Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold331
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: 1394875
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 5 of 8
Found at i:850360 original size:13 final size:13
Alignment explanation
Indices: 850342--850367 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
850332 ACACACAATA
850342 TGTATCGATACAT
1 TGTATCGATACAT
850355 TGTATCGATACAT
1 TGTATCGATACAT
850368 CCCAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:850363 original size:32 final size:33
Alignment explanation
Indices: 850322--850385 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
850312 CCTTAACTGT
*
850322 TTGTATCGATACA-CACAATATGTATCGATACA
1 TTGTATCGATACATCACAAAATGTATCGATACA
*
850354 TTGTATCGATACATCCCAAAATGTATCGATAC
1 TTGTATCGATACATCACAAAATGTATCGATAC
850386 GTTGGCTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.31
Consensus pattern (33 bp):
TTGTATCGATACATCACAAAATGTATCGATACA
Found at i:852458 original size:15 final size:16
Alignment explanation
Indices: 852427--852459 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
852417 AGAAGATAAT
*
852427 AAATTGAAAATTATTG
1 AAATTAAAAATTATTG
852443 AAATTAAAAATT-TTG
1 AAATTAAAAATTATTG
852458 AA
1 AA
852460 CAAAAGATTG
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:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (16 bp):
AAATTAAAAATTATTG
Found at i:854080 original size:13 final size:13
Alignment explanation
Indices: 854062--854086 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
854052 AAATTGCACA
854062 GTATCGATACATT
1 GTATCGATACATT
854075 GTATCGATACAT
1 GTATCGATACAT
854087 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:854118 original size:21 final size:20
Alignment explanation
Indices: 854074--854126 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
854064 ATCGATACAT
**
854074 TGTATCGATACATGACCAAA
1 TGTATCGATACATGAAAAAA
*
854094 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAA-AA
*
854115 TGTATTGATACA
1 TGTATCGATACA
854127 GGTCATTGGT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (20 bp):
TGTATCGATACATGAAAAAA
Found at i:854195 original size:13 final size:13
Alignment explanation
Indices: 854177--854202 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
854167 TACACACAGT
854177 ATGTATCGATACA
1 ATGTATCGATACA
854190 ATGTATCGATACA
1 ATGTATCGATACA
854203 TCATAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:854219 original size:33 final size:32
Alignment explanation
Indices: 854159--854222 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
854149 TAGCCAAACT
**
854159 TGTATCGATACACACAGTATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
854191 TGTATCGATACATCATAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
854223 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:855826 original size:3 final size:3
Alignment explanation
Indices: 855812--855857 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
855802 CATCAAGGAC
*
855812 GAT GAA GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
855858 GTGACTCAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.30
Consensus pattern (3 bp):
GAT
Found at i:860424 original size:13 final size:13
Alignment explanation
Indices: 860406--860449 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
860396 TAGCATTCTC
*
860406 TGTATCGATACAT
1 TGTATCGATACAA
*
860419 TGTATCGATACAG
1 TGTATCGATACAA
860432 TGTATCGATACAA
1 TGTATCGATACAA
860445 TGTAT
1 TGTAT
860450 TTATATGAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:860909 original size:20 final size:21
Alignment explanation
Indices: 860877--860928 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 21
860867 CCCCTAGGCA
*
860877 GCACCCACCAGGTCGCGACC-G
1 GCACCC-CCAGGTCGCAACCGG
860898 GCACCCCCAGGTCGCAACCGG
1 GCACCCCCAGGTCGCAACCGG
860919 GCAGCCCCCA
1 GCA-CCCCCA
