Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 152 of 163
Found at i:41851347 original size:58 final size:58
Alignment explanation
Indices: 41851251--41851398 Score: 226
Period size: 57 Copynumber: 2.6 Consensus size: 58
41851241 ACCCAGGGGC
* * * *
41851251 AAAAATGGAATTTTAGAAAATTCGAGGATAAAATGGTAATTTTTGGTGAAATCGGGGTT
1 AAAAATGGAATTTTGGAAAGTTCGGGGGT-AAATGGTAATTTTTGGTGAAATCGGGGTT
*
41851310 AAAAATGGAATTTTGGAAAGTTCGGGGGTAAATGGTAATTTTTTGTGAAATCGGGGTT
1 AAAAATGGAATTTTGGAAAGTTCGGGGGTAAATGGTAATTTTTGGTGAAATCGGGGTT
*
41851368 -AAAATGGAATTTTGGAAAGTTTGGGGGTAAA
1 AAAAATGGAATTTTGGAAAGTTCGGGGGTAAA
41851399 AACATAATTT
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
57 30 0.36
58 28 0.34
59 25 0.30
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.32
Consensus pattern (58 bp):
AAAAATGGAATTTTGGAAAGTTCGGGGGTAAATGGTAATTTTTGGTGAAATCGGGGTT
Found at i:41851400 original size:29 final size:29
Alignment explanation
Indices: 41851304--41851400 Score: 87
Period size: 29 Copynumber: 3.4 Consensus size: 29
41851294 TGGTGAAATC
* *
41851304 GGGGTTAAAAATGGAATTTTGGAAAGTTC
1 GGGGGTAAAAATGGAATTTTGGAAAGTTT
41851333 GGGGGT--AAATGGTAATTTTTTGTGAAA---T
1 GGGGGTAAAAATGG-AA--TTTTG-GAAAGTTT
* *
41851361 CGGGGTTAAAATGGAATTTTGGAAAGTTT
1 GGGGGTAAAAATGGAATTTTGGAAAGTTT
41851390 GGGGGTAAAAA
1 GGGGGTAAAAA
41851401 CATAATTTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 18
0.70 0.06 0.23
Matches are distributed among these distances:
26 4 0.07
27 11 0.20
28 7 0.13
29 17 0.31
30 11 0.20
31 4 0.07
ACGTcount: A:0.33, C:0.02, G:0.33, T:0.32
Consensus pattern (29 bp):
GGGGGTAAAAATGGAATTTTGGAAAGTTT
Found at i:41851410 original size:57 final size:58
Alignment explanation
Indices: 41851251--41851410 Score: 196
Period size: 58 Copynumber: 2.7 Consensus size: 58
41851241 ACCCAGGGGC
* * * * **
41851251 AAAAATGGAATTTTAGAAAATTCGAGGATAAAATGGTAATTTTTGGTGAAATCGGGGTT
1 AAAAATGGAATTTTGGAAAGTTCGGGGGTAAAA-CATAATTTTTGGTGAAATCGGGGTT
*** *
41851310 AAAAATGGAATTTTGGAAAGTTCGGGGGTAAATGGTAATTTTTTGTGAAATCGGGGTT
1 AAAAATGGAATTTTGGAAAGTTCGGGGGTAAAACATAATTTTTGGTGAAATCGGGGTT
*
41851368 -AAAATGGAATTTTGGAAAGTTTGGGGGTAAAAACATAATTTTT
1 AAAAATGGAATTTTGGAAAGTTCGGGGGT-AAAACATAATTTTT
41851411 AAAAAAGTTT
Statistics
Matches: 90, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
57 27 0.30
58 35 0.39
59 28 0.31
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (58 bp):
AAAAATGGAATTTTGGAAAGTTCGGGGGTAAAACATAATTTTTGGTGAAATCGGGGTT
Found at i:41851431 original size:31 final size:31
Alignment explanation
Indices: 41851383--41851442 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
41851373 GGAATTTTGG
* *
41851383 AAAGTTTGGGGGTAAAAACATAATTTTTAAA
1 AAAGTTTAGGGGCAAAAACATAATTTTTAAA
**
41851414 AAAGTTTAGGGGCAAAAATGTAATTTTTA
1 AAAGTTTAGGGGCAAAAACATAATTTTTA
41851443 GAAGTTTCGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.43, C:0.03, G:0.20, T:0.33
Consensus pattern (31 bp):
AAAGTTTAGGGGCAAAAACATAATTTTTAAA
Found at i:41851460 original size:29 final size:29
Alignment explanation
Indices: 41851384--41851477 Score: 82
Period size: 31 Copynumber: 3.1 Consensus size: 29
41851374 GAATTTTGGA
* * * *
41851384 AAGTTTGGGGGTAAAAACATAATTTTTAAAA
1 AAGTTTCGGGGTCAAAATATAATTTTT--AG
* *
41851415 AAGTTTAGGGG-CAAAAATGTAATTTTTAG
1 AAGTTTCGGGGTC-AAAATATAATTTTTAG
*
41851444 AAGTTTCGGGGTCAAAATACAATTTCTTAG
1 AAGTTTCGGGGTCAAAATATAATTT-TTAG
41851474 AAGT
1 AAGT
41851478 CTAAAGACCT
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
29 21 0.40
30 9 0.17
31 22 0.42
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.33
Consensus pattern (29 bp):
AAGTTTCGGGGTCAAAATATAATTTTTAG
Found at i:41853464 original size:17 final size:17
Alignment explanation
Indices: 41853438--41853474 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
41853428 ACATTTAATT
*
41853438 TTTATTTTAAATTTAAA
1 TTTATATTAAATTTAAA
*
41853455 TTTATATTAAGTTTAAA
1 TTTATATTAAATTTAAA
41853472 TTT
1 TTT
41853475 TAGAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTATATTAAATTTAAA
Found at i:41861491 original size:26 final size:27
Alignment explanation
Indices: 41861430--41861491 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
41861420 AATTTTATTA
*
41861430 TTTTAAAAAA-TTAAATATAATTTTAC
1 TTTTAAAAAATTTAAATATAATTTAAC
*
41861456 TTTT-ATAAATTTAAAT-T-ATTTAAAC
1 TTTTAAAAAATTTAAATATAATTT-AAC
41861481 TTTTAAAAAAT
1 TTTTAAAAAAT
41861492 AGATCATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 4 0.13
25 11 0.37
26 15 0.50
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (27 bp):
TTTTAAAAAATTTAAATATAATTTAAC
Found at i:41868982 original size:23 final size:23
Alignment explanation
Indices: 41868950--41869058 Score: 146
Period size: 23 Copynumber: 4.7 Consensus size: 23
41868940 GCTGGGGAAA
*
41868950 CAGTAAGCACACACAGCGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
* * *
41868973 TAGTAGGCACACACAGTGCAAAA
1 CAGTAAGCACACACAGTGCAAAT
41868996 CAGTAAGCACACACAGTGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
* * * *
41869019 TAGTAAGCACATATAGTGCGAAT
1 CAGTAAGCACACACAGTGCAAAT
41869042 CAGTAAGCACACACAGT
1 CAGTAAGCACACACAGT
41869059 ATTGAACAGT
Statistics
Matches: 72, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 72 1.00
ACGTcount: A:0.42, C:0.24, G:0.19, T:0.15
Consensus pattern (23 bp):
CAGTAAGCACACACAGTGCAAAT
Found at i:41869058 original size:46 final size:46
Alignment explanation
Indices: 41868947--41869058 Score: 170
Period size: 46 Copynumber: 2.4 Consensus size: 46
41868937 AGTGCTGGGG
* *
41868947 AAACAGTAAGCACACACAGCGCAAATTAGTAGGCACACACAGTGCA
1 AAACAGTAAGCACACACAGTGCAAATTAGTAAGCACACACAGTGCA
* * *
41868993 AAACAGTAAGCACACACAGTGCAAATTAGTAAGCACATATAGTGCG
1 AAACAGTAAGCACACACAGTGCAAATTAGTAAGCACACACAGTGCA
*
41869039 AATCAGTAAGCACACACAGT
1 AAACAGTAAGCACACACAGT
41869059 ATTGAACAGT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 60 1.00
ACGTcount: A:0.44, C:0.23, G:0.19, T:0.14
Consensus pattern (46 bp):
AAACAGTAAGCACACACAGTGCAAATTAGTAAGCACACACAGTGCA
Found at i:41883982 original size:1 final size:1
Alignment explanation
Indices: 41883978--41884004 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
41883968 GTGTGTGTGT
41883978 GGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGG
41884005 TGAAGAAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:41902431 original size:13 final size:13
Alignment explanation
Indices: 41902413--41902439 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41902403 CCACAAATTC
41902413 TCTATTTTATTTT
1 TCTATTTTATTTT
41902426 TCTATTTTATTTT
1 TCTATTTTATTTT
41902439 T
1 T
41902440 TTAACAAGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (13 bp):
TCTATTTTATTTT
Found at i:41904006 original size:18 final size:18
Alignment explanation
Indices: 41903983--41904021 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
41903973 AGTATACAAG
41903983 TCATACATACATAATCAT
1 TCATACATACATAATCAT
41904001 TCATACATACATAATCAT
1 TCATACATACATAATCAT
41904019 TCA
1 TCA
41904022 CTTACTTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (18 bp):
TCATACATACATAATCAT
Found at i:41905489 original size:14 final size:14
Alignment explanation
Indices: 41905440--41905489 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
41905430 AAATTATAAC
41905440 ATAAGTAACTAAAAT
1 ATAA-TAACTAAAAT
** *
41905455 ATAATATTTCAAAT
1 ATAATAACTAAAAT
41905469 ATAAATAACTAAAAT
1 AT-AATAACTAAAAT
41905484 ATAATA
1 ATAATA
41905490 TAAAAAAACA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
14 13 0.46
15 15 0.54
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (14 bp):
ATAATAACTAAAAT
Found at i:41919137 original size:24 final size:26
Alignment explanation
Indices: 41919092--41919139 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
41919082 CAAAAAATTG
* *
41919092 TATAAATTTATTAAATATTAATATAA
1 TATAAATATATTAAATAATAATATAA
41919118 TATAAATAT-TTAAA-AATAATAT
1 TATAAATATATTAAATAATAATAT
41919140 GGGTAGATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 5 0.25
26 8 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
TATAAATATATTAAATAATAATATAA
Found at i:41920118 original size:39 final size:39
Alignment explanation
Indices: 41920073--41920273 Score: 116
Period size: 39 Copynumber: 5.2 Consensus size: 39
41920063 ATTTTTTTAT
41920073 TTTATAATTTATTAGAATATTTTATAAGTTTTTATAATA
1 TTTATAATTTATTAGAATATTTTATAAGTTTTTATAATA
* *
41920112 TTTATAATTTTTTATGAA-AGTTTT-T-A-CTTTTATAAGT-
1 TTTATAATTTATTA-GAATA-TTTTATAAGTTTTTATAA-TA
* * * * *
41920149 TTATATAAATTGTTA-AATATTTT-TAATATGTTTTATTATT
1 TT-TATAATTTATTAGAATATTTTATAA-GT-TTTTATAATA
* * * *
41920189 TTTATAATTTATTTGAAAAATCTATAAGTTTTTATAA-A
1 TTTATAATTTATTAGAATATTTTATAAGTTTTTATAATA
* * * * *
41920227 TTTAATATTTTATT-TATTAATTTTATAAGTTTATATAAAA
1 TTT-ATAATTTATTAGAAT-ATTTTATAAGTTTTTATAATA
