Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167982.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_24, whole genome shotgun sequence
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: 18142777
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 63000 characters in sequence are not A, C, G, or T
File 52 of 84
Found at i:12001477 original size:21 final size:22
Alignment explanation
Indices: 12001451--12001511 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
12001441 GTAAAATTTC
12001451 AATTTACTACTAAA-TATCAAT
1 AATTTACTACTAAATTATCAAT
*
12001472 AATTTATTACTAAATTATCAAT
1 AATTTACTACTAAATTATCAAT
* * *
12001494 TATTTACTATTATATTAT
1 AATTTACTACTAAATTAT
12001512 TATGTACTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 13 0.38
22 21 0.62
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.48
Consensus pattern (22 bp):
AATTTACTACTAAATTATCAAT
Found at i:12001510 original size:22 final size:22
Alignment explanation
Indices: 12001452--12001548 Score: 74
Period size: 22 Copynumber: 4.5 Consensus size: 22
12001442 TAAAATTTCA
* *
12001452 ATTTACTACTA-AATATCAATA
1 ATTTACTACTATATTATCAATT
* *
12001473 ATTTATTACTAAATTATCAATT
1 ATTTACTACTATATTATCAATT
* *
12001495 ATTTACTATTATATTAT-TATGT
1 ATTTACTACTATATTATCAAT-T
* * *
12001517 ACTTACTATTATATTATC-ATCA
1 ATTTACTACTATATTATCAAT-T
12001539 ATTTACTACT
1 ATTTACTACT
12001549 TAATTTATGA
Statistics
Matches: 61, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
21 12 0.20
22 49 0.80
ACGTcount: A:0.38, C:0.12, G:0.01, T:0.48
Consensus pattern (22 bp):
ATTTACTACTATATTATCAATT
Found at i:12001713 original size:22 final size:21
Alignment explanation
Indices: 12001452--12001714 Score: 60
Period size: 22 Copynumber: 12.2 Consensus size: 21
12001442 TAAAATTTCA
* * * *
12001452 ATTTACTACTAAATATCAATA
1 ATTTACTATTAATTATCATTG
* *
12001473 ATTTATTACTAAATTATCAATT-
1 ATTTACTA-TTAATTATC-ATTG
*
12001495 ATTTACTATTATATTATTA-TG
1 ATTTACTATTA-ATTATCATTG
* **
12001516 TACTTACTATTATATTATCATCA
1 -ATTTACTATTA-ATTATCATTG
*
12001539 ATTTACTACTTAATTTATGATT-
1 ATTTACTA-TTAA-TTATCATTG
* ** * *
12001561 ATTTATTACAAAGTTATTATCG
1 ATTTACTATTAA-TTATCATTG
* * *
12001583 ATTTAGTACTAAATTATCCA-TA
1 ATTTACTA-TTAATTAT-CATTG
*
12001605 ATTT-CCATTAAGTTATCATTG
1 ATTTACTATTAA-TTATCATTG
*
12001626 A-TTA--ATT-ATTCTCTATTG
1 ATTTACTATTAATTATC-ATTG
* * * *
12001644 ATTTATTTTTAAATTCTCAATG
1 ATTTACTATT-AATTATCATTG
* * *
12001666 ATTAACTACTAAATTGTCAATT-
1 ATTTACTA-TTAATTATC-ATTG
12001688 ATTTACTATTAAGTTATCATTG
1 ATTTACTATTAA-TTATCATTG
12001710 ATTTA
1 ATTTA
12001715 TCACTAAGTT
Statistics
Matches: 176, Mismatches: 42, Indels: 47
0.66 0.16 0.18
Matches are distributed among these distances:
17 4 0.02
18 6 0.03
19 6 0.03
20 8 0.05
21 33 0.19
22 95 0.54
23 24 0.14
ACGTcount: A:0.36, C:0.11, G:0.05, T:0.49
Consensus pattern (21 bp):
ATTTACTATTAATTATCATTG
Found at i:12006423 original size:15 final size:13
Alignment explanation
Indices: 12006395--12006436 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 13
12006385 TTAGCAAATC
12006395 AATTGAAACAAAA
1 AATTGAAACAAAA
12006408 AATTGAAAGGCAAAA
1 AATTGAAA--CAAAA
*
12006423 AATAGAAA-AAAA
1 AATTGAAACAAAA
12006435 AA
1 AA
12006437 GTATGTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 6 0.23
13 8 0.31
15 12 0.46
ACGTcount: A:0.71, C:0.05, G:0.12, T:0.12
Consensus pattern (13 bp):
AATTGAAACAAAA
Found at i:12007237 original size:2 final size:2
Alignment explanation
Indices: 12007232--12007260 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12007222 TATATATATA
12007232 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
12007261 TAAGATTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:12007890 original size:16 final size:17
Alignment explanation
Indices: 12007849--12007883 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 17
12007839 TCTATGTTAT
12007849 ATAAAAAAGTTAATAAC
1 ATAAAAAAGTTAATAAC
12007866 AGTAAAAAAGTTTAATAA
1 A-TAAAAAAG-TTAATAA
12007884 TAAAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.06
18 8 0.50
19 7 0.44
ACGTcount: A:0.63, C:0.03, G:0.09, T:0.26
Consensus pattern (17 bp):
ATAAAAAAGTTAATAAC
Found at i:12008255 original size:2 final size:2
Alignment explanation
Indices: 12008250--12008274 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12008240 TCTCTCTCTC
12008250 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
12008275 TAGATGATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12009724 original size:22 final size:21
Alignment explanation
Indices: 12009688--12009728 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
12009678 TAGATAAGTG
12009688 TAATTAACTAATTAGTATTATA
1 TAATTAACTAATTAG-ATTATA
**
12009710 TAATTAACTTGTTAGATTA
1 TAATTAACTAATTAGATTA
12009729 AACTATAGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.46
Consensus pattern (21 bp):
TAATTAACTAATTAGATTATA
Found at i:12011751 original size:60 final size:63
Alignment explanation
Indices: 12011687--12011812 Score: 177
Period size: 60 Copynumber: 2.0 Consensus size: 63
12011677 CTATATATAT
* *
12011687 ATATATAAATATATTTTATTATTTATTTAAATTTAAATTTA-A-ATAT-ATTATATTAATAAA
1 ATATATAAATATATTTAATTATTTATTTAAATTTAAATTTATATATATAACTATATTAATAAA
* * *
12011747 ATATATACATATATTTAATTATTTATTTAATTTTATATTTATATATATGAACTATATTAATAAA
1 ATATATAAATATATTTAATTATTTATTTAAATTTAAATTTATATATAT-AACTATATTAATAAA
12011811 AT
1 AT
12011813 TATTATTTAA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
60 37 0.65
61 1 0.02
62 4 0.07
64 15 0.26
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.52
Consensus pattern (63 bp):
ATATATAAATATATTTAATTATTTATTTAAATTTAAATTTATATATATAACTATATTAATAAA
Found at i:12012377 original size:105 final size:104
Alignment explanation
Indices: 12012196--12012408 Score: 401
Period size: 105 Copynumber: 2.0 Consensus size: 104
12012186 ATAGAATTCA
12012196 TTTGATATTATTCATTAAAACTTTTTTATCTTTTTTTAATTAAAAATATATAATTTTGTAAAGAA
1 TTTGATATTATTCATTAAAACTTTTTTATCTTTTTTTAATTAAAAATATATAATTTTGTAAAGAA
12012261 AATATCAAATGAAGTATCACGTGGCATCTGGATTGTGTT
66 AATATCAAATGAAGTATCACGTGGCATCTGGATTGTGTT
12012300 TTTGATATTATTCATTAAAACTTTTTTATCTTTTTTTTTAA-TAAAAATATATAATTTTGTAAAG
1 TTTGATATTATTCATTAAAACTTTTTTATC--TTTTTTTAATTAAAAATATATAATTTTGTAAAG
12012364 AAAATATCAAATGAAGTATCACGTGGCATCTGGATTGTGTT
64 AAAATATCAAATGAAGTATCACGTGGCATCTGGATTGTGTT
12012405 TTTG
1 TTTG
12012409 CCCTTTTTTT
Statistics
Matches: 107, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
104 30 0.28
105 68 0.64
106 9 0.08
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.46
Consensus pattern (104 bp):
TTTGATATTATTCATTAAAACTTTTTTATCTTTTTTTAATTAAAAATATATAATTTTGTAAAGAA
AATATCAAATGAAGTATCACGTGGCATCTGGATTGTGTT
Found at i:12013731 original size:34 final size:34
Alignment explanation
Indices: 12013684--12013752 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
12013674 ATATATACAC
12013684 AATTTTTTAATTCATTAAATTTACAATAAACATT
1 AATTTTTTAATTCATTAAATTTACAATAAACATT
* *
12013718 AATTTTTTCATTCATTAAATTTATAATAAACATT
1 AATTTTTTAATTCATTAAATTTACAATAAACATT
12013752 A
1 A
12013753 TTGTGTAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (34 bp):
AATTTTTTAATTCATTAAATTTACAATAAACATT
Found at i:12015318 original size:29 final size:29
Alignment explanation
Indices: 12015276--12015333 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
12015266 TCCAACCATG
*
12015276 CACCTAATCTTCATGCAATGTATATATGT
1 CACCTAATCTTCATGCAATCTATATATGT
*
12015305 CACCTAGTCTTCATGCAATCTATATATGT
1 CACCTAATCTTCATGCAATCTATATATGT
12015334 GACATATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.38
Consensus pattern (29 bp):
CACCTAATCTTCATGCAATCTATATATGT
Found at i:12021989 original size:21 final size:21
Alignment explanation
Indices: 12021963--12022006 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
12021953 AATCTTTTGA
12021963 TTTTAA-T-AAATTAATTTTATT
1 TTTTAATTCAAATT-ATTTT-TT
12021984 TTTTAATTCAAATTATTTTTT
1 TTTTAATTCAAATTATTTTTT
12022005 TT
1 TT
12022007 ACATAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 10 0.48
22 6 0.29
23 5 0.24
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTAATTCAAATTATTTTTT
Found at i:12022294 original size:17 final size:17
Alignment explanation
Indices: 12022274--12022310 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
12022264 TGATAAGATA
12022274 ATCTTGATAATAAAATT
1 ATCTTGATAATAAAATT
* *
12022291 ATCTTGATGATTAAATT
1 ATCTTGATAATAAAATT
12022308 ATC
1 ATC
12022311 AGAATGATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (17 bp):
ATCTTGATAATAAAATT
Found at i:12023859 original size:31 final size:31
Alignment explanation
Indices: 12023821--12023885 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
12023811 AAGTTGATAT
*
12023821 AACCAAACCTTTAAGGGGGGCGGCACTACAC
1 AACCAAACCTGTAAGGGGGGCGGCACTACAC
* *
12023852 AACCAAACCTGTAAGGGGGGCGGTACTACTC
1 AACCAAACCTGTAAGGGGGGCGGCACTACAC
12023883 AAC
1 AAC
12023886 ACGGGACCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.28, G:0.26, T:0.14
Consensus pattern (31 bp):
AACCAAACCTGTAAGGGGGGCGGCACTACAC
Found at i:12035890 original size:28 final size:28
Alignment explanation
Indices: 12035829--12035892 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
12035819 GGTTTCAGGC
* * *
12035829 TCGATTTCAATTCAATTAGACTTCAAGT
1 TCGATTTCAATTCAATTAGACCTAAAAT
12035857 TCGATTTCAATTCAATT-GAGCCTAAAAT
1 TCGATTTCAATTCAATTAGA-CCTAAAAT
*
12035885 TTGATTTC
1 TCGATTTC
12035893 GATCGCCCCC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 2 0.06
28 29 0.94
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (28 bp):
TCGATTTCAATTCAATTAGACCTAAAAT
