Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 89 of 126
Found at i:27460145 original size:15 final size:15
Alignment explanation
Indices: 27460125--27460175 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 15
27460115 ACTACAAAAC
27460125 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
27460140 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
27460159 ATTTATTATTAA-AT
1 ATTTATTATTAATAT
27460173 ATT
1 ATT
27460176 AATATTGGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 5 0.17
15 7 0.23
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:27460277 original size:16 final size:19
Alignment explanation
Indices: 27460258--27460307 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 19
27460248 TGAAATATCA
27460258 AATAATTTATTAA-A-A-T
1 AATAATTTATTAATATATT
27460274 AATAAATTATATTAATTATATT
1 AAT-AATT-TATTAA-TATATT
27460296 AATAATTTATTA
1 AATAATTTATTA
27460308 TATGAGTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 3 0.11
17 4 0.14
18 6 0.21
20 6 0.21
21 5 0.18
22 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AATAATTTATTAATATATT
Found at i:27461364 original size:28 final size:29
Alignment explanation
Indices: 27461326--27461381 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
27461316 CAAATTGACA
*
27461326 ATTTTTTTT-AATTTGATACTTAAACTTG
1 ATTTTTTTTAAAGTTGATACTTAAACTTG
*
27461354 ATTTTTTTTAAAGTTGGTACTTAAACTT
1 ATTTTTTTTAAAGTTGATACTTAAACTT
27461382 TTTGGGATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.29, C:0.07, G:0.09, T:0.55
Consensus pattern (29 bp):
ATTTTTTTTAAAGTTGATACTTAAACTTG
Found at i:27461701 original size:59 final size:59
Alignment explanation
Indices: 27461584--27461713 Score: 163
Period size: 59 Copynumber: 2.2 Consensus size: 59
27461574 TAATAAATTT
* *
27461584 AGATACCAAATTGAATAAAAAAAAGCTTAGGTGCCAAATTAGAAAAAAAATATCAAGTTC
1 AGATACCAAATTGAATAAAAAAAAGCTTAAGTACCAAATTAG-AAAAAAATATCAAGTTC
* * * * *
27461644 AGATATCAAATTGAATCTAAAAAAAGTTTAAGTATCAAATTAG-AAAAAATATTAAGTTC
1 AGATACCAAATTGAAT-AAAAAAAAGCTTAAGTACCAAATTAGAAAAAAATATCAAGTTC
*
27461703 AAATACCAAAT
1 AGATACCAAAT
27461714 ATTGTATTAA
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
59 24 0.40
60 15 0.25
61 21 0.35
ACGTcount: A:0.54, C:0.10, G:0.11, T:0.25
Consensus pattern (59 bp):
AGATACCAAATTGAATAAAAAAAAGCTTAAGTACCAAATTAGAAAAAAATATCAAGTTC
Found at i:27464442 original size:28 final size:28
Alignment explanation
Indices: 27464410--27464467 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
27464400 ATGATTAAGT
27464410 AGAGGGACCAAATGAATAAATTAACCAA
1 AGAGGGACCAAATGAATAAATTAACCAA
*
27464438 AGAGGGACCAAATGAATAAATTAATCAA
1 AGAGGGACCAAATGAATAAATTAACCAA
27464466 AG
1 AG
27464468 GAAATTAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.53, C:0.12, G:0.19, T:0.16
Consensus pattern (28 bp):
AGAGGGACCAAATGAATAAATTAACCAA
Found at i:27465664 original size:71 final size:75
Alignment explanation
Indices: 27465543--27465718 Score: 234
Period size: 71 Copynumber: 2.3 Consensus size: 75
27465533 CATATTCTCA
* *
27465543 TCAGCTTAGTGTGAGCAGCATCGTAGGGAACAATTATACCGTATCTA-T-GG-CCGCATGTGATG
1 TCAGCTTAGTGTGAGCAGCATCGTAGGGAACAATTATACCGTATCAAGTAGGACCACATGTGATG
27465605 TGAGTCCTTG
66 TGAGTCCTTG
* *
27465615 T-AGCTTAATGTGAGCAGCATCGTAGGGAACAGTTATACCGTATCAATGGCTGAGGTACCACATG
1 TCAGCTTAGTGTGAGCAGCATCGTAGGGAACAATTATACCGTATCAA--G-T-AGG-ACCACATG
27465679 TGATGTGAGTCCTTG
61 TGATGTGAGTCCTTG
*
27465694 TCAGCTTAGTGTGAGTAGCATCGTA
1 TCAGCTTAGTGTGAGCAGCATCGTA
27465719 TACTGGTAAC
Statistics
Matches: 89, Mismatches: 6, Indels: 10
0.85 0.06 0.10
Matches are distributed among these distances:
71 42 0.47
72 1 0.01
75 1 0.01
77 2 0.02
79 22 0.25
80 21 0.24
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (75 bp):
TCAGCTTAGTGTGAGCAGCATCGTAGGGAACAATTATACCGTATCAAGTAGGACCACATGTGATG
TGAGTCCTTG
Found at i:27466252 original size:21 final size:21
Alignment explanation
Indices: 27466228--27466280 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
27466218 CATACTTGTT
*
27466228 TCGGTAGAACTCATGCATGTA
1 TCGGTAGAACTCATGCATGCA
27466249 TCGGTAGAACTCATGCATGCA
1 TCGGTAGAACTCATGCATGCA
27466270 TCGGTAGAACT
1 TCGGTAGAACT
27466281 ACTGATACCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (21 bp):
TCGGTAGAACTCATGCATGCA
Found at i:27469223 original size:24 final size:24
Alignment explanation
Indices: 27469196--27469259 Score: 110
Period size: 24 Copynumber: 2.7 Consensus size: 24
27469186 AATTAATTTG
*
27469196 GGCTCGTAAGAGCTAACCATTCTA
1 GGCTCGTAAGAGCTAACCATCCTA
27469220 GGCTCGTAAGAGCTAACCATCCTA
1 GGCTCGTAAGAGCTAACCATCCTA
*
27469244 GGCTCGTGAGAGCTAA
1 GGCTCGTAAGAGCTAA
27469260 TGTTGTCTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (24 bp):
GGCTCGTAAGAGCTAACCATCCTA
Found at i:27478229 original size:17 final size:18
Alignment explanation
Indices: 27478209--27478269 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 18
27478199 TACATTTCCT
27478209 TTGTCATTGCATTTTA-A
1 TTGTCATTGCATTTTACA
* *
27478226 TTGTCACTGCA-TCTACA
1 TTGTCATTGCATTTTACA
* *
27478243 TTGTTATTGCA-TTTCCA
1 TTGTCATTGCATTTTACA
27478260 TGTGTCATTG
1 T-TGTCATTG
27478270 TAAATTAATG
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
16 3 0.09
17 25 0.71
18 7 0.20
ACGTcount: A:0.20, C:0.18, G:0.15, T:0.48
Consensus pattern (18 bp):
TTGTCATTGCATTTTACA
Found at i:27483407 original size:18 final size:18
Alignment explanation
Indices: 27483384--27483428 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
27483374 GAGAAGGAAT
27483384 AGCATACTGACTCGTTCG
1 AGCATACTGACTCGTTCG
* *
27483402 AGCATACTGGCTCGTTTG
1 AGCATACTGACTCGTTCG
27483420 AGCAATACT
1 AGC-ATACT
27483429 AGCTTGTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (18 bp):
AGCATACTGACTCGTTCG
Found at i:27485813 original size:18 final size:19
Alignment explanation
Indices: 27485779--27485951 Score: 175
Period size: 18 Copynumber: 9.5 Consensus size: 19
27485769 TTTGCAATCT
*
27485779 AGTATTGCTCTTA-CGAGCC
1 AGTA-TGCTCTAATCGAGCC
27485798 AGTATGCTC-AATCGAGCC
1 AGTATGCTCTAATCGAGCC
*
27485816 AGTATGCTCAAAT-GAGCC
1 AGTATGCTCTAATCGAGCC
* *
27485834 AATATGCTCTAA-CGAGCT
1 AGTATGCTCTAATCGAGCC
27485852 AGTATGCTCTAA-CGAGCC
1 AGTATGCTCTAATCGAGCC
27485870 AGTATGCTCTAAT-GAGCC
1 AGTATGCTCTAATCGAGCC
* *
27485888 AGTATGCTC-AAACGAGCG
1 AGTATGCTCTAATCGAGCC
*
27485906 AGTTTGCTCTAAT-GAGCC
1 AGTATGCTCTAATCGAGCC
* * * *
27485924 AATATGCTTTAA-CAAGCT
1 AGTATGCTCTAATCGAGCC
27485942 AGTATGCTCT
1 AGTATGCTCT
27485952 TCCTTCCGCA
Statistics
Matches: 129, Mismatches: 18, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
17 3 0.02
18 117 0.91
19 9 0.07
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (19 bp):
AGTATGCTCTAATCGAGCC
Found at i:27485824 original size:36 final size:36
Alignment explanation
Indices: 27485779--27485951 Score: 204
Period size: 36 Copynumber: 4.8 Consensus size: 36
27485769 TTTGCAATCT
*
27485779 AGTATTGCTCTTACGAGCCAGTATGCTC-AATCGAGCC
1 AGTA-TGCTCTAACGAGCCAGTATGCTCTAAT-GAGCC
* * * * *
27485816 AGTATGCTCAAATGAGCCAATATGCTCTAACGAGCT
1 AGTATGCTCTAACGAGCCAGTATGCTCTAATGAGCC
27485852 AGTATGCTCTAACGAGCCAGTATGCTCTAATGAGCC
1 AGTATGCTCTAACGAGCCAGTATGCTCTAATGAGCC
* * *
27485888 AGTATGCTCAAACGAGCGAGTTTGCTCTAATGAGCC
1 AGTATGCTCTAACGAGCCAGTATGCTCTAATGAGCC
* * * *
27485924 AATATGCTTTAACAAGCTAGTATGCTCT
1 AGTATGCTCTAACGAGCCAGTATGCTCT
27485952 TCCTTCCGCA
Statistics
Matches: 115, Mismatches: 20, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
36 109 0.95
37 6 0.05
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (36 bp):
AGTATGCTCTAACGAGCCAGTATGCTCTAATGAGCC
Found at i:27485849 original size:54 final size:55
Alignment explanation
Indices: 27485784--27485931 Score: 203
Period size: 54 Copynumber: 2.7 Consensus size: 55
27485774 AATCTAGTAT
*
27485784 TGCTCTTACGAGCCAGTATGCTC-AATCGAGCCAGTATGCTCAAATGAGCCAATA
1 TGCTCTAACGAGCCAGTATGCTCTAATCGAGCCAGTATGCTCAAATGAGCCAATA
* * *
27485838 TGCTCTAACGAGCTAGTATGCTCTAA-CGAGCCAGTATGCTCTAATGAGCCAGTA
1 TGCTCTAACGAGCCAGTATGCTCTAATCGAGCCAGTATGCTCAAATGAGCCAATA
* * * *
27485892 TGCTCAAACGAGCGAGTTTGCTCTAAT-GAGCCAATATGCT
1 TGCTCTAACGAGCCAGTATGCTCTAATCGAGCCAGTATGCT
27485932 TTAACAAGCT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
54 82 0.98
55 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (55 bp):
TGCTCTAACGAGCCAGTATGCTCTAATCGAGCCAGTATGCTCAAATGAGCCAATA
Found at i:27492583 original size:12 final size:12
Alignment explanation
Indices: 27492568--27492593 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
27492558 AATTAAAGAA
27492568 ATAATAGCATTC
1 ATAATAGCATTC
27492580 ATAATAGCATTC
1 ATAATAGCATTC
27492592 AT
1 AT
27492594 CATGATAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATAATAGCATTC
Found at i:27495336 original size:24 final size:24
Alignment explanation
Indices: 27495309--27495356 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
27495299 TATCTACAAG
*
27495309 TTAAATATTAAAT-TTAATTTAATA
1 TTAAA-ATTAAATATTAAATTAATA
*
27495333 TTAAAATTTAATATTAAATTAATA
1 TTAAAATTAAATATTAAATTAATA
27495357 AAATACTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TTAAAATTAAATATTAAATTAATA
Found at i:27495339 original size:18 final size:19
Alignment explanation
Indices: 27495312--27495354 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
27495302 CTACAAGTTA
27495312 AATATT-AAATTTAAT-TT
1 AATATTAAAATTTAATATT
27495329 AATATTAAAATTTAATATT
1 AATATTAAAATTTAATATT
27495348 AA-ATTAA
1 AATATTAA
