Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397286.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_459.0, 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: 854433
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 16369 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:7798 original size:6 final size:6
Alignment explanation
Indices: 7739--7800 Score: 56
Period size: 6 Copynumber: 10.3 Consensus size: 6
7729 ACTCTACCTA
* * * *
7739 TTATCTT TTA-TT TTATGT TTATTA TTATTA TTATTAT TTATTT TT-TTA
1 TTAT-TT TTATTT TTATTT TTATTT TTATTT TTATT-T TTATTT TTATTT
7787 TTATTT TTATTT TT
1 TTATTT TTATTT TT
7801 CACTTTTAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
5 9 0.20
6 29 0.63
7 8 0.17
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.76
Consensus pattern (6 bp):
TTATTT
Found at i:7807 original size:24 final size:24
Alignment explanation
Indices: 7760--7807 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
7750 TTTATGTTTA
*
7760 TTATTATTATTATTATTTATTTTT
1 TTATTATTATTATTATTTACTTTT
*
7784 TTATTATTTTTATT-TTTCACTTTT
1 TTATTATTATTATTATTT-ACTTTT
7808 AATCTATCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (24 bp):
TTATTATTATTATTATTTACTTTT
Found at i:9472 original size:59 final size:59
Alignment explanation
Indices: 9395--9540 Score: 152
Period size: 59 Copynumber: 2.5 Consensus size: 59
9385 TCTAAGCTCG
* * * * * * **
9395 ACTTATCTAAAAACAAGTTCAATTTAAAGTTGAGAATTTTTAAATTAAATTTAGGTTTA
1 ACTTATCTCATAATAAGTTCAATTTAAAGTTGAAAATTCTTAAACTAAATCAAGGTTTA
** * *
9454 A-TCTATCTCA-AGATAAGTTTGATTTAAAGTTGAAAATTCTTAAACTGAATCAAGGTTTG
1 ACT-TATCTCATA-ATAAGTTCAATTTAAAGTTGAAAATTCTTAAACTAAATCAAGGTTTA
9513 ACTTATCTCATAATAAGTTCAATTTAAA
1 ACTTATCTCATAATAAGTTCAATTTAAA
9541 AATTTTAGAA
Statistics
Matches: 70, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
58 2 0.03
59 66 0.94
60 2 0.03
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (59 bp):
ACTTATCTCATAATAAGTTCAATTTAAAGTTGAAAATTCTTAAACTAAATCAAGGTTTA
Found at i:19815 original size:22 final size:22
Alignment explanation
Indices: 19787--19839 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
19777 TTAAAATTAT
* *
19787 TTAATTAAGCTGTTGGGCTTAA
1 TTAATTAAACTGTTGAGCTTAA
* *
19809 TTAATTAAATTGTTTAGCTTAA
1 TTAATTAAACTGTTGAGCTTAA
19831 TTAATTAAA
1 TTAATTAAA
19840 TTGCTTAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.36, C:0.06, G:0.13, T:0.45
Consensus pattern (22 bp):
TTAATTAAACTGTTGAGCTTAA
Found at i:19890 original size:35 final size:36
Alignment explanation
Indices: 19828--19895 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 36
19818 TTGTTTAGCT
****
19828 TAATTAATTAAATTGCTTAATTAAGTT-ATTGGACC
1 TAATTAATTAAATTAAACAATTAAGTTAATTGGACC
*
19863 TAATTAATTAAATTAAACAATTTAGTTAATTGG
1 TAATTAATTAAATTAAACAATTAAGTTAATTGG
19896 GCTTCTTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 22 0.81
36 5 0.19
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (36 bp):
TAATTAATTAAATTAAACAATTAAGTTAATTGGACC
Found at i:21058 original size:28 final size:28
Alignment explanation
Indices: 21017--21071 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
21007 TGTTACAAAT
*
21017 AAATAAATTACACCAAATATGAATAAAC
1 AAATAAATTACACCAAATATAAATAAAC
*
21045 AAATAAATTGCACCAAATATAAATAAA
1 AAATAAATTACACCAAATATAAATAAA
21072 GTTTCAATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.62, C:0.13, G:0.04, T:0.22
Consensus pattern (28 bp):
AAATAAATTACACCAAATATAAATAAAC
Found at i:25385 original size:10 final size:8
Alignment explanation
Indices: 25362--25397 Score: 54
Period size: 8 Copynumber: 4.2 Consensus size: 8
25352 CAACTAATTT
25362 TTTATATA
1 TTTATATA
25370 TTTATATA
1 TTTATATA
25378 TTAATATATA
1 TT--TATATA
25388 TTTATATA
1 TTTATATA
25396 TT
1 TT
25398 AAGAAGAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 18 0.69
10 8 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TTTATATA
Found at i:25387 original size:18 final size:18
Alignment explanation
Indices: 25364--25399 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
25354 ACTAATTTTT
25364 TATATATTTATATATTAA
1 TATATATTTATATATTAA
25382 TATATATTTATATATTAA
1 TATATATTTATATATTAA
25400 GAAGAATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATATTTATATATTAA
Found at i:26411 original size:73 final size:73
Alignment explanation
Indices: 26257--26429 Score: 199
Period size: 73 Copynumber: 2.4 Consensus size: 73
26247 AACATTATCA
* * * * * *
26257 CTTAATTGACTAAGTCTTTTCTGTCTCTGAACCCAGTTTTTGATAGCAGGCTCTTAGTCGACTAA
1 CTTAGTTGACTAAGTCGTTTCTGTCTCTAAACCCAGTTTCTGACAGCAAGCTCTTAGTCGACTAA
26322 CAACACTT
66 CAACACTT
* * *
26330 CTTAGTTGATTAAGTCGTTTCTGTCTCTAAACCCAGTTTCTGACAGTAAGCTCTTGGTCGACTAA
1 CTTAGTTGACTAAGTCGTTTCTGTCTCTAAACCCAGTTTCTGACAGCAAGCTCTTAGTCGACTAA
*
26395 C-ACTGTCTT
66 CAAC--ACTT
*
26404 -TTGGTTGACTAAGT-GTTCTCTGTCTC
1 CTTAGTTGACTAAGTCGTT-TCTGTCTC
26430 ACAGTTTGCT
Statistics
Matches: 85, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
72 5 0.06
73 77 0.91
74 3 0.04
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.39
Consensus pattern (73 bp):
CTTAGTTGACTAAGTCGTTTCTGTCTCTAAACCCAGTTTCTGACAGCAAGCTCTTAGTCGACTAA
CAACACTT
Found at i:27298 original size:21 final size:22
Alignment explanation
Indices: 27274--27317 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
27264 ATCTACATTA
27274 ATTTGAAAT-TACAAGTTATAT
1 ATTTGAAATATACAAGTTATAT
* *
27295 ATTTTAAATAATATAAGTTATAT
1 ATTTGAAAT-ATACAAGTTATAT
27318 GTTAATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.42
23 11 0.58
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (22 bp):
ATTTGAAATATACAAGTTATAT
Found at i:27680 original size:212 final size:201
Alignment explanation
Indices: 27412--27802 Score: 408
Period size: 212 Copynumber: 1.9 Consensus size: 201
27402 AATGTTATGA
* * *
27412 ATATATATAATTATATAAATATATTATATATACATATATTTAATTTATAGATAAGCATTACTATA
1 ATATATATAATTAAATAAATATATTATATATACACATATTTAATTTATACATAAGCATTACTATA
* * * ** **
27477 ATTTGTAATAGACTTTGTTTATATGATTACACTTAATAACTTTATTAATTATCATGTTAGATTTT
66 ATTTATAATAAACTTTATTTATATGATTACACTTAATAACTTTATTAACCATCACCTTAGATTTT
* * *
27542 ATATCATATTGTTTATAATTAGTTATTATTTATACAAACTTTGATANNNNNNNNNNTAACATATA
131 ATAACATATTGTTTAGAATTAGTTATTATTTACACAAACTTTGATA----------TAACATATA
27607 ATTTGTATAATTAATT
186 ATTTGTATAATTAATT
***
27623 ATATATATAA-TAAACT-AATATATTATATATTTACACATATTTAATTTATACATAAGCATTNNN
1 ATATATATAATTAAA-TAAATATATTATATA--TACACATATTTAATTTATACATAAGCATTACT
******* * * * *
27686 NNNNNNNATAATAAATTTTATTTATATGATTACATTTAATAATTTTATTAGCCATCACCTTAGAT
63 ATAATTTATAATAAACTTTATTTATATGATTACACTTAATAACTTTATTAACCATCACCTTAGAT
27751 TTTATAACATATTGTTTAGAATTAGTTATTATTTACACAAACTTTGATATAA
128 TTTATAACATATTGTTTAGAATTAGTTATTATTTACACAAACTTTGATATAA
27803 AACATTTTAA
Statistics
Matches: 150, Mismatches: 27, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
202 3 0.02
210 16 0.11
211 11 0.07
212 120 0.80
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.45
Consensus pattern (201 bp):
ATATATATAATTAAATAAATATATTATATATACACATATTTAATTTATACATAAGCATTACTATA
ATTTATAATAAACTTTATTTATATGATTACACTTAATAACTTTATTAACCATCACCTTAGATTTT
ATAACATATTGTTTAGAATTAGTTATTATTTACACAAACTTTGATATAACATATAATTTGTATAA
TTAATT
Found at i:46553 original size:16 final size:16
Alignment explanation
Indices: 46532--46574 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
46522 TACCATATTT
46532 ATGTGTGTGTGTGTGC
1 ATGTGTGTGTGTGTGC
* * *
46548 ATGTGTATATGTTTGC
1 ATGTGTGTGTGTGTGC
*
46564 ATGTGCGTGTG
1 ATGTGTGTGTG
46575 CTCTCAAAGT
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:0.12, C:0.07, G:0.37, T:0.44
Consensus pattern (16 bp):
ATGTGTGTGTGTGTGC
Found at i:48774 original size:2 final size:2
Alignment explanation
Indices: 48762--48807 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
48752 TGGACATGCT
*
48762 TA TA CA 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
48804 TA TA
1 TA TA
48808 AATGATGCAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:55191 original size:11 final size:12
Alignment explanation
Indices: 55167--55195 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
55157 TGTATTTAAT
55167 TTTTTATTTGTA
1 TTTTTATTTGTA
55179 TTTTTATTT-TA
1 TTTTTATTTGTA
55190 TTTTTA
1 TTTTTA
55196 GTGTCCCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.79
Consensus pattern (12 bp):
TTTTTATTTGTA
Found at i:59132 original size:46 final size:46
Alignment explanation
Indices: 59079--59171 Score: 150
Period size: 46 Copynumber: 2.0 Consensus size: 46
59069 AATAAGATTT
*
59079 TCACGTAATTTGTTCAAAACTATGTGACAAATAGATATTGAGTTAA
1 TCACGTAATTTGTTCAAAACTATCTGACAAATAGATATTGAGTTAA
* * *
59125 TCACGTAATTTGTTCAAAACTGTCTGATAAATAGATATTGGGTTAA
1 TCACGTAATTTGTTCAAAACTATCTGACAAATAGATATTGAGTTAA
59171 T
1 T
59172 GCTTTTGATT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (46 bp):
TCACGTAATTTGTTCAAAACTATCTGACAAATAGATATTGAGTTAA
Found at i:69554 original size:15 final size:16
Alignment explanation
Indices: 69522--69554 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
69512 ACATGTTAAC
69522 AAAATTAACATACAAA
1 AAAATTAACATACAAA
69538 AAAATTGAA-ATACAAA
1 AAAATT-AACATACAAA
69554 A
1 A
69555 TTAAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.70, C:0.09, G:0.03, T:0.18
Consensus pattern (16 bp):
AAAATTAACATACAAA
Found at i:78257 original size:18 final size:19
Alignment explanation
Indices: 78213--78266 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 19
78203 TACATATATA
* *
78213 TATATATATATATTAATATT
1 TATAAATATAT-TTAAAATT
78233 TATAAATATATTTAAAATT
1 TATAAATATATTTAAAATT
*
78252 TA-AAAT-TAATTAAAA
1 TATAAATATATTTAAAA
78267 AATATGTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 8 0.26
18 4 0.13
19 9 0.29
20 10 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TATAAATATATTTAAAATT
Found at i:80119 original size:2 final size:2
Alignment explanation
Indices: 80112--80139 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
80102 CCAGGTAATT
80112 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
80140 ATTCTCATTA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:82091 original size:97 final size:98
Alignment explanation
Indices: 81919--82106 Score: 333
Period size: 97 Copynumber: 1.9 Consensus size: 98
81909 AAGCCTTTTG
*
81919 ACTAATACAAATGTCAAAGGACCATGTAGTTCAGATGGATATCCGAGTTTCTTGATTTAACGTGT
1 ACTAATACAAATGTCAAAGGACCATGTAGTTCAGATGGATATCCGAGTTTCTTGATTTAACATGT
81984 TATAATCTCCTGATGTTGTATAGCAGCTGTTTA
66 TATAATCTCCTGATGTTGTATAGCAGCTGTTTA
* * *
82017 ACTAGTACAAATGTCAGAGGACCATGTAG-TCAGATGGATATCTGAGTTTCTTGATTTAACATGT
1 ACTAATACAAATGTCAAAGGACCATGTAGTTCAGATGGATATCCGAGTTTCTTGATTTAACATGT
82081 TATAATCTCCTGATGTTGTATAGCAG
66 TATAATCTCCTGATGTTGTATAGCAG
82107 GATGTACTAT
Statistics
Matches: 86, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
97 59 0.69
98 27 0.31
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (98 bp):
ACTAATACAAATGTCAAAGGACCATGTAGTTCAGATGGATATCCGAGTTTCTTGATTTAACATGT
TATAATCTCCTGATGTTGTATAGCAGCTGTTTA
Found at i:83399 original size:23 final size:23
Alignment explanation
Indices: 83363--83411 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
83353 TAGATTATGC
*
83363 TTTTCTGTTTTATTTTA-TTTAT
1 TTTTCTGTGTTATTTTATTTTAT
83385 TTTTCATGTGTTATTTTATTTTAT
1 TTTTC-TGTGTTATTTTATTTTAT
83409 TTT
1 TTT
83412 ATTTATTAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 5 0.21
23 11 0.46
24 8 0.33
ACGTcount: A:0.14, C:0.04, G:0.06, T:0.76
Consensus pattern (23 bp):
TTTTCTGTGTTATTTTATTTTAT
Found at i:86527 original size:2 final size:2
Alignment explanation
Indices: 86520--86560 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
86510 GCATAAAAAC
86520 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
86561 TATCACTTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:92720 original size:15 final size:15
Alignment explanation
Indices: 92698--92734 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 15
92688 AAGTCCTTAC
92698 ATATATATAATATAATA
1 ATATATAT-ATAT-ATA
92715 ATATATATATATATA
1 ATATATATATATATA
92730 ATATA
1 ATATA
92735 ATCAATATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 8 0.40
16 4 0.20
