Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 135 of 318
Found at i:41318073 original size:55 final size:53
Alignment explanation
Indices: 41318003--41318120 Score: 150
Period size: 55 Copynumber: 2.2 Consensus size: 53
41317993 TGACCATGGC
*
41318003 AAGAAGACAATATAGTGTAAAACCTAGTCATAGTGG-CTATGGCATCATATGG-GAA
1 AAGAAGACAACATAGTGTAAAACCTAGT--T-G-GGACTATGGCATCATATGGAGAA
* *
41318058 AAGAAGACCACATAGTGTAAGACCTAGTTGGGACTATGGCATCATATGGAGAA
1 AAGAAGACAACATAGTGTAAAACCTAGTTGGGACTATGGCATCATATGGAGAA
*
41318111 AAGATGACAA
1 AAGAAGACAA
41318121 GGACGGTTGG
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
51 2 0.04
52 17 0.30
53 12 0.21
55 25 0.45
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.21
Consensus pattern (53 bp):
AAGAAGACAACATAGTGTAAAACCTAGTTGGGACTATGGCATCATATGGAGAA
Found at i:41318280 original size:28 final size:28
Alignment explanation
Indices: 41318218--41318339 Score: 127
Period size: 28 Copynumber: 4.3 Consensus size: 28
41318208 TGAATTGTAG
* *
41318218 GAGCCTTTGTGGCTAATTCTATTATATGT
1 GAGCCTTTGTGG-TGATTCTGTTATATGT
* * * * *
41318247 GGGCCTTTGTGTTGTTTTTGTTATATAT
1 GAGCCTTTGTGGTGATTCTGTTATATGT
41318275 GAGCCTTTGTGGTGATTCTGTTATATGT
1 GAGCCTTTGTGGTGATTCTGTTATATGT
* * * *
41318303 GAGCCTTTATGGCTAATTCTGCTATGTGT
1 GAGCCTTTGTGG-TGATTCTGTTATATGT
41318332 GAGCCTTT
1 GAGCCTTT
41318340 AAAGTTGTAC
Statistics
Matches: 76, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
28 45 0.59
29 31 0.41
ACGTcount: A:0.16, C:0.13, G:0.25, T:0.47
Consensus pattern (28 bp):
GAGCCTTTGTGGTGATTCTGTTATATGT
Found at i:41320702 original size:29 final size:28
Alignment explanation
Indices: 41320668--41320770 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
41320658 TACTCAATCA
*
41320668 CGCACACTTAGTGCCATATGATTCAAGCC
1 CGCACACTTAGTGCCATAT-ATTCAAGCT
* * *
41320697 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCATATA-TTCAAGCT
* *
41320726 CGCACACTTAGTGCCGTACATTACAAGCT
1 CGCACACTTAGTGCCATATATT-CAAGCT
*
41320755 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
41320771 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATATTCAAGCT
Found at i:41327526 original size:20 final size:20
Alignment explanation
Indices: 41327497--41327540 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
41327487 AGGCTAAACC
*
41327497 ATGAGTATTCTCATTATCAT
1 ATGAGCATTCTCATTATCAT
41327517 ATGAGCATTCTCATTATCAT
1 ATGAGCATTCTCATTATCAT
41327537 ATGA
1 ATGA
41327541 TGCCACGAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (20 bp):
ATGAGCATTCTCATTATCAT
Found at i:41329128 original size:560 final size:559
Alignment explanation
Indices: 41328051--41329167 Score: 2173
Period size: 561 Copynumber: 2.0 Consensus size: 559
41328041 TACAACCCCC
*
41328051 ATGTAATATCCTAAATTAGGGCTTAATCGGAATAGTGGTTTCGTGACCACAAATCCGAGATAGAA
1 ATGTAATATCCTAAATTAGGGCTTAATCGAAATAGTGGTTTCGTGACCACAAATCCGAGATAGAA
41328116 ATAATTATTTTACAATGATTTTGATGTTTATGATATGATTGCATGATTGTGTGAAAATTTCGTGA
66 ATAATTATTTTACAATGATTTTGATGTTTATGATATGATTGCATGATTGTGTGAAAATTTCGTGA
41328181 TGAAATTCTATGCCTAAAGTGCTTAAATTGAAAGTAGGGACTAAATCGAATAAGTTGCAAAACTT
131 TGAAATTCTATGCCTAAAGTGCTTAAATTGAAAGTAGGGACTAAATCGAATAAGTTGCAAAACTT
41328246 GCATTCTAGAAGTTTTAGTATGAAATTGTTTTGGAATATTAATGAGGAGGTCTTAAATAGCAATT
196 GCATTCTAGAAGTTTTAGTATGAAATTGTTTTGGAATATTAATGAGGAGGTCTTAAATAGCAATT
41328311 TTACCAATTTTAAGTTCATGGACAAAATTAGGACATGGAAGGAATTTTTGGAAAGTTTAGTAGTA
261 TTACCAATTTTAAGTTCATGGACAAAATTAGGACATGGAAGGAATTTTTGGAAAGTTTAGTAGTA
41328376 AGGGTATTTTGGTCATTTAGTTATTAAAATGAATTAAAAACAAAATTAAAAGCCAATTTTTGTCC
326 AGGGTATTTTGGTCATTTAGTTATTAAAATGAATTAAAAACAAAATTAAAAGCCAATTTTTGTCC
41328441 ATCTTCTTCATTAGGCCGAAATTTCAAGGGTTCTCCATAGCTAGGGTTTGTTTCAAGCTTCCAAG
391 ATCTTCTTCATTAGGCCGAAATTTCAAGGGTTCTCCATAGCTAGGGTTTGTTTCAAGCTTCCAAG
*
41328506 CTCCATAGTAAGTGATTCCAAGCCCCATTTTTAATGATTTTTACGTTTTTGAGATCCCGGTAAGT
456 CTCCATAGTAAGTGATTCCAAGCCCCATTTTTAATGATTTTTACGTTTTTGAGATCCCGGTAACT
*
41328571 CGATAAAGCTTATGTTAGCAATAATTTCACCTATGGGTAT
521 CGATAAAGCTTATGTTAGCAATAATTTAACCTA-GGGTAT
41328611 ATGTAATATCCTAAATTAGGGCTTAATCGAAATAGTGGTTTCGTGACCACAAATCCGAGATAGAA
1 ATGTAATATCCTAAATTAGGGCTTAATCGAAATAGTGGTTTCGTGACCACAAATCCGAGATAGAA
41328676 ATAATTATTTTACAATGATTTTGATGTTTATGATATGATTGCATGATTGTGTGAAAATTTCGTGA
66 ATAATTATTTTACAATGATTTTGATGTTTATGATATGATTGCATGATTGTGTGAAAATTTCGTGA
41328741 TGAAATTCTATGCCTAAAGTGCTTAAATTGAAAGTAGGGACTAAATCGAATAAGTTGCAAAACTT
131 TGAAATTCTATGCCTAAAGTGCTTAAATTGAAAGTAGGGACTAAATCGAATAAGTTGCAAAACTT
41328806 GCATTCTAGAAGTTTTTAGTATGAAATTGTTTTGGAATATTAATGAGGAGGTCTTAAATAGCAAT
196 GCATTCTAGAAG-TTTTAGTATGAAATTGTTTTGGAATATTAATGAGGAGGTCTTAAATAGCAAT
41328871 TTTACCAATTTTAAGTTCATGGACAAAATTAGGACATGGAAGGAATTTTTGGAAAGTTTAGTAGT
260 TTTACCAATTTTAAGTTCATGGACAAAATTAGGACATGGAAGGAATTTTTGGAAAGTTTAGTAGT
41328936 AAGGGTATTTTGGTCATTTAGTTATTAAAATGAATTAAAAACAAAATTAAAAGCCAATTTTTGTC
325 AAGGGTATTTTGGTCATTTAGTTATTAAAATGAATTAAAAACAAAATTAAAAGCCAATTTTTGTC
41329001 CATCTTCTTCATTAGGCCGAAATTTCAAGGGTTCTCCATAGCTAGGGTTTGTTTCAAGCTTCCAA
390 CATCTTCTTCATTAGGCCGAAATTTCAAGGGTTCTCCATAGCTAGGGTTTGTTTCAAGCTTCCAA
*
41329066 GCTCCATAGTAAGTGATTCCAAGCCCCGTTTTTAATGATTTTTACGTTTTTGAGAT-CCGGTAAC
455 GCTCCATAGTAAGTGATTCCAAGCCCCATTTTTAATGATTTTTACGTTTTTGAGATCCCGGTAAC
41329130 TCGATAAAGCTTATGTTAGCAATAATTTAACCTAGGGT
520 TCGATAAAGCTTATGTTAGCAATAATTTAACCTAGGGT
41329168 TTATATTTGG
Statistics
Matches: 552, Mismatches: 4, Indels: 3
0.99 0.01 0.01
Matches are distributed among these distances:
559 4 0.01
560 246 0.45
561 302 0.55
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (559 bp):
ATGTAATATCCTAAATTAGGGCTTAATCGAAATAGTGGTTTCGTGACCACAAATCCGAGATAGAA
ATAATTATTTTACAATGATTTTGATGTTTATGATATGATTGCATGATTGTGTGAAAATTTCGTGA
TGAAATTCTATGCCTAAAGTGCTTAAATTGAAAGTAGGGACTAAATCGAATAAGTTGCAAAACTT
GCATTCTAGAAGTTTTAGTATGAAATTGTTTTGGAATATTAATGAGGAGGTCTTAAATAGCAATT
TTACCAATTTTAAGTTCATGGACAAAATTAGGACATGGAAGGAATTTTTGGAAAGTTTAGTAGTA
AGGGTATTTTGGTCATTTAGTTATTAAAATGAATTAAAAACAAAATTAAAAGCCAATTTTTGTCC
ATCTTCTTCATTAGGCCGAAATTTCAAGGGTTCTCCATAGCTAGGGTTTGTTTCAAGCTTCCAAG
CTCCATAGTAAGTGATTCCAAGCCCCATTTTTAATGATTTTTACGTTTTTGAGATCCCGGTAACT
CGATAAAGCTTATGTTAGCAATAATTTAACCTAGGGTAT
Found at i:41329951 original size:46 final size:46
Alignment explanation
Indices: 41329901--41330076 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
41329891 TGGTTGAGCA
41329901 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
41329947 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
41329992 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
41330040 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
41330077 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:41330057 original size:93 final size:93
Alignment explanation
Indices: 41329898--41330069 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
41329888 GGATGGTTGA
* *
41329898 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
41329963 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
41329991 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
41330056 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
41330070 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:41338806 original size:29 final size:29
Alignment explanation
Indices: 41338773--41338874 Score: 150
Period size: 29 Copynumber: 3.5 Consensus size: 29
41338763 TGACGAGATC
41338773 GGCACTAAGTGTGCGTGCTGGAAATATAT
1 GGCACTAAGTGTGCGTGCTGGAAATATAT
41338802 GGCACTAAGTGTGCGTGCTGGAAATATAT
1 GGCACTAAGTGTGCGTGCTGGAAATATAT
** * *
41338831 GGCACTAAGTGTGCAAGCTGGAAAAATAC
1 GGCACTAAGTGTGCGTGCTGGAAATATAT
**
41338860 GGCACTGGGTGTGCG
1 GGCACTAAGTGTGCG
41338875 AGCTCGGAGG
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.27, C:0.16, G:0.33, T:0.24
Consensus pattern (29 bp):
GGCACTAAGTGTGCGTGCTGGAAATATAT
Found at i:41346664 original size:29 final size:29
Alignment explanation
Indices: 41346631--41346732 Score: 150
Period size: 29 Copynumber: 3.5 Consensus size: 29
41346621 TGACGAGATC
41346631 GGCACTAAGTGTGCGTGCTGGAAATATAT
1 GGCACTAAGTGTGCGTGCTGGAAATATAT
41346660 GGCACTAAGTGTGCGTGCTGGAAATATAT
1 GGCACTAAGTGTGCGTGCTGGAAATATAT
** * *
41346689 GGCACTAAGTGTGCAAGCTGGAAAAATAC
1 GGCACTAAGTGTGCGTGCTGGAAATATAT
**
41346718 GGCACTGGGTGTGCG
1 GGCACTAAGTGTGCG
41346733 AGCTCGGAGG
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.27, C:0.16, G:0.33, T:0.24
Consensus pattern (29 bp):
GGCACTAAGTGTGCGTGCTGGAAATATAT
Found at i:41352381 original size:42 final size:42
Alignment explanation
Indices: 41352283--41352427 Score: 161
Period size: 43 Copynumber: 3.4 Consensus size: 42
41352273 AGCTCGTACA
*
41352283 ATGCCAATGTCCCTA-AC-GTGGTCTTACATGTAATCAAATATCG
1 ATGCCAATGTCCC-AGACAG-GGTCTTACATGAAATCAAATA-CG
* **
41352326 ATGCCACTGTCCCAGACAGGGTCCAACATGAAATCAAATACG
1 ATGCCAATGTCCCAGACAGGGTCTTACATGAAATCAAATACG
* *
41352368 ATGCCAATGTCCCAGACAAGGTCTTACACGTAAATCATAAGT-CG
1 ATGCCAATGTCCCAGACAGGGTCTTACATG-AAATCA-AA-TACG
41352412 ATGCCAATGTCCCAGA
1 ATGCCAATGTCCCAGA
41352428 TGTGGTCTTA
Statistics
Matches: 88, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
42 28 0.32
43 38 0.43
44 21 0.24
45 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACAGGGTCTTACATGAAATCAAATACG
Found at i:41353546 original size:19 final size:20
Alignment explanation
Indices: 41353504--41353548 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
41353494 AATTATTTTG
*
41353504 AAATAAGAAAATAATTAGTA
1 AAATAAGAAAATAATGAGTA
41353524 AAATAAGAAAA-AGATGA-TA
1 AAATAAGAAAATA-ATGAGTA
41353543 AAATAA
1 AAATAA
41353549 TGGGTGTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.69, C:0.00, G:0.11, T:0.20
Consensus pattern (20 bp):
AAATAAGAAAATAATGAGTA
Found at i:41354298 original size:545 final size:540
Alignment explanation
Indices: 41353200--41354241 Score: 1145
Period size: 545 Copynumber: 1.9 Consensus size: 540
41353190 TTTTGAGACC
* * * *
41353200 ACAAAATCGAGTCATAAAAATAATTAACTGTTATATTCTATGTTTATTATATGTGTAAATGCATG
1 ACAAAACCAAGTCATAAAAATAATTAACTGTTATATTCTATGCTTATTATATGTGTAAATGCATA
* *
41353265 TGTGAAAGTTTCATGCTTTGATTTTGTCATTTGTATGTGAAATTTATAAGATAGGACTCATGTGA
66 TGTGAAAGTTTCATGCTCTAATTTTGTCATTTGTATGTGAAATTTATAAGATAGGACTCATGTGA
* * * *** *
41353330 TAAGACTTGAAAATGTGATAGGTAAATTTTAAAGTGCCAAATAATGCATGAAGTATTGACATGGG
131 TAAGAATTGAAAAGGTGATAGGTAAATTTTAAAGGGCCAAATAATGCAT--AGTACAAAAATGGG
* *
41353395 GACTTGCATGTCAAATAGACCACTTTTAATATAGTGGCCGGCCATATTGATGGTTGATGGATAAT
194 GACTTGCATGTCAAATAGACCACTTTTAATATAGTGGCCGGCCATAATGATGATTGATGGATAAT
* * *
41353460 ATATGTTTTATTTAAGTATTATAATAAGTAATGGAATTATTTTGAAATAAGAAAATAATTAGTAA
259 ATATATTTTAATTAAATATTATAATAAGTAATGGAATTATTTTGAAATAAGAAAATAATTAGTAA
** * * ** * *
41353525 AATAAGAAAAAGATGATAAAATAATGGGTGTTCATCTTTCTTTCTTCATTGCCGAAATTGAGAAA
324 AATAAGAAAAAGAAAACAAAATAAAGAATGCTCATCTTTCTTTCTTCATTGCCGAAATTAAGAAA
* * * ** * *
41353590 GAAAAATATTGAAGAAGAAGCCAAGGCATTCGGCCATGGTTATCTCAATTTAAAGGTATGTAATG
389 GAAAAAGATTGAAAAAGAAACCAAGGCATTCGGCCATGGCAATCTCAATTGAAAGGTATGCAATG
* * * *
41353655 TGATTTTTTTTTGTAATTGATTATGAAATTAAATTGATAAGTACTGTGACAGCCCTAATTTGACC
454 TGA-TTTTTATTCTAATTGATTATGAAATTAAATTGATAAG-A-TGTGACAGCCCTAAGTTAACC
* ** * **
41353720 CTAGTCGGGAAGTGGTTTCGGGACC
516 CTAGTCGAGAAGTGAATTCGGAAAA
* * *
41353745 ACAAAACCAAGTCATAAAAATAATTGATTGTTATATTCTATGCTTATTATATGTGTACATGCATA
1 ACAAAACCAAGTCATAAAAATAATTAACTGTTATATTCTATGCTTATTATATGTGTAAATGCATA
* **
41353810 TGTGAAAGTTTCATGCTCTAATTTTGTCATTTGTATGTGAAA-TTATTAA-ATAGGATTTGTGTG
66 TGTGAAAGTTTCATGCTCTAATTTTGTCATTTGTATGTGAAATTTA-TAAGATAGGACTCATGTG
* ** * * *
41353873 A-AATAATTGTGGAAGGTGATAGGT-AATTTTAAAAAGGGGTCTATTAATGCAT-GTCACAAAAA
130 ATAAGAATTG-AAAAGGTGATAGGTAAATTTT--AAA-GGGCCAAATAATGCATAGT-ACAAAAA
** * * * * * *
41353935 GTTTGGACTTTCATGTCAAATA-TCCAATTTTTTTATTATGGTGGCCGGCCATAATGATTATTGA
190 -TGGGGACTTGCATGTCAAATAGACC-A--CTTTTAATATAGTGGCCGGCCATAATGATGATTGA
* * *
41353999 TGGGTAATATATATGTTTAATTAAATATTATAATAAG-AATTTGCATTATTTTGAAATAA-AATA
251 TGGATAATATATAT-TTTAATTAAATATTATAATAAGTAA-TGGAATTATTTTGAAATAAGAA-A
* ** *
41354062 ATAATTATTAAAATAAGGTAAAGAAAACAAAATTTAAAGAATGCTCATCTTTC-TTGTTCATTGC
313 ATAATTAGTAAAATAAGAAAAAGAAAACAAAA--TAAAGAATGCTCATCTTTCTTTCTTCATTGC
*
41354126 CGAAATTAAGAAAG-AAAAGATTGAAAAAGAAACCAAGGCATTCGGCCATGGCAATTTCAATTGA
