Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009610.1 Hibiscus syriacus cultivar Beakdansim tig00116996_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3811333
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 18
Found at i:4161 original size:29 final size:29
Alignment explanation
Indices: 4127--4185 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
4117 CTTAAATTAA
*
4127 TTTGATGTCTTTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
4156 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
4185 T
1 T
4186 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.51
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:9073 original size:23 final size:23
Alignment explanation
Indices: 9040--9099 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
9030 AATCTTATAT
* *
9040 GACACTACGGTGTAATTCTACGC
1 GACACTTCGGTGCAATTCTACGC
*
9063 GACACTTCGGTGCAATTCTACGT
1 GACACTTCGGTGCAATTCTACGC
*
9086 GGCACTTCGGTGCA
1 GACACTTCGGTGCA
9100 TTTATATGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.27
Consensus pattern (23 bp):
GACACTTCGGTGCAATTCTACGC
Found at i:14888 original size:63 final size:64
Alignment explanation
Indices: 14749--14910 Score: 179
Period size: 63 Copynumber: 2.5 Consensus size: 64
14739 ATTGATCAAG
* * * **
14749 GTGTATCGATGCACATGAAGTGCATCGATGCACTCTTTTAAAATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCA
* * * *
14813 GTGTATCAATGCACAAGTAGTGCATCGATGCACCCCCTT-AAATACAAACATCGAATAG-GATTT
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAAT-GCCA-TC
14876 A
64 A
*
14877 -TGTATCGATGCA-TAGATAGTGCATCGATGCACCC
1 GTGTATCGATGCACAAG-TAGTGCATCGATGCACCC
14911 GTCAAGGGAT
Statistics
Matches: 84, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
62 2 0.02
63 46 0.55
64 36 0.43
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.26
Consensus pattern (64 bp):
GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCA
Found at i:15580 original size:23 final size:23
Alignment explanation
Indices: 15560--15611 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
15550 ATGGCACTAT
15560 GGTGCAATTCTACGCGACACTTC
1 GGTGCAATTCTACGCGACACTTC
* *
15583 GTTGCAATTCTACGTGACACTTC
1 GGTGCAATTCTACGCGACACTTC
15606 GGTGCA
1 GGTGCA
15612 TTTATACTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (23 bp):
GGTGCAATTCTACGCGACACTTC
Found at i:19528 original size:3 final size:3
Alignment explanation
Indices: 19520--19636 Score: 234
Period size: 3 Copynumber: 39.0 Consensus size: 3
19510 CAACCCAAAT
19520 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
19568 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
19616 TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
19637 AGAATGAGAA
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 114 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:31876 original size:2 final size:2
Alignment explanation
Indices: 31871--31896 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31861 TATAAAATTA
31871 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
31897 TGATTAACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33191 original size:15 final size:15
Alignment explanation
Indices: 33171--33212 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
33161 TTGGGCGGGC
* **
33171 GGATGCGGTGTGGGT
1 GGATGCGGTGCGAAT
33186 GGATGCGGTGCGAAT
1 GGATGCGGTGCGAAT
33201 GGATGCGGTGCG
1 GGATGCGGTGCG
33213 GATGCGGATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.12, C:0.12, G:0.55, T:0.21
Consensus pattern (15 bp):
GGATGCGGTGCGAAT
Found at i:37250 original size:45 final size:44
Alignment explanation
Indices: 37161--37259 Score: 117
Period size: 45 Copynumber: 2.2 Consensus size: 44
37151 CAGGAAGTGA
* * *
37161 ATCGATGCACCTATTAAAATGGAAACATCGAATACAATTGGTGC
1 ATCGATGCACCCATTAAAATGAAAACATCGAAGACAATTGGTGC
* *** *
37205 ATCGATGCATCCCCTTAAAATGAAAACATCGAAGGTGATTTGTGC
1 ATCGATGCA-CCCATTAAAATGAAAACATCGAAGACAATTGGTGC
37250 ATCGATGCAC
1 ATCGATGCAC
37260 GGGTACTGCA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 10 0.22
45 36 0.78
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.25
Consensus pattern (44 bp):
ATCGATGCACCCATTAAAATGAAAACATCGAAGACAATTGGTGC
Found at i:37312 original size:20 final size:20
Alignment explanation
Indices: 37247--37323 Score: 75
Period size: 20 Copynumber: 3.7 Consensus size: 20
37237 AGGTGATTTG
* * *
37247 TGCATCGATGCACGGGT-AC
1 TGCATCGATGCACTGTTGAA
*
37266 TGCATCGATGCACATGCTAAAGAA
1 TGCATCGATGCAC-TG-T--TGAA
37290 TGCATCGATGCACTGTTGAA
1 TGCATCGATGCACTGTTGAA
37310 TGCATCGATGCACT
1 TGCATCGATGCACT
37324 TCAAGAGAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
19 13 0.27
20 18 0.38
22 1 0.02
23 2 0.04
24 14 0.29
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (20 bp):
TGCATCGATGCACTGTTGAA
Found at i:42650 original size:21 final size:21
Alignment explanation
Indices: 42621--42660 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
42611 GACTCCTCGC
42621 TGTCATCATCATCGTCGTCGT
1 TGTCATCATCATCGTCGTCGT
* *
42642 TGTCGTCATCGTCGTCGTC
1 TGTCATCATCATCGTCGTC
42661 CTGAGCAGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.30, G:0.23, T:0.38
Consensus pattern (21 bp):
TGTCATCATCATCGTCGTCGT
Found at i:43022 original size:18 final size:18
Alignment explanation
Indices: 42999--43038 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
42989 AAAGGCGATG
42999 GCGGCATCATATATGGAT
1 GCGGCATCATATATGGAT
*
43017 GCGGCATCATATATGGTT
1 GCGGCATCATATATGGAT
43035 GCGG
1 GCGG
43039 TGGCTGCTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.28
Consensus pattern (18 bp):
GCGGCATCATATATGGAT
Found at i:44588 original size:111 final size:111
Alignment explanation
Indices: 44394--44726 Score: 594
Period size: 111 Copynumber: 3.0 Consensus size: 111
44384 ATTACAAAAA
* *
44394 TTAATTCTTACTCTAATAATCATGCATTAAATAAATCAAATAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
44459 AATTAAAACGTTAAAATATTACTGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATATTACTGTATCAGCAAAGTGTCGAGATAT
*
44505 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTATTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
44570 AATTAAAACGTTAAAATATTACTGTATTAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATATTACTGTATCAGCAAAGTGTCGAGATAT
*
44616 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* * *
44681 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATATTACTGTATCAGCAAAGTGTCGAGATAT
44727 ATGATTTCCA
Statistics
Matches: 212, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 212 1.00
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATATTACTGTATCAGCAAAGTGTCGAGATAT
Found at i:44998 original size:50 final size:47
Alignment explanation
Indices: 44944--45060 Score: 128
Period size: 50 Copynumber: 2.4 Consensus size: 47
44934 CCCCCTGCAC
* *
44944 CGCGCTATACCCCACGTGTCAGAT-ACCCAGGTATAGCGCGGATCAGGGGA
1 CGCGCTATA-CCCACGTGCCAGATCA-CC--GTATAGCGCGGAGCAGGGGA
* *
44994 CGCGCTATACCCACGTGGCGCCAGATCACCGTATATCGCGGAGCAGGGGG
1 CGCGCTATACCCACGT---GCCAGATCACCGTATAGCGCGGAGCAGGGGA
45044 CGCGCTATACCCACGTG
1 CGCGCTATACCCACGTG
45061 ACGCCAAATC
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
47 1 0.02
49 7 0.12
50 42 0.71
52 8 0.14
53 1 0.02
ACGTcount: A:0.21, C:0.32, G:0.31, T:0.15
Consensus pattern (47 bp):
CGCGCTATACCCACGTGCCAGATCACCGTATAGCGCGGAGCAGGGGA
Found at i:45066 original size:50 final size:50
Alignment explanation
Indices: 44974--45099 Score: 171
Period size: 50 Copynumber: 2.5 Consensus size: 50
44964 AGATACCCAG
* * * *
44974 GTATAGCGCGGATCAGGGGACGCGCTATACCCACGTGGCGCCAGATCACC
1 GTATAACGCGGATCAGGGGGCGCGCTATACCCACGTGACGCCAAATCACC
* * *
45024 GTATATCGCGGAGCAGGGGGCGCGCTATACCCACGTGACGCCAAATCAGC
1 GTATAACGCGGATCAGGGGGCGCGCTATACCCACGTGACGCCAAATCACC
* *
45074 GTATAACGCAGTTCAGGGGGCGCGCT
1 GTATAACGCGGATCAGGGGGCGCGCT
45100 TTACTACTAC
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 66 1.00
ACGTcount: A:0.22, C:0.29, G:0.33, T:0.15
Consensus pattern (50 bp):
GTATAACGCGGATCAGGGGGCGCGCTATACCCACGTGACGCCAAATCACC
Found at i:52586 original size:21 final size:21
Alignment explanation
Indices: 52561--52623 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
52551 TTGATGAAAA
52561 TTTATTTAAAATATTATTATT
1 TTTATTTAAAATATTATTATT
52582 TTTA-TTAAAATTATTATTATT
1 TTTATTTAAAA-TATTATTATT
* *
52603 TCTATTGAAAATATTATTATT
1 TTTATTTAAAATATTATTATT
52624 GGGAATTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.16
21 27 0.71
22 5 0.13
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTATTTAAAATATTATTATT
Found at i:53439 original size:60 final size:61
Alignment explanation
Indices: 53346--53461 Score: 189
Period size: 60 Copynumber: 1.9 Consensus size: 61
53336 GAATAACAAT
* * *
53346 TATTCTTTTAACCATTGAAGATTTTATTTTAAGACTCATG-CCCAAATAAAATGTGTTGTC
1 TATTCCTTTAACCATTAAAGATTTTATTTTAAGACTCAGGTCCCAAATAAAATGTGTTGTC
*
53406 TATTCCTTTAACCATTAAAGATTTTATTTTAAGACTCAGGTCCCAAATAAAGTGTG
1 TATTCCTTTAACCATTAAAGATTTTATTTTAAGACTCAGGTCCCAAATAAAATGTG
53462 GTGTACAACG
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
60 37 0.73
61 14 0.27
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.40
Consensus pattern (61 bp):
TATTCCTTTAACCATTAAAGATTTTATTTTAAGACTCAGGTCCCAAATAAAATGTGTTGTC
Found at i:63144 original size:24 final size:26
Alignment explanation
Indices: 63094--63148 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 26
63084 TTTTGAAACG
63094 TTAGATACCTAAATGAATCGAAAAATAT
1 TTAGATACCTAAATGAA-C-AAAAATAT
*
63122 TTAGATACCTAAATGAAAAAATAATAT
1 TTAGATACCTAAATGAACAAA-AATAT
63149 AATTTATACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 3 0.12
27 5 0.20
28 17 0.68
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.29
Consensus pattern (26 bp):
TTAGATACCTAAATGAACAAAAATAT
Found at i:78328 original size:41 final size:41
Alignment explanation
Indices: 78274--78353 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
78264 ACAAGACCAT
78274 ATTCATGTCCGTTTATTTATTTTTAAAAGTGTTTATGTTTA
1 ATTCATGTCCGTTTATTTATTTTTAAAAGTGTTTATGTTTA
* * * *
78315 ATTCGTGTTCGTTTATTTATTTTTGAAGGTGTTTATGTT