17 8 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:92728 original size:23 final size:24
Alignment explanation
Indices: 92698--92742 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
92688 AAGTCCTTAC
92698 ATATATATAATATAAT-AATATAT
1 ATATATATAATATAATCAATATAT
92721 ATATATATAATATAATCAATAT
1 ATATATATAATATAATCAATAT
92743 CCTTTTGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
ATATATATAATATAATCAATATAT
Found at i:96853 original size:74 final size:74
Alignment explanation
Indices: 96765--96945 Score: 202
Period size: 74 Copynumber: 2.4 Consensus size: 74
96755 TTGATCTTTG
* * * *
96765 CTCTAACCAATTATAGAAGGCTCTACCCGATTAAGAGTGCTCTATTTTCAAGCTTCTT-TTCTTC
1 CTCTAACTAGTTATAGAAGGCTCTAACCGATTAAGAGTGCTCTATCTTCAAGCTT-TTATTCTTC
*
96829 AGTCGACTTC
65 AGTAGACTTC
* * * * *
96839 CTCTAACTAGTTATAGCAGGCTCTAACTGATTAAGAGTTCTCTGTCTTCAGGCTTTTATTCTTCA
1 CTCTAACTAGTTATAGAAGGCTCTAACCGATTAAGAGTGCTCTATCTTCAAGCTTTTATTCTTCA
*
96904 GTAGATTTC
66 GTAGACTTC
* * * * *
96913 TTTTAACTAGTTATAGTAGGTTCTAACCAATTA
1 CTCTAACTAGTTATAGAAGGCTCTAACCGATTA
96946 CAAACATTAT
Statistics
Matches: 89, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
73 2 0.02
74 87 0.98
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.39
Consensus pattern (74 bp):
CTCTAACTAGTTATAGAAGGCTCTAACCGATTAAGAGTGCTCTATCTTCAAGCTTTTATTCTTCA
GTAGACTTC
Found at i:101184 original size:20 final size:18
Alignment explanation
Indices: 101135--101184 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 18
101125 TATCGATACA
101135 ATCGATACATTCAAATGT
1 ATCGATACATTCAAATGT
**
101153 ATTAATACATTCGAGAATGT
1 ATCGATACATTC-A-AATGT
*
101173 ATCGATAGATTC
1 ATCGATACATTC
101185 TGCTAAAGAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 10 0.40
19 1 0.04
20 14 0.56
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (18 bp):
ATCGATACATTCAAATGT
Found at i:101218 original size:11 final size:11
Alignment explanation
Indices: 101197--101245 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
101187 CTAAAGATGA
101197 ACATGTATCGAT
1 ACAT-TATCGAT
101209 ACATTATCGAT
1 ACATTATCGAT
*
101220 ACATTATCCA-
1 ACATTATCGAT
101230 A-ATGTATCGAT
1 ACAT-TATCGAT
101241 ACATT
1 ACATT
101246 TGAAATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
9 2 0.06
10 6 0.19
11 18 0.56
12 6 0.19
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (11 bp):
ACATTATCGAT
Found at i:113269 original size:36 final size:36
Alignment explanation
Indices: 113167--113282 Score: 153
Period size: 36 Copynumber: 3.2 Consensus size: 36
113157 GTGTTTCGGT
* *
113167 AAAGGCATGTTGTGAAGGTTACT-CTTGATCCTGGTA
1 AAAGGCATGTTGTGAAGGTTA-TGCATGATCTTGGTA
* *
113203 AAAAGCATGTTGTGAAGGTTATGCCTGATCTTGGTA
1 AAAGGCATGTTGTGAAGGTTATGCATGATCTTGGTA
* *
113239 AAAGGCATGTTGTAAAGGTTATGCATGATCTTGTTGA
1 AAAGGCATGTTGTGAAGGTTATGCATGATCTTGGT-A
113276 AAAGGCA
1 AAAGGCA
113283 AACTGATAGT
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
35 1 0.01
36 62 0.87
37 8 0.11
ACGTcount: A:0.29, C:0.11, G:0.28, T:0.32
Consensus pattern (36 bp):
AAAGGCATGTTGTGAAGGTTATGCATGATCTTGGTA
Found at i:116952 original size:142 final size:142
Alignment explanation
Indices: 116584--118539 Score: 1787
Period size: 142 Copynumber: 13.8 Consensus size: 142
116574 TTCATCAAGC
* ** * * * * *
116584 TGATGTTGCAACAATGTTTGAATTCCTCATTTTTGTCATATAATGGT-ATAGGATTAAATGTTGG
1 TGATGTTGCAATAATGTTTGAATTCCTTGTTTTTGTCATGTAATGATGA-AAGATTAAATGCTAG
* * * * * * *
116648 AATTCCCAAGTCATGTTTAGAAGCCTCAAGCTCCTT-CAACACAATG-AA-TGCTTGTTGGACGA
65 AATTCCCAAGTCATGTTCACAAGCCTCAACCT-CTTCCAACGC-A-GCAAGTGCTTGCTAGATGA
*
116710 TTGGTAATAGACCT-GA
127 TTGGTGATAG-CCTAGA
** * * * * * *
116726 TGATGTTATAATATTGTTTGAATTCCGTGTTTTTGTTATGCAACGATGAAAGATTAAATGTTAGA
1 TGATGTTGCAATAATGTTTGAATTCCTTGTTTTTGTCATGTAATGATGAAAGATTAAATGCTAGA
* * * * * *
116791 ATTCCCAAGTCATGCTCACAAACCTTAGCCTTTTCCAACGCAGTAAGTGCTTGCTAGATGATTGG
66 ATTCCCAAGTCATGTTCACAAGCCTCAACCTCTTCCAACGCAGCAAGTGCTTGCTAGATGATTGG
116856 TGATAGCCTAGA
131 TGATAGCCTAGA
* ** *
116868 TGATGTTACAATAATGTTTGAATTCCTCATTGTTGTCATGTAATGATGAAAGATTAAATGCTAGA
1 TGATGTTGCAATAATGTTTGAATTCCTTGTTTTTGTCATGTAATGATGAAAGATTAAATGCTAGA
* * * * * * *
116933 GTTCCCAATTTATGTTCACAAGCCTCAACCTCCTCCAATGCAGCAAGTGCTTAG-TAAATGATTA
66 ATTCCCAAGTCATGTTCACAAGCCTCAACCTCTTCCAACGCAGCAAGTGCTT-GCTAGATGATTG
* *
116997 CTGATAGCCTAAA
130 GTGATAGCCTAGA
* *
117010 TAATGTTGCAATAATGTTTTAATTCCTTGTTTTTGTCATGTAAT--T--AA-ATGT---TG-T--
1 TGATGTTGCAATAATGTTTGAATTCCTTGTTTTTGTCATGTAATGATGAAAGAT-TAAATGCTAG
* * * * * **
117064 AATTCCCAAGTCATGTTCACAAGCCTTAACCTCCTT-CAATGCAACAAGCGCTTGCCAGACAATT
65 AATTCCCAAGTCATGTTCACAAGCCTCAACCT-CTTCCAACGCAGCAAGTGCTTGCTAGATGATT
* * * *
117128 GCTTATAGCCCAAA
129 GGTGATAGCCTAGA
* * * * * * *
117142 TGATGTTGCAATAATGTTTGAATT-TTTCGTTCTTGTGATGTAAAGGT-AAAGGATGAAATGTTA
1 TGATGTTGCAATAATGTTTGAATTCCTT-GTTTTTGTCATGTAATGATGAAA-GATTAAATGCTA
* * * * *
117205 GAATTCCTAAGTCATGTTCACAAGCCTCAGCCTCTTCCAACGTAACAAGTGCTTGCTAGATAATT
64 GAATTCCCAAGTCATGTTCACAAGCCTCAACCTCTTCCAACGCAGCAAGTGCTTGCTAGATGATT
* *
117270 AGTGATAGCCCAGA
129 GGTGATAGCCTAGA
* * * *
117284 TGATGTTGCAATAATGTTTGAAATT-CTTATTTTTGTCATGTGATGAAGAATA-ATTAAATACTA
1 TGATGTTGCAATAATGTTTG-AATTCCTTGTTTTTGTCATGTAATGATGAA-AGATTAAATGCTA
** * * * * * * *
117347 GAATTCATAAGTTATGTTCACAAGCCTCAACCTCTTCCAACGTAGTACGTGCTTACTAAATGATC
64 GAATTCCCAAGTCATGTTCACAAGCCTCAACCTCTTCCAACGCAGCAAGTGCTTGCTAGATGATT
* *
117412 GGTGATAGCATAAA
129 GGTGATAGCCTAGA
* * *
117426 TGATGTTGCAACAATGTTTGAATTCCTTGTTTTTGTCATGTAATGGTGAAAGATCAAATGCTAGA
1 TGATGTTGCAATAATGTTTGAATTCCTTGTTTTTGTCATGTAATGATGAAAGATTAAATGCTAGA
* * * * * * * *
117491 ATTCCTAAGCCATGTTCACAAGCCTCAACCTTTTCTAATGTAACAAGTGCTTGCCAGATGATTGG
66 ATTCCCAAGTCATGTTCACAAGCCTCAACCTCTTCCAACGCAGCAAGTGCTTGCTAGATGATTGG
117556 TGATAGCCTAGA
131 TGATAGCCTAGA
* * * * ** * *
117568 TAATGTTACAATAATGGTTGAATTTCTCCTTTTTGTCATGTAATGATGAAGGATTAAATGCTAGG
1 TGATGTTGCAATAATGTTTGAATTCCTTGTTTTTGTCATGTAATGATGAAAGATTAAATGCTAGA
** * * * * * * **
117633 ATTTGCAAG-CTATGTTCACAAGTCTCAACCTCTTCTAACGCAGAAAATGCTTGGTAAACAATTG
66 ATTCCCAAGTC-ATGTTCACAAGCCTCAACCTCTTCCAACGCAGCAAGTGCTTGCTAGATGATTG
*
117697 GTGATAGCCCAGA
130 GTGATAGCCTAGA
* * ** *
117710 TGATGTTGCAATAATGTTTGAATTCCTTGTTTTTGTCATGTTAT-AGTGAAGGATTAAATTTTGG
1 TGATGTTGCAATAATGTTTGAATTCCTTGTTTTTGTCATGTAATGA-TGAAAGATTAAATGCTAG
* * * * * * * *
117774 AATTCCCAAGTCATGTTCATAAGCCTCAACCTCCTCTAATGCAGTAAGTGCTTGCTAAATTATTA
65 AATTCCCAAGTCATGTTCACAAGCCTCAACCTCTTCCAACGCAGCAAGTGCTTGCTAGATGATTG
*
117839 GTAATAGCCTAGA
130 GTGATAGCCTAGA
* * *
117852 TGATGTTTCAATAATGTTTGAATTCCTTGTTTTTGTCATGTAATGGT-AAAGGGTTAAATGCTAG
1 TGATGTTGCAATAATGTTTGAATTCCTTGTTTTTGTCATGTAATGATGAAA-GATTAAATGCTAG
* * * * ** *
117916 AATTCCCAAGTCATGTTCATAAACCTCAACTTCCTCCAACATAGCAATTGCTTGCTAGATGATTG
65 AATTCCCAAGTCATGTTCACAAGCCTCAACCTCTTCCAACGCAGCAAGTGCTTGCTAGATGATTG
*
117981 GTGATAGCCTTGA
130 GTGATAGCCTAGA
* * *
117994 TGATGTTGCCATAATGTTTGAATACCTCG-TTTTGTCATGTAATGATGAAAGATTAAATGCTAGA
1 TGATGTTGCAATAATGTTTGAATTCCTTGTTTTTGTCATGTAATGATGAAAGATTAAATGCTAGA
* * *
118058 ATTCCCAAGTCATGTTCACATGCCTCAACTTCCTT-CAACGCAACAAGTGCTTGCTAGATGATTG
66 ATTCCCAAGTCATGTTCACAAGCCTCAACCT-CTTCCAACGCAGCAAGTGCTTGCTAGATGATTG
*
118122 GTGATAAG-CTACA
130 GTGAT-AGCCTAGA
* ** * * * * *
118135 TGATGTTGCAATAATATTTGAATTCCTCATTTTTGTCATTTAATGATGAAGGATTGAATGTTGGA
1 TGATGTTGCAATAATGTTTGAATTCCTTGTTTTTGTCATGTAATGATGAAAGATTAAATGCTAGA
* * ** * * * *
118200 ATTCCCAAGTTATGTTCACAAGCCTCAACCTCCTT-CGACATAGTAAATGCTTGCTAGACGATTA
66 ATTCCCAAGTCATGTTCACAAGCCTCAACCT-CTTCCAACGCAGCAAGTGCTTGCTAGATGATTG
*
118264 GTGATAGCAC-ATA
130 GTGATAGC-CTAGA
* * * * **
118277 TGATGTTGCAGTAATGTTTGAATTCTTTGTTTTTGTCCTGTAAT-AGTGAAGGATTCTATGCTAG
1 TGATGTTGCAATAATGTTTGAATTCCTTGTTTTTGTCATGTAATGA-TGAAAGATTAAATGCTAG
* * * * ** * ** * * *
118341 AATTCCCAAATCATGTTTACAAGACTTATTCTCCTATAATGCAGCAAGTGCTTGCCAGACGATTG
65 AATTCCCAAGTCATGTTCACAAGCCTCAACCTCTTCCAACGCAGCAAGTGCTTGCTAGATGATTG
118406 GTGATAGCCTAGA
130 GTGATAGCCTAGA
* *
118419 TGATGTTGCAATCATGTTTGAATTTCTTTGTTTTTTTGTCATGTAATGATGAAAGATTAAATGCT
1 TGATGTTGCAATAATGTTTGAA-TTCCTTG--TTTTTGTCATGTAATGATGAAAGATTAAATGCT
* * * * *
118484 AGAATTCCCAAATCATGTTCAAAAGCCTTAACCTCCTCCGACGCAGCAAGTGCTTG
63 AGAATTCCCAAGTCATGTTCACAAGCCTCAACCTCTTCCAACGCAGCAAGTGCTTG
118540 AACTCTCACC
Statistics
Matches: 1477, Mismatches: 292, Indels: 87
0.80 0.16 0.05
Matches are distributed among these distances:
131 3 0.00
132 94 0.06
133 2 0.00
134 2 0.00
135 4 0.00
137 4 0.00
138 3 0.00
139 2 0.00
140 3 0.00
141 141 0.10
142 1124 0.76
143 19 0.01
144 1 0.00
145 74 0.05
146 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (142 bp):
TGATGTTGCAATAATGTTTGAATTCCTTGTTTTTGTCATGTAATGATGAAAGATTAAATGCTAGA
ATTCCCAAGTCATGTTCACAAGCCTCAACCTCTTCCAACGCAGCAAGTGCTTGCTAGATGATTGG
TGATAGCCTAGA
Found at i:121642 original size:333 final size:333
Alignment explanation
Indices: 121036--121698 Score: 778
Period size: 333 Copynumber: 2.0 Consensus size: 333
121026 ACATAAAAAG
* * *
121036 TGTATTTGGTATCTCGTTTTAGCATCTATGCAATACTTCTCATGTATTAGACGTGTAAATACTCC
1 TGTATTTGGTATCTCGCTTTAGCATCTATGCAATACTTCTCATGTATCAGACGTATAAATACTCC
* * ** * *
121101 TTAGACTTGAGACACCAAGTTGTCTTGCACATGGAATGCTATATTTTGATTGCATGTGGAGTGCC
66 TTAGACTTGAGACACCAAGTTGTCTTGCAAATAGAATGCTATACGTTGATTGCACGTGGAGTGAC
* * ** * * *
121166 AACTCATGATGTTTTTGGATATGGTATGAAGCATGTGAAAGAAAACAAGTGGTCGAGATAGGAAT
131 AACTCAGGATGTTTTTAGATATAATATGAAACATGTGAAAGAAAACAAGTGATCGAGAAAGGAAT
* *** * ** * *
121231 TATCACTTTAAATGATTCAAGGGGACGTATCCTAATGGTTATTGGTTGATATTAGTTTAACCAAA
196 CATCACCACAAATGATTCAAGGGGACATATCCTAATGGTTATTACTTGATAATAGCTTAACCAAA
* * *
121296 TCCTTACCCAAGGTGATTTAGAGATTATGAAATGAATT-TCATAAGACTCAATAAAATTAATGAT
261 TCCTTACCCAAGGTGATTTAGAGATTAAGAAATGAGTTCT-ATAAGACTCAATAAAACTAATGAT
121360 CTAACTATA
325 CTAACTATA
* * * * *
121369 TGTATTTGGTATCTTGCTTTAGCATCTATGCAATACTTTTCATGTGTCAGTCGTATAAATATTCC
1 TGTATTTGGTATCTCGCTTTAGCATCTATGCAATACTTCTCATGTATCAGACGTATAAATACTCC
* *
121434 TTAGACTTGAGACATCAAGTTGTCTTG-AAAGTAGAGTGCTATACGTTGATTGCACGTGGAGTGA
66 TTAGACTTGAGACACCAAGTTGTCTTGCAAA-TAGAATGCTATACGTTGATTGCACGTGGAGTGA
* * * *
121498 CTACTTAGGATGTTTTTTAG-TATAATATGAAATATGTG-AAGAAAA-ATGAGTGATTGAGAAAG
130 CAACTCAGGATG-TTTTTAGATATAATATGAAACATGTGAAAGAAAACA--AGTGATCGAGAAAG
* * * * * * *
121560 GAATCATTACCACAAGTGATTCAATGGGACATATCCTAGTGGTTCTTACTTGATAATAGCTTGAT
192 GAATCATCACCACAAATGATTCAAGGGGACATATCCTAATGGTTATTACTTGATAATAGCTTAAC
** * ** *
121625 CAAATCCTTGGCCAAGGTGATTTGGAGATTAAGAAATGAGTTCTATAAGTTTTAATAAAACTAAT
257 CAAATCCTTACCCAAGGTGATTTAGAGATTAAGAAATGAGTTCTATAAGACTCAATAAAACTAAT
121690 GATCTAACT
322 GATCTAACT
121699 GTAGTAACAA
Statistics
Matches: 273, Mismatches: 52, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
331 1 0.00
332 9 0.03
333 256 0.94
334 7 0.03
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (333 bp):
TGTATTTGGTATCTCGCTTTAGCATCTATGCAATACTTCTCATGTATCAGACGTATAAATACTCC
TTAGACTTGAGACACCAAGTTGTCTTGCAAATAGAATGCTATACGTTGATTGCACGTGGAGTGAC
AACTCAGGATGTTTTTAGATATAATATGAAACATGTGAAAGAAAACAAGTGATCGAGAAAGGAAT
CATCACCACAAATGATTCAAGGGGACATATCCTAATGGTTATTACTTGATAATAGCTTAACCAAA
TCCTTACCCAAGGTGATTTAGAGATTAAGAAATGAGTTCTATAAGACTCAATAAAACTAATGATC
TAACTATA
Found at i:122331 original size:45 final size:45
Alignment explanation
Indices: 122277--122521 Score: 253
Period size: 45 Copynumber: 5.5 Consensus size: 45
122267 ATATGCCATG
* * * *
122277 GTTAAGTTGTTACACACCATGTACAAAAACGTGTGACACGCCACA
1 GTTAGGTTGTTACACGCCATGTACAAAAACGTGTGACACGTCATA
* * *
122322 GTTAGGTTGTTACACGCCATGTGCAAAAACGTGCGACACGTTAT-
1 GTTAGGTTGTTACACGCCATGTACAAAAACGTGTGACACGTCATA
* * ** * * * *
122366 GATTAGGTTGTTACACGTCATGTATAAAAATATATTACATGCCATA
1 G-TTAGGTTGTTACACGCCATGTACAAAAACGTGTGACACGTCATA
* * * *
122412 ATTAGGTTGTTACATGCCATGTACAAAAACATGTGACACGTCATG
1 GTTAGGTTGTTACACGCCATGTACAAAAACGTGTGACACGTCATA
* * * *
122457 GTTAAGTTGTTACACGCCATGCACAAATACGT-T-ACACGTCATG
1 GTTAGGTTGTTACACGCCATGTACAAAAACGTGTGACACGTCATA
122500 GTTAGGTTGTTACACGCCATGT
1 GTTAGGTTGTTACACGCCATGT
122522 TAAAAAAAAT
Statistics
Matches: 162, Mismatches: 36, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
43 30 0.19
44 2 0.01
45 130 0.80
