Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 116 of 198
Found at i:37003220 original size:20 final size:19
Alignment explanation
Indices: 37003177--37003220 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
37003167 AAAAACTTAG
* *
37003177 ATTTTCTAGAAGATATCAT
1 ATTTTCTAGAAAATAACAT
*
37003196 ATTTTCTAGAAAATCAACCT
1 ATTTTCTAGAAAAT-AACAT
37003216 ATTTT
1 ATTTT
37003221 TCGTTAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (19 bp):
ATTTTCTAGAAAATAACAT
Found at i:37004699 original size:41 final size:41
Alignment explanation
Indices: 37004603--37004724 Score: 154
Period size: 41 Copynumber: 2.9 Consensus size: 41
37004593 AATACACCGG
* * *
37004603 TTTGTGGACAAACCACCAGTAATTGTAGATATACTGCCAAAAA
1 TTTGTGGACAAGCCACCAGT-ATTGTAGATAAATTGCC-AAAA
* * *
37004646 TATGTGGACAAGCCACCAGTATTGTATACAAATTGCCAAAA
1 TTTGTGGACAAGCCACCAGTATTGTAGATAAATTGCCAAAA
* *
37004687 TTTGTGGACAAGCCATCAATATTGTAGATAAATTGCCA
1 TTTGTGGACAAGCCACCAGTATTGTAGATAAATTGCCA
37004725 GTACTTCCTC
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
41 37 0.54
42 13 0.19
43 18 0.26
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (41 bp):
TTTGTGGACAAGCCACCAGTATTGTAGATAAATTGCCAAAA
Found at i:37004937 original size:6 final size:6
Alignment explanation
Indices: 37004928--37005010 Score: 112
Period size: 6 Copynumber: 13.8 Consensus size: 6
37004918 AATGTAGAAT
* * * * *
37004928 AGTGAT AGTGAC AGTGAT AGTGAC AGTGAC AGTGAT AGTGAC GGTGAT
1 AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC
*
37004976 AGTGAC AGTGAC AGTGAT AGTGAC AGTGAC AGTGA
1 AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC AGTGA
37005011 TAGTATCAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 66 1.00
ACGTcount: A:0.33, C:0.10, G:0.35, T:0.23
Consensus pattern (6 bp):
AGTGAC
Found at i:37004949 original size:18 final size:18
Alignment explanation
Indices: 37004926--37005014 Score: 124
Period size: 18 Copynumber: 4.9 Consensus size: 18
37004916 TAAATGTAGA
* *
37004926 ATAGTGATAGTGACAGTG
1 ATAGTGACAGTGATAGTG
*
37004944 ATAGTGACAGTGACAGTG
1 ATAGTGACAGTGATAGTG
*
37004962 ATAGTGACGGTGATAGTG
1 ATAGTGACAGTGATAGTG
*
37004980 ACAGTGACAGTGATAGTG
1 ATAGTGACAGTGATAGTG
*
37004998 ACAGTGACAGTGATAGT
1 ATAGTGACAGTGATAGT
37005015 ATCAATAAAC
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 66 1.00
ACGTcount: A:0.33, C:0.09, G:0.34, T:0.25
Consensus pattern (18 bp):
ATAGTGACAGTGATAGTG
Found at i:37021562 original size:29 final size:29
Alignment explanation
Indices: 37021528--37021589 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
37021518 ATGTGGTTAT
37021528 GTTTGGGTTATTACCGACTTTGTTACTTA
1 GTTTGGGTTATTACCGACTTTGTTACTTA
37021557 GTTTGGGTTATTACCGACTTTGTTACTTA
1 GTTTGGGTTATTACCGACTTTGTTACTTA
37021586 GTTT
1 GTTT
37021590 TTTTGGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.16, C:0.13, G:0.21, T:0.50
Consensus pattern (29 bp):
GTTTGGGTTATTACCGACTTTGTTACTTA
Found at i:37034019 original size:17 final size:18
Alignment explanation
Indices: 37033977--37034020 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
37033967 GCCCAATATT
37033977 CCCACACGCCCGTATGGGG
1 CCCACACGCCCG-ATGGGG
* *
37033996 CCAACACGCCCG-TGTGG
1 CCCACACGCCCGATGGGG
37034013 CCCACACG
1 CCCACACG
37034021 GCCCAATTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 11 0.50
19 11 0.50
ACGTcount: A:0.18, C:0.45, G:0.27, T:0.09
Consensus pattern (18 bp):
CCCACACGCCCGATGGGG
Found at i:37036309 original size:139 final size:138
Alignment explanation
Indices: 37036027--37036449 Score: 686
Period size: 138 Copynumber: 3.1 Consensus size: 138
37036017 GTGAACATAG
*
37036027 ATATAATTAATCTATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCAAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCAAATTTATT
* * *
37036092 AATATCAACAATTATATTAATTAATTTCAATTAAAATATAAAAGACATGGAAATTAATATTCTTT
66 AATATAAAAAATTATATTAATTAATTTCAATCAAAATATAAAAGACATGGAAATTAATATTCTTT
37036157 TGGAAAGA
131 TGGAAAGA
*
37036165 ATATAATTAATATATGAATTTGATTTATACAAAATATTAATTGTATATATTTTA-CTAAATTTAT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATC-AAATTTAT
* *
37036229 TAATATAAAAAAATTATATTAATTACTTTCAATCAAAATATAAAAGACATGGAAATTAATATTAT
65 TAATAT-AAAAAATTATATTAATTAATTTCAATCAAAATATAAAAGACATGGAAATTAATATTCT
*
37036294 TTTGGAAAGG
129 TTTGGAAAGA
*
37036304 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCAAATTTATT
* * * * * *
37036369 AGTATAAATAATTATATTAATTAATTTCGATCAAAATATAAAGGACATGAAAATTAATGTTCTTT
66 AATATAAAAAATTATATTAATTAATTTCAATCAAAATATAAAAGACATGGAAATTAATATTCTTT
37036434 TGGAAAGA
131 TGGAAAGA
37036442 ATATAATT
1 ATATAATT
37036450 TATTTTTCTA
Statistics
Matches: 263, Mismatches: 19, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
137 1 0.00
138 134 0.51
139 127 0.48
140 1 0.00
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (138 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCAAATTTATT
AATATAAAAAATTATATTAATTAATTTCAATCAAAATATAAAAGACATGGAAATTAATATTCTTT
TGGAAAGA
Found at i:37036340 original size:71 final size:71
Alignment explanation
Indices: 37036124--37036340 Score: 180
Period size: 71 Copynumber: 3.1 Consensus size: 71
37036114 AATTTCAATT
*
37036124 AAAATATAAAAGACATGGAAATTAATATTCTTTTGGAAAGAATATAATTAATATATGAATTTGAT
1 AAAATATAAAAGACATGGAAATTAATATTATTTTGGAAAGAATATAATTAATATATGAATTTGAT
*
37036189 TTATAC
66 TCATAC
** * ** * * * * * *
37036195 AAAATATTAATTGTATAT--ATTTTACTA-AATTTAT-TAATATAAAAAAATT-ATAT-T-AATT
1 AAAATA-TAAAAG-ACATGGAAATTAATATTATTT-TGGAA-AGAATATAATTAATATATGAATT
***
37036253 ACTTTCA-ATC
62 TGATTCATA-C
*
37036263 AAAATATAAAAGACATGGAAATTAATATTATTTTGGAAAGGATATAATTAATATATGAATTTGAT
1 AAAATATAAAAGACATGGAAATTAATATTATTTTGGAAAGAATATAATTAATATATGAATTTGAT
37036328 TCATAC
66 TCATAC
37036334 AAAATAT
1 AAAATAT
37036341 TAATTGTATA
Statistics
Matches: 102, Mismatches: 31, Indels: 26
0.64 0.19 0.16
Matches are distributed among these distances:
66 3 0.03
67 5 0.05
68 28 0.27
69 11 0.11
70 10 0.10
71 37 0.36
72 5 0.05
73 3 0.03
ACGTcount: A:0.48, C:0.05, G:0.08, T:0.39
Consensus pattern (71 bp):
AAAATATAAAAGACATGGAAATTAATATTATTTTGGAAAGAATATAATTAATATATGAATTTGAT
TCATAC
Found at i:37036556 original size:75 final size:75
Alignment explanation
Indices: 37036428--37036572 Score: 245
Period size: 75 Copynumber: 1.9 Consensus size: 75
37036418 AAAATTAATG
* * * * *
37036428 TTCTTTTGGAAAGAATATAATTTATTTTTCTAACTTTTCATTTGTCTTTTCTATTATTAAGGGAA
1 TTCTTTTGGAAAGAATATAACTCATTTTTCTAACTTTCCATTTGTCTTCTCTATTAATAAGGGAA
37036493 TAATCCTATA
66 TAATCCTATA
37036503 TTCTTTTGGAAAGAATATAACTCATTTTTCTAACTTTCCATTTGTCTTCTCTATTAATAAGGGAA
1 TTCTTTTGGAAAGAATATAACTCATTTTTCTAACTTTCCATTTGTCTTCTCTATTAATAAGGGAA
37036568 TAATC
66 TAATC
37036573 ATGGTTTTCC
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 65 1.00
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.48
Consensus pattern (75 bp):
TTCTTTTGGAAAGAATATAACTCATTTTTCTAACTTTCCATTTGTCTTCTCTATTAATAAGGGAA
TAATCCTATA
Found at i:37047527 original size:10 final size:11
Alignment explanation
Indices: 37047514--37047562 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 11
37047504 TAAATAAAGC
37047514 TAATAATA-AT
1 TAATAATATAT
37047524 TAAT-ATATAT
1 TAATAATATAT
*
37047534 T-ATAATAGAT
1 TAATAATATAT
*
37047544 ATAATTATATAT
1 -TAATAATATAT
37047556 TAATAAT
1 TAATAAT
37047563 TATCATCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
9 5 0.16
10 12 0.39
11 7 0.23
12 7 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (11 bp):
TAATAATATAT
Found at i:37047552 original size:22 final size:20
Alignment explanation
Indices: 37047514--37047562 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 20
37047504 TAAATAAAGC
37047514 TAATAATAATTAATATATAT
1 TAATAATAATTAATATATAT
37047534 T-ATAATAGATATAATTATATAT
1 TAATAATA-AT-TAA-TATATAT
37047556 TAATAAT
1 TAATAAT
37047563 TATCATCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 6 0.24
20 3 0.12
21 3 0.12
22 8 0.32
23 5 0.20
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
TAATAATAATTAATATATAT
Found at i:37047691 original size:30 final size:30
Alignment explanation
Indices: 37047634--37047695 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
37047624 TCTTTTTGAA
***
37047634 AATATTTACAAAAAGAGGCATTTAATTTTT
1 AATATTTACAAAAAGAGGCACAAAATTTTT
37047664 AATATTTACAAAAAGA-GCAACAAAATTTTT
1 AATATTTACAAAAAGAGGC-ACAAAATTTTT
37047694 AA
1 AA
37047696 AAATAATTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 2 0.07
30 26 0.93
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34
Consensus pattern (30 bp):
AATATTTACAAAAAGAGGCACAAAATTTTT
Found at i:37067952 original size:26 final size:26
Alignment explanation
Indices: 37067906--37067955 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
37067896 AGCCCAAGAA
*
37067906 GTTAAGATAGGGATGTCTACACAACT
1 GTTAAGATAGGGATATCTACACAACT
* *
37067932 GTTAAGATAGGGCTATTTACACAA
1 GTTAAGATAGGGATATCTACACAA
37067956 ATTTTAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (26 bp):
GTTAAGATAGGGATATCTACACAACT
Found at i:37067962 original size:26 final size:26
Alignment explanation
Indices: 37067906--37067962 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
37067896 AGCCCAAGAA
* *
37067906 GTTAAGATAGGGATGTCTACACAACT
1 GTTAAGATAGGGATATCTACACAAAT
* *
37067932 GTTAAGATAGGGCTATTTACACAAAT
1 GTTAAGATAGGGATATCTACACAAAT
*
37067958 TTTAA
1 GTTAA
37067963 TATATTGTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (26 bp):
GTTAAGATAGGGATATCTACACAAAT
Found at i:37069155 original size:27 final size:29
Alignment explanation
Indices: 37069125--37069197 Score: 96
Period size: 27 Copynumber: 2.6 Consensus size: 29
37069115 GAATAGTATA
37069125 TGTGGCAAAGCCACCAGTAACAGTA-AT-
1 TGTGGCAAAGCCACCAGTAACAGTATATG
* * *
37069152 TGTGGCAAAGCCACTAGTATCAGTATGTG
1 TGTGGCAAAGCCACCAGTAACAGTATATG
*
37069181 TGTGGCAGAGCCACCAG
1 TGTGGCAAAGCCACCAG
37069198 AAATAGTACT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 23 0.59
28 1 0.03
29 15 0.38
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (29 bp):
TGTGGCAAAGCCACCAGTAACAGTATATG
Found at i:37069205 original size:29 final size:25
Alignment explanation
Indices: 37069111--37069205 Score: 82
Period size: 27 Copynumber: 3.5 Consensus size: 25
37069101 CAGCAGAGCT
37069111 ACCAGAATAGTATATGTGGCAAAGCC
1 ACCAGAATAGTAT-TGTGGCAAAGCC
*
37069137 ACCAGTAACAGTAATTGTGGCAAAGCC
1 ACCAG-AATAGT-ATTGTGGCAAAGCC
* * *
37069164 ACTAGTATCAGTATGTGTGTGGCAGAGCC
1 ACCAGAAT-AGTA--T-TGTGGCAAAGCC
37069193 ACCAGAAATAGTA
1 ACCAG-AATAGTA
37069206 CTTCCTCTAG
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
26 7 0.13
27 24 0.44
28 3 0.05
29 19 0.35
30 2 0.04