1 ATTCATGTCCGTTTATTTATTTTTAAAAGTGTTTATGTT
78354 CGTTCGCTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.20, C:0.06, G:0.16, T:0.57
Consensus pattern (41 bp):
ATTCATGTCCGTTTATTTATTTTTAAAAGTGTTTATGTTTA
Found at i:79442 original size:24 final size:24
Alignment explanation
Indices: 79399--79501 Score: 77
Period size: 24 Copynumber: 4.3 Consensus size: 24
79389 TATAAAAAAA
* * *
79399 ATAAACGAGCTT-CTAAATGAGCTT
1 ATAAACGAGCTTGCT-CATGAACAT
* *
79423 ATAAACGAGTTTGTTCATGAACAT
1 ATAAACGAGCTTGCTCATGAACAT
*
79447 ATAGACGAGCTTGCTCATGAACTAT
1 ATAAACGAGCTTGCTCATGAAC-AT
* * * *
79472 ATAGACAAGCTTGTTCGTG-A-AT
1 ATAAACGAGCTTGCTCATGAACAT
79494 ATAAACGA
1 ATAAACGA
79502 ACCGAACACA
Statistics
Matches: 64, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
22 8 0.12
24 37 0.58
25 19 0.30
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (24 bp):
ATAAACGAGCTTGCTCATGAACAT
Found at i:79492 original size:25 final size:25
Alignment explanation
Indices: 79433--79496 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
79423 ATAAACGAGT
*
79433 TTGTTCATGAAC-ATATAGACGAGC
1 TTGTTCATGAACTATATAGACAAGC
*
79457 TTGCTCATGAACTATATAGACAAGC
1 TTGTTCATGAACTATATAGACAAGC
*
79482 TTGTTCGTGAA-TATA
1 TTGTTCATGAACTATA
79497 AACGAACCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 15 0.43
25 20 0.57
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (25 bp):
TTGTTCATGAACTATATAGACAAGC
Found at i:84334 original size:2 final size:2
Alignment explanation
Indices: 84327--84367 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
84317 TTGTAATTGA
84327 AT AT AT 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 AT AT AT A
84368 ATAGTATAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:85206 original size:28 final size:28
Alignment explanation
Indices: 85174--85230 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
85164 TTCTCAGTTT
85174 ATATTATGTCGTCGAGCCAATGCTTGAA
1 ATATTATGTCGTCGAGCCAATGCTTGAA
*
85202 ATATTATGTCGTCGAGCCAGTGCTTGAA
1 ATATTATGTCGTCGAGCCAATGCTTGAA
85230 A
1 A
85231 GCAACGACAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.32
Consensus pattern (28 bp):
ATATTATGTCGTCGAGCCAATGCTTGAA
Found at i:85439 original size:59 final size:60
Alignment explanation
Indices: 85375--85522 Score: 174
Period size: 59 Copynumber: 2.5 Consensus size: 60
85365 ACAATTTTGC
* * *
85375 AACTTTTAATTGTC-ACGAGACTCAATAAAACAACATCTTATAGTCAGGAGACCAT-TTTT
1 AACTTTTAATGGTCGA-GAGACTCAACAAAACAACATCTTATAATCAGGAGACCATGTTTT
* * **
85434 AACTTTTAATGGTCGAGAGACTCAACAAAACAACGTCTTATAATCAGGGGATTATGTTTT
1 AACTTTTAATGGTCGAGAGACTCAACAAAACAACATCTTATAATCAGGAGACCATGTTTT
* * * *
85494 AACTTTTAATAGTTGACAGACTCGACAAA
1 AACTTTTAATGGTCGAGAGACTCAACAAA
85523 GTAATATCCT
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
59 46 0.61
60 30 0.39
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (60 bp):
AACTTTTAATGGTCGAGAGACTCAACAAAACAACATCTTATAATCAGGAGACCATGTTTT
Found at i:87422 original size:2 final size:2
Alignment explanation
Indices: 87415--87446 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
87405 ATAACCAAAG
87415 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
87447 TTAGGGCCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:88617 original size:18 final size:18
Alignment explanation
Indices: 88594--88636 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
88584 AGCCTCAGAG
88594 GATGAAGACGAAGACGAA
1 GATGAAGACGAAGACGAA
* * *
88612 GATGAAGATGATGGCGAA
1 GATGAAGACGAAGACGAA
88630 GATGAAG
1 GATGAAG
88637 GTGAGAGTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.07, G:0.37, T:0.12
Consensus pattern (18 bp):
GATGAAGACGAAGACGAA
Found at i:88618 original size:12 final size:12
Alignment explanation
Indices: 88594--88636 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
88584 AGCCTCAGAG
88594 GATGAAGACGAA
1 GATGAAGACGAA
* *
88606 GACGAAGATGAA
1 GATGAAGACGAA
* *
88618 GATGATGGCGAA
1 GATGAAGACGAA
88630 GATGAAG
1 GATGAAG
88637 GTGAGAGTGG
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.44, C:0.07, G:0.37, T:0.12
Consensus pattern (12 bp):
GATGAAGACGAA
Found at i:92059 original size:9 final size:9
Alignment explanation
Indices: 92045--92074 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
92035 ATGGGCTGGC
92045 TGAACAAGT
1 TGAACAAGT
92054 TGAACAAGT
1 TGAACAAGT
*
92063 TGATCAAGT
1 TGAACAAGT
92072 TGA
1 TGA
92075 CAGCTTGACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.27
Consensus pattern (9 bp):
TGAACAAGT
Found at i:94801 original size:35 final size:35
Alignment explanation
Indices: 94723--94802 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 35
94713 ATTTAAATTC
*
94723 AACAAACTTACAATAAGAATTAAATGGTAAATGAT
1 AACAAAATTACAATAAGAATTAAATGGTAAATGAT
*
94758 AACCAAATTACAATAACTGATATTAAATGGT-AAT-A-
1 AACAAAATTACAATAA--GA-ATTAAATGGTAAATGAT
94793 AACAAAATTA
1 AACAAAATTA
94803 ACTGAAATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
35 23 0.59
36 1 0.03
37 5 0.13
38 10 0.26
ACGTcount: A:0.55, C:0.10, G:0.09, T:0.26
Consensus pattern (35 bp):
AACAAAATTACAATAAGAATTAAATGGTAAATGAT
Found at i:95060 original size:18 final size:18
Alignment explanation
Indices: 95012--95083 Score: 96
Period size: 18 Copynumber: 4.2 Consensus size: 18
95002 ACTCCTCGCT
*
95012 GTCATCATCGTCGTCGTC
1 GTCATCATCGTCGTCATC
*
95030 GTCACCAT--T-GTCATC
1 GTCATCATCGTCGTCATC
95045 GTCATCATCGTCGTCATC
1 GTCATCATCGTCGTCATC
*
95063 GTCATCATCGTCGTCGTC
1 GTCATCATCGTCGTCATC
95081 GTC
1 GTC
95084 GTCTTGAGCA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
15 12 0.26
16 1 0.02
17 1 0.02
18 33 0.70
ACGTcount: A:0.14, C:0.33, G:0.19, T:0.33
Consensus pattern (18 bp):
GTCATCATCGTCGTCATC
Found at i:95082 original size:9 final size:9
Alignment explanation
Indices: 95012--95086 Score: 78
Period size: 9 Copynumber: 8.3 Consensus size: 9
95002 ACTCCTCGCT
*
95012 GTCATCATC
1 GTCATCGTC
*
95021 GTCGTCGTC
1 GTCATCGTC
* * *
95030 GTCACCATT
1 GTCATCGTC
95039 GTCATCGTC
1 GTCATCGTC
*
95048 ATCATCGTC
1 GTCATCGTC
95057 GTCATCGTC
1 GTCATCGTC
*
95066 ATCATCGTC
1 GTCATCGTC
*
95075 GTCGTCGTC
1 GTCATCGTC
95084 GTC
1 GTC
95087 TTGAGCAGGT
Statistics
Matches: 52, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 52 1.00
ACGTcount: A:0.13, C:0.33, G:0.20, T:0.33
Consensus pattern (9 bp):
GTCATCGTC
Found at i:97250 original size:111 final size:111
Alignment explanation
Indices: 96920--97252 Score: 594
Period size: 111 Copynumber: 3.0 Consensus size: 111
96910 ATTACAAAAA
*
96920 TTAATTCTTATTCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
96985 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCAATATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
97031 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* * *
97096 AATTAAAACATTAAAATGTTACCGTATTAGTAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
97142 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
97207 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTTGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
97253 ATGATTTCAA
Statistics
Matches: 211, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 211 1.00
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.37
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:97575 original size:50 final size:50
Alignment explanation
Indices: 97521--97645 Score: 144
Period size: 50 Copynumber: 2.5 Consensus size: 50
97511 AGATACCCAT
* * *
97521 GTATAGCGCAGATCAGGGGGCGCGCTATACCCATGTGGCGCCAGATCACC
1 GTATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
* ** * * *
97571 GTATATCGCGGGGCAGGGGGCGCGTTATACCCACGTGGTGCCAAATCAGC
1 GTATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
* *
97621 GTATAGCACGGTTCA-GGGGCGCGCT
1 GTATAGCGCGGATCAGGGGGCGCGCT
97646 TTACTGTTAT
Statistics
Matches: 61, Mismatches: 14, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
49 9 0.15
50 52 0.85
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (50 bp):
GTATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
Found at i:104848 original size:23 final size:23
Alignment explanation
Indices: 104780--104848 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
104770 ATATCTTATA
* *
104780 TGGCACTACGGTGCATTTCTAGG
1 TGGCACTTCGGTGCATTTCTACG
* *** *
104803 CGGCACTTTAATGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
104826 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
104849 AGTTGTGGTG
Statistics
Matches: 33, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.32
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:106882 original size:15 final size:15
Alignment explanation
Indices: 106849--106891 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
106839 TGCCTGTGAG
* **
106849 ATAAGCCATGTGACT
1 ATAAGCTATGTGAAA
106864 ATAAGCTATGTGAAA
1 ATAAGCTATGTGAAA
*
106879 ATAAGTTATGTGA
1 ATAAGCTATGTGA
106892 TTATATGATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.30
Consensus pattern (15 bp):
ATAAGCTATGTGAAA
Found at i:107174 original size:21 final size:21
Alignment explanation
Indices: 107144--107223 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
107134 TCCTTAAGGA
107144 GTGGTCATTCGGGACATCTAT
1 GTGGTCATTCGGGACATCTAT
* ** *
107165 GTGGTTATTCAAGACAAAC-AT
1 GTGGTCATTCGGGAC-ATCTAT
* *
107186 GTGGTCCTTCGGGACATTCTAC
1 GTGGTCATTCGGGACA-TCTAT
107208 GTGGTCATTCGGGACA
1 GTGGTCATTCGGGACA
107224 AATTCTATGT
Statistics
Matches: 45, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
20 1 0.02
21 26 0.58
22 18 0.40
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.30
Consensus pattern (21 bp):
GTGGTCATTCGGGACATCTAT
Found at i:107363 original size:42 final size:41
Alignment explanation
Indices: 107304--107388 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 41
107294 TCAATATTTT
107304 AGTTCTCAAAAGTGTACATGGGTTAATAAAAGAGATAACATA
1 AGTTCTCAAAAGTGTACATGGGTTAATAAAAGAGA-AACATA
107346 AGTTCTCAAAAGTGTACATGGGTTAATAAAAGAGAAACATA
1 AGTTCTCAAAAGTGTACATGGGTTAATAAAAGAGAAACATA
107387 AG
1 AG
107389 AAACCTTGTG
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 8 0.19