41920267 TTT-TAAT
1 TTTATAAT
41920274 ATTTTTATGT
Statistics
Matches: 124, Mismatches: 23, Indels: 31
0.70 0.13 0.17
Matches are distributed among these distances:
36 7 0.06
37 12 0.10
38 19 0.15
39 57 0.46
40 26 0.21
41 3 0.02
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.57
Consensus pattern (39 bp):
TTTATAATTTATTAGAATATTTTATAAGTTTTTATAATA
Found at i:41920124 original size:20 final size:20
Alignment explanation
Indices: 41920070--41920125 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
41920060 GACATTTTTT
*
41920070 TATTTTATAATTTATTAGAA
1 TATTTTATAATTTTTTAGAA
* *
41920090 TATTTTATAAGTTTTTATAA
1 TATTTTATAATTTTTTAGAA
41920110 TA-TTTATAATTTTTTA
1 TATTTTATAATTTTTTA
41920126 TGAAAGTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 13 0.41
20 19 0.59
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.61
Consensus pattern (20 bp):
TATTTTATAATTTTTTAGAA
Found at i:41920268 original size:20 final size:20
Alignment explanation
Indices: 41920188--41920271 Score: 57
Period size: 20 Copynumber: 4.2 Consensus size: 20
41920178 GTTTTATTAT
*
41920188 TTTTATAA-TTTATTTGAAAA
1 TTTTATAAGTTTATAT-AAAA
* * *
41920208 ATCTATAAGTTTTTAT-AAA
1 TTTTATAAGTTTATATAAAA
* * * *
41920227 TTTAAT-ATTTTATTTATTAA
1 TTTTATAAGTTTATATA-AAA
41920247 TTTTATAAGTTTATATAAAA
1 TTTTATAAGTTTATATAAAA
41920267 TTTTA
1 TTTTA
41920272 ATATTTTTAT
Statistics
Matches: 45, Mismatches: 15, Indels: 8
0.66 0.22 0.12
Matches are distributed among these distances:
18 6 0.13
19 6 0.13
20 20 0.44
21 13 0.29
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (20 bp):
TTTTATAAGTTTATATAAAA
Found at i:41920290 original size:39 final size:38
Alignment explanation
Indices: 41920211--41920290 Score: 92
Period size: 39 Copynumber: 2.1 Consensus size: 38
41920201 TTGAAAAATC
* *
41920211 TATAAGTTTTTATAAATTTAATATTTTATTTATTAATTT
1 TATAAGTTTATATAAATTTAATATTTTATGTATT-ATTT
41920250 TATAAGTTTATATAAAATTTTAATATTTTTATGT-TT-TTT
1 TATAAGTTTATAT-AAA-TTTAATA-TTTTATGTATTATTT
41920289 TA
1 TA
41920291 CGATTTTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
39 17 0.47
40 3 0.08
41 9 0.25
42 7 0.19
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (38 bp):
TATAAGTTTATATAAATTTAATATTTTATGTATTATTT
Found at i:41925096 original size:22 final size:22
Alignment explanation
Indices: 41925048--41925088 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
41925038 ATTTAAAGGT
41925048 TTTTTAGATTTATATATATTTA
1 TTTTTAGATTTATATATATTTA
*
41925070 GTTTTA-A-TTATATATATTT
1 TTTTTAGATTTATATATATTT
41925089 TGATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 1 0.06
22 5 0.28
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (22 bp):
TTTTTAGATTTATATATATTTA
Found at i:41925104 original size:26 final size:25
Alignment explanation
Indices: 41925071--41925122 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
41925061 ATATATTTAG
41925071 TTTTAATTATATATATTTTGATTTT
1 TTTTAATTATATATATTTTGATTTT
* * *
41925096 TTTTAAATTATATTTTTTTTTATTTT
1 TTTT-AATTATATATATTTTGATTTT
41925122 T
1 T
41925123 AGGCAATTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (25 bp):
TTTTAATTATATATATTTTGATTTT
Found at i:41947213 original size:2 final size:2
Alignment explanation
Indices: 41947206--41947263 Score: 74
Period size: 2 Copynumber: 32.0 Consensus size: 2
41947196 ATGGAGAATA
41947206 AT AT AT AT A- AT AT A- AT AT AT AT AT AT AT AT -T AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41947244 AT -T AT AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
41947264 CACCAATGAG
Statistics
Matches: 50, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
1 6 0.12
2 44 0.88
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:41947220 original size:5 final size:5
Alignment explanation
Indices: 41947203--41947262 Score: 50
Period size: 5 Copynumber: 11.6 Consensus size: 5
41947193 ATAATGGAGA
* * * *
41947203 ATAAT AT-AT ATAAT ATAAT ATATAT ATATAT ATTAT ATTAT ATTAT ATTAT
1 ATAAT ATAAT ATAAT ATAAT ATA-AT ATA-AT ATAAT ATAAT ATAAT ATAAT
41947254 ATATAT ATA
1 ATA-AT ATA
41947263 TCACCAATGA
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
4 4 0.08
5 31 0.62
6 15 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (5 bp):
ATAAT
Found at i:41954185 original size:20 final size:20
Alignment explanation
Indices: 41954133--41954194 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
41954123 AATGTATGAG
* ** *
41954133 TAGAAATGAACTAATATAAA
1 TAGAAGTGAACTTGTATAGA
41954153 TAGAAGTGAACTTGTATAGA
1 TAGAAGTGAACTTGTATAGA
41954173 TAGAAGTGAACTTGTATAGA
1 TAGAAGTGAACTTGTATAGA
41954193 TA
1 TA
41954195 TAGGATGTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.47, C:0.05, G:0.19, T:0.29
Consensus pattern (20 bp):
TAGAAGTGAACTTGTATAGA
Found at i:41955721 original size:19 final size:18
Alignment explanation
Indices: 41955687--41955743 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
41955677 ATTTTAATGT
*
41955687 TATACAATTATTTAAAAAA
1 TATATAATT-TTTAAAAAA
*
41955706 TAATATAATTTTT-AAAAC
1 T-ATATAATTTTTAAAAAA
*
41955724 TTTATAATCTTTTAAAAAA
1 TATATAAT-TTTTAAAAAA
41955743 T
1 T
41955744 TAAAATTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
17 6 0.19
18 9 0.29
19 9 0.29
20 7 0.23
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (18 bp):
TATATAATTTTTAAAAAA
Found at i:41955746 original size:26 final size:26
Alignment explanation
Indices: 41955717--41955766 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
41955707 AATATAATTT
*
41955717 TTAAAACTTT-ATAATCTTTTAAAAAA
1 TTAAAA-TTTCATAATCTTTCAAAAAA
*
41955743 TTAAAATTTCATAATGTTTCAAAA
1 TTAAAATTTCATAATCTTTCAAAA
41955767 TCTAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 18 0.86
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (26 bp):
TTAAAATTTCATAATCTTTCAAAAAA
Found at i:41956628 original size:31 final size:31
Alignment explanation
Indices: 41956573--41956631 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
41956563 GTTCAAACCC
*
41956573 CAATGTGAGAACAATTTCTTAGTTTGGGTCA
1 CAATGTGAGAACAATTTCTAAGTTTGGGTCA
*
41956604 CAATGTGGGAACAATTATC-AAGTTTGGG
1 CAATGTGAGAACAATT-TCTAAGTTTGGG
41956632 GATTAACTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 23 0.92
32 2 0.08
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.32
Consensus pattern (31 bp):
CAATGTGAGAACAATTTCTAAGTTTGGGTCA
Found at i:41956885 original size:31 final size:31
Alignment explanation
Indices: 41956789--41956908 Score: 103
Period size: 31 Copynumber: 4.0 Consensus size: 31
41956779 CTTAATATAA
* *
41956789 AATTTGGTACCTGAACTTGACA-TATTTTCCT
1 AATTTGGTACCTAAACTTGACACTATTTT-TT
*
41956820 AATTTGGTATCTAAACTT-----T-TTTTGATGT
1 AATTTGGTACCTAAACTTGACACTATTTT--T-T
*
41956848 AATTTGGTA-CTCAAACTTGACACTTTTTTTT
1 AATTTGGTACCT-AAACTTGACACTATTTTTT
41956879 AATTTGGTACCTAAACTTGACACTATTTTT
1 AATTTGGTACCTAAACTTGACACTATTTTT
41956909 AAGTCTGTAC
Statistics
Matches: 74, Mismatches: 5, Indels: 20
0.75 0.05 0.20
Matches are distributed among these distances:
26 4 0.05
27 3 0.04
28 16 0.22
31 43 0.58
32 3 0.04
33 1 0.01
34 4 0.05
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.47
Consensus pattern (31 bp):
AATTTGGTACCTAAACTTGACACTATTTTTT
Found at i:41957896 original size:7 final size:7
Alignment explanation
Indices: 41957886--41957911 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
41957876 TGTGAAATTA
41957886 TTAAATC
1 TTAAATC
41957893 TTAAATC
1 TTAAATC
41957900 TTAAATC
1 TTAAATC
41957907 TTAAA
1 TTAAA
41957912 ATTTAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (7 bp):
TTAAATC
Found at i:41965001 original size:3 final size:3
Alignment explanation
Indices: 41964993--41965019 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
41964983 TTTATTGACC
41964993 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
41965020 ATTTTCAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:41971240 original size:11 final size:11
Alignment explanation
Indices: 41971220--41971249 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
41971210 CCAAATATGC
41971220 AAAA-AAAAAA
1 AAAAGAAAAAA
41971230 AAAAGAAAAAA
1 AAAAGAAAAAA
41971241 AAAAGAAAA
1 AAAAGAAAA
41971250 GGTCGGGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.21
11 15 0.79
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:41971241 original size:16 final size:16
Alignment explanation
Indices: 41971220--41971250 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41971210 CCAAATATGC
41971220 AAAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAAGA
*
41971236 AAAAAAAAAGAAAAG
1 AAAAAAAAAAAAAAG
41971251 GTCGGGCTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAGA
Found at i:41973357 original size:24 final size:24
Alignment explanation
Indices: 41973323--41973370 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