860929 CACTAGCAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 12 0.43
21 10 0.36
22 6 0.21
ACGTcount: A:0.19, C:0.50, G:0.27, T:0.04
Consensus pattern (21 bp):
GCACCCCCAGGTCGCAACCGG
Found at i:862911 original size:21 final size:20
Alignment explanation
Indices: 862867--862919 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
862857 ATCGATACAT
**
862867 TGTATCGATACATGACCAAA
1 TGTATCGATACATGAAAAAA
*
862887 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAA-AA
*
862908 TGTATCAATACA
1 TGTATCGATACA
862920 GGTCATTGGC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (20 bp):
TGTATCGATACATGAAAAAA
Found at i:866264 original size:8 final size:8
Alignment explanation
Indices: 866251--866276 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
866241 TTTGACTAAA
866251 ATTTTGTG
1 ATTTTGTG
866259 ATTTTGTG
1 ATTTTGTG
866267 ATTTTGTG
1 ATTTTGTG
866275 AT
1 AT
866277 GAATGATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:866497 original size:13 final size:13
Alignment explanation
Indices: 866479--866542 Score: 110
Period size: 13 Copynumber: 4.9 Consensus size: 13
866469 CAGCATTCTC
*
866479 TGTATCGATACAT
1 TGTATCGATACAG
866492 TGTATCGATACAG
1 TGTATCGATACAG
*
866505 TGTATCGATACAT
1 TGTATCGATACAG
866518 TGTATCGATACAG
1 TGTATCGATACAG
866531 TGTATCGATACA
1 TGTATCGATACA
866543 AAGGGTTTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 48 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:866515 original size:26 final size:26
Alignment explanation
Indices: 866479--866542 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
866469 CAGCATTCTC
866479 TGTATCGATACATTGTATCGATACAG
1 TGTATCGATACATTGTATCGATACAG
866505 TGTATCGATACATTGTATCGATACAG
1 TGTATCGATACATTGTATCGATACAG
866531 TGTATCGATACA
1 TGTATCGATACA
866543 AAGGGTTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (26 bp):
TGTATCGATACATTGTATCGATACAG
Found at i:868391 original size:22 final size:22
Alignment explanation
Indices: 868365--868409 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
868355 GGAAATTGTT
868365 AAATTATCTC-ATTAAGGGAGAG
1 AAATT-TCTCGATTAAGGGAGAG
* *
868387 AAATTTTTCGATTAAGGGGGAG
1 AAATTTCTCGATTAAGGGAGAG
868409 A
1 A
868410 GAAAAGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.29
Consensus pattern (22 bp):
AAATTTCTCGATTAAGGGAGAG
Found at i:868973 original size:13 final size:13
Alignment explanation
Indices: 868955--868979 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
868945 AGATTGCACA
868955 GTATCGATACATT
1 GTATCGATACATT
868968 GTATCGATACAT
1 GTATCGATACAT
868980 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:868992 original size:20 final size:21
Alignment explanation
Indices: 868967--869017 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
868957 ATCGATACAT
**
868967 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
868987 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
869008 TGTATCGATA
1 TGTATCGATA
869018 TAGGTCATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:869101 original size:32 final size:33
Alignment explanation
Indices: 869060--869127 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
869050 CCTTAACTGT
* *
869060 TTGTATCGATACA-CACAATATGTGTCGATACA
1 TTGTATCGATACATCACAAAATGTATCGATACA
*
869092 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACATCACAAAATGTATCGATACA
869125 TTG
1 TTG
869128 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACATCACAAAATGTATCGATACA
Found at i:869703 original size:34 final size:35
Alignment explanation
Indices: 869665--869731 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
869655 CCTTACAACA
869665 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
869699 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
869732 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:870205 original size:13 final size:13
Alignment explanation
