Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009582.1 Hibiscus syriacus cultivar Beakdansim tig00116959_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4978262
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 24
Found at i:2808713 original size:29 final size:29
Alignment explanation
Indices: 2808680--2808743 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
2808670 AAAAATTCGG
*
2808680 TTAATTCGGTTCAG-TTAATAATTTTCAAA
1 TTAATTCAGTT-AGTTTAATAATTTTCAAA
* *
2808709 TTAATTCAGTTTGTTTAATAATTTTTAAA
1 TTAATTCAGTTAGTTTAATAATTTTCAAA
*
2808738 TAAATT
1 TTAATT
2808744 TTAGTTTGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 1 0.03
29 29 0.97
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.50
Consensus pattern (29 bp):
TTAATTCAGTTAGTTTAATAATTTTCAAA
Found at i:2808843 original size:29 final size:29
Alignment explanation
Indices: 2808804--2808867 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
2808794 AAAAAATAGG
2808804 TTAATTCGGTTCGATTAATAATTTTCAAA
1 TTAATTCGGTTCGATTAATAATTTTCAAA
*
2808833 TTAATTCGGTTCGGTTAATAATTTTCAAA
1 TTAATTCGGTTCGATTAATAATTTTCAAA
*
2808862 TAAATT
1 TTAATT
2808868 TTTTTTCAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.45
Consensus pattern (29 bp):
TTAATTCGGTTCGATTAATAATTTTCAAA
Found at i:2808872 original size:138 final size:137
Alignment explanation
Indices: 2808752--2809039 Score: 362
Period size: 141 Copynumber: 2.1 Consensus size: 137
2808742 TTTTAGTTTG
* *
2808752 ATTAACCGAAATTTTTCTTAGATTAATTCGGTTAATAA-TTTAAAAAAATAGGTTAATTCGGTTC
1 ATTAACCAAAATTTTGCTTAGATTAATTCGGTTAATAATTTTAAAAAAA-A-GTTAATTCGGTTC
* * * *
2808816 GATTAATAATTTTCAAATTAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTTTTTCAATTAA
64 GATTAATAATTTTCAAATTAATTCGGTTCAGTGAATAATTTTCAAATAAATTTTTTTTAAATAAA
2808881 CCGAACCGA
129 CCGAACCGA
* * * *
2808890 ATTAACCAAAATTTTGCTTCGATTAATTTGGTTATTAATTTTTTTTAAAAAAAAGTTAATTTGGT
1 ATTAACCAAAATTTTGCTTAGATTAATTCGGTTAATAA----TTTTAAAAAAAAGTTAATTCGGT
* * ** ** *
2808955 TCGGTTAATAATTTTCAAATTCATTCGGTTCAGTGAATAATTTTCAAATAAATTTTGGTTCGATT
62 TCGATTAATAATTTTCAAATTAATTCGGTTCAGTGAATAATTTTCAAATAAATTTTTTTTAAATA
2809020 AACCGAACCGA
127 AACCGAACCGA
2809031 ATTAACCAA
1 ATTAACCAA
2809040 TTTTTTCTTT
Statistics
Matches: 132, Mismatches: 13, Indels: 7
0.87 0.09 0.05
Matches are distributed among these distances:
138 33 0.25
141 88 0.67
142 1 0.01
143 10 0.08
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.41
Consensus pattern (137 bp):
ATTAACCAAAATTTTGCTTAGATTAATTCGGTTAATAATTTTAAAAAAAAGTTAATTCGGTTCGA
TTAATAATTTTCAAATTAATTCGGTTCAGTGAATAATTTTCAAATAAATTTTTTTTAAATAAACC
GAACCGA
Found at i:2812847 original size:23 final size:23
Alignment explanation
Indices: 2812798--2812852 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
2812788 CTGAAATAAT
* * * *
2812798 AAAAAATATTATTTTTATTCAAT
1 AAAAAATAATAATTTAATTCAAA
*
2812821 AAAAAATAATAATTTAATTGAAA
1 AAAAAATAATAATTTAATTCAAA
2812844 AAAATAATA
1 AAAA-AATA
2812853 TATAGAGGGG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (23 bp):
AAAAAATAATAATTTAATTCAAA
Found at i:2813301 original size:16 final size:18
Alignment explanation
Indices: 2813270--2813302 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
2813260 AAATTATTTA
2813270 TAATTATTTATTTAAAAT
1 TAATTATTTATTTAAAAT
2813288 TAATT-TTT-TTTAAAA
1 TAATTATTTATTTAAAA
2813303 ATATGTTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TAATTATTTATTTAAAAT
Found at i:2814487 original size:143 final size:141
Alignment explanation
Indices: 2814210--2814673 Score: 503
Period size: 143 Copynumber: 3.3 Consensus size: 141
2814200 AAGTTTGTGA
* * * *
2814210 ACTGAAAAGTTTCTGTCATGGTGCATTATTTTACCTATGAGAAATATACGTTTTTTTATATGAAG
1 ACTGAAAAGGTTCTGCCATGGTGCATTATTTTACCTATGAGAAATGTACGTTTTTTGATATGAAG
* ** * *
2814275 TGATATATCACCAA-TGAAAAGTTTTCTTAAATGAATTGGCATATCACTGAAAAGTTGCTGAAAA
66 TGATATATCA-CAACTGAAAAGTTTTCTTAAATGAGTTGATATATCACTTAAAAGTTGCTGAAGA
*
2814339 TGATTAATTAGGC
130 GGATTAATT-GGC
* *
2814352 ACTGAAAAGGTTCTGCCATGGTACATTATTTTTCCTATGAGAAATGTACGTTTTTCTGATATGAA
1 ACTGAAAAGGTTCTGCCATGGTGCATTATTTTACCTATGAGAAATGTACGTTTTT-TGATATGAA
* **
2814417 GTGATATATCATAACTGAGCAGTTTTCTTAAATGAGTTGATATATCACTTAAAAGTTAG-TGAAG
65 GTGATATATCACAACTGAAAAGTTTTCTTAAATGAGTTGATATATCACTTAAAAGTT-GCTGAAG
2814481 AGGATTAATTGGGC
129 AGGATTAATT-GGC
* * * * * * *
2814495 GCT-AAAATTTGTT-TGCCATAGTGCATTAATTTGCCTATGAGAAATGCAC-TTTTTTGTTATGA
1 ACTGAAAA--GGTTCTGCCATGGTGCATTATTTTACCTATGAGAAATGTACGTTTTTTGATATGA
* * * * *
2814557 AGTGATATATCACAACTGAAAAGTTTTCTAAAATGTGTTGATGTATCA-TTGAAAATTTGTTGAA
64 AGTGATATATCACAACTGAAAAGTTTTCTTAAATGAGTTGATATATCACTT-AAAAGTTGCTGAA
2814621 GAGGATTAATTGGC
128 GAGGATTAATTGGC
* * * * *
2814635 AC--AATTAGATTATGCCATGTTGCATTATTTTGCCTATGA
1 ACTGAA-AAGGTTCTGCCATGGTGCATTATTTTACCTATGA
2814674 TATATCATTT
Statistics
Matches: 275, Mismatches: 38, Indels: 21
0.82 0.11 0.06
Matches are distributed among these distances:
138 2 0.01
139 26 0.09
140 8 0.03
141 70 0.25
142 61 0.22
143 104 0.38
144 4 0.01
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.38
Consensus pattern (141 bp):
ACTGAAAAGGTTCTGCCATGGTGCATTATTTTACCTATGAGAAATGTACGTTTTTTGATATGAAG
TGATATATCACAACTGAAAAGTTTTCTTAAATGAGTTGATATATCACTTAAAAGTTGCTGAAGAG
GATTAATTGGC
Found at i:2816005 original size:63 final size:61
Alignment explanation
Indices: 2815932--2816088 Score: 192
Period size: 63 Copynumber: 2.5 Consensus size: 61
2815922 TGTTGAAGGC
* * * * *
2815932 GCATCGATGCATATGAAGTGCATCGATGCATTAATTTAA-AAACA-AACATCGAATGTCGTCAGT
1 GCATCGATGCATA-GGAGTGCATCGATGCATT--TCTAATAAA-AGAACATCGAATGCCCTCAAT
2815995 GCATCGATGCATAAGGAGTGCATCGATGCATTTCTAATAAAATGAACATCGAATGCCCTCAAT
1 GCATCGATGCAT-AGGAGTGCATCGATGCATTTCTAATAAAA-GAACATCGAATGCCCTCAAT
2816058 GCATCGATGCATCAGGAGTGCATCGATGCAT
1 GCATCGATGCAT-AGGAGTGCATCGATGCAT
2816089 GCCTCCATTA
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
61 5 0.06
62 3 0.04
63 75 0.89
64 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (61 bp):
GCATCGATGCATAGGAGTGCATCGATGCATTTCTAATAAAAGAACATCGAATGCCCTCAAT
Found at i:2817216 original size:18 final size:18
Alignment explanation
Indices: 2817193--2817228 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2817183 AGGAATGATA
*
2817193 TGTGGTCCTTTGGGACAT
1 TGTGGTCCTTCGGGACAT
2817211 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
2817229 ATATGTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.19, G:0.33, T:0.36
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:2817248 original size:121 final size:121
Alignment explanation
Indices: 2817090--2817350 Score: 486
Period size: 121 Copynumber: 2.1 Consensus size: 121
2817080 CGAGGGTCTA
2817090 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
* *
2817155 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTTGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTAGTCCTTCGGGACAT
2817211 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
2817276 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTAGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTAGTCCTTCGGGACAT
*
2817332 TGTGGTCCTTTTGGGACAT
1 TGTGGTCC-TTCGGGACAT
2817351 TGTGGTCCTT
Statistics
Matches: 136, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
121 127 0.93
122 9 0.07
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (121 bp):
TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTAGTCCTTCGGGACAT
Found at i:2817289 original size:59 final size:59
Alignment explanation
Indices: 2817105--2817289 Score: 150
Period size: 59 Copynumber: 3.1 Consensus size: 59
2817095 TCCTTCGGGA
2817105 CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAG
1 CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAG
* * * * * * *
2817164 CATATGTATATGATTCTTAAGGAATGATATGTG--GTCCT-TTG-G-GACAT--TGTGGTCCTTC
1 CATA--TATGT-ATTCTT-TGGAA-CATGTGTGAAGT-CTGGTGAGACACATACT-TGATCC--C
**
2817222 GGG
57 TAG
2817225 ACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAG
1 -CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAG
2817285 CATAT
1 CATAT
2817290 GTATATGATT
Statistics
Matches: 91, Mismatches: 18, Indels: 34
0.64 0.13 0.24
Matches are distributed among these distances:
57 6 0.07
58 7 0.08
59 24 0.26
60 11 0.12
61 11 0.12
62 19 0.21
63 7 0.08
64 6 0.07
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (59 bp):
CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAG
Found at i:2817341 original size:18 final size:18
Alignment explanation
Indices: 2817318--2817360 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
2817308 ATGATATGTA
2817318 GTCCTTCGGGACATTGTG
1 GTCCTTCGGGACATTGTG
*
2817336 GTCCTTTTGGGACATTGTG
1 GTCC-TTCGGGACATTGTG
2817355 GTCCTT
1 GTCCTT
2817361 TTGGGACATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.09, C:0.21, G:0.30, T:0.40
Consensus pattern (18 bp):
GTCCTTCGGGACATTGTG
Found at i:2817349 original size:19 final size:19
Alignment explanation
Indices: 2817325--2817369 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
2817315 GTAGTCCTTC
2817325 GGGACATTGTGGTCCTTTT
1 GGGACATTGTGGTCCTTTT
2817344 GGGACATTGTGGTCCTTTT
1 GGGACATTGTGGTCCTTTT
2817363 GGGACAT
1 GGGACAT
2817370 ATATGTATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.13, C:0.16, G:0.33, T:0.38
Consensus pattern (19 bp):
GGGACATTGTGGTCCTTTT
Found at i:2817424 original size:141 final size:139
Alignment explanation
Indices: 2817193--2817473 Score: 490
Period size: 141 Copynumber: 2.0 Consensus size: 139
2817183 AGGAATGATA
2817193 TGTGGTCCTTTGGGACATTGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGT
1 TGTGGTCCTTTGGGACATTGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGT
2817258 CTGGTGAGACACATACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTAGTCCT
66 CTGGTGAGACACATACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTAGTCCT
*
2817323 TCGGGACAT
131 TAGGGACAT
*
2817332 TGTGGTCCTTTTGGGACATTGTGGTCCTTTTGGGACATATATGTATTCTTTGGAACATGTGTGAA
1 TGTGGTCC-TTTGGGACATTGTGGTCC-TTCGGGACATATATGTATTCTTTGGAACATGTGTGAA
* * *
2817397 GTCTGGTGAGACGCATACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTC
64 GTCTGGTGAGACACATACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTAGTC
*
2817462 CTTATGGACAT
129 CTTAGGGACAT
2817473 T
1 T
2817474 ATTATATGGC
Statistics
Matches: 134, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
139 8 0.06
140 18 0.13
141 108 0.81
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.37
Consensus pattern (139 bp):
TGTGGTCCTTTGGGACATTGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGT
CTGGTGAGACACATACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTAGTCCT
TAGGGACAT
Found at i:2817508 original size:23 final size:23
Alignment explanation
Indices: 2817481--2817532 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
2817471 ATTATTATAT
*
2817481 GGCACTATGGTGCAATTCTATGC
1 GGCACTACGGTGCAATTCTATGC
*
2817504 GGCACTACGGTGCAATTCTATGT
1 GGCACTACGGTGCAATTCTATGC
2817527 GGCACT
1 GGCACT
2817533 TCAGTGCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.29
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTATGC
Found at i:2817548 original size:23 final size:23
Alignment explanation
Indices: 2817481--2817540 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
2817471 ATTATTATAT
**
2817481 GGCACTATGGTGCAATTCTATGC
1 GGCACTACAGTGCAATTCTATGC
* *
2817504 GGCACTACGGTGCAATTCTATGT
1 GGCACTACAGTGCAATTCTATGC
*
2817527 GGCACTTCAGTGCA
1 GGCACTACAGTGCA
2817541 TTTATATGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.22, C:0.23, G:0.27, T:0.28
Consensus pattern (23 bp):
GGCACTACAGTGCAATTCTATGC
Found at i:2821387 original size:19 final size:20
Alignment explanation
Indices: 2821358--2821395 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
2821348 AAAAATTTAT
2821358 TGAAGGTGCATCGATGCATA
1 TGAAGGTGCATCGATGCATA
2821378 TGAA-GTGCATCGATGCAT
1 TGAAGGTGCATCGATGCAT
2821396 TAATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAAGGTGCATCGATGCATA
Found at i:2821438 original size:63 final size:62
Alignment explanation
Indices: 2821363--2821521 Score: 203
Period size: 63 Copynumber: 2.5 Consensus size: 62
2821353 TTTATTGAAG
* * * *
2821363 GTGCATCGATGCATATGAAGTGCATCGATGCATTAAT-TTAAATACAAACATCGAATGTCGTCA
1 GTGCATCGATGCATA-GGAGTGCATCGATGCATTAATAATAAA-ACAAACATCGAATGCCCTCA
* * **
2821426 GTGCATCGATGCATAAGGAGTGCATCGATTCATTTATAATAAAATGAACATCGAATGCCCTCA
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
2821489 GTGCATCGATGCATCAGGAGTGCATCGATGCAT
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCAT
2821522 GCCTCCATTA
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
63 79 0.94
64 5 0.06
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (62 bp):
GTGCATCGATGCATAGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
Found at i:2822647 original size:18 final size:18
Alignment explanation
Indices: 2822624--2822659 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2822614 AGGAATGATA
2822624 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
2822642 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
2822660 ATATGTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:2822681 original size:121 final size:121
Alignment explanation
Indices: 2822521--2822780 Score: 502
Period size: 121 Copynumber: 2.1 Consensus size: 121
2822511 CGAGGGTCTA
* *
2822521 TGTGGTCATTCGGGACATATATGTATTTTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
2822586 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
2822642 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
2822707 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
2822763 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
2822781 TGTGGTCCTT
Statistics
Matches: 137, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 137 1.00
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.35
Consensus pattern (121 bp):
TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
Found at i:2822720 original size:59 final size:59
Alignment explanation
Indices: 2822536--2822720 Score: 134
Period size: 59 Copynumber: 3.1 Consensus size: 59
2822526 TCATTCGGGA
*
2822536 CATATATGTATTTTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAG
1 CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAG
* * * * * *
2822595 CATATGTATATGATTCTTAAGGAATGATATGTG--GTCCT--TCG-G-GACAT--TGTGGTCCTT
1 CATA--TATGT-ATTCTT-TGGAA-CATGTGTGAAGT-CTGGT-GAGACACATACT-TGATCC--
**
2822652 CGGG
56 CTAG
2822656 ACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAG
1 -CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAG
2822716 CATAT
1 CATAT
2822721 GTATATGATT
Statistics
Matches: 90, Mismatches: 17, Indels: 38
0.62 0.12 0.26
Matches are distributed among these distances:
57 6 0.07
58 7 0.08
59 23 0.26
60 12 0.13
61 12 0.13
62 17 0.19
63 7 0.08
64 6 0.07
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (59 bp):
CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAG
Found at i:2822768 original size:18 final size:18
Alignment explanation
Indices: 2822745--2822798 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
2822735 AGGAATGATA
2822745 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
2822763 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
*
2822781 TGTGGTCCTTTGGGACAT
1 TGTGGTCCTTCGGGACAT
2822799 ATATATATTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.11, C:0.20, G:0.33, T:0.35
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:2822874 original size:139 final size:139
Alignment explanation
Indices: 2822624--2822902 Score: 495
Period size: 139 Copynumber: 2.0 Consensus size: 139
2822614 AGGAATGATA
*
2822624 TGTGGTCCTTCGGGACATTGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGT
1 TGTGGTCCTTCGGGACATTGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGT
*
2822689 CTGGTGAGACACATACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCT
66 CTGGTAAGACACATACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCT
*
2822754 TCGGGACAT
131 TAGGGACAT
*
2822763 TGTGGTCCTTCGGGACATTGTGGTCCTTTGGGACATATATATATTCTTTGGAACATGTGTGAAGT
1 TGTGGTCCTTCGGGACATTGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGT
* *
2822828 CTGGTAAGACGCATACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCT
66 CTGGTAAGACACATACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCT
*
2822893 TATGGACAT
131 TAGGGACAT
2822902 T
1 T
2822903 ATTATATGGC
Statistics
Matches: 133, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
139 133 1.00
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (139 bp):
TGTGGTCCTTCGGGACATTGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGT
CTGGTAAGACACATACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCT
TAGGGACAT
Found at i:2822946 original size:23 final size:23
Alignment explanation
Indices: 2822910--2822969 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
2822900 ATTATTATAT
* *
2822910 GGCACAACGATGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
2822933 GGCACTACGGTGCAATTCTATGT
1 GGCACTACGGTGCAATTCTACGC
*
2822956 GGCACTTCGGTGCA
1 GGCACTACGGTGCA
2822970 TTTATATGAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.23, C:0.27, G:0.27, T:0.23
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:2822977 original size:23 final size:23
Alignment explanation
Indices: 2822900--2822977 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
2822890 CCTTATGGAC
* * *
2822900 ATTATTATATGGCACAACGATGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * *
2822924 ATTCTACGCGGCACTACGGTGCA
1 ATTATATGTGGCACTACGGTGCA
* *
2822947 ATTCTATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
2822970 TTTATATG
1 ATTATATG
2822978 AGCTGTGGTG
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 40 0.93
24 3 0.07
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.32
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:2824859 original size:24 final size:24
Alignment explanation
Indices: 2824830--2824884 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
2824820 AAAAATGCTC
2824830 AAGATAA-TTCCTAAAATATCACAA
1 AAGATAATTTCCT-AAATATCACAA
*
2824854 AAGATAATTTCCTAAATATCTCAA
1 AAGATAATTTCCTAAATATCACAA
*
2824878 ATGATAA
1 AAGATAA
2824885 CTCCCTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 23 0.82
25 5 0.18
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.29
Consensus pattern (24 bp):
AAGATAATTTCCTAAATATCACAA
Found at i:2831407 original size:8 final size:9
Alignment explanation
Indices: 2831386--2831410 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2831376 TTATATATGA
2831386 AAAAAATAT
1 AAAAAATAT
2831395 AAAAAATAT
1 AAAAAATAT
2831404 AAAAAAT
1 AAAAAAT
2831411 TATATATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAAATAT
Found at i:2834234 original size:13 final size:13
Alignment explanation
Indices: 2834216--2834242 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2834206 CTCTTTCAGT
2834216 TATAAGCCATTGC
1 TATAAGCCATTGC
2834229 TATAAGCCATTGC
1 TATAAGCCATTGC
2834242 T
1 T
2834243 TGTCTAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (13 bp):
TATAAGCCATTGC