41973313 CTAAGACTTG
*
41973323 AAAGTTTAGGAGTAAAGTGATAAAA
1 AAAGTTTAGGACTAAA-TGATAAAA
*
41973348 AAAG-TTAGGACTGAATGATAAAA
1 AAAGTTTAGGACTAAATGATAAAA
41973371 TAAGAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.38
24 9 0.43
25 4 0.19
ACGTcount: A:0.52, C:0.02, G:0.23, T:0.23
Consensus pattern (24 bp):
AAAGTTTAGGACTAAATGATAAAA
Found at i:41981558 original size:34 final size:34
Alignment explanation
Indices: 41981515--41981590 Score: 143
Period size: 34 Copynumber: 2.2 Consensus size: 34
41981505 TGTGTTCGGT
41981515 TCGTTTATGTTCACGAACAAGCTTGATTATTGAC
1 TCGTTTATGTTCACGAACAAGCTTGATTATTGAC
*
41981549 TCGTTTATGTTCACGAACAAGCTTGATTATTGGC
1 TCGTTTATGTTCACGAACAAGCTTGATTATTGAC
41981583 TCGTTTAT
1 TCGTTTAT
41981591 TGACTCATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.41
Consensus pattern (34 bp):
TCGTTTATGTTCACGAACAAGCTTGATTATTGAC
Found at i:41981720 original size:24 final size:24
Alignment explanation
Indices: 41981686--41981731 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
41981676 TCATTAATAT
*
41981686 TGTTCATGAACATGTTCAATTATA
1 TGTTCAAGAACATGTTCAATTATA
*
41981710 TGTTCAAGAACATGTTCGATTA
1 TGTTCAAGAACATGTTCAATTA
41981732 AGTTAAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (24 bp):
TGTTCAAGAACATGTTCAATTATA
Found at i:41987497 original size:2 final size:2
Alignment explanation
Indices: 41987490--41987519 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
41987480 TTTTCTACTT
*
41987490 GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
41987520 AGGGAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:41987793 original size:34 final size:34
Alignment explanation
Indices: 41987748--41987850 Score: 152
Period size: 34 Copynumber: 3.0 Consensus size: 34
41987738 AGAATATGAA
*
41987748 AAGTTAAGGAAGATGGAAGGTTAAAGATCAAGGG
1 AAGTTAAGGAAGATGGAAGGTTAAAGATCAAAGG
* *
41987782 AGGTTAAGGAAGATGGAAGGTTAAAGGTCAAAGG
1 AAGTTAAGGAAGATGGAAGGTTAAAGATCAAAGG
* *
41987816 AAGTTAAGAAAGATGGAAGGTTAAAAGATGAAAGG
1 AAGTTAAGGAAGATGGAAGGTT-AAAGATCAAAGG
41987851 TTGAAATTCC
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
34 51 0.84
35 10 0.16
ACGTcount: A:0.46, C:0.02, G:0.35, T:0.17
Consensus pattern (34 bp):
AAGTTAAGGAAGATGGAAGGTTAAAGATCAAAGG
Found at i:41987802 original size:17 final size:17
Alignment explanation
Indices: 41987750--41987852 Score: 81
Period size: 17 Copynumber: 6.2 Consensus size: 17
41987740 AATATGAAAA
41987750 GTTAAGGAAGATGGAAG
1 GTTAAGGAAGATGGAAG
* ** * *
41987767 GTTAAAGATCAAGGGAG
1 GTTAAGGAAGATGGAAG
41987784 GTTAAGGAAGATGGAAG
1 GTTAAGGAAGATGGAAG
41987801 GTTAAAGGTCAA-A-GGAA-
1 GTT-AAGG--AAGATGGAAG
*
41987818 GTTAAGAAAGATGGAAG
1 GTTAAGGAAGATGGAAG
*
41987835 GTTAA--AAGATGAAAG
1 GTTAAGGAAGATGGAAG
41987850 GTT
1 GTT
41987853 GAAATTCCAT
Statistics
Matches: 68, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
14 2 0.03
15 13 0.19
16 7 0.10
17 35 0.51
18 8 0.12
19 1 0.01
20 2 0.03
ACGTcount: A:0.44, C:0.02, G:0.35, T:0.19
Consensus pattern (17 bp):
GTTAAGGAAGATGGAAG
Found at i:41993233 original size:34 final size:35
Alignment explanation
Indices: 41993178--41993246 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 35
41993168 AAGAATATGA
41993178 AAAGTTAAGAAAGATGAAAGGTT-AAAGATCAAAG
1 AAAGTTAAGAAAGATGAAAGGTTAAAAGATCAAAG
* *
41993212 AAAGTTAAGGAAA-ATGGAAGGTTAAAAGATGAAAG
1 AAAGTTAA-GAAAGATGAAAGGTTAAAAGATCAAAG
41993247 GTTGAACATC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 17 0.55
35 14 0.45
ACGTcount: A:0.55, C:0.01, G:0.26, T:0.17
Consensus pattern (35 bp):
AAAGTTAAGAAAGATGAAAGGTTAAAAGATCAAAG
Found at i:41997336 original size:18 final size:18
Alignment explanation
Indices: 41997313--41997350 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
41997303 TAATATAGTT
41997313 TTATTCG-GTTTATTCGAA
1 TTATTCGAG-TTATTCGAA
41997331 TTATTCGAGTTATTCGAA
1 TTATTCGAGTTATTCGAA
41997349 TT
1 TT
41997351 CGAAAATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.24, C:0.11, G:0.16, T:0.50
Consensus pattern (18 bp):
TTATTCGAGTTATTCGAA
Found at i:42002163 original size:14 final size:14
Alignment explanation
Indices: 42002096--42002167 Score: 65
Period size: 14 Copynumber: 4.9 Consensus size: 14
42002086 CTATCGTTTG
*
42002096 ATAAAACTTAAAAT
1 ATAAAAATTAAAAT
*
42002110 TTAAAAATTTTAAAAAT
1 ATAAAAA--TT-AAAAT
42002127 ATAAAAATTAAAA-
1 ATAAAAATTAAAAT
42002140 ATAACTAAATTAAAAT
1 ATAA--AAATTAAAAT
*
42002156 ATAGAAATTAAA
1 ATAAAAATTAAA
42002168 GCAACAACTT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
13 4 0.08
14 17 0.35
15 11 0.23
16 5 0.10
17 11 0.23
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (14 bp):
ATAAAAATTAAAAT
Found at i:42011620 original size:28 final size:29
Alignment explanation
Indices: 42011563--42011621 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
42011553 GGAACATTTC
*
42011563 TTTTCTAATTTTTAAAATTTTGTTATATA
1 TTTTCTAAATTTTAAAATTTTGTTATATA
*
42011592 TTTT-TAAATTTTAAAATATTTTTTA-ATA
1 TTTTCTAAATTTTAAAAT-TTTGTTATATA
42011620 TT
1 TT
42011622 ATATATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 17 0.63
29 10 0.37
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (29 bp):
TTTTCTAAATTTTAAAATTTTGTTATATA
Found at i:42011631 original size:28 final size:28
Alignment explanation
Indices: 42011568--42011631 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
42011558 ATTTCTTTTC
*
42011568 TAATTTTTAAAATTTTGTTATATATTTT
1 TAATTTTTAAAATTTTGTTATATATTTA
* *
42011596 TAAATTTTAAAATATTTTTTA-ATA-TTA
1 TAATTTTTAAAAT-TTTGTTATATATTTA
42011623 TATATTTTT
1 TA-ATTTTT
42011632 GATTTTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
27 4 0.13
28 20 0.67
29 6 0.20
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (28 bp):
TAATTTTTAAAATTTTGTTATATATTTA
Found at i:42016851 original size:2 final size:2
Alignment explanation
Indices: 42016844--42016920 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
42016834 AGAAAGAAGA
42016844 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42016886 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42016921 GGCAACTGAC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42025828 original size:21 final size:20
Alignment explanation
Indices: 42025785--42025830 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
42025775 AAATATTGAG
*
42025785 AATTAATTTTTTATAATTAT
1 AATTAATTTATTATAATTAT
42025805 AATTAATTTGATTA-AATATAT
1 AATTAATTT-ATTATAAT-TAT
42025826 AATTA
1 AATTA
42025831 TTAAGGGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
AATTAATTTATTATAATTAT
Found at i:42028231 original size:102 final size:102
Alignment explanation
Indices: 42028045--42028260 Score: 405
Period size: 102 Copynumber: 2.1 Consensus size: 102
42028035 CAGCAAAAAA
*
42028045 TTGAGTATAGCTATTGTCTGAGGGATTCAACACGTCTATAAGGAGGGCAACAAGACAGCGGATGG
1 TTGA-TATAACTATTGTCTGAGGGATTCAACACGTCTATAAGGAGGGCAACAAGACAGCGGATGG
42028110 CTGCACATGCACCTCATCAACCACCCGGTTTCTACAGT
65 CTGCACATGCACCTCATCAACCACCCGGTTTCTACAGT
42028148 TTGATATAACTATTGTCTGAGGGATTCAACACGTCTATAAGGAGGGCAACAAGACAGCGGATGGC
1 TTGATATAACTATTGTCTGAGGGATTCAACACGTCTATAAGGAGGGCAACAAGACAGCGGATGGC
*
42028213 TGCACATGCACCTCATCAACCATCCGGTTTCTACAGT
66 TGCACATGCACCTCATCAACCACCCGGTTTCTACAGT
42028250 TTGATATAACT
1 TTGATATAACT
42028261 GCCAGTTAAG
Statistics
Matches: 111, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
102 107 0.96
103 4 0.04
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (102 bp):
TTGATATAACTATTGTCTGAGGGATTCAACACGTCTATAAGGAGGGCAACAAGACAGCGGATGGC
TGCACATGCACCTCATCAACCACCCGGTTTCTACAGT
Found at i:42030073 original size:10 final size:10
Alignment explanation
Indices: 42030052--42030087 Score: 63
Period size: 10 Copynumber: 3.5 Consensus size: 10
42030042 TTCTAACTTT
42030052 GAAAAATCATA
1 GAAAAAT-ATA
42030063 GAAAAATATA
1 GAAAAATATA
42030073 GAAAAATATA
1 GAAAAATATA
42030083 GAAAA
1 GAAAA
42030088 TTTATTAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 18 0.72
11 7 0.28
ACGTcount: A:0.69, C:0.03, G:0.11, T:0.17
Consensus pattern (10 bp):
GAAAAATATA
Found at i:42030615 original size:24 final size:26
Alignment explanation
Indices: 42030588--42030635 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
42030578 AGAGAAATGT
42030588 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
42030612 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
42030636 CCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:42030787 original size:24 final size:24
Alignment explanation
Indices: 42030712--42030789 Score: 102
Period size: 24 Copynumber: 3.2 Consensus size: 24
42030702 ACTGATCAGA
* *
42030712 CTGTTTCCCAACACTTATGTGCTT
1 CTGTTCCCCAGCACTTATGTGCTT
* *
42030736 CTATTTCTCCAGCACTTATGTGCTT
1 CT-GTTCCCCAGCACTTATGTGCTT
*
42030761 CTGTTCCCCAGCACTTATGCGCTT
1 CTGTTCCCCAGCACTTATGTGCTT