Indices: 870187--870212 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
870177 CAATTTTTTG
870187 TGTATCGATACAT
1 TGTATCGATACAT
870200 TGTATCGATACAT
1 TGTATCGATACAT
870213 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:873107 original size:84 final size:84
Alignment explanation
Indices: 873017--873181 Score: 201
Period size: 84 Copynumber: 2.0 Consensus size: 84
873007 CATTTTCCAC
* * * *
873017 TTGCAACTCATTTC-TTTTCTCCTCTAATTCATTTATTTTCTCTTTAAAAGAAT-T-ATTTTCTA
1 TTGCAACTC-TTTCATATTCTCCTCTAATTCACTTAATTTCT-TTT-AAAGAATATCATTCTCTA
873079 AACTCATTGATTTACTTTCATT
63 AACTCATTGATTTACTTTCATT
* * *
873101 TTGCAACTCTTTCATATTCTTCTCTAATTCACTTAATTTCTTTTCAAGAATATCATTCTCTACAC
1 TTGCAACTCTTTCATATTCTCCTCTAATTCACTTAATTTCTTTTAAAGAATATCATTCTCTAAAC
* *
873166 TTATTGATTTATTTTC
66 TCATTGATTTACTTTC
873182 TTCTTTGAGT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
82 6 0.09
83 8 0.12
84 55 0.80
ACGTcount: A:0.25, C:0.20, G:0.04, T:0.52
Consensus pattern (84 bp):
TTGCAACTCTTTCATATTCTCCTCTAATTCACTTAATTTCTTTTAAAGAATATCATTCTCTAAAC
TCATTGATTTACTTTCATT
Found at i:874745 original size:34 final size:35
Alignment explanation
Indices: 874707--874773 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
874697 CCTTACAACA
874707 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
874741 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
874774 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:875249 original size:13 final size:13
Alignment explanation
Indices: 875231--875256 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
875221 CAATTTTTTG
875231 TGTATCGATACAT
1 TGTATCGATACAT
875244 TGTATCGATACAT
1 TGTATCGATACAT
875257 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:876205 original size:19 final size:20
Alignment explanation
Indices: 876181--876233 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
876171 ACATTATGCT
* *
876181 TTGTATCGATACGTGCTC-A
1 TTGTATCGATACATACTCAA
876200 TTGTATCGATACATACTCAA
1 TTGTATCGATACATACTCAA
*
876220 TTGTATTGATACAT
1 TTGTATCGATACAT
876234 GAAACTAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (20 bp):
TTGTATCGATACATACTCAA
Found at i:876224 original size:20 final size:19
Alignment explanation
Indices: 876162--876233 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 19
876152 CACATCCAGA
*
876162 TGTATCGATACATTA-TGCTT
1 TGTATCGATACA-TACT-CAT
* *
876182 TGTATCGATACGTGCTCAT
1 TGTATCGATACATACTCAT
876201 TGTATCGATACATACTCAAT
1 TGTATCGATACATACTC-AT
*
876221 TGTATTGATACAT
1 TGTATCGATACAT
876234 GAAACTAGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
19 18 0.41
20 26 0.59
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (19 bp):
TGTATCGATACATACTCAT
Found at i:876297 original size:13 final size:13
Alignment explanation
Indices: 876279--876311 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
876269 GATACATGGG
876279 ACATTGTATCAAT
1 ACATTGTATCAAT
*
876292 ACATTGTATCGAT
1 ACATTGTATCAAT
876305 ACATTGT
1 ACATTGT
876312 GCCTAACGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (13 bp):
ACATTGTATCAAT
Found at i:878243 original size:14 final size:14
Alignment explanation
Indices: 878226--878276 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 14
878216 CTTAATTTAA
878226 AAAAATTTATATAT
1 AAAAATTTATATAT
878240 AAAAATTT-TA-ATT
1 AAAAATTTATATA-T
*
878253 AAAATTTTCATATAT
1 AAAAATTT-ATATAT
*
878268 GAAAATTTA
1 AAAAATTTA
878277 ATTATAGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
12 1 0.03
13 10 0.33
14 9 0.30
15 9 0.30
16 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (14 bp):
AAAAATTTATATAT
Found at i:878265 original size:26 final size:26
Alignment explanation
Indices: 878219--878280 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
878209 GTAAAATCTT
*
878219 AATTTAA-AAAAATTTATATATA-AA
1 AATTTAATTAAAATTTATATATAGAA