27495355 TAAAATACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.25
18 14 0.58
19 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATATTAAAATTTAATATT
Found at i:27495340 original size:13 final size:13
Alignment explanation
Indices: 27495324--27495350 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
27495314 TATTAAATTT
27495324 AATTTAATATTAA
1 AATTTAATATTAA
27495337 AATTTAATATTAA
1 AATTTAATATTAA
27495350 A
1 A
27495351 TTAATAAAAT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATTTAATATTAA
Found at i:27500397 original size:30 final size:30
Alignment explanation
Indices: 27500352--27500436 Score: 138
Period size: 30 Copynumber: 2.9 Consensus size: 30
27500342 ATGTTAACAA
*
27500352 GACA-TCCCTCACATTTTCAAGTGGTTCTAG
1 GACACTCCC-CACATTTCCAAGTGGTTCTAG
27500382 GACACTCCCCACATTTCCAAGTGGTTCTAG
1 GACACTCCCCACATTTCCAAGTGGTTCTAG
27500412 GACAC-CCCCACATTTCCAAGTGGTT
1 GACACTCCCCACATTTCCAAGTGGTT
27500437 ATCTTGTCTC
Statistics
Matches: 53, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
29 20 0.38
30 29 0.55
31 4 0.08
ACGTcount: A:0.24, C:0.32, G:0.16, T:0.28
Consensus pattern (30 bp):
GACACTCCCCACATTTCCAAGTGGTTCTAG
Found at i:27504151 original size:29 final size:30
Alignment explanation
Indices: 27504072--27504185 Score: 151
Period size: 29 Copynumber: 3.9 Consensus size: 30
27504062 ATGTTAATAA
* *
27504072 GACACCCCTCATATTTTCAAGTGGTTCTAG
1 GACACCCCTCACATTTCCAAGTGGTTCTAG
* * **
27504102 GACACCCCTCATATTTTCAAGCAGTTCTAG
1 GACACCCCTCACATTTCCAAGTGGTTCTAG
27504132 GACA-CCCTCACATTTCCAAGTGGTTCTAG
1 GACACCCCTCACATTTCCAAGTGGTTCTAG
*
27504161 GACACTCC-CACATTTCCAAGTGGTT
1 GACACCCCTCACATTTCCAAGTGGTT
27504186 ATCTTGTCTC
Statistics
Matches: 76, Mismatches: 7, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
29 42 0.55
30 34 0.45
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.30
Consensus pattern (30 bp):
GACACCCCTCACATTTCCAAGTGGTTCTAG
Found at i:27507321 original size:3 final size:3
Alignment explanation
Indices: 27507313--27507348 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
27507303 TTTCTACCAG
27507313 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
27507349 TAAAACGTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:27519308 original size:19 final size:18
Alignment explanation
Indices: 27519273--27519312 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
27519263 TGTTTCTTTT
27519273 TTCTTTTTTTTGCTCATC
1 TTCTTTTTTTTGCTCATC
**
27519291 TTCTTTGTTTTTTTTCATC
1 TTCTTT-TTTTTGCTCATC
27519310 TTC
1 TTC
27519313 CTTACTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.05, C:0.20, G:0.05, T:0.70
Consensus pattern (18 bp):
TTCTTTTTTTTGCTCATC
Found at i:27521265 original size:19 final size:19
Alignment explanation
Indices: 27521225--27521265 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
27521215 AAGGTAGTAA
*
27521225 GGTCGATTCCACAGGGATT
1 GGTCGATTCCACAGGGACT
* *
27521244 GGTCGATTTCACATGGACT
1 GGTCGATTCCACAGGGACT
27521263 GGT
1 GGT
27521266 TGTTGTAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.20, C:0.20, G:0.32, T:0.29
Consensus pattern (19 bp):
GGTCGATTCCACAGGGACT
Found at i:27536864 original size:50 final size:51
Alignment explanation
Indices: 27536782--27536965 Score: 248
Period size: 50 Copynumber: 3.6 Consensus size: 51
27536772 TTTCATTTAA
* * * * *
27536782 TACTCAAGATGACATATTA-TCATCGGACCTTTAATTCGTCATGGATTCATT
1 TACTCACGATGACA-CTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
*
27536833 TACTCACGATGACA-TTTGTCATCGGACCTTTAATCCGTAAAGGA-TCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* * *
27536882 TACTCACGATGACACTTAGTCACCGAACCTTTAATCCGTAAAGGATACATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
27536933 TACTCACGATGACACTTAGTCATCGGACTCTTT
1 TACTCACGATGACACTTAGTCATCGGAC-CTTT
27536966 CGTTTATAGC
Statistics
Matches: 118, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
49 21 0.18
50 50 0.42
51 43 0.36
52 4 0.03
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
Found at i:27543151 original size:4 final size:4
Alignment explanation
Indices: 27543142--27543181 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
27543132 AAAGAGAAAA
27543142 GGAG GGAG GGAG GGAG GGAG GGAG GGAG GGAG GGAG GGAG
1 GGAG GGAG GGAG GGAG GGAG GGAG GGAG GGAG GGAG GGAG
27543182 AAAGGAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.25, C:0.00, G:0.75, T:0.00
Consensus pattern (4 bp):
GGAG
Found at i:27544685 original size:3 final size:3
Alignment explanation
Indices: 27544677--27544703 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
27544667 GAAACAAGCT
27544677 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
27544704 AAGGGAAACT
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:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:27546302 original size:25 final size:24
Alignment explanation
Indices: 27546273--27546325 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
27546263 ATATAATGAT
*
27546273 TTATTTTTATAT-TAGATAAATATAA
1 TTATTTGTATATGTA-ATAAATA-AA
*
27546298 TTATTTGTATATGTAATATATAAA
1 TTATTTGTATATGTAATAAATAAA
27546322 TTAT
1 TTAT
27546326 CAATGATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 6 0.24
25 17 0.68
26 2 0.08
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (24 bp):
TTATTTGTATATGTAATAAATAAA
Found at i:27548617 original size:327 final size:327
Alignment explanation
Indices: 27548023--27549009 Score: 1902
Period size: 327 Copynumber: 3.0 Consensus size: 327
27548013 ATTTCCTTCT
* *
27548023 CTTCATTATCTTCGATACCTTACATACATCCTTTAAATATCTGAGTCATCACTTCATTGTGATTT
1 CTTCATTATCTTCGATACCTTACATAAATTCTTTAAATATCTGAGTCATCACTTCATTGTGATTT
27548088 AGGAAGAAGCATATACACAGGTGACAAGTACTTCCTTCGAATAGACAAATGTTACATCCTTATTC
66 AGGAAGAAGCATATACACAGGTGACAAGTACTTCCTTCGAATAGACAAATGTTACATCCTTATTC
*
27548153 ATAATACATTTTCGATACTAACTCATCACTTCGCCTTCTCTCTATAATTCACTATCTTCAATTGA
131 ATAATACATTTTCGATACTAACTTATCACTTCGCCTTCTCTCTATAATTCACTATCTTCAATTGA
27548218 GCCTTAGTCTTTATATAATACCTTACCATATAGTCCATATAAACAATTTGTACTTACTGATTTCA
196 GCCTTAGTCTTTATATAATACCTTACCATATAGTCCATATAAACAATTTGTACTTACTGATTTCA
27548283 CTGTTTACTTTTATGAGCAATACAGAATACGCCAATTCTGTAGCACAGAACCAGTCACAATATCA
261 CTGTTTACTTTTATGAGCAATACAGAATACGCCAATTCTGTAGCACAGAACCAGTCACAATATCA
27548348 TC
326 TC
*
27548350 CTTCATTATCTTTGATACCTTACATAAATTCTTTAAATATCTGAGTCATCACTTCATTGTGATTT
1 CTTCATTATCTTCGATACCTTACATAAATTCTTTAAATATCTGAGTCATCACTTCATTGTGATTT
*
27548415 AGGAAGAAGCATATACACAGGTGACAAGTACTTCCTTCAAATAGACAAATGTTACATCCTTATTC
66 AGGAAGAAGCATATACACAGGTGACAAGTACTTCCTTCGAATAGACAAATGTTACATCCTTATTC
27548480 ATAATACATTTTCGATACTAACTTATCACTTCGCCTTCTCTCTATAATTCACTATCTTCAATTGA
131 ATAATACATTTTCGATACTAACTTATCACTTCGCCTTCTCTCTATAATTCACTATCTTCAATTGA
27548545 GCCTTAGTCTTTATATAATACCTTACCATATAGTCCATATAAACAATTTGTACTTACTGATTTCA
196 GCCTTAGTCTTTATATAATACCTTACCATATAGTCCATATAAACAATTTGTACTTACTGATTTCA
27548610 CTGTTTACTTTTATGAGCAATACAGAATACGCCAATTCTGTAGCACAGAACCAGTCACAATATCA
261 CTGTTTACTTTTATGAGCAATACAGAATACGCCAATTCTGTAGCACAGAACCAGTCACAATATCA
27548675 TC
326 TC
27548677 CTTCATTATCTTCGATACCTTACATAAATTCTTTAAATATCTGAGTCATCACTTCATTGTGATTT
1 CTTCATTATCTTCGATACCTTACATAAATTCTTTAAATATCTGAGTCATCACTTCATTGTGATTT
*
27548742 AAGAAGAAGCATATACACAGGTGACAAGTACTTCCTTCGAATAGACAAATGTTACATCCTTATTC
66 AGGAAGAAGCATATACACAGGTGACAAGTACTTCCTTCGAATAGACAAATGTTACATCCTTATTC
*
27548807 ATAATACATTTTCGATACTAACTTATCACTTCGCCTTCTCTTTATAATTCACTATCTTCAATTGA
131 ATAATACATTTTCGATACTAACTTATCACTTCGCCTTCTCTCTATAATTCACTATCTTCAATTGA
*
27548872 GCCTTAGTCTTTATATAATACCTTACCATATAGTCCATATAAACAATTTATACTTACTGATTTCA
196 GCCTTAGTCTTTATATAATACCTTACCATATAGTCCATATAAACAATTTGTACTTACTGATTTCA
27548937 CTGTTTACTTTTATGAGCAATACAGAATACGCCAATTCTGTAGCACAGAACCAGTCACAATATCA
261 CTGTTTACTTTTATGAGCAATACAGAATACGCCAATTCTGTAGCACAGAACCAGTCACAATATCA
27549002 TC
326 TC
27549004 CTTCAT
1 CTTCAT
27549010 AAGTTATTAC
Statistics
Matches: 650, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
327 650 1.00
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.36
Consensus pattern (327 bp):
CTTCATTATCTTCGATACCTTACATAAATTCTTTAAATATCTGAGTCATCACTTCATTGTGATTT
AGGAAGAAGCATATACACAGGTGACAAGTACTTCCTTCGAATAGACAAATGTTACATCCTTATTC
ATAATACATTTTCGATACTAACTTATCACTTCGCCTTCTCTCTATAATTCACTATCTTCAATTGA
GCCTTAGTCTTTATATAATACCTTACCATATAGTCCATATAAACAATTTGTACTTACTGATTTCA
CTGTTTACTTTTATGAGCAATACAGAATACGCCAATTCTGTAGCACAGAACCAGTCACAATATCA
TC
Found at i:27549210 original size:26 final size:28
Alignment explanation
Indices: 27549176--27549238 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 28
27549166 TCTTAGTTCA
27549176 CCACAAAGGCGGTT-CTTA-AAAGTGTG
1 CCACAAAGGCGGTTCCTTACAAAGTGTG
* * *
27549202 CCACGAAGG-TGTTCCTTACAAAGTTTG
1 CCACAAAGGCGGTTCCTTACAAAGTGTG
27549229 CCACAAAGGC
1 CCACAAAGGC
27549239 ATTCATTTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
25 3 0.10
26 12 0.40
27 15 0.50
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (28 bp):
CCACAAAGGCGGTTCCTTACAAAGTGTG
Found at i:27552003 original size:24 final size:24
Alignment explanation
Indices: 27551952--27552006 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
27551942 TCTTTTAGTT
*
27551952 AAACTCTGTTTATTTGTTTCAATT
1 AAACTCTGTTTATTTGTTTCAATC
* *
27551976 AAACTCTGTTTATTTGTTTGAGTC
1 AAACTCTGTTTATTTGTTTCAATC
27552000 AAACTCT
1 AAACTCT
27552007 TATTACTCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.49
Consensus pattern (24 bp):
AAACTCTGTTTATTTGTTTCAATC