Found at i:2837668 original size:20 final size:20
Alignment explanation
Indices: 2837612--2837669 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
2837602 GAATAGTAGT
* *
2837612 ATACTGTATAAATAATACCG
1 ATACTGTATAAACAATATCG
*
2837632 ATACTGTATAAATAATATCG
1 ATACTGTATAAACAATATCG
* *
2837652 ATACTGTGTGAACAATAT
1 ATACTGTATAAACAATAT
2837670 AAATAGTATC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (20 bp):
ATACTGTATAAACAATATCG
Found at i:2837668 original size:23 final size:20
Alignment explanation
Indices: 2837612--2837658 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
2837602 GAATAGTAGT
2837612 ATACTGTATAAATAATACCG
1 ATACTGTATAAATAATACCG
*
2837632 ATACTGTATAAATAATATCG
1 ATACTGTATAAATAATACCG
2837652 ATACTGT
1 ATACTGT
2837659 GTGAACAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.34
Consensus pattern (20 bp):
ATACTGTATAAATAATACCG
Found at i:2837770 original size:19 final size:20
Alignment explanation
Indices: 2837746--2837787 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
2837736 AATGTAAAAT
*
2837746 GTGTATCGGT-ACTGCTATA
1 GTGTATCGATAACTGCTATA
2837765 GTGTATCGATACACTGCTATA
1 GTGTATCGATA-ACTGCTATA
2837786 GT
1 GT
2837788 CATTTCAGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
21 11 0.55
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.36
Consensus pattern (20 bp):
GTGTATCGATAACTGCTATA
Found at i:2838818 original size:30 final size:31
Alignment explanation
Indices: 2838784--2838841 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
2838774 GAACAGATAA
* * *
2838784 TTTATCCCATTCAGATGTTAGAA-GGGGTCG
1 TTTATCACATACAAATGTTAGAATGGGGTCG
2838814 TTTATCACATACAAATGTTAGAATGGGG
1 TTTATCACATACAAATGTTAGAATGGGG
2838842 AACGAGGTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (31 bp):
TTTATCACATACAAATGTTAGAATGGGGTCG
Found at i:2838917 original size:29 final size:29
Alignment explanation
Indices: 2838852--2838954 Score: 109
Period size: 29 Copynumber: 3.6 Consensus size: 29
2838842 AACGAGGTCC
* * * * *
2838852 CATGCAGAATTAGGACGGGGACT-AAGCC
1 CATGCAGAATCAGGACGGGAAATAAATCA
* *
2838880 CATGTAGAATCAGGATGGGAAATAAATCA
1 CATGCAGAATCAGGACGGGAAATAAATCA
* *
2838909 CATGCAGAATCAGGACGGGGAATAAATCT
1 CATGCAGAATCAGGACGGGAAATAAATCA
*
2838938 CATGCAGAATTAGGACG
1 CATGCAGAATCAGGACG
2838955 AGGATTATGC
Statistics
Matches: 62, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
28 18 0.29
29 44 0.71
ACGTcount: A:0.38, C:0.17, G:0.28, T:0.17
Consensus pattern (29 bp):
CATGCAGAATCAGGACGGGAAATAAATCA
Found at i:2839074 original size:2 final size:2
Alignment explanation
Indices: 2839056--2839089 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2839046 ATATGTCGCG
* *
2839056 TA TA AA TA TA TA AA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2839090 CTATTATCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:2839654 original size:26 final size:26
Alignment explanation
Indices: 2839623--2839673 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
2839613 CGGTTAACAG
** *
2839623 GTCGGTCAAACGGGTCGGGTCAATGT
1 GTCGGTCAAACAAGTCAGGTCAATGT
2839649 GTCGGTCAAACAAGTCAGGTCAATG
1 GTCGGTCAAACAAGTCAGGTCAATG
2839674 GTTCAATGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.25, C:0.20, G:0.33, T:0.22
Consensus pattern (26 bp):
GTCGGTCAAACAAGTCAGGTCAATGT
Found at i:2841171 original size:167 final size:167
Alignment explanation
Indices: 2840895--2841229 Score: 670
Period size: 167 Copynumber: 2.0 Consensus size: 167
2840885 ACTCGTTCAA
2840895 CCTATCGGTTGCCTCGCCGGACCTCTTTCTCCCGGCCTCATCGCAGTTCCCCGACCACAATGTCT
1 CCTATCGGTTGCCTCGCCGGACCTCTTTCTCCCGGCCTCATCGCAGTTCCCCGACCACAATGTCT
2840960 CCGCCATTGCCGAAGTTCTCGGCCATAACCTACCATCCAAAACCGTAGGATCAGCTTGTTCTGAC
66 CCGCCATTGCCGAAGTTCTCGGCCATAACCTACCATCCAAAACCGTAGGATCAGCTTGTTCTGAC
2841025 CACAATGCCACCTCTCCACCGAGTACCAATTTAGCTT
131 CACAATGCCACCTCTCCACCGAGTACCAATTTAGCTT
2841062 CCTATCGGTTGCCTCGCCGGACCTCTTTCTCCCGGCCTCATCGCAGTTCCCCGACCACAATGTCT
1 CCTATCGGTTGCCTCGCCGGACCTCTTTCTCCCGGCCTCATCGCAGTTCCCCGACCACAATGTCT
2841127 CCGCCATTGCCGAAGTTCTCGGCCATAACCTACCATCCAAAACCGTAGGATCAGCTTGTTCTGAC
66 CCGCCATTGCCGAAGTTCTCGGCCATAACCTACCATCCAAAACCGTAGGATCAGCTTGTTCTGAC
2841192 CACAATGCCACCTCTCCACCGAGTACCAATTTAGCTT
131 CACAATGCCACCTCTCCACCGAGTACCAATTTAGCTT
2841229 C
1 C
2841230 ATCTTCACTC
Statistics
Matches: 168, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
167 168 1.00
ACGTcount: A:0.20, C:0.39, G:0.17, T:0.24
Consensus pattern (167 bp):
CCTATCGGTTGCCTCGCCGGACCTCTTTCTCCCGGCCTCATCGCAGTTCCCCGACCACAATGTCT
CCGCCATTGCCGAAGTTCTCGGCCATAACCTACCATCCAAAACCGTAGGATCAGCTTGTTCTGAC
CACAATGCCACCTCTCCACCGAGTACCAATTTAGCTT
Found at i:2866245 original size:26 final size:27
Alignment explanation
Indices: 2866201--2866251 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
2866191 TGTAACGCTA
2866201 ATGTGAGAGAAGAAGAACTA-CTTAGG
1 ATGTGAGAGAAGAAGAACTATCTTAGG
*
2866227 ATGTGAGAGTAAGGA-AACTATCTTA
1 ATGTGAGAG-AAGAAGAACTATCTTA
2866252 CCGTTTTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.41, C:0.08, G:0.27, T:0.24
Consensus pattern (27 bp):
ATGTGAGAGAAGAAGAACTATCTTAGG
Found at i:2871822 original size:21 final size:21
Alignment explanation
Indices: 2871753--2871832 Score: 99
Period size: 21 Copynumber: 3.8 Consensus size: 21
2871743 CCCGATTCAC
2871753 CTGTCATCGTTCAAGAGGCCT
1 CTGTCATCGTTCAAGAGGCCT
* * *
2871774 CTCTTATCATTCAAGAGGCC-
1 CTGTCATCGTTCAAGAGGCCT
*
2871794 CTTATCATCGTTCAAGAGGCCT
1 C-TGTCATCGTTCAAGAGGCCT
*
2871816 CTGTCATCGTTCGAGAG
1 CTGTCATCGTTCAAGAG
2871833 CCCGATTCAC
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.02
21 47 0.96
22 1 0.02
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (21 bp):
CTGTCATCGTTCAAGAGGCCT
Found at i:2873205 original size:14 final size:15
Alignment explanation
Indices: 2873172--2873210 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
2873162 CGTGAAATTG
2873172 ATTT-ATTTGTAAAA
1 ATTTGATTTGTAAAA
*
2873186 AGTTGATTTGT-AAA
1 ATTTGATTTGTAAAA
2873200 ATTTGATTTGT
1 ATTTGATTTGT
2873211 TTAATTGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.51
Consensus pattern (15 bp):
ATTTGATTTGTAAAA
Found at i:2873328 original size:63 final size:64
Alignment explanation
Indices: 2873188--2873338 Score: 225
Period size: 63 Copynumber: 2.4 Consensus size: 64
2873178 TTGTAAAAAG
*
2873188 TTGATTTGTAAAATTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTACTTGTTTAA
1 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTACTTGTTTAA
* *** *
2873252 TTGATTTGTAAAAGTTGATTTGTTTAATTGAT-ATGTAAATAATTCTT-TTTTTTGCTTGTTTAA
1 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGA-GGAAATAAGAATTATTTTTTACTTGTTTAA
2873315 TTGATTTGTAAAAGTTGATTTGTT
1 TTGATTTGTAAAAGTTGATTTGTT
2873339 GTTTTAAATT
Statistics
Matches: 80, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
63 40 0.50
64 40 0.50
ACGTcount: A:0.29, C:0.02, G:0.16, T:0.53
Consensus pattern (64 bp):
TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTACTTGTTTAA
Found at i:2873422 original size:20 final size:20
Alignment explanation
Indices: 2873397--2873442 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
2873387 AAGGTACACT
2873397 TTCGCAACGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
*
2873417 TTCGCAACGTGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
2873437 TTCGCA
1 TTCGCA
2873443 TTGCGATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
TTCGCAACGCGAAAGTCAAA
Found at i:2874882 original size:12 final size:12
Alignment explanation
Indices: 2874867--2874931 Score: 69
Period size: 12 Copynumber: 5.4 Consensus size: 12
2874857 ATTTATATTG
2874867 AAATTCAAACTC
1 AAATTCAAACTC
* * *
2874879 AAATTGAAATTT
1 AAATTCAAACTC
2874891 AAATTCAAACTC
1 AAATTCAAACTC
*
2874903 AAATTGAAA-TC
1 AAATTCAAACTC
2874914 TAAATTCAAACTC
1 -AAATTCAAACTC
*
2874927 CAATT
1 AAATT
2874932 ACATATGAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
11 2 0.05
12 38 0.90
13 2 0.05
ACGTcount: A:0.49, C:0.17, G:0.03, T:0.31
Consensus pattern (12 bp):
AAATTCAAACTC
Found at i:2874886 original size:18 final size:18
Alignment explanation
Indices: 2874863--2874899 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2874853 CGAAATTTAT
2874863 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
2874881 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
2874899 A
1 A
2874900 CTCAAATTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:2874888 original size:6 final size:6
Alignment explanation
Indices: 2874867--2874923 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
2874857 ATTTATATTG
* * * * *
2874867 AAATTC AAACTC AAATTG AAATTT AAATTC AAACTC AAATTG AAA-TC
1 AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC
2874914 TAAATTC AAA
1 -AAATTC AAA
2874924 CTCCAATTAC
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
5 1 0.03
6 37 0.93
7 2 0.05
ACGTcount: A:0.53, C:0.14, G:0.04, T:0.30
Consensus pattern (6 bp):
AAATTC
Found at i:2874894 original size:24 final size:24
Alignment explanation
Indices: 2874867--2874931 Score: 112
Period size: 24 Copynumber: 2.7 Consensus size: 24
2874857 ATTTATATTG
*
2874867 AAATTCAAACTCAAATTGAAATTT
1 AAATTCAAACTCAAATTGAAATCT
2874891 AAATTCAAACTCAAATTGAAATCT
1 AAATTCAAACTCAAATTGAAATCT
*
2874915 AAATTCAAACTCCAATT
1 AAATTCAAACTCAAATT
2874932 ACATATGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.49, C:0.17, G:0.03, T:0.31
Consensus pattern (24 bp):
AAATTCAAACTCAAATTGAAATCT
Found at i:2875333 original size:25 final size:25
Alignment explanation