878243 AATTTTAATTAAAATTT-TCATATATGAA
1 AA-TTTAATTAAAATTTAT-ATATA-GAA
878271 AATTTAATTA
1 AATTTAATTA
878281 TAGATTCCAC
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
24 2 0.06
25 6 0.19
26 12 0.38
27 8 0.25
28 4 0.12
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (26 bp):
AATTTAATTAAAATTTATATATAGAA
Found at i:878276 original size:27 final size:26
Alignment explanation
Indices: 878219--878280 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 26
878209 GTAAAATCTT
878219 AATTTAA--AAAAATTTATATATAAA
1 AATTTAATTAAAAATTTATATATAAA
* *
878243 AATTTTAATTAAAATTTTCATATATGAA
1 AA-TTTAATTAAAAATTT-ATATATAAA
878271 AATTTAATTA
1 AATTTAATTA
878281 TAGATTCCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 2 0.06
25 5 0.16
27 15 0.47
28 10 0.31
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (26 bp):
AATTTAATTAAAAATTTATATATAAA
Found at i:878327 original size:28 final size:27
Alignment explanation
Indices: 878241--878327 Score: 68
Period size: 28 Copynumber: 3.1 Consensus size: 27
878231 TTTATATATA
* *
878241 AAAATTTTAATTAAAATTTTCAT-ATATG
1 AAAA-TTTAATTAAAAATTTCATAAT-TT
* * * *
878269 AAAATTTAATTATAGATTCCACAATTAT
1 AAAATTTAATTAAAAATTTCATAATT-T
*
878297 AAAGTTTAATTAAAAATTTCATACATTT
1 AAAATTTAATTAAAAATTTCATA-ATTT
878325 AAA
1 AAA
878328 TTAAATTTTA
Statistics
Matches: 45, Mismatches: 11, Indels: 6
0.73 0.18 0.10
Matches are distributed among these distances:
27 14 0.31
28 28 0.62
29 3 0.07
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.41
Consensus pattern (27 bp):
AAAATTTAATTAAAAATTTCATAATTT
Found at i:881892 original size:28 final size:27
Alignment explanation
Indices: 881855--881935 Score: 78
Period size: 24 Copynumber: 3.0 Consensus size: 27
881845 ATTTATTTTT
881855 AATTTAATTAATATATTAATTTAAAAATA
1 AATTT-ATTAATATATT-ATTTAAAAATA
* **
881884 AATTTATTAAAATATT-TTT--ATTTA
1 AATTTATTAATATATTATTTAAAAATA
881908 AATTTATTAATTAGTATTATTTAAAAAT
1 AATTTATTAA-TA-TATTATTTAAAAAT
881936 TTTAATGATA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
24 13 0.32
25 1 0.02
26 7 0.17
27 3 0.07
28 10 0.24
29 7 0.17
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (27 bp):
AATTTATTAATATATTATTTAAAAATA
Found at i:882778 original size:14 final size:15
Alignment explanation
Indices: 882759--882798 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
882749 TATATTAACT
882759 TTAAAATAAATTTA-
1 TTAAAATAAATTTAG
*
882773 TTAAAATAATTTTAG
1 TTAAAATAAATTTAG
882788 TT-AAATAAATT
1 TTAAAATAAATT
882799 AATTTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 21 0.91
15 2 0.09
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (15 bp):
TTAAAATAAATTTAG
Found at i:885384 original size:19 final size:20
Alignment explanation
Indices: 885360--885413 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
885350 ACATTATGCT
* **
885360 TTGTATCAATACATGTTC-A
1 TTGTATCGATACATGCACAA
885379 TTGTATCGATACATGCACAA
1 TTGTATCGATACATGCACAA
885399 TTGTATCGATACATG
1 TTGTATCGATACATG
885414 AAACTGGCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGCACAA
Found at i:887045 original size:3 final size:3
Alignment explanation
Indices: 887030--887060 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
887020 AACCATCAAA
*
887030 GAT GAT GAA GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
887061 TTGACTCGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:891255 original size:13 final size:13
Alignment explanation
Indices: 891237--891273 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
891227 ATATTCTTTA
891237 TATCGATACATTG
1 TATCGATACATTG
891250 TATCGATACATTG
1 TATCGATACATTG
*
891263 TATGGATACAT
1 TATCGATACAT
891274 GGGTTACTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:893190 original size:28 final size:30
Alignment explanation
Indices: 893134--893191 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
893124 AATAAATTTT
*