Found at i:12036085 original size:16 final size:16
Alignment explanation
Indices: 12036066--12036097 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12036056 GGCCACCGAC
12036066 CCCTCTAATCACCCAT
1 CCCTCTAATCACCCAT
*
12036082 CCCTCTAGTCACCCAT
1 CCCTCTAATCACCCAT
12036098 ACCTTGTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.50, G:0.03, T:0.25
Consensus pattern (16 bp):
CCCTCTAATCACCCAT
Found at i:12036358 original size:15 final size:17
Alignment explanation
Indices: 12036340--12036394 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 17
12036330 AAAAACTACT
12036340 AAAAAAACTTT-CAAAA
1 AAAAAAACTTTGCAAAA
*
12036356 AAAAAAACTTTGTAAAA
1 AAAAAAACTTTGCAAAA
* *
12036373 AAAAGATACCTTGCAAAA
1 AAAA-AAACTTTGCAAAA
12036391 AAAA
1 AAAA
12036395 TAAAAAAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
16 11 0.33
17 8 0.24
18 14 0.42
ACGTcount: A:0.65, C:0.11, G:0.05, T:0.18
Consensus pattern (17 bp):
AAAAAAACTTTGCAAAA
Found at i:12036359 original size:16 final size:16
Alignment explanation
Indices: 12036340--12036376 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
12036330 AAAAACTACT
12036340 AAAAAAACTTTCAAAA
1 AAAAAAACTTTCAAAA
**
12036356 AAAAAAACTTTGTAAA
1 AAAAAAACTTTCAAAA
12036372 AAAAA
1 AAAAA
12036377 GATACCTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.70, C:0.08, G:0.03, T:0.19
Consensus pattern (16 bp):
AAAAAAACTTTCAAAA
Found at i:12038162 original size:200 final size:200
Alignment explanation
Indices: 12037819--12038219 Score: 698
Period size: 200 Copynumber: 2.0 Consensus size: 200
12037809 TGTTATCAAT
12037819 GTAATGGAACATTTTAATAACTATTTCAATAAAAAAGTCTAAATTTATTTTCCTTGAATAAAATT
1 GTAATGGAACATTTTAATAACTATTTCAATAAAAAAGTCTAAATTTATTTTCCTTGAATAAAATT
*
12037884 TGAGCATCAATAAATAAATAACAAATTTTCAATAAATAAAAAAAATCAATAAAATTATTTTTTTA
66 TGAGCATCAATAAATAAATAACAAATTTCCAATAAATAAAAAAAATCAATAAAATTATTTTTTTA
** *
12037949 AATATTGAAAATAAGATTATTTTTATCAAAATTAATGGATAACACGTAGTTAATT-AGTACCGTT
131 AATATAAAAAATAAGACTATTTTTATCAAAATTAATGGATAACACGTAGTTAATTGA-TACCGTT
12038013 TTAAAC
195 TTAAAC
*
12038019 GTAATGGAACATTTTAATAACTATTTCAATAAAAAAAGTCTTAATTTATTTTCCTTGAATAAAAT
1 GTAATGGAACATTTTAATAACTATTTCAAT-AAAAAAGTCTAAATTTATTTTCCTTGAATAAAAT
*
12038084 TTGAGTATCAATAAATAAATAACAAATTTCCAATAAATAAAAAAAATCAATAAAATTA-TTTTTT
65 TTGAGCATCAATAAATAAATAACAAATTTCCAATAAATAAAAAAAATCAATAAAATTATTTTTTT
* *
12038148 AAATATAAAAAATAAGACTGTTTTTATCAAAATTAATGGATAACTCGTAGTTAATTGATACCGTT
130 AAATATAAAAAATAAGACTATTTTTATCAAAATTAATGGATAACACGTAGTTAATTGATACCGTT
12038213 TTAAAC
195 TTAAAC
12038219 G
1 G
12038220 GGCGCTGTAG
Statistics
Matches: 191, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
200 101 0.53
201 90 0.47
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.37
Consensus pattern (200 bp):
GTAATGGAACATTTTAATAACTATTTCAATAAAAAAGTCTAAATTTATTTTCCTTGAATAAAATT
TGAGCATCAATAAATAAATAACAAATTTCCAATAAATAAAAAAAATCAATAAAATTATTTTTTTA
AATATAAAAAATAAGACTATTTTTATCAAAATTAATGGATAACACGTAGTTAATTGATACCGTTT
TAAAC
Found at i:12038330 original size:18 final size:18
Alignment explanation
Indices: 12038301--12038336 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
12038291 AAATTATTTT
12038301 TTTAATAAATTTTAATTAA
1 TTTAATAAATTTT-ATTAA
12038320 TTTAA-AAATTTTATTAA
1 TTTAATAAATTTTATTAA
12038337 AAAGATAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 7 0.41
19 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAATAAATTTTATTAA
Found at i:12048362 original size:57 final size:57
Alignment explanation
Indices: 12048274--12048675 Score: 626
Period size: 57 Copynumber: 6.9 Consensus size: 57
12048264 TCTTGTATAG
* *
12048274 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAATTTATTTTTAA
*
12048331 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTGAAACTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATA--TTTTTTTGAAA-TTT-ATTTTTAA
*
12048392 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTG-AAATTTATTTTTAA
* * *
12048450 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAATTTATTTTTAA
*
12048507 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAT-ATTTTTTTG-AAATTTATTTTTAA
*
12048566 GGAAAATTGATACTTTCAACTTTTTCC-CAAAAATATTTTTTGGAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTTTGAAATTTATTTTTAA
**
12048623 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGATTTTTATTT
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAATTTATTT
12048676 AAAGAATATA
Statistics
Matches: 318, Mismatches: 18, Indels: 18
0.90 0.05 0.05
Matches are distributed among these distances:
56 6 0.02
57 137 0.43
58 61 0.19
59 62 0.19
60 12 0.04
61 40 0.13
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.46
Consensus pattern (57 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAATTTATTTTTAA
Found at i:12048582 original size:116 final size:115
Alignment explanation
Indices: 12048274--12048664 Score: 635
Period size: 116 Copynumber: 3.4 Consensus size: 115
12048264 TCTTGTATAG
* * *
12048274 GGAAAATTGATACTTTCAACTTTTCCCCAAAAAT-ATTTTTTTG-AAATTTATTTCTAAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTTTAAGGAAAA
* *
12048337 TTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTGAAACTTTGATTTTCAA
66 TTGATACTTTCAACTTTTCCCCAAAAATA--TTTTTTGGAAA-TTT-ATTTT-AA
12048392 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATC-TTTTTTTGAAAATTTATTTTTAAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTTTAAGGAAAA
12048456 TTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
66 TTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTT-TAA
12048507 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTTTAAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTTTAAGGAAAA
*
12048572 TTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGGAAATTTATTTTTAA
66 TTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTA-TTTTAA
*
12048623 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTT
12048665 GATTTTTATT
Statistics
Matches: 262, Mismatches: 6, Indels: 12
0.94 0.02 0.04
Matches are distributed among these distances:
115 41 0.16
116 120 0.46
117 13 0.05
118 41 0.16
119 47 0.18
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (115 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTTTAAGGAAAA
TTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTTAA
Found at i:12048745 original size:20 final size:19
Alignment explanation
Indices: 12048695--12048746 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 19
12048685 AAAACAAAAT
*
12048695 AAAAGTAAAAGTAAATAAAG
1 AAAAGTAAAA-AAAATAAAG
12048715 --AAG-AAAAAAAATAAAG
1 AAAAGTAAAAAAAATAAAG
12048731 AAAAGTAAAACAAAAT
1 AAAAGTAAAA-AAAAT
12048747 TAAAAATAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
16 8 0.30
17 4 0.15
18 6 0.22
19 4 0.15
20 5 0.19
ACGTcount: A:0.75, C:0.02, G:0.12, T:0.12
Consensus pattern (19 bp):
AAAAGTAAAAAAAATAAAG
Found at i:12048751 original size:27 final size:27
Alignment explanation
Indices: 12048721--12048777 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
12048711 AAAGAAGAAA
12048721 AAAAATAAAGA-AAAG-TAAAACAAAATT
1 AAAAAT-AAGATAAAGATAAAA-AAAATT
*
12048748 AAAAATAAGATAAAGATAAAAAATATT
1 AAAAATAAGATAAAGATAAAAAAAATT
12048775 AAA
1 AAA
12048778 TAAATCTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 4 0.15
27 18 0.67
28 5 0.19
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.18
Consensus pattern (27 bp):
AAAAATAAGATAAAGATAAAAAAAATT
Found at i:12049737 original size:43 final size:41
Alignment explanation
Indices: 12049656--12049740 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 41
12049646 AATAAAAATC
* *
12049656 AAAATAAAAAAATACTAGATAATTAGAAAAGATAAGATAAA
1 AAAATAAAAAAATAATAGATAATTAAAAAAGATAAGATAAA
* *
12049697 AAAATAATAATAATAATCAGATAA-TAAAAAAGAATCAGATAAA
1 AAAATAA-AAAAATAAT-AGATAATTAAAAAAG-ATAAGATAAA
12049740 A
1 A
12049741 TTAACAGATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
41 7 0.19
42 14 0.38
43 16 0.43
ACGTcount: A:0.68, C:0.04, G:0.08, T:0.20
Consensus pattern (41 bp):
AAAATAAAAAAATAATAGATAATTAAAAAAGATAAGATAAA
Found at i:12049944 original size:20 final size:21
Alignment explanation
Indices: 12049921--12049961 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
12049911 GGCCTTACCC
12049921 ATTTGGGCCAGG-CCCAATTG
1 ATTTGGGCCAGGACCCAATTG
*
12049941 ATTTGGGCCTGGACCCAATTG
1 ATTTGGGCCAGGACCCAATTG
12049962 GGTGTCTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (21 bp):
ATTTGGGCCAGGACCCAATTG
Found at i:12051823 original size:48 final size:48
Alignment explanation
Indices: 12051767--12052341 Score: 582
Period size: 48 Copynumber: 11.9 Consensus size: 48
12051757 AACATATAAG
* * **
12051767 ATTTTAAAGTTATTAAGCCTCTATTGAGAGGAGCTTTTTCAAGATAGA
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATAGA
* * * * * *
12051815 ATTTTAAAGTTATTGAGCCTTTACTGAAAGGAGTTTTTTCAAGATAAA
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATAGA
* * * * * *
12051863 ATTTTAAAGTTGTAGAACCTTTGCTGAAATGAGTTTTTTCAAGATAGA
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATAGA
*
12051911 ATTTTAAAGTTGTTAAGCCTCTGCTGAGAGGAGCTTTTTTCAAGAT-GA
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC-TTTTTCAAGATAGA
** *
12051959 ATTTTTAAAGTTGTTGAGTTTCTACTGAGAGGAGCTTTTTCAAGATAGA
1 A-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATAGA
* * * * * * *
12052008 ATTTTAAAGTTGTTGGGCTTTTGTTGAGTGAAGCTTTTTCAAGATAAA
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATAGA
* *
12052056 ATTTTAAAGTTGTCG-GCCTCTACTGAGAGGTA-CTTTTTCAAGAT-GTA
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGG-AGCTTTTTCAAGATAG-A
* * *
12052103 TTTTTAAAGTTGTTGAGCCTATGCTGAGAGAAGCTTTTTTCAAGATAGA