Found at i:27553991 original size:24 final size:24
Alignment explanation
Indices: 27553940--27553994 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
27553930 TCTTTTAGTT
*
27553940 AAACTCTGTTTATTTGTTTCAATT
1 AAACTCTGTTTATTTGTTTCAATC
* * *
27553964 AAACTTTGTTTATTTGTTTGAGTC
1 AAACTCTGTTTATTTGTTTCAATC
27553988 AAACTCT
1 AAACTCT
27553995 TATTACTCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.25, C:0.13, G:0.11, T:0.51
Consensus pattern (24 bp):
AAACTCTGTTTATTTGTTTCAATC
Found at i:27557647 original size:17 final size:17
Alignment explanation
Indices: 27557615--27557663 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
27557605 AACCAAAACT
* *
27557615 TATTTTATATTAAAATGA
1 TATTTTATAAT-AAATAA
27557633 TATTTTATAATAAATAA
1 TATTTTATAATAAATAA
*
27557650 CATTTTAT-ATAAAT
1 TATTTTATAATAAAT
27557664 TTAATAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 6 0.21
17 12 0.43
18 10 0.36
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (17 bp):
TATTTTATAATAAATAA
Found at i:27557942 original size:18 final size:18
Alignment explanation
Indices: 27557892--27557942 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
27557882 TTAAGAATAA
27557892 TATTAAAATTTAAAA-TTAT
1 TATTAAAA--TAAAATTTAT
** *
27557911 TATTAATGTTAAATTTAT
1 TATTAAAATAAAATTTAT
27557929 TATTAAAATAAAAT
1 TATTAAAATAAAAT
27557943 ATTAATCTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
17 4 0.16
18 15 0.60
19 6 0.24
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TATTAAAATAAAATTTAT
Found at i:27561963 original size:20 final size:20
Alignment explanation
Indices: 27561938--27561992 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
27561928 AGTTATACAC
*
27561938 TGTTATTTTTCTTGAGATAT
1 TGTTATTTTTCCTGAGATAT
*
27561958 TGTTATTTTTCCTGAGATGT
1 TGTTATTTTTCCTGAGATAT
27561978 TGTTATTTTTCCTGA
1 TGTTATTTTTCCTGA
27561993 AAATAGTGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.16, C:0.09, G:0.16, T:0.58
Consensus pattern (20 bp):
TGTTATTTTTCCTGAGATAT
Found at i:27565220 original size:27 final size:28
Alignment explanation
Indices: 27565173--27565227 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
27565163 AGGTTTTTGC
27565173 ATATATTGAGTTAAAAAATATG-AAAAG
1 ATATATTGAGTTAAAAAATATGTAAAAG
* *
27565200 ATATATTTA-TTAAAATTATATGTAAAAG
1 ATATATTGAGTTAAAA-AATATGTAAAAG
27565228 CTAAATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.25
27 13 0.54
28 5 0.21
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (28 bp):
ATATATTGAGTTAAAAAATATGTAAAAG
Found at i:27569737 original size:29 final size:30
Alignment explanation
Indices: 27569693--27569933 Score: 146
Period size: 29 Copynumber: 8.3 Consensus size: 30
27569683 AAAGAATGCC
*
27569693 ATAAAGGAAATGCCTTTATGGCGATCTTTG
1 ATAAAGGAAATGCCTTTATGGCGATCTCTG
* * * *
27569723 CTAAA-GAAATGCCTTAATGACAATCTCT-
1 ATAAAGGAAATGCCTTTATGGCGATCTCTG
* *
27569751 ATAAAGGAAATGTCTTTGTGGCGATCTCTG
1 ATAAAGGAAATGCCTTTATGGCGATCTCTG
* *
27569781 TTAAA-GAAATGCCTGTT-TGGCAATCTCT-
1 ATAAAGGAAATGCCT-TTATGGCGATCTCTG
** *
27569809 ATAAAGGAAACACTTTTATGGCGATCTCTG
1 ATAAAGGAAATGCCTTTATGGCGATCTCTG
* * * * *
27569839 TTAAA--AAAGTGTCTTTGTGGCAACCTCTG
1 ATAAAGGAAA-TGCCTTTATGGCGATCTCTG
* * * * *
27569868 TTAAA-GAAATGTCTTTGTGGCAAACTCTAG
1 ATAAAGGAAATGCCTTTATGGCGATCTCT-G
* * *
27569898 A-CAA-GAAA-GCCTTTGTGGCGTTCTCT-
1 ATAAAGGAAATGCCTTTATGGCGATCTCTG
27569924 ATAAAGGAAA
1 ATAAAGGAAA
27569934 GCATCTGTGG
Statistics
Matches: 165, Mismatches: 35, Indels: 24
0.74 0.16 0.11
Matches are distributed among these distances:
26 1 0.01
27 2 0.01
28 31 0.19
29 113 0.68
30 18 0.11
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (30 bp):
ATAAAGGAAATGCCTTTATGGCGATCTCTG
Found at i:27569786 original size:58 final size:57
Alignment explanation
Indices: 27569693--27569888 Score: 200
Period size: 58 Copynumber: 3.4 Consensus size: 57
27569683 AAAGAATGCC
* * * *
27569693 ATAAAGGAAATGCCTTTATGGCGATCTTTGCTAAAGAAATGCCTTAATGACAATCTCT
1 ATAAAGGAAATGTCTTTATGGCGATCTCTGTTAAAGAAATGCCTT-ATGGCAATCTCT
* *
27569751 ATAAAGGAAATGTCTTTGTGGCGATCTCTGTTAAAGAAATGCCTGTTTGGCAATCTCT
1 ATAAAGGAAATGTCTTTATGGCGATCTCTGTTAAAGAAATGCCT-TATGGCAATCTCT
** * * *
27569809 ATAAAGGAAA-CACTTTTATGGCGATCTCTGTTAAA-AAAGTGTCTTTGTGGCAACCTCT
1 ATAAAGGAAATGTC-TTTATGGCGATCTCTGTTAAAGAAA-TG-CCTTATGGCAATCTCT
* *
27569867 GTTAAA-GAAATGTCTTTGTGGC
1 -ATAAAGGAAATGTCTTTATGGC
27569889 AAACTCTAGA
Statistics
Matches: 116, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
57 4 0.03
58 104 0.90
59 8 0.07
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (57 bp):
ATAAAGGAAATGTCTTTATGGCGATCTCTGTTAAAGAAATGCCTTATGGCAATCTCT
Found at i:27569933 original size:28 final size:28
Alignment explanation
Indices: 27569902--27570091 Score: 89
Period size: 28 Copynumber: 6.8 Consensus size: 28
27569892 CTCTAGACAA
27569902 GAAAGCCTTTGTGGCGTTCTCTATAAAG
1 GAAAGCCTTTGTGGCGTTCTCTATAAAG
* * *** * * *
27569930 GAAAGCATCTGTGGCAAACTATAGATAG
1 GAAAGCCTTTGTGGCGTTCTCTATAAAG
* * *
27569958 GAAATCCTTTGTGGCATTCTCTGTAAAG
1 GAAAGCCTTTGTGGCGTTCTCTATAAAG
* * * **
27569986 GAAAGTCTTCGTGGAAAAGTT-TGGAT-AA-
1 GAAAGCCTTTGTGG---CGTTCTCTATAAAG
* * * *
27570014 GAAAACCTTTGTGACGTTCTCTGTAAAT
1 GAAAGCCTTTGTGGCGTTCTCTATAAAG
* **** * *
27570042 GAAAGCCTCTGTGGCAAAATCTAGATAG
1 GAAAGCCTTTGTGGCGTTCTCTATAAAG
27570070 GAAAGCCTTTGTGGCGTTCTCT
1 GAAAGCCTTTGTGGCGTTCTCT
27570092 GTTAAAAAAC
Statistics
Matches: 107, Mismatches: 49, Indels: 12
0.64 0.29 0.07
Matches are distributed among these distances:
25 3 0.03
26 2 0.02
27 2 0.02
28 94 0.88
29 2 0.02
30 2 0.02
31 2 0.02
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (28 bp):
GAAAGCCTTTGTGGCGTTCTCTATAAAG
Found at i:27569943 original size:56 final size:56
Alignment explanation
Indices: 27569883--27570093 Score: 253
Period size: 56 Copynumber: 3.8 Consensus size: 56
27569873 GAAATGTCTT
* *
27569883 TGTGGCAAACTCTAGACAAGAAAGCCTTTGTGGCGTTCTCTATAAAGGAAAGCATC
1 TGTGGCAAACTCTAGATAAGAAAGCCTTTGTGGCGTTCTCTGTAAAGGAAAGCATC
* * * * *
27569939 TGTGGCAAACTATAGATAGGAAATCCTTTGTGGCATTCTCTGTAAAGGAAAGTCTTC
1 TGTGGCAAACTCTAGATAAGAAAGCCTTTGTGGCGTTCTCTGTAAAGGAAAG-CATC
* * * * * * * *
27569996 -GTGGAAAAGTTTGGATAAGAAAACCTTTGTGACGTTCTCTGTAAATGAAAGCCTC
1 TGTGGCAAACTCTAGATAAGAAAGCCTTTGTGGCGTTCTCTGTAAAGGAAAGCATC
* *
27570051 TGTGGCAAAATCTAGATAGGAAAGCCTTTGTGGCGTTCTCTGT
1 TGTGGCAAACTCTAGATAAGAAAGCCTTTGTGGCGTTCTCTGT
27570094 TAAAAAACAG
Statistics
Matches: 129, Mismatches: 24, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
55 3 0.02
56 123 0.95
57 3 0.02
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (56 bp):
TGTGGCAAACTCTAGATAAGAAAGCCTTTGTGGCGTTCTCTGTAAAGGAAAGCATC
Found at i:27570017 original size:112 final size:112
Alignment explanation
Indices: 27569851--27570093 Score: 308
Period size: 112 Copynumber: 2.2 Consensus size: 112
27569841 AAAAAAGTGT
** * * * *
27569851 CTTTGTGGCAACCTCTGTTAAAGAAATGTCTTTGTGGCAAACTCTAGACAAGAAAGCCTTTGTGG
1 CTTTGTGGCATTCTCTG-TAAAGAAATGTCTTCGTGGAAAACTCTAGACAAGAAAACCTTTGTGA
* *
27569916 CGTTCTCTATAAAGGAAAGCATCTGTGGCAAACTATAGATAGGAAATC
65 CGTTCTCTATAAAGGAAAGCATCTGTGGCAAAATATAGATAGGAAAGC
* * * *
27569964 CTTTGTGGCATTCTCTGTAAAGGAAA-GTCTTCGTGGAAAAGTTTGGATAAGAAAACCTTTGTGA
1 CTTTGTGGCATTCTCTGTAAA-GAAATGTCTTCGTGGAAAACTCTAGACAAGAAAACCTTTGTGA
* * * *
27570028 CGTTCTCTGTAAATGAAAGCCTCTGTGGCAAAATCTAGATAGGAAAGC
65 CGTTCTCTATAAAGGAAAGCATCTGTGGCAAAATATAGATAGGAAAGC
*
27570076 CTTTGTGGCGTTCTCTGT
1 CTTTGTGGCATTCTCTGT
27570094 TAAAAAACAG
Statistics
Matches: 112, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
112 93 0.83
113 19 0.17
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.30
Consensus pattern (112 bp):
CTTTGTGGCATTCTCTGTAAAGAAATGTCTTCGTGGAAAACTCTAGACAAGAAAACCTTTGTGAC
GTTCTCTATAAAGGAAAGCATCTGTGGCAAAATATAGATAGGAAAGC
Found at i:27570173 original size:112 final size:112
Alignment explanation
Indices: 27569851--27570162 Score: 261
Period size: 112 Copynumber: 2.8 Consensus size: 112
27569841 AAAAAAGTGT
** * * * * * * *
27569851 CTTTGTGGCAACCTCTGTTAAAGAAATGTCTTTGTGGCAAACTCT-AGACAAGAAAGCCTTTGTG
1 CTTTGTGGCATTCTCTG-TAAAGAAAAGCCTTCGTGGAAAACTTTGA-ATAAGAAAACCTTTGTG
* ** * * * * * *
27569915 GCGTTCTCTATAAAGGAAAGCATCTGTGGCAAACTATAGATAGGAAATC
64 ACAATCTCTGTAAATGAAAGCCTCTGTGGCAAAATCTAGATAGGAAAGC
* * * *
27569964 CTTTGTGGCATTCTCTGTAAAGGAAAGTCTTCGTGGAAAAGTTTGGATAAGAAAACCTTTGTGAC
1 CTTTGTGGCATTCTCTGTAAAGAAAAGCCTTCGTGGAAAACTTTGAATAAGAAAACCTTTGTGAC
**
27570029 GTTCTCTGTAAATGAAAGCCTCTGTGGCAAAATCTAGATAGGAAAGC
66 AATCTCTGTAAATGAAAGCCTCTGTGGCAAAATCTAGATAGGAAAGC
* * * ***
27570076 CTTTGTGGCGTTCTCTGTTAAA-AAACAGCCTTCGTGGCAATCTTTGAATAAGGAATGTCTTTGT
1 CTTTGTGGCATTCTCTG-TAAAGAAA-AGCCTTCGTGGAAAACTTTGAATAA-GAAAACCTTTGT
* * *
27570140 GGCAATCTTTGTAAA-GGAAGCCT
63 GACAATCTCTGTAAATGAAAGCCT
27570163 TCGTGGAAAA
Statistics
Matches: 162, Mismatches: 33, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
112 96 0.59
113 46 0.28
114 20 0.12
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (112 bp):
CTTTGTGGCATTCTCTGTAAAGAAAAGCCTTCGTGGAAAACTTTGAATAAGAAAACCTTTGTGAC
AATCTCTGTAAATGAAAGCCTCTGTGGCAAAATCTAGATAGGAAAGC
Found at i:27583155 original size:24 final size:24
Alignment explanation
Indices: 27583122--27583174 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
27583112 ATTCACAAAC
*
27583122 ATAAAGAAACATGCCCACGAACAT
1 ATAAACAAACATGCCCACGAACAT
** *
27583146 ATAAACAAACATGTTCGCGAACAT
1 ATAAACAAACATGCCCACGAACAT
27583170 ATAAA
1 ATAAA