893134 TTATCAAGGGGGAGAAAATCTTTTCAACGA
1 TTATCAAGGGGGAGAAAATCTTTTAAACGA
893164 TTATCAAGGGGGA-AAAAT-TTTTAAACGA
1 TTATCAAGGGGGAGAAAATCTTTTAAACGA
893192 GAGCCTTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 9 0.33
29 5 0.19
30 13 0.48
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.28
Consensus pattern (30 bp):
TTATCAAGGGGGAGAAAATCTTTTAAACGA
Found at i:893845 original size:52 final size:51
Alignment explanation
Indices: 893721--893853 Score: 137
Period size: 52 Copynumber: 2.6 Consensus size: 51
893711 AAACCCTTGT
* * * *
893721 ATGTATCGAT--ACA-CATTGTATCGATACCTTATGCTTTGTATCGATATA
1 ATGTATCGATACACACCATTGTATCGATACATTAGGCTCTGTATCGATACA
* *
893769 ATGTATCGATACACACCAGATGTATCGATAGATTAGGCTCTGTATCGATACA
1 ATGTATCGATACACACCA-TTGTATCGATACATTAGGCTCTGTATCGATACA
* ***
893821 ATGTATGGATACATGTTCATTGTATCGATACAT
1 ATGTATCGATACA-CACCATTGTATCGATACAT
893854 GCACAATTGT
Statistics
Matches: 68, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
48 10 0.15
50 3 0.04
51 2 0.03
52 51 0.75
53 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (51 bp):
ATGTATCGATACACACCATTGTATCGATACATTAGGCTCTGTATCGATACA
Found at i:893864 original size:20 final size:20
Alignment explanation
Indices: 893818--893874 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
893808 CTGTATCGAT
* *
893818 ACAA-TGTATGGATACATGT
1 ACAATTGTATCGATACATGC
*
893837 TC-ATTGTATCGATACATGC
1 ACAATTGTATCGATACATGC
893856 ACAATTGTATCGATACATG
1 ACAATTGTATCGATACATG
893875 AAACTGGCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 1 0.03
19 15 0.47
20 16 0.50
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (20 bp):
ACAATTGTATCGATACATGC
Found at i:893945 original size:20 final size:19
Alignment explanation
Indices: 893922--893989 Score: 67
Period size: 20 Copynumber: 3.8 Consensus size: 19
893912 TACATGGCAC
893922 ATTGTATCGATACATGATGA
1 ATTGTATCGATACAT-ATGA
893942 ATTGTATCGATAC-----A
1 ATTGTATCGATACATATGA
893956 A-TGTATCGATACATAATGA
1 ATTGTATCGATACAT-ATGA
*
893975 ATTGTATCAATACAT
1 ATTGTATCGATACAT
893990 TGCTTCAAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.28
14 2 0.05
19 2 0.05
20 25 0.62
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (19 bp):
ATTGTATCGATACATATGA
Found at i:893962 original size:13 final size:13
Alignment explanation
Indices: 893944--893968 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
893934 CATGATGAAT
893944 TGTATCGATACAA
1 TGTATCGATACAA
893957 TGTATCGATACA
1 TGTATCGATACA
893969 TAATGAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:893966 original size:33 final size:33
Alignment explanation
Indices: 893924--893988 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
893914 CATGGCACAT
* *
893924 TGTATCGATACATGATGAATTGTATCGATACAA
1 TGTATCGATACATAATGAATTGTATCAATACAA
893957 TGTATCGATACATAATGAATTGTATCAATACA
1 TGTATCGATACATAATGAATTGTATCAATACA
893989 TTGCTTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATAATGAATTGTATCAATACAA
Found at i:897293 original size:85 final size:85
Alignment explanation
Indices: 897204--897387 Score: 232
Period size: 85 Copynumber: 2.2 Consensus size: 85
897194 AAGATAAAGA
* *
897204 TTAGAGTATCTCCCT-AGAGGAGTGAAG-ATAAAGTTTTCCCAAAAATTATAAGAAGGAAAAGCT
1 TTAGAGTATCTCCCTCAGAGGAAT-AAGTATAAAGTTTTCCCAAAAATTATAAGAAAGAAAAGCT
897267 TGAATTTTTTTGAAGATCGGGG
65 TGAA-TTTTTTGAAGATCGGGG
* * * * * * *
897289 TTAGAGTATC-CTCTCGGAGGAATAGGTATAGATTTTTCCCAAAAATTATATGAAAGAAAAGTTT
1 TTAGAGTATCTCCCTCAGAGGAATAAGTATAAAGTTTTCCCAAAAATTATAAGAAAGAAAAGCTT
*
897353 GAATTTTTTGATGATCGGGG
66 GAATTTTTTGAAGATCGGGG
897373 TTAGAGTAT-TCCCTC
1 TTAGAGTATCTCCCTC
897388 GGAATAGTCT
Statistics
Matches: 85, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
84 34 0.40
85 51 0.60
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.33
Consensus pattern (85 bp):
TTAGAGTATCTCCCTCAGAGGAATAAGTATAAAGTTTTCCCAAAAATTATAAGAAAGAAAAGCTT