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (25 bp):
ACCAGAATAGTATTGTGGCAAAGCC
Found at i:37069369 original size:27 final size:27
Alignment explanation
Indices: 37069321--37069593 Score: 347
Period size: 27 Copynumber: 10.2 Consensus size: 27
37069311 CCTAGAAGTC
* * *
37069321 ATTTTGCCCTATCGAGAGTATTTCGATA
1 ATTTTACCC-ATCGAGGGTATTTCGGTA
* * *
37069349 ACTTTACCCATCGGGGGTATTTTGGTA
1 ATTTTACCCATCGAGGGTATTTCGGTA
37069376 ATTTTACCCATC-AGGGTATTTCGGTA
1 ATTTTACCCATCGAGGGTATTTCGGTA
* *
37069402 ATTTTACCCATAGAGGGTATTTTGGTA
1 ATTTTACCCATCGAGGGTATTTCGGTA
*
37069429 ATTTTACCCATTGAGGGTATTTCGGTA
1 ATTTTACCCATCGAGGGTATTTCGGTA
* *
37069456 ATTTTACCCAT-TAGGGTATTTCGATA
1 ATTTTACCCATCGAGGGTATTTCGGTA
* *
37069482 ATTTTACCCATTGAGGGTATTTCGATA
1 ATTTTACCCATCGAGGGTATTTCGGTA
* *
37069509 ATTTTACCCATCGGGGGTATTTCAGTA
1 ATTTTACCCATCGAGGGTATTTCGGTA
* *
37069536 ATTTCACTCATCGA-GGTA-TTCGGTA
1 ATTTTACCCATCGAGGGTATTTCGGTA
37069561 ATTTTACCCATCGAGGGTATTTCGGTA
1 ATTTTACCCATCGAGGGTATTTCGGTA
*
37069588 GTTTTA
1 ATTTTA
37069594 GGCCGATAAC
Statistics
Matches: 214, Mismatches: 27, Indels: 9
0.86 0.11 0.04
Matches are distributed among these distances:
25 18 0.08
26 55 0.26
27 134 0.63
28 7 0.03
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (27 bp):
ATTTTACCCATCGAGGGTATTTCGGTA
Found at i:37069408 original size:53 final size:54
Alignment explanation
Indices: 37069338--37069593 Score: 324
Period size: 53 Copynumber: 4.8 Consensus size: 54
37069328 CCTATCGAGA
* * * *
37069338 GTATTTCGATAACTTTACCCATCGGGGGTATTTTGGTAATTTTACCCA-TCAGG
1 GTATTTCGGTAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCATTCAGG
* * *
37069391 GTATTTCGGTAATTTTACCCATAGAGGGTATTTTGGTAATTTTACCCATTGAGG
1 GTATTTCGGTAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCATTCAGG
* * *
37069445 GTATTTCGGTAATTTTACCCAT-TAGGGTATTTCGATAATTTTACCCATTGAGG
1 GTATTTCGGTAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCATTCAGG
* * * * *
37069498 GTATTTCGATAATTTTACCCATCGGGGGTATTTCAGTAATTTCACTCA-TC-GAG
1 GTATTTCGGTAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCATTCAG-G
*
37069551 GTA-TTCGGTAATTTTACCCATCGAGGGTATTTCGGTAGTTTTA
1 GTATTTCGGTAATTTTACCCATCGAGGGTATTTCGGTAATTTTA
37069594 GGCCGATAAC
Statistics
Matches: 179, Mismatches: 21, Indels: 7
0.86 0.10 0.03
Matches are distributed among these distances:
52 36 0.20
53 98 0.55
54 45 0.25
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (54 bp):
GTATTTCGGTAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCATTCAGG
Found at i:37069472 original size:80 final size:80
Alignment explanation
Indices: 37069338--37069593 Score: 345
Period size: 80 Copynumber: 3.2 Consensus size: 80
37069328 CCTATCGAGA
* * * *
37069338 GTATTTCGATAACTTTACCCATCGGGGGTATTTTGGTAATTTTACCCATCAGGGTATTTCGGTAA
1 GTATTTCGGTAATTTTACCCATCGGGGGTATTTCGGTAATTTTACCCATTAGGGTATTTCGGTAA
37069403 TTTTACCCATAGAGG
66 TTTTACCCATAGAGG
* * * *
37069418 GTATTTTGGTAATTTTACCCATTGAGGGTATTTCGGTAATTTTACCCATTAGGGTATTTCGATAA
1 GTATTTCGGTAATTTTACCCATCGGGGGTATTTCGGTAATTTTACCCATTAGGGTATTTCGGTAA
*
37069483 TTTTACCCATTGAGG
66 TTTTACCCATAGAGG
* * * * *
37069498 GTATTTCGATAATTTTACCCATCGGGGGTATTTCAGTAATTTCACTCA-TCGAGGTA-TTCGGTA
1 GTATTTCGGTAATTTTACCCATCGGGGGTATTTCGGTAATTTTACCCATTAG-GGTATTTCGGTA
*
37069561 ATTTTACCCATCGAGG
65 ATTTTACCCATAGAGG
*
37069577 GTATTTCGGTAGTTTTA
1 GTATTTCGGTAATTTTA
37069594 GGCCGATAAC
Statistics
Matches: 154, Mismatches: 21, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
79 38 0.25
80 116 0.75
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (80 bp):
GTATTTCGGTAATTTTACCCATCGGGGGTATTTCGGTAATTTTACCCATTAGGGTATTTCGGTAA
TTTTACCCATAGAGG
Found at i:37080588 original size:56 final size:57
Alignment explanation
Indices: 37080527--37080653 Score: 157
Period size: 56 Copynumber: 2.2 Consensus size: 57
37080517 GGTTTTCTCC
* * *
37080527 AAAAATGAAAATGGAGAAATGAAATCAACTGGAAATGATTATGG-TTTCTCCAAAAT
1 AAAAATAAAAATGAAGAAATGAAATCAACTGGAAATGAATATGGTTTTCTCCAAAAT
* * *** *
37080583 AAAAATTAAAATGAAGAAATGGAATCCTTTGGAAATGAATGTGGTTTTCTCCAAAAT
1 AAAAATAAAAATGAAGAAATGAAATCAACTGGAAATGAATATGGTTTTCTCCAAAAT
*
37080640 GAAAATAAAAATGA
1 AAAAATAAAAATGA
37080654 TCTGGAAATG
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
56 36 0.60
57 24 0.40
ACGTcount: A:0.49, C:0.08, G:0.17, T:0.26
Consensus pattern (57 bp):
AAAAATAAAAATGAAGAAATGAAATCAACTGGAAATGAATATGGTTTTCTCCAAAAT
Found at i:37082111 original size:20 final size:19
Alignment explanation
Indices: 37082075--37082113 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
37082065 TTTTTCTAAA
* *
37082075 ATTTAAAATTATTAAAATT
1 ATTTAAAACTATAAAAATT
37082094 ATTTAAAAACTATAAAAATT
1 ATTT-AAAACTATAAAAATT
37082114 TATATATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTTAAAACTATAAAAATT
Found at i:37085918 original size:42 final size:42
Alignment explanation
Indices: 37085858--37086205 Score: 378
Period size: 42 Copynumber: 8.3 Consensus size: 42
37085848 AAGGAAATCA
* *
37085858 TTCATTACATTTAAAGGCCCAGATGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGATGTGGAGGTCCATTTACTT
* * ** * * *
37085900 TTCATTACATTTAGAGGCCTAGGCGTGTAAGTTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGATGTGGAGGTCCATTTACTT
*
37085942 TTCATTGCATTTAGAGGCCC-GAGTGTGGAGGTTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGA-TGTGGAGGTCCATTTACTT
* *
37085984 TTCATTGCATTTAGAGGCTC-GAAGTGTGGAGGTCCATTTATTT
1 TTCATTGCATTTAGAGGCCCAG-A-TGTGGAGGTCCATTTACTT
* * ** *
37086027 TTCATTGCATTTAGAGGCTCAGGTGTGGAAATTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGATGTGGAGGTCCATTTACTT
* * * * **
37086069 TTCATTGCATTTAGAGGCTCGGGTATGGAAATCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGATGTGGAGGTCCATTTACTT
* **
37086111 TTCATTGCATTTAGAGGCTCAGATGTGGAGGTTAATTTACTT
1 TTCATTGCATTTAGAGGCCCAGATGTGGAGGTCCATTTACTT
* * *
37086153 TACATTGCATTTAAAGGCCCA-AGTGTAGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGA-TGTGGAGGTCCATTTACTT
37086195 TTCATTGCATT
1 TTCATTGCATT
37086206 GTATAATAAG
Statistics
Matches: 264, Mismatches: 38, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
41 2 0.01
42 222 0.84
43 39 0.15
44 1 0.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.39
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGATGTGGAGGTCCATTTACTT
Found at i:37086039 original size:127 final size:126
Alignment explanation
Indices: 37085858--37086205 Score: 434
Period size: 127 Copynumber: 2.8 Consensus size: 126
37085848 AAGGAAATCA
* * * *
37085858 TTCATTACATTTAAAGGCCCAGATGTGGAGGTCCATTTACTTTTCATTACATTTAGAGGCCTAGG
1 TTCATTGCATTTAGAGGCTCAGATGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCTAGG
* * ** *
37085923 CGTGTAAGTTCATTTACTTTTCATTGCATTTAGAGGCCCGAGTGTGGAGGTTCATTTACTT
66 AGTGTAAGTTCATTTACTTTTCATTGCATTTAGAGGCCCGAGTATGGAAATCCATTTACTT
*
37085984 TTCATTGCATTTAGAGGCTC-GAAGTGTGGAGGTCCATTTATTTTTCATTGCATTTAGAGG-CTC
1 TTCATTGCATTTAGAGGCTCAG-A-TGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCT-
* * * * *
37086047 AGGTGTGGAAATTCATTTACTTTTCATTGCATTTAGAGGCTCGGGTATGGAAATCCATTTACTT
63 AGGAGTGTAAGTTCATTTACTTTTCATTGCATTTAGAGGCCCGAGTATGGAAATCCATTTACTT
** * * *
37086111 TTCATTGCATTTAGAGGCTCAGATGTGGAGGTTAATTTACTTTACATTGCATTTAAAGGCCCA--
1 TTCATTGCATTTAGAGGCTCAGATGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCTAGG
*
37086174 AGTGTAGAGGTCCATTTACTTTTCATTGCATT
66 AGTGTA-A-GTTCATTTACTTTTCATTGCATT
37086206 GTATAATAAG
Statistics
Matches: 191, Mismatches: 24, Indels: 14
0.83 0.10 0.06
Matches are distributed among these distances:
124 4 0.02
125 2 0.01
126 73 0.38
127 111 0.58
128 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.39
Consensus pattern (126 bp):
TTCATTGCATTTAGAGGCTCAGATGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCTAGG
AGTGTAAGTTCATTTACTTTTCATTGCATTTAGAGGCCCGAGTATGGAAATCCATTTACTT
Found at i:37087447 original size:21 final size:22
Alignment explanation
Indices: 37087421--37087465 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
37087411 AAAGCTTTGA
*
37087421 TTTTTAAGA-AAAA-TTGTGATT
1 TTTTTAAAACAAAACTT-TGATT
37087442 TTTTTAAAACAAAACTTTGATT
1 TTTTTAAAACAAAACTTTGATT
37087464 TT
1 TT
37087466 GCAAAAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 11 0.52
23 2 0.10
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (22 bp):
TTTTTAAAACAAAACTTTGATT
Found at i:37087474 original size:140 final size:141
Alignment explanation
Indices: 37087207--37087464 Score: 373
Period size: 140 Copynumber: 1.9 Consensus size: 141
37087197 GTTTTTAGTC
* * *
37087207 ATTTTAAAGTAAAAGTTTAAATTTTTTAAAATAAAGTTTTGATCTTTTTCAACTATTTCAAAATA
1 ATTTTAAAGGAAAAGTTTAAATATTTTAAAACAAAGTTTTGATCTTTTTCAACTATTTCAAAATA
* * *
37087272 AAGTTTTGATTTTTAAGAAAAATGGTGATTTTTTTTTAAAAGAGAAAGGTTAGATTTAAAAAA-A
66 AAGCTTTGATTTTTAAGAAAAATGGTGA-TTTTTTTTAAAACAGAAAGCTTAGATTTAAAAAAGA
37087336 AAACATTTAGCT
130 AAACATTTAGCT
* * *
37087348 ATTTTAAAGGAAAAGTTTAAA-ATTTTAGAACAATGTTTTGATCTTTTTCAACTGTTTCAAAATA
1 ATTTTAAAGGAAAAGTTTAAATATTTTAAAACAAAGTTTTGATCTTTTTCAACTATTTCAAAATA
* *
37087412 AAGCTTTGATTTTTAAGAAAAATTGTGA-TTTTTTTAAAACA-AAA-CTTTGATTT
66 AAGCTTTGATTTTTAAGAAAAATGGTGATTTTTTTTAAAACAGAAAGCTTAGATTT
37087465 TGCAAAAAAA
Statistics
Matches: 106, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
136 7 0.07
137 3 0.03
138 12 0.11
140 64 0.60
141 20 0.19
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (141 bp):
ATTTTAAAGGAAAAGTTTAAATATTTTAAAACAAAGTTTTGATCTTTTTCAACTATTTCAAAATA
AAGCTTTGATTTTTAAGAAAAATGGTGATTTTTTTTAAAACAGAAAGCTTAGATTTAAAAAAGAA
AACATTTAGCT
Found at i:37088044 original size:16 final size:17
Alignment explanation
Indices: 37088015--37088060 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
37088005 ATAATTTTTA
*
37088015 TTTATTTTTATTTCATC
1 TTTATTTATATTTCATC
*
37088032 TTTATTTAT-TTTCATG
1 TTTATTTATATTTCATC
*
37088048 TCTATTTATATTT
1 TTTATTTATATTT
37088061 ATGGTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.70
Consensus pattern (17 bp):
TTTATTTATATTTCATC
Found at i:37090153 original size:17 final size:18
Alignment explanation
Indices: 37090133--37090166 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
37090123 TTTTTTCATT
37090133 TGACTTTATTT-TTTTAC
1 TGACTTTATTTGTTTTAC
*
37090150 TGACTTTGTTTGTTTTA
1 TGACTTTATTTGTTTTA
37090167 TGTCTGTGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.15, C:0.09, G:0.12, T:0.65
Consensus pattern (18 bp):
TGACTTTATTTGTTTTAC
Found at i:37099253 original size:24 final size:24
Alignment explanation
Indices: 37099225--37099272 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
37099215 ATGAAGAATG
37099225 AATGCAAAATTATGAATTCTTGAT
1 AATGCAAAATTATGAATTCTTGAT