Indices: 2875305--2875354 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
2875295 CATTATTTTC
*
2875305 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
*
2875330 CAAATAATGTACTCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
2875355 TAATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:2875759 original size:6 final size:6
Alignment explanation
Indices: 2875750--2875784 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
2875740 TTGTGATTAA
**
2875750 GATTTT GATTTT GATTTT GATTGC GATTTT GATTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTT
2875785 CCTTTTGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.17, C:0.03, G:0.20, T:0.60
Consensus pattern (6 bp):
GATTTT
Found at i:2878082 original size:24 final size:24
Alignment explanation
Indices: 2878048--2878101 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2878038 CTGAAACATC
2878048 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2878072 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2878096 ATCAAA
1 ATCAAA
2878102 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2878115 original size:24 final size:24
Alignment explanation
Indices: 2878048--2878115 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
2878038 CTGAAACATC
* * *
2878048 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
2878072 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
2878096 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
2878116 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:2878248 original size:12 final size:12
Alignment explanation
Indices: 2878227--2878260 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2878217 GGTTGTGGGT
*
2878227 TTTGAGATTGTG
1 TTTGATATTGTG
2878239 TTTGATATTGTG
1 TTTGATATTGTG
*
2878251 TTTGGTATTG
1 TTTGATATTG
2878261 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:2878931 original size:22 final size:22
Alignment explanation
Indices: 2878916--2878961 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
2878906 GATGTCGTTT
2878916 GATATAGGAACGGATGTCGCCG
1 GATATAGGAACGGATGTCGCCG
*
2878938 GATATAGGAACGGATATCGCCG
1 GATATAGGAACGGATGTCGCCG
2878960 GA
1 GA
2878962 GAGAGTGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.35, T:0.17
Consensus pattern (22 bp):
GATATAGGAACGGATGTCGCCG
Found at i:2879115 original size:20 final size:20
Alignment explanation
Indices: 2879073--2879161 Score: 56
Period size: 20 Copynumber: 4.5 Consensus size: 20
2879063 ATAAAACCTA
* *
2879073 TTGCGAAATT-AAAATTCGTG
1 TTGCG-AATTCAAAAATCGAG
*
2879093 TTGTGAATTCAAAAATCGAG
1 TTGCGAATTCAAAAATCGAG
* *
2879113 TTGCGAAATCAGAAATC-ACG
1 TTGCGAATTCAAAAATCGA-G
* *** *
2879133 TTGGGAATTTGGAAATCGCG
1 TTGCGAATTCAAAAATCGAG
2879153 TTGCGAATT
1 TTGCGAATT
2879162 TGACTTATGT
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
19 5 0.09
20 49 0.91
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (20 bp):
TTGCGAATTCAAAAATCGAG
Found at i:2879162 original size:20 final size:20
Alignment explanation
Indices: 2879105--2879163 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
2879095 GTGAATTCAA
* * **
2879105 AAATCGAGTTGCGAAATCAG
1 AAATCGCGTTGCGAATTTGG
* *
2879125 AAATCACGTTGGGAATTTGG
1 AAATCGCGTTGCGAATTTGG
2879145 AAATCGCGTTGCGAATTTG
1 AAATCGCGTTGCGAATTTG
2879164 ACTTATGTGT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (20 bp):
AAATCGCGTTGCGAATTTGG
Found at i:2879195 original size:20 final size:20
Alignment explanation
Indices: 2879172--2879218 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2879162 TGACTTATGT
*
2879172 GTTGCGATTTACATATTCAC
1 GTTGCGATTTACATATGCAC
* *
2879192 GTTGCAATTTACATATGCGC
1 GTTGCGATTTACATATGCAC
2879212 GTTGCGA
1 GTTGCGA
2879219 ATTTGGAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACATATGCAC
Found at i:2884936 original size:23 final size:24
Alignment explanation
Indices: 2884899--2884949 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
2884889 TGATTAAATG
2884899 TAAATTAATATAGTTTAATTTATA
1 TAAATTAATATAGTTTAATTTATA
*
2884923 TAAATT-ATATAGTTTAATTTATG
1 TAAATTAATATAGTTTAATTTATA
2884946 TAAA
1 TAAA
2884950 GAAAAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (24 bp):
TAAATTAATATAGTTTAATTTATA
Found at i:2888476 original size:24 final size:24
Alignment explanation
Indices: 2888421--2888477 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
2888411 CGGTTAGGGT
*
2888421 TTTTAGGTTCAGGTTTGAATTTAG
1 TTTTGGGTTCAGGTTTGAATTTAG
* *
2888445 GTTCGGGTTCAGGTTTGAATTT-G
1 TTTTGGGTTCAGGTTTGAATTTAG
2888468 ATTTTGGGTT
1 -TTTTGGGTT
2888478 TGGGGTTTGG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 1 0.04
24 26 0.96
ACGTcount: A:0.16, C:0.05, G:0.30, T:0.49
Consensus pattern (24 bp):
TTTTGGGTTCAGGTTTGAATTTAG
Found at i:2889677 original size:13 final size:12
Alignment explanation
Indices: 2889629--2889721 Score: 68
Period size: 13 Copynumber: 7.7 Consensus size: 12
2889619 GTTAGGGTTT
*
2889629 TTTAGGTTCGGG
1 TTTAGGTTTGGG
**
2889641 TTCGGGTTT-GG
1 TTTAGGTTTGGG
2889652 -TTAGTGTTTGGG
1 TTTAG-GTTTGGG
2889664 TTTAGGTTTAGGG
1 TTTAGGTTT-GGG
2889677 TTTAGGTTTGAGG
1 TTTAGGTTTG-GG
*
2889690 TTT-GAGTTTAAGG
1 TTTAG-GTTT-GGG
2889703 TTTAGG-TTGGG
1 TTTAGGTTTGGG
*
2889714 GTTAGGTT
1 TTTAGGTT
2889722 ATAAAAGATG
Statistics
Matches: 64, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
10 2 0.03
11 13 0.20
12 17 0.27
13 31 0.48
14 1 0.02
ACGTcount: A:0.12, C:0.02, G:0.40, T:0.46
Consensus pattern (12 bp):
TTTAGGTTTGGG
Found at i:2889709 original size:6 final size:6
Alignment explanation
Indices: 2889652--2889710 Score: 57
Period size: 6 Copynumber: 9.2 Consensus size: 6
2889642 TCGGGTTTGG
*
2889652 TTAGTGT TTGGGT TTAGGT TTAGGGT TTAGGT TTGAGGT TT-GAGT TTAAGGT
1 TTAG-GT TTAGGT TTAGGT TTA-GGT TTAGGT TT-AGGT TTAG-GT TT-AGGT
2889704 TTAGGT T
1 TTAGGT T
2889711 GGGGTTAGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
5 1 0.02
6 24 0.53
7 19 0.42
8 1 0.02
ACGTcount: A:0.15, C:0.00, G:0.36, T:0.49
Consensus pattern (6 bp):
TTAGGT
Found at i:2890512 original size:12 final size:12
Alignment explanation
Indices: 2890470--2890512 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 12
2890460 AATAAACTAT
2890470 TTATAATTAATA
1 TTATAATTAATA
2890482 TTAAAATAATTATATA
1 TT---ATAATTA-ATA
2890498 TTATAATTAATA
1 TTATAATTAATA
2890510 TTA
1 TTA
2890513 ATATTAGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 8 0.30
13 7 0.26
15 7 0.26
16 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
TTATAATTAATA
Found at i:2890525 original size:28 final size:27
Alignment explanation
Indices: 2890447--2890613 Score: 91
Period size: 28 Copynumber: 6.2 Consensus size: 27
2890437 TTCATCCATA
*
2890447 TATAATTTATATTAATA-AAC-TAT-T
1 TATAATTAATATTAATATAACTTATAT
* *
2890471 TATAATTAATATTAAAATAATTATATAT
1 TATAATTAATATTAATATAACT-TATAT
**
2890499 TATAATTAATATT-A-AT-A-TTAGCT
1 TATAATTAATATTAATATAACTTATAT
**
2890522 TAT-ATTAATA-TAATATAGTTTATAATT
1 TATAATTAATATTAATATAACTTAT-A-T
* **
2890549 TGTAATTAATATTAATATAAAATATAGT
1 TATAATTAATATTAATATAACTTATA-T
*
2890577 CTATAAAATTAATATTAATATAAACTATATGT
1 -TAT--AATTAATATTAATAT-AACT-TATAT
2890609 TATAA
1 TATAA
2890614 ATTATATAGT
Statistics
Matches: 109, Mismatches: 17, Indels: 29
0.70 0.11 0.19
Matches are distributed among these distances:
21 1 0.01
22 8 0.07
23 8 0.07
24 16 0.15
25 6 0.06
26 2 0.02
27 7 0.06
28 23 0.21
29 14 0.13
31 18 0.17
32 3 0.03
33 3 0.03
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (27 bp):
TATAATTAATATTAATATAACTTATAT
Found at i:2890529 original size:44 final size:44
Alignment explanation
Indices: 2890479--2890562 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 44
2890469 TTTATAATTA
2890479 ATATTAAAATAATTATA-TATTATAATTAAT-ATTAATATTAGCTT
1 ATATTAAAATAA-TATAGT-TTATAATTAATAATTAATATTAGCTT
* **
2890523 ATATTAATATAATATAGTTTATAATTTGTAATTAATATTA
1 ATATTAAAATAATATAGTTTATAATTAATAATTAATATTA
2890563 ATATAAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
43 13 0.37
44 22 0.63
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (44 bp):
ATATTAAAATAATATAGTTTATAATTAATAATTAATATTAGCTT
Found at i:2890590 original size:31 final size:30
Alignment explanation
Indices: 2890552--2890744 Score: 144
Period size: 31 Copynumber: 6.0 Consensus size: 30
2890542 TATAATTTGT
*
2890552 AATTAATATTAATATAAAATATAGTCTATAA
1 AATTAATATTAATATAAACTATAGT-TATAA
2890583 AATTAATATTAATATAAACTATATGTTAT-A
1 AATTAATATTAATATAAACTATA-GTTATAA
*
2890613 AATTATATAGTATAGTTTATAAACTATAGTTA-AA
1 AATTA-ATA-T-TA--ATATAAACTATAGTTATAA
*
2890647 TAATTAATATTAATAT--AGTATAGTTTATAA
1 -AATTAATATTAATATAAACTATAG-TTATAA
*
2890677 ACTATATACTATATTAATATAAATTATAGTTA-AGA
1 A--AT-TA--ATATTAATATAAACTATAGTTATA-A
* *
2890712 TAATTAACATTAATATAAACTATATTTTATAA
1 -AATTAATATTAATATAAACTATA-GTTATAA
2890744 A
1 A
2890745 TTATATACTA
Statistics
Matches: 133, Mismatches: 8, Indels: 42
0.73 0.04 0.23
Matches are distributed among these distances:
28 6 0.05
29 4 0.03
30 11 0.08
31 47 0.35
32 11 0.08
33 6 0.05
34 21 0.16
35 20 0.15
36 7 0.05
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.42
Consensus pattern (30 bp):
AATTAATATTAATATAAACTATAGTTATAA
Found at i:2890593 original size:65 final size:66
Alignment explanation
Indices: 2890523--2890756 Score: 261
Period size: 65 Copynumber: 3.6 Consensus size: 66
2890513 ATATTAGCTT
* * *
2890523 ATATTAATAT-AA-TATAGTTTATAATTTGTA-ATTAATATTAATATAAAATATAGTCTATAA-A
1 ATATTAATATAAACTATAGTTTATAAATTATATACT-ATATTAATATAAAATATAGT-TA-AATA
2890584 ATTA
63 ATTA
* *
2890588 ATATTAATATAAACTATA-TGTTATAAATTATATAGTATAGTT--TATAAACTATAGTTAAATAA