GAATTTTTTGAAGATCGGGG
Found at i:897414 original size:84 final size:83
Alignment explanation
Indices: 897235--897416 Score: 226
Period size: 84 Copynumber: 2.2 Consensus size: 83
897225 GTGAAGATAA
*
897235 AGTTTTCCCAAAAATTATAAGAAGGAAAAGCTTGAATTTTTTTGAAGATCGGGGTTAGAGTATCC
1 AGTTTTCCCAAAAATTATAAGAAAGAAAAGCTTGAATTTTTTTGAAGATCGGGGTTAGAGTATCC
*
897300 TCTCGGAGGAATAGGTATAG
66 TCTC-G-GGAATAGCTATAG
* * * *
897320 ATTTTTCCCAAAAATTATATGAAAGAAAAGTTTGAA-TTTTTTGATGATCGGGGTTAGAGTATTC
1 AGTTTTCCCAAAAATTATAAGAAAGAAAAGCTTGAATTTTTTTGAAGATCGGGGTTAGAGTA-TC
897384 C-CTC-GGAATAGTCTAGCTAG
65 CTCTCGGGAATAG-CTA--TAG
*
897404 AGTTTCCCCAAAA
1 AGTTTTCCCAAAA
897417 TTGATAATTT
Statistics
Matches: 85, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
81 7 0.08
82 2 0.02
84 41 0.48
85 35 0.41
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (83 bp):
AGTTTTCCCAAAAATTATAAGAAAGAAAAGCTTGAATTTTTTTGAAGATCGGGGTTAGAGTATCC
TCTCGGGAATAGCTATAG
Found at i:900704 original size:73 final size:74
Alignment explanation
Indices: 900590--900757 Score: 205
Period size: 73 Copynumber: 2.3 Consensus size: 74
900580 CCATTGACTC
* * **
900590 GTGTGGGCTTTAAAGTAGGT-AAGAAAAAGCATCCTGTTTTTTGAGGACTGAAATGGATAAGTGC
1 GTGTGGGCTTTGAGGTAGGTAAAGAAAAAGCATCCTACTTTTTGAGGACTGAAATGGATAAGTGC
** *
900654 CATTAGCTT
66 CACCAACTT
* * * * *
900663 GTGTGAGCTTTGAGGTAGGTAAAG-AAAAGCATCCTACTTTTTTAGGACTGAAGTGGATAGGTGT
1 GTGTGGGCTTTGAGGTAGGTAAAGAAAAAGCATCCTACTTTTTGAGGACTGAAATGGATAAGTGC
*
900727 TACCAACTT
66 CACCAACTT
900736 GTGTGGGCTTTGAGGTAGGTAA
1 GTGTGGGCTTTGAGGTAGGTAA
900758 GCATTTTACT
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
73 77 0.96
74 3 0.04
ACGTcount: A:0.28, C:0.11, G:0.30, T:0.32
Consensus pattern (74 bp):
GTGTGGGCTTTGAGGTAGGTAAAGAAAAAGCATCCTACTTTTTGAGGACTGAAATGGATAAGTGC
CACCAACTT
Found at i:900995 original size:63 final size:63
Alignment explanation
Indices: 900927--901045 Score: 150
Period size: 63 Copynumber: 1.9 Consensus size: 63
900917 ACTAAGGTAG
* * * * * *
900927 GTAGGTGCCACTAGCTTATGTGGG-TTTTAAGATGGATAAGCATCTTTCTTTTTGAGAACTGCA
1 GTAGGTGCCACCAGCGTATGTGGGCTTTGAA-ATGGATAAGCACCTTACTCTTTGAGAACTGCA
* *
900990 GTAGGTGCCACCAGCGTGTGTGGGCTTTGAAATGGGTAAGCACCTTACTCTTTGAG
1 GTAGGTGCCACCAGCGTATGTGGGCTTTGAAATGGATAAGCACCTTACTCTTTGAG
901046 GGTTGAGGGA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
63 42 0.89
64 5 0.11
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.33
Consensus pattern (63 bp):
GTAGGTGCCACCAGCGTATGTGGGCTTTGAAATGGATAAGCACCTTACTCTTTGAGAACTGCA
Found at i:901236 original size:65 final size:64
Alignment explanation
Indices: 901132--901254 Score: 158
Period size: 65 Copynumber: 1.9 Consensus size: 64
901122 TAAAGATAGA
* * * *
901132 TAGGTGCCACCAGCTTGTGTGGGCTTTAAGATAGTTAAGAAAAAAGTGTCTTGCTCTTTTGTAGG
1 TAGGTGCCACCAGCTTGTATAGGCTTCAAGATAGTTAAG-AAAAAGTATCTTGCTCTTTTGTAGG
* **
901197 TAGGTGTCACCAGCTTGTATAGGCTTCGCGATA-TGTAAGAAAAAGTATCTTGCTCTTT
1 TAGGTGCCACCAGCTTGTATAGGCTTCAAGATAGT-TAAGAAAAAGTATCTTGCTCTTT
901255 GAGAACTAAG
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
64 19 0.38
65 31 0.62
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.34
Consensus pattern (64 bp):
TAGGTGCCACCAGCTTGTATAGGCTTCAAGATAGTTAAGAAAAAGTATCTTGCTCTTTTGTAGG
Found at i:901285 original size:73 final size:72
Alignment explanation
Indices: 901192--901531 Score: 328
Period size: 73 Copynumber: 4.7 Consensus size: 72
901182 TTGCTCTTTT
* * * * * *
901192 GTAGGTAGGTGTCACCAGCTTGTATAGGCTTCGCGATATGTAAGAAAAAGTATCTTGCTCTTTGA
1 GTAGGTAGGTGCCACCAGCTTATGTGGGCTTTGCGGTATGTAAGAAAAAGTATCTTGCTCTTT-A
*
901257 GAACTAAG
65 AAACTAAG
* * * * *
901265 GTAGGTAGATGCCACAAGCTTATGTGGGCTTTGCGGTATATAAGAAAAAGTGTC-CGACTCTTTA
1 GTAGGTAGGTGCCACCAGCTTATGTGGGCTTTGCGGTATGTAAGAAAAAGTATCTTG-CTCTTTA
901329 AAGACTAAG
65 AA-ACTAAG
* * * * *
901338 GTAGGTAGGTGCCACCAACTTGTGTGTGCTTTGAGGTATGTAAGAAAAAGCATCTTAG-TCATTT