42030785 CTGTT
1 CTGTT
42030790 AAGTATTTCG
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
24 26 0.57
25 20 0.43
ACGTcount: A:0.14, C:0.31, G:0.14, T:0.41
Consensus pattern (24 bp):
CTGTTCCCCAGCACTTATGTGCTT
Found at i:42033477 original size:216 final size:216
Alignment explanation
Indices: 42033079--42033493 Score: 568
Period size: 216 Copynumber: 1.9 Consensus size: 216
42033069 GCCAAGATGA
* * *
42033079 CCCCACATGAGGTTGCGATTGGGAGTACATGCATTGAGTTCATTATCATAAGCTCCAACCCCAAA
1 CCCCACATGAGGTCGCGATCGGGAGTACATGCATCGAGTTCATTATCATAAGCTCCAACCCCAAA
* * *
42033144 TACCATATCGATGAGTGCATCACCTCTCGATTAGTATGATTCATATTTTTTTAATCCTTTCACTA
66 TACCATATCGATGAGTGCATCACCTCTCGATCAATATGATTCATATTTTTCTAATCCTTTCACTA
* *
42033209 ACTCCTTTTTTTTACAAAAGCAACACATTATGCACCATTATAGCCTTGAGTTGCGTTTCAACTTT
131 ACTCCATTTTTTTACAAAAGCAACACATTATGCACCATTATAGCCCTGAGTTGCGTTTCAACTTT
42033274 TTCTGTACTGTCATTGTCATT
196 TTCTGTACTGTCATTGTCATT
* * *
42033295 CCCCACATGAGGTCGCGATCGGGAGTGCATGCGTCGAGTTCATCT-TCATCAGCTCCAACCCCAA
1 CCCCACATGAGGTCGCGATCGGGAGTACATGCATCGAGTTCAT-TATCATAAGCTCCAACCCCAA
* * **
42033359 ATACTATA-CTGATGGGTGCATCACCTCTCTG-TCAATATGATTCATATTTTTCTGGTCCTTTCA
65 ATACCATATC-GATGAGTGCATCACCTCTC-GATCAATATGATTCATATTTTTCTAATCCTTTCA
* * ** * * *
42033422 CTAACTCCATTTTTTTACATAAGCACCACATTATGCACTGTTGTCA-CCCTGAGTTGCGTTTTAG
128 CTAACTCCATTTTTTTACAAAAGCAACACATTATGCACCATTAT-AGCCCTGAGTTGCGTTTCAA
42033486 CTTTTTCT
192 CTTTTTCT
42033494 CCATCGTCAT
Statistics
Matches: 173, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
215 1 0.01
216 169 0.98
217 3 0.02
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (216 bp):
CCCCACATGAGGTCGCGATCGGGAGTACATGCATCGAGTTCATTATCATAAGCTCCAACCCCAAA
TACCATATCGATGAGTGCATCACCTCTCGATCAATATGATTCATATTTTTCTAATCCTTTCACTA
ACTCCATTTTTTTACAAAAGCAACACATTATGCACCATTATAGCCCTGAGTTGCGTTTCAACTTT
TTCTGTACTGTCATTGTCATT
Found at i:42036912 original size:24 final size:24
Alignment explanation
Indices: 42036884--42036930 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
42036874 GACTAATAAG
*
42036884 AGTTTGACTCAAACAAATAAACAT
1 AGTTTAACTCAAACAAATAAACAT
* *
42036908 AGTTTAATTGAAACAAATAAACA
1 AGTTTAACTCAAACAAATAAACA
42036931 GAGTAACTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.53, C:0.13, G:0.09, T:0.26
Consensus pattern (24 bp):
AGTTTAACTCAAACAAATAAACAT
Found at i:42040247 original size:2 final size:2
Alignment explanation
Indices: 42040240--42040264 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42040230 CCCCAACTAT
42040240 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
42040265 TAAATATAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:42043034 original size:86 final size:86
Alignment explanation
Indices: 42042940--42043213 Score: 539
Period size: 86 Copynumber: 3.2 Consensus size: 86
42042930 TTTCATAGTA
42042940 GAATCAAAATGTTCAGCTAATTATAAAGATCTAATCCTTATATTTAAGCTTTAATAAAATGCATA
1 GAATCAAAATGTTCAGCTAATTATAAAGATCTAATCCTTATATTTAAGCTTTAATAAAATGCATA
42043005 AAAATAAAAGTTTTAATAATT
66 AAAATAAAAGTTTTAATAATT
42043026 GAATCAAAATGTTCAGCTAATTATAAAGATCTAATCCTTATATTTAAGCTTTAATAAAATGCATA
1 GAATCAAAATGTTCAGCTAATTATAAAGATCTAATCCTTATATTTAAGCTTTAATAAAATGCATA
42043091 AAAATAAAAGTTTTAATAATT
66 AAAATAAAAGTTTTAATAATT
*
42043112 GAATCAAAATGTTCAGCTAATTATAAAGATCTAATCCTTATATTTAAGCTTTAATAAAACGCATA
1 GAATCAAAATGTTCAGCTAATTATAAAGATCTAATCCTTATATTTAAGCTTTAATAAAATGCATA
42043177 AAAATAAAAGTTTTAATAATT
66 AAAATAAAAGTTTTAATAATT
42043198 GAATCAAAATGTTCAG
1 GAATCAAAATGTTCAG
42043214 TTATCTAATT
Statistics
Matches: 187, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 187 1.00
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.35
Consensus pattern (86 bp):
GAATCAAAATGTTCAGCTAATTATAAAGATCTAATCCTTATATTTAAGCTTTAATAAAATGCATA
AAAATAAAAGTTTTAATAATT
Found at i:42043305 original size:22 final size:22
Alignment explanation
Indices: 42043261--42043305 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
42043251 TAATAGAAAC
*
42043261 AAACAAGCATCTGATCCTGACA
1 AAACAAGCATCTGATCATGACA
42043283 AAACAAAGCATCTGATCAT-ACA
1 AAAC-AAGCATCTGATCATGACA
42043305 A
1 A
42043306 CCAATTAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.47, C:0.24, G:0.11, T:0.18
Consensus pattern (22 bp):
AAACAAGCATCTGATCATGACA
Found at i:42045315 original size:17 final size:17
Alignment explanation
Indices: 42045290--42045330 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
42045280 TAAACTTATT
* *
42045290 TTTAGATTTATTTTAAG
1 TTTAAATTTATTTTAAA
42045307 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
42045324 TTTAAAT
1 TTTAAAT
42045331 ATTCAAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:42047060 original size:28 final size:27
Alignment explanation
Indices: 42047014--42047080 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
42047004 TTAACTTCTT
** * *
42047014 AAAAATTACATTTTGCCCCTAAACTTTC
1 AAAAATTACA-TTCCCCCCCAAACTTCC
42047042 AAAAATTACATTCCCCCCCAAACTTCC
1 AAAAATTACATTCCCCCCCAAACTTCC
*
42047069 AAAAATCACATT
1 AAAAATTACATT
42047081 TTTACCCCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 24 0.71
28 10 0.29
ACGTcount: A:0.40, C:0.30, G:0.01, T:0.28
Consensus pattern (27 bp):
AAAAATTACATTCCCCCCCAAACTTCC
Found at i:42047215 original size:88 final size:86
Alignment explanation
Indices: 42047061--42047317 Score: 302
Period size: 87 Copynumber: 2.9 Consensus size: 86
42047051 ATTCCCCCCC
* * * *
42047061 AAACTTCCAAAAATCACATTTTTACCCCTAAAAATTTCCAAAAAATACATTTTTGCCCTCTATCT
1 AAACTTCCAAAAATTACATTTTTACCCC--CAAACTTCC-AAAAATACATTTTTGCCCTCGATCT
42047126 TCCAAAAATTACATTTTT-TACCCTT
63 TCCAAAAATTACATTTTTGT-CCC-T
* *
42047151 AAACTTTCAAAAATTACATTTTTACCCCCAAACTTCCAAAAACTACATTTTTGCTCTCGATCTTC
1 AAACTTCCAAAAATTACATTTTTACCCCCAAACTTCCAAAAA-TACATTTTTGCCCTCGATCTTC
42047216 CAAAAATTACATTTTTGTCCCT
65 CAAAAATTACATTTTTGTCCCT
** * * * *
42047238 AAACTTCCAAAAATTATGTTTTTGCCCCCGAACTTCCAAAAATCACATTTTTACCCT-GAATTTT
1 AAACTTCCAAAAATTACATTTTTACCCCCAAACTTCCAAAAAT-ACATTTTTGCCCTCG-ATCTT
* *
42047302 CCCAAAATGACATTTT
64 CCAAAAATTACATTTT
42047318 ACCCCTAAAA
Statistics
Matches: 147, Mismatches: 16, Indels: 11
0.84 0.09 0.06
Matches are distributed among these distances:
86 2 0.01
87 72 0.49
88 46 0.31
89 1 0.01
90 26 0.18
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.36
Consensus pattern (86 bp):
AAACTTCCAAAAATTACATTTTTACCCCCAAACTTCCAAAAATACATTTTTGCCCTCGATCTTCC
AAAAATTACATTTTTGTCCCT
Found at i:42047259 original size:29 final size:29
Alignment explanation
Indices: 42046986--42047289 Score: 260
Period size: 29 Copynumber: 10.5 Consensus size: 29
42046976 AACTTTTTCT
* * * *
42046986 AAAATTACA-TTTTGACCATTAACTTCTTA
1 AAAATTACATTTTTGCCCCTAAACTTC-CA
*
42047015 AAAATTACA-TTTTGCCCCTAAACTTTCA
1 AAAATTACATTTTTGCCCCTAAACTTCCA
** *
42047043 AAAATTACA--TTCCCCCCCAAACTTCCA
1 AAAATTACATTTTTGCCCCTAAACTTCCA
* * *
42047070 AAAATCACATTTTTACCCCTAAAAATTTCCA
1 AAAATTACATTTTTGCCCCT--AAACTTCCA
* *
42047101 AAAAATACATTTTTGCCCTCT-ATCTTCCA
1 AAAATTACATTTTTGCCC-CTAAACTTCCA
* * *
42047130 AAAATTACATTTTTTACCCTTAAACTTTCA
1 AAAATTACA-TTTTTGCCCCTAAACTTCCA
* *
42047160 AAAATTACATTTTTACCCCCAAACTTCCA
1 AAAATTACATTTTTGCCCCTAAACTTCCA
* * * *
42047189 AAAACTACATTTTTG-CTCTCGATCTTCCA
1 AAAATTACATTTTTGCCCCT-AAACTTCCA
*
42047218 AAAATTACATTTTTGTCCCTAAACTTCCA
1 AAAATTACATTTTTGCCCCTAAACTTCCA
** **
42047247 AAAATTATGTTTTTGCCCCCGAACTTCCA
1 AAAATTACATTTTTGCCCCTAAACTTCCA
*
42047276 AAAATCACATTTTT
1 AAAATTACATTTTT
42047290 ACCCTGAATT
Statistics
Matches: 221, Mismatches: 45, Indels: 18
0.78 0.16 0.06
Matches are distributed among these distances:
27 22 0.10
28 12 0.05
29 136 0.62
30 26 0.12
31 23 0.10
32 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAATTACATTTTTGCCCCTAAACTTCCA
Found at i:42047303 original size:29 final size:29
Alignment explanation
Indices: 42046986--42047336 Score: 223
Period size: 29 Copynumber: 12.1 Consensus size: 29
42046976 AACTTTTTCT
* * * *
42046986 AAAATTACATTTTGACCAT-TAACTTCTTA
1 AAAATTACATTTTTACCCTGAAACTTC-CA
** *
42047015 AAAATTACATTTTGCCCCT-AAACTTTCA
1 AAAATTACATTTTTACCCTGAAACTTCCA
** **
42047043 AAAATTACA--TTCCCCCCCAAACTTCCA
1 AAAATTACATTTTTACCCTGAAACTTCCA
* * *
42047070 AAAATCACATTTTTACCCCTAAAAATTTCCA
1 AAAATTACATTTTTA-CCCT-GAAACTTCCA
* * ** *
42047101 AAAAATACATTTTTGCCCTCTATCTTCCA
1 AAAATTACATTTTTACCCTGAAACTTCCA
* *
42047130 AAAATTACATTTTTTACCCTTAAACTTTCA
1 AAAATTACA-TTTTTACCCTGAAACTTCCA
**
42047160 AAAATTACATTTTTACCCCCAAACTTCCA
1 AAAATTACATTTTTACCCTGAAACTTCCA
* * * *
42047189 AAAACTACATTTTTGCTCTCG-ATCTTCCA
1 AAAATTACATTTTTACCCT-GAAACTTCCA
*
42047218 AAAATTACATTTTTGTCCCT-AAACTTCCA
1 AAAATTACATTTTT-ACCCTGAAACTTCCA
** * *
42047247 AAAATTATGTTTTTGCCCCCG-AACTTCCA
1 AAAATTACATTTTT-ACCCTGAAACTTCCA
* ** *
42047276 AAAATCACATTTTTACCCTGAATTTTCCC
1 AAAATTACATTTTTACCCTGAAACTTCCA
* *