1 ATATTAATATAAACTATAGT-TTATAAATTATATACTATA-TTAATATAAAATATAGTTAAATAA
2890650 TTA
64 TTA
* * *
2890653 ATATTAATAT--AGTATAGTTTATAAACTATATACTATATTAATATAAATTATAGTTAAGATAAT
1 ATATTAATATAAACTATAGTTTATAAATTATATACTATATTAATATAAAATATAGTTAA-ATAAT
2890716 TA
65 TA
* *
2890718 ACATTAATATAAACTATATTTTATAAATTATATACTATA
1 ATATTAATATAAACTATAGTTTATAAATTATATACTATA
2890757 GGTTATAAAG
Statistics
Matches: 145, Mismatches: 12, Indels: 22
0.81 0.07 0.12
Matches are distributed among these distances:
62 2 0.01
63 22 0.15
64 18 0.12
65 43 0.30
66 15 0.10
67 41 0.28
68 4 0.03
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (66 bp):
ATATTAATATAAACTATAGTTTATAAATTATATACTATATTAATATAAAATATAGTTAAATAATT
A
Found at i:2890604 original size:24 final size:25
Alignment explanation
Indices: 2890559--2890605 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
2890549 TGTAATTAAT
**
2890559 ATTAATATAAAATATAGTCTATAAA
1 ATTAATATAAAATATAAACTATAAA
*
2890584 ATTAATAT-TAATATAAACTATA
1 ATTAATATAAAATATAAACTATA
2890606 TGTTATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTAATATAAAATATAAACTATAAA
Found at i:2890691 original size:130 final size:130
Alignment explanation
Indices: 2890523--2890765 Score: 348
Period size: 130 Copynumber: 1.9 Consensus size: 130
2890513 ATATTAGCTT
** * *
2890523 ATATTAATATAATATAGTTTATAATTTGTAATTAATATTAATATAAAATATAGTCTATA-A-AAT
1 ATATTAATATAATATAGTTTATAAACTATAACTAATATTAATATAAAATATAGT-TA-AGATAAT
* * *
2890586 TAATATTAATATAAACTATATGTTATAAATTATATAGTATAGTTTATAAACTATAGTTAAATAAT
64 TAACATTAATATAAACTATATGTTATAAATTATATACTATAGGTTATAAACTATAGTTAAATAAT
2890651 TA
129 TA
* *
2890653 ATATTAATATAGTATAGTTTATAAACTATATACT-ATATTAATATAAATTATAGTTAAGATAATT
1 ATATTAATATAATATAGTTTATAAACTATA-ACTAATATTAATATAAAATATAGTTAAGATAATT
*
2890717 AACATTAATATAAACTATATTTTATAAATTATATACTATAGGTTATAAA
65 AACATTAATATAAACTATATGTTATAAATTATATACTATAGGTTATAAA
2890766 GTGTAAACTA
Statistics
Matches: 100, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
128 1 0.01
129 3 0.03
130 94 0.94
131 2 0.02
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (130 bp):
ATATTAATATAATATAGTTTATAAACTATAACTAATATTAATATAAAATATAGTTAAGATAATTA
ACATTAATATAAACTATATGTTATAAATTATATACTATAGGTTATAAACTATAGTTAAATAATTA
Found at i:2890704 original size:15 final size:15
Alignment explanation
Indices: 2890686--2890750 Score: 62
Period size: 15 Copynumber: 4.3 Consensus size: 15
2890676 AACTATATAC
2890686 TATATTAATATAAAT
1 TATATTAATATAAAT
*
2890701 TATAGTTAAGAT-AAT
1 TATA-TTAATATAAAT
* *
2890716 TAACATTAATATAAAC
1 T-ATATTAATATAAAT
*
2890732 TATATT-TTATAAAT
1 TATATTAATATAAAT
2890746 TATAT
1 TATAT
2890751 ACTATAGGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
14 11 0.28
15 18 0.45
16 11 0.28
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (15 bp):
TATATTAATATAAAT
Found at i:2890775 original size:21 final size:21
Alignment explanation
Indices: 2890725--2890777 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2890715 TTAACATTAA
** *
2890725 TATAAACTATATTTTATAAAT
1 TATAAACTATAGGTTATAAAG
*
2890746 TATATACTATAGGTTATAAAG
1 TATAAACTATAGGTTATAAAG
*
2890767 TGTAAACTATA
1 TATAAACTATA
2890778 TAGTACACTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.42
Consensus pattern (21 bp):
TATAAACTATAGGTTATAAAG
Found at i:2890871 original size:24 final size:21
Alignment explanation
Indices: 2890820--2890919 Score: 74
Period size: 20 Copynumber: 5.0 Consensus size: 21
2890810 TATAGGTTAC
2890820 ATATATAGTTTATATA-ACAT
1 ATATATAGTTTATATATACAT
*
2890840 ATAAATAGATTGTATATATACAT
1 ATATATAG-TT-TATATATACAT
*
2890863 ATACTATAG---GT-TAT--AT
1 ATA-TATAGTTTATATATACAT
2890879 ATATATAGTTTATATATACTAT
1 ATATATAGTTTATATATAC-AT
*
2890901 ATA--TAGTTTATACATACAT
1 ATATATAGTTTATATATACAT
2890920 GTACTATAAG
Statistics
Matches: 64, Mismatches: 5, Indels: 23
0.70 0.05 0.25
Matches are distributed among these distances:
15 5 0.08
16 5 0.08
18 4 0.06
19 6 0.09
20 20 0.31
21 2 0.03
22 11 0.17
23 7 0.11
24 4 0.06
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (21 bp):
ATATATAGTTTATATATACAT
Found at i:2890938 original size:35 final size:36
Alignment explanation
Indices: 2890899--2890972 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
2890889 TATATATACT
*
2890899 ATATATAGTTTA-TACATACATGTACTATAAGTTAC
1 ATATATAGTTTACTACATACATATACTATAAGTTAC
** *
2890934 ATATATAGTTTACTTGTATACATATACTATAGGTTAC
1 ATATATAGTTTAC-TACATACATATACTATAAGTTAC
2890971 AT
1 AT
2890973 TTATTAACTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 12 0.36
37 21 0.64
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (36 bp):
ATATATAGTTTACTACATACATATACTATAAGTTAC
Found at i:2890954 original size:57 final size:58
Alignment explanation
Indices: 2890808--2890965 Score: 189
Period size: 57 Copynumber: 2.7 Consensus size: 58
2890798 TTGTTTATAA
* *
2890808 ACTATAGGTTACATATATAGTTTATATA-ACATATAAATAGATTGTATATATACATAT
1 ACTATAGGTTACATATATAGTTTATATATACATATATATAGATTGTATACATACATAT
* *
2890865 ACTATAGGTTATATATATATAGTTTATATATAC-TATATATAG-TT-TATACATACATGT
1 ACTATAGG-T-TACATATATAGTTTATATATACATATATATAGATTGTATACATACATAT
* *
2890922 ACTATAAGTTACATATATAGTTTACTTGTATACATATACTATAG
1 ACTATAGGTTACATATATAGTTTA--TATATACATATA-TATAG
2890966 GTTACATTTA
Statistics
Matches: 87, Mismatches: 7, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
55 14 0.16
56 1 0.01
57 32 0.37
58 7 0.08
59 31 0.36
60 2 0.02
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (58 bp):
ACTATAGGTTACATATATAGTTTATATATACATATATATAGATTGTATACATACATAT
Found at i:2891505 original size:15 final size:17
Alignment explanation
Indices: 2891487--2891572 Score: 69
Period size: 15 Copynumber: 5.4 Consensus size: 17
2891477 CTATATATTT
2891487 TATATAG-TT-TATACA
1 TATATAGTTTATATACA
2891502 TATATAGTTTATATACA
1 TATATAGTTTATATACA
2891519 TATATA-TATATATATACA
1 TATATAGT-T-TATATACA
* * *
2891537 -CTATA-TTAATATAAA
1 TATATAGTTTATATACA
*
2891552 T-TATAGTTTATAAAC-
1 TATATAGTTTATATACA
2891567 TATATA
1 TATATA
2891573 CTTTTTATAG
Statistics
Matches: 58, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
15 18 0.31
16 14 0.24
17 18 0.31
18 8 0.14
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (17 bp):
TATATAGTTTATATACA
Found at i:2891543 original size:89 final size:88
Alignment explanation
Indices: 2891434--2891622 Score: 292
Period size: 89 Copynumber: 2.1 Consensus size: 88
2891424 TTATATTAGT
* *
2891434 TATACATATATATACAATATTAGTATAAATTATAATTTATAAACTATATA-TTTTATATAGTTTA
1 TATATATATATATACAATATTAATATAAATTATAATTTATAAACTATATACTTTT-TATAGTTTA
2891498 TACATATATAGTTTATATACATA-
65 TACATATATAGTTTATATACATAG
*
2891521 TATATATATATATACACTATATTAATATAAATTATAGTTTATAAACTATATACTTTTTATAGTTT
1 TATATATATATATACA--ATATTAATATAAATTATAATTTATAAACTATATACTTTTTATAGTTT
*
2891586 ATACGTATATAGTTTATATACATAG
64 ATACATATATAGTTTATATACATAG
*
2891611 TTTATATATATA
1 TATATATATATA
2891623 ATTCATAAAC
Statistics
Matches: 93, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
87 15 0.16
89 63 0.68
90 15 0.16
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (88 bp):
TATATATATATATACAATATTAATATAAATTATAATTTATAAACTATATACTTTTTATAGTTTAT
ACATATATAGTTTATATACATAG
Found at i:2891684 original size:18 final size:19
Alignment explanation
Indices: 2891661--2891696 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
2891651 TTATAAAAAT
2891661 ATATAGTTTATA-ATATAA
1 ATATAGTTTATATATATAA
2891679 ATATAGTTTATATATATA
1 ATATAGTTTATATATATA
2891697 GTTTATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (19 bp):
ATATAGTTTATATATATAA
Found at i:2891695 original size:13 final size:13
Alignment explanation
Indices: 2891578--2891707 Score: 89
Period size: 13 Copynumber: 9.2 Consensus size: 13
2891568 ATATACTTTT
2891578 TATAGTTTATACGTA
1 TATAGTTTATA--TA
2891593 TATAGTTTATATA
1 TATAGTTTATATA
*
2891606 CATAGTTTATATA
1 TATAGTTTATATA
* * *
2891619 TATAATTCATAAA
1 TATAGTTTATATA
* * *
2891632 CATAATTTATATG
1 TATAGTTTATATA
*
2891645 TATAGCTTATAAAAATA
1 TATAG-TT-T--ATATA
2891662 TATAGTTTATAATATAAA
1 TATAG-TT-T-ATAT--A
2891680 TATAGTTTATATA
1 TATAGTTTATATA
2891693 TATAGTTTATATA
1 TATAGTTTATATA
2891706 TA
1 TA
2891708 AACTTATATT
Statistics
Matches: 94, Mismatches: 15, Indels: 14
0.76 0.12 0.11
Matches are distributed among these distances:
13 51 0.54
14 2 0.02
15 16 0.17
16 5 0.05
17 14 0.15
18 6 0.06
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:2891709 original size:30 final size:32
Alignment explanation
Indices: 2891659--2891727 Score: 99
Period size: 31 Copynumber: 2.2 Consensus size: 32
2891649 GCTTATAAAA
2891659 ATATATAGTTTATAATATAAA-TATAGTT-TAT
1 ATATATAGTTTATAATATAAACTATA-TTATAT
2891690 ATATATAGTTTAT-ATATAAACTTATATTATAT
1 ATATATAGTTTATAATATAAAC-TATATTATAT
2891722 ATATAT
1 ATATAT
2891728 TATAATTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
30 7 0.20
31 15 0.43
32 13 0.37
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (32 bp):
ATATATAGTTTATAATATAAACTATATTATAT
Found at i:2894024 original size:31 final size:34
Alignment explanation
Indices: 2893956--2894067 Score: 108
Period size: 34 Copynumber: 3.4 Consensus size: 34
2893946 AAACAACAAC
* * * *
2893956 GATACTGTAATAC-CAACAATGAAATCACAATATT
1 GATACTGTAATACTCAGCACTGGAAT-ACAATACT
2893990 GATACTGTAATACT-AGCACTGG-A-ACAATACT
1 GATACTGTAATACTCAGCACTGGAATACAATACT
* * *
2894021 GATATTGTAATA-TCAGCACTGGAATTACAGTACA
1 GATACTGTAATACTCAGCACTGGAA-TACAATACT
2894055 GATACTGTAATAC
1 GATACTGTAATAC
2894068 CAATACTAGA
Statistics
Matches: 64, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