376 CGAAATTAAGAAAGAAAAAGATTGAAAAAGAAACCAAGGCATTCGGCCATGGCAATCTCAATTGA
* * *
41354190 AAGGTATGCATTGTGA-TTTTATTCTAATTGA-TATTGAGATTAAGTTGATAAG
441 AAGGTATGCAATGTGATTTTTATTCTAATTGATTA-TGAAATTAAATTGATAAG
41354242 TGTATAGTCT
Statistics
Matches: 415, Mismatches: 66, Indels: 31
0.81 0.13 0.06
Matches are distributed among these distances:
543 14 0.03
544 31 0.07
545 125 0.30
546 41 0.10
547 45 0.11
548 121 0.29
549 23 0.06
550 15 0.04
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (540 bp):
ACAAAACCAAGTCATAAAAATAATTAACTGTTATATTCTATGCTTATTATATGTGTAAATGCATA
TGTGAAAGTTTCATGCTCTAATTTTGTCATTTGTATGTGAAATTTATAAGATAGGACTCATGTGA
TAAGAATTGAAAAGGTGATAGGTAAATTTTAAAGGGCCAAATAATGCATAGTACAAAAATGGGGA
CTTGCATGTCAAATAGACCACTTTTAATATAGTGGCCGGCCATAATGATGATTGATGGATAATAT
ATATTTTAATTAAATATTATAATAAGTAATGGAATTATTTTGAAATAAGAAAATAATTAGTAAAA
TAAGAAAAAGAAAACAAAATAAAGAATGCTCATCTTTCTTTCTTCATTGCCGAAATTAAGAAAGA
AAAAGATTGAAAAAGAAACCAAGGCATTCGGCCATGGCAATCTCAATTGAAAGGTATGCAATGTG
ATTTTTATTCTAATTGATTATGAAATTAAATTGATAAGATGTGACAGCCCTAAGTTAACCCTAGT
CGAGAAGTGAATTCGGAAAA
Found at i:41356344 original size:39 final size:39
Alignment explanation
Indices: 41356290--41356413 Score: 194
Period size: 39 Copynumber: 3.2 Consensus size: 39
41356280 ATTTGATGTG
41356290 TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTA
1 TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTA
*
41356329 TATCCGGACTTAGGGTCCGCAAGCTATGTGCTGGAATTA
1 TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTA
* * * *
41356368 TATCCAGACTTAAGGTCCGCAGGCTACGTGCTGGAAATA
1 TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTA
*
41356407 TGTCCGG
1 TATCCGG
41356414 GCTAAAGTCC
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 77 1.00
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.27
Consensus pattern (39 bp):
TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTA
Found at i:41357204 original size:19 final size:20
Alignment explanation
Indices: 41357163--41357206 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
41357153 TACTCGTCAC
*
41357163 ACTATCTATCATTTTGGGGT
1 ACTATCTATCATTTTGGGCT
41357183 ACTA-CTAT-ATTTTGGAGCT
1 ACTATCTATCATTTTGG-GCT
41357202 ACTAT
1 ACTAT
41357207 GGCATGTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 7 0.33
19 10 0.48
20 4 0.19
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (20 bp):
ACTATCTATCATTTTGGGCT
Found at i:41357347 original size:6 final size:6
Alignment explanation
Indices: 41357336--41357380 Score: 58
Period size: 6 Copynumber: 7.7 Consensus size: 6
41357326 TGGCGATGTA
*
41357336 TATTTT TA-TTT TATTTT TATTGTA TATTTT TA-TTT TATTTT TATT
1 TATTTT TATTTT TATTTT TATT-TT TATTTT TATTTT TATTTT TATT
41357381 GTGTATGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 10 0.29
6 19 0.56
7 5 0.15
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (6 bp):
TATTTT
Found at i:41357352 original size:11 final size:11
Alignment explanation
Indices: 41357336--41357380 Score: 72
Period size: 11 Copynumber: 3.9 Consensus size: 11
41357326 TGGCGATGTA
41357336 TATTTTTATTT
1 TATTTTTATTT
41357347 TATTTTTATTGT
1 TATTTTTATT-T
41357359 ATATTTTTATTT
1 -TATTTTTATTT
41357371 TATTTTTATT
1 TATTTTTATT
41357381 GTGTATGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 20 0.62
12 2 0.06
13 10 0.31
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (11 bp):
TATTTTTATTT
Found at i:41357359 original size:24 final size:24
Alignment explanation
Indices: 41357332--41357391 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
41357322 AGTTTGGCGA
41357332 TGTATATTTTTATTTTATTTTTAT
1 TGTATATTTTTATTTTATTTTTAT
41357356 TGTATATTTTTATTTTATTTTTAT
1 TGTATATTTTTATTTTATTTTTAT
*
41357380 TGTGTATGTTTT
1 TGTATAT-TTTT
41357392 TAAAATATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 30 0.88
25 4 0.12
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.73
Consensus pattern (24 bp):
TGTATATTTTTATTTTATTTTTAT
Found at i:41358880 original size:40 final size:40
Alignment explanation
Indices: 41358843--41358988 Score: 206
Period size: 40 Copynumber: 3.7 Consensus size: 40
41358833 TGAGGAATTG
*
41358843 TATCCGAGCTTAAAGACCCGCAGGCTATATGCTGGAATGT
1 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATGT
*
41358883 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTAGAATGT
1 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATGT
* * *
41358923 TATCCGGGCTTAAAGACCCGCAGGCT-TCGTGCTAGAATGC
1 TATCCGGGCTTAAAGACCCGCAGGCTAT-ATGCTGGAATGT
* *
41358963 TATCCGGG-ATAGAGACCCGCAGGCTA
1 TATCCGGGCTTAAAGACCCGCAGGCTA
41358989 CGAGCTGGTA
Statistics
Matches: 98, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
39 16 0.16
40 82 0.84
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATGT
Found at i:41361087 original size:39 final size:40
Alignment explanation
Indices: 41361040--41361137 Score: 137
Period size: 39 Copynumber: 2.5 Consensus size: 40
41361030 GGACTAGGAT
*
41361040 CCGAAGGCATTCGTGCGAGTTAATAAATCCGGGCTAAG-C
1 CCGAAGGCATTCGTGCGAGTTAATAAACCCGGGCTAAGTC
* * * *
41361079 CCGAAGGCATT-GGGCAAGTTACTAAACCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTAATAAACCCGGGCTAAGTC
41361118 CCGAAGGCATTCGTGCGAGT
1 CCGAAGGCATTCGTGCGAGT
41361138 CGCTATAATC
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
38 21 0.42
39 23 0.46
40 6 0.12
ACGTcount: A:0.27, C:0.23, G:0.30, T:0.20
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTAATAAACCCGGGCTAAGTC
Found at i:41362065 original size:40 final size:40
Alignment explanation
Indices: 41362020--41362187 Score: 149
Period size: 40 Copynumber: 4.2 Consensus size: 40
41362010 CGGAATATAA
*
41362020 CCGGATATAACCACGT-GCACAAATACCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* *** * *
41362060 CCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
41362100 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
*** * * * * *
41362140 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
41362180 CCGGATAT
1 CCGGATAT
41362188 TATTCAATTT
Statistics
Matches: 101, Mismatches: 26, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
39 1 0.01
40 100 0.99
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:41362170 original size:80 final size:80
Alignment explanation
Indices: 41362036--41362185 Score: 196
Period size: 80 Copynumber: 1.9 Consensus size: 80
41362026 ATAACCACGT
* *
41362036 GCACAAATACCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATACCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGGCTTAGCC
41362101 CGGATGTAGCCACTA
66 CGGATGTAGCCACTA
* * * * * *
41362116 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGGCTTAG
1 GCACAAATACCTTCGGGTCTTAACCCGGATAGAATGTCTC-GCACGAA-TGCCTTCGGGGCTTAG
41362179 CCCGGAT
64 CCCGGAT
41362186 ATTATTCAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
79 3 0.05
80 57 0.95
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (80 bp):
GCACAAATACCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGGCTTAGCC
CGGATGTAGCCACTA
Found at i:41369353 original size:40 final size:40
Alignment explanation
Indices: 41369308--41369476 Score: 187
Period size: 40 Copynumber: 4.2 Consensus size: 40
41369298 CGGAATATAA
41369308 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
41369348 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
41369388 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * * *
41369428 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
41369468 CCGGATATA
1 CCGGATATA
41369477 TTCAATTTCT
Statistics
Matches: 108, Mismatches: 20, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 1 0.01
40 107 0.99
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:41373394 original size:27 final size:27
Alignment explanation
Indices: 41373352--41373418 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
41373342 ATTTAAACCC
*
41373352 TAGGGT-ATATCGGTAATTTTGCTCTT
1 TAGGGTAATTTCGGTAATTTTGCTCTT
41373378 TAGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGTAATTTCGGTAATTTTGCTCTT
41373405 TAGGGGTAATTTCG
1 TA-GGGTAATTTCG
41373419 TGATCTACGC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 6 0.16
27 21 0.55
28 11 0.29
ACGTcount: A:0.19, C:0.10, G:0.25, T:0.45
Consensus pattern (27 bp):
TAGGGTAATTTCGGTAATTTTGCTCTT
Found at i:41379324 original size:28 final size:28
Alignment explanation
Indices: 41379263--41379360 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
41379253 TCACAAATTG
** * *
41379263 GCACTAAGTGTGCGGGTTCAAATTATACA
1 GCACTAAGTGTGCAAGTTC-GATTATATA
*
41379292 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCAAGTTCGATTATATA
* *
41379320 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCAAGTTCGATTATAT-A
41379348 GCACTAAGTGTGC
1 GCACTAAGTGTGC
41379361 GGGCTTATTG
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.02
28 43 0.72
29 16 0.27
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCAAGTTCGATTATATA
Found at i:41387002 original size:28 final size:28
Alignment explanation
Indices: 41386941--41387038 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
41386931 TCACAAATTG
** * *
41386941 GCACTAAGTGTGCGGGTTCAAATTATACA
1 GCACTAAGTGTGCAAGTTC-GATTATATA
*
41386970 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCAAGTTCGATTATATA
* *
41386998 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCAAGTTCGATTATAT-A
41387026 GCACTAAGTGTGC
1 GCACTAAGTGTGC
41387039 GGGCTTATTG
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.02
28 43 0.72
29 16 0.27
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCAAGTTCGATTATATA
Found at i:41388699 original size:40 final size:41
Alignment explanation
Indices: 41388614--41388720 Score: 130
Period size: 40 Copynumber: 2.7 Consensus size: 41
41388604 ATACCAGCTC
* * * *
41388614 ATAGCCTGCGGGTCTCT-AGCCTGGATAGCAGTCTAGCACG
1 ATAGCCTGCGGGTCTTTAAGCCCGGATAACAGTCCAGCACG
* *
41388654 A-AGCCTGCGGGTCTTTAAGCCCGGATAACATTCCAGCA-T
1 ATAGCCTGCGGGTCTTTAAGCCCGGATAACAGTCCAGCACG
*
41388693 ATAGCCTGCGGGTCTTTAAGCCCAGATA
1 ATAGCCTGCGGGTCTTTAAGCCCGGATA
41388721 CAATTCCTCA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 15 0.26
40 43 0.74
ACGTcount: A:0.23, C:0.27, G:0.26, T:0.23
Consensus pattern (41 bp):
ATAGCCTGCGGGTCTTTAAGCCCGGATAACAGTCCAGCACG
Found at i:41389486 original size:2 final size:2
Alignment explanation
Indices: 41389481--41389505 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41389471 ATATAGCCGA
41389481 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
41389506 GTTCATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41399924 original size:2 final size:2
Alignment explanation
Indices: 41399919--41399943 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41399909 ATATAGCCGA
41399919 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
41399944 GTTCATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41403291 original size:27 final size:27
Alignment explanation
Indices: 41403261--41403405 Score: 209
Period size: 27 Copynumber: 5.4 Consensus size: 27
41403251 GGGCAAAATA
* * * *
41403261 GTAATTTTACCCCACAAGGGTATCTCG
1 GTAATTCTACCCTACAGGGGTATTTCG
41403288 GTAATTCTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCG
* * *
41403315 GTATTTCTACCCTACAAGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCG
*
41403342 ATAATTCTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCG
*
41403369 GTAATTCTACCTTACAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCG
41403396 GTAATTCTAC
1 GTAATTCTAC
41403406 AACTTATCCA
Statistics
Matches: 105, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 105 1.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (27 bp):
GTAATTCTACCCTACAGGGGTATTTCG
Found at i:41408689 original size:40 final size:40
Alignment explanation
Indices: 41408623--41408789 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 40
41408613 AAATTGAATG
* * *
41408623 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
41408662 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
41408702 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
41408742 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
41408782 ATATCCGG
1 ATATCCGG
41408790 TTATATTCCG
Statistics