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (45 bp):
GTTAGGTTGTTACACGCCATGTACAAAAACGTGTGACACGTCATA
Found at i:122395 original size:90 final size:88
Alignment explanation
Indices: 122273--122521 Score: 282
Period size: 90 Copynumber: 2.8 Consensus size: 88
122263 TGTTATATGC
* * *
122273 CATGGTTAAGTTGTTACACACCATGTACAAAAACGTGTGACACGCCACAGTTAGGTTGTTACACG
1 CATGATTAAGTTGTTACACGCCATGTACAAAAACGT-T-ACACGCCATAGTTAGGTTGTTACACG
* *
122338 CCATGTGCAAAAACGTGCGACACGT
64 CCATGTACAAAAACATGCGACACGT
* * * * ** * * *
122363 TATGATTAGGTTGTTACACGTCATGTATAAAAATATATTACATGCCATAATTAGGTTGTTACATG
1 CATGATTAAGTTGTTACACGCCATGTA-CAAAA-ACGTTACACGCCATAGTTAGGTTGTTACACG
*
122428 CCATGTACAAAAACATGTGACACGT
64 CCATGTACAAAAACATGCGACACGT
* * * * *
122453 CATGGTTAAGTTGTTACACGCCATGCACAAATACGTTACACGTCATGGTTAGGTTGTTACACGCC
1 CATGATTAAGTTGTTACACGCCATGTACAAAAACGTTACACGCCATAGTTAGGTTGTTACACGCC
122518 ATGT
66 ATGT
122522 TAAAAAAAAT
Statistics
Matches: 128, Mismatches: 29, Indels: 6
0.79 0.18 0.04
Matches are distributed among these distances:
88 30 0.23
89 3 0.02
90 88 0.69
91 5 0.04
92 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (88 bp):
CATGATTAAGTTGTTACACGCCATGTACAAAAACGTTACACGCCATAGTTAGGTTGTTACACGCC
ATGTACAAAAACATGCGACACGT
Found at i:122471 original size:21 final size:21
Alignment explanation
Indices: 122447--122524 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
122437 AAAACATGTG
*
122447 ACACGTCATGGTTAAGTTGTT
1 ACACGCCATGGTTAAGTTGTT
*** * *
122468 ACACGCCATGCACAAATACGTT
1 ACACGCCATGGTTAAGT-TGTT
* *
122490 ACACGTCATGGTTAGGTTGTT
1 ACACGCCATGGTTAAGTTGTT
122511 ACACGCCAT-GTTAA
1 ACACGCCATGGTTAA
122525 AAAAAATNNN
Statistics
Matches: 41, Mismatches: 15, Indels: 3
0.69 0.25 0.05
Matches are distributed among these distances:
20 4 0.10
21 23 0.56
22 14 0.34
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (21 bp):
ACACGCCATGGTTAAGTTGTT
Found at i:122531 original size:135 final size:134
Alignment explanation
Indices: 122282--122529 Score: 336
Period size: 135 Copynumber: 1.8 Consensus size: 134
122272 CCATGGTTAA
* * **
122282 GTTGTTACACACCATGTACAAAAACGTGTGACACGCCACAGTTAGGTTGTTACACGCCATGTGCA
1 GTTGTTACACACCATGTACAAAAACATGTGACACGCCACAGTTAAGTTGTTACACGCCATGCACA
* * *
122347 AAAACGTGCGACACGTTATGATTAGGTTGTTACACGTCATGTATAAAAATATATTACATGCCATA
66 AAAACGT-CGACACGTCATGATTAGGTTGTTACACGCCATGTAAAAAAATATATTACATGCCATA
122412 ATTAG
130 ATTAG
** * **
122417 GTTGTTACATGCCATGTACAAAAACATGTGACACGTCATGGTTAAGTTGTTACACGCCATGCACA
1 GTTGTTACACACCATGTACAAAAACATGTGACACGCCACAGTTAAGTTGTTACACGCCATGCACA
* * *
122482 AATACGT-TACACGTCATGGTTAGGTTGTTACACGCCATGTTAAAAAAA
66 AAAACGTCGACACGTCATGATTAGGTTGTTACACGCCATG-TAAAAAAA
122530 ATNNNNNNNN
Statistics
Matches: 97, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
133 28 0.29
134 7 0.07
135 62 0.64
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (134 bp):
GTTGTTACACACCATGTACAAAAACATGTGACACGCCACAGTTAAGTTGTTACACGCCATGCACA
AAAACGTCGACACGTCATGATTAGGTTGTTACACGCCATGTAAAAAAATATATTACATGCCATAA
TTAG
Found at i:125249 original size:12 final size:12
Alignment explanation
Indices: 125200--125278 Score: 61
Period size: 12 Copynumber: 6.3 Consensus size: 12
125190 ATGTCATATA
*
125200 TTTTATTA-CAT
1 TTTTATTATAAT
125211 TTTTATTATAAT
1 TTTTATTATAAT
* *
125223 CTTTTATTTTTAT
1 -TTTTATTATAAT
*
125236 TTTTAATATAATT
1 TTTTATTATAA-T
*
125249 TTCTATATTATATT
1 TT-T-TATTATAAT
*
125263 TTTTATTTTAAT
1 TTTTATTATAAT
125275 TTTT
1 TTTT
125279 TTCTTTAAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
11 8 0.15
12 21 0.40
13 14 0.26
14 4 0.08
15 6 0.11
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTATTATAAT
Found at i:125286 original size:13 final size:13
Alignment explanation
Indices: 125210--125279 Score: 61
Period size: 13 Copynumber: 5.4 Consensus size: 13
125200 TTTTATTACA
*
125210 TTTTTATTATAAT
1 TTTTTATTTTAAT
* *
125223 CTTTTATTTTTA-
1 TTTTTATTTTAAT
* *
125235 TTTTTAATATAAT
1 TTTTTATTTTAAT
* *
125248 TTTCTATATTATAT
1 TTTTTATTTTA-AT
125262 TTTTTATTTTAAT
1 TTTTTATTTTAAT
125275 TTTTT
1 TTTTT
125280 TCTTTAAAAG
Statistics
Matches: 42, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
12 8 0.19
13 23 0.55
14 11 0.26
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTATTTTAAT
Found at i:125324 original size:28 final size:28
Alignment explanation
Indices: 125263--125324 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
125253 ATATTATATT
*
125263 TTTTATTTTAATTTTTTTCTTTAAAAGA
1 TTTTATTTTAATTTTTTTCTTTAAAACA
* * *
125291 TATTATTTTATTTTTATTTC-TTAATACA
1 TTTTATTTTAATTTT-TTTCTTTAAAACA
125319 TTTTAT
1 TTTTAT
125325 ACGTATATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (28 bp):
TTTTATTTTAATTTTTTTCTTTAAAACA
Found at i:126510 original size:24 final size:23
Alignment explanation
Indices: 126466--126510 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
126456 TTTAATATTT
* **
126466 TTAAATAATTTTTTATTAAATAA
1 TTAAATAATTTTTAAAAAAATAA
126489 TTAATATAATTTTTAAAAAAAT
1 TTAA-ATAATTTTTAAAAAAAT
126511 GACCTTACAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 4 0.22
24 14 0.78
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTAAATAATTTTTAAAAAAATAA
Found at i:126646 original size:5 final size:5
Alignment explanation
Indices: 126636--126703 Score: 54
Period size: 5 Copynumber: 13.6 Consensus size: 5
126626 AAGGTAAAGT
126636 TTTTA TTTTA TTTTA -TTTA TTTATA TTATTA -TTTA TATTTA -TTTA
1 TTTTA TTTTA TTTTA TTTTA TTT-TA TT-TTA TTTTA T-TTTA TTTTA
* *
126681 TTTT- TTTCAA TTTTA TTCTA TTT
1 TTTTA TTT-TA TTTTA TTTTA TTT
126704 GCTCATATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
4 14 0.27
5 23 0.45
6 13 0.25
7 1 0.02
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:126669 original size:12 final size:13
Alignment explanation
Indices: 126637--126683 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
126627 AGGTAAAGTT
*
126637 TTTATTTTATTTTA
1 TTTA-TTTATATTA
126651 TTTATTTATATTA
1 TTTATTTATATTA
126664 -TTATTTATATTTA
1 TTTATTTATA-TTA
126677 TTTATTT
1 TTTATTT
126684 TTTTCAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 9 0.30
13 11 0.37
14 10 0.33
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTATTTATATTA
Found at i:129931 original size:11 final size:11
Alignment explanation
Indices: 129915--129939 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
129905 AAAGAACAAT
129915 TATAAGAGAAA
1 TATAAGAGAAA
129926 TATAAGAGAAA
1 TATAAGAGAAA
129937 TAT
1 TAT
129940 TTATATAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.16, T:0.24
Consensus pattern (11 bp):
TATAAGAGAAA
Found at i:132504 original size:23 final size:23
Alignment explanation
Indices: 132478--132528 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
132468 GTTTAGAGTT
* *
132478 TGTGAAATGGCATGGTGGAAATG
1 TGTGAAACGGCATAGTGGAAATG
* *
132501 TGTGACACGGCATAGTGGGAATG
1 TGTGAAACGGCATAGTGGAAATG
132524 TGTGA
1 TGTGA
132529 CACATCATGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.08, G:0.39, T:0.25
Consensus pattern (23 bp):
TGTGAAACGGCATAGTGGAAATG
Found at i:132529 original size:23 final size:23
Alignment explanation
Indices: 132486--132531 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
132476 TTTGTGAAAT
*
132486 GGCATGGTGGAAATGTGTGACAC
1 GGCATAGTGGAAATGTGTGACAC
*
132509 GGCATAGTGGGAATGTGTGACAC
1 GGCATAGTGGAAATGTGTGACAC
132532 ATCATGGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.13, G:0.39, T:0.22
Consensus pattern (23 bp):
GGCATAGTGGAAATGTGTGACAC
Found at i:132545 original size:23 final size:22
Alignment explanation
Indices: 132487--132551 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 22
132477 TTGTGAAATG
*
132487 GCATGGTGGAAATGTGTGACACG
1 GCATGGTGG-AATGTGTGACACA
*
132510 GCATAGTGGGAATGTGTGACACA
1 GCATGGT-GGAATGTGTGACACA
* *
132533 TCATGGTGAGAATATGTGA
1 GCATGGTG-GAATGTGTGA
132552 GATGGTTGTG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 1 0.03
23 32 0.91
24 2 0.06
ACGTcount: A:0.29, C:0.11, G:0.35, T:0.25
Consensus pattern (22 bp):
GCATGGTGGAATGTGTGACACA
Found at i:132743 original size:23 final size:23
Alignment explanation
Indices: 132717--132772 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
132707 TGGTGTGAAC
**
132717 ATGTGACACGTCATGGTAAGAAT
1 ATGTGACACAACATGGTAAGAAT
* * *
132740 ATGTGAGACAACATGGTGAGCAT
1 ATGTGACACAACATGGTAAGAAT
132763 ATGTGACACA
1 ATGTGACACA
132773 GTTGTGACAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.23
Consensus pattern (23 bp):
ATGTGACACAACATGGTAAGAAT
Found at i:132803 original size:24 final size:24
Alignment explanation
Indices: 132774--132830 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
132764 TGTGACACAG
*
132774 TTGTGACATGATAGGGTTCAGAGT
1 TTGTGACACGATAGGGTTCAGAGT
132798 TTGTGACACGATAGGGTTCAGAGT
1 TTGTGACACGATAGGGTTCAGAGT
132822 TTGTGACAC
1 TTGTGACAC
132831 CATGGAGAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.25, C:0.12, G:0.32, T:0.32
Consensus pattern (24 bp):
TTGTGACACGATAGGGTTCAGAGT
Found at i:133092 original size:23 final size:23
Alignment explanation
Indices: 133063--133121 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
133053 TTAAAGTTTA
*
133063 TGACACGCCATGG-TGGTAATGTG
1 TGACACGCCATGGCTGG-AATATG
* *
133086 TGACACGGCATGGCTTGAATATG
1 TGACACGCCATGGCTGGAATATG
*
133109 TGACACACCATGG
1 TGACACGCCATGG
133122 ATTGAAATAG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 28 0.93
24 2 0.07
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (23 bp):
TGACACGCCATGGCTGGAATATG
Found at i:133126 original size:23 final size:23
Alignment explanation
Indices: 133084--133127 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
133074 GGTGGTAATG
** *
133084 TGTGACACGGCATGGCTTGAATA
1 TGTGACACACCATGGATTGAATA
133107 TGTGACACACCATGGATTGAA
1 TGTGACACACCATGGATTGAA
133128 ATAGAAAAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (23 bp):
TGTGACACACCATGGATTGAATA
Found at i:133666 original size:21 final size:21
Alignment explanation
Indices: 133641--133696 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
133631 GGTTAACTGG
*
133641 TTTTTGGGGTTTTTAGCTTAT
1 TTTTTGAGGTTTTTAGCTTAT
133662 TTTTTGAGGTTTTTAGCTTAT
1 TTTTTGAGGTTTTTAGCTTAT
133683 TTTTTGAGGTTTTT
1 TTTTTGAGGTTTTT
133697 CATGTGTCAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.11, C:0.04, G:0.21, T:0.64
Consensus pattern (21 bp):
TTTTTGAGGTTTTTAGCTTAT
Found at i:133949 original size:61 final size:61
Alignment explanation
Indices: 133830--133958 Score: 170
Period size: 61 Copynumber: 2.1 Consensus size: 61
133820 GCGAGTAATG
* * ** **
133830 ACATTTTACTTGATATGCATGGTGTGCAACAACATTTTACTTGATATGCATGGCATGCAACA
1 ACATTTTACTTGATATGCATGATGT-CAACAACATATTACTTGATATAAATAACATGCAACA
*
133892 ACATTTTACTTGATATGCATGCATGT-AACAACATATTACTTGGTATAAATAACATGCAACA
1 ACATTTTACTTGATATGCATG-ATGTCAACAACATATTACTTGATATAAATAACATGCAACA
133953 ACATTT
1 ACATTT
133959 ATTTCTTTCT
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
61 35 0.59
62 21 0.36
63 3 0.05
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (61 bp):
ACATTTTACTTGATATGCATGATGTCAACAACATATTACTTGATATAAATAACATGCAACA
Found at i:133955 original size:31 final size:30
Alignment explanation
Indices: 133830--133958 Score: 159
Period size: 31 Copynumber: 4.2 Consensus size: 30
133820 GCGAGTAATG
**
133830 ACATTTTACTTGATATGCATGGTGTGCAACA
1 ACATTTTACTTGATATGCAT-GCATGCAACA
133861 ACATTTTACTTGATATGCATGGCATGCAACA
1 ACATTTTACTTGATATGCAT-GCATGCAACA
*
133892 ACATTTTACTTGATATGCATGCATGTAACA
1 ACATTTTACTTGATATGCATGCATGCAACA
* * ** *
133922 ACATATTACTTGGTATAAATAACATGCAACA
1 ACATTTTACTTGATATGCAT-GCATGCAACA
133953 ACATTT
1 ACATTT
133959 ATTTCTTTCT
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
30 25 0.29
31 62 0.71
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (30 bp):
ACATTTTACTTGATATGCATGCATGCAACA
Found at i:140445 original size:7 final size:7
Alignment explanation
Indices: 140435--140459 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
140425 TCCACTTACC
140435 ACTTGCA
1 ACTTGCA
140442 ACTTGCA
1 ACTTGCA
140449 ACTTGCA
1 ACTTGCA
140456 ACTT
1 ACTT
140460 CCTTTTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.32
Consensus pattern (7 bp):
ACTTGCA
