Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 15 of 325
Found at i:5797613 original size:38 final size:39
Alignment explanation
Indices: 5797529--5797663 Score: 107
Period size: 39 Copynumber: 3.4 Consensus size: 39
5797519 ACCAATATGG
*
5797529 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
* * *
5797568 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAGTTGA
* * * * *
5797606 TACCCAGTACCTCATTGAATCTA-TCCGAAGAAATA-TAGTGA
1 CACCCAGTGCCTCATCGGA--TAGTCCGAAGTAATAGT--TGA
*
5797647 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
5797664 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
38 18 0.25
39 36 0.49
40 4 0.05
41 15 0.21
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
Found at i:5799239 original size:5 final size:5
Alignment explanation
Indices: 5799221--5799256 Score: 63
Period size: 5 Copynumber: 7.0 Consensus size: 5
5799211 TTTCTTTTAT
5799221 ATATA ATAATA ATATA ATATA ATATA ATATA ATATA
1 ATATA AT-ATA ATATA ATATA ATATA ATATA ATATA
5799257 CTTAATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:5805778 original size:46 final size:46
Alignment explanation
Indices: 5805672--5805991 Score: 417
Period size: 46 Copynumber: 7.0 Consensus size: 46
5805662 TTTGACATGA
* * * * ** * * *
5805672 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTTTTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGC
** * *
5805719 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
*** *** * *
5805765 TGCCATGGTATCTTTCAACCATGGTC-TATTTATTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
5805810 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
*
5805856 TGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
*
5805902 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
5805948 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
5805992 AGAGCACACT
Statistics
Matches: 248, Mismatches: 24, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
45 40 0.16
46 179 0.72
47 29 0.12
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
Found at i:5808164 original size:18 final size:20
Alignment explanation
Indices: 5808149--5808185 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5808139 TAATAATAAA
*
5808149 ATATCTCATTAAAATAATAT
1 ATATCTAATTAAAATAATAT
5808169 ATATCTAATT-AAATAAT
1 ATATCTAATTAAAATAAT
5808186 CATAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATCTAATTAAAATAATAT
Found at i:5811894 original size:35 final size:35
Alignment explanation
Indices: 5811809--5811935 Score: 119
Period size: 35 Copynumber: 3.6 Consensus size: 35
5811799 TCCTCATTGA
* * ** * *
5811809 AATATCATACCTACATTTCACAACTCCGTATGAAA
1 AATACCATACCTACGTTTCACAACTCAATATGGAT
* * ** *
5811844 AATGCCATATCTACGTTTCTTAACTCAGTATGGAT
1 AATACCATACCTACGTTTCACAACTCAATATGGAT
* * *
5811879 AATATCATACTTACGTTTCACAACTCAATATGGTT
1 AATACCATACCTACGTTTCACAACTCAATATGGAT
*
5811914 AATACCATACCTATGTTTCACA
1 AATACCATACCTACGTTTCACA
5811936 CTTTTCCATG
Statistics
Matches: 72, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
35 72 1.00
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.34
Consensus pattern (35 bp):
AATACCATACCTACGTTTCACAACTCAATATGGAT
Found at i:5814578 original size:2 final size:2
Alignment explanation
Indices: 5814573--5814606 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5814563 TTTCCAGTTT
*
5814573 CA CA CA CA CA CA CA CA CA CA CA CA CA AA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
5814607 AAAAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:5816321 original size:44 final size:44
Alignment explanation
Indices: 5816258--5816345 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
5816248 TCTTGACAGA
5816258 TTGAATCCATCCTAAAATCAATGCTTTCTTCTCCTACTCAACAT
1 TTGAATCCATCCTAAAATCAATGCTTTCTTCTCCTACTCAACAT
5816302 TTGAATCCATCCTAAAATCAATGCTTTCTTCTCCTACTCAACAT
1 TTGAATCCATCCTAAAATCAATGCTTTCTTCTCCTACTCAACAT
5816346 CTCACCACAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.36
Consensus pattern (44 bp):
TTGAATCCATCCTAAAATCAATGCTTTCTTCTCCTACTCAACAT
Found at i:5820807 original size:19 final size:18
Alignment explanation
Indices: 5820765--5820821 Score: 78
Period size: 18 Copynumber: 3.1 Consensus size: 18
5820755 GTGTACTTCG
5820765 ATAAAAATTTTAAAATAT
1 ATAAAAATTTTAAAATAT
5820783 ATAAAAATTTTAAAATAT
1 ATAAAAATTTTAAAATAT
* **
5820801 TTGAAAAACGTTAAAATAT
1 AT-AAAAATTTTAAAATAT
5820820 AT
1 AT
5820822 TTTTATAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 19 0.56
19 15 0.44
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (18 bp):
ATAAAAATTTTAAAATAT
Found at i:5834491 original size:16 final size:16
Alignment explanation
Indices: 5834440--5834493 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
5834430 TAATGTCTTC
5834440 TAAAATA-TATAATATA
1 TAAAATATTATAA-ATA
*
5834456 TAAAA-ATAATATAATA
1 TAAAATATTATA-AATA
*
5834472 TAAAATATTATAAATT
1 TAAAATATTATAAATA
5834488 TAAAAT
1 TAAAAT
5834494 GGGTCAAGCC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
15 1 0.03
16 25 0.78
17 6 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAAATATTATAAATA
Found at i:5835491 original size:35 final size:35
Alignment explanation
Indices: 5835448--5835514 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
5835438 ATTACTGTCA
* * *
5835448 TATGTAATTCTTGTTAATTTGTGAAAATTAAAATG
1 TATGTAATTATTATTAATTTGTGAAAAATAAAATG
5835483 TATGTAATTATTATTAATTTGTGAAAAATAAA
1 TATGTAATTATTATTAATTTGTGAAAAATAAA
5835515 TTTTAATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.42, C:0.01, G:0.12, T:0.45
Consensus pattern (35 bp):
TATGTAATTATTATTAATTTGTGAAAAATAAAATG
Found at i:5835761 original size:21 final size:20
Alignment explanation
Indices: 5835733--5835777 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 20
5835723 ATTTTAACAG
5835733 AACTGCTGATGTGGCAAGTT
1 AACTGCTGATGTGGCAAGTT
*
5835753 AACTAGCTGATGTGGCCAGTT
1 AACT-GCTGATGTGGCAAGTT
5835774 AACT
1 AACT
5835778 TGCCACGTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (20 bp):
AACTGCTGATGTGGCAAGTT
Found at i:5837429 original size:46 final size:45
Alignment explanation
Indices: 5837379--5837543 Score: 190
Period size: 46 Copynumber: 3.6 Consensus size: 45
5837369 TGTTTGGGCA
5837379 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
5837425 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
5837472 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
5837518 CCCGAGCTCGTTGAGTTGAGTCCGAG
1 TCCGAACTCGTTGAGTTGAGTCCGAG
5837544 ATCGCTAATG
Statistics
Matches: 100, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 58 0.58
47 32 0.32
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.27
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:5837534 original size:93 final size:93
Alignment explanation
Indices: 5837375--5837543 Score: 302
Period size: 93 Copynumber: 1.8 Consensus size: 93
5837365 AGGATGTTTG
* *
5837375 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
5837440 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
5837468 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
5837533 TTGAGTCCGAG
66 TTGAGTCCGAG
5837544 ATCGCTAATG
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:5840522 original size:21 final size:20
Alignment explanation
Indices: 5840496--5840540 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
5840486 CTACGTGACA
5840496 AGTTAACTGGCCACATCAGC
1 AGTTAACTGGCCACATCAGC
* *
5840516 TAGTTAACTTGCTACATCAGC
1 -AGTTAACTGGCCACATCAGC
5840537 AGTT
1 AGTT
5840541 CTGTTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (20 bp):
AGTTAACTGGCCACATCAGC
Found at i:5840636 original size:30 final size:31
Alignment explanation
Indices: 5840571--5840636 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
5840561 ACTATTAATC
* *
5840571 AGTGACTGTTTTGTCACTTTTTTATAACGTT
1 AGTGACTGTTTTGTCACTTTTTCATAAAGTT
*
5840602 AGTGACTGTTTTGTTA-TTTTTCA-AAAGTT
1 AGTGACTGTTTTGTCACTTTTTCATAAAGTT
5840631 GAGTGA
1 -AGTGA
5840637 TTGAAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 5 0.16
30 11 0.35
31 15 0.48
ACGTcount: A:0.23, C:0.09, G:0.20, T:0.48
Consensus pattern (31 bp):
AGTGACTGTTTTGTCACTTTTTCATAAAGTT
Found at i:5852018 original size:17 final size:18
Alignment explanation
Indices: 5851993--5852030 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
5851983 TTTCTTCAAC
* *
5851993 TTCTTTTTCA-ATTTCTT
1 TTCTGTTTCACATTCCTT
5852010 TTCTGTTTCACATTCCTT
1 TTCTGTTTCACATTCCTT
5852028 TTC
1 TTC
5852031 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.11, C:0.24, G:0.03, T:0.63
Consensus pattern (18 bp):
TTCTGTTTCACATTCCTT
Found at i:5856162 original size:24 final size:24
Alignment explanation
Indices: 5856130--5856177 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
5856120 TCTTTAAGGT
* *
5856130 GGCATTAGGTCCATCATGGATGGA
1 GGCATTAGGCCCACCATGGATGGA
5856154 GGCATTAGGCCCACCATGGATGGA
1 GGCATTAGGCCCACCATGGATGGA
5856178 CATTCCTACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.25, C:0.21, G:0.33, T:0.21
Consensus pattern (24 bp):
GGCATTAGGCCCACCATGGATGGA
Found at i:5861240 original size:27 final size:27
Alignment explanation
Indices: 5861187--5861243 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
5861177 CATTTACTAT
5861187 TTATAAAAAAATTATTATTTTAATTTAA
1 TTATAAAAAAATTATTATTTT-ATTTAA
5861215 TTAT-AAAAAATATATATATTTT-TTTAA
1 TTATAAAAAAAT-TAT-TATTTTATTTAA
5861242 TT
1 TT
5861244 TTTTAAGCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 14 0.52
28 7 0.26
29 6 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TTATAAAAAAATTATTATTTTATTTAA
Found at i:5862320 original size:22 final size:22
Alignment explanation
Indices: 5862295--5862340 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
5862285 TTCATTTTAG
5862295 TTGCCCAAAACTTTTAAGGCGC
1 TTGCCCAAAACTTTTAAGGCGC
5862317 TTGCCCAAAACTTTTAAGGCGC
1 TTGCCCAAAACTTTTAAGGCGC
5862339 TT
1 TT
5862341 TCATTTTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (22 bp):
TTGCCCAAAACTTTTAAGGCGC
Found at i:5866707 original size:22 final size:22
Alignment explanation
Indices: 5866678--5866734 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
5866668 TAGCACGTTA
5866678 AGTGCTCTCTGTTTAGCACATCT
1 AGTGCTCTCTGTTTAGCAC-TCT
* *
5866701 -GTGCTCTCTGTATAGCACTTT
1 AGTGCTCTCTGTTTAGCACTCT
5866722 AGTGCTCTCTGTT
1 AGTGCTCTCTGTT
5866735 CGTTTGTGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.07
22 28 0.93
ACGTcount: A:0.14, C:0.25, G:0.19, T:0.42
Consensus pattern (22 bp):
AGTGCTCTCTGTTTAGCACTCT
Found at i:5872438 original size:29 final size:28
Alignment explanation
Indices: 5872405--5872459 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
5872395 CTCTCACAAC
5872405 TAAAATTAAAAAAATATATATATAATTTT
1 TAAAATTAAAAAAATATATA-ATAATTTT
* * *
5872434 TAAAATTCAAAATATTTATAATAATT
1 TAAAATTAAAAAAATATATAATAATT
5872460 CCAGAATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
TAAAATTAAAAAAATATATAATAATTTT
Found at i:5876084 original size:20 final size:20
Alignment explanation
Indices: 5876059--5876108 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
5876049 TGGCTTAAAA
5876059 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
5876079 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
5876096 GTGGTAGTGGATT
1 TTGGTAGTGGATT
5876109 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:5880721 original size:20 final size:20
Alignment explanation
Indices: 5880696--5880745 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
5880686 TGGCTTAAAA
5880696 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
5880716 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
5880733 GTGGTAGTGGATT
1 TTGGTAGTGGATT
5880746 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:5882835 original size:17 final size:17
Alignment explanation
Indices: 5882813--5882848 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
5882803 GGTTGATACT
5882813 CATATAATAAATTTATG
1 CATATAATAAATTTATG
5882830 CATATAATAAATTTATG
1 CATATAATAAATTTATG
5882847 CA
1 CA
5882849 CCAAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (17 bp):
CATATAATAAATTTATG
Found at i:5888313 original size:29 final size:27
Alignment explanation
Indices: 5888249--5888320 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
5888239 TTATGGATTT
*
5888249 TTTATAAAAATAATATTAAAAAAATTA
1 TTTATGAAAATAATATTAAAAAAATTA
* * * *
5888276 ATTACGAAAATGATATTAAACCTAAATTA
1 TTTATGAAAATAATATTAAA--AAAATTA
5888305 TTTATGAAAA-AATATT
1 TTTATGAAAATAATATT
5888321 TTTTCTGCAG
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
27 16 0.46
28 5 0.14
29 14 0.40
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (27 bp):
TTTATGAAAATAATATTAAAAAAATTA
Found at i:5892172 original size:35 final size:35
Alignment explanation
Indices: 5892117--5892191 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
5892107 GTGTGAGTGC
** *
5892117 GGTCCATAACAAGTGTTGTCCTAAGTCCTTAAAGT
1 GGTCCATAACAAGTAATGTCCTAAGTCCTAAAAGT
* * *
5892152 GGTCCATAACGAGTAATGTCCTAATTCGTAAAAGT
1 GGTCCATAACAAGTAATGTCCTAAGTCCTAAAAGT
5892187 GGTCC
1 GGTCC
5892192 GTAATTGTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.29
Consensus pattern (35 bp):
GGTCCATAACAAGTAATGTCCTAAGTCCTAAAAGT
Found at i:5895843 original size:3 final size:3
Alignment explanation
Indices: 5895835--5895860 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5895825 GCTAGGGTTT
5895835 TGG TGG TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TG
5895861 TGAGGATGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
TGG
Found at i:5899206 original size:16 final size:15
Alignment explanation
Indices: 5899185--5899217 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
5899175 GTAGCTTTTC
5899185 ATGAATTATAATAATT
1 ATGAATTATAA-AATT
5899201 ATGAATTATAAAATT
1 ATGAATTATAAAATT
5899216 AT
1 AT
5899218 TTCAACATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (15 bp):
ATGAATTATAAAATT
Found at i:5904128 original size:54 final size:52
Alignment explanation
Indices: 5904046--5904149 Score: 131
Period size: 54 Copynumber: 2.0 Consensus size: 52
5904036 CAATCTCTAT
*
5904046 TAATTGGATGATAAATTAAAAAAAATATAATT-GAGTGATAAAAA-AATTTTA
1 TAATTGAATGATAAATTAAAAAAAATATAATTAG-GTGATAAAAAGAATTTTA
* *
5904097 TAATTGAATGATGAATTTAAAATATATATATAATTAGGTGATAAAAAGAATTT
1 TAATTGAATGAT-AAATTAAAA-A-AAATATAATTAGGTGATAAAAAGAATTT
5904150 CCATGGGTCA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
51 11 0.24
52 8 0.18
53 1 0.02
54 19 0.42
55 6 0.13
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (52 bp):
TAATTGAATGATAAATTAAAAAAAATATAATTAGGTGATAAAAAGAATTTTA
Found at i:5924181 original size:28 final size:30
Alignment explanation
Indices: 5924124--5924181 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
5924114 TCTACAATTG
5924124 AAGTAAAATTATGACCAAAAATTTGTGTTT
1 AAGTAAAATTATGACCAAAAATTTGTGTTT
5924154 AAGTAAAATTATGA-CAAAAA-TTGTGTTT
1 AAGTAAAATTATGACCAAAAATTTGTGTTT
5924182 GTCAGTCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 8 0.29
29 6 0.21
30 14 0.50
ACGTcount: A:0.45, C:0.05, G:0.14, T:0.36
Consensus pattern (30 bp):
AAGTAAAATTATGACCAAAAATTTGTGTTT
Found at i:5925357 original size:33 final size:33
Alignment explanation
Indices: 5925320--5925384 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
5925310 ATTTGTATAT
*
5925320 ATATTT-TAAATTTATTATTATATTTTTTTGAAA
1 ATATTTATAAATTTATTA-TATATTTCTTTGAAA
* *
5925353 ATATTTATATATTTTTTATATATTTCTTTGAA
1 ATATTTATAAATTTATTATATATTTCTTTGAA
5925385 TTTTTTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 19 0.68
34 9 0.32
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.62
Consensus pattern (33 bp):
ATATTTATAAATTTATTATATATTTCTTTGAAA
Found at i:5928647 original size:28 final size:28
Alignment explanation
Indices: 5928603--5928674 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 28
5928593 TAAAAATATT
* *
5928603 TTTTTAAAAAATCTTT-ATAATTTTTATA
1 TTTTTAAATAAT-TTTAATAATTTTAATA
*
5928631 CTTTTCT-AATAATTTTAATAGTTTTAATA
1 -TTTT-TAAATAATTTTAATAATTTTAATA
5928660 TTTTTAAATAATTTT
1 TTTTTAAATAATTTT
5928675 CATTTTTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
27 1 0.03
28 16 0.43
29 19 0.51
30 1 0.03
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.58
Consensus pattern (28 bp):
TTTTTAAATAATTTTAATAATTTTAATA
Found at i:5928664 original size:18 final size:18
Alignment explanation
Indices: 5928637--5928686 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
5928627 TATACTTTTC
* *
5928637 TAATAATTTTAATAGTTT
1 TAATATTTTTAATAATTT
5928655 TAATATTTTTAAATAATTT
1 TAATATTTTT-AATAATTT
* *
5928674 TCATTTTTTTAAT
1 TAATATTTTTAAT
5928687 TTTTGAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
TAATATTTTTAATAATTT
Found at i:5928683 original size:28 final size:27
Alignment explanation
Indices: 5928638--5928690 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
5928628 ATACTTTTCT
5928638 AATAATTTTAATAGTTTTAATATTTTTA
1 AATAATTTTAATAGTTTTAAT-TTTTTA
* **
5928666 AATAATTTTCATTTTTTTAATTTTT
1 AATAATTTTAATAGTTTTAATTTTT
5928691 GAAAATTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (27 bp):
AATAATTTTAATAGTTTTAATTTTTTA
Found at i:5928696 original size:28 final size:28
Alignment explanation
Indices: 5928604--5928696 Score: 66
Period size: 28 Copynumber: 3.3 Consensus size: 28
5928594 AAAAATATTT
* *
5928604 TTTTAAAA-AATCTTT-ATAATTTTTATA
1 TTTTAAAATAAT-TTTAATAGTTTTAATA
**
5928631 CTTTTCTAATAATTTTAATAGTTTTAATA
1 -TTTTAAAATAATTTTAATAGTTTTAATA
* * **
5928660 TTTTTAAATAATTTTCATTTTTTTAAT-
1 TTTTAAAATAATTTTAATAGTTTTAATA
5928687 TTTTGAAAAT
1 TTTT-AAAAT
5928697 TTTAAAAAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
27 4 0.08
28 35 0.67
29 13 0.25
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.58
Consensus pattern (28 bp):
TTTTAAAATAATTTTAATAGTTTTAATA
Found at i:5937039 original size:76 final size:76
Alignment explanation
Indices: 5936887--5937165 Score: 389
Period size: 76 Copynumber: 3.6 Consensus size: 76
5936877 GGGAAGGATA
* * * * *
5936887 AAAAATTGTTATTAAGATTATCATTTATTACACTTATCTATTTTTTAACTTCAATTGGGGAGGAA
1 AAAAA-TGTTATTAGGATTACCATTTATTACACTTAT-T-TTTTTTAACTTTAATTAGGAAGGAA
5936952 ATGACTTTTTATAG
63 ATGACTTTTTATAG
*
5936966 AAAAATGTTATTAGGATTACCATTTATTACGCTTATTTTTTTTAACTTTAATTAGGAAGGAAATG
1 AAAAATGTTATTAGGATTACCATTTATTACACTTATTTTTTTTAACTTTAATTAGGAAGGAAATG
5937031 ACTTTTTATAG
66 ACTTTTTATAG
* *
5937042 AAAAATATTATTAGGATTACCATTTATTACACTTATTTATTTTTTTTAACTTTAATTCGGAAGGA
1 AAAAATGTTATTAGGATTACCATTTATTACAC----TTATTTTTTTTAACTTTAATTAGGAAGGA
*
5937107 AATTACTTTTTATAG
62 AATGACTTTTTATAG
*
5937122 AAAAATGTTACTAGGATTACCATTTATTACACTT-TTTTTATTTA
1 AAAAATGTTATTAGGATTACCATTTATTACACTTATTTTT-TTTA
5937166 TTTTCTAACT
Statistics
Matches: 183, Mismatches: 12, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
75 5 0.03
76 72 0.39
77 1 0.01
78 28 0.15
79 5 0.03
80 72 0.39
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (76 bp):
AAAAATGTTATTAGGATTACCATTTATTACACTTATTTTTTTTAACTTTAATTAGGAAGGAAATG
ACTTTTTATAG
Found at i:5937123 original size:80 final size:80
Alignment explanation
Indices: 5936887--5937181 Score: 404
Period size: 80 Copynumber: 3.7 Consensus size: 80
5936877 GGGAAGGATA
* * * * * *
5936887 AAAAATTGTTATTAAGATTATCATTTATTACACTTATCTA--TTTTTTAACTTCAATTGGGGAGG
1 AAAAA-TGTTATTAGGATTACCATTTATTACACTTATTTATTTTTTTTAACTTTAATTAGGAAGG
5936950 AAATGACTTTTTATAG
65 AAATGACTTTTTATAG
*
5936966 AAAAATGTTATTAGGATTACCATTTATTACGC----TTATTTTTTTTAACTTTAATTAGGAAGGA
1 AAAAATGTTATTAGGATTACCATTTATTACACTTATTTATTTTTTTTAACTTTAATTAGGAAGGA
5937027 AATGACTTTTTATAG
66 AATGACTTTTTATAG
* *
5937042 AAAAATATTATTAGGATTACCATTTATTACACTTATTTATTTTTTTTAACTTTAATTCGGAAGGA
1 AAAAATGTTATTAGGATTACCATTTATTACACTTATTTATTTTTTTTAACTTTAATTAGGAAGGA
*
5937107 AATTACTTTTTATAG
66 AATGACTTTTTATAG
* *
5937122 AAAAATGTTACTAGGATTACCATTTATTACACTTTTTTTATTTATTTTCTAACTTTAATT
1 AAAAATGTTATTAGGATTACCATTTATTACAC-TTATTTATTT-TTTT-TAACTTTAATT
5937182 TACTTTTTTT
Statistics
Matches: 193, Mismatches: 14, Indels: 14
0.87 0.06 0.06
Matches are distributed among these distances:
74 2 0.01
76 66 0.34
78 24 0.12
79 5 0.03
80 72 0.37
81 9 0.05
82 4 0.02
83 11 0.06
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.47
Consensus pattern (80 bp):
AAAAATGTTATTAGGATTACCATTTATTACACTTATTTATTTTTTTTAACTTTAATTAGGAAGGA
AATGACTTTTTATAG
Found at i:5940315 original size:52 final size:52
Alignment explanation
Indices: 5940237--5940351 Score: 178
Period size: 52 Copynumber: 2.2 Consensus size: 52
5940227 ATGCTTACGT
* *
5940237 CTATCAAAGCTCTATTGCGTTACAATGAATCAAACATA-CTGTTATTATTTCA
1 CTATCAAAGCTCTATTACATTACAATGAATCAAACA-AGCTGTTATTATTTCA
*
5940289 CTATCAAGGCTCTATTACATTACAATGAATCAAACAAGCTGTTATTATTTCA
1 CTATCAAAGCTCTATTACATTACAATGAATCAAACAAGCTGTTATTATTTCA
*
5940341 CTGTCAAAGCT
1 CTATCAAAGCT
5940352 TAATGTATGA
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
51 1 0.02
52 56 0.98
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (52 bp):
CTATCAAAGCTCTATTACATTACAATGAATCAAACAAGCTGTTATTATTTCA
Found at i:5942594 original size:3 final size:3
Alignment explanation
Indices: 5942586--5942617 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5942576 AATGAGCAAT
5942586 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
5942618 CGAATGAGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5943492 original size:6 final size:6
Alignment explanation
Indices: 5943481--5943514 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
5943471 AGAAAAGAGT
* *
5943481 GTAGTA GTAGTA GTAGTC GTAGTC GTAGTC GTAG
1 GTAGTC GTAGTC GTAGTC GTAGTC GTAGTC GTAG
5943515 GCCTCACTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.24, C:0.09, G:0.35, T:0.32
Consensus pattern (6 bp):
GTAGTC
Found at i:5954898 original size:34 final size:35
Alignment explanation
Indices: 5954824--5954900 Score: 129
Period size: 36 Copynumber: 2.2 Consensus size: 35
5954814 AGTATTTTTG
*
5954824 AAAGGATGCAGAATCAACATCGAGTCGAGCAACATT
1 AAAGTATGCAGAATCAACATCGAGTCGAG-AACATT
5954860 AAAGTATGCAGAATCAACATCGAGTCGAG-ACATT
1 AAAGTATGCAGAATCAACATCGAGTCGAGAACATT
5954894 AAAGTAT
1 AAAGTAT
5954901 CTCGTGGAGC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
34 12 0.30
36 28 0.70
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.19
Consensus pattern (35 bp):
AAAGTATGCAGAATCAACATCGAGTCGAGAACATT
Found at i:5965900 original size:20 final size:20
Alignment explanation
Indices: 5965872--5965909 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5965862 AGAAGATAAT
5965872 AGAAAATAAAAAAAATTAAA
1 AGAAAATAAAAAAAATTAAA
*
5965892 AGAACATAAAAAAAATTA
1 AGAAAATAAAAAAAATTA
5965910 TTTAAAACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (20 bp):
AGAAAATAAAAAAAATTAAA
Found at i:6006542 original size:20 final size:20
Alignment explanation
Indices: 6006517--6006556 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
6006507 CTCACCAATA
6006517 ACGGTCTTGTTCCAAGGCTT
1 ACGGTCTTGTTCCAAGGCTT
6006537 ACGGTCTTGTTCCAAGGCTT
1 ACGGTCTTGTTCCAAGGCTT
6006557 TAAGACAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (20 bp):
ACGGTCTTGTTCCAAGGCTT
Found at i:6008257 original size:17 final size:18
Alignment explanation
Indices: 6008227--6008263 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
6008217 TACGGTTATA
*
6008227 AATTATAAATTTTTAAAT
1 AATTATAAAATTTTAAAT
6008245 AATT-TAAAATTTTAAAT
1 AATTATAAAATTTTAAAT
6008262 AA
1 AA
6008264 AAAACTTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATTATAAAATTTTAAAT
Found at i:6009425 original size:20 final size:20
Alignment explanation
Indices: 6009397--6009434 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6009387 GACAATTTGT
* *
6009397 TAGATATATTGGTAAATCCA
1 TAGAAATATTAGTAAATCCA
6009417 TAGAAATATTAGTAAATC
1 TAGAAATATTAGTAAATC
6009435 GTCAAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (20 bp):
TAGAAATATTAGTAAATCCA
Found at i:6009451 original size:20 final size:20
Alignment explanation
Indices: 6009405--6009473 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 20
6009395 GTTAGATATA
* *
6009405 TTGGTAAATCCAT-AGAAATA
1 TTGGTAAATCC-TCAAAAATT
* * *
6009425 TTAGTAAATCGTCAAATATT
1 TTGGTAAATCCTCAAAAATT
* *
6009445 TTGGTAATTCCTTAAAAATT
1 TTGGTAAATCCTCAAAAATT
6009465 TTGGTAAAT
1 TTGGTAAAT
6009474 GGTAAATCAT
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
19 1 0.03
20 36 0.97
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (20 bp):
TTGGTAAATCCTCAAAAATT
Found at i:6009476 original size:27 final size:27
Alignment explanation
Indices: 6009446--6009499 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
6009436 TCAAATATTT
* *
6009446 TGGTAATTCCTTAAAAATTTTGGTAAA
1 TGGTAAATCATTAAAAATTTTGGTAAA
* *
6009473 TGGTAAATCATTAGATATTTTGGTAAA
1 TGGTAAATCATTAAAAATTTTGGTAAA
6009500 GTCAGAGAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.41
Consensus pattern (27 bp):
TGGTAAATCATTAAAAATTTTGGTAAA
Found at i:6009763 original size:20 final size:20
Alignment explanation
Indices: 6009740--6009814 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
6009730 TAAACTATTG
* **
6009740 GATATATAGGTAAATTGTTA
1 GATATATTGGTAAATCCTTA
*
6009760 GATATTTTGGTAAATCCTTA
1 GATATATTGGTAAATCCTTA
* *
6009780 GAGATATTGGTAAAGTCTCATA
1 GATATATTGGTAAA-TC-CTTA
6009802 -A-ATATTGGTAAAT
1 GATATATTGGTAAAT
6009815 TGACGGAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
19 1 0.02
20 39 0.85
21 3 0.07
22 3 0.07
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.39
Consensus pattern (20 bp):
GATATATTGGTAAATCCTTA
Found at i:6009812 original size:60 final size:60
Alignment explanation
Indices: 6009743--6009855 Score: 145
Period size: 60 Copynumber: 1.9 Consensus size: 60
6009733 ACTATTGGAT
** * *
6009743 ATATAGGTAAATTGTTAGATATTTTGGTAAATCCTTAGAGATATTGGTAAAGTCTCATAA
1 ATATAGGTAAATTGACAGAAATTTTGGTAAATCCTTAGAGATATTGATAAAGTCTCATAA
* * * * *
6009803 ATATTGGTAAATTGACGGAAATTTTGGTAAATCGTTAGATATTTTGATAAAGT
1 ATATAGGTAAATTGACAGAAATTTTGGTAAATCCTTAGAGATATTGATAAAGT
6009856 GATAGAAACT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 44 1.00
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.39
Consensus pattern (60 bp):
ATATAGGTAAATTGACAGAAATTTTGGTAAATCCTTAGAGATATTGATAAAGTCTCATAA
Found at i:6009846 original size:20 final size:20
Alignment explanation
Indices: 6009748--6009996 Score: 80
Period size: 20 Copynumber: 12.3 Consensus size: 20
6009738 TGGATATATA
* *
6009748 GGTAAATTGTTAGATATTTT
1 GGTAAATCGTTAGAAATTTT
* * *
6009768 GGTAAATCCTTAGAGATATT
1 GGTAAATCGTTAGAAATTTT
* * *
6009788 GGTAAAGTC-TCATAAATATT
1 GGTAAA-TCGTTAGAAATTTT
* ***
6009808 GGTAAATTGACGGAAATTTT
1 GGTAAATCGTTAGAAATTTT
*
6009828 GGTAAATCGTTAGATATTTT
1 GGTAAATCGTTAGAAATTTT
* * *
6009848 GATAAAGT-GATAGAAACTTT
1 GGTAAA-TCGTTAGAAATTTT
* * *
6009868 GGT-AATTGTTA-ATA-CTT
1 GGTAAATCGTTAGAAATTTT
** *
6009885 GGTATGGT-GTTTAGAAAATTT
1 GGTA-AATCG-TTAGAAATTTT
* *
6009906 GGAAATATTGGTAAGTAGAAATTTT
1 GGTAA-A-TCGT---TAGAAATTTT
* * *
6009931 GGTAGATCGTTAGATATATT
1 GGTAAATCGTTAGAAATTTT
* * *
6009951 GGTAAGTTC-TTAAAAATATT
1 GGTAA-ATCGTTAGAAATTTT
*
6009971 GGTAAATCGTTAGATATTTT
1 GGTAAATCGTTAGAAATTTT
6009991 GGTAAA
1 GGTAAA
6009997 GTTGAGGAAC
Statistics
Matches: 166, Mismatches: 46, Indels: 34
0.67 0.19 0.14
Matches are distributed among these distances:
17 5 0.03
18 4 0.02
19 12 0.07
20 116 0.70
21 10 0.06
22 2 0.01
23 4 0.02
24 1 0.01
25 12 0.07
ACGTcount: A:0.35, C:0.04, G:0.21, T:0.39
Consensus pattern (20 bp):
GGTAAATCGTTAGAAATTTT
Found at i:6009957 original size:36 final size:37
Alignment explanation
Indices: 6009910--6009995 Score: 102
Period size: 40 Copynumber: 2.3 Consensus size: 37
6009900 AAATTTGGAA
* * *
6009910 ATATTGGTAAG-TAGAAATTTTGGTAGATCGTTAGAT
1 ATATTGGTAAGTTAAAAATATTGGTAAATCGTTAGAT
6009946 ATATTGGTAAGTTCTTAAAAATATTGGTAAATCGTTAGAT
1 ATATTGGTAAG---TTAAAAATATTGGTAAATCGTTAGAT
*
6009986 ATTTTGGTAA
1 ATATTGGTAA
6009996 AGTTGAGGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
36 11 0.26
40 31 0.74
ACGTcount: A:0.35, C:0.03, G:0.21, T:0.41
Consensus pattern (37 bp):
ATATTGGTAAGTTAAAAATATTGGTAAATCGTTAGAT
Found at i:6010095 original size:40 final size:39
Alignment explanation
Indices: 6010051--6010127 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 39
6010041 GAAAATTTGA
*
6010051 AAATATTGGTAAAATC-TTAGAAATTTTGGTAAAGTCTTAT
1 AAATATTGGTAAAA-CAATAGAAATTTTGGTAAA-TCTTAT
6010091 AAATATTGGTAAAACAATAGAAATTTTGGTAAATCTT
1 AAATATTGGTAAAACAATAGAAATTTTGGTAAATCTT
6010128 TAGAAATCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
39 5 0.14
40 30 0.86
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (39 bp):
AAATATTGGTAAAACAATAGAAATTTTGGTAAATCTTAT
Found at i:6010224 original size:20 final size:20
Alignment explanation
Indices: 6010051--6010225 Score: 106
Period size: 20 Copynumber: 8.8 Consensus size: 20
6010041 GAAAATTTGA
*
6010051 AAATATTGGTAAAATC-TTAG
1 AAATTTTGGT-AAATCTTTAG
*
6010071 AAATTTTGGTAAAGTC-TTAT
1 AAATTTTGGTAAA-TCTTTAG
* * **
6010091 AAATATTGGTAAAACAATAG
1 AAATTTTGGTAAATCTTTAG
6010111 AAATTTTGGTAAATCTTTAG
1 AAATTTTGGTAAATCTTTAG
** *
6010131 AAATCCTGATAAAT-TGTTAG
1 AAATTTTGGTAAATCT-TTAG
** * **
6010151 TTATATTGGTGAAAT-GATAG
1 AAATTTTGGT-AAATCTTTAG
* *
6010171 AAATTTTGGTAACTCATTAG
1 AAATTTTGGTAAATCTTTAG
* **
6010191 ATATTTAAGTAAATCTTTAG
1 AAATTTTGGTAAATCTTTAG
*
6010211 AAATTTCGGTAAATC
1 AAATTTTGGTAAATC
6010226 GTTAAATATT
Statistics
Matches: 116, Mismatches: 34, Indels: 10
0.73 0.21 0.06
Matches are distributed among these distances:
19 8 0.07
20 104 0.90
21 4 0.03
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.38
Consensus pattern (20 bp):
AAATTTTGGTAAATCTTTAG
Found at i:6010399 original size:20 final size:20
Alignment explanation
Indices: 6010376--6010479 Score: 91
Period size: 20 Copynumber: 5.2 Consensus size: 20
6010366 GATAAAATGA
*
6010376 TAGAAATTTTAATAAATCGT
1 TAGAAATTTTGATAAATCGT
* * *
6010396 TAGATATTTTGTTAAATCCT
1 TAGAAATTTTGATAAATCGT
* * * **
6010416 TAGAAATGTTGGTAAAACAA
1 TAGAAATTTTGATAAATCGT
*
6010436 TAGAAATCTTGATAAATCGT
1 TAGAAATTTTGATAAATCGT
* * *
6010456 TAGATATATTGATAAATAGT
1 TAGAAATTTTGATAAATCGT
6010476 TAGA
1 TAGA
6010480 TGTATTGGTA
Statistics
Matches: 66, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.38
Consensus pattern (20 bp):
TAGAAATTTTGATAAATCGT
Found at i:6010480 original size:20 final size:20
Alignment explanation
Indices: 6010444--6010492 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
6010434 AATAGAAATC
*
6010444 TTGATAAATCGTTAGATATA
1 TTGATAAATAGTTAGATATA
*
6010464 TTGATAAATAGTTAGATGTA
1 TTGATAAATAGTTAGATATA
*
6010484 TTGGTAAAT
1 TTGATAAAT
6010493 CCTTAATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.39, C:0.02, G:0.18, T:0.41
Consensus pattern (20 bp):
TTGATAAATAGTTAGATATA
Found at i:6010488 original size:60 final size:60
Alignment explanation
Indices: 6010360--6010491 Score: 156
Period size: 60 Copynumber: 2.2 Consensus size: 60
6010350 AAGTCTCCTT
* ** * * * *
6010360 AATATTGATAAAATGATAGAAATTTTAATAAATCGTTAGATATTTTGTTAAATCCTTAGA
1 AATATTGGTAAAACAATAGAAATCTTAATAAATCGTTAGATATATTGATAAATACTTAGA
* * *
6010420 AATGTTGGTAAAACAATAGAAATCTTGATAAATCGTTAGATATATTGATAAATAGTTAGA
1 AATATTGGTAAAACAATAGAAATCTTAATAAATCGTTAGATATATTGATAAATACTTAGA
**
6010480 TGTATTGGTAAA
1 AATATTGGTAAA
6010492 TCCTTAATTA
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.43, C:0.05, G:0.15, T:0.37
Consensus pattern (60 bp):
AATATTGGTAAAACAATAGAAATCTTAATAAATCGTTAGATATATTGATAAATACTTAGA
Found at i:6012063 original size:14 final size:15
Alignment explanation
Indices: 6012034--6012067 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
6012024 CATTTTCATT
6012034 TTCTTCTCCTTATTC
1 TTCTTCTCCTTATTC
6012049 TTCTTCTCC-TATTC
1 TTCTTCTCCTTATTC
6012063 TTCTT
1 TTCTT
6012068 ATTATTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.06, C:0.32, G:0.00, T:0.62
Consensus pattern (15 bp):
TTCTTCTCCTTATTC
Found at i:6014789 original size:131 final size:132
Alignment explanation
Indices: 6014469--6014989 Score: 613
Period size: 132 Copynumber: 4.0 Consensus size: 132
6014459 TTTAGAGAGT
* * *
6014469 ATGAGTGAAATTCTAAAGGAATC-TTCGATCATTCTG-GACAAAC-AGGAAATCGCAACCCAGCA
1 ATGAGTGAAATTCTAAAGGGA-CATTCGATTATTTTGAG-CAAACGA-GAAATCGCAACCCAGCA
* * * * * * ** * * *
6014531 CGATAGGGCACGATTCCCCGAATTGTCATACATCGAATATTACCCTCGTTTTGAAGAGTTTTTAG
63 CGTTAGGGCACGATTCCGCGAATTGCCAAATATCGAACATCGCCTTCGTTTTAAAGAATTTTTAG
*
6014596 AAAAC
128 AAGAC
* * * * *
6014601 ATAAGTGAAATTCAAAAGGGACTTTCGATCATTTTGAACAAACGAGAAATCGCAACCCAGCACGT
1 ATGAGTGAAATTCTAAAGGGACATTCGATTATTTTGAGCAAACGAGAAATCGCAACCCAGCACGT
* *
6014666 TAAGGCACGATTCCGCAAATTGCCAAATATCGAACATCGCCTTCG-TTTAAAGAATTTTTA-AAG
66 TAGGGCACGATTCCGCGAATTGCCAAATATCGAACATCGCCTTCGTTTTAAAGAATTTTTAGAA-
6014729 GAC
130 GAC
* * * * * *
6014732 ATGGGTGAAATTCTAAAGGGACCTTCAATTACTTTGAGCAAACGAGAAATTGCAACCCAACACGT
1 ATGAGTGAAATTCTAAAGGGACATTCGATTATTTTGAGCAAACGAGAAATCGCAACCCAGCACGT
* *
6014797 TAGGGCACGATTCCGCGAATTGCCAAATATCGAATATCGCCTTCGTTTTAAAGGATTTTTAGAAG
66 TAGGGCACGATTCCGCGAATTGCCAAATATCGAACATCGCCTTCGTTTTAAAGAATTTTTAGAAG
6014862 AC
131 AC
* * * * * *
6014864 ATGAGTGAAATTTTGAAGGGATATTCGATTATTTTGAGCAAACGATAAATTGCACCCCAGCACGT
1 ATGAGTGAAATTCTAAAGGGACATTCGATTATTTTGAGCAAACGAGAAATCGCAACCCAGCACGT
* *
6014929 TAGGGCACGATTTCGCGAATTGCCAAATATCAAATC-TCGCCTTCGTTTTAAAGAATTTTTA
66 TAGGGCACGATTCCGCGAATTGCCAAATATCGAA-CATCGCCTTCGTTTTAAAGAATTTTTA
6014990 AACGAATAAT
Statistics
Matches: 335, Mismatches: 47, Indels: 14
0.85 0.12 0.04
Matches are distributed among these distances:
130 2 0.01
131 113 0.34
132 217 0.65
133 3 0.01
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (132 bp):
ATGAGTGAAATTCTAAAGGGACATTCGATTATTTTGAGCAAACGAGAAATCGCAACCCAGCACGT
TAGGGCACGATTCCGCGAATTGCCAAATATCGAACATCGCCTTCGTTTTAAAGAATTTTTAGAAG
AC
Found at i:6014940 original size:263 final size:264
Alignment explanation
Indices: 6014514--6014991 Score: 676
Period size: 263 Copynumber: 1.8 Consensus size: 264
6014504 GGACAAACAG
* * * *
6014514 GAAATCGCAACCCAGCACGATAGGGCACGATTCCCCGAATTGTCATACATCGAATATTACCCTCG
1 GAAATCGCAACCCAACACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAATATCACCCTCG
*
6014579 TTTTGAAGAGTTTTTAGAAAACATAAGTGAAATTCAAAAGGGACTTTCGATCATTTTGAACAAAC
66 TTTTAAAGAGTTTTTAGAAAACATAAGTGAAATTCAAAAGGGACTTTCGATCATTTTGAACAAAC
*
6014644 GAGAAATCGCAACCCAGCACGTTAAGGCACGATTCCGCAAATTGCCAAATATCGAA-CATCGCCT
131 GAGAAATCGCAACCCAGCACGTTAAGGCACGATTCCGCAAATTGCCAAATATCAAATC-TCGCCT
6014708 TCG-TTTAAAGAATTTTTAAAGGACATGGGTGAAATTCTAAAGGGACCTTCAATTACTTTGAGCA
195 TCGTTTTAAAGAATTTTTAAAGGACATGGGTGAAATTCTAAAGGGACCTTCAATTACTTTGAGCA
6014772 AACGA
260 AACGA
* * * * * *
6014777 GAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAATATCGAATATCGCCTTCG
1 GAAATCGCAACCCAACACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAATATCACCCTCG
* * *** * *
6014842 TTTTAAAG-GATTTTTAGAAGACATGAGTGAAATTTTGAAGGGA-TATTCGATTATTTTGAGCAA
66 TTTTAAAGAG-TTTTTAGAAAACATAAGTGAAATTCAAAAGGGACT-TTCGATCATTTTGAACAA
* * * * * *
6014905 ACGATAAATTGCACCCCAGCACGTTAGGGCACGATTTCGCGAATTGCCAAATATCAAATCTCGCC
129 ACGAGAAATCGCAACCCAGCACGTTAAGGCACGATTCCGCAAATTGCCAAATATCAAATCTCGCC
6014970 TTCGTTTTAAAGAATTTTTAAA
194 TTCGTTTTAAAGAATTTTTAAA
6014992 CGAATAATTA
Statistics
Matches: 186, Mismatches: 25, Indels: 7
0.85 0.11 0.03
Matches are distributed among these distances:
262 2 0.01
263 166 0.89
264 18 0.10
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (264 bp):
GAAATCGCAACCCAACACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAATATCACCCTCG
TTTTAAAGAGTTTTTAGAAAACATAAGTGAAATTCAAAAGGGACTTTCGATCATTTTGAACAAAC
GAGAAATCGCAACCCAGCACGTTAAGGCACGATTCCGCAAATTGCCAAATATCAAATCTCGCCTT
CGTTTTAAAGAATTTTTAAAGGACATGGGTGAAATTCTAAAGGGACCTTCAATTACTTTGAGCAA
ACGA
Found at i:6017139 original size:24 final size:24
Alignment explanation
Indices: 6017124--6017196 Score: 121
Period size: 24 Copynumber: 3.0 Consensus size: 24
6017114 TAGCTCTACT
6017124 TCAGCTTAGAAGTTTAGCCTCAGC
1 TCAGCTTAGAAGTTTAGCCTCAGC
*
6017148 TCAGCTTAGGAGTTTAGCCTCAGC
1 TCAGCTTAGAAGTTTAGCCTCAGC
6017172 TCAGCTTA-AGAGTTTAGCCTCAGC
1 TCAGCTTAGA-AGTTTAGCCTCAGC
6017196 T
1 T
6017197 TAGACACGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (24 bp):
TCAGCTTAGAAGTTTAGCCTCAGC
Found at i:6032801 original size:3 final size:3
Alignment explanation
Indices: 6032793--6032832 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
6032783 GTAGGGAAGC
*
6032793 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
6032833 TAATTAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:6033058 original size:13 final size:13
Alignment explanation
Indices: 6033040--6033064 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6033030 AATAACTGTT
6033040 TTTGGTTATATTA
1 TTTGGTTATATTA
6033053 TTTGGTTATATT
1 TTTGGTTATATT
6033065 TATGAAAACA
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:0.20, C:0.00, G:0.16, T:0.64
Consensus pattern (13 bp):
TTTGGTTATATTA
Found at i:6046023 original size:15 final size:15
Alignment explanation
Indices: 6046005--6046034 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6045995 CTCCTTACTA
*
6046005 TTACAATTCACCACC
1 TTACAAGTCACCACC
6046020 TTACAAGTCACCACC
1 TTACAAGTCACCACC
6046035 GCCGCCTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.40, G:0.03, T:0.23
Consensus pattern (15 bp):
TTACAAGTCACCACC
Found at i:6046112 original size:48 final size:48
Alignment explanation
Indices: 6046054--6046822 Score: 588
Period size: 48 Copynumber: 15.9 Consensus size: 48
6046044 ACCTAGTCCT
* *
6046054 CCACCACCTTACTACTACAAGTCTCCACCTCCACCATCTCCTTCACCA
1 CCACCTCCTTACTACTACAAGTCACCACCTCCACCATCTCCTTCACCA
* * * * * * *
6046102 CCTCCTCCTTACTATTACAAATCACCACCACCCCCTTCACCTAGTC-CC-
1 CCACCTCCTTACTACTACAAGTCACCACCTCCACCATCTCCT--TCACCA
* *
6046150 CCACCAT-CATACTACTACAACTCACCACCTCCACCATCTCCTTCACCA
1 CCACC-TCCTTACTACTACAAGTCACCACCTCCACCATCTCCTTCACCA
* * * * *
6046198 CCTCCTCCTTACTACTACAAATCACCACCACCACCCTCACCTAGTC-CC-
1 CCACCTCCTTACTACTACAAGTCACCACCTCCACCATCTCCT--TCACCA
* *
6046246 CCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCTTCACCA
1 CCACCTCCTTACTACTACAAGTCACCACCTCCACCATCTCCTTCACCA
* * * * * **
6046294 CCCCCTCCTTACTATTACAAGTCTCCACCCCCACCCTCAGCTAGTC-CC-
1 CCACCTCCTTACTACTACAAGTCACCACCTCCACCATCTCCT--TCACCA
* *
6046342 CCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCTTCACCA
1 CCACCTCCTTACTACTACAAGTCACCACCTCCACCATCTCCTTCACCA
* * * * * * *
6046390 CCTCCTCCTTACTATTACAAGTCTCCACCCCCGCCCTCACCTAGTC-CC-
1 CCACCTCCTTACTACTACAAGTCACCACCTCCACCATCTCCT--TCACCA
* * * *
6046438 CCACCACCATACTACTACAAGTCACCACCTCCACCGTCTCCCTCACCA
1 CCACCTCCTTACTACTACAAGTCACCACCTCCACCATCTCCTTCACCA
* * * * *
6046486 CCTCCTCCTTACTACTACAAATCACCACCACCACCCTCACCTAGTC-CC-
1 CCACCTCCTTACTACTACAAGTCACCACCTCCACCATCTCCT--TCACCA
* * *
6046534 CCACCACCATACTACTACAAGTCACCACCTCCACCATCTCCCTCACCA
1 CCACCTCCTTACTACTACAAGTCACCACCTCCACCATCTCCTTCACCA
* * * * * *** *
6046582 CCTCCTCCTTACTACTACAAATCACCACCACCACCTTCACCTAGTCCT
1 CCACCTCCTTACTACTACAAGTCACCACCTCCACCATCTCCTTCACCA
* * * *
6046630 CCACCACCATACTACTACAAGTCTCCAGTACCTCCACCATCTCCTAGTCCCCCA
1 CCACCTCCTTACTACTACAAGTCACC---ACCTCCACCATCTCCT--T-CACCA
* * * * * * * *
6046684 CCACCTCCATACTACTACAAATCTCCTCCTCTACCGTCTCCATCACCC
1 CCACCTCCTTACTACTACAAGTCACCACCTCCACCATCTCCTTCACCA
* * * * * * *
6046732 CCTCCTCCTTACTACTACAAATCACCACCACCTCCTTCTCCATCACCC
1 CCACCTCCTTACTACTACAAGTCACCACCTCCACCATCTCCTTCACCA
* * * * * *
6046780 CCGCCACCTTACTATTATAAGTCACCTCCTCCACCACCTCCTT
1 CCACCTCCTTACTACTACAAGTCACCACCTCCACCATCTCCTT
6046823 ATCACTACTA
Statistics
Matches: 559, Mismatches: 134, Indels: 56
0.75 0.18 0.07
Matches are distributed among these distances:
46 10 0.02
47 11 0.02
48 465 0.83
49 12 0.02
50 10 0.02
51 25 0.04
54 26 0.05
ACGTcount: A:0.25, C:0.50, G:0.03, T:0.22
Consensus pattern (48 bp):
CCACCTCCTTACTACTACAAGTCACCACCTCCACCATCTCCTTCACCA
Found at i:6046127 original size:96 final size:96
Alignment explanation
Indices: 6046021--6046706 Score: 1032
Period size: 96 Copynumber: 7.1 Consensus size: 96
6046011 TTCACCACCT
* * * * * * *
6046021 TACAAGTCACCACCGCCGCCTTCACCTAGTCCTCCACCACCTTACTACTACAAGTCTCCACCTCC
1 TACAAATCACCACCACCACCCTCACCTAGTCCCCCACCACCATACTACTACAAGTCACCACCTCC
*
6046086 ACCATCTCCTTCACCACCTCCTCCTTACTAT
66 ACCATCTCCTTCACCACCTCCTCCTTACTAC
* *
6046117 TACAAATCACCACCACC-CCCTTCACCTAGTCCCCCACCATCATACTACTACAACTCACCACCTC
1 TACAAATCACCACCACCACCC-TCACCTAGTCCCCCACCACCATACTACTACAAGTCACCACCTC
6046181 CACCATCTCCTTCACCACCTCCTCCTTACTAC
65 CACCATCTCCTTCACCACCTCCTCCTTACTAC
6046213 TACAAATCACCACCACCACCCTCACCTAGTCCCCCACCACCATACTACTACAAGTCACCACCTCC
1 TACAAATCACCACCACCACCCTCACCTAGTCCCCCACCACCATACTACTACAAGTCACCACCTCC
* *
6046278 ACCATCTCCTTCACCACCCCCTCCTTACTAT
66 ACCATCTCCTTCACCACCTCCTCCTTACTAC
* * * *
6046309 TACAAGTCTCCACCCCCACCCTCAGCTAGTCCCCCACCACCATACTACTACAAGTCACCACCTCC
1 TACAAATCACCACCACCACCCTCACCTAGTCCCCCACCACCATACTACTACAAGTCACCACCTCC
*
6046374 ACCATCTCCTTCACCACCTCCTCCTTACTAT
66 ACCATCTCCTTCACCACCTCCTCCTTACTAC
* * * *
6046405 TACAAGTCTCCACCCCCGCCCTCACCTAGTCCCCCACCACCATACTACTACAAGTCACCACCTCC
1 TACAAATCACCACCACCACCCTCACCTAGTCCCCCACCACCATACTACTACAAGTCACCACCTCC
* *
6046470 ACCGTCTCCCTCACCACCTCCTCCTTACTAC
66 ACCATCTCCTTCACCACCTCCTCCTTACTAC
6046501 TACAAATCACCACCACCACCCTCACCTAGTCCCCCACCACCATACTACTACAAGTCACCACCTCC
1 TACAAATCACCACCACCACCCTCACCTAGTCCCCCACCACCATACTACTACAAGTCACCACCTCC
*
6046566 ACCATCTCCCTCACCACCTCCTCCTTACTAC
66 ACCATCTCCTTCACCACCTCCTCCTTACTAC
* * *
6046597 TACAAATCACCACCACCACCTTCACCTAGTCCTCCACCACCATACTACTACAAGTCTCCAGTACC
1 TACAAATCACCACCACCACCCTCACCTAGTCCCCCACCACCATACTACTACAAGTCACC---ACC
* * *
6046662 TCCACCATCTCCTAGTCCCCCACCACCTCCATACTAC
63 TCCACCATCTCCT--T-CACCACCTCCTCCTTACTAC
6046699 TACAAATC
1 TACAAATC
6046707 TCCTCCTCTA
Statistics
Matches: 547, Mismatches: 35, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
95 2 0.00
96 501 0.92
97 3 0.01
99 15 0.03
101 1 0.00
102 25 0.05
ACGTcount: A:0.25, C:0.50, G:0.03, T:0.21
Consensus pattern (96 bp):
TACAAATCACCACCACCACCCTCACCTAGTCCCCCACCACCATACTACTACAAGTCACCACCTCC
ACCATCTCCTTCACCACCTCCTCCTTACTAC
Found at i:6048559 original size:31 final size:30
Alignment explanation
Indices: 6048515--6048573 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
6048505 ATTATTTATT
6048515 TATTTGAAAG-TTTTAGTTTAAGTCATTGAAC
1 TATTTGAAAGTTTTTA-TTT-AGTCATTGAAC
* *
6048546 TATTTTAACGTTTTTATTTAGTCATTGA
1 TATTTGAAAGTTTTTATTTAGTCATTGA
6048574 GTTATTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 9 0.36
31 11 0.44
32 5 0.20
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.51
Consensus pattern (30 bp):
TATTTGAAAGTTTTTATTTAGTCATTGAAC
Found at i:6058317 original size:5 final size:5
Alignment explanation
Indices: 6058307--6058332 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
6058297 ATTGAAATAC
6058307 ATATA ATATA ATATA ATATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA A
6058333 ACGTTAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:6063184 original size:18 final size:18
Alignment explanation
Indices: 6063161--6063198 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
6063151 AAATTGAACA
* *
6063161 AATGCCTGCAAACCGGTT
1 AATGCCCGCAAACCGATT
6063179 AATGCCCGCAAACCGATT
1 AATGCCCGCAAACCGATT
6063197 AA
1 AA
6063199 ACCCAAGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.29, G:0.18, T:0.18
Consensus pattern (18 bp):
AATGCCCGCAAACCGATT
Found at i:6065330 original size:42 final size:42
Alignment explanation
Indices: 6065271--6065382 Score: 161
Period size: 42 Copynumber: 2.7 Consensus size: 42
6065261 CGTTTCCTCG
* *
6065271 ATGCCATAGTCCAACTATGGTCTTACACATCTTCACATATTA
1 ATGCCATAGCCCAACTATGGTCTTACACATATTCACATATTA
* *
6065313 ATGCCATAGCCCAACTATGATCTTACATATATTCACATATTA
1 ATGCCATAGCCCAACTATGGTCTTACACATATTCACATATTA
* * *
6065355 ATGCCATAACCCAGCTATAGTCTTACAC
1 ATGCCATAGCCCAACTATGGTCTTACAC
6065383 GTAATCATAT
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.33, C:0.27, G:0.09, T:0.31
Consensus pattern (42 bp):
ATGCCATAGCCCAACTATGGTCTTACACATATTCACATATTA
Found at i:6065522 original size:50 final size:50
Alignment explanation
Indices: 6065345--6065528 Score: 214
Period size: 50 Copynumber: 3.7 Consensus size: 50
6065335 TTACATATAT
** * * *
6065345 TCACATATTAATGCCATAACCCAGCTATAGTCTTACA-CGTAATCATAT-A
1 TCACATATCGATGCCATAGCCCAGCTATGGTCTTACATCG-AATCACATAA
* * **
6065394 TCACGTATTGATGCCATAGCCCAGCTATCATCTT--ATGCGAGATCACATAA
1 TCACATATCGATGCCATAGCCCAGCTATGGTCTTACAT-CGA-ATCACATAA
* *
6065444 TCACATACCGATGCCATAGCCCAGCTATGGTCTTACATAGAATCACATAA
1 TCACATATCGATGCCATAGCCCAGCTATGGTCTTACATCGAATCACATAA
6065494 TCACATATCGATGCCATAGCCCAGCTATGGTCTTA
1 TCACATATCGATGCCATAGCCCAGCTATGGTCTTA
6065529 TACACATAAT
Statistics
Matches: 116, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
47 1 0.01
48 1 0.01
49 37 0.32
50 73 0.63
51 2 0.02
52 2 0.02
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.28
Consensus pattern (50 bp):
TCACATATCGATGCCATAGCCCAGCTATGGTCTTACATCGAATCACATAA
Found at i:6069091 original size:31 final size:32
Alignment explanation
Indices: 6069051--6069110 Score: 113
Period size: 31 Copynumber: 1.9 Consensus size: 32
6069041 TTAATTTCCG
6069051 ATATCTCATTTGTAACCTTTTTACTTATTATC
1 ATATCTCATTTGTAACCTTTTTACTTATTATC
6069083 ATAT-TCATTTGTAACCTTTTTACTTATT
1 ATATCTCATTTGTAACCTTTTTACTTATT
6069111 TCACAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.25, C:0.17, G:0.03, T:0.55
Consensus pattern (32 bp):
ATATCTCATTTGTAACCTTTTTACTTATTATC
Found at i:6071439 original size:21 final size:21
Alignment explanation
Indices: 6071415--6071481 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
6071405 ACTCATATGA
*
6071415 GTTTTAGTTCAACCCTTTTGG
1 GTTTCAGTTCAACCCTTTTGG
* * * *
6071436 GTTTCAGTTTAGCTCTTTTGA
1 GTTTCAGTTCAACCCTTTTGG
* * *
6071457 GCTTCAGTTTAACCCTTATGG
1 GTTTCAGTTCAACCCTTTTGG
6071478 GTTT
1 GTTT
6071482 TCGTTCAGCT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.15, C:0.18, G:0.19, T:0.48
Consensus pattern (21 bp):
GTTTCAGTTCAACCCTTTTGG
Found at i:6071472 original size:42 final size:42
Alignment explanation
Indices: 6071420--6071523 Score: 111
Period size: 42 Copynumber: 2.5 Consensus size: 42
6071410 TATGAGTTTT
* * * * **
6071420 AGTTCAACCCTTTTGGG-TTTCAGTTTAGCTCTTTTGAGCTTC
1 AGTTTAACCCTTATGGGTTTTC-GTTCAGCTCCTAAGAGCTTC
6071462 AGTTTAACCCTTATGGGTTTTCGTTCAGCTCCTAAGAGCTTC
1 AGTTTAACCCTTATGGGTTTTCGTTCAGCTCCTAAGAGCTTC
* * *
6071504 CGTTTAACCCATACGGGTTT
1 AGTTTAACCCTTATGGGTTT
6071524 CCGATTAGCA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 48 0.92
43 4 0.08
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.40
Consensus pattern (42 bp):
AGTTTAACCCTTATGGGTTTTCGTTCAGCTCCTAAGAGCTTC
Found at i:6073519 original size:47 final size:47
Alignment explanation
Indices: 6073468--6073644 Score: 213
Period size: 47 Copynumber: 3.8 Consensus size: 47
6073458 TGGTTGAACA
*
6073468 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAACG
* *
6073515 TCCGAACTCGTTGAGTTGAGTCCGAG-T---TTGTGAGATGT-AACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGTGAA--A--CG
*
6073562 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCG-AACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAACG
* *
6073608 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
6073645 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 8, Indels: 21
0.79 0.06 0.15
Matches are distributed among these distances:
43 6 0.05
44 5 0.04
45 1 0.01
46 37 0.33
47 52 0.46
48 2 0.02
50 5 0.04
51 4 0.04
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (47 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAACG
Found at i:6074397 original size:19 final size:20
Alignment explanation
Indices: 6074369--6074407 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
6074359 TCCCATTATT
6074369 TATTTATTTTT-TGTTTTAA
1 TATTTATTTTTATGTTTTAA
*
6074388 TATTTGTTTTTATGTTTTAA
1 TATTTATTTTTATGTTTTAA
6074408 ATGTATTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.72
Consensus pattern (20 bp):
TATTTATTTTTATGTTTTAA
Found at i:6074425 original size:25 final size:23
Alignment explanation
Indices: 6074388--6074433 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
6074378 TTTGTTTTAA
*
6074388 TATTTGTTTTTATGTTTTAAATG
1 TATTTGTTTTTATATTTTAAATG
6074411 TATTTGATTTATTATATTTTAAA
1 TATTTG-TTT-TTATATTTTAAA
6074434 GTTTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 3 0.15
25 11 0.55
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (23 bp):
TATTTGTTTTTATATTTTAAATG
Found at i:6091393 original size:19 final size:19
Alignment explanation
Indices: 6091348--6091402 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
6091338 TTAAACATGG
* *
6091348 TATAATTTTAAATTA-TGT
1 TATAATTTTAAAATATTTT
6091366 TAT--TTTTAAAATATTTT
1 TATAATTTTAAAATATTTT
*
6091383 TATAATTTTAAAGTATTTT
1 TATAATTTTAAAATATTTT
6091402 T
1 T
6091403 TAACGTGATG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 9 0.29
17 5 0.16
18 3 0.10
19 14 0.45
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (19 bp):
TATAATTTTAAAATATTTT
Found at i:6095515 original size:21 final size:21
Alignment explanation
Indices: 6095489--6095529 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6095479 AGACGAGCAA
* *
6095489 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
6095510 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
6095530 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:6100894 original size:5 final size:5
Alignment explanation
Indices: 6100884--6100916 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
6100874 GAATTAAAGA
*
6100884 GTATG GTATG GTATG GTATG GTATA GT-TG GTAT
1 GTATG GTATG GTATG GTATG GTATG GTATG GTAT
6100917 CCAAGAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 22 0.88
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.42
Consensus pattern (5 bp):
GTATG
Found at i:6107087 original size:46 final size:46
Alignment explanation
Indices: 6107040--6107313 Score: 334
Period size: 46 Copynumber: 6.0 Consensus size: 46
6107030 GCTCTCTGAT
** * * *
6107040 ATGAAATGTGTAAGACCATGGTTGAAAGATATCATGGCAACCTGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** * * *
6107086 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACGTGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
6107132 ATGAAATGAATAAGACCATGGTAGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** * * *
6107178 GGGAAATGAATAAGACCATGGTTGAAAGATATCATGGCAGCGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
6107224 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAAATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * * *
6107270 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATG
6107314 TCAAAGATAA
Statistics
Matches: 200, Mismatches: 27, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
45 1 0.00
46 199 1.00
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:6107193 original size:92 final size:92
Alignment explanation
Indices: 6107036--6107298 Score: 373
Period size: 92 Copynumber: 2.9 Consensus size: 92
6107026 GTGTGCTCTC
** * * * * *
6107036 TGATATGAAATGTGTAAGACCATGGTTGAAAGATATCATGGCAACCTGATATGAAATGTGTAAGA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAGTAAGA
6107101 CCATGGTTGAAAGATACCATGACAACG
66 CCATGGTTGAAAGATACCATGACAACG
* * *
6107128 TGATATGAAATGAATAAGACCATGGTAGAAAGATACCATGGCAACATGACGGGAAATGAATAAGA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAGTAAGA
* * *
6107193 CCATGGTTGAAAGATATCATGGCAGCG
66 CCATGGTTGAAAGATACCATGACAACG
* * *
6107220 TGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAAATGACAGAAAATGAGTAAGA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAGTAAGA
*
6107285 CCATAGTTGAAAGA
66 CCATGGTTGAAAGA
6107299 CACTATGGCA
Statistics
Matches: 151, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
92 151 1.00
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (92 bp):
TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAGTAAGA
CCATGGTTGAAAGATACCATGACAACG
Found at i:6107297 original size:138 final size:138
Alignment explanation
Indices: 6107050--6107313 Score: 377
Period size: 138 Copynumber: 1.9 Consensus size: 138
6107040 ATGAAATGTG
* **
6107050 TAAGACCATGGTTGAAAGATATCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATATCATGGCAACCTGACATGAAATGAATAAGACCATGGTTGAAAGA
** * * *
6107115 TACCATGACAACGTGATATGAAATGAATAAGACCATGGTAGAAAGATACCATGGCAACATGACGG
66 TACCATGACAAAATGACATGAAATGAATAAGACCATAGTAGAAAGACACCATGGCAACATGACGG
6107180 GAAATGAA
131 GAAATGAA
* *
6107188 TAAGACCATGGTTGAAAGATATCATGGCAGCGTGACATGAAATGAATAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATATCATGGCAACCTGACATGAAATGAATAAGACCATGGTTGAAAGA
* * * * *
6107253 TACCATGGCAAAATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
66 TACCATGACAAAATGACATG-AAATGAATAAGACCATAGTAGAAAGACACCATGGCAACATG
6107314 TCAAAGATAA
Statistics
Matches: 110, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
137 1 0.01
138 109 0.99
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (138 bp):
TAAGACCATGGTTGAAAGATATCATGGCAACCTGACATGAAATGAATAAGACCATGGTTGAAAGA
TACCATGACAAAATGACATGAAATGAATAAGACCATAGTAGAAAGACACCATGGCAACATGACGG
GAAATGAA
Found at i:6109821 original size:51 final size:51
Alignment explanation
Indices: 6109747--6109958 Score: 343
Period size: 51 Copynumber: 4.2 Consensus size: 51
6109737 CTGATCACAT
6109747 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
* * * * *
6109798 TTATTACTTGTCATTGATAAGATAAGTGTAGCTAAAGCTACCACTTATCAT
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
*
6109849 TTATCACTTGTCACTGATCAGACAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
* *
6109900 TTATCACTTGTCATTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
*
6109951 TTGTCACT
1 TTATCACT
6109959 GATCAGAAGT
Statistics
Matches: 146, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 146 1.00
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
Found at i:6109861 original size:102 final size:102
Alignment explanation
Indices: 6109744--6109958 Score: 385
Period size: 102 Copynumber: 2.1 Consensus size: 102
6109734 ACACTGATCA
* *
6109744 CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTATTACTTGT
1 CATTTATCACTTGTCACTGATCAGACAAGTGTAGCTAAAACTACCACTTATCACTTATCACTTGT
6109809 CATTGATAAGATAAGTGTAGCTAAAGCTACCACTTAT
66 CATTGATAAGATAAGTGTAGCTAAAGCTACCACTTAT
6109846 CATTTATCACTTGTCACTGATCAGACAAGTGTAGCTAAAACTACCACTTATCACTTATCACTTGT
1 CATTTATCACTTGTCACTGATCAGACAAGTGTAGCTAAAACTACCACTTATCACTTATCACTTGT
*
6109911 CATTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
66 CATTGATAAGATAAGTGTAGCTAAAGCTACCACTTAT
* *
6109948 CACTTGTCACT
1 CATTTATCACT
6109959 GATCAGAAGT
Statistics
Matches: 108, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 108 1.00
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (102 bp):
CATTTATCACTTGTCACTGATCAGACAAGTGTAGCTAAAACTACCACTTATCACTTATCACTTGT
CATTGATAAGATAAGTGTAGCTAAAGCTACCACTTAT
Found at i:6112803 original size:43 final size:43
Alignment explanation
Indices: 6112742--6112828 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
6112732 TCTATTGTAA
6112742 AGCATGGTTATAACAATTTATTAATAATTATTTATTTTATTTT
1 AGCATGGTTATAACAATTTATTAATAATTATTTATTTTATTTT
6112785 AGCATGGTTATAACAATTTATTAATAATTATTTATTTTATTTT
1 AGCATGGTTATAACAATTTATTAATAATTATTTATTTTATTTT
6112828 A
1 A
6112829 CGTAAAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.53
Consensus pattern (43 bp):
AGCATGGTTATAACAATTTATTAATAATTATTTATTTTATTTT
Found at i:6115623 original size:13 final size:13
Alignment explanation
Indices: 6115585--6115626 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
6115575 GGTTGGAGAG
6115585 AAATTATAAAATA
1 AAATTATAAAATA
*
6115598 AAAATA-AAAATA
1 AAATTATAAAATA
*
6115610 AAATTATGAAATA
1 AAATTATAAAATA
6115623 AAAT
1 AAAT
6115627 AGTATATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (13 bp):
AAATTATAAAATA
Found at i:6117105 original size:3 final size:3
Alignment explanation
Indices: 6117097--6117125 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
6117087 TAATATATAC
6117097 GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
6117126 AGAAAAGGGA
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:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:6118346 original size:22 final size:22
Alignment explanation
Indices: 6118290--6118349 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
6118280 TTAAATTTTA
*
6118290 AAATCTA-AAATAAAAAAAAGTT
1 AAATCTATAAA-AAAAAAAAGAT
* *
6118312 AAAT-TACTGAAAATAAAAAGAT
1 AAATCTA-TAAAAAAAAAAAGAT
6118334 AAATCTATAAAAAAAA
1 AAATCTATAAAAAAAA
6118350 TATAAAAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
21 2 0.07
22 24 0.80
23 4 0.13
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (22 bp):
AAATCTATAAAAAAAAAAAGAT
Found at i:6124909 original size:21 final size:21
Alignment explanation
Indices: 6124883--6124923 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6124873 ATCTGCTCAA
* *
6124883 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
6124904 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
6124924 TCGCTTGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:6135021 original size:15 final size:17
Alignment explanation
Indices: 6135001--6135042 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
6134991 TTTCAATCGC
6135001 TTTGTTTCATTT-T-AT
1 TTTGTTTCATTTCTGAT
*
6135016 TTTGTTTTATTTCTGAT
1 TTTGTTTCATTTCTGAT
*
6135033 TTTTTTTCAT
1 TTTGTTTCAT
6135043 GTTAATTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 11 0.50
16 1 0.05
17 10 0.45
ACGTcount: A:0.12, C:0.07, G:0.07, T:0.74
Consensus pattern (17 bp):
TTTGTTTCATTTCTGAT
Found at i:6153357 original size:11 final size:11
Alignment explanation
Indices: 6153341--6153366 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6153331 AAACATTTGA
6153341 TTTTTTTTTAT
1 TTTTTTTTTAT
6153352 TTTTTTTTTAT
1 TTTTTTTTTAT
6153363 TTTT
1 TTTT
6153367 ACAATTCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTAT
Found at i:6154914 original size:11 final size:11
Alignment explanation
Indices: 6154898--6154923 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6154888 AATTAATAAA
6154898 AATATTTAATT
1 AATATTTAATT
6154909 AATATTTAATT
1 AATATTTAATT
6154920 AATA
1 AATA
6154924 AAACATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AATATTTAATT
Found at i:6154949 original size:28 final size:28
Alignment explanation
Indices: 6154888--6154949 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
6154878 TTCACTTAGA
* * *
6154888 AATTAATAAAAATATTTAATTAATATTT
1 AATTAATAAAAACATTTAATTAACATCT
6154916 AATTAAT-AAAACATTTAATTAACCATCT
1 AATTAATAAAAACATTTAATTAA-CATCT
*
6154944 AGTTAA
1 AATTAA
6154950 CGTTTTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 14 0.48
28 15 0.52
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (28 bp):
AATTAATAAAAACATTTAATTAACATCT
Found at i:6169448 original size:22 final size:23
Alignment explanation
Indices: 6169423--6169470 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
6169413 ACACTATCCA
*
6169423 AATAATAATAA-AAAATAGTAAT
1 AATAATAATAACAAAATAGTAAC
*
6169445 AAT-ATAATAACAAAATTGTAAC
1 AATAATAATAACAAAATAGTAAC
6169467 AATA
1 AATA
6169471 CAACAACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (23 bp):
AATAATAATAACAAAATAGTAAC
Found at i:6169478 original size:22 final size:22
Alignment explanation
Indices: 6169434--6169481 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
6169424 ATAATAATAA
* * *
6169434 AAAATAGTAATAATATAATAAC
1 AAAATAGTAACAATACAACAAC
*
6169456 AAAATTGTAACAATACAACAAC
1 AAAATAGTAACAATACAACAAC
6169478 AAAA
1 AAAA
6169482 AATAATAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.65, C:0.10, G:0.04, T:0.21
Consensus pattern (22 bp):
AAAATAGTAACAATACAACAAC
Found at i:6171898 original size:39 final size:39
Alignment explanation
Indices: 6171791--6171925 Score: 123
Period size: 39 Copynumber: 3.4 Consensus size: 39
6171781 GACCTCGAGT
* * *
6171791 CGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAAC--TATTACTTCGGCTAG-TC
** ** *
6171832 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
*
6171870 CGATGAGACACTGGGTGTCAACTATTACTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTATTACTTCG-GCTAGTC
*
6171909 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
6171926 CCATATTGGT
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
38 19 0.25
39 36 0.47
40 4 0.05
41 15 0.20
42 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
Found at i:6175029 original size:60 final size:59
Alignment explanation
Indices: 6174896--6175028 Score: 144
Period size: 60 Copynumber: 2.2 Consensus size: 59
6174886 ATAAATATAT
* * * * * **
6174896 ATTTTTTAATTTTTAGATTTAGTACTAAATTGATAGATTTTGTAAATGTTGATGGCTAA
1 ATTTTTTAATTTTTAGAATTAGAACTAAAATGACAAATTTTGTAAACATTGATGGCTAA
* *
6174955 ATTATTTAACTTTTTAGAATTAGAACTAAAATGACAAATTTTGTAAACATTGA--GCGTCA
1 ATTTTTTAA-TTTTTAGAATTAGAACTAAAATGACAAATTTTGTAAACATTGATGGC-TAA
6175014 ATTTTGTTAATTTTT
1 ATTTT-TTAATTTTT
6175029 TTAATATTTA
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
58 2 0.03
59 19 0.31
60 40 0.66
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.47
Consensus pattern (59 bp):
ATTTTTTAATTTTTAGAATTAGAACTAAAATGACAAATTTTGTAAACATTGATGGCTAA
Found at i:6178357 original size:21 final size:21
Alignment explanation
Indices: 6178333--6178372 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6178323 AAGATATACT
*
6178333 TATATAAATATATATTAAAGA
1 TATATAAATATATAATAAAGA
*
6178354 TATATACATATATAATAAA
1 TATATAAATATATAATAAA
6178373 ATACATGAAT
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:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
TATATAAATATATAATAAAGA
Found at i:6178446 original size:18 final size:19
Alignment explanation
Indices: 6178425--6178463 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
6178415 AATAAAAATA
6178425 ATAAAAT-ACATAATATAT
1 ATAAAATCACATAATATAT
6178443 ATAAAATGCACATAATATAT
1 ATAAAAT-CACATAATATAT
6178463 A
1 A
6178464 CGTATATAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
20 12 0.63
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.31
Consensus pattern (19 bp):
ATAAAATCACATAATATAT
Found at i:6178723 original size:18 final size:20
Alignment explanation
Indices: 6178700--6178738 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
6178690 ATACATATAC
*
6178700 ATATATACTAA-AAC-ATGT
1 ATATATAATAATAACAATGT
6178718 ATATATAATAATAACAATGT
1 ATATATAATAATAACAATGT
6178738 A
1 A
6178739 AAAATAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 3 0.17
20 5 0.28
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.33
Consensus pattern (20 bp):
ATATATAATAATAACAATGT
Found at i:6179273 original size:6 final size:6
Alignment explanation
Indices: 6179262--6179286 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6179252 ACCGGACCTT
6179262 CGCCGG CGCCGG CGCCGG CGCCGG C
1 CGCCGG CGCCGG CGCCGG CGCCGG C
6179287 CACAGTACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.52, G:0.48, T:0.00
Consensus pattern (6 bp):
CGCCGG
Found at i:6194754 original size:52 final size:50
Alignment explanation
Indices: 6194546--6194755 Score: 189
Period size: 52 Copynumber: 4.2 Consensus size: 50
6194536 TTGCACATAG
* * * *
6194546 TCACATATCAC-ACACCGAAGCCATAGCCCCGCCATGGTCTTACAC-GGA
1 TCACATATCACTTCACCGAAGCCATAGCCCAGCTATGGTCTTATACGGGA
* * * *
6194594 TCACATATCA--T-ACCG-AGCCATATCCCAGATATGGTCCTATACGGAA
1 TCACATATCACTTCACCGAAGCCATAGCCCAGCTATGGTCTTATACGGGA
* * **
6194640 TCACATTATCACATCACACCGAAACCATAGCCCAGCTATGGTCTTATACAAGA
1 TCACA-TATCAC-T-TCACCGAAGCCATAGCCCAGCTATGGTCTTATACGGGA
* * *
6194693 ACACGTATCACGTTGCACCGATGCCATAGCCCAGCTATGGTCTTATACGGGA
1 TCACATATCAC-TT-CACCGAAGCCATAGCCCAGCTATGGTCTTATACGGGA
*
6194745 GCACATATCAC
1 TCACATATCAC
6194756 ATCTTTTACG
Statistics
Matches: 127, Mismatches: 26, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
45 21 0.17
46 11 0.09
47 5 0.04
48 10 0.08
52 53 0.42
53 27 0.21
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.21
Consensus pattern (50 bp):
TCACATATCACTTCACCGAAGCCATAGCCCAGCTATGGTCTTATACGGGA
Found at i:6200120 original size:25 final size:25
Alignment explanation
Indices: 6200067--6200120 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
6200057 AAAATTTATA
* *
6200067 TGATAGGAAAATTGTATGAAAATAT
1 TGATAGGAAAATTGTATCAAAATAG
* **
6200092 TGATAGGAAAATTTTATCAATTTAG
1 TGATAGGAAAATTGTATCAAAATAG
6200117 TGAT
1 TGAT
6200121 TAGTTAGAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.43, C:0.02, G:0.19, T:0.37
Consensus pattern (25 bp):
TGATAGGAAAATTGTATCAAAATAG
Found at i:6205547 original size:8 final size:7
Alignment explanation
Indices: 6205528--6205559 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
6205518 AGCTCAATAA
6205528 TAAAAAT
1 TAAAAAT
6205535 TAAAAAT
1 TAAAAAT
6205542 TAAAAAT
1 TAAAAAT
*
6205549 TAAAAAA
1 TAAAAAT
6205556 TAAA
1 TAAA
6205560 CAGAAAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (7 bp):
TAAAAAT
Found at i:6213903 original size:24 final size:23
Alignment explanation
Indices: 6213875--6213925 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
6213865 AATGGAGTCC
*
6213875 ATCG-ACAAAACTTATTAGTCACTT
1 ATCGAACAAAACTT-TCAG-CACTT
*
6213899 ATCGAATAAAACTTTCAGCACTT
1 ATCGAACAAAACTTTCAGCACTT
6213922 ATCG
1 ATCG
6213926 GTTAGTTGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 9 0.38
24 7 0.29
25 8 0.33
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (23 bp):
ATCGAACAAAACTTTCAGCACTT
Found at i:6219966 original size:26 final size:26
Alignment explanation
Indices: 6219930--6219981 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
6219920 CTTTGTCGTC
6219930 GGAGTTCTGCGAGAAAATGGCATGCA
1 GGAGTTCTGCGAGAAAATGGCATGCA
6219956 GGAGTTCTGCGAGAAAATGGCATGCA
1 GGAGTTCTGCGAGAAAATGGCATGCA
6219982 TGAAACTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.35, T:0.19
Consensus pattern (26 bp):
GGAGTTCTGCGAGAAAATGGCATGCA
Found at i:6230603 original size:24 final size:24
Alignment explanation
Indices: 6230576--6230627 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
6230566 TTAGTAAGTC
*
6230576 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
6230600 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
6230624 AAAT
1 AAAT
6230628 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:6240510 original size:18 final size:18
Alignment explanation
Indices: 6240483--6240517 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6240473 AAATAGATAT
*
6240483 ATATAGTTACATGTATAG
1 ATATAGTTACATATATAG
*
6240501 ATATATTTACATATATA
1 ATATAGTTACATATATA
6240518 AATGAAAGTA
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:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (18 bp):
ATATAGTTACATATATAG
Found at i:6242636 original size:18 final size:19
Alignment explanation
Indices: 6242587--6242636 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
6242577 TATAATATAA
6242587 TTATTTAATTAATAAATATC
1 TTATTTAA-TAATAAATATC
6242607 TT-TTATAAAATAATAAATAT-
1 TTATT-T--AATAATAAATATC
6242627 TTATTTAATA
1 TTATTTAATA
6242637 TCTAATACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
18 4 0.15
19 2 0.08
20 6 0.23
21 12 0.46
22 2 0.08
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TTATTTAATAATAAATATC
Found at i:6245130 original size:47 final size:47
Alignment explanation
Indices: 6245054--6245191 Score: 237
Period size: 47 Copynumber: 3.0 Consensus size: 47
6245044 CACTAATGAA
*
6245054 CAGAGAGCACTGAAGTGCT--ATA-CAGAGAGCACAAATGTGCTAAT
1 CAGAGAGCACTGACGTGCTAAATATCAGAGAGCACAAATGTGCTAAT
*
6245098 CAGAGAGCATTGACGTGCTAAATATCAGAGAGCACAAATGTGCTAAT
1 CAGAGAGCACTGACGTGCTAAATATCAGAGAGCACAAATGTGCTAAT
6245145 CAGAGAGCACTGACGTGCTAAATATCAGAGAGCACAAATGTGCTAAT
1 CAGAGAGCACTGACGTGCTAAATATCAGAGAGCACAAATGTGCTAAT
6245192 AATCAGAAAG
Statistics
Matches: 88, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
44 17 0.19
46 3 0.03
47 68 0.77
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (47 bp):
CAGAGAGCACTGACGTGCTAAATATCAGAGAGCACAAATGTGCTAAT
Found at i:6245187 original size:25 final size:24
Alignment explanation
Indices: 6245054--6245203 Score: 134
Period size: 22 Copynumber: 6.4 Consensus size: 24
6245044 CACTAATGAA
*
6245054 CAGAGAGCACTGAA-GTGCT-ATA-
1 CAGAGAGCAC-AAATGTGCTAATAT
6245076 CAGAGAGCACAAATGTGCT-A-AT
1 CAGAGAGCACAAATGTGCTAATAT
*** *
6245098 CAGAGAGCATTGACGTGCTAAATAT
1 CAGAGAGCACAAATGTGCT-AATAT
6245123 CAGAGAGCACAAATGTGCT-A-AT
1 CAGAGAGCACAAATGTGCTAATAT
** *
6245145 CAGAGAGCACTGACGTGCTAAATAT
1 CAGAGAGCACAAATGTGCT-AATAT
6245170 CAGAGAGCACAAATGTGCTAATAAT
1 CAGAGAGCACAAATGTGCTAAT-AT
*
6245195 CAGAAAGCA
1 CAGAGAGCA
6245204 TGCTGAGGTC
Statistics
Matches: 103, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
21 3 0.03
22 49 0.48
23 1 0.01
24 5 0.05
25 45 0.44
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.19
Consensus pattern (24 bp):
CAGAGAGCACAAATGTGCTAATAT
Found at i:6247795 original size:18 final size:19
Alignment explanation
Indices: 6247746--6247795 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
6247736 TATAATATAA
6247746 TTATTTAATTAATAAATATC
1 TTATTTAA-TAATAAATATC
6247766 TT-TTATAAAATAATAAATAT-
1 TTATT-T--AATAATAAATATC
6247786 TTATTTAATA
1 TTATTTAATA
6247796 TCTAATACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
18 4 0.15
19 2 0.08
20 6 0.23
21 12 0.46
22 2 0.08
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TTATTTAATAATAAATATC
Found at i:6250119 original size:50 final size:51
Alignment explanation
Indices: 6250056--6250264 Score: 127
Period size: 50 Copynumber: 4.2 Consensus size: 51
6250046 TAGCTCTTAT
* * * *
6250056 GAGCATCCTGATATATGGCTTTAATGAGCTTTCCGATTAATGGCTCTAC-G
1 GAGCTTCCCGATATATGGCTTTAATGAGCTTCCCGATTAATGGCTCTACAA
*** ** **
6250106 GAGCTTCCCGATAT-TGGCTCGCATGAGCTTTCCAAATT--TGGCTCT-CTT
1 GAGCTTCCCGATATATGGCTTTAATGAGC-TTCCCGATTAATGGCTCTACAA
* *
6250154 GAGCTTCCCCAT-TATGGCTCGT-ATGAGCTTCCCGA-TAATTGGCTC-ACAA
1 GAGCTTCCCGATATATGGCT-TTAATGAGCTTCCCGATTAA-TGGCTCTACAA
* * * * *
6250203 AAGCTTCCCGTTACATGGC-TTACATGAGCTTCCCG-TTATATAGCTCGA-AA
1 GAGCTTCCCGATATATGGCTTTA-ATGAGCTTCCCGATTA-ATGGCTCTACAA
6250253 GAGCTTCCCGAT
1 GAGCTTCCCGAT
6250265 TACATGCTCG
Statistics
Matches: 121, Mismatches: 24, Indels: 28
0.70 0.14 0.16
Matches are distributed among these distances:
46 1 0.01
47 7 0.06
48 30 0.25
49 27 0.22
50 54 0.45
51 2 0.02
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.32
Consensus pattern (51 bp):
GAGCTTCCCGATATATGGCTTTAATGAGCTTCCCGATTAATGGCTCTACAA
Found at i:6250133 original size:24 final size:24
Alignment explanation
Indices: 6250106--6250264 Score: 106
Period size: 25 Copynumber: 6.5 Consensus size: 24
6250096 TGGCTCTACG
6250106 GAGCTTCCCGATATTGGCTCGCAT
1 GAGCTTCCCGATATTGGCTCGCAT
* * * *
6250130 GAGCTTTCC-AAATTTGGCTCTCTT
1 GAGCTTCCCGATA-TTGGCTCGCAT
* *
6250154 GAGCTTCCCCAT-TATGGCTCGTAT
1 GAGCTTCCCGATAT-TGGCTCGCAT
* *
6250178 GAGCTTCCCGATAATTGGCTCACAA
1 GAGCTTCCCGAT-ATTGGCTCGCAT
* * * **
6250203 AAGCTTCCCGTTACATGGCTTACAT
1 GAGCTTCCCGATA-TTGGCTCGCAT
* * * *
6250228 GAGCTTCCCGTTATATAGCTCGAAA
1 GAGCTTCCCGATAT-TGGCTCGCAT
6250253 GAGCTTCCCGAT
1 GAGCTTCCCGAT
6250265 TACATGCTCG
Statistics
Matches: 102, Mismatches: 26, Indels: 13
0.72 0.18 0.09
Matches are distributed among these distances:
23 3 0.03
24 44 0.43
25 54 0.53
26 1 0.01
ACGTcount: A:0.21, C:0.28, G:0.20, T:0.31
Consensus pattern (24 bp):
GAGCTTCCCGATATTGGCTCGCAT
Found at i:6258592 original size:17 final size:17
Alignment explanation
Indices: 6258561--6258595 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
6258551 ACCTTTAATC
**
6258561 TTTTAAATTTTTAAAAA
1 TTTTAAATTAATAAAAA
6258578 TTTTAAATTAATAAAAA
1 TTTTAAATTAATAAAAA
6258595 T
1 T
6258596 AAAATTTTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTTAAATTAATAAAAA
Found at i:6274208 original size:3 final size:3
Alignment explanation
Indices: 6274193--6274278 Score: 163
Period size: 3 Copynumber: 28.7 Consensus size: 3
6274183 TTAAACATAA
*
6274193 AAG AAG GAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
6274241 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
6274279 CCGTCATAAG
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:6280539 original size:20 final size:21
Alignment explanation
Indices: 6280501--6280542 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
6280491 TAACAATTAC
6280501 AAATAATATTTAATTATATTT
1 AAATAATATTTAATTATATTT
6280522 AAATAA-ATTT-ATTAATATTT
1 AAATAATATTTAATT-ATATTT
6280542 A
1 A
6280543 TTTTTAGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 3 0.15
20 11 0.55
21 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AAATAATATTTAATTATATTT
Found at i:6292669 original size:14 final size:14
Alignment explanation
Indices: 6292650--6292677 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6292640 TTGTAGCAGG
6292650 ATAAAAATAAAAAA
1 ATAAAAATAAAAAA
6292664 ATAAAAATAAAAAA
1 ATAAAAATAAAAAA
6292678 GAGAGAGAGA
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:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (14 bp):
ATAAAAATAAAAAA
Found at i:6295505 original size:20 final size:20
Alignment explanation
Indices: 6295480--6295522 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
6295470 TAAGCGTCTT
6295480 TAAAATAGTAACAAAATTAA
1 TAAAATAGTAACAAAATTAA
*
6295500 TAAAATAGTGACAAAATTAA
1 TAAAATAGTAACAAAATTAA
6295520 TAA
1 TAA
6295523 TAAAACAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.63, C:0.05, G:0.07, T:0.26
Consensus pattern (20 bp):
TAAAATAGTAACAAAATTAA
Found at i:6295592 original size:22 final size:21
Alignment explanation
Indices: 6295567--6295611 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
6295557 ATCATAATAG
* *
6295567 TACCAACATAATAGTGAAAAAA
1 TACCAACAAAATAG-CAAAAAA
*
6295589 TACCAAGAAAATAGCAAAAAA
1 TACCAACAAAATAGCAAAAAA
6295610 TA
1 TA
6295612 AAATAGTAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.62, C:0.13, G:0.09, T:0.16
Consensus pattern (21 bp):
TACCAACAAAATAGCAAAAAA
Done.