30 1 0.02
31 26 0.41
32 1 0.02
33 1 0.02
34 35 0.55
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (34 bp):
GATACTGTAATACTCAGCACTGGAATACAATACT
Found at i:2894301 original size:18 final size:18
Alignment explanation
Indices: 2894264--2894308 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
2894254 TAATGGAATG
*
2894264 TAAGATTACCGGCAGAAA
1 TAAGATTACCGACAGAAA
*
2894282 TAGGATTACCGAC-GAGAA
1 TAAGATTACCGACAGA-AA
2894300 TAAGATTAC
1 TAAGATTAC
2894309 TAGGAATGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (18 bp):
TAAGATTACCGACAGAAA
Found at i:2905777 original size:2 final size:2
Alignment explanation
Indices: 2905765--2905834 Score: 133
Period size: 2 Copynumber: 35.5 Consensus size: 2
2905755 TTTGTTAAAC
2905765 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2905806 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 T
2905835 CAATTTCGAT
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 66 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2916465 original size:26 final size:26
Alignment explanation
Indices: 2916429--2916479 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
2916419 GCTTTATTGC
*
2916429 ATTCGTTTCCTATGTTTAAAAAGTTG
1 ATTCGTTTCCTATATTTAAAAAGTTG
*
2916455 ATTCTTTTCCTATATTTAAAAAGTT
1 ATTCGTTTCCTATATTTAAAAAGTT
2916480 TATTTGCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.49
Consensus pattern (26 bp):
ATTCGTTTCCTATATTTAAAAAGTTG
Found at i:2922266 original size:31 final size:31
Alignment explanation
Indices: 2922217--2922301 Score: 82
Period size: 32 Copynumber: 2.7 Consensus size: 31
2922207 TAACCAAAAT
* * *
2922217 CAAAATTAACCCAAACCGAAAG-AATCCGAAC
1 CAAATTTAACCC-GACCGAAAGTAATACGAAC
* *
2922248 CAAATTTTAACTCGACCGAAAGTAATACGAAT
1 CAAA-TTTAACCCGACCGAAAGTAATACGAAC
*
2922280 CGAATTTAACCCGACCCGAAAG
1 CAAATTTAACCCGA-CCGAAAG
2922302 CAACCTGAAG
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
31 21 0.48
32 23 0.52
ACGTcount: A:0.45, C:0.26, G:0.13, T:0.16
Consensus pattern (31 bp):
CAAATTTAACCCGACCGAAAGTAATACGAAC
Found at i:2922390 original size:19 final size:19
Alignment explanation
Indices: 2922338--2922390 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
2922328 CGAATAATAA
2922338 ATTA-ATTTA-AATAAAAT
1 ATTATATTTATAATAAAAT
*
2922355 -TTATAATTTATTA-AAAAT
1 ATTAT-ATTTATAATAAAAT
2922373 ATTATATTTATAATAAAA
1 ATTATATTTATAATAAAA
2922391 ATAATAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
16 3 0.10
18 17 0.59
19 9 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTATATTTATAATAAAAT
Found at i:2922512 original size:38 final size:38
Alignment explanation
Indices: 2922438--2922514 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
2922428 ATTTAAAAGT
**
2922438 AAGAATCTAATCGTAAGATTGAAAACAATACTAAATAA
1 AAGAATCTAATCGTAAGATTGAAAACAATAAGAAATAA
* * *
2922476 AAGAATCTAATTGTAAGCTTGAAAACAGTAAGAAATAA
1 AAGAATCTAATCGTAAGATTGAAAACAATAAGAAATAA
2922514 A
1 A
2922515 GTTTACTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.55, C:0.09, G:0.13, T:0.23
Consensus pattern (38 bp):
AAGAATCTAATCGTAAGATTGAAAACAATAAGAAATAA
Found at i:2923011 original size:16 final size:16
Alignment explanation
Indices: 2922992--2923043 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
2922982 CGAAAATCAA
2922992 CCGATCCGATATTGAC
1 CCGATCCGATATTGAC
* * ** *
2923008 CCGACCCGAAATCAAA
1 CCGATCCGATATTGAC
*
2923024 CCGATCTGATATTGAC
1 CCGATCCGATATTGAC
2923040 CCGA
1 CCGA
2923044 CCCAAAAATC
Statistics
Matches: 25, Mismatches: 11, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.31, C:0.33, G:0.17, T:0.19
Consensus pattern (16 bp):
CCGATCCGATATTGAC
Found at i:2923018 original size:32 final size:32
Alignment explanation
Indices: 2922981--2923060 Score: 126
Period size: 32 Copynumber: 2.5 Consensus size: 32
2922971 GTTGACCTAA
2922981 CCGAAAATCAACCGATCCGATATTGACCCGAC
1 CCGAAAATCAACCGATCCGATATTGACCCGAC
*
2923013 CCG-AAATCAAACCGATCTGATATTGACCCGAC
1 CCGAAAATC-AACCGATCCGATATTGACCCGAC
*
2923045 CCAAAAATCAACCGAT
1 CCGAAAATCAACCGAT
2923061 AAGAACTAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
31 5 0.11
32 34 0.77
33 5 0.11
ACGTcount: A:0.38, C:0.33, G:0.14, T:0.16
Consensus pattern (32 bp):
CCGAAAATCAACCGATCCGATATTGACCCGAC
Found at i:2923704 original size:12 final size:12
Alignment explanation
Indices: 2923687--2923712 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2923677 ATAAAATCAG
2923687 TAAAAATATTAT
1 TAAAAATATTAT
2923699 TAAAAATATTAT
1 TAAAAATATTAT
2923711 TA
1 TA
2923713 TTTCTACCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAAAAATATTAT
Found at i:2923854 original size:21 final size:21
Alignment explanation
Indices: 2923828--2923867 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2923818 TAAAGAGCTC
2923828 AATAATAACATTTTCGATAGA
1 AATAATAACATTTTCGATAGA
**
2923849 AATAATAATGTTTTCGATA
1 AATAATAACATTTTCGATA
2923868 ATTTTTTATC
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:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (21 bp):
AATAATAACATTTTCGATAGA
Found at i:2928082 original size:9 final size:8
Alignment explanation
Indices: 2928057--2928102 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
2928047 GACAACCCAT
2928057 TTTTATTA
1 TTTTATTA
2928065 TTTTATTA
1 TTTTATTA
2928073 TTTTATTTA
1 TTTTA-TTA
2928082 TTTTATTTA
1 TTTTA-TTA
* *
2928091 ATTTACTA
1 TTTTATTA
2928099 TTTT
1 TTTT
2928103 TTCTGAGTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
8 18 0.53
9 16 0.47
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTATTA
Found at i:2928082 original size:17 final size:16
Alignment explanation
Indices: 2928057--2928102 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
2928047 GACAACCCAT
2928057 TTTTATTATTTTATTA
1 TTTTATTATTTTATTA
2928073 TTTTATTTATTTTATTTA
1 TTTTA-TTATTTTA-TTA
* *
2928091 ATTTACTATTTT
1 TTTTATTATTTT
2928103 TTCTGAGTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 5 0.19
17 14 0.54
18 7 0.27
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTATTATTTTATTA
Found at i:2931147 original size:20 final size:20
Alignment explanation
Indices: 2931122--2931199 Score: 79
Period size: 20 Copynumber: 3.9 Consensus size: 20
2931112 TGATAATTGA
2931122 TTAATTATTAAAATATATAT
1 TTAATTATTAAAATATATAT
* * *
2931142 TTAATTATCAAAATATAAAA
1 TTAATTATTAAAATATATAT
2931162 TT-ATTA-TAAAATATATTAAT
1 TTAATTATTAAAATATA-T-AT
*
2931182 TTAATCATTTAAAATATA
1 TTAATTA-TTAAAATATA
2931200 ATAAATAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
18 8 0.17
19 4 0.09
20 22 0.48
21 3 0.07
23 9 0.20
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAATTATTAAAATATATAT
Found at i:2931312 original size:31 final size:31
Alignment explanation
Indices: 2931277--2931337 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
2931267 GATTGAATTA
* *
2931277 GATTGGGATTAGGGTTTAAGTCTAAGAATCG
1 GATTGGGATCAGGGTTTAAGTCTAAAAATCG
*
2931308 GATTGGGATCAGGGTTTTAGTCTAAAAATC
1 GATTGGGATCAGGGTTTAAGTCTAAAAATC
2931338 AGAATGGATC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.30, C:0.08, G:0.30, T:0.33
Consensus pattern (31 bp):
GATTGGGATCAGGGTTTAAGTCTAAAAATCG
Found at i:2932102 original size:46 final size:45
Alignment explanation
Indices: 2932018--2932116 Score: 110
Period size: 46 Copynumber: 2.2 Consensus size: 45
2932008 TCATTAAAAA
* * * *
2932018 TATTAATTTACTAATAGATAATAAAAAGATTGATAAATTACTAAT
1 TATTAATTTACTAATAAATAATAAAAACAATGACAAATTACTAAT
* *
2932063 CTATTAATTTTCTAATAAATAATAAAAACAAT-ACCAAATTATTAAT
1 -TATTAATTTACTAATAAATAATAAAAACAATGA-CAAATTACTAAT
*
2932109 TAATAATT
1 TATTAATT
2932117 ATTTTACTAC
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
45 8 0.18
46 37 0.82
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.38
Consensus pattern (45 bp):
TATTAATTTACTAATAAATAATAAAAACAATGACAAATTACTAAT
Found at i:2935659 original size:10 final size:10
Alignment explanation
Indices: 2935646--2935721 Score: 53
Period size: 10 Copynumber: 6.9 Consensus size: 10
2935636 ATGAACACAA
2935646 ATAAACGAAT
1 ATAAACGAAT
2935656 ATAAACGAATGGAT
1 ATAAACG-A---AT
*
2935670 ATAAACGAAC
1 ATAAACGAAT
*
2935680 ATAAACGAACACA
1 ATAAACG-A-A-T
2935693 ATAAACGAAT
1 ATAAACGAAT
* *
2935703 GTAAACGAAC
1 ATAAACGAAT
2935713 ATAAACGAA
1 ATAAACGAA
2935722 CACAATAAAC
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
10 31 0.58
11 3 0.06
12 2 0.04
13 8 0.15
14 9 0.17
ACGTcount: A:0.58, C:0.14, G:0.13, T:0.14
Consensus pattern (10 bp):
ATAAACGAAT
Found at i:2935659 original size:24 final size:24
Alignment explanation
Indices: 2935632--2935713 Score: 94
Period size: 24 Copynumber: 3.5 Consensus size: 24
2935622 CATTTAAATG
*
2935632 ATAAATGAACACAAATAAACGAAT
1 ATAAACGAACACAAATAAACGAAT
*** * *
2935656 ATAAACGAATGGATATAAACGAAC
1 ATAAACGAACACAAATAAACGAAT
2935680 ATAAACGAACAC-AATAAACGAAT
1 ATAAACGAACACAAATAAACGAAT
*
2935703 GTAAACGAACA
1 ATAAACGAACA
2935714 TAAACGAACA
Statistics
Matches: 46, Mismatches: 12, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 19 0.41
24 27 0.59
ACGTcount: A:0.59, C:0.15, G:0.12, T:0.15
Consensus pattern (24 bp):
ATAAACGAACACAAATAAACGAAT
Found at i:2935713 original size:33 final size:33
Alignment explanation
Indices: 2935671--2935746 Score: 134
Period size: 33 Copynumber: 2.3 Consensus size: 33
2935661 CGAATGGATA
* *
2935671 TAAACGAACATAAACGAACACAATAAACGAATG
1 TAAACGAACATAAACGAACACAATAAACAAACG
2935704 TAAACGAACATAAACGAACACAATAAACAAACG
1 TAAACGAACATAAACGAACACAATAAACAAACG
2935737 TAAACGAACA
1 TAAACGAACA
2935747 CAAATGAATG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.59, C:0.20, G:0.11, T:0.11