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC-TTTTTCAAGATAGA
* * * * * *
12052152 ATTTTAAAATTATTGAGCTTCTGCTAAGAGGAGCTTTTTCCAGATAAA
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATAGA
* * *
12052200 ATTTTGAAGTTGTTGAGCCTCTGCTAAAAGGAGCTTTTTTCAAGATGAGA
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC-TTTTTCAAGAT-AGA
* * * * *
12052250 ATTTTTAAAGTTGTTGAGTCTTTGTTGAAATGAGCTTTTTTCAAGATAGAA
1 A-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC-TTTTTCAAGATAG-A
* * * *
12052301 AATTTAAAGTTGTTGAGCCTCTGCTGAAAGGAACCTTTTCA
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCA
12052342 GATTTCAAAT
Statistics
Matches: 441, Mismatches: 73, Indels: 25
0.82 0.14 0.05
Matches are distributed among these distances:
47 36 0.08
48 233 0.53
49 98 0.22
50 33 0.07
51 41 0.09
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (48 bp):
ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATAGA
Found at i:12052014 original size:97 final size:97
Alignment explanation
Indices: 12051767--12052332 Score: 590
Period size: 97 Copynumber: 5.8 Consensus size: 97
12051757 AACATATAAG
* * * * *
12051767 ATTTTAAAGTTATTAAGCCTCTATTGAGAGGAGCTTTTTCAAGATAGAATTTTAAAGTTATTGAG
1 ATTTTAAAGTTGTTGAGCTTCTACTGAGAGGAGCTTTTTCAAGATAGAATTTTAAAGTTGTTGAG
* * *
12051832 CCTTTACTGAAAGGAG-TTTTTTCAAGATAAA
66 CCTCTGCTGAAAGGAGCTTTTTTCAAGATGAA
* * * * * * *
12051863 ATTTTAAAGTTGTAGAACCTT-TGCTGAAATGAGTTTTTTCAAGATAGAATTTTAAAGTTGTTAA
1 ATTTTAAAGTTGTTG-AGCTTCTACTGAGAGGAGCTTTTTCAAGATAGAATTTTAAAGTTGTTGA
*
12051927 GCCTCTGCTGAGAGGAGCTTTTTTCAAGATGAA
65 GCCTCTGCTGAAAGGAGCTTTTTTCAAGATGAA
* * *
12051960 TTTTTAAAGTTGTTGAGTTTCTACTGAGAGGAGCTTTTTCAAGATAGAATTTTAAAGTTGTTGGG
1 ATTTTAAAGTTGTTGAGCTTCTACTGAGAGGAGCTTTTTCAAGATAGAATTTTAAAGTTGTTGAG
* * * ** * *
12052025 CTTTTGTTGAGTGAAGC-TTTTTCAAGATAAA
66 CCTCTGCTGAAAGGAGCTTTTTTCAAGATGAA
* * *
12052056 ATTTTAAAGTTGTCG-GCCTCTACTGAGAGGTA-CTTTTTCAAGAT-GTATTTTTAAAGTTGTTG
1 ATTTTAAAGTTGTTGAGCTTCTACTGAGAGG-AGCTTTTTCAAGATAG-AATTTTAAAGTTGTTG
* * *
12052118 AGCCTATGCTGAGAGAAGCTTTTTTCAAGAT-AGA
64 AGCCTCTGCTGAAAGGAGCTTTTTTCAAGATGA-A
* * * * * * *
12052152 ATTTTAAAATTATTGAGCTTCTGCTAAGAGGAGCTTTTTCCAGATAAAATTTTGAAGTTGTTGAG
1 ATTTTAAAGTTGTTGAGCTTCTACTGAGAGGAGCTTTTTCAAGATAGAATTTTAAAGTTGTTGAG
*
12052217 CCTCTGCTAAAAGGAGCTTTTTTCAAGATGAGA
66 CCTCTGCTGAAAGGAGCTTTTTTCAAGATGA-A
** * * *
12052250 ATTTTTAAAGTTGTTGAGTCTT-TGTTGAAATGAGCTTTTTTCAAGATAGAAAATTTAAAGTTGT
1 A-TTTTAAAGTTGTTGAG-CTTCTACTGAGAGGAGC-TTTTTCAAGATAG-AATTTTAAAGTTGT
12052314 TGAGCCTCTGCTGAAAGGA
62 TGAGCCTCTGCTGAAAGGA
12052333 ACCTTTTCAG
Statistics
Matches: 388, Mismatches: 67, Indels: 25
0.81 0.14 0.05
Matches are distributed among these distances:
94 1 0.00
95 55 0.14
96 117 0.30
97 144 0.37
98 4 0.01
99 23 0.06
100 14 0.04
101 30 0.08
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (97 bp):
ATTTTAAAGTTGTTGAGCTTCTACTGAGAGGAGCTTTTTCAAGATAGAATTTTAAAGTTGTTGAG
CCTCTGCTGAAAGGAGCTTTTTTCAAGATGAA
Found at i:12052728 original size:16 final size:16
Alignment explanation
Indices: 12052687--12052729 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
12052677 TTATTAAATT
*
12052687 AAACAAAAATATAAAA
1 AAACAAAAAAATAAAA
* * *
12052703 AAAGAGAAAAATACAA
1 AAACAAAAAAATAAAA
12052719 AAACAAAAAAA
1 AAACAAAAAAA
12052730 AGGGGGCTGA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.81, C:0.07, G:0.05, T:0.07
Consensus pattern (16 bp):
AAACAAAAAAATAAAA
Found at i:12053754 original size:24 final size:24
Alignment explanation
Indices: 12053706--12053754 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
12053696 CCAGTTTAGG
12053706 TAAAAATATTTTTTTTTGAATTTTT
1 TAAAAATATTTTTTTTT-AATTTTT
12053731 TAAAAATATTATTTTTGTT-ATTTT
1 TAAAAATATT-TTTTT-TTAATTTT
12053755 AATTATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 15 0.68
26 5 0.23
27 2 0.09
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (24 bp):
TAAAAATATTTTTTTTTAATTTTT
Found at i:12053961 original size:21 final size:21
Alignment explanation
Indices: 12053918--12053961 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
12053908 AAAAGGTTAT
* *
12053918 AATTAAATAAAAATAATACAA
1 AATTAAATAAAAATAAGAAAA
12053939 AATTAAATAAAAATAAGAAAA
1 AATTAAATAAAAATAAGAAAA
12053960 AA
1 AA
12053962 AAATTTATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.20
Consensus pattern (21 bp):
AATTAAATAAAAATAAGAAAA
Found at i:12054816 original size:18 final size:18
Alignment explanation
Indices: 12054787--12054822 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
12054777 AAATTATCTT
12054787 TTTAATAAATTTTAATTAA
1 TTTAATAAATTTT-ATTAA
12054806 TTTAA-AAATTTTATTAA
1 TTTAATAAATTTTATTAA
12054823 AAAGATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 7 0.41
19 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAATAAATTTTATTAA
Found at i:12056899 original size:3 final size:3
Alignment explanation
Indices: 12056891--12056922 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
12056881 CTTTTGTCTT
*
12056891 TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12056923 GTTTTGGAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:12058639 original size:24 final size:22
Alignment explanation
Indices: 12058603--12058656 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
12058593 TACATGATAT
12058603 AATTATATAATAT-ATAAAATAA
1 AATTATATAATATCAT-AAATAA
*
12058625 AATTATATATCATATCATATATAA
1 AATTATATA--ATATCATAAATAA
*
12058649 TATTATAT
1 AATTATAT
12058657 TACAAAATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 9 0.33
24 16 0.59
25 2 0.07
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTATATAATATCATAAATAA
Found at i:12059743 original size:6 final size:6
Alignment explanation
Indices: 12059732--12059764 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
12059722 TTCACCTTTA
12059732 TTTTGT TTTTGT TTTTGT TTTT-T TTTATGT TTT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTT-TGT TTT
12059765 CAGTAAATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 4 0.16
6 17 0.68
7 4 0.16
ACGTcount: A:0.03, C:0.00, G:0.12, T:0.85
Consensus pattern (6 bp):
TTTTGT
Found at i:12062223 original size:2 final size:2
Alignment explanation
Indices: 12062216--12062263 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
12062206 TGATAGGGCT
12062216 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12062258 TA TA TA
1 TA TA TA
12062264 CACTCGAAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12062623 original size:2 final size:2
Alignment explanation
Indices: 12062616--12062648 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12062606 CAATGTTAGA
12062616 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12062649 AAGGATCAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12063159 original size:26 final size:26
Alignment explanation
Indices: 12063123--12063173 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
12063113 TAATATGAGT
12063123 AAGGTTAATTAACACAAGCATAAAAA
1 AAGGTTAATTAACACAAGCATAAAAA
12063149 AAGGTTAATTAACACAAGCATAAAA
1 AAGGTTAATTAACACAAGCATAAAA
12063174 TTTTTTAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.57, C:0.12, G:0.12, T:0.20
Consensus pattern (26 bp):
AAGGTTAATTAACACAAGCATAAAAA
Found at i:12068444 original size:2 final size:2
Alignment explanation
Indices: 12068437--12068462 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12068427 AGCAAGCACA
12068437 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
12068463 GTGCGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12072234 original size:264 final size:263
Alignment explanation
Indices: 12071732--12072257 Score: 1007
Period size: 264 Copynumber: 2.0 Consensus size: 263
12071722 TGGATATCAC
12071732 TTACAGGTTTCAAAAGAACACGCAACAAGCTTAATGTATGGGGCAAGGGAAGAGATAACAGGTAA
1 TTACAGGTTTCAAAAGAACACGCAACAAGCTTAATGTATGGGGCAAGGGAAGAGATAACAGGTAA
12071797 TGTCAATGTCCCTAACTGGAATAGATTATGGCAGTTACCCATTCTAAGTAAATTCAAATATTGCA
66 TGTCAATGTCCCTAACTGGAATAGATTATGGCAGTTACCCATTCTAAGTAAATTCAAATATTGCA
*
12071862 TAGAGATTGAGGTTAAAACACTACTTGTATATGAAAGACTAAAGCATATGAAAATAATAGATTGT
131 TAGAGATTGAGGTTAAAACACTACTTGTATATGAAAGACTAAAGCATATGAAAATAATAGACTGT
*
12071927 GTGACATGTCAACGATGTTAAAAGTAGGACAAAACTATAATACATGCAATAAGAGATTACCCCAT
196 GTGACATGTCAACGATGTTAAAAGTAAGACAAAACTATAATACATGCAATAAGAGATTACCCCAT
12071992 TGG
261 TGG
* *
12071995 TTACTGGTTTCAAAAGAACACGCAACAAGCTTAATGTATGGTGCAAGGGAAGAGATAACAGGTAA
1 TTACAGGTTTCAAAAGAACACGCAACAAGCTTAATGTATGGGGCAAGGGAAGAGATAACAGGTAA
12072060 TGTCAATGTCCCTAACTGGAATAGATTATGGCAGTTACCCATTCTAAGTAAATTCAAAATATTGC
66 TGTCAATGTCCCTAACTGGAATAGATTATGGCAGTTACCCATTCTAAGTAAATTC-AAATATTGC
12072125 ATAGAGATTGAGGTTAAAACACTACTTGTATATGAAAGACTAAAGCATATGAAAATAATAGACTG
130 ATAGAGATTGAGGTTAAAACACTACTTGTATATGAAAGACTAAAGCATATGAAAATAATAGACTG
12072190 TGTGACATGTCAACGATGTTAAAAGTAAGACAAAACTATAATACATGCAATAAGAGATTACCCCA
195 TGTGACATGTCAACGATGTTAAAAGTAAGACAAAACTATAATACATGCAATAAGAGATTACCCCA
12072255 TTG
260 TTG
12072258 CCAAGGAAGT
Statistics
Matches: 258, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
263 118 0.46
264 140 0.54
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.26
Consensus pattern (263 bp):
TTACAGGTTTCAAAAGAACACGCAACAAGCTTAATGTATGGGGCAAGGGAAGAGATAACAGGTAA
TGTCAATGTCCCTAACTGGAATAGATTATGGCAGTTACCCATTCTAAGTAAATTCAAATATTGCA
TAGAGATTGAGGTTAAAACACTACTTGTATATGAAAGACTAAAGCATATGAAAATAATAGACTGT
GTGACATGTCAACGATGTTAAAAGTAAGACAAAACTATAATACATGCAATAAGAGATTACCCCAT
TGG
Found at i:12074173 original size:13 final size:13
Alignment explanation
Indices: 12074155--12074181 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12074145 AACATGGGCT
12074155 AAGATCATTTATA