Found at i:143620 original size:31 final size:31
Alignment explanation
Indices: 143552--143622 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
143542 TAGGGCATGG
** *
143552 CATGTCACCCCATAGTTCTGCTAGCACTCAA
1 CATGTCACCCCATAAATCTGCTACCACTCAA
** * *
143583 TGTGTCACGCCATAAATCTGCTACCACTTAA
1 CATGTCACCCCATAAATCTGCTACCACTCAA
143614 CATGTCACC
1 CATGTCACC
143623 ACAAGATGTC
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.34, G:0.13, T:0.27
Consensus pattern (31 bp):
CATGTCACCCCATAAATCTGCTACCACTCAA
Found at i:143885 original size:138 final size:138
Alignment explanation
Indices: 143554--144068 Score: 587
Period size: 138 Copynumber: 3.8 Consensus size: 138
143544 GGGCATGGCA
* * * * *
143554 TGTCACCCCATAGTTCTGCTAGCACTCAATGTGTCACGCCATAAATCTGCTACCACTTAACATGT
1 TGTCACCCCATAGTTCTACTAGCACTCAACGTGTCACCCCATAAATCTGCTACCACTCAACGTGT
** * * *
143619 CACCACAAGATGTCATCAACATCTAACAATTGAG-GTGTGGCATGTC-CCC-CCATAATACAACA
66 CACCACAAGATGTCATCAACATCTAACAATTGAGAGCATGGCATGTCACCCACAATACTGCAACA
*
143681 ACTTAG-T
131 ACTCAGCT
* * ** * * *
143688 GTATCACCCCATAGTTCTGCTAGCACTCAGTGTGTCACACTATAAATCTGCTACCACTCAATGTG
1 -TGTCACCCCATAGTTCTACTAGCACTCAACGTGTCACCCCATAAATCTGCTACCACTCAACGTG
* *
143753 TCACCACAAGGTGTCATCAACATCTAACAATTGAG-GCATGACATGTCACCGCACAATACTGCAA
65 TCACCACAAGATGTCATCAACATCTAACAATTGAGAGCATGGCATGTCACC-CACAATACTGCAA
143817 CAACTCAGCT
129 CAACTCAGCT
* * * *
143827 TGTCACCCTATAGTTCTACCAGCACTCAACGTGTCACCCCATAAATCT-ATCACGACTCAACGTG
1 TGTCACCCCATAGTTCTACTAGCACTCAACGTGTCACCCCATAAATCTGCT-ACCACTCAACGTG
* * * *
143891 TCACCACAAGATGTCATCGACATCTAACAATTG-GAGCGTGGCGTATCACCCCACAATACTGCAA
65 TCACCACAAGATGTCATCAACATCTAACAATTGAGAGCATGGCATGTCA-CCCACAATACTGCAA
* *
143955 CAACTCAACA
129 CAACTCAGCT
* * * * **
143965 TGTCATCCCATAGTTCTACTAGCACTCAGCGTGTCACCCTATAAATTTGCTACCACTCAGTGTGT
1 TGTCACCCCATAGTTCTACTAGCACTCAACGTGTCACCCCATAAATCTGCTACCACTCAACGTGT
* * *
144030 CACTATAAGTTGTCATCAACATCTAACAATT-AGAGCATG
66 CACCACAAGATGTCATCAACATCTAACAATTGAGAGCATG
144069 TGGCTAATAA
Statistics
Matches: 322, Mismatches: 49, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
135 100 0.31
136 2 0.01
137 3 0.01
138 213 0.66
139 4 0.01
ACGTcount: A:0.31, C:0.30, G:0.14, T:0.25
Consensus pattern (138 bp):
TGTCACCCCATAGTTCTACTAGCACTCAACGTGTCACCCCATAAATCTGCTACCACTCAACGTGT
CACCACAAGATGTCATCAACATCTAACAATTGAGAGCATGGCATGTCACCCACAATACTGCAACA
ACTCAGCT
Found at i:147104 original size:23 final size:23
Alignment explanation
Indices: 147075--147241 Score: 155
Period size: 23 Copynumber: 7.3 Consensus size: 23
147065 TCAGTCATGT
147075 TGTTACACACCATGTTCAAAAAA
1 TGTTACACACCATGTTCAAAAAA
** *
147098 TGTTACACGTCATGTTTAAAAAA
1 TGTTACACACCATGTTCAAAAAA
**
147121 TGTTACATGCCATGTTC-AAAAA
1 TGTTACACACCATGTTCAAAAAA
* *
147143 TGTTATACA-CAAGTTCAAAAAA
1 TGTTACACACCATGTTCAAAAAA
* *
147165 TGCTACACACTATGTTC-AAAAA
1 TGTTACACACCATGTTCAAAAAA
* *
147187 TGTTACAC-GCAAGTT-AAAAAA
1 TGTTACACACCATGTTCAAAAAA
* *
147208 TGGTCACACGCCATGTTCGATAAAAA
1 T-GTTACACACCATGTTC-A-AAAAA
147234 TGTTACAC
1 TGTTACAC
147242 GGCATGTGCT
Statistics
Matches: 114, Mismatches: 22, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
21 16 0.14
22 41 0.36
23 44 0.39
25 7 0.06
26 6 0.05
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.28
Consensus pattern (23 bp):
TGTTACACACCATGTTCAAAAAA
Found at i:147144 original size:22 final size:22
Alignment explanation
Indices: 147075--147248 Score: 145
Period size: 22 Copynumber: 7.7 Consensus size: 22
147065 TCAGTCATGT
*
147075 TGTTACACACCATGTTCAAAAAA
1 TGTTACACGCCATGTTC-AAAAA
* *
147098 TGTTACACGTCATGTTTAAAAAA
1 TGTTACACGCCATG-TTCAAAAA
*
147121 TGTTACATGCCATGTTCAAAAA
1 TGTTACACGCCATGTTCAAAAA
* * *
147143 TGTTATAC-ACAAGTTCAAAAAA
1 TGTTACACGCCATGTTC-AAAAA
* * *
147165 TGCTACACACTATGTTCAAAAA
1 TGTTACACGCCATGTTCAAAAA
* *
147187 TGTTACACG-CAAGTTAAAAAA
1 TGTTACACGCCATGTTCAAAAA
*
147208 TGGTCACACGCCATGTTCGATAAAAA
1 T-GTTACACGCCATGTTC---AAAAA
*
147234 TGTTACACGGCATGT
1 TGTTACACGCCATGT
147249 GCTAACACAT
Statistics
Matches: 118, Mismatches: 25, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
21 16 0.14
22 43 0.36
23 39 0.33
24 2 0.02
25 12 0.10
26 6 0.05
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (22 bp):
TGTTACACGCCATGTTCAAAAA
Found at i:147180 original size:44 final size:43
Alignment explanation
Indices: 147078--147241 Score: 166
Period size: 44 Copynumber: 3.6 Consensus size: 43
147068 GTCATGTTGT
* * *
147078 TACACACCATGTTCAAAAAATGTTACACGTCATGTTTAAAAAATGT
1 TACACACCATGTTC-AAAAATGTTACAC-ACAAG-TTAAAAAATGC
** *
147124 TACATGCCATGTTCAAAAATGTTATACACAAGTTCAAAAAATGC
1 TACACACCATGTTCAAAAATGTTACACACAAGTT-AAAAAATGC
* * *
147168 TACACACTATGTTCAAAAATGTTACACGCAAGTTAAAAAATGG
1 TACACACCATGTTCAAAAATGTTACACACAAGTTAAAAAATGC
*
147211 TCACACGCCATGTTCGATAAAAATGTTACAC
1 T-ACACACCATGTTC---AAAAATGTTACAC
147242 GGCATGTGCT
Statistics
Matches: 99, Mismatches: 14, Indels: 9
0.81 0.11 0.07
Matches are distributed among these distances:
43 11 0.11
44 51 0.52
45 12 0.12
46 12 0.12
47 13 0.13
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.27
Consensus pattern (43 bp):
TACACACCATGTTCAAAAATGTTACACACAAGTTAAAAAATGC
Found at i:158276 original size:23 final size:23
Alignment explanation
Indices: 158233--158313 Score: 74
Period size: 23 Copynumber: 3.5 Consensus size: 23
158223 ATGACAGGGT
*
158233 GAGAATATGTGACACGACTTGGAA
1 GAGAATATGTGAGACGACTT-GAA
* * *
158257 G-GAATATGTGAGATGTCTTGAG
1 GAGAATATGTGAGACGACTTGAA
* * *
158279 GAGAATATGTGAGACAACATGAT
1 GAGAATATGTGAGACGACTTGAA
*
158302 GAGCATATGTGA
1 GAGAATATGTGA
158314 CATGACAGGA
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
22 3 0.07
23 42 0.91
24 1 0.02
ACGTcount: A:0.36, C:0.09, G:0.31, T:0.25
Consensus pattern (23 bp):
GAGAATATGTGAGACGACTTGAA
Found at i:158382 original size:23 final size:24
Alignment explanation
Indices: 158356--158409 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
158346 AGAGGAAATT
* *
158356 TGTGACACAGA-AAGGTGATAATG
1 TGTGACACAGACAAGGTGACAATA
* *
158379 TGTGAGA-TGACAAGGTGACAATA
1 TGTGACACAGACAAGGTGACAATA
158402 TGTGACAC
1 TGTGACAC
158410 GGCTGTGACA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 2 0.08
23 22 0.92
ACGTcount: A:0.37, C:0.11, G:0.30, T:0.22
Consensus pattern (24 bp):
TGTGACACAGACAAGGTGACAATA
Found at i:160024 original size:16 final size:18
Alignment explanation
Indices: 159978--160024 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
159968 TAAACCGAGG
*
159978 TATTTTGAAATAAAATAA
1 TATTTTAAAATAAAATAA
*
159996 TATTTTATTAATAAAAT-A
1 TATTTTA-AAATAAAATAA
160014 -ATTTTAAAATA
1 TATTTTAAAATA
160025 TTAATATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 4 0.16
17 6 0.24
18 7 0.28
19 8 0.32
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
TATTTTAAAATAAAATAA
Found at i:163794 original size:41 final size:41
Alignment explanation
Indices: 163749--163829 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
163739 TGGGCTATTC
* **
163749 TTCACCTT-AGTGGGGTTTTCTAACCTTGCCAAGATTGGTGG
1 TTCACATTAAGTGGGG-TTTCTAACCTCACCAAGATTGGTGG
*
163790 TTCACATTAAGTGGGGTTTCTAACCTCACCACGATTGGTG
1 TTCACATTAAGTGGGGTTTCTAACCTCACCAAGATTGGTG
163830 TCTTTCACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 28 0.80
42 7 0.20
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.35
Consensus pattern (41 bp):
TTCACATTAAGTGGGGTTTCTAACCTCACCAAGATTGGTGG
Found at i:164045 original size:31 final size:31
Alignment explanation
Indices: 164004--164143 Score: 174
Period size: 31 Copynumber: 4.5 Consensus size: 31
163994 GTTACAGTTG
* * *
164004 GCATGTAACAACATTTGACTTGGTATGCTTA
1 GCATGTAACAACATTTTACTTGATATGCATA
* *
164035 GCGTGTAACAACATTTTACTTGATATGCATG
1 GCATGTAACAACATTTTACTTGATATGCATA
*
164066 GCATGTAACAACATTTTACTTGATATGCATG
1 GCATGTAACAACATTTTACTTGATATGCATA
* *
164097 GTATGTAACAACATGTTACTT-AGTATGCATA
1 GCATGTAACAACATTTTACTTGA-TATGCATA
* *
164128 GCGTGTAACGACATTT
1 GCATGTAACAACATTT
164144 ATTTCTTTCT
Statistics
Matches: 95, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
30 1 0.01
31 94 0.99
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.35
Consensus pattern (31 bp):
GCATGTAACAACATTTTACTTGATATGCATA
Found at i:165331 original size:15 final size:15
Alignment explanation
Indices: 165311--165344 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
165301 GCCTTGGAGC
165311 CCACCTCGGATGAGG
1 CCACCTCGGATGAGG
165326 CCACCTCGGATGAGG
1 CCACCTCGGATGAGG
165341 CCAC
1 CCAC
165345 ATGGAAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.29, T:0.12
Consensus pattern (15 bp):
CCACCTCGGATGAGG
Found at i:168899 original size:20 final size:21
Alignment explanation
Indices: 168860--168900 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
168850 ACTTAATATG
* *
168860 GGCCTCCAGCAGCTTTAAATA
1 GGCCTCCAGCAACTTCAAATA
168881 GGCCT-CAGCAACTTCAAATA
1 GGCCTCCAGCAACTTCAAATA
168901 AGCCATCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (21 bp):
GGCCTCCAGCAACTTCAAATA
Found at i:169130 original size:21 final size:21
Alignment explanation
Indices: 169100--169145 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
169090 TATCAAAATA
169100 ATCTTAATTTAAACCTTCTTC
1 ATCTTAATTTAAACCTTCTTC
* **
169121 ATCTTCATTTAAATGTTCTTC
1 ATCTTAATTTAAACCTTCTTC
169142 ATCT
1 ATCT
169146 CTAAGTTCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.22, G:0.02, T:0.50
Consensus pattern (21 bp):
ATCTTAATTTAAACCTTCTTC
Found at i:173080 original size:62 final size:61
Alignment explanation
Indices: 172943--173124 Score: 208
Period size: 62 Copynumber: 3.0 Consensus size: 61
172933 AGACACGATC
* * *
172943 ACCTACTCATGGGAGCTGCCCACGCCACC-AATACAAATTGGGGCTTCAAGT--CCCTTTTT
1 ACCTACTCATGGGAACTGCCCACGCCACCTAATACAAA-TAGGGCTTCAGGTCCCCCTTTTT
* ** * *
173002 ACCTACTCGTTTGAACTGCCCATGCCACCTAATACGAATCAGGGCTTCAGGTCCCCCTTTTT
1 ACCTACTCATGGGAACTGCCCACGCCACCTAATACAAAT-AGGGCTTCAGGTCCCCCTTTTT
* * * *
173064 TCCTACTCATGGGAACTGCCCACGTCACCTAATATAAATTGAGGCTTCAGGTCCCCCTTTT
1 ACCTACTCATGGGAACTGCCCACGCCACCTAATACAAATAG-GGCTTCAGGTCCCCCTTTT
173125 ACAATCAAAT
Statistics
Matches: 101, Mismatches: 17, Indels: 7
0.81 0.14 0.06
Matches are distributed among these distances:
59 25 0.25
60 17 0.17
61 1 0.01
62 58 0.57
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28
Consensus pattern (61 bp):
ACCTACTCATGGGAACTGCCCACGCCACCTAATACAAATAGGGCTTCAGGTCCCCCTTTTT
Found at i:179604 original size:60 final size:60
Alignment explanation
Indices: 179480--179660 Score: 215
Period size: 60 Copynumber: 3.0 Consensus size: 60
179470 AGACACGATC
* *
179480 ACCTACTCATGGGAGCTGCCCACGCCACC-AATACAAATTGGGCTTCAAGT-CCCTTTTT
1 ACCTACTCATGGGAACTGCCCACGCCACCTAATACAAATTGGGCTTCAGGTCCCCTTTTT
* ** * * *
179538 ACCTACTCGTTTGAACTGCCCATGCCACCTAATACGAATCAGGGCTTCAGGTCCCCTTTTT
1 ACCTACTCATGGGAACTGCCCACGCCACCTAATACAAAT-TGGGCTTCAGGTCCCCTTTTT
* * * *
179599 -TCTACTCATGGGAACTGCCCACGTCACCTAATATAAATTGAGGCTTCAGGTCCCCCTTTT
1 ACCTACTCATGGGAACTGCCCACGCCACCTAATACAAATTG-GGCTTCAGGTCCCCTTTTT
179659 AC
1 AC
179661 AATCAAATAT
Statistics
Matches: 99, Mismatches: 19, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
58 24 0.24
59 9 0.09
60 58 0.59
61 8 0.08
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28
Consensus pattern (60 bp):
ACCTACTCATGGGAACTGCCCACGCCACCTAATACAAATTGGGCTTCAGGTCCCCTTTTT
Found at i:186417 original size:32 final size:32
Alignment explanation
Indices: 186381--186452 Score: 144
Period size: 32 Copynumber: 2.2 Consensus size: 32
186371 GCTTCTTCAT
186381 GTGACATAACATTTGTTTGGTGTTCTTTAATC
1 GTGACATAACATTTGTTTGGTGTTCTTTAATC
186413 GTGACATAACATTTGTTTGGTGTTCTTTAATC
1 GTGACATAACATTTGTTTGGTGTTCTTTAATC
186445 GTGACATA
1 GTGACATA
186453 CACAGCCGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.24, C:0.12, G:0.19, T:0.44
Consensus pattern (32 bp):
GTGACATAACATTTGTTTGGTGTTCTTTAATC
Found at i:186853 original size:22 final size:22
Alignment explanation
Indices: 186825--186903 Score: 97
Period size: 22 Copynumber: 3.6 Consensus size: 22
186815 GCTATGTTTA
186825 AAAAATGTTACACGTCATGTTC
1 AAAAATGTTACACGTCATGTTC
* *
186847 AAAAATGTTACACG-CAAGTTAA
1 AAAAATGTTACACGTCATGTT-C
* *
186869 AAAAATGCTACATGTCATGTTC