37099249 AATGCAAAATTATGAATTCTTGAT
1 AATGCAAAATTATGAATTCTTGAT
37099273 CTCATTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (24 bp):
AATGCAAAATTATGAATTCTTGAT
Found at i:37099864 original size:10 final size:10
Alignment explanation
Indices: 37099849--37099893 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
37099839 GCCTACACAA
37099849 AAAAAAAACT
1 AAAAAAAACT
37099859 AAAAAAAACT
1 AAAAAAAACT
37099869 AAAAAATAA--
1 AAAAAA-AACT
*
37099878 AAAATAAACT
1 AAAAAAAACT
37099888 AAAAAA
1 AAAAAA
37099894 GATAGAGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
8 2 0.07
9 5 0.17
10 21 0.70
11 2 0.07
ACGTcount: A:0.82, C:0.07, G:0.00, T:0.11
Consensus pattern (10 bp):
AAAAAAAACT
Found at i:37099874 original size:19 final size:20
Alignment explanation
Indices: 37099850--37099893 Score: 58
Period size: 18 Copynumber: 2.3 Consensus size: 20
37099840 CCTACACAAA
37099850 AAAAAAACT-AAAAA-AAACT
1 AAAAAAA-TAAAAAATAAACT
37099869 -AAAAAATAAAAAATAAACT
1 AAAAAAATAAAAAATAAACT
37099888 AAAAAA
1 AAAAAA
37099894 GATAGAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.05
18 11 0.50
19 5 0.23
20 5 0.23
ACGTcount: A:0.82, C:0.07, G:0.00, T:0.11
Consensus pattern (20 bp):
AAAAAAATAAAAAATAAACT
Found at i:37100364 original size:42 final size:42
Alignment explanation
Indices: 37100300--37100562 Score: 343
Period size: 42 Copynumber: 6.3 Consensus size: 42
37100290 AAGGAAAGCA
*
37100300 TTCATTGCATTTAGAGGCCCAGGTGTAGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
37100342 TTCACTGCATTTAGAGGCCCAGGCGTAGAGGTCCGTTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* **
37100384 TTCATTGCATTTAGAAG-CTTGGTTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGG-TGTGGAGGTCCATTTACTT
* *
37100426 TACATTGCATTTAGAGGCCC-GAGTGTGGAGGTCAATTTACTT
1 TTCATTGCATTTAGAGGCCCAG-GTGTGGAGGTCCATTTACTT
** * *
37100468 TTCATTGCATTTAGAATCGCAAGTGTGGAGG-CTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTC-CATTTACTT
*
37100510 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
37100552 TTCATTGCATT
1 TTCATTGCATT
37100563 GTATATGAAG
Statistics
Matches: 192, Mismatches: 23, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
41 4 0.02
42 185 0.96
43 3 0.02
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Found at i:37102341 original size:69 final size:69
Alignment explanation
Indices: 37102230--37102500 Score: 234
Period size: 69 Copynumber: 3.9 Consensus size: 69
37102220 TATTCACACT
* * *
37102230 TATAAGATCAAGGCTTGCAAGCG-AAAAG-CTACAACCCCCAAAACAGTTAGCAATAGCAAAGCT
1 TATAAGATCAAGGCTCGC-AGCGAAAAAGTC-GCAACCCCCAAAACAGTTAGCAAGAGCAAAGCT
37102293 CCTAGC
64 CCTAGC
* * * *
37102299 TATAAGATCAAGGCTTGCAG-GAAAAGAGTCGCAACCCCCAAAATAGTTAACAAAAGCAAAGCTC
1 TATAAGATCAAGGCTCGCAGCGAAAA-AGTCGCAACCCCCAAAACAGTTAGCAAGAGCAAAGCTC
* *
37102363 CCAAC
65 CTAGC
* * * * * * *
37102368 TATCAGATCAAGGCTCACAG-GTGAAAAG-C-C-ACTGCTCTAGAATAGTTAGCAAGAGCAAAGC
1 TATAAGATCAAGGCTCGCAGCG-AAAAAGTCGCAAC--CCCCAAAACAGTTAGCAAGAGCAAAGC
37102429 TCCTAGC
63 TCCTAGC
* * * * *
37102436 TGTAAGGTCAAGGCTCGTAAGCG-AAAAGTCGCAGCTCCCAAAACAGTTAGCAAGAGCAAAGCTC
1 TATAAGATCAAGGCTCG-CAGCGAAAAAGTCGCAACCCCCAAAACAGTTAGCAAGAGCAAAGCTC
37102500 C
65 C
37102501 CAGTTGTAAT
Statistics
Matches: 163, Mismatches: 28, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
66 2 0.01
67 2 0.01
68 51 0.31
69 101 0.62
70 6 0.04
71 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (69 bp):
TATAAGATCAAGGCTCGCAGCGAAAAAGTCGCAACCCCCAAAACAGTTAGCAAGAGCAAAGCTCC
TAGC
Found at i:37102555 original size:69 final size:69
Alignment explanation
Indices: 37102406--37102579 Score: 170
Period size: 69 Copynumber: 2.5 Consensus size: 69
37102396 CCACTGCTCT
* * * * *
37102406 AGAATAGTTAGCAAGAGCAAAGCTCCTAGCTGTAAGGTCAAGGCTCGTAAGCGAAAAGTCGCAGC
1 AGAATAGTTAGCAAGAGCAAAGCTCCCAGCTGTAAGCTAAAGACTCATAAGCGAAAAGTCGCAGC
37102471 TCCC
66 TCCC
* * * * * * **
37102475 AAAACAGTTAGCAAGAGCAAAGCTCCCAGTTGTAATCTAAAGACTCATAGGCGAAGAGTCGTGGC
1 AGAATAGTTAGCAAGAGCAAAGCTCCCAGCTGTAAGCTAAAGACTCATAAGCGAAAAGTCGCAGC
37102540 -CTCC
66 TC-CC
* ** * *
37102544 AGAATAATTAGCGCGAACAAAGCTCCCAGCAGTAAG
1 AGAATAGTTAGCAAGAGCAAAGCTCCCAGCTGTAAG
37102580 ATCAAGGCTC
Statistics
Matches: 82, Mismatches: 22, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
68 1 0.01
69 81 0.99
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (69 bp):
AGAATAGTTAGCAAGAGCAAAGCTCCCAGCTGTAAGCTAAAGACTCATAAGCGAAAAGTCGCAGC
TCCC
Found at i:37102805 original size:58 final size:58
Alignment explanation
Indices: 37102679--37102855 Score: 275
Period size: 58 Copynumber: 3.1 Consensus size: 58
37102669 CTGTAGTATC
* * * *
37102679 AGTATAAAACAGACCGCAAATTCATATTCCTAGCTTATAA-TTTGAGAAAAATCTCTA
1 AGTAAAAAATAGATCGCAAATTCATATTCCCAGCTTATAATTTTGAGAAAAATCTCTA
* *
37102736 TGTAAAAAATAGATCGCGAATTCATATTCCCAGCTTATAATTTTGAGAAAAATCTCTA
1 AGTAAAAAATAGATCGCAAATTCATATTCCCAGCTTATAATTTTGAGAAAAATCTCTA
* *
37102794 AGTAGAAAATAGATCGCAAATTCATGTTCCCAGCTTATAATTTTGAGAAAAATCTCTA
1 AGTAAAAAATAGATCGCAAATTCATATTCCCAGCTTATAATTTTGAGAAAAATCTCTA
37102852 AGTA
1 AGTA
37102856 TCAGACGGCT
Statistics
Matches: 109, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
57 34 0.31
58 75 0.69
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (58 bp):
AGTAAAAAATAGATCGCAAATTCATATTCCCAGCTTATAATTTTGAGAAAAATCTCTA
Found at i:37108212 original size:25 final size:25
Alignment explanation
Indices: 37108182--37108238 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
37108172 AATACACCTA
37108182 TTAGAGATTAGAACTCATAACACAT
1 TTAGAGATTAGAACTCATAACACAT
37108207 TTAGAGATTAGAACTCATAACACAT
1 TTAGAGATTAGAACTCATAACACAT
37108232 TTAGAGA
1 TTAGAGA
37108239 ATTTTTTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (25 bp):
TTAGAGATTAGAACTCATAACACAT
Found at i:37112338 original size:22 final size:22
Alignment explanation
Indices: 37112310--37112395 Score: 127
Period size: 22 Copynumber: 3.9 Consensus size: 22
37112300 ATACTCAACA
37112310 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
37112332 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
* * * **
37112354 CATGAGGGTTTAGTTCGTTAAA
1 CATGAGAGCTTAGTACGTTAGC
37112376 CATGAGAGCTTAGTACGTTA
1 CATGAGAGCTTAGTACGTTA
37112396 TGTGCAAAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 56 1.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:37118337 original size:33 final size:33
Alignment explanation
Indices: 37118295--37118360 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
37118285 TTGCGAGGGT
37118295 GGCGGTTGTTGAGCAGCTAGATTCGTTCGAACA
1 GGCGGTTGTTGAGCAGCTAGATTCGTTCGAACA
37118328 GGCGGTTGTTGAGCAGCTAGATTCGTTCGAACA
1 GGCGGTTGTTGAGCAGCTAGATTCGTTCGAACA
37118361 AACTCTGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.27
Consensus pattern (33 bp):
GGCGGTTGTTGAGCAGCTAGATTCGTTCGAACA
Found at i:37119741 original size:13 final size:13
Alignment explanation
Indices: 37119723--37119750 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
37119713 ATCTTAACCT
37119723 TTTCTATTTGAAC
1 TTTCTATTTGAAC
37119736 TTTCTATTTGAAC
1 TTTCTATTTGAAC
37119749 TT
1 TT
37119751 CCTACTTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.57
Consensus pattern (13 bp):
TTTCTATTTGAAC
Found at i:37125442 original size:42 final size:42
Alignment explanation
Indices: 37125380--37125548 Score: 196
Period size: 42 Copynumber: 4.0 Consensus size: 42
37125370 GTTTTTACTA
* * **
37125380 AAAGCGCCGCTAAAGAACATGACCTTTAACGGCGTTT-TGGCG
1 AAAGCGCCGCTAAAGGACATGTCCTTTAGTGGCGTTTGTGG-G
* * *
37125422 ACAGCGTCGCTAAAGGACATGTCTTTTAGTGGCGTTTGTGGG
1 AAAGCGCCGCTAAAGGACATGTCCTTTAGTGGCGTTTGTGGG
* *
37125464 AAAGCGCCGCTAAAGGTCATGTCCTTTAGTGGCATTTGTGGG
1 AAAGCGCCGCTAAAGGACATGTCCTTTAGTGGCGTTTGTGGG
* * * * *
37125506 AAAGCGCCGCTAAAGGTCATGTTCTATAGTGACGTTTATGGG
1 AAAGCGCCGCTAAAGGACATGTCCTTTAGTGGCGTTTGTGGG
37125548 A
1 A
37125549 GGTGTCGCTA
Statistics
Matches: 109, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
42 106 0.97
43 3 0.03
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (42 bp):
AAAGCGCCGCTAAAGGACATGTCCTTTAGTGGCGTTTGTGGG
Found at i:37125517 original size:84 final size:84
Alignment explanation
Indices: 37125380--37125568 Score: 204
Period size: 84 Copynumber: 2.3 Consensus size: 84
37125370 GTTTTTACTA
** * * * *
37125380 AAAGCGCCGCTAAAGAACATGACCTTTAACGGCGTTTTGGCGACAGCGTCGCTAAAGGACATG-T
1 AAAGCGCCGCTAAAGGTCATGTCCTTTAACGGCATTTTGGCGAAAGCGCCGCTAAAGGACATGTT
* * *
37125444 CTTTTAGTGGCGTTTGTGGG
66 C-TATAGTGACGTTTATGGG
** *
37125464 AAAGCGCCGCTAAAGGTCATGTCCTTTAGTGGCATTTGTGG-GAAAGCGCCGCTAAAGGTCATGT
1 AAAGCGCCGCTAAAGGTCATGTCCTTTAACGGCATTT-TGGCGAAAGCGCCGCTAAAGGACATGT
37125528 TCTATAGTGACGTTTATGGG
65 TCTATAGTGACGTTTATGGG
* * *
37125548 -AGGTGTCGCTAAAGGTCATGT
1 AAAGCGCCGCTAAAGGTCATGT
37125569 TCTATAGCTG
Statistics
Matches: 88, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
83 18 0.20
84 65 0.74
85 5 0.06
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.28
Consensus pattern (84 bp):
AAAGCGCCGCTAAAGGTCATGTCCTTTAACGGCATTTTGGCGAAAGCGCCGCTAAAGGACATGTT
CTATAGTGACGTTTATGGG
Found at i:37125569 original size:41 final size:42
Alignment explanation
Indices: 37125410--37125575 Score: 185
Period size: 42 Copynumber: 4.0 Consensus size: 42
37125400 GACCTTTAAC
* * * *
37125410 GGCGTTT-TGGCGACAGCGTCGCTAAAGGACATG-TCTTTTAGT
1 GGCGTTTGTGG-GAAAGCGCCGCTAAAGGTCATGTTC-TATAGT
* *
37125452 GGCGTTTGTGGGAAAGCGCCGCTAAAGGTCATGTCCTTTAGT
1 GGCGTTTGTGGGAAAGCGCCGCTAAAGGTCATGTTCTATAGT
*
37125494 GGCATTTGTGGGAAAGCGCCGCTAAAGGTCATGTTCTATAGT
1 GGCGTTTGTGGGAAAGCGCCGCTAAAGGTCATGTTCTATAGT
* * * * *
37125536 GACGTTTATGGG-AGGTGTCGCTAAAGGTCATGTTCTATAG
1 GGCGTTTGTGGGAAAGCGCCGCTAAAGGTCATGTTCTATAG
37125576 CTGCATTTTT
Statistics
Matches: 109, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
41 25 0.23
42 80 0.73
43 4 0.04
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (42 bp):
GGCGTTTGTGGGAAAGCGCCGCTAAAGGTCATGTTCTATAGT
Found at i:37125832 original size:29 final size:30
Alignment explanation
Indices: 37125791--37125849 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
37125781 TTTTGTTCAA
37125791 TGTGCAATATTATATA-TAAAT-TTCAATTT
1 TGTGCAATATTATATATTAAATGTT-AATTT
* *
37125820 TGTGTAATTTTATATATTAAATGTTAATTT
1 TGTGCAATATTATATATTAAATGTTAATTT
37125850 GATCTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 14 0.54
30 10 0.38
31 2 0.08
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.53
Consensus pattern (30 bp):
TGTGCAATATTATATATTAAATGTTAATTT
Found at i:37125858 original size:30 final size:29
Alignment explanation
Indices: 37125800--37125860 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
