAAA-GTGGTTGCTAAGTGCTGATTCCACCGTATCACTGAATA
* *
357497 TGAAAGGGGTTGCTATGTGCTGATTCC-CCGTATCACTGAATA
1 T-AAAGTGGTTGCTAAGTGCTGATTCCACCGTATCACTGAATA
*
357539 T-AAGTTGGTTGCTAAGTGTTGATTCCACCG
1 TAAAG-TGGTTGCTAAGTGCTGATTCCACCG
357569 AGTAACGGCT
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
40 3 0.05
41 18 0.30
42 16 0.27
43 20 0.33
44 3 0.05
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.34
Consensus pattern (42 bp):
TAAAGTGGTTGCTAAGTGCTGATTCCACCGTATCACTGAATA
Found at i:359800 original size:61 final size:58
Alignment explanation
Indices: 359734--359851 Score: 173
Period size: 61 Copynumber: 2.0 Consensus size: 58
359724 TAAAGTGATC
* *
359734 ATTTAATATGAAATTTAATTTAATATTTATCTTATAGATAAATATTCTATTAATTTAATAG
1 ATTTAATATGAAATTTAACTTAATATTTATC-T-T-GATAAATATTATATTAATTTAATAG
* *
359795 ATTTAATATTAAATTTAACTTAATATTTATCTTGATAAGTATTATATTAATTTAATA
1 ATTTAATATGAAATTTAACTTAATATTTATCTTGATAAATATTATATTAATTTAATA
359852 TTAAAGTGAT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 22 0.42
59 1 0.02
60 1 0.02
61 29 0.55
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.50
Consensus pattern (58 bp):
ATTTAATATGAAATTTAACTTAATATTTATCTTGATAAATATTATATTAATTTAATAG
Found at i:359864 original size:58 final size:60
Alignment explanation
Indices: 359738--359870 Score: 157
Period size: 58 Copynumber: 2.2 Consensus size: 60
359728 GTGATCATTT
* * * *
359738 AATATGAAATTTAATTTAATATTTATCTTATAGATAAATATTCTATTAATTTAATAGATTT
1 AATATTAAATTTAACTTAATATTTATCTTATAGATAAATATTATATTAATTTAATA-ATTA
*
359799 AATATTAAATTTAACTTAATATTTATC-T-T-GATAAGTATTATATTAATTTAAT-ATTA
1 AATATTAAATTTAACTTAATATTTATCTTATAGATAAATATTATATTAATTTAATAATTA
*
359855 AAGTGATTAAGTTTAA
1 AA-T-ATTAAATTTAA
359871 TTATAGTTGA
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
56 5 0.08
57 1 0.02
58 31 0.48
59 1 0.02
60 1 0.02
61 25 0.39
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (60 bp):
AATATTAAATTTAACTTAATATTTATCTTATAGATAAATATTATATTAATTTAATAATTA
Found at i:362445 original size:25 final size:25
Alignment explanation
Indices: 362416--362488 Score: 92
Period size: 25 Copynumber: 2.9 Consensus size: 25
362406 GCAAACCAAA
* * *
362416 TAAAGCCTTTGTGACGAGTTATCTG
1 TAAAGCCCTTGTGACAAATTATCTG
* *
362441 TAAAGCCCTTATGGCAAATTATCTG
1 TAAAGCCCTTGTGACAAATTATCTG
*
362466 TAAAGCCCTTGTGGCAAATTATC
1 TAAAGCCCTTGTGACAAATTATC
362489 CAAAAAGGCT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (25 bp):
TAAAGCCCTTGTGACAAATTATCTG
Found at i:362495 original size:25 final size:25
Alignment explanation
Indices: 362442--362495 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
362432 AGTTATCTGT
***
362442 AAAGCCCTTATGGCAAATTATCTGT
1 AAAGCCCTTATGGCAAATTATCCAA
*
362467 AAAGCCCTTGTGGCAAATTATCCAA
1 AAAGCCCTTATGGCAAATTATCCAA
362492 AAAG
1 AAAG
362496 GCTATGTGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (25 bp):
AAAGCCCTTATGGCAAATTATCCAA
Found at i:370820 original size:279 final size:280
Alignment explanation
Indices: 370197--370962 Score: 963
Period size: 279 Copynumber: 2.7 Consensus size: 280
370187 CTACGAACCT
* * * * *
370197 AGCATAAATGTTGGATCTGGTGCCTTGAGGGTAGTATATTTGT-TTGTAAACTTGTAATTTTTTC
1 AGCA-AAATGTTGGATCTGGTGCCCTAAGTGTAGTATTTTTGTCTTGTACACTTGTAATTTTTTC
* * **
370261 AAACAGATTAGTTAATAAAAAAATTCATTG-ATTACATTAATATACTTTGTATAATTGTCCTCAC
65 GAACAGATTGGTTAATAAAATTATTCA-TGAATTACATT-A-ATACTTTGTAT-ATTGTCCTCAC
* *
370325 ATAG-TTTTGCACT-CAAAGCAAAATGGAAGCAAATGTTGCTCATTGGTTGTCTAATGTTTAAAC
126 ATGGTTTTTGCA-TGCAAAGCAAAATAGAAGCAAATGTTGCTCATTGGTTGTCTAATGTTTAAAC
* * *
370388 TAATACTAAGTAGTATTACGTAGTCAGATCATAATACATAATGACAACTATATCAGCAGACAAAC
190 TAATACTAAGCAG--TTA-G-AGTCAGATCATAATACACAAAGACAACTATATCAGCAGACAAAC
* *
370453 CTAAACATATCCTTACTCTAATCGAAAATG
251 CTAAACACATACTTACTCTAATCGAAAATG
* * * *
370483 AGCAAACTATTGGATCTGGTGCCCTAAGTGTAGTATTTTCGTCTCTGTACAATTGTAATTTTTTC
1 AGCAAAATGTTGGATCTGGTGCCCTAAGTGTAGTATTTTTGTCT-TGTACACTTGTAATTTTTTC
* * * *
370548 GAATAGATTGGTCAATAAAATTATTCATGAATTACATTAATACTATGTATATTTTCCTCACATGG
65 GAACAGATTGGTTAATAAAATTATTCATGAATTACATTAATACTTTGTATATTGTCCTCACATGG
* *
370613 TTTTTTCATGCAATGCAAAATAGAAGCAAATGTTGCTCATTGGTTGTCTAATGTTTAAACTAATA
130 TTTTTGCATGCAAAGCAAAATAGAAGCAAATGTTGCTCATTGGTTGTCTAATGTTTAAACTAATA
** ** * * *
370678 CTAAGCAG-T-G-GTTGGATTGTAATACGCAAAGACAACTTATATTAGTAGACAAACCTAAACAC
195 CTAAGCAGTTAGAGTCAGATCATAATACACAAAGACAAC-TATATCAGCAGACAAACCTAAACAC
*
370740 ATACTTAGTCTAATCGAAAATG
259 ATACTTACTCTAATCGAAAATG
* *
370762 AGCAAAATGTTGGATTTGGTGCCCTAAGTGTAGTATTTTTGTCTAAGTACACTTGTAATTTTTTC
1 AGCAAAATGTTGGATCTGGTGCCCTAAGTGTAGTATTTTTGTCT-TGTACACTTGTAATTTTTTC
* * *
370827 GAACAGATTGGTTAATACAATTATTCATGAATTACATTAATACTTTGCATATTGCCCTCACATGG
65 GAACAGATTGGTTAATAAAATTATTCATGAATTACATTAATACTTTGTATATTGTCCTCACATGG
** * * *
370892 TTTTTGCATG-AAAAAAAAATAGAAGAAAATGTTGCTTATTGGTTATCTAATGTTTAAACTAATA
130 TTTTTGCATGCAAAGCAAAATAGAAGCAAATGTTGCTCATTGGTTGTCTAATGTTTAAACTAATA
370956 CTAAGCA
195 CTAAGCA
370963 CTATTATGAG
Statistics
Matches: 419, Mismatches: 55, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
278 74 0.18
279 167 0.40
280 1 0.00
282 1 0.00
284 14 0.03
285 107 0.26
286 8 0.02
287 47 0.11
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (280 bp):
AGCAAAATGTTGGATCTGGTGCCCTAAGTGTAGTATTTTTGTCTTGTACACTTGTAATTTTTTCG
AACAGATTGGTTAATAAAATTATTCATGAATTACATTAATACTTTGTATATTGTCCTCACATGGT
TTTTGCATGCAAAGCAAAATAGAAGCAAATGTTGCTCATTGGTTGTCTAATGTTTAAACTAATAC
TAAGCAGTTAGAGTCAGATCATAATACACAAAGACAACTATATCAGCAGACAAACCTAAACACAT
ACTTACTCTAATCGAAAATG
Found at i:374274 original size:34 final size:34
Alignment explanation
Indices: 374230--374297 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
374220 GCACAGTTGA
* *
374230 ACAGTCTTGGGCCTAAGCCCTTTTCAGTATCAGTG
1 ACAGTCTTGGGCCTAAGCCCATCTCAGTA-CAGTG
*
374265 ACAGT-TTGGGCCTTAGCCCATCTCAGTACAGTG
1 ACAGTCTTGGGCCTAAGCCCATCTCAGTACAGTG
374298 TCAAAAATGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 5 0.17
34 20 0.67
35 5 0.17
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (34 bp):
ACAGTCTTGGGCCTAAGCCCATCTCAGTACAGTG
Found at i:376160 original size:20 final size:20
Alignment explanation
Indices: 376135--376172 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
376125 AAAGGTTAAC
376135 TTAGTAAAATAATAATAATG
1 TTAGTAAAATAATAATAATG
* *
376155 TTAGTATAATGATAATAA
1 TTAGTAAAATAATAATAA
376173 AATAAAACAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.37
Consensus pattern (20 bp):
TTAGTAAAATAATAATAATG
Found at i:377129 original size:37 final size:38
Alignment explanation
Indices: 377038--377131 Score: 127
Period size: 37 Copynumber: 2.4 Consensus size: 38
377028 CTATATGATT
* * *
377038 AGCACTAAGTATGCGAATTAAATGATGAGGTTGAATAGTG
1 AGCACTAAGTGTGCGAATTAAATGAT--GGTTAAATAATG
377078 AGCACTAAGTGTGCGAATTAAATGAT-GTTAAATAATG
1 AGCACTAAGTGTGCGAATTAAATGATGGTTAAATAATG
*
377115 GGCACTAAGTGTGCGAA
1 AGCACTAAGTGTGCGAA
377132 ACCGAGGTCA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
37 25 0.50
40 25 0.50
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.27
Consensus pattern (38 bp):
AGCACTAAGTGTGCGAATTAAATGATGGTTAAATAATG
Found at i:378140 original size:70 final size:70
Alignment explanation
Indices: 378055--378338 Score: 334
Period size: 70 Copynumber: 4.0 Consensus size: 70
378045 TGGTGTAAAA
* * * * * * *
378055 ATGCTGCCGATTTTGGTGTCTATATGCTGTCCAATTTCGGTATAAAAATGCTGTCCAATTTGATA
1 ATGCTGCCCAATTTGGTGTATATATGCTGTCAAATTTTGGTGTAAAAATGTTGTCCAATTTGATA
378120 TATAT
66 TATAT
* * * *
378125 ATGCTGCCCAATTTGGTGTATATATACTGTCAAATTTTGATGTAAAAATATTGTCAAAATTGATA
1 ATGCTGCCCAATTTGGTGTATATATGCTGTCAAATTTTGGTGTAAAAATGTTGTC-CAATT--T-
*
378190 TATATATAT
62 GATATATAT
* * *
378199 ATGCTGCCCAATTTGGTGTATATATGCTCTCAAATTTTGGTGTAAAAAATGTTGTTCAATTTTAT
1 ATGCTGCCCAATTTGGTGTATATATGCTGTCAAATTTTGGTGT-AAAAATGTTGTCCAATTTGAT
378264 ATATAT
65 ATATAT
** * * * *
378270 ATGCTGCCCAATTTATTGTATAAATGCTGTCCAATTTTGGTGTATAAATGTTGTCCAATTTGATG
1 ATGCTGCCCAATTTGGTGTATATATGCTGTCAAATTTTGGTGTAAAAATGTTGTCCAATTTGATA
378335 TATA
66 TATA
378339 AGAGTTGTCC
Statistics
Matches: 182, Mismatches: 27, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
70 67 0.37
71 51 0.28
72 1 0.01
73 1 0.01
74 52 0.29
75 10 0.05
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (70 bp):
ATGCTGCCCAATTTGGTGTATATATGCTGTCAAATTTTGGTGTAAAAATGTTGTCCAATTTGATA
TATAT
Found at i:378220 original size:74 final size:72
Alignment explanation
Indices: 378055--378338 Score: 308
Period size: 74 Copynumber: 3.9 Consensus size: 72
378045 TGGTGTAAAA
* * * * * * * * *
378055 ATGCTGCCGATTTTGGTGTCTATATGCTGTCCAATTTCGGTATAAAAATGCTGTCCAATT--TGA
1 ATGCTGCCCAATTTGGTGTATATATGCTGTCAAATTTTGGTGTAAAAATGTTGTCAAATTGATTA
378118 TATATAT
66 TATATAT
* * *
378125 ATGCTGCCCAATTTGGTGTATATATACTGTCAAATTTTGATGTAAAAATATTGTCAAAATTGATA
1 ATGCTGCCCAATTTGGTGTATATATGCTGTCAAATTTTGGTGTAAAAATGTTGTC-AAATTGAT-
378190 TATATATAT
64 TATATATAT
*
378199 ATGCTGCCCAATTTGGTGTATATATGCTCTCAAATTTTGGTGTAAAAAATGTTGTTC-AATT--T