Matches: 103, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
39 16 0.16
40 85 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:41416697 original size:40 final size:40
Alignment explanation
Indices: 41416631--41416797 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 40
41416621 AAATTGAATG
* * *
41416631 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
41416670 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
41416710 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
41416750 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
41416790 ATATCCGG
1 ATATCCGG
41416798 TTATATTCCG
Statistics
Matches: 103, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
39 16 0.16
40 85 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:41423534 original size:42 final size:42
Alignment explanation
Indices: 41423443--41423584 Score: 119
Period size: 43 Copynumber: 3.3 Consensus size: 42
41423433 GACCACGCCC
*
41423443 GGGACATTGGCATCG-ACTTATGATTT-ACGTGTAAGACCATGTCT
1 GGGACATTGGCATCGTA-TT-TGATTTCAC--GTAAGACCCTGTCT
* *
41423487 AGGACATTGGCATCGTATTTGATTTCACGAAAGACCCTGTCT
1 GGGACATTGGCATCGTATTTGATTTCACGTAAGACCCTGTCT
* * * * *
41423529 GGGACAGTGACATCATTATTTGATTACATGTAAGACCAC-GTCT
1 GGGACATTGGCATC-GTATTTGATTTCACGTAAGACC-CTGTCT
**
41423572 GGGATGTTGGCAT
1 GGGACATTGGCAT
41423585 TGTACGAGCT
Statistics
Matches: 80, Mismatches: 14, Indels: 9
0.78 0.14 0.09
Matches are distributed among these distances:
42 23 0.29
43 37 0.46
44 19 0.24
45 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (42 bp):
GGGACATTGGCATCGTATTTGATTTCACGTAAGACCCTGTCT
Found at i:41424389 original size:22 final size:22
Alignment explanation
Indices: 41424351--41424393 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
41424341 TTGGCATGAT
41424351 TTTGGTATGGTTATAATCATGGA
1 TTTGGTATGGTTATAAT-ATGGA
*
41424374 TTTGGT-TGTTTATAATATGG
1 TTTGGTATGGTTATAATATGG
41424394 TATGAATGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 9 0.47
23 6 0.32
ACGTcount: A:0.23, C:0.02, G:0.26, T:0.49
Consensus pattern (22 bp):
TTTGGTATGGTTATAATATGGA
Found at i:41429574 original size:40 final size:40
Alignment explanation
Indices: 41429516--41429733 Score: 327
Period size: 40 Copynumber: 5.5 Consensus size: 40
41429506 CGGATGATAA
* *
41429516 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
41429556 CCGGGCTAAG-CCCTGAAGGCCTTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCC-GAAGGCATTTGTGCGAGTTACTATAT
41429596 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
41429636 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
41429676 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
41429716 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
41429734 TACTTGGTTT
Statistics
Matches: 166, Mismatches: 8, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
39 20 0.12
40 142 0.86
41 4 0.02
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:41431144 original size:42 final size:43
Alignment explanation
Indices: 41431085--41431194 Score: 134
Period size: 43 Copynumber: 2.6 Consensus size: 43
41431075 GGGTGTTACA
* * * *
41431085 AAGACCATGTCTGGGACATTGGTATCG-TATTTGATTTCGTGT
1 AAGACCATGTCTGGGACAGTGGCATCGATATTTGATTACATGT
*
41431127 AAGACCCTGTCTGGGACAGTGGCATCGATATTTGATTACATGT
1 AAGACCATGTCTGGGACAGTGGCATCGATATTTGATTACATGT
* *
41431170 AAGACCACGACTGGGAC-GTTGGCAT
1 AAGACCATGTCTGGGACAG-TGGCAT
41431195 TGTACAAGCT
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 25 0.43
43 33 0.57
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (43 bp):
AAGACCATGTCTGGGACAGTGGCATCGATATTTGATTACATGT
Found at i:41450447 original size:40 final size:39
Alignment explanation
Indices: 41450403--41450531 Score: 111
Period size: 40 Copynumber: 3.3 Consensus size: 39
41450393 GACTCGCTCA
*
41450403 AATGCCTTCGGGAC-GAAGCCC-GGTTATAGCGACTTGCAC
1 AATGCCTTCGGGACTGAA-CCCGGGTT-TAGCAACTTGCAC
* *
41450442 GAATGCCTTCGGGACTTAACCCGGGTTTAGTAACTTGCAC
1 -AATGCCTTCGGGACTGAACCCGGGTTTAGCAACTTGCAC
* * * * ** *
41450482 AAAGCCTTCGGGA-TTAGCCCGGATTTATTAACTCGCAC
1 AATGCCTTCGGGACTGAACCCGGGTTTAGCAACTTGCAC
41450520 GAATGCCTTCGG
1 -AATGCCTTCGG
41450532 ATCCTAGTCC
Statistics
Matches: 77, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
38 21 0.27
39 22 0.29
40 28 0.36
41 6 0.08
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTGAACCCGGGTTTAGCAACTTGCAC
Found at i:41450531 original size:78 final size:80
Alignment explanation
Indices: 41450438--41450584 Score: 210
Period size: 78 Copynumber: 1.9 Consensus size: 80
41450428 ATAGCGACTT
* * *
41450438 GCACGAATGCCTTCGGGA-CTTAACCCGGGTTTAGTAACTT-GCACAAAGCCTTCGGGA-TTAGC
1 GCACGAATGCCTTC-GGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGC
41450500 CCGGATTTATTAACTC
65 CCGGATTTATTAACTC
** *
41450516 GCACGAATGCCTTCGGATCCTAGTCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTTAGCC
1 GCACGAATGCCTTCGGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCC
41450581 CGGA
66 CGGA
41450585 CATCATTCGA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
77 3 0.05
78 30 0.50
79 17 0.28
80 10 0.17
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (80 bp):
GCACGAATGCCTTCGGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCC
CGGATTTATTAACTC
Found at i:41450568 original size:40 final size:37
Alignment explanation
Indices: 41450419--41450584 Score: 125
Period size: 40 Copynumber: 4.2 Consensus size: 37
41450409 TTCGGGACGA
* ** *
41450419 AGCCCGGTTATAGCGACTTGCACGAATGCCTTCGGGACTT
1 AGCCCGGATATAGTAACTTGCAC-AAAGCCTTC-GGA-TT
* * *
41450459 AACCCGGGTTTAGTAACTTGCACAAAGCCTTCGGGATT
1 AGCCCGGATATAGTAACTTGCACAAAGCCTTC-GGATT
* * * *
41450497 AGCCCGGATTTATTAACTCGCACGAATGCCTTCGGATCCT
1 AGCCCGGATATAGTAACTTGCAC-AAAGCCTTCGGAT--T
* *
41450537 AGTCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTT
1 AGCCCGGATATAGTAACTT-GCACAAAGCCTTC-GGA-TT
41450577 AGCCCGGA
1 AGCCCGGA
41450585 CATCATTCGA
Statistics
Matches: 102, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
38 25 0.25
39 20 0.20
40 49 0.48
41 7 0.07
42 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (37 bp):
AGCCCGGATATAGTAACTTGCACAAAGCCTTCGGATT
Found at i:41458514 original size:40 final size:39
Alignment explanation
Indices: 41458470--41458598 Score: 111
Period size: 40 Copynumber: 3.3 Consensus size: 39
41458460 GACTCGCTCA
*
41458470 AATGCCTTCGGGAC-GAAGCCC-GGTTATAGCGACTTGCAC
1 AATGCCTTCGGGACTGAA-CCCGGGTT-TAGCAACTTGCAC
* *
41458509 GAATGCCTTCGGGACTTAACCCGGGTTTAGTAACTTGCAC
1 -AATGCCTTCGGGACTGAACCCGGGTTTAGCAACTTGCAC
* * * * ** *
41458549 AAAGCCTTCGGGA-TTAGCCCGGATTTATTAACTCGCAC
1 AATGCCTTCGGGACTGAACCCGGGTTTAGCAACTTGCAC
41458587 GAATGCCTTCGG
1 -AATGCCTTCGG
41458599 ATCCTAGTCC
Statistics
Matches: 77, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
38 21 0.27
39 22 0.29
40 28 0.36
41 6 0.08
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTGAACCCGGGTTTAGCAACTTGCAC
Found at i:41458598 original size:78 final size:80
Alignment explanation
Indices: 41458505--41458651 Score: 210
Period size: 78 Copynumber: 1.9 Consensus size: 80
41458495 ATAGCGACTT
* * *
41458505 GCACGAATGCCTTCGGGA-CTTAACCCGGGTTTAGTAACTT-GCACAAAGCCTTCGGGA-TTAGC
1 GCACGAATGCCTTC-GGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGC
41458567 CCGGATTTATTAACTC
65 CCGGATTTATTAACTC
** *
41458583 GCACGAATGCCTTCGGATCCTAGTCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTTAGCC
1 GCACGAATGCCTTCGGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCC
41458648 CGGA
66 CGGA
41458652 CATCATTCGA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
77 3 0.05
78 30 0.50
79 17 0.28
80 10 0.17
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (80 bp):
GCACGAATGCCTTCGGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCC
CGGATTTATTAACTC
Found at i:41458635 original size:40 final size:37
Alignment explanation
Indices: 41458486--41458651 Score: 125
Period size: 40 Copynumber: 4.2 Consensus size: 37
41458476 TTCGGGACGA
* ** *
41458486 AGCCCGGTTATAGCGACTTGCACGAATGCCTTCGGGACTT
1 AGCCCGGATATAGTAACTTGCAC-AAAGCCTTC-GGA-TT
* * *
41458526 AACCCGGGTTTAGTAACTTGCACAAAGCCTTCGGGATT
1 AGCCCGGATATAGTAACTTGCACAAAGCCTTC-GGATT
* * * *
41458564 AGCCCGGATTTATTAACTCGCACGAATGCCTTCGGATCCT
1 AGCCCGGATATAGTAACTTGCAC-AAAGCCTTCGGAT--T
* *
41458604 AGTCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTT
1 AGCCCGGATATAGTAACTT-GCACAAAGCCTTC-GGA-TT
41458644 AGCCCGGA
1 AGCCCGGA
41458652 CATCATTCGA
Statistics
Matches: 102, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
38 25 0.25
39 20 0.20
40 49 0.48
41 7 0.07
42 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (37 bp):
AGCCCGGATATAGTAACTTGCACAAAGCCTTCGGATT
Found at i:41463423 original size:9 final size:9
Alignment explanation
Indices: 41463409--41463433 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
41463399 ACAAGTTTTG
41463409 CAATTTATT
1 CAATTTATT
41463418 CAATTTATT
1 CAATTTATT
41463427 CAATTTA
1 CAATTTA
41463434 GTCCTTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (9 bp):
CAATTTATT
Found at i:41465686 original size:27 final size:27
Alignment explanation
Indices: 41465655--41465950 Score: 337
Period size: 27 Copynumber: 11.0 Consensus size: 27
41465645 TAGAATACTT
**
41465655 TAGTTTACCAAATTACCAAAATACCCC
1 TAGTTTATAAAATTACCAAAATACCCC
* * *
41465682 TAGTTTGTAAAATTACTAAAATACCCT
1 TAGTTTATAAAATTACCAAAATACCCC
* *
41465709 TGGTTTATAAAATCACCAAAATACCCC
1 TAGTTTATAAAATTACCAAAATACCCC
* * * *
41465736 TGGTTTGTAAAATTACTAAAATACCCT
1 TAGTTTATAAAATTACCAAAATACCCC
*
41465763 TAGTTTATAAAATTACCAAAATACCCT
1 TAGTTTATAAAATTACCAAAATACCCC
* **
41465790 TAGTTTGTAAAATTACCAAAATACCAT
1 TAGTTTATAAAATTACCAAAATACCCC
* *
41465817 TGGTTTACAAAATTACCAAAATA-CCC
1 TAGTTTATAAAATTACCAAAATACCCC
* * * *
41465843 TTGCTTTATAAAATTACTAGAATACCCT
1 TAG-TTTATAAAATTACCAAAATACCCC
41465871 TAGTTTATAAAATTACCAAAATACCCC
1 TAGTTTATAAAATTACCAAAATACCCC
41465898 T-GATTTATAAAATTACCAAAATACCCC
1 TAG-TTTATAAAATTACCAAAATACCCC
* *
41465925 T-GATTTGTGAAATTACCAAAATACCC
1 TAG-TTTATAAAATTACCAAAATACCC
41465951 TTGTAGGGTA
Statistics
Matches: 231, Mismatches: 35, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
26 4 0.02
27 223 0.97
28 4 0.02
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.32
Consensus pattern (27 bp):
TAGTTTATAAAATTACCAAAATACCCC
Found at i:41465729 original size:54 final size:54
Alignment explanation
Indices: 41465664--41465950 Score: 389
Period size: 54 Copynumber: 5.3 Consensus size: 54
41465654 TTAGTTTACC
41465664 AAATTACCAAAATACCCCTAGTTTGTAAAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACTAAAATACCCTTGGTTTATA
* * *
41465718 AAATCACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTAGTTTATA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACTAAAATACCCTTGGTTTATA
* * * *
41465772 AAATTACCAAAATACCCTTAGTTTGTAAAATTACCAAAATACCATTGGTTTACA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACTAAAATACCCTTGGTTTATA
* * * *
41465826 AAATTACCAAAATA-CCCTTGCTTTATAAAATTACTAGAATACCCTTAGTTTATA
1 AAATTACCAAAATACCCCTAG-TTTGTAAAATTACTAAAATACCCTTGGTTTATA
* * * * * *
41465880 AAATTACCAAAATACCCCT-GATTTATAAAATTACCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATACCCCTAG-TTTGTAAAATTACTAAAATACCCTTGGTTTATA
41465934 AAATTACCAAAATACCC
1 AAATTACCAAAATACCC
41465951 TTGTAGGGTA
Statistics
Matches: 205, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
53 4 0.02
54 197 0.96
55 4 0.02
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (54 bp):
AAATTACCAAAATACCCCTAGTTTGTAAAATTACTAAAATACCCTTGGTTTATA
Found at i:41465801 original size:81 final size:81
Alignment explanation
Indices: 41465664--41465952 Score: 384
Period size: 81 Copynumber: 3.6 Consensus size: 81
41465654 TTAGTTTACC
* * * *
41465664 AAATTACCAAAATACCCCT-AGTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAATCACCAA
1 AAATTACCAAAATACCCCTGA-TTTATAAAATTACCAAAATACCCTTAGTTTATAAAATTACCAA
*
41465728 AATACCCCTGGTTTGTA
65 AATACCCCTGGTTTATA
* * *
41465745 AAATTACTAAAATA-CCCTTAGTTTATAAAATTACCAAAATACCCTTAGTTTGTAAAATTACCAA
1 AAATTACCAAAATACCCCTGA-TTTATAAAATTACCAAAATACCCTTAGTTTATAAAATTACCAA
** *
41465809 AATACCATTGGTTTACA
65 AATACCCCTGGTTTATA
* * * *