42 35 0.81
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.25
Consensus pattern (41 bp):
AGTTCTCAAAAGTGTACATGGGTTAATAAAAGAGAAACATA
Found at i:107376 original size:20 final size:20
Alignment explanation
Indices: 107311--107377 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
107301 TTTAGTTCTC
107311 AAAAGTGTACATGGGTTAAT
1 AAAAGTGTACATGGGTTAAT
* ** *
107331 AAAAGAGATAACATAAGTT-CT
1 AAAAGTG-T-ACATGGGTTAAT
107352 CAAAAGTGTACATGGGTTAAT
1 -AAAAGTGTACATGGGTTAAT
107373 AAAAG
1 AAAAG
107378 AGAAACATAA
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
20 18 0.51
21 4 0.11
22 13 0.37
ACGTcount: A:0.46, C:0.07, G:0.21, T:0.25
Consensus pattern (20 bp):
AAAAGTGTACATGGGTTAAT
Found at i:107489 original size:6 final size:6
Alignment explanation
Indices: 107478--107534 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
107468 CTAAATGGAT
** * * *
107478 TAATGA TAATGA TAATGA TAATGA TAATGA CGATGA T-GTGA TCAGGA
1 TAATGA TAATGA TAATGA TAATGA TAATGA TAATGA TAATGA TAATGA
107525 TAATGA TAAT
1 TAATGA TAAT
107535 ATGTGTGCAT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
5 4 0.10
6 38 0.90
ACGTcount: A:0.44, C:0.04, G:0.21, T:0.32
Consensus pattern (6 bp):
TAATGA
Found at i:108470 original size:25 final size:26
Alignment explanation
Indices: 108439--108496 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
108429 AGGTACTTTA
* *
108439 GTCATTTACACTTTG-GGGTATTTTG
1 GTCATTTACACTTCGAGGGCATTTTG
*
108464 GTTATTTACACTTCGAGGGCATTTTG
1 GTCATTTACACTTCGAGGGCATTTTG
108490 GTCATTT
1 GTCATTT
108497 CCTTCAATCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 13 0.46
26 15 0.54
ACGTcount: A:0.17, C:0.14, G:0.22, T:0.47
Consensus pattern (26 bp):
GTCATTTACACTTCGAGGGCATTTTG
Found at i:109156 original size:204 final size:205
Alignment explanation
Indices: 108801--109209 Score: 754
Period size: 204 Copynumber: 2.0 Consensus size: 205
108791 TATTAAAGTT
108801 TTAATGAGGATAAATTGAATTTAGAGATTCTGTGGTTATTTGCTTTTTGATAATCAATGAACTTG
1 TTAATGAGGATAAATTGAATTTAGAGATTCTGTGGTTATTTGCTTTTTGATAATCAATGAACTTG
108866 AAATCATCTTATTAGTCATTTTGTGTCTATGTAGGTAGTTGAGCCTTATTCAGTTTAATTTATTT
66 AAATCATCTTATTAGTCATTTTGTGTCTATGTAGGTAGTTGAGCCTTATTCAGTTTAATTTATTT
108931 TAGTTCGTAATCAGATCGAGTTTAGAAATTTT-AC-ACACATATGTAACCATAT-T-TCCAATCA
131 TAGTTCGTAATCAGATCGAGTTTAGAAATTTTAACTACACATATGTAACCATATATATCCAATCA
108992 TGCATTTACC
196 TGCATTTACC
109002 TTAATGAGGATAAATTGAATTTAGAGATTCTGTGGTTATTTGCTTTTTGGATAATCAATGAACTT
1 TTAATGAGGATAAATTGAATTTAGAGATTCTGTGGTTATTTGCTTTTT-GATAATCAATGAACTT
109067 GAAATCATTCTTATTAGTCATTTTGTGTCTATGTAGGTAGTTTGAGCCTTATTCAGTTTAATTTA
65 GAAATCA-TCTTATTAGTCATTTTGTGTCTATGTAGGTAG-TTGAGCCTTATTCAGTTTAATTTA
*
109132 TTTTAGTTCGTAATCAGATCGAGTTTAGAAATTTTAACTACACATATGTAACCATATATATTCAA
128 TTTTAGTTCGTAATCAGATCGAGTTTAGAAATTTTAACTACACATATGTAACCATATATATCCAA
109197 TCATGCATTTACC
193 TCATGCATTTACC
109210 AATACCAACA
Statistics
Matches: 200, Mismatches: 1, Indels: 7
0.96 0.00 0.03
Matches are distributed among these distances:
201 48 0.24
202 23 0.12
203 32 0.16
204 59 0.29
205 2 0.01
206 18 0.09
207 1 0.00
208 17 0.09
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (205 bp):
TTAATGAGGATAAATTGAATTTAGAGATTCTGTGGTTATTTGCTTTTTGATAATCAATGAACTTG
AAATCATCTTATTAGTCATTTTGTGTCTATGTAGGTAGTTGAGCCTTATTCAGTTTAATTTATTT
TAGTTCGTAATCAGATCGAGTTTAGAAATTTTAACTACACATATGTAACCATATATATCCAATCA
TGCATTTACC
Found at i:115895 original size:27 final size:27
Alignment explanation
Indices: 115853--115920 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
115843 TTGTAGGAAT
115853 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
115878 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
115905 TATAGAGATATGATTT
1 TATAGAGATATGATTT
115921 TGTAAATAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 7 0.17
27 34 0.83
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:122264 original size:15 final size:15
Alignment explanation
Indices: 122246--122276 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
122236 AAATTTTAAA
122246 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
122261 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
122276 T
1 T
122277 CTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:126483 original size:71 final size:71
Alignment explanation
Indices: 126238--126479 Score: 396
Period size: 73 Copynumber: 3.4 Consensus size: 71
126228 AAGATTAAGT
* * * *
126238 TCAATTCAATAAAAATATGTAAAATTAAATAGAATTCAAAAGATAATTTTTTTAAATAAAGTGGT
1 TCAATTTAATAAAAATATGTAAAATTAAATAGAATTCAAGAGA-GAGTTTTTT-AATAAAGTGGT
126303 ATAAATAC
64 ATAAATAC
126311 TCAATTTAATAAAAATATGTAAAATTAAATAGAATTCAAGAGAGATGTTTTTTTAATAAAGTGGT
1 TCAATTTAATAAAAATATGTAAAATTAAATAGAATTCAAGAGAGA-G-TTTTTTAATAAAGTGGT
126376 ATAAATAC
64 ATAAATAC
*
126384 TCAATTTAATAAAAATATGTAAAATTAAATAGAATTCAAGAGAGAGTTTTTTAATAAAGTGCTAT
1 TCAATTTAATAAAAATATGTAAAATTAAATAGAATTCAAGAGAGAGTTTTTTAATAAAGTGGTAT
126449 AAATAC
66 AAATAC
126455 TCAATTTAAT-AAAATATGTAAAATT
1 TCAATTTAATAAAAATATGTAAAATT
126480 TAAAATAATA
Statistics
Matches: 162, Mismatches: 5, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
70 15 0.09
71 34 0.21
72 2 0.01
73 105 0.65
74 6 0.04
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (71 bp):
TCAATTTAATAAAAATATGTAAAATTAAATAGAATTCAAGAGAGAGTTTTTTAATAAAGTGGTAT
AAATAC
Found at i:128536 original size:12 final size:12
Alignment explanation
Indices: 128519--128543 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
128509 AATGTTAAAT
128519 GAATATATTTAC
1 GAATATATTTAC
128531 GAATATATTTAC
1 GAATATATTTAC
128543 G
1 G
128544 GACATTAAAC
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:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (12 bp):
GAATATATTTAC
Found at i:131055 original size:153 final size:161
Alignment explanation
Indices: 130747--131035 Score: 472
Period size: 153 Copynumber: 1.9 Consensus size: 161
130737 GTCGGTCGTG
* *
130747 ATCTCATTAAAATGTTTAAGCTGGTTAGTTACTCTAATCTAATTTATATATATTTTTATTCTTAT
1 ATCTCATTAAAATGTTTAAGCTGGTTAGTTACCCTAATCTAATTTATATATATTATTATTCTTAT
*
130812 TTTAAATACTTATTATGATATAATTATAAGGTTAAATTATGTAATTAGATTTTACTCTCTTTTCT
66 TTTAAATACTTATTATGATATAATTATAAGGTTAAATTATGTAATTAGATTTTACTCTCTTATCT
*
130877 CTTATTTAATTTATCGTATTTTTTTACTCTA
131 CTAATTTAATTTATCGTATTTTTTTACTCTA
130908 ATCTCATTAAAATGTTTAAGCTGGTTAG-TACCCTAATCTAATTT-T-TATA-TATT-TT-TTA-
1 ATCTCATTAAAATGTTTAAGCTGGTTAGTTACCCTAATCTAATTTATATATATTATTATTCTTAT
130966 TTTAAATACTTATTATGATATAATTAT-AGGTTAAATTATGTAATTAGATTTTACTCTCTTAT-T
66 TTTAAATACTTATTATGATATAATTATAAGGTTAAATTATGTAATTAGATTTTACTCTCTTATCT
131029 -TAATTTA
131 CTAATTTA
131036 TCTTATTTTT
Statistics
Matches: 124, Mismatches: 4, Indels: 10
0.90 0.03 0.07
Matches are distributed among these distances:
151 6 0.05
152 1 0.01
153 34 0.27
154 27 0.22
155 3 0.02
156 2 0.02
157 3 0.02
158 4 0.03
159 1 0.01
160 15 0.12
161 28 0.23
ACGTcount: A:0.32, C:0.09, G:0.07, T:0.52
Consensus pattern (161 bp):
ATCTCATTAAAATGTTTAAGCTGGTTAGTTACCCTAATCTAATTTATATATATTATTATTCTTAT
TTTAAATACTTATTATGATATAATTATAAGGTTAAATTATGTAATTAGATTTTACTCTCTTATCT
CTAATTTAATTTATCGTATTTTTTTACTCTA
Found at i:131607 original size:77 final size:78
Alignment explanation
Indices: 131480--131637 Score: 309
Period size: 77 Copynumber: 2.0 Consensus size: 78
131470 GGCCAAGAGA
131480 ACAACTTACGATGACAGCTAAGAGAACAAAGCAAGCGACGGTTTTCTCCATTGT-GAATTTCAAA
1 ACAACTTACGATGACAGCTAAGAGAACAAAGCAAGCGACGGTTTTCTCCATTGTAGAATTTCAAA
131544 AAAGAAAGAAAAC
66 AAAGAAAGAAAAC
131557 ACAACTTACGATGACAGCTAAGAGAACAAAGCAAGCGACGGTTTTCTCCATTGTAGAATTTCAAA
1 ACAACTTACGATGACAGCTAAGAGAACAAAGCAAGCGACGGTTTTCTCCATTGTAGAATTTCAAA
131622 AAAGAAAGAAAAC
66 AAAGAAAGAAAAC
131635 ACA
1 ACA
131638 GAGCTTGAGA
Statistics
Matches: 80, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 54 0.68
78 26 0.32
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.19
Consensus pattern (78 bp):
ACAACTTACGATGACAGCTAAGAGAACAAAGCAAGCGACGGTTTTCTCCATTGTAGAATTTCAAA
AAAGAAAGAAAAC
Found at i:132452 original size:13 final size:13
Alignment explanation
Indices: 132434--132495 Score: 70
Period size: 13 Copynumber: 4.5 Consensus size: 13
132424 TTAAGGCTAG
132434 AGATGACAATTAT
1 AGATGACAATTAT
132447 AGATGACAATTAT
1 AGATGACAATTAT
*
132460 AAGTGGATGATAATTAT
1 -A---GATGACAATTAT
132477 AGATGACAATTAT
1 AGATGACAATTAT
*
132490 AAATGA
1 AGATGA
132496 AGACTTTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
13 29 0.69
14 1 0.02
16 1 0.02
17 11 0.26
ACGTcount: A:0.47, C:0.05, G:0.18, T:0.31
Consensus pattern (13 bp):
AGATGACAATTAT
Found at i:132475 original size:30 final size:30
Alignment explanation
Indices: 132435--132491 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
132425 TAAGGCTAGA
132435 GATGACAATTATAGATGACAATTATAAGTG
1 GATGACAATTATAGATGACAATTATAAGTG
*
132465 GATGATAATTATAGATGACAATTATAA
1 GATGACAATTATAGATGACAATTATAA
132492 ATGAAGACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.32
Consensus pattern (30 bp):
GATGACAATTATAGATGACAATTATAAGTG
Found at i:132690 original size:29 final size:29
Alignment explanation
Indices: 132633--132695 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
132623 TTTGAGAATT
* *
132633 ATATTTATCTCATTTTTAATGTTTAGTAC
1 ATATTTATATCATTTTTAATATTTAGTAC
* *
132662 TTATTTATAT-ATTTTTAATATATTTGTAC
1 ATATTTATATCATTTTTAATAT-TTAGTAC
132691 ATATT
1 ATATT
132696 AGTGATGAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
28 10 0.36
29 18 0.64
ACGTcount: A:0.30, C:0.06, G:0.05, T:0.59
Consensus pattern (29 bp):
ATATTTATATCATTTTTAATATTTAGTAC
Found at i:133468 original size:27 final size:27
Alignment explanation
Indices: 133436--133502 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
133426 GATAATGGCT
133436 CTGAATCATTCAGAATGTACTTCTGTG
1 CTGAATCATTCAGAATGTACTTCTGTG
* *
133463 TTGAATCATTAAGAATGTACTTCTGTG
1 CTGAATCATTCAGAATGTACTTCTGTG
133490 CTGAATCATTCAG
1 CTGAATCATTCAG
133503 CATTGTTTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.37
Consensus pattern (27 bp):
CTGAATCATTCAGAATGTACTTCTGTG