1 ATGCTGCCCAATTTGGTGTATATATGCTGTCAAATTTTGGTGT-AAAAATGTTG-TCAAATTGAT
378261 TATATATAT
64 TATATATAT
** * * * *
378270 ATGCTGCCCAATTTATTGTATAAATGCTGTCCAATTTTGGTGTATAAATGTTGTCCAATTTGATG
1 ATGCTGCCCAATTTGGTGTATATATGCTGTCAAATTTTGGTGTAAAAATGTTGT-CAAATTGAT-
378335 TATA
64 TATA
378339 AGAGTTGTCC
Statistics
Matches: 180, Mismatches: 23, Indels: 18
0.81 0.10 0.08
Matches are distributed among these distances:
69 1 0.01
70 55 0.31
71 54 0.30
72 1 0.01
73 2 0.01
74 56 0.31
75 9 0.05
76 2 0.01
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (72 bp):
ATGCTGCCCAATTTGGTGTATATATGCTGTCAAATTTTGGTGTAAAAATGTTGTCAAATTGATTA
TATATAT
Found at i:378290 original size:145 final size:144
Alignment explanation
Indices: 378055--378338 Score: 370
Period size: 145 Copynumber: 2.0 Consensus size: 144
378045 TGGTGTAAAA
* * * * *
378055 ATGCTGCCGATTTTGGTGTCTATATGCTGTCCAATTTCGGTATAAAAATGCTGTCCAATTTGATA
1 ATGCTGCCCAATTTGGTGTATATATGCTCTCAAATTTCGGTATAAAAATGCTGTCCAATTTGATA
* *
378120 TATATATGCTGCCCAATTTGGTGTATATATACTGTCAAATTTTGATGTAAAAATATTGTCAAAAT
66 TATATATGCTGCCCAATTTAGTGTATAAATACTGTCAAATTTTGATGTAAAAATATTGTCAAAAT
378185 TGATATATATATAT
131 TGATATATATATAT
* * * * *
378199 ATGCTGCCCAATTTGGTGTATATATGCTCTCAAATTTTGGTGTAAAAAATGTTGTTCAATTTTAT
1 ATGCTGCCCAATTTGGTGTATATATGCTCTCAAATTTCGGTAT-AAAAATGCTGTCCAATTTGAT
* * * * * * * *
378264 ATATATATGCTGCCCAATTTATTGTATAAATGCTGTCCAATTTTGGTGTATAAATGTTGTCCAAT
65 ATATATATGCTGCCCAATTTAGTGTATAAATACTGTCAAATTTTGATGTAAAAATATTGTCAAAA
*
378329 TTGATGTATA
130 TTGATATATA
378339 AGAGTTGTCC
Statistics
Matches: 118, Mismatches: 21, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
144 36 0.31
145 82 0.69
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (144 bp):
ATGCTGCCCAATTTGGTGTATATATGCTCTCAAATTTCGGTATAAAAATGCTGTCCAATTTGATA
TATATATGCTGCCCAATTTAGTGTATAAATACTGTCAAATTTTGATGTAAAAATATTGTCAAAAT
TGATATATATATAT
Found at i:378336 original size:23 final size:23
Alignment explanation
Indices: 378034--378339 Score: 157
Period size: 23 Copynumber: 12.9 Consensus size: 23
378024 TGTCTATATT
* *
378034 CTGTCCAATTTTGGTGTAAAAATG
1 CTGTCCAA-TTTGATGTATAAATG
* * * *
378058 CTG-CCGATTTTGGTGTCTATATG
1 CTGTCC-AATTTGATGTATAAATG
* * *
378081 CTGTCCAATTTCGGTATAAAAATG
1 CTGTCCAATTT-GATGTATAAATG
* *
378105 CTGTCCAATTTGATATATATATG
1 CTGTCCAATTTGATGTATAAATG
* * * *
378128 CTGCCCAATTTGGTGTATATATA
1 CTGTCCAATTTGATGTATAAATG
* * *
378151 CTGTCAAATTTTGATGTAAAAATA
1 CTGTCCAA-TTTGATGTATAAATG
* * * *
378175 TTGTCAAAATTGATATATATATATATG
1 CTGTCCAATTTG--ATGTATA-A-ATG
* * *
378202 CTGCCCAATTTGGTGTATATATG
1 CTGTCCAATTTGATGTATAAATG
* * * *
378225 CTCTCAAATTTTGGTGTAAAAAATG
1 CTGTCCAA-TTTGATGT-ATAAATG
* * * * *
378250 TTGTTCAATTTTATATATATATG
1 CTGTCCAATTTGATGTATAAATG
*
378273 CTGCCCAATTT-ATTGTATAAATG
1 CTGTCCAATTTGA-TGTATAAATG
*
378296 CTGTCCAATTTTGGTGTATAAATG
1 CTGTCCAA-TTTGATGTATAAATG
*
378320 TTGTCCAATTTGATGTATAA
1 CTGTCCAATTTGATGTATAA
378340 GAGTTGTCCA
Statistics
Matches: 213, Mismatches: 56, Indels: 27
0.72 0.19 0.09
Matches are distributed among these distances:
22 1 0.00
23 105 0.49
24 77 0.36
25 19 0.09
26 1 0.00
27 10 0.05
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.41
Consensus pattern (23 bp):
CTGTCCAATTTGATGTATAAATG
Found at i:378337 original size:47 final size:47
Alignment explanation
Indices: 378028--378339 Score: 209
Period size: 47 Copynumber: 6.6 Consensus size: 47
378018 ATTCGGTGTC
* * * * *
378028 TATATTCTGTCCAATTTTGGTGTAAAAATGCTG-CCGATTTTGGTGTC
1 TATATGCTGTCCAA-TTTGGTGTATAAATGCTGTCCAATTTTGATGTA
* * *
378075 TATATGCTGTCCAATTTCGGTATAAAAATGCTGTCCAA-TTTGATATA
1 TATATGCTGTCCAATTT-GGTGTATAAATGCTGTCCAATTTTGATGTA
* * * *
378122 TATATGCTGCCCAATTTGGTGTATATATACTGTCAAATTTTGATGTA
1 TATATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTTGATGTA
* * ** * * * * * *
378169 AAAATATTGTCAAAATTGATATATATATATATGCTGCCCAA-TTTGGTGTA
1 TATATGCTGTCCAATTTG--GTGTATA-A-ATGCTGTCCAATTTTGATGTA
* * * * * *
378219 TATATGCTCTCAAATTTTGGTGTAAAAAATGTTGTTCAATTTT-ATATA
1 TATATGCTGTCCAA-TTTGGTGT-ATAAATGCTGTCCAATTTTGATGTA
* ** *
378267 TATATGCTGCCCAATTTATTGTATAAATGCTGTCCAATTTTGGTGTA
1 TATATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTTGATGTA
* * *
378314 TAAATGTTGTCCAATTTGATGTATAA
1 TATATGCTGTCCAATTTGGTGTATAA
378340 GAGTTGTCCA
Statistics
Matches: 198, Mismatches: 56, Indels: 22
0.72 0.20 0.08
Matches are distributed among these distances:
46 34 0.17
47 98 0.49
48 25 0.13
49 11 0.06
50 19 0.10
51 11 0.06
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (47 bp):
TATATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTTGATGTA
Found at i:381519 original size:5 final size:5
Alignment explanation
Indices: 381509--381537 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
381499 AGCTTTTGGT
381509 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
381538 TCTCTCTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:381756 original size:34 final size:35
Alignment explanation
Indices: 381694--381776 Score: 114
Period size: 35 Copynumber: 2.4 Consensus size: 35
381684 TAGCCCTTGG
* *
381694 TTCTTTCCTCTTTTCTTTGTGGCCGAATATTGCCT
1 TTCTTTCCTCTTCTCTTTGTGGCCGAATACTGCCT
*
381729 TTCTTTCTTCTTCTCTTT-TGGCCGAATACTGCCT
1 TTCTTTCCTCTTCTCTTTGTGGCCGAATACTGCCT
*
381763 TTCTCTCCCTCTTC
1 TTCT-TTCCTCTTC
381777 ATCTATTCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
34 19 0.45
35 23 0.55
ACGTcount: A:0.07, C:0.31, G:0.11, T:0.51
Consensus pattern (35 bp):
TTCTTTCCTCTTCTCTTTGTGGCCGAATACTGCCT
Found at i:382800 original size:27 final size:27
Alignment explanation
Indices: 382406--382792 Score: 431
Period size: 27 Copynumber: 14.3 Consensus size: 27
382396 TAATGGGCCT
* **
382406 AAATAACCGAAATACCCTTAAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
382433 AAATGACCGAAATA-CCTCCGAAGGATA
1 AAATGACCGAAATACCCT-CGAAGGGTA
*
382460 AAATGACTGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* * ** *
382487 AAATAACCAAAATACCCTTAAAAGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* **
382514 AAATGACTGAAATACCCTTAAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
382541 AAATGGCCGAAATACCC-CTGAAGGGTA
1 AAATGACCGAAATACCCTC-GAAGGGTA
382568 AAATGACCGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* * **
382595 AAAGGACCAAAATACATTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* * *
382622 AAATGATCGAAATACCCCCCGAGGGGTA
1 AAATGACCGAAATA-CCCTCGAAGGGTA
* *
382650 AAATGATCGAAATACGCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* * *
382677 AAATGATCGAAATACCTTCAAAGGGT-
1 AAATGACCGAAATACCCTCGAAGGGTA
* * *
382703 AAAGGATCGAAATACCC-CCAATGGGTA
1 AAATGACCGAAATACCCTCGAA-GGGTA
*
382730 AAATGACCGAAATACCCCCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
382757 AAATGACTGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
382784 AAATGACCG
1 AAATGACCG
382793 TTATACCCCT
Statistics
Matches: 305, Mismatches: 47, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
25 3 0.01
26 22 0.07
27 250 0.82
28 30 0.10
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.17
Consensus pattern (27 bp):
AAATGACCGAAATACCCTCGAAGGGTA
Found at i:382996 original size:26 final size:26
Alignment explanation
Indices: 382967--383037 Score: 106
Period size: 26 Copynumber: 2.7 Consensus size: 26
382957 TTGCCACATA
* * *
382967 TACTGTTACTGGCAGCTTTGCTTCGT
1 TACTATTACTGGCAGCTTTGCTGCAT
382993 TACTATTACTGGCAGCTTTGCTGCAT
1 TACTATTACTGGCAGCTTTGCTGCAT
*
383019 CACTATTACTGGCAGCTTT
1 TACTATTACTGGCAGCTTT
383038 ACCGCGATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (26 bp):
TACTATTACTGGCAGCTTTGCTGCAT
Found at i:385622 original size:26 final size:26
Alignment explanation
Indices: 385599--385659 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
385589 TACCTATAGT
385599 AGTTTCAGAATATCATAACATATATC
1 AGTTTCAGAATATCATAACATATATC
* *
385625 AGTTTCAGAATATCATAGCATGTATC
1 AGTTTCAGAATATCATAACATATATC
385651 AGTTTCAGA
1 AGTTTCAGA
385660 GCACTTACAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (26 bp):
AGTTTCAGAATATCATAACATATATC
Found at i:385810 original size:26 final size:26
Alignment explanation
Indices: 385781--385838 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
385771 AGCCGAGTTT
385781 TGTAACCTGGCTCTGATACTACTAAA
1 TGTAACCTGGCTCTGATACTACTAAA
385807 TGTAACCTGGCTCTGATACTACTAAA
1 TGTAACCTGGCTCTGATACTACTAAA
385833 TGTAAC
1 TGTAAC
385839 ACCCTAAACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (26 bp):
TGTAACCTGGCTCTGATACTACTAAA
Found at i:394435 original size:13 final size:13
Alignment explanation
Indices: 394414--394464 Score: 68
Period size: 13 Copynumber: 4.0 Consensus size: 13
394404 AAAATTATAA
394414 ATTTTATTTTTTT
1 ATTTTATTTTTTT
* *
394427 ATTTCATTTTTAT
1 ATTTTATTTTTTT
*
394440 -TTTTATTTTTGT
1 ATTTTATTTTTTT
394452 ATTTTATTTTTTT
1 ATTTTATTTTTTT
394465 CTTATAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
12 10 0.31
13 22 0.69
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (13 bp):