Consensus pattern (33 bp):
TAAACGAACATAAACGAACACAATAAACAAACG
Found at i:2935722 original size:10 final size:10
Alignment explanation
Indices: 2935670--2935746 Score: 64
Period size: 10 Copynumber: 7.1 Consensus size: 10
2935660 ACGAATGGAT
2935670 ATAAACGAAC
1 ATAAACGAAC
2935680 ATAAACGAACAC
1 ATAAACG-A-AC
*
2935692 AATAAACGAAT
1 -ATAAACGAAC
*
2935703 GTAAACGAAC
1 ATAAACGAAC
2935713 ATAAACGAACAC
1 ATAAACG-A-AC
*
2935725 AATAAACAAAC
1 -ATAAACGAAC
*
2935736 GTAAACGAAC
1 ATAAACGAAC
2935746 A
1 A
2935747 CAAATGAATG
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
10 29 0.55
11 5 0.09
12 6 0.11
13 13 0.25
ACGTcount: A:0.60, C:0.19, G:0.10, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:2935765 original size:24 final size:23
Alignment explanation
Indices: 2935704--2935777 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
2935694 TAAACGAATG
*
2935704 TAAACGAACATAAACGAACACAA
1 TAAACGAACGTAAACGAACACAA
*
2935727 TAAACAAACGTAAACGAACACAAA
1 TAAACGAACGTAAACGAACAC-AA
* * * *
2935751 TGAATGAACGTAAACAAATACAA
1 TAAACGAACGTAAACGAACACAA
2935774 TAAA
1 TAAA
2935778 TTGTTAAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
23 24 0.57
24 18 0.43
ACGTcount: A:0.61, C:0.18, G:0.09, T:0.12
Consensus pattern (23 bp):
TAAACGAACGTAAACGAACACAA
Found at i:2940526 original size:14 final size:14
Alignment explanation
Indices: 2940506--2940555 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
2940496 GATTGAGCTA
2940506 AACATAAATGAAC-
1 AACATAAATGAACG
**
2940519 ACACATAAACAAACG
1 A-ACATAAATGAACG
2940534 AACATAAATGAACG
1 AACATAAATGAACG
2940548 AACATAAA
1 AACATAAA
2940556 CAAACATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 1 0.03
14 29 0.94
15 1 0.03
ACGTcount: A:0.62, C:0.18, G:0.08, T:0.12
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:2940539 original size:28 final size:28
Alignment explanation
Indices: 2940506--2940560 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
2940496 GATTGAGCTA
2940506 AACATAAATGAAC-ACACATAAACAAACG
1 AACATAAATGAACGA-ACATAAACAAACG
2940534 AACATAAATGAACGAACATAAACAAAC
1 AACATAAATGAACGAACATAAACAAAC
2940561 ATAAATGAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 25 0.96
29 1 0.04
ACGTcount: A:0.62, C:0.20, G:0.07, T:0.11
Consensus pattern (28 bp):
AACATAAATGAACGAACATAAACAAACG
Found at i:2940556 original size:24 final size:24
Alignment explanation
Indices: 2940505--2940575 Score: 81
Period size: 28 Copynumber: 2.8 Consensus size: 24
2940495 AGATTGAGCT
2940505 AAACATAAATGAAC-ACACATAAAC
1 AAACATAAATGAACGA-ACATAAAC
2940529 AAACGAACATAAATGAACGAACATAAAC
1 --A--AACATAAATGAACGAACATAAAC
*
2940557 AAACATAAATGAACTAACA
1 AAACATAAATGAACGAACA
2940576 CATTATCTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
24 17 0.41
26 2 0.05
28 21 0.51
29 1 0.02
ACGTcount: A:0.62, C:0.18, G:0.07, T:0.13
Consensus pattern (24 bp):
AAACATAAATGAACGAACATAAAC
Found at i:2942326 original size:97 final size:97
Alignment explanation
Indices: 2942160--2942354 Score: 381
Period size: 97 Copynumber: 2.0 Consensus size: 97
2942150 GTACTCCGCA
2942160 AGCAACGCCGAAGGAACTCCCAACTGATTTCGAAAATGCATAGGATTAATTCCTTTAACCTAAAA
1 AGCAACGCCGAAGGAACTCCCAACTGATTTCGAAAATGCATAGGATTAATTCCTTTAACCTAAAA
2942225 TTGTGAGTAACATAGTGAACTTTGGGAAAGCT
66 TTGTGAGTAACATAGTGAACTTTGGGAAAGCT
*
2942257 AGCAACGCCGAAGGAACTCCCAACTGATTTCGATAATGCATAGGATTAATTCCTTTAACCTAAAA
1 AGCAACGCCGAAGGAACTCCCAACTGATTTCGAAAATGCATAGGATTAATTCCTTTAACCTAAAA
2942322 TTGTGAGTAACATAGTGAACTTTGGGAAAGCT
66 TTGTGAGTAACATAGTGAACTTTGGGAAAGCT
2942354 A
1 A
2942355 AATAATACCA
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 97 1.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.26
Consensus pattern (97 bp):
AGCAACGCCGAAGGAACTCCCAACTGATTTCGAAAATGCATAGGATTAATTCCTTTAACCTAAAA
TTGTGAGTAACATAGTGAACTTTGGGAAAGCT
Found at i:2943265 original size:25 final size:25
Alignment explanation
Indices: 2943237--2943284 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
2943227 CATTTTCAAA
*
2943237 TCAAATCAGATAAAATAGTCATAAT
1 TCAAATCAGATAAAATAATCATAAT
*
2943262 TCAAATCATATAAAATAATCATA
1 TCAAATCAGATAAAATAATCATA
2943285 TAGCACACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.54, C:0.12, G:0.04, T:0.29
Consensus pattern (25 bp):
TCAAATCAGATAAAATAATCATAAT
Found at i:2944908 original size:16 final size:16
Alignment explanation
Indices: 2944887--2944959 Score: 112
Period size: 16 Copynumber: 4.6 Consensus size: 16
2944877 GTCTCCAACG
2944887 TTTATGTTCGTGTTCT
1 TTTATGTTCGTGTTCT
*
2944903 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCT
2944919 TTTATGTTCGTGTT-T
1 TTTATGTTCGTGTTCT
*
2944934 GTTTATGTTCGTGTTCG
1 -TTTATGTTCGTGTTCT
2944951 TTTATGTTC
1 TTTATGTTC
2944960 ATTTATTTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.08, C:0.11, G:0.21, T:0.60
Consensus pattern (16 bp):
TTTATGTTCGTGTTCT
Found at i:2946185 original size:18 final size:20
Alignment explanation
Indices: 2946144--2946186 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
2946134 CATATATTTA
2946144 CATTTTAGTTACTAATTTTC
1 CATTTTAGTTACTAATTTTC
* *
2946164 CATTTT-GTTA-TTATTTTG
1 CATTTTAGTTACTAATTTTC
2946182 CATTT
1 CATTT
2946187 GGTGCTCTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 11 0.52
19 4 0.19
20 6 0.29
ACGTcount: A:0.21, C:0.12, G:0.07, T:0.60
Consensus pattern (20 bp):
CATTTTAGTTACTAATTTTC
Found at i:2946659 original size:30 final size:30
Alignment explanation
Indices: 2946625--2946681 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
2946615 TATATTTTTG
*
2946625 TTATTTGCATGTATGCACTTTATTTTTCTT
1 TTATTTACATGTATGCACTTTATTTTTCTT
*
2946655 TTATTTACATTTATGCACTTTATTTTT
1 TTATTTACATGTATGCACTTTATTTTT
2946682 TTGTTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.19, C:0.12, G:0.07, T:0.61
Consensus pattern (30 bp):
TTATTTACATGTATGCACTTTATTTTTCTT
Found at i:2947830 original size:91 final size:91
Alignment explanation
Indices: 2947675--2947857 Score: 366
Period size: 91 Copynumber: 2.0 Consensus size: 91
2947665 AAATTAAGTT
2947675 AAATCGATCTCCTCTTGGCCCCAAAAAAGCTTAAGGATCGTTGTAACAATATACCCAATTTAAGT
1 AAATCGATCTCCTCTTGGCCCCAAAAAAGCTTAAGGATCGTTGTAACAATATACCCAATTTAAGT
2947740 TGGTAAATCATCATTGAAAGAAGTAG
66 TGGTAAATCATCATTGAAAGAAGTAG
2947766 AAATCGATCTCCTCTTGGCCCCAAAAAAGCTTAAGGATCGTTGTAACAATATACCCAATTTAAGT
1 AAATCGATCTCCTCTTGGCCCCAAAAAAGCTTAAGGATCGTTGTAACAATATACCCAATTTAAGT
2947831 TGGTAAATCATCATTGAAAGAAGTAG
66 TGGTAAATCATCATTGAAAGAAGTAG
2947857 A
1 A
2947858 TGATTAGAAA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 92 1.00
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (91 bp):
AAATCGATCTCCTCTTGGCCCCAAAAAAGCTTAAGGATCGTTGTAACAATATACCCAATTTAAGT
TGGTAAATCATCATTGAAAGAAGTAG
Found at i:2959421 original size:60 final size:61
Alignment explanation
Indices: 2959314--2959442 Score: 138
Period size: 60 Copynumber: 2.1 Consensus size: 61
2959304 TAAGTGACTA
*
2959314 TTTAGTAACTTTTAATAGTCAAGGGACTCGACAAACCAACTCTCTATAGTCA-GAGGACCAT
1 TTTA-TAACTTTTAATAGTCAAGGGACTCAACAAACCAACTCTCTATAGTCATGAGGACCAT
* * * * * *
2959375 TTTATAACTTTTAATAGTTAGGGGACTTAACAAAGCGATA-TC-CTATAGTTATGGGGACCAT
1 TTTATAACTTTTAATAGTCAAGGGACTCAACAAA-CCA-ACTCTCTATAGTCATGAGGACCAT
2959436 TTGTATA
1 TT-TATA
2959443 TTTTACCTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
60 34 0.60
61 18 0.32
62 5 0.09
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (61 bp):
TTTATAACTTTTAATAGTCAAGGGACTCAACAAACCAACTCTCTATAGTCATGAGGACCAT
Found at i:2960194 original size:20 final size:20
Alignment explanation
Indices: 2960171--2960222 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
2960161 AACGCGATCC
2960171 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
2960191 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
2960211 CCAAAATCGCAA
1 CCAGAATCGCAA
2960223 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:2960303 original size:20 final size:20
Alignment explanation
Indices: 2960278--2960471 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
2960268 GATTTTCCAT
* *
2960278 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
2960298 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
2960318 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
2960338 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
2960358 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
2960378 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
2960398 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
2960418 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
2960439 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
2960459 AATCGCAACGCGA
1 AATCGCAACGCGA
2960472 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:2960323 original size:40 final size:39
Alignment explanation
Indices: 2960274--2960471 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
2960264 TTGCGATTTT
* ** *
2960274 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
2960312 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
2960353 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
2960393 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
2960432 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
2960472 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:2960361 original size:60 final size:60
Alignment explanation
Indices: 2960278--2960470 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
2960268 GATTTTCCAT
* ** * *
2960278 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