Found at i:133852 original size:32 final size:31
Alignment explanation
Indices: 133799--133868 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 31
133789 AATAACAAAG
133799 TAATATCTGTTTATAATTTTATTAAATATTAA
1 TAATA-CTGTTTATAATTTTATTAAATATTAA
133831 TAATACTGTTTATAATCTTTATTAAATATTAA
1 TAATACTGTTTATAAT-TTTATTAAATATTAA
133863 TAATAC
1 TAATAC
133869 ATATAACTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
31 11 0.30
32 26 0.70
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (31 bp):
TAATACTGTTTATAATTTTATTAAATATTAA
Found at i:136875 original size:103 final size:100
Alignment explanation
Indices: 136682--136885 Score: 381
Period size: 103 Copynumber: 2.0 Consensus size: 100
136672 CTCCTCTATC
136682 ACCCATACATTTGGAGCACAGGATCAAGCTTTCAGGGAACGTCCTATTGGACAGTTGTTACGACG
1 ACCCATACATTTGGAGCACAGGATCAAGCTTTCAGGGAACGTCCTATTGGACAGTTGTTACGACG
136747 TCCAGGTTGATGTGCCTTTCCCGTTAGAAATGGAA
66 TCCAGGTTGATGTGCCTTTCCCGTTAGAAATGGAA
136782 ACCCATACATTTGGAGCACAGGATCAAGCTTTCAGGGAACTGTCCTATTGGATCCAGTTGTTACG
1 ACCCATACATTTGGAGCACAGGATCAAGCTTTCAGGGAAC-GTCCTATTGGA--CAGTTGTTACG
136847 ACGTCCAGGTTGATGTGCCTTTCCCGTTAGAAATGGAA
63 ACGTCCAGGTTGATGTGCCTTTCCCGTTAGAAATGGAA
136885 A
1 A
136886 AGTCTGCATT
Statistics
Matches: 101, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
100 40 0.40
101 11 0.11
103 50 0.50
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (100 bp):
ACCCATACATTTGGAGCACAGGATCAAGCTTTCAGGGAACGTCCTATTGGACAGTTGTTACGACG
TCCAGGTTGATGTGCCTTTCCCGTTAGAAATGGAA
Found at i:138667 original size:20 final size:21
Alignment explanation
Indices: 138642--138734 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
138632 TTTTCCCAAT
*
138642 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
138662 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
138683 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
138703 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
138724 TCGCAATGCGA
1 TCGCAATGCGA
138735 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:138687 original size:41 final size:41
Alignment explanation
Indices: 138642--138734 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
138632 TTTTCCCAAT
138642 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
138683 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
138724 TCGCAATGCGA
1 TCGCAATGCGA
138735 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:138747 original size:41 final size:41
Alignment explanation
Indices: 138661--138795 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
138651 GAATAAGTAA
** *
138661 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
138702 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
138743 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
138784 TTCGCAACGCGA
1 ATCGCAACGCGA
138796 TACTGACTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 5 0.06
41 74 0.91
42 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:138748 original size:20 final size:20
Alignment explanation
Indices: 138723--138816 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
138713 AATTGGGAAA
*
138723 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
138743 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
138764 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
138784 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
138804 TTCGCAACGCGAT
1 ATCGCAACGCGAT
138817 TTACATAATC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.71
21 12 0.19
22 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:139031 original size:22 final size:22
Alignment explanation
Indices: 139003--139046 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
138993 CACTCTCTCA
*
139003 CCCATCTTCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
139025 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
139047 TATCTAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:140592 original size:18 final size:18
Alignment explanation
Indices: 140571--140615 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
140561 TCCACTTCGG
*
140571 GAGCCATCACCTCACCCA
1 GAGCCATCACCCCACCCA
*
140589 GAGCTATCACCCCACCCA
1 GAGCCATCACCCCACCCA
140607 GAGCCATCA
1 GAGCCATCA
140616 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.29, C:0.47, G:0.13, T:0.11
Consensus pattern (18 bp):
GAGCCATCACCCCACCCA
Found at i:141173 original size:19 final size:19
Alignment explanation
Indices: 141081--141182 Score: 79
Period size: 19 Copynumber: 5.6 Consensus size: 19
141071 TAGTTTACTT
* **
141081 TCGCAACACGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
141100 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
141120 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
141139 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
141153 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
141172 TCGCAATGCGA
1 TCGCAACGCGA
141183 TTTTGTGTTT
Statistics
Matches: 68, Mismatches: 9, Indels: 12
0.76 0.10 0.13
Matches are distributed among these distances:
14 10 0.15
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 35 0.51
20 17 0.25
ACGTcount: A:0.41, C:0.24, G:0.22, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:141232 original size:18 final size:18
Alignment explanation
Indices: 141190--141326 Score: 137
Period size: 18 Copynumber: 7.9 Consensus size: 18
141180 CGATTTTGTG
141190 TTTCGCGTTGCGATTT--
1 TTTCGCGTTGCGATTTCA
*
141206 TGT--CGTTGCGATTTCA
1 TTTCGCGTTGCGATTTCA
141222 TTTCGCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTCA
141240 TTTCGCGTTGCGATTT--
1 TTTCGCGTTGCGATTTCA
*
141256 TGT--CGTTGCGATTTCA
1 TTTCGCGTTGCGATTTCA
* **
141272 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGAT-TTCA
*
141291 TTTCCGCGTTGCGATGGTCA
1 TTT-CGCGTTGCGAT-TTCA
141311 TTTCGCGTTGCGATTT
1 TTTCGCGTTGCGATTT
141327 TAAGTTTCGT
Statistics
Matches: 100, Mismatches: 11, Indels: 18
0.78 0.09 0.14
Matches are distributed among these distances:
14 22 0.22
16 8 0.08
18 38 0.38
19 16 0.16
20 16 0.16
ACGTcount: A:0.11, C:0.21, G:0.25, T:0.43
Consensus pattern (18 bp):
TTTCGCGTTGCGATTTCA
Found at i:141255 original size:50 final size:51
Alignment explanation
Indices: 141190--141305 Score: 189
Period size: 50 Copynumber: 2.3 Consensus size: 51
141180 CGATTTTGTG
* **
141190 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCATTTCGCGTTGCGAT-TTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCATTTCGCATTGCGATAGCCA
141240 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCATTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCATTTCGCATTGCGATAGCCA
141291 TTTCCGCGTTGCGAT
1 TTT-CGCGTTGCGAT
141306 GGTCATTTCG
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
50 45 0.74
51 5 0.08
52 11 0.18
ACGTcount: A:0.11, C:0.22, G:0.24, T:0.43
Consensus pattern (51 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTCATTTCGCATTGCGATAGCCA
Found at i:141304 original size:20 final size:19
Alignment explanation
Indices: 141270--141324 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
141260 GTTGCGATTT
*
141270 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
* *
141289 CATTTCCGCGTTGCGATGGT
1 CATTT-CGCGTTGCGATAGC
141309 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
141325 TTTAAGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:143290 original size:19 final size:19
Alignment explanation
Indices: 143266--143336 Score: 106
Period size: 19 Copynumber: 3.7 Consensus size: 19
143256 CAAACAGACT
*
143266 ATCGCAACGCGAAATGGAA
1 ATCGCAACGCGAAATGAAA
*
143285 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
143304 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
143323 ATCGCAACGAGAAA
1 ATCGCAACGCGAAA
143337 ATCGCAATGC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:143337 original size:33 final size:36
Alignment explanation
Indices: 143266--143348 Score: 109
Period size: 38 Copynumber: 2.3 Consensus size: 36
143256 CAAACAGACT
* *
143266 ATCGCAACGCGAAATGGAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAA
143304 ATCGCAATGCGAAATGAAAATCGCAA-CG-A-GAAA
1 ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
143337 ATCGCAATGCGA
1 ATCGCAATGCGA
143349 TTTTCATTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
33 16 0.37
34 1 0.02
36 2 0.05
38 24 0.56
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (36 bp):
ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
Found at i:143422 original size:19 final size:19
Alignment explanation
Indices: 143368--143422 Score: 92
Period size: 19 Copynumber: 2.9 Consensus size: 19
143358 CGCATTGCGA
* *
143368 TTTTCTCGTTGCGATAACC
1 TTTTCGCGTTGCGATAGCC
143387 TTTTCGCGTTGCGATAGCC
1 TTTTCGCGTTGCGATAGCC
143406 TTTTCGCGTTGCGATAG
1 TTTTCGCGTTGCGATAG
143423 TCAATGAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.13, C:0.24, G:0.24, T:0.40
Consensus pattern (19 bp):
TTTTCGCGTTGCGATAGCC
Found at i:144436 original size:23 final size:23
Alignment explanation
Indices: 144409--144461 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
144399 CATATTCGAA
* *
144409 ATTTGATCTT-GTCAATACCCGG
1 ATTTGATATTGGTCAATACACGG
144431 ACTTTGATATTGGTCAATACACGG
1 A-TTTGATATTGGTCAATACACGG
144455 ATTTGAT
1 ATTTGAT
144462 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 1 0.04
23 14 0.52
24 12 0.44
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (23 bp):
ATTTGATATTGGTCAATACACGG
Found at i:144648 original size:12 final size:12
Alignment explanation
Indices: 144631--144655 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
144621 ATATAATCCT
144631 GAAGAAGAAAAA
1 GAAGAAGAAAAA
144643 GAAGAAGAAAAA
1 GAAGAAGAAAAA
144655 G
1 G
144656 TCCCCGAGAA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:146986 original size:33 final size:31
Alignment explanation
Indices: 146898--147025 Score: 152
Period size: 32 Copynumber: 4.0 Consensus size: 31
146888 GAAATTACTA
* * *
146898 TCGCAATGCGAAATAAAATCGC-ACGAGAGAA
1 TCGCAATGCGAAATGAAATCGCAACGCGA-AT
*
146929 TCGCAATGCGAAATGAAATCGCAACGCTAATT
1 TCGCAATGCGAAATGAAATCGCAACGCGAA-T
*
