Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008981.1 Hibiscus syriacus cultivar Beakdansim tig00112343_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: 1473337
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
File 4 of 7
Found at i:776345 original size:21 final size:21
Alignment explanation
Indices: 776295--776347 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
776285 AATCAGTTCC
776295 CAGAATCGCAATGCGATAGTA
1 CAGAATCGCAATGCGATAGTA
* ** *
776316 CA-AATTCGCATTGCGATTTTT
1 CAGAA-TCGCAATGCGATAGTA
776337 CAGAATCGCAA
1 CAGAATCGCAA
776348 CACGAATATG
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
20 2 0.08
21 21 0.84
22 2 0.08
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (21 bp):
CAGAATCGCAATGCGATAGTA
Found at i:776389 original size:20 final size:20
Alignment explanation
Indices: 776340--776389 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
776330 GATTTTTCAG
* *
776340 AATCGCAACACGAATATGAA
1 AATCGCAACGCGAACATGAA
776360 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGAACATGA-A
776380 AATCGCAACG
1 AATCGCAACG
776390 AGTATCCGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.46, C:0.24, G:0.16, T:0.14
Consensus pattern (20 bp):
AATCGCAACGCGAACATGAA
Found at i:776401 original size:20 final size:20
Alignment explanation
Indices: 776378--776592 Score: 205
Period size: 20 Copynumber: 10.6 Consensus size: 20
776368 CGCGAACATA
776378 TAAATCGCAACGAGTATCCG
1 TAAATCGCAACGAGTATCCG
*
776398 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACGAGTATCCG
** *
776419 TAAATCGCAACGAAAATACG
1 TAAATCGCAACGAGTATCCG
**
776439 TAAAATCGCAACGCTTATCCG
1 T-AAATCGCAACGAGTATCCG
* * *
776460 TAAATCGAAACGAGAATACG
1 TAAATCGCAACGAGTATCCG
* * *
776480 TAAATCGTAACGCGTATCTG
1 TAAATCGCAACGAGTATCCG
* *
776500 TAAATCGCAACGAGAATACG
1 TAAATCGCAACGAGTATCCG
* * *
776520 TAAATCGTAATGCGTATCCG
1 TAAATCGCAACGAGTATCCG
** *
776540 TAAATCGCAACGACAATACG
1 TAAATCGCAACGAGTATCCG
* *
776560 TAAAATCGTAACGCGTATCCG
1 T-AAATCGCAACGAGTATCCG
776581 TAAATCGCAACG
1 TAAATCGCAACG
776593 TGATTTTTAA
Statistics
Matches: 151, Mismatches: 41, Indels: 6
0.76 0.21 0.03
Matches are distributed among these distances:
20 101 0.67
21 50 0.33
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (20 bp):
TAAATCGCAACGAGTATCCG
Found at i:776503 original size:40 final size:41
Alignment explanation
Indices: 776378--776592 Score: 326
Period size: 41 Copynumber: 5.3 Consensus size: 41
776368 CGCGAACATA
* * *
776378 TAAATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCG
1 TAAATCGCAACGAGAATACGTAAAATCGTAACGCGTATCCG
* * *
776419 TAAATCGCAACGAAAATACGTAAAATCGCAACGCTTATCCG
1 TAAATCGCAACGAGAATACGTAAAATCGTAACGCGTATCCG
* *
776460 TAAATCGAAACGAGAATACGT-AAATCGTAACGCGTATCTG
1 TAAATCGCAACGAGAATACGTAAAATCGTAACGCGTATCCG
*
776500 TAAATCGCAACGAGAATACGT-AAATCGTAATGCGTATCCG
1 TAAATCGCAACGAGAATACGTAAAATCGTAACGCGTATCCG
*
776540 TAAATCGCAACGACAATACGTAAAATCGTAACGCGTATCCG
1 TAAATCGCAACGAGAATACGTAAAATCGTAACGCGTATCCG
776581 TAAATCGCAACG
1 TAAATCGCAACG
776593 TGATTTTTAA
Statistics
Matches: 159, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 73 0.46
41 86 0.54
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (41 bp):
TAAATCGCAACGAGAATACGTAAAATCGTAACGCGTATCCG
Found at i:776878 original size:33 final size:33
Alignment explanation
Indices: 776840--776933 Score: 145
Period size: 33 Copynumber: 2.8 Consensus size: 33
776830 TTCCAAATCG
776840 CGTTGCGATTTTCATTTCGC-TTTACGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTT-CGATTCCCT
*
776873 CGTTGCGATTTTCATTTCGCATTTCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTTCGATTCCCT
* *
776906 CGTTGCGATTTTCATTTCTCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTTCGAT
776934 AGTCATTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 54 0.95
34 3 0.05
ACGTcount: A:0.13, C:0.24, G:0.16, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTTCGATTCCCT
Found at i:776930 original size:19 final size:19
Alignment explanation
Indices: 776875--776933 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
776865 GATTCCCTCG
*
776875 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCTCA
* *
776894 TTTCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCTCA
776908 TTGCGATTTTCATTTCTCA
1 TTGCGATTTTCATTTCTCA
776927 TTGCGAT
1 TTGCGAT
776934 AGTCATTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
14 8 0.27
16 3 0.10
17 3 0.10
19 16 0.53
ACGTcount: A:0.14, C:0.22, G:0.15, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCTCA
Found at i:776939 original size:19 final size:19
Alignment explanation
Indices: 776903--776941 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
776893 ATTTCGATTC
* **
776903 TCTCGTTGCGATTTTCATT
1 TCTCATTGCGATAGTCATT
776922 TCTCATTGCGATAGTCATT
1 TCTCATTGCGATAGTCATT
776941 T
1 T
776942 TTGCCTTCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.21, G:0.15, T:0.49
Consensus pattern (19 bp):
TCTCATTGCGATAGTCATT
Found at i:778905 original size:94 final size:93
Alignment explanation
Indices: 778744--778965 Score: 338
Period size: 94 Copynumber: 2.4 Consensus size: 93
778734 TGTTTCAAAC
* * *
778744 TTAGCAGAATTGTA-AGCAACCGAACAAATTTACTTTCAACCAAAAGATAAAATAAAGACAAATA
1 TTAGCAGAATTG-ACAGCAACCGAATAAATTTAC-TTCAACCAAAAGACAAAAAAAAGACAAATA
*
778808 CTAACTTCACAGTGTTAAAGAATATACAGT
64 CTAACTTCACAGTGTTAAAGAATAAACAGT
*
778838 TTAGCAGAATTGACAACAACCGAATAAATTTACTTCAACCAAAAGACAAAACAAAAGACAAATAC
1 TTAGCAGAATTGACAGCAACCGAATAAATTTACTTCAACCAAAAGACAAAA-AAAAGACAAATAC
* *
778903 TAACTTTATAGTGTTAAAGAATAAACAGT
65 TAACTTCACAGTGTTAAAGAATAAACAGT
*
778932 TTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 TTAGCAGAATTGACAGCAACCGAATAAATTTACT
778966 AAGCAATCTA
Statistics
Matches: 117, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
93 18 0.15
94 99 0.85
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (93 bp):
TTAGCAGAATTGACAGCAACCGAATAAATTTACTTCAACCAAAAGACAAAAAAAAGACAAATACT
AACTTCACAGTGTTAAAGAATAAACAGT
Found at i:779210 original size:94 final size:94
Alignment explanation
Indices: 779049--779270 Score: 383
Period size: 94 Copynumber: 2.4 Consensus size: 94
779039 TAGATTGTTT
* *
779049 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTAAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTAAAGTTAGT
779114 ATTTGTCTTTTGTTTTGTCTTTTAGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTAGTTGAA
*
779143 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTAAAGTTAGT
*
779208 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTAGTTGAA
*
779237 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAA
779271 GTTTGAAACA
Statistics
Matches: 122, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
93 19 0.16
94 103 0.84
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.46
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTAAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTAGTTGAA
Found at i:781044 original size:34 final size:34
Alignment explanation
Indices: 780952--781037 Score: 165
Period size: 34 Copynumber: 2.6 Consensus size: 34
780942 TAAAAGTTGA
780952 TTTGTTTAATTGATGTGAACATAATTCTTATTTG
1 TTTGTTTAATTGATGTGAACATAATTCTTATTTG
780986 TTTGTTTAATTGATGTGAACATAATTCTTATTTG
1 TTTGTTTAATTGATGTGAACATAATTCTTATTTG
781020 TTTGTTTAATTGAT-TGAA
1 TTTGTTTAATTGATGTGAA
781038 ATATAATGGT
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 4 0.08
34 48 0.92
ACGTcount: A:0.27, C:0.05, G:0.15, T:0.53
Consensus pattern (34 bp):
TTTGTTTAATTGATGTGAACATAATTCTTATTTG
Found at i:781169 original size:19 final size:18
Alignment explanation
Indices: 781147--781235 Score: 68
Period size: 19 Copynumber: 5.2 Consensus size: 18
781137 CGAAACTAAA
781147 TTCGCATTGCGATTTTCAT
1 TTCGC-TTGCGATTTTCAT
*
781166 TTCGCTTTGCGA--TTC-C
1 TTCGC-TTGCGATTTTCAT
*
781182 CTCG-TTGCGATTTTCAT
1 TTCGCTTGCGATTTTCAT
781199 TTCGCATTGCGA--TTC-T
1 TTCGC-TTGCGATTTTCAT
*
781215 CTCG-TTGCGATTTTCAT
1 TTCGCTTGCGATTTTCAT
781232 TTCG
1 TTCG
781236 TATTACGATA
Statistics
Matches: 55, Mismatches: 7, Indels: 18
0.69 0.09 0.22
Matches are distributed among these distances:
14 12 0.22
16 13 0.24
17 13 0.24
19 17 0.31
ACGTcount: A:0.11, C:0.25, G:0.18, T:0.46
Consensus pattern (18 bp):
TTCGCTTGCGATTTTCAT
Found at i:781195 original size:33 final size:33
Alignment explanation
Indices: 781153--781244 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
781143 TAAATTCGCA
*
781153 TTGCGATTTTCATTTCGCTTTGCGATTCCCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCCCTCG
*
781186 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCCCTCG
* *
781219 TTGCGATTTTCATTTCGTATTACGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
781245 AGTTATTTCC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCCCTCG
Found at i:783761 original size:24 final size:24
Alignment explanation
Indices: 783734--783780 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
783724 CAAAATCCGA
783734 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
* *
783758 GTATTGACCAATATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
783781 AATACTGACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:783789 original size:24 final size:24
Alignment explanation
Indices: 783738--783789 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
783728 ATCCGAGTAT
** *
783738 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
* *
783762 TGACCAATATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
783786 TGAC
1 TGAC
783790 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:784662 original size:21 final size:21
Alignment explanation
Indices: 784638--784683 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
784628 TATTCGCATT
784638 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
784659 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
784680 GCGA
1 GCGA
784684 TAGTTAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:784755 original size:19 final size:19
Alignment explanation
Indices: 784731--784773 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