1 AAGATCATTTATA
12074168 AAGATCATTTATA
1 AAGATCATTTATA
12074181 A
1 A
12074182 CCCATAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (13 bp):
AAGATCATTTATA
Found at i:12081324 original size:19 final size:18
Alignment explanation
Indices: 12081288--12081331 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
12081278 TAATAATTAA
12081288 ATAATTAATTAACAAATT
1 ATAATTAATTAACAAATT
12081306 ATAATATAATTATAC-AATT
1 ATAAT-TAATTA-ACAAATT
*
12081325 AAAATTA
1 ATAATTA
12081332 CACATTATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 7 0.30
19 14 0.61
20 2 0.09
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAATTAATTAACAAATT
Found at i:12084252 original size:63 final size:63
Alignment explanation
Indices: 12084177--12084326 Score: 150
Period size: 62 Copynumber: 2.4 Consensus size: 63
12084167 TAAAGACGTC
* * *
12084177 TTTTTACC-AAAAATACCTTGAATAATCCCT-T-ATAAAAAATTTAATAGAGG-TTATTTAAGGT
1 TTTTTGCCAAAAAACACCTTGAATAAT-CCTATCAT-AAAAATTT-ATAG-GGATTATTCAAGGT
12084238 G-
62 GT
* * *
12084239 TTTTTGCCAAAAAACATCTTTAATAATCCTATCATAAAAATTTTTAGGGATTATTCAAGGTGT
1 TTTTTGCCAAAAAACACCTTGAATAATCCTATCATAAAAATTTATAGGGATTATTCAAGGTGT
* *
12084302 TTTTTGCC-AGAAACACTTTGAATAA
1 TTTTTGCCAAAAAACACCTTGAATAA
12084327 CCCAATTCAA
Statistics
Matches: 73, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
61 2 0.03
62 37 0.51
63 32 0.44
64 2 0.03
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (63 bp):
TTTTTGCCAAAAAACACCTTGAATAATCCTATCATAAAAATTTATAGGGATTATTCAAGGTGT
Found at i:12084840 original size:20 final size:20
Alignment explanation
Indices: 12084802--12084843 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
12084792 AAAGATAAAA
12084802 AAAATTAAAATTATATTAAT
1 AAAATTAAAATTATATTAAT
*
12084822 AAAATATAAAA-TATTTTAAT
1 AAAAT-TAAAATTATATTAAT
12084842 AA
1 AA
12084844 TATTTAATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATTAAAATTATATTAAT
Found at i:12086096 original size:12 final size:12
Alignment explanation
Indices: 12086079--12086104 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12086069 TTCGTCTTTA
12086079 TTATTATTATTG
1 TTATTATTATTG
12086091 TTATTATTATTG
1 TTATTATTATTG
12086103 TT
1 TT
12086105 GTTGTTTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTATTATTATTG
Found at i:12088050 original size:59 final size:57
Alignment explanation
Indices: 12087987--12088267 Score: 223
Period size: 61 Copynumber: 4.8 Consensus size: 57
12087977 TTATTTAAGG
* *
12087987 AAAATTGATACTTTTAACTTTTCTTAAAAATATTTTTTCTTTAAATTTTATTTTTAAAA
1 AAAATTGATACTTTCAACTTTTCTCAAAAATATTTTTT-TTTAAATTTTA-TTTTAAAA
* * * * *
12088046 AAAATTGGTACTTCCAACTTTTCCTCAAAAATGCTTTTTTTTTTAAATTTTAATTTCAAGA
1 AAAATTGATACTTTCAACTTTT-CTCAAAAAT--ATTTTTTTTTAAATTTT-ATTTTAAAA
* * * * *
12088107 AAAATTGGTACTTTCAATTTTTTCTCAAAAATATTTTTTTTGAAAACTTTATTTT-AAG
1 AAAATTGATACTTTCAA-CTTTTCTCAAAAATATTTTTTTT-TAAATTTTATTTTAAAA
* **** *
12088165 GAAATTGATAC-TTCAACTTTTCTTCAAAAATATTTTAAGGT---TTTTATTTTCAAAG
1 AAAATTGATACTTTCAACTTTTC-TCAAAAATATTTTTTTTTAAATTTTATTTT-AAAA
* * * *
12088220 AAAATTAATATTTTCAATTTTTTCTCAAAAATA-TTTTTTTGAAATTTT
1 AAAATTGATACTTTCAA-CTTTTCTCAAAAATATTTTTTTTTAAATTTT
12088268 TATTCTCTAT
Statistics
Matches: 175, Mismatches: 33, Indels: 29
0.74 0.14 0.12
Matches are distributed among these distances:
53 8 0.05
55 14 0.08
56 19 0.11
57 23 0.13
58 14 0.08
59 31 0.18
60 14 0.08
61 41 0.23
62 11 0.06
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTCTCAAAAATATTTTTTTTTAAATTTTATTTTAAAA
Found at i:12088110 original size:61 final size:60
Alignment explanation
Indices: 12087980--12088200 Score: 243
Period size: 61 Copynumber: 3.7 Consensus size: 60
12087970 GAAGTTTTTA
* * * * *
12087980 TTTAAGGAAAATTGATACTTTTAACTTTT-CTTAAAAATATTTTTTCTTTAAATTTTATT
1 TTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTTAAATTTTAAT
* * * *
12088039 TTTAAAAAAAATTGGTACTTCCAACTTTTCCTCAAAAATGCTTTTTTTTTTAAATTTTAAT
1 TTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAT-ATTTTTTTTTTAAATTTTAAT
* * * * ** *
12088100 TTCAAGAAAAATTGGTACTTTCAATTTTTTCTCAAAAATATTTTTTTTGAAAACTTT-AT
1 TTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTTAAATTTTAAT
* *
12088159 TTTAAG-GAAATTGATAC-TTCAACTTTTCTTCAAAAATATTTT
1 TTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTT
12088201 AAGGTTTTTA
Statistics
Matches: 136, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
57 22 0.16
58 9 0.07
59 31 0.23
60 22 0.16
61 52 0.38
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.49
Consensus pattern (60 bp):
TTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTTAAATTTTAAT
Found at i:12088330 original size:51 final size:53
Alignment explanation
Indices: 12088275--12088383 Score: 125
Period size: 51 Copynumber: 2.1 Consensus size: 53
12088265 TTTTATTCTC
* * **
12088275 TATTTAAAG-AAAATTTGATATTTCAACTTTTCCTTTTTTTTT-GAAA-AATTT
1 TATTTAAAGAAAAATTAG-TATTCCAAAATTTCCTTTTTTTTTGGAAATAATTT
* * *
12088326 TATTTAAGGAAAAATTAGTATTCCAAAATTTCTTTTTTTTTTGGAAATATTTT
1 TATTTAAAGAAAAATTAGTATTCCAAAATTTCCTTTTTTTTTGGAAATAATTT
12088379 TATTT
1 TATTT
12088384 TTTTCTTTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
51 28 0.58
52 11 0.23
53 9 0.19
ACGTcount: A:0.33, C:0.06, G:0.07, T:0.53
Consensus pattern (53 bp):
TATTTAAAGAAAAATTAGTATTCCAAAATTTCCTTTTTTTTTGGAAATAATTT
Found at i:12089858 original size:5 final size:5
Alignment explanation
Indices: 12089804--12089871 Score: 70
Period size: 5 Copynumber: 13.6 Consensus size: 5
12089794 CCTATTATCT
* *
12089804 TAAAA TAATAA TAGAA TAAAA TTAAA -AAAA TCAAAA TAAAA -ACAAA
1 TAAAA TAA-AA TAAAA TAAAA TAAAA TAAAA T-AAAA TAAAA TA-AAA
12089850 -AAAA TAAAA TAAAA TAAAA TAA
1 TAAAA TAAAA TAAAA TAAAA TAA
12089872 CCAACAGTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
4 7 0.13
5 38 0.70
6 9 0.17
ACGTcount: A:0.76, C:0.03, G:0.01, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:12090568 original size:22 final size:21
Alignment explanation
Indices: 12090543--12090585 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
12090533 GACAACAAAA
* *
12090543 TTTAATTTAAATATATTATCTT
1 TTTAAATTAAATAAATT-TCTT
12090565 TTTAAATTAAATAAATTTCTT
1 TTTAAATTAAATAAATTTCTT
12090586 AATAATCTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTAAATTAAATAAATTTCTT
Found at i:12094001 original size:2 final size:2
Alignment explanation
Indices: 12093994--12094029 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
12093984 TAAATATGCC
12093994 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12094030 CCACACACAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12102283 original size:19 final size:18
Alignment explanation
Indices: 12102241--12102304 Score: 78
Period size: 18 Copynumber: 3.6 Consensus size: 18
12102231 TGAGCAAAAT
*
12102241 ATCATGCAAAT-AATTAA
1 ATCATGCAATTAAATTAA
*
12102258 ATCATGCAATTAAATCAA
1 ATCATGCAATTAAATTAA
12102276 ATTCATGCAA-TAATATTAA
1 A-TCATGCAATTAA-ATTAA
12102295 ATCATGCAAT
1 ATCATGCAAT
12102305 AATGCAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
17 10 0.25
18 17 0.43
19 13 0.32
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.31
Consensus pattern (18 bp):
ATCATGCAATTAAATTAA
Found at i:12102313 original size:36 final size:37
Alignment explanation
Indices: 12102237--12102332 Score: 112
Period size: 37 Copynumber: 2.6 Consensus size: 37
12102227 TATATGAGCA
12102237 AAATATCATGCAAATAATTAAATCATGCAATTAAATC
1 AAATATCATGCAAATAATTAAATCATGCAATTAAATC
12102274 AAAT-TCATGC-AATAATATTAAATCATGCAA-T-AATGC
1 AAATATCATGCAAAT-A-ATTAAATCATGCAATTAAAT-C
*
12102310 AAATAATCATGTAAATAA-TAAAT
1 AAAT-ATCATGCAAATAATTAAAT
12102333 AATTATGCAA
Statistics
Matches: 52, Mismatches: 1, Indels: 13
0.79 0.02 0.20
Matches are distributed among these distances:
35 6 0.12
36 18 0.35
37 19 0.37
38 6 0.12
39 3 0.06
ACGTcount: A:0.52, C:0.11, G:0.06, T:0.30
Consensus pattern (37 bp):
AAATATCATGCAAATAATTAAATCATGCAATTAAATC
Found at i:12102334 original size:19 final size:19
Alignment explanation
Indices: 12102237--12102368 Score: 109
Period size: 19 Copynumber: 7.1 Consensus size: 19
12102227 TATATGAGCA
12102237 AAAT-ATCATGCAAATAAT
1 AAATAATCATGCAAATAAT
* *
12102255 -TA-AATCATGCAATTAAAT
1 AAATAATCATGCAAAT-AAT
12102273 CAAAT--TCATGC-AATAAT
1 -AAATAATCATGCAAATAAT
*
12102290 -ATTAAATCATGC-AATAAT
1 AAAT-AATCATGCAAATAAT
*
12102308 GCAAATAATCATGTAAATAAT
1 --AAATAATCATGCAAATAAT
*
12102329 AAATAATTATGCAAATAAT
1 AAATAATCATGCAAATAAT
*
12102348 AATTAATCATGCAAATAAT
1 AAATAATCATGCAAATAAT
12102367 AA
1 AA
12102369 TTTCTCATAG
Statistics
Matches: 91, Mismatches: 11, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
15 2 0.02
17 14 0.15
18 17 0.19
19 42 0.46
20 8 0.09
21 8 0.09
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.30
Consensus pattern (19 bp):
AAATAATCATGCAAATAAT
Found at i:12102514 original size:13 final size:13
Alignment explanation
Indices: 12102454--12102525 Score: 56
Period size: 13 Copynumber: 5.4 Consensus size: 13
12102444 AGAATAAAAT
12102454 ATAAAAATAT-AAA
1 ATAAAAA-ATCAAA
*
12102467 ATAAATATAAACAAA
1 ATAAA-A-AATCAAA
* *
12102482 ACAAAAAAGCAAA
1 ATAAAAAATCAAA
** *
12102495 AGCAAAAATTAAA
1 ATAAAAAATCAAA
12102508 ATAAAAAATCAAA
1 ATAAAAAATCAAA
12102521 ATAAA
1 ATAAA
12102526 TAAAAGAAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
13 35 0.76
14 3 0.07
15 8 0.17
ACGTcount: A:0.75, C:0.07, G:0.03, T:0.15
Consensus pattern (13 bp):
ATAAAAAATCAAA
Found at i:12103359 original size:16 final size:15
Alignment explanation
Indices: 12103323--12103352 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12103313 CAAATCTCAA
12103323 ATTTTTCTATGATTT
1 ATTTTTCTATGATTT
*