1 GTAGGTAGGTGCCACCAGCTTATGTGGGCTTTGCGGTATGTAAGAAAAAGTATCTT-GCTC-TTT
*
901402 AAAAC-ATGG
64 AAAACTA-AG
* * * * * *
901411 GTAGATAGGTGCCACCAGCTTATATGGGCTTTGTGGTATGTAAAAAAAAGTATCATGCTTTTTGA
1 GTAGGTAGGTGCCACCAGCTTATGTGGGCTTTGCGGTATGTAAGAAAAAGTATCTTGCTCTTT-A
** *
901476 GGACT-GG
65 AAACTAAG
* *
901483 GTAGGTAGATGCCACCAGCTTATGTGGGCTTTGTGGTATGTAAGAAAAA
1 GTAGGTAGGTGCCACCAGCTTATGTGGGCTTTGCGGTATGTAAGAAAAA
901532 ACGTCCTACT
Statistics
Matches: 219, Mismatches: 39, Indels: 19
0.79 0.14 0.07
Matches are distributed among these distances:
72 55 0.25
73 157 0.72
74 6 0.03
75 1 0.00
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (72 bp):
GTAGGTAGGTGCCACCAGCTTATGTGGGCTTTGCGGTATGTAAGAAAAAGTATCTTGCTCTTTAA
AACTAAG
Found at i:905880 original size:22 final size:22
Alignment explanation
Indices: 905840--905882 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
905830 ATTCATCACA
*
905840 GTATCGATACATCATTGTTCAT
1 GTATCGATACATCACTGTTCAT
**
905862 GTATCGATATGTCACTGTTCA
1 GTATCGATACATCACTGTTCA
905883 CACTATTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.40
Consensus pattern (22 bp):
GTATCGATACATCACTGTTCAT
Found at i:908089 original size:84 final size:84
Alignment explanation
Indices: 907916--908076 Score: 200
Period size: 84 Copynumber: 1.9 Consensus size: 84
907906 ACTCAAAGAA
* * * * * *
907916 GAAAATAAATCAATAAGTGTAGAGAATGATTTTCTTGAAAAGAAATTAAGTGAATTAGAGAAGAA
1 GAAAATAAATCAATAAGTGTAGAAAATAATTTTCTTAAAAAGAAAATAAATGAAATAGAGAAGAA
*
907981 TATGAAAGAGTTACAAAAT
66 TAAGAAAGAGTTACAAAAT
* * *
908000 GAAAATAAATCAATGAGTTTAGAAAATAATTCTT-TTAAAAAGAAAATAAATGAAATAGAGGAGA
1 GAAAATAAATCAATAAGTGTAGAAAATAATT-TTCTTAAAAAGAAAATAAATGAAATAGAGAAGA
908064 A-AAGAAATGAGTT
65 ATAAGAAA-GAGTT
908077 GCAAGTGGAA
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
83 5 0.08
84 58 0.89
85 2 0.03
ACGTcount: A:0.53, C:0.03, G:0.18, T:0.25
Consensus pattern (84 bp):
GAAAATAAATCAATAAGTGTAGAAAATAATTTTCTTAAAAAGAAAATAAATGAAATAGAGAAGAA
TAAGAAAGAGTTACAAAAT
Found at i:910632 original size:13 final size:13
Alignment explanation
Indices: 910614--910638 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
910604 AGTTTGCTTA
910614 GTATCGATACATT
1 GTATCGATACATT
910627 GTATCGATACAT
1 GTATCGATACAT
910639 AAACTGGCAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:911574 original size:20 final size:19
Alignment explanation
Indices: 911520--911574 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
911510 AAAACCCTTA
*
911520 AAAGTATCGATACACAATTC
1 AAAGTATCGATACA-TATTC
911540 AAAGTATCGATACATATTGC
1 AAAGTATCGATACATATT-C
*
911560 AATGTATCGATACAT
1 AAAGTATCGATACAT
911575 CAAAAATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 3 0.09
20 29 0.91
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (19 bp):
AAAGTATCGATACATATTC
Found at i:911663 original size:13 final size:13
Alignment explanation
Indices: 911645--911670 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
911635 TACACCAAGT
911645 ATGTATCGATACA
1 ATGTATCGATACA
911658 ATGTATCGATACA
1 ATGTATCGATACA
911671 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:911668 original size:32 final size:33
Alignment explanation
Indices: 911627--911690 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
911617 TAGCCAAACT
* **
911627 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
911659 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
911691 TAGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:916613 original size:51 final size:52
Alignment explanation
Indices: 916504--916639 Score: 159
Period size: 52 Copynumber: 2.6 Consensus size: 52
916494 GGCCTGCATG
* * * *
916504 TATCGATACATTGAAGAATGTATTGATAGATTTGGGTCAAAAACAAAGAATT
1 TATCGATACAATGAAGAATGTATAGATACATTTAGGTCAAAAACAAAGAATT
* * * * *
916556 TATCGATATAATGAAGAATATATAGATACATTTAGGTTAAAACCTAA-AATT