37125790 ATGTGCAATA
*
37125800 TTATATATAAATTTCAATTTTGTGTAATT
1 TTATATATAAATTTCAATTTTGTCTAATT
37125829 TTATATATTAAATGTT-AA-TTTGATCTAATT
1 TTATATA-TAAAT-TTCAATTTTG-TCTAATT
37125859 TT
1 TT
37125861 CAAAAATCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 11 0.39
30 15 0.54
31 2 0.07
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.56
Consensus pattern (29 bp):
TTATATATAAATTTCAATTTTGTCTAATT
Found at i:37127672 original size:22 final size:22
Alignment explanation
Indices: 37127647--37127688 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
37127637 CAATTTAATC
* *
37127647 TAATTTAATATATATTTCATTT
1 TAATATAATACATATTTCATTT
*
37127669 TAATATCATACATATTTCAT
1 TAATATAATACATATTTCAT
37127689 GTGTTATTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (22 bp):
TAATATAATACATATTTCATTT
Found at i:37128552 original size:18 final size:19
Alignment explanation
Indices: 37128524--37128573 Score: 84
Period size: 18 Copynumber: 2.7 Consensus size: 19
37128514 AGAATTTCTG
*
37128524 AAAATTCAAAAAATACATA
1 AAAATTCAAAAAACACATA
37128543 AAAATT-AAAAAACACATA
1 AAAATTCAAAAAACACATA
37128561 AAAATTCAAAAAA
1 AAAATTCAAAAAA
37128574 AAAAATAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 17 0.59
19 12 0.41
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.18
Consensus pattern (19 bp):
AAAATTCAAAAAACACATA
Found at i:37137120 original size:20 final size:19
Alignment explanation
Indices: 37137092--37137143 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
37137082 AATTACGGTT
*
37137092 TTAATTGAGAAATTTGTAAAA
1 TTAA-TGAGAAATGTGT-AAA
* *
37137113 TTCATGAGTAAATGTGTGAA
1 TTAATGAG-AAATGTGTAAA
37137133 TTAATGAGAAA
1 TTAATGAGAAA
37137144 AATGGTCTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 3 0.12
20 13 0.50
21 10 0.38
ACGTcount: A:0.44, C:0.02, G:0.19, T:0.35
Consensus pattern (19 bp):
TTAATGAGAAATGTGTAAA
Found at i:37137546 original size:20 final size:20
Alignment explanation
Indices: 37137521--37137562 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
37137511 TTAAAATTCA
* *
37137521 AATTACTGATTATATGATTG
1 AATTACTGATTACATGAATG
*
37137541 AATTACTGTTTACATGAATG
1 AATTACTGATTACATGAATG
37137561 AA
1 AA
37137563 AGTGAAATGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.40
Consensus pattern (20 bp):
AATTACTGATTACATGAATG
Found at i:37137879 original size:23 final size:23
Alignment explanation
Indices: 37137853--37137912 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
37137843 CTCATTGGAA
37137853 CTTACCATTTCAGCTAGT-ATGAG
1 CTTACCATTTCAGCTAGTCA-GAG
*
37137876 CTTA-C-TGTTCAGCTCGTCAGAG
1 CTTACCAT-TTCAGCTAGTCAGAG
*
37137898 CTTACCATTTTAGCT
1 CTTACCATTTCAGCT
37137913 TAATAGAGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
21 1 0.03
22 17 0.55
23 12 0.39
24 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.37
Consensus pattern (23 bp):
CTTACCATTTCAGCTAGTCAGAG
Found at i:37138122 original size:20 final size:21
Alignment explanation
Indices: 37138092--37138132 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
37138082 TATGAATAAG
37138092 ATATGTGTTTATACAGATGAA
1 ATATGTGTTTATACAGATGAA
*
37138113 ATAT-TGTTTATACGGATGAA
1 ATATGTGTTTATACAGATGAA
37138133 CCACTGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.39
Consensus pattern (21 bp):
ATATGTGTTTATACAGATGAA
Found at i:37138140 original size:20 final size:20
Alignment explanation
Indices: 37138097--37138144 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
37138087 ATAAGATATG
* *
37138097 TGTTTATACAGATGAAATAT
1 TGTTTATACAGATGAAACAC
* *
37138117 TGTTTATACGGATGAACCAC
1 TGTTTATACAGATGAAACAC
37138137 TGTTTATA
1 TGTTTATA
37138145 TGAATGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (20 bp):
TGTTTATACAGATGAAACAC
Found at i:37139097 original size:13 final size:13
Alignment explanation
Indices: 37139079--37139103 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37139069 ATATGTTTGG
37139079 ATATGAAATTGAT
1 ATATGAAATTGAT
37139092 ATATGAAATTGA
1 ATATGAAATTGA
37139104 GATTGAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (13 bp):
ATATGAAATTGAT
Found at i:37144573 original size:20 final size:19
Alignment explanation
Indices: 37144545--37144596 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
37144535 AATTACGGTT
*
37144545 TTAATTGAGAAATTTGTAAAA
1 TTAA-TGAGAAATGTGT-AAA
* *
37144566 TTCATGAGTAAATGTGTGAA
1 TTAATGAG-AAATGTGTAAA
37144586 TTAATGAGAAA
1 TTAATGAGAAA
37144597 AATAGGCTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 3 0.12
20 13 0.50
21 10 0.38
ACGTcount: A:0.44, C:0.02, G:0.19, T:0.35
Consensus pattern (19 bp):
TTAATGAGAAATGTGTAAA
Found at i:37145384 original size:22 final size:22
Alignment explanation
Indices: 37145310--37145397 Score: 83
Period size: 22 Copynumber: 3.9 Consensus size: 22
37145300 TATCGATATA
*
37145310 TCAGCTCGTAAGAGCTTACTGTTT
1 TCAGCTCGTATGAGCTTACTG--T
*
37145334 TCAGCTCAT-TGGAGCTTACCAT-T
1 TCAGCTCGTAT-GAGCTTA-C-TGT
37145357 TCAGCTCGTATGAGCTTACTGT
1 TCAGCTCGTATGAGCTTACTGT
37145379 TCAGCTCGTCA-GAGCTTAC
1 TCAGCTCGT-ATGAGCTTAC
37145398 CATTTTAGCT
Statistics
Matches: 55, Mismatches: 3, Indels: 14
0.76 0.04 0.19
Matches are distributed among these distances:
21 1 0.02
22 19 0.35
23 17 0.31
24 16 0.29
25 1 0.02
26 1 0.02
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.34
Consensus pattern (22 bp):
TCAGCTCGTATGAGCTTACTGT
Found at i:37145397 original size:45 final size:46
Alignment explanation
Indices: 37145310--37145408 Score: 137
Period size: 45 Copynumber: 2.2 Consensus size: 46
37145300 TATCGATATA
**
37145310 TCAGCTCGTAAGAGCTTACTGTTTTCAGCTCATTGGAGCTTACCATT
1 TCAGCTCGTAAGAGCTTACTG-TTTCAGCTCATCAGAGCTTACCATT
* *
37145357 TCAGCTCGTATGAGCTTACTG-TTCAGCTCGTCAGAGCTTACCATT
1 TCAGCTCGTAAGAGCTTACTGTTTCAGCTCATCAGAGCTTACCATT
*
37145402 TTAGCTC
1 TCAGCTC
37145409 AATAGAGCAT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 27 0.57
47 20 0.43
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.35
Consensus pattern (46 bp):
TCAGCTCGTAAGAGCTTACTGTTTCAGCTCATCAGAGCTTACCATT
Found at i:37145416 original size:23 final size:22
Alignment explanation
Indices: 37145310--37145408 Score: 85
Period size: 23 Copynumber: 4.3 Consensus size: 22
37145300 TATCGATATA
**
37145310 TCAGCTCGTAAGAGCTTACTGTTT
1 TCAGCTCGT-AGAGCTTAC-CATT
* *
37145334 TCAGCTCATTGGAGCTTACCATT
1 TCAGCTC-GTAGAGCTTACCATT
37145357 TCAGCTCGTATGAGCTTA-C-TGT
1 TCAGCTCGTA-GAGCTTACCAT-T
37145379 TCAGCTCGTCAGAGCTTACCATT
1 TCAGCTCGT-AGAGCTTACCATT
*
37145402 TTAGCTC
1 TCAGCTC
37145409 AATAGAGCAT
Statistics
Matches: 62, Mismatches: 7, Indels: 13
0.76 0.09 0.16
Matches are distributed among these distances:
21 1 0.02
22 19 0.31
23 25 0.40
24 16 0.26
25 1 0.02
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.35
Consensus pattern (22 bp):
TCAGCTCGTAGAGCTTACCATT
Found at i:37145617 original size:20 final size:20
Alignment explanation
Indices: 37145593--37145664 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
37145583 TAAAATATGT
*
37145593 GTTTATACGAATGAATTATT
1 GTTTATACGAATGAATTATA
* **
37145613 GTTTATACGGATGAACCACTA
1 GTTTATACGAATGAATTA-TA
* *
37145634 G-TTATATGAATGAATTACA
1 GTTTATACGAATGAATTATA
37145653 GTTTATACGAAT
1 GTTTATACGAAT
37145665 AGAAATGAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
19 2 0.05
20 36 0.90
21 2 0.05
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.38
Consensus pattern (20 bp):
GTTTATACGAATGAATTATA
Found at i:37159713 original size:2 final size:2
Alignment explanation
Indices: 37159706--37159748 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
37159696 TTGCTCATGA
37159706 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37159748 A
1 A
37159749 CACATGTACC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:37167088 original size:45 final size:45
Alignment explanation
Indices: 37167020--37167122 Score: 143
Period size: 45 Copynumber: 2.3 Consensus size: 45
37167010 TTGGACTATC
* * * * *
37167020 CACCATGTTTGTTTGCCATTTGGATTGTTCATCATTTATGTTGTT
1 CACCATGTGTGTTTGCCAATTGGACTATTCACCATTTATGTTGTT
* *
37167065 CTCCATGTGTGTTTGCCAATTGGACTATTCGCCATTTATGTTGTT
1 CACCATGTGTGTTTGCCAATTGGACTATTCACCATTTATGTTGTT
37167110 CACCATGTGTGTT
1 CACCATGTGTGTT
37167123 CACCATTGCA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.16, C:0.18, G:0.19, T:0.47
Consensus pattern (45 bp):
CACCATGTGTGTTTGCCAATTGGACTATTCACCATTTATGTTGTT
Found at i:37170837 original size:25 final size:25
Alignment explanation
Indices: 37170777--37170847 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
37170767 TGTACTTTAG
37170777 CTTGTGAGAGCTTACCGATTCTCAA
1 CTTGTGAGAGCTTACCGATTCTCAA
* *
37170802 CTCGT-ATGAGCTTACCGATT-TACAG
1 CTTGTGA-GAGCTTACCGATTCT-CAA
* *
37170827 GTTGTGAGAGCATACCGATTC
1 CTTGTGAGAGCTTACCGATTC
37170848 ATAGCTCGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
24 2 0.05
25 34 0.92
26 1 0.03
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (25 bp):
CTTGTGAGAGCTTACCGATTCTCAA
Found at i:37187680 original size:44 final size:44
Alignment explanation
Indices: 37187601--37188208 Score: 224
Period size: 44 Copynumber: 13.8 Consensus size: 44
37187591 GCCACCAAAC
* * * *
37187601 CTTATCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGTAGAT
* * **
37187645 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA-CGGCGAAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGTAG-AT
* * ***** *
37187689 CTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCA-AA
1 CTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGATTGTAGAT
* * * * * *
37187732 CATTGTCTCCCTGAGCAGCAGTAGAGAAGGTTGAAGATTGTAGAT
1 C-TTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGTAGAT
* * **
37187777 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA-CGGCGAAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGTAG-AT
* * * ***** * *
37187821 CTTATCTTTCC-AAG-A-TAGTGGGAAGCACATTTAAGCCACCAAAC
1 CTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGATTGTAGAT
* * * *
37187865 CTTATCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGTAGAT
* * **
37187909 CTTATCTCCCTAAGCAGTAGTGGAGCAGATGGAAGA-CGGCGAAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGTAG-AT
* * * ***** * *
37187953 CTTATCTTTCC-AAG-A-TAGTGGGAAGCACATTTAAGCCACCAAAC
1 CTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGATTGTAGAT
* * * *
37187997 CTTATCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGTAGAT
* * **
37188041 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA-CGGCGAAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGTAG-AT
* * ***** * *
37188085 CTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAAAC
1 CTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGATTGTAGAT
* * ** * *
37188129 CTTGTCTCCCTGAGCAGCGGTGGAGAAGGTTGAAGATTGTAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGTAGAT
* * *
37188173 ATTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGA
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA
37188209 CGGCAAATCT
Statistics
Matches: 389, Mismatches: 141, Indels: 68
0.65 0.24 0.11
Matches are distributed among these distances:
42 16 0.04
43 34 0.09
44 303 0.78
45 25 0.06
46 11 0.03
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.24
Consensus pattern (44 bp):
CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGTAGAT
Found at i:37187746 original size:132 final size:132
Alignment explanation
Indices: 37187509--37188289 Score: 1393
Period size: 132 Copynumber: 5.9 Consensus size: 132
37187499 GTGAAACACC
* *
37187509 AGATCATATCTCCCTAAGCAGTAGTGGAGCGGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
37187574 GTGGGAAGCAGATTTAAGCCACCAAACCTTATCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATT
66 GTGGGAAGCAGATTTAAGCCACCAAACCTTATCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATT
37187639 GT
131 GT
37187641 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
* * *
37187706 GTGGGAAGCAGATTTAAGCCACCAAACATTGTCTCCCTGAGCAGCAGTAGAGAAGGTTGAAGATT
66 GTGGGAAGCAGATTTAAGCCACCAAACCTTATCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATT
37187771 GT
131 GT
37187773 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
*
37187838 GTGGGAAGCACATTTAAGCCACCAAACCTTATCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATT
66 GTGGGAAGCAGATTTAAGCCACCAAACCTTATCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATT
37187903 GT
131 GT
*
37187905 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATGGAAGACGGCGAATCTTATCTTTCCAAGATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
*
37187970 GTGGGAAGCACATTTAAGCCACCAAACCTTATCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATT
66 GTGGGAAGCAGATTTAAGCCACCAAACCTTATCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATT
37188035 GT
131 GT
37188037 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
* *
37188102 GTGGGAAGCAGATTTAAGCCACCAAACCTTGTCTCCCTGAGCAGCGGTGGAGAAGGTTGAAGATT
66 GTGGGAAGCAGATTTAAGCCACCAAACCTTATCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATT
37188167 GT
131 GT
* * *
37188169 AGATATTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGACGGCAAATCTTATCTTTCCAAGATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
* * * * *
37188234 GTGGGAAGCAGATTT-AGCCACCAAGCCTTGTCTCCCTAAGCAGTAGTGGAGCAGGT
66 GTGGGAAGCAGATTTAAGCCACCAAACCTTATCTCCCTGAGCAGCAGTGGAGAAGGT
37188290 CGTACCCAAT
Statistics
Matches: 627, Mismatches: 22, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
131 36 0.06
132 591 0.94
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (132 bp):
AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
GTGGGAAGCAGATTTAAGCCACCAAACCTTATCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATT
GT
Found at i:37189743 original size:33 final size:31
Alignment explanation
Indices: 37189681--37189743 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
37189671 AGTCCTTTTT
* ** *
37189681 TATATATTTCTCTTAAAATCAATATTTTATG
1 TATATATTTCTCTAAAAAAAAATAATTTATG
37189712 TATATATTTCTACTAAAAAAAACATAATTTAT
1 TATATATTTCT-CTAAAAAAAA-ATAATTTAT
37189744 ATTCACATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 11 0.42
32 7 0.27
33 8 0.31
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.46
Consensus pattern (31 bp):
TATATATTTCTCTAAAAAAAAATAATTTATG
Found at i:37208861 original size:111 final size:110
Alignment explanation
Indices: 37208667--37208889 Score: 392
Period size: 111 Copynumber: 2.0 Consensus size: 110
37208657 AAATTGTACC
* *
37208667 TTTCCAATTCGTCTAGGATAAACGCTTCGACCAAGTAGTCTTCTCCATTATCCTCAAGCTCATAT
1 TTTCCAATTCGTCTAGGATAAAAGCTTCGACCAAGTAGTCTTCTCCATTATCCTCAAGCTCACAT
37208732 CTACCGAGTGTGGGCTCACTTTGAACCAAAAAAATTTTCACAAAAA
66 CTACCGAGTGTGGGCTCACTTTGAACC-AAAAAATTTTCACAAAAA
*
37208778 TTTCCAATTTGTCTAGGATAAAAGCTTCGACCAAGTAGTCTTCTCCATTATCCTCAAGCTCACAT
1 TTTCCAATTCGTCTAGGATAAAAGCTTCGACCAAGTAGTCTTCTCCATTATCCTCAAGCTCACAT
**
37208843 CTGTCGAGTGTGGGCTCACTTTGAACCAAAAAATTTTCACAAAAA
66 CTACCGAGTGTGGGCTCACTTTGAACCAAAAAATTTTCACAAAAA
37208888 TT
1 TT
37208890 ACTAGTGGCA
Statistics
Matches: 107, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
110 20 0.19
111 87 0.81
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (110 bp):
TTTCCAATTCGTCTAGGATAAAAGCTTCGACCAAGTAGTCTTCTCCATTATCCTCAAGCTCACAT
CTACCGAGTGTGGGCTCACTTTGAACCAAAAAATTTTCACAAAAA
Found at i:37209205 original size:61 final size:58
Alignment explanation
Indices: 37209097--37209208 Score: 152
Period size: 61 Copynumber: 1.9 Consensus size: 58
37209087 ATCACTTTAA
* * *
37209097 TATTCAATTAATATAATACTTTCCAAGATAAATATTAGATTAAATTTAATACTAAATC
1 TATTAAATTAATAGAATACTTTCCAAGATAAATATTAAATTAAATTTAATACTAAATC
* *
37209155 TATTAAATTAATAGAATACTTATCTACAATATAAATATTAAATTAGATTTAATA
1 TATTAAATTAATAGAATACTT-TC--CAAGATAAATATTAAATTAAATTTAATA
37209209 TTAAGATAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
58 19 0.41
59 2 0.04
61 25 0.54
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (58 bp):
TATTAAATTAATAGAATACTTTCCAAGATAAATATTAAATTAAATTTAATACTAAATC
Found at i:37220007 original size:130 final size:130
Alignment explanation
Indices: 37219741--37219996 Score: 404
Period size: 130 Copynumber: 2.0 Consensus size: 130
37219731 CCTTAGCTAA
* * * * *
37219741 ATTTTTAAGGATTTTTTATAAATGAGTAGTCTGTTTAGAAATTTAAATTGCAAAAAACCAAACAA
1 ATTTTTAAGGATTTCTTATAAATGAGTAGTCTGCTCAGAAATTTAAACTGCAAAAAACCAAAAAA
*
37219806 TTAGTGACTTAAGGCCCTTGCTGTAAGAATGATTAAATTTTAAAGTTCACTTTTTTAGAAAATAC
66 TTAGTGACTTAAGGCCCTTGCTGTAAGAATGATTAAATTTTAAAATTCACTTTTTTAGAAAATAC
* * *
37219871 ATTTTTAAGGATTTCTTGTAAATGAGTAGTCTGCTCAGAAATTTGAACTGCGAAAAACCAAAAAA
1 ATTTTTAAGGATTTCTTATAAATGAGTAGTCTGCTCAGAAATTTAAACTGCAAAAAACCAAAAAA
* * *
37219936 TTAGTGACTTAAGGCCCTTGTTGTAAGAGTGATTAAATTTTAAAATTCAGTTTTTTAGAAA
66 TTAGTGACTTAAGGCCCTTGCTGTAAGAATGATTAAATTTTAAAATTCACTTTTTTAGAAA
37219997 GTTTTATTTT
Statistics
Matches: 114, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
130 114 1.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.37
Consensus pattern (130 bp):
ATTTTTAAGGATTTCTTATAAATGAGTAGTCTGCTCAGAAATTTAAACTGCAAAAAACCAAAAAA
TTAGTGACTTAAGGCCCTTGCTGTAAGAATGATTAAATTTTAAAATTCACTTTTTTAGAAAATAC
Found at i:37221350 original size:28 final size:28
Alignment explanation
Indices: 37221311--37221368 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
37221301 ATAAAAAAAA
37221311 TTCATTACATTAATATACTTTGTATAAT
1 TTCATTACATTAATATACTTTGTATAAT
*
37221339 TTCATTATATTAATATACTTTGTATAAT
1 TTCATTACATTAATATACTTTGTATAAT
37221367 TT
1 TT
37221369 TTGTCATATG
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:0.34, C:0.09, G:0.03, T:0.53
Consensus pattern (28 bp):
TTCATTACATTAATATACTTTGTATAAT
Found at i:37224950 original size:54 final size:54
Alignment explanation
Indices: 37224861--37225047 Score: 198
Period size: 54 Copynumber: 3.5 Consensus size: 54
37224851 ACATGCCAGA
*
37224861 AAAAGGAAGCCTTTGTAGCGATCTAAGAAAAGAAAGCCTTTGTGTTTATCTATG
1 AAAAGGAAGCCTTTGTGGCGATCTAAGAAAAGAAAGCCTTTGTGTTTATCTATG
* * * * * *
37224915 AAAAGAAAGCCTTTGTGGCGATCTAACAAATGAAAGTCTTTATGGATTT-T-AATG
1 AAAAGGAAGCCTTTGTGGCGATCTAAGAAAAGAAAGCCTTTGT-G-TTTATCTATG
* * * * **
37224969 AAAAGGAAGCCTTTATGGCTATCTATGAAAAGAAAACCTTTGTGGCTATCTATG
1 AAAAGGAAGCCTTTGTGGCGATCTAAGAAAAGAAAGCCTTTGTGTTTATCTATG
* * *
37225023 ACAAGGAAGCCTTCGTGGTGATCTA
1 AAAAGGAAGCCTTTGTGGCGATCTA
37225048 TGAAGGGAAT
Statistics
Matches: 105, Mismatches: 24, Indels: 8
0.77 0.18 0.06
Matches are distributed among these distances:
52 1 0.01
53 2 0.02
54 97 0.92
55 2 0.02
56 3 0.03
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (54 bp):
AAAAGGAAGCCTTTGTGGCGATCTAAGAAAAGAAAGCCTTTGTGTTTATCTATG
Found at i:37225048 original size:27 final size:27
Alignment explanation
Indices: 37224861--37225051 Score: 161
Period size: 27 Copynumber: 7.1 Consensus size: 27
37224851 ACATGCCAGA
* * *
37224861 AAAAGGAAGCCTTTGTAGCGATCTAAG
1 AAAAGGAAGCCTTTGTGGCTATCTATG
* **
37224888 AAAAGAAAGCCTTTGTGTTTATCTATG
1 AAAAGGAAGCCTTTGTGGCTATCTATG
* * **
37224915 AAAAGAAAGCCTTTGTGGCGATCTAAC
1 AAAAGGAAGCCTTTGTGGCTATCTATG
* * * * * *
37224942 AAATGAAAGTCTTTATGGAT-TTTAATG
1 AAAAGGAAGCCTTTGTGGCTATCT-ATG
*
37224969 AAAAGGAAGCCTTTATGGCTATCTATG
1 AAAAGGAAGCCTTTGTGGCTATCTATG
* *
37224996 AAAAGAAAACCTTTGTGGCTATCTATG
1 AAAAGGAAGCCTTTGTGGCTATCTATG
* *
37225023 ACAAGGAAGCCTTCGTGG-TGATCTATG
1 AAAAGGAAGCCTTTGTGGCT-ATCTATG
37225050 AA
1 AA
37225052 GGGAATGCCC
Statistics
Matches: 129, Mismatches: 32, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
26 3 0.02
27 124 0.96
28 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (27 bp):
AAAAGGAAGCCTTTGTGGCTATCTATG
Found at i:37240732 original size:23 final size:22
Alignment explanation
Indices: 37240688--37240732 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
37240678 TAAAGAATTT
*
37240688 TTTTAGGGCTGAAAATATTATA
1 TTTTAGGGCTGAAAATAATATA
37240710 TTTTA-GGCTTGAAAATCAATATA
1 TTTTAGGGC-TGAAAAT-AATATA
37240733 AATCAAGGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 3 0.15
22 12 0.60
23 5 0.25
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.40
Consensus pattern (22 bp):
TTTTAGGGCTGAAAATAATATA
Found at i:37254963 original size:85 final size:84
Alignment explanation
Indices: 37254821--37254993 Score: 337
Period size: 85 Copynumber: 2.0 Consensus size: 84
37254811 AGCCCAGCAC
37254821 TCCACCAACATTGTTTATTTAGCATTCCAGCGTTTCGTGCTCACAAGCATTTACCAGAAATGATT
1 TCCACCAACATTGTTTATTTAGCATTCCAGCGTTTCGTGCTCACAAGCATTTACCAGAAATGATT
37254886 TGTAATGTTGCTACTAAGA
66 TGTAATGTTGCTACTAAGA
37254905 TCCACCAACATTGTTTATTTTAGCATTCCAGCGTTTCGTGCTCACAAGCATTTACCAGAAATGAT
1 TCCACCAACATTGTTTA-TTTAGCATTCCAGCGTTTCGTGCTCACAAGCATTTACCAGAAATGAT
37254970 TTGTAATGTTGCTACTAAGA
65 TTGTAATGTTGCTACTAAGA
37254990 TCCA
1 TCCA
37254994 TCATGCATTG
Statistics
Matches: 88, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
84 17 0.19
85 71 0.81
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (84 bp):
TCCACCAACATTGTTTATTTAGCATTCCAGCGTTTCGTGCTCACAAGCATTTACCAGAAATGATT
TGTAATGTTGCTACTAAGA
Found at i:37255172 original size:34 final size:34
Alignment explanation
Indices: 37255129--37255195 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
37255119 CCATGTTCTG
37255129 CACCAATCAACTCAACAGTACATTATACAAATTT
1 CACCAATCAACTCAACAGTACATTATACAAATTT
*