1 AAAAATGTTACACGTCATGTTC
*
186891 AAAAATATTACAC
1 AAAAATGTTACAC
186904 ACAAGTTCAA
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 5 0.11
22 36 0.78
23 5 0.11
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.28
Consensus pattern (22 bp):
AAAAATGTTACACGTCATGTTC
Found at i:186886 original size:44 final size:44
Alignment explanation
Indices: 186824--186915 Score: 139
Period size: 44 Copynumber: 2.1 Consensus size: 44
186814 TGCTATGTTT
* * *
186824 AAAAAATGTTACACGTCATGTTCAAAAATGTTACACGCAAGTTA
1 AAAAAATGCTACACGTCATGTTCAAAAATATTACACACAAGTTA
* *
186868 AAAAAATGCTACATGTCATGTTCAAAAATATTACACACAAGTTC
1 AAAAAATGCTACACGTCATGTTCAAAAATATTACACACAAGTTA
186912 AAAA
1 AAAA
186916 GTTATCACAC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (44 bp):
AAAAAATGCTACACGTCATGTTCAAAAATATTACACACAAGTTA
Found at i:186911 original size:21 final size:21
Alignment explanation
Indices: 186825--186915 Score: 67
Period size: 22 Copynumber: 4.2 Consensus size: 21
186815 GCTATGTTTA
* *
186825 AAAAATGTTACACGTCATGTTC
1 AAAAATATTACAC-TCAAGTTC
* *
186847 AAAAATGTTACACGCAAGTT-
1 AAAAATATTACACTCAAGTTC
* * *
186867 AAAAAAATGCTACATGTCATGTTC
1 AAAAATAT--TACA-CTCAAGTTC
*
186891 AAAAATATTACACACAAGTTC
1 AAAAATATTACACTCAAGTTC
186912 AAAA
1 AAAA
186916 GTTATCACAC
Statistics
Matches: 54, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
20 6 0.11
21 15 0.28
22 21 0.39
23 5 0.09
24 7 0.13
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.26
Consensus pattern (21 bp):
AAAAATATTACACTCAAGTTC
Found at i:186942 original size:11 final size:11
Alignment explanation
Indices: 186923--186958 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
186913 AAAGTTATCA
186923 CACACCATGTT
1 CACACCATGTT
*
186934 CACAGCATGTT
1 CACACCATGTT
186945 ACACACCATGTT
1 -CACACCATGTT
186957 CA
1 CA
186959 ATAAAAATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.31, C:0.33, G:0.11, T:0.25
Consensus pattern (11 bp):
CACACCATGTT
Found at i:187225 original size:54 final size:54
Alignment explanation
Indices: 187161--187265 Score: 156
Period size: 54 Copynumber: 1.9 Consensus size: 54
187151 CCACAGCACA
* * * *
187161 ATGACGATGGTGCTCAATAGAGAGTTGACAGAGCTAATACAGTTCAGAGAGCTG
1 ATGACGATGGTGCTCAACAAAGAGTTGACAAAGCTAATACAGTTCAAAGAGCTG
* *
187215 ATGACGATGGTGCTCAACAAAGAGTTGACAAAGTTGATACAGTTCAAAGAG
1 ATGACGATGGTGCTCAACAAAGAGTTGACAAAGCTAATACAGTTCAAAGAG
187266 TTGACAGAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.36, C:0.14, G:0.28, T:0.22
Consensus pattern (54 bp):
ATGACGATGGTGCTCAACAAAGAGTTGACAAAGCTAATACAGTTCAAAGAGCTG
Found at i:194102 original size:34 final size:34
Alignment explanation
Indices: 194064--194161 Score: 142
Period size: 34 Copynumber: 2.9 Consensus size: 34
194054 AATAATATCT
* *
194064 TAAATCATAGTCCAATTTAACCTATTTTAGCCCA
1 TAAATTATAGTCCAATTTAACCCATTTTAGCCCA
* * *
194098 TAAATTATAATCTAATTTAACCCATTTTAGCTCA
1 TAAATTATAGTCCAATTTAACCCATTTTAGCCCA
*
194132 TAAATTATAGCCCAATTTAACCCATTTTAG
1 TAAATTATAGTCCAATTTAACCCATTTTAG
194162 TCCAAGTCAA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 56 1.00
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.38
Consensus pattern (34 bp):
TAAATTATAGTCCAATTTAACCCATTTTAGCCCA
Found at i:194217 original size:10 final size:10
Alignment explanation
Indices: 194202--194229 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
194192 TTATCACCAA
194202 AAACCGACCG
1 AAACCGACCG
194212 AAACCGACCG
1 AAACCGACCG
194222 AAACCGAC
1 AAACCGAC
194230 ATTCAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.43, C:0.39, G:0.18, T:0.00
Consensus pattern (10 bp):
AAACCGACCG
Found at i:210251 original size:15 final size:16
Alignment explanation
Indices: 210231--210267 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
210221 TATAATTTAA
210231 ATATTTGAA-TAATAT
1 ATATTTGAAGTAATAT
*
210246 ATATTTGAAGTGATAT
1 ATATTTGAAGTAATAT
210262 ATATTT
1 ATATTT
210268 TTAATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (16 bp):
ATATTTGAAGTAATAT
Found at i:211153 original size:73 final size:73
Alignment explanation
Indices: 211061--211214 Score: 200
Period size: 73 Copynumber: 2.1 Consensus size: 73
211051 ATAATTTATC
* * *
211061 AAGAGCTTACTGTTAGAAACTGAGTTCAAAAACAGAAATGACTTAATCGACCAAGAAGTTATGTT
1 AAGAGCTTACTGTCAGAAACTGAGTTCAAAAACAGAAACGACTTAATCGACCAAGAAGTAATGTT
*
211126 AGTCGACT
66 AGTCAACT
* * * * * * * *
211134 AAGAGCTTACTGTCAGAAACTGGGTTCAGAGATAGAGACGACTTAATTGACTAAGTAGTAATGTT
1 AAGAGCTTACTGTCAGAAACTGAGTTCAAAAACAGAAACGACTTAATCGACCAAGAAGTAATGTT
211199 AGTCAACT
66 AGTCAACT
211207 AAGAGCTT
1 AAGAGCTT
211215 TCTATATGAA
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (73 bp):
AAGAGCTTACTGTCAGAAACTGAGTTCAAAAACAGAAACGACTTAATCGACCAAGAAGTAATGTT
AGTCAACT
Found at i:212731 original size:21 final size:22
Alignment explanation
Indices: 212706--212749 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
212696 GACGAGGAAG
*
212706 AAGAAAACAAGAGAA-AAGAAA
1 AAGAAAACAAGAAAAGAAGAAA
*
212727 AAGAAAAGAAGAAAAGAAGAAA
1 AAGAAAACAAGAAAAGAAGAAA
212749 A
1 A
212750 GCATTGCCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.77, C:0.02, G:0.20, T:0.00
Consensus pattern (22 bp):
AAGAAAACAAGAAAAGAAGAAA
Found at i:212740 original size:8 final size:8
Alignment explanation
Indices: 212703--212750 Score: 57
Period size: 8 Copynumber: 6.4 Consensus size: 8
212693 AAGGACGAGG
212703 AAGAAGAA
1 AAGAAGAA
* *
212711 AACAAGAG
1 AAGAAGAA
212719 AA-AAG-A
1 AAGAAGAA
212725 AA-AAGAA
1 AAGAAGAA
212732 AAGAAGAA
1 AAGAAGAA
212740 AAGAAGAA
1 AAGAAGAA
212748 AAG
1 AAG
212751 CATTGCCTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
6 5 0.14
7 6 0.17
8 24 0.69
ACGTcount: A:0.75, C:0.02, G:0.23, T:0.00
Consensus pattern (8 bp):
AAGAAGAA
Found at i:227597 original size:73 final size:73
Alignment explanation
Indices: 227507--227691 Score: 271
Period size: 73 Copynumber: 2.5 Consensus size: 73
227497 AACAGAGAAC
* * *
227507 ACTTAATCCACTAAGAAGTTTTGTTAGTCGACTAAGAGCTTACTACCAGAAACTAGGTTCAGAGA
1 ACTTAATCAACTAAGAAGTTATGTTAGTCGACTAAGAGCCTACTACCAGAAACTAGGTTCAGAGA
227572 TAGAAACA
66 TAGAAACA
* * * *
227580 ACTTAATCGACAAAGAAGTTATGTTAGTCGACTAAGAGCCTATTACCAGAAACTGGGTTCAGAGA
1 ACTTAATCAACTAAGAAGTTATGTTAGTCGACTAAGAGCCTACTACCAGAAACTAGGTTCAGAGA
*
227645 TAGAGACA
66 TAGAAACA
* **
227653 ACTTAATCAACTAAGTAGCAATGTTAGTCGACTAAGAGC
1 ACTTAATCAACTAAGAAGTTATGTTAGTCGACTAAGAGC
227692 ATTCTGTCTG
Statistics
Matches: 100, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 100 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.25
Consensus pattern (73 bp):
ACTTAATCAACTAAGAAGTTATGTTAGTCGACTAAGAGCCTACTACCAGAAACTAGGTTCAGAGA
TAGAAACA
Found at i:228981 original size:2 final size:2
Alignment explanation
Indices: 228976--229001 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
228966 ATATTGAGAA
228976 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
229002 TGGTTGAATC
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:229358 original size:92 final size:95
Alignment explanation
Indices: 229223--229499 Score: 270
Period size: 92 Copynumber: 3.0 Consensus size: 95
229213 AGAGTGAAAT
* * * *
229223 TAAGAGTTTGAAGTATGAAATTGACAAA-TTGAAGGGATTGTTGGAGTATGATAAAAATAATTAA
1 TAAGAGTTCGAAATGTGAAATTGA-AAAGTTGAA-AGATTGTTGGAGTATGATAAAAATAATTAA
*
229287 AAACTGAAAGAAAAAGAAAAAGCAGTAGGAGAA
64 AAACTGAAAGAAAAAG-AAAAGCAATAGGAGAA
* * *
229320 TGAGAG-TCGAAGTGTG-AATTGAAAAG-TG-AAGATTGTTGGAGTATGAT-AAAATAGTT-AAA
1 TAAGAGTTCGAAATGTGAAATTGAAAAGTTGAAAGATTGTTGGAGTATGATAAAAATAATTAAAA
* * * *
229379 A--G-CAGAAAATGGAAAA-CAATGGGAGTA
66 ACTGAAAGAAAA-AGAAAAGCAATAGGAGAA
* * * *
229406 TAAGAGTTTGAAATGTGAAATTGAAAAGTTGAAAAAATTATTGGGGTATGATAAAAATAATTAAA
1 TAAGAGTTCGAAATGTGAAATTGAAAAGTTG-AAAGATTGTTGGAGTATGATAAAAATAATTAAA
* *
229471 AGCTGAAAGAAAAAGAGAAGCAATAGGAG
65 AACTGAAAGAAAAAGAAAAGCAATAGGAG
229500 TATATGTTTT
Statistics
Matches: 145, Mismatches: 22, Indels: 27
0.75 0.11 0.14
Matches are distributed among these distances:
86 13 0.09
87 18 0.12
88 12 0.08
89 2 0.01
90 4 0.03
91 24 0.17
92 25 0.17
93 4 0.03
94 5 0.03
95 11 0.08
96 22 0.15
97 5 0.03
ACGTcount: A:0.49, C:0.03, G:0.25, T:0.23
Consensus pattern (95 bp):
TAAGAGTTCGAAATGTGAAATTGAAAAGTTGAAAGATTGTTGGAGTATGATAAAAATAATTAAAA
ACTGAAAGAAAAAGAAAAGCAATAGGAGAA
Found at i:233156 original size:12 final size:13
Alignment explanation
Indices: 233141--233176 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
233131 AGAGATTTTT
233141 GAGGCAGCAAGA-
1 GAGGCAGCAAGAG
233153 GAGGCAGCAA-AG
1 GAGGCAGCAAGAG
233165 GAGGCAGCAAGA
1 GAGGCAGCAAGA
233177 AACTATTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.05
12 20 0.91
13 1 0.05
ACGTcount: A:0.42, C:0.17, G:0.42, T:0.00
Consensus pattern (13 bp):
GAGGCAGCAAGAG
Found at i:234876 original size:60 final size:60
Alignment explanation
Indices: 234782--234962 Score: 229
Period size: 60 Copynumber: 3.0 Consensus size: 60
234772 TAACATCAAC
*
234782 ACCTACTCGTGGGAACTCCCCATGACACCAAATATAAGTCAGGGCTTCAAGTCCCCCTTT
1 ACCTACTCGTGGGAACTCCCCATGCCACCAAATATAAGTCAGGGCTTCAAGTCCCCCTTT
* * * * * * * * *
234842 ACCTACTTGTGGGAACTTCCTACT-CTACCGAATATAAGTCGGGGCTTTAGGTCTCCCTTT
1 ACCTACTCGTGGGAACTCCCCA-TGCCACCAAATATAAGTCAGGGCTTCAAGTCCCCCTTT
* * *
234902 TCCTACTCGTGGGAACTCCCCATGCCACCAAATATGAGTCAGGGCTTCAAGTCCCCTTTT
1 ACCTACTCGTGGGAACTCCCCATGCCACCAAATATAAGTCAGGGCTTCAAGTCCCCCTTT
234962 A
1 A
234963 TTATCAATTA
Statistics
Matches: 96, Mismatches: 23, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
59 1 0.01
60 94 0.98
61 1 0.01
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (60 bp):
ACCTACTCGTGGGAACTCCCCATGCCACCAAATATAAGTCAGGGCTTCAAGTCCCCCTTT
Found at i:236598 original size:11 final size:11
Alignment explanation
Indices: 236555--236589 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
236545 GATCTTTTCC
236555 TTATTTTAATA
1 TTATTTTAATA
*
236566 TTATTTTAATG
1 TTATTTTAATA
*
236577 TTATTTTATTA
1 TTATTTTAATA
236588 TT
1 TT
236590 TTAGTATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:237043 original size:2 final size:2
Alignment explanation
Indices: 237036--237067 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
237026 ATCAACCCAT
*
237036 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
237068 GATACAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:238654 original size:33 final size:32
Alignment explanation
Indices: 238611--238673 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 32
238601 ATTAAAACAA
238611 AAAATATTAAAATAAAATATATATTATAAAAATC
1 AAAATATTAAAATAAAATATA-A-TATAAAAATC
238645 AAAA-ATTAAAATAAAATATAATATAAAAA
1 AAAATATTAAAATAAAATATAATATAAAAA
238674 ATTAAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 8 0.28
32 1 0.03
33 16 0.55
34 4 0.14
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (32 bp):
AAAATATTAAAATAAAATATAATATAAAAATC
Found at i:238687 original size:24 final size:25
Alignment explanation
Indices: 238645--238730 Score: 75
Period size: 28 Copynumber: 3.2 Consensus size: 25
238635 TATAAAAATC
238645 AAAAATTAAAATAAAATATAATATA
1 AAAAATTAAAATAAAATATAATATA
**
238670 AAAAATTAAAATTTATATAATAT-ATGGA
1 AAAAATTAAAA--TA-A-AATATAATATA
238698 AAAGTAATTAAAATAAAATATATAATATA
1 AAA--AATTAAAAT-AAA-ATATAATATA
238727 AAAA
1 AAAA
238731 TTATATTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 16
0.71 0.06 0.24
Matches are distributed among these distances:
25 11 0.23
27 4 0.08
28 13 0.27
29 12 0.25
30 8 0.17
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.30
Consensus pattern (25 bp):
AAAAATTAAAATAAAATATAATATA
Found at i:238732 original size:26 final size:26
Alignment explanation
Indices: 238645--238733 Score: 69
Period size: 26 Copynumber: 3.3 Consensus size: 26
238635 TATAAAAATC
238645 AAAAATTAAAAT-AAA-ATATAATAT
1 AAAAATTAAAATAAAATATATAATAT
*
238669 AAAAAATTAAAATTTATATAATATATGGA-A-
1 -AAAAATTAAAA--TA-A-AATATAT-AATAT
*
238699 AAGTAATTAAAATAAAATATATAATAT
1 AA-AAATTAAAATAAAATATATAATAT
238726 AAAAATTA
1 AAAAATTA
238734 TATTAAAGAA
Statistics
Matches: 50, Mismatches: 4, Indels: 19
0.68 0.05 0.26
Matches are distributed among these distances:
25 12 0.24
26 13 0.26
27 4 0.08
28 2 0.04
29 3 0.06