784721 CGATACCGGA
784731 GATCGCGTTGCGAATTATC
1 GATCGCGTTGCGAATTATC
784750 GATCGCGTTGCGAATTATC
1 GATCGCGTTGCGAATTATC
784769 GATCG
1 GATCG
784774 TATTGCGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (19 bp):
GATCGCGTTGCGAATTATC
Found at i:784779 original size:19 final size:19
Alignment explanation
Indices: 784731--784781 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
784721 CGATACCGGA
*
784731 GATCGCGTTGCGAATTATC
1 GATCGCATTGCGAATTATC
*
784750 GATCGCGTTGCGAATTATC
1 GATCGCATTGCGAATTATC
*
784769 GATCGTATTGCGA
1 GATCGCATTGCGA
784782 TTTAGTTGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (19 bp):
GATCGCATTGCGAATTATC
Found at i:785732 original size:2 final size:2
Alignment explanation
Indices: 785725--785804 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
785715 CAAAGAATAC
785725 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
785767 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
785805 GTATGTATTT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:790205 original size:14 final size:14
Alignment explanation
Indices: 790186--790214 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
790176 TTGTGCATTG
790186 CCATATGAACCTTA
1 CCATATGAACCTTA
790200 CCATATGAACCTTA
1 CCATATGAACCTTA
790214 C
1 C
790215 TTGGTATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.31, G:0.07, T:0.28
Consensus pattern (14 bp):
CCATATGAACCTTA
Found at i:793903 original size:41 final size:42
Alignment explanation
Indices: 793858--793937 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
793848 TTAATAGTGA
*
793858 GAAAATA-TTTTCAGTGTTTGATAGTTGTAATTGGTTTTACG
1 GAAAATATTTTTCAGTGTTTGATAGTTGTAATTGATTTTACG
793899 GAAAATATTTTTCAGTGTTTGATAGTTGTAATTGATTTT
1 GAAAATATTTTTCAGTGTTTGATAGTTGTAATTGATTTT
793938 TCCCATATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
41 7 0.19
42 30 0.81
ACGTcount: A:0.28, C:0.04, G:0.20, T:0.49
Consensus pattern (42 bp):
GAAAATATTTTTCAGTGTTTGATAGTTGTAATTGATTTTACG
Found at i:794164 original size:17 final size:17
Alignment explanation
Indices: 794117--794172 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 17
794107 AAATACTCAT
794117 TATTAA-AATATT-TAA
1 TATTAATAATATTATAA
*
794132 TATTACAT-ATAATATAA
1 TATTA-ATAATATTATAA
*
794149 TTTTAATAATATTAT-A
1 TATTAATAATATTATAA
794165 TATTAATA
1 TATTAATA
794173 TATACCTAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
15 5 0.15
16 15 0.45
17 13 0.39
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
TATTAATAATATTATAA
Found at i:794242 original size:26 final size:29
Alignment explanation
Indices: 794188--794248 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 29
794178 CTAGATATAT
* *
794188 TATAATAATATATGATATTATATTTTTAA
1 TATAATAATATATGATATTAAATTATTAA
*
794217 TTTAATAATATAT-A-A-TAAATTATTAA
1 TATAATAATATATGATATTAAATTATTAA
794243 TATAAT
1 TATAAT
794249 TCATATTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 14 0.50
27 1 0.04
28 1 0.04
29 12 0.43
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (29 bp):
TATAATAATATATGATATTAAATTATTAA
Found at i:794342 original size:19 final size:19
Alignment explanation
Indices: 794304--794349 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
794294 TAATAATGAG
*
794304 TAATATTAATTTATATATT
1 TAATATTAATTAATATATT
794323 TAATATTAATATAATA-ATT
1 TAATATTAAT-TAATATATT
*
794342 TAGTATTA
1 TAATATTA
794350 TGTTAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TAATATTAATTAATATATT
Found at i:794356 original size:30 final size:27
Alignment explanation
Indices: 794310--794371 Score: 72
Period size: 30 Copynumber: 2.2 Consensus size: 27
794300 TGAGTAATAT
*
794310 TAATTTATATATTTAATATTAATA-TAA
1 TAATTTATATATTTAATA-AAATACTAA
794337 TAATTTAGTATTATGTTAATAAAATACTAA
1 TAATTTA-TA-TAT-TTAATAAAATACTAA
794367 TAATT
1 TAATT
794372 AAAATTAAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 7 0.23
28 2 0.07
29 7 0.23
30 14 0.47
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (27 bp):
TAATTTATATATTTAATAAAATACTAA
Found at i:800444 original size:21 final size:20
Alignment explanation
Indices: 800419--800472 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
800409 CATAATTTAA
800419 AAATAATATAAATAGATATCT
1 AAATAATATAAA-AGATATCT
* * *
800440 AAATAAAATCAAAAGTTCTCT
1 AAATAATAT-AAAAGATATCT
800461 AAATAAT-TAAAA
1 AAATAATATAAAA
800473 AAATTAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 4 0.14
20 1 0.04
21 20 0.71
22 3 0.11
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.30
Consensus pattern (20 bp):
AAATAATATAAAAGATATCT
Found at i:800947 original size:45 final size:45
Alignment explanation
Indices: 800868--800954 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 45
800858 GAATTAATCA
* *
800868 TTTAATTTTATCAAATCTAATAATCAAAAGGAACTAATCATTTGAT
1 TTTAATTTTAT-AAATCCAATAATCAAAAGGAACTAAGCATTTGAT
* *
800914 TTTAATTTTCAT-AATCCAATGATCGAAAGGAACTAAGCATT
1 TTTAATTTT-ATAAATCCAATAATCAAAAGGAACTAAGCATT
800955 GTACATATTC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
45 25 0.69
46 9 0.25
47 2 0.06
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (45 bp):
TTTAATTTTATAAATCCAATAATCAAAAGGAACTAAGCATTTGAT
Found at i:806314 original size:16 final size:16
Alignment explanation
Indices: 806279--806311 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
806269 ACTTGTTATC
*
806279 TTAAAAAAATATTTCA
1 TTAAAAAAATATTTAA
806295 TTAAAAAAATA-TTAA
1 TTAAAAAAATATTTAA
806310 TT
1 TT
806312 TAATAATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
TTAAAAAAATATTTAA
Found at i:807478 original size:13 final size:13
Alignment explanation
Indices: 807457--807501 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
807447 TGAAAGTTAG
807457 TAAAAAAAAGAAA
1 TAAAAAAAAGAAA
*
807470 -AAGAAAAAATAAA
1 TAA-AAAAAAGAAA
*
807483 TAAAAAAAATAAA
1 TAAAAAAAAGAAA
807496 TAAAAA
1 TAAAAA
807502 GGACCAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 2 0.07
13 25 0.86
14 2 0.07
ACGTcount: A:0.84, C:0.00, G:0.04, T:0.11
Consensus pattern (13 bp):
TAAAAAAAAGAAA
Found at i:807487 original size:17 final size:16
Alignment explanation
Indices: 807458--807499 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
807448 GAAAGTTAGT
807458 AAAAA-AAAGAAAAAGA
1 AAAAATAAAGAAAAA-A
*
807474 AAAAATAAATAAAAAA
1 AAAAATAAAGAAAAAA
807490 AATAAATAAA
1 AA-AAATAAA
807500 AAGGACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.86, C:0.00, G:0.05, T:0.10
Consensus pattern (16 bp):
AAAAATAAAGAAAAAA
Found at i:816104 original size:14 final size:15
Alignment explanation
Indices: 816085--816114 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
816075 AATTAAAATA
816085 AAATTGT-AAAATTT
1 AAATTGTAAAAATTT
816099 AAATTGTAAAAATTT
1 AAATTGTAAAAATTT
816114 A
1 A
816115 TATTACTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (15 bp):
AAATTGTAAAAATTT
Found at i:818306 original size:43 final size:41
Alignment explanation
Indices: 818185--818324 Score: 129
Period size: 43 Copynumber: 3.2 Consensus size: 41
818175 GCTAAAGTTC
* ** *
818185 GCGGCGTTTGTTAACGAAAAACGCCGCAATAGGTGACGATATATA
1 GCGGCGTTTGTT---GAAAAACACCGCAATAGGTGTTG-TATTTA
*
818230 GCAGCGTTTGTTGAAAAA-ACGCTGCAATAGGTGTTGCTATTTA
1 GCGGCGTTTGTTGAAAAACAC-C-GCAATAGGTGTTG-TATTTA
* *
818273 GCGGCGTTTGTCTTAAAAACACCGCAATAGGTGTTGTCGTTTA
1 GCGGCGTTTGT-TGAAAAACACCGCAATAGGTGTTGT-ATTTA
818316 GCGGCGTTT
1 GCGGCGTTT
818325 TTCCCCCAAA
Statistics
Matches: 81, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
41 1 0.01
42 8 0.10
43 52 0.64
44 7 0.09
45 13 0.16
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.29
Consensus pattern (41 bp):
GCGGCGTTTGTTGAAAAACACCGCAATAGGTGTTGTATTTA
Found at i:818336 original size:86 final size:86
Alignment explanation
Indices: 818246--818413 Score: 210
Period size: 86 Copynumber: 2.0 Consensus size: 86
818236 TTTGTTGAAA
* * * **
818246 AAACGCTGCAATAGGTGTTGCTATTTAGCGGCGTTTGTCTTAAAAACACCGCAATAGGTGTTGTC
1 AAACGCCGCAATAGGTATCGCTATTTAGCGGCGTTTGTCCCAAAAACACCGCAATAGGTGTTGTC
818311 GTTTAGCGGCGTTTTTCCCCC
66 GTTTAGCGGCGTTTTTCCCCC
* * * * *** *
818332 AAACGCCGCAGTAGGTATCGTTGTTTAGCGGCGTTTTTCCCAAAAATGTCGCAATAGGTGTTGTT
1 AAACGCCGCAATAGGTATCGCTATTTAGCGGCGTTTGTCCCAAAAACACCGCAATAGGTGTTGTC
*
818397 GTTTAGCGGTGTTTTTC
66 GTTTAGCGGCGTTTTTC
818414 AAACAAGCGC
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
86 68 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.35
Consensus pattern (86 bp):
AAACGCCGCAATAGGTATCGCTATTTAGCGGCGTTTGTCCCAAAAACACCGCAATAGGTGTTGTC
GTTTAGCGGCGTTTTTCCCCC
Found at i:818341 original size:43 final size:43
Alignment explanation
Indices: 818244--818430 Score: 182
Period size: 43 Copynumber: 4.3 Consensus size: 43
818234 CGTTTGTTGA
* * * **
818244 AAAAACGCTGCAATAGGTGTTG-CTATTTAGCGGCGTTTGTCTT
1 AAAAACGCCGCAATAGGTGTTGTC-GTTTAGCGGCGTTTTTCCC
*
818287 AAAAACACCGCAATAGGTGTTGTCGTTTAGCGGCGTTTTTCCC
1 AAAAACGCCGCAATAGGTGTTGTCGTTTAGCGGCGTTTTTCCC
** * * * *
818330 CCAAACGCCGCAGTAGGTATCGTTGTTTAGCGGCGTTTTTCCC
1 AAAAACGCCGCAATAGGTGTTGTCGTTTAGCGGCGTTTTTCCC
* * * *
818373 AAAAATGTCGCAATAGGTGTTGTTGTTTAGCGGTGTTTTT--C
1 AAAAACGCCGCAATAGGTGTTGTCGTTTAGCGGCGTTTTTCCC
818414 AAACAAGCGCCGCAATA
1 AAA-AA-CGCCGCAATA
818431 AGCGTTGAGA
Statistics
Matches: 118, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
41 4 0.03
42 2 0.02
43 111 0.94
44 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.32
Consensus pattern (43 bp):
AAAAACGCCGCAATAGGTGTTGTCGTTTAGCGGCGTTTTTCCC
Found at i:818450 original size:86 final size:86
Alignment explanation
Indices: 818295--818455 Score: 193
Period size: 86 Copynumber: 1.9 Consensus size: 86
818285 TTAAAAACAC
*** * * *
818295 CGCAATAGGTGTTGTCGTTTAGCGGCGTTTTTCCCCCAAACGCCGCAGTAGGTATCGTTGTTTAG
1 CGCAATAGGTGTTGTCGTTTAGCGGCGTTTTTCAAACAAACGCCGCAATAGGTATCGTAGTTTAA
818360 CGGCGTTTTTCCCAAAAATGT
66 CGGCGTTTTTCCCAAAAATGT
* * *
818381 CGCAATAGGTGTTGTTGTTTAGCGGTGTTTTTCAAACAAGCGCCGCAATAAGCGT-T-G-AGATT
1 CGCAATAGGTGTTGTCGTTTAGCGGCGTTTTTCAAACAAACGCCGCAAT-AG-GTATCGTAG-TT
818443 TAACGGCGTTTTT
63 TAACGGCGTTTTT
818456 ATCGAAAACG