37255163 CACCAATCAACTCAACAGTACATTATGCAAATT
1 CACCAATCAACTCAACAGTACATTATACAAATT
37255196 CCAATTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.43, C:0.27, G:0.04, T:0.25
Consensus pattern (34 bp):
CACCAATCAACTCAACAGTACATTATACAAATTT
Found at i:37262661 original size:24 final size:24
Alignment explanation
Indices: 37262634--37262684 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
37262624 ATAGATAGGA
37262634 TACAAATGACATGTCATTAGGGGT
1 TACAAATGACATGTCATTAGGGGT
37262658 TACAAATGACATGTCATTAGGGGT
1 TACAAATGACATGTCATTAGGGGT
37262682 TAC
1 TAC
37262685 CATGATTTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (24 bp):
TACAAATGACATGTCATTAGGGGT
Found at i:37265923 original size:9 final size:9
Alignment explanation
Indices: 37265911--37265972 Score: 52
Period size: 9 Copynumber: 6.7 Consensus size: 9
37265901 TATTAAAAAC
37265911 GAGAGACTT
1 GAGAGACTT
*
37265920 GAGAAACTT
1 GAGAGACTT
**
37265929 GAGAAGGTTT
1 GAG-AGACTT
*
37265939 GAGAGATTTT
1 GAGAGA-CTT
*
37265949 GAGAGAATT
1 GAGAGACTT
*
37265958 GAGAGAGTT
1 GAGAGACTT
37265967 GAGAGA
1 GAGAGA
37265973 ATGATATGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
9 29 0.66
10 15 0.34
ACGTcount: A:0.37, C:0.03, G:0.35, T:0.24
Consensus pattern (9 bp):
GAGAGACTT
Found at i:37265970 original size:18 final size:19
Alignment explanation
Indices: 37265937--37265974 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
37265927 TTGAGAAGGT
*
37265937 TTGAGAGATTTTGAGAGAA
1 TTGAGAGATGTTGAGAGAA
37265956 TTGAGAGA-GTTGAGAGAA
1 TTGAGAGATGTTGAGAGAA
37265974 T
1 T
37265975 GATATGAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.34, T:0.29
Consensus pattern (19 bp):
TTGAGAGATGTTGAGAGAA
Found at i:37278757 original size:25 final size:26
Alignment explanation
Indices: 37278723--37278773 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
37278713 AAGTTGTAAA
37278723 TAAAAAAATATC-TCTAGA-AATTTTC
1 TAAAAAAATATCTTC-AGAGAATTTTC
*
37278748 TAAAATAATATCTTCAGAGAATTTTC
1 TAAAAAAATATCTTCAGAGAATTTTC
37278774 CCTCTACAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.37
Consensus pattern (26 bp):
TAAAAAAATATCTTCAGAGAATTTTC
Found at i:37278888 original size:21 final size:22
Alignment explanation
Indices: 37278862--37278915 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
37278852 ATTCAACTAT
*
37278862 TATTAAACTTAAT-CACTTTAA
1 TATTAAACTTAATACAATTTAA
*
37278883 TATTAAA-TTAATATAATTTAA
1 TATTAAACTTAATACAATTTAA
37278904 TATTAAATCTTA
1 TATTAAA-CTTA
37278916 TTAAAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 5 0.18
21 20 0.71
23 3 0.11
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (22 bp):
TATTAAACTTAATACAATTTAA
Found at i:37278895 original size:11 final size:11
Alignment explanation
Indices: 37278879--37278911 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
37278869 CTTAATCACT
37278879 TTAATATTAAA
1 TTAATATTAAA
*
37278890 TTAATA-TAAT
1 TTAATATTAAA
37278900 TTAATATTAAA
1 TTAATATTAAA
37278911 T
1 T
37278912 CTTATTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:37279182 original size:18 final size:18
Alignment explanation
Indices: 37279156--37279190 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
37279146 CCGCTGTTGA
*
37279156 CCATCGGGATGTCATCGG
1 CCATCGGGATGCCATCGG
*
37279174 CCATTGGGATGCCATCG
1 CCATCGGGATGCCATCG
37279191 TCGCAGCCAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.29, G:0.31, T:0.23
Consensus pattern (18 bp):
CCATCGGGATGCCATCGG
Found at i:37285773 original size:13 final size:12
Alignment explanation
Indices: 37285755--37285788 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
37285745 TACATAATAT
37285755 AAATATTATAAAC
1 AAATA-TATAAAC
37285768 AAATATA-AAAC
1 AAATATATAAAC
37285779 AAATATATAA
1 AAATATATAA
37285789 GGAGATAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 11 0.55
12 4 0.20
13 5 0.25
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (12 bp):
AAATATATAAAC
Found at i:37289512 original size:5 final size:5
Alignment explanation
Indices: 37289502--37289538 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
37289492 TTTTTAGAGT
*
37289502 AATAA AATAA AATAA CATAA AATAA AAT-A AATAA AAT
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AAT
37289539 TCAAGAGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 4 0.14
5 25 0.86
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (5 bp):
AATAA
Found at i:37289523 original size:15 final size:14
Alignment explanation
Indices: 37289502--37289538 Score: 65
Period size: 15 Copynumber: 2.6 Consensus size: 14
37289492 TTTTTAGAGT
37289502 AATAAAATAAAATA
1 AATAAAATAAAATA
37289516 ACATAAAATAAAATA
1 A-ATAAAATAAAATA
37289531 AATAAAAT
1 AATAAAAT
37289539 TCAAGAGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (14 bp):
AATAAAATAAAATA
Found at i:37300797 original size:31 final size:29
Alignment explanation
Indices: 37300733--37300801 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
37300723 ACGATAACGT
* *
37300733 AAGTGACTAAAACGTAATATTTCAAACAT
1 AAGTGACTAAAACGTAATATTGCAAACAA
* *
37300762 AAGTGACTAAAATGTAATCTTAGGCAAACAA
1 AAGTGACTAAAACGTAATATT--GCAAACAA
37300793 AAGTGACTA
1 AAGTGACTA
37300802 TTTTGAGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.56
31 15 0.44
ACGTcount: A:0.48, C:0.13, G:0.14, T:0.25
Consensus pattern (29 bp):
AAGTGACTAAAACGTAATATTGCAAACAA
Found at i:37310909 original size:14 final size:14
Alignment explanation
Indices: 37310890--37310916 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
37310880 CTAAATATGA
37310890 TAATCCAATTCAAT
1 TAATCCAATTCAAT
37310904 TAATCCAATTCAA
1 TAATCCAATTCAA
37310917 CATCTTAAAA
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:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (14 bp):
TAATCCAATTCAAT
Found at i:37318645 original size:35 final size:35
Alignment explanation
Indices: 37318604--37318688 Score: 143
Period size: 35 Copynumber: 2.4 Consensus size: 35
37318594 GATTTTCTTC
*
37318604 CAAATTATTATTCATTCATTCATAATGATATGGTA
1 CAAATTATTATTCATTCATTCATAATCATATGGTA
*
37318639 CAAATTATTATTCATTCATTCGTAATCATATGGTA
1 CAAATTATTATTCATTCATTCATAATCATATGGTA
*
37318674 CAAATAATTATTCAT
1 CAAATTATTATTCAT
37318689 GAATTTATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 47 1.00
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (35 bp):
CAAATTATTATTCATTCATTCATAATCATATGGTA
Found at i:37319439 original size:16 final size:15
Alignment explanation
Indices: 37319420--37319454 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
37319410 AATCAAATAA
*
37319420 AAAAATAAAAAAGGTG
1 AAAAACAAAAAA-GTG
37319436 AAAAACAAAAAAGTG
1 AAAAACAAAAAAGTG
37319451 AAAA
1 AAAA
37319455 TGGAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.74, C:0.03, G:0.14, T:0.09
Consensus pattern (15 bp):
AAAAACAAAAAAGTG
Found at i:37319484 original size:23 final size:21
Alignment explanation
Indices: 37319437--37319484 Score: 51
Period size: 23 Copynumber: 2.2 Consensus size: 21
37319427 AAAAAGGTGA
*
37319437 AAAACAAAAAAGTGAAAATGG
1 AAAACAAAAAAGTGAAAAAGG
* *
37319458 AAAATAAAAAATGATGAAAAAGT
1 AAAACAAAAAA-G-TGAAAAAGG
37319481 AAAA
1 AAAA
37319485 ATAGAGAGGC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 10 0.45
22 1 0.05
23 11 0.50
ACGTcount: A:0.71, C:0.02, G:0.15, T:0.12
Consensus pattern (21 bp):
AAAACAAAAAAGTGAAAAAGG
Found at i:37320802 original size:44 final size:44
Alignment explanation
Indices: 37320739--37320984 Score: 307
Period size: 44 Copynumber: 5.6 Consensus size: 44
37320729 AAAACCTAGA
* *
37320739 TCCCTAACCAGTAGTGGAATAGGTTGAAGATTGTAAGTCCTATC
1 TCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATC
*
37320783 TCCCTAACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATC
1 TCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATC
* * * * * * *
37320827 TCCATGGCCAGTAGAGGAATAGGTAGAAGATTGCAAGTCCTAAC
1 TCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATC
* *
37320871 TCCCTGACCAGCAGTGGAATAGGTGGAAGATTGTAAGCCCTAGT-
1 TCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTA-TC
* * * *
37320915 TCCCTGACCAGCAATGGAATAGGTGGAAGACTGTAAGCCCTAGT-
1 TCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTA-TC
*
37320959 TCCTTGACCAGCAGTGGAATAGGTTG
1 TCCCTGACCAGCAGTGGAATAGGTTG
37320985 GGAAATTACA
Statistics
Matches: 179, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
44 179 1.00
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.24
Consensus pattern (44 bp):
TCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATC
Found at i:37320978 original size:132 final size:132
Alignment explanation
Indices: 37320739--37320982 Score: 339
Period size: 132 Copynumber: 1.8 Consensus size: 132
37320729 AAAACCTAGA
* * * *
37320739 TCCCTAACCAGTAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTAACCAGCAGTGGAATA
1 TCCCTAACCAGCAGTGGAATAGGTGGAAGATTGTAAGCCCTATCTCCCTAACCAGCAATGGAATA
* * * * *
37320804 GGTTGAAGATTGTAAGTCCTATCTCCATGGCCAGTAGAGGAATAGGTAGAAGATTGCAAGTCCTA
66 GGTGGAAGACTGTAAGCCCTATCTCCATGACCAGCAGAGGAATAGGTAGAAGATTGCAAGTCCTA
37320869 AC
131 AC
* *
37320871 TCCCTGACCAGCAGTGGAATAGGTGGAAGATTGTAAGCCCTAGT-TCCCTGACCAGCAATGGAAT
1 TCCCTAACCAGCAGTGGAATAGGTGGAAGATTGTAAGCCCTA-TCTCCCTAACCAGCAATGGAAT
* *
37320935 AGGTGGAAGACTGTAAGCCCTAGT-TCCTTGACCAGCAGTGGAATAGGT
65 AGGTGGAAGACTGTAAGCCCTA-TCTCCATGACCAGCAGAGGAATAGGT
37320983 TGGGAAATTA
Statistics
Matches: 97, Mismatches: 13, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
132 95 0.98
133 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (132 bp):
TCCCTAACCAGCAGTGGAATAGGTGGAAGATTGTAAGCCCTATCTCCCTAACCAGCAATGGAATA
GGTGGAAGACTGTAAGCCCTATCTCCATGACCAGCAGAGGAATAGGTAGAAGATTGCAAGTCCTA
AC
Found at i:37321500 original size:50 final size:50
Alignment explanation
Indices: 37321423--37321795 Score: 294
Period size: 50 Copynumber: 7.5 Consensus size: 50
37321413 GACTGAGAAT
* * * *
37321423 AGCGAATCTTAC-TCCCCAAGCAATGCAGTGGAACAGATTAAAGCCACATC
1 AGCGAATCTTACTTCCCCGA-CATTGCAGTGAAACAGATTAAAGCTACATC
* * * * *
37321473 GGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAAC
1 AGCGAATCTTACTTCCCCGACATTGCAGTGAAACAGATTAAAGCTACATC
* *
37321523 AGCGAATCTTAC-T-CCCGA-AGTGATGCAGTGGAACAGATTAAAGCCACATC
1 AGCGAATCTTACTTCCCCGACA-T--TGCAGTGAAACAGATTAAAGCTACATC
* * * * *
37321573 GGTGAATCATT-CTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAAC
1 AGCGAATC-TTACTTCCCCGACATTGCAGTGAAACAGATTAAAGCTACATC
* * * *
37321623 AGTGAATCTTAC-TCCCC-AGCTAATGCAGTGCAACAGATTAAAGCCACATC
1 AGCGAATCTTACTTCCCCGA-C-ATTGCAGTGAAACAGATTAAAGCTACATC
* * * * * *
37321673 GGTGAATCTTGCTTCCCCGACATTACAGTTAAAAAGATTAAAGCTACAAT-