41465826 AAATTACCAAAATACCCTTGCTTTATAAAATTACTAGAATACCCTTAGTTTATAAAATTACCAAA
1 AAATTACCAAAATACCCCTGATTTATAAAATTACCAAAATACCCTTAGTTTATAAAATTACCAAA
*
41465891 ATACCCCTGATTTATA
66 ATACCCCTGGTTTATA
* *
41465907 AAATTACCAAAATACCCCTGATTTGTGAAATTACCAAAATACCCTT
1 AAATTACCAAAATACCCCTGATTTATAAAATTACCAAAATACCCTT
41465953 GTAGGGTAGA
Statistics
Matches: 179, Mismatches: 27, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
80 4 0.02
81 172 0.96
82 3 0.02
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.32
Consensus pattern (81 bp):
AAATTACCAAAATACCCCTGATTTATAAAATTACCAAAATACCCTTAGTTTATAAAATTACCAAA
ATACCCCTGGTTTATA
Found at i:41465965 original size:27 final size:27
Alignment explanation
Indices: 41465881--41466131 Score: 283
Period size: 27 Copynumber: 9.3 Consensus size: 27
41465871 TAGTTTATAA
*** *
41465881 AATTACCAAAATACCCCTG-ATTTATAA
1 AATTACCAAAATACCCCTGTA-GGGTAG
**
41465908 AATTACCAAAATACCCCTG-ATTTGT-G
1 AATTACCAAAATACCCCTGTA-GGGTAG
*
41465934 AAATTACCAAAATACCCTTGTAGGGTAG
1 -AATTACCAAAATACCCCTGTAGGGTAG
*
41465962 AATTACCAGAATACCCCTGTAGGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAG
*
41465989 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAG
* *
41466016 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAG
* *
41466043 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAG
*
41466070 AATTACCAAAATACCCCTATAGGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAG
* * * * *
41466097 AATTACCGAGATACCCTTGTGGGGTAA
1 AATTACCAAAATACCCCTGTAGGGTAG
41466124 AATTACCA
1 AATTACCA
41466132 TTTTACCCCT
Statistics
Matches: 199, Mismatches: 22, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
27 197 0.99
28 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (27 bp):
AATTACCAAAATACCCCTGTAGGGTAG
Found at i:41466511 original size:22 final size:22
Alignment explanation
Indices: 41466477--41466536 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
41466467 ACACGTTATC
41466477 GATGGC-TCTGTGCCAACCTAAA
1 GATGGCTTC-GTGCCAACCTAAA
* * * * *
41466499 TATGGCTTCGTGCCATCTTGAC
1 GATGGCTTCGTGCCAACCTAAA
41466521 GATGGCTTCGTGCCAA
1 GATGGCTTCGTGCCAA
41466537 ACGTATTTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
22 28 0.93
23 2 0.07
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.28
Consensus pattern (22 bp):
GATGGCTTCGTGCCAACCTAAA
Found at i:41466724 original size:27 final size:27
Alignment explanation
Indices: 41466694--41466758 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
41466684 ATTCTGTTAA
* * *
41466694 GTGGCTTTGCCA-TATTATCTGATTCTG
1 GTGGCTTTGCCACAAATATCT-ATACTG
*
41466721 GTGGCTATGCCACAAATATCTATACTG
1 GTGGCTTTGCCACAAATATCTATACTG
*
41466748 GAGGCTTTGCC
1 GTGGCTTTGCC
41466759 TCAACTTACT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
27 25 0.81
28 6 0.19
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (27 bp):
GTGGCTTTGCCACAAATATCTATACTG
Found at i:41466939 original size:6 final size:6
Alignment explanation
Indices: 41466924--41467047 Score: 58
Period size: 6 Copynumber: 19.8 Consensus size: 6
41466914 ATTCTGTTAC
* * * *
41466924 CTGATA CTGATT CTGATT TTGATT CTG-TT ACCTGATA CTAATT CTGATT
1 CTGATT CTGATT CTGATT CTGATT CTGATT --CTGATT CTGATT CTGATT
* * * *
41466973 CTGATT CTG-TCAC CTAATT CTGATT CTGATATT CTG-TCAC CTCATT
1 CTGATT CTGAT--T CTGATT CTGATT CTG--ATT CTGAT--T CTGATT
*
41467019 CTGATT CTGATT TTGATT CT-AGTT CTGAT
1 CTGATT CTGATT CTGATT CTGA-TT CTGAT
41467048 AATGTTTCTT
Statistics
Matches: 88, Mismatches: 17, Indels: 26
0.67 0.13 0.20
Matches are distributed among these distances:
5 5 0.06
6 66 0.75
7 8 0.09
8 9 0.10
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.47
Consensus pattern (6 bp):
CTGATT
Found at i:41466952 original size:31 final size:31
Alignment explanation
Indices: 41466901--41467038 Score: 158
Period size: 31 Copynumber: 4.5 Consensus size: 31
41466891 TTGCATTCAC
* *
41466901 ATTCTGATTTTTTATTCTGTTACCTGATACTG
1 ATTCTGA-TTTTGATTCTGTCACCTGATACTG
* *
41466933 ATTCTGATTTTGATTCTGTTACCTGATACTA
1 ATTCTGATTTTGATTCTGTCACCTGATACTG
* * *
41466964 ATTCTGATTCTGATTCTGTCACCTAATTCTG
1 ATTCTGATTTTGATTCTGTCACCTGATACTG
* *
41466995 ATTCTGA---T-ATTCTGTCACCTCATTCTG
1 ATTCTGATTTTGATTCTGTCACCTGATACTG
41467022 ATTCTGATTTTGATTCT
1 ATTCTGATTTTGATTCT
41467039 AGTTCTGATA
Statistics
Matches: 94, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
27 25 0.27
28 1 0.01
30 1 0.01
31 60 0.64
32 7 0.07
ACGTcount: A:0.20, C:0.19, G:0.12, T:0.49
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTCACCTGATACTG
Found at i:41467014 original size:27 final size:27
Alignment explanation
Indices: 41466961--41467029 Score: 115
Period size: 27 Copynumber: 2.6 Consensus size: 27
41466951 TTACCTGATA
41466961 CTAATTCTGATTCTG--ATTCTGTCAC
1 CTAATTCTGATTCTGATATTCTGTCAC
41466986 CTAATTCTGATTCTGATATTCTGTCAC
1 CTAATTCTGATTCTGATATTCTGTCAC
*
41467013 CTCATTCTGATTCTGAT
1 CTAATTCTGATTCTGAT
41467030 TTTGATTCTA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 15 0.37
27 26 0.63
ACGTcount: A:0.20, C:0.23, G:0.12, T:0.45
Consensus pattern (27 bp):
CTAATTCTGATTCTGATATTCTGTCAC
Found at i:41468943 original size:39 final size:39
Alignment explanation
Indices: 41468812--41469002 Score: 172
Period size: 40 Copynumber: 4.8 Consensus size: 39
41468802 GGATATAACG
* ** **
41468812 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGG-TTATAGCG
1 ACTCGCAC-AATGCCTTCGGGACTTAGCCCGGATT-TAGTA
* *
41468852 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCAC-AATGCCTTCGGGACTTAGCCCGGATTTAGTA
* *
41468892 ACTTGCACAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * * *
41468930 ACTCGCACGAATGCCTTC-GGATCCTAGTCCGGATATAGTC
1 ACTCGCAC-AATGCCTTCGGGA-CTTAGCCCGGATTTAGTA
* *
41468970 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAATGCCTTCGGGACTTAGCCCGGA
41469003 CATCATTCGA
Statistics
Matches: 124, Mismatches: 21, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
38 24 0.19
39 21 0.17
40 69 0.56
41 10 0.08
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.24
Consensus pattern (39 bp):
ACTCGCACAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:41468947 original size:78 final size:80
Alignment explanation
Indices: 41468852--41469002 Score: 209
Period size: 78 Copynumber: 1.9 Consensus size: 80
41468842 GGTTATAGCG
* * * *
41468852 ACTCGCACGAATGCCTTCGGGA-CTTAACCCGGGTTTAGTAACTT-GCACAATGCCTTCGGG-CT
1 ACTCGCACGAATGCCTTC-GGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACT
41468914 TAGCCCGGATTTATTA
65 TAGCCCGGATTTATTA
** *
41468930 ACTCGCACGAATGCCTTCGGATCCTAGTCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTT
1 ACTCGCACGAATGCCTTCGGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTT
41468995 AGCCCGGA
66 AGCCCGGA
41469003 CATCATTCGA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
77 3 0.05
78 34 0.54
79 15 0.24
80 11 0.17
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.25
Consensus pattern (80 bp):
ACTCGCACGAATGCCTTCGGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTT
AGCCCGGATTTATTA
Found at i:41476968 original size:39 final size:39
Alignment explanation
Indices: 41476837--41477027 Score: 172
Period size: 40 Copynumber: 4.8 Consensus size: 39
41476827 GGATATAACG
* ** **
41476837 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGG-TTATAGCG
1 ACTCGCAC-AATGCCTTCGGGACTTAGCCCGGATT-TAGTA
* *
41476877 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCAC-AATGCCTTCGGGACTTAGCCCGGATTTAGTA
* *
41476917 ACTTGCACAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * * *
41476955 ACTCGCACGAATGCCTTC-GGATCCTAGTCCGGATATAGTC
1 ACTCGCAC-AATGCCTTCGGGA-CTTAGCCCGGATTTAGTA
* *
41476995 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAATGCCTTCGGGACTTAGCCCGGA
41477028 CATCATTCGA
Statistics
Matches: 124, Mismatches: 21, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
38 24 0.19
39 21 0.17
40 69 0.56
41 10 0.08
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.24
Consensus pattern (39 bp):
ACTCGCACAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:41476972 original size:78 final size:80
Alignment explanation
Indices: 41476877--41477027 Score: 209
Period size: 78 Copynumber: 1.9 Consensus size: 80
41476867 GGTTATAGCG
* * * *
41476877 ACTCGCACGAATGCCTTCGGGA-CTTAACCCGGGTTTAGTAACTT-GCACAATGCCTTCGGG-CT
1 ACTCGCACGAATGCCTTC-GGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACT
41476939 TAGCCCGGATTTATTA
65 TAGCCCGGATTTATTA
** *
41476955 ACTCGCACGAATGCCTTCGGATCCTAGTCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTT
1 ACTCGCACGAATGCCTTCGGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTT
41477020 AGCCCGGA
66 AGCCCGGA
41477028 CATCATTCGA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
77 3 0.05
78 34 0.54
79 15 0.24
80 11 0.17
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.25
Consensus pattern (80 bp):
ACTCGCACGAATGCCTTCGGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTT
AGCCCGGATTTATTA
Found at i:41484187 original size:28 final size:28
Alignment explanation
Indices: 41484151--41484260 Score: 152
Period size: 28 Copynumber: 4.0 Consensus size: 28
41484141 CTGCCAGAAT
* * *
41484151 AGAT-ATTGTGACAGAGTCACCAGATAC
1 AGATAATTGTGGCAGAGCCACCAGAAAC
*
41484178 AGATAATTGTGGCAGGGCCACCAGAAAC
1 AGATAATTGTGGCAGAGCCACCAGAAAC
*
41484206 AGATATTTGTGGCAGAGCCACCAGAAAC
1 AGATAATTGTGGCAGAGCCACCAGAAAC
*
41484234 AGATATTTGTGGCAGAGCCACCA-AAAC
1 AGATAATTGTGGCAGAGCCACCAGAAAC
41484261 GCTTCCTCCA
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
27 8 0.11
28 68 0.89
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (28 bp):
AGATAATTGTGGCAGAGCCACCAGAAAC
Found at i:41484421 original size:26 final size:26
Alignment explanation
Indices: 41484367--41484424 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
41484357 TCAACCCTAG
* *
41484367 GGGTATAATGGTCATTTTGCACCTAA
1 GGGTATAATGGTAATTTTGCAACTAA
*
41484393 GGGTATAATGGTAATTTT-CATACTTA
1 GGGTATAATGGTAATTTTGCA-ACTAA
41484419 GGGTAT
1 GGGTAT
41484425 TTTATAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 2 0.07
26 26 0.93
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.38
Consensus pattern (26 bp):
GGGTATAATGGTAATTTTGCAACTAA
Found at i:41493647 original size:33 final size:34
Alignment explanation
Indices: 41493570--41493650 Score: 94
Period size: 33 Copynumber: 2.4 Consensus size: 34
41493560 TCTGGGCCAT
*
41493570 ACTGTTATCTGAATAAGGGGCTAAGGCCCAGTTT
1 ACTGTTATCTGAATAAGGGGCTAAGGCCCAGTTC
* * **
41493604 AATGTAATCTGAA-AA-GGGCTCTGGCCCAGTATC
1 ACTGTTATCTGAATAAGGGGCTAAGGCCCAGT-TC
41493637 ACTGTTATCTGAAT
1 ACTGTTATCTGAAT
41493651 GGGCTTAGGC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
32 13 0.34
33 14 0.37
34 11 0.29
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (34 bp):
ACTGTTATCTGAATAAGGGGCTAAGGCCCAGTTC
Found at i:41493655 original size:32 final size:30
Alignment explanation
Indices: 41493570--41493663 Score: 71
Period size: 32 Copynumber: 2.9 Consensus size: 30
41493560 TCTGGGCCAT
* *
41493570 ACTGTTATCTGAATAAGGGGCTAAGGCCCAGTTT
1 ACTGTTATCTGAAT---GGGCT-TGGCCCAGTTC
* * *
41493604 AATGTAATCTGAAAAGGGCTCTGGCCCAGTATC
1 ACTGTTATCTG-AATGGGCT-TGGCCCAGT-TC
41493637 ACTGTTATCTGAATGGGCTTAGGCCCA
1 ACTGTTATCTGAATGGGCTT-GGCCCA
41493664 ATGGGCTTGA
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
31 1 0.02
32 26 0.54
33 10 0.21
34 9 0.19
35 2 0.04
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.28
Consensus pattern (30 bp):
ACTGTTATCTGAATGGGCTTGGCCCAGTTC
Found at i:41504616 original size:93 final size:93
Alignment explanation
Indices: 41504501--41504673 Score: 301
Period size: 93 Copynumber: 1.9 Consensus size: 93
41504491 CGCCCATAAG
* *
41504501 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCA
41504566 ACGAGCTCGGATGCCTAGTTACATCTCA
66 ACGAGCTCGGATGCCTAGTTACATCTCA
* *
41504594 CGAACTCGGACTCAACTCAACGAGTTCGGATGCTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
41504659 ACGAGTTCGGATGCC
66 ACGAGCTCGGATGCC
41504674 CAAATATCCC
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.20
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCA
Found at i:41504669 original size:46 final size:46
Alignment explanation
Indices: 41504494--41504672 Score: 220