27583175 TGAACATGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.21, G:0.11, T:0.17
Consensus pattern (24 bp):
ATAAACAAACATGCCCACGAACAT
Found at i:27583180 original size:24 final size:24
Alignment explanation
Indices: 27583139--27583208 Score: 88
Period size: 24 Copynumber: 3.0 Consensus size: 24
27583129 AACATGCCCA
*
27583139 CGAACATATAAACAAACATGTTCG
1 CGAACATATAAACGAACATGTTCG
*
27583163 CGAACATATAAATGAACATGTTCG
1 CGAACATATAAACGAACATGTTCG
* **
27583187 AGAATGT-TAAACGAACATGTTC
1 CGAACATATAAACGAACATGTTC
27583209 ACAACTGCTA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 14 0.35
24 26 0.65
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.24
Consensus pattern (24 bp):
CGAACATATAAACGAACATGTTCG
Found at i:27583220 original size:23 final size:23
Alignment explanation
Indices: 27583171--27583224 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
27583161 CGCGAACATA
* * *
27583171 TAAATGAACATGTTCGAGAATGT
1 TAAACGAACATGTTCGACAATGC
27583194 TAAACGAACATGTTC-ACAACTGC
1 TAAACGAACATGTTCGACAA-TGC
27583217 TAAACGAA
1 TAAACGAA
27583225 TCGAGCCCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 3 0.11
23 24 0.89
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.24
Consensus pattern (23 bp):
TAAACGAACATGTTCGACAATGC
Found at i:27584855 original size:111 final size:110
Alignment explanation
Indices: 27584667--27584904 Score: 275
Period size: 111 Copynumber: 2.2 Consensus size: 110
27584657 AAATGGAAAT
* * * * * *
27584667 CTTTGTGGCAATCTTTAAAACGGAAGCCTTTGTGGCGATCTTTGATAAATAAAAGCTTTTGCGGT
1 CTTTGTGGTAATCTTTAAAACGGAAGCCTTTGTAGCGATCTTTGACAAATAAAAGCCTTTGAGAT
* *
27584732 GATCTATGAAAC-GAA-ATCTTGTATGGTAATCTTTGATAACTGGAAG
66 GATATATGAAACGGAACA-CTT-TATGGTAATCTTTGATAAAT-GAAG
* * * * *
27584778 CATTTGTGGTGATCTTTGAAATGGAA-CCTTTGTATCGATCTTTGACAAATAGAAGCCTTTGAGA
1 C-TTTGTGGTAATCTTTAAAACGGAAGCCTTTGTAGCGATCTTTGACAAATAAAAGCCTTTGAGA
* * *
27584842 TGATATCTGAAACGGAACACTTTGTGGTGATCTTTGATAAATGAAG
65 TGATATATGAAACGGAACACTTTATGGTAATCTTTGATAAATGAAG
27584888 CTTTGTGGTAATCTTTA
1 CTTTGTGGTAATCTTTA
27584905 TTAAAAGAAG
Statistics
Matches: 106, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
109 14 0.13
110 5 0.05
111 60 0.57
112 26 0.25
113 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (110 bp):
CTTTGTGGTAATCTTTAAAACGGAAGCCTTTGTAGCGATCTTTGACAAATAAAAGCCTTTGAGAT
GATATATGAAACGGAACACTTTATGGTAATCTTTGATAAATGAAG
Found at i:27584878 original size:56 final size:55
Alignment explanation
Indices: 27584684--27584901 Score: 190
Period size: 56 Copynumber: 3.9 Consensus size: 55
27584674 GCAATCTTTA
* * * *
27584684 AAACGGAAGCCTTTGTGGCGATCTTTGATAAATAAAAGCTTTTGCGGTGATCTATG
1 AAACGGAA-CCTTTGTGGTGATCTTTGATAAATAGAAGCCTTTGAGGTGATCTATG
* * * * * * * * *
27584740 AAACGAAATCTTGTATGGTAATCTTTGATAACTGGAAGCATTTGTGGTGATCTTTG
1 AAACGGAACCTT-TGTGGTGATCTTTGATAAATAGAAGCCTTTGAGGTGATCTATG
* * * * * *
27584796 AAATGGAACCTTTGT-ATCGATCTTTGACAAATAGAAGCCTTTGAGATGATATCTG
1 AAACGGAACCTTTGTGGT-GATCTTTGATAAATAGAAGCCTTTGAGGTGATCTATG
* *
27584851 AAACGGAACACTTTGTGGTGATCTTTGATAAAT-GAAG-CTTTGTGGTAATCT
1 AAACGGAAC-CTTTGTGGTGATCTTTGATAAATAGAAGCCTTTGAGGTGATCT
27584902 TTATTAAAAG
Statistics
Matches: 126, Mismatches: 32, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
54 11 0.09
55 45 0.36
56 69 0.55
57 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (55 bp):
AAACGGAACCTTTGTGGTGATCTTTGATAAATAGAAGCCTTTGAGGTGATCTATG
Found at i:27584891 original size:27 final size:27
Alignment explanation
Indices: 27584689--27584976 Score: 110
Period size: 27 Copynumber: 10.4 Consensus size: 27
27584679 CTTTAAAACG
*
27584689 GAAGCCTTTGTGGCGATCTTTGATAAAT
1 GAAG-CTTTGTGGTGATCTTTGATAAAT
* * * *
27584717 AAAAGCTTTTGCGGTGATCTATG--AAAC
1 -GAAGC-TTTGTGGTGATCTTTGATAAAT
* * * *
27584744 GAAATCTTGTATGGTAATCTTTGATAACT
1 G-AAGCTT-TGTGGTGATCTTTGATAAAT
27584773 GGAAGCATTTGTGGTGATCTTTG--AAAT
1 -GAAGC-TTTGTGGTGATCTTTGATAAAT
* * *
27584800 GGAACCTTTGT-ATCGATCTTTGACAAAT
1 -GAAGCTTTGTGGT-GATCTTTGATAAAT
* * * * **
27584828 AGAAGCCTTTGAGATGATATCTGA-AACG
1 -GAAG-CTTTGTGGTGATCTTTGATAAAT
*
27584856 GAACACTTTGTGGTGATCTTTGATAAAT
1 GAA-GCTTTGTGGTGATCTTTGATAAAT
* *
27584884 GAAGCTTTGTGGTAATCTTT-ATTAAAA
1 GAAGCTTTGTGGTGATCTTTGA-TAAAT
* * * *
27584911 GAAGCCTTTATGG-CAACTTTTGATAAAG
1 GAAG-CTTTGTGGTGATC-TTTGATAAAT
*
27584939 GAAGCCTTTGT--AGATCTTTGATAAAT
1 GAAG-CTTTGTGGTGATCTTTGATAAAT
* *
27584965 GAGGCCTTGTGG
1 GAAGCTTTGTGG
27584977 CAAATAAAGA
Statistics
Matches: 192, Mismatches: 46, Indels: 44
0.68 0.16 0.16
Matches are distributed among these distances:
25 6 0.03
26 28 0.15
27 68 0.35
28 39 0.20
29 46 0.24
30 5 0.03
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (27 bp):
GAAGCTTTGTGGTGATCTTTGATAAAT
Found at i:27589389 original size:16 final size:15
Alignment explanation
Indices: 27589370--27589404 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
27589360 ATTTGGTTGA
*
27589370 AAAAATTATTTAATT
1 AAAAATTAATTAATT
27589385 GAAAAATTAATTAATT
1 -AAAAATTAATTAATT
27589401 AAAA
1 AAAA
27589405 TTAGTTTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (15 bp):
AAAAATTAATTAATT
Found at i:27609249 original size:3 final size:3
Alignment explanation
Indices: 27609241--27609292 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
27609231 GTATTGAGGC
*
27609241 AGA AGA AGA AGAA AGA A-A AGA AGA AAA AGA AGA AGA A-A AGGA AGA
1 AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA A-GA AGA
*
27609286 AAA AGA A
1 AGA AGA A
27609293 TATGTTGCCC
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
2 4 0.10
3 32 0.78
4 5 0.12
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:27609263 original size:12 final size:13
Alignment explanation
Indices: 27609241--27609292 Score: 67
Period size: 12 Copynumber: 4.3 Consensus size: 13
27609231 GTATTGAGGC
27609241 AGAAGAAGAAGAA
1 AGAAGAAGAAGAA
27609254 AGAA-AAGAAGAA
1 AGAAGAAGAAGAA
27609266 A-AAGAAGAAGAA
1 AGAAGAAGAAGAA
*
27609278 A-AGGAAGAA-AA
1 AGAAGAAGAAGAA
27609289 AGAA
1 AGAA
27609293 TATGTTGCCC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
11 5 0.14
12 26 0.74
13 4 0.11
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (13 bp):
AGAAGAAGAAGAA
Found at i:27609270 original size:21 final size:21
Alignment explanation
Indices: 27609241--27609292 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
27609231 GTATTGAGGC
*
27609241 AGAAGAAGAAGAAAGAAAA-GA
1 AGAAAAAGAAG-AAGAAAAGGA
27609262 AGAAAAAGAAGAAGAAAAGGA
1 AGAAAAAGAAGAAGAAAAGGA
27609283 AGAAAAAGAA
1 AGAAAAAGAA
27609293 TATGTTGCCC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 7 0.24
21 22 0.76
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (21 bp):
AGAAAAAGAAGAAGAAAAGGA
Found at i:27611180 original size:18 final size:18
Alignment explanation
Indices: 27611148--27611183 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
27611138 TTACAACTGC
*
27611148 AAAAAGGAGCTAGATCTG
1 AAAAAGGAGCAAGATCTG
*
27611166 AAAAAGGAGGAAGATCTG
1 AAAAAGGAGCAAGATCTG
27611184 CAATTACAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.08, G:0.31, T:0.14
Consensus pattern (18 bp):
AAAAAGGAGCAAGATCTG
Found at i:27612980 original size:21 final size:20
Alignment explanation
Indices: 27612940--27612980 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
27612930 CATAAAAGTG
* *
27612940 CCTAAAATCCATTTATTTCA
1 CCTAAAATACATTAATTTCA
27612960 CCTAAAATACACTTAATTTCA
1 CCTAAAATACA-TTAATTTCA
27612981 TCATTTAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
CCTAAAATACATTAATTTCA
Found at i:27616220 original size:21 final size:21
Alignment explanation
Indices: 27616191--27616243 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
27616181 CTGCTACTTT
*
27616191 TACCGATACAAG-TATACAAAC
1 TACCAATACAAGCTATAC-AAC
** *
27616212 TACCAATACTTGCTATTCAAC
1 TACCAATACAAGCTATACAAC
27616233 TACCAATACAA
1 TACCAATACAA
27616244 CCCAAGTCAG
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.43, C:0.26, G:0.06, T:0.25
Consensus pattern (21 bp):
TACCAATACAAGCTATACAAC
Found at i:27616882 original size:24 final size:24
Alignment explanation
Indices: 27616847--27616898 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
27616837 AGATCTCATG
*
27616847 AGCCCAAGATGGTTAGCTCTTACA
1 AGCCCAAAATGGTTAGCTCTTACA
*
27616871 AGCCCAAAATGGTTAGCTCTTACG
1 AGCCCAAAATGGTTAGCTCTTACA
27616895 AGCC
1 AGCC
27616899 TAGAATAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (24 bp):
AGCCCAAAATGGTTAGCTCTTACA
Found at i:27616909 original size:24 final size:24
Alignment explanation
Indices: 27616847--27616909 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
27616837 AGATCTCATG
* *
27616847 AGCCCAAGATGGTTAGCTCTTACA
1 AGCCCAAAATAGTTAGCTCTTACA
* *
27616871 AGCCCAAAATGGTTAGCTCTTACG
1 AGCCCAAAATAGTTAGCTCTTACA
* *
27616895 AGCCTAGAATAGTTA
1 AGCCCAAAATAGTTA
27616910 ACTAATATAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (24 bp):
AGCCCAAAATAGTTAGCTCTTACA
Found at i:27619500 original size:3 final size:3
Alignment explanation
Indices: 27619494--27619521 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
27619484 TTGAATGAAC
27619494 TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA T
27619522 AAAGAAGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:27619801 original size:7 final size:7
Alignment explanation
Indices: 27619789--27619813 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
27619779 TTAGGGATAT
27619789 AAATTTA
1 AAATTTA
27619796 AAATTTA
1 AAATTTA