146961 TCGCAATGCGAAATGAAAATCGCAACGAGGGAA-
1 TCGCAATGCGAAATG-AAATCGCAAC--GCGAAT
146994 TCGCAATGCGAAATGAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAATCGCAACGCGAAT
147025 T
1 T
147026 TAATTTCGCG
Statistics
Matches: 84, Mismatches: 7, Indels: 12
0.82 0.07 0.12
Matches are distributed among these distances:
30 4 0.05
31 23 0.27
32 29 0.35
33 25 0.30
35 3 0.04
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (31 bp):
TCGCAATGCGAAATGAAATCGCAACGCGAAT
Found at i:146999 original size:65 final size:63
Alignment explanation
Indices: 146898--147026 Score: 222
Period size: 65 Copynumber: 2.0 Consensus size: 63
146888 GAAATTACTA
*
146898 TCGCAATGCGAAATAAAATCGCACGAGAGAATCGCAATGCGAAATGAAATCGCAACGCTAATT
1 TCGCAATGCGAAATAAAATCGCACGAGAGAATCGCAATGCGAAATGAAATCGCAACGCGAATT
*
146961 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAATCGCAACGCGAATT
1 TCGCAATGCGAAAT-AAAATCGC-ACGAGAGAATCGCAATGCGAAATGAAATCGCAACGCGAATT
147026 T
1 T
147027 AATTTCGCGT
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
63 14 0.23
64 8 0.13
65 40 0.65
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.17
Consensus pattern (63 bp):
TCGCAATGCGAAATAAAATCGCACGAGAGAATCGCAATGCGAAATGAAATCGCAACGCGAATT
Found at i:147041 original size:19 final size:20
Alignment explanation
Indices: 147019--147061 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
147009 AAATCGCAAC
147019 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
147038 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
147058 GCGA
1 GCGA
147062 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:147046 original size:14 final size:14
Alignment explanation
Indices: 147047--147080 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
147037 TGCGATTTTC
147047 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
147061 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
147075 ATTTTC
1 ATTTTC
147081 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:147221 original size:14 final size:14
Alignment explanation
Indices: 147202--147237 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
147192 CATCAATTAA
*
147202 ACAAATCAACTTTT
1 ACAAATCAACCTTT
147216 ACAAATC-ACCTTT
1 ACAAATCAACCTTT
147229 ACAAATCAA
1 ACAAATCAA
147238 TTAAACAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (14 bp):
ACAAATCAACCTTT
Found at i:148619 original size:21 final size:21
Alignment explanation
Indices: 148553--148619 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
148543 GTGAATCGGG
*
148553 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
148573 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
148595 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
148616 CTCT
1 CTCT
148620 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:148638 original size:42 final size:41
Alignment explanation
Indices: 148553--148675 Score: 104
Period size: 42 Copynumber: 2.9 Consensus size: 41
148543 GTGAATCGGG
* * * * *
148553 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
148595 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * * *
148637 CTCTTCAACGATAGGAGTGGAATCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
148676 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.24, C:0.17, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:150704 original size:19 final size:19
Alignment explanation
Indices: 150653--150764 Score: 117
Period size: 19 Copynumber: 6.1 Consensus size: 19
150643 GTCTTTGGTT
*
150653 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
150672 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
150692 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
150710 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
150725 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
150744 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
150763 GA
1 GA
150765 TTTTGGTTTC
Statistics
Matches: 78, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
14 10 0.13
15 2 0.03
18 2 0.03
19 47 0.60
20 17 0.22
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:150793 original size:19 final size:19
Alignment explanation
Indices: 150760--150826 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
150750 AAAATCGCAA
**
150760 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
150779 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
150798 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
150818 TGCGATTTT
1 TGCGATTTT
150827 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:151395 original size:41 final size:41
Alignment explanation
Indices: 151349--151426 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
151339 CGAAAGTCAG
* * *
151349 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTGTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTGTAT
*
151390 TATCGCATTGCGATAGTAAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
151427 CCCAATTCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTGTAT
Found at i:151423 original size:20 final size:20
Alignment explanation
Indices: 151330--151423 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
151320 CGCTATGTAA
* *
151330 ATCGCATTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* *
151350 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* * * *
151370 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTAAGT
151391 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
151411 ATCGCATTGCGAT
1 ATCGCATTGCGAT
151424 TTTCCCAATT
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.72
21 12 0.20
22 2 0.03
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:151442 original size:41 final size:41
Alignment explanation
Indices: 151349--151444 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
151339 CGAAAGTCAG
* * * ** *
151349 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
*
151390 TATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAA
151432 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
151445 TTACTTATTC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 44 0.96
42 2 0.04
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
Found at i:157068 original size:2 final size:2
Alignment explanation
Indices: 157061--157090 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
157051 GGCGAGTATT
157061 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
157091 TGCGTCGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:159383 original size:3 final size:3
Alignment explanation
Indices: 159377--159401 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
159367 ATTAAAAAAA
159377 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
159402 TATTTATTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:161714 original size:36 final size:35
Alignment explanation
Indices: 161641--161714 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
161631 TTTTTATATT
* *
161641 TTTAATTTTGTAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATATATAAATATTATCAA
*
161676 TTTAATTTT-TAAAGAAAATATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATATATAAATATTAT-CAA
161712 TTT
1 TTT
161715 GTAATATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
34 4 0.12
35 25 0.74
36 5 0.15
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (35 bp):
TTTAATTTTGTAAAAAAATATATAAATATTATCAA
Found at i:163353 original size:18 final size:19
Alignment explanation
Indices: 163330--163366 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
163320 AAACTTGTAT
163330 AACATTT-AAATTATTCAA
1 AACATTTAAAATTATTCAA
163348 AACATTTACAAATTATTCA
1 AACATTTA-AAATTATTCA
163367 GAGCTTATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.38
Consensus pattern (19 bp):
AACATTTAAAATTATTCAA
Found at i:163883 original size:31 final size:31
Alignment explanation
Indices: 163845--164054 Score: 366
Period size: 31 Copynumber: 6.8 Consensus size: 31
163835 AGCTCGATCA
* ** *
163845 ATGTCCCGAAGAACCTAGGTAATTAGTCTAT
1 ATGTCCCGAAGAACATAGGTAAACAGTCCAT
163876 ATGTCCCGAAGAACATAGGTAAACAGTCCAT
1 ATGTCCCGAAGAACATAGGTAAACAGTCCAT
*
163907 ATGTCCCGAAGAACATAGGTAAACAATCCAT
1 ATGTCCCGAAGAACATAGGTAAACAGTCCAT
163938 ATGTCCCGAAGAACATAGGTAAACAGTCCAT
1 ATGTCCCGAAGAACATAGGTAAACAGTCCAT
*
163969 ATGTCCCAAAGAACATAGGTAAACAGTCCAT
1 ATGTCCCGAAGAACATAGGTAAACAGTCCAT
164000 ATGTCCCGAAGAACATAGGTAAACAGTCCAT
1 ATGTCCCGAAGAACATAGGTAAACAGTCCAT
164031 ATGTCCCGAAGAACATAGGTAAAC
1 ATGTCCCGAAGAACATAGGTAAAC
164055 CCTCGACCCT
Statistics
Matches: 171, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 171 1.00
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (31 bp):
ATGTCCCGAAGAACATAGGTAAACAGTCCAT
Found at i:165060 original size:17 final size:17
Alignment explanation
Indices: 165005--165070 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 17
164995 TTATTTAGGG
165005 GGGAATC-GATACCCCCA
1 GGGAATCTG-TACCCCCA
* *
165022 GGGGAATCTGT--TCCCG
1 -GGGAATCTGTACCCCCA
165038 GGGAATC-GATACCCCCA
1 GGGAATCTG-TACCCCCA
165055 GGGAATCTGTACCCCC
1 GGGAATCTGTACCCCC
165071 TGGACATTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
14 1 0.03
15 8 0.21
16 3 0.08
17 17 0.44
18 9 0.23
19 1 0.03
ACGTcount: A:0.23, C:0.33, G:0.27, T:0.17
Consensus pattern (17 bp):
GGGAATCTGTACCCCCA
Found at i:175643 original size:2 final size:2
Alignment explanation
Indices: 175636--175669 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
175626 GAGTAGAATA
175636 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
175670 TACAATTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:177536 original size:18 final size:17
Alignment explanation
Indices: 177482--177530 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
177472 TTGGACTCCT
* *
177482 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
177500 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
177518 AGTGCATTCGATG
1 AGTGCA-TCGATG
177531 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:177614 original size:64 final size:62
Alignment explanation
Indices: 177482--177637 Score: 172
Period size: 64 Copynumber: 2.5 Consensus size: 62