Period size: 46 Copynumber: 3.9 Consensus size: 46
41504484 TGTAACCCGC
** *
41504494 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGATGCTCGCAT
* *
41504540 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGATG-CTCG---CAT
* *
41504590 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGATGCTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGATGCTCGCAT
* *
41504633 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGATGC
41504673 CCAAATATCC
Statistics
Matches: 115, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 71 0.62
47 32 0.28
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGATGCTCGCAT
Found at i:41511400 original size:49 final size:48
Alignment explanation
Indices: 41511328--41511513 Score: 246
Period size: 49 Copynumber: 3.8 Consensus size: 48
41511318 TGAGGTCACG
* *
41511328 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAT-GTTGGTCGCA
** * * *
41511377 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATTAGATGGTGAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAT-GT-TGGTCGCA
*
41511427 TGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGACTGTTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA-TGTTGGTCGCA
* *
41511476 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGAT
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAT
41511514 AGCTTCGGCT
Statistics
Matches: 118, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
48 1 0.01
49 75 0.64
50 41 0.35
51 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (48 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGTTGGTCGCA
Found at i:41511488 original size:99 final size:99
Alignment explanation
Indices: 41511317--41511501 Score: 327
Period size: 99 Copynumber: 1.9 Consensus size: 99
41511307 ATGAACTATT
* *
41511317 GTGAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGT
1 GTGAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATAATTGGTCGCATGTGT
41511382 AGTACTAAGTGCAGGCTACTACGTGTATTAGATG
66 AGTACTAAGTGCAGGCTACTACGTGTATTAGATG
*
41511416 GTGAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGACT-GTTGGTCGCATGTG
1 GTGAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGA-TAATTGGTCGCATGTG
41511480 TAGTACTAAGTGCAGGCTACTA
65 TAGTACTAAGTGCAGGCTACTA
41511502 TGCGTACCAG
Statistics
Matches: 82, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
99 81 0.99
100 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (99 bp):
GTGAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATAATTGGTCGCATGTGT
AGTACTAAGTGCAGGCTACTACGTGTATTAGATG
Found at i:41514547 original size:2 final size:2
Alignment explanation
Indices: 41514540--41514567 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
41514530 TCACATAATC
41514540 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
41514568 CCCATGTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41519272 original size:17 final size:17
Alignment explanation
Indices: 41519232--41519278 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
41519222 GGTCAAACAT
*
41519232 TATTATAATTGTGGTAAT
1 TATTATAATT-TGGTAAC
41519250 TATTAT-ATTTGGTTAAC
1 TATTATAATTTGG-TAAC
*
41519267 TATTATGATTTG
1 TATTATAATTTG
41519279 ATTCATATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 3 0.12
17 12 0.46
18 11 0.42
ACGTcount: A:0.30, C:0.02, G:0.15, T:0.53
Consensus pattern (17 bp):
TATTATAATTTGGTAAC
Found at i:41527317 original size:539 final size:519
Alignment explanation
Indices: 41526101--41527157 Score: 1555
Period size: 539 Copynumber: 2.0 Consensus size: 519
41526091 AGGTCAATGT
* * ** * ***
41526101 ACCTGTTTTACTGTGACAGAAATACAAGAGCAATGCTTATGCAGCTGTTCAAATTTGGTTACATA
1 ACCTGGTTTACTGTGACAGAAATAAAAGAAAAATGCCTATGCAGCTGTTCAAAGAAGG-TACATA
* * *
41526166 CATTGCATGAGCTATGACCACAGAGAAAAGAGAAAT--AGGGAGGGTGGAAGGAACTCCAGTTCC
65 CATTGCATAAGCTATGACCACAGAGAAAAGAGAAATAGAGGGAGGGTGGAAGGAAC-CCAGATCT
*
41526229 ATTGCTATGACCAGGCTAATAAATGAAAGGAGATGTGGTTGTGAGGGAAATGGTGAAAAAGAAAG
129 A-TGC-A-GA-C-GACTAATAAATGAAAGGAGATGTGGTTGTGAGGGAAATGGTGAAAAAGAAAG
*
41526294 GGGGGGAGAATAGGGGGCATTGATCAGGACTCTTGTTTCCATTTCAACTTGAGTTTCAGAAAGGA
189 GGGGGGAGAATAGGGGGCATTGATCAGGACTCTTGTTTCCATTACAACTTGAGTTTCAGAAAGGA
41526359 ACACATATTTGGGCCCAAATTTCATTCTAATTAACTAATTTAATAAAAGTTTATGTCTTAGACCA
254 ACACATATTTGGGCCCAAATTTCATTCTAATTAACTAATTTAATAAAAGTTTATGTCTTAGACCA
*
41526424 GCCCAGCTCTGAATTGTCTTTTGCTCAAAGTTTCAGAACTAACAGTCAGCTAAAGAGAATATAAA
319 GCCCAGCTCTGAATTGTCTTTTGCTCAAAATTTCAGAACTAACAGTCAGCTAAAGAGAATATAAA
* * * *
41526489 AGTATTGAAACCAATATGCTTTAGATTTAAAGGTGTAGATAAAATATCTCATAAACTTAAAAATT
384 AGTATGGAAACCAATATGCTTCAGATTTAAACGTGTAGATAAAATATCTCATAAACTGAAAAATT
41526554 TCAGCTTGATCAAAACAAAAATTATTCACAACTATTTCCTTCAGTCAAATTCATTATTATTCAAG
449 TCAGCTTGATCAAAACAAAAATTATTCACAACTATTTCCTTCAGTCAAATTCATTATTATTCAAG
41526619 GTCAACGC
514 G--AACGC
* * ** * ***
41526627 ACCTGTTTTACTGTGACAGAAATACAAGAGCAATGCTTATGCAGCTGTTCAAATTTGGTTACATA
1 ACCTGGTTTACTGTGACAGAAATAAAAGAAAAATGCCTATGCAGCTGTTCAAAGAAGG-TACATA
* *
41526692 CATTGCATGAGCTATGACCACAGAGAAAAGAGAAATAGAGGGAGGGTGGAAGGAACTCCAGTTCT
65 CATTGCATAAGCTATGACCACAGAGAAAAGAGAAATAGAGGGAGGGTGGAAGGAAC-CCAGATCT
*
41526757 ATTGCTATGACTGGGCTAATAAATGAAAGGAGATGTGGTGGTTGTGAGGGAAATGGTGAAAAAGA
129 A-TGC-A-GAC--GACTAATAAATGAAAGGAGA--T-GTGGTTGTGAGGGAAATGGTGAAAAAGA
*
41526822 AGAGGGGGGGGGGGGGGGGAATAGGGGGCATTGATCAGGACTCTTGTTTCCATTACAACTTGAGT
186 A-A-------GGGGGGGAGAATAGGGGGCATTGATCAGGACTCTTGTTTCCATTACAACTTGAGT
41526887 TTCAGAAAGGAACACATATTTGGGCCCAAATTTCATTCTAATTAACTAATTTAATAAAAGTTTAT
243 TTCAGAAAGGAACACATATTTGGGCCCAAATTTCATTCTAATTAACTAATTTAATAAAAGTTTAT
41526952 GTCTTAGACCAGCCCAGCTCTGAATTGTCTTTTGCTCAAAATTTCAGAACTAACAGTCAGCTAAA
308 GTCTTAGACCAGCCCAGCTCTGAATTGTCTTTTGCTCAAAATTTCAGAACTAACAGTCAGCTAAA
41527017 GAGAATATAAAAGTA-GGAAACCAATATGCTTCAGATTTAAACGTGTAGATAAAATATCTCATAA
373 GAGAATATAAAAGTATGGAAACCAATATGCTTCAGATTTAAACGTGTAGATAAAATATCTCATAA
*
41527081 ACTGAAAAATTTCAGCTTGATCAAAA-AAAAATTATTTACAACTATTTCCTTCAGTCAAATTCAT
438 ACTGAAAAATTTCAGCTTGATCAAAACAAAAATTATTCACAACTATTTCCTTCAGTCAAATTCAT
*
41527145 TATTATTTAAGGA
503 TATTATTCAAGGA
41527158 TGCATTTGGT
Statistics
Matches: 506, Mismatches: 11, Indels: 19
0.94 0.02 0.04
Matches are distributed among these distances:
526 101 0.20
527 1 0.00
528 56 0.11
530 1 0.00
531 29 0.06
532 1 0.00
535 1 0.00
537 48 0.09
538 71 0.14
539 197 0.39
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (519 bp):
ACCTGGTTTACTGTGACAGAAATAAAAGAAAAATGCCTATGCAGCTGTTCAAAGAAGGTACATAC
ATTGCATAAGCTATGACCACAGAGAAAAGAGAAATAGAGGGAGGGTGGAAGGAACCCAGATCTAT
GCAGACGACTAATAAATGAAAGGAGATGTGGTTGTGAGGGAAATGGTGAAAAAGAAAGGGGGGGA
GAATAGGGGGCATTGATCAGGACTCTTGTTTCCATTACAACTTGAGTTTCAGAAAGGAACACATA
TTTGGGCCCAAATTTCATTCTAATTAACTAATTTAATAAAAGTTTATGTCTTAGACCAGCCCAGC
TCTGAATTGTCTTTTGCTCAAAATTTCAGAACTAACAGTCAGCTAAAGAGAATATAAAAGTATGG
AAACCAATATGCTTCAGATTTAAACGTGTAGATAAAATATCTCATAAACTGAAAAATTTCAGCTT
GATCAAAACAAAAATTATTCACAACTATTTCCTTCAGTCAAATTCATTATTATTCAAGGAACGC
Found at i:41529048 original size:270 final size:270
Alignment explanation
Indices: 41528567--41529081 Score: 888
Period size: 270 Copynumber: 1.9 Consensus size: 270
41528557 AGCTAATATA
* *
41528567 TGCTTCCAAAAACGTTGTCAAGCATGATTTATAGATACATCCTCCCAGCATAAAAATGCTCTAAT
1 TGCTTCCAAAAACGTTGTCAAGCATGATTTACAGATACATCCTCCAAGCATAAAAATGCTCTAAT
* * *
41528632 ACATTAACAAAAAAAAACTTCACTAACTGGAAAAATTTAGCATGCTCGTTGTGTTCTACTTGTTT
66 ACATTAACAAAAAAAAACTTCACTAACTGGAAAAATTTAGCATGCTCGTCGTGTTCTACCTGTCT
41528697 AAAATCCAATTCTCGAAAGTAAATTTTACTCTAGCATCCCCCAATGGTGCATAAAACTGCCTTAA
131 AAAATCCAATTCTCGAAAGTAAATTTTACTCTAGCATCCCCCAATGGTGCATAAAACTGCCTTAA
* * *
41528762 ACATGCTAAGAGAAACAAATGCATGCAACCAAGGATTACAAGCAGAGTTGCTTCCAAATACATAA
196 AAAAGCTAAGAGAAACAAATGCATGCAACCAAAGATTACAAGCAGAGTTGCTTCCAAATACATAA
41528827 ATAAATGAAC
261 ATAAATGAAC
* *
41528837 TGCTTCCAAAAACTTTGTCAAGCATGATTTACAGATACATCCTCCAAGCATAATAATGCTCTAAT
1 TGCTTCCAAAAACGTTGTCAAGCATGATTTACAGATACATCCTCCAAGCATAAAAATGCTCTAAT
* *
41528902 ACATTAACAAAAACAAACTTCACTAACTGG-AAAATTTAGCATGCTGGTCGTGTTCTACCTGTCT
66 ACATTAACAAAAAAAAACTTCACTAACTGGAAAAATTTAGCATGCTCGTCGTGTTCTACCTGTCT
* *
41528966 AAAATCCAATTCTTGAAAAGTAAATTTTACTCTAGCATCCCCCAATGGTGCATACAACTGCCTTA
131 AAAATCCAATTCTCG-AAAGTAAATTTTACTCTAGCATCCCCCAATGGTGCATAAAACTGCCTTA
41529031 AAAAAGCTAAGAGAAACAAATGCATGCAACCAAAGATTACAAGCAGAGTTG
195 AAAAAGCTAAGAGAAACAAATGCATGCAACCAAAGATTACAAGCAGAGTTG
41529082 TCAAGGGCAC
Statistics
Matches: 230, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
269 44 0.19
270 186 0.81
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (270 bp):
TGCTTCCAAAAACGTTGTCAAGCATGATTTACAGATACATCCTCCAAGCATAAAAATGCTCTAAT
ACATTAACAAAAAAAAACTTCACTAACTGGAAAAATTTAGCATGCTCGTCGTGTTCTACCTGTCT
AAAATCCAATTCTCGAAAGTAAATTTTACTCTAGCATCCCCCAATGGTGCATAAAACTGCCTTAA
AAAAGCTAAGAGAAACAAATGCATGCAACCAAAGATTACAAGCAGAGTTGCTTCCAAATACATAA
ATAAATGAAC
Found at i:41533534 original size:22 final size:22
Alignment explanation
Indices: 41533482--41533535 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
41533472 AATAACTCTA
*
41533482 CATAAGTCAACTAAAAAACCTT
1 CATAAGTCGACTAAAAAACCTT
41533504 CATAAGTCGACTAAAAAACCTT
1 CATAAGTCGACTAAAAAACCTT
41533526 CATAAGTCGA
1 CATAAGTCGA
41533536 GCAACATATC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.46, C:0.22, G:0.09, T:0.22
Consensus pattern (22 bp):
CATAAGTCGACTAAAAAACCTT
Found at i:41543932 original size:12 final size:12
Alignment explanation
Indices: 41543915--41543948 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
41543905 GTATCTAATT
41543915 TTATTGTTATTA
1 TTATTGTTATTA
41543927 TTATTGTTATTA
1 TTATTGTTATTA
*
41543939 TTATTTTTAT
1 TTATTGTTAT
41543949 ATAAATTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (12 bp):
TTATTGTTATTA
Found at i:41544221 original size:15 final size:16
Alignment explanation
Indices: 41544201--41544240 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
41544191 TAGTTAGATC
41544201 AAATAAATCA-TTAAA
1 AAATAAATCATTTAAA
41544216 AAATAAAAT-ATTTAAA
1 AAAT-AAATCATTTAAA
41544232 AAATAAATC
1 AAATAAATC
41544241 TCAATTCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (16 bp):
AAATAAATCATTTAAA
Found at i:41544536 original size:29 final size:28
Alignment explanation
Indices: 41544503--41544559 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
41544493 TAATTATTTG
* *
41544503 AACTAATTAATTACATTATAAAAATATTA
1 AACTAATTAATAACATTACAAAAA-ATTA
*
41544532 AACTAATTAATAATATTACAAAAAATTA
1 AACTAATTAATAACATTACAAAAAATTA
41544560 GAGATCAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (28 bp):
AACTAATTAATAACATTACAAAAAATTA
Found at i:41546429 original size:38 final size:38
Alignment explanation
Indices: 41546375--41546549 Score: 206
Period size: 38 Copynumber: 4.6 Consensus size: 38
41546365 TACTACACTA
* * * **
41546375 GCACAAAGCCTGCTAGGCACTATGCCTGATTAACATTG
1 GCACAAAGCCTACTAGGCACTAAGCCTGAATAACACCG
*
41546413 GCACAAAGTCTACTAGGCACTAAGCCTGAATAACACCG
1 GCACAAAGCCTACTAGGCACTAAGCCTGAATAACACCG
** *
41546451 GCATTAAGCCTACTAGGCACTAAGCCTGAATAACACCA
1 GCACAAAGCCTACTAGGCACTAAGCCTGAATAACACCG
** * * *
41546489 GCATTAAGCCTGCTAGGCACTAAGCCTAAATAACACCA
1 GCACAAAGCCTACTAGGCACTAAGCCTGAATAACACCG
* *
41546527 GCACTAAGCCTGCTAGGCACTAA
1 GCACAAAGCCTACTAGGCACTAA
41546550 ACTTGAATCA
Statistics
Matches: 124, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 124 1.00
ACGTcount: A:0.34, C:0.29, G:0.18, T:0.19
Consensus pattern (38 bp):
GCACAAAGCCTACTAGGCACTAAGCCTGAATAACACCG
Found at i:41546458 original size:22 final size:22
Alignment explanation
Indices: 41546428--41546538 Score: 75
Period size: 22 Copynumber: 5.6 Consensus size: 22
41546418 AAGTCTACTA
41546428 GGCACTAAGCCTGAATAACACC
1 GGCACTAAGCCTGAATAACACC
* *
41546450 GGCATTAAGCCT-ACT---A--
1 GGCACTAAGCCTGAATAACACC
41546466 GGCACTAAGCCTGAATAACACC
1 GGCACTAAGCCTGAATAACACC
* * *
41546488 AGCATTAAGCCTG-CT---A--
1 GGCACTAAGCCTGAATAACACC
*
41546504 GGCACTAAGCCTAAATAACACC
1 GGCACTAAGCCTGAATAACACC
*
41546526 AGCACTAAGCCTG
1 GGCACTAAGCCTG
41546539 CTAGGCACTA
Statistics
Matches: 64, Mismatches: 13, Indels: 24
0.63 0.13 0.24
Matches are distributed among these distances:
16 21 0.33
17 3 0.05
18 2 0.03
20 2 0.03