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
85 1 0.02
86 57 0.90
87 3 0.05
88 2 0.03
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (86 bp):
CGCAATAGGTGTTGTCGTTTAGCGGCGTTTTTCAAACAAACGCCGCAATAGGTATCGTAGTTTAA
CGGCGTTTTTCCCAAAAATGT
Found at i:820253 original size:22 final size:22
Alignment explanation
Indices: 820225--820271 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
820215 GCTTTACAAA
820225 AAGTAAACATTCAAGGATCAAG
1 AAGTAAACATTCAAGGATCAAG
820247 AAGTAAACATTCAAGGATCAAG
1 AAGTAAACATTCAAGGATCAAG
820269 AAG
1 AAG
820272 GCTTTACAAA
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:0.51, C:0.13, G:0.19, T:0.17
Consensus pattern (22 bp):
AAGTAAACATTCAAGGATCAAG
Found at i:822282 original size:41 final size:41
Alignment explanation
Indices: 822187--822467 Score: 293
Period size: 41 Copynumber: 6.8 Consensus size: 41
822177 ACAATCAAAT
*
822187 TACGAGTCTATAGCGGCGTTTG-GTATTAAAACGCCACAAAAG
1 TACGAGTCTATAGCGGCGTTTGTGTA--AAAACGCCACTAAAG
* * *
822229 TACGTGTCTATAGCGGCGTTTGTGTAAAAATGTCACTAAAG
1 TACGAGTCTATAGCGGCGTTTGTGTAAAAACGCCACTAAAG
*
822270 TACGAGTCTATAGCGGCGTTTG-GTATTAAAACGCCACAAAAG
1 TACGAGTCTATAGCGGCGTTTGTGTA--AAAACGCCACTAAAG
*
822312 TAC-ATGTCTATAGCGGCGTTTGTGTAAAAACGCCACTAAAA
1 TACGA-GTCTATAGCGGCGTTTGTGTAAAAACGCCACTAAAG
* * * * *
822353 TACTAGTTTATAGCGGCGTTTGTATAAAAACGCCACTACAT
1 TACGAGTCTATAGCGGCGTTTGTGTAAAAACGCCACTAAAG
* * * * *
822394 TACGATTCTTTAGCGGCGTTTTTATACAAACGCCACTAAAG
1 TACGAGTCTATAGCGGCGTTTGTGTAAAAACGCCACTAAAG
* * * *
822435 TA-TAGTATTTTGCGGCGTTTGT-TCAAAAACGCC
1 TACGAGTCTATAGCGGCGTTTGTGT-AAAAACGCC
822468 GCTACATCCG
Statistics
Matches: 204, Mismatches: 28, Indels: 16
0.82 0.11 0.06
Matches are distributed among these distances:
39 1 0.00
40 26 0.13
41 117 0.57
42 54 0.26
43 6 0.03
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (41 bp):
TACGAGTCTATAGCGGCGTTTGTGTAAAAACGCCACTAAAG
Found at i:822284 original size:83 final size:83
Alignment explanation
Indices: 822187--822433 Score: 345
Period size: 83 Copynumber: 3.0 Consensus size: 83
822177 ACAATCAAAT
822187 TACGAGTCTATAGCGGCGTTTGGTATTAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTTGT
1 TACGAGTCTATAGCGGCGTTTGGTATTAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTTGT
* * *
822252 GTAAAAATGTCACTAAAG
66 GTAAAAACGCCACTAAAA
*
822270 TACGAGTCTATAGCGGCGTTTGGTATTAAAACGCCACAAAAGTACATGTCTATAGCGGCGTTTGT
1 TACGAGTCTATAGCGGCGTTTGGTATTAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTTGT
822335 GTAAAAACGCCACTAAAA
66 GTAAAAACGCCACTAAAA
* * * * * * * *
822353 TACTAGTTTATAGCGGCGTTT-GTATAAAAACGCCACTACATTACGAT-TCTTTAGCGGCGTTTT
1 TACGAGTCTATAGCGGCGTTTGGTATTAAAACGCCACAAAAGTACG-TGTCTATAGCGGCGTTTG
* *
822416 TATACAAACGCCACTAAA
65 TGTAAAAACGCCACTAAA
822434 GTATAGTATT
Statistics
Matches: 148, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
82 49 0.33
83 99 0.67
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (83 bp):
TACGAGTCTATAGCGGCGTTTGGTATTAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTTGT
GTAAAAACGCCACTAAAA
Found at i:822373 original size:124 final size:122
Alignment explanation
Indices: 822191--822467 Score: 321
Period size: 124 Copynumber: 2.2 Consensus size: 122
822181 TCAAATTACG
*
822191 AGTCTATAGCGGCGTTTG-GTATTAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTTGTGTA
1 AGTCTATAGCGGCGTTTGTGTA--AAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTTGTATA
* *
822255 AAAATGTCACTAAAGTACGAGTCTATAGCGGCGTTTGGTATTA-AAACGCCACAAAAGTAC
64 AAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTT-GTA-TACAAACGCCACAAAAGTAC
*
822315 ATGTCTATAGCGGCGTTTGTGTAAAAACGCCACTAAAA-TAC-TAGTTTATAGCGGCGTTTGTAT
1 A-GTCTATAGCGGCGTTTGTGTAAAAACGCCAC-AAAAGTACGT-GTCTATAGCGGCGTTTGTAT
* * * * * * *
822378 AAAAACGCCACTACATTACGATTCTTTAGCGGCGTTTTTATACAAACGCCACTAAAGTAT
63 AAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATACAAACGCCACAAAAGTAC
* * *
822438 AGTATTTTGCGGCGTTTGT-TCAAAAACGCC
1 AGTCTATAGCGGCGTTTGTGT-AAAAACGCC
822468 GCTACATCCG
Statistics
Matches: 133, Mismatches: 14, Indels: 14
0.83 0.09 0.09
Matches are distributed among these distances:
121 1 0.01
122 26 0.20
123 19 0.14
124 63 0.47
125 21 0.16
126 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (122 bp):
AGTCTATAGCGGCGTTTGTGTAAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTTGTATAAA
AACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATACAAACGCCACAAAAGTAC
Found at i:822473 original size:81 final size:82
Alignment explanation
Indices: 822195--822474 Score: 273
Period size: 83 Copynumber: 3.4 Consensus size: 82
822185 ATTACGAGTC
* * * * * *
822195 TATAGCGGCGTTTGGTATTAAAACGCCACAAAAGTACG-TGTCTATAGCGGCGTTTGTGTAAAAA
1 TATAGCGGCGTTT-GTATAAAAACGCCACTACATTACGAT-TCTTTAGCGGCGTTTGTATAAAAA
* * * * *
822259 TGTCACTAAAGTACGAGTC
64 CGCCACTAAAATACTAGTT
* * * * * *
822278 TATAGCGGCGTTTGGTATTAAAACGCCACAAAAGTAC-ATGTCTATAGCGGCGTTTGTGTAAAAA
1 TATAGCGGCGTTT-GTATAAAAACGCCACTACATTACGAT-TCTTTAGCGGCGTTTGTATAAAAA
822342 CGCCACTAAAATACTAGTT
64 CGCCACTAAAATACTAGTT
* *
822361 TATAGCGGCGTTTGTATAAAAACGCCACTACATTACGATTCTTTAGCGGCGTTTTTATACAAACG
1 TATAGCGGCGTTTGTATAAAAACGCCACTACATTACGATTCTTTAGCGGCGTTTGTATAAAAACG
*
822426 CCACTAAAGTA-TAGTAT
66 CCACTAAAATACTAGT-T
* *
822443 T-TTGCGGCGTTTGT-TCAAAAACGCCGCTACAT
1 TATAGCGGCGTTTGTAT-AAAAACGCCACTACAT
822475 CCGCCGCTAA
Statistics
Matches: 177, Mismatches: 16, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
80 1 0.01
81 31 0.18
82 53 0.30
83 92 0.52
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (82 bp):
TATAGCGGCGTTTGTATAAAAACGCCACTACATTACGATTCTTTAGCGGCGTTTGTATAAAAACG
CCACTAAAATACTAGTT
Found at i:830050 original size:78 final size:79
Alignment explanation
Indices: 829910--830068 Score: 257
Period size: 78 Copynumber: 2.0 Consensus size: 79
829900 TGGAAAAAAT
* * *
829910 AACATTTTAGGTAGCGTCCAATATTAACATTTCCGGTAGAAAAAATAATGTTTTAGGTAGCGTTT
1 AACATTTTAAGTAGCGCCCAATATTAACATTTCCAGTAGAAAAAATAATGTTTTAGGTAGCGTTT
** *
829975 TTTCGGAAATGTTA
66 TACCGAAAATGTTA
829989 AACATTTTAAGTAGCGCCCAATATTAACATTTCCAGTAG-AAAAATAATGTTTTAGGTAGCGTTT
1 AACATTTTAAGTAGCGCCCAATATTAACATTTCCAGTAGAAAAAATAATGTTTTAGGTAGCGTTT
830053 TACCGAAAATGTTA
66 TACCGAAAATGTTA
830067 AA
1 AA
830069 AAATATATTA
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
78 38 0.51
79 36 0.49
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.35
Consensus pattern (79 bp):
AACATTTTAAGTAGCGCCCAATATTAACATTTCCAGTAGAAAAAATAATGTTTTAGGTAGCGTTT
TACCGAAAATGTTA
Found at i:830519 original size:31 final size:29
Alignment explanation
Indices: 830450--830519 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 29
830440 CATCGATTAT
830450 TAAAAGTTA-TTAAATGATCATCCGACTA
1 TAAAAGTTACTTAAATGATCATCCGACTA
* *
830478 TAGAATGTTACTTTAATGACTC-TCTCGACTA
1 TA-AAAGTTACTTAAATGA-TCATC-CGACTA
830509 CTAAAAGTTAC
1 -TAAAAGTTAC
830520 AAATCATCTG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
28 2 0.06
29 6 0.18
30 9 0.26
31 15 0.44
32 2 0.06
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.34
Consensus pattern (29 bp):
TAAAAGTTACTTAAATGATCATCCGACTA
Found at i:833900 original size:27 final size:26
Alignment explanation
Indices: 833853--833931 Score: 113
Period size: 27 Copynumber: 3.0 Consensus size: 26
833843 GAGTAGAGTA
833853 GATGATATATATTTATCGGGTCGGGTG
1 GATGATATATATTT-TCGGGTCGGGTG
* *
833880 GATGATATAAAATTTTAGGGTCGGGTG
1 GATGATAT-ATATTTTCGGGTCGGGTG
*
833907 GATGATACATATTTTCGGGTCGGGT
1 GATGATATATATTTTCGGGTCGGGT
833932 CAGGTTGATC
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
26 15 0.33
27 26 0.57
28 5 0.11
ACGTcount: A:0.24, C:0.08, G:0.33, T:0.35
Consensus pattern (26 bp):
GATGATATATATTTTCGGGTCGGGTG
Found at i:834260 original size:27 final size:26
Alignment explanation
Indices: 834222--834296 Score: 78
Period size: 27 Copynumber: 2.8 Consensus size: 26
834212 TCAGAGTCTA
834222 GTGGAAGATATATATTTATCGGATCGG
1 GTGGAAGATATATATTT-TCGGATCGG
* * * *
834249 GTGGACGATATAAAATTTTAGGGTCGG
1 GTGGAAGATAT-ATATTTTCGGATCGG
* *
834276 GTGGATGATACATATTTTCGG
1 GTGGAAGATATATATTTTCGG
834297 GTCGAGTCAG
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
26 8 0.21
27 26 0.67
28 5 0.13
ACGTcount: A:0.28, C:0.08, G:0.31, T:0.33
Consensus pattern (26 bp):
GTGGAAGATATATATTTTCGGATCGG
Found at i:837528 original size:10 final size:11
Alignment explanation
Indices: 837503--837529 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
837493 TATTCTTATT
837503 AAAAAATAAAG
1 AAAAAATAAAG
837514 AAAAAATAAAG
1 AAAAAATAAAG
837525 AAAAA
1 AAAAA
837530 GAGAATCGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.07
Consensus pattern (11 bp):
AAAAAATAAAG
Found at i:839523 original size:34 final size:35
Alignment explanation
Indices: 839485--839554 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
839475 CGTACCTCTG
* *
839485 ATCATCGTATT-CAAAAACTACACCAACAGCAACA
1 ATCATCGTATTAAAAAAACTACACCAACAACAACA
*
839519 ATCATCGTATTAAAAAAACTACAGCAACAACAACA
1 ATCATCGTATTAAAAAAACTACACCAACAACAACA
839554 A
1 A
839555 CAATCACAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 11 0.34
35 21 0.66
ACGTcount: A:0.51, C:0.26, G:0.06, T:0.17
Consensus pattern (35 bp):
ATCATCGTATTAAAAAAACTACACCAACAACAACA
Found at i:840262 original size:31 final size:31
Alignment explanation
Indices: 840197--840281 Score: 102
Period size: 31 Copynumber: 2.7 Consensus size: 31
840187 AGTTGGGTAA
* *
840197 TGCTCGACTCGTGCTCGTT-AAAAACTTTTTT
1 TGCTCGACTCATGCTCGTTAAAAAAC-TTTGT
840228 TGCTCGACTCATGCTCGTTAAGAAAAC-TTGT
1 TGCTCGACTCATGCTCGTTAA-AAAACTTTGT
*
840259 TGCTCGACTCATTGCTTGTTAAA
1 TGCTCGACTCA-TGCTCGTTAAA
840282 CTTGTTGCTC
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
31 33 0.69
32 10 0.21
33 5 0.10
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (31 bp):
TGCTCGACTCATGCTCGTTAAAAAACTTTGT
Found at i:840296 original size:16 final size:16
Alignment explanation
Indices: 840277--840326 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
840267 TCATTGCTTG
*
840277 TTAAACTTGTTGCTCA
1 TTAAGCTTGTTGCTCA
* * *
840293 TTAAGCTCGTTACTCG
1 TTAAGCTTGTTGCTCA