42047305 AAAATGACA-TTTTACCCCTAAAACTTTCCA
1 AAAATTACATTTTTA-CCCTGAAAC-TTCCA
42047335 AA
1 AA
42047337 TTTGCATTTT
Statistics
Matches: 252, Mismatches: 57, Indels: 25
0.75 0.17 0.07
Matches are distributed among these distances:
26 6 0.02
27 16 0.06
28 19 0.08
29 151 0.60
30 40 0.16
31 20 0.08
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAATTACATTTTTACCCTGAAACTTCCA
Found at i:42047797 original size:97 final size:97
Alignment explanation
Indices: 42047631--42047824 Score: 325
Period size: 97 Copynumber: 2.0 Consensus size: 97
42047621 AAAATATTTA
* * * * *
42047631 AAATCGAGGCAATATTCCTTTATTTCGGGTTTTGAAAATCTGTGCCTTAACTTACTAGGTGCGAT
1 AAATCAAGGCAATATTCCTTTATCTCGGATTTTGAAAATCTGTGCCTTAACTTACTAGGCGCGAC
42047696 TTTTCTTCAAACCGAGATAATCGAATACCCTT
66 TTTTCTTCAAACCGAGATAATCGAATACCCTT
*
42047728 AAATCAAGGCAATATTCCTTTATCTCGGATTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGAC
1 AAATCAAGGCAATATTCCTTTATCTCGGATTTTGAAAATCTGTGCCTTAACTTACTAGGCGCGAC
*
42047793 TTTTCTTCAAACCGGGATAATCGAATACCCTT
66 TTTTCTTCAAACCGAGATAATCGAATACCCTT
42047825 TTTCAAGGTT
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
97 90 1.00
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (97 bp):
AAATCAAGGCAATATTCCTTTATCTCGGATTTTGAAAATCTGTGCCTTAACTTACTAGGCGCGAC
TTTTCTTCAAACCGAGATAATCGAATACCCTT
Found at i:42048578 original size:6 final size:6
Alignment explanation
Indices: 42048569--42048607 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
42048559 TTTAATAAGA
42048569 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATA
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATA
42048608 AAGTAATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.33
Consensus pattern (6 bp):
ATATAG
Found at i:42050873 original size:16 final size:16
Alignment explanation
Indices: 42050852--42050888 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
42050842 AGAATGAATT
42050852 ATAAATTTTTAA-AATA
1 ATAAA-TTTTAATAATA
42050868 ATAAATTTTAATAATA
1 ATAAATTTTAATAATA
42050884 ATAAA
1 ATAAA
42050889 ATTATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATAAATTTTAATAATA
Found at i:42078730 original size:14 final size:14
Alignment explanation
Indices: 42078701--42078729 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
42078691 TGTGTCATTT
42078701 AATTCAAATTTAAA
1 AATTCAAATTTAAA
42078715 AATT-AAATTTAAA
1 AATTCAAATTTAAA
42078728 AA
1 AA
42078730 AATTCTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTCAAATTTAAA
Found at i:42082126 original size:43 final size:43
Alignment explanation
Indices: 42082078--42082289 Score: 164
Period size: 43 Copynumber: 5.0 Consensus size: 43
42082068 AATCTGTTAA
* * *
42082078 TTTTAGCGACGTTTGTAAAAAAAGCGGCGCTAAAGATCATGGT
1 TTTTAGCGGCGTTTGTAAGAAAAGCGCCGCTAAAGATCATGGT
*
42082121 TTTTAGCGGCGTTTGTAAGAAAAGCGCCGTTAAAGAAT-AT-GT
1 TTTTAGCGGCGTTTGTAAGAAAAGCGCCGCTAAAG-ATCATGGT
* * * * *
42082163 TCTTTAGCGGCGTTCGTGAGAAAAGCACCGCTATAGATCATGTT
1 T-TTTAGCGGCGTTTGTAAGAAAAGCGCCGCTAAAGATCATGGT
* ** ** * *
42082207 TTTTAACGGCGTTT-TTGGGTAAGCGTCGCTAAAGA-CAATGGC
1 TTTTAGCGGCGTTTGTAAGAAAAGCGCCGCTAAAGATC-ATGGT
* * * * *
42082249 CTTTAGCGGCGTTTATGCA-AAAAGCGCTGCTAAATATCATG
1 TTTTAGCGGCGTTTGT-AAGAAAAGCGCCGCTAAAGATCATG
42082290 TTCTATAGCG
Statistics
Matches: 131, Mismatches: 30, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
41 1 0.01
42 34 0.26
43 91 0.69
44 5 0.04
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (43 bp):
TTTTAGCGGCGTTTGTAAGAAAAGCGCCGCTAAAGATCATGGT
Found at i:42086995 original size:29 final size:26
Alignment explanation
Indices: 42086924--42086979 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
42086914 AAATACGTAG
42086924 ATAGCATAGTATTGATACTCAAAATA
1 ATAGCATAGTATTGATACTCAAAATA
42086950 ATAGCATAGTATTGATACTCAAAATA
1 ATAGCATAGTATTGATACTCAAAATA
42086976 ATAG
1 ATAG
42086980 GAGCCATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.30
Consensus pattern (26 bp):
ATAGCATAGTATTGATACTCAAAATA
Found at i:42092168 original size:2 final size:2
Alignment explanation
Indices: 42092163--42092198 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
42092153 AATTAACCCA
42092163 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42092199 GATGTTGTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42093015 original size:2 final size:2
Alignment explanation
Indices: 42093008--42093061 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
42092998 ACTCATTTCT
42093008 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
42093050 TC TC TC TC TC TC
1 TC TC TC TC TC TC
42093062 GCTCGCTCGC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:42095379 original size:11 final size:13
Alignment explanation
Indices: 42095362--42095398 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 13
42095352 TATGTTTAAA
42095362 TTTAAAATA-TAC
1 TTTAAAATATTAC
42095374 -TTAAAATATTAC
1 TTTAAAATATTAC
42095386 TTTAAAATCATTA
1 TTTAAAAT-ATTA
42095399 ATATTTTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 8 0.36
12 3 0.14
13 7 0.32
14 4 0.18
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTAAAATATTAC
Found at i:42099259 original size:20 final size:21
Alignment explanation
Indices: 42099234--42099272 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
42099224 TCACCGATAA
42099234 AAAT-AATATCAAA-AATTTAT
1 AAATAAAT-TCAAATAATTTAT
42099254 AAATAAATTCAAATAATTT
1 AAATAAATTCAAATAATTT
42099273 TTTCATTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATAAATTCAAATAATTTAT
Found at i:42104528 original size:22 final size:21
Alignment explanation
Indices: 42104503--42104544 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
42104493 AGGTAACATG
*
42104503 TAAAAATTAAAGTTTAAAATTT
1 TAAAAATTAAA-ATTAAAATTT
42104525 TAAAAATTAAAATTAAAATT
1 TAAAAATTAAAATTAAAATT
42104545 ATTATTATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
TAAAAATTAAAATTAAAATTT
Found at i:42113457 original size:19 final size:20
Alignment explanation
Indices: 42113418--42113458 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
42113408 TTAATGATAT
*
42113418 TTTATTAAATGAAAATAATA
1 TTTAATAAATGAAAATAATA
*
42113438 TTTAATAAAT-AAAATTATA
1 TTTAATAAATGAAAATAATA
42113457 TT
1 TT
42113459 ATAAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
TTTAATAAATGAAAATAATA
Found at i:42114374 original size:41 final size:41
Alignment explanation
Indices: 42114312--42114412 Score: 168
Period size: 41 Copynumber: 2.5 Consensus size: 41
42114302 GGCGCTTCCC
*
42114312 ACTTGACCTTTAGCGGGGCTTATGTGAAAGCGCCGCTAATG
1 ACTTGACCTTTAGCGGCGCTTATGTGAAAGCGCCGCTAATG
42114353 ACTTGACCTTTAGCGGCGCTTATGTGAAAGCGCCGCTAATG
1 ACTTGACCTTTAGCGGCGCTTATGTGAAAGCGCCGCTAATG
* *
42114394 TC-TGACCTTTAGCGCCGCT
1 ACTTGACCTTTAGCGGCGCT
42114413 ACTGACCTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 16 0.28
41 41 0.72
ACGTcount: A:0.20, C:0.26, G:0.27, T:0.28
Consensus pattern (41 bp):
ACTTGACCTTTAGCGGCGCTTATGTGAAAGCGCCGCTAATG
Found at i:42114456 original size:105 final size:107
Alignment explanation
Indices: 42114264--42114457 Score: 266
Period size: 105 Copynumber: 1.8 Consensus size: 107
42114254 GCTTTCGACA
* * * * *
42114264 CTTATGAGAAAAGCGCCGCTAATGACCTGACCTTTAGCGGCGCTTCCCACTTGACCTTTAGCGGG
1 CTTATGAGAAAAGCGCCGCTAATGACCTGACCTTTAGCGCCGCTACCCACCTAACCTTTAGCGGC
*
42114329 GCTTATGTGAAAGCGCCGCTAATGACTTGACCTTTAGCGGCG
66 GCTTATGGGAAAGCGCCGCTAATGACTTGACCTTTAGCGGCG
* * ** *
42114371 CTTATGTG-AAAGCGCCGCTAATG-TCTGACCTTTAGCGCCGCTACTGACCTAACCTTTAGTGGC
1 CTTATGAGAAAAGCGCCGCTAATGACCTGACCTTTAGCGCCGCTACCCACCTAACCTTTAGCGGC
*
42114434 GTTTATGGGAAAGCGCCGCTAATG
66 GCTTATGGGAAAGCGCCGCTAATG
42114458 GCCTGACTTT
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
105 53 0.71
106 15 0.20
107 7 0.09
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.26
Consensus pattern (107 bp):
CTTATGAGAAAAGCGCCGCTAATGACCTGACCTTTAGCGCCGCTACCCACCTAACCTTTAGCGGC
GCTTATGGGAAAGCGCCGCTAATGACTTGACCTTTAGCGGCG
Found at i:42114557 original size:12 final size:12
Alignment explanation
Indices: 42114542--42114566 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42114532 CCTATTGCTT
42114542 TACCTTTTGCGG
1 TACCTTTTGCGG
42114554 TACCTTTTGCGG
1 TACCTTTTGCGG
42114566 T
1 T
42114567 GTTTTCTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.24, G:0.24, T:0.44
Consensus pattern (12 bp):
TACCTTTTGCGG
Found at i:42116256 original size:23 final size:23
Alignment explanation
Indices: 42116230--42116322 Score: 107
Period size: 23 Copynumber: 4.0 Consensus size: 23
42116220 TTAATGTTCA
*
42116230 CGAACATGTTCATTTAAC-TTAAT
1 CGAACATGTTCA-TGAACATTAAT
* * *
42116253 CGAATATGTTCACGAACAATAAT
1 CGAACATGTTCATGAACATTAAT
*
42116276 CGAACATGTTCATGAACATTAAA
1 CGAACATGTTCATGAACATTAAT
*
42116299 CGAACATGTTCATTAACATATAAT
1 CGAACATGTTCATGAACAT-TAAT
42116323 TGGACACGTT