177472 TTGGACTCCT
* * * * *
177482 AGTGCATCGGTGCACT-AAGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAAAAATAGCC
1 AGTGCATCGATGCA-TGGAGAGTGCATCGATGAATCAAATGCATTCGATGTTTGAAAAATAG-C
** *
177545 TAGTGCATCGATGCATGGATTGTGCATCGATGAATCAAATGCATTCGATGTTTTAATTAAATCAG
1 -AGTGCATCGATGCATGGAGAGTGCATCGATGAATCAAATGCATTCGATGTTTGAA--AAAT-AG
177610 -
62 C
177610 AGTGCATCGATGCATGGAGAGTGCATCG
1 AGTGCATCGATGCATGGAGAGTGCATCG
177638 GTGCATGGAG
Statistics
Matches: 78, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
63 1 0.01
64 71 0.91
66 4 0.05
67 2 0.03
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.28
Consensus pattern (62 bp):
AGTGCATCGATGCATGGAGAGTGCATCGATGAATCAAATGCATTCGATGTTTGAAAAATAGC
Found at i:177632 original size:19 final size:19
Alignment explanation
Indices: 177608--177665 Score: 107
Period size: 19 Copynumber: 3.1 Consensus size: 19
177598 TAATTAAATC
*
177608 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGGTGCATGG
177627 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGGTGCATGG
177646 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGGTGCATGG
177665 A
1 A
177666 ATGCATTCTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.24, C:0.16, G:0.40, T:0.21
Consensus pattern (19 bp):
AGAGTGCATCGGTGCATGG
Found at i:177643 original size:83 final size:85
Alignment explanation
Indices: 177546--177730 Score: 216
Period size: 83 Copynumber: 2.2 Consensus size: 85
177536 AAAATAGCCT
* ** *
177546 AGTGCATCGATGCATGGATTGTGCATCGATGAATCAAATGCATTCGATGTTTTAATTAAATCA-G
1 AGTGCATCGGTGCATGGAGAGTGCATCGATGAATCAAATGCATTCGATGTTTCAATTAAATCATG
177610 AGTGCATCGATGCATGG-A-G
66 A-TGCATCGATGCATGGTATG
* * ** * * *
177629 AGTGCATCGGTGCATGGAGAGTGCATCGGTGCATGGAATGCATTCTATGTTTCAATTTATTCATT
1 AGTGCATCGGTGCATGGAGAGTGCATCGATGAATCAAATGCATTCGATGTTTCAATTAAATCA-T
177694 GATGCATCGATGCATGGTATTG
65 GATGCATCGATGCATGGTA-TG
177716 A-TGCATCGGTGCATG
1 AGTGCATCGGTGCATG
177731 CCTTTGAAAC
Statistics
Matches: 86, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
83 52 0.60
84 15 0.17
85 3 0.03
86 14 0.16
87 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (85 bp):
AGTGCATCGGTGCATGGAGAGTGCATCGATGAATCAAATGCATTCGATGTTTCAATTAAATCATG
ATGCATCGATGCATGGTATG
Found at i:177717 original size:21 final size:21
Alignment explanation
Indices: 177691--177730 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
177681 CAATTTATTC
177691 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
177712 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
177731 CCTTTGAAAC
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:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:180448 original size:22 final size:19
Alignment explanation
Indices: 180393--180449 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 19
180383 AACCCTCAGA
180393 GGGTATCGATTCCCCTATG
1 GGGTATCGATTCCCCTATG
*
180412 GGGTGAATCGGTTCCCCTTCAATG
1 GGGT--ATCGATTCCCC-T--ATG
180436 GGGTATCGATTCCC
1 GGGTATCGATTCCC
180450 TCTGCACTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
19 4 0.13
21 10 0.32
22 10 0.32
24 7 0.23
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (19 bp):
GGGTATCGATTCCCCTATG
Found at i:184278 original size:22 final size:21
Alignment explanation
Indices: 184236--184275 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
184226 GAGTTTGTTT
*
184236 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
184257 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
184276 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:189783 original size:289 final size:289
Alignment explanation
Indices: 189264--189840 Score: 1082
Period size: 289 Copynumber: 2.0 Consensus size: 289
189254 CCAACTAATG
*
189264 ACAATGATTTGTTCATCAATAATTGGCCATTGTTATTTTGTTCGTCAAACTCTGTGATATATCAA
1 ACAATGATTTGTTCATCAATAATTGGCCATTGTTATTTTGTTCGTCAAACTCTATGATATATCAA
*
189329 TGCAGTTAGCCGTTGCTTCAATTTGATAAGTTGTGCGGTCAGTGGGCTTTGAGTTAGTCAAAATA
66 TGCAGTTAGCCGTTGCTTCAATTTGATAAGTTGTGCGGTCAGTGGGCTTTGAGTTAGTAAAAATA
189394 AGGTAGCTCCTTACCATCCTGTAATTCCCTGTTCCCCTCCCCAAGATTTGAATCCTGACCTGAGT
131 AGGTAGCTCCTTACCATCCTGTAATTCCCTGTTCCCCTCCCCAAGATTTGAATCCTGACCTGAGT
189459 TAAAAACTCCTAGTTGTCTCAGATGGCAGCCCCTTTGAGATGGGGATAGTTATAAATGTTGTCTA
196 TAAAAACTCCTAGTTGTCTCAGATGGCAGCCCCTTTGAGATGGGGATAGTTATAAATGTTGTCTA
189524 TTTAAATTGAAGCAAAGAAGCTTAGAACT
261 TTTAAATTGAAGCAAAGAAGCTTAGAACT
189553 ACAATGATTTGTTCATCAATAATTGGCCATTGTTATTTTGTTCGTCAAACTCTATGATATATCAA
1 ACAATGATTTGTTCATCAATAATTGGCCATTGTTATTTTGTTCGTCAAACTCTATGATATATCAA
189618 TGCAGTTAGCCGTTGCTTCAATTTGATAAGTTGTGCGGTCAGTGGGCTTTGAGTTAGTAAAAATA
66 TGCAGTTAGCCGTTGCTTCAATTTGATAAGTTGTGCGGTCAGTGGGCTTTGAGTTAGTAAAAATA
* * **
189683 GGGTAGCTCCTTACCATCCTGTAATTCCCTGTTCCCTTCCCCGTGATTTGAATCCTGACCTGAGT
131 AGGTAGCTCCTTACCATCCTGTAATTCCCTGTTCCCCTCCCCAAGATTTGAATCCTGACCTGAGT
* *
189748 TAAAAGCTCCTAGTTGTCTCAGATGGCAGCCCCTTTGAGATGGTGATAGTTATAAATGTTGTCTA
196 TAAAAACTCCTAGTTGTCTCAGATGGCAGCCCCTTTGAGATGGGGATAGTTATAAATGTTGTCTA
189813 TTTAAATTGAAGCAAAGAAGCTTAGAAC
261 TTTAAATTGAAGCAAAGAAGCTTAGAAC
189841 CCATGTTTTC
Statistics
Matches: 280, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
289 280 1.00
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.35
Consensus pattern (289 bp):
ACAATGATTTGTTCATCAATAATTGGCCATTGTTATTTTGTTCGTCAAACTCTATGATATATCAA
TGCAGTTAGCCGTTGCTTCAATTTGATAAGTTGTGCGGTCAGTGGGCTTTGAGTTAGTAAAAATA
AGGTAGCTCCTTACCATCCTGTAATTCCCTGTTCCCCTCCCCAAGATTTGAATCCTGACCTGAGT
TAAAAACTCCTAGTTGTCTCAGATGGCAGCCCCTTTGAGATGGGGATAGTTATAAATGTTGTCTA
TTTAAATTGAAGCAAAGAAGCTTAGAACT
Found at i:191450 original size:28 final size:28
Alignment explanation
Indices: 191414--191469 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
191404 ATAACAAATG
* * * *
191414 ATTTGATTGATATAATTTAAATAATTAA
1 ATTTAATTGATAAAATTAAAAAAATTAA
191442 ATTTAATTGATAAAATTAAAAAAATTAA
1 ATTTAATTGATAAAATTAAAAAAATTAA
191470 TGATCAGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (28 bp):
ATTTAATTGATAAAATTAAAAAAATTAA
Found at i:191816 original size:6 final size:6
Alignment explanation
Indices: 191807--191846 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
191797 CCGTCGCCAA
191807 TACCAT TACCAT TACCAT TACCAT TACCAT TACCAT TACC
1 TACCAT TACCAT TACCAT TACCAT TACCAT TACCAT TACC
191847 GACTTCTTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.33
Consensus pattern (6 bp):
TACCAT
Found at i:196487 original size:2 final size:2
Alignment explanation
Indices: 196480--196506 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
196470 ATGTTTTAAT
196480 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
196507 TAATCTTGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:198782 original size:60 final size:60
Alignment explanation
Indices: 198672--198788 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 60
198662 TATTTGACAC
* * * * * *
198672 GATGCCTTCAAGTTTCAGGGGGAGGCATTCAACTGCGAGCTTCTTGGACCTCAATGTTGA
1 GATGCCTTCAAGTTTCAGGGGAAGGCATTCAACTACCAACTTCTTCGACCTAAATGTTGA
* * *
198732 GATGCCTTCAAG-TTCAAGGGTAATGCATTCAACTACCAACTTGTTCGACCTAAATGT
1 GATGCCTTCAAGTTTC-AGGGGAAGGCATTCAACTACCAACTTCTTCGACCTAAATGT
198789 CGGCATCGTA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
59 3 0.06
60 44 0.94
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (60 bp):
GATGCCTTCAAGTTTCAGGGGAAGGCATTCAACTACCAACTTCTTCGACCTAAATGTTGA
Found at i:198899 original size:19 final size:19
Alignment explanation
Indices: 198875--198913 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
198865 CTATTCGTTC
198875 AGCCAGAATCACCGCAGTT
1 AGCCAGAATCACCGCAGTT
*
198894 AGCCAGAATCATCGCAGTT
1 AGCCAGAATCACCGCAGTT
198913 A
1 A
198914 AAAATGGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.18
Consensus pattern (19 bp):
AGCCAGAATCACCGCAGTT
Found at i:200703 original size:724 final size:723
Alignment explanation
Indices: 199279--200726 Score: 2761
Period size: 724 Copynumber: 2.0 Consensus size: 723
199269 TAACAACCAT
*
199279 ACTCACTTGATGTACCTGAGGGATCAACCAGGGTCATCCTACCTTGGACTCCGACATTATATGAC
1 ACTCACTTGATGTACCTGAGGGATCAACCAGGGTCATCCTAACTTGGACTCCGACATTATATGAC
199344 AAACCATCATGCCCATGGTCAAAGAAAACTCCAATATAGTTATTGCGATGATGATTTTAGTTATA
66 AAACCATCATGCCCATGGTCAAAGAAAACTCCAATATAGTTATTGCGATGATGATTTTAGTTATA
199409 CAATCATAATATGGGTACACTGTATCATACAGAAAAGCATGGAAGGCAAAGTAAAATATCATTAA
131 CAATCATAATATGGGTACACTGTATCATACAGAAAAGCATGGAAGGCAAAGTAAAATATCATTAA
**
199474 AAAAATTCACGGCAAGTGGCATGCATCTTTAAACGAACTACCAAGTTGATTTAGGGTAGTGCGCA
196 AAAAATTCACGGCAAGTGGCATGCATCTTTAAACGAACTACCAAGTTGATTTAGGGTAGTGCAAA
*
199539 TATTAAATCCTAGGACAATTATCGACTTTGAAACTTGCCATACATATCAAAATGATCGAGTGCTT
261 TATTAAATCCTAGGACAATTATCGACTTCGAAACTTGCCATACATATCAAAATGATCGAGTGCTT
*
199604 AGTGATCGATGCCAATTCTAGCGGTTTTTTAGACTTACCCATAGTGAGTTAATGATGTGTAATAC
326 AGTGATCGATGCCAATTCTAGCGGTTTTTTAGACTTACCCACAGTGAGTTAATGATGTGTAATAC
199669 TGCAAGCCTGTGGTTCAAATTGATGGGCATTCTTGTATGTAAAATACAAACAATTTTTAGTATTG
391 TGCAAGCCTGTGGTTCAAATTGATGGGCATTCTTGTATGTAAAATACAAACAATTTTTAGTATTG
199734 GCAGCTGTCTAAGATGGTAATTGTAATATTTTTCCAGTTGTTTTTGCCTTGTTGAATGAGAAGAT
456 GCAGCTGTCTAAGATGGTAATTGTAATATTTTTCCAGTTGTTTTTGCCTTGTTGAATGAGAAGAT
199799 ACAAATTCTTGAGTTTTTTTCCTCAGAAACTTACGCTTACATGTTATCACAAGGGAAGAAATATG
521 ACAAATTCTTGAGTTTTTTTCCTCAGAAACTTACGCTTACATGTTATCACAAGGGAAGAAATATG
199864 TGTCATTTCAGATTATAAAGCTAAGATCAAAGCAACAATGGAGTCTTTGGGTCTAATGTGGCAAC
586 TGTCATTTCAGATTATAAAGCTAAGATCAAAGCAACAATGGAGTCTTTGGGTCTAATGTGGCAAC
*
199929 CACCCTATGTCCAACATTGGTACTGTATCTGACACATTGTTGTTAATTATCATTGCTGCTAATGA
651 CACCCTATGTCCAACATTGGTACTGTATCCGACACATTGTTGTTAATTATCATTGCTGCTAATGA
199994 TGAGGCCA
716 TGAGGCCA
*
200002 ACTCACTTGATGTACCTGAGGGATCAACCAGGGTCATCCTAACTTGGACTCCGACATTATCTGAC
1 ACTCACTTGATGTACCTGAGGGATCAACCAGGGTCATCCTAACTTGGACTCCGACATTATATGAC
200067 AAACCATCATGCCCATGGTCAAAGAAAACTCCAATATAGTTATTGCGATGATGATTTTAGTTATA
66 AAACCATCATGCCCATGGTCAAAGAAAACTCCAATATAGTTATTGCGATGATGATTTTAGTTATA
*
200132 CAATCATAATATGGGTACACTGTATCATACAGGAAAGCATGGAAGGCAAAGTAAAATATCATTAA
131 CAATCATAATATGGGTACACTGTATCATACAGAAAAGCATGGAAGGCAAAGTAAAATATCATTAA