12103338 AATTTTCTATGATTT
1 ATTTTTCTATGATTT
12103353 GGTTTTTGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.63
Consensus pattern (15 bp):
ATTTTTCTATGATTT
Found at i:12104077 original size:32 final size:31
Alignment explanation
Indices: 12104019--12104137 Score: 106
Period size: 32 Copynumber: 3.9 Consensus size: 31
12104009 ATTAATAGTT
*
12104019 ATGCAATTAACA-ATGTAAATCATGCAAATAAAC
1 ATGCAATTAA-ATATATAAATCATGCAAAT--AC
12104052 ATGCAATTAAATATAT-AATCATGC-AAT-C
1 ATGCAATTAAATATATAAATCATGCAAATAC
* * *
12104080 ATGTAAATAATAATATATAAACCATGCAAATA-
1 ATG-CAATTA-AATATATAAATCATGCAAATAC
*
12104112 ATGCAAATAAATATAT-AATCATGCAA
1 ATGCAATTAAATATATAAATCATGCAA
12104138 TCAAATTAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
28 4 0.06
29 13 0.18
30 14 0.19
31 13 0.18
32 15 0.21
33 13 0.18
ACGTcount: A:0.52, C:0.13, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGCAATTAAATATATAAATCATGCAAATAC
Found at i:12104089 original size:20 final size:20
Alignment explanation
Indices: 12104036--12104090 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
12104026 TAACAATGTA
* *
12104036 AATCATGCAAATAAACATGC
1 AATCATGTAAATAATCATGC
* ** *
12104056 AATTAAATATATAATCATGC
1 AATCATGTAAATAATCATGC
12104076 AATCATGTAAATAAT
1 AATCATGTAAATAAT
12104091 AATATATAAA
Statistics
Matches: 25, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.51, C:0.13, G:0.07, T:0.29
Consensus pattern (20 bp):
AATCATGTAAATAATCATGC
Found at i:12104137 original size:20 final size:20
Alignment explanation
Indices: 12104112--12104235 Score: 92
Period size: 20 Copynumber: 5.8 Consensus size: 20
12104102 CATGCAAATA
12104112 ATGCAAATAAATATATAATC
1 ATGCAAATAAATATATAATC
12104132 ATGC-AATCAAATTAAATATAATC
1 ATGCAAAT-AAA-T--ATATAATC
*
12104155 ATACAAATAAATATATTAATAATC
1 ATGCAAAT-AA-ATA-T-ATAATC
*
12104179 ATGCAAATATAT-TAATATATC
1 ATGCAAATAAATAT-ATA-ATC
*
12104200 AT-CAAATAAATATATTAATA
1 ATGCAAATAAATATA-TAATC
*
12104220 ATGCAAAAAAATATAT
1 ATGCAAATAAATATAT
12104236 TAGGCAAATA
Statistics
Matches: 85, Mismatches: 7, Indels: 24
0.73 0.06 0.21
Matches are distributed among these distances:
19 3 0.04
20 26 0.31
21 20 0.24
22 3 0.04
23 13 0.15
24 19 0.22
25 1 0.01
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.32
Consensus pattern (20 bp):
ATGCAAATAAATATATAATC
Found at i:12104143 original size:24 final size:24
Alignment explanation
Indices: 12104115--12104184 Score: 74
Period size: 23 Copynumber: 3.0 Consensus size: 24
12104105 GCAAATAATG
12104115 CAAATAAATATATAATCATGCAAT
1 CAAATAAATATATAATCATGCAAT
* *
12104139 CAAATTAA-ATATAATCATACAAAT
1 CAAATAAATATATAATCATGC-AAT
*
12104163 -AAATATAT-TAATAATCATGCAA
1 CAAATAAATAT-ATAATCATGCAA
12104185 ATATATTAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
23 19 0.50
24 19 0.50
ACGTcount: A:0.56, C:0.11, G:0.03, T:0.30
Consensus pattern (24 bp):
CAAATAAATATATAATCATGCAAT
Found at i:12104185 original size:24 final size:24
Alignment explanation
Indices: 12104149--12104237 Score: 95
Period size: 24 Copynumber: 4.0 Consensus size: 24
12104139 CAAATTAAAT
*
12104149 ATAATCATACAAATAAATATATTA
1 ATAATCATGCAAATAAATATATTA
12104173 ATAATCATGC----AAATATATTA
1 ATAATCATGCAAATAAATATATTA
12104193 ATATATCAT-CAAATAAATATATTA
1 ATA-ATCATGCAAATAAATATATTA
*
12104217 AT-A--ATGCAAAAAAATATATTA
1 ATAATCATGCAAATAAATATATTA
12104238 GGCAAATAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 15
0.77 0.03 0.20
Matches are distributed among these distances:
20 16 0.28
21 19 0.33
22 1 0.02
24 21 0.37
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.34
Consensus pattern (24 bp):
ATAATCATGCAAATAAATATATTA
Found at i:12104218 original size:44 final size:47
Alignment explanation
Indices: 12104126--12104221 Score: 146
Period size: 44 Copynumber: 2.1 Consensus size: 47
12104116 AAATAAATAT
12104126 ATAATCATGCAATCAAATTAAATATAATCATACAAATAAATATATTA
1 ATAATCATGCAATCAAATTAAATATAATCATACAAATAAATATATTA
*
12104173 ATAATCATGCAAAT-ATATT-AATAT-ATCAT-CAAATAAATATATTA
1 ATAATCATGC-AATCAAATTAAATATAATCATACAAATAAATATATTA
12104217 ATAAT
1 ATAAT
12104222 GCAAAAAAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
44 20 0.43
45 5 0.11
46 5 0.11
47 14 0.30
48 3 0.06
ACGTcount: A:0.54, C:0.09, G:0.02, T:0.34
Consensus pattern (47 bp):
ATAATCATGCAATCAAATTAAATATAATCATACAAATAAATATATTA
Found at i:12108660 original size:47 final size:47
Alignment explanation
Indices: 12108587--12108684 Score: 169
Period size: 47 Copynumber: 2.1 Consensus size: 47
12108577 GTAGATTTGG
* * *
12108587 CTATAAAAGTTGTCCTATTTATAATGATGGCTTTTAGTGAAAACCAA
1 CTATAAAAGTTATCCTATTTACAATGATGGCTTTTAGCGAAAACCAA
12108634 CTATAAAAGTTATCCTATTTACAATGATGGCTTTTAGCGAAAACCAA
1 CTATAAAAGTTATCCTATTTACAATGATGGCTTTTAGCGAAAACCAA
12108681 CTAT
1 CTAT
12108685 CTCAAATGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (47 bp):
CTATAAAAGTTATCCTATTTACAATGATGGCTTTTAGCGAAAACCAA
Found at i:12115158 original size:58 final size:58
Alignment explanation
Indices: 12115054--12115184 Score: 147
Period size: 58 Copynumber: 2.3 Consensus size: 58
12115044 CTTAATTGAT
* * * * * *
12115054 GCTTGGACTTAATCATAGCACATAACTTTACTACCTAGGTTGTCTCAATGCCCCTTAA
1 GCTTGAACTCAATCATAGCACATAACCTTACTACCTAAGTTATCTCAATGCCCCTCAA
* * * * *
12115112 GCTTGAACTCAATCATAGCACATAACCTTGCTACTTAAGTTATCTCAGTGTCTCTCAA
1 GCTTGAACTCAATCATAGCACATAACCTTACTACCTAAGTTATCTCAATGCCCCTCAA
12115170 GCTTGCAA-TCAATCA
1 GCTTG-AACTCAATCA
12115185 CAGTTTGAAC
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
58 59 0.97
59 2 0.03
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (58 bp):
GCTTGAACTCAATCATAGCACATAACCTTACTACCTAAGTTATCTCAATGCCCCTCAA
Found at i:12115223 original size:66 final size:66
Alignment explanation
Indices: 12115148--12115279 Score: 210
Period size: 66 Copynumber: 2.0 Consensus size: 66
12115138 CTTGCTACTT
* * *
12115148 AAGTTATCTCAGTGTCTCTCAAGCTTGCAATCAATCACAGTTTGAACTCAATCTTGCACTCCATC
1 AAGTTATCTCAATGCCTCTCAAGCTTGCAATCAATCACAGTCTGAACTCAATCTTGCACTCCATC
12115213 A
66 A
* * *
12115214 AAGTTATCTCAATGCCTCTCAAGCTTGCGATCAATCATAGTCTGAACTTAATCTTGCACTCCATC
1 AAGTTATCTCAATGCCTCTCAAGCTTGCAATCAATCACAGTCTGAACTCAATCTTGCACTCCATC
12115279 A
66 A
12115280 TAGGTTGACT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (66 bp):
AAGTTATCTCAATGCCTCTCAAGCTTGCAATCAATCACAGTCTGAACTCAATCTTGCACTCCATC
A
Found at i:12116200 original size:12 final size:12
Alignment explanation
Indices: 12116183--12116209 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
12116173 TACATCATCT
12116183 TCACACGCTATG
1 TCACACGCTATG
12116195 TCACACGCTATG
1 TCACACGCTATG
12116207 TCA
1 TCA
12116210 ACTTCACACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.26
Consensus pattern (12 bp):
TCACACGCTATG
Found at i:12117302 original size:28 final size:28
Alignment explanation
Indices: 12117265--12117352 Score: 78
Period size: 29 Copynumber: 3.2 Consensus size: 28
12117255 AAAATTCTTC
*
12117265 AATTATTTATT-T-TTTAAATGAATTTAT
1 AATT-TTTATTATATTTAAATCAATTTAT
*
12117292 -ATTTTTATTATATTTAAATCAATTTTT
1 AATTTTTATTATATTTAAATCAATTTAT
* *
12117319 AATTTTTTGTTGTATTTAAAT-AAGTTT-T
1 AA-TTTTTATTATATTTAAATCAA-TTTAT
12117347 AATTTT
1 AATTTT
12117353 AAATATGAGA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
25 6 0.12
26 4 0.08
27 17 0.33
28 6 0.12
29 19 0.37
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.61
Consensus pattern (28 bp):
AATTTTTATTATATTTAAATCAATTTAT
Found at i:12117460 original size:29 final size:30
Alignment explanation
Indices: 12117380--12117465 Score: 74
Period size: 30 Copynumber: 2.9 Consensus size: 30
12117370 ATGATAAATT
*
12117380 TTTATTT-AAGTACAAAAT-AAATGTTAAAGA
1 TTTATTTGAA-TATAAAATAAAAT-TTAAAGA
*
12117410 TTTATTTGAATATAAATTAAAATTTAAA-A
1 TTTATTTGAATATAAAATAAAATTTAAAGA
*
12117439 TTTTATTTTG-ATA-AAAATAAAAATTAA
1 -TTTA-TTTGAATATAAAATAAAATTTAA
12117466 TAAATTATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
29 13 0.27
30 25 0.52
31 10 0.21
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.42
Consensus pattern (30 bp):
TTTATTTGAATATAAAATAAAATTTAAAGA
Found at i:12117499 original size:26 final size:24
Alignment explanation
Indices: 12117450--12117514 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 24
12117440 TTTATTTTGA
* *
12117450 TAAAAATAAAAATTAATAAATTATT
1 TAAAAA-AAAAATTAACAAATTATC
*
12117475 TAAATAAAAAAATATAACAATTTATC
1 TAAA-AAAAAAAT-TAACAAATTATC
12117501 T-AAAAAAAAATTAA
1 TAAAAAAAAAATTAA
12117515 AGTTTAGAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
23 3 0.09
24 8 0.23
25 12 0.34
26 12 0.34
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (24 bp):
TAAAAAAAAAATTAACAAATTATC
Found at i:12117767 original size:18 final size:17
Alignment explanation
Indices: 12117734--12117768 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12117724 TTTGATCGAA
*
12117734 ATATAATAAAATTATAT
1 ATATAATAAAAATATAT
12117751 ATATAATTAAAAATATAT
1 ATATAA-TAAAAATATAT
12117769 GAAATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAATAAAAATATAT
Found at i:12119891 original size:24 final size:23
Alignment explanation
Indices: 12119849--12119896 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
12119839 ACTTCTTTTG
*
12119849 TTTCTTTATTTTTCGTACAGGAC
1 TTTCTTTATTTTTCGTACAAGAC
* *
12119872 TTTCTTTCTTTTTTCTTACAAGAC
1 TTTCTTT-ATTTTTCGTACAAGAC
12119896 T
1 T
12119897 ATTTGATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.17, C:0.19, G:0.08, T:0.56
Consensus pattern (23 bp):
TTTCTTTATTTTTCGTACAAGAC
Found at i:12123488 original size:4 final size:4
Alignment explanation
Indices: 12123479--12123508 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
12123469 ATATTTCAAC