ATTTTATTTTTTT
Found at i:394439 original size:19 final size:18
Alignment explanation
Indices: 394414--394470 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
394404 AAAATTATAA
394414 ATTTTATTTTTTTATTTCAT
1 ATTTTATTTTTTT-TTT-AT
*
394434 -TTTTATTTTTATTTTTGT
1 ATTTTATTTTT-TTTTTAT
*
394452 ATTTTATTTTTTTCTTAT
1 ATTTTATTTTTTTTTTAT
394470 A
1 A
394471 ATTTGGTCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
18 7 0.22
19 23 0.72
20 2 0.06
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.77
Consensus pattern (18 bp):
ATTTTATTTTTTTTTTAT
Found at i:394444 original size:25 final size:25
Alignment explanation
Indices: 394415--394462 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
394405 AAATTATAAA
*
394415 TTTTATTTTTTTATTTCATTTTTAT
1 TTTTATTTTTGTATTTCATTTTTAT
*
394440 TTTTATTTTTGTATTTTATTTTT
1 TTTTATTTTTGTATTTCATTTTT
394463 TTCTTATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.81
Consensus pattern (25 bp):
TTTTATTTTTGTATTTCATTTTTAT
Found at i:394474 original size:19 final size:20
Alignment explanation
Indices: 394407--394471 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 20
394397 AATTAGAAAA
394407 ATTATAAATTTTATTTTTTT
1 ATTATAAATTTTATTTTTTT
* *
394427 ATT-TCATTTTTATTTTTATT
1 ATTATAAATTTTATTTTT-TT
**
394447 -TT-TGTATTTTATTTTTTT
1 ATTATAAATTTTATTTTTTT
*
394465 CTTATAA
1 ATTATAA
394472 TTTGGTCCTA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
18 2 0.06
19 27 0.77
20 6 0.17
ACGTcount: A:0.23, C:0.03, G:0.02, T:0.72
Consensus pattern (20 bp):
ATTATAAATTTTATTTTTTT
Found at i:395184 original size:30 final size:30
Alignment explanation
Indices: 395132--395211 Score: 105
Period size: 30 Copynumber: 2.8 Consensus size: 30
395122 ACCCATGAAA
*
395132 CCCTAAA-CTCTAAATCCTTAACTCTTAAC
1 CCCTAAACCCCTAAATCCTTAACTCTTAAC
395161 CCCTAAACCCCTAAA-CCTCTAACTCTTAAC
1 CCCTAAACCCCTAAATCCT-TAACTCTTAAC
*
395191 CCCTAAA-CCTTAAAT-CTTAAC
1 CCCTAAACCCCTAAATCCTTAAC
395212 CCGAACCTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
28 4 0.09
29 18 0.39
30 24 0.52
ACGTcount: A:0.35, C:0.38, G:0.00, T:0.28
Consensus pattern (30 bp):
CCCTAAACCCCTAAATCCTTAACTCTTAAC
Found at i:395191 original size:22 final size:21
Alignment explanation
Indices: 395166--395213 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 21
395156 TTAACCCCTA
*
395166 AACCCCTAAACCTCTAACTCTT
1 AACCCCTAAACCT-TAAATCTT
395188 AACCCCTAAACCTTAAATCTT
1 AACCCCTAAACCTTAAATCTT
395209 AACCC
1 AACCC
395214 GAACCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.35, C:0.40, G:0.00, T:0.25
Consensus pattern (21 bp):
AACCCCTAAACCTTAAATCTT
Found at i:395356 original size:15 final size:16
Alignment explanation
Indices: 395330--395361 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
395320 CCTAACATCT
395330 AACCCTTAAATCCATA
1 AACCCTTAAATCCATA
395346 AACCC-TAAATCCATA
1 AACCCTTAAATCCATA
395361 A
1 A
395362 CTGATCTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (16 bp):
AACCCTTAAATCCATA
Found at i:395385 original size:7 final size:7
Alignment explanation
Indices: 395369--395402 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
395359 TAACTGATCT
*
395369 TAACCTC
1 TAACCCC
395376 TAACCCC
1 TAACCCC
395383 TAACCCC
1 TAACCCC
*
395390 TAGCCCC
1 TAACCCC
395397 TAACCC
1 TAACCC
395403 ATAAACCTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.53, G:0.03, T:0.18
Consensus pattern (7 bp):
TAACCCC
Found at i:396204 original size:41 final size:41
Alignment explanation
Indices: 396142--396300 Score: 264
Period size: 41 Copynumber: 3.9 Consensus size: 41
396132 TTTTATTATT
*
396142 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCAGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
* * ** *
396183 ATTAGCGGCGCTTTTTTAAAAACGCCGCTAAAGATCTGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
396224 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
396265 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCC
396301 CCAAAAACTC
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 109 1.00
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (41 bp):
ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
Found at i:396461 original size:40 final size:40
Alignment explanation
Indices: 396337--396471 Score: 107
Period size: 40 Copynumber: 3.4 Consensus size: 40
396327 TGGCTTAGGC
* *
396337 TTTTT-GCGGCGCTTTTCA-AAAAACGCCGCTAATGCT-TA
1 TTTTTAGCGGCG-TTTTTATAAAAGCGCCGCTAATGCTCTA
* ** * * *
396375 TTTTTAGCAGCGTTTTCGGT-GAAGCGTCGCTAATTCTCTA
1 TTTTTAGCGGCGTTTT-TATAAAAGCGCCGCTAATGCTCTA
** *
396415 CCTTTAGCGGCGTTTTTATAAAAGCGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTATAAAAGCGCCGCTAATGCTCTA
* *
396455 TTTTTAGTGGTGTTTTT
1 TTTTTAGCGGCGTTTTT
396472 TTGTCCAAGC
Statistics
Matches: 72, Mismatches: 20, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
38 9 0.12
39 19 0.26
40 44 0.61
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.39
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTATAAAAGCGCCGCTAATGCTCTA
Found at i:399496 original size:14 final size:14
Alignment explanation
Indices: 399479--399505 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
399469 ATATTTATAA
399479 TTTGAAAACTTAAG
1 TTTGAAAACTTAAG
399493 TTTGAAAACTTAA
1 TTTGAAAACTTAA
399506 TTTAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.37
Consensus pattern (14 bp):
TTTGAAAACTTAAG
Found at i:399832 original size:34 final size:34
Alignment explanation
Indices: 399784--399960 Score: 212
Period size: 34 Copynumber: 5.2 Consensus size: 34
399774 TTTCTTGTCT
*
399784 TTTCTTGCAGGGAATATTTCCTGTTCACACATCA
1 TTTCTTGCAGGGAATCTTTCCTGTTCACACATCA
* *
399818 TTTCTTGCAAGGAATCTTTCCTGTTCACGCATCA
1 TTTCTTGCAGGGAATCTTTCCTGTTCACACATCA
* * * *
399852 TTTCTTGCAGGGAATCTTT-CTTTCTCACCTCGTCT
1 TTTCTTGCAGGGAATCTTTCCTGT-TCA-CACATCA
* **
399887 TTTCTTGCAGGGAATTTTTCCTGTTCATGCATCA
1 TTTCTTGCAGGGAATCTTTCCTGTTCACACATCA
* * *
399921 TTCCTTGCAGGGAATCTTTCCTATTCACACATCT
1 TTTCTTGCAGGGAATCTTTCCTGTTCACACATCA
399955 TTTCTT
1 TTTCTT
399961 ACATCATTTC
Statistics
Matches: 119, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
33 3 0.03
34 88 0.74
35 25 0.21
36 3 0.03
ACGTcount: A:0.18, C:0.25, G:0.14, T:0.42
Consensus pattern (34 bp):
TTTCTTGCAGGGAATCTTTCCTGTTCACACATCA
Found at i:399907 original size:69 final size:67
Alignment explanation
Indices: 399784--399960 Score: 219
Period size: 69 Copynumber: 2.6 Consensus size: 67
399774 TTTCTTGTCT
*
399784 TTTCTTGCAGGGAATATTTCCTGTTCACACATCATTTCTTGCAAGGAATCTTTCCTGTTCACGCA
1 TTTCTTGCAGGGAATCTTT-CTGTTCACACATCATTTCTTGCAAGGAATCTTTCCTGTTCACGCA
399849 TCA
65 TCA
* * * * * * *
399852 TTTCTTGCAGGGAATCTTTCTTTCTCACCTCGTCTTTTCTTGCAGGGAATTTTTCCTGTTCATGC
1 TTTCTTGCAGGGAATCTTTCTGT-TCA-CACATCATTTCTTGCAAGGAATCTTTCCTGTTCACGC
399917 ATCA
64 ATCA
* * *
399921 TTCCTTGCAGGGAATCTTTCCTATTCACACATCTTTTCTT
1 TTTCTTGCAGGGAATCTTT-CTGTTCACACATCATTTCTT
399961 ACATCATTTC
Statistics
Matches: 94, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
67 3 0.03
68 32 0.34
69 56 0.60
70 3 0.03
ACGTcount: A:0.18, C:0.25, G:0.14, T:0.42
Consensus pattern (67 bp):
TTTCTTGCAGGGAATCTTTCTGTTCACACATCATTTCTTGCAAGGAATCTTTCCTGTTCACGCAT
CA
Found at i:402096 original size:12 final size:13
Alignment explanation
Indices: 402064--402102 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
402054 GATAATATAA
* *
402064 TGTTAGAAAAATT
1 TGTTATAAATATT
402077 TGTTATAAATATT
1 TGTTATAAATATT
402090 T-TTATAAATATT
1 TGTTATAAATATT
402102 T
1 T
402103 ACGAAGTGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (13 bp):
TGTTATAAATATT
Found at i:403287 original size:87 final size:86
Alignment explanation
Indices: 403138--403387 Score: 304
Period size: 87 Copynumber: 2.9 Consensus size: 86
403128 ATCGGCGATC
* * * * * *
403138 ATCGATTATGAAAAGGGATGGTGACAACCATCAACTATGAAAAGGGATAGCTTTGGCTATCAATT
1 ATCGATTATGAAAAGGGATGGTGACGACCATCAACTATGAAAAGGGAT-GGTATGACCATCAAAT
*
403203 ATGAAAAGGGATAGCTT-TGACT
65 ATGAAAAGGGATAGCTTCAG-CT
*
403225 ATCGATTATGAAAAGGGATAGTGACGACCATCAACTATGAAAAGGGATGGTGATGACCATCAAAT
1 ATCGATTATGAAAAGGGATGGTGACGACCATCAACTATGAAAAGGGATGGT-ATGACCATCAAAT
403290 ATGAAAAGGGATAGCTTCAGCT
65 ATGAAAAGGGATAGCTTCAGCT
** * * * * * * *
403312 ATCGATTATGAAAAGGGATGGTTTCGGCCATCGATTATGAAAAGGGATGGTTTCTACCGTCGAAT
1 ATCGATTATGAAAAGGGATGGTGACGACCATCAACTATGAAAAGGGATGGTAT-GACCATCAAAT
403377 ATGAAAAGGGA
65 ATGAAAAGGGA
403388 CGGTTACGAC
Statistics
Matches: 142, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
86 3 0.02
87 138 0.97
88 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.25
Consensus pattern (86 bp):
ATCGATTATGAAAAGGGATGGTGACGACCATCAACTATGAAAAGGGATGGTATGACCATCAAATA
TGAAAAGGGATAGCTTCAGCT
Found at i:403360 original size:29 final size:29
Alignment explanation
Indices: 403137--403400 Score: 212
Period size: 29 Copynumber: 9.1 Consensus size: 29
403127 TATCGGCGAT
** *
403137 CATCGATTATGAAAAGGGATGGTGACAAC
1 CATCGATTATGAAAAGGGATGGTTTCGAC
* * * *