30 10 0.20
31 5 0.10
32 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.31
Consensus pattern (26 bp):
AAAAATTAAAATAAAATATATAATAT
Found at i:238758 original size:33 final size:33
Alignment explanation
Indices: 238708--238793 Score: 104
Period size: 33 Copynumber: 2.6 Consensus size: 33
238698 AAAGTAATTA
*
238708 AAAT-AAAATATATAATATA-AAAATTATATTAAAG
1 AAATGAAAATA-A-AATATATAAAATTATAAT-AAG
* *
238742 AAATGAAAATAAAATATATAAGATTATAATAAT
1 AAATGAAAATAAAATATATAAAATTATAATAAG
238775 AAATGAAAATAAAATATAT
1 AAATGAAAATAAAATATAT
238794 GACATTAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
33 27 0.57
34 14 0.30
35 6 0.13
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (33 bp):
AAATGAAAATAAAATATATAAAATTATAATAAG
Found at i:239027 original size:15 final size:15
Alignment explanation
Indices: 239007--239046 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
238997 TGTTATTTTT
239007 CCTGCAATCATATTA
1 CCTGCAATCATATTA
*
239022 CCTGCAACCATATTA
1 CCTGCAATCATATTA
*
239037 CTTGCAATCA
1 CCTGCAATCA
239047 CATTCCTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.33, C:0.30, G:0.07, T:0.30
Consensus pattern (15 bp):
CCTGCAATCATATTA
Found at i:244866 original size:251 final size:252
Alignment explanation
Indices: 243537--245902 Score: 2721
Period size: 252 Copynumber: 9.4 Consensus size: 252
243527 ATAAAAGAGA
* * * *
243537 AATAACTAAATTTTAAATCTTAACATAAATATGTGAGAGTTAACATAACAAGTCAATTAAGTAAA
1 AATAATTAAATTTTAAATCTTAACGTAAGTATGTGAGAGTTAACGTAACAAGTCAATTAAGTAAA
********** * * * *
243602 AANNNNNNNNNNTTAATGAAAAGTAAATATTTAAATTTATATTCTTGGGCTAAAAGTATTTAATG
66 AACAATGTAAATTTAATGAAAAGTAAATATTTAAATTTATATTCTCGGGCTGAAAGTGTTTAACG
** *
243667 ATATAGTAATTTTAATTTTTAAATAAAAGATAATAAGGATAAAGATAATTATAGTTCAAAGTTGA
131 ATATAAAAATTTTAATTTTTAAATAAAAGATAATAAGGATAAAAATAATTATAGTTCAAAGTTGA
*
243732 CATGGAAAAGCCTTAGACGTAAAACTGTAAGAATTGACGTAAAAGCTTGTAAAGGTAG
196 CATGAAAAAGCCTT-GACGTAAAACTGTAAGAATTGACGTAAAAGCTTGTAAAGGTAG
* ** * *
243790 AACAATGCAATTTTAAATCTTAACGTAAGTATGTGAGACTTAATGTAACAAGTCAATTTAA-TAA
1 AATAATTAAATTTTAAATCTTAACGTAAGTATGTGAGAGTTAACGTAACAAGTCAA-TTAAGTAA
* * *
243854 AATCAATGTAAATTTAATGAAAAGTAAATATTTAAATTTATATTCTCAGGGTTGAAAGTATTTAA
65 AAACAATGTAAATTTAATGAAAAGTAAATATTTAAATTTATATTCTC-GGGCTGAAAGTGTTTAA
* *
243919 CGATGTAAAAATTTTACTTTTTAAATAAAAGATAATAAGGATAAAAATAATTATAGTTCAAAGTT
129 CGATATAAAAATTTTAATTTTTAAATAAAAGATAATAAGGATAAAAATAATTATAGTTCAAAGTT
* * *
243984 GACATGAAAAAGACTTGACGTAAAACTGTAAGAATTAACGTAAAAGCTTGTAAAAGT-G
194 GACATGAAAAAGCCTTGACGTAAAACTGTAAGAATTGACGTAAAAGCTTGTAAAGGTAG
*
244042 AAATAATTAAATTTTAAATCTTAACTTAAGTATGTGAGAGTTAACGTAACAAGTCAATTAAGTAA
1 -AATAATTAAATTTTAAATCTTAACGTAAGTATGTGAGAGTTAACGTAACAAGTCAATTAAGTAA
********** * * *
244107 AAANNNNNNNNNNTTAATGAAAAGTAAATATTTAAATTTATATTCTTGGGGCTAAAAGTGTTTTA
65 AAACAATGTAAATTTAATGAAAAGTAAATATTTAAATTTATATTC-TCGGGCTGAAAGTGTTTAA
* * *
244172 CGAT-TGAAAAATTTTAATTTTTAAAT-TAAGAATAATAAGAATAAAAATAATTATAGTTCAAAT
129 CGATAT-AAAAATTTTAATTTTTAAATAAAAG-ATAATAAGGATAAAAATAATTATAGTTCAAAG
* * * * * * * *
244235 TTGACATGAAAAAGGCTTGACATAAAACTGTATGAATAGATGTAGAAGCTTTTAAAGAT-G
192 TTGACATGAAAAAGCCTTGACGTAAAACTGTAAGAATTGACGTAAAAGCTTGTAAAGGTAG
* * * *
244295 AAATAATTAAAGTTTAAATCTTAATGTAAGTATATGAGAGTTAACATAACAAGTCAATTAAGTAA
1 -AATAATTAAATTTTAAATCTTAACGTAAGTATGTGAGAGTTAACGTAACAAGTCAATTAAGTAA
* ********** *
244360 AAATAATGTAAATTTAATGAAAAGTAAATNNNNNNNNNNATATTATCGGGCTGAAAGTGTTTAAC
65 AAACAATGTAAATTTAATGAAAAGTAAATATTTAAATTTATATTCTCGGGCTGAAAGTGTTTAAC
* *
244425 GATATAAAAATTTTAATTTCTAAAT-TAAGAATAATAAGGATAAAAATAATTATAGTTCAAAGTT
130 GATATAAAAATTTTAATTTTTAAATAAAAG-ATAATAAGGATAAAAATAATTATAGTTCAAAGTT
* * * * * * ******
244489 AATATCG-AAAAGCCTTAACGTAAAACTTTAAGAATTGACGTAAAAACTTATAANNNNNN
194 GACAT-GAAAAAGCCTTGACGTAAAACTGTAAGAATTGACGTAAAAGCTTGTAAAGGTAG
**** * * * * * *
244548 NNNNACTAAATTTTAAATCTTAACGTAAGTGTGTGAGAGTTGACGTGACAAGTCAATCAAATAAA
1 AATAATTAAATTTTAAATCTTAACGTAAGTATGTGAGAGTTAACGTAACAAGTCAATTAAGTAAA
* *
244613 AACAATGTAAATTTAATGAAAAGTAAATATTTAAATTTATATTCTCGAGCTGAAAGTGTTTAACA
66 AACAATGTAAATTTAATGAAAAGTAAATATTTAAATTTATATTCTCGGGCTGAAAGTGTTTAACG
** * *
244678 ATATACCAATTTTAATTTTTAAATAAAAGATAATAAGGAT-AAAATAATTAAAGTTCAAAATTGA
131 ATATAAAAATTTTAATTTTTAAATAAAAGATAATAAGGATAAAAATAATTATAGTTCAAAGTTGA
* * * *
244742 CATGAAAAAGTCTTGACATAAAATTGTAAGAATTGACATAAAAGCTTGTAAAGGTAG
196 CATGAAAAAGCCTTGACGTAAAACTGTAAGAATTGACGTAAAAGCTTGTAAAGGTAG
* * * * * * * *
244799 AACAATTGAATTTTAAATCTCAACGTAAATATGTGAGAGTTGACGTGATATGTCAATTAAGTAAA
1 AATAATTAAATTTTAAATCTTAACGTAAGTATGTGAGAGTTAACGTAACAAGTCAATTAAGTAAA
* ** * *
244864 AACAATGTAAATTTAATGAAAAGCAAATATTTAAATTTATATTCTTAGGCTGAAATTGTTTAATG
66 AACAATGTAAATTTAATGAAAAGTAAATATTTAAATTTATATTCTCGGGCTGAAAGTGTTTAACG
* *
244929 ATATAAAAATTTTAATTTTTAAATAAAA-AAAATAAAGATAAAAATAATTATAGTTCAAAGTTGA
131 ATATAAAAATTTTAATTTTTAAATAAAAGATAATAAGGATAAAAATAATTATAGTTCAAAGTTGA
*** * ** *
244993 CAT-AAAAAAATTTGACGTAAAACTGTAATAATTGATATAAAAGCTTGTAAAGGTGG
196 CATGAAAAAGCCTTGACGTAAAACTGTAAGAATTGACGTAAAAGCTTGTAAAGGTAG
* * ** *
245049 AATAATTAAATTTTAAATCTTAACGTAAGTCTGTGAGATTTAATATAATAAGTCAATTAAGTAAA
1 AATAATTAAATTTTAAATCTTAACGTAAGTATGTGAGAGTTAACGTAACAAGTCAATTAAGTAAA
* * * * *
245114 AACAATGTAAATTTAATGAAAAGTAAATATTTAAATTTTTATTCTTGGACTAAAAGTGTTTAATG
66 AACAATGTAAATTTAATGAAAAGTAAATATTTAAATTTATATTCTCGGGCTGAAAGTGTTTAACG
* * * *
245179 TTATAAAAATTTTAATTTTTAATTAAAAAATAATAAAGATAAAAATAATTATAGTTCAAAGTTGA
131 ATATAAAAATTTTAATTTTTAAATAAAAGATAATAAGGATAAAAATAATTATAGTTCAAAGTTGA
* * *
245244 CATGGAAAAGTCC-TGACGTAAAACTGTAAGAATTGACAT-AAAGCTTATAAAGGTTA-
196 CATGAAAAAG-CCTTGACGTAAAACTGTAAGAATTGACGTAAAAGCTTGTAAAGG-TAG
* * * * * * *
245300 AATAATGAAATATTAAATCTTAACGTAAGTGTATGAAACTTAACATAACAAGTCAATTAAGTAAA
1 AATAATTAAATTTTAAATCTTAACGTAAGTATGTGAGAGTTAACGTAACAAGTCAATTAAGTAAA
* * *
245365 AATAATGTAAATTTAATGAAAAATAAATAGTTAAATTTATATTCTCGGGCTGAAAGTGTTTAACG
66 AACAATGTAAATTTAATGAAAAGTAAATATTTAAATTTATATTCTCGGGCTGAAAGTGTTTAACG
* * *
245430 ATATACAAATTTTAATTTTTAAATAAAAGATAATAAGGTTAAAAATAATTATAGTTCAAAATTGA
131 ATATAAAAATTTTAATTTTTAAATAAAAGATAATAAGGATAAAAATAATTATAGTTCAAAGTTGA
* * *
245495 CGTGAAAAAGCCATG-CTGTAAAATTGTATA-AATTGACGTAAAAGCTTGTAAAGGTAG
196 CATGAAAAAGCCTTGAC-GTAAAACTGTA-AGAATTGACGTAAAAGCTTGTAAAGGTAG
* * *
245552 AATAACTAAATTTTAAATCTTAACATAAGTGTGTGAGAGTTAACGTAACAAGTCAATTAAGTAAA
1 AATAATTAAATTTTAAATCTTAACGTAAGTATGTGAGAGTTAACGTAACAAGTCAATTAAGTAAA
* * * ** * * *
245617 AATAATATAAATTTAATGAAAAGTAAATACTTAAATTTATATTCTCAAGTTTAGAGTGTTTAACG
66 AACAATGTAAATTTAATGAAAAGTAAATATTTAAATTTATATTCTCGGGCTGAAAGTGTTTAACG
* * ** * * *
245682 ATATAAAAATTTTAATTGTTAAAT-TAAGAATAGCAAGTATAAAAATAATTATAGTTTAAACTTG
131 ATATAAAAATTTTAATTTTTAAATAAAAG-ATAATAAGGATAAAAATAATTATAGTTCAAAGTTG
* * * * * *
245746 ACATAAAAAAGCCTTGACGTAAAACTGTATGAATTGACATAAAAACTTATTAAGGTAG
195 ACATGAAAAAGCCTTGACGTAAAACTGTAAGAATTGACGTAAAAGCTTGTAAAGGTAG
* * * * * * *
245804 AATAATTAAAATTTAAATTTTAACATAACTATGTGAGAGTTAACCTAATAAGTTAATTAAGTAAA
1 AATAATTAAATTTTAAATCTTAACGTAAGTATGTGAGAGTTAACGTAACAAGTCAATTAAGTAAA
245869 AACAATGTAAATTTAATGAAAAGTAAATATTTAA
66 AACAATGTAAATTTAATGAAAAGTAAATATTTAA
245903 NNNNNNNNNN
Statistics
Matches: 1785, Mismatches: 303, Indels: 51
0.83 0.14 0.02
Matches are distributed among these distances:
250 197 0.11
251 478 0.27
252 600 0.34
253 417 0.23
254 93 0.05
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.33
Consensus pattern (252 bp):
AATAATTAAATTTTAAATCTTAACGTAAGTATGTGAGAGTTAACGTAACAAGTCAATTAAGTAAA
AACAATGTAAATTTAATGAAAAGTAAATATTTAAATTTATATTCTCGGGCTGAAAGTGTTTAACG
ATATAAAAATTTTAATTTTTAAATAAAAGATAATAAGGATAAAAATAATTATAGTTCAAAGTTGA
CATGAAAAAGCCTTGACGTAAAACTGTAAGAATTGACGTAAAAGCTTGTAAAGGTAG
Found at i:250849 original size:252 final size:251
Alignment explanation
Indices: 250405--251889 Score: 1789
Period size: 252 Copynumber: 5.9 Consensus size: 251
250395 NNNNNNNNNN
* * *
250405 AATTTAATGAAAAGTAAATATTTAAATTTATATTATCGGGCTGAAAGTGTTTAATGATATAAAAT
1 AATTTAATGAAAAGTAAATATTTAAATTTATATTCTCGAGCTGAAAGTGTTTAACGATATAAAAT
* * * *
250470 TTTAATTTTTAAAT-TAAGAATAATAAGGATAACAATAATTATAGTTCAAAGTTGA-TATCG-AA
66 TTTAATTTTTAAATAAAAG-ATAATAAGGATAAAAATAATTAAAGTTCAAAATTGACT-T-GAAA
* * * * *
250532 AAGCCTTGACGTAAAACCT-TAAGAATTGACAGAAAAAATTTTCAAGGTGGAATAACTAAATTTT
128 AAGCCTTGACATAAAA-CTATAAGAATTGACATAAAAACTTGTAAAGGTGGAATAACTAAATTTT
* * * * *
250596 AAATTTTAACGTAAATGTGTGAGAGTTGACGTGACAAGTCAATTAAGTAAAAATAATGTA
192 AAATCTTAACGTAAGTGTGTGAGAGTTAACGTAACAAGTCAATTAAGTAAAAACAATGTA
* *
250656 AATTTAATGAAAAGTAAATATTTGAATTTATATTCTCGAGCTGAAAGTATTTAACGATATAGAAA
1 AATTTAATGAAAAGTAAATATTTAAATTTATATTCTCGAGCTGAAAGTGTTTAACGATATA-AAA
* * *
250721 TTTTAATTTTTAAATAAATGATAGTAAGGATAAAAATAATTAAAGTTTAAAATTGACTTGAAAAA
65 TTTTAATTTTTAAATAAAAGATAATAAGGATAAAAATAATTAAAGTTCAAAATTGACTTGAAAAA
** * *
250786 GCCTTGACATAAAACTATAAGAATTGA-AGTAAAAGTTTGTAAATGTGGAATAATTAAATTTTAA
130 GCCTTGACATAAAACTATAAGAATTGACA-TAAAAACTTGTAAAGGTGGAATAACTAAATTTTAA
* * * * * *
250850 ATCTCAACGTAAATGTGAGAGAGTTGACGTGACAAGTCAATTAAGTAAAAACAATATA
194 ATCTTAACGTAAGTGTGTGAGAGTTAACGTAACAAGTCAATTAAGTAAAAACAATGTA
*
250908 AATTTAATGAAAAGTAAATATTTAAATTTATATTCTCTG-GCTGAAAGTGTTTAATGATATATAA
1 AATTTAATGAAAAGTAAATATTTAAATTTATATTCTC-GAGCTGAAAGTGTTTAACGATATA-AA
*
250972 ATTTTAATTTTTAAATAAAAGATAATAAGGATAAAAATAATTAAAGTTCAAAATTGACATGAAAA
64 ATTTTAATTTTTAAATAAAAGATAATAAGGATAAAAATAATTAAAGTTCAAAATTGACTTGAAAA
* * * * *
251037 AGCCTTGACATAAAACTGTAAGAATTGACATAAAAGCTTGTAAAAGTGAAATAATTAAATTTTAA
129 AGCCTTGACATAAAACTATAAGAATTGACATAAAAACTTGTAAAGGTGGAATAACTAAATTTTAA
*
251102 ATCTTAACGTAAGTGTGTGAGAGTTAACGTAACAAGTGAATTAAGTAAAAACAATGTA
194 ATCTTAACGTAAGTGTGTGAGAGTTAACGTAACAAGTCAATTAAGTAAAAACAATGTA
* *
251160 AATTTAATGAAAAGTAAATATTTAAATTTATATTTTC-AGGTTGAAAGTGTTTAACGATATAAAA
1 AATTTAATGAAAAGTAAATATTTAAATTTATATTCTCGA-GCTGAAAGTGTTTAACGATAT-AAA
* * * * *
251224 ATTTTAATTTTTAAATAAAAGATAACAAGGATAAAAATGATTATAGCTCAAAATTGACATAGAAA
64 ATTTTAATTTTTAAATAAAAGATAATAAGGATAAAAATAATTAAAGTTCAAAATTGAC-TTGAAA
* * * * * * *
251289 TA-TCTTGACATAAAATTGTAAGAATTGATATAAGAACTTGTAAAGGTGGAATAACAAAATTTTA
128 AAGCCTTGACATAAAACTATAAGAATTGACATAAAAACTTGTAAAGGTGGAATAACTAAATTTTA
* *
251353 AATCTTAACGTAAGTGTGAGAGAGTTAACGTAACAAGTCAATTAAGTAAAAACAATATA
193 AATCTTAACGTAAGTGTGTGAGAGTTAACGTAACAAGTCAATTAAGTAAAAACAATGTA
* * * * *
251412 AATTTAGTAAAAAGAAAATATTTAAATTTATATTCTTG-GTTTGAAA-TGTTTAACGATATAAAA
1 AATTTAATGAAAAGTAAATATTTAAATTTATATTCTCGAG-CTGAAAGTGTTTAACGATAT-AAA
* * * * *
251475 ATTTTAATTTTTAAATAAAAGATAATGAGGATAAAAGTAATTATAGTTCAAAATTGGCATGAAAA
64 ATTTTAATTTTTAAATAAAAGATAATAAGGATAAAAATAATTAAAGTTCAAAATTGACTTG-AAA
* * * * *
251540 AAACATTGACGTAAAACTATAAGAATTGATATAAAAACTTGTGAAGGTGGAATAACTAAATTTTA
128 AAGCCTTGACATAAAACTATAAGAATTGACATAAAAACTTGTAAAGGTGGAATAACTAAATTTTA
*
251605 AATCTTAACGTAAGTGTGTGAGAGTTAACATAACAAGTCAATTAAGTAAAAACAATGTA
193 AATCTTAACGTAAGTGTGTGAGAGTTAACGTAACAAGTCAATTAAGTAAAAACAATGTA
* * *
251664 AATTTAATG-AAAGAAAATATTTAAATTTATATTTTC-AGGCTAAAAGTGTTTAACGATATAATA
1 AATTTAATGAAAAGTAAATATTTAAATTTATATTCTCGA-GCTGAAAGTGTTTAACGATATAA-A
* * * *
251727 TTTTTAATTTTTAAATTAAAA-ATAATAAAGATAAAAATTAATTATAA-TTTAAAATT-ACTATT
64 ATTTTAATTTTTAAA-TAAAAGATAATAAGGATAAAAA-TAATTA-AAGTTCAAAATTGACT-TG
* * * ** * * * * * * * *
251789 AGAAGAG-TTTAATGTAAAATTGTTAGAATTGACGTAAAATCTTATGAAGGTGTAATAAAC-AAA
125 A-AAAAGCCTTGACATAAAACTATAAGAATTGACATAAAAACTTGTAAAGGTGGAAT-AACTAAA
* * * *
251852 TTTAAAATCTTAACGTAAATGTGTTAAAGTTAACGTAA
188 TTTTAAATCTTAACGTAAGTGTGTGAGAGTTAACGTAA
251890 TTAGTGATAA
Statistics
Matches: 1084, Mismatches: 124, Indels: 51
0.86 0.10 0.04
Matches are distributed among these distances:
250 1 0.00
251 165 0.15
252 880 0.81
253 37 0.03
254 1 0.00
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (251 bp):
AATTTAATGAAAAGTAAATATTTAAATTTATATTCTCGAGCTGAAAGTGTTTAACGATATAAAAT
TTTAATTTTTAAATAAAAGATAATAAGGATAAAAATAATTAAAGTTCAAAATTGACTTGAAAAAG
CCTTGACATAAAACTATAAGAATTGACATAAAAACTTGTAAAGGTGGAATAACTAAATTTTAAAT
CTTAACGTAAGTGTGTGAGAGTTAACGTAACAAGTCAATTAAGTAAAAACAATGTA
Found at i:251862 original size:756 final size:755
Alignment explanation
Indices: 250405--251889 Score: 1977
Period size: 756 Copynumber: 2.0 Consensus size: 755