1 TATCGATACAATGAAGAATGTATAGATACATTTAGGTCAAAAACAAAGAATT
*
916607 TATCGATACAATGAA-AATTGTATCGATACATTT
1 TATCGATACAATGAAGAA-TGTATAGATACATTT
916640 TCATTCTAGA
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
50 2 0.03
51 31 0.44
52 38 0.54
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (52 bp):
TATCGATACAATGAAGAATGTATAGATACATTTAGGTCAAAAACAAAGAATT
Found at i:916725 original size:20 final size:20
Alignment explanation
Indices: 916695--916748 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
916685 CATTTCAAAC
* *
916695 ATGTATTGATACATT-CACTT
1 ATGTATCGATACATTAC-CCT
916715 ATGTATCGATACATTACCCT
1 ATGTATCGATACATTACCCT
916735 ATTGTATCGATACA
1 A-TGTATCGATACA
916749 GTTTGTTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTACCCT
Found at i:923237 original size:20 final size:20
Alignment explanation
Indices: 923214--923261 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
923204 CATTTCAGAC
923214 ATGTATCAATACATTCACTT
1 ATGTATCAATACATTCACTT
** *
923234 ATGTATTGATACATTCATTT
1 ATGTATCAATACATTCACTT
923254 ATTGTATC
1 A-TGTATC
923262 GATAAAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (20 bp):
ATGTATCAATACATTCACTT
Found at i:924543 original size:20 final size:19
Alignment explanation
Indices: 924518--924588 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 19
924508 CTACTGTTTA
924518 TATCGATACATGGCACATTG
1 TATCGATACATGG-ACATTG
*
924538 TATCGATACAATCGATACATTG
1 TATCGATAC-AT-G-GACATTG
924560 TATCGATACATGAAGA-ATTG
1 TATCGATACATG--GACATTG
924580 TATCGATAC
1 TATCGATAC
924589 TTTGTCCCAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
20 23 0.51
21 6 0.13
22 16 0.36
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (19 bp):
TATCGATACATGGACATTG
Found at i:924566 original size:13 final size:13
Alignment explanation
Indices: 924532--924570 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
924522 GATACATGGC
924532 ACATTGTATCGAT
1 ACATTGTATCGAT
924545 ACA----ATCGAT
1 ACATTGTATCGAT
924554 ACATTGTATCGAT
1 ACATTGTATCGAT
924567 ACAT
1 ACAT
924571 GAAGAATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 8
0.73 0.00 0.27
Matches are distributed among these distances:
9 9 0.41
13 13 0.59
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:925273 original size:15 final size:15
Alignment explanation
Indices: 925235--925278 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
925225 AACCATCAAA
* *
925235 GATGATAAAGATAAT
1 GATGATAATGATGAT
925250 GATGATAATGATGAT
1 GATGATAATGATGAT
925265 GATGATAATGATGA
1 GATGATAATGATGA
925279 AGTTGACTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.25, T:0.30
Consensus pattern (15 bp):
GATGATAATGATGAT
Found at i:930323 original size:34 final size:35
Alignment explanation
Indices: 930285--930351 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
930275 CCTTACAACA
930285 CTATC-TTTC-AAGACTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGACTAAGATAG-AACCTCTCTCT
930319 CTATCTTTTTCAAAGACTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGACTAAGATAGAACCTCTC
930352 AATTACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.33, C:0.25, G:0.09, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGACTAAGATAGAACCTCTCTCT
Found at i:930838 original size:13 final size:13
Alignment explanation
Indices: 930820--930844 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
930810 CTATTCACAA
930820 TGTATCGATACAC
1 TGTATCGATACAC
930833 TGTATCGATACA
1 TGTATCGATACA
930845 TGAATAGTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:930922 original size:22 final size:22
Alignment explanation
Indices: 930833--930950 Score: 87
Period size: 22 Copynumber: 5.1 Consensus size: 22
930823 ATCGATACAC
*
930833 TGTATCGATACATGAATAGTGA
1 TGTATCGATACATGAACAGTGA
*
930855 TGAACATATCGATACATGAATAGTGA
1 TG----TATCGATACATGAACAGTGA
**
930881 TACAT-GA-ACAGTTATGAACAGTGA
1 TGTATCGATAC----ATGAACAGTGA
930905