1 AGCGAATCTTACTTCCCCGACATTGCAGTGAAACAGATTAAAGCTAC-ATC
* * * * * * * * *
37321723 AACGAATCTTACTTCCCAGGCAGTGTAGTGGAACCGATTGAAGCTACAGC
1 AGCGAATCTTACTTCCCCGACATTGCAGTGAAACAGATTAAAGCTACATC
*
37321773 AGCGAATCTTATTTCCCCGACAT
1 AGCGAATCTTACTTCCCCGACAT
37321796 CACAGTTAAG
Statistics
Matches: 250, Mismatches: 58, Indels: 30
0.74 0.17 0.09
Matches are distributed among these distances:
47 1 0.00
48 7 0.03
49 10 0.04
50 207 0.83
51 17 0.07
52 7 0.03
53 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (50 bp):
AGCGAATCTTACTTCCCCGACATTGCAGTGAAACAGATTAAAGCTACATC
Found at i:37321596 original size:100 final size:99
Alignment explanation
Indices: 37321423--37321804 Score: 505
Period size: 100 Copynumber: 3.8 Consensus size: 99
37321413 GACTGAGAAT
* *
37321423 AGCGAATCTTACTCCCCAAGCAATGCAGTGGAACAGATTAAAGCCACATCGGCGAATCTTGCTTC
1 AGCGAATCTTACT-CCCAAGTAATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTC
37321488 CCCGACATTGCAGTTAAAAAGATTAAAGCTACAAC
65 CCCGACATTGCAGTTAAAAAGATTAAAGCTACAAC
*
37321523 AGCGAATCTTACTCCCGAAGTGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCATT-CTT
1 AGCGAATCTTACTCCC-AAGTAATGCAGTGGAACAGATTAAAGCCACATCGGTGAATC-TTGCTT
37321587 CCCCGACATTGCAGTTAAAAAGATTAAAGCTACAAC
64 CCCCGACATTGCAGTTAAAAAGATTAAAGCTACAAC
* * *
37321623 AGTGAATCTTACTCCCCAGCTAATGCAGTGCAACAGATTAAAGCCACATCGGTGAATCTTGCTTC
1 AGCGAATCTTACTCCCAAG-TAATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTC
* *
37321688 CCCGACATTACAGTTAAAAAGATTAAAGCTACAAT
65 CCCGACATTGCAGTTAAAAAGATTAAAGCTACAAC
* * * * * * * * * * * **
37321723 AACGAATCTTACTTCCCAGGCAGTGTAGTGGAACCGATTGAAGCTACAGCAGCGAATCTTATTTC
1 AGCGAATCTTAC-TCCCAAGTAATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTC
**
37321788 CCCGACATCACAGTTAA
65 CCCGACATTGCAGTTAA
37321805 GCAGATCAAA
Statistics
Matches: 251, Mismatches: 26, Indels: 10
0.87 0.09 0.03
Matches are distributed among these distances:
99 7 0.03
100 237 0.94
101 7 0.03
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (99 bp):
AGCGAATCTTACTCCCAAGTAATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCC
CCGACATTGCAGTTAAAAAGATTAAAGCTACAAC
Found at i:37326721 original size:90 final size:90
Alignment explanation
Indices: 37326568--37326737 Score: 306
Period size: 90 Copynumber: 1.9 Consensus size: 90
37326558 ATAAATGATC
37326568 TACTTATAGATAATATGACATTTCAAAAGCCTCGTTGGTGAAGGAAAAAATTTTAGATAACCTTT
1 TACTTATAGATAATATGACATTTCAAAAGCCTCGTTGGTGAAGGAAAAAATTTTAGATAACCTTT
37326633 GATGGGATAAGGACTTATATATCCT
66 GATGGGATAAGGACTTATATATCCT
*
37326658 TACTTATAGATAATATGACATTTCAAAAGCCTCGTTGGTGAAGGAAGAAATTTT-GAATAACCTT
1 TACTTATAGATAATATGACATTTCAAAAGCCTCGTTGGTGAAGGAAAAAATTTTAG-ATAACCTT
*
37326722 TGATGGGATAATGACT
65 TGATGGGATAAGGACT
37326738 AAGTGTAAAT
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
89 1 0.01
90 76 0.99
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (90 bp):
TACTTATAGATAATATGACATTTCAAAAGCCTCGTTGGTGAAGGAAAAAATTTTAGATAACCTTT
GATGGGATAAGGACTTATATATCCT
Found at i:37341913 original size:21 final size:23
Alignment explanation
Indices: 37341882--37341925 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
37341872 TATTCACATT
*
37341882 TAGATTTAAATTTTAAA-ATAAA
1 TAGATTTAAATTTCAAATATAAA
37341904 TAGA-TTAAATTTCAAATATAAA
1 TAGATTTAAATTTCAAATATAAA
37341926 AAAATATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (23 bp):
TAGATTTAAATTTCAAATATAAA
Found at i:37342810 original size:22 final size:23
Alignment explanation
Indices: 37342775--37342818 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
37342765 ATTAGCAAAC
37342775 AAATATATAAATAT-AAATAAAT
1 AAATATATAAATATAAAATAAAT
* *
37342797 AAATATCTATATATAAAATAAA
1 AAATATATAAATATAAAATAAA
37342819 ATATAAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
AAATATATAAATATAAAATAAAT
Found at i:37342812 original size:14 final size:14
Alignment explanation
Indices: 37342775--37342826 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
37342765 ATTAGCAAAC
37342775 AAATATATAAATAT
1 AAATATATAAATAT
*
37342789 AAATAAATAAATAT
1 AAATATATAAATAT
**
37342803 CTATATATAAA-AT
1 AAATATATAAATAT
37342816 AAA-ATATAAAT
1 AAATATATAAAT
37342827 TGAATAATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
12 7 0.23
13 3 0.10
14 21 0.68
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATATATAAATAT
Found at i:37343287 original size:20 final size:20
Alignment explanation
Indices: 37343262--37343314 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
37343252 TTAAAGGAGC
* *
37343262 AATTAAATCCATTTGATTAA
1 AATTAAATCAAATTGATTAA
*
37343282 AATTAAATCAAATTGATTAG
1 AATTAAATCAAATTGATTAA
* *
37343302 AATAAAATAAAAT
1 AATTAAATCAAAT
37343315 CAGGATATGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.34
Consensus pattern (20 bp):
AATTAAATCAAATTGATTAA
Found at i:37347826 original size:54 final size:54
Alignment explanation
Indices: 37347734--37348078 Score: 309
Period size: 54 Copynumber: 6.4 Consensus size: 54
37347724 GCATGAAGTT
* * * **
37347734 TGCTTACAAAATTTTAAAAATATTACAG-TCCGCTGATTTACGATCACGACCTTC
1 TGCTTACAAGATTTTAAGAATCTTA-AGATCCATTGATTTACGATCACGACCTTC
* * * * * * *
37347788 TGCTAACAAGATTTTTAGAATCTTACGACCCGTTGATTTACGATCAGGATCTTC
1 TGCTTACAAGATTTTAAGAATCTTAAGATCCATTGATTTACGATCACGACCTTC
* * * ** *
37347842 TACTTACAAGATTTTAAGCATTTTAAAGAT-TGTTGATTTACGATCACGACCTTT
1 TGCTTACAAGATTTTAAGAATCTT-AAGATCCATTGATTTACGATCACGACCTTC
* * * *
37347896 TGCTTAGATGATTTTAAGAATCTTGCAG-TTCATTGATTTACGATCACGACCTTC
1 TGCTTACAAGATTTTAAGAATCTT-AAGATCCATTGATTTACGATCACGACCTTC
* * * * * *
37347950 TGCTTAAAAGATTTTAAAAATCTTATGATCCACTGATTTATGATCACAACCTTC
1 TGCTTACAAGATTTTAAGAATCTTAAGATCCATTGATTTACGATCACGACCTTC
* * * * * * * *
37348004 TACTTATAAGATTTTAAGAATCTCAAGGTCTATTGAATTATGATCACGACGTTC
1 TGCTTACAAGATTTTAAGAATCTTAAGATCCATTGATTTACGATCACGACCTTC
*
37348058 TGCTTACAAGATTTTTAGAAT
1 TGCTTACAAGATTTTAAGAAT
37348079 ATTATAGTTT
Statistics
Matches: 233, Mismatches: 54, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
53 3 0.01
54 227 0.97
55 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (54 bp):
TGCTTACAAGATTTTAAGAATCTTAAGATCCATTGATTTACGATCACGACCTTC
Found at i:37348096 original size:162 final size:162
Alignment explanation
Indices: 37347734--37348097 Score: 408
Period size: 162 Copynumber: 2.2 Consensus size: 162
37347724 GCATGAAGTT
* * * *
37347734 TGCTTACAAAATTTTAAAAATATTACAGTCCGCTGATTTACGATCACGACCTTCTGCTAACAAGA
1 TGCTTACAAGATTTTAAGAATATTACAGTTCGTTGATTTACGATCACGACCTTCTGCTAACAAGA
* * ** ** * *
37347799 TTTTTAGAATCTTACGACCCGTTGATTTACGATCAGGATCTTCTACTTACAAGATTTTAAGCATT
66 TTTTAAAAATCTTACGACCCACTGATTTACGATCACAACCTTCTACTTACAAGATTTTAAGCAAT
* * * *
37347864 TTAAAGATTGTTGATTTACGATCACGACCTTT
131 CTAAAGATTATTGAATTACGATCACGACCTTC
* * * * *
37347896 TGCTTAGATGATTTTAAGAATCTTGCAGTTCATTGATTTACGATCACGACCTTCTGCTTAA-AAG
1 TGCTTACAAGATTTTAAGAATATTACAGTTCGTTGATTTACGATCACGACCTTCTGC-TAACAAG
* * * *
37347960 ATTTTAAAAATCTTATGATCCACTGATTTATGATCACAACCTTCTACTTATAAGATTTTAAG-AA
65 ATTTTAAAAATCTTACGACCCACTGATTTACGATCACAACCTTCTACTTACAAGATTTTAAGCAA
* * * *
37348024 TCTCAAGGTCTATTGAATTATGATCACGACGTTC
130 TCTAAAGAT-TATTGAATTACGATCACGACCTTC
* * *
37348058 TGCTTACAAGATTTTTAGAATATTATAGTTTGTTGATTTA
1 TGCTTACAAGATTTTAAGAATATTACAGTTCGTTGATTTA
37348098 GGATTCTCAA
Statistics
Matches: 163, Mismatches: 37, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
161 7 0.04
162 153 0.94
163 3 0.02
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (162 bp):
TGCTTACAAGATTTTAAGAATATTACAGTTCGTTGATTTACGATCACGACCTTCTGCTAACAAGA
TTTTAAAAATCTTACGACCCACTGATTTACGATCACAACCTTCTACTTACAAGATTTTAAGCAAT
CTAAAGATTATTGAATTACGATCACGACCTTC
Found at i:37351045 original size:14 final size:14
Alignment explanation
Indices: 37351026--37351053 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
37351016 GAAATTAATG
37351026 ATTGTTACTCGAAT
1 ATTGTTACTCGAAT
37351040 ATTGTTACTCGAAT
1 ATTGTTACTCGAAT
37351054 GAATGATGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (14 bp):
ATTGTTACTCGAAT
Found at i:37357098 original size:43 final size:43
Alignment explanation
Indices: 37357034--37357120 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 43
37357024 ATTTAACTTT
37357034 TTTTTAACATTAACGACCACCATGTTTAAGTTGGATCGAAAAC
1 TTTTTAACATTAACGACCACCATGTTTAAGTTGGATCGAAAAC
* * *
37357077 TTTTTAACATTAAC-AGTCACCATGTTTAGGTTGGGTCGAAAAC
1 TTTTTAACATTAACGA-CCACCATGTTTAAGTTGGATCGAAAAC
37357120 T
1 T
37357121 ACAGCCTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 1 0.03
43 39 0.98
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Consensus pattern (43 bp):
TTTTTAACATTAACGACCACCATGTTTAAGTTGGATCGAAAAC
Found at i:37359601 original size:9 final size:9
Alignment explanation
Indices: 37359571--37359617 Score: 53
Period size: 8 Copynumber: 5.2 Consensus size: 9
37359561 AAGCCCTTTT
37359571 AAAATT-TA
1 AAAATTATA
*
37359579 AAATTTATAAA
1 AAAATTAT--A
37359590 AAAATTATA
1 AAAATTATA
37359599 AAAATTAT-
1 AAAATTATA
37359607 AAAATTATA
1 AAAATTATA
37359616 AA
1 AA
37359618 TTTTTTATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
8 13 0.39
9 12 0.36
11 8 0.24
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
AAAATTATA
Found at i:37359606 original size:20 final size:19
Alignment explanation
Indices: 37359571--37359610 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
37359561 AAGCCCTTTT
*
37359571 AAAATTTAAAATTTATAAA
1 AAAATTTAAAAATTATAAA
37359590 AAAATTATAAAAATTATAAA
1 AAAATT-TAAAAATTATAAA
37359610 A
1 A
37359611 TTATAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATTTAAAAATTATAAA
Found at i:37359771 original size:13 final size:12
Alignment explanation
Indices: 37359740--37359777 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
37359730 AAATTTAAAA
37359740 TTTTATAACTTT
1 TTTTATAACTTT
37359752 TTTTATAACTTT
1 TTTTATAACTTT
37359764 TGTTTATAA-TTT
1 T-TTTATAACTTT
37359776 TT
1 TT
37359778 ATGATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 1 0.04
12 17 0.68
13 7 0.28
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (12 bp):
TTTTATAACTTT
Found at i:37359779 original size:22 final size:20
Alignment explanation
Indices: 37359751--37359796 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
37359741 TTTATAACTT
*
37359751 TTTTTATAACTTTTGTTTATAA
1 TTTTTATAA-TTTT-TTAATAA
*
37359773 TTTTTATGATTTTTTAATAA
1 TTTTTATAATTTTTTAATAA
37359793 TTTT
1 TTTT
37359797 AAAATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.45
21 4 0.18
22 8 0.36
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.67
Consensus pattern (20 bp):
TTTTTATAATTTTTTAATAA
Found at i:37362331 original size:3 final size:3
Alignment explanation