250395 NNNNNNNNNN
* *
250405 AATTTAATGAAAAGTAAATATTTAAATTTATATTATCGGGCTGAAAGTGTTTAATGATATAAAAT
1 AATTTAATGAAAAGTAAATATTTAAATTTATATTATCAGGCTGAAAGTGTTTAACGATATAAAAT
* * * * * * *
250470 TTTAATTTTTAAATTAAGAATAATAAGGATAACAATAATTATAGTTCAAAGTTGATATCGAAAAG
66 TTTAATTTTTAAATAAAGAATAACAAGGATAAAAATAATTATAGCTCAAAATTGACATAGAAAAG
* * * *
250535 CCTTGACGTAAAACCTTAAGAATTGACAGAAAAAATTTTCAAGGTGGAATAACTAAATTTTAAAT
131 CCTTGACATAAAACCTTAAGAATTGACAGAAAAAATTGTAAAGGTGGAATAACAAAATTTTAAAT
* * * * * * *
250600 TTTAACGTAAATGTGTGAGAGTTGACGTGACAAGTCAATTAAGTAAAAATAATGTAAATTTAATG
196 CTTAACGTAAATGTGAGAGAGTTAACGTAACAAGTCAATTAAGTAAAAACAATATAAATTTAATA
* * *
250665 AAAAGTAAATATTTGAATTTATATTCTCGAGCTGAAAGTATTTAACGATATAGAAATTTTAATTT
261 AAAAGAAAATATTTAAATTTATATTCTCGAGCTGAAAGTATTTAACGATATAAAAATTTTAATTT
* * * * * *
250730 TTAAATAAATGATAGTAAGGATAAAAATAATTAAAGTTTAAAATTGACTTGAAAAAGCCTTGACA
326 TTAAATAAAAGATAATAAGGATAAAAATAATTAAAGTTCAAAATTGACATGAAAAAACATTGACA
** * *
250795 TAAAACTATAAGAATTGAAGTAAAAGTTTGTAAATGTGGAATAATTAAATTTTAAATCTCAACGT
391 TAAAACTATAAGAATTGAAGTAAAAACTTGTAAAGGTGGAATAACTAAATTTTAAATCTCAACGT
* * * *
250860 AAATGTGAGAGAGTTGACGTGACAAGTCAATTAAGTAAAAACAATATAAATTTAATGAAAAGTAA
456 AAATGTGAGAGAGTTAACATAACAAGTCAATTAAGTAAAAACAATATAAATTTAATGAAAAGAAA
* * *
250925 ATATTTAAATTTATATTCTCTGGCTGAAAGTGTTTAATGATATATAAATTTTAATTTTTAAATAA
521 ATATTTAAATTTATATTCTCAGGCTAAAAGTGTTTAACGATATATAAATTTTAATTTTTAAATAA
* *
250990 AAGATAATAAGGATAAAAATAATTAAAGTTCAAAATTGACATGAAAAAGCCTTGACATAAAACTG
586 AAGATAATAAAGATAAAAATAATTAAAGTTCAAAATTGACATGAAAAAGCCTTAACATAAAACTG
* ** * *
251055 TAAGAATTGACATAAAAGCTTGTAAAAGTGAAATAATTAAATTTTAAATCTTAACGTAAGTGTGT
651 TAAGAATTGACATAAAAGCTTATAAAAGTGAAATAAACAAATTTAAAATCTTAACGTAAATGTGT
*
251120 GAGAGTTAACGTAACAAGTGAATTAAGTAAAAACAATGTA
716 GAAAGTTAACGTAACAAGTGAATTAAGTAAAAACAATGTA
* *
251160 AATTTAATGAAAAGTAAATATTTAAATTTATATTTTCAGGTTGAAAGTGTTTAACGATATAAAAA
1 AATTTAATGAAAAGTAAATATTTAAATTTATATTATCAGGCTGAAAGTGTTTAACGATAT-AAAA
*
251225 TTTTAATTTTTAAATAAA-AGATAACAAGGATAAAAATGATTATAGCTCAAAATTGACATAGAAA
65 TTTTAATTTTTAAATAAAGA-ATAACAAGGATAAAAATAATTATAGCTCAAAATTGACATAGAAA
* * * * * *
251289 TA-TCTTGACATAAAA-TTGTAAGAATTGATATAAGAACTTGTAAAGGTGGAATAACAAAATTTT
129 -AGCCTTGACATAAAACCT-TAAGAATTGACAGAAAAAATTGTAAAGGTGGAATAACAAAATTTT
*
251352 AAATCTTAACGTAAGTGTGAGAGAGTTAACGTAACAAGTCAATTAAGTAAAAACAATATAAATTT
192 AAATCTTAACGTAAATGTGAGAGAGTTAACGTAACAAGTCAATTAAGTAAAAACAATATAAATTT
* * * *
251417 AGTAAAAAGAAAATATTTAAATTTATATTCTTG-GTTTGAAA-TGTTTAACGATATAAAAATTTT
257 AATAAAAAGAAAATATTTAAATTTATATTCTCGAG-CTGAAAGTATTTAACGATATAAAAATTTT
* * * *
251480 AATTTTTAAATAAAAGATAATGAGGATAAAAGTAATTATAGTTCAAAATTGGCATGAAAAAAACA
321 AATTTTTAAATAAAAGATAATAAGGATAAAAATAATTAAAGTTCAAAATTGACATG-AAAAAACA
* *
251545 TTGACGTAAAACTATAAGAATTGATA-TAAAAACTTGTGAAGGTGGAATAACTAAATTTTAAATC
385 TTGACATAAAACTATAAGAATTGA-AGTAAAAACTTGTAAAGGTGGAATAACTAAATTTTAAATC
* * * *
251609 TTAACGTAAGTGTGTGAGAGTTAACATAACAAGTCAATTAAGTAAAAACAATGTAAATTTAATG-
449 TCAACGTAAATGTGAGAGAGTTAACATAACAAGTCAATTAAGTAAAAACAATATAAATTTAATGA
* *
251673 AAAGAAAATATTTAAATTTATATTTTCAGGCTAAAAGTGTTTAACGATATA-ATATTTTTAATTT
514 AAAGAAAATATTTAAATTTATATTCTCAGGCTAAAAGTGTTTAACGATATATA-AATTTTAATTT
* * * *
251737 TTAAATTAAAA-ATAATAAAGATAAAAATTAATTATAA-TTTAAAATT-ACTATTAGAAGAG-TT
578 TTAAA-TAAAAGATAATAAAGATAAAAA-TAATTA-AAGTTCAAAATTGAC-ATGA-AAAAGCCT
** * * * * * * *
251798 TAATGTAAAATTGTTAGAATTGACGTAAAATCTTATGAAGGTGTAATAAACAAATTTAAAATCTT
638 TAACATAAAACTGTAAGAATTGACATAAAAGCTTATAAAAGTGAAATAAACAAATTTAAAATCTT
*
251863 AACGTAAATGTGTTAAAGTTAACGTAA
703 AACGTAAATGTGTGAAAGTTAACGTAA
251890 TTAGTGATAA
Statistics
Matches: 629, Mismatches: 88, Indels: 25
0.85 0.12 0.03
Matches are distributed among these distances:
754 1 0.00
755 205 0.33
756 415 0.66
757 8 0.01
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (755 bp):
AATTTAATGAAAAGTAAATATTTAAATTTATATTATCAGGCTGAAAGTGTTTAACGATATAAAAT
TTTAATTTTTAAATAAAGAATAACAAGGATAAAAATAATTATAGCTCAAAATTGACATAGAAAAG
CCTTGACATAAAACCTTAAGAATTGACAGAAAAAATTGTAAAGGTGGAATAACAAAATTTTAAAT
CTTAACGTAAATGTGAGAGAGTTAACGTAACAAGTCAATTAAGTAAAAACAATATAAATTTAATA
AAAAGAAAATATTTAAATTTATATTCTCGAGCTGAAAGTATTTAACGATATAAAAATTTTAATTT
TTAAATAAAAGATAATAAGGATAAAAATAATTAAAGTTCAAAATTGACATGAAAAAACATTGACA
TAAAACTATAAGAATTGAAGTAAAAACTTGTAAAGGTGGAATAACTAAATTTTAAATCTCAACGT
AAATGTGAGAGAGTTAACATAACAAGTCAATTAAGTAAAAACAATATAAATTTAATGAAAAGAAA
ATATTTAAATTTATATTCTCAGGCTAAAAGTGTTTAACGATATATAAATTTTAATTTTTAAATAA
AAGATAATAAAGATAAAAATAATTAAAGTTCAAAATTGACATGAAAAAGCCTTAACATAAAACTG
TAAGAATTGACATAAAAGCTTATAAAAGTGAAATAAACAAATTTAAAATCTTAACGTAAATGTGT
GAAAGTTAACGTAACAAGTGAATTAAGTAAAAACAATGTA
Found at i:267893 original size:17 final size:17
Alignment explanation
Indices: 267871--267903 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
267861 CTTCATAGAG
267871 AAAAAATTCTTAGTGCT
1 AAAAAATTCTTAGTGCT
*
267888 AAAAAATTTTTAGTGC
1 AAAAAATTCTTAGTGC
267904 GTGCATACAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (17 bp):
AAAAAATTCTTAGTGCT
Found at i:273669 original size:2 final size:2
Alignment explanation
Indices: 273662--273692 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
273652 AAATAAATAA
273662 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
273693 GATGAAATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:275031 original size:23 final size:23
Alignment explanation
Indices: 274977--275031 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
274967 GAACCAAAAC
*
274977 TTTGATTTGTTTGATTGTAGATA
1 TTTGATTTTTTTGATTGTAGATA
* *
275000 CTTGATTTTTTTTATTGTAGATA
1 TTTGATTTTTTTGATTGTAGATA
275023 TTTGATTTT
1 TTTGATTTT
275032 GATTAATACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.20, C:0.02, G:0.16, T:0.62
Consensus pattern (23 bp):
TTTGATTTTTTTGATTGTAGATA
Found at i:278912 original size:12 final size:14
Alignment explanation
Indices: 278878--278906 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
278868 TTATTTCTTT
278878 TAAAAAATATAACA
1 TAAAAAATATAACA
278892 TAAAAAATAT-ACA
1 TAAAAAATATAACA
278905 TA
1 TA
278907 CAAATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAAAAATATAACA
Found at i:279829 original size:22 final size:22
Alignment explanation
Indices: 279787--279830 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
279777 AATTTTATTA
* *
279787 TTTATTATTTATTATTTTAATT
1 TTTATTATTTATTAATATAATT
279809 TTTATATATTT-TTAATATAATT
1 TTTAT-TATTTATTAATATAATT
279831 AATTATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTATTATTTATTAATATAATT
Found at i:280697 original size:15 final size:15
Alignment explanation
Indices: 280679--280720 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
280669 CGTTATTGGC
* *
280679 TAAGATGTTACTATT
1 TAAGGTGTTACTAAT
*
280694 TAAGGTATTACTAAT
1 TAAGGTGTTACTAAT
280709 TAAGGTGTTACT
1 TAAGGTGTTACT
280721 GGCCGAGGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (15 bp):
TAAGGTGTTACTAAT
Found at i:281028 original size:35 final size:35
Alignment explanation
Indices: 280947--281037 Score: 92
Period size: 35 Copynumber: 2.6 Consensus size: 35
280937 ACTATTTTAT
* * * * *
280947 GCAAAACAACTAAAACAATTGAAGTGCTACTTCAT
1 GCAAAAAAATTAAAACGAGTGAAGTGCTACTTCAC
* * *
280982 GCAGAATAATTAGAACGAGTGAAGTGCTACTTCAC
1 GCAAAAAAATTAAAACGAGTGAAGTGCTACTTCAC
* *
281017 GTAAAAAAATTAAAATGAGTG
1 GCAAAAAAATTAAAACGAGTG
281038 GAGCACTACT
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.23
Consensus pattern (35 bp):
GCAAAAAAATTAAAACGAGTGAAGTGCTACTTCAC
Found at i:281346 original size:29 final size:29
Alignment explanation
Indices: 281314--281379 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
281304 ATCATATCTA
281314 TTCACGTACAGCTTT-TTCTATTGTACATG
1 TTCACGTACAG-TTTCTTCTATTGTACATG
* * * *
281343 TTCACATACAGTTTCTTCTCTTGTACCTT
1 TTCACGTACAGTTTCTTCTATTGTACATG
281372 TTCACGTA
1 TTCACGTA
281380 TACCTCATCT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 3 0.10
29 28 0.90
ACGTcount: A:0.20, C:0.24, G:0.11, T:0.45
Consensus pattern (29 bp):
TTCACGTACAGTTTCTTCTATTGTACATG
Found at i:290592 original size:34 final size:37
Alignment explanation
Indices: 290548--290779 Score: 154
Period size: 40 Copynumber: 6.0 Consensus size: 37
290538 TGATAATATT
* *
290548 TAAATTTAAATAATCAAAACAAATAT-T-TTA-AACA
1 TAAACTTAAATAATCAAAACAAATATCTATAACAACA
*
290582 TAAACTTAAATAACTAAAAACAAATATCCATATAACAACA
1 TAAACTTAAATAA-TCAAAACAAATAT-C-TATAACAACA
* *
290622 TAAACTTAAATAA-CTAAACACAAATATCCAAATAATAACA
1 TAAACTTAAATAATC-AAA-ACAAATAT-C-TATAACAACA
* * *
290662 TAAACTTAAATAA-CTAAACACAAAGATCCAAACAAACAACA
1 TAAACTTAAATAATC-AAA-ACAAATAT-C-TA-TAACAACA
* *
290703 TAAACTTAAATAA-CTAAACACAAATATCCAAATAACAACT
1 TAAACTTAAATAATC-AAA-ACAAATAT-C-TATAACAACA
* *
290743 TAAACTTAAATAATTAAAAACAAATATCCA-AACAACA
1 TAAACTTAAATAA-TCAAAACAAATATCTATAACAACA
290780 ACTTAAACAA
Statistics
Matches: 172, Mismatches: 15, Indels: 19
0.83 0.07 0.09
Matches are distributed among these distances:
34 12 0.07
35 12 0.07
37 6 0.03
38 2 0.01
39 6 0.03
40 94 0.55
41 40 0.23
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.22
Consensus pattern (37 bp):
TAAACTTAAATAATCAAAACAAATATCTATAACAACA
Found at i:290622 original size:40 final size:40
Alignment explanation
Indices: 290578--290787 Score: 321
Period size: 40 Copynumber: 5.2 Consensus size: 40
290568 AAATATTTTA
* *
290578 AACATAAACTTAAATAACTAAAAACAAATATCCATATAAC
1 AACATAAACTTAAATAACTAAACACAAATATCCAAATAAC
*
290618 AACATAAACTTAAATAACTAAACACAAATATCCAAATAAT
1 AACATAAACTTAAATAACTAAACACAAATATCCAAATAAC
* *
290658 AACATAAACTTAAATAACTAAACACAAAGATCCAAACAAAC
1 AACATAAACTTAAATAACTAAACACAAATATCCAAA-TAAC
290699 AACATAAACTTAAATAACTAAACACAAATATCCAAATAAC
1 AACATAAACTTAAATAACTAAACACAAATATCCAAATAAC
* * * *
290739 AACTTAAACTTAAATAATTAAAAACAAATATCCAAACAAC
1 AACATAAACTTAAATAACTAAACACAAATATCCAAATAAC
*
290779 AACTTAAAC
1 AACATAAAC
290788 AACATTAGAA
Statistics
Matches: 157, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 120 0.76
41 37 0.24
ACGTcount: A:0.60, C:0.19, G:0.00, T:0.20
Consensus pattern (40 bp):
AACATAAACTTAAATAACTAAACACAAATATCCAAATAAC
Found at i:290727 original size:81 final size:80
Alignment explanation
Indices: 290578--290787 Score: 339
Period size: 81 Copynumber: 2.6 Consensus size: 80
290568 AAATATTTTA
* *
290578 AACATAAACTTAAATAACTAAAAACAAATATCCATATAACAACATAAACTTAAATAACTAAACAC
1 AACATAAACTTAAATAACTAAAAACAAATATCCAAACAACAACATAAACTTAAATAACTAAACAC
*
290643 AAATATCCAAATAAT
66 AAATATCCAAATAAC
* *
290658 AACATAAACTTAAATAACTAAACACAAAGATCCAAACAAACAACATAAACTTAAATAACTAAACA
1 AACATAAACTTAAATAACTAAAAACAAATATCCAAAC-AACAACATAAACTTAAATAACTAAACA
290723 CAAATATCCAAATAAC
65 CAAATATCCAAATAAC
* * *
290739 AACTTAAACTTAAATAATTAAAAACAAATATCCAAACAACAACTTAAAC
1 AACATAAACTTAAATAACTAAAAACAAATATCCAAACAACAACATAAAC
290788 AACATTAGAA
Statistics
Matches: 119, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
80 44 0.37
81 75 0.63
ACGTcount: A:0.60, C:0.19, G:0.00, T:0.20
Consensus pattern (80 bp):
AACATAAACTTAAATAACTAAAAACAAATATCCAAACAACAACATAAACTTAAATAACTAAACAC
AAATATCCAAATAAC
Found at i:294679 original size:32 final size:32
Alignment explanation
Indices: 294628--294696 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
294618 ACCCTTAATA
*
294628 TATTATTATTAAATTATAAAAATCAATACTAT
1 TATTATTATTAAATAATAAAAATCAATACTAT
* * * *
294660 TATTATTTTTTAATAATAAAAATTAATATTAT
1 TATTATTATTAAATAATAAAAATCAATACTAT
294692 T-TTAT
1 TATTAT
294697 GATTTAGTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 4 0.12
32 28 0.88
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (32 bp):
TATTATTATTAAATAATAAAAATCAATACTAT
Found at i:294844 original size:15 final size:15
Alignment explanation
Indices: 294824--294861 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
294814 TAGATATATA
294824 TTATAATTAATAA-TT
1 TTATAATT-ATAATTT
294839 TTATAAGTTATAATTT
1 TTATAA-TTATAATTT
294855 TTATAAT
1 TTATAAT
294862 GTTAACGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTATAATTATAATTT
Found at i:295383 original size:339 final size:340
Alignment explanation
Indices: 294817--295792 Score: 1151
Period size: 339 Copynumber: 2.9 Consensus size: 340
294807 GTGTGCGTAG