403166 CATCAACTATGAAAAGGGATAGCTTT-GGC
1 CATCGATTATGAAAAGGGAT-GGTTTCGAC
* * *
403195 TATCAATTATGAAAAGGGATAGCTTT-GAC
1 CATCGATTATGAAAAGGGAT-GGTTTCGAC
* * **
403224 TATCGATTATGAAAAGGGATAGTGACGAC
1 CATCGATTATGAAAAGGGATGGTTTCGAC
* * *
403253 CATCAACTATGAAAAGGGATGGTGAT-GAC
1 CATCGATTATGAAAAGGGATGGT-TTCGAC
* * * *
403282 CATCAAATATGAAAAGGGATAGCTTC-AGC
1 CATCGATTATGAAAAGGGATGGTTTCGA-C
* *
403311 TATCGATTATGAAAAGGGATGGTTTCGGC
1 CATCGATTATGAAAAGGGATGGTTTCGAC
*
403340 CATCGATTATGAAAAGGGATGGTTTCTAC
1 CATCGATTATGAAAAGGGATGGTTTCGAC
* * * *
403369 CGTCGAATATGAAAAGGGACGGTTACGAC
1 CATCGATTATGAAAAGGGATGGTTTCGAC
403398 CAT
1 CAT
403401 TGTTTAGCAC
Statistics
Matches: 189, Mismatches: 40, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
28 3 0.02
29 184 0.97
30 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.25
Consensus pattern (29 bp):
CATCGATTATGAAAAGGGATGGTTTCGAC
Found at i:407181 original size:57 final size:57
Alignment explanation
Indices: 407094--407205 Score: 165
Period size: 57 Copynumber: 1.9 Consensus size: 57
407084 AAAAATGATG
* *
407094 AAATGGAGAAATAGGAAACATTTGGAAATGATTATGGTTTTCT-CCTAAATGAAAAAAA
1 AAATGGAGAAATA-GAAACATTTGGAAATGAATATGGTTTT-TGCCAAAATGAAAAAAA
407152 AAATGGAGAAATA-AAATCATTTGGAAATGAATATGGTTTTTGCCAAAATGAAAA
1 AAATGGAGAAATAGAAA-CATTTGGAAATGAATATGGTTTTTGCCAAAATGAAAA
407206 TGACCTAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
56 4 0.08
57 33 0.66
58 13 0.26
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (57 bp):
AAATGGAGAAATAGAAACATTTGGAAATGAATATGGTTTTTGCCAAAATGAAAAAAA
Found at i:409035 original size:3 final size:3
Alignment explanation
Indices: 409027--409062 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
409017 AATTAAATGA
409027 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
409063 TATTCATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:416140 original size:38 final size:36
Alignment explanation
Indices: 416084--416158 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 36
416074 AAAAAATACA
* * *
416084 TAAATCACCGGTATATCTAATGTTTTTCTGTGTCATTT
1 TAAATCACCAGTAAATCTAATATTTTT-T-TGTCATTT
416122 TAAATCACCAGTAAATCTAATATTTTTTTGTCATTT
1 TAAATCACCAGTAAATCTAATATTTTTTTGTCATTT
416158 T
1 T
416159 TTTAATTAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
36 9 0.26
37 1 0.03
38 24 0.71
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.48
Consensus pattern (36 bp):
TAAATCACCAGTAAATCTAATATTTTTTTGTCATTT
Found at i:416461 original size:3 final size:3
Alignment explanation
Indices: 416455--416494 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
416445 GTTGTTGTTT
416455 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
416495 GGAGCAAGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:417010 original size:18 final size:16
Alignment explanation
Indices: 416978--417012 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
416968 TAATAAATAG
416978 AACAAAGAACAAAAGA
1 AACAAAGAACAAAAGA
416994 AACAGAAGAAGCAAAAGA
1 AACA-AAGAA-CAAAAGA
417012 A
1 A
417013 CTATAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 5 0.29
18 8 0.47
ACGTcount: A:0.71, C:0.11, G:0.17, T:0.00
Consensus pattern (16 bp):
AACAAAGAACAAAAGA
Found at i:418606 original size:3 final size:3
Alignment explanation
Indices: 418598--418626 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
418588 ATAATGGGAA
418598 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
418627 AGCCACTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:418844 original size:24 final size:24
Alignment explanation
Indices: 418816--418867 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
418806 TTCCTAGAAG
* *
418816 ATTTAATATTTATGAGTATAATAT
1 ATTTAACATTTATGAGCATAATAT
* *
418840 ATTTAGCATTTATTAGCATAATAT
1 ATTTAACATTTATGAGCATAATAT
418864 ATTT
1 ATTT
418868 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAACATTTATGAGCATAATAT
Found at i:423227 original size:24 final size:24
Alignment explanation
Indices: 423193--423244 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
423183 TTTCTAGAAG
* *
423193 ATTTAGTATTTATGAGTAAAATAT
1 ATTTAGCATTTATGAGCAAAATAT
* *
423217 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCAAAATAT
423241 ATTT
1 ATTT
423245 GACCTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCAAAATAT
Found at i:424633 original size:13 final size:13
Alignment explanation
Indices: 424615--424639 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
424605 GAATTGTTCA
424615 ATTAAAGAATTTG
1 ATTAAAGAATTTG
424628 ATTAAAGAATTT
1 ATTAAAGAATTT
424640 TCTTGAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (13 bp):
ATTAAAGAATTTG
Found at i:425217 original size:16 final size:16
Alignment explanation
Indices: 425179--425220 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
425169 TATTAAATTA
425179 AATTTAATA-TTTATC
1 AATTTAATATTTTATC
** *
425194 AAGATAATATTTTATT
1 AATTTAATATTTTATC
425210 AATTTAATATT
1 AATTTAATATT
425221 AATGTGATTA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (16 bp):
AATTTAATATTTTATC
Found at i:428443 original size:45 final size:45
Alignment explanation
Indices: 428379--428467 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
428369 AACAGATACT
* *
428379 CGGTGGATTCAACACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
*
428424 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
1 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGT
428468 TCAGTTCACA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (45 bp):
CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:428536 original size:51 final size:50
Alignment explanation
Indices: 428474--428664 Score: 231
Period size: 51 Copynumber: 3.8 Consensus size: 50
428464 ATGTTCAGTT
* *
428474 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATCCGGTA
* * * *
428525 CACCTAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATCCGGTA
* * * * *
428576 CGCATAGTAGCCTACACATAGTACTACACATGCGACC-TATCATTCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATACCA-TCCGGTA
* *
428626 CACGTATTAGCCTGCACATAGTACTACACACGTGACCAT
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCAT
428665 CACTTTCACT
Statistics
Matches: 116, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
49 2 0.02
50 39 0.34
51 73 0.63
52 2 0.02
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCATACCATCCGGTA
Found at i:428656 original size:101 final size:101
Alignment explanation
Indices: 428476--428660 Score: 291
Period size: 101 Copynumber: 1.8 Consensus size: 101
428466 GTTCAGTTCA
* *
428476 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACCTAGTAGCCTGCA
1 CATAGTAGCCTACACATAGTACTACACATGCGACCA-TACCATCCGATACACCTAGTAGCCTGCA
428541 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
65 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
* * * *
428578 CATAGTAGCCTACACATAGTACTACACATGCGACC-TATCATTCCGGTACACGTATTAGCCTGCA
1 CATAGTAGCCTACACATAGTACTACACATGCGACCATACCA-TCCGATACACCTAGTAGCCTGCA
428642 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
428661 CCATCACTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
100 4 0.05
101 39 0.51
102 33 0.43
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.23
Consensus pattern (101 bp):
CATAGTAGCCTACACATAGTACTACACATGCGACCATACCATCCGATACACCTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATCCGGTACG
Found at i:435693 original size:26 final size:26
Alignment explanation
Indices: 435663--435714 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
435653 GGAAATCAAG
435663 TAAGCAGTATTGTTCTTGATATTTCC
1 TAAGCAGTATTGTTCTTGATATTTCC
435689 TAAGCAGTATTGTTCTTGATATTTCC
1 TAAGCAGTATTGTTCTTGATATTTCC
435715 ACATTCCTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (26 bp):
TAAGCAGTATTGTTCTTGATATTTCC
Found at i:440747 original size:16 final size:17
Alignment explanation
Indices: 440721--440761 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
440711 ATAATATGTT
*
440721 TTATAAGTATTAATATA
1 TTATAAATATTAATATA
*
440738 -TATAAATATTATTATA
1 TTATAAATATTAATATA
440754 TTATAAAT
1 TTATAAAT
440762 TATAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
TTATAAATATTAATATA
Found at i:441490 original size:9 final size:9
Alignment explanation
Indices: 441476--441542 Score: 80
Period size: 9 Copynumber: 7.4 Consensus size: 9
441466 TTTTTTTGGT
441476 AATTAACCG
1 AATTAACCG
*
441485 AATTAAACG
1 AATTAACCG
*
441494 AATTACCCG
1 AATTAACCG
441503 AATTAACCG
1 AATTAACCG
*
441512 AATTACCCG
1 AATTAACCG
**
441521 AATTAACTA
1 AATTAACCG
*
441530 AATTAACCA
1 AATTAACCG
441539 AATT
1 AATT
441543 GAATCACTAC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 49 1.00
ACGTcount: A:0.46, C:0.21, G:0.07, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:444938 original size:2 final size:2
Alignment explanation
Indices: 444931--444961 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
444921 ATCTTAAATT
444931 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