21 3 0.05
22 33 0.52
ACGTcount: A:0.35, C:0.30, G:0.18, T:0.17
Consensus pattern (22 bp):
GGCACTAAGCCTGAATAACACC
Found at i:41546506 original size:76 final size:76
Alignment explanation
Indices: 41546369--41546549 Score: 227
Period size: 76 Copynumber: 2.4 Consensus size: 76
41546359 AACATTTACT
* * * * *** *
41546369 ACACTAGCACAAAGCCTGCTAGGCACTATGCCTGATTAACATTGGCACAAAGTCTACTAGGCACT
1 ACACCAGCACTAAGCCTGCTAGGCACTAAGCCTGAATAACACCAGCACAAAGCCTACTAGGCACT
*
41546434 AAGCCTGAATA
66 AAGCCTAAATA
* * * ** *
41546445 ACACCGGCATTAAGCCTACTAGGCACTAAGCCTGAATAACACCAGCATTAAGCCTGCTAGGCACT
1 ACACCAGCACTAAGCCTGCTAGGCACTAAGCCTGAATAACACCAGCACAAAGCCTACTAGGCACT
41546510 AAGCCTAAATA
66 AAGCCTAAATA
41546521 ACACCAGCACTAAGCCTGCTAGGCACTAA
1 ACACCAGCACTAAGCCTGCTAGGCACTAA
41546550 ACTTGAATCA
Statistics
Matches: 87, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
76 87 1.00
ACGTcount: A:0.35, C:0.29, G:0.18, T:0.19
Consensus pattern (76 bp):
ACACCAGCACTAAGCCTGCTAGGCACTAAGCCTGAATAACACCAGCACAAAGCCTACTAGGCACT
AAGCCTAAATA
Found at i:41548112 original size:108 final size:108
Alignment explanation
Indices: 41547934--41548144 Score: 341
Period size: 108 Copynumber: 2.0 Consensus size: 108
41547924 GACATGCCCG
* * *
41547934 TGTGCCATGGTCGTGGGAAAACTGATGAGGTTACTGACTTGGGTCACATGGACAACCGCACACCC
1 TGTGCCATGGCCGTGGGAAAACTGAGGAGGTTACTGACTTGGGTCACAAGGACAACCGCACACCC
41547999 ATGTGCCAGCCCGTGTGCCACACACGACCAGTAGACACGCCTA
66 ATGTGCCAGCCCGTGTGCCACACACGACCAGTAGACACGCCTA
* * * *
41548042 TGTGCCATGGCCGTGGGAAAACTGGGGAGGTTACTGACTTGGGTCACAAGGCCGACCGCACGCCC
1 TGTGCCATGGCCGTGGGAAAACTGAGGAGGTTACTGACTTGGGTCACAAGGACAACCGCACACCC
* *
41548107 ATGTGCCAGCCCGTGTGCTACACACGGCCAGTAGACAC
66 ATGTGCCAGCCCGTGTGCCACACACGACCAGTAGACAC
41548145 ACCCGTGTGT
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
108 94 1.00
ACGTcount: A:0.23, C:0.30, G:0.29, T:0.18
Consensus pattern (108 bp):
TGTGCCATGGCCGTGGGAAAACTGAGGAGGTTACTGACTTGGGTCACAAGGACAACCGCACACCC
ATGTGCCAGCCCGTGTGCCACACACGACCAGTAGACACGCCTA
Found at i:41549315 original size:42 final size:42
Alignment explanation
Indices: 41549251--41549378 Score: 134
Period size: 42 Copynumber: 3.0 Consensus size: 42
41549241 AGCTCGTACA
* * *
41549251 ATGCCATATCCCAGATATGGTCTTAC-TGTTATCACATATCG
1 ATGCCATGTCCCAGACATGGTCTTACATGTAATCACATATCG
* * * * *
41549292 ATGCCACTGTCCCAGACAGGGTCTTACACGAAATC-GATAGCG
1 ATGCCA-TGTCCCAGACATGGTCTTACATGTAATCACATATCG
* *
41549334 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCATATCTCG
1 ATGCC-ATGTCCCAGACATGGTCTTACATGTAATCACATATCG
41549377 AT
1 AT
41549379 AACCTAATGT
Statistics
Matches: 69, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
41 6 0.09
42 52 0.75
43 11 0.16
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (42 bp):
ATGCCATGTCCCAGACATGGTCTTACATGTAATCACATATCG
Found at i:41551847 original size:16 final size:16
Alignment explanation
Indices: 41551826--41551857 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
41551816 GCTTGGTAAG
41551826 TTTAATTCTTATTATA
1 TTTAATTCTTATTATA
41551842 TTTAATTCTTATTATA
1 TTTAATTCTTATTATA
41551858 CGAACTTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTAATTCTTATTATA
Found at i:41552275 original size:20 final size:23
Alignment explanation
Indices: 41552226--41552276 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
41552216 TATCATGTAA
*
41552226 AATGTTAGAATTGGCTTGGTTAT
1 AATGTTTGAATTGGCTTGGTTAT
41552249 AATGTTTGAATTGG-TTGG-TAT
1 AATGTTTGAATTGGCTTGGTTAT
41552270 -ATGTTTG
1 AATGTTTG
41552277 CAAGTATTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 7 0.26
21 3 0.11
22 4 0.15
23 13 0.48
ACGTcount: A:0.24, C:0.02, G:0.27, T:0.47
Consensus pattern (23 bp):
AATGTTTGAATTGGCTTGGTTAT
Found at i:41558834 original size:29 final size:29
Alignment explanation
Indices: 41558800--41558904 Score: 86
Period size: 29 Copynumber: 3.6 Consensus size: 29
41558790 TACTCGATTT
* * *
41558800 CGCACACTTAGTGCCATGCGATTTAAGCC
1 CGCACACTTAGTGCCATACCATTCAAGCC
** * * *
41558829 CGCACACACAGTGCCATACCCTTCGAGCT
1 CGCACACTTAGTGCCATACCATTCAAGCC
* * *
41558858 CGCACACTTAGTGCCATA-TATTTCCAGCA
1 CGCACACTTAGTGCCATACCA-TTCAAGCC
*
41558887 TGCACACTTAGTGCCATA
1 CGCACACTTAGTGCCATA
41558905 TATTTCCAGC
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.24
Consensus pattern (29 bp):
CGCACACTTAGTGCCATACCATTCAAGCC
Found at i:41558892 original size:58 final size:59
Alignment explanation
Indices: 41558838--41558960 Score: 169
Period size: 58 Copynumber: 2.1 Consensus size: 59
41558828 CCGCACACAC
* *
41558838 AGTGCCATACCCTTCGAGC-TCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
1 AGTGCCATACACTTCCAGCATCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
* * * * *
41558896 AGTGCCATATATTTCCAGCAT-GCACTCTCAGTGCCATATTTTTCCAGCATGCACACTT
1 AGTGCCATACACTTCCAGCATCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
41558954 AGTGCCA
1 AGTGCCA
41558961 ATCTCGTCAC
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
58 56 0.98
59 1 0.02
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.29
Consensus pattern (59 bp):
AGTGCCATACACTTCCAGCATCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
Found at i:41558905 original size:29 final size:29
Alignment explanation
Indices: 41558859--41558960 Score: 177
Period size: 29 Copynumber: 3.5 Consensus size: 29
41558849 CTTCGAGCTC
41558859 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
41558888 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
* * *
41558917 GCACTCTCAGTGCCATATTTTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
41558946 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
41558961 ATCTCGTCAC
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 68 1.00
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.30
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:41566814 original size:29 final size:29
Alignment explanation
Indices: 41566780--41566884 Score: 86
Period size: 29 Copynumber: 3.6 Consensus size: 29
41566770 TACTCGATTT
* * *
41566780 CGCACACTTAGTGCCATGCGATTTAAGCC
1 CGCACACTTAGTGCCATACCATTCAAGCC
** * * *
41566809 CGCACACACAGTGCCATACCCTTCGAGCT
1 CGCACACTTAGTGCCATACCATTCAAGCC
* * *
41566838 CGCACACTTAGTGCCATA-TATTTCCAGCA
1 CGCACACTTAGTGCCATACCA-TTCAAGCC
*
41566867 TGCACACTTAGTGCCATA
1 CGCACACTTAGTGCCATA
41566885 TATTTCCAGC
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.24
Consensus pattern (29 bp):
CGCACACTTAGTGCCATACCATTCAAGCC
Found at i:41566872 original size:58 final size:59
Alignment explanation
Indices: 41566818--41566940 Score: 178
Period size: 58 Copynumber: 2.1 Consensus size: 59
41566808 CCGCACACAC
* *
41566818 AGTGCCATACCCTTCGAGC-TCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
1 AGTGCCATACACTTCCAGCATCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
* * * *
41566876 AGTGCCATATATTTCCAGCAT-GCACACTCAGTGCCATATTTTTCCAGCATGCACACTT
1 AGTGCCATACACTTCCAGCATCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
41566934 AGTGCCA
1 AGTGCCA
41566941 ATCTCGTCAC
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 57 0.98
59 1 0.02
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.28
Consensus pattern (59 bp):
AGTGCCATACACTTCCAGCATCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
Found at i:41566885 original size:29 final size:29
Alignment explanation
Indices: 41566839--41566940 Score: 186
Period size: 29 Copynumber: 3.5 Consensus size: 29
41566829 CTTCGAGCTC
41566839 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
41566868 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
* *
41566897 GCACACTCAGTGCCATATTTTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
41566926 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
41566941 ATCTCGTCAC
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 70 1.00
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.29
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:41569083 original size:23 final size:23
Alignment explanation
Indices: 41569057--41569100 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
41569047 CTAGTTATGC
* *
41569057 AAATACAAAAATTTTTATAACTT
1 AAATACAAAAAGTTTCATAACTT
41569080 AAATACAAAAAGTTTCATAAC
1 AAATACAAAAAGTTTCATAAC
41569101 CCTAAACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.55, C:0.11, G:0.02, T:0.32
Consensus pattern (23 bp):
AAATACAAAAAGTTTCATAACTT
Found at i:41569106 original size:24 final size:23
Alignment explanation
Indices: 41569057--41569106 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
41569047 CTAGTTATGC
* * *
41569057 AAATACAAAAATTTTTATAACTT
1 AAATACAAAAAGTTTCATAACCT
41569080 AAATACAAAAAGTTTCATAACCCT
1 AAATACAAAAAGTTTCATAA-CCT
41569104 AAA
1 AAA
41569107 CCCATATACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.54, C:0.14, G:0.02, T:0.30
Consensus pattern (23 bp):
AAATACAAAAAGTTTCATAACCT
Found at i:41569781 original size:21 final size:21
Alignment explanation
Indices: 41569755--41569799 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
41569745 TATTATTAAT
*
41569755 TTTGTTATTATTTTAAAGGCA
1 TTTGTTAATATTTTAAAGGCA
*
41569776 TTTGTTAATATTTTAGAGGCA
1 TTTGTTAATATTTTAAAGGCA
41569797 TTT
1 TTT
41569800 ACATGTTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.04, G:0.16, T:0.53
Consensus pattern (21 bp):
TTTGTTAATATTTTAAAGGCA
Found at i:41573565 original size:10 final size:10
Alignment explanation
Indices: 41573517--41573571 Score: 56
Period size: 10 Copynumber: 5.2 Consensus size: 10
41573507 AGTGGAATGT
*
41573517 ATAAAAAAAA
1 ATAAATAAAA
*
41573527 ATAGACATGAAA
1 ATA-A-ATAAAA
41573539 ATAAATAAAA
1 ATAAATAAAA
*
41573549 ATGAAATAAGA
1 AT-AAATAAAA
41573560 ATAAATAAAA
1 ATAAATAAAA
41573570 AT
1 AT
41573572 TATACAAGTG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
10 19 0.51
11 11 0.30
12 7 0.19
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (10 bp):
ATAAATAAAA
Found at i:41574461 original size:152 final size:151
Alignment explanation
Indices: 41574200--41574575 Score: 515
Period size: 152 Copynumber: 2.5 Consensus size: 151
41574190 AAATTTAAAT
* * * * *
41574200 TTTCTTTTAGAATGACTTAAAAAATAGATTTTTATTTTTCAAAATCTAAACTTTCTCC-TTTTTA
1 TTTCCTTTAAAATGACTAAAAAAACAAATTTTTATTTTTCAAAATCTAAACTTTCTCCTTTTTTA
* *
41574264 AAAAAAAACACTATTTTTCTTAAAGATTAAAACTTTTATTTTGAAATAGTTGAAAACAATCAAAA
66 AAAAAAAACACTATTTTTCTTAAAGATTAAAACTTTTACTTTGAAATAGTTGAAAAAAATCAAAA
* *
41574329 TTTTGTTTTAAAAGTTAAAAC
131 CTTTATTTTAAAAGTTAAAAC
*
41574350 TTTCCTTTAAAATGACTAAAAAAACAAAATTTTATTTTTCAAAATCTAAACTTTCTCCTTTTTTT
1 TTTCCTTTAAAATGACTAAAAAAACAAATTTTTATTTTTCAAAATCTAAACTTTCTCC-TTTTTT
* * * * *
41574415 TAAAAAAAACTCTATTTTTCTTAAAGATTAAAGCTTTTACTTTGAAATGGTTGAAAAAAATTAAA
65 AAAAAAAAACACTATTTTTCTTAAAGATTAAAACTTTTACTTTGAAATAGTTGAAAAAAATCAAA
* *
41574480 ACTTTATTTTAAAATTTTAAAC
130 ACTTTATTTTAAAAGTTAAAAC
* * *
41574502 TTTCCTTTAAAGTAACTATAAAAAACATATTTTTATTTGTT-AAAATCTAAACTTTCT-CTGTTT
1 TTTCCTTTAAAATGACTA-AAAAAACAAATTTTTATTT-TTCAAAATCTAAACTTTCTCCT-TTT
41574565 TTAAAAAAAAA
63 TTAAAAAAAAA
41574576 TCAAAACTTT
Statistics
Matches: 199, Mismatches: 22, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
150 52 0.26
151 1 0.01
152 111 0.56
153 33 0.17
154 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (151 bp):
TTTCCTTTAAAATGACTAAAAAAACAAATTTTTATTTTTCAAAATCTAAACTTTCTCCTTTTTTA
AAAAAAAACACTATTTTTCTTAAAGATTAAAACTTTTACTTTGAAATAGTTGAAAAAAATCAAAA
CTTTATTTTAAAAGTTAAAAC
Found at i:41575204 original size:22 final size:22
Alignment explanation
Indices: 41575176--41575252 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
41575166 ACTAAATCAG
41575176 ACGCCCGTGTGAGACCGGGGAC
1 ACGCCCGTGTGAGACCGGGGAC
*
41575198 ACGCCCGTGTGAGACTGGGGAC
1 ACGCCCGTGTGAGACCGGGGAC
41575220 ACGCCCGTGTGAGACCGGGGAC
1 ACGCCCGTGTGAGACCGGGGAC
41575242 ACGCCCGTGTG
1 ACGCCCGTGTG
41575253 CTTTCAACAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.17, C:0.31, G:0.40, T:0.12
Consensus pattern (22 bp):
ACGCCCGTGTGAGACCGGGGAC
Found at i:41578212 original size:16 final size:16
Alignment explanation
Indices: 41578191--41578221 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
41578181 TAGGCCCCTA
41578191 AATGTAATGAAAAGTC
1 AATGTAATGAAAAGTC