*
840309 TTAAGCTTGATGCTCA
1 TTAAGCTTGTTGCTCA
840325 TT
1 TT
840327 GCTAGCCTCG
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42
Consensus pattern (16 bp):
TTAAGCTTGTTGCTCA
Found at i:845279 original size:16 final size:17
Alignment explanation
Indices: 845256--845304 Score: 66
Period size: 16 Copynumber: 2.9 Consensus size: 17
845246 CACGTTTAGA
845256 TATTTTAAAAATATATT
1 TATTTTAAAAATATATT
845273 T-TTTTAAATAATAT-TT
1 TATTTTAAA-AATATATT
*
845289 TATTTAAAAAATATAT
1 TATTTTAAAAATATAT
845305 ATGACATATG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
16 15 0.54
17 13 0.46
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTTTAAAAATATATT
Found at i:845821 original size:31 final size:30
Alignment explanation
Indices: 845781--845865 Score: 143
Period size: 30 Copynumber: 2.8 Consensus size: 30
845771 ACCTAACGCG
*
845781 TTTAGTACCTAAACTATCAGATTTTATCCGT
1 TTTAGTACCTAAACTTTC-GATTTTATCCGT
*
845812 TTTAATACCTAAACTTTCGATTTTATCCGT
1 TTTAGTACCTAAACTTTCGATTTTATCCGT
845842 TTTAGTACCTAAACTTTCGATTTT
1 TTTAGTACCTAAACTTTCGATTTT
845866 TTTTCAAAAC
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 35 0.69
31 16 0.31
ACGTcount: A:0.27, C:0.19, G:0.08, T:0.46
Consensus pattern (30 bp):
TTTAGTACCTAAACTTTCGATTTTATCCGT
Found at i:846585 original size:48 final size:49
Alignment explanation
Indices: 846491--846589 Score: 182
Period size: 49 Copynumber: 2.0 Consensus size: 49
846481 GTTGATGTGT
*
846491 CTATGCTTAAAAAATATGTAGTATAAAAATTATAAAACTTTTATGGGTC
1 CTATGCTTAAAAAATATATAGTATAAAAATTATAAAACTTTTATGGGTC
846540 CTATGCTTAAAAAATATATAGTATAAAAATTATAAAA-TTTTATGGGTC
1 CTATGCTTAAAAAATATATAGTATAAAAATTATAAAACTTTTATGGGTC
846588 CT
1 CT
846590 GGGCGGGCGC
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 13 0.27
49 36 0.73
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.37
Consensus pattern (49 bp):
CTATGCTTAAAAAATATATAGTATAAAAATTATAAAACTTTTATGGGTC
Found at i:849063 original size:20 final size:20
Alignment explanation
Indices: 849038--849098 Score: 122
Period size: 20 Copynumber: 3.0 Consensus size: 20
849028 CTTTGGGTGC
849038 GTTTGACTCACGAAATGTAA
1 GTTTGACTCACGAAATGTAA
849058 GTTTGACTCACGAAATGTAA
1 GTTTGACTCACGAAATGTAA
849078 GTTTGACTCACGAAATGTAA
1 GTTTGACTCACGAAATGTAA
849098 G
1 G
849099 ATTATCAGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (20 bp):
GTTTGACTCACGAAATGTAA
Found at i:857391 original size:20 final size:23
Alignment explanation
Indices: 857366--857422 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
857356 AGAATAATTA
*
857366 TGTCTTTGTGACA-TTTTA-TT-
1 TGTCTTTGTGACACGTTTATTTC
* *
857386 TGTCTTTATAACACGTTTATTTC
1 TGTCTTTGTGACACGTTTATTTC
857409 TGTCTTTGTGACAC
1 TGTCTTTGTGACAC
857423 ATTTTTCTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 11 0.38
21 4 0.14
22 2 0.07
23 12 0.41
ACGTcount: A:0.18, C:0.16, G:0.14, T:0.53
Consensus pattern (23 bp):
TGTCTTTGTGACACGTTTATTTC
Found at i:858962 original size:21 final size:21
Alignment explanation
Indices: 858930--858971 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
858920 GATGTAAAGA
*
858930 AGTTTCAGGCAATGATTGCTG
1 AGTTTCAGGCAAGGATTGCTG
*
858951 AGTTTACA-GCAAGGGTTGCTG
1 AGTTT-CAGGCAAGGATTGCTG
858972 CATTGGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.24, C:0.14, G:0.31, T:0.31
Consensus pattern (21 bp):
AGTTTCAGGCAAGGATTGCTG
Found at i:866671 original size:31 final size:31
Alignment explanation
Indices: 866618--866706 Score: 135
Period size: 31 Copynumber: 2.9 Consensus size: 31
866608 TAAACATAAT
*
866618 ATATTATCACTTTCA-TTTTATTTAATTAAG
1 ATATGATCACTTTCATTTTTATTTAATTAAG
* *
866648 ATATGATCACTTTTATTTTTATTTAGTTAAG
1 ATATGATCACTTTCATTTTTATTTAATTAAG
*
866679 ATATGATCACTTTCATTTTAATTTAATT
1 ATATGATCACTTTCATTTTTATTTAATT
866707 GAGGCGTGGT
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 13 0.25
31 39 0.75
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.54
Consensus pattern (31 bp):
ATATGATCACTTTCATTTTTATTTAATTAAG
Found at i:867265 original size:26 final size:27
Alignment explanation
Indices: 867216--867268 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
867206 ACTTATTATG
*
867216 TATTTTATTATTAACTTAATTTTAAAA
1 TATTTTATTATTAACTTAAATTTAAAA
*
867243 TATTTTATT-TTAATTTAAATTTAAAA
1 TATTTTATTATTAACTTAAATTTAAAA
867269 ATATATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (27 bp):
TATTTTATTATTAACTTAAATTTAAAA
Found at i:867280 original size:31 final size:32
Alignment explanation
Indices: 867242--867354 Score: 126
Period size: 31 Copynumber: 3.6 Consensus size: 32
867232 TAATTTTAAA
867242 ATATTTTATT-TTAATTTAAATTTAAAAATAT
1 ATATTTTATTATTAATTTAAATTTAAAAATAT
* * *
867273 ATATTTTATTCTT-ATCTAAATTTTTAAAA-AT
1 ATATTTTATTATTAATTTAAA-TTTAAAAATAT
* *
867304 ATATTTTATTATTATTTTAACTTTAGAAAATAT
1 ATATTTTATTATTAATTTAAATTTA-AAAATAT
*
867337 ATATTTTA-TCTTAATTTA
1 ATATTTTATTATTAATTTA
867355 CTAAATATTC
Statistics
Matches: 68, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
31 33 0.49
32 25 0.37
33 10 0.15
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.56
Consensus pattern (32 bp):
ATATTTTATTATTAATTTAAATTTAAAAATAT
Found at i:867295 original size:58 final size:63
Alignment explanation
Indices: 867216--867350 Score: 174
Period size: 63 Copynumber: 2.2 Consensus size: 63
867206 ACTTATTATG
* *
867216 TATTTTATTATTAACTTAA-TTTT-AAA-ATATTTTATT-TTAATTTAAATTTA-AAAATATA
1 TATTTTATTCTTAACTAAATTTTTAAAATATATTTTATTATTAATTTAAATTTAGAAAATATA
* * *
867274 TATTTTATTCTTATCTAAATTTTTAAAAATATATTTTATTATTATTTTAACTTTAGAAAATATA
1 TATTTTATTCTTAACTAAATTTTT-AAAATATATTTTATTATTAATTTAAATTTAGAAAATATA
867338 TATTTTA-TCTTAA
1 TATTTTATTCTTAA
867351 TTTACTAAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
58 16 0.25
59 4 0.06
61 3 0.05
62 10 0.15
63 17 0.26
64 15 0.23
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.56
Consensus pattern (63 bp):
TATTTTATTCTTAACTAAATTTTTAAAATATATTTTATTATTAATTTAAATTTAGAAAATATA
Found at i:867360 original size:26 final size:27
Alignment explanation
Indices: 867331--867399 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 27
867321 TAACTTTAGA
* *
867331 AAATATATATT-TTA-TCTTAATTTACT
1 AAATATATATTATTACT-TTAAATTAAT
867357 AAATATTCATATTATTACTTTAAATTAAT
1 AAATA-T-ATATTATTACTTTAAATTAAT
*
867386 AAATATATTTTATT
1 AAATATATATTATT
867400 CTCATTGCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
26 5 0.14
27 8 0.22
28 6 0.17
29 16 0.44
30 1 0.03
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (27 bp):
AAATATATATTATTACTTTAAATTAAT
Found at i:867474 original size:28 final size:29
Alignment explanation
Indices: 867424--867497 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 29
867414 AAAATATTGT
*
867424 AAAATAAAACATATAATTAAAA-TAAAATA
1 AAAATAAAACATAT-TTTAAAATTAAAATA
**
867453 AAAATAAAA-ATATTTTACAAATTAAGTTA
1 AAAATAAAACATATTTTA-AAATTAAAATA
* *
867482 ATAATAAAATATATTT
1 AAAATAAAACATATTT
867498 AATATGTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
27 3 0.08
28 7 0.18
29 22 0.58
30 6 0.16
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (29 bp):
AAAATAAAACATATTTTAAAATTAAAATA
Found at i:868015 original size:21 final size:21
Alignment explanation
Indices: 867937--868016 Score: 65
Period size: 21 Copynumber: 3.8 Consensus size: 21
867927 AAATCAGTTC
*
867937 CCAGAATCGCAACGCGATTAT
1 CCAGAATCGCAATGCGATTAT
**
867958 GAAGAATCGCAATGCGA-TAGT
1 CCAGAATCGCAATGCGATTA-T
* * * *
867979 ACA-AATTAGCATTGCGATTTT
1 CCAGAA-TCGCAATGCGATTAT
868000 CCAGAATCGCAATGCGA
1 CCAGAATCGCAATGCGA
868017 ATATGAAAAT
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 4 0.09
21 37 0.84
22 3 0.07
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (21 bp):
CCAGAATCGCAATGCGATTAT
Found at i:868109 original size:20 final size:20
Alignment explanation
Indices: 868065--868235 Score: 166
Period size: 20 Copynumber: 8.4 Consensus size: 20
868055 GATTCTGACT
* *
868065 ATCGCAACGAGTATTCGTAAA
1 ATCGCAACGCGTATCCGT-AA
868086 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
868106 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
*
868127 ATCGCAACGCGTATCCATAA
1 ATCGCAACGCGTATCCGTAA
* ** *
868147 ATTGCAAC-AATAATACGTAA
1 ATCGCAACGCGT-ATCCGTAA
*
868167 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
868187 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
868207 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
868227 ATCGCAACG
1 ATCGCAACG
868236 ACAATACGTA
Statistics
Matches: 119, Mismatches: 26, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
19 1 0.01
20 85 0.71
21 33 0.28
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:868110 original size:41 final size:41
Alignment explanation
Indices: 868065--868250 Score: 268
Period size: 40 Copynumber: 4.6 Consensus size: 41
868055 GATTCTGACT
** *
868065 ATCGCAACGAGTATTCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
*
868106 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCATAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
* * * *
868147 ATTGCAACAATAATACGT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
* *
868187 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
868227 ATCGCAACGACAATACGTAAAATC
1 ATCGCAACGACAATACGTAAAATC
868251 ACAATGCGAT
Statistics
Matches: 129, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
40 72 0.56
41 57 0.44
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (41 bp):
ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:868877 original size:21 final size:21
Alignment explanation
Indices: 868816--868908 Score: 106
Period size: 20 Copynumber: 4.6 Consensus size: 21
868806 TTCTAAACTT
*
868816 AAAATCGCAAC-ATGAAAATG
1 AAAATCGCAACGACGAAAATG
868836 AAAATCGCAAC-ACGAAAATG
1 AAAATCGCAACGACGAAAATG
**
868856 ACTATCGCAACGA-GAGAAATG
1 AAAATCGCAACGACGA-AAATG
868877 AAAATCGCAACG-CG-AAATG
1 AAAATCGCAACGACGAAAATG
*
868896 AAAATTGCAACGA
1 AAAATCGCAACGA
868909 GATAATCGCA
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
19 16 0.25
20 30 0.48
21 17 0.27
ACGTcount: A:0.51, C:0.18, G:0.18, T:0.13
Consensus pattern (21 bp):