444962 TTACATACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:446306 original size:17 final size:17
Alignment explanation
Indices: 446284--446332 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
446274 TTTACTTTAT
446284 TAATAT-ATATAATAATA
1 TAATATAATATAAT-ATA
*
446301 TAATATAATATATTATA
1 TAATATAATATAATATA
446318 TAATA-AA-ATAATATA
1 TAATATAATATAATATA
446333 CATAACATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 7 0.24
16 2 0.07
17 14 0.48
18 6 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATATAATATAATATA
Found at i:446331 original size:20 final size:22
Alignment explanation
Indices: 446284--446337 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
446274 TTTACTTTAT
446284 TAATATATATAATAATATAATA
1 TAATATATATAATAATATAATA
446306 TAATATAT-TATATAATA-AA-A
1 TAATATATATA-ATAATATAATA
*
446326 TAATATACATAA
1 TAATATATATAA
446338 CATAAAAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 9 0.31
21 6 0.21
22 14 0.48
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
TAATATATATAATAATATAATA
Found at i:453524 original size:14 final size:13
Alignment explanation
Indices: 453473--453524 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
453463 TATTAATATG
*
453473 TATAATAATATAA
1 TATAATAAAATAA
* *
453486 TATAAT-ATATTA
1 TATAATAAAATAA
453498 TATAATAAAATAA
1 TATAATAAAATAA
*
453511 TATACATAACATAA
1 TATA-ATAAAATAA
453525 AAATCTTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
12 11 0.33
13 14 0.42
14 8 0.24
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (13 bp):
TATAATAAAATAA
Found at i:456818 original size:24 final size:24
Alignment explanation
Indices: 456782--456912 Score: 103
Period size: 24 Copynumber: 5.5 Consensus size: 24
456772 ATACATATAT
* *
456782 AATTGGACTGCATTTGTACATCAA
1 AATTGGACAGCATTTATACATCAA
*
456806 AATTTGACAGCA--TATACAT-ATA
1 AATTGGACAGCATTTATACATCA-A
*
456828 TAATTGGACTGCATTTATACATCAA
1 -AATTGGACAGCATTTATACATCAA
*
456853 AATTTGACAGCA--TATACAT-ATA
1 AATTGGACAGCATTTATACATCA-A
* *
456875 TAATTGGACTGCATTTGTACATCAA
1 -AATTGGACAGCATTTATACATCAA
* *
456900 AATTTGATAGCAT
1 AATTGGACAGCAT
456913 ATACATTCAT
Statistics
Matches: 84, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
21 2 0.02
22 15 0.18
23 20 0.24
24 30 0.36
25 15 0.18
26 2 0.02
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (24 bp):
AATTGGACAGCATTTATACATCAA
Found at i:456823 original size:47 final size:47
Alignment explanation
Indices: 456772--456918 Score: 276
Period size: 47 Copynumber: 3.1 Consensus size: 47
456762 CGATCCAACA
456772 ATACATATATAATTGGACTGCATTTGTACATCAAAATTTGACAGCAT
1 ATACATATATAATTGGACTGCATTTGTACATCAAAATTTGACAGCAT
*
456819 ATACATATATAATTGGACTGCATTTATACATCAAAATTTGACAGCAT
1 ATACATATATAATTGGACTGCATTTGTACATCAAAATTTGACAGCAT
*
456866 ATACATATATAATTGGACTGCATTTGTACATCAAAATTTGATAGCAT
1 ATACATATATAATTGGACTGCATTTGTACATCAAAATTTGACAGCAT
456913 ATACAT
1 ATACAT
456919 TCATTTACTC
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 97 1.00
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (47 bp):
ATACATATATAATTGGACTGCATTTGTACATCAAAATTTGACAGCAT
Found at i:457196 original size:14 final size:15
Alignment explanation
Indices: 457172--457206 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
457162 TATATACATT
457172 ACCATATAAATACTA
1 ACCATATAAATACTA
457187 ACCATA-AAATACTA
1 ACCATATAAATACTA
457201 ATCCAT
1 A-CCAT
457207 GATTAAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (15 bp):
ACCATATAAATACTA
Found at i:464249 original size:19 final size:16
Alignment explanation
Indices: 464211--464240 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
464201 ATGTTTCAAC
464211 TTAA-AAATGTTGTTA
1 TTAATAAATGTTGTTA
464226 TTAATAAATGTTGTT
1 TTAATAAATGTTGTT
464241 GTATTTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (16 bp):
TTAATAAATGTTGTTA
Found at i:467633 original size:22 final size:22
Alignment explanation
Indices: 467605--467650 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
467595 GGCGAATACA
467605 TCAATGCAACTAAACTTGGTTT
1 TCAATGCAACTAAACTTGGTTT
467627 TCAATGCAACTAAACTTGGTTT
1 TCAATGCAACTAAACTTGGTTT
467649 TC
1 TC
467651 TCCCCCCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (22 bp):
TCAATGCAACTAAACTTGGTTT
Found at i:479669 original size:37 final size:36
Alignment explanation
Indices: 479618--479693 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
479608 ATTCCAAAAA
*
479618 TAATATTATGTTAATAGT-TTCTTATTAAATTTAAT-T
1 TAATATTATCTTAATAGTATT-TTATT-AATTTAATAT
479654 TAATACTTATCTTAATAGTATTTTATTAATTTAATAT
1 TAATA-TTATCTTAATAGTATTTTATTAATTTAATAT
479691 TAA
1 TAA
479694 AGTGATTATC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
36 13 0.36
37 21 0.58
38 2 0.06
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (36 bp):
TAATATTATCTTAATAGTATTTTATTAATTTAATAT
Found at i:479823 original size:62 final size:60
Alignment explanation
Indices: 479705--479820 Score: 144
Period size: 62 Copynumber: 1.9 Consensus size: 60
479695 GTGATTATCG
* * * *
479705 TAATATTAAATTTAATTTAATGTTTATCTACAAGTTAAACATTCTATTATTTTAATATGATT
1 TAATATTAAATTTAATCTAATATTTATCT--AAGATAAACATTATATTATTTTAATATGATT
* * *
479767 TAATATTAAATTTAATCTAATATTTATCT-GGATAAATATTATATTAATTTAATA
1 TAATATTAAATTTAATCTAATATTTATCTAAGATAAACATTATATTATTTTAATA
479821 ATAAAGTGAT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
59 20 0.43
62 27 0.57
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.49
Consensus pattern (60 bp):
TAATATTAAATTTAATCTAATATTTATCTAAGATAAACATTATATTATTTTAATATGATT
Found at i:481949 original size:19 final size:18
Alignment explanation
Indices: 481920--481964 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 18
481910 GAATAAATTA
481920 AATGAGAATAACTTTCAAG
1 AATG-GAATAACTTTCAAG
481939 AATAGGAATAACTTTCAAG
1 AAT-GGAATAACTTTCAAG
481958 AATGGAA
1 AATGGAA
481965 ATGGAACTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.16
19 20 0.80
20 1 0.04
ACGTcount: A:0.49, C:0.09, G:0.18, T:0.24
Consensus pattern (18 bp):
AATGGAATAACTTTCAAG
Found at i:497561 original size:6 final size:6
Alignment explanation
Indices: 497550--497574 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
497540 TTTCATTATA
497550 TAATTT TAATTT TAATTT TAATTT T
1 TAATTT TAATTT TAATTT TAATTT T
497575 TTAAAGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TAATTT
Found at i:498070 original size:25 final size:26
Alignment explanation
Indices: 498036--498095 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
498026 ACTTAACATC
*
498036 ATGCGAGCTCAAT-TGTAAACTCGAT
1 ATGCGAGCTCAATCTGCAAACTCGAT
* *
498061 ATGCGAGCTCAATCTGCAAACTTGGT
1 ATGCGAGCTCAATCTGCAAACTCGAT
498087 ATGCGAGCT
1 ATGCGAGCT
498096 TAACATACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
25 13 0.42
26 18 0.58
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (26 bp):
ATGCGAGCTCAATCTGCAAACTCGAT
Found at i:502712 original size:37 final size:37
Alignment explanation
Indices: 502653--502741 Score: 90
Period size: 37 Copynumber: 2.4 Consensus size: 37
502643 TAAATATCAG
*
502653 TCAGTATATCAGTAAAACTTGCTC-AGTTAAGCTCCAA
1 TCAGTATAACAGTAAAACTTGCTCGA-TTAAGCTCCAA
* * * * * *
502690 TCAGTATAACGGTACAATTTGCTCGATTGAGCTTCAT
1 TCAGTATAACAGTAAAACTTGCTCGATTAAGCTCCAA
*
502727 TCAGTATAATAGTAA
1 TCAGTATAACAGTAA
502742 GTTTGGATTG
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
37 40 0.98
38 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Consensus pattern (37 bp):
TCAGTATAACAGTAAAACTTGCTCGATTAAGCTCCAA
Found at i:505354 original size:28 final size:28
Alignment explanation
Indices: 505322--505400 Score: 131
Period size: 28 Copynumber: 2.8 Consensus size: 28
505312 ACAGTACAGG
505322 GTGGGCCTTAGCCCAATATAGTAATAGT
1 GTGGGCCTTAGCCCAATATAGTAATAGT
* * *
505350 GTGGGCTTTAGCCCAGTACAGTAATAGT
1 GTGGGCCTTAGCCCAATATAGTAATAGT
505378 GTGGGCCTTAGCCCAATATAGTA
1 GTGGGCCTTAGCCCAATATAGTA
505401 GCCAGTATAG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.28
Consensus pattern (28 bp):
GTGGGCCTTAGCCCAATATAGTAATAGT
Found at i:505804 original size:27 final size:27
Alignment explanation
Indices: 505757--506030 Score: 336
Period size: 27 Copynumber: 10.1 Consensus size: 27
505747 TATAACAGTT
* *
505757 ATTTTACCCTATGGA-GCTATTTCGGTC
1 ATTTTACCCT-TCGAGGGTATTTCGGTC
*
505784 ATTTTACCCTTCGGGGGTATTTCGGTC
1 ATTTTACCCTTCGAGGGTATTTCGGTC
* *
505811 ATTTTACCCTTCAAAGGTATCTT-GGTC
1 ATTTTACCCTTCGAGGGTAT-TTCGGTC
* * **
505838 ATTTTACCCTCCGGGGGTATTTCAATC
1 ATTTTACCCTTCGAGGGTATTTCGGTC
* * *
505865 ATTTTACCCTCCGAAGGTATTTCGATC
1 ATTTTACCCTTCGAGGGTATTTCGGTC
* *
505892 ATTTTACCCTTTGAGGGTATTTTGGTC
1 ATTTTACCCTTCGAGGGTATTTCGGTC
505919 ATTTTACCCTTCGAGGGTATTTCGGTC
1 ATTTTACCCTTCGAGGGTATTTCGGTC
* * *
505946 ATTTTACCTTTAGAGGGTATTTTGGTC
1 ATTTTACCCTTCGAGGGTATTTCGGTC
* *
505973 ATTTTACCCTTTGGGGGTATTTCGGTC
1 ATTTTACCCTTCGAGGGTATTTCGGTC
*
506000 ATTTTACCCATCGAGGGTATTTCGGTC
1 ATTTTACCCTTCGAGGGTATTTCGGTC
506027 ATTT
1 ATTT
506031 GCCCATGAAT
Statistics