27619803 AAATTTA
1 AAATTTA
27619810 AAAT
1 AAAT
27619814 AATATAGTTT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATTTA
Found at i:27619862 original size:24 final size:24
Alignment explanation
Indices: 27619835--27619883 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
27619825 TATTTGGTTT
* *
27619835 ATTCGAATTATTCAAGTT-ATTCGA
1 ATTCGAA-AATTCAACTTGATTCGA
27619859 ATTCGAAAATTCAACTTGATTCGA
1 ATTCGAAAATTCAACTTGATTCGA
27619883 A
1 A
27619884 AAAATCTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (24 bp):
ATTCGAAAATTCAACTTGATTCGA
Found at i:27624790 original size:42 final size:42
Alignment explanation
Indices: 27624731--27624853 Score: 185
Period size: 42 Copynumber: 2.9 Consensus size: 42
27624721 GCTACAGGAA
*
27624731 ACACCACATGCTGATTCTGTACATCCTGCACACCTTGATGAG
1 ACACCACATGCTGATTCTGTACATCCTGCACAACTTGATGAG
* * *
27624773 ACACCACATGTTGATTCTGTACATCCTGCATATCTTGATGAG
1 ACACCACATGCTGATTCTGTACATCCTGCACAACTTGATGAG
*
27624815 ACACCACATGCTGA-TCTTGTATATCCTGCACAACTTGAT
1 ACACCACATGCTGATTC-TGTACATCCTGCACAACTTGAT
27624854 CAGTAGAATT
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
41 2 0.03
42 71 0.97
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (42 bp):
ACACCACATGCTGATTCTGTACATCCTGCACAACTTGATGAG
Found at i:27627587 original size:14 final size:14
Alignment explanation
Indices: 27627568--27627596 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
27627558 TAACTACTAA
27627568 TAGTTGCTGATAAT
1 TAGTTGCTGATAAT
27627582 TAGTTGCTGATAAT
1 TAGTTGCTGATAAT
27627596 T
1 T
27627597 GGTTATGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.45
Consensus pattern (14 bp):
TAGTTGCTGATAAT
Found at i:27632473 original size:17 final size:14
Alignment explanation
Indices: 27632440--27632466 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
27632430 ATTAATAATT
27632440 AAATTTGACTCTTA
1 AAATTTGACTCTTA
27632454 AAATTTGACTCTT
1 AAATTTGACTCTT
27632467 TTTAAAAGGT
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:0.33, C:0.15, G:0.07, T:0.44
Consensus pattern (14 bp):
AAATTTGACTCTTA
Found at i:27634765 original size:22 final size:21
Alignment explanation
Indices: 27634723--27634762 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
27634713 TAAAACAACG
*
27634723 TAGTTTTGCTTTTTAACTTAA
1 TAGTTTTGATTTTTAACTTAA
27634744 TAGTTTTGATTTTTAACTT
1 TAGTTTTGATTTTTAACTT
27634763 TAAAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.07, G:0.10, T:0.60
Consensus pattern (21 bp):
TAGTTTTGATTTTTAACTTAA
Found at i:27636814 original size:21 final size:21
Alignment explanation
Indices: 27636788--27636830 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
27636778 ATAAAAAAAA
27636788 AATCAAAGTAATAGCGATCCC
1 AATCAAAGTAATAGCGATCCC
*
27636809 AATCAAAGTAATAGGGATCCC
1 AATCAAAGTAATAGCGATCCC
27636830 A
1 A
27636831 TGTGACGGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.44, C:0.21, G:0.16, T:0.19
Consensus pattern (21 bp):
AATCAAAGTAATAGCGATCCC
Found at i:27650931 original size:16 final size:18
Alignment explanation
Indices: 27650892--27650925 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27650882 TAAGTTTATA
27650892 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
27650909 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
27650926 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:27652384 original size:20 final size:20
Alignment explanation
Indices: 27652359--27652408 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
27652349 CACTAGATTT
*
27652359 GTATAACCTTTTAGGACAAG
1 GTATAACCTTTGAGGACAAG
27652379 GTATAACCTTTGAGGACAAG
1 GTATAACCTTTGAGGACAAG
*
27652399 GTTTAACCTT
1 GTATAACCTT
27652409 ACAATCACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (20 bp):
GTATAACCTTTGAGGACAAG
Found at i:27653330 original size:32 final size:33
Alignment explanation
Indices: 27653277--27653341 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
27653267 GAATAGATTT
* * *
27653277 CTCCCCCTTAATAAAAGTCATTTTGAAATTAAG
1 CTCCCCCATAATAAAAATCATTTTCAAATTAAG
*
27653310 CTCCCCCAT-ATAAAAATCATTTTCAATTTAAG
1 CTCCCCCATAATAAAAATCATTTTCAAATTAAG
27653342 GCAAAAAGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 20 0.71
33 8 0.29
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (33 bp):
CTCCCCCATAATAAAAATCATTTTCAAATTAAG
Found at i:27656066 original size:57 final size:57
Alignment explanation
Indices: 27655999--27656126 Score: 211
Period size: 57 Copynumber: 2.2 Consensus size: 57
27655989 TAGAAGAGGA
* * *
27655999 GTTCTATCGGTAGAAGCCCCAGGGTAGACGACTTTACAAAATATTACTGTTGGAGTC
1 GTTCTATCGGTAGAAGCCCCAAGGTAAACGACTTTACAAAATATTACTGTTGAAGTC
* *
27656056 GTTCTATCGGTAGAAGTCTCAAGGTAAACGACTTTACAAAATATTACTGTTGAAGTC
1 GTTCTATCGGTAGAAGCCCCAAGGTAAACGACTTTACAAAATATTACTGTTGAAGTC
27656113 GTTCTATCGGTAGA
1 GTTCTATCGGTAGA
27656127 TGCTTCATTG
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 66 1.00
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (57 bp):
GTTCTATCGGTAGAAGCCCCAAGGTAAACGACTTTACAAAATATTACTGTTGAAGTC
Found at i:27660762 original size:12 final size:11
Alignment explanation
Indices: 27660736--27660761 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
27660726 ATGAAATATC
27660736 TTTTGTTTTTT
1 TTTTGTTTTTT
27660747 TTTTGTTTTTT
1 TTTTGTTTTTT
27660758 TTTT
1 TTTT
27660762 TTACAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTGTTTTTT
Found at i:27662375 original size:14 final size:15
Alignment explanation
Indices: 27662340--27662380 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
27662330 TTAGCCATTT
*
27662340 TTATTTTTATTTTAA
1 TTATTTTTGTTTTAA
27662355 -TATTTTTGTTTTAA
1 TTATTTTTGTTTTAA
*
27662369 TTTTTTTTGTTT
1 TTATTTTTGTTT
27662381 GATTCTTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (15 bp):
TTATTTTTGTTTTAA
Found at i:27668120 original size:18 final size:18
Alignment explanation
Indices: 27668097--27668139 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
27668087 TAGGAACTTC
27668097 ACACGGGCGTGTGGCCCA
1 ACACGGGCGTGTGGCCCA
27668115 ACACGGGCGTGTGGCCCA
1 ACACGGGCGTGTGGCCCA
27668133 ACACGGG
1 ACACGGG
27668140 TTCGAAACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.19, C:0.33, G:0.40, T:0.09
Consensus pattern (18 bp):
ACACGGGCGTGTGGCCCA
Found at i:27670615 original size:23 final size:23
Alignment explanation
Indices: 27670574--27670621 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
27670564 CTTTTTGTTT
* *
27670574 TTTATTTTATTTTATTATTCTTA
1 TTTATTTAATTTTATTATTATTA
27670597 TTTATTTAATTATTA-TATTATTA
1 TTTATTTAATT-TTATTATTATTA
27670620 TT
1 TT
27670622 ATTGTTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTATTTAATTTTATTATTATTA
Found at i:27672959 original size:51 final size:51
Alignment explanation
Indices: 27672885--27673123 Score: 282
Period size: 51 Copynumber: 4.6 Consensus size: 51
27672875 GCTATAAACG
* *
27672885 AAAGGATCCGATGATTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATA
1 AAAGG-TCCGATGACTAGGTGTCATCGTGAGTAAATGAATCCTTTACGGATA
* *
27672937 AAAGGTCTGATGACTAGGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAGGTGTCATCGTGAGTAAATGAATCCTTTACGGATA
* * * *
27672988 AAAGGTCCGATGACTAGGTGTCATCGTGAGTAAATGAATCCATGATGGATT
1 AAAGGTCCGATGACTAGGTGTCATCGTGAGTAAATGAATCCTTTACGGATA
* * * * * *
27673039 AAAGGTCCAATGACTCA-ATGTTATCATGAGTATATGAATTCCTATACGGAATA
1 AAAGGTCCGATGACT-AGGTGTCATCGTGAGTAAATGAA-TCCTTTACGG-ATA
* **
27673092 AGAGGTCCGATGACTATATGTCATCGTGAGTA
1 AAAGGTCCGATGACTAGGTGTCATCGTGAGTA
27673124 TTAAATGAAA
Statistics
Matches: 161, Mismatches: 22, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
51 120 0.75
52 13 0.08
53 28 0.17
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (51 bp):
AAAGGTCCGATGACTAGGTGTCATCGTGAGTAAATGAATCCTTTACGGATA
Found at i:27673171 original size:59 final size:61
Alignment explanation
Indices: 27673072--27673189 Score: 177
Period size: 59 Copynumber: 2.0 Consensus size: 61
27673062 TCATGAGTAT
* * * *
27673072 ATGAATTCCTATACGGAATAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATGAA
1 ATGAATTCCAATACGGAACAAGAGGTCCGATGACTATATGTCATCGTGAGAAATAAATGAA
*
27673133 ATGAATTCCAATAC-GAACAAG-GGTCCGATGACTTTATGTCATCGTGAGAAATAAATG
1 ATGAATTCCAATACGGAACAAGAGGTCCGATGACTATATGTCATCGTGAGAAATAAATG
27673190 CGAGTGAAAC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
59 33 0.63
60 6 0.12
61 13 0.25
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.28
Consensus pattern (61 bp):
ATGAATTCCAATACGGAACAAGAGGTCCGATGACTATATGTCATCGTGAGAAATAAATGAA
Found at i:27675007 original size:376 final size:372
Alignment explanation
Indices: 27674296--27675031 Score: 816
Period size: 376 Copynumber: 2.0 Consensus size: 372
27674286 CATTGGCAAA
* * * *
27674296 GTGATCGCCTCCAAACGTACTCCCGTTCAGTGTAAGTTTTTGAGTTTATGCAAGTATACAGGTCA
1 GTGATCGCCTCCAAACGTACTCCCATTCAGTGTAAGTTTTCGACTTTA-GCAAGTACACAGGTCA
* * *
27674361 AGTTGTAATATAGTTTGTACATGAAATACTCGGCAGTATTTCGAGGATCGTACCTAAAGGAGGCT
65 AGTTGTAATATAGTGTGTACATGAAACACTCGGCAGTATTCCGAGGATCGTACCTAAAGGAGGCT
* ** * * *
27674426 GAGAGTGATAGTGATTTATATCACTGCAAAGAAAAGAAGTAATTAGTACTACCTTTAGGGATTAT
130 AAGAGCAATAGTGATTTAGATCACTACAAAGAAAAGAAGTAATTAGTAATACCTTTAGGGATTAT
* * * * *
27674491 AGTACGAAAGTAAAATAATGATTTGTGATTGTAAAACATAAAATAAAGTAAATAAAGTAAAAGAA
195 AGTACAAAAATAAAATAAAGAGTTGTGATTGTAAAACATAAAATAAAATAAATAAAGTAAAAG-A
* * * *
27674556 TGAGATATGTAGATTCAATGATCGAATTTGGGGAGATTAGGTCACTTGAGTATGGATTCTTCAAT
259 TGAGAGATGTAGATTCAATAAACGAATTTGGGGAGATTAGGTCACTTCAGTATGGATTCTTCAAT