AAAATCGCAACGACGAAAATG
Found at i:868895 original size:40 final size:40
Alignment explanation
Indices: 868816--868910 Score: 122
Period size: 40 Copynumber: 2.4 Consensus size: 40
868806 TTCTAAACTT
868816 AAAATCGCAAC-ATGAAAATGAAAATCGCAACACGAAAATG
1 AAAATCGCAACGA-GAAAATGAAAATCGCAACACGAAAATG
** *
868856 ACTATCGCAACGAGAGAAATGAAAATCGCAACGCG-AAATG
1 AAAATCGCAACGAGA-AAATGAAAATCGCAACACGAAAATG
*
868896 AAAATTGCAACGAGA
1 AAAATCGCAACGAGA
868911 TAATCGCAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
40 28 0.60
41 19 0.40
ACGTcount: A:0.51, C:0.18, G:0.19, T:0.13
Consensus pattern (40 bp):
AAAATCGCAACGAGAAAATGAAAATCGCAACACGAAAATG
Found at i:868955 original size:19 final size:19
Alignment explanation
Indices: 868933--869045 Score: 92
Period size: 20 Copynumber: 6.1 Consensus size: 19
868923 GAAACCAAAA
*
868933 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
868952 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
868966 TCTCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
**
868985 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* **
869004 TCCACGTTGCGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
*
869024 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
869044 TC
1 TC
869046 AACCAAAAGA
Statistics
Matches: 76, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
14 10 0.13
16 2 0.03
17 3 0.04
19 28 0.37
20 32 0.42
21 1 0.01
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:869166 original size:25 final size:24
Alignment explanation
Indices: 869112--869166 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
869102 TTATGTTTAT
* *
869112 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
869136 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
869162 TGTTT
1 TGTTT
869167 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:870878 original size:94 final size:94
Alignment explanation
Indices: 870717--871096 Score: 593
Period size: 94 Copynumber: 4.1 Consensus size: 94
870707 TAGATTGCTT
* * *
870717 AGTAAATTTATTCGGTTGCTGTCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
870782 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
* *
870811 AGTAAATTTATTTGGTTGCTGCCAATTCTGCTAAACCGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
870876 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * *
870905 AGTAAATTTGTTCGATTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACCCTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
870970 ATTTGTCTTTGTTTAGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * * * *
870999 AGTAAATTTGTTCAGTTGCTGTCAATTCTGCTAAACTATGTATTCTTTAATACTATGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
871064 ATTTGTCTTTGTTTTATCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
871092 AGTAA
1 AGTAA
871097 TACAATCCAT
Statistics
Matches: 265, Mismatches: 20, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
93 26 0.10
94 239 0.90
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:871333 original size:19 final size:19
Alignment explanation
Indices: 871182--871333 Score: 215
Period size: 19 Copynumber: 8.3 Consensus size: 19
871172 AAAAATGACT
*
871182 ATCGCAACGCAAAATGAAA
1 ATCGCAACGCGAAATGAAA
871201 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
871220 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
871239 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
871258 ATCGCAACGCAAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
871277 ATCGCAACGCAAAATGAAA
1 ATCGCAACGCGAAATGAAA
* *
871296 ATCG-AA-ACG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
871310 ATCGCAACGCGAAATAAAA
1 ATCGCAACGCGAAATGAAA
871329 ATCGC
1 ATCGC
871334 GTTGCGATTT
Statistics
Matches: 120, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
14 7 0.06
15 3 0.03
16 2 0.02
17 1 0.01
18 3 0.03
19 104 0.87
ACGTcount: A:0.49, C:0.21, G:0.19, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:871875 original size:21 final size:21
Alignment explanation
Indices: 871851--871917 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
871841 TCATTCCTCG
871851 AGAGTCCCCTCCCACCATTCA
1 AGAGTCCCCTCCCACCATTCA
* * ** * * *
871872 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCATTCA
871893 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCATTCA
871914 AGAG
1 AGAG
871918 CCCGATTCAC
Statistics
Matches: 31, Mismatches: 14, Indels: 3
0.65 0.29 0.06
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCATTCA
Found at i:871875 original size:42 final size:42
Alignment explanation
Indices: 871829--871917 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 42
871819 CCTATCGTTG
*
871829 AAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCACCATTC
1 AAGAGGCCACTATCA-TCCTCGAAGAGGT-CCCTCCCACCATTC
* * *
871871 AAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCACCATTC
1 AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
871913 AAGAG
1 AAGAG
871918 CCCGATTCAC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
41 4 0.10
42 35 0.85
43 2 0.05
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.20
Consensus pattern (42 bp):
AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
Found at i:873294 original size:14 final size:13
Alignment explanation
Indices: 873275--873310 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
873265 ATTGTTTAAT
873275 TGATTTGTAAAAG
1 TGATTTGTAAAAG
873288 ATGATTTGTAAAAG
1 -TGATTTGTAAAAG
873302 TGAATTTGT
1 TG-ATTTGT
873311 TTAATTGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 2 0.10
14 19 0.90
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (13 bp):
TGATTTGTAAAAG
Found at i:873492 original size:19 final size:19
Alignment explanation
Indices: 873417--873482 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
873407 AAAAATGACT
873417 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
873436 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
873450 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
873469 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
873483 CTAAATTCGC
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 24 0.60
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:873535 original size:33 final size:33
Alignment explanation
Indices: 873492--873639 Score: 152
Period size: 33 Copynumber: 4.3 Consensus size: 33
873482 ACTAAATTCG
* *
873492 CGTTGTGATTTTCATTTCGCTTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
873525 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCT
1 CGTTGCGATTTTCATTTCGCATTGCGAT--TC---TCT
* * * *
873563 GCGTTGCGATATTCATATTCGCGTTGCGATTTTCA
1 -CGTTGCGATTTTCAT-TTCGCATTGCGATTCTCT
* *
873598 CGTTACGATTTTCATTTCGCATTGCGATTATCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
873631 CATTGCGAT
1 CGTTGCGAT
873640 AATAATTTCC
Statistics
Matches: 95, Mismatches: 13, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
33 48 0.51
34 13 0.14
35 4 0.04
38 4 0.04
39 14 0.15
40 12 0.13
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:873571 original size:20 final size:19
Alignment explanation
Indices: 873488--873597 Score: 95
Period size: 20 Copynumber: 5.9 Consensus size: 19
873478 CGAAACTAAA
* *
873488 TTCGCGTTGTGATTTTCAT
1 TTCGCGTTGCGATATTCAT
*
873507 TTCGCTTTGCG--ATTC--
1 TTCGCGTTGCGATATTCAT
* *
873522 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATATTCAT
* *
873540 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATATTCAT
873559 TTCTGCGTTGCGATATTCAT
1 TTC-GCGTTGCGATATTCAT
*
873579 ATTCGCGTTGCGATTTTCA
1 -TTCGCGTTGCGATATTCA
873598 CGTTACGATT
Statistics
Matches: 71, Mismatches: 13, Indels: 13
0.73 0.13 0.13
Matches are distributed among these distances:
14 8 0.11
16 3 0.04
17 3 0.04
19 26 0.37
20 28 0.39
21 3 0.04
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.45
Consensus pattern (19 bp):
TTCGCGTTGCGATATTCAT
Found at i:873607 original size:73 final size:72
Alignment explanation
Indices: 873491--873625 Score: 207
Period size: 73 Copynumber: 1.9 Consensus size: 72
873481 AACTAAATTC
* * * * *
873491 GCGTTGTGATTTTCATTTCGCTTTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATAGT
1 GCGTTGCGATATTCATTTCGCGTTGCGATTCTCACGTTACGATTTTCATTTCGCATTGCGATAGT
873556 CATTTCT
66 CATTTCT
*
873563 GCGTTGCGATATTCATATTCGCGTTGCGATTTTCACGTTACGATTTTCATTTCGCATTGCGAT
1 GCGTTGCGATATTCAT-TTCGCGTTGCGATTCTCACGTTACGATTTTCATTTCGCATTGCGAT
873626 TATCTCATTG
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
72 14 0.25
73 42 0.75
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.44
Consensus pattern (72 bp):
GCGTTGCGATATTCATTTCGCGTTGCGATTCTCACGTTACGATTTTCATTTCGCATTGCGATAGT
CATTTCT
Found at i:873705 original size:20 final size:20
Alignment explanation
Indices: 873633--873705 Score: 51
Period size: 20 Copynumber: 3.6 Consensus size: 20
873623 GATTATCTCA
* * *
873633 TTGCGATAATAATTTCCGCG
1 TTGCGATAGTCATTTCCGTG
* **
873653 TTGCGATAGACA-TTAAGATG
1 TTGCGATAGTCATTTCCG-TG
873673 ATTGCGA-ACGTCATTTCCGTG
1 -TTGCGATA-GTCATTTCCGTG
873694 TTGCGATAGTCA
1 TTGCGATAGTCA
873706 AATGAATGCC
Statistics
Matches: 39, Mismatches: 9, Indels: 10
0.67 0.16 0.17
Matches are distributed among these distances:
19 3 0.08
20 21 0.54
21 12 0.31
22 3 0.08
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGTG
Found at i:875745 original size:3 final size:3
Alignment explanation
Indices: 875737--875805 Score: 93
Period size: 3 Copynumber: 23.0 Consensus size: 3
875727 CTTTGGGGAT
* * * *
875737 TTC TTC TTC TTC TTT TTC TTC TTC TTC TTT TTC TTC TTA TTC TTT TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
875785 TTC TTC TTC TTT TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC
875806 AGTGTTATAT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.72
Consensus pattern (3 bp):
TTC
Found at i:875754 original size:15 final size:15
Alignment explanation
Indices: 875736--875805 Score: 131
Period size: 15 Copynumber: 4.7 Consensus size: 15
875726 TCTTTGGGGA
875736 TTTCTTCTTCTTCTT
1 TTTCTTCTTCTTCTT
875751 TTTCTTCTTCTTCTT
1 TTTCTTCTTCTTCTT
*
875766 TTTCTTCTTATTCTT