41578207 AATGTAATGAAAAGT
1 AATGTAATGAAAAGT
41578222 AAACTAGAAA
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:0.52, C:0.03, G:0.19, T:0.26
Consensus pattern (16 bp):
AATGTAATGAAAAGTC
Found at i:41578292 original size:42 final size:42
Alignment explanation
Indices: 41578228--41578716 Score: 439
Period size: 42 Copynumber: 11.3 Consensus size: 42
41578218 AAGTAAACTA
* *
41578228 GAAAAGTAAACGGACCTCCACACCTGGGTCTCTAAATGCAAT
1 GAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
* * ** *
41578270 GAAAAGTCAAAT-GACCTTCACACATGGATCTCTAAATGAAAT
1 GAAAAGT-AAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
* * * * *
41578312 GAAAAGTGAATGGACCTCAAAACTTGGACCTCTAAATGCAAT
1 GAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
** ** * *
41578354 GAAAAGTCAATGCAATAAAAAGTAAACAGACCTCCACACCTGGGTCTCTAAATGCAAT
1 GAAAAGT--A---AAT-GGACCT---C-CA-C-----ACCTGGGCCTCTAAATGCAAT
* * ** *
41578412 GAAAAGTCAAAT-GACCTCTACACCTAGGTTTCTAAATGAAAT
1 GAAAAGT-AAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
* * *
41578454 GAAAAGTGAATGGACCTCAACACTTGGGCCTCTAAATGCAAT
1 GAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
* * * *
41578496 AAAAAGTAAATGGACCTCCACACATGGGTCTTTAAATGCAAT
1 GAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
41578538 GAAAAG-AGAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
1 GAAAAGTA-AATGGACCTCCACACCTGGGCCTCTAAATGCAAT
* *
41578580 GAAGAG-AGAATGGACCTCTACACCTGGGCCTCTAAATGCAAT
1 GAAAAGTA-AATGGACCTCCACACCTGGGCCTCTAAATGCAAT
* *
41578622 GAAGAG-AGAACGGACCTCCACACCTGGGCCTCTAAATGCAAT
1 GAAAAGTA-AATGGACCTCCACACCTGGGCCTCTAAATGCAAT
*
41578664 GAAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGCAAT
1 GAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
41578706 GAAAAGTAAAT
1 GAAAAGTAAAT
41578717 AGAGCCTAAA
Statistics
Matches: 372, Mismatches: 54, Indels: 42
0.79 0.12 0.09
Matches are distributed among these distances:
41 7 0.02
42 320 0.86
43 4 0.01
47 4 0.01
48 3 0.01
49 1 0.00
51 1 0.00
52 3 0.01
54 3 0.01
57 1 0.00
58 25 0.07
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (42 bp):
GAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
Found at i:41578367 original size:16 final size:16
Alignment explanation
Indices: 41578346--41578376 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41578336 TGGACCTCTA
*
41578346 AATGCAATGAAAAGTC
1 AATGCAATAAAAAGTC
41578362 AATGCAATAAAAAGT
1 AATGCAATAAAAAGT
41578377 AAACAGACCT
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:0.55, C:0.10, G:0.16, T:0.19
Consensus pattern (16 bp):
AATGCAATAAAAAGTC
Found at i:41578411 original size:142 final size:142
Alignment explanation
Indices: 41578229--41578507 Score: 463
Period size: 142 Copynumber: 2.0 Consensus size: 142
41578219 AGTAAACTAG
*
41578229 AAAAGTAAACGGACCTCCACACCTGGGTCTCTAAATGCAATGAAAAGTCAAATGACCT-TCACAC
1 AAAAGTAAACAGACCTCCACACCTGGGTCTCTAAATGCAATGAAAAGTCAAATGACCTCT-ACAC
*
41578293 AT-GGATCTCTAAATGAAATGAAAAGTGAATGGACCTCAAAACTTGGACCTCTAAATGCAATGAA
65 ATAGG-TCTCTAAATGAAATGAAAAGTGAATGGACCTCAAAACTTGGACCTCTAAATGCAATAAA
*
41578357 AAGTCAATGCAATA
129 AAGTAAATGCAATA
*
41578371 AAAAGTAAACAGACCTCCACACCTGGGTCTCTAAATGCAATGAAAAGTCAAATGACCTCTACACC
1 AAAAGTAAACAGACCTCCACACCTGGGTCTCTAAATGCAATGAAAAGTCAAATGACCTCTACACA
* * *
41578436 TAGGTTTCTAAATGAAATGAAAAGTGAATGGACCTCAACACTTGGGCCTCTAAATGCAATAAAAA
66 TAGGTCTCTAAATGAAATGAAAAGTGAATGGACCTCAAAACTTGGACCTCTAAATGCAATAAAAA
41578501 GTAAATG
131 GTAAATG
41578508 GACCTCCACA
Statistics
Matches: 128, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
142 125 0.98
143 3 0.02
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (142 bp):
AAAAGTAAACAGACCTCCACACCTGGGTCTCTAAATGCAATGAAAAGTCAAATGACCTCTACACA
TAGGTCTCTAAATGAAATGAAAAGTGAATGGACCTCAAAACTTGGACCTCTAAATGCAATAAAAA
GTAAATGCAATA
Found at i:41578446 original size:100 final size:100
Alignment explanation
Indices: 41578262--41578465 Score: 234
Period size: 100 Copynumber: 2.0 Consensus size: 100
41578252 TGGGTCTCTA
* * * *
41578262 AATGCAATGAAAAGTCAAATGACCTTCACACATGGATCTCTAAATGAAATGAAAAGTGAATGGAC
1 AATGCAATAAAAAGTCAAAAGACCTCCACACATGGATCTCTAAATGAAATGAAAAGTAAATGGAC
* *
41578327 CTCAAAACTTGGACCTCTAAATGCAATGAAAAGTC
66 CTCAAAACTAGGACCTCTAAATGAAATGAAAAGTC
* * *
41578362 AATGCAATAAAAAGT-AAACAGACCTCCACACCTGGGTCTCTAAATGCAATGAAAAGTCAAAT-G
1 AATGCAATAAAAAGTCAAA-AGACCTCCACACATGGATCTCTAAATGAAATGAAAAGT-AAATGG
* * ** *
41578425 ACCTCTACACCTAGG-TTTCTAAATGAAATGAAAAGTG
64 ACCTC-AAAACTAGGACCTCTAAATGAAATGAAAAGTC
41578462 AATG
1 AATG
41578466 GACCTCAACA
Statistics
Matches: 87, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
99 3 0.03
100 75 0.86
101 9 0.10
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.22
Consensus pattern (100 bp):
AATGCAATAAAAAGTCAAAAGACCTCCACACATGGATCTCTAAATGAAATGAAAAGTAAATGGAC
CTCAAAACTAGGACCTCTAAATGAAATGAAAAGTC
Found at i:41578526 original size:126 final size:126
Alignment explanation
Indices: 41578362--41578712 Score: 510
Period size: 126 Copynumber: 2.8 Consensus size: 126
41578352 ATGAAAAGTC
*
41578362 AATGCAATAAAAAGTAAACAGACCTCCACACCTGGGTCTCTAAATGCAATGAAAAGTCAAAT-GA
1 AATGCAATAAAAAGTAAACGGACCTCCACACCTGGGTCTCTAAATGCAATGAAAAGT-AAATGGA
* ** * *
41578426 CCTCTACACCTAGGTTTCTAAATGAAATGAAAAGTGAATGGACCTCAACACTTGGGCCTCTA
65 CCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTGAATGGACCTCAACACCTGGGCCTCTA
* * *
41578488 AATGCAATAAAAAGTAAATGGACCTCCACACATGGGTCTTTAAATGCAATGAAAAG-AGAATGGA
1 AATGCAATAAAAAGTAAACGGACCTCCACACCTGGGTCTCTAAATGCAATGAAAAGTA-AATGGA
* * * *
41578552 CCTCCACACCTGGGCCTCTAAATGCAATGAAGAGAGAATGGACCTCTACACCTGGGCCTCTA
65 CCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTGAATGGACCTCAACACCTGGGCCTCTA
* * *
41578614 AATGCAATGAAGAG-AGAACGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAGTAAATGGA
1 AATGCAATAAAAAGTA-AACGGACCTCCACACCTGGGTCTCTAAATGCAATGAAAAGTAAATGGA
41578678 CCTCCACACCTAGGCCTCTAAATGCAATGAAAAGT
65 CCTCCACACCTAGGCCTCTAAATGCAATGAAAAGT
41578713 AAATAGAGCC
Statistics
Matches: 199, Mismatches: 22, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
124 1 0.01
125 4 0.02
126 193 0.97
127 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (126 bp):
AATGCAATAAAAAGTAAACGGACCTCCACACCTGGGTCTCTAAATGCAATGAAAAGTAAATGGAC
CTCCACACCTAGGCCTCTAAATGCAATGAAAAGTGAATGGACCTCAACACCTGGGCCTCTA
Found at i:41587251 original size:19 final size:19
Alignment explanation
Indices: 41587215--41587253 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
41587205 TTTTCATCAT
* *
41587215 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
41587234 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
41587253 A
1 A
41587254 AAATTAAAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Found at i:41587764 original size:26 final size:27
Alignment explanation
Indices: 41587713--41587801 Score: 108
Period size: 28 Copynumber: 3.2 Consensus size: 27
41587703 GTGACAGAGT
*
41587713 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATA-TTTGTGGCAGGGC
*
41587742 CA-CAGAACAGATATATGTGGCAGGGC
1 CACCAGAACAGATATTTGTGGCAGGGC
**
41587768 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGAT-ATTTGTGGCAGGGC
41587796 CACCAG
1 CACCAG
41587802 GACGCTTCCT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
26 13 0.25
27 17 0.32
28 21 0.40
29 2 0.04
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.20
Consensus pattern (27 bp):
CACCAGAACAGATATTTGTGGCAGGGC
Found at i:41587954 original size:28 final size:28
Alignment explanation
Indices: 41587907--41587971 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
41587897 AAATTAACCC
*
41587907 TAGGGGTATAAAGGTCATTTAGCATACA
1 TAGGGGTATAAAGGTAATTTAGCATACA
* *
41587935 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTAGCATACA
41587963 TAGGGGTAT
1 TAGGGGTAT
41587972 TCTAGTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTAGCATACA
Found at i:41595098 original size:19 final size:19
Alignment explanation
Indices: 41595062--41595100 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
41595052 TTTTCATCAT
* *
41595062 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
41595081 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
41595100 A
1 A
41595101 ATAATTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Found at i:41595624 original size:26 final size:26
Alignment explanation
Indices: 41595564--41595652 Score: 115
Period size: 27 Copynumber: 3.2 Consensus size: 26
41595554 GTGACAGAGT
41595564 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATA-TTTGTGGCAG-GC
*
41595593 CACCAGAACAGATATATGTGGCAGGC
1 CACCAGAACAGATATTTGTGGCAGGC
*
41595619 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGAT-ATTTGTGGCA-GGC
41595647 CACCAG
1 CACCAG
41595653 GACGCTTCCT
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
26 15 0.27
27 18 0.33
28 15 0.27
29 7 0.13
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.20
Consensus pattern (26 bp):
CACCAGAACAGATATTTGTGGCAGGC
Found at i:41595805 original size:28 final size:28
Alignment explanation
Indices: 41595758--41595822 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
41595748 AAATTAACCC
*
41595758 TAGGGGTATAAAGGTCATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
*
41595786 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
41595814 TAGGGGTAT
1 TAGGGGTAT
41595823 TCTAGTAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.31, C:0.08, G:0.28, T:0.34
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTTGCATACA
Found at i:41602630 original size:37 final size:37
Alignment explanation
Indices: 41602588--41602664 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
41602578 TTAAAATTAA
*
41602588 TTATATTATGAATTGATACACATAATTTTGGACCTTC
1 TTATATTATGAATTGATACACATAATTTTGGACCGTC
41602625 TTATATTATGAATTGATACACATAATTTTGGACCGTC
1 TTATATTATGAATTGATACACATAATTTTGGACCGTC
41602662 TTA
1 TTA
41602665 GGCAGGAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (37 bp):
TTATATTATGAATTGATACACATAATTTTGGACCGTC
Found at i:41604036 original size:4 final size:4
Alignment explanation
Indices: 41604013--41604077 Score: 55
Period size: 4 Copynumber: 16.5 Consensus size: 4
41604003 TGAATAAACA
* * *
41604013 AATG AACG AAT- AAGTG AATG AATG TATG AATG -ATG AATG AATG AATT
1 AATG AATG AATG AA-TG AATG AATG AATG AATG AATG AATG AATG AATG
*
41604060 AAAG AAAT- AATG AATG AA
1 AATG -AATG AATG AATG AA
41604078 ATTGGGGCAC
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
3 8 0.17
4 36 0.75
5 4 0.08
ACGTcount: A:0.52, C:0.02, G:0.22, T:0.25
Consensus pattern (4 bp):
AATG
Found at i:41607623 original size:3 final size:3
Alignment explanation
Indices: 41607615--41607658 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
41607605 ATTCGATCTT
41607615 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
41607659 TTTAAAAGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:41611891 original size:53 final size:54
Alignment explanation
Indices: 41611763--41612017 Score: 256
Period size: 55 Copynumber: 4.8 Consensus size: 54
41611753 ACACGGGTAC
* * * **
41611763 CTTACCATTGCCATGACTTGTCATGGTCTTATTTGGTATCC-T---TT-TGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* * *
41611812 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTAGCCTTGCCTTATG-AA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* * * *
41611865 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTAT-GAAA
* * * *
41611920 CTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTA-GAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* *
41611973 CCTTACCAATTGCCATGCCTTGGCATGGTCTTACACGGTATCCTT
1 -CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTATCCTT
41612018 AAACCCTAAT
Statistics
Matches: 171, Mismatches: 24, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
49 36 0.21
50 1 0.01
52 2 0.01
53 49 0.29
54 10 0.06
55 71 0.42
56 2 0.01
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (54 bp):
CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
Found at i:41611954 original size:108 final size:110
Alignment explanation
Indices: 41611810--41612007 Score: 312
Period size: 108 Copynumber: 1.8 Consensus size: 110
41611800 ATCCTTTTGA
* *