* * *
27674621 TATCGGTTTTGTG-GATTTTGCTTTAATCAACTAGTTATTACCTTAGCAG
324 TATCGGTTTTG-GAGAATTTCCTTCAATCAACTAGTTATTACCTTAGCAG
* ** *
27674670 GTGATCGCCTCCGAACGTACTCCCATTTGGTGTAGAG-TTTCGACTTCTA-CAAGTACACGGGTC
1 GTGATCGCCTCCAAACGTACTCCCATTCAGTGTA-AGTTTTCGACTT-TAGCAAGTACACAGGTC
* * *
27674733 ATA-TTGTAAATATAGTGTGTTACAATGGAACACTTGGTAGTATTCCGAGGATCGTACCTAAAGG
64 A-AGTTGT-AATATAGTGTG-TAC-ATGAAACACTCGGCAGTATTCCGAGGATCGTACCTAAAGG
* * *
27674797 AGGCGTAAG-GCAATAGTG-TATTAGATCTCTACAAAGAATAGAATTAATTAGTAAT-CACTTTA
125 AGGC-TAAGAGCAATAGTGAT-TTAGATCACTACAAAGAAAAGAAGTAATTAGTAATAC-CTTTA
27674859 GGGATTATAGTACAAAAATAAAATAAAGAGTTG-G-TTGTGAAAAGCATAAAA-AGAAATAAA-A
187 GGGATTATAGTACAAAAATAAAATAAAGAGTTGTGATTGT-AAAA-CATAAAATA-AAATAAATA
* * * * *
27674920 GAAGTAAAAG-TTA-AGATGTAGAAGTTCGATAAACGACTTTGGGGATATTAGGTCGCTTCAGTA
249 -AAGTAAAAGATGAGAGATGTAG-A-TTCAATAAACGAATTTGGGGAGATTAGGTCACTTCAGTA
* *
27674983 T-GAGTTCTTCAATTGTTGGGTTTTGGAGAATTTCCTTCAATCAACTAGT
311 TGGA-TTCTTCAATT-ATCGGTTTTGGAGAATTTCCTTCAATCAACTAGT
27675032 CACTACTAGA
Statistics
Matches: 302, Mismatches: 42, Indels: 34
0.80 0.11 0.09
Matches are distributed among these distances:
373 24 0.08
374 57 0.19
375 60 0.20
376 158 0.52
377 3 0.01
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (372 bp):
GTGATCGCCTCCAAACGTACTCCCATTCAGTGTAAGTTTTCGACTTTAGCAAGTACACAGGTCAA
GTTGTAATATAGTGTGTACATGAAACACTCGGCAGTATTCCGAGGATCGTACCTAAAGGAGGCTA
AGAGCAATAGTGATTTAGATCACTACAAAGAAAAGAAGTAATTAGTAATACCTTTAGGGATTATA
GTACAAAAATAAAATAAAGAGTTGTGATTGTAAAACATAAAATAAAATAAATAAAGTAAAAGATG
AGAGATGTAGATTCAATAAACGAATTTGGGGAGATTAGGTCACTTCAGTATGGATTCTTCAATTA
TCGGTTTTGGAGAATTTCCTTCAATCAACTAGTTATTACCTTAGCAG
Found at i:27675331 original size:41 final size:41
Alignment explanation
Indices: 27675242--27675331 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 41
27675232 TTAATAAAAA
* *
27675242 ATTATATTGTTGTTTTGGTGCTTTTTTTACTGTTTTGGTTG
1 ATTATTTTGCTGTTTTGGTGCTTTTTTTACTGTTTTGGTTG
* *
27675283 CTT-TTTTGCTGTTTTGGTGTTGTTTTTTACTGTTTTGGTT-
1 ATTATTTTGCTGTTTTGGTGCT-TTTTTTACTGTTTTGGTTG
27675323 ATTATTTTG
1 ATTATTTTG
27675332 GTGCTTTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
40 17 0.40
41 25 0.60
ACGTcount: A:0.08, C:0.06, G:0.21, T:0.66
Consensus pattern (41 bp):
ATTATTTTGCTGTTTTGGTGCTTTTTTTACTGTTTTGGTTG
Found at i:27675356 original size:20 final size:20
Alignment explanation
Indices: 27675252--27675321 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
27675242 ATTATATTGT
27675252 TGTTTTGGTGCTTTTTTTAC
1 TGTTTTGGTGCTTTTTTTAC
*
27675272 TGTTTTGGTTGC-TTTTTTGC
1 TGTTTTGG-TGCTTTTTTTAC
*
27675292 TGTTTTGGTGTTGTTTTTTAC
1 TGTTTTGGTGCT-TTTTTTAC
27675313 TGTTTTGGT
1 TGTTTTGGT
27675322 TATTATTTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
19 2 0.05
20 23 0.52
21 19 0.43
ACGTcount: A:0.03, C:0.07, G:0.24, T:0.66
Consensus pattern (20 bp):
TGTTTTGGTGCTTTTTTTAC
Found at i:27675386 original size:12 final size:12
Alignment explanation
Indices: 27675371--27675436 Score: 59
Period size: 12 Copynumber: 5.8 Consensus size: 12
27675361 TTATTTTTTC
*
27675371 TATTTTTGCTAT
1 TATTTTTGCTGT
* *
27675383 TATTTTTGTTGC
1 TATTTTTGCTGT
* *
27675395 TGTTTTTGTTGT
1 TATTTTTGCTGT
27675407 TA-TTTT--TGT
1 TATTTTTGCTGT
27675416 TA-TTTTGCTGT
1 TATTTTTGCTGT
27675427 TATTTTTGCT
1 TATTTTTGCT
27675437 ATTTTGGTTG
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
9 9 0.20
11 9 0.20
12 27 0.60
ACGTcount: A:0.09, C:0.06, G:0.15, T:0.70
Consensus pattern (12 bp):
TATTTTTGCTGT
Found at i:27675400 original size:24 final size:23
Alignment explanation
Indices: 27675336--27675413 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 23
27675326 ATTTTGGTGC
27675336 TTTTTTTACTGTTTTGATGCTATTA
1 TTTTTTTACTGTTTT--TGCTATTA
* *
27675361 TTATTTTTTCTATTTTTGCTATTA
1 TT-TTTTTACTGTTTTTGCTATTA
* * *
27675385 TTTTTGTTGCTGTTTTTGTTGTTA
1 TTTTT-TTACTGTTTTTGCTATTA
27675409 TTTTT
1 TTTTT
27675414 GTTATTTTGC
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
23 3 0.07
24 29 0.64
25 2 0.04
26 11 0.24
ACGTcount: A:0.12, C:0.06, G:0.12, T:0.71
Consensus pattern (23 bp):
TTTTTTTACTGTTTTTGCTATTA
Found at i:27675415 original size:9 final size:9
Alignment explanation
Indices: 27675403--27675457 Score: 56
Period size: 9 Copynumber: 5.6 Consensus size: 9
27675393 GCTGTTTTTG
27675403 TTGTTATTT
1 TTGTTATTT
27675412 TTGTTATTT
1 TTGTTATTT
27675421 TGCTGTTATTT
1 T--TGTTATTT
*
27675432 TTGCTATTTT
1 TTGTTA-TTT
27675442 GGTTGTTATTT
1 --TTGTTATTT
27675453 TTGTT
1 TTGTT
27675458 GTTTGGATGT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 19 0.49
10 3 0.08
11 12 0.31
12 5 0.13
ACGTcount: A:0.09, C:0.04, G:0.16, T:0.71
Consensus pattern (9 bp):
TTGTTATTT
Found at i:27675427 original size:20 final size:20
Alignment explanation
Indices: 27675398--27675474 Score: 100
Period size: 20 Copynumber: 3.8 Consensus size: 20
27675388 TTGTTGCTGT
27675398 TTTTGTTGTTATTTTTGTTA
1 TTTTGTTGTTATTTTTGTTA
* *
27675418 TTTTGCTGTTATTTTTGCTA
1 TTTTGTTGTTATTTTTGTTA
*
27675438 TTTTGGTTGTTATTTTTGTTG
1 TTTT-GTTGTTATTTTTGTTA
* *
27675459 TTTGGATGTTATTTTT
1 TTTTGTTGTTATTTTT
27675475 ATGCGTTTGA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
20 33 0.67
21 16 0.33
ACGTcount: A:0.09, C:0.03, G:0.18, T:0.70
Consensus pattern (20 bp):
TTTTGTTGTTATTTTTGTTA
Found at i:27675448 original size:41 final size:41
Alignment explanation
Indices: 27675391--27675474 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
27675381 ATTATTTTTG
* * * *
27675391 TTGCTGTTTTTGTTGTTATTTTTGTTATTTTGCTGTTATTT
1 TTGCTATTTTGGTTGTTATTTTTGTTATTTGGATGTTATTT
*
27675432 TTGCTATTTTGGTTGTTATTTTTGTTGTTTGGATGTTATTT
1 TTGCTATTTTGGTTGTTATTTTTGTTATTTGGATGTTATTT
27675473 TT
1 TT
27675475 ATGCGTTTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.08, C:0.04, G:0.19, T:0.69
Consensus pattern (41 bp):
TTGCTATTTTGGTTGTTATTTTTGTTATTTGGATGTTATTT
Found at i:27675451 original size:12 final size:11
Alignment explanation
Indices: 27675398--27675460 Score: 62
Period size: 10 Copynumber: 5.9 Consensus size: 11
27675388 TTGTTGCTGT
27675398 TTTTGTTGTTA
1 TTTTGTTGTTA
27675409 -TTT-TTGTTA
1 TTTTGTTGTTA
*
27675418 TTTTGCTGTTA
1 TTTTGTTGTTA
*
27675429 -TTT-TTGCTA
1 TTTTGTTGTTA
27675438 TTTTGGTTGTTA
1 TTTT-GTTGTTA
27675450 TTTTTGTTGTT
1 -TTTTGTTGTT
27675461 TGGATGTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
9 10 0.24
10 12 0.29
11 5 0.12
12 11 0.26
13 4 0.10
ACGTcount: A:0.08, C:0.03, G:0.17, T:0.71
Consensus pattern (11 bp):
TTTTGTTGTTA
Found at i:27675482 original size:21 final size:20
Alignment explanation
Indices: 27675439--27675483 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
27675429 TTTTTGCTAT
* * *
27675439 TTTGGTTGTTATTTTTGTTG
1 TTTGGATGTTATTTTTATCG
27675459 TTTGGATGTTATTTTTATGCG
1 TTTGGATGTTATTTTTAT-CG
27675480 TTTG
1 TTTG
27675484 AACTATTGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.09, C:0.02, G:0.24, T:0.64
Consensus pattern (20 bp):
TTTGGATGTTATTTTTATCG
Found at i:27676984 original size:13 final size:13
Alignment explanation
Indices: 27676957--27676992 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
27676947 GTCAAAGTCT
*
27676957 AAAATGGTTTGGGG
1 AAAA-GGTTTAGGG
27676971 AAAAGGTTTAGGG
1 AAAAGGTTTAGGG
27676984 AAAAGGTTT
1 AAAAGGTTT
27676993 TCATGGATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 17 0.81
14 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.28
Consensus pattern (13 bp):
AAAAGGTTTAGGG
Found at i:27679993 original size:23 final size:23
Alignment explanation
Indices: 27679964--27680008 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
27679954 ATAGTAAGTA
27679964 AAGAAGTTACCCGATTGAACGTG
1 AAGAAGTTACCCGATTGAACGTG
*
27679987 AAGAAGTTACCTGATTGAACGT
1 AAGAAGTTACCCGATTGAACGT
27680009 TAATGTCCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (23 bp):
AAGAAGTTACCCGATTGAACGTG
Found at i:27689058 original size:41 final size:41
Alignment explanation
Indices: 27688930--27689049 Score: 150
Period size: 41 Copynumber: 2.9 Consensus size: 41
27688920 AGGAAGTGCT
* * * *
27688930 GCTAAAAGTCAGAACATTAACGACGTTTTTTAAGAAGTATC
1 GCTAAAAATCAGAGCATTAGCGACGTTTTTTAAGAAGCATC
* * * *
27688971 GCTAAAGATCAAAGCATTAGCGACATTTTTTAGGAAGCATC
1 GCTAAAAATCAGAGCATTAGCGACGTTTTTTAAGAAGCATC
* *
27689012 GCTAAAAATCAGAGCATTAGCGACGTTTATTAAAAAGC
1 GCTAAAAATCAGAGCATTAGCGACGTTTTTTAAGAAGC
27689050 GCCACTAAAG
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 65 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (41 bp):
GCTAAAAATCAGAGCATTAGCGACGTTTTTTAAGAAGCATC
Found at i:27693227 original size:43 final size:43
Alignment explanation
Indices: 27693179--27693391 Score: 164
Period size: 43 Copynumber: 5.0 Consensus size: 43
27693169 AATTTGTTAA
* * *
27693179 TTTTAGCGGTGTTTATGGAAAAAATGCTGCTAAAGATCATGTT
1 TTTTAGCGGCGTTTATGGAAAAAACGCCGCTAAAGATCATGTT
* * * *
27693222 TTTTAGTGGCGTTTGTGGTAAAAACGCCGTTAAAGATCATGTT
1 TTTTAGCGGCGTTTATGGAAAAAACGCCGCTAAAGATCATGTT
* * * *
27693265 TTTTAGCGGCGTTT-TTGATAAAAGCGTCGCTAAAGA-CTATGCT
1 TTTTAGCGGCGTTTATGGA-AAAAACGCCGCTAAAGATC-ATGTT
* * * * * * *
27693308 CTTTAGCGGCGGTTGTGGTAAAAGCGCCACTAAAGACCATGTT
1 TTTTAGCGGCGTTTATGGAAAAAACGCCGCTAAAGATCATGTT
* * * *
27693351 CTTTAGCGGCGCTTGTAT--TAAAAGCGCCGCTAAAGACCATG
1 TTTTAGCGGCG-TT-TATGGAAAAAACGCCGCTAAAGATCATG
27693392 GTCTAAAACG
Statistics
Matches: 140, Mismatches: 24, Indels: 12
0.80 0.14 0.07
Matches are distributed among these distances:
42 3 0.02
43 131 0.94
44 4 0.03
45 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (43 bp):
TTTTAGCGGCGTTTATGGAAAAAACGCCGCTAAAGATCATGTT
Found at i:27693313 original size:86 final size:86
Alignment explanation
Indices: 27693223--27693387 Score: 224
Period size: 86 Copynumber: 1.9 Consensus size: 86
27693213 GATCATGTTT
* * ** * * * *
27693223 TTTAGTGGCGTTTGTGGTAAAAACGCCGTTAAAGATCATGTTTTTTAGCGGCGTTTTTGA-TAAA
1 TTTAGCGGCGGTTGTGGTAAAAACGCCACTAAAGACCATGTTCTTTAGCGGCGCTTGT-ATTAAA
*
27693287 AGCGTCGCTAAAGACTATGCTC
65 AGCGCCGCTAAAGACTATGCTC
*
27693309 TTTAGCGGCGGTTGTGGTAAAAGCGCCACTAAAGACCATGTTCTTTAGCGGCGCTTGTATTAAAA
1 TTTAGCGGCGGTTGTGGTAAAAACGCCACTAAAGACCATGTTCTTTAGCGGCGCTTGTATTAAAA
27693374 GCGCCGCTAAAGAC
66 GCGCCGCTAAAGAC
27693388 CATGGTCTAA
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
85 1 0.01
86 67 0.99
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.30
Consensus pattern (86 bp):
TTTAGCGGCGGTTGTGGTAAAAACGCCACTAAAGACCATGTTCTTTAGCGGCGCTTGTATTAAAA
GCGCCGCTAAAGACTATGCTC
Found at i:27697807 original size:3 final size:3
Alignment explanation
Indices: 27697799--27697853 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
27697789 TTGAATTTCC
27697799 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
27697847 TTA TTA T
1 TTA TTA T
27697854 ATGGATGTTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:27708017 original size:7 final size:7
Alignment explanation
Indices: 27708005--27708035 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
27707995 TTTATAATAG
27708005 CATTATA
1 CATTATA
27708012 CATTATA
1 CATTATA
27708019 CATTATA
1 CATTATA
27708026 CATTATA
1 CATTATA
27708033 CAT
1 CAT
27708036 ATGTGTAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (7 bp):
CATTATA
Found at i:27715796 original size:7 final size:7
Alignment explanation
Indices: 27715784--27715814 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
27715774 TTTATAATAG
27715784 CATTATA
1 CATTATA
27715791 CATTATA
1 CATTATA
27715798 CATTATA
1 CATTATA
27715805 CATTATA
1 CATTATA
27715812 CAT
1 CAT
27715815 ATGTGTAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (7 bp):
CATTATA
Found at i:27716172 original size:18 final size:18
Alignment explanation
Indices: 27716144--27716204 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
27716134 TCTCAAAAAT
27716144 TATTATTTAACTTTTTATA
1 TATT-TTTAACTTTTTATA
27716163 TATTTTTAACTTTTTA-A
1 TATTTTTAACTTTTTATA
* *
27716180 -AATCTTAACCTTTTTATA
1 TATTTTTAA-CTTTTTATA
27716198 TATTTTT
1 TATTTTT
27716205 TTAAAATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 6 0.17
17 8 0.23
18 13 0.37
19 8 0.23
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTTTTAACTTTTTATA
Found at i:27732746 original size:40 final size:39
Alignment explanation
Indices: 27732696--27732778 Score: 123
Period size: 40 Copynumber: 2.1 Consensus size: 39
27732686 TTCCTCTTTG
*
27732696 AACAATCTTATGCTAC-ACCGAGTCATAAGTCTTCCTTTCA
1 AACAATCTTATGCT-CTACCGAGTCATAAGTCTTCCATT-A
*
27732736 AACAATCTTATGCTCTATCGAGTCATAAGTCTTCCATTA
1 AACAATCTTATGCTCTACCGAGTCATAAGTCTTCCATTA
27732775 AACA
1 AACA
27732779 TATTCTCACG
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
39 6 0.15
40 34 0.85
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.33
Consensus pattern (39 bp):
AACAATCTTATGCTCTACCGAGTCATAAGTCTTCCATTA
Found at i:27732820 original size:41 final size:42
Alignment explanation
Indices: 27732754--27732937 Score: 158
Period size: 42 Copynumber: 4.4 Consensus size: 42
27732744 TATGCTCTAT
* * * *
27732754 CGAGTCATAAGTCTTCCATTAAACATATTCTCACGCTCTTTC
1 CGAGACATGAGTCTTCCTTTTAACATATTCTCACGCTCTTTC
* * *
27732796 CGAGACATGAGTCTT-CTTTTAACATAGTCTCATGCTCTTTT
1 CGAGACATGAGTCTTCCTTTTAACATATTCTCACGCTCTTTC
* * *
27732837 CGAGACATGAGTCTTCCTTTAAACATAATT-TCATGTTCATTT-
1 CGAGACATGAGTCTTCCTTTTAACAT-ATTCTCACGCTC-TTTC
* * * * * * *
27732879 CAAGTCACGAGTCTTCCATTTATACATAATCTCACGCTCATCC
1 CGAGACATGAGTCTTCCTTTTA-ACATATTCTCACGCTCTTTC
*
27732922 CGAGACATGACTCTTC
1 CGAGACATGAGTCTTC
27732938 TATTTATACA
Statistics
Matches: 112, Mismatches: 24, Indels: 11
0.76 0.16 0.07
Matches are distributed among these distances:
41 36 0.32
42 49 0.44
43 27 0.24
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.36
Consensus pattern (42 bp):
CGAGACATGAGTCTTCCTTTTAACATATTCTCACGCTCTTTC
Found at i:27732856 original size:21 final size:21
Alignment explanation
Indices: 27732791--27732856 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
27732781 TTCTCACGCT
*
27732791 CTTTCCGAGACATGAGTCTT-
1 CTTTTCGAGACATGAGTCTTC
27732811 CTTTT--A-ACAT-AGTCTCATGC
1 CTTTTCGAGACATGAGTCT--T-C
27732831 TCTTTTCGAGACATGAGTCTTC
1 -CTTTTCGAGACATGAGTCTTC
27732853 CTTT
1 CTTT
27732857 AAACATAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 17
0.67 0.02 0.31
Matches are distributed among these distances:
16 5 0.14
17 4 0.11
18 2 0.06
20 4 0.11
21 9 0.25
22 1 0.03
23 2 0.06
24 4 0.11
25 5 0.14
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (21 bp):
CTTTTCGAGACATGAGTCTTC
Found at i:27739889 original size:40 final size:39
Alignment explanation
Indices: 27739839--27739921 Score: 112
Period size: 40 Copynumber: 2.1 Consensus size: 39
27739829 TTCCTCTTTG
*
27739839 AACAATCTTATGCTACACCGAGTCATAAGTCTTCCTTTCA
1 AACAATCTTATGCTACACCGAGTCATAAGTCTTCCATT-A
* ** *
27739879 AACAATCTTATGTTGTATCGAGTCATAAGTCTTCCATTA
1 AACAATCTTATGCTACACCGAGTCATAAGTCTTCCATTA
27739918 AACA
1 AACA
27739922 TATTCTCACG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
39 5 0.13
40 33 0.87
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.34
Consensus pattern (39 bp):
AACAATCTTATGCTACACCGAGTCATAAGTCTTCCATTA
Found at i:27740013 original size:43 final size:43
Alignment explanation
Indices: 27739897--27740050 Score: 170
Period size: 42 Copynumber: 3.6 Consensus size: 43
27739887 TATGTTGTAT
* * * *
27739897 CGAGTCATAAGTCTTCCA-TTAAACATATTCTCACGCTCTTTT
1 CGAGTCATGAGTCTTCCATTTAAACATAATCTCACGCTCATTC
* *
27739939 CGAGACATGAGTCTTCC-TTTAAACATAATCTCATGCTCATTC
1 CGAGTCATGAGTCTTCCATTTAAACATAATCTCACGCTCATTC
* * *
27739981 CGAGTCATGAGTATTCCATTTATACATAATCTCACGCGT-ATCC
1 CGAGTCATGAGTCTTCCATTTAAACATAATCTCACGC-TCATTC
* * *
27740024 CGAGGCATGAGTTTTCCATTTATACAT
1 CGAGTCATGAGTCTTCCATTTAAACAT
27740051 CAGGTGATTC
Statistics
Matches: 96, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
42 50 0.52
43 45 0.47
44 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (43 bp):
CGAGTCATGAGTCTTCCATTTAAACATAATCTCACGCTCATTC
Found at i:27742298 original size:21 final size:21
Alignment explanation
Indices: 27742239--27742298 Score: 50
Period size: 24 Copynumber: 2.7 Consensus size: 21
27742229 CTATACGCCT
* *
27742239 AAATGAGTAAGACCATAACTG
1 AAATGAGTAAGATCATAACGG
*
27742260 AAA-GATGTTATAGCATCATGACGG
1 AAATGA-G-TA-AG-ATCATAACGG
27742284 AAATGAGTAAGATCA
1 AAATGAGTAAGATCA
27742299 CAGTTGAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
20 2 0.06
21 8 0.26
22 4 0.13
23 4 0.13
24 11 0.35
25 2 0.06
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.22
Consensus pattern (21 bp):
AAATGAGTAAGATCATAACGG
Found at i:27742307 original size:45 final size:45
Alignment explanation
Indices: 27742239--27742324 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
27742229 CTATACGCCT
*
27742239 AAATGAGTAAGACCATAACTGAAAGATGTTATAG-CATCATGACGG
1 AAATGAGTAAGACCACAACTGAAAGATGTTAT-GCCATCATGACGG
* ** *
27742284 AAATGAGTAAGATCACAGTTGAAATATGTTATGCCATCATG
1 AAATGAGTAAGACCACAACTGAAAGATGTTATGCCATCATG
27742325 TAAAAGCACG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 1 0.03
45 34 0.97
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.26
Consensus pattern (45 bp):
AAATGAGTAAGACCACAACTGAAAGATGTTATGCCATCATGACGG
Found at i:27743131 original size:23 final size:23
Alignment explanation
Indices: 27743097--27743163 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
27743087 GTAATTTAAA
* **
27743097 ACAAATATAATGTTTGAAGAGTCG
1 ACAAAAATAATGGCTGAAGAGT-G
*
27743121 A-AAAAATAATGGCTGAAGAGTT
1 ACAAAAATAATGGCTGAAGAGTG
27743143 ACAAAAATAATGGCTGAAGAG
1 ACAAAAATAATGGCTGAAGAG
27743164 ATAAAAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 1 0.03
23 36 0.95
24 1 0.03
ACGTcount: A:0.48, C:0.07, G:0.22, T:0.22
Consensus pattern (23 bp):
ACAAAAATAATGGCTGAAGAGTG
Found at i:27743171 original size:23 final size:23
Alignment explanation
Indices: 27743121--27743173 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
27743111 TGAAGAGTCG
*
27743121 AAAAAATAATGGCTGAAGAGTTA
1 AAAAAATAATGGCTGAAGAGATA
*
27743144 CAAAAATAATGGCTGAAGAGATA
1 AAAAAATAATGGCTGAAGAGATA
27743167 AAAAAAT
1 AAAAAAT
27743174 TAAAGCAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.57, C:0.06, G:0.19, T:0.19
Consensus pattern (23 bp):
AAAAAATAATGGCTGAAGAGATA
Found at i:27748639 original size:18 final size:19
Alignment explanation
Indices: 27748604--27748642 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
27748594 AATAAATATA
27748604 AATACAATTTAAATTTAAT
1 AATACAATTTAAATTTAAT
27748623 AATA-AATTGTAAA-TTAAT
1 AATACAATT-TAAATTTAAT
27748641 AA
1 AA
27748643 AAAGAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (19 bp):
AATACAATTTAAATTTAAT
Found at i:27749019 original size:23 final size:23
Alignment explanation
Indices: 27748993--27749037 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
27748983 AAACAAATAC
27748993 AATGGCTGAAGAGTTACAAAAAT
1 AATGGCTGAAGAGTTACAAAAAT
*
27749016 AATGGTTGAAGAGTTACAAAAA