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
22 3 0.05
23 52 0.90
24 3 0.05
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (23 bp):
CGAACATGTTCATGAACATTAAT
Found at i:42116456 original size:23 final size:24
Alignment explanation
Indices: 42116426--42116470 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
42116416 ATCATTAATA
42116426 AATAAACGAGC-TATAAACGAGTT
1 AATAAACGAGCTTATAAACGAGTT
*
42116449 AATAAACGAGCTTTTAAACGAG
1 AATAAACGAGCTTATAAACGAG
42116471 CTTGTTCGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.47, C:0.13, G:0.18, T:0.22
Consensus pattern (24 bp):
AATAAACGAGCTTATAAACGAGTT
Found at i:42116473 original size:12 final size:12
Alignment explanation
Indices: 42116427--42116473 Score: 62
Period size: 12 Copynumber: 4.0 Consensus size: 12
42116417 TCATTAATAA
42116427 ATAAACGAGC-T
1 ATAAACGAGCTT
42116438 ATAAACGAG-TT
1 ATAAACGAGCTT
42116449 AATAAACGAGCTT
1 -ATAAACGAGCTT
*
42116462 TTAAACGAGCTT
1 ATAAACGAGCTT
42116474 GTTCGTGAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
11 10 0.31
12 20 0.62
13 2 0.06
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.26
Consensus pattern (12 bp):
ATAAACGAGCTT
Found at i:42119577 original size:28 final size:28
Alignment explanation
Indices: 42119525--42119581 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
42119515 TATCTATTTA
*
42119525 TAATTACTTTACTTTTTTATTTATAATT
1 TAATTACTTTACTTTTTTATATATAATT
42119553 TAATTA-TTTA-TTTTTTATAAATATAATT
1 TAATTACTTTACTTTTTTAT--ATATAATT
42119581 T
1 T
42119582 TGATATTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 8 0.31
27 4 0.15
28 14 0.54
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (28 bp):
TAATTACTTTACTTTTTTATATATAATT
Found at i:42121550 original size:12 final size:12
Alignment explanation
Indices: 42121533--42121561 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
42121523 GGCCGGGCAG
42121533 CAGCAGCAGCAC
1 CAGCAGCAGCAC
42121545 CAGCAGCAGCAC
1 CAGCAGCAGCAC
42121557 CAGCA
1 CAGCA
42121562 CCGAAGCGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.41, G:0.24, T:0.00
Consensus pattern (12 bp):
CAGCAGCAGCAC
Found at i:42134977 original size:13 final size:13
Alignment explanation
Indices: 42134959--42134987 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
42134949 ACACAATGAT
42134959 GGCTGGTGATGGG
1 GGCTGGTGATGGG
42134972 GGCTGGTGATGGG
1 GGCTGGTGATGGG
42134985 GGC
1 GGC
42134988 ATCGCATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.10, G:0.62, T:0.21
Consensus pattern (13 bp):
GGCTGGTGATGGG
Found at i:42138041 original size:7 final size:7
Alignment explanation
Indices: 42138029--42138063 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
42138019 ATATTATATA
42138029 AAAGCAC
1 AAAGCAC
42138036 AAAGCAC
1 AAAGCAC
42138043 AAAGCAC
1 AAAGCAC
42138050 AAAGCAC
1 AAAGCAC
42138057 AAAGCAC
1 AAAGCAC
42138064 GATACCATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.57, C:0.29, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAGCAC
Found at i:42139003 original size:19 final size:19
Alignment explanation
Indices: 42138959--42139003 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
42138949 CTTAAAATTC
*
42138959 AAAATAAAATTATTGATAT
1 AAAATAAAATTATTGATAA
*
42138978 AACATAAAATTATTGA-AA
1 AAAATAAAATTATTGATAA
42138996 AGAAATAA
1 A-AAATAA
42139004 TAACCCTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 2 0.09
19 20 0.91
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (19 bp):
AAAATAAAATTATTGATAA
Found at i:42141707 original size:18 final size:18
Alignment explanation
Indices: 42141677--42141713 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
42141667 ATTTTATAAT
42141677 TTTTAAAACATTATTAAA
1 TTTTAAAACATTATTAAA
42141695 TTTTATAAA-ATTATTAAA
1 TTTTA-AAACATTATTAAA
42141713 T
1 T
42141714 AAAATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTTAAAACATTATTAAA
Found at i:42143057 original size:31 final size:31
Alignment explanation
Indices: 42142989--42143058 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
42142979 CTTAATACTA
* * * *
42142989 AATTTAGTTTTCAATATTTATATATTTTATC
1 AATTTAATTTTAAATATTTATAAAATTTATC
*
42143020 AATTTAATTTTAAATATTTATAAAATTTGTC
1 AATTTAATTTTAAATATTTATAAAATTTATC
*
42143051 ATTTTAAT
1 AATTTAAT
42143059 CGGAACCGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.56
Consensus pattern (31 bp):
AATTTAATTTTAAATATTTATAAAATTTATC
Found at i:42145390 original size:3 final size:3
Alignment explanation
Indices: 42145382--42145422 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
42145372 GGAAAAAGTA
*
42145382 AAG AAG AAG CAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
42145423 AAAGGAAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.66, C:0.02, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:42158866 original size:36 final size:36
Alignment explanation
Indices: 42158821--42158920 Score: 155
Period size: 36 Copynumber: 2.8 Consensus size: 36
42158811 ACAACATAAT
42158821 GCTCGCATACAACATATGGGTTCGCACATATTCATG
1 GCTCGCATACAACATATGGGTTCGCACATATTCATG
* * * *
42158857 GTTTGCATACAAGATATGGGTTCGCACATGTTCATG
1 GCTCGCATACAACATATGGGTTCGCACATATTCATG
*
42158893 GCTCGCATACAACATATAGGTTCGCACA
1 GCTCGCATACAACATATGGGTTCGCACA
42158921 CAACATGGGG
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (36 bp):
GCTCGCATACAACATATGGGTTCGCACATATTCATG
Found at i:42159018 original size:19 final size:19
Alignment explanation
Indices: 42158947--42159018 Score: 78
Period size: 18 Copynumber: 3.9 Consensus size: 19
42158937 AATAACATGG
*
42158947 GGCTCGCACATGTATA-TA
1 GGCTCGCACATATATATTA
*
42158965 GGCTCGCACAACATATATTA
1 GGCTCGCAC-ATATATATTA
* *
42158985 -GCTCGCATA-AAATATTA
1 GGCTCGCACATATATATTA
42159002 GGCTCGCACATATATAT
1 GGCTCGCACATATATAT
42159019 AAACTCGCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
17 7 0.16
18 18 0.41
19 17 0.39
20 2 0.05
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (19 bp):
GGCTCGCACATATATATTA
Found at i:42170914 original size:26 final size:27
Alignment explanation
Indices: 42170872--42170924 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
42170862 GATTGAATAT
*
42170872 ATTGATTCATGCTCATTGTCT-TTTAAA
1 ATTGATTCAGGCTCATT-TCTATTTAAA
42170899 ATTGATT-AGGCTCATTTCTATTTAAA
1 ATTGATTCAGGCTCATTTCTATTTAAA
42170925 TTTAATCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 3 0.12
26 14 0.58
27 7 0.29
ACGTcount: A:0.28, C:0.13, G:0.11, T:0.47
Consensus pattern (27 bp):
ATTGATTCAGGCTCATTTCTATTTAAA
Found at i:42172030 original size:22 final size:20
Alignment explanation
Indices: 42172005--42172064 Score: 50
Period size: 24 Copynumber: 2.9 Consensus size: 20
42171995 TGGAAATAAA
42172005 AAATAAAAAAATAAAATCATCC
1 AAATAAAAAAATAAAATC--CC
* *
42172027 AAATTCAAAATAATACAATCCC
1 AAA-T-AAAAAAATAAAATCCC
*
42172049 AAA-AATAAAATAAAAT
1 AAATAAAAAAATAAAAT
42172065 AAAATAAAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
19 10 0.32
22 8 0.26
23 1 0.03
24 12 0.39
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.20
Consensus pattern (20 bp):
AAATAAAAAAATAAAATCCC
Found at i:42186505 original size:18 final size:19
Alignment explanation
Indices: 42186472--42186507 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
42186462 AATCTAAAAA
42186472 AAAATCTTTGAAGAAATTG
1 AAAATCTTTGAAGAAATTG
*
42186491 AAAATC-TTGAGGAAATT
1 AAAATCTTTGAAGAAATT
42186508 CAGTATAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.31
Consensus pattern (19 bp):
AAAATCTTTGAAGAAATTG
Found at i:42192177 original size:16 final size:16
Alignment explanation
Indices: 42192132--42192177 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
42192122 ATAATAAAAA
*
42192132 AATATTTTATATATAA-
1 AATAATTTATATA-AAT
42192148 AATAATTTA-A-AAAT
1 AATAATTTATATAAAT
42192162 AATAATTTATATAAAT
1 AATAATTTATATAAAT
42192178 TAGCAAACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 2 0.08
14 10 0.38
15 2 0.08
16 12 0.46
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATAATTTATATAAAT
Found at i:42192610 original size:8 final size:8
Alignment explanation
Indices: 42192597--42192650 Score: 90
Period size: 8 Copynumber: 6.8 Consensus size: 8
42192587 GCTTCTATAT
42192597 ATCAAGCA
1 ATCAAGCA
42192605 ATCAAGCA
1 ATCAAGCA
42192613 ATCAAGCA
1 ATCAAGCA
42192621 ATCAAGCA
1 ATCAAGCA
*
42192629 TTCAAGCA
1 ATCAAGCA
42192637 ATCAAGCA
1 ATCAAGCA
*
42192645 TTCAAG
1 ATCAAG
42192651 AACAAGATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 43 1.00
ACGTcount: A:0.46, C:0.24, G:0.13, T:0.17
Consensus pattern (8 bp):
ATCAAGCA
Found at i:42194526 original size:18 final size:17
Alignment explanation
Indices: 42194499--42194546 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 17
42194489 CCCATTTTGG
42194499 ATTTATTTTAAATTTAA
1 ATTTATTTTAAATTTAA
42194516 ATTTATGTTTAAATTTAA