12123479 TTGT TTGT TTGT TTGT TTGT TTGT TT-T TTG
1 TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTG
12123509 CAGGATGGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (4 bp):
TTGT
Found at i:12123602 original size:2 final size:2
Alignment explanation
Indices: 12123595--12123634 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
12123585 AACCGATTAC
12123595 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12123635 CATTGTCACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12125194 original size:25 final size:26
Alignment explanation
Indices: 12125139--12125195 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
12125129 AAAAAAAAGC
*
12125139 ATAAAAATAAAAATCAAAACAGAAGG
1 ATAAAAATAAAAATCAAAACAGAAGA
12125165 A-AAAAATAAAAATCAAAA-ATGAA-A
1 ATAAAAATAAAAATCAAAACA-GAAGA
12125189 ATAAAAA
1 ATAAAAA
12125196 AGAAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 2 0.07
25 25 0.89
26 1 0.04
ACGTcount: A:0.75, C:0.05, G:0.07, T:0.12
Consensus pattern (26 bp):
ATAAAAATAAAAATCAAAACAGAAGA
Found at i:12125338 original size:13 final size:13
Alignment explanation
Indices: 12125316--12125357 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
12125306 AAGGAAAAAT
12125316 AAAC-AAAAATAA
1 AAACAAAAAATAA
*
12125328 AGACAAAAAATAAA
1 AAACAAAAAAT-AA
*
12125342 AAATAAAAAATAA
1 AAACAAAAAATAA
12125355 AAA
1 AAA
12125358 ATAGATCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 3 0.12
13 11 0.44
14 11 0.44
ACGTcount: A:0.83, C:0.05, G:0.02, T:0.10
Consensus pattern (13 bp):
AAACAAAAAATAA
Found at i:12125344 original size:7 final size:7
Alignment explanation
Indices: 12125310--12125360 Score: 59
Period size: 7 Copynumber: 7.0 Consensus size: 7
12125300 CTCAAAAAGG
12125310 AAAAATA
1 AAAAATA
12125317 AACAAA-A
1 AA-AAATA
*
12125324 ATAAAGACA
1 A-AAA-ATA
12125333 AAAAATA
1 AAAAATA
12125340 AAAAATA
1 AAAAATA
12125347 AAAAATA
1 AAAAATA
12125354 AAAAATA
1 AAAAATA
12125361 GATCATTTAG
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
7 29 0.74
8 8 0.21
9 2 0.05
ACGTcount: A:0.82, C:0.04, G:0.02, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:12133407 original size:51 final size:51
Alignment explanation
Indices: 12133254--12133395 Score: 266
Period size: 51 Copynumber: 2.8 Consensus size: 51
12133244 TCGAAGAGGA
12133254 CTTCCAACATTATTCAAGTATTCATGTCATTCATTCCATGCATACCAAAAC
1 CTTCCAACATTATTCAAGTATTCATGTCATTCATTCCATGCATACCAAAAC
12133305 CTTCCAACATTATTCAAGTATTCATGTCATTCATTCCATGCATACCAAAAC
1 CTTCCAACATTATTCAAGTATTCATGTCATTCATTCCATGCATACCAAAAC
* *
12133356 CTTCCAACATTATTCAAGTATTTATATCATTCATTCCATG
1 CTTCCAACATTATTCAAGTATTCATGTCATTCATTCCATG
12133396 TCCACCAAAA
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 89 1.00
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (51 bp):
CTTCCAACATTATTCAAGTATTCATGTCATTCATTCCATGCATACCAAAAC
Found at i:12140996 original size:270 final size:270
Alignment explanation
Indices: 12140515--12141002 Score: 841
Period size: 270 Copynumber: 1.8 Consensus size: 270
12140505 AAAATAATTT
* * *
12140515 AAAAAACTAAATTAATTATATTTTTATTTTTATTGTTAACCTTAAATTACTCTCAATTCAATTCA
1 AAAAAACTAAATTAATTATATTTATATTTTTATTATTAACCTTAAATCACTCTCAATTCAATTCA
*
12140580 TATTAAAAGTATTAAAATTTTAAAATTTTTTTAATTTGACAAATTAAATCAATCAATATATAATT
66 TATTAAAAGTATTAAAATTTTAAAATTTTCTTAATTTGACAAATTAAATCAATCAATATATAATT
* *
12140645 AATAAATTAATAAATACTACAATTACAATTATAAAATAGTTGATTCTTTAATCAATTATTTGATA
131 AATAAATTAATAAATACTACAATTACAATTATAAAATAGTTAATTCTCTAATCAATTATTTGATA
12140710 CATTTATATTTGATTAAATATAGTATTCAGTAATTGATGTATTTCATGTATAAATATATAAAGTA
196 CATTTATATTTGATTAAATATAGTATTCAGTAATTGATGTATTTCATGTATAAATATATAAAGTA
12140775 AATATAACTC
261 AATATAACTC
* * * **
12140785 AAAAAACTAAATTGATTATATTTATGTTTTTATTATTGATTTTAAATCACTCTCAATTCAATTCA
1 AAAAAACTAAATTAATTATATTTATATTTTTATTATTAACCTTAAATCACTCTCAATTCAATTCA
12140850 TATTAAAAGTATTAAAATTTTAAAATTTTCTTAATTTGACAAATTAAATCAATCAATATATAATT
66 TATTAAAAGTATTAAAATTTTAAAATTTTCTTAATTTGACAAATTAAATCAATCAATATATAATT
* * * *
12140915 AATAAATTAATAAATACTATAATTAGAATTATAAAATAGTTAATTCTCTAATTAATTATTTTATA
131 AATAAATTAATAAATACTACAATTACAATTATAAAATAGTTAATTCTCTAATCAATTATTTGATA
12140980 CATTTATATTTGATTAAATATAG
196 CATTTATATTTGATTAAATATAG
12141003 CATCCATTTG
Statistics
Matches: 203, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
270 203 1.00
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (270 bp):
AAAAAACTAAATTAATTATATTTATATTTTTATTATTAACCTTAAATCACTCTCAATTCAATTCA
TATTAAAAGTATTAAAATTTTAAAATTTTCTTAATTTGACAAATTAAATCAATCAATATATAATT
AATAAATTAATAAATACTACAATTACAATTATAAAATAGTTAATTCTCTAATCAATTATTTGATA
CATTTATATTTGATTAAATATAGTATTCAGTAATTGATGTATTTCATGTATAAATATATAAAGTA
AATATAACTC
Found at i:12141870 original size:31 final size:32
Alignment explanation
Indices: 12141797--12141872 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
12141787 CATTAAATAT
* * *
12141797 GATTTCAGTTGTTAAAATACTAATGCACGTTT
1 GATTTCATTTGATAAAATACTAATGCACGTTG
*
12141829 GACTTCATTTGATAAAATA-TGAATGCAC-TTG
1 GATTTCATTTGATAAAATACT-AATGCACGTTG
12141860 GATTTCATTTGAT
1 GATTTCATTTGAT
12141873 TTCATTTGTA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
31 15 0.39
32 23 0.61
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.41
Consensus pattern (32 bp):
GATTTCATTTGATAAAATACTAATGCACGTTG
Found at i:12142689 original size:3 final size:3
Alignment explanation
Indices: 12142681--12142709 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
12142671 ATTTATTTAT
12142681 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12142710 TCCTTTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12143021 original size:15 final size:15
Alignment explanation
Indices: 12142973--12143023 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
12142963 AAAAGACTCT
12142973 GGTTTA-AAGTTTCTG
1 GGTTTAGAA-TTTCTG
*
12142988 GGTTTAGAATCTT-TA
1 GGTTTAGAAT-TTCTG
*
12143003 GGTTTTGAATTTCTG
1 GGTTTAGAATTTCTG
12143018 GGTTTA
1 GGTTTA
12143024 CAGATTCTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
14 2 0.07
15 23 0.79
16 4 0.14
ACGTcount: A:0.20, C:0.06, G:0.25, T:0.49
Consensus pattern (15 bp):
GGTTTAGAATTTCTG
Found at i:12143484 original size:15 final size:15
Alignment explanation
Indices: 12143466--12143495 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12143456 TTCAATTTAC
*
12143466 ATTTTTATTTATTTT
1 ATTTTTATATATTTT
12143481 ATTTTTATATATTTT
1 ATTTTTATATATTTT
12143496 TCTTTATTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
ATTTTTATATATTTT
Found at i:12143617 original size:25 final size:24
Alignment explanation
Indices: 12143583--12143629 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
12143573 TTTTATAATT
*
12143583 TTTTTAAAAAATAATAATAAAAAAA
1 TTTTT-AAAAATAAAAATAAAAAAA
12143608 TTTTTAAAAATAAAAATAAAAA
1 TTTTTAAAAATAAAAATAAAAA
12143630 GTAAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (24 bp):
TTTTTAAAAATAAAAATAAAAAAA
Found at i:12143625 original size:30 final size:32
Alignment explanation
Indices: 12143589--12143649 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 32
12143579 AATTTTTTTA
* *
12143589 AAAAATAATAA-TAAAAAA-ATTTTTAAAAAT
1 AAAAATAAAAAGTAAAAAATATTTCTAAAAAT
12143619 AAAAATAAAAAGTAAAAAATATTTCTAAAAA
1 AAAAATAAAAAGTAAAAAATATTTCTAAAAA
12143650 CGAATTTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 10 0.37
31 7 0.26
32 10 0.37
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (32 bp):
AAAAATAAAAAGTAAAAAATATTTCTAAAAAT
Found at i:12153016 original size:141 final size:141
Alignment explanation
Indices: 12152762--12153043 Score: 530
Period size: 141 Copynumber: 2.0 Consensus size: 141
12152752 TTTGGACCTC
* *
12152762 CGCTGACTTCTTGTTTGCGTTGGAATGGAAATTCCTCGCCCTTTTTTAATAATAATAATTAATAA
1 CGCTGACTTCTAGTTTGCGTTGGAATGGAAATTCCTCGCCCCTTTTTAATAATAATAATTAATAA
12152827 AAAAATACTTAACTTAATTTGTCTCAGGAAATTTCTAATTACTTTGGATTTGGTGAAACATTTGA
66 AAAAATACTTAACTTAATTTGTCTCAGGAAATTTCTAATTACTTTGGATTTGGTGAAACATTTGA
12152892 CACGTCAGACT
131 CACGTCAGACT
12152903 CGCTGACTTCTAGTTTGCGTTGGAATGGAAATTCCTCGCCCCTTTTTAATAATAATAATTAATAA
1 CGCTGACTTCTAGTTTGCGTTGGAATGGAAATTCCTCGCCCCTTTTTAATAATAATAATTAATAA
12152968 AAAAATACTTAACTTAATTTGTCTC-GGCAAATTTCTAATTACTTTGGATTTGGTGAAACATTTG
66 AAAAATACTTAACTTAATTTGTCTCAGG-AAATTTCTAATTACTTTGGATTTGGTGAAACATTTG
12153032 ACACGTCAGACT
130 ACACGTCAGACT
12153044 TTATTTTTTT
Statistics
Matches: 138, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
140 2 0.01
141 136 0.99
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (141 bp):
CGCTGACTTCTAGTTTGCGTTGGAATGGAAATTCCTCGCCCCTTTTTAATAATAATAATTAATAA
AAAAATACTTAACTTAATTTGTCTCAGGAAATTTCTAATTACTTTGGATTTGGTGAAACATTTGA
CACGTCAGACT
Found at i:12153563 original size:16 final size:16
Alignment explanation
Indices: 12153538--12153569 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12153528 ACATTATCTT
*
12153538 TTTTTTTATTTAATAA
1 TTTTTATATTTAATAA
12153554 TTTTTATATTTAATAA
1 TTTTTATATTTAATAA
12153570 ATATTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTTATATTTAATAA
Found at i:12155630 original size:31 final size:31
Alignment explanation
Indices: 12155579--12155639 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
12155569 AAAACTTTTA
* *
12155579 TTTTTTATATTTTAAAATTAATTTTTATGAT
1 TTTTTTATATTTTAAAATTAAATATTATGAT
* * *
12155610 TTTTTTATTTTTTGATATTAAATATTATGA
1 TTTTTTATATTTTAAAATTAAATATTATGA
12155640 AACTTGGGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (31 bp):
TTTTTTATATTTTAAAATTAAATATTATGAT
Found at i:12156723 original size:2 final size:2
Alignment explanation
Indices: 12156716--12156745 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12156706 AATCAGTTCA