*
294817 ATATATATTATAATTAATAATTTTATAAGTTATAATTTTTATAATGTTAACGTAAAATAAAAAGT
1 ATATATATTATAATTAATAATTTTATAAGTTATAATTTTT-TAATGTTAACATAAAATAAAAAGT
* * *
294882 AAATATATTTATAATTAAAGT-ATATATATATTAAAAGTATTTTAGTATATATATAACCA-TAAT
65 AAATATATTTATATTTAAAGTAATATATACATTAAAAGTATTTTAGTATATATATAA-TAGTAAT
* * **
294945 TATATTTTTTATAAATGAACCCAATATATATAACA-TATAGATATTAACAAACATTACAAATTAA
129 TATATTCTTTATAAATGAACCCAATATATATAA-AGTA-ATATATTAA-AAACATTACAAGGTAA
* * * * **
295009 TTAATAATCATAGTTTTATTAA-TTACTTTAATTAATTATATGGGTTTCTCCTTAATTTTATGAA
191 TTAATAATCATAGTTTCATGAATTTA-TTTAATTAATTATATGGGTTTGTCTTTAATTACATGAA
* ** * *
295073 ATT-AAAAAAAATAACTAAGCTTCAAAACTATTCTAATTTCTTAACTTCTTTTTA-G-ATA-ATT
255 ATTAAAAAAAAATAACT-AGCTTCAAAACTATTCTAATCTCACAACTTCTCTTAAGGTATATATT
295134 A-A-GTTTATATAAACAAAGGT
319 ATAGGTTTATATAAACAAAGGT
* *
295154 ATATATATTATAATTAATAATTGTATAAGTTATAATTTTTGTAATGTTAACACAAAATAAAATA-
1 ATATATATTATAATTAATAATTTTATAAGTTATAATTTTT-TAATGTTAACATAAAATAAAA-AG
* * * *
295218 TAAATATATTTATATTTAAAGTACACACACACATTAAAAGTATTTTAGTATATGTATAATAGTAA
64 TAAATATATTTATATTTAAAGTA-ATATATACATTAAAAGTATTTTAGTATATATATAATAGTAA
295283 TTATATTCTTTATAAATGAACCCAATATATATAAAGTAAATATATTAAAAGACATTACAAGGTAA
128 TTATATTCTTTATAAATGAACCCAATATATATAAAGT-AATATATTAAAA-ACATTACAAGGTAA
* * * * *
295348 TTAATAATTATACTTTCATGAATTTATTTAATTAATTATTTGAGTTTGTCTTTAATTACAAGAAA
191 TTAATAATCATAGTTTCATGAATTTATTTAATTAATTATATGGGTTTGTCTTTAATTACATGAAA
* * * * *
295413 TTAAAAAAAAATAACTAGGTTTAGAAATTATTTTAATCTCACAACTTCTCTTAAGGTTTTTATAT
256 TTAAAAAAAAATAACTAGCTTCA-AAACTATTCTAATCTCACAACTTCTCTTAAGG--TATATAT
295478 TATAGGTTTATATAAACAAAGGT
318 TATAGGTTTATATAAACAAAGGT
* * *
295501 GTATATGTTATAATTAATAATTTTATAAGTTATAATTTTTTAAATGTCAACATAAAA-AAGAAAG
1 ATATATATTATAATTAATAATTTTATAAGTTATAATTTTTT-AATGTTAACATAAAATAA-AAAG
* *
295565 TAAATATATTTATATTTAAAGT-ATATATA-TTCTAAAAGTA--TTACTATATATATAATATAGT
64 TAAATATATTTATATTTAAAGTAATATATACAT-TAAAAGTATTTTAGTATATATAT-A-ATAGT
* * * * **
295626 AATTGTATGTC-TTATAAACGAACCCAACATATATAATGT-ATATATTAAAAAACATGCCAAGGT
126 AATTATAT-TCTTTATAAATGAACCCAATATATATAAAGTAATATATT-AAAAACATTACAAGGT
* * *
295689 AATTAATAATCATAGTTTCATGAATTAATTTAATTAATTATATGGGTTTGTTTTTCATTACATGA
189 AATTAATAATCATAGTTTCATGAATTTATTTAATTAATTATATGGGTTTGTCTTTAATTACATGA
* * *
295754 AATTAAAAAAAAATATCTAGATTTCGAAACTATTCTAAT
254 AATTAAAAAAAAATAACTAG-CTTCAAAACTATTCTAAT
295793 ATCAAAGACT
Statistics
Matches: 546, Mismatches: 67, Indels: 46
0.83 0.10 0.07
Matches are distributed among these distances:
337 79 0.14
338 5 0.01
339 144 0.26
340 40 0.07
341 1 0.00
343 115 0.21
344 10 0.02
345 53 0.10
346 7 0.01
347 92 0.17
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (340 bp):
ATATATATTATAATTAATAATTTTATAAGTTATAATTTTTTAATGTTAACATAAAATAAAAAGTA
AATATATTTATATTTAAAGTAATATATACATTAAAAGTATTTTAGTATATATATAATAGTAATTA
TATTCTTTATAAATGAACCCAATATATATAAAGTAATATATTAAAAACATTACAAGGTAATTAAT
AATCATAGTTTCATGAATTTATTTAATTAATTATATGGGTTTGTCTTTAATTACATGAAATTAAA
AAAAAATAACTAGCTTCAAAACTATTCTAATCTCACAACTTCTCTTAAGGTATATATTATAGGTT
TATATAAACAAAGGT
Found at i:296161 original size:31 final size:31
Alignment explanation
Indices: 296124--296184 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
296114 AGTGGATTTT
296124 TTTTATTTAATTATTT-AAATAACAATAAAAA
1 TTTTATTTAATT-TTTCAAATAACAATAAAAA
296155 TTTTATTTAATTTTTCAAATAACAATAAAA
1 TTTTATTTAATTTTTCAAATAACAATAAAA
296185 TAGAACTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 3 0.10
31 26 0.90
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (31 bp):
TTTTATTTAATTTTTCAAATAACAATAAAAA
Found at i:296474 original size:136 final size:136
Alignment explanation
Indices: 296240--296672 Score: 670
Period size: 136 Copynumber: 3.2 Consensus size: 136
296230 AACTTACTTA
* * * *** *
296240 TAGGGTACTCTAACTCGATATAACC-GGATCGGGTACTCACACGTACCCTATAATAGGGTACCTA
1 TAGGGTACCCTAACTCAATCTAACCAGG-TCGGGTACTCACTTATACCCTATAATAGGGTACCCA
* * * *
296304 TTGCCATCTCTAATTTTAAGAATCAAATTAGAACTTGATATGGATAATGAAGTCACTATTTGAAC
65 TTGCTATCTCTAATTTTGAGAATCAAAATAGAACTTGATATGGATAACGAAGTCACTATTTGAAC
296369 TTGATTT
130 TTGATTT
* *
296376 TAAGGTACCCTAACTCAATCTAACCAGGTCGGGCACTCACTTATACCCTATAATAGGGTACCCAT
1 TAGGGTACCCTAACTCAATCTAACCAGGTCGGGTACTCACTTATACCCTATAATAGGGTACCCAT
* *
296441 TGCTATCTCTAATTTTGAGAATCAAAATAGAACTTGACATGGATAACGAAGTCACTATTTAAACT
66 TGCTATCTCTAATTTTGAGAATCAAAATAGAACTTGATATGGATAACGAAGTCACTATTTGAACT
296506 TGATTT
131 TGATTT
* * *
296512 TAGGGTACCCTAACTCAATCTAACTAGGTCTGGTACTCACTTATACCCTATAATAGGCTACCCAT
1 TAGGGTACCCTAACTCAATCTAACCAGGTCGGGTACTCACTTATACCCTATAATAGGGTACCCAT
* *
296577 TGCTATCTCTAATTTTGAAAATCAAAATAGAACTTGATATGGATAACGAAGTCATTATTTGAACT
66 TGCTATCTCTAATTTTGAGAATCAAAATAGAACTTGATATGGATAACGAAGTCACTATTTGAACT
296642 TGATTT
131 TGATTT
296648 TAGGGTACCCTAACTCAATCTAACC
1 TAGGGTACCCTAACTCAATCTAACC
296673 CGATACAACT
Statistics
Matches: 271, Mismatches: 25, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
136 269 0.99
137 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (136 bp):
TAGGGTACCCTAACTCAATCTAACCAGGTCGGGTACTCACTTATACCCTATAATAGGGTACCCAT
TGCTATCTCTAATTTTGAGAATCAAAATAGAACTTGATATGGATAACGAAGTCACTATTTGAACT
TGATTT
Found at i:298211 original size:3 final size:3
Alignment explanation
Indices: 298205--298230 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
298195 TGTAGTAGTA
298205 GTG GTG GTG GTG GTG GTG GTG GTG GT
1 GTG GTG GTG GTG GTG GTG GTG GTG GT
298231 AGTAGCACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
GTG
Found at i:305587 original size:29 final size:29
Alignment explanation
Indices: 305526--305601 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 29
305516 CAATGTTGAA
* * * * *
305526 AAAAAATACTGTTATTACACGCCATGCTG
1 AAAAAATATTGTTGTTACATGCCATACTC
*
305555 AAAAAATATTGTTGTTACATGCCATATTC
1 AAAAAATATTGTTGTTACATGCCATACTC
305584 -AAAAATATT-TTGTTACAT
1 AAAAAATATTGTTGTTACAT
305602 TTTAATGTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 9 0.22
28 9 0.22
29 23 0.56
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (29 bp):
AAAAAATATTGTTGTTACATGCCATACTC
Found at i:308694 original size:37 final size:37
Alignment explanation
Indices: 308644--308719 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
308634 TTATAAGCTG
308644 TTCAATTGTCAAATATTTTATCTCTAAATGCATAGTC
1 TTCAATTGTCAAATATTTTATCTCTAAATGCATAGTC
308681 TTCAATTGTCAAATATTTTATCTCTAAATGCATAGTC
1 TTCAATTGTCAAATATTTTATCTCTAAATGCATAGTC
308718 TT
1 TT
308720 TGTAATACCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.45
Consensus pattern (37 bp):
TTCAATTGTCAAATATTTTATCTCTAAATGCATAGTC
Found at i:309668 original size:47 final size:47
Alignment explanation
Indices: 309478--309656 Score: 211
Period size: 47 Copynumber: 3.9 Consensus size: 47
309468 TCACGGTAGG
* * ***
309478 GTTCAGAGTTTGTGACACACCATGGAGGAAATCTATGATACTTTAGA
1 GTTCAGAGTTTGTGACACACCATGGAGGGAATCTATGACACGCCAGA
* * *
309525 GTTTAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGA
1 GTTCAGAGTTTGTGACACACCATGGAGGGAATCTATGACACGCCAGA
* *
309572 GTTCAGAGTTTG-G-CATACCATGGAGGGAATATATGACACGCCA-A
1 GTTCAGAGTTTGTGACACACCATGGAGGGAATCTATGACACGCCAGA
* * *
309616 TGTTCAGAGTTTGTGACCCAGCATGGAGGGAATCTGTGACA
1 -GTTCAGAGTTTGTGACACACCATGGAGGGAATCTATGACA
309657 TGCTAATGTT
Statistics
Matches: 111, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
44 1 0.01
45 38 0.34
46 2 0.02
47 70 0.63
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.26
Consensus pattern (47 bp):
GTTCAGAGTTTGTGACACACCATGGAGGGAATCTATGACACGCCAGA
Found at i:309714 original size:92 final size:91
Alignment explanation
Indices: 309490--309720 Score: 243
Period size: 92 Copynumber: 2.5 Consensus size: 91
309480 TCAGAGTTTG
* * * *
309490 TGACACACCATGGAGGAAATCTATGATACTTTAGAGTTTAGAGTTTGTGACACGCCATGGAGGGA
1 TGACATACCATGGAGGAAATCTATGACACGTTAGA-TTCAGAGTTTGTGACACGCCATGGAGGGA
*
309555 ATCTGTGACACGCCAGAGTTCAGAGTT
65 ATCTGTGACACGCCAGAGTTCAAAGTT
* * * ** *
309582 TGGCATACCATGGAGGGAATATATGACACGCCA-ATGTTCAGAGTTTGTGACCCAG-CATGGAGG
1 TGACATACCATGGAGGAAATCTATGACACGTTAGA--TTCAGAGTTTGTGACAC-GCCATGGAGG
* *
309645 GAATCTGTGACATGCTA-ATGTTCAAAGTT
63 GAATCTGTGACACGCCAGA-GTTCAAAGTT
* * *
309674 TGACATGCCATGAAGGAAATCTGTGACACGTTAGGATTCAGAGTTTG
1 TGACATACCATGGAGGAAATCTATGACACGTTA-GATTCAGAGTTTG
309721 ACACGTCAGC
Statistics
Matches: 113, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
91 2 0.02
92 109 0.96
93 1 0.01
94 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.26
Consensus pattern (91 bp):
TGACATACCATGGAGGAAATCTATGACACGTTAGATTCAGAGTTTGTGACACGCCATGGAGGGAA
TCTGTGACACGCCAGAGTTCAAAGTT
Found at i:309741 original size:22 final size:22
Alignment explanation
Indices: 309697--309742 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
309687 AGGAAATCTG
* *
309697 TGACACGTTAGGATTCAGAGTT
1 TGACACGTCAGCATTCAGAGTT
* *
309719 TGACACGTCAGCATTTAGGGTT
1 TGACACGTCAGCATTCAGAGTT
309741 TG
1 TG
309743 TGACACAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (22 bp):
TGACACGTCAGCATTCAGAGTT
Found at i:310511 original size:31 final size:31
Alignment explanation
Indices: 310473--310664 Score: 213
Period size: 31 Copynumber: 6.2 Consensus size: 31
310463 GCGTTTTACA
* * **
310473 ACATTTGACTTGTTATGCATGACGTGTCATG
1 ACATTTTACTTGTTATGCATGGCGTGTCACC
* * *
310504 ACATTTGACTTGATATGCATGTCGTGTCACC
1 ACATTTTACTTGTTATGCATGGCGTGTCACC
* * *
310535 ACATTTTACTTGTTATGCATGGCATGTGACG
1 ACATTTTACTTGTTATGCATGGCGTGTCACC
* * * *
310566 ACCTTTTACTTGTTATGCATGGCATGTGACA
1 ACATTTTACTTGTTATGCATGGCGTGTCACC
* * * *
310597 ACCTTTTACTTATTATGCATGACGTGTAACC
1 ACATTTTACTTGTTATGCATGGCGTGTCACC
*
310628 ACATTTTACTTGTTATGCATGGCGTGTAACC
1 ACATTTTACTTGTTATGCATGGCGTGTCACC
310659 ACATTT
1 ACATTT
310665 GTACCATGTT
Statistics
Matches: 141, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 141 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (31 bp):
ACATTTTACTTGTTATGCATGGCGTGTCACC
Found at i:312479 original size:23 final size:23
Alignment explanation
Indices: 312452--312543 Score: 73
Period size: 23 Copynumber: 4.0 Consensus size: 23
312442 AGGGTGATAT
312452 GCCATGCCCGAATG-AGGTGACACA
1 GCCATGCCCGAATGCA-GTGACA-A
*
312476 -CCATGCCCTAATGCAGTGACAA
1 GCCATGCCCGAATGCAGTGACAA
* **
312498 GCCATGCCTC-AGTGGGGTGACAA
1 GCCATGCC-CGAATGCAGTGACAA
* **
312521 GCCATGCTCGAATGTTGTGACAA
1 GCCATGCCCGAATGCAGTGACAA
312544 ACTATGCNNN
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
22 2 0.04
23 52 0.93
24 2 0.04
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (23 bp):
GCCATGCCCGAATGCAGTGACAA
Found at i:316282 original size:51 final size:51
Alignment explanation
Indices: 316206--316307 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
316196 AGAAGTTAAG
316206 CTAAATATAACATAAAGGGCAATATGCATAATATGTAGCTAATCATCATCA
1 CTAAATATAACATAAAGGGCAATATGCATAATATGTAGCTAATCATCATCA
*
316257 CTAAATATAGCATAAAGGGCAATATGCATAATATGTAGCTAATCATCATCA
1 CTAAATATAACATAAAGGGCAATATGCATAATATGTAGCTAATCATCATCA
316308 ATACTTACTA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (51 bp):
CTAAATATAACATAAAGGGCAATATGCATAATATGTAGCTAATCATCATCA
Found at i:340857 original size:6 final size:6
Alignment explanation
Indices: 340846--340915 Score: 65
Period size: 6 Copynumber: 11.7 Consensus size: 6
340836 GACATGCAAA
* *
340846 AAGATG AAGATG -A-A-G AAGATG ACATGGAAG AAGATG AAAATG AAGATG
1 AAGATG AAGATG AAGATG AAGATG A-A--GATG AAGATG AAGATG AAGATG
*
340894 AAGATG AAGTTG AAGATG AAGA
1 AAGATG AAGATG AAGATG AAGA
340916 CAAAGACAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
3 1 0.02
4 2 0.04
5 2 0.04
6 41 0.79
7 1 0.02
8 1 0.02
9 4 0.08
ACGTcount: A:0.51, C:0.01, G:0.31, T:0.16
Consensus pattern (6 bp):
AAGATG
Found at i:340858 original size:30 final size:30
Alignment explanation
Indices: 340824--340891 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
340814 CTTGATTGAG
340824 GATGAAGAAGATGACATGCAAAAAGATGAA
1 GATGAAGAAGATGACATGCAAAAAGATGAA
* *
340854 GATGAAGAAGATGACATGGAAGAAGATGAA
1 GATGAAGAAGATGACATGCAAAAAGATGAA
*
340884 AATGAAGA
1 GATGAAGA
340892 TGAAGATGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.53, C:0.04, G:0.29, T:0.13
Consensus pattern (30 bp):
GATGAAGAAGATGACATGCAAAAAGATGAA
Done.