1 TTTCTTCTTCTTCTT
875781 TTTCTTCTTCTTCTT
1 TTTCTTCTTCTTCTT
875796 TTTCTTCTTC
1 TTTCTTCTTC
875806 AGTGTTATAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 53 1.00
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTCTTCTTCTTCTT
Found at i:876014 original size:24 final size:24
Alignment explanation
Indices: 875980--876033 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
875970 CTGAAAAATC
875980 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
*
876004 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
876028 ATCAAA
1 ATCAAA
876034 TTTCGAATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:876047 original size:24 final size:24
Alignment explanation
Indices: 875980--876047 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
875970 CTGAAAAATC
* * *
875980 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
876004 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
876028 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
876048 TAGTACTCAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:876916 original size:20 final size:21
Alignment explanation
Indices: 876893--876972 Score: 112
Period size: 21 Copynumber: 3.9 Consensus size: 21
876883 GTCAGAATCT
876893 CGTTGCGA-TTTACGGATATG
1 CGTTGCGATTTTACGGATATG
*
876913 CGTTGCGATTTTACGTAT-TG
1 CGTTGCGATTTTACGGATATG
*
876933 TCGTTGCGA-TTTACGGATACG
1 -CGTTGCGATTTTACGGATATG
876954 CGTTGCGATTTTACGGATA
1 CGTTGCGATTTTACGGATA
876973 CTTGTTGCGA
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
20 26 0.49
21 27 0.51
ACGTcount: A:0.19, C:0.16, G:0.28, T:0.38
Consensus pattern (21 bp):
CGTTGCGATTTTACGGATATG
Found at i:876973 original size:21 final size:21
Alignment explanation
Indices: 876893--877046 Score: 108
Period size: 20 Copynumber: 7.6 Consensus size: 21
876883 GTCAGAATCT
*
876893 CGTTGCGA-TTTACGGATATG
1 CGTTGCGATTTTACGGATACG
* *
876913 CGTTGCGATTTTACGTAT-TG
1 CGTTGCGATTTTACGGATACG
876933 TCGTTGCGA-TTTACGGATACG
1 -CGTTGCGATTTTACGGATACG
*
876954 CGTTGCGATTTTACGGATACT
1 CGTTGCGATTTTACGGATACG
* ** *
876975 TGTTGCGATAGT-CAGA-ATCG
1 CGTTGCGATTTTACGGATA-CG
* *
876995 CGTTGCGATTTATA-TG-TTCG
1 CGTTGCGATTT-TACGGATACG
** *
877015 CGTTGCGATTTT-CATATTCG
1 CGTTGCGATTTTACGGATACG
877035 CGTTGCGATTTT
1 CGTTGCGATTTT
877047 GGAAAATCGC
Statistics
Matches: 108, Mismatches: 16, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
19 2 0.02
20 67 0.62
21 39 0.36
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.40
Consensus pattern (21 bp):
CGTTGCGATTTTACGGATACG
Found at i:876980 original size:41 final size:41
Alignment explanation
Indices: 876891--876983 Score: 141
Period size: 41 Copynumber: 2.3 Consensus size: 41
876881 TAGTCAGAAT
* * *
876891 CTCGTTGCGATTTACGGATATGCGTTGCGATTTTACGTATT
1 CTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATA
*
876932 GTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATA
1 CTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATA
*
876973 CTTGTTGCGAT
1 CTCGTTGCGAT
876984 AGTCAGAATC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.17, C:0.17, G:0.27, T:0.39
Consensus pattern (41 bp):
CTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATA
Found at i:877561 original size:21 final size:21
Alignment explanation
Indices: 877537--877608 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 21
877527 TAAAAATTAA
877537 AATTGAATTTATAAATTTGTT
1 AATTGAATTTATAAATTTGTT
* * * *
877558 AATTGACTTCAACTATATTT-TA
1 AATTGAATT-TA-TAAATTTGTT
877580 AATGTGGAATTTATAAATTTGTT
1 AAT-T-GAATTTATAAATTTGTT
877603 AATTGA
1 AATTGA
877609 CTTCAACTAT
Statistics
Matches: 38, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
21 10 0.26
22 12 0.32
23 12 0.32
24 4 0.11
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (21 bp):
AATTGAATTTATAAATTTGTT
Found at i:877577 original size:23 final size:23
Alignment explanation
Indices: 877551--877622 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 23
877541 GAATTTATAA
877551 ATTTGTTAATTGACTTCAACTAT
1 ATTTGTTAATTGACTTCAACTAT
* * * *
877574 ATTT-TAAATGTGGAATT-TA-TAA
1 ATTTGTTAAT-T-GACTTCAACTAT
877596 ATTTGTTAATTGACTTCAACTAT
1 ATTTGTTAATTGACTTCAACTAT
877619 ATTT
1 ATTT
877623 TAAATGTGTC
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
21 4 0.11
22 12 0.33
23 16 0.44
24 4 0.11
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.49
Consensus pattern (23 bp):
ATTTGTTAATTGACTTCAACTAT
Found at i:877596 original size:45 final size:45
Alignment explanation
Indices: 877541--877630 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
877531 AATTAAAATT
877541 GAATTTATAAATTTGTTAATTGACTTCAACTATATTTTAAATGTG
1 GAATTTATAAATTTGTTAATTGACTTCAACTATATTTTAAATGTG
877586 GAATTTATAAATTTGTTAATTGACTTCAACTATATTTTAAATGTG
1 GAATTTATAAATTTGTTAATTGACTTCAACTATATTTTAAATGTG
877631 TCGTGAACTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.47
Consensus pattern (45 bp):
GAATTTATAAATTTGTTAATTGACTTCAACTATATTTTAAATGTG
Found at i:877625 original size:21 final size:21
Alignment explanation
Indices: 877556--877625 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
877546 TATAAATTTG
877556 TTAATTGACTTCAACTATATT
1 TTAATTGACTTCAACTATATT
* * *
877577 TTAAATGTGGAATT-TA-TAAATTT
1 TT-AAT-T-GACTTCAACTATA-TT
877600 GTTAATTGACTTCAACTATATT
1 -TTAATTGACTTCAACTATATT
877622 TTAA
1 TTAA
877626 ATGTGTCGTG
Statistics
Matches: 36, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
21 10 0.28
22 10 0.28
23 10 0.28
24 6 0.17
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.47
Consensus pattern (21 bp):
TTAATTGACTTCAACTATATT
Found at i:886043 original size:124 final size:123
Alignment explanation
Indices: 885832--886054 Score: 324
Period size: 124 Copynumber: 1.8 Consensus size: 123
885822 AAAATAAATT
* ** *
885832 AAGTTCCAAAGGTTAAAGTAAATGTAAGCAAGGTAATCCATGGAAACTGCCTCGACAGTATGATG
1 AAGTTCCAAAGGTTAAACTAAATACAAGCAAGGTAATCCATGGAAACTGCCTCGACAGAATGATG
* *
885897 TGGTTTAAGACCACTGTGAACAATTTTAGGAGTACACTCTCCGTGCCAATAATAACCG
66 TGGTTTAAGACCAATGCGAACAATTTTAGGAGTACACTCTCCGTGCCAATAATAACCG
* *
885955 AAGTTCCAAAGGTTAAACTACAATACATA-CAAGGTAATCCA-GAGAGACTGCCTCTACAGAATG
1 AAGTTCCAAAGGTTAAACTA-AATACA-AGCAAGGTAATCCATG-GAAACTGCCTCGACAGAATG
*
886018 GTGTGGTTTAAGACCAATGCGAACAATTTTAGGAGTA
63 ATGTGGTTTAAGACCAATGCGAACAATTTTAGGAGTA
886055 TATGCACGAA
Statistics
Matches: 88, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
123 20 0.23
124 67 0.76
125 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (123 bp):
AAGTTCCAAAGGTTAAACTAAATACAAGCAAGGTAATCCATGGAAACTGCCTCGACAGAATGATG
TGGTTTAAGACCAATGCGAACAATTTTAGGAGTACACTCTCCGTGCCAATAATAACCG
Found at i:894473 original size:35 final size:35
Alignment explanation
Indices: 894405--894474 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
894395 CAATGACTTA
***
894405 CTTTGTTTTTATGCCATTAATTCACTCGTAATCAC
1 CTTTGTTTTTATGCCATTAATTCACTAAAAATCAC
*
894440 CTTT-TTTTTCATGCCATTAATTCTCTAAAAATCAC
1 CTTTGTTTTT-ATGCCATTAATTCACTAAAAATCAC
894475 TTAGTTTCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 5 0.17
35 25 0.83
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.46
Consensus pattern (35 bp):
CTTTGTTTTTATGCCATTAATTCACTAAAAATCAC
Found at i:895437 original size:54 final size:54
Alignment explanation
Indices: 895373--895480 Score: 173
Period size: 54 Copynumber: 2.0 Consensus size: 54
895363 AAACGGTACA
* *
895373 GTGAAGAGTGTTCATGTAAT-AATTTTTCGATTTAAAGACGATGAATCAAAATCG
1 GTGAAGAGTGTTCATATAATAAATATTT-GATTTAAAGACGATGAATCAAAATCG
*
895427 GTGAAGAGTGTTCATATGATAAATATTTGATTTAAAGACGATGAATCAAAATCG
1 GTGAAGAGTGTTCATATAATAAATATTTGATTTAAAGACGATGAATCAAAATCG
895481 CATCCGAATC
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
54 44 0.88
55 6 0.12
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.32
Consensus pattern (54 bp):
GTGAAGAGTGTTCATATAATAAATATTTGATTTAAAGACGATGAATCAAAATCG
Found at i:899557 original size:67 final size:67
Alignment explanation
Indices: 899419--899567 Score: 192
Period size: 67 Copynumber: 2.2 Consensus size: 67
899409 AAAATTTTGT
* * *
899419 TGCTCGTTAAGCTCATTAAAATTTTGCTCAACTTGTGCTCGTTAAGAAAATTTGTTGCTAAACTC
1 TGCTCGTTAAGCTCATTAAAATTTTACTCAACTCGTGCTCGTTAAGAAAATTTGTTACTAAACTC
**
899484 TT
66 GC
* * **
899486 TGCTCGTTAAGCTCATTAAAATTTTATTCGAA-TCGTGCTCGTTAAGAAAATTTGTTATTCGACT
1 TGCTCGTTAAGCTCATTAAAATTTTACTC-AACTCGTGCTCGTTAAGAAAATTTGTTACTAAACT
899550 CGC
65 CGC
*
899553 TGCTCATTAAGCTCA
1 TGCTCGTTAAGCTCA
899568 CTGCTCGTTA
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
67 69 0.97
68 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (67 bp):
TGCTCGTTAAGCTCATTAAAATTTTACTCAACTCGTGCTCGTTAAGAAAATTTGTTACTAAACTC
GC
Found at i:899656 original size:43 final size:44
Alignment explanation
Indices: 899580--899662 Score: 141
Period size: 43 Copynumber: 1.9 Consensus size: 44
899570 GCTCGTTAAC
899580 TTAAGCTCACCAGATTTTTTATTTTACTTTTTTAACTATACTCG
1 TTAAGCTCACCAGATTTTTTATTTTACTTTTTTAACTATACTCG
* *
899624 TTAAGCTCACCGGA-TTTTTATTTTATTTTTTTAACTATA
1 TTAAGCTCACCAGATTTTTTATTTTACTTTTTTAACTATA
899663 AATAAAAATC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
43 24 0.65
44 13 0.35
ACGTcount: A:0.25, C:0.16, G:0.07, T:0.52
Consensus pattern (44 bp):
TTAAGCTCACCAGATTTTTTATTTTACTTTTTTAACTATACTCG
Found at i:915199 original size:53 final size:56
Alignment explanation
Indices: 915117--915244 Score: 124
Period size: 59 Copynumber: 2.3 Consensus size: 56
915107 AAGTCAACAG
*
915117 AAAAG-TATATAAATGAGTCCCAGATTAT-AAGA-TTT-TTCAGTCTATT-GACTATT
1 AAAAGTTATA-AAATGAGTCCCAGACTATAAAGATTTTGTTCAGTC-ATTCGACTATT
* *
915170 AAAAGTTATAAAATG-GTCCCTTGACTATAAAGAGTTTTTTGTTGAGTCATTCGACTATT
1 AAAAGTTATAAAATGAGTCCC-AGACTATAAAGA---TTTTGTTCAGTCATTCGACTATT
*
915229 AAAAGTTACAAAATGA
1 AAAAGTTATAAAATGA
915245 TCACTCGATT
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
52 5 0.08
53 15 0.25
54 8 0.13
58 6 0.10
59 27 0.44
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (56 bp):
AAAAGTTATAAAATGAGTCCCAGACTATAAAGATTTTGTTCAGTCATTCGACTATT
Found at i:919793 original size:3 final size:3
Alignment explanation