200197 AAAAATTCACGGCAAGTGGCATGCATCTTTAAACGAACTACCAAGTTGATTTAGGGTAGTGCAAA
196 AAAAATTCACGGCAAGTGGCATGCATCTTTAAACGAACTACCAAGTTGATTTAGGGTAGTGCAAA
* *
200262 TATTGAATCCTAGGATAATTATCGACTTCGAAACTTGCCATACATATCAAAATGATCGAGTGCTT
261 TATTAAATCCTAGGACAATTATCGACTTCGAAACTTGCCATACATATCAAAATGATCGAGTGCTT
200327 AGTGATCGATGCCAATTCTAGCGGTTTTTTTAGACTTACCCACAGTGAGTTAATGATGTGTAATA
326 AGTGATCGATGCCAATTCTAGCGG-TTTTTTAGACTTACCCACAGTGAGTTAATGATGTGTAATA
200392 CTGCAAGCCTGTGGTTCAAATTGATGGGCATTCTTGTATGTAAAATACAAACAATTTTTAGTATT
390 CTGCAAGCCTGTGGTTCAAATTGATGGGCATTCTTGTATGTAAAATACAAACAATTTTTAGTATT
*
200457 GGCAGCTGTCTAAGATGGTAATTGTAATATTTTTCCAGTTGTTTTTTCCTTGTTGAATGAGAAGA
455 GGCAGCTGTCTAAGATGGTAATTGTAATATTTTTCCAGTTGTTTTTGCCTTGTTGAATGAGAAGA
* *
200522 TACAAATTCTTGAGTTTTTTTCCTCAGAAACTTACGCTTACATGTTGTCACGAGGGAAGAAATAT
520 TACAAATTCTTGAGTTTTTTTCCTCAGAAACTTACGCTTACATGTTATCACAAGGGAAGAAATAT
*
200587 GTGTCATTTCAGATTATGAAGCTAAGATCAAAGCAACAATGGAGTCTTTGGGTCTAATGTGGCAA
585 GTGTCATTTCAGATTATAAAGCTAAGATCAAAGCAACAATGGAGTCTTTGGGTCTAATGTGGCAA
200652 CCACCCTATGTCCAACATTGGTACTGTATCCGACACATTGTTGTTAATTATCATTGCTGCTAATG
650 CCACCCTATGTCCAACATTGGTACTGTATCCGACACATTGTTGTTAATTATCATTGCTGCTAATG
200717 ATGAGGCCA
715 ATGAGGCCA
200726 A
1 A
200727 TTACGTGTGC
Statistics
Matches: 710, Mismatches: 14, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
723 341 0.48
724 369 0.52
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (723 bp):
ACTCACTTGATGTACCTGAGGGATCAACCAGGGTCATCCTAACTTGGACTCCGACATTATATGAC
AAACCATCATGCCCATGGTCAAAGAAAACTCCAATATAGTTATTGCGATGATGATTTTAGTTATA
CAATCATAATATGGGTACACTGTATCATACAGAAAAGCATGGAAGGCAAAGTAAAATATCATTAA
AAAAATTCACGGCAAGTGGCATGCATCTTTAAACGAACTACCAAGTTGATTTAGGGTAGTGCAAA
TATTAAATCCTAGGACAATTATCGACTTCGAAACTTGCCATACATATCAAAATGATCGAGTGCTT
AGTGATCGATGCCAATTCTAGCGGTTTTTTAGACTTACCCACAGTGAGTTAATGATGTGTAATAC
TGCAAGCCTGTGGTTCAAATTGATGGGCATTCTTGTATGTAAAATACAAACAATTTTTAGTATTG
GCAGCTGTCTAAGATGGTAATTGTAATATTTTTCCAGTTGTTTTTGCCTTGTTGAATGAGAAGAT
ACAAATTCTTGAGTTTTTTTCCTCAGAAACTTACGCTTACATGTTATCACAAGGGAAGAAATATG
TGTCATTTCAGATTATAAAGCTAAGATCAAAGCAACAATGGAGTCTTTGGGTCTAATGTGGCAAC
CACCCTATGTCCAACATTGGTACTGTATCCGACACATTGTTGTTAATTATCATTGCTGCTAATGA
TGAGGCCA
Found at i:204763 original size:2 final size:2
Alignment explanation
Indices: 204756--204785 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
204746 CCTAAAACAA
204756 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
204786 AATTTCAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:205667 original size:22 final size:22
Alignment explanation
Indices: 205616--205663 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
205606 AGTATTTACT
205616 AAAAAA-TAATCATTAATTTAA
1 AAAAAATTAATCATTAATTTAA
* * *
205637 TAATAATTAAT-ATTATTTTAA
1 AAAAAATTAATCATTAATTTAA
205658 AAAAAA
1 AAAAAA
205664 ATTAGATTCA
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAAAATTAATCATTAATTTAA
Found at i:232366 original size:4 final size:4
Alignment explanation
Indices: 232357--232381 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
232347 AATTGTGCTT
232357 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
232382 AAAAATTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:234120 original size:21 final size:20
Alignment explanation
Indices: 234069--234141 Score: 101
Period size: 21 Copynumber: 3.5 Consensus size: 20
234059 AAATGACCAA
*
234069 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGATAGT
*
234089 CAAATTTGCAACGCGATAGT
1 CAAATTCGCAACGCGATAGT
234109 CGAAATTCGCAACGCGATAGT
1 C-AAATTCGCAACGCGATAGT
*
234130 CCAAAATCGCAA
1 -CAAATTCGCAA
234142 TGCATTTGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
20 19 0.40
21 27 0.57
22 1 0.02
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (20 bp):
CAAATTCGCAACGCGATAGT
Found at i:234486 original size:20 final size:20
Alignment explanation
Indices: 234457--234527 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 20
234447 AGATAATTAA
*
234457 GTTGCAAATTTGACTTTCGC
1 GTTGCGAATTTGACTTTCGC
*
234477 GTTGCGAATTT-CCATTATCGC
1 GTTGCGAATTTGAC-TT-TCGC
* *
234498 GTTGCGATTTTGGACTATCGC
1 GTTGCGAATTT-GACTTTCGC
234519 GTTGCGAAT
1 GTTGCGAAT
234528 CTAGAAACTG
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
19 1 0.02
20 12 0.29
21 26 0.63
22 1 0.02
23 1 0.02
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTCGC
Found at i:234499 original size:21 final size:21
Alignment explanation
Indices: 234473--234527 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
234463 AATTTGACTT
*
234473 TCGCGTTGCGAATTTCCATTA
1 TCGCGTTGCGAATTTCCACTA
* **
234494 TCGCGTTGCGATTTTGGACTA
1 TCGCGTTGCGAATTTCCACTA
234515 TCGCGTTGCGAAT
1 TCGCGTTGCGAAT
234528 CTAGAAACTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGAATTTCCACTA
Found at i:236420 original size:15 final size:15
Alignment explanation
Indices: 236400--236431 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
236390 CCGGTTTGAT
*
236400 CGGTTCAACCCAACC
1 CGGTTCAACACAACC
236415 CGGTTCAACACAACC
1 CGGTTCAACACAACC
236430 CG
1 CG
236432 ACTGACCGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.44, G:0.16, T:0.12
Consensus pattern (15 bp):
CGGTTCAACACAACC
Found at i:236462 original size:25 final size:24
Alignment explanation
Indices: 236434--236488 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
236424 ACAACCCGAC
236434 TGACCGGC-CCGAACCGTTGACCCAT
1 TGACCGGCGCCG-ACCGTTGA-CCAT
* **
236459 TGACCAGCGTTGACCGTTGACCAT
1 TGACCGGCGCCGACCGTTGACCAT
236483 TGACCG
1 TGACCG
236489 ATGTTGACCA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 9 0.36
25 15 0.60
26 1 0.04
ACGTcount: A:0.20, C:0.35, G:0.25, T:0.20
Consensus pattern (24 bp):
TGACCGGCGCCGACCGTTGACCAT
Found at i:239719 original size:79 final size:80
Alignment explanation
Indices: 239617--239771 Score: 222
Period size: 79 Copynumber: 1.9 Consensus size: 80
239607 AATTTCATAA
* * * *
239617 AAATTAATTTGTAATTAGATTATTAAAATATAAACTGTAAAA-AATATTTTTTATTTATATTATT
1 AAATAAATTTGTAATTACATTATTAAAATATAAACTGTAAAACAATAATTTTTAATTATATTATT
*
239681 AAAGTATTAAATATT
66 AAAATATTAAATATT
* * *
239696 AAATAAATTTTTAATTACATTATTAAAATATTAATTGTAAAACCAATAATTTTTAATTATATTAT
1 AAATAAATTTGTAATTACATTATTAAAATATAAACTGTAAAA-CAATAATTTTTAATTATATTAT
239761 TAAAATATTAA
65 TAAAATATTAA
239772 TCTAACTAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
79 37 0.56
81 29 0.44
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (80 bp):
AAATAAATTTGTAATTACATTATTAAAATATAAACTGTAAAACAATAATTTTTAATTATATTATT
AAAATATTAAATATT
Found at i:239748 original size:42 final size:40
Alignment explanation
Indices: 239614--239772 Score: 176
Period size: 40 Copynumber: 4.0 Consensus size: 40
239604 TTAAATTTCA
* * * * *
239614 TAAAAATTAATTTGTAATTAGATTATTAAAATATAAACTG
1 TAAAAAATAATTTTTAATTATATTATTAAAATATTAATTG
* * * * *
239654 TAAAAAATATTTTTTATTTATATTATTAAAGTATTAAATA
1 TAAAAAATAATTTTTAATTATATTATTAAAATATTAATTG
* * *
239694 TTAAATA-AATTTTTAATTACATTATTAAAATATTAATTG
1 TAAAAAATAATTTTTAATTATATTATTAAAATATTAATTG
239733 TAAAACCAATAATTTTTAATTATATTATTAAAATATTAAT
1 TAAAA--AATAATTTTTAATTATATTATTAAAATATTAAT
239773 CTAACTAAAG
Statistics
Matches: 96, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
39 30 0.31
40 36 0.38
41 1 0.01
42 29 0.30
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (40 bp):
TAAAAAATAATTTTTAATTATATTATTAAAATATTAATTG
Found at i:239850 original size:16 final size:17
Alignment explanation
Indices: 239821--239852 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
239811 ACTTGTAACT
239821 AATTATAGAATATTATA
1 AATTATAGAATATTATA
239838 AATTATA-AATATTAT
1 AATTATAGAATATTAT
239853 TTTCGAGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
AATTATAGAATATTATA
Found at i:241832 original size:43 final size:43
Alignment explanation
Indices: 241771--241856 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
241761 AAACCATATC
241771 AACAATTCCCTTAAAAACTCATTATATATATTCGTCATTATTT
1 AACAATTCCCTTAAAAACTCATTATATATATTCGTCATTATTT
241814 AACAATTCCCTTAAAAACTCATTATATATATTCGTCATTATTT
1 AACAATTCCCTTAAAAACTCATTATATATATTCGTCATTATTT
241857 CACTCATCTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.37, C:0.19, G:0.02, T:0.42
Consensus pattern (43 bp):
AACAATTCCCTTAAAAACTCATTATATATATTCGTCATTATTT
Found at i:243455 original size:25 final size:24
Alignment explanation
Indices: 243412--243484 Score: 94
Period size: 24 Copynumber: 3.0 Consensus size: 24
243402 TGTAAAAAAT
243412 TAAACGAGCTTGTTT-ATGAACATA
1 TAAACGAGCTT-TTTCATGAACATA
*
243436 TAATACGAGCTTTTTCATGAACCTA
1 TAA-ACGAGCTTTTTCATGAACATA
* *
243461 TAAACGAGCTTGTTCGTGAACATA
1 TAAACGAGCTTTTTCATGAACATA
243485 AACGAACCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
24 24 0.56
25 19 0.44
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Consensus pattern (24 bp):
TAAACGAGCTTTTTCATGAACATA
Found at i:243480 original size:24 final size:24
Alignment explanation
Indices: 243412--243489 Score: 97
Period size: 25 Copynumber: 3.3 Consensus size: 24
243402 TGTAAAAAAT
* *
243412 TAAACGAGCTTGTTTATGAACATA
1 TAAACGAGCTTGTTCATGAACCTA
*
243436 TAATACGAGCTTTTTCATGAACCTA
1 TAA-ACGAGCTTGTTCATGAACCTA
*
243461 TAAACGAGCTTGTTCGTGAA-C-A
1 TAAACGAGCTTGTTCATGAACCTA
243483 TAAACGA
1 TAAACGA
243490 ACCAAACACA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
22 8 0.17
23 1 0.02
24 18 0.38
25 21 0.44
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (24 bp):
TAAACGAGCTTGTTCATGAACCTA
Found at i:245072 original size:3 final size:3
Alignment explanation
Indices: 245064--245092 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
245054 GTCTGCAGGT
245064 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
245093 TTGCTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:247727 original size:563 final size:565
Alignment explanation
Indices: 246623--248130 Score: 2710
Period size: 563 Copynumber: 2.7 Consensus size: 565
246613 AGGGACAGCC
*
246623 AATCATACACAGGTCTTTCATGGTTTTTTCTTCAACTTGACTTGTTAGTATTTACTTTTTGACTG
1 AATCATACACAGGTCTTTCATGGTTTTTTCTTCAACGTGACTTGTTAGTATTTACTTTTTGACTG