Indices: 37362325--37362366 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
37362315 TTATTAACCA
37362325 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
37362367 GATTTATTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:37362711 original size:6 final size:6
Alignment explanation
Indices: 37362700--37362734 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
37362690 TAATTCTTAA
37362700 ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
37362735 TTCTTTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:37362909 original size:46 final size:46
Alignment explanation
Indices: 37362859--37362959 Score: 132
Period size: 46 Copynumber: 2.2 Consensus size: 46
37362849 AATTTTAAAT
* **
37362859 ACATACATGCATATATTCTTCGTATTTTATAAC-TTTATGTATATAC
1 ACATACATGCATATATT-TTCATATTTTATAACTTTTAAATATATAC
* * *
37362905 ACATACTTACATATATTTTTATATTTTATAACTTTTAAATATATAC
1 ACATACATGCATATATTTTCATATTTTATAACTTTTAAATATATAC
37362951 ACATACATG
1 ACATACATG
37362960 TATGTCTTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
45 13 0.28
46 33 0.72
ACGTcount: A:0.37, C:0.14, G:0.04, T:0.46
Consensus pattern (46 bp):
ACATACATGCATATATTTTCATATTTTATAACTTTTAAATATATAC
Found at i:37368000 original size:6 final size:6
Alignment explanation
Indices: 37367989--37368042 Score: 56
Period size: 6 Copynumber: 8.7 Consensus size: 6
37367979 AAAAAATAAG
* *
37367989 AAAAGA AAAAGA AAATAAA ATAAAAA AAGAAGA AAAAG- AAAAGA AAAAGA
1 AAAAGA AAAAGA AAA-AGA A-AAAGA AA-AAGA AAAAGA AAAAGA AAAAGA
37368039 AAAA
1 AAAA
37368043 TGAGAGGCCA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
5 5 0.12
6 23 0.55
7 12 0.29
8 2 0.05
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (6 bp):
AAAAGA
Found at i:37368000 original size:11 final size:11
Alignment explanation
Indices: 37367989--37368041 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
37367979 AAAAAATAAG
37367989 AAAAGAAAA-A
1 AAAAGAAAAGA
* *
37367999 GAAAATAAAATA
1 -AAAAGAAAAGA
37368011 AAAA-AAGAAGA
1 AAAAGAA-AAGA
37368022 AAAAGAAAAGA
1 AAAAGAAAAGA
37368033 AAAAGAAAA
1 AAAAGAAAA
37368042 ATGAGAGGCC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
10 2 0.05
11 32 0.86
12 3 0.08
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:37368533 original size:100 final size:105
Alignment explanation
Indices: 37368408--37368616 Score: 252
Period size: 108 Copynumber: 2.0 Consensus size: 105
37368398 CATTGTGATA
** * * *
37368408 ATCTTATTCATTTCGTATCTTAGCAAAATTTTCTA-T-CTTAATTGA-T-TTT-GAGCTTTGTTC
1 ATCTTATTCATTTCGTATCTTAGCAAAATTCGCTATTGATTAATTGATTGTTTAGAGCTCTGCTC
37368468 TCAATAAAATTTCATCTTAT-CCATTGTGATAATCCTTTTC
66 TCAATAAAATTTCATCTT-TCCCATTGTGATAATCCTTTTC
* *
37368508 ATCTTATTCATTTTG-AGTCTTAGCAAAATTCGCTATTTTGATTAATTTATTTGTTTAGAGCTCT
1 ATCTTATTCATTTCGTA-TCTTAGCAAAATTCGCTA--TTGATTAATTGA-TTGTTTAGAGCTCT
*
37368572 GCTCTCAATAAAATTTCATCTTTCCCATTGTGATAATCTTTTTC
62 GCTCTCAATAAAATTTCATCTTTCCCATTGTGATAATCCTTTTC
37368616 A
1 A
37368617 AGTATTTTCT
Statistics
Matches: 91, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
99 1 0.01
100 30 0.33
103 1 0.01
104 7 0.08
106 1 0.01
107 4 0.04
108 47 0.52
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.48
Consensus pattern (105 bp):
ATCTTATTCATTTCGTATCTTAGCAAAATTCGCTATTGATTAATTGATTGTTTAGAGCTCTGCTC
TCAATAAAATTTCATCTTTCCCATTGTGATAATCCTTTTC
Found at i:37369434 original size:40 final size:40
Alignment explanation
Indices: 37369390--37369470 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
37369380 CTTTACAGGT
37369390 CATGTTCCTTAGAGAACAGATCAATAAAGTTACCCATACC
1 CATGTTCCTTAGAGAACAGATCAATAAAGTTACCCATACC
37369430 CATGTTCCTTAGAGAACAGATCAATAAAGTTACCCATACC
1 CATGTTCCTTAGAGAACAGATCAATAAAGTTACCCATACC
37369470 C
1 C
37369471 CTGAAGTTGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.25
Consensus pattern (40 bp):
CATGTTCCTTAGAGAACAGATCAATAAAGTTACCCATACC
Found at i:37369672 original size:89 final size:89
Alignment explanation
Indices: 37369541--37369769 Score: 314
Period size: 89 Copynumber: 2.6 Consensus size: 89
37369531 AAAGGAGTAG
* * * * * * *
37369541 ACTAGAAGCAACATATCTTGTCTTCCTGTACTGGCAGTGAAGCAGATCGAAGACACAAGCCTGAA
1 ACTAAAAGCAACAGATCTTGTCTTCCTGTACCGACAGCGAAGCAGATCAAACACACAAGCCTGAA
37369606 CTCCCTGAGTTTACAGCAGAGCAA
66 CTCCCTGAGTTTACAGCAGAGCAA
* * *
37369630 ACTAAAAGCAGCAGATCTTGTCTTCCTGTACCGACAGCGAAGCAGATCAAACACACAATCCTGAC
1 ACTAAAAGCAACAGATCTTGTCTTCCTGTACCGACAGCGAAGCAGATCAAACACACAAGCCTGAA
* *
37369695 CTCCCTGAGTTTACAGCGGAGCAG
66 CTCCCTGAGTTTACAGCAGAGCAA
* * * *
37369719 ACTAAAAGCAACAGATCTTGTCTTCCTGTACTGGCAGTGAAGCGGATCAAA
1 ACTAAAAGCAACAGATCTTGTCTTCCTGTACCGACAGCGAAGCAGATCAAA
37369770 AAACTAATCT
Statistics
Matches: 123, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
89 123 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (89 bp):
ACTAAAAGCAACAGATCTTGTCTTCCTGTACCGACAGCGAAGCAGATCAAACACACAAGCCTGAA
CTCCCTGAGTTTACAGCAGAGCAA
Found at i:37370315 original size:41 final size:41
Alignment explanation
Indices: 37370258--37370457 Score: 247
Period size: 41 Copynumber: 4.8 Consensus size: 41
37370248 AAAGGACAGA
* *
37370258 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAG
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCAAG
*
37370299 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAG
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCAAG
* * *
37370340 TCTTATCTCTCTGAAGTTGCAGTAGAGCAAATCATATGAAG
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCAAG
* * * * * * *
37370381 TCTCATTTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAA
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-T-CACAT--CAAG
37370426 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGAT
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGAT
37370458 TAAAGCTATA
Statistics
Matches: 137, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
41 103 0.75
42 1 0.01
43 3 0.02
44 1 0.01
45 29 0.21
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.29
Consensus pattern (41 bp):
TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCAAG
Found at i:37370444 original size:45 final size:42
Alignment explanation
Indices: 37370224--37370456 Score: 188
Period size: 41 Copynumber: 5.5 Consensus size: 42
37370214 TTCTATCTTC
* * *
37370224 CTGAAGTTGCAGT-GAAGCAGATTAAAAGGACAGATCTTATCTCT
1 CTGAAGTTGCAGTAG-AGCAGAATAAGATGA-A-ATCTTATCTCT
* ** *
37370268 CTGAAGTTGCAGTAGAGCAG-AT-CGCATCCAGTCTTATCTCT
1 CTGAAGTTGCAGTAGAGCAGAATAAG-ATGAAATCTTATCTCT
* * ** *
37370309 CTGAAGTTGCAGTAGAGCAG-ATCACATCCAGTCTTATCTCT
1 CTGAAGTTGCAGTAGAGCAGAATAAGATGAAATCTTATCTCT
* * * * * *
37370350 CTGAAGTTGCAGTAGAGCA-AATCATATGAAGTCTCATTTCC
1 CTGAAGTTGCAGTAGAGCAGAATAAGATGAAATCTTATCTCT
* *
37370391 CTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATCTCT
1 CTGAAGTTGCAGTAGAGCAGAAT-AAGAT-G-AAATCTTATCTCT
37370436 CTGAAGTTGCAGTAGAGCAGA
1 CTGAAGTTGCAGTAGAGCAGA
37370457 TTAAAGCTAT
Statistics
Matches: 157, Mismatches: 24, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
41 100 0.64
42 3 0.02
43 5 0.03
44 19 0.12
45 30 0.19
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (42 bp):
CTGAAGTTGCAGTAGAGCAGAATAAGATGAAATCTTATCTCT
Found at i:37372198 original size:3 final size:3
Alignment explanation
Indices: 37372192--37372216 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
37372182 TTATTAATCA
37372192 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
37372217 TATTCATTTA
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:37372730 original size:46 final size:46
Alignment explanation
Indices: 37372679--37372780 Score: 125
Period size: 46 Copynumber: 2.2 Consensus size: 46
37372669 GTAATTTTAA
* **
37372679 ATACATACATACATATATTCTTCGTATTTTATAA-CTTTATGTATAT
1 ATACATACATACATATATT-TTCATATTTTATAATCTTTAAATATAT
* * *
37372725 ATACATACTTACATATATTTTTATATTTTATAATTTTTAAATATAT
1 ATACATACATACATATATTTTCATATTTTATAATCTTTAAATATAT
*
37372771 ACACATACAT
1 ATACATACAT
37372781 GTATTTCTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
45 12 0.26
46 35 0.74
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (46 bp):
ATACATACATACATATATTTTCATATTTTATAATCTTTAAATATAT
Found at i:37372786 original size:42 final size:41
Alignment explanation
Indices: 37372656--37372786 Score: 113
Period size: 42 Copynumber: 3.1 Consensus size: 41
37372646 ACACTTGCAC
** *
37372656 ATTTTTGTATTTCGTAA-TTTTAAATACAT-ACATACATAT
1 ATTTTTGTATTTTATAATTTTTAAATATATAACATACATAT
* * * *
37372695 ATTCTTCGTATTTTATAACTTTATGTATATATACATACTTACATAT
1 ATT-TTTGTATTTTATAA-TTT-T-TAAATATATA-ACATACATAT
* *
37372741 ATTTTTATATTTTATAATTTTTAAATATATACACATACATGT
1 ATTTTTGTATTTTATAATTTTTAAATATATA-ACATACATAT
37372783 ATTT
1 ATTT
37372787 CTTTTTACCC
Statistics
Matches: 71, Mismatches: 14, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
39 3 0.04
40 11 0.15
42 22 0.31
43 2 0.03
44 9 0.13
45 12 0.17
46 12 0.17
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.51
Consensus pattern (41 bp):
ATTTTTGTATTTTATAATTTTTAAATATATAACATACATAT
Found at i:37372824 original size:4 final size:4
Alignment explanation
Indices: 37372815--37372840 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
37372805 TCTTTTCATA
37372815 TATT TATT TATT TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TA
37372841 CATGTCCACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:37377008 original size:2 final size:2
Alignment explanation
Indices: 37377001--37377035 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
37376991 TAGTTGTAGG
37377001 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
37377036 GCCACCCAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:37380302 original size:19 final size:19
Alignment explanation
Indices: 37380274--37380311 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
37380264 TAAAAGAAAG
* *
37380274 AAAGGGAAAGGGAAAAGAA
1 AAAGGAAAAGGAAAAAGAA
37380293 AAAGGAAAAGGAAAAAGAA
1 AAAGGAAAAGGAAAAAGAA
37380312 CACAAAGAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (19 bp):
AAAGGAAAAGGAAAAAGAA
Found at i:37381569 original size:31 final size:31
Alignment explanation
Indices: 37381532--37381600 Score: 113
Period size: 31 Copynumber: 2.2 Consensus size: 31
37381522 ATTAAAGCCC
37381532 AATGACTTAAATAAAATTTTTTGAATAG-TT
1 AATGACTTAAATAAAATTTTTTGAATAGTTT
*
37381562 AAGTGACTTAAATGAAATTTTTTGAATAGTTT
1 AA-TGACTTAAATAAAATTTTTTGAATAGTTT
37381594 AATGACT
1 AATGACT
37381601 ATTTTGTAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
30 2 0.06
31 30 0.83
32 4 0.11
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.42
Consensus pattern (31 bp):
AATGACTTAAATAAAATTTTTTGAATAGTTT
Done.