Indices: 919745--919780 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
919735 CTTAATTTAC
919745 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
919781 AAATTTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:928076 original size:36 final size:37
Alignment explanation
Indices: 928036--928116 Score: 128
Period size: 38 Copynumber: 2.2 Consensus size: 37
928026 TTTTGTTCGG
*
928036 GTCGGGTCGGG-TTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGACGA
*
928072 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGACGG
1 GTCGGGTCGGG-TTTTTTAAGTGTGATATTCGGGACGA
928110 GTCGGGT
1 GTCGGGT
928117 TTAGGGTGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
36 11 0.27
38 30 0.73
ACGTcount: A:0.12, C:0.11, G:0.41, T:0.36
Consensus pattern (37 bp):
GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGACGA
Found at i:928159 original size:216 final size:209
Alignment explanation
Indices: 927761--928522 Score: 763
Period size: 216 Copynumber: 3.6 Consensus size: 209
927751 CTTATTCATA
927761 TATTAAATAAAAATATTTTTTTATTATTTCGGGTC--G--GG-T-----TTCTAATTCATATATT
1 TATTAAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGATCGAACTTCTAATT-ATATATT
* *
927816 CGGGTCGAGTCTGG-TGAAACTTTATTTTGGTCAGGTCGGATCGGGTTTTTTTAAGTGTGATATT
65 CGGGTCGGGTC-GGATGAAACTTTA--TT--TC-GGTCGGGTCGGGTTTTTTTAAGTGTGATA-T
*
927880 CGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAATCGGACCGACCCGAAAATATATATAATTC
123 ----TCGGG-CGGG-TCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTC
* *
927945 AGATCAGGTCGGATTAAGTCACTGTTTT
182 GGATCGGGTCGGATTAAGTCACTGTTTT
*
927973 TATTAAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGAT-GAAACTT-T-ATT-T-TGTT
1 TATTAAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGATCG-AACTTCTAATTATATATT
* ** *
928033 CGGGTCGGGTCGGGTTTTTAAGTGTGATATTCGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGA
65 CGGGTCGGGTC-GG-ATGAAACT-T--TATT----TCG-GTCGGGTCGGGTTTTTTTAAGTGTGA
*
928098 TATTCGGGACGGGTCGGGTTTAGGGTGAAAAAAACCGGACCGACTCGAAAATATATATAATTCGG
120 TATTCGGG-CGGGTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCGG
* * *
928163 GTCGGGTCAGATTAAATCACTGTTTT
184 ATCGGGTCGGATTAAGTCACTGTTTT
* * * *
928189 TATTAAATAAAAATATTTTTTTATTATTTCGGGTCGGGTTGGGTCGGATTTCTAATTCATATATT
1 TATTAAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGATCGAACTTCTAATT-ATATATT
* * * * *
928254 CTGGTCGGGTCGGATGAAACTTTATTTTGTTCAGGTCGGG-TTTTTTAAGAGTGATATT----CG
65 CGGGTCGGGTCGGATGAAACTTTATTTCGGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGCG
* *
928314 GGTCGGGTTTAGGGTGAAAACAACCGGACCGACCCG-AAA-ATATATAATTCGGTTCGGGTCGGA
130 GGTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCGGATCGGGTCGGA
*
928377 TTAAGTCACTATTTT
195 TTAAGTCACTGTTTT
* *
928392 TATTAAATAAAAATAATTTTTTATTATTTTGGGTCGGGTCGGAT-----TTCTAATTCATATATT
1 TATTAAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGATCGAACTTCTAATT-ATATATT
* * * *
928452 AGGGTCGGGTCGGATGAAACTTTATTTTGTTCAGGTCGGG-TTTTTTAAGTGTGATATTCGGGTC
65 CGGGTCGGGTCGGATGAAACTTTATTTCGGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGG-C
*
928516 GAGTCGG
129 GGGTCGG
928523 ATCGGGTTTT
Statistics
Matches: 478, Mismatches: 43, Indels: 67
0.81 0.07 0.11
Matches are distributed among these distances:
198 71 0.15
203 82 0.17
204 3 0.01
205 36 0.08
210 17 0.04
211 9 0.02
212 37 0.08
214 1 0.00
216 122 0.26
217 27 0.06
218 5 0.01
219 8 0.02
220 9 0.02
221 16 0.03
222 35 0.07
ACGTcount: A:0.25, C:0.12, G:0.26, T:0.38
Consensus pattern (209 bp):
TATTAAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGATCGAACTTCTAATTATATATTC
GGGTCGGGTCGGATGAAACTTTATTTCGGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGCGG
GTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCGGATCGGGTCGGAT
TAAGTCACTGTTTT
Found at i:928540 original size:38 final size:38
Alignment explanation
Indices: 928487--928569 Score: 134
Period size: 38 Copynumber: 2.2 Consensus size: 38
928477 TTTGTTCAGG
928487 TCGGG-TTTTTTAAGTGTGATATTCGGGTC-GAGTCGGA
1 TCGGGTTTTTTTAAGTGTGATATTCGGGTCAG-GTCGGA
*
928524 TCGGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCGGG
1 TCGGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCGGA
928562 TCGGGTTT
1 TCGGGTTT
928570 AGGGTGAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
37 5 0.12
38 37 0.86
39 1 0.02
ACGTcount: A:0.13, C:0.11, G:0.36, T:0.40
Consensus pattern (38 bp):
TCGGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCGGA
Found at i:935461 original size:130 final size:130
Alignment explanation
Indices: 935320--935567 Score: 408
Period size: 130 Copynumber: 1.9 Consensus size: 130
935310 TATTTATATA
*
935320 ATCAATTTGGTCCTAAATTAAA-AAAATTTTAATAAATTAATCATTTAATTAGGATCTGACATGT
1 ATCAATTTGGTCCTAAATTAAATAAAA-TTTAATAAATTAATCATTTAATCAGGATCTGACATGT
* * *
935384 GTTAGCACATGATCATGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATAC
65 GTTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATAC
935449 T
130 T
935450 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * *
935515 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
935568 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
130 105 0.96
131 4 0.04
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.37
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATACT
Found at i:937171 original size:14 final size:15
Alignment explanation
Indices: 937135--937172 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
937125 GAAATCATTG
937135 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
937150 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
937165 AAAAATTA
1 AAAAATTA
937173 GAGATGGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:937456 original size:212 final size:211
Alignment explanation
Indices: 937101--937527 Score: 730
Period size: 212 Copynumber: 2.0 Consensus size: 211
937091 CCTTTATTAA
* *
937101 GTTGATAGTTGATAATTTGGGAGAGAAATCATTGAAAAATTATATAGAAATAAAATTATGTAAAA
1 GTTGATAGTTGATAATTTGAGAGAGAAATCATTAAAAAATTATATAGAAATAAAATTATGTAAAA
* * *
937166 AAAATTAGAGATGGGAAAGGATGTCGTTGGATATAGGAACGGATGTCGCCGGAGAGAGTGGGAGA
66 AAAATTAGAGATGAGAAAGGATATCGTTAGATATAGGAACGGATGTCGCCGGAGAGAGTGGGAGA
* *
937231 TGGAGATGGAATGAGTTGCGATTTAGGGATTTTGGTTATGAGTTGTTGCTGTTGCGTAGTTTATA
131 TGGAGATGGAATGAGTTGCGATTTAGGGATTTTAGTTATGAGTTGTTGCTGCTGCGTAGTTTATA
*
937296 TATCCAAAACATTTGT
196 TACCCAAAACATTTGT
*
937312 GTTGATAGTTGATAGTTTGAGAGAGAAATCATTAAAAAATTATATAGAAAT-AAATTATGTAAAA
1 GTTGATAGTTGATAATTTGAGAGAGAAATCATTAAAAAATTATATAGAAATAAAATTATGT--AA
* *
937376 AAAAAATTAGATATGAGAAAGGATATTGTTAGATATAGGAACGGATGTCGCCGGAGAGAGTGGGA
64 AAAAAATTAGAGATGAGAAAGGATATCGTTAGATATAGGAACGGATGTCGCCGGAGAGAGTGGGA
937441 GATGGAGATGGAATGAGTTGCGATTTAGGGATTTTAGTTATGAGTTGTTGCTGCTGCGTAGTTTA
129 GATGGAGATGGAATGAGTTGCGATTTAGGGATTTTAGTTATGAGTTGTTGCTGCTGCGTAGTTTA
937506 TATACCCAAAACATTTGT
194 TATACCCAAAACATTTGT
937524 GTTG
1 GTTG
937528 CGAAAATAAA
Statistics
Matches: 203, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
210 9 0.04
211 48 0.24
212 146 0.72
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (211 bp):
GTTGATAGTTGATAATTTGAGAGAGAAATCATTAAAAAATTATATAGAAATAAAATTATGTAAAA
AAAATTAGAGATGAGAAAGGATATCGTTAGATATAGGAACGGATGTCGCCGGAGAGAGTGGGAGA
TGGAGATGGAATGAGTTGCGATTTAGGGATTTTAGTTATGAGTTGTTGCTGCTGCGTAGTTTATA
TACCCAAAACATTTGT
Found at i:937550 original size:17 final size:19
Alignment explanation
Indices: 937523--937561 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
937513 AAAACATTTG
937523 TGTTGCGAAAA-TAAAAGT
1 TGTTGCGAAAATTAAAAGT
*
937541 TGTTGC-AAAATTAAAATT
1 TGTTGCGAAAATTAAAAGT
937559 TGT
1 TGT
937562 GTTGCGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.36
Consensus pattern (19 bp):
TGTTGCGAAAATTAAAAGT
Found at i:937576 original size:20 final size:20
Alignment explanation
Indices: 937549--937608 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
937539 GTTGTTGCAA
*
937549 AATT-AAAATTTGTGTTGCG
1 AATTCAAAATTCGTGTTGCG
* **
937568 AATTCAAAAATCAAGTTGCG
1 AATTCAAAATTCGTGTTGCG
**
937588 AAAACAAAATTCGTGTTGCG
1 AATTCAAAATTCGTGTTGCG
937608 A
1 A
937609 TTTAGAAAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
19 4 0.13
20 27 0.87
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (20 bp):
AATTCAAAATTCGTGTTGCG
Found at i:937626 original size:40 final size:40
Alignment explanation
Indices: 937540--937631 Score: 98
Period size: 40 Copynumber: 2.3 Consensus size: 40
937530 AAAATAAAAG
* *
937540 TTGTTGCAAAATTAAAATTTGTGTTGCGAATTCAAAAATC
1 TTGTTGCAAAATCAAAATTCGTGTTGCGAATTCAAAAATC
** *
937580 AAGTTGCGAAAA-CAAAATTCGTGTTGCG-ATTTAGAAAATC
1 TTGTTGC-AAAATCAAAATTCGTGTTGCGAATTCA-AAAATC
937620 TTGTTGCTAAAA
1 TTGTTGC-AAAA
937632 GGAAACTTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
39 4 0.10
40 34 0.81
41 4 0.10
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (40 bp):
TTGTTGCAAAATCAAAATTCGTGTTGCGAATTCAAAAATC
Found at i:937685 original size:20 final size:20
Alignment explanation
Indices: 937652--937752 Score: 64
Period size: 20 Copynumber: 5.0 Consensus size: 20
937642 ATTGCGAAAA
*
937652 AGAAATTCGCGTTGCGAATTC
1 AGAAA-TCGAGTTGCGAATTC
937673 AGAAATCGAGTTGCGAATT-
1 AGAAATCGAGTTGCGAATTC
* * * *
937692 TGAAATTCCGTGTTGTGAATTT
1 AGAAA-T-CGAGTTGCGAATTC
* * *
937714 GGATATCGCGTTGCG-ATTGC
1 AGAAATCGAGTTGCGAATT-C
937734 AGAAA-CTGAGTTGCGAATT
1 AGAAATC-GAGTTGCGAATT
937753 TGGAAACTAT
Statistics
Matches: 62, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
19 8 0.13
20 31 0.50
21 20 0.32
22 3 0.05
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.32
Consensus pattern (20 bp):
AGAAATCGAGTTGCGAATTC
Found at i:937728 original size:61 final size:61
Alignment explanation
Indices: 937657--937792 Score: 165
Period size: 61 Copynumber: 2.2 Consensus size: 61
937647 GAAAAAGAAA
* * *
937657 TTCGCGTTGCGAATT-CAGAAA-TCGAGTTGCGAATTT-GAAATTCCGTGTTGTGAATTTGGA-
1 TTCGCGTTGCGAATTGCAGAAACT-GAGTTGCGAATTTGGAAA--CCATGTTGCGAAATTGGAG
*
937717 TATCGCGTTGCG-ATTGCAGAAACTGAGTTGCGAATTTGGAAACTATGTTGCGAAATTGGAG
1 T-TCGCGTTGCGAATTGCAGAAACTGAGTTGCGAATTTGGAAACCATGTTGCGAAATTGGAG