12156716 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12156746 GGATAAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12166438 original size:23 final size:24
Alignment explanation
Indices: 12166407--12166455 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
12166397 CCTCTTAAAA
*
12166407 TTATATTTTATTTTTTAAAAATAT
1 TTATATTTTATATTTTAAAAATAT
*
12166431 TTAT-TTTTATATTTTAAAATTAT
1 TTATATTTTATATTTTAAAAATAT
12166454 TT
1 TT
12166456 TTATGATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TTATATTTTATATTTTAAAAATAT
Found at i:12166470 original size:23 final size:20
Alignment explanation
Indices: 12166401--12166467 Score: 62
Period size: 22 Copynumber: 3.1 Consensus size: 20
12166391 TTATTGCCTC
*
12166401 TTAAAATTATATTTTATTTT
1 TTAAAATTATTTTTTATTTT
* *
12166421 TTAAAAATATTTATTTTTATATT
1 TT-AAAAT-TAT-TTTTTATTTT
12166444 TTAAAATTATTTTTATGATTTT
1 TTAAAATTATTTTT-T-ATTTT
12166466 TT
1 TT
12166468 TAATTTTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
20 6 0.16
21 8 0.22
22 13 0.35
23 10 0.27
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (20 bp):
TTAAAATTATTTTTTATTTT
Found at i:12169425 original size:25 final size:25
Alignment explanation
Indices: 12169363--12169426 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 25
12169353 TATAAATTTT
* *
12169363 TTATTAAAAATTTTTTTAATCGCAA
1 TTATTATAATTTTTTTTAATCGCAA
** * *
12169388 TTACGATATTTTTTTTTAATTGCAA
1 TTATTATAATTTTTTTTAATCGCAA
12169413 TTATTATAATTTTT
1 TTATTATAATTTTT
12169427 ATCATTATTT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.33, C:0.06, G:0.05, T:0.56
Consensus pattern (25 bp):
TTATTATAATTTTTTTTAATCGCAA
Found at i:12172834 original size:2 final size:2
Alignment explanation
Indices: 12172827--12172854 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12172817 ACACCTTAGA
12172827 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
12172855 CAACCGAAAT
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:12174830 original size:2 final size:2
Alignment explanation
Indices: 12174823--12174848 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12174813 TGTTTTTAAG
12174823 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
12174849 GAACAGCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12176902 original size:22 final size:21
Alignment explanation
Indices: 12176876--12176917 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
12176866 AAAAAAAAGT
*
12176876 TTTTTTAAGGCGTTTTTGTTG
1 TTTTTTAAGGCATTTTTGTTG
*
12176897 TTTTTTAAGGTATTTTTGTTG
1 TTTTTTAAGGCATTTTTGTTG
12176918 AAAAATGCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.02, G:0.21, T:0.64
Consensus pattern (21 bp):
TTTTTTAAGGCATTTTTGTTG
Found at i:12179193 original size:19 final size:19
Alignment explanation
Indices: 12179121--12179195 Score: 55
Period size: 20 Copynumber: 3.8 Consensus size: 19
12179111 TCAAAATTTA
*
12179121 ATAAAAACGATATTTT-AAG
1 ATAAAAATG-TATTTTAAAG
**
12179140 ATAGAAAATGTAATCTTTAGTG
1 ATA-AAAATGT-AT-TTTAAAG
*
12179162 A-AAAAATTATATTTTAAAG
1 ATAAAAA-TGTATTTTAAAG
12179181 ATAAAAATGTATTTT
1 ATAAAAATGTATTTT
12179196 TGTTAAAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
19 17 0.40
20 18 0.42
21 6 0.14
22 2 0.05
ACGTcount: A:0.49, C:0.03, G:0.11, T:0.37
Consensus pattern (19 bp):
ATAAAAATGTATTTTAAAG
Found at i:12179420 original size:19 final size:18
Alignment explanation
Indices: 12179384--12179472 Score: 54
Period size: 19 Copynumber: 4.7 Consensus size: 18
12179374 TTCATAATTT
* *
12179384 AATAAAAACAATATTTTTA
1 AATAAAAA-TATAATTTTA
*
12179403 AGATAAAAATATAATTTTT
1 A-ATAAAAATATAATTTTA
**
12179422 GTTAAAAA-ATAATTTTTTA
1 AATAAAAATATAA--TTTTA
* *
12179441 AATACAAAACATAATTTTT
1 AATA-AAAATATAATTTTA
*
12179460 ATTAAAAATATAA
1 AATAAAAATATAA
12179473 AAATAAATAT
Statistics
Matches: 54, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
17 4 0.07
18 14 0.26
19 21 0.39
20 11 0.20
21 4 0.07
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.39
Consensus pattern (18 bp):
AATAAAAATATAATTTTA
Found at i:12179429 original size:18 final size:17
Alignment explanation
Indices: 12179406--12179472 Score: 64
Period size: 18 Copynumber: 3.6 Consensus size: 17
12179396 ATTTTTAAGA
12179406 TAAAAATATAATTTTTGT
1 TAAAAATATAATTTTT-T
12179424 TAAAAA-ATAATTTTTT
1 TAAAAATATAATTTTTT
*
12179440 AAATACAAAACATAATTTTTAT
1 ---TA-AAAATATAATTTTT-T
12179462 TAAAAATATAA
1 TAAAAATATAA
12179473 AAATAAATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
16 1 0.02
17 9 0.21
18 14 0.33
19 4 0.10
20 4 0.10
21 9 0.21
22 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
TAAAAATATAATTTTTT
Found at i:12179439 original size:38 final size:39
Alignment explanation
Indices: 12179387--12179472 Score: 113
Period size: 38 Copynumber: 2.2 Consensus size: 39
12179377 ATAATTTAAT
* * *
12179387 AAAAACAATATTTTTAAGATA-AAAATATAATTTTTGTTA
1 AAAAATAATATTTTTAA-ATACAAAACATAATTTTTATTA
12179426 AAAAATAAT-TTTTTAAATACAAAACATAATTTTTATTA
1 AAAAATAATATTTTTAAATACAAAACATAATTTTTATTA
12179464 AAAATATAA
1 AAAA-ATAA
12179473 AAATAAATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
37 3 0.07
38 27 0.64
39 12 0.29
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (39 bp):
AAAAATAATATTTTTAAATACAAAACATAATTTTTATTA
Found at i:12179537 original size:37 final size:37
Alignment explanation
Indices: 12179477--12179550 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
12179467 ATATAAAAAT
* *
12179477 AAATATAAAATATTTTTATTTAATATTATTACATATA
1 AAATATAAAATATATTTACTTAATATTATTACATATA
* *
12179514 AAATTTAAAATATATTTGCTTAATATTATTACATATA
1 AAATATAAAATATATTTACTTAATATTATTACATATA
12179551 GATGTTATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
AAATATAAAATATATTTACTTAATATTATTACATATA
Found at i:12191059 original size:9 final size:9
Alignment explanation
Indices: 12191045--12191069 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
12191035 TAGTATGTAT
12191045 TTTTATTAC
1 TTTTATTAC
12191054 TTTTATTAC
1 TTTTATTAC
12191063 TTTTATT
1 TTTTATT
12191070 GATGATACTT
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:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTTATTAC
Found at i:12204096 original size:17 final size:17
Alignment explanation
Indices: 12204047--12204100 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
12204037 TAATATAATA
*
12204047 TTTATAAAATT-ATATT
1 TTTATTAAATTAATATT
* *
12204063 TTAATTATAAATAAATATT
1 TTTA-T-TAAATTAATATT
12204082 TTTATTAAATTAATATT
1 TTTATTAAATTAATATT
12204099 TT
1 TT
12204101 AAATAAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
16 3 0.10
17 14 0.47
18 5 0.17
19 8 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTATTAAATTAATATT
Found at i:12204107 original size:17 final size:17
Alignment explanation
Indices: 12204053--12204107 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
12204043 AATATTTATA
12204053 AAATT-ATATTTTAATTAT
1 AAATTAATATTTTAA--AT
* * *
12204071 AAATAAATATTTTTATT
1 AAATTAATATTTTAAAT
12204088 AAATTAATATTTTAAAT
1 AAATTAATATTTTAAAT
12204105 AAA
1 AAA
12204108 ATATTAAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
17 18 0.60
18 4 0.13
19 8 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATTAATATTTTAAAT
Found at i:12204137 original size:41 final size:41
Alignment explanation
Indices: 12204070--12204172 Score: 106
Period size: 41 Copynumber: 2.5 Consensus size: 41
12204060 ATTTTAATTA
* *
12204070 TAAATAAATATTTTTATTAAATTAATATTTTAAATAAAAT-AT
1 TAAAT-AATAATTTTATTAAATTAATA-TATAAATAAAATAAT
* *
12204112 TAAATAATAATTTTATT-AATATAATATATAATTAAATTAAT
1 TAAATAATAATTTTATTAAAT-TAATATATAAATAAAATAAT
12204153 TAAA-AATATATTTTA-TAAAT
1 TAAATAATA-ATTTTATTAAAT
12204173 CAAGATCGGA
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
40 17 0.32
41 31 0.58
42 5 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (41 bp):
TAAATAATAATTTTATTAAATTAATATATAAATAAAATAAT
Found at i:12216175 original size:19 final size:20
Alignment explanation
Indices: 12216139--12216178 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
12216129 ATTAAAAAAT
*
12216139 AAAAAACAATAAAGAGGAAA
1 AAAAAACAATAAAAAGGAAA
*
12216159 AAAAAATAA-AAAAAGGAAA
1 AAAAAACAATAAAAAGGAAA
12216178 A
1 A
12216179 GTGATATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.80, C:0.03, G:0.12, T:0.05
Consensus pattern (20 bp):
AAAAAACAATAAAAAGGAAA
Found at i:12217130 original size:8 final size:8
Alignment explanation
Indices: 12217043--12217133 Score: 63
Period size: 8 Copynumber: 12.1 Consensus size: 8
12217033 TATTACATTA
12217043 AAATAT-T
1 AAATATAT
12217050 AAATA-AT
1 AAATATAT
12217057 AACAT-TAT
1 AA-ATATAT
*
12217065 TAATATACT
1 AAATATA-T
*
12217074 ATATATAT
1 AAATATAT
12217082 AAATATA-
1 AAATATAT
*
12217089 AAATAAAT
1 AAATATAT
*
12217097 AAATATTT
1 AAATATAT
*
12217105 AAAAATAT
1 AAATATAT
12217113 -AAT-TAT
1 AAATATAT
12217119 --ATATAT
1 AAATATAT
12217125 AAATATAT
1 AAATATAT
12217133 A
1 A
12217134 TACTTGAGGT
Statistics
Matches: 65, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
5 2 0.03
6 6 0.09
7 18 0.28
8 33 0.51
9 6 0.09
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.38
Consensus pattern (8 bp):
AAATATAT
Found at i:12217366 original size:13 final size:12
Alignment explanation
Indices: 12217344--12217374 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
12217334 GTCAAAGACT
12217344 AAAAAACAAAAA
1 AAAAAACAAAAA
12217356 AAAATAACAAAAA
1 AAAA-AACAAAAA
12217369 AAAAAA
1 AAAAAA
12217375 AAACCCCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.90, C:0.06, G:0.00, T:0.03
Consensus pattern (12 bp):
AAAAAACAAAAA
Found at i:12227674 original size:20 final size:20