Matches: 212, Mismatches: 32, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
26 4 0.02
27 206 0.97
28 2 0.01
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.42
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCGGTC
Found at i:507372 original size:10 final size:10
Alignment explanation
Indices: 507349--507387 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
507339 TAAACCCAGG
*
507349 CTCCTCAAATA
1 CTCC-CAAACA
507360 CTCCCAAACA
1 CTCCCAAACA
507370 CTCCCAAACA
1 CTCCCAAACA
*
507380 CACCCAAA
1 CTCCCAAA
507388 TTACTTAACC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 22 0.85
11 4 0.15
ACGTcount: A:0.41, C:0.46, G:0.00, T:0.13
Consensus pattern (10 bp):
CTCCCAAACA
Found at i:512099 original size:18 final size:17
Alignment explanation
Indices: 512076--512111 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
512066 CGAGAGTCTC
*
512076 CCTACAGTTTTCAGTTTT
1 CCTACAGTCTT-AGTTTT
512094 CCTACAGTCTTAGTTTT
1 CCTACAGTCTTAGTTTT
512111 C
1 C
512112 TCTAGTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.17, C:0.25, G:0.11, T:0.47
Consensus pattern (17 bp):
CCTACAGTCTTAGTTTT
Found at i:513023 original size:28 final size:28
Alignment explanation
Indices: 512921--513025 Score: 129
Period size: 28 Copynumber: 3.8 Consensus size: 28
512911 GTACAGCGTA
* * * * *
512921 GGCCTTAGCCCAAAATAGAAACAATGTG
1 GGCCTTAGCCCAATACAGTAATAGTGTG
*
512949 GGCCTTAGCCCAACACAGTAATAGTGTG
1 GGCCTTAGCCCAATACAGTAATAGTGTG
* *
512977 GGCCTTAACCCAGTACAGTAATAGTGTG
1 GGCCTTAGCCCAATACAGTAATAGTGTG
*
513005 GGCCGTAGCCCAATACAGTAA
1 GGCCTTAGCCCAATACAGTAA
513026 CCAGTACAGT
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 66 1.00
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.20
Consensus pattern (28 bp):
GGCCTTAGCCCAATACAGTAATAGTGTG
Found at i:513384 original size:27 final size:27
Alignment explanation
Indices: 513336--513663 Score: 396
Period size: 27 Copynumber: 12.3 Consensus size: 27
513326 AGGTATAACA
*
513336 GTCATTTTA-CCTT-GAGGGTATTTTG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * *
513361 GTTATTTTACCCTTCAAGGGTATTTCA
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
513388 ATCATTTTACCC-TCTGGGGGTATTTCG
1 GTCATTTTACCCTTC-GAGGGTATTTCG
* *
513415 ATCATTTTACCC-TCTAGGAGTATTTCG
1 GTCATTTTACCCTTCGAGG-GTATTTCG
* *
513442 GTTATTTTACTCTTCGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
513469 GTCATTTTA-CCTTTGAGGGTATTTTG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
513495 ATCATTTTACCCTTCGAGGGTATTTCA
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * *
513522 GTCATTTTACCCTTTGAAGGTATTTCA
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * *
513549 GTCATTTTACCCATCGAGGATATTTCA
1 GTCATTTTACCCTTCGAGGGTATTTCG
513576 GTCATTTTACCCTTCGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
*
513603 GTCATTTTACCCTTCGGGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
513630 GTCATTTTTCCCATCGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
513657 GTCATTT
1 GTCATTT
513664 GCCCATAAAT
Statistics
Matches: 260, Mismatches: 37, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
25 8 0.03
26 30 0.12
27 217 0.83
28 5 0.02
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTTCGAGGGTATTTCG
Found at i:521924 original size:141 final size:141
Alignment explanation
Indices: 521777--522061 Score: 543
Period size: 141 Copynumber: 2.0 Consensus size: 141
521767 TTTAAAAACC
521777 TTTCTTAATAATTTTAAGAGTTAATTTTATAACTTCATGAATTATATATTTATTTTATCATTTAT
1 TTTCTTAATAATTTTAAGAGTTAATTTTATAACTTCATGAATTATATATTTATTTTATCATTTAT
521842 AATATTTTATTGAGTTAACTAAATAATAAATTATATCTCATTAAAAATATTCCTCAAATTTATTA
66 AATATTTTATTGAGTTAACTAAATAATAAATTATATCTCATTAAAAATATTCCTCAAATTTATTA
521907 TCAAAAGAAAT
131 TCAAAAGAAAT
* *
521918 TTTCTTAATAATTTTAAGAGTTAATTTTCTAACTTCATGAATTATATATTTATTTTATTATTTAT
1 TTTCTTAATAATTTTAAGAGTTAATTTTATAACTTCATGAATTATATATTTATTTTATCATTTAT
521983 AATATTTTATTGAGTTAACTAAATAATAAATTATATCTCATTAAAAATATTCCTCAAATTTATTA
66 AATATTTTATTGAGTTAACTAAATAATAAATTATATCTCATTAAAAATATTCCTCAAATTTATTA
*
522048 TCGAAAGAAAT
131 TCAAAAGAAAT
522059 TTT
1 TTT
522062 GAGAGAAGAA
Statistics
Matches: 141, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
141 141 1.00
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.48
Consensus pattern (141 bp):
TTTCTTAATAATTTTAAGAGTTAATTTTATAACTTCATGAATTATATATTTATTTTATCATTTAT
AATATTTTATTGAGTTAACTAAATAATAAATTATATCTCATTAAAAATATTCCTCAAATTTATTA
TCAAAAGAAAT
Found at i:522045 original size:70 final size:70
Alignment explanation
Indices: 521830--522048 Score: 180
Period size: 70 Copynumber: 3.1 Consensus size: 70
521820 ATATATTTAT
*
521830 TTTATCATTTATAATATTTTATTGAGTTAACTAAATAATAAATTATATCTCATTAAAAATATTCC
1 TTTATTATTTATAATATTTTATTGAGTTAACTAAATAATAAATTATATCTCATTAAAAATATTCC
521895 TCAAA
66 TCAAA
** * * * * * * * * * * * * *
521900 TTTATTATCAAAAGAAATTTTCTT-A-ATAATTTTAAGAGTTAATTTTCTAACTTCATGAATTAT
1 TTTATTATTTATA-ATATTTTATTGAGTTAA-CTAAATA-ATAA-ATTATATC-TCATTAA--AA
*
521963 ATATT--T--AT
59 ATATTCCTCAAA
521971 TTTATTATTTATAATATTTTATTGAGTTAACTAAATAATAAATTATATCTCATTAAAAATATTCC
1 TTTATTATTTATAATATTTTATTGAGTTAACTAAATAATAAATTATATCTCATTAAAAATATTCC
522036 TCAAA
66 TCAAA
522041 TTTATTAT
1 TTTATTAT
522049 CGAAAGAAAT
Statistics
Matches: 103, Mismatches: 33, Indels: 26
0.64 0.20 0.16
Matches are distributed among these distances:
66 6 0.06
68 7 0.07
69 8 0.08
70 34 0.33
71 27 0.26
72 8 0.08
73 7 0.07
75 6 0.06
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (70 bp):
TTTATTATTTATAATATTTTATTGAGTTAACTAAATAATAAATTATATCTCATTAAAAATATTCC
TCAAA
Found at i:528635 original size:2 final size:2
Alignment explanation
Indices: 528628--528660 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
528618 CACCAAATCC
*
528628 TA TA TA TA TA TA TA TA CA 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
528661 TAGTATTATT
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:529585 original size:43 final size:42
Alignment explanation
Indices: 529498--529598 Score: 132
Period size: 43 Copynumber: 2.4 Consensus size: 42
529488 GCTCTCTATA
529498 TCGCACACTTAGTGCCCATTAATCAACATCTCCATTTTAATT
1 TCGCACACTTAGTGCCCATTAATCAACATCTCCATTTTAATT
* * * * *
529540 TCGCACACTCAGTGCCCTTTTATTCAACCTCGT-CATTTTAGTT
1 TCGCACACTTAGTGCCC-ATTAATCAACATC-TCCATTTTAATT
529583 TCGCACACTTAGTGCC
1 TCGCACACTTAGTGCC
529599 GTTTATATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
42 16 0.31
43 34 0.67
44 1 0.02
ACGTcount: A:0.23, C:0.31, G:0.11, T:0.36
Consensus pattern (42 bp):
TCGCACACTTAGTGCCCATTAATCAACATCTCCATTTTAATT
Found at i:543449 original size:16 final size:17
Alignment explanation
Indices: 543418--543451 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
543408 TGTATACGTA
543418 TATATATACCTTATATC
1 TATATATACCTTATATC
*
543435 TATATAT-CTTTATATC
1 TATATATACCTTATATC
543451 T
1 T
543452 TATTATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.32, C:0.15, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATACCTTATATC
Found at i:543460 original size:20 final size:20
Alignment explanation
Indices: 543435--543491 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
543425 ACCTTATATC
*
543435 TATATATCTTTATATCTTAT
1 TATATATCTATATATCTTAT
* *
543455 TATATATCCATATGTCTTAT
1 TATATATCTATATATCTTAT
*
543475 TATATATATATATATCT
1 TATATATCTATATATCT
543492 CTTTTACATT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.11, G:0.02, T:0.54
Consensus pattern (20 bp):
TATATATCTATATATCTTAT
Found at i:557339 original size:22 final size:23
Alignment explanation
Indices: 557291--557339 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
557281 ATATTTTTTG
* * *
557291 AATTGGAAAAGGTCTTTTAAAATT
1 AATTGAAAAAGG-CTTTGAAAAAT
557315 AATTGAAAAAGG-TTTGAAAAAT
1 AATTGAAAAAGGCTTTGAAAAAT
557337 AAT
1 AAT
557340 ACTTGACCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 11 0.50
24 11 0.50
ACGTcount: A:0.49, C:0.02, G:0.16, T:0.33
Consensus pattern (23 bp):
AATTGAAAAAGGCTTTGAAAAAT
Found at i:569650 original size:41 final size:41
Alignment explanation
Indices: 569593--569814 Score: 340
Period size: 41 Copynumber: 5.4 Consensus size: 41
569583 ACATATTCAT
* *
569593 CGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCCA-ATCAC
1 CGGCACTTAGCCTGCTAGGTTTATAACCTGATT-CAGATCAC
569634 CGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCAC
1 CGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCAC
* *
569675 CGACACTTAGCCTGCTAGGTTTATAACCTGATTCAGTTCAC
1 CGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCAC
*
569716 CGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAAATCAC
1 CGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCAC
* * *
569757 CGACTCTTAGCCTGCTAGG-TTATAACCTGGTTCAGATCAC
1 CGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCAC
*
569797 CGGCTCTTAGCCTGCTAG
1 CGGCACTTAGCCTGCTAG
569815 ACTTAAAGTC
Statistics
Matches: 168, Mismatches: 12, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
40 38 0.23
41 130 0.77