1 AATGGCTGAAGAGTTACAAAAA
27749038 AAAAAATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.49, C:0.07, G:0.22, T:0.22
Consensus pattern (23 bp):
AATGGCTGAAGAGTTACAAAAAT
Found at i:27749047 original size:23 final size:23
Alignment explanation
Indices: 27748999--27749048 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
27748989 ATACAATGGC
* ***
27748999 TGAAGAGTTACAAAAATAATGGT
1 TGAAGAGTTACAAAAAAAAAAAT
27749022 TGAAGAGTTACAAAAAAAAAAAT
1 TGAAGAGTTACAAAAAAAAAAAT
27749045 TGAA
1 TGAA
27749049 ATAATAGGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (23 bp):
TGAAGAGTTACAAAAAAAAAAAT
Found at i:27751696 original size:3 final size:3
Alignment explanation
Indices: 27751688--27751732 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
27751678 TACATCCCAA
27751688 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
27751733 GAATAGAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:27752812 original size:20 final size:20
Alignment explanation
Indices: 27752789--27752891 Score: 66
Period size: 20 Copynumber: 4.8 Consensus size: 20
27752779 AAAAGTCAAC
27752789 GGTCAAAGTCAACGGTCAGT
1 GGTCAAAGTCAACGGTCAGT
*
27752809 GGTCAACGGTCAAAGTCAACGGTCAACT
1 GGTC-A------AAGTCAACGGTC-AGT
27752837 -GTCAAAGTCAACGGTCAGT
1 GGTCAAAGTCAACGGTCAGT
* * **
27752856 GGTCAAAGGTCAA-AGTTAAC
1 GGTCAAA-GTCAACGGTCAGT
27752876 GGTCAAAGTCAACGGT
1 GGTCAAAGTCAACGGT
27752892 TTGACTTGGT
Statistics
Matches: 65, Mismatches: 7, Indels: 22
0.69 0.07 0.23
Matches are distributed among these distances:
19 7 0.11
20 34 0.52
21 6 0.09
26 1 0.02
27 15 0.23
28 2 0.03
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.19
Consensus pattern (20 bp):
GGTCAAAGTCAACGGTCAGT
Found at i:27752821 original size:27 final size:27
Alignment explanation
Indices: 27752783--27752880 Score: 120
Period size: 27 Copynumber: 3.9 Consensus size: 27
27752773 TTGAAAAAAA
27752783 GTCAACGGTCAAAGTCAACGGTCAGTG
1 GTCAACGGTCAAAGTCAACGGTCAGTG
27752810 GTCAACGGTCAAAGTCAA----C---G
1 GTCAACGGTCAAAGTCAACGGTCAGTG
*
27752830 GTCAACTGTCAAAGTCAACGGTCAGTG
1 GTCAACGGTCAAAGTCAACGGTCAGTG
* *
27752857 GTCAAAGGTCAAAGTTAACGGTCA
1 GTCAACGGTCAAAGTCAACGGTCA
27752881 AAGTCAACGG
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
20 18 0.30
23 1 0.02
24 1 0.02
27 40 0.67
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.19
Consensus pattern (27 bp):
GTCAACGGTCAAAGTCAACGGTCAGTG
Found at i:27752852 original size:47 final size:47
Alignment explanation
Indices: 27752783--27752881 Score: 171
Period size: 47 Copynumber: 2.1 Consensus size: 47
27752773 TTGAAAAAAA
*
27752783 GTCAACGGTCAAAGTCAACGGTCAGTGGTCAACGGTCAAAGTCAACG
1 GTCAACGGTCAAAGTCAACGGTCAGTGGTCAAAGGTCAAAGTCAACG
* *
27752830 GTCAACTGTCAAAGTCAACGGTCAGTGGTCAAAGGTCAAAGTTAACG
1 GTCAACGGTCAAAGTCAACGGTCAGTGGTCAAAGGTCAAAGTCAACG
27752877 GTCAA
1 GTCAA
27752882 AGTCAACGGT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.19
Consensus pattern (47 bp):
GTCAACGGTCAAAGTCAACGGTCAGTGGTCAAAGGTCAAAGTCAACG
Found at i:27753476 original size:17 final size:17
Alignment explanation
Indices: 27753450--27753482 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
27753440 AAGTCAAGGG
*
27753450 AAAAAGAAAGAAAAAGA
1 AAAAAAAAAGAAAAAGA
27753467 AAAAAAAAAGAAAAAG
1 AAAAAAAAAGAAAAAG
27753483 GTTTGGGGCA
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:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAGAAAAAGA
Found at i:27758924 original size:3 final size:3
Alignment explanation
Indices: 27758916--27758945 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
27758906 TACATCCCAA
27758916 AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
27758946 GAATAGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:27760038 original size:7 final size:7
Alignment explanation
Indices: 27760002--27760097 Score: 56
Period size: 7 Copynumber: 14.3 Consensus size: 7
27759992 TTGAAAAAAA
27760002 GTCAACG
1 GTCAACG
* *
27760009 GCCAA-A
1 GTCAACG
27760015 GTCAACG
1 GTCAACG
**
27760022 GTCAGTG
1 GTCAACG
27760029 GTCAACG
1 GTCAACG
*
27760036 GTCAACT
1 GTCAACG
*
27760043 GTCAA-A
1 GTCAACG
27760049 GTCAACG
1 GTCAACG
**
27760056 GTCAGTG
1 GTCAACG
*
27760063 GTCAAAG
1 GTCAACG
*
27760070 GTCAA-A
1 GTCAACG
*
27760076 GTTAACG
1 GTCAACG
*
27760083 GTCAA-A
1 GTCAACG
27760089 GTCAACG
1 GTCAACG
27760096 GT
1 GT
27760098 TTGACTTGGT
Statistics
Matches: 64, Mismatches: 21, Indels: 8
0.69 0.23 0.09
Matches are distributed among these distances:
6 18 0.28
7 46 0.72
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:27760049 original size:34 final size:34
Alignment explanation
Indices: 27760002--27760074 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
27759992 TTGAAAAAAA
*
27760002 GTCAACGGCCAAAGTCAACGGTCAGTGGTCAACG
1 GTCAACGGCCAAAGTCAACGGTCAGTGGTCAAAG
* *
27760036 GTCAACTGTCAAAGTCAACGGTCAGTGGTCAAAG
1 GTCAACGGCCAAAGTCAACGGTCAGTGGTCAAAG
27760070 GTCAA
1 GTCAA
27760075 AGTTAACGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.32, C:0.23, G:0.27, T:0.18
Consensus pattern (34 bp):
GTCAACGGCCAAAGTCAACGGTCAGTGGTCAAAG
Found at i:27760054 original size:13 final size:13
Alignment explanation
Indices: 27759999--27760097 Score: 75
Period size: 13 Copynumber: 7.9 Consensus size: 13
27759989 TTTTTGAAAA
*
27759999 AAAGTCAACGGCC
1 AAAGTCAACGGTC
27760012 AAAGTCAACGGTC
1 AAAGTCAACGGTC
27760025 --AGT----GGTC
1 AAAGTCAACGGTC
* *
27760032 AACGGTCAACTGTC
1 AA-AGTCAACGGTC
27760046 AAAGTCAACGGTC
1 AAAGTCAACGGTC
** *
27760059 AGTGGTCAAAGGTC
1 A-AAGTCAACGGTC
*
27760073 AAAGTTAACGGTC
1 AAAGTCAACGGTC
27760086 AAAGTCAACGGT
1 AAAGTCAACGGT
27760098 TTGACTTGGT
Statistics
Matches: 65, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
7 4 0.06
10 2 0.03
11 3 0.05
13 41 0.63
14 15 0.23
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.18
Consensus pattern (13 bp):
AAAGTCAACGGTC
Found at i:27760054 original size:20 final size:20
Alignment explanation
Indices: 27760029--27760097 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
27760019 ACGGTCAGTG
27760029 GTCAACGGTCAACTGTCAAA
1 GTCAACGGTCAACTGTCAAA
*
27760049 GTCAACGGTC-AGTGGTCAAA
1 GTCAACGGTCAACT-GTCAAA
* * *
27760069 GGTCAA-AGTTAACGGTCAAA
1 -GTCAACGGTCAACTGTCAAA
27760089 GTCAACGGT
1 GTCAACGGT
27760098 TTGACTTGGT
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 7 0.18
20 26 0.67
21 6 0.15
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.20
Consensus pattern (20 bp):
GTCAACGGTCAACTGTCAAA
Found at i:27760058 original size:27 final size:27
Alignment explanation
Indices: 27760002--27760087 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 27
27759992 TTGAAAAAAA
* * **
27760002 GTCAACGGCCAAA-GTCAACGGTCAGTG
1 GTCAACGGTCAAAGGTCAA-AGTCAACG
**
27760029 GTCAACGGTCAACTGTCAAAGTCAACG
1 GTCAACGGTCAAAGGTCAAAGTCAACG
** *
27760056 GTCAGTGGTCAAAGGTCAAAGTTAACG
1 GTCAACGGTCAAAGGTCAAAGTCAACG
27760083 GTCAA
1 GTCAA
27760088 AGTCAACGGT
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
27 42 0.89
28 5 0.11
ACGTcount: A:0.33, C:0.22, G:0.27, T:0.19
Consensus pattern (27 bp):
GTCAACGGTCAAAGGTCAAAGTCAACG
Found at i:27760170 original size:21 final size:22
Alignment explanation
Indices: 27760144--27760189 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
27760134 TGGTTCAAAA
27760144 GGGTTTGGTTTAAAT-GAATTT
1 GGGTTTGGTTTAAATAGAATTT
*
27760165 GGGTTTGGTTTAAATAGGATTT
1 GGGTTTGGTTTAAATAGAATTT
27760187 GGG
1 GGG
27760190 CTTAATGGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.22, C:0.00, G:0.35, T:0.43
Consensus pattern (22 bp):
GGGTTTGGTTTAAATAGAATTT
Found at i:27760678 original size:9 final size:10
Alignment explanation
Indices: 27760655--27760690 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
27760645 TAAGGCAAGG
27760655 GAAAAAGAAA
1 GAAAAAGAAA
27760665 GAAAAAGAAA
1 GAAAAAGAAA
27760675 -AAAAAGAAA
1 GAAAAAGAAA
27760684 GAAAAAG
1 GAAAAAG
27760691 GTTTGGGGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (10 bp):
GAAAAAGAAA
Found at i:27765387 original size:14 final size:15
Alignment explanation
Indices: 27765370--27765399 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
27765360 TAATTAGTTT
27765370 TTTTTATTTT-TTTA
1 TTTTTATTTTATTTA
27765384 TTTTTATTTTATTTA
1 TTTTTATTTTATTTA
27765399 T
1 T
27765400 AAATTACTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTATTTTATTTA
Found at i:27766970 original size:15 final size:15
Alignment explanation
Indices: 27766919--27766973 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
27766909 TATATATATG
27766919 TATAT-TTTAGAGTTT
1 TATATATTTAGA-TTT
**
27766934 TATATAATTTTTATTAT
1 TATAT-ATTTAGATT-T
27766951 T-TATATTTAGATTT
1 TATATATTTAGATTT
27766965 TATATATTT
1 TATATATTT
27766974 TTCTCAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 2 0.06
15 19 0.59
16 5 0.16
17 6 0.19
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (15 bp):
TATATATTTAGATTT
Found at i:27766989 original size:33 final size:32
Alignment explanation
Indices: 27766915--27766975 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 32
27766905 TACGTATATA
27766915 TATGTATATTTTAGAGTTTTATATAATTTTTAT
1 TATGTATA-TTTAGAGTTTTATATAATTTTTAT
*
27766948 TATTTATATTTAGA-TTTTATAT-ATTTTT
1 TATGTATATTTAGAGTTTTATATAATTTTT
27766976 CTCAATTTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 6 0.22
31 8 0.30
32 6 0.22
33 7 0.26
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (32 bp):
TATGTATATTTAGAGTTTTATATAATTTTTAT
Done.