937778 TTCGCGTTGCGAATT
1 TTCGCGTTGCGAATT
937793 TGTTGGTTAT
Statistics
Matches: 66, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
60 28 0.42
61 33 0.50
62 5 0.08
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.33
Consensus pattern (61 bp):
TTCGCGTTGCGAATTGCAGAAACTGAGTTGCGAATTTGGAAACCATGTTGCGAAATTGGAG
Found at i:942368 original size:22 final size:22
Alignment explanation
Indices: 942316--942358 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
942306 TTCTCTTTTT
942316 TCAAATATTAGTCTTCAATTTA
1 TCAAATATTAGTCTTCAATTTA
942338 TCAAATATTAGTCTTCAATTT
1 TCAAATATTAGTCTTCAATTT
942359 TTTTAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.47
Consensus pattern (22 bp):
TCAAATATTAGTCTTCAATTTA
Found at i:942616 original size:18 final size:19
Alignment explanation
Indices: 942581--942617 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
942571 CACGGAATGT
942581 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
942601 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
942618 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:946207 original size:15 final size:16
Alignment explanation
Indices: 946170--946207 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
946160 AATGTGCTTC
946170 ATTTATATTCTGAATAT
1 ATTT-TATTCTGAATAT
*
946187 ATTTTATTCTGATTA-
1 ATTTTATTCTGAATAT
946202 ATTTTA
1 ATTTTA
946208 ACCTAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 10 0.50
17 4 0.20
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (16 bp):
ATTTTATTCTGAATAT
Found at i:949022 original size:43 final size:43
Alignment explanation
Indices: 948963--949107 Score: 220
Period size: 43 Copynumber: 3.4 Consensus size: 43
948953 TTTCAAGAAA
*
948963 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT-GATAGAC
1 AAACGCCACAATAGGTGTTGATATTTAGCGGCGTTTGGA-AGAC
*
949006 AAATGCCACAATAGGTGTTGATATTTAGCGGCGTTTGGAAGAC
1 AAACGCCACAATAGGTGTTGATATTTAGCGGCGTTTGGAAGAC
* * *
949049 AAACGCCGCAATAGATGTTGATATTTAGCGGCATTTGGAAGAC
1 AAACGCCACAATAGGTGTTGATATTTAGCGGCGTTTGGAAGAC
*
949092 AAACGCCACAGTAGGT
1 AAACGCCACAATAGGT
949108 TTCGATTTAT
Statistics
Matches: 92, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
43 90 0.98
44 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.26
Consensus pattern (43 bp):
AAACGCCACAATAGGTGTTGATATTTAGCGGCGTTTGGAAGAC
Found at i:949126 original size:86 final size:86
Alignment explanation
Indices: 948963--949127 Score: 237
Period size: 86 Copynumber: 1.9 Consensus size: 86
948953 TTTCAAGAAA
* * *
948963 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGATAGACAAATGCCACAATAGGTGTTGAT
1 AAACGCCGCAATAGATGTTGATATTTAGCGGCATTTGATAGACAAACGCCACAATAGGTGTTGAT
*
949028 ATTTAGCGGCGTTTGGAAGAC
66 ATTTAGCAGCGTTTGGAAGAC
*
949049 AAACGCCGCAATAGATGTTGATATTTAGCGGCATTTGGA-AGACAAACGCCACAGTAGGT-TTCG
1 AAACGCCGCAATAGATGTTGATATTTAGCGGCATTT-GATAGACAAACGCCACAATAGGTGTT-G
949112 AT-TTATAGCAGCGTTT
64 ATATT-TAGCAGCGTTT
949128 TTCTCAGAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
85 4 0.06
86 65 0.92
87 2 0.03
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (86 bp):
AAACGCCGCAATAGATGTTGATATTTAGCGGCATTTGATAGACAAACGCCACAATAGGTGTTGAT
ATTTAGCAGCGTTTGGAAGAC
Found at i:949139 original size:43 final size:43
Alignment explanation
Indices: 948963--949183 Score: 119
Period size: 43 Copynumber: 5.1 Consensus size: 43
948953 TTTCAAGAAA
* * * * *
948963 AAACGCCGCAATAGGTGTTGATATT-TAGCGGCG-TTTGATAGAC
1 AAACGCCACAGTAGGTGTTGAT-TTATAGCAGCGTTTTTAT-CAC
* * * ** **
949006 AAATGCCACAATAGGTGTTGATATT-TAGCGGCGTTTGGAAGAC
1 AAACGCCACAGTAGGTGTTGAT-TTATAGCAGCGTTTTTATCAC
* * * * * ** **
949049 AAACGCCGCAATAGATGTTGATATT-TAGCGGCATTTGGAAGAC
1 AAACGCCACAGTAGGTGTTGAT-TTATAGCAGCGTTTTTATCAC
* *
949092 AAACGCCACAGTAGGT-TTCGATTTATAGCAGCGTTTTTCTCAG
1 AAACGCCACAGTAGGTGTT-GATTTATAGCAGCGTTTTTATCAC
* * **
949135 AAACGCCGCAGTAGGTGTTGATTTTTAGTGGCGTTTTTATCAC
1 AAACGCCACAGTAGGTGTTGATTTATAGCAGCGTTTTTATCAC
949178 AAACGC
1 AAACGC
949184 TGCAATAAGT
Statistics
Matches: 149, Mismatches: 25, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
42 4 0.03
43 139 0.93
44 6 0.04
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.29
Consensus pattern (43 bp):
AAACGCCACAGTAGGTGTTGATTTATAGCAGCGTTTTTATCAC
Found at i:949139 original size:86 final size:86
Alignment explanation
Indices: 948963--949162 Score: 235
Period size: 86 Copynumber: 2.3 Consensus size: 86
948953 TTTCAAGAAA
* *
948963 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGATAGACAAATGCCACAATAGGTGTTGAT
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCATTTGATAGACAAACGCCACAATAGGTGTTGAT
* *
949028 ATTTAGCGGCGTTTGGAAGAC
66 ATTTAGCAGCGTTTGGAACAC
* *
949049 AAACGCCGCAATAGATGTTGATATTTAGCGGCATTTGGA-AGACAAACGCCACAGTAGGT-TTCG
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCATTT-GATAGACAAACGCCACAATAGGTGTT-G
**** *
949112 AT-TTATAGCAGCGTTTTTCTCAG
64 ATATT-TAGCAGCGTTTGGAACAC
* *
949135 AAACGCCGCAGTAGGTGTTGATTTTTAG
1 AAACGCCGCAATAGGTGTTGATATTTAG
949163 TGGCGTTTTT
Statistics
Matches: 97, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
85 4 0.04
86 91 0.94
87 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (86 bp):
AAACGCCGCAATAGGTGTTGATATTTAGCGGCATTTGATAGACAAACGCCACAATAGGTGTTGAT
ATTTAGCAGCGTTTGGAACAC
Found at i:949196 original size:43 final size:43
Alignment explanation
Indices: 949117--949272 Score: 118
Period size: 43 Copynumber: 3.6 Consensus size: 43
949107 TTTCGATTTA
* * * * * * **
949117 TAGCAGCGTTTTTCTCAGAAACGCCGCAGTAGGTGTTGATTTT
1 TAGCGGCGTTTTTATCACAAACGCCGCAATAAGTGTTAAGGTT
* *
949160 TAGTGGCGTTTTTATCACAAACGCTGCAATAAGTGTTAAGGTT
1 TAGCGGCGTTTTTATCACAAACGCCGCAATAAGTGTTAAGGTT
* ** * * *
949203 TAGCGGCGTTTTTTAGCTTAAACGCCGCAATATGTGTT-TGATT
1 TAGCGGCG-TTTTTATCACAAACGCCGCAATAAGTGTTAAGGTT
* *
949246 TGGCGGCGTCTTTAAT-ACAAACGCCGC
1 TAGCGGCGT-TTTTATCACAAACGCCGC
949273 TAAAGATCGA
Statistics
Matches: 88, Mismatches: 23, Indels: 5
0.76 0.20 0.04
Matches are distributed among these distances:
42 10 0.11
43 54 0.61
44 24 0.27
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (43 bp):
TAGCGGCGTTTTTATCACAAACGCCGCAATAAGTGTTAAGGTT
Found at i:949707 original size:21 final size:21
Alignment explanation
Indices: 949640--949696 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
949630 ATATGTTACT
949640 TCTCTTTGTGCTGCCGCTGCC
1 TCTCTTTGTGCTGCCGCTGCC
*
949661 TCTCTTTGTGCTGTCGCTGCC
1 TCTCTTTGTGCTGCCGCTGCC
949682 TCTCTTTGTGCTGCC
1 TCTCTTTGTGCTGCC
949697 ACTGTTTCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.00, C:0.35, G:0.23, T:0.42
Consensus pattern (21 bp):
TCTCTTTGTGCTGCCGCTGCC
Found at i:949721 original size:42 final size:42
Alignment explanation
Indices: 949640--949722 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
949630 ATATGTTACT
* * *
949640 TCTCTTTGTGCTGCCGCTGCCTCTCTTTGTGCTGTCGCTGCC
1 TCTCTTTGTGCTGCCACTGCCTCTCTCTCTGCTGTCGCTGCC
**
949682 TCTCTTTGTGCTGCCACTGTTTCTCTCTCTGCT-TCCGCTGC
1 TCTCTTTGTGCTGCCACTGCCTCTCTCTCTGCTGT-CGCTGC
949723 TGCTCTGGCT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 1 0.03
42 34 0.97
ACGTcount: A:0.01, C:0.36, G:0.20, T:0.42
Consensus pattern (42 bp):
TCTCTTTGTGCTGCCACTGCCTCTCTCTCTGCTGTCGCTGCC
Found at i:949765 original size:21 final size:21
Alignment explanation
Indices: 949704--949759 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
949694 GCCACTGTTT
949704 CTCTCTCTGCTTCCGCTGCTG
1 CTCTCTCTGCTTCCGCTGCTG
**
949725 CTCTGGCTGCTTCCGCTGCTG
1 CTCTCTCTGCTTCCGCTGCTG
949746 CTCTCTCTGCTTCC
1 CTCTCTCTGCTTCC
949760 CTTGCTTCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.00, C:0.43, G:0.20, T:0.38
Consensus pattern (21 bp):
CTCTCTCTGCTTCCGCTGCTG
Found at i:952759 original size:60 final size:59
Alignment explanation
Indices: 952692--952816 Score: 187
Period size: 60 Copynumber: 2.1 Consensus size: 59
952682 CACATACGAA
* * * *
952692 TTTTATCTTGGCGTACCAAGTAACATAGTTGAGCCTTAGCTCTTTATCATTCACATGGT
1 TTTTATCTTGGCGTACCAAGTAACATAGTTGAGCATTAACTCCTTATCATTCACATAGT
* *
952751 TTCTTATCTTGGCTTACCTAGTAACATAGTTGAGCATTAACTCCTTATCATTCACATAGT
1 TT-TTATCTTGGCGTACCAAGTAACATAGTTGAGCATTAACTCCTTATCATTCACATAGT
952811 TTTTAT
1 TTTTAT
952817 TCATGGATTT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
59 6 0.10
60 53 0.90
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.42
Consensus pattern (59 bp):
TTTTATCTTGGCGTACCAAGTAACATAGTTGAGCATTAACTCCTTATCATTCACATAGT
Found at i:954484 original size:57 final size:57
Alignment explanation
Indices: 954416--954605 Score: 353
Period size: 57 Copynumber: 3.3 Consensus size: 57
954406 ATTAAAACAG
954416 AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
1 AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
954473 AAGTACTTATGCATAAAACTACTTATAACAACAAAATACATTATAATTTAGAAACATTA
1 AAGTACTTATGCATAAAACTAC-T-TAACAACAAAATACATTATAATTTAGAAACATTA
*
954532 AAGTACTTATGCATAAAACTACTTAAAAACAAAATACATTATAATTTAGAAACATTA
1 AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
954589 AAGTACTTATGCATAAA
1 AAGTACTTATGCATAAA
954606 CAGTCTTCAC
Statistics
Matches: 130, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
57 72 0.55
58 2 0.02
59 56 0.43
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.30
Consensus pattern (57 bp):
AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
Found at i:956583 original size:2 final size:2
Alignment explanation
Indices: 956578--956602 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
956568 AAGAGAGTCC
956578 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
956603 AAATAGTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:959586 original size:21 final size:21
Alignment explanation
Indices: 959562--959610 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
959552 ATTTTTAGCC
959562 CAATGTATATGTAAGAGAATG
1 CAATGTATATGTAAGAGAATG
959583 CAATGTATATGTAAGAGAATG
1 CAATGTATATGTAAGAGAATG
959604 CAATGTA
1 CAATGTA
959611 CGCGATTCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.43, C:0.06, G:0.22, T:0.29
Consensus pattern (21 bp):
CAATGTATATGTAAGAGAATG
Done.