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.29
Consensus pattern (41 bp):
CGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCAC
Found at i:569866 original size:122 final size:123
Alignment explanation
Indices: 569588--569859 Score: 365
Period size: 122 Copynumber: 2.2 Consensus size: 123
569578 ATTTAACATA
* * * * *
569588 TTCATCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCCAATCACCGGCACTTAGCCTGCTAGG
1 TTCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAAATCACCGACACTTAGCCTGCTAGG
**
569653 TTTATAACCTGATTCAGATCACCGACACTTAGCCTGCTAGGTTTATAACCTGATTCAG
66 TTTATAACCTGATTCAGATCACCGACACTTAGCCTGCTAGACTTATAACCTGATTCAG
*
569711 TTCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAAATCACCGACTCTTAGCCTGCTAGG
1 TTCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAAATCACCGACACTTAGCCTGCTAGG
* * * *
569776 -TTATAACCTGGTTCAGATCACCGGCTCTTAGCCTGCTAGACTTA-AAGTCC-GAATT-AT
66 TTTATAACCTGATTCAGATCACCGACACTTAGCCTGCTAGACTTATAA--CCTG-ATTCAG
569833 TTCACCGGC-CTTAAGCCTGCTAGGTTT
1 TTCACCGGCACTT-AGCCTGCTAGGTTT
569860 TAAACCTAAA
Statistics
Matches: 133, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
121 5 0.04
122 64 0.48
123 64 0.48
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.31
Consensus pattern (123 bp):
TTCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAAATCACCGACACTTAGCCTGCTAGG
TTTATAACCTGATTCAGATCACCGACACTTAGCCTGCTAGACTTATAACCTGATTCAG
Found at i:572953 original size:25 final size:25
Alignment explanation
Indices: 572920--572981 Score: 97
Period size: 25 Copynumber: 2.5 Consensus size: 25
572910 ACGAGCTGTA
572920 AACGGTAAGCTCCTTCCAGCTGAAT
1 AACGGTAAGCTCCTTCCAGCTGAAT
**
572945 AACGGTAAGCTCCTTTGAGCTGAAT
1 AACGGTAAGCTCCTTCCAGCTGAAT
*
572970 AGCGGTAAGCTC
1 AACGGTAAGCTC
572982 GTACGAGCTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (25 bp):
AACGGTAAGCTCCTTCCAGCTGAAT
Found at i:572989 original size:25 final size:24
Alignment explanation
Indices: 572904--572993 Score: 92
Period size: 25 Copynumber: 3.7 Consensus size: 24
572894 GTACATGTAT
*
572904 GCTCATACGAGCTGTAA-ACGGTAA
1 GCTCCTACGAGCTG-AATACGGTAA
* *
572928 GCTCCTTCCAGCTGAATAACGGTAA
1 GCTCCTACGAGCTGAAT-ACGGTAA
**
572953 GCTCCTTTGAGCTGAATAGCGGTAA
1 GCTCCTACGAGCTGAATA-CGGTAA
*
572978 GCTCGTACGAGCTGAA
1 GCTCCTACGAGCTGAA
572994 ATCCGTAATC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
23 2 0.04
24 12 0.22
25 41 0.75
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (24 bp):
GCTCCTACGAGCTGAATACGGTAA
Found at i:574334 original size:11 final size:11
Alignment explanation
Indices: 574320--574346 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
574310 TAAACACTTG
574320 ATAAATAAATC
1 ATAAATAAATC
574331 ATAAATAAATC
1 ATAAATAAATC
574342 ATAAA
1 ATAAA
574347 GAATAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (11 bp):
ATAAATAAATC
Found at i:584337 original size:50 final size:51
Alignment explanation
Indices: 584273--584408 Score: 195
Period size: 50 Copynumber: 2.7 Consensus size: 51
584263 AGTGAAAGTG
* * * *
584273 ATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA-ATG-
1 ATGGTCACATGTGTAGTACTATATGCAGGCTACTACGTGTACCAGATAGGA
* *
584322 ATGGGTCGCATGTGTAGTACTATATGCAGGCTACTACGTGTATCAGATAGGA
1 AT-GGTCACATGTGTAGTACTATATGCAGGCTACTACGTGTACCAGATAGGA
584374 ATGGTCACATGTGTAGTACTATATGCAGGCTACTA
1 ATGGTCACATGTGTAGTACTATATGCAGGCTACTA
584409 TGTGAACTGA
Statistics
Matches: 77, Mismatches: 7, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
49 2 0.03
50 39 0.51
51 34 0.44
52 2 0.03
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATATGCAGGCTACTACGTGTACCAGATAGGA
Found at i:584412 original size:26 final size:26
Alignment explanation
Indices: 584331--584412 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
584321 GATGGGTCGC
584331 ATGTGTAGTACTATATGCAGGCTACT
1 ATGTGTAGTACTATATGCAGGCTACT
* * * *
584357 ACGTGTA-T-CAGATAGGAATGG-TCAC-
1 ATGTGTAGTAC-TATATGCA-GGCT-ACT
584382 ATGTGTAGTACTATATGCAGGCTACT
1 ATGTGTAGTACTATATGCAGGCTACT
584408 ATGTG
1 ATGTG
584413 AACTGAACAT
Statistics
Matches: 41, Mismatches: 8, Indels: 14
0.65 0.13 0.22
Matches are distributed among these distances:
24 1 0.02
25 17 0.41
26 22 0.54
27 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.32
Consensus pattern (26 bp):
ATGTGTAGTACTATATGCAGGCTACT
Found at i:588883 original size:56 final size:56
Alignment explanation
Indices: 588742--588937 Score: 193
Period size: 56 Copynumber: 3.5 Consensus size: 56
588732 TCGAGTCTAA
* * * * * *
588742 GTTTGCCTTAGGTCGTGAAG-TCA-TCTCGCACATACTTTTTAGAAAAC-TCAAAAAG
1 GTTTGCCTTAGGTCGT-AAGACCAGT-TTGCACATACTTATCAGAAAACATGAACAAG
*** ** ** *
588797 GTCCACCTTAGGTCACAAGACTGGTTTGCACATACTTATCAGAAAACATGAACAGG
1 GTTTGCCTTAGGTCGTAAGACCAGTTTGCACATACTTATCAGAAAACATGAACAAG
* *
588853 GTTTGCCTTAGGTCG-AGAGACCAGTTTGCACATACTTGTTAGAAAACATGAACAAG
1 GTTTGCCTTAGGTCGTA-AGACCAGTTTGCACATACTTATCAGAAAACATGAACAAG
588909 GTTTGCCTTAGGTCGTAAGACCAGTTTGC
1 GTTTGCCTTAGGTCGTAAGACCAGTTTGC
588938 TTATCAGAAT
Statistics
Matches: 113, Mismatches: 23, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
54 3 0.03
55 31 0.27
56 78 0.69
57 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (56 bp):
GTTTGCCTTAGGTCGTAAGACCAGTTTGCACATACTTATCAGAAAACATGAACAAG
Found at i:592667 original size:21 final size:22
Alignment explanation
Indices: 592643--592704 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
592633 TGCCTGAAAT
* *
592643 GACACACGAGGTGTCTGA-TAC
1 GACACACAAAGTGTCTGAGTAC
*
592664 GACACATAAAGTGTCTGATGTAC
1 GACACACAAAGTGTCTGA-GTAC
* *
592687 GACACATAAAGTGCCTGA
1 GACACACAAAGTGTCTGA
592705 TGATCAAAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 15 0.43
23 20 0.57
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (22 bp):
GACACACAAAGTGTCTGAGTAC
Found at i:592691 original size:23 final size:23
Alignment explanation
Indices: 592653--592706 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
592643 GACACACGAG
592653 GTGTCTGA--TACGACACATAAA
1 GTGTCTGATGTACGACACATAAA
592674 GTGTCTGATGTACGACACATAAA
1 GTGTCTGATGTACGACACATAAA
*
592697 GTGCCTGATG
1 GTGTCTGATG
592707 ATCAAAGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 8 0.27
23 22 0.73
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (23 bp):
GTGTCTGATGTACGACACATAAA
Found at i:593307 original size:3 final size:3
Alignment explanation
Indices: 593299--593326 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
593289 ACATTAATTT
593299 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
593327 AATTTCTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:594029 original size:5 final size:5
Alignment explanation
Indices: 594009--594065 Score: 69
Period size: 5 Copynumber: 11.4 Consensus size: 5
593999 TTTAGTTTTT
* * * * *
594009 TAATA TATTT TAATA TAATA TAATA TGATA TAAAA TAATA TAATA TAAAA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
594059 TAATA TA
1 TAATA TA
594066 TAAAACATAA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:594039 original size:15 final size:15
Alignment explanation
Indices: 594019--594065 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
594009 TAATATATTT
*
594019 TAATATAATATAATA
1 TAATATAAAATAATA
*
594034 TGATATAAAATAATA
1 TAATATAAAATAATA
594049 TAATATAAAATAATA
1 TAATATAAAATAATA
594064 TA
1 TA
594066 TAAAACATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (15 bp):
TAATATAAAATAATA
Found at i:603275 original size:38 final size:38
Alignment explanation
Indices: 603223--603361 Score: 181
Period size: 38 Copynumber: 3.7 Consensus size: 38
603213 TGAATTATAT
** *
603223 TGTTATTCGTGCTTTGTGCCTAGCAGGCTTTATGCCGG
1 TGTTATTCAAGCTTTGTGCCTAGCAGGCTTTGTGCCGG
* *
603261 TGTTATTCAAGCTTTGTGCCTAGCAAGCTTTGTGTCGG
1 TGTTATTCAAGCTTTGTGCCTAGCAGGCTTTGTGCCGG
* * * *
603299 TGTTATTTAGGC-TTGTGCCAAGCAGGCTTTGTGCTGG
1 TGTTATTCAAGCTTTGTGCCTAGCAGGCTTTGTGCCGG
*
603336 TGTTATTCAAGTTTTGTGCCTAGCAG
1 TGTTATTCAAGCTTTGTGCCTAGCAG
603362 TCTTAGTTCC
Statistics
Matches: 85, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
37 30 0.35
38 55 0.65
ACGTcount: A:0.14, C:0.18, G:0.28, T:0.40
Consensus pattern (38 bp):
TGTTATTCAAGCTTTGTGCCTAGCAGGCTTTGTGCCGG
Found at i:606467 original size:30 final size:29
Alignment explanation
Indices: 606432--606510 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
606422 CGGCTAAATA
*
606432 AGGCCTATAGGCCGATTTTAATTTTTAATT
1 AGGCCTATAGGCCGATTTTAA-CTTTAATT
* *
606462 AGGCCTTTAGGCCAATTTTAACTTTAATT
1 AGGCCTATAGGCCGATTTTAACTTTAATT
***
606491 AGGGAAATAGGCCGATTTTA
1 AGGCCTATAGGCCGATTTTA
606511 GGAGAGAAAC
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 22 0.54
30 19 0.46
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (29 bp):
AGGCCTATAGGCCGATTTTAACTTTAATT
Found at i:608424 original size:16 final size:16
Alignment explanation
Indices: 608403--608444 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
608393 TTATTAAATT
*
608403 ATATATTTTAATTATA
1 ATATATTTTAATAATA