1 ATTTAT-TTTAAATTTAA
* *
42194534 AATTATTCTAAAT
1 ATTTATTTTAAAT
42194547 AATGAAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 12 0.43
18 16 0.57
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (17 bp):
ATTTATTTTAAATTTAA
Found at i:42197039 original size:6 final size:6
Alignment explanation
Indices: 42197028--42197097 Score: 63
Period size: 6 Copynumber: 12.0 Consensus size: 6
42197018 TTAGAATAAT
** * * *
42197028 TTTAAA TTTAAA CATAAA TTTAAA TTTAAA TTTTAA --CAAA TTCAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
**
42197074 TTTAAA AATAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
42197098 ATAAATCCAA
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
4 2 0.04
6 48 0.96
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:42197692 original size:49 final size:49
Alignment explanation
Indices: 42197549--42197762 Score: 175
Period size: 49 Copynumber: 4.4 Consensus size: 49
42197539 ATGTTTTCGT
* * * *
42197549 GGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCGT-GCTTC-C
1 GGTACTAGATTCGCCGTTACGACTTAAATCTTTCCCTTCATATCTTCAC
* * * * * *
42197596 -GTGATGTAAGTTTTGCCATTACGACTT-AACCTTTCCCTTCATTTCTTCAC
1 GGT-A-CT-AGATTCGCCGTTACGACTTAAATCTTTCCCTTCATATCTTCAC
* * * *
42197646 GGTACTAGATTCGCCGTTACGGCTTAAATCTTTTCCTTCGTATCTTCAT
1 GGTACTAGATTCGCCGTTACGACTTAAATCTTTCCCTTCATATCTTCAC
* ** * * *
42197695 GGTACTGGATTCATCGTTGCGACTTAAATCTTTTCCCATCATATCTTCAT
1 GGTACTAGATTCGCCGTTACGACTTAAATC-TTTCCCTTCATATCTTCAC
*
42197745 GGTACTAGATTAGCCGTT
1 GGTACTAGATTCGCCGTT
42197763 GCGATCCACC
Statistics
Matches: 128, Mismatches: 31, Indels: 13
0.74 0.18 0.08
Matches are distributed among these distances:
46 2 0.02
47 1 0.01
48 29 0.23
49 62 0.48
50 32 0.25
51 2 0.02
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.39
Consensus pattern (49 bp):
GGTACTAGATTCGCCGTTACGACTTAAATCTTTCCCTTCATATCTTCAC
Found at i:42197763 original size:50 final size:50
Alignment explanation
Indices: 42197627--42197766 Score: 176
Period size: 49 Copynumber: 2.8 Consensus size: 50
42197617 CGACTTAACC
* * * * *
42197627 TTTCCCTTCATTTCTTCACGGTACTAGATTCGCCGTTACGGCTTAAATCT
1 TTTCCCTTCATATCTTCATGGTACTAGATTAGCCGTTGCGACTTAAATCT
* * *
42197677 TTT-CCTTCGTATCTTCATGGTACTGGATTCA-TCGTTGCGACTTAAATCT
1 TTTCCCTTCATATCTTCATGGTACTAGATT-AGCCGTTGCGACTTAAATCT
*
42197726 TTTCCCATCATATCTTCATGGTACTAGATTAGCCGTTGCGA
1 TTTCCCTTCATATCTTCATGGTACTAGATTAGCCGTTGCGA
42197767 TCCACCCTTT
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
49 41 0.55
50 34 0.45
ACGTcount: A:0.19, C:0.25, G:0.16, T:0.40
Consensus pattern (50 bp):
TTTCCCTTCATATCTTCATGGTACTAGATTAGCCGTTGCGACTTAAATCT
Found at i:42199012 original size:51 final size:50
Alignment explanation
Indices: 42198900--42199124 Score: 219
Period size: 50 Copynumber: 4.5 Consensus size: 50
42198890 TTTCGGGATT
*
42198900 TCTTAGATCTTTCCCTTCATGTTTTTGAGGTACACGGTCCGTCGTTGCGA
1 TCTTAGATCTTTCCCTTCATGTTTTTGAGGTACACGGTCCGCCGTTGCGA
* * * * *
42198950 -CTTAGACCTTTCCCTT-TTGTATCTTTGTGGTAC-TGGATCCGCCGTCGCGA
1 TCTTAGATCTTTCCCTTCATGT-T-TTTGAGGTACACGG-TCCGCCGTTGCGA
* *
42199000 TCTTAGATCTTTCCCTTCATGTTTCTGAGGTACACGGTCCGCCGTAGCG-
1 TCTTAGATCTTTCCCTTCATGTTTTTGAGGTACACGGTCCGCCGTTGCGA
* * * * * * *
42199049 GCTTATACCTTTCCCTT-TTGTATCTTTGTGGTAC-TGGATCCGCCGTTGCGG
1 TCTTAGATCTTTCCCTTCATGT-T-TTTGAGGTACACGG-TCCGCCGTTGCGA
42199100 TCTTAGATCTTTCCCTTCATGTTTT
1 TCTTAGATCTTTCCCTTCATGTTTT
42199125 CATGGTATTG
Statistics
Matches: 140, Mismatches: 24, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
48 6 0.04
49 35 0.25
50 60 0.43
51 33 0.24
52 6 0.04
ACGTcount: A:0.12, C:0.26, G:0.21, T:0.40
Consensus pattern (50 bp):
TCTTAGATCTTTCCCTTCATGTTTTTGAGGTACACGGTCCGCCGTTGCGA
Found at i:42199073 original size:100 final size:100
Alignment explanation
Indices: 42198900--42199123 Score: 385
Period size: 100 Copynumber: 2.2 Consensus size: 100
42198890 TTTCGGGATT
* * *
42198900 TCTTAGATCTTTCCCTTCATGTTTTTGAGGTACACGGTCCGTCGTTGCGACTTAGACCTTTCCCT
1 TCTTAGATCTTTCCCTTCATGTTTCTGAGGTACACGGTCCGCCGTAGCGACTTAGACCTTTCCCT
42198965 TTTGTATCTTTGTGGTACTGGATCCGCCGTCGCGA
66 TTTGTATCTTTGTGGTACTGGATCCGCCGTCGCGA
* *
42199000 TCTTAGATCTTTCCCTTCATGTTTCTGAGGTACACGGTCCGCCGTAGCGGCTTATACCTTTCCCT
1 TCTTAGATCTTTCCCTTCATGTTTCTGAGGTACACGGTCCGCCGTAGCGACTTAGACCTTTCCCT
* *
42199065 TTTGTATCTTTGTGGTACTGGATCCGCCGTTGCGG
66 TTTGTATCTTTGTGGTACTGGATCCGCCGTCGCGA
42199100 TCTTAGATCTTTCCCTTCATGTTT
1 TCTTAGATCTTTCCCTTCATGTTT
42199124 TCATGGTATT
Statistics
Matches: 117, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 117 1.00
ACGTcount: A:0.12, C:0.26, G:0.21, T:0.40
Consensus pattern (100 bp):
TCTTAGATCTTTCCCTTCATGTTTCTGAGGTACACGGTCCGCCGTAGCGACTTAGACCTTTCCCT
TTTGTATCTTTGTGGTACTGGATCCGCCGTCGCGA
Found at i:42203098 original size:71 final size:70
Alignment explanation
Indices: 42203005--42203155 Score: 218
Period size: 71 Copynumber: 2.1 Consensus size: 70
42202995 ACGTCTCGTG
42203005 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGAT-T-AGCACTT-TGTGTACTCTCTGATTAGTA
1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATCTCAGCACTTATGTG--CTCTCTG-TTAGTA
42203067 CTTTGTGTA
63 CTTTG-GTA
* *
42203076 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGTTGCTCAGCACTTATGTGCTCTTTGTTAGTACT
1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGAT-CTCAGCACTTATGTGCTCTCTGTTAGTACT
42203141 TTGGTA
65 TTGGTA
42203147 CTCTCTGTT
1 CTCTCTGTT
42203156 TGTTCCGTAT
Statistics
Matches: 74, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
71 45 0.61
72 11 0.15
73 7 0.09
74 7 0.09
75 4 0.05
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.46
Consensus pattern (70 bp):
CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATCTCAGCACTTATGTGCTCTCTGTTAGTACTT
TGGTA
Found at i:42203109 original size:25 final size:25
Alignment explanation
Indices: 42202979--42203135 Score: 150
Period size: 23 Copynumber: 6.5 Consensus size: 25
42202969 GAACACTAGC
*
42202979 GTGCTCTCTG-T-TTAGCAC-GTCT
1 GTGCTCTCTGTTATTAGCACTGTGT
42203001 CGTGCTCTCTGTTATTAGCACTGTGT
1 -GTGCTCTCTGTTATTAGCACTGTGT
*
42203027 GTGCTCTCTG--ATTAGCACTTTGT
1 GTGCTCTCTGTTATTAGCACTGTGT
* * *
42203050 GTACTCTCTG--ATTAGTACTTTGT
1 GTGCTCTCTGTTATTAGCACTGTGT
*
42203073 GTACTCTCTGTTATTAGCACTGTGT
1 GTGCTCTCTGTTATTAGCACTGTGT
* * *
42203098 GTGCTCTCTGTTGCTCAGCACT-TAT
1 GTGCTCTCTGTT-ATTAGCACTGTGT
*
42203123 GTGCTCTTTGTTA
1 GTGCTCTCTGTTA
42203136 GTACTTTGGT
Statistics
Matches: 116, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
23 53 0.46
24 1 0.01
25 52 0.45
26 10 0.09
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (25 bp):
GTGCTCTCTGTTATTAGCACTGTGT
Found at i:42205939 original size:6 final size:6
Alignment explanation
Indices: 42205924--42205952 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
42205914 AAATAACATG
42205924 AATA-A AATATA AATATA AATATA AATATA
1 AATATA AATATA AATATA AATATA AATATA
42205953 TACAATCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AATATA
Found at i:42216383 original size:29 final size:34
Alignment explanation
Indices: 42216342--42216404 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 34
42216332 ATCTTTATAA
*
42216342 TTTTATAAGATTAAA-TTTAA-TTT-TTATTATT
1 TTTTATAAGATTAAAGTATAATTTTGTTATTATT
42216373 TTTTAT-A-ATTAAAGTATAATTTTGTTATTATT
1 TTTTATAAGATTAAAGTATAATTTTGTTATTATT
42216405 GATTTAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 6 0.21
30 5 0.18
31 9 0.32
32 8 0.29
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (34 bp):
TTTTATAAGATTAAAGTATAATTTTGTTATTATT
Found at i:42217185 original size:15 final size:16
Alignment explanation
Indices: 42217165--42217194 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42217155 CCAAGTTTGA
42217165 TCTTTT-TAAATTTAG
1 TCTTTTATAAATTTAG
42217180 TCTTTTATAAATTTA
1 TCTTTTATAAATTTA
42217195 CACTATGACC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (16 bp):
TCTTTTATAAATTTAG
Found at i:42219882 original size:26 final size:26
Alignment explanation
Indices: 42219824--42219880 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
42219814 TTTCTGTACT
42219824 ATTAAAA-AAAATTAAATAATATTAA
1 ATTAAAATAAAATTAAATAATATTAA
*
42219849 ATTAAAATAAAATT-AATATTTATT-A
1 ATTAAAATAAAATTAAATA-ATATTAA
42219874 ATTAAAA
1 ATTAAAA
42219881 ATTATCATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 19 0.66
26 10 0.34
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
ATTAAAATAAAATTAAATAATATTAA
Found at i:42221070 original size:18 final size:19
Alignment explanation
Indices: 42221047--42221082 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
42221037 AAATCTATTT
42221047 ATCAAA-CTTATATTTTTG
1 ATCAAATCTTATATTTTTG
*
42221065 ATCAAATCTTTTATTTTT
1 ATCAAATCTTATATTTTT
42221083 TGAGTGGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.31, C:0.11, G:0.03, T:0.56