*
246688 CTGATGAGGTACAATTCATTTTGAAATAACATTTATGTTAAATTATGATTTTTCTTACATAATAT
66 CTGATGAGGTACAATTCATTTTGAAATAACATTTATGTTAAATAATGATTTTTCTTACATAATAT
246753 TCATGTATTGTT-TGCATGTTTTAATTTGATATTCTGTGAAGAATAACTGTATTCTGAGTTCAAT
131 TCATGTATT-TTGTGCATGTTTTAATTTGATATTCTGTGAAGAATAACTGTATTCTGAGTTCAAT
*
246817 TAGAAATATAGCTATTTTTATGCATGAAAGAACATAGAAAAATAGGATCTTACACTCTATTTCAT
195 TAGAAATATAGCTATTTTTATGCATGAAAGAACATAGAAAAATAAGATCTTACAC-CTATTTCAT
*
246882 GTTAACCTTTTTCATTTGTAGCAATATAATTTTTTTTTGTGATTAATGCTTTCCAAACTTCTGTT
259 GTTAACCTTTTTCATTGGTAGCAATATAATTTTTTTTTGTGATTAATGCTTTCCAAACTTCTGTT
246947 CTTATATTTAACAATTGCAAGTATGAAAGATGTTTT-TTTTAGAAACTTTGCCTTTTGAATTTAC
324 CTTATATTTAACAATTGCAAGTATGAAAGATGTTTTGTTTTAGAAACTTTGCCTTTTGAATTTAC
* *
247011 ATTCAATTTTTTGTTTGTTTGCTTGTTTTTAATTACTGAATTTTCATCTCTTGTTCATCATAAGC
389 ATTCAATGTTTTGTTTGTTTGCTTGTTTTTAATTACTAAATTTTCATCTCTTGTTCATCATAAGC
*
247076 AAGAAATGAAAAGCTTGAGCTTGAAGAAGAGCATCGCCGTGGCAATCAACAAATCCACAAGATGT
454 AAGAAATGAAAAGCTTGAGCTTGAAGAAGAGCATCGCCGTGGCAATCAACAAATACACAAGATGT
247141 TGAATGATGTTAGGATGCATGAAGAACAAGTTCATGATATTCAGGAG
519 TGAATGATGTTAGGATGCATGAAGAACAAGTTCATGATATTCAGGAG
* *
247188 AATCATACACAGGTCTTTCATGGTTTTTTCTTCAACGTGACTTGTCAGTATTTACTTTTTGGCTG
1 AATCATACACAGGTCTTTCATGGTTTTTTCTTCAACGTGACTTGTTAGTATTTACTTTTTGACTG
*
247253 CTGATGAGGTACAATTCATTTTGAAATAACATTTATGTTAAATAATGATTTTTATTACATAATAT
66 CTGATGAGGTACAATTCATTTTGAAATAACATTTATGTTAAATAATGATTTTTCTTACATAATAT
*
247318 TCATGTATTTTGTGCATGTTTTAATTTGATATTCTGTGAAGAATAACTGTATTCCGAGTTCAATT
131 TCATGTATTTTGTGCATGTTTTAATTTGATATTCTGTGAAGAATAACTGTATTCTGAGTTCAATT
247383 AGAAATATAGCTA-TTTTATGCATGAAAGAACATAG-AAAATAAGATCTTACA-CTATTTCATGT
196 AGAAATATAGCTATTTTTATGCATGAAAGAACATAGAAAAATAAGATCTTACACCTATTTCATGT
247445 TAACCTTTTTCATTGGTAGCAATATAATTTTTTTTTTTGTGATTAATGCTTTCCAAACTTCTGTT
261 TAACCTTTTTCATTGGTAGCAATATAA--TTTTTTTTTGTGATTAATGCTTTCCAAACTTCTGTT
*
247510 CTTATATTTAACAATTGCAAGTATGAAAGATGTTTTGTTTTAGAAACATTGCCTTTTGAATTTAC
324 CTTATATTTAACAATTGCAAGTATGAAAGATGTTTTGTTTTAGAAACTTTGCCTTTTGAATTTAC
*
247575 GTTCAA-GTTTTGTTTGTTTGCTTGTTTTTAATTACTAAATTTTCATCTCTTGTTCATCATAAGC
389 ATTCAATGTTTTGTTTGTTTGCTTGTTTTTAATTACTAAATTTTCATCTCTTGTTCATCATAAGC
* * *
247639 AAGAAATGAAAAGCTTGAGCTTGAAGAAGAGCATCGCTGTGGCACTCAGCAAATACACAAGATGT
454 AAGAAATGAAAAGCTTGAGCTTGAAGAAGAGCATCGCCGTGGCAATCAACAAATACACAAGATGT
247704 TGAATGATGTTAGGATGCATGAAGAACAAGTTCATGATATTCAGGAG
519 TGAATGATGTTAGGATGCATGAAGAACAAGTTCATGATATTCAGGAG
*
247751 AATCATACACAGGTCTTTCATGGTTTTTTCTTCAACGTGACTTGTTAGTATTTATTTTTTGACTG
1 AATCATACACAGGTCTTTCATGGTTTTTTCTTCAACGTGACTTGTTAGTATTTACTTTTTGACTG
*
247816 CTGATGAGGTACAATTCATTTTGAAATAACATTTATGTTAAATAATGATTTTTCTTATATAATAT
66 CTGATGAGGTACAATTCATTTTGAAATAACATTTATGTTAAATAATGATTTTTCTTACATAATAT
* *
247881 TCATGTTTTTTGTGCATGTTTTAATTTGATATTTTGTGAAGAATAACTGTATTCTGAGTTCAATT
131 TCATGTATTTTGTGCATGTTTTAATTTGATATTCTGTGAAGAATAACTGTATTCTGAGTTCAATT
247946 AGAAATATAGCTATTTTTATGCATGAAAGAACATAGAAAAATAAGATCTTACACTCTATTTCATG
196 AGAAATATAGCTATTTTTATGCATGAAAGAACATAGAAAAATAAGATCTTACAC-CTATTTCATG
*
248011 TTAACCTTTTTCACTGGTAGC-A-AT-ATTTTTTTTTGTGATTAATGCTTTCCAAACTTCTGTTC
260 TTAACCTTTTTCATTGGTAGCAATATAATTTTTTTTTGTGATTAATGCTTTCCAAACTTCTGTTC
*
248073 TTATATTTAACAATTGCAAGTATGAAAGATGTTTTGGTTTAGAAACTTTGCCTTTTGA
325 TTATATTTAACAATTGCAAGTATGAAAGATGTTTTGTTTTAGAAACTTTGCCTTTTGA
248131 TGTACTAATT
Statistics
Matches: 908, Mismatches: 27, Indels: 19
0.95 0.03 0.02
Matches are distributed among these distances:
561 37 0.04
562 93 0.10
563 451 0.50
564 79 0.09
565 217 0.24
566 1 0.00
567 30 0.03
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (565 bp):
AATCATACACAGGTCTTTCATGGTTTTTTCTTCAACGTGACTTGTTAGTATTTACTTTTTGACTG
CTGATGAGGTACAATTCATTTTGAAATAACATTTATGTTAAATAATGATTTTTCTTACATAATAT
TCATGTATTTTGTGCATGTTTTAATTTGATATTCTGTGAAGAATAACTGTATTCTGAGTTCAATT
AGAAATATAGCTATTTTTATGCATGAAAGAACATAGAAAAATAAGATCTTACACCTATTTCATGT
TAACCTTTTTCATTGGTAGCAATATAATTTTTTTTTGTGATTAATGCTTTCCAAACTTCTGTTCT
TATATTTAACAATTGCAAGTATGAAAGATGTTTTGTTTTAGAAACTTTGCCTTTTGAATTTACAT
TCAATGTTTTGTTTGTTTGCTTGTTTTTAATTACTAAATTTTCATCTCTTGTTCATCATAAGCAA
GAAATGAAAAGCTTGAGCTTGAAGAAGAGCATCGCCGTGGCAATCAACAAATACACAAGATGTTG
AATGATGTTAGGATGCATGAAGAACAAGTTCATGATATTCAGGAG
Found at i:252984 original size:362 final size:362
Alignment explanation
Indices: 252286--253012 Score: 1332
Period size: 362 Copynumber: 2.0 Consensus size: 362
252276 TCCAATGTTC
**
252286 TGTATGTGTTGTACTAATTATGTGTCATGAGTTTCTTTTGATTGGTGATTTGGTTGCAGATTGTT
1 TGTATGTGTTGTACTAATTATGTGTCATGAGTTTCTTTTGATTGGTGATTTGGTTGCAGATTGCC
* *
252351 GTGCTAAAGTGGTTATGATATTTGCTCTATATTGTCTTACATCTGAGGCATTTGACAGGTAGAAA
66 GTGCTAAAGTGGTTATGATATTTGCTCTATATCGTCATACATCTGAGGCATTTGACAGGTAGAAA
* *
252416 AATTGCCAGCCAGAAGGAGGACCTCCGTGAGCTGTTTGAACATTTCAATGTGAGTGTTTGGCCTG
131 AATTGCCAGCCAGAAGGAGGACCTCCGTGAGATGGTTGAACATTTCAATGTGAGTGTTTGGCCTG
252481 AGAATTAAGTATCCTTTAAGTTTCTTAATTGCAGCATTTTGTTGTTTTCTTGTTGGTACATGATC
196 AGAATTAAGTATCCTTTAAGTTTCTTAATTGCAGCATTTTGTTGTTTTCTTGTTGGTACATGATC
252546 TGTCATCATGTACTTAATATAATACTTCATTATTTTTCTGAATTAGGTGTATATAACACTTGCTT
261 TGTCATCATGTACTTAATATAATACTTCATTATTTTTCTGAATTAGGTGTATATAACACTTGCTT
*
252611 TTTTTCCCCAGTTTTAAAAATAAATCATTTTATTATA
326 TTTTCCCCCAGTTTTAAAAATAAATCATTTTATTATA
252648 TGTATGTGTTGTACTAATTATGTGTCATGAGTTTCTTTTGATTGGTGATTTGGTTGCAGATTGCC
1 TGTATGTGTTGTACTAATTATGTGTCATGAGTTTCTTTTGATTGGTGATTTGGTTGCAGATTGCC
*
252713 GTGCTAAAGTGGTTATGGA-ATTTGCTCTATATCGTCATATATCTGAGGCATTTGACAGGTAGAA
66 GTGCTAAAGTGGTTAT-GATATTTGCTCTATATCGTCATACATCTGAGGCATTTGACAGGTAGAA
252777 AAATTGCCAGCCAGAAGGAGGACCTCCGTGAGATGGTTGAACATTTCAATGTGAGTGTTTGGCCT
130 AAATTGCCAGCCAGAAGGAGGACCTCCGTGAGATGGTTGAACATTTCAATGTGAGTGTTTGGCCT
*
252842 GAGAATTAAGTATGCTTTAAGTTTCTTAATTGCAGCATTTTGTTGTTTTCTTGTTGGTACATGAT
195 GAGAATTAAGTATCCTTTAAGTTTCTTAATTGCAGCATTTTGTTGTTTTCTTGTTGGTACATGAT
*
252907 CTGTCATCATGTACTTAATATAATACTTCATTATTTTTTCTGAATTATGTGTATATAACACTTGC
260 CTGTCATCATGTACTTAATATAATACTTCATTA-TTTTTCTGAATTAGGTGTATATAACACTTGC
252972 -TTTTTCCCCCAGTTTTAAAAATAAATCATTTTATTATA
324 TTTTTTCCCCCAGTTTTAAAAATAAATCATTTTATTATA
253010 TGT
1 TGT
253013 TGGTGCAGCT
Statistics
Matches: 353, Mismatches: 10, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
362 321 0.91
363 32 0.09
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (362 bp):
TGTATGTGTTGTACTAATTATGTGTCATGAGTTTCTTTTGATTGGTGATTTGGTTGCAGATTGCC
GTGCTAAAGTGGTTATGATATTTGCTCTATATCGTCATACATCTGAGGCATTTGACAGGTAGAAA
AATTGCCAGCCAGAAGGAGGACCTCCGTGAGATGGTTGAACATTTCAATGTGAGTGTTTGGCCTG
AGAATTAAGTATCCTTTAAGTTTCTTAATTGCAGCATTTTGTTGTTTTCTTGTTGGTACATGATC
TGTCATCATGTACTTAATATAATACTTCATTATTTTTCTGAATTAGGTGTATATAACACTTGCTT
TTTTCCCCCAGTTTTAAAAATAAATCATTTTATTATA
Found at i:261029 original size:209 final size:212
Alignment explanation
Indices: 260669--261092 Score: 701
Period size: 209 Copynumber: 2.0 Consensus size: 212
260659 TTAGAGTTTT
* *
260669 TGATTGTACTGTGTTCGTTTATAACAATGTTTCTTTCAGGTCCAAATTAGATCCTTGAGCATTTC
1 TGATTGTACTGTGTTCGTTTATAACAATGTTCCTTTCAGGTCCAAATTAGATCCTTGAGCAGTTC
* *
260734 GGTGTGTTTTTGGGTTATTCTTCGACTCAAAAGGACTTTCGGTGTTATTATCCTCGTACTAAGAA
66 GGTGTGTTTCTAGGTTATTCTTCGACTCAAAAGGACTTTCGGTGTTATTATCCTCGTACTAAGAA
* *
260799 ATTATTTATTACTATGGACGTTAC-TTTCTTTGAAAAAATACC-GTTTTTCCTTAATACTTCTAT
131 ATTATTTATTAATATGGACGTTACTTTTCTTTGAAAAAATACCTGTTTTTCCTTAAAACTTCTAT
260862 TCA-GGGAGTCATATAA
196 TCAGGGGAGTCATATAA
*
260878 TGATTGTACTGTGTTCGTTTATAACAATGTTCCTTTCAGGTCCAAATTAGATCCTTTAGCAGTTC
1 TGATTGTACTGTGTTCGTTTATAACAATGTTCCTTTCAGGTCCAAATTAGATCCTTGAGCAGTTC
* * *
260943 GGTTTGTTTCTAGGTTATTCTTCGACTCAAAAGGACTTTCGGTGTTATTATTCTTGTACTAAGAA
66 GGTGTGTTTCTAGGTTATTCTTCGACTCAAAAGGACTTTCGGTGTTATTATCCTCGTACTAAGAA
* * * *
261008 ATTCTTTATTAATATGGACGTTACTTTTTTTTGAATAAATACCTTTTTTTCCTTAAAACTTCTAT
131 ATTATTTATTAATATGGACGTTACTTTTCTTTGAAAAAATACCTGTTTTTCCTTAAAACTTCTAT
261073 TCAGGGGAGTCATATAA
196 TCAGGGGAGTCATATAA
261090 TGA
1 TGA
261093 ATATCAGTTT
Statistics
Matches: 198, Mismatches: 14, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
209 144 0.73
210 16 0.08
211 22 0.11
212 16 0.08
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (212 bp):
TGATTGTACTGTGTTCGTTTATAACAATGTTCCTTTCAGGTCCAAATTAGATCCTTGAGCAGTTC
GGTGTGTTTCTAGGTTATTCTTCGACTCAAAAGGACTTTCGGTGTTATTATCCTCGTACTAAGAA
ATTATTTATTAATATGGACGTTACTTTTCTTTGAAAAAATACCTGTTTTTCCTTAAAACTTCTAT
TCAGGGGAGTCATATAA
Found at i:262024 original size:152 final size:152
Alignment explanation
Indices: 261745--262040 Score: 427
Period size: 152 Copynumber: 1.9 Consensus size: 152
261735 CAAATGGCCT
* * * * *
261745 TTCACGGTAAAATACAAAGCTGATGGTAGCATTGAAAGATACAAAGGCAAGATTAGTGGTGAAAG
1 TTCACGATAAAATACAAAGCTGATGGTAGCATTGAAAAATACAAAGACAAGATTAGTGGGGAAAA
* *
261810 GATTTACTCAATCTTTTGGAGTTGATTATCAAGAAACGTTTGCTCCGGTAGCAAAACTAAACACT
66 GATTTACTCAATCTTTTGGAGTTGATTATCAAGAAAAGTTTGCTCCAGTAGCAAAACTAAACACT
* *
261875 TTGAGAGTGTTACAAATTGGTA
131 GTGAAAGTGTTACAAATTGGTA
* *
261897 TTCACGATAAAATACAAAGTTGATGGTAGCATTGAAAAATAC-AAGACGAGATTAGTGGCGGGAA
1 TTCACGATAAAATACAAAGCTGATGGTAGCATTGAAAAATACAAAGACAAGATTAGT-G-GGGAA
* *
261961 AAGATTTACTC-ATCTTTTGGAGTTGA-TATCGAGAAAAGTTTGCTCCAGTAGTAAAACTAAAAC
64 AAGATTTACTCAATCTTTTGGAGTTGATTATCAAGAAAAGTTTGCTCCAGTAGCAAAACT-AAAC
262024 ACTGTGAAAGTGTTACA
128 ACTGTGAAAGTGTTACA
262041 TCATAGAAGT
Statistics
Matches: 128, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
151 40 0.31
152 74 0.58
153 14 0.11
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.28
Consensus pattern (152 bp):
TTCACGATAAAATACAAAGCTGATGGTAGCATTGAAAAATACAAAGACAAGATTAGTGGGGAAAA
GATTTACTCAATCTTTTGGAGTTGATTATCAAGAAAAGTTTGCTCCAGTAGCAAAACTAAACACT
GTGAAAGTGTTACAAATTGGTA
Found at i:263379 original size:8 final size:8
Alignment explanation
Indices: 263362--263391 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
263352 AAAATCAAAT
*
263362 TCTTCATC
1 TCTTCTTC
263370 TCTTCTTC
1 TCTTCTTC
263378 TCTTCTTC
1 TCTTCTTC
263386 TCTTCT
1 TCTTCT
263392 ACCTACGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.03, C:0.37, G:0.00, T:0.60
Consensus pattern (8 bp):
TCTTCTTC
Done.