608419 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
608434 AT-TATGTTTAA
1 ATATAT-TTTAA
608445 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:608429 original size:15 final size:15
Alignment explanation
Indices: 608394--608435 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
608384 TTAAGAATTT
*
608394 TATTAAATTAT-ATA
1 TATTTAATTATAATA
608408 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
608422 TATTTAATAATAAT
1 TATTTAATTATAAT
608436 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:608640 original size:44 final size:45
Alignment explanation
Indices: 608590--608678 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
608580 CCTCTATTCT
608590 ATTCAACCAAACACA-AGA-TTACTATTACGCCTCTATTCCATTAC
1 ATTCAACCAAACA-ATAGATTTACTATTACGCCTCTATTCCATTAC
* *
608634 ATTCAACCAAACAATTGATTTGCTATTACGCCTCTATTCCATTAC
1 ATTCAACCAAACAATAGATTTACTATTACGCCTCTATTCCATTAC
608679 GCCTTTATTC
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
43 1 0.02
44 15 0.37
45 25 0.61
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.33
Consensus pattern (45 bp):
ATTCAACCAAACAATAGATTTACTATTACGCCTCTATTCCATTAC
Found at i:608679 original size:16 final size:16
Alignment explanation
Indices: 608658--608706 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
608648 TTGATTTGCT
608658 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
608674 ATTACGCCTTTATTCC
1 ATTACGCCTCTATTCC
*
608690 ATTACGGCTCTATTCC
1 ATTACGCCTCTATTCC
608706 A
1 A
608707 ATACAGCGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.20, C:0.33, G:0.08, T:0.39
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:609499 original size:23 final size:26
Alignment explanation
Indices: 609444--609503 Score: 81
Period size: 23 Copynumber: 2.4 Consensus size: 26
609434 TAACGTTAAG
* *
609444 TTTTATAATATTTTATTACATTTTCA
1 TTTTATAATATTTAATTACATTATCA
609470 TTTTATAAT-TTTAATTAC-TTAT-A
1 TTTTATAATATTTAATTACATTATCA
609493 TTTTATAATAT
1 TTTTATAATAT
609504 AAGAACATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 10 0.32
24 4 0.13
25 8 0.26
26 9 0.29
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTTATAATATTTAATTACATTATCA
Found at i:615675 original size:36 final size:36
Alignment explanation
Indices: 615630--615725 Score: 131
Period size: 36 Copynumber: 2.7 Consensus size: 36
615620 AATTATCACT
*
615630 CTTA-AATATCACAACTATATCATTAGGCCAAATCA
1 CTTATAATATCACAACTATATCAATAGGCCAAATCA
* * *
615665 CTTATAATATCACAAGTATATCAATAGGCCGAATTA
1 CTTATAATATCACAACTATATCAATAGGCCAAATCA
* *
615701 CTTATAATATCACAAGTACATCAAT
1 CTTATAATATCACAACTATATCAAT
615726 TCAAATATAC
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
35 4 0.07
36 51 0.93
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (36 bp):
CTTATAATATCACAACTATATCAATAGGCCAAATCA
Found at i:615935 original size:43 final size:42
Alignment explanation
Indices: 615874--615988 Score: 114
Period size: 43 Copynumber: 2.7 Consensus size: 42
615864 AAAGCTCGTA
*
615874 CAATGCCAAC-GTCCCAGACGTGGTCTTACATGTAATC-ATATAT
1 CAATGCC-ACTGTCCCAGACGTGGTCTTACACG-AATCGA-ATAT
615917 CAATGCCACTGTCCCAGACAG-GGTCTTACACGAATCGAATAT
1 CAATGCCACTGTCCCAGAC-GTGGTCTTACACGAATCGAATAT
* * *
615959 -GATGTCGA-TGTCCCAGACATGGTCTTACAC
1 CAATG-CCACTGTCCCAGACGTGGTCTTACAC
615989 TTAAACACAA
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
41 23 0.37
42 12 0.19
43 27 0.43
44 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (42 bp):
CAATGCCACTGTCCCAGACGTGGTCTTACACGAATCGAATAT
Found at i:625891 original size:13 final size:13
Alignment explanation
Indices: 625873--625899 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
625863 TTATTATCGT
625873 TATATGTTTATGG
1 TATATGTTTATGG
625886 TATATGTTTATGG
1 TATATGTTTATGG
625899 T
1 T
625900 CTACAAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (13 bp):
TATATGTTTATGG
Found at i:627550 original size:48 final size:48
Alignment explanation
Indices: 627481--627684 Score: 205
Period size: 48 Copynumber: 4.2 Consensus size: 48
627471 TCGGAATAAA
* * * *
627481 AACAGATTTCTCGGTGGCCTGCACACAGTCTGTACCACCTTTGTGTAAT
1 AACAGA-TTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTAAT
* * * * **
627530 AACAGATTCTCGGTGGCCTGCGCATAGTCCGTGCCACCCTTGTATCTT
1 AACAGATTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTAAT
* * * *
627578 AACA-AGTTATTGGTGACTTGCACACAATCCGTGCCACCCTTGTGTCAA-
1 AACAGA-TTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGT-AAT
* * * *
627626 AACAGAATATTGGTGGCCTGTACACAGTCCGTGCCACCCTTGTGTCAT
1 AACAGATTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTAAT
627674 AACAGATTATC
1 AACAGATTATC
627685 AGTACGCATA
Statistics
Matches: 125, Mismatches: 26, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
47 2 0.02
48 116 0.93
49 7 0.06
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (48 bp):
AACAGATTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTAAT
Found at i:627664 original size:96 final size:96
Alignment explanation
Indices: 627500--627677 Score: 232
Period size: 96 Copynumber: 1.9 Consensus size: 96
627490 CTCGGTGGCC
* * * * * * *
627500 TGCACACAGTCTGTACCACCTTTGTGTAATAACAGATTCTCGGTGGCCTGCGCATAGTCCGTGCC
1 TGCACACAATCCGTACCACCCTTGTGTAATAACAGAATATCGGTGGCCTGCACACAGTCCGTGCC
*
627565 ACCCTTGTATCTTAACAAGTTATTGGTGACT
66 ACCCTTGTATCATAACAAGTTATTGGTGACT
* * *
627596 TGCACACAATCCGTGCCACCCTTGTGTCAA-AACAGAATATTGGTGGCCTGTACACAGTCCGTGC
1 TGCACACAATCCGTACCACCCTTGTGT-AATAACAGAATATCGGTGGCCTGCACACAGTCCGTGC
*
627660 CACCCTTGTGTCATAACA
65 CACCCTTGTATCATAACA
627678 GATTATCAGT
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
96 67 0.97
97 2 0.03
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (96 bp):
TGCACACAATCCGTACCACCCTTGTGTAATAACAGAATATCGGTGGCCTGCACACAGTCCGTGCC
ACCCTTGTATCATAACAAGTTATTGGTGACT
Found at i:629422 original size:48 final size:48
Alignment explanation
Indices: 629351--629547 Score: 207
Period size: 48 Copynumber: 4.1 Consensus size: 48
629341 TACTATGCGT
629351 ACCGATAATCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCC
1 ACCGATAATCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCC
* * * * * *
629399 ACCGATATTCTGTTGTGACACAAGGGTGGCACAGCCAGTGTGCAGGTC
1 ACCGATAATCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCC
* * ** * * *
629447 ACCAATAA-CTTGTTAAGGTACAAGGGTGGCACGAACTATGTGTAGGCC
1 ACCGATAATC-TGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCC
* * * * * *
629495 ACCAAGAATCTGTTATTACACAAAGGTGGTACGGACTGTGTGCAGGTC
1 ACCGATAATCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCC
629543 ACCGA
1 ACCGA
629548 GAAATCTATT
Statistics
Matches: 116, Mismatches: 31, Indels: 4
0.77 0.21 0.03
Matches are distributed among these distances:
47 1 0.01
48 114 0.98
49 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.22
Consensus pattern (48 bp):
ACCGATAATCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCC
Found at i:629536 original size:96 final size:96
Alignment explanation
Indices: 629370--629545 Score: 235
Period size: 96 Copynumber: 1.8 Consensus size: 96
629360 CTGTTATGAC
* * * * * * * *
629370 ACAAGGGTGGCACGGACTGTGTGCAGGCCACCGATATTCTGTTGTGACACAAGGGTGGCACAGCC
1 ACAAGGGTGGCACGAACTATGTGCAGGCCACCAAGAATCTGTTATGACACAAAGGTGGCACAGAC
629435 AGTGTGCAGGTCACCAATAACTTGTTAAGGT
66 AGTGTGCAGGTCACCAATAACTTGTTAAGGT
* * * *
629466 ACAAGGGTGGCACGAACTATGTGTAGGCCACCAAGAATCTGTTATTACACAAAGGTGGTACGGAC
1 ACAAGGGTGGCACGAACTATGTGCAGGCCACCAAGAATCTGTTATGACACAAAGGTGGCACAGAC
*
629531 TGTGTGCAGGTCACC
66 AGTGTGCAGGTCACC
629546 GAGAAATCTA
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
96 67 1.00
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.22
Consensus pattern (96 bp):
ACAAGGGTGGCACGAACTATGTGCAGGCCACCAAGAATCTGTTATGACACAAAGGTGGCACAGAC
AGTGTGCAGGTCACCAATAACTTGTTAAGGT
Found at i:633220 original size:22 final size:22
Alignment explanation
Indices: 633192--633252 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
633182 TTTATTGTTC
633192 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
*
633214 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTG
**
633236 AGCCATGAGAGCTTAGT
1 AAACATGAGAGCTTAGT
633253 TTTATGGATT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:641855 original size:65 final size:66
Alignment explanation
Indices: 641748--641894 Score: 206
Period size: 66 Copynumber: 2.2 Consensus size: 66
641738 GATACACGGA
* * * *
641748 TCTCCATCACACCAGATAGACTCATAGAGTCAAACATGTCCC-ATAAGTGAAGCATAAAACTAAC
1 TCTCCAACACACCA-ATAGACTCATAAAGTCAAACATATCCCAAAAAGTGAAGCATAAAACTAAC
641812 AC
65 AC
* * * *
641814 TCTCCAACACACCAATTGAGTCATAAAGTCGAACATATCCCAAAAAGTGAAGCATAAAGCTAACA
1 TCTCCAACACACCAATAGACTCATAAAGTCAAACATATCCCAAAAAGTGAAGCATAAAACTAACA
641879 C
66 C
641880 TCTCCAACACACCAA
1 TCTCCAACACACCAA
641895 ACATGTCTCG
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
65 22 0.31
66 50 0.69
ACGTcount: A:0.42, C:0.29, G:0.11, T:0.18
Consensus pattern (66 bp):
TCTCCAACACACCAATAGACTCATAAAGTCAAACATATCCCAAAAAGTGAAGCATAAAACTAACA
C
Done.