Consensus pattern (19 bp):
ATCAAATCTTATATTTTTG
Found at i:42222824 original size:4 final size:4
Alignment explanation
Indices: 42222817--42222846 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
42222807 TCTCTCTCTA
42222817 TATG TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TA
42222847 CACACTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:42223857 original size:34 final size:34
Alignment explanation
Indices: 42223815--42223885 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
42223805 AAGGAACGGT
* *
42223815 TTTTGAAGCAAGGTAAATCATTACATTCTTAATG
1 TTTTGAAGCAAGGTAAAGCATTAAATTCTTAATG
42223849 TTTTGAAGCAAGGTAAAGCATTAAATTCTTAATG
1 TTTTGAAGCAAGGTAAAGCATTAAATTCTTAATG
42223883 TTT
1 TTT
42223886 GAGTCATCCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.39
Consensus pattern (34 bp):
TTTTGAAGCAAGGTAAAGCATTAAATTCTTAATG
Found at i:42225207 original size:6 final size:6
Alignment explanation
Indices: 42225165--42225206 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
42225155 TTTACATAAC
*
42225165 AGCCTG AGCCTG AGCCTG AGCCTG AGCCTG AGCCTG TGCCTG
1 AGCCTG AGCCTG AGCCTG AGCCTG AGCCTG AGCCTG AGCCTG
42225207 TCCCCTTCCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.14, C:0.33, G:0.33, T:0.19
Consensus pattern (6 bp):
AGCCTG
Found at i:42240193 original size:10 final size:9
Alignment explanation
Indices: 42240097--42240321 Score: 92
Period size: 9 Copynumber: 24.3 Consensus size: 9
42240087 TCGTAAAAAG
42240097 AAATTATAA
1 AAATTATAA
42240106 AAATTATATA
1 AAATTATA-A
* *
42240116 AAGTAATAA
1 AAATTATAA
*
42240125 AAAGTATTAA
1 AAATTA-TAA
*
42240135 AAAGTTTTAA
1 AAA-TTATAA
42240145 AATATT-T-A
1 AA-ATTATAA
42240153 AAATTA-AA
1 AAATTATAA
*
42240161 AAATTAGAGA
1 AAATTATA-A
42240171 AAATTATAA
1 AAATTATAA
*
42240180 AAATTATTAT
1 AAATTA-TAA
*
42240190 AAA-TAAAA
1 AAATTATAA
42240198 AAATTATAA
1 AAATTATAA
**
42240207 AAA--A-GG
1 AAATTATAA
*
42240213 AAATTACAA
1 AAATTATAA
* *
42240222 ATA-TATTA
1 AAATTATAA
*
42240230 AATTTATAA
1 AAATTATAA
*
42240239 AAAATAT-A
1 AAATTATAA
42240247 AAATCTATATA
1 AAAT-TATA-A
42240258 AAATTATGAAA
1 AAATTAT--AA
*
42240269 AAAATATAA
1 AAATTATAA
42240278 GAAATTATAAAAA
1 -AAATTAT---AA
42240291 AAATTATTTAA
1 AAATTA--TAA
*
42240302 AAATAATAA
1 AAATTATAA
42240311 AAATTA-AA
1 AAATTATAA
42240319 AAA
1 AAA
42240322 AAAAGGATGA
Statistics
Matches: 162, Mismatches: 29, Indels: 51
0.67 0.12 0.21
Matches are distributed among these distances:
6 3 0.02
7 4 0.02
8 28 0.17
9 54 0.33
10 42 0.26
11 21 0.13
12 7 0.04
13 2 0.01
14 1 0.01
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (9 bp):
AAATTATAA
Found at i:42240243 original size:11 final size:10
Alignment explanation
Indices: 42240233--42240322 Score: 55
Period size: 11 Copynumber: 9.0 Consensus size: 10
42240223 TATATTAAAT
42240233 TTATAAAAAA
1 TTATAAAAAA
42240243 -TAT--AAAA
1 TTATAAAAAA
*
42240250 TCTATATAAAA
1 T-TATAAAAAA
42240261 TTATGAAAAAA
1 TTAT-AAAAAA
* *
42240272 ATATAAGAAA
1 TTATAAAAAA
42240282 TTATAAAAAAAA
1 TTAT--AAAAAA
*
42240294 TTATTTAAAAA
1 TTA-TAAAAAA
*
42240305 TAAT-AAAAA
1 TTATAAAAAA
42240314 TTA-AAAAAA
1 TTATAAAAAA
42240323 AAAGGATGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
7 4 0.06
9 18 0.29
10 12 0.19
11 20 0.32
12 8 0.13
13 1 0.02
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:42240276 original size:21 final size:22
Alignment explanation
Indices: 42240246--42240316 Score: 69
Period size: 21 Copynumber: 3.3 Consensus size: 22
42240236 TAAAAAATAT
*
42240246 AAAATCTATATAAAATTATGAAA
1 AAAAT-TATATAAAATTATAAAA
42240269 AAAA-TATA-AGAAATTATAAAA
1 AAAATTATATA-AAATTATAAAA
* *
42240290 AAAATTATTTAAAA--ATAATA
1 AAAATTATATAAAATTATAAAA
42240310 AAAATTA
1 AAAATTA
42240317 AAAAAAAAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
20 13 0.31
21 18 0.43
22 6 0.14
23 5 0.12
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (22 bp):
AAAATTATATAAAATTATAAAA
Found at i:42240304 original size:33 final size:32
Alignment explanation
Indices: 42240257--42240325 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 32
42240247 AAATCTATAT
*
42240257 AAAATTATGAAAAAA-ATATAAGAAATTATAAAA
1 AAAATTATGAAAAAATA-ATAA-AAATTAAAAAA
**
42240290 AAAATTATTTAAAAATAATAAAAATTAAAAAA
1 AAAATTATGAAAAAATAATAAAAATTAAAAAA
42240322 AAAA
1 AAAA
42240326 GGATGATTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 14 0.44
33 17 0.53
34 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (32 bp):
AAAATTATGAAAAAATAATAAAAATTAAAAAA
Found at i:42240434 original size:17 final size:17
Alignment explanation
Indices: 42240412--42240463 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
42240402 TATATATAAA
*
42240412 ATTTTAGATATTTTTTT
1 ATTTTATATATTTTTTT
*
42240429 ATTTTATA-ATTTTTGTA
1 ATTTTATATATTTTT-TT
42240446 ATTTTATATTATTTTTTT
1 ATTTTATA-TATTTTTTT
42240464 TTATATTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 6 0.21
17 16 0.55
18 1 0.03
19 6 0.21
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (17 bp):
ATTTTATATATTTTTTT
Found at i:42240479 original size:31 final size:32
Alignment explanation
Indices: 42240419--42240481 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 32
42240409 AAAATTTTAG
*
42240419 ATATTTTTTTATTTTATAATTTTTGTAATTTT
1 ATATTTTTTTATTTTATAATTTTTCTAATTTT
42240451 ATATTATTTTT-TTTTAT-ATTTTTCTAATTTT
1 ATATT-TTTTTATTTTATAATTTTTCTAATTTT
42240482 CTAATGTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 13 0.45
32 11 0.38
33 5 0.17
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (32 bp):
ATATTTTTTTATTTTATAATTTTTCTAATTTT
Found at i:42240492 original size:31 final size:33
Alignment explanation
Indices: 42240424--42240493 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 33
42240414 TTTAGATATT
* *
42240424 TTTTTATTTTATAATTTTTGTAATTTTATATTA
1 TTTTTATTTTATAATTTTTCTAATTTTATAATA
* *
42240457 TTTTT-TTTTAT-ATTTTTCTAATTTTCTAATG
1 TTTTTATTTTATAATTTTTCTAATTTTATAATA
42240488 TTTTTA
1 TTTTTA
42240494 AATGATTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 21 0.66
32 6 0.19
33 5 0.16
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (33 bp):
TTTTTATTTTATAATTTTTCTAATTTTATAATA
Found at i:42240544 original size:20 final size:20
Alignment explanation
Indices: 42240508--42240546 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
42240498 ATTTTAATAT
42240508 TATATATTTTTACAATTTTC
1 TATATATTTTTACAATTTTC
*
42240528 TATA-ATTTGTTATAATTTT
1 TATATATTT-TTACAATTTT
42240547 TTGTGCACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (20 bp):
TATATATTTTTACAATTTTC
Found at i:42240580 original size:22 final size:21
Alignment explanation
Indices: 42240530--42240590 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
42240520 CAATTTTCTA
42240530 TAATTTGTTATAATTTTTTGTG
1 TAATTT-TTATAATTTTTTGTG
* * *
42240552 CACTTTTCTATAATTTTTTTTG
1 TAATTTT-TATAATTTTTTGTG
* *
42240574 TAATTTTAAGAATTTTT
1 TAATTTTTATAATTTTT
42240591 AATCGTTTCC
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
21 9 0.29
22 22 0.71
ACGTcount: A:0.25, C:0.05, G:0.08, T:0.62
Consensus pattern (21 bp):
TAATTTTTATAATTTTTTGTG
Found at i:42243285 original size:14 final size:14
Alignment explanation
Indices: 42243252--42243278 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42243242 ATAATATATA
42243252 TATAAAAATTAAAG
1 TATAAAAATTAAAG
42243266 TATAAAAATTAAA
1 TATAAAAATTAAA
42243279 TCTTAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (14 bp):
TATAAAAATTAAAG
Found at i:42243610 original size:24 final size:24
Alignment explanation
Indices: 42243570--42243628 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
42243560 CCGCTCATAT
* *
42243570 TATTTTTAATTCT-TTTTAAAATA
1 TATTTTTTATTTTATTTTAAAATA
*
42243593 T-TTATTTTATTTTATTTTAATATA
1 TATT-TTTTATTTTATTTTAAAATA
42243617 TATTTTTTATTT
1 TATTTTTTATTT
42243629 ATTGAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 2 0.07
23 8 0.27
24 18 0.60
25 2 0.07
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (24 bp):
TATTTTTTATTTTATTTTAAAATA
Found at i:42243620 original size:22 final size:23
Alignment explanation
Indices: 42243589--42243631 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
42243579 TTCTTTTTAA
*
42243589 AATATTTATTTTAT-TTTATTTT
1 AATATATATTTTATATTTATTTT
*
42243611 AATATATATTTTTTATTTATT
1 AATATATATTTTATATTTATT
42243632 GAAAATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
AATATATATTTTATATTTATTTT
Found at i:42246394 original size:20 final size:20
Alignment explanation
Indices: 42246356--42246394 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
42246346 CAGCAAGAAG
*
42246356 AGAAACATAATTTGTATTAT
1 AGAAACATAACTTGTATTAT
42246376 AGAAACATAAGCTTG-ATTA
1 AGAAACATAA-CTTGTATTA
42246395 CATTAATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (20 bp):
AGAAACATAACTTGTATTAT
Done.