41611810 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTAGCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATAGCCTTGCCTTA-GAAACCTCACCAA
41611873 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
65 TTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
* ** *
41611918 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATAGCCTTGCCTTAGAAACCTCACCAAT
41611983 TGCCATGCCTTGGCATGGTCTTACA
66 TGCCATGCCTTGGCATGGTCTTACA
41612008 CGGTATCCTT
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
107 1 0.01
108 48 0.59
109 7 0.09
110 25 0.31
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.34
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATAGCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
Found at i:41615083 original size:25 final size:25
Alignment explanation
Indices: 41615055--41615133 Score: 67
Period size: 25 Copynumber: 3.3 Consensus size: 25
41615045 ACTCGGCCCT
*
41615055 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACATTCACATTC
** * *
41615080 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATACACATTC-ACATTC
*
41615102 ATCACATATATACACCTTCACATTC
1 ATCACATATATACACATTCACATTC
41615127 ATCACAT
1 ATCACAT
41615134 CGGCCATTAG
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 11 0.28
23 5 0.13
24 5 0.13
25 18 0.46
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.33
Consensus pattern (25 bp):
ATCACATATATACACATTCACATTC
Found at i:41615179 original size:49 final size:49
Alignment explanation
Indices: 41615019--41615405 Score: 638
Period size: 49 Copynumber: 8.0 Consensus size: 49
41615009 TCACATTTAT
* * * * * * *
41615019 ACACTTCCACATCCATCACGTTGGCCACTCGGCCCTATCACATATAT--
1 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
* *
41615066 ACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
41615115 AC-C-TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
41615162 ACACTTTCACATTCATCACAACGGCCATTAGGCCTTATCACATATATAC
1 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
41615211 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
41615260 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
41615309 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
41615358 ACACTTTCACATTCATCACATCGGCCAATAGGCCTTATCACATATATA
1 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
41615406 TCTCTCATAC
Statistics
Matches: 324, Mismatches: 12, Indels: 6
0.95 0.04 0.02
Matches are distributed among these distances:
47 86 0.27
48 2 0.01
49 236 0.73
ACGTcount: A:0.30, C:0.31, G:0.09, T:0.30
Consensus pattern (49 bp):
ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
Found at i:41621319 original size:25 final size:25
Alignment explanation
Indices: 41621291--41621369 Score: 67
Period size: 25 Copynumber: 3.3 Consensus size: 25
41621281 ACTCGGCCCT
*
41621291 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACATTCACATTC
** * *
41621316 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATACACATTC-ACATTC
*
41621338 ATCACATATATACACCTTCACATTC
1 ATCACATATATACACATTCACATTC
41621363 ATCACAT
1 ATCACAT
41621370 CGGCCATTAG
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 11 0.28
23 5 0.13
24 5 0.13
25 18 0.46
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.33
Consensus pattern (25 bp):
ATCACATATATACACATTCACATTC
Found at i:41621415 original size:49 final size:49
Alignment explanation
Indices: 41621255--41621592 Score: 549
Period size: 49 Copynumber: 7.0 Consensus size: 49
41621245 TCACATTTAT
* * * * * * *
41621255 ACACTTCCACATCCATCACGTTGGCCACTCGGCCCTATCACATATAT--
1 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
* *
41621302 ACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
41621351 AC-C-TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
41621398 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
41621447 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
41621496 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
41621545 ACACTTTCACATTCATCACATCGTCCATTAGGCCTTATCACATATATA
1 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
41621593 TATCTCATAC
Statistics
Matches: 277, Mismatches: 10, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
47 86 0.31
48 2 0.01
49 189 0.68
ACGTcount: A:0.30, C:0.31, G:0.08, T:0.31
Consensus pattern (49 bp):
ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
Found at i:41624315 original size:24 final size:24
Alignment explanation
Indices: 41624283--41624511 Score: 363
Period size: 24 Copynumber: 9.6 Consensus size: 24
41624273 TATCTCAAAT
41624283 GCACTATGTGTGCGATTCACTATG
1 GCACTATGTGTGCGATTCACTATG
41624307 GCACTATGTGTGCGATT-ACTATG
1 GCACTATGTGTGCGATTCACTATG
41624330 GCACTATGTGTGCGATTCACTATG
1 GCACTATGTGTGCGATTCACTATG
41624354 GCACTATGTGTGCGATT-ACTATG
1 GCACTATGTGTGCGATTCACTATG
41624377 GCACTATGTGTGCGATTCACTATG
1 GCACTATGTGTGCGATTCACTATG
41624401 GCACTATGTGTGCGATTCACTATG
1 GCACTATGTGTGCGATTCACTATG
*
41624425 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTCACTATG
* * *
41624449 GCACTAAGTGTGCGATTTACTATA
1 GCACTATGTGTGCGATTCACTATG
* ** *
41624473 GCACTACGTGTGCGATTTGCTATA
1 GCACTATGTGTGCGATTCACTATG
*
41624497 GCTCTATGTGTGCGA
1 GCACTATGTGTGCGA
41624512 ACATAATAAG
Statistics
Matches: 196, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
23 46 0.23
24 150 0.77
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.34
Consensus pattern (24 bp):
GCACTATGTGTGCGATTCACTATG
Found at i:41624447 original size:48 final size:47
Alignment explanation
Indices: 41624283--41624511 Score: 368
Period size: 47 Copynumber: 4.8 Consensus size: 47
41624273 TATCTCAAAT
41624283 GCACTATGTGTGCGATTCACTATGGCACTATGTGTGCGATTACTATG
1 GCACTATGTGTGCGATTCACTATGGCACTATGTGTGCGATTACTATG
41624330 GCACTATGTGTGCGATTCACTATGGCACTATGTGTGCGATTACTATG
1 GCACTATGTGTGCGATTCACTATGGCACTATGTGTGCGATTACTATG
41624377 GCACTATGTGTGCGATTCACTATGGCACTATGTGTGCGATTCACTATG
1 GCACTATGTGTGCGATTCACTATGGCACTATGTGTGCGATT-ACTATG
* * *
41624425 GCACTATGTGTGCGATTTACTATGGCACTAAGTGTGCGATTTACTATA
1 GCACTATGTGTGCGATTCACTATGGCACTATGTGTGCGA-TTACTATG
* ** * *
41624473 GCACTACGTGTGCGATTTGCTATAGCTCTATGTGTGCGA
1 GCACTATGTGTGCGATTCACTATGGCACTATGTGTGCGA
41624512 ACATAATAAG
Statistics
Matches: 172, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
47 88 0.51
48 82 0.48
49 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.34
Consensus pattern (47 bp):
GCACTATGTGTGCGATTCACTATGGCACTATGTGTGCGATTACTATG
Found at i:41630256 original size:13 final size:13
Alignment explanation
Indices: 41630238--41630265 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
41630228 CTTGAGTATC
41630238 AGGTGGGAGATAA
1 AGGTGGGAGATAA
41630251 AGGTGGGAGATAA
1 AGGTGGGAGATAA
41630264 AG
1 AG
41630266 TGTTTCTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.46, T:0.14
Consensus pattern (13 bp):
AGGTGGGAGATAA
Found at i:41632090 original size:24 final size:24
Alignment explanation
Indices: 41632058--41632204 Score: 264
Period size: 24 Copynumber: 6.2 Consensus size: 24
41632048 TATCTCAAAT
41632058 GCACTATGTGTGCGATTCACTATG
1 GCACTATGTGTGCGATTCACTATG
41632082 GCACTATGTGTGCGATT-ACTATG
1 GCACTATGTGTGCGATTCACTATG
41632105 GCACTATGTGTGCGATTCAC--TG
1 GCACTATGTGTGCGATTCACTATG
41632127 GCACTATGTGTGCGATTCACTATG
1 GCACTATGTGTGCGATTCACTATG
41632151 GCACTATGTGTGCGATTCACTATG
1 GCACTATGTGTGCGATTCACTATG
*
41632175 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTCACTATG
41632199 GCACTA
1 GCACTA
41632205 GTACAAGGTA
Statistics
Matches: 119, Mismatches: 1, Indels: 6
0.94 0.01 0.05
Matches are distributed among these distances:
22 22 0.18
23 23 0.19
24 74 0.62
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.33
Consensus pattern (24 bp):
GCACTATGTGTGCGATTCACTATG
Found at i:41632141 original size:69 final size:70
Alignment explanation
Indices: 41632058--41632191 Score: 261
Period size: 69 Copynumber: 1.9 Consensus size: 70
41632048 TATCTCAAAT
41632058 GCACTATGTGTGCGATTCACTATGGCACTATGTGTGCGATT-ACTATGGCACTATGTGTGCGATT
1 GCACTATGTGTGCGATTCACTATGGCACTATGTGTGCGATTCACTATGGCACTATGTGTGCGATT
41632122 CACTG
66 CACTG
41632127 GCACTATGTGTGCGATTCACTATGGCACTATGTGTGCGATTCACTATGGCACTATGTGTGCGATT
1 GCACTATGTGTGCGATTCACTATGGCACTATGTGTGCGATTCACTATGGCACTATGTGTGCGATT
41632192 TACTATGGCA
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
69 41 0.64
70 23 0.36
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (70 bp):
GCACTATGTGTGCGATTCACTATGGCACTATGTGTGCGATTCACTATGGCACTATGTGTGCGATT
CACTG
Found at i:41634702 original size:40 final size:40
Alignment explanation
Indices: 41634304--41634690 Score: 526
Period size: 40 Copynumber: 9.7 Consensus size: 40
41634294 AGGTCTCGAC
41634304 GATG-ATCCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGT
41634343 GATGTATCCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGT
* **
41634383 GATGTATCCGGGATAAGTTCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGT
** ** *
41634423 GATGTATCCGGAATAAGTTCTGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGT
41634463 GATGTATCCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGT
*
41634503 GATGTATCCGGGCCAAGCCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGT
** **
41634543 GATGTATCC-GAATAAGTTCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGT
* ***
41634582 GATGTATCCGGGATAAATTCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGT
* * * * *
41634622 GATATATCCGTGCTAAACCCCGAAGAGCATTCATGCTGGT
1 GATGTATCCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGT
* * * *
41634662 GTTATATCCGGGCTAGGTCCCGAAGAGCA
1 GATGTATCCGGGCTAAGCCCCGAAGAGCA
41634691 ATCATGCTGG
Statistics
Matches: 316, Mismatches: 30, Indels: 3
0.91 0.09 0.01
Matches are distributed among these distances:
39 38 0.12
40 278 0.88
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
GATGTATCCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGT
Found at i:41636879 original size:69 final size:70
Alignment explanation
Indices: 41636747--41636879 Score: 223
Period size: 69 Copynumber: 1.9 Consensus size: 70
41636737 TAGTTTATTA
* * * *
41636747 CTAATTAATTTGCTGCTGTAATGCTGTAAATTATTGGCTGTCCAAATTAGGACAAATTTATGGTA
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGTA
41636812 CTTAG
66 CTTAG
41636817 CTAATTAATATGCTGCTGTAATACT-TAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGT
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGT
41636880 GTTATGTGCT
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
69 36 0.61
70 23 0.39
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (70 bp):
CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGTA
CTTAG
Found at i:41638252 original size:47 final size:47
Alignment explanation
Indices: 41638196--41638448 Score: 380
Period size: 47 Copynumber: 5.4 Consensus size: 47
41638186 GATGTACAAG
*
41638196 ATATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
1 ATATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
*
41638243 ATATATATATGTGATAAGGCCGAGTGGCCAATGTGATGAATGTGAAA
1 ATATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
*
41638290 GTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
1 ATATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
* * *
41638337 ATATATATATGTGATAAGGCCGAGTGGCCAACGTGATGAATGTGGAA
1 ATATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
* * * * *
41638384 GTGTATATATGTGATAAGACCTAATGGCCAATGTGATGGATGTGAAA
1 ATATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
* * *
41638431 GTGTATAAATGTGATAAG
1 ATATATATATGTGATAAG
41638449 TCCCGAAGGG
Statistics
Matches: 189, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 189 1.00
ACGTcount: A:0.36, C:0.08, G:0.28, T:0.28
Consensus pattern (47 bp):
ATATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
Found at i:41644560 original size:34 final size:34
Alignment explanation
Indices: 41644499--41644563 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
41644489 TAAGCCCTTA
* * *
41644499 ACAGTAGCAATATTACTGTGGGCCTTAGCCCGCT
1 ACAGTAGCAATATCACTCTGGGACTTAGCCCGCT
* *
41644533 ACAGTAGCAGTATCAGTCTGGGACTTAGCCC
1 ACAGTAGCAATATCACTCTGGGACTTAGCCC
41644564 AATTCAATAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.25
Consensus pattern (34 bp):
ACAGTAGCAATATCACTCTGGGACTTAGCCCGCT
Done.