Alignment explanation
Indices: 12227636--12227674 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12227626 CAAATTGCAT
* *
12227636 ACATAATTAAAAGATAAATA
1 ACATAATTAAAACAAAAATA
12227656 ACATAATTAAAACAAAAAT
1 ACATAATTAAAACAAAAAT
12227675 GTTAACAGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.67, C:0.08, G:0.03, T:0.23
Consensus pattern (20 bp):
ACATAATTAAAACAAAAATA
Found at i:12229997 original size:17 final size:17
Alignment explanation
Indices: 12229975--12230013 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
12229965 TATGAATGAA
* *
12229975 AAAAATTGGAGAAAACC
1 AAAAATTGGACAAAAAC
*
12229992 AAAAATTTGACAAAAAC
1 AAAAATTGGACAAAAAC
12230009 AAAAA
1 AAAAA
12230014 AGAAATAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.67, C:0.10, G:0.10, T:0.13
Consensus pattern (17 bp):
AAAAATTGGACAAAAAC
Found at i:12230674 original size:21 final size:22
Alignment explanation
Indices: 12230634--12230674 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
12230624 GAAAATCAAA
* *
12230634 AAGAAAAGCACCAAATAAAAAG
1 AAGAAAAGCAACAAACAAAAAG
12230656 AAGAAAAG-AACAAACAAAA
1 AAGAAAAGCAACAAACAAAA
12230675 GTGTAACACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.73, C:0.12, G:0.12, T:0.02
Consensus pattern (22 bp):
AAGAAAAGCAACAAACAAAAAG
Found at i:12230751 original size:525 final size:522
Alignment explanation
Indices: 12229758--12230804 Score: 1400
Period size: 525 Copynumber: 2.0 Consensus size: 522
12229748 AATACTATAC
* *
12229758 ATCATAATCAATCTCACAAAAAACAAAAGCAACAAAGCAAAAAAATAAATCTCAACCCATAGGAA
1 ATCACAATCAATCTCACAAAAAACAAAAGCAACAAAGCAAAAAAATAAATCTCAACCCATAGAAA
* * *
12229823 ACCTAAAAAAATCTAATAAGAGAGTAAACTTGAACAACCTAATAAAAGAAATAACAAACAAAACA
66 ACCTAAAAAAATATAATAAAAGAGTAAACTTGAAAAACCTAATAAAAGAAATAACAAACAAAACA
* * * *
12229888 TGCCAATGAGAATATAAGAAAATGAAATATAGAAGTAAGTAAAAGAAGGGAAACAAATCACACAA
131 TGCCAACGAGAACATAAGAAAATGAAATATAGAAGGAAGTAAAAGAAGAGAAACAAATCACACAA
* * * *** **
12229953 GTAAATCAGAGATATGAATGAAAAAAATTGGAGAAAACCAAAAATTTGACAAAAACAAAAAAGAA
196 GTAAATAAGAAATACGAATGAAAAAAATCAAAGAAAACCAAAAATTCAACAAAAACAAAAAAGAA
* * * *
12230018 ATAATTGAAAAGAAAATTAGGATATAGGTAAAATGAAAACAGTTGATTGATAAAAAAAAAATCCA
261 ATAATCGAAAAGAAAAATAAGATATAGGCAAAATGAAAACAGTTGATTGATAAAAAAAAAATCCA
* *
12230083 AAATAAAGCAAGCAACATAAAGAAAAAAAAAAAGCACCAAGTAAAAAGAAGAAAAGAATAAACAA
326 AAATAAA-CAAGCAACATAAAGAAAAAAAAAAAGCACCAAATAAAAAGAAGAAAAGAACAAACAA
* * * * *
12230148 AGGTGTGACACATGACTAAACAAAACACGGTTAAGAGGAAGTAAAAATTAGTAAATTTAATAGTA
390 AAGTGTAACACATAACTAAACAAAACACAGTTAAGAGGAAGTAAAAATTAATAAATTTAATAGTA
*
12230213 TGGATGAATGGATGTGATTATAATATATTTTTACTTCATAAAAAGGTAATTACTGTTTGATTAGT
455 TGGATGAATGGATGTGATTATAATATATTTTTACTTCATAAAAAAGTAATTACTGTTTGATTAGT
12230278 TAT
520 TAT
* *
12230281 ATCACAATCAATCTCACAAAAAACAAATGCAACAAAATG-AGAAAAAA-AAGATC-CTAACCGAT
1 ATCACAATCAATCTCACAAAAAACAAAAGCAAC-AAA-GCA-AAAAAATAA-ATCTC-AACCCAT
* * *
12230343 -GAAAACCTCAAAAAATATGATAAAAGAGTAAACTTGAAAAACCTAATAGAAGAAATAACAAACA
61 AGAAAACCTAAAAAAATATAATAAAAGAGTAAACTTGAAAAACCTAATAAAAGAAATAACAAACA
* * * *
12230407 AAATATGTCGACGA-ATACATAAGAAAATGAAGTATAGAAGGAAGTAAAA-ACA-AGAAACAAAT
126 AAACATGCCAACGAGA-ACATAAGAAAATGAAATATAGAAGGAAGTAAAAGA-AGAGAAACAAAT
* * * *
12230469 CACATAGGTAAATAAGAAATACGAATGAAAAGAAATCAAAGAAAATCGAAAAA-TCAACAAAAGC
189 CACACAAGTAAATAAGAAATACGAATGAAAA-AAATCAAAGAAAA-CCAAAAATTCAACAAAAAC
*
12230533 AAAAAGAGAAATAATCGAAGAGAAAAATAAGATATAGGCAAAATGAAAACAGTTGATTGAT-AAA
252 AAAAA-AGAAATAATCGAAAAGAAAAATAAGATATAGGCAAAATGAAAACAGTTGATTGATAAAA
* ** *
12230597 AAAAATTTTAAAA-AAA-AA-CAACTTAAAGAAAATCAAAAAGAAAAGCACCAAATAAAAAGAAG
316 AAAAAATCCAAAATAAACAAGCAACATAAAG--AA--AAAAA-AAAAGCACCAAATAAAAAGAAG
* *
12230659 AAAAGAACAAACAAAAGTGTAACACATAACTAATCAAAACATAGTTAA-AGGGAAGTAAAAATTA
376 AAAAGAACAAACAAAAGTGTAACACATAACTAAACAAAACACAGTTAAGA-GGAAGTAAAAATTA
12230723 ATAAATTTAATAGTATGGATGAATGGATGTGATTATAATATATTTTTACTTCATAAAAAAGTAAT
440 ATAAATTTAATAGTATGGATGAATGGATGTGATTATAATATATTTTTACTTCATAAAAAAGTAAT
*
12230788 TAGTGTTTGATTAGTTA
505 TACTGTTTGATTAGTTA
12230805 CATTATTGAA
Statistics
Matches: 458, Mismatches: 50, Indels: 30
0.85 0.09 0.06
Matches are distributed among these distances:
520 9 0.02
521 2 0.00
522 2 0.00
523 71 0.16
524 147 0.32
525 227 0.50
ACGTcount: A:0.57, C:0.10, G:0.14, T:0.20
Consensus pattern (522 bp):
ATCACAATCAATCTCACAAAAAACAAAAGCAACAAAGCAAAAAAATAAATCTCAACCCATAGAAA
ACCTAAAAAAATATAATAAAAGAGTAAACTTGAAAAACCTAATAAAAGAAATAACAAACAAAACA
TGCCAACGAGAACATAAGAAAATGAAATATAGAAGGAAGTAAAAGAAGAGAAACAAATCACACAA
GTAAATAAGAAATACGAATGAAAAAAATCAAAGAAAACCAAAAATTCAACAAAAACAAAAAAGAA
ATAATCGAAAAGAAAAATAAGATATAGGCAAAATGAAAACAGTTGATTGATAAAAAAAAAATCCA
AAATAAACAAGCAACATAAAGAAAAAAAAAAAGCACCAAATAAAAAGAAGAAAAGAACAAACAAA
AGTGTAACACATAACTAAACAAAACACAGTTAAGAGGAAGTAAAAATTAATAAATTTAATAGTAT
GGATGAATGGATGTGATTATAATATATTTTTACTTCATAAAAAAGTAATTACTGTTTGATTAGTT
AT
Found at i:12230955 original size:24 final size:24
Alignment explanation
Indices: 12230928--12231001 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
12230918 GGCAAAATTA
12230928 ATTTATAAATAGTTGAGGATCAGG
1 ATTTATAAATAGTTGAGGATCAGG
** * *
12230952 ATTTCA-ACGTAGAAT-AGGATTA--
1 ATTT-ATAAATAG-TTGAGGATCAGG
12230974 ATTTATAAATAGTTGAGGATCAGG
1 ATTTATAAATAGTTGAGGATCAGG
12230998 ATTT
1 ATTT
12231002 CAACGTAGAA
Statistics
Matches: 36, Mismatches: 8, Indels: 12
0.64 0.14 0.21
Matches are distributed among these distances:
21 2 0.06
22 14 0.39
24 18 0.50
25 2 0.06
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.35
Consensus pattern (24 bp):
ATTTATAAATAGTTGAGGATCAGG
Found at i:12230991 original size:46 final size:46
Alignment explanation
Indices: 12230924--12231016 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
12230914 ATTAGGCAAA
12230924 ATTAATTTATAAATAGTTGAGGATCAGGATTTCAACGTAGAATAGG
1 ATTAATTTATAAATAGTTGAGGATCAGGATTTCAACGTAGAATAGG
12230970 ATTAATTTATAAATAGTTGAGGATCAGGATTTCAACGTAGAATAGG
1 ATTAATTTATAAATAGTTGAGGATCAGGATTTCAACGTAGAATAGG
12231016 A
1 A
12231017 CAAATACACA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.32
Consensus pattern (46 bp):
ATTAATTTATAAATAGTTGAGGATCAGGATTTCAACGTAGAATAGG
Found at i:12230992 original size:22 final size:22
Alignment explanation
Indices: 12230924--12230993 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
12230914 ATTAGGCAAA
12230924 ATTAATTTATAAATAGTTGAGG
1 ATTAATTTATAAATAGTTGAGG
* ** *
12230946 ATCAGGATTTCA-ACGTAGAAT-AGG
1 ATTA--ATTT-ATAAATAG-TTGAGG
12230970 ATTAATTTATAAATAGTTGAGG
1 ATTAATTTATAAATAGTTGAGG
12230992 AT
1 AT
12230994 CAGGATTTCA
Statistics
Matches: 34, Mismatches: 8, Indels: 12
0.63 0.15 0.22
Matches are distributed among these distances:
21 2 0.06
22 16 0.47
24 14 0.41
25 2 0.06
ACGTcount: A:0.40, C:0.04, G:0.20, T:0.36
Consensus pattern (22 bp):
ATTAATTTATAAATAGTTGAGG
Found at i:12231016 original size:24 final size:24
Alignment explanation
Indices: 12230943--12231016 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
12230933 TAAATAGTTG
12230943 AGGATCAGGATTTCAACGTAGAAT
1 AGGATCAGGATTTCAACGTAGAAT
* ** *
12230967 AGGATTA--ATTT-ATAAATAG-TT
1 AGGATCAGGATTTCA-ACGTAGAAT
12230988 GAGGATCAGGATTTCAACGTAGAAT
1 -AGGATCAGGATTTCAACGTAGAAT
12231013 AGGA
1 AGGA
12231017 CAAATACACA
Statistics
Matches: 36, Mismatches: 8, Indels: 12
0.64 0.14 0.21
Matches are distributed among these distances:
21 2 0.06
22 14 0.39
24 18 0.50
25 2 0.06
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.28
Consensus pattern (24 bp):
AGGATCAGGATTTCAACGTAGAAT
Found at i:12231232 original size:14 final size:14
Alignment explanation
Indices: 12231208--12231241 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
12231198 TAAAATTTTA
*
12231208 AAAAGATTTACAATT
1 AAAA-ATTTACAAAT
12231223 AAAAATTTACAAAT
1 AAAAATTTACAAAT
12231237 AAAAA
1 AAAAA
12231242 ATAGAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (14 bp):
AAAAATTTACAAAT
Found at i:12239009 original size:17 final size:17
Alignment explanation
Indices: 12238968--12239002 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
12238958 TTTAATATTA
12238968 AAATTTAAATTTTTTAT
1 AAATTTAAATTTTTTAT
*
12238985 AAAGTTAAA-TTTTTAT
1 AAATTTAAATTTTTTAT
12239001 AA
1 AA
12239003 TTTTTAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (17 bp):
AAATTTAAATTTTTTAT
Found at i:12241442 original size:2 final size:2
Alignment explanation
Indices: 12241435--12241467 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
12241425 GGAGATGTAC
12241435 AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12241468 GACGGTATGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12242128 original size:15 final size:17
Alignment explanation
Indices: 12242108--12242153 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 17
12242098 TATAGATTTA
12242108 AAAAAATATT-TTT-TG
1 AAAAAATATTATTTATG
12242123 AAAAAA-ATTATTTATG
1 AAAAAATATTATTTATG
12242139 AATAAAATATATATT
1 AA-AAAATAT-TATT
12242154 AATATTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 3 0.12
15 9 0.35
16 4 0.15
17 4 0.15
18 2 0.08
19 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (17 bp):
AAAAAATATTATTTATG
Found at i:12242128 original size:16 final size:17
Alignment explanation
Indices: 12242107--12242150 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
12242097 TTATAGATTT
*
12242107 AAAAAAATAT-TTTTTG
1 AAAAAAATATATTTATG
12242123 AAAAAAAT-TATTTATG
1 AAAAAAATATATTTATG
*
12242139 AATAAAATATAT
1 AAAAAAATATAT
12242151 ATTAATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 1 0.04
16 20 0.83
17 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (17 bp):
AAAAAAATATATTTATG
Done.