Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015354.1 Kokia drynarioides strain JFW-HI SEQ_130401, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1324750
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 502 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:357076 original size:25 final size:27
Alignment explanation
Indices: 357035--357100 Score: 84
Period size: 26 Copynumber: 2.5 Consensus size: 27
357025 TCATAGTAAA
*
357035 CATTTTTTTTTTCTTCTTT-TCTTTTCT
1 CATTTTATTTTTCTTCTTTCT-TTTTCT
357062 C-TTTTATTTTT-TTCTTTCTTTTTCT
1 CATTTTATTTTTCTTCTTTCTTTTTCT
*
357087 CATTTTCTTTTTCT
1 CATTTTATTTTTCT
357101 AAGTGACTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
25 13 0.38
26 19 0.56
27 2 0.06
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (27 bp):
CATTTTATTTTTCTTCTTTCTTTTTCT
Found at i:357099 original size:24 final size:24
Alignment explanation
Indices: 357052--357100 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
357042 TTTTTCTTCT
* *
357052 TTTCTTTTCTCTTTTATTTTTTTC
1 TTTCTTTTCTCATTTATCTTTTTC
357076 TTTCTTTTTCTCATTT-TCTTTTTC
1 TTTC-TTTTCTCATTTATCTTTTTC
357100 T
1 T
357101 AAGTGACTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTCTTTTCTCATTTATCTTTTTC
Found at i:358099 original size:18 final size:18
Alignment explanation
Indices: 358076--358122 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
358066 CGAGTTGGTG
*
358076 TAGGGGGAGGTCTACCAT
1 TAGGGGCAGGTCTACCAT
*
358094 TAGGGGCAAGTCTACCAT
1 TAGGGGCAGGTCTACCAT
*
358112 CAGGGGCAGGT
1 TAGGGGCAGGT
358123 TGCTCGAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.23, C:0.19, G:0.38, T:0.19
Consensus pattern (18 bp):
TAGGGGCAGGTCTACCAT
Found at i:378376 original size:12 final size:13
Alignment explanation
Indices: 378359--378387 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
378349 CAAATTAATT
378359 TAATTA-AAAATA
1 TAATTATAAAATA
378371 TAATTATAAAATA
1 TAATTATAAAATA
378384 TAAT
1 TAAT
378388 AATGCTCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAATTATAAAATA
Found at i:399044 original size:20 final size:20
Alignment explanation
Indices: 399021--399093 Score: 62
Period size: 20 Copynumber: 3.7 Consensus size: 20
399011 TTTAAATTTT
399021 GATTTCAAGATTTAGGTTTA
1 GATTTCAAGATTTAGGTTTA
* * *
399041 GATTTTAAG-TTTAAGTTTT
1 GATTTCAAGATTTAGGTTTA
*
399060 GAATTTGAA-ATTTAAGGTTTA
1 G-ATTTCAAGATTT-AGGTTTA
*
399081 G-GTTCAAGATTTA
1 GATTTCAAGATTTA
399094 AGGATTTCAG
Statistics
Matches: 41, Mismatches: 8, Indels: 9
0.71 0.14 0.16
Matches are distributed among these distances:
19 14 0.34
20 21 0.51
21 6 0.15
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.47
Consensus pattern (20 bp):
GATTTCAAGATTTAGGTTTA
Found at i:399115 original size:22 final size:19
Alignment explanation
Indices: 399067--399106 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 19
399057 TTTGAATTTG
399067 AAATTTAAGGTTTAGGTTC
1 AAATTTAAGGTTTAGGTTC
399086 AAGATTTAAGGATTTCAGGTT
1 AA-ATTTAAGG-TTT-AGGTT
399107 TAGAATTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 8 0.44
21 3 0.17
22 5 0.28
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.40
Consensus pattern (19 bp):
AAATTTAAGGTTTAGGTTC
Found at i:399221 original size:20 final size:21
Alignment explanation
Indices: 399196--399238 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
399186 GGATTATGGA
399196 TTTAAGGTTTT-TATTTAAGG
1 TTTAAGGTTTTATATTTAAGG
*
399216 TTTAAGGTTTTATATTTTAGG
1 TTTAAGGTTTTATATTTAAGG
399237 TT
1 TT
399239 CATAGTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.23, C:0.00, G:0.19, T:0.58
Consensus pattern (21 bp):
TTTAAGGTTTTATATTTAAGG
Found at i:399490 original size:16 final size:17
Alignment explanation
Indices: 399457--399491 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
399447 TAATGTGATA
399457 AAATTTTATTAATATTT
1 AAATTTTATTAATATTT
*
399474 AAATTTT-TTAATTTTT
1 AAATTTTATTAATATTT
399490 AA
1 AA
399492 GATCATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
AAATTTTATTAATATTT
Found at i:402946 original size:2 final size:2
Alignment explanation
Indices: 402939--402980 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
402929 GCATGCAAAT
* *
402939 CA CA CA CA CA CA CA CA CA CA TA CA CA CG CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
402981 TACATGGTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.48, C:0.48, G:0.02, T:0.02
Consensus pattern (2 bp):
CA
Found at i:411447 original size:6 final size:6
Alignment explanation
Indices: 411419--411464 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
411409 TGGACCCAAT
*
411419 TTTAAA TTTTAAA -TT-AT TTTAAA TTTAAA TTTAAA TTT-AA TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
411465 AGAGAGTCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
4 1 0.03
5 9 0.26
6 18 0.53
7 6 0.18
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:411447 original size:16 final size:17
Alignment explanation
Indices: 411417--411449 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
411407 ATTGGACCCA
411417 ATTTTAAATTTTAAATT
1 ATTTTAAATTTTAAATT
411434 ATTTTAAA-TTTAAATT
1 ATTTTAAATTTTAAATT
411450 TAAATTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTTAAATTTTAAATT
Found at i:411449 original size:23 final size:23
Alignment explanation
Indices: 411419--411464 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
411409 TGGACCCAAT
*
411419 TTTAAATTTTAAA-TTATTTTAAA
1 TTTAAA-TTTAAATTTAATTTAAA
411442 TTTAAATTTAAATTTAATTTAAA
1 TTTAAATTTAAATTTAATTTAAA
411465 AGAGAGTCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTAAATTTAAATTTAATTTAAA
Found at i:411460 original size:17 final size:17
Alignment explanation
Indices: 411419--411464 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
411409 TGGACCCAAT
*
411419 TTTAAATTTTAAATT-AT
1 TTTAAA-TTTAAATTAAA
411436 TTTAAATTTAAATTTAAA
1 TTTAAATTTAAA-TTAAA
411454 TTT-AATTTAAA
1 TTTAAATTTAAA
411465 AGAGAGTCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 6 0.23
17 16 0.62
18 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTAAATTTAAATTAAA
Found at i:411462 original size:11 final size:11
Alignment explanation
Indices: 411426--411464 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
411416 AATTTTAAAT
*
411426 TTTAAA-TTAT
1 TTTAAATTTAA
411436 TTTAAATTTAAA
1 TTTAAATTT-AA
411448 TTTAAATTTAA
1 TTTAAATTTAA
411459 TTTAAA
1 TTTAAA
411465 AGAGAGTCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 6 0.23
11 10 0.38
12 10 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:412091 original size:13 final size:13
Alignment explanation
Indices: 412066--412099 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
412056 TTAAGTATAA
412066 TAAATAA-ATTAT
1 TAAATAATATTAT
412078 TAAATAATATTAT
1 TAAATAATATTAT
*
412091 TAAGTAATA
1 TAAATAATA
412100 AAAAATTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (13 bp):
TAAATAATATTAT
Found at i:413012 original size:30 final size:30
Alignment explanation
Indices: 412978--413043 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
412968 TAAAATTTCC
*
412978 AAAAATCAC-GTTTTAACCCTTAAACTTCTT
1 AAAAATCACAGTTTTAACCC-CAAACTTCTT
* *
413008 AAAAATTACATTTTTAACCCCAAACTTCTT
1 AAAAATCACAGTTTTAACCCCAAACTTCTT
*
413038 CAAAAT
1 AAAAAT
413044 TATATTTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 22 0.71
31 9 0.29
ACGTcount: A:0.41, C:0.23, G:0.02, T:0.35
Consensus pattern (30 bp):
AAAAATCACAGTTTTAACCCCAAACTTCTT
Found at i:413062 original size:29 final size:30
Alignment explanation
Indices: 412988--413139 Score: 118
Period size: 30 Copynumber: 5.2 Consensus size: 30
412978 AAAAATCACG
412988 TTTTAACCCTTAAACTTCTTAAAAATTACAT
1 TTTTAACCC-TAAACTTCTTAAAAATTACAT
* * *
413019 TTTTAACCCCAAACTTCTTCAAAATTATAT
1 TTTTAACCCTAAACTTCTTAAAAATTACAT
* *
413049 TTTT-GCCCTAAACTTC-CAAAAA-TACA-
1 TTTTAACCCTAAACTTCTTAAAAATTACAT
** * *
413075 TTTT-ACCTCCGAACTTC-CAAAAATCACAT
1 TTTTAACC-CTAAACTTCTTAAAAATTACAT
* * **
413104 TTTTTACCCTCGAACTTCTCCAAAATTACAT
1 TTTTAACCCT-AAACTTCTTAAAAATTACAT
413135 TTTTA
1 TTTTA
413140 CCAACGAACT
Statistics
Matches: 99, Mismatches: 16, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
26 6 0.06
27 16 0.16
28 7 0.07
29 15 0.15
30 32 0.32
31 23 0.23
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (30 bp):
TTTTAACCCTAAACTTCTTAAAAATTACAT
Found at i:413120 original size:86 final size:86
Alignment explanation
Indices: 413008--413166 Score: 214
Period size: 86 Copynumber: 1.8 Consensus size: 86
412998 TAAACTTCTT
* * * *
413008 AAAAATTACATTTTTAACCCCAAACTTCTTCAAAATTATATTTTTGCC-CTAAACTTCCAAAAAT
1 AAAAATCACATTTTTAACCCCAAACTTCTCCAAAATTACATTTTTACCAC-AAACTTCCAAAAAT
413072 -ACATTTTACCTCCGAACTTCC
65 CACATTTTACCTCCGAACTTCC
* * *
413093 AAAAATCACATTTTTTACCCTCGAACTTCTCCAAAATTACATTTTTACCAACGAACTTCCAAAAA
1 AAAAATCACATTTTTAACCC-CAAACTTCTCCAAAATTACATTTTTACC-ACAAACTTCCAAAAA
413158 TCACATTTT
64 TCACATTTT
413167 TGTCCTTGAA
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
85 18 0.29
86 24 0.38
87 13 0.21
88 8 0.13
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.35
Consensus pattern (86 bp):
AAAAATCACATTTTTAACCCCAAACTTCTCCAAAATTACATTTTTACCACAAACTTCCAAAAATC
ACATTTTACCTCCGAACTTCC
Found at i:413140 original size:30 final size:30
Alignment explanation
Indices: 412977--413253 Score: 168
Period size: 29 Copynumber: 9.5 Consensus size: 30
412967 TTAAAATTTC
* * * **
412977 CAAAAATCACGTTTTAACCCTTAAACTTCT
1 CAAAAATTACATTTTTACCCTCGAACTTCT
* *
413007 TAAAAATTACATTTTTAACCC-CAAACTTCTT
1 CAAAAATTACATTTTT-ACCCTCGAACTTC-T
* * *
413038 C-AAAATTATATTTTTGCCCT-AAACTTC-
1 CAAAAATTACATTTTTACCCTCGAACTTCT
413065 CAAAAA-TACA-TTTTA-CCTCCGAACTTC-
1 CAAAAATTACATTTTTACCCT-CGAACTTCT
*
413092 CAAAAATCACATTTTTTACCCTCGAACTTCT
1 CAAAAATTACA-TTTTTACCCTCGAACTTCT
* **
413123 CCAAAATTACATTTTTACCAACGAACTTC-
1 CAAAAATTACATTTTTACCCTCGAACTTCT
* ** * *
413152 CAAAAATCACATTTTTGTCCTTGAACATC-
1 CAAAAATTACATTTTTACCCTCGAACTTCT
** *
413181 CAAAAATTACCATTTTGCCCCT-GAACATCT
1 CAAAAATTA-CATTTTTACCCTCGAACTTCT
* * *
413211 -AAAAATTACCA-TTTTGCCCTCAAATTTCT
1 CAAAAATTA-CATTTTTACCCTCGAACTTCT
*
413240 -AAAAATCACATTTT
1 CAAAAATTACATTTT
413254 AAACCTCAAA
Statistics
Matches: 198, Mismatches: 34, Indels: 31
0.75 0.13 0.12
Matches are distributed among these distances:
25 3 0.02
26 4 0.02
27 16 0.08
28 16 0.08
29 72 0.36
30 70 0.35
31 17 0.09
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.35
Consensus pattern (30 bp):
CAAAAATTACATTTTTACCCTCGAACTTCT
Found at i:413177 original size:29 final size:28
Alignment explanation
Indices: 413059--413196 Score: 136
Period size: 30 Copynumber: 4.8 Consensus size: 28
413049 TTTTGCCCTA
413059 AACTTCCAAAAAT-ACA-TTTTACCTCCG
1 AACTTCCAAAAATCACATTTTTACCT-CG
413086 AACTTCCAAAAATCACATTTTTTACCCTCG
1 AACTTCCAAAAATCACA-TTTTTA-CCTCG
* * *
413116 AACTTCTCCAAAATTACATTTTTACCAACG
1 AACTTC-CAAAAATCACATTTTTACC-TCG
* *
413146 AACTTCCAAAAATCACATTTTTGTCCTTG
1 AACTTCCAAAAATCACATTTTT-ACCTCG
* *
413175 AACATCCAAAAATTACCATTTT
1 AACTTCCAAAAATCA-CATTTT
413197 GCCCCTGAAC
Statistics
Matches: 93, Mismatches: 10, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
27 13 0.14
28 3 0.03
29 30 0.32
30 35 0.38
31 12 0.13
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (28 bp):
AACTTCCAAAAATCACATTTTTACCTCG
Found at i:413183 original size:116 final size:116
Alignment explanation
Indices: 412974--413263 Score: 261
Period size: 116 Copynumber: 2.5 Consensus size: 116
412964 TCCTTAAAAT
* * *
412974 TTCCAAAAATCACGTTTTAACCCTTAAACTTCTTAAAAATTACATTTTTAACCCCAAACTTCTTC
1 TTCCAAAAATCACGTTTTAACCCTCAAACTTCTCAAAAATTACATTTTTAACCACAAACTTC-TC
* * *
413039 AAAATTATATTTTTGCCCTAAACTTCCAAAAA-TA-CATTTTACCTCCGAAC
65 AAAATCACATTTTTGCCCTAAACATCCAAAAATTACCATTTTACCTCCGAAC
* * * * *
413089 TTCCAAAAATCACATTTTTTACCCTCGAACTTCTCCAAAATTACATTTTT-ACCAACGAACTTC-
1 TTCCAAAAATCAC-GTTTTAACCCTCAAACTTCTCAAAAATTACATTTTTAACC-ACAAACTTCT
* * *
413152 CAAAAATCACATTTTTGTCCTTGAACATCCAAAAATTACCATTTTGCC-CCTGAAC
64 C-AAAATCACATTTTTG-CCCTAAACATCCAAAAATTACCATTTTACCTCC-GAAC
* * * * * * * * *
413207 ATCTAAAAATTACCATTTT-GCCCTCAAATTTCT-AAAAATCACATTTTAAACCTCAAA
1 TTCCAAAAATCA-CGTTTTAACCCTCAAACTTCTCAAAAATTACATTTTTAACCACAAA
413264 ATTTCCAAAA
Statistics
Matches: 140, Mismatches: 26, Indels: 17
0.77 0.14 0.09
Matches are distributed among these distances:
114 1 0.01
115 29 0.21
116 66 0.47
117 18 0.13
118 25 0.18
119 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (116 bp):
TTCCAAAAATCACGTTTTAACCCTCAAACTTCTCAAAAATTACATTTTTAACCACAAACTTCTCA
AAATCACATTTTTGCCCTAAACATCCAAAAATTACCATTTTACCTCCGAAC
Found at i:413319 original size:30 final size:29
Alignment explanation
Indices: 413231--413325 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 29
413221 ATTTTGCCCT
* *
413231 CAAA-TTTCTAAAAA-TCACATTTTAAACC
1 CAAATTTTCCAAAAATTCA-ATTTTAATCC
* *
413259 TCAAAATTTCCAAAAGTTCAATTTTAATCC
1 -CAAATTTTCCAAAAATTCAATTTTAATCC
*
413289 CAAATTTTCCAAAAATTCCAATTTTGATCC
1 CAAATTTTCCAAAAATT-CAATTTTAATCC
413319 CTAAATT
1 C-AAATT
413326 CTTTGAAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
29 19 0.34
30 29 0.52
31 8 0.14
ACGTcount: A:0.41, C:0.21, G:0.02, T:0.36
Consensus pattern (29 bp):
CAAATTTTCCAAAAATTCAATTTTAATCC
Found at i:425684 original size:39 final size:39
Alignment explanation
Indices: 425634--425972 Score: 205
Period size: 39 Copynumber: 8.7 Consensus size: 39
425624 TTGAAGATTT
* * * * *
425634 CAATCTCTTACCCCGAGTCTGAGGCAGATCACAATCATC
1 CAATCTTTTACCCCAAGCCTGGGGCAGATCACAATCAGC
* ** *
425673 AAATCTTTTACCCCAAGCCTACGGCAGATCACCATCAGC
1 CAATCTTTTACCCCAAGCCTGGGGCAGATCACAATCAGC
* *** ** *
425712 CAATTTTTTACCCCAAGCCT-GGGCAGATTGTAGCCATC
1 CAATCTTTTACCCCAAGCCTGGGGCAGATCACAATCAGC
* * * * * * *
425750 CGATCTCTTACCCCGAGCTTGGGGTAGATCACTATTAGC
1 CAATCTTTTACCCCAAGCCTGGGGCAGATCACAATCAGC
* * * ** * **
425789 CAATCTCTTACCCCGAGCTTGGGGCAGATTGCAACCATT
1 CAATCTTTTACCCCAAGCCTGGGGCAGATCACAATCAGC
* *
425828 CGATCTTTTACCCCAAGCCTGGGGCAGATCACCATCAGC
1 CAATCTTTTACCCCAAGCCTGGGGCAGATCACAATCAGC
* *** ** *
425867 CAATCTTTTACCCCAAACCT-GGGCAGATTGTAGCCATC
1 CAATCTTTTACCCCAAGCCTGGGGCAGATCACAATCAGC
* *** * * *
425905 CAATCTCTTACCTTGAGCATGGGGCAGATCACCATCAAC
1 CAATCTTTTACCCCAAGCCTGGGGCAGATCACAATCAGC
** * *
425944 CAATCTCATACCCTAAGCCAGGGGCAGAT
1 CAATCTTTTACCCCAAGCCTGGGGCAGAT
425973 TGCAACCATC
Statistics
Matches: 220, Mismatches: 78, Indels: 4
0.73 0.26 0.01
Matches are distributed among these distances:
38 50 0.23
39 170 0.77
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (39 bp):
CAATCTTTTACCCCAAGCCTGGGGCAGATCACAATCAGC
Found at i:425916 original size:155 final size:156
Alignment explanation
Indices: 425634--425981 Score: 468
Period size: 155 Copynumber: 2.2 Consensus size: 156
425624 TTGAAGATTT
* ** *
425634 CAATCTCTTACCCCGAG-TCTGAGGCAGATCACAATCA-TCAAATCTTTTACCCCAAGCCTACGG
1 CAATCTCTTACCCCGAGCT-TGGGGCAGATTGCAACCATTCAAATCTTTTACCCCAAGCCTACGG
* * *
425697 CAGATCACCATCAGCCAATTTTTTACCCCAAGCCTGGGCAGATTGTAGCCATCCGATCTCTTACC
65 CAGATCACCATCAGCCAATCTTTTACCCCAAACCTGGGCAGATTGTAGCCATCCAATCTCTTACC
* * * * *
425762 CCGAGCTTGGGGTAGATCACTATTAGC
130 CCGAGCATGGGGCAGATCACCATCAAC
* **
425789 CAATCTCTTACCCCGAGCTTGGGGCAGATTGCAACCATTC-GATCTTTTACCCCAAGCCTGGGGC
1 CAATCTCTTACCCCGAGCTTGGGGCAGATTGCAACCATTCAAATCTTTTACCCCAAGCCTACGGC
*
425853 AGATCACCATCAGCCAATCTTTTACCCCAAACCTGGGCAGATTGTAGCCATCCAATCTCTTACCT
66 AGATCACCATCAGCCAATCTTTTACCCCAAACCTGGGCAGATTGTAGCCATCCAATCTCTTACCC
*
425918 TGAGCATGGGGCAGATCACCATCAAC
131 CGAGCATGGGGCAGATCACCATCAAC
* ** **
425944 CAATCTCATACCCTAAGCCAGGGGCAGATTGCAACCAT
1 CAATCTCTTACCCCGAGCTTGGGGCAGATTGCAACCAT
425982 CCAATATCCT
Statistics
Matches: 169, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
155 166 0.98
156 3 0.02
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (156 bp):
CAATCTCTTACCCCGAGCTTGGGGCAGATTGCAACCATTCAAATCTTTTACCCCAAGCCTACGGC
AGATCACCATCAGCCAATCTTTTACCCCAAACCTGGGCAGATTGTAGCCATCCAATCTCTTACCC
CGAGCATGGGGCAGATCACCATCAAC
Found at i:425931 original size:77 final size:77
Alignment explanation
Indices: 425634--425986 Score: 346
Period size: 77 Copynumber: 4.5 Consensus size: 77
425624 TTGAAGATTT
* * ** * * * * * **
425634 CAATCTCTTACCCCGAGTCTGAGGCAGATCACAATCATCAAATCTTTTACCCCAAGCCTACGGCA
1 CAATCTCTTACCCCAAGCCTG-GGCAGATTGCAACCATCCAATCTCTTACCCCGAGCATGGGGCA
425699 GATCACCATCAGC
65 GATCACCATCAGC
* * * * * * *
425712 CAATTTTTTACCCCAAGCCTGGGCAGATTGTAGCCATCCGATCTCTTACCCCGAGCTTGGGGTAG
1 CAATCTCTTACCCCAAGCCTGGGCAGATTGCAACCATCCAATCTCTTACCCCGAGCATGGGGCAG
* *
425777 ATCACTATTAGC
66 ATCACCATCAGC
* * * * * * *
425789 CAATCTCTTACCCCGAGCTTGGGGCAGATTGCAACCATTCGATCTTTTACCCCAAGCCTGGGGCA
1 CAATCTCTTACCCCAAGCCT-GGGCAGATTGCAACCATCCAATCTCTTACCCCGAGCATGGGGCA
425854 GATCACCATCAGC
65 GATCACCATCAGC
* * * * **
425867 CAATCTTTTACCCCAAACCTGGGCAGATTGTAGCCATCCAATCTCTTACCTTGAGCATGGGGCAG
1 CAATCTCTTACCCCAAGCCTGGGCAGATTGCAACCATCCAATCTCTTACCCCGAGCATGGGGCAG
*
425932 ATCACCATCAAC
66 ATCACCATCAGC
* * *
425944 CAATCTCATACCCTAAGCCAGGGGCAGATTGCAACCATCCAAT
1 CAATCTCTTACCCCAAGCC-TGGGCAGATTGCAACCATCCAAT
425987 ATCCTAAAAA
Statistics
Matches: 220, Mismatches: 53, Indels: 4
0.79 0.19 0.01
Matches are distributed among these distances:
77 119 0.54
78 101 0.46
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (77 bp):
CAATCTCTTACCCCAAGCCTGGGCAGATTGCAACCATCCAATCTCTTACCCCGAGCATGGGGCAG
ATCACCATCAGC
Found at i:426472 original size:16 final size:16
Alignment explanation
Indices: 426430--426496 Score: 71
Period size: 16 Copynumber: 4.1 Consensus size: 16
426420 ATTGGACCCA
*
426430 ATTTTAAATTTTAATTT
1 ATTTTAAA-TTTAAATT
*
426447 AGTTTAAATTTAAATT
1 ATTTTAAATTTAAATT
* *
426463 ATTTTGAATTTAAACTC
1 ATTTTAAATTTAAA-TT
*
426480 ATTCTAAATTTAAATT
1 ATTTTAAATTTAAATT
426496 A
1 A
426497 AATTTAATGT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
16 21 0.51
17 20 0.49
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.52
Consensus pattern (16 bp):
ATTTTAAATTTAAATT
Found at i:426491 original size:17 final size:16
Alignment explanation
Indices: 426451--426494 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
426441 TAATTTAGTT
* *
426451 TAAATTTAAATTATTT
1 TAAATTTAAATCATTC
*
426467 TGAATTTAAACTCATTC
1 TAAATTTAAA-TCATTC
426484 TAAATTTAAAT
1 TAAATTTAAAT
426495 TAAATTTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAAATTTAAATCATTC
Found at i:428139 original size:29 final size:29
Alignment explanation
Indices: 428089--428286 Score: 136
Period size: 29 Copynumber: 6.8 Consensus size: 29
428079 AAGGTCCTTG
* *
428089 AACTTC-CAAAAATCATGC-TTTTAACTCCG
1 AACTTCTCAAAAATCA--CATTTTAACCCCA
* *
428118 AACTTCTCAAAAATTACATTTTCACCCCCA
1 AACTTCTCAAAAATCACATTTT-AACCCCA
* * * **
428148 AACTTCTCTAAAATTATATTTTTTGCCCCTA
1 AACTTCTCAAAAATCACA-TTTTAACCCC-A
*
428179 AACTTCT-AAAAATCACATTTTTACCCCCA
1 AACTTCTCAAAAATCACA-TTTTAACCCCA
* * *
428208 AACTTC-CAAAAATCACATTTTAGCCTCG
1 AACTTCTCAAAAATCACATTTTAACCCCA
* * * * *
428236 AACTTCTCCAAAATTACATTTTTACCATCG
1 AACTTCTCAAAAATCACATTTTAACC-CCA
428266 AACTT-TCAAAAATCACATTTT
1 AACTTCTCAAAAATCACATTTT
428287 TCCCTCGAAC
Statistics
Matches: 139, Mismatches: 22, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
28 15 0.11
29 56 0.40
30 56 0.40
31 12 0.09
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.34
Consensus pattern (29 bp):
AACTTCTCAAAAATCACATTTTAACCCCA
Found at i:428259 original size:58 final size:58
Alignment explanation
Indices: 428089--428315 Score: 201
Period size: 58 Copynumber: 3.9 Consensus size: 58
428079 AAGGTCCTTG
* *
428089 AACTTCCAAAAATCATGC-TTTTA-ACTCCGAACTTCTCAAAAATTACATTTTCACCCCCA
1 AACTTCCAAAAATCA--CATTTTAGCCT-CGAACTTCTCAAAAATTACATTTTTACCCCCA
* * * * * * *
428148 AACTTCTCTAAAATTATATTTTTTGCCCCTAAACTTCT-AAAAATCACATTTTTACCCCCA
1 AACTTC-CAAAAATCACA-TTTTAGCCTC-GAACTTCTCAAAAATTACATTTTTACCCCCA
* ** *
428208 AACTTCCAAAAATCACATTTTAGCCTCGAACTTCTCCAAAATTACATTTTTACCATCG
1 AACTTCCAAAAATCACATTTTAGCCTCGAACTTCTCAAAAATTACATTTTTACCCCCA
* ** * *
428266 AACTTTCAAAAATCACATTTTTCCCTCGAACAT-ACAAAAATTACCATTTT
1 AACTTCCAAAAATCACATTTTAGCCTCGAACTTCTCAAAAATTA-CATTTT
428316 GCCCTTGAAC
Statistics
Matches: 135, Mismatches: 26, Indels: 15
0.77 0.15 0.09
Matches are distributed among these distances:
57 15 0.11
58 60 0.44
59 14 0.10
60 38 0.28
61 8 0.06
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (58 bp):
AACTTCCAAAAATCACATTTTAGCCTCGAACTTCTCAAAAATTACATTTTTACCCCCA
Found at i:428283 original size:87 final size:87
Alignment explanation
Indices: 428186--428373 Score: 222
Period size: 87 Copynumber: 2.2 Consensus size: 87
428176 CTAAACTTCT
* * * *
428186 AAAAATCACATTTTTACCCCCAAACTTCCAAAAATCA-CATTTTAG-CCTCGAACTTCTCCAAAA
1 AAAAATCACATTTTT-CCCCCAAACATACAAAAATCACCATTTT-GCCCTCGAACATC-CAAAAA
*
428249 TTA-CATTTTTACCATCGAACTTTC-
63 TTACCATTTTTACCATC-AAATTTCG
* * * *
428273 AAAAATCACATTTTTCCCTCGAACATACAAAAATTACCATTTTGCCCTTGAACATCCAAAAATTA
1 AAAAATCACATTTTTCCCCCAAACATACAAAAATCACCATTTTGCCCTCGAACATCCAAAAATTA
*
428338 CCATTTTTACCCTCAAATTTCG
66 CCATTTTTACCATCAAATTTCG
428360 AAAAATCACATTTT
1 AAAAATCACATTTT
428374 CAACCTTAAA
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
86 31 0.36
87 56 0.64
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.32
Consensus pattern (87 bp):
AAAAATCACATTTTTCCCCCAAACATACAAAAATCACCATTTTGCCCTCGAACATCCAAAAATTA
CCATTTTTACCATCAAATTTCG
Found at i:428287 original size:29 final size:29
Alignment explanation
Indices: 428116--428373 Score: 168
Period size: 29 Copynumber: 8.8 Consensus size: 29
428106 CTTTTAACTC
* * *
428116 CGAACTTCTCAAAAATTACATTTTCACCCC
1 CGAACTT-TCAAAAATCACATTTTTACCCT
* * * * *
428146 CAAACTTCTCTAAAATTATATTTTTTGCCC-
1 CGAACTT-TCAAAAATCACA-TTTTTACCCT
* *
428176 CTAAAC-TTCTAAAAATCACATTTTTACCCC
1 C-GAACTTTC-AAAAATCACATTTTTACCCT
* * *
428206 CAAACTTCCAAAAATCACA-TTTTAGCCT
1 CGAACTTTCAAAAATCACATTTTTACCCT
* * *
428234 CGAACTTCTCCAAAATTACATTTTTACCAT
1 CGAACTT-TCAAAAATCACATTTTTACCCT
428264 CGAACTTTCAAAAATCACATTTTT-CCCT
1 CGAACTTTCAAAAATCACATTTTTACCCT
* * * *
428292 CGAACATACAAAAATTACCA-TTTTGCCCT
1 CGAACTTTCAAAAATCA-CATTTTTACCCT
* * * *
428321 TGAACATCCAAAAATTACCATTTTTACCCT
1 CGAACTTTCAAAAATCA-CATTTTTACCCT
*
428351 C-AAATTTCGAAAAATCACATTTT
1 CGAACTTTC-AAAAATCACATTTT
428374 CAACCTTAAA
Statistics
Matches: 185, Mismatches: 32, Indels: 23
0.77 0.13 0.10
Matches are distributed among these distances:
28 34 0.18
29 82 0.44
30 58 0.31
31 11 0.06
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (29 bp):
CGAACTTTCAAAAATCACATTTTTACCCT
Found at i:428429 original size:30 final size:29
Alignment explanation
Indices: 428381--428438 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
428371 TTTCAACCTT
428381 AAATTTTCCAAAAGTTCAATTTTAATCCC
1 AAATTTTCCAAAAGTTCAATTTTAATCCC
* *
428410 AAATTTTCCAAAAATTTCAATTTTGATCC
1 AAATTTTCC-AAAAGTTCAATTTTAATCC
428439 TTAAGTTCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 9 0.35
30 17 0.65
ACGTcount: A:0.38, C:0.19, G:0.03, T:0.40
Consensus pattern (29 bp):
AAATTTTCCAAAAGTTCAATTTTAATCCC
Found at i:432915 original size:116 final size:116
Alignment explanation
Indices: 432762--433008 Score: 383
Period size: 116 Copynumber: 2.1 Consensus size: 116
432752 AGAACTCATG
*
432762 CTTGTATCGATAGAAGTACAGGGTAGGAGAGAGGTTGTTCTCTGACTTGAGTTGTTTCGATAGTT
1 CTTGTATCGATAGAAGCACAGGGTAGGAGAGAGGTTGTTCTCTGACTTGAGTTGTTTCGATAGTT
* * * *
432827 GTTTAACA-TGTAT-TGATAGTTTTGTACATTGAGGTATCAGTAGTTTAAATA
66 GTATAACAGT-TATCAG-TAGTTCTGTACATTGAGGTATCAATAGTTTAAATA
* *
432878 CTTGTATCGGTAGAAGCATAGGGTAGGAGAGAGGTTGTTCTCTGACTTGAGTTGTTTCGATAGTT
1 CTTGTATCGATAGAAGCACAGGGTAGGAGAGAGGTTGTTCTCTGACTTGAGTTGTTTCGATAGTT
*
432943 GTATAACAGTTATCAGTAGTTCTGTACATTGTGGTATCAATAGTTTAAATA
66 GTATAACAGTTATCAGTAGTTCTGTACATTGAGGTATCAATAGTTTAAATA
432994 CTTGT-TCGATAGAAG
1 CTTGTATCGATAGAAG
433009 TTGCAGGGTA
Statistics
Matches: 120, Mismatches: 9, Indels: 5
0.90 0.07 0.04
Matches are distributed among these distances:
115 9 0.08
116 109 0.91
117 2 0.02
ACGTcount: A:0.27, C:0.10, G:0.26, T:0.38
Consensus pattern (116 bp):
CTTGTATCGATAGAAGCACAGGGTAGGAGAGAGGTTGTTCTCTGACTTGAGTTGTTTCGATAGTT
GTATAACAGTTATCAGTAGTTCTGTACATTGAGGTATCAATAGTTTAAATA
Found at i:439141 original size:15 final size:15
Alignment explanation
Indices: 439118--439165 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
439108 CAATCTCCCA
*
439118 ATCTCCATAG-TATCC
1 ATCTTCATAGATAT-C
439133 ATCTTCATAGATATC
1 ATCTTCATAGATATC
* *
439148 ATCCTCATAGATGTC
1 ATCTTCATAGATATC
439163 ATC
1 ATC
439166 ATCGTAACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 26 0.90
16 3 0.10
ACGTcount: A:0.29, C:0.27, G:0.08, T:0.35
Consensus pattern (15 bp):
ATCTTCATAGATATC
Found at i:442490 original size:33 final size:33
Alignment explanation
Indices: 442451--442525 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
442441 TCATCTTCCA
442451 CATCATCATTATCATTCCCAATTTCTGGTTCTT
1 CATCATCATTATCATTCCCAATTTCTGGTTCTT
* *
442484 CATCATCACTATCATTCCCTATTTCTGGTTCTT
1 CATCATCATTATCATTCCCAATTTCTGGTTCTT
*
442517 CTTCATCAT
1 CATCATCAT
442526 GCTCCTCATC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.20, C:0.29, G:0.05, T:0.45
Consensus pattern (33 bp):
CATCATCATTATCATTCCCAATTTCTGGTTCTT
Found at i:444193 original size:17 final size:17
Alignment explanation
Indices: 444136--444185 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 17
444126 AACTCAATCA
*
444136 AAATTAATAAAATAAAC
1 AAATAAATAAAATAAAC
444153 GAGTAATAAAATAAAATAAAC
1 -A--AAT-AAATAAAATAAAC
444174 AAATAAATAAAA
1 AAATAAATAAAA
444186 CTAACAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 8 0.29
18 4 0.14
20 4 0.14
21 12 0.43
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.20
Consensus pattern (17 bp):
AAATAAATAAAATAAAC
Found at i:445682 original size:20 final size:21
Alignment explanation
Indices: 445644--445683 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
445634 CCTAAATAAT
* *
445644 AATAATAATATTAATAAACAA
1 AATAATAATAATAAAAAACAA
445665 AATAA-AATAATAAAAAACA
1 AATAATAATAATAAAAAACA
445684 TATCTAGAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (21 bp):
AATAATAATAATAAAAAACAA
Found at i:450452 original size:46 final size:47
Alignment explanation
Indices: 450343--450471 Score: 147
Period size: 47 Copynumber: 2.8 Consensus size: 47
450333 TGAACAGTGT
* * * *
450343 CACCAAAATC-GTAGATAAATTGCCAATAACCAATATCGTGGACAAGC
1 CACCAAAATCTGTAGATAAACTACCAATAATCAA-ATCATGGACAAGC
* *
450390 CACCAAAATCT-CAGATAAACTACCAATAATCAAATCATGGACAAGG
1 CACCAAAATCTGTAGATAAACTACCAATAATCAAATCATGGACAAGC
* *
450436 CACC-ACATTTGTAGATAAACTACCACATAATCAAAT
1 CACCAAAATCTGTAGATAAACTACCA-ATAATCAAAT
450472 TGTGAACAGT
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
45 4 0.06
46 28 0.40
47 38 0.54
ACGTcount: A:0.45, C:0.24, G:0.11, T:0.20
Consensus pattern (47 bp):
CACCAAAATCTGTAGATAAACTACCAATAATCAAATCATGGACAAGC
Found at i:453617 original size:2 final size:2
Alignment explanation
Indices: 453600--453640 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
453590 TTTATTATTC
* *
453600 TA TA CA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
453641 TCTTTTTATC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:454357 original size:26 final size:26
Alignment explanation
Indices: 454326--454383 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
454316 AAATGCATGC
454326 AACTAAACTAAGTAATGAAAAGTAAA
1 AACTAAACTAAGTAATGAAAAGTAAA
454352 AACTAAACTAAGTAATGAAAAGTAAA
1 AACTAAACTAAGTAATGAAAAGTAAA
454378 AACTAA
1 AACTAA
454384 TCCAGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.62, C:0.09, G:0.10, T:0.19
Consensus pattern (26 bp):
AACTAAACTAAGTAATGAAAAGTAAA
Found at i:454757 original size:12 final size:12
Alignment explanation
Indices: 454736--454782 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
454726 TCAGTACAAA
454736 TTCTTCTTCTTT
1 TTCTTCTTCTTT
* *
454748 TTCTTTTTCTCT
1 TTCTTCTTCTTT
*
454760 TGCTTCTTCTTT
1 TTCTTCTTCTTT
454772 CTTC-TCTTCTT
1 -TTCTTCTTCTT
454783 CCTCCTCTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
12 26 0.93
13 2 0.07
ACGTcount: A:0.00, C:0.28, G:0.02, T:0.70
Consensus pattern (12 bp):
TTCTTCTTCTTT
Found at i:455303 original size:18 final size:18
Alignment explanation
Indices: 455277--455311 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
455267 GCATGGGATT
*
455277 CCTTACCTTTCTTTTTCA
1 CCTTACCTTTCTCTTTCA
*
455295 CCTTGCCTTTCTCTTTC
1 CCTTACCTTTCTCTTTC
455312 TTCGATGGTG
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:0.06, C:0.37, G:0.03, T:0.54
Consensus pattern (18 bp):
CCTTACCTTTCTCTTTCA
Found at i:457953 original size:48 final size:48
Alignment explanation
Indices: 457879--458053 Score: 253
Period size: 48 Copynumber: 3.7 Consensus size: 48
457869 TATGCTTCAC
* *
457879 TAAGTGTTTT-TTTTTTAAATGCATCTTTGTTTAATAATCTGCATCAT
1 TAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTGCATTAT
* * *
457926 TAAGTGTTTTGTTTGTTAAATGGATCTTTGTTTATTAATCTTCATTAT
1 TAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTGCATTAT
* * *
457974 TAACTGTTTTGTTTGTAAAATGCATCTTTGTTTAATAATATGCATTAT
1 TAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTGCATTAT
* *
458022 TAAATGTTTTTTTTGTTAAATGCATCTTTGTT
1 TAAGTGTTTTGTTTGTTAAATGCATCTTTGTT
458054 AAATGCCTTG
Statistics
Matches: 113, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
47 10 0.09
48 103 0.91
ACGTcount: A:0.25, C:0.08, G:0.13, T:0.54
Consensus pattern (48 bp):
TAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTGCATTAT
Found at i:458767 original size:20 final size:20
Alignment explanation
Indices: 458734--458772 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
458724 AATGAGTAAT
*
458734 AAAATAAAACAAA-TAATTA
1 AAAATAAAAAAAATTAATTA
458753 AAAACTAAAAAAAATTAATT
1 AAAA-TAAAAAAAATTAATT
458773 TATGGAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 8 0.47
21 5 0.29
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAATAAAAAAAATTAATTA
Found at i:460246 original size:3 final size:3
Alignment explanation
Indices: 460238--460296 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
460228 GAATAGCCTA
460238 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
460286 AAT AAT AAT AA
1 AAT AAT AAT AA
460297 ACAAAATAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:460317 original size:14 final size:15
Alignment explanation
Indices: 460241--460310 Score: 58
Period size: 15 Copynumber: 4.7 Consensus size: 15
460231 TAGCCTAAAT
*
460241 AATAATAATAATA-AT
1 AATAATAATAA-ACAA
*
460256 AATAATAATAATA-AT
1 AATAATAATAA-ACAA
*
460271 AATAATAATAATA-AT
1 AATAATAATAA-ACAA
460286 AATAATAATAAACAA
1 AATAATAATAAACAA
460301 AATAA-AATAA
1 AATAATAATAA
460311 CGAAAATCAT
Statistics
Matches: 53, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
14 6 0.11
15 47 0.89
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.29
Consensus pattern (15 bp):
AATAATAATAAACAA
Found at i:461421 original size:14 final size:14
Alignment explanation
Indices: 461402--461429 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
461392 CCAGGGGTCG
461402 GTGTCGTGACATAC
1 GTGTCGTGACATAC
461416 GTGTCGTGACATAC
1 GTGTCGTGACATAC
461430 CAAGTCCTAT
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:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (14 bp):
GTGTCGTGACATAC
Found at i:464674 original size:18 final size:19
Alignment explanation
Indices: 464647--464737 Score: 91
Period size: 18 Copynumber: 4.9 Consensus size: 19
464637 CCAGCACATA
464647 TATATATATTTCTAATACT
1 TATATATATTTCTAATACT
* *
464666 TAT-TATATTT-TTATTCT
1 TATATATATTTCTAATACT
**
464683 TATATATATTTCTAGCACT
1 TATATATATTTCTAATACT
* *
464702 TAT-TATATTT-TTATTCTT
1 TATATATATTTCTAATAC-T
464720 TATATATATTTCTAATAC
1 TATATATATTTCTAATAC
464738 GCATTATATA
Statistics
Matches: 55, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
17 10 0.18
18 25 0.45
19 16 0.29
20 4 0.07
ACGTcount: A:0.31, C:0.10, G:0.01, T:0.58
Consensus pattern (19 bp):
TATATATATTTCTAATACT
Found at i:464694 original size:36 final size:37
Alignment explanation
Indices: 464647--464746 Score: 157
Period size: 36 Copynumber: 2.7 Consensus size: 37
464637 CCAGCACATA
464647 TATATATATTTCTAATACTTATTATATTTTTATTC-T
1 TATATATATTTCTAATACTTATTATATTTTTATTCTT
**
464683 TATATATATTTCTAGCACTTATTATATTTTTATTCTT
1 TATATATATTTCTAATACTTATTATATTTTTATTCTT
**
464720 TATATATATTTCTAATACGCATTATAT
1 TATATATATTTCTAATACTTATTATAT
464747 ATATATATTA
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 33 0.58
37 24 0.42
ACGTcount: A:0.31, C:0.10, G:0.02, T:0.57
Consensus pattern (37 bp):
TATATATATTTCTAATACTTATTATATTTTTATTCTT
Found at i:464959 original size:205 final size:205
Alignment explanation
Indices: 464742--465153 Score: 788
Period size: 205 Copynumber: 2.0 Consensus size: 205
464732 TAATACGCAT
464742 TATATATATATATTACATTGCCATAACATAGTATTTACTAACCTTTGCCCTGAAATTATTTTAGA
1 TATATATATATATTACATTGCCATAACATAGTATTTACTAACCTTTGCCCTGAAATTATTTTAGA
464807 ATCATGACATTAACATACACTGACTCTACCATGACATTATTCTTTTGCCATGACAATAACTGAAT
66 ATCATGACATTAACATACACTGACTCTACCATGACATTATTCTTTTGCCATGACAATAACTGAAT
*
464872 TAAATCACATTATCAATTCTGATCCCTATGGAGAACGATAACGTACTTATCACTTTATTACCTGA
131 TAAATCACATTATCAATTCCGATCCCTATGGAGAACGATAACGTACTTATCACTTTATTACCTGA
464937 GCGACATGTA
196 GCGACATGTA
464947 TATATATATATATTACATTGCCATAACATAGTATTTACTAACCTTTGCCCTGAAATTATTTTAGA
1 TATATATATATATTACATTGCCATAACATAGTATTTACTAACCTTTGCCCTGAAATTATTTTAGA
* *
465012 GTTATGACATTAACATACACTGACTCTACCATGACATTATTCTTTTGCCATGACAATAACTGAAT
66 ATCATGACATTAACATACACTGACTCTACCATGACATTATTCTTTTGCCATGACAATAACTGAAT
465077 TAAATCACATTATCAATTCCGATCCCTATGGAGAACGATAACGTACTTATCACTTTATTACCTGA
131 TAAATCACATTATCAATTCCGATCCCTATGGAGAACGATAACGTACTTATCACTTTATTACCTGA
*
465142 GCGACGTGTA
196 GCGACATGTA
465152 TA
1 TA
465154 CTTGTACAGT
Statistics
Matches: 203, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
205 203 1.00
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Consensus pattern (205 bp):
TATATATATATATTACATTGCCATAACATAGTATTTACTAACCTTTGCCCTGAAATTATTTTAGA
ATCATGACATTAACATACACTGACTCTACCATGACATTATTCTTTTGCCATGACAATAACTGAAT
TAAATCACATTATCAATTCCGATCCCTATGGAGAACGATAACGTACTTATCACTTTATTACCTGA
GCGACATGTA
Found at i:467178 original size:28 final size:28
Alignment explanation
Indices: 467135--467201 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
467125 GAATGGCCAC
* *
467135 AAAAGGCTTTCGCATA-CTAGAACAACCA
1 AAAAGGCTTCCACATATC-AGAACAACCA
*
467163 AAAAGTCTTCCACATATCAGAACAACCA
1 AAAAGGCTTCCACATATCAGAACAACCA
*
467191 CAAAGGCTTCC
1 AAAAGGCTTCC
467202 TTTCGGTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 32 0.97
29 1 0.03
ACGTcount: A:0.42, C:0.28, G:0.12, T:0.18
Consensus pattern (28 bp):
AAAAGGCTTCCACATATCAGAACAACCA
Found at i:476686 original size:20 final size:21
Alignment explanation
Indices: 476661--476699 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
476651 AATTATGTTT
476661 ATTTAAAATAA-AAACATTAA
1 ATTTAAAATAAGAAACATTAA
*
476681 ATTTAAATTAAGAAACATT
1 ATTTAAAATAAGAAACATT
476700 TGACTTTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (21 bp):
ATTTAAAATAAGAAACATTAA
Found at i:477044 original size:15 final size:15
Alignment explanation
Indices: 477000--477045 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
476990 TCATGTTACA
477000 TTTTAATCACTTATG
1 TTTTAATCACTTATG
* *
477015 TTTGAA--ATGTTATG
1 TTTTAATCA-CTTATG
477029 TTTTAATCACTTATG
1 TTTTAATCACTTATG
477044 TT
1 TT
477046 ATTATTTTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
13 1 0.04
14 10 0.42
15 12 0.50
16 1 0.04
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.54
Consensus pattern (15 bp):
TTTTAATCACTTATG
Found at i:477269 original size:6 final size:6
Alignment explanation
Indices: 477258--477286 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
477248 ACGCCTCTCT
477258 TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
477287 TTCCCTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.34, G:0.00, T:0.52
Consensus pattern (6 bp):
TCTTCA
Found at i:477425 original size:113 final size:113
Alignment explanation
Indices: 477291--477521 Score: 349
Period size: 113 Copynumber: 2.1 Consensus size: 113
477281 ATCTTCTTCC
* * *
477291 CTTTTGATTCCAATATCTTTAGTTACAAATCTATTTCAAAGCTTAAATCTTTAAAAT-TCATTAA
1 CTTTTGATTCCAATATATTTAGTTACAAATCTATCTCAAAACTTAAATCTTTAAAATCT-ATTAA
*
477355 CCAAAAGATTCAATATATTTGGTTACAATATTTTCTTCCCGTTAAGTTT
65 CCAAAAGATTCAATATATTTGGTTACAATATCTTCTTCCCGTTAAGTTT
* *
477404 CTTTTGATTCCAATATATTTAGTTACAAATCTGTCTCAAAACTTGAATCTTTAAAATCTATTAAC
1 CTTTTGATTCCAATATATTTAGTTACAAATCTATCTCAAAACTTAAATCTTTAAAATCTATTAAC
* * * *
477469 TAAAATATTCAATATCTTTGGTTTCAATATCTTCTTCCCGTTAAGTTT
66 CAAAAGATTCAATATATTTGGTTACAATATCTTCTTCCCGTTAAGTTT
477517 -TTTTG
1 CTTTTG
477522 GGTTAATGTG
Statistics
Matches: 107, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
112 5 0.05
113 101 0.94
114 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.07, T:0.45
Consensus pattern (113 bp):
CTTTTGATTCCAATATATTTAGTTACAAATCTATCTCAAAACTTAAATCTTTAAAATCTATTAAC
CAAAAGATTCAATATATTTGGTTACAATATCTTCTTCCCGTTAAGTTT
Found at i:490744 original size:24 final size:26
Alignment explanation
Indices: 490691--490741 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 26
490681 TAATTGTGTC
*
490691 TTGGCTGGAGTTGCTTTTCTTGCTTA
1 TTGGCTGGAGTTGCTTTTCATGCTTA
*
490717 TTGG-TGG-GTTGTTTTTCATG-TTA
1 TTGGCTGGAGTTGCTTTTCATGCTTA
490740 TT
1 TT
490742 TGGCAGGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 5 0.22
24 11 0.48
25 3 0.13
26 4 0.17
ACGTcount: A:0.08, C:0.10, G:0.27, T:0.55
Consensus pattern (26 bp):
TTGGCTGGAGTTGCTTTTCATGCTTA
Found at i:492599 original size:18 final size:18
Alignment explanation
Indices: 492576--492618 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
492566 CTGGACACTC
492576 TGGGCAGGAAGCCGAGGG
1 TGGGCAGGAAGCCGAGGG
492594 TGGGCAGGAAGCCGAGGG
1 TGGGCAGGAAGCCGAGGG
492612 TGGGCAG
1 TGGGCAG
492619 AAAGGACCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.21, C:0.16, G:0.56, T:0.07
Consensus pattern (18 bp):
TGGGCAGGAAGCCGAGGG
Found at i:496323 original size:11 final size:11
Alignment explanation
Indices: 496296--496330 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
496286 TTATTTATTT
*
496296 TTAAATTTACTA
1 TTAAATTTA-AA
496308 TTAAATTTAAA
1 TTAAATTTAAA
496319 TTAAATTTAAA
1 TTAAATTTAAA
496330 T
1 T
496331 ATTTTATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 13 0.59
12 9 0.41
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:496960 original size:26 final size:27
Alignment explanation
Indices: 496923--496992 Score: 79
Period size: 26 Copynumber: 2.5 Consensus size: 27
496913 ATACATATTT
*
496923 AATTATTTATATTTAATCA-TATAATA
1 AATTATTAATATTTAATCATTATAATA
* *
496949 AATTATTAATATAATTTATCATTTTAATA
1 AATTATTAATAT--TTAATCATTATAATA
496978 AATTATTTAATATTT
1 AATTA-TTAATATTT
496993 CAATTTTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 11 0.30
28 8 0.22
29 11 0.30
30 7 0.19
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (27 bp):
AATTATTAATATTTAATCATTATAATA
Found at i:496966 original size:29 final size:30
Alignment explanation
Indices: 496933--496990 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
496923 AATTATTTAT
496933 ATTTAATCA-TATAATAAATTA-TTAATATA
1 ATTT-ATCATTATAATAAATTATTTAATATA
*
496962 ATTTATCATTTTAATAAATTATTTAATAT
1 ATTTATCATTATAATAAATTATTTAATAT
496991 TTCAATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 4 0.15
29 15 0.58
30 7 0.27
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (30 bp):
ATTTATCATTATAATAAATTATTTAATATA
Found at i:502076 original size:13 final size:13
Alignment explanation
Indices: 502058--502082 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
502048 TTCAATTTTT
502058 TTTTAAATAATAA
1 TTTTAAATAATAA
502071 TTTTAAATAATA
1 TTTTAAATAATA
502083 TTCTTCACAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTTAAATAATAA
Found at i:513218 original size:21 final size:21
Alignment explanation
Indices: 513180--513220 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
513170 TTTTTTAGTA
*
513180 TCGGTAGAAGCATGACTTGTT
1 TCGGTAGAAGCATCACTTGTT
**
513201 TCGGTAGAAGTTTCACTTGT
1 TCGGTAGAAGCATCACTTGT
513221 ATTAGTAGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.15, G:0.27, T:0.37
Consensus pattern (21 bp):
TCGGTAGAAGCATCACTTGTT
Found at i:515334 original size:35 final size:35
Alignment explanation
Indices: 515295--515365 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
515285 GAAATGCCTG
515295 ACTGGTAAAGTAATTACAGTTGAATCTGGTAGGTT
1 ACTGGTAAAGTAATTACAGTTGAATCTGGTAGGTT
515330 ACTGGTAAAGTAATTACAGTTGAATCTGGTAGGTT
1 ACTGGTAAAGTAATTACAGTTGAATCTGGTAGGTT
515365 A
1 A
515366 AGTAATGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.32, C:0.08, G:0.25, T:0.34
Consensus pattern (35 bp):
ACTGGTAAAGTAATTACAGTTGAATCTGGTAGGTT
Found at i:520902 original size:29 final size:29
Alignment explanation
Indices: 520860--520917 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
520850 ATTGGCTTTT
*
520860 GTTAATTTTATTTTTGTAGCTGCAATTAA
1 GTTAATTTTATTTTGGTAGCTGCAATTAA
520889 GTTAATTTTATTTTGGTAGCTGCAATTAA
1 GTTAATTTTATTTTGGTAGCTGCAATTAA
520918 TTCTACTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.28, C:0.07, G:0.16, T:0.50
Consensus pattern (29 bp):
GTTAATTTTATTTTGGTAGCTGCAATTAA
Found at i:523637 original size:15 final size:15
Alignment explanation
Indices: 523619--523648 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
523609 TGATAAAAAG
523619 TAGGTTAATAATTGT
1 TAGGTTAATAATTGT
523634 TAGGTTAATAATTGT
1 TAGGTTAATAATTGT
523649 GAGCTGAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (15 bp):
TAGGTTAATAATTGT
Found at i:537670 original size:9 final size:9
Alignment explanation
Indices: 537658--537691 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
537648 TTTTAGCAAT
537658 TTTTTCTTC
1 TTTTTCTTC
537667 TTTTTCTT-
1 TTTTTCTTC
537675 TTCTTTCTTC
1 TT-TTTCTTC
537685 TTTTTCT
1 TTTTTCT
537692 CATTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 2 0.09
9 19 0.83
10 2 0.09
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:545702 original size:12 final size:12
Alignment explanation
Indices: 545681--545709 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
545671 GAGATGAAGG
545681 TTTT-GGAGTGT
1 TTTTGGGAGTGT
545692 TTTTGGGAGTGT
1 TTTTGGGAGTGT
545704 TTTTGG
1 TTTTGG
545710 ATGCATGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.07, C:0.00, G:0.38, T:0.55
Consensus pattern (12 bp):
TTTTGGGAGTGT
Found at i:548941 original size:12 final size:12
Alignment explanation
Indices: 548920--548955 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
548910 GTTCGAAGGC
548920 ATAAAATAAAAG
1 ATAAAATAAAAG
* *
548932 ATAAACTAAAAC
1 ATAAAATAAAAG
548944 ATAAAATAAAAG
1 ATAAAATAAAAG
548956 CAAAGTTTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.17
Consensus pattern (12 bp):
ATAAAATAAAAG
Found at i:549400 original size:35 final size:35
Alignment explanation
Indices: 549354--549423 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
549344 AATTAGTTTA
549354 TCATGGTTTCTTTATTCATCAATAACACAATATAT
1 TCATGGTTTCTTTATTCATCAATAACACAATATAT
549389 TCATGGTTTCTTTATTCATCAATAACACAATATAT
1 TCATGGTTTCTTTATTCATCAATAACACAATATAT
549424 GAAAACATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (35 bp):
TCATGGTTTCTTTATTCATCAATAACACAATATAT
Found at i:576242 original size:40 final size:40
Alignment explanation
Indices: 576197--576285 Score: 169
Period size: 40 Copynumber: 2.2 Consensus size: 40
576187 ACTCGAGTAA
576197 AATTTAAAATACGATCCTAAATACATGAATTATTTAATGT
1 AATTTAAAATACGATCCTAAATACATGAATTATTTAATGT
*
576237 AATTTAAAATATGATCCTAAATACATGAATTATTTAATGT
1 AATTTAAAATACGATCCTAAATACATGAATTATTTAATGT
576277 AATTTAAAA
1 AATTTAAAA
576286 AAATTAATTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.38
Consensus pattern (40 bp):
AATTTAAAATACGATCCTAAATACATGAATTATTTAATGT
Found at i:593393 original size:75 final size:74
Alignment explanation
Indices: 593305--593464 Score: 196
Period size: 75 Copynumber: 2.1 Consensus size: 74
593295 ATTGATAACT
* * * * *
593305 GTATAAATTAAATTAGAAGCT-GATATATTAAGATTTATTTAAAATAATGAATGAAGTTTTGGCA
1 GTATAAATTAAATTAGAAGCTCG-TACATCAACATTTATTTAAAATAATAAATGAA-ATTTGGCA
* * *
593369 TATCATTTATG
64 TATCACTAATA
* * *
593380 GTATAAATTAAATTAGAAGTTCGTGCATCAACATTTATTTGAAATAATAAATGAAATTTGGCATA
1 GTATAAATTAAATTAGAAGCTCGTACATCAACATTTATTTAAAATAATAAATGAAATTTGGCATA
593445 TCACTAATA
66 TCACTAATA
593454 GTATAAATTAA
1 GTATAAATTAA
593465 GTAAATTAAA
Statistics
Matches: 73, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
74 26 0.36
75 46 0.63
76 1 0.01
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.38
Consensus pattern (74 bp):
GTATAAATTAAATTAGAAGCTCGTACATCAACATTTATTTAAAATAATAAATGAAATTTGGCATA
TCACTAATA
Found at i:597685 original size:74 final size:75
Alignment explanation
Indices: 597561--598155 Score: 538
Period size: 83 Copynumber: 7.5 Consensus size: 75
597551 TCAGAAACAA
* * * *
597561 TGAATGAAGTTTTGGCATATCACT-ATGATATAAATTAAATTAGAAGTTCGTATATCAAGATTTG
1 TGAATGAAGTTTTGGTATACCACTAATGATATAAATTAAATTAGAAATTCGTATATCAAAATTTG
597625 TTT-GAAGTAG
66 TTTGGAA-TAG
*
597635 TGAATGGAGTTTTGGTATACCACTAATG-TATAAATTAAATTAGAAATTCGTATATCAAAATTTG
1 TGAATGAAGTTTTGGTATACCACTAATGATATAAATTAAATTAGAAATTCGTATATCAAAATTTG
597699 TTTGGAATAG
66 TTTGGAATAG
* * * * * *
597709 TGAATGAAGTTTTGGTATATCAATAATGGTATAAATTAAATTAGAAGTTCGTATATTAAGATTTG
1 TGAATGAAGTTTTGGTATACCACTAATGATATAAATTAAATTAGAAATTCGTATATCAAAATTTG
597774 TTT-GAAGTAG
66 TTTGGAA-TAG
* *
597784 TGAATGAAGCTTTGGTATACCACTAATGTATAAATTAAATAAACTAAATTAGAAGTTCGTATATC
1 TGAATGAAGTTTTGGTATACCACTAATG-AT--A-TAAAT----TAAATTAGAAATTCGTATATC
597849 AAAATTTGTTTGGAATAG
58 AAAATTTGTTTGGAATAG
* *
597867 TGAATGAAGTTTTGATATACCACTAATGGTATAAATTAAATAAATGAAATTAGCAATTCGTATAT
1 TGAATGAAGTTTTGGTATACCACTAAT-G-AT--A-TAAAT---T-AAATTAGAAATTCGTATAT
*
597932 CAAGATTTGTTTGGAATAG
57 CAAAATTTGTTTGGAATAG
* * * *
597951 TGAAAT-ATGTTTTGGTATATCACTATTGTATAAATTAAATAAACTAAATTAGAAATTTGTATAT
1 TG-AATGAAGTTTTGGTATACCACTAATG-AT--A-TAAAT----TAAATTAGAAATTCGTATAT
*
598015 CAAAATTTGTTTAGAATAG
57 CAAAATTTGTTTGGAATAG
* * *
598034 TGAA-GAAGTTTTAGTATACCACTAATGATATAAATTAAATAAATTAAATTAGAAGTTCATATAT
1 TGAATGAAGTTTTGGTATACCACTAATG------A-T--ATAAATTAAATTAGAAATTCGTATAT
** *
598098 CAAGGTTTTTTTGGAAT-G
57 CAAAATTTGTTTGGAATAG
* *
598116 ATGAATGAAGTTTTGGTATATCACTAATGGTATAAATTAA
1 -TGAATGAAGTTTTGGTATACCACTAATGATATAAATTAA
598156 GTAAATTAAA
Statistics
Matches: 448, Mismatches: 47, Indels: 51
0.82 0.09 0.09
Matches are distributed among these distances:
74 89 0.20
75 79 0.18
76 1 0.00
77 1 0.00
78 1 0.00
79 5 0.01
82 21 0.05
83 144 0.32
84 94 0.21
85 3 0.01
87 6 0.01
88 4 0.01
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.38
Consensus pattern (75 bp):
TGAATGAAGTTTTGGTATACCACTAATGATATAAATTAAATTAGAAATTCGTATATCAAAATTTG
TTTGGAATAG
Found at i:597868 original size:83 final size:83
Alignment explanation
Indices: 597739--598174 Score: 594
Period size: 83 Copynumber: 5.2 Consensus size: 83
597729 CAATAATGGT
* *
597739 ATAAATTAAATTAGAAGTTCGTATATTAAGATTTGTTT-GAAGTAGTGAATGAAGCTTTGGTATA
1 ATAAATTAAATTAGAAGTTCGTATATCAAGATTTGTTTGGAA-TAGTGAATGAAGTTTTGGTATA
597803 CCACTAATGTATAAATTAA
65 CCACTAATGTATAAATTAA
* * *
597822 ATAAACTAAATTAGAAGTTCGTATATCAAAATTTGTTTGGAATAGTGAATGAAGTTTTGATATAC
1 ATAAATTAAATTAGAAGTTCGTATATCAAGATTTGTTTGGAATAGTGAATGAAGTTTTGGTATAC
597887 CACTAATGGTATAAATTAA
66 CACTAAT-GTATAAATTAA
* *
597906 ATAAATGAAATTAGCAA-TTCGTATATCAAGATTTGTTTGGAATAGTGAAAT-ATGTTTTGGTAT
1 ATAAATTAAATTAG-AAGTTCGTATATCAAGATTTGTTTGGAATAGTG-AATGAAGTTTTGGTAT
* *
597969 ATCACTATTGTATAAATTAA
64 ACCACTAATGTATAAATTAA
* * * * * *
597989 ATAAACTAAATTAGAAATTTGTATATCAAAATTTGTTTAGAATAGTGAA-GAAGTTTTAGTATAC
1 ATAAATTAAATTAGAAGTTCGTATATCAAGATTTGTTTGGAATAGTGAATGAAGTTTTGGTATAC
598053 CACTAATGATATAAATTAA
66 CACTAATG-TATAAATTAA
* * *
598072 ATAAATTAAATTAGAAGTTCATATATCAAGGTTTTTTTGGAAT-GATGAATGAAGTTTTGGTATA
1 ATAAATTAAATTAGAAGTTCGTATATCAAGATTTGTTTGGAATAG-TGAATGAAGTTTTGGTATA
*
598136 TCACTAATGGTATAAATTAA
65 CCACTAAT-GTATAAATTAA
*
598156 GTAAATTAAATTAGAAGTT
1 ATAAATTAAATTAGAAGTT
598175 TTTTTCTTAA
Statistics
Matches: 311, Mismatches: 32, Indels: 19
0.86 0.09 0.05
Matches are distributed among these distances:
82 23 0.07
83 162 0.52
84 120 0.39
85 6 0.02
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.38
Consensus pattern (83 bp):
ATAAATTAAATTAGAAGTTCGTATATCAAGATTTGTTTGGAATAGTGAATGAAGTTTTGGTATAC
CACTAATGTATAAATTAA
Found at i:598002 original size:167 final size:166
Alignment explanation
Indices: 597664--598174 Score: 645
Period size: 167 Copynumber: 3.1 Consensus size: 166
597654 CCACTAATGT
* * * *
597664 ATAAATTAAATTAGAAATTCGTATATCAAAATTTGTTTGGAATAGTGAATGAAGTTTTGGTATA-
1 ATAAACTAAATTAGAAGTTCGTATATCAAAATTTGTTTAGAATAGTGAA-GAAGTTTTAGTATAC
* ** *
597728 -TC-AAT-A-AT--GGT--ATAAATTAAATTAGAAGTTCGTATATTAAGATTTGTTT-GAAGTAG
65 CACTAATGATATAAATTAAATAAATTAAATTAGAAGTTCGTATATCAAGATTTGTTTGGAA-TAG
* * *
597784 TGAATGAAGCTTTGGTATACCACTAATGTATAAATTAA
129 TGAATGAAGTTTTGGTATATCACTATTGTATAAATTAA
*
597822 ATAAACTAAATTAGAAGTTCGTATATCAAAATTTGTTTGGAATAGTGAATGAAGTTTT-GATATA
1 ATAAACTAAATTAGAAGTTCGTATATCAAAATTTGTTTAGAATAGTGAA-GAAGTTTTAG-TATA
* *
597886 CCACTAATGGTATAAATTAAATAAATGAAATTAGCAA-TTCGTATATCAAGATTTGTTTGGAATA
64 CCACTAATGATATAAATTAAATAAATTAAATTAG-AAGTTCGTATATCAAGATTTGTTTGGAATA
*
597950 GTGAAAT-ATGTTTTGGTATATCACTATTGTATAAATTAA
128 GTG-AATGAAGTTTTGGTATATCACTATTGTATAAATTAA
* *
597989 ATAAACTAAATTAGAAATTTGTATATCAAAATTTGTTTAGAATAGTGAAGAAGTTTTAGTATACC
1 ATAAACTAAATTAGAAGTTCGTATATCAAAATTTGTTTAGAATAGTGAAGAAGTTTTAGTATACC
* * *
598054 ACTAATGATATAAATTAAATAAATTAAATTAGAAGTTCATATATCAAGGTTTTTTTGGAAT-GAT
66 ACTAATGATATAAATTAAATAAATTAAATTAGAAGTTCGTATATCAAGATTTGTTTGGAATAG-T
*
598118 GAATGAAGTTTTGGTATATCACTAATGGTATAAATTAA
130 GAATGAAGTTTTGGTATATCACT-ATTGTATAAATTAA
* *
598156 GTAAATTAAATTAGAAGTT
1 ATAAACTAAATTAGAAGTT
598175 TTTTTCTTAA
Statistics
Matches: 310, Mismatches: 25, Indels: 27
0.86 0.07 0.07
Matches are distributed among these distances:
157 1 0.00
158 60 0.19
160 1 0.00
161 3 0.01
163 2 0.01
165 7 0.02
166 86 0.28
167 142 0.46
168 8 0.03
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (166 bp):
ATAAACTAAATTAGAAGTTCGTATATCAAAATTTGTTTAGAATAGTGAAGAAGTTTTAGTATACC
ACTAATGATATAAATTAAATAAATTAAATTAGAAGTTCGTATATCAAGATTTGTTTGGAATAGTG
AATGAAGTTTTGGTATATCACTATTGTATAAATTAA
Found at i:598113 original size:250 final size:242
Alignment explanation
Indices: 597664--598171 Score: 691
Period size: 250 Copynumber: 2.1 Consensus size: 242
597654 CCACTAATGT
597664 ATAAATTAAATTAGAAATTCGTATATCAAAATTTGTTTGGAATAGTGAATGAAGTTTTGGTATAT
1 ATAAATTAAATTAGAAATTCGTATATCAAAATTTGTTTGGAATAGTGAATGAAGTTTTGGTATAT
* * * *
597729 CAATAATGGTATAAATTAAATTAGAAGTTCGTATATTAAGATTTGTTTGAAGTAGTGAATGAAGC
66 CAATAATGATATAAATTAAATTAGAAATTCGTATATCAAAATTTGTTTGAAGTAGTGAATGAAGC
* *
597794 TTTGGTATACCACTAATGTATAAATTAAATAAACTAAATTAGAAGTTCGTATATCAAAATTTGTT
131 TTTAGTATACCACTAATGTATAAATTAAATAAACTAAATTAGAAGTTCATATATCAAAATTTGTT
597859 TGGAAT-AGTGAATGAAGTTTTGATATACCACTAATGGTATAAATTAA
196 TGGAATGA-TGAATGAAGTTTTGATATACCACTAATGGTATAAATTAA
* * * *
597906 ATAAATGAAATTAGCAATTCGTATATCAAGATTTGTTTGGAATAGTGAAAT-ATGTTTTGGTATA
1 ATAAATTAAATTAGAAATTCGTATATCAAAATTTGTTTGGAATAGTG-AATGAAGTTTTGGTATA
* * *
597970 TCACTATTGTATAAATTAAATAAACTAAATTAGAAATTTGTATATCAAAATTTGTTTAGAA-TAG
65 TCAATAATG-AT--A-TAAAT----TAAATTAGAAATTCGTATATCAAAATTTGTTT-GAAGTAG
* *
598034 TGAA-GAAGTTTTAGTATACCACTAATGATATAAATTAAATAAATTAAATTAGAAGTTCATATAT
121 TGAATGAAGCTTTAGTATACCACTAATG-TATAAATTAAATAAACTAAATTAGAAGTTCATATAT
** * * *
598098 CAAGGTTTTTTTGGAATGATGAATGAAGTTTTGGTATATCACTAATGGTATAAATTAA
185 CAAAATTTGTTTGGAATGATGAATGAAGTTTTGATATACCACTAATGGTATAAATTAA
*
598156 GTAAATTAAATTAGAA
1 ATAAATTAAATTAGAA
598172 GTTTTTTTCT
Statistics
Matches: 231, Mismatches: 23, Indels: 16
0.86 0.09 0.06
Matches are distributed among these distances:
242 63 0.27
243 4 0.02
245 1 0.00
246 5 0.02
249 21 0.09
250 133 0.58
251 4 0.02
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.38
Consensus pattern (242 bp):
ATAAATTAAATTAGAAATTCGTATATCAAAATTTGTTTGGAATAGTGAATGAAGTTTTGGTATAT
CAATAATGATATAAATTAAATTAGAAATTCGTATATCAAAATTTGTTTGAAGTAGTGAATGAAGC
TTTAGTATACCACTAATGTATAAATTAAATAAACTAAATTAGAAGTTCATATATCAAAATTTGTT
TGGAATGATGAATGAAGTTTTGATATACCACTAATGGTATAAATTAA
Found at i:598898 original size:22 final size:22
Alignment explanation
Indices: 598873--598914 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
598863 ATTTGAAAGG
598873 ATAA-ACTTTAAGATTTAAAATT
1 ATAATACTTTAA-ATTTAAAATT
*
598895 ATAATATTTTAAATTTAAAA
1 ATAATACTTTAAATTTAAAA
598915 CTATTTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
ATAATACTTTAAATTTAAAATT
Found at i:599838 original size:22 final size:22
Alignment explanation
Indices: 599810--599856 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
599800 TTGATGTACT
599810 TGTTTTCGTTTACAACAATTCA
1 TGTTTTCGTTTACAACAATTCA
599832 TGTTTTCGTTTACAACAATTCA
1 TGTTTTCGTTTACAACAATTCA
599854 TGT
1 TGT
599857 AAGAATGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.47
Consensus pattern (22 bp):
TGTTTTCGTTTACAACAATTCA
Found at i:601974 original size:18 final size:18
Alignment explanation
Indices: 601947--601989 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
601937 TGTTTATTTG
601947 ATTT-TTATT-AATTTACA
1 ATTTATTATTAAATTTA-A
601964 ATTTATTATTAAATTTAA
1 ATTTATTATTAAATTTAA
601982 ATTGTATT
1 ATT-TATT
601990 TATATTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.17
18 9 0.39
19 10 0.43
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (18 bp):
ATTTATTATTAAATTTAA
Found at i:608444 original size:158 final size:158
Alignment explanation
Indices: 608136--608616 Score: 705
Period size: 158 Copynumber: 3.0 Consensus size: 158
608126 ATTTCAGGAT
* * *
608136 TTACATGTTATATGGGTG-TTGGTCTTAGATGTCTTACCGATGGTTGAGATCCAACATATGTTGC
1 TTACATGTTATATGGGTGCTT-GTCTTAGATGTCCTACCGATGGCTGAGATCCGACATATGTTGC
* * * *
608200 GAATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGTCTAACATCTTGATCCACAGCTCATGTGA
65 GAATTCTCCACAGCTCGTGTGAGCAGCATCATGTAGTCTAACATCTCGACCCACAGCTCGTGTGA
* * * *
608265 GCAAACTCGCTTTACATCTCGTGTGAGCA
130 GCAGACCCACTTCACATCTCGTGTGAGCA
*
608294 TTACATGTTATATGGGTGCTTGTCTTAGATGTCCTATCGATGGCTGAGATCCGACATATGTTGCG
1 TTACATGTTATATGGGTGCTTGTCTTAGATGTCCTACCGATGGCTGAGATCCGACATATGTTGCG
* * *
608359 AATTCTCCACAACTCGTGTGAGCAGCATCTTGTAGTCTAACATCTCGACCCACAGCTCGTGTGAA
66 AATTCTCCACAGCTCGTGTGAGCAGCATCATGTAGTCTAACATCTCGACCCACAGCTCGTGTGAG
* *
608424 CAGACCCACTTCATAGCTCGTGTGAGCA
131 CAGACCCACTTCACATCTCGTGTGAGCA
*
608452 TTACATGTTATATGGGTGCTGGTCTTAGATGTCCTACCGATGGCTGAGATCCGACATATGTTGC-
1 TTACATGTTATATGGGTGCTTGTCTTAGATGTCCTACCGATGGCTGAGATCCGACATATGTTGCG
* * ** *
608516 AGGTTCTCTACAGCTTATGTGAGCAGCATCATGTAGTCTAACATCTCGACCCACAACTCGTGTGA
66 A-ATTCTCCACAGCTCGTGTGAGCAGCATCATGTAGTCTAACATCTCGACCCACAGCTCGTGTGA
*
608581 GCAGACCCATTTCACATCTCGTGTGAGCA
130 GCAGACCCACTTCACATCTCGTGTGAGCA
*
608610 CTACATG
1 TTACATG
608617 ATACAAAGAT
Statistics
Matches: 291, Mismatches: 30, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
157 1 0.00
158 288 0.99
159 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.31
Consensus pattern (158 bp):
TTACATGTTATATGGGTGCTTGTCTTAGATGTCCTACCGATGGCTGAGATCCGACATATGTTGCG
AATTCTCCACAGCTCGTGTGAGCAGCATCATGTAGTCTAACATCTCGACCCACAGCTCGTGTGAG
CAGACCCACTTCACATCTCGTGTGAGCA
Found at i:623016 original size:137 final size:139
Alignment explanation
Indices: 622624--623017 Score: 596
Period size: 139 Copynumber: 2.8 Consensus size: 139
622614 CAGAGCGCCA
* * * *
622624 CAGGTTCGAACACTTTGCTTGAATCGATTATTGCATCAACATCAACAGGGAGCCCTAGTTGTAGT
1 CAGGTTCGAACACTTTGCTTGAATCGATTACTGCATCACCATCAACGGGGAGCCCTAGTTGCAGT
* * * *
622689 GCAACATATTCTAGTGAGATGGTGCATTCCCCACACGACAAATAAAATGTGTGCATCTCTAGGCG
66 GCGACATCTTCTAGTGAGATGGTGCATTCCCCACATGACAAATGAAATGTGTGCATCTCTAGGCG
622754 CCAACACCG
131 CCAACACCG
* * *
622763 TAGGTTCGAACACTTTGCTTGAATCGATTACTGCATCACCATCAACGGGGAGCCCTGGTTGCTGT
1 CAGGTTCGAACACTTTGCTTGAATCGATTACTGCATCACCATCAACGGGGAGCCCTAGTTGCAGT
622828 GCGACATCTTCTAGTGAGATGGTGCATTCCCCACATGACAAATGAAATGTGTGCATCTCTAGGCG
66 GCGACATCTTCTAGTGAGATGGTGCATTCCCCACATGACAAATGAAATGTGTGCATCTCTAGGCG
*
622893 CCAACTCC-
131 CCAACACCG
** *
622901 CAGGTTCGAACACTTTGCTTGAATCGATTACCACATCACCATCAATGGGGAG-CCTAGTTGCAGT
1 CAGGTTCGAACACTTTGCTTGAATCGATTACTGCATCACCATCAACGGGGAGCCCTAGTTGCAGT
* * *
622965 GCGACATCTTCCAGTGTGATGGTGCATTCCCCACATGGA-GAATGAAATGTGTG
66 GCGACATCTTCTAGTGAGATGGTGCATTCCCCACAT-GACAAATGAAATGTGTG
623018 AGTCTTTTGG
Statistics
Matches: 233, Mismatches: 21, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
137 57 0.24
138 50 0.21
139 126 0.54
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (139 bp):
CAGGTTCGAACACTTTGCTTGAATCGATTACTGCATCACCATCAACGGGGAGCCCTAGTTGCAGT
GCGACATCTTCTAGTGAGATGGTGCATTCCCCACATGACAAATGAAATGTGTGCATCTCTAGGCG
CCAACACCG
Found at i:623456 original size:16 final size:15
Alignment explanation
Indices: 623435--623466 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
623425 CTTTAACACA
623435 AATCTAATCTAATAAT
1 AATCTAATCTAA-AAT
623451 AATCTAATCTAAAAT
1 AATCTAATCTAAAAT
623466 A
1 A
623467 TAAATAATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (15 bp):
AATCTAATCTAAAAT
Found at i:628101 original size:74 final size:77
Alignment explanation
Indices: 627997--628141 Score: 233
Period size: 74 Copynumber: 1.9 Consensus size: 77
627987 GCTCCAGTTT
* *
627997 CACTAGAACTGTAATCCCCTATACCCGGCCTAGAAGATATGACCAGATCTAAAGGGTCACTATTA
1 CACTAGAACTGTAATCCCCTATACCCGGCCTAAAAGATATGACCAGATCCAAAGGGTCACTATTA
628062 TAATTTTGATAC
66 TAATTTTGATAC
* *
628074 CACTA-AA-TGTAA-CCCCTATACCTGGCCTAAAAGATATGACCGGATCCAAAGGGTCACTATTA
1 CACTAGAACTGTAATCCCCTATACCCGGCCTAAAAGATATGACCAGATCCAAAGGGTCACTATTA
628136 TAATTT
66 TAATTT
628142 CACCCGCATG
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
74 52 0.81
75 5 0.08
76 2 0.03
77 5 0.08
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.27
Consensus pattern (77 bp):
CACTAGAACTGTAATCCCCTATACCCGGCCTAAAAGATATGACCAGATCCAAAGGGTCACTATTA
TAATTTTGATAC
Found at i:631104 original size:195 final size:198
Alignment explanation
Indices: 630745--631105 Score: 478
Period size: 195 Copynumber: 1.8 Consensus size: 198
630735 GACGCGATAA
* * * *
630745 CTGAGGTACAGCTTATGTTGCAAGTTCTCTACAACTCGTGTGAGCAGCATCATGAGTCGAGAAAT
1 CTGAGGTACAGCATATGTTGCAAGTTCTCAACAACTCATGTGAGCAGCATCATGAGTCGAGAAAA
* *
630810 GAGAAATGAATCCCAAGAATGGATTACAGGCCCTACAATGGTTGGGATTTATGCATAAGTGCATA
66 GAGAAATGAATCCCAAGAATGGATTACAGGCCCTACAATGGCTGGGATTTATGCATAAATGCATA
* * * *
630875 TTCTCGACAGCTCGTGTGAGCAGCATTGTTAAGGGAAACAAATATAGGCACAGATACCATATCAA
131 TTCTCAACAACTCGTATGAGCAACATTGTTAAGGGAAACAAATATAGGCACAGATACCATATCAA
630940 TGG
196 TGG
* * * * *
630943 CTGAGGTACCGCATATGTTGCAAGTTCTCAATAGCTCATGTGAGTAGCATCGTGAGTCG-GAAAA
1 CTGAGGTACAGCATATGTTGCAAGTTCTCAACAACTCATGTGAGCAGCATCATGAGTCGAGAAAA
* * * * * *
631007 GAGATATGAAT-CCTA-AATGGATTATAGGCCTTACGATGGCTGGGATTTATGCTTAAATGCATA
66 GAGAAATGAATCCCAAGAATGGATTACAGGCCCTACAATGGCTGGGATTTATGCATAAATGCATA
* *
631070 TTCTCAACAACTTGTATGAGTAACATCT-TTAAGGGA
131 TTCTCAACAACTCGTATGAGCAACAT-TGTTAAGGGA
631106 CAGTTTACAG
Statistics
Matches: 139, Mismatches: 23, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
195 70 0.50
196 4 0.03
197 14 0.10
198 51 0.37
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (198 bp):
CTGAGGTACAGCATATGTTGCAAGTTCTCAACAACTCATGTGAGCAGCATCATGAGTCGAGAAAA
GAGAAATGAATCCCAAGAATGGATTACAGGCCCTACAATGGCTGGGATTTATGCATAAATGCATA
TTCTCAACAACTCGTATGAGCAACATTGTTAAGGGAAACAAATATAGGCACAGATACCATATCAA
TGG
Found at i:631909 original size:7 final size:7
Alignment explanation
Indices: 631897--631929 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
631887 ATTTTATATG
631897 GAATTTT
1 GAATTTT
631904 GAATTTT
1 GAATTTT
631911 GAATTTT
1 GAATTTT
631918 -AATTATT
1 GAATT-TT
631925 GAATT
1 GAATT
631930 AAAAGTTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 4 0.17
7 16 0.67
8 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (7 bp):
GAATTTT
Found at i:639548 original size:45 final size:45
Alignment explanation
Indices: 639493--639581 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
639483 CTCAAAATGA
* * *
639493 TTACCAATATCCGATTTCTCATTTTGCATAGGTGAAAACTAACCC
1 TTACAAATATCCGATTTCTCATTCTGCACAGGTGAAAACTAACCC
*
639538 TTACAAATATCCGATTTCTCGTTCTGCACAGGTGAAAACTAACC
1 TTACAAATATCCGATTTCTCATTCTGCACAGGTGAAAACTAACC
639582 TTGGAGTTCT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (45 bp):
TTACAAATATCCGATTTCTCATTCTGCACAGGTGAAAACTAACCC
Found at i:644369 original size:15 final size:15
Alignment explanation
Indices: 644345--644377 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
644335 TTTATTTTAA
644345 TTTTGTTATTT-ACT
1 TTTTGTTATTTCACT
644359 TTTTAGTTATTTCACT
1 TTTT-GTTATTTCACT
644375 TTT
1 TTT
644378 CGTTGTGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 7 0.41
16 6 0.35
ACGTcount: A:0.15, C:0.09, G:0.06, T:0.70
Consensus pattern (15 bp):
TTTTGTTATTTCACT
Found at i:649711 original size:21 final size:21
Alignment explanation
Indices: 649663--649739 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
649653 GGAGTTTTTA
*
649663 GTATCGGTAGAAGTATGACAT
1 GTATCGGTAGAAGTATCACAT
* * *
649684 GTTTCGGTAGAAGTCTCACTT
1 GTATCGGTAGAAGTATCACAT
* *
649705 GTATCGGTAGTATTGTTTCA-A-
1 GTATCGGTAG-A-AGTATCACAT
649726 GTATCGGTAGAAGT
1 GTATCGGTAGAAGT
649740 CAATGCTGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
19 2 0.04
20 1 0.02
21 36 0.80
22 1 0.02
23 5 0.11
ACGTcount: A:0.26, C:0.12, G:0.27, T:0.35
Consensus pattern (21 bp):
GTATCGGTAGAAGTATCACAT
Found at i:670766 original size:17 final size:16
Alignment explanation
Indices: 670722--670772 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
670712 TCTTGCATAG
* *
670722 AATATAAAAAGAAACA
1 AATAAAAAAAGAAATA
* *
670738 GATAAAAGAAGAAATA
1 AATAAAAAAAGAAATA
670754 AAGTAAAAAAAGAAATA
1 AA-TAAAAAAAGAAATA
670771 AA
1 AA
670773 CATAAATGTA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 13 0.46
17 15 0.54
ACGTcount: A:0.75, C:0.02, G:0.12, T:0.12
Consensus pattern (16 bp):
AATAAAAAAAGAAATA
Found at i:682136 original size:43 final size:44
Alignment explanation
Indices: 682088--682204 Score: 114
Period size: 43 Copynumber: 2.7 Consensus size: 44
682078 TCGCTTTTGG
* *
682088 ACAATTCGCATATAACAGTTCTCACATAAACAGTTTACATA-AA
1 ACAATTTGCATATAACAGTTCTCACATAAACAGTTTACACATAA
* * *
682131 ACAATTTGCACTTTAACAGTT-TGCACA-CAACATTTTACACATAA
1 ACAATTTGCA-TATAACAGTTCT-CACATAAACAGTTTACACATAA
* * * *
682175 ATAATTTGCATGTTACAGTTCACACATAAA
1 ACAATTTGCATATAACAGTTCTCACATAAA
682205 TAGATCGCAG
Statistics
Matches: 59, Mismatches: 10, Indels: 9
0.76 0.13 0.12
Matches are distributed among these distances:
43 33 0.56
44 26 0.44
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.31
Consensus pattern (44 bp):
ACAATTTGCATATAACAGTTCTCACATAAACAGTTTACACATAA
Found at i:682149 original size:44 final size:45
Alignment explanation
Indices: 682100--682204 Score: 112
Period size: 44 Copynumber: 2.4 Consensus size: 45
682090 AATTCGCATA
*
682100 TAACAGTTCTCACATAAACAGTTTACATA-AAACAATTTGCACT-T
1 TAACAGTTCTCACATAAACAGTTTACACATAAACAATTTGCA-TGT
* * *
682144 TAACAGTT-TGCACA-CAACATTTTACACATAAATAATTTGCATGT
1 TAACAGTTCT-CACATAAACAGTTTACACATAAACAATTTGCATGT
*
682188 T-ACAGTTCACACATAAA
1 TAACAGTTCTCACATAAA
682205 TAGATCGCAG
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
43 23 0.46
44 27 0.54
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (45 bp):
TAACAGTTCTCACATAAACAGTTTACACATAAACAATTTGCATGT
Found at i:682252 original size:29 final size:29
Alignment explanation
Indices: 682241--682331 Score: 182
Period size: 29 Copynumber: 3.1 Consensus size: 29
682231 AACCAACTCA
682241 CATACAATAGTTCACATATAATTAGTTCG
1 CATACAATAGTTCACATATAATTAGTTCG
682270 CATACAATAGTTCACATATAATTAGTTCG
1 CATACAATAGTTCACATATAATTAGTTCG
682299 CATACAATAGTTCACATATAATTAGTTCG
1 CATACAATAGTTCACATATAATTAGTTCG
682328 CATA
1 CATA
682332 TATTAGATCA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 62 1.00
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (29 bp):
CATACAATAGTTCACATATAATTAGTTCG
Found at i:682271 original size:58 final size:58
Alignment explanation
Indices: 682191--682329 Score: 170
Period size: 58 Copynumber: 2.4 Consensus size: 58
682181 TGCATGTTAC
* * * *
682191 AGTTCACACATAAATAGATCGCAGATAACAGTTCACACATAACCAACTCACATACAAT
1 AGTTCACATATAATTAGTTCGCAGACAACAGTTCACACATAACCAACTCACATACAAT
* * * ** ** *
682249 AGTTCACATATAATTAGTTCGCATACAATAGTTCACATATAATTAGTTCGCATACAAT
1 AGTTCACATATAATTAGTTCGCAGACAACAGTTCACACATAACCAACTCACATACAAT
682307 AGTTCACATATAATTAGTTCGCA
1 AGTTCACATATAATTAGTTCGCA
682330 TATATTAGAT
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 69 1.00
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (58 bp):
AGTTCACATATAATTAGTTCGCAGACAACAGTTCACACATAACCAACTCACATACAAT
Found at i:682355 original size:58 final size:58
Alignment explanation
Indices: 682241--682355 Score: 169
Period size: 58 Copynumber: 2.0 Consensus size: 58
682231 AACCAACTCA
* * *
682241 CATACAATAGTTCACATATAATTAGTTCGCATACAATAGTTCACATATAATTAGTTCG
1 CATACAATAGTTCACATATAATTAGTTCGCATACAATAGATCACATACAATCAGTTCG
* *
682299 CATACAATAGTTCACATATAATTAGTTCGCATATATTAGATCA-ACTACAATCAGTTC
1 CATACAATAGTTCACATATAATTAGTTCGCATACAATAGATCACA-TACAATCAGTTC
682356 AATCTAGTGA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 1 0.02
58 50 0.98
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (58 bp):
CATACAATAGTTCACATATAATTAGTTCGCATACAATAGATCACATACAATCAGTTCG
Found at i:682811 original size:40 final size:40
Alignment explanation
Indices: 682756--682836 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
682746 GATACACAGT
682756 TCACAGTTCACTATATGGCATTGTTCGCAAGCAATAAGGC
1 TCACAGTTCACTATATGGCATTGTTCGCAAGCAATAAGGC
*
682796 TCACAGTTCACTATATGGCATTGTTCGTAAGCAATAAGGC
1 TCACAGTTCACTATATGGCATTGTTCGCAAGCAATAAGGC
682836 T
1 T
682837 TGCAATGCAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.30
Consensus pattern (40 bp):
TCACAGTTCACTATATGGCATTGTTCGCAAGCAATAAGGC
Found at i:682996 original size:15 final size:15
Alignment explanation
Indices: 682976--683006 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
682966 TACAATACAT
682976 AGGTTCACATAACAC
1 AGGTTCACATAACAC
682991 AGGTTCACATAACAC
1 AGGTTCACATAACAC
683006 A
1 A
683007 AATTAAGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.26, G:0.13, T:0.19
Consensus pattern (15 bp):
AGGTTCACATAACAC
Found at i:688898 original size:13 final size:13
Alignment explanation
Indices: 688880--688913 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
688870 TCTCGTTTCG
688880 AAACTAAAAATAA
1 AAACTAAAAATAA
*
688893 AAACTAAAACTAA
1 AAACTAAAAATAA
688906 AAACTAAA
1 AAACTAAA
688914 GGTCCTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.74, C:0.12, G:0.00, T:0.15
Consensus pattern (13 bp):
AAACTAAAAATAA
Found at i:688900 original size:7 final size:7
Alignment explanation
Indices: 688880--688913 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
688870 TCTCGTTTCG
688880 AAACTAA
1 AAACTAA
688887 AAA-TAA
1 AAACTAA
688893 AAACT-A
1 AAACTAA
688899 AAACTAA
1 AAACTAA
688906 AAACTAA
1 AAACTAA
688913 A
1 A
688914 GGTCCTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 12 0.48
7 13 0.52
ACGTcount: A:0.74, C:0.12, G:0.00, T:0.15
Consensus pattern (7 bp):
AAACTAA
Found at i:693881 original size:3 final size:3
Alignment explanation
Indices: 693868--693932 Score: 57
Period size: 3 Copynumber: 22.3 Consensus size: 3
693858 TTTGGGTATT
* * *
693868 GAA GCA GAA GAA G-A GAA -AA AAA TAA GAA GGAA -AA GAA G-A GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -GAA GAA GAA GAA GAA
693910 GGAA GAA GAA GAA GAA GAA GAA G
1 -GAA GAA GAA GAA GAA GAA GAA G
693933 TTGTTCCGAC
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
2 8 0.15
3 38 0.73
4 6 0.12
ACGTcount: A:0.65, C:0.02, G:0.32, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:707919 original size:20 final size:20
Alignment explanation
Indices: 707882--707920 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
707872 GCTAAGAATC
*
707882 TGAAACAACATAATGAAAAG
1 TGAAACAACATAAAGAAAAG
707902 TGAAACAA-ATAAAAGAAAA
1 TGAAACAACAT-AAAGAAAA
707921 TAAATGAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.67, C:0.08, G:0.13, T:0.13
Consensus pattern (20 bp):
TGAAACAACATAAAGAAAAG
Found at i:717194 original size:27 final size:27
Alignment explanation
Indices: 717156--717214 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
717146 TAGACTCGTA
717156 GGGTAAGACTATTACTATTTTCTAGAC
1 GGGTAAGACTATTACTATTTTCTAGAC
*
717183 GGGTAAGACTATTACTATTTTCTAGAT
1 GGGTAAGACTATTACTATTTTCTAGAC
717210 GGGTA
1 GGGTA
717215 CTCAGGGTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (27 bp):
GGGTAAGACTATTACTATTTTCTAGAC
Found at i:719887 original size:13 final size:13
Alignment explanation
Indices: 719848--719899 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
719838 TGATAATTCT
719848 TAATATTATA-TTA
1 TAAT-TTATATTTA
* *
719861 TAAATTAAATTTTA
1 TAATTTATA-TTTA
719875 TAATTTATATTTA
1 TAATTTATATTTA
719888 TAATTTAATATT
1 TAATTT-ATATT
719900 AATTATTATC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
12 4 0.12
13 13 0.41
14 15 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAATTTATATTTA
Found at i:744455 original size:21 final size:21
Alignment explanation
Indices: 744430--744477 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
744420 ATAAGAGTGT
744430 GTCCCATTGCTAAGAATGGGC
1 GTCCCATTGCTAAGAATGGGC
744451 GTCCCATTGCTAAGAATGGGC
1 GTCCCATTGCTAAGAATGGGC
744472 GTCCCA
1 GTCCCA
744478 AGATGATGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.23, C:0.27, G:0.27, T:0.23
Consensus pattern (21 bp):
GTCCCATTGCTAAGAATGGGC
Found at i:748244 original size:10 final size:10
Alignment explanation
Indices: 748231--748286 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
748221 AATATATATA
748231 TTCTTTCTTT
1 TTCTTTCTTT
748241 TTCTTTCTTCT
1 TTCTTTCTT-T
**
748252 TATC-AAC-TT
1 T-TCTTTCTTT
748261 TTCTTTCTTT
1 TTCTTTCTTT
*
748271 TTCTTTTTTT
1 TTCTTTCTTT
748281 TTCTTT
1 TTCTTT
748287 TTGTGACTGG
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
8 2 0.05
9 3 0.08
10 27 0.73
11 3 0.08
12 2 0.05
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (10 bp):
TTCTTTCTTT
Found at i:748655 original size:24 final size:24
Alignment explanation
Indices: 748626--748671 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
748616 ACATTCATCC
*
748626 AATTCATGCATTA-GCATTCAAAAT
1 AATTCATGAATTATGCA-TCAAAAT
748650 AATTCATGAATTATGCATCAAA
1 AATTCATGAATTATGCATCAAA
748672 TTGAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.33
Consensus pattern (24 bp):
AATTCATGAATTATGCATCAAAAT
Found at i:748881 original size:17 final size:16
Alignment explanation
Indices: 748861--748913 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 16
748851 TACAATGCAT
*
748861 ATGCTAAAACAAATAAA
1 ATGCAAAAAC-AATAAA
748878 ATGCAAAAACAATAAAA
1 ATGCAAAAACAAT-AAA
748895 ATGCAATAAA-AATTAAA
1 ATGCAA-AAACAA-TAAA
748912 AT
1 AT
748914 AAATGCATGC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
16 3 0.09
17 25 0.78
18 4 0.12
ACGTcount: A:0.66, C:0.09, G:0.06, T:0.19
Consensus pattern (16 bp):
ATGCAAAAACAATAAA
Found at i:750569 original size:23 final size:23
Alignment explanation
Indices: 750539--750592 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
750529 TGGTTGCAAA
750539 ATTGTTCTCATCCCAAACAAGAG
1 ATTGTTCTCATCCCAAACAAGAG
750562 ATTGTTCTCATCCCAAACAAGAG
1 ATTGTTCTCATCCCAAACAAGAG
750585 ATTGTTCT
1 ATTGTTCT
750593 GGCTACTTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.31
Consensus pattern (23 bp):
ATTGTTCTCATCCCAAACAAGAG
Found at i:751190 original size:13 final size:14
Alignment explanation
Indices: 751162--751191 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
751152 ATTCCTGCAT
751162 AAAACTTAAAGAAA
1 AAAACTTAAAGAAA
*
751176 AAAAGTTAAAGAAA
1 AAAACTTAAAGAAA
751190 AA
1 AA
751192 CAAAAAGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.73, C:0.03, G:0.10, T:0.13
Consensus pattern (14 bp):
AAAACTTAAAGAAA
Found at i:765667 original size:15 final size:15
Alignment explanation
Indices: 765647--765682 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
765637 TTTATATTTT
765647 CTTTTATTTGTTTCA
1 CTTTTATTTGTTTCA
*
765662 CTTTTACTTGTTTCA
1 CTTTTATTTGTTTCA
765677 -TTTTAT
1 CTTTTAT
765683 ATTCTTTGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.14, C:0.14, G:0.06, T:0.67
Consensus pattern (15 bp):
CTTTTATTTGTTTCA
Found at i:767529 original size:3 final size:3
Alignment explanation
Indices: 767523--767557 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
767513 GAAGATGGCC
*
767523 AGA AGA AGA AGA ATGA AGA AGA AAA AGA AGA AGA A
1 AGA AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA A
767558 AATGACATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:768027 original size:19 final size:19
Alignment explanation
Indices: 768003--768046 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
767993 TACTTTTCAA
*
768003 GCATTTTTATTTTGTCATT
1 GCATTTTTATTTTGTCAGT
*
768022 GCATTTTTATTTTGTTAGT
1 GCATTTTTATTTTGTCAGT
768041 GCATTT
1 GCATTT
768047 CTTTTGTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.16, C:0.09, G:0.14, T:0.61
Consensus pattern (19 bp):
GCATTTTTATTTTGTCAGT
Found at i:768675 original size:18 final size:18
Alignment explanation
Indices: 768635--768676 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
768625 CTTGAAAAAG
*
768635 AAAAATGAGAAAAGGGAA
1 AAAAATGAGAAAAGAGAA
*
768653 GAAAATGA-AAAAGAAGAA
1 AAAAATGAGAAAAG-AGAA
768671 AAAAAT
1 AAAAAT
768677 TTATAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.07
Consensus pattern (18 bp):
AAAAATGAGAAAAGAGAA
Found at i:772328 original size:45 final size:43
Alignment explanation
Indices: 772264--772514 Score: 175
Period size: 45 Copynumber: 5.7 Consensus size: 43
772254 CCAGAATGAA
* * *
772264 TAAGACCATAGTTGGAAGATATTATGGCATCAAACCGGAAACATG
1 TAAGACCATAGTTGAAAGATACTATGGCAT-TAACCGGAAA-ATG
* * * * **
772309 TAAGACCATAATTGAAAGATACCATGGCATTTATCTGGCATGA-G
1 TAAGACCATAGTTGAAAGATACTATGGCA-TTAACCGG-AAAATG
*
772353 TAAGACCATAGTTGAAAGATACTATGGCATTAACCCGAAAATG
1 TAAGACCATAGTTGAAAGATACTATGGCATTAACCGGAAAATG
* * ** **** *
772396 TATAAGACCATAGTTGAAAGATAATGTGGCATTATTCGTTGCATA
1 --TAAGACCATAGTTGAAAGATACTATGGCATTAACCGGAAAATG
* * * *
772441 TAAGACCATAGTTGAAAGATACTATGACATCATATC-GAAAATTA
1 TAAGACCATAGTTGAAAGATACTATGGCATTA-ACCGGAAAA-TG
*
772485 TCAATG-CCATAGTTGAAATATACTATGGCA
1 T-AA-GACCATAGTTGAAAGATACTATGGCA
772515 CTTTTTCGGA
Statistics
Matches: 160, Mismatches: 37, Indels: 18
0.74 0.17 0.08
Matches are distributed among these distances:
42 2 0.01
43 35 0.22
44 33 0.21
45 87 0.54
46 3 0.02
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (43 bp):
TAAGACCATAGTTGAAAGATACTATGGCATTAACCGGAAAATG
Found at i:772368 original size:44 final size:43
Alignment explanation
Indices: 772263--772560 Score: 174
Period size: 45 Copynumber: 6.7 Consensus size: 43
772253 ACCAGAATGA
* * ** * *
772263 ATAAGACCATAGTTGGAAGATATTATGGCATCAAACCGGAAACATG
1 ATAAGACCATAGTTGAAAGATACTATGGCATTTATCTGG---CATG
* *
772309 -TAAGACCATAATTGAAAGATACCATGGCATTTATCTGGCATG
1 ATAAGACCATAGTTGAAAGATACTATGGCATTTATCTGGCATG
* * * **
772351 AGTAAGACCATAGTTGAAAGATACTATGGCATTAACCCGAAAATG
1 A-TAAGACCATAGTTGAAAGATACTATGGCATTTATCTG-GCATG
* * *
772396 TATAAGACCATAGTTGAAAGATAATGTGGCA-TTATTCGTTGCAT-
1 -ATAAGACCATAGTTGAAAGATACTATGGCATTTA-TC-TGGCATG
* * ** *
772440 ATAAGACCATAGTTGAAAGATACTATGACATCATATC-GAAAATT
1 ATAAGACCATAGTTGAAAGATACTATGGCAT-TTATCTG-GCATG
* * * ** *
772484 ATCAATG-CCATAGTTGAAATATACTATGGCACTTTTTCGGAGTTTT
1 AT-AA-GACCATAGTTGAAAGATACTATGGCA-TTTATCTG-GCATG
* *
772530 ATAAGACCATGGTTGAAAGATACCATGGCAT
1 ATAAGACCATAGTTGAAAGATACTATGGCAT
772561 ACTTTGGAAC
Statistics
Matches: 197, Mismatches: 40, Indels: 32
0.73 0.15 0.12
Matches are distributed among these distances:
42 4 0.02
43 29 0.15
44 40 0.20
45 115 0.58
46 9 0.05
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (43 bp):
ATAAGACCATAGTTGAAAGATACTATGGCATTTATCTGGCATG
Found at i:772480 original size:88 final size:86
Alignment explanation
Indices: 772263--772560 Score: 282
Period size: 88 Copynumber: 3.4 Consensus size: 86
772253 ACCAGAATGA
* * *
772263 ATAAGACCATAGTTGGAAGATATTATGGCATCAAACCGGAAACATG--TAAGACCATAATTGAAA
1 ATAAGACCATAGTTGAAAGATACTATGGCATC-AACC-GAAA-ATGTATAAGACCATAGTTGAAA
* *
772326 GATACCATGGCATTTATC-TGGCAT
63 GATACTATGGCATTT-TCGTAGCAT
*
772350 GAGTAAGACCATAGTTGAAAGATACTATGGCATTAACCCGAAAATGTATAAGACCATAGTTGAAA
1 -A-TAAGACCATAGTTGAAAGATACTATGGCATCAA-CCGAAAATGTATAAGACCATAGTTGAAA
* * *
772415 GATAATGTGGCATTATTCGTTGCAT
63 GATACTATGGCATT-TTCGTAGCAT
* *
772440 ATAAGACCATAGTTGAAAGATACTATGACATCATATCGAAAAT-TATCAATG-CCATAGTTGAAA
1 ATAAGACCATAGTTGAAAGATACTATGGCATCA-ACCGAAAATGTAT-AA-GACCATAGTTGAAA
* * **
772503 TATACTATGGCACTTTTTCGGAGTTTT
63 GATACTATGGCA--TTTTCGTAG-CAT
* *
772530 ATAAGACCATGGTTGAAAGATACCATGGCAT
1 ATAAGACCATAGTTGAAAGATACTATGGCAT
772561 ACTTTGGAAC
Statistics
Matches: 177, Mismatches: 21, Indels: 22
0.80 0.10 0.10
Matches are distributed among these distances:
87 6 0.03
88 67 0.38
89 67 0.38
90 37 0.21
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (86 bp):
ATAAGACCATAGTTGAAAGATACTATGGCATCAACCGAAAATGTATAAGACCATAGTTGAAAGAT
ACTATGGCATTTTCGTAGCAT
Found at i:775034 original size:17 final size:17
Alignment explanation
Indices: 775001--775061 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
774991 CATTAAATTA
*
775001 CAATGACAAATGGAAATG
1 CAATGAC-AATGCAAATG
*
775019 TAATGACAATGCAAATG
1 CAATGACAATGCAAATG
* *
775036 CAGTGACAAT-TAAATTG
1 CAATGACAATGCAAA-TG
775053 CAATGACAA
1 CAATGACAA
775062 AGGGAATGTG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
16 3 0.08
17 27 0.75
18 6 0.17
ACGTcount: A:0.48, C:0.13, G:0.18, T:0.21
Consensus pattern (17 bp):
CAATGACAATGCAAATG
Found at i:775526 original size:12 final size:12
Alignment explanation
Indices: 775509--775579 Score: 63
Period size: 12 Copynumber: 5.8 Consensus size: 12
775499 TCCTCTTCAG
775509 CCTCTTTTCCTT
1 CCTCTTTTCCTT
*
775521 CCTCTTTTTCTT
1 CCTCTTTTCCTT
**
775533 CCTCTTTTCGAT
1 CCTCTTTTCCTT
*
775545 CCTCTTCTTCC-A
1 CCTCTT-TTCCTT
*
775557 CTTCTTTTCCTT
1 CCTCTTTTCCTT
*
775569 TCTCTTCTTCC
1 CCTCTT-TTCC
775580 ACTTCTTCCA
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
11 4 0.09
12 35 0.76
13 7 0.15
ACGTcount: A:0.03, C:0.39, G:0.01, T:0.56
Consensus pattern (12 bp):
CCTCTTTTCCTT
Found at i:775536 original size:24 final size:24
Alignment explanation
Indices: 775509--775586 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
775499 TCCTCTTCAG
* **
775509 CCTCTTTTCCTTCCTCTTTTTCTT
1 CCTCTTTTCCTTCCTCTTCTTCCA
**
775533 CCTCTTTTCGATCCTCTTCTTCCA
1 CCTCTTTTCCTTCCTCTTCTTCCA
* *
775557 CTTCTTTTCCTTTCTCTTCTTCCA
1 CCTCTTTTCCTTCCTCTTCTTCCA
*
775581 CTTCTT
1 CCTCTT
775587 CCACTTGTGT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.04, C:0.38, G:0.01, T:0.56
Consensus pattern (24 bp):
CCTCTTTTCCTTCCTCTTCTTCCA
Found at i:778202 original size:173 final size:173
Alignment explanation
Indices: 777913--778261 Score: 680
Period size: 173 Copynumber: 2.0 Consensus size: 173
777903 CGTATCATCA
777913 AGTCTAGAAGACCAATCTTTTCTTGATGGATTCACCATCTTCTCAAGAATATTCTTGATTTTTCG
1 AGTCTAGAAGACCAATCTTTTCTTGATGGATTCACCATCTTCTCAAGAATATTCTTGATTTTTCG
777978 ATTGGATACTTCAATTTGTCCGTTGGTTTGCGGATGGTAAGTGGTCGCCATTCTATGATTAAGTC
66 ATTGGATACTTCAATTTGTCCGTTGGTTTGCGGATGGTAAGTGGTCGCCATTCTATGATTAAGTC
*
778043 CATATCGCTTCAGTGCGGCTGCTACCTGGTTGCAATGGTAGTG
131 CATATCGCTTCAGTGCGGCTGCTAACTGGTTGCAATGGTAGTG
778086 AGTCTAGAAGACCAATCTTTTCTTGATGGATTCACCATCTTCTCAAGAATATTCTTGATTTTTCG
1 AGTCTAGAAGACCAATCTTTTCTTGATGGATTCACCATCTTCTCAAGAATATTCTTGATTTTTCG
778151 ATTGGATACTTCAATTTGTCCGTTGGTTTGCGGATGGTAAGTGGTCGCCATTCTATGATTAAGTC
66 ATTGGATACTTCAATTTGTCCGTTGGTTTGCGGATGGTAAGTGGTCGCCATTCTATGATTAAGTC
*
778216 CATATCGCTTTAGTGCGGCTGCTAACTGGTTGCAATGGTAGTG
131 CATATCGCTTCAGTGCGGCTGCTAACTGGTTGCAATGGTAGTG
778259 AGT
1 AGT
778262 GCCTTGGTCC
Statistics
Matches: 174, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
173 174 1.00
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (173 bp):
AGTCTAGAAGACCAATCTTTTCTTGATGGATTCACCATCTTCTCAAGAATATTCTTGATTTTTCG
ATTGGATACTTCAATTTGTCCGTTGGTTTGCGGATGGTAAGTGGTCGCCATTCTATGATTAAGTC
CATATCGCTTCAGTGCGGCTGCTAACTGGTTGCAATGGTAGTG
Found at i:784596 original size:23 final size:25
Alignment explanation
Indices: 784570--784615 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
784560 CCAATTAGGG
784570 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
784593 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
784616 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:786653 original size:33 final size:33
Alignment explanation
Indices: 786569--786654 Score: 95
Period size: 32 Copynumber: 2.6 Consensus size: 33
786559 AAAATGGTAG
* * * *
786569 CTGATATTTGTTATCATTTTACAAAATTAACGT
1 CTGATATTTGTTATAATTTCACAAAATGAAAGT
*
786602 -TG-TAATTTGTTATAATTTCACAACATGAAAGT
1 CTGAT-ATTTGTTATAATTTCACAAAATGAAAGT
*
786634 CTGATATTTGTTATTATTTCA
1 CTGATATTTGTTATAATTTCA
786655 TAGAACTACA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
31 1 0.02
32 25 0.57
33 17 0.39
34 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (33 bp):
CTGATATTTGTTATAATTTCACAAAATGAAAGT
Done.