2960338 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
2960398 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
2960459 AATCGCAACGCG
1 AATCGCAACGCG
2960471 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:2960901 original size:32 final size:32
Alignment explanation
Indices: 2960848--2960917 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
2960838 TTCACTTAGA
*
2960848 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTA-GATTCTCTCGTTGCGAT
2960881 TTTCATTTCGCGTT-GTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTAG-ATTCTCTCGTTGCGAT
2960913 TTTCA
1 TTTCA
2960918 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
31 1 0.03
32 20 0.57
33 14 0.40
ACGTcount: A:0.11, C:0.21, G:0.19, T:0.49
Consensus pattern (32 bp):
TTTCATTTCGCGTTAGATTCTCTCGTTGCGAT
Found at i:2961056 original size:14 final size:14
Alignment explanation
Indices: 2961037--2961091 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
2961027 GAGATGACTG
2961037 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
2961051 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
2961070 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
2961084 TCGCAACG
1 TCGCAACG
2961092 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:2961058 original size:33 final size:33
Alignment explanation
Indices: 2961016--2961107 Score: 130
Period size: 33 Copynumber: 2.8 Consensus size: 33
2961006 GATAAATGAA
* ***
2961016 AATCGCAACGCGAGATGACTGTCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
2961049 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
**
2961082 AATCGCAACGCGAAACCAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCGCA
2961108 TTGCGATTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.41, C:0.25, G:0.24, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:2961125 original size:19 final size:18
Alignment explanation
Indices: 2961103--2961199 Score: 84
Period size: 19 Copynumber: 5.7 Consensus size: 18
2961093 GAAACCAAAA
*
2961103 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
2961122 TCGCGTTGCGA-TTC---
1 TCGCGTTGCGATTTCATT
*
2961136 TCTCGTTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
2961154 TCGCGTTGCGA-TTC---
1 TCGCGTTGCGATTTCATT
* *
2961168 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATT-TCATT
2961187 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2961200 CTCTCGTTGC
Statistics
Matches: 64, Mismatches: 5, Indels: 18
0.74 0.06 0.21
Matches are distributed among these distances:
14 20 0.31
15 4 0.06
16 2 0.03
17 6 0.09
18 10 0.16
19 22 0.34
ACGTcount: A:0.10, C:0.25, G:0.23, T:0.42
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:2961144 original size:14 final size:14
Alignment explanation
Indices: 2961125--2961213 Score: 88
Period size: 14 Copynumber: 5.7 Consensus size: 14
2961115 TTTCATTTCG
2961125 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2961139 CGTTGCGATTTCATTTCG
1 CGTTGCGA-TTC---TCT
2961157 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2961171 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
2961188 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
2961204 CGTTGCGATT
1 CGTTGCGATT
2961214 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 18
0.76 0.02 0.21
Matches are distributed among these distances:
14 28 0.44
15 4 0.06
16 5 0.08
17 8 0.12
18 11 0.17
19 8 0.12
ACGTcount: A:0.09, C:0.26, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2961196 original size:33 final size:33
Alignment explanation
Indices: 2961108--2961221 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
2961098 CAAAATCGCA
2961108 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2961141 TTGCGA-TTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
2961173 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2961206 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2961222 AACCAAAAGA
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
32 32 0.42
33 44 0.58
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2963068 original size:92 final size:92
Alignment explanation
Indices: 2962896--2963444 Score: 956
Period size: 92 Copynumber: 6.1 Consensus size: 92
2962886 TAGATTGCTT
*
2962896 AGTAAATTT-ATCGGTTGCTGCCAA-TCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
2962959 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
2962987 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATATAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
2963052 TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
2963079 AGTAAATTTGTTCGGTTGCTGCCAATTCTACTAAACTGTGTATTCTTTAACACTGTG-AA-ATAG
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
2963142 TTGTCTTTG--TTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
2963167 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATA-
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
2963231 TT-TCTTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
*
2963257 AGTAAATTTGTTCGGTTG-TGCCAATTCTACTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
2963321 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2963349 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
*
2963414 TTGTCTTTGTTCTGTCTTTTGGTTG-A
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
2963440 AGTAA
1 AGTAA
2963445 TGCAATCCAT
Statistics
Matches: 439, Mismatches: 9, Indels: 20
0.94 0.02 0.04
Matches are distributed among these distances:
88 78 0.18
89 46 0.10
90 51 0.12
91 19 0.04
92 168 0.38
93 77 0.18
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (92 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
TTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2963404 original size:270 final size:274
Alignment explanation
Indices: 2962896--2963444 Score: 961
Period size: 270 Copynumber: 2.0 Consensus size: 274
2962886 TAGATTGCTT
2962896 AGTAAATTTATCGGTTGCTGCCAATCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATT
1 AGTAAATTTATCGGTTGCTGCCAATCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATT
*
2962961 TGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGT
66 TGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTACTAAACTGT
2963026 ATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTT
131 ATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTT
2963091 CGGTTGCTGCCAATTCTACTAAACTGTGTATTCTTTAACACTGTG-AA-ATAGTTGTCTTTG-T-
196 CGGTTGCTGCCAATTCTACTAAACTGTGTATTCTTTAACACTGTGAAATATAGTTGTCTTTGTTC
2963152 TGTCTTTTGGTTGAA
261 TGTCTTTTGGTTG-A
*
2963167 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTT-ATCGGTTGCTGCCAA-TCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2963231 -TT-TCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTG-TGCCAATTCTACTAAACT
64 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTACTAAACT
*
2963293 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
129 GTATATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
* *
2963358 GTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATATTTGTCTTTG
193 GTTCGGTTGCTGCCAATTCTACTAAACTGTGTATTCTTTAACACTGTGAAATATAGTTGTCTTTG
2963423 TTCTGTCTTTTGGTTGA
258 TTCTGTCTTTTGGTTGA
2963440 AGTAA
1 AGTAA
2963445 TGCAATCCAT
Statistics
Matches: 266, Mismatches: 5, Indels: 12
0.94 0.02 0.04
Matches are distributed among these distances:
269 41 0.15
270 128 0.48
271 13 0.05
272 28 0.11
273 43 0.16
274 13 0.05
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (274 bp):
AGTAAATTTATCGGTTGCTGCCAATCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATT
TGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTACTAAACTGT
ATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTT
CGGTTGCTGCCAATTCTACTAAACTGTGTATTCTTTAACACTGTGAAATATAGTTGTCTTTGTTC
TGTCTTTTGGTTGA
Found at i:2963537 original size:14 final size:14
Alignment explanation
Indices: 2963518--2963572 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
2963508 GAGATGACTG
2963518 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
2963532 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
2963551 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
2963565 TCGCAACG
1 TCGCAACG
2963573 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:2963539 original size:33 final size:33
Alignment explanation
Indices: 2963497--2963588 Score: 130
Period size: 33 Copynumber: 2.8 Consensus size: 33
2963487 GATAAATGAA
* ***
2963497 AATCGCAACGCGAGATGACTGTCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
2963530 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
**
2963563 AATCGCAACGCGAAACCAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCGCA
2963589 TTGCGATTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.41, C:0.25, G:0.24, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:2963606 original size:19 final size:19
Alignment explanation
Indices: 2963584--2963681 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 19
2963574 GAAACCAAAA
*
2963584 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2963603 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2963617 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
2963636 TCGCGTTGCG--CTTC---
1 TCGCGTTGCGATTTTCATT
* * *
2963650 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
2963669 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2963682 CTCTCGTTGC
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 19 0.31
16 5 0.08
17 6 0.10
19 31 0.51
ACGTcount: A:0.09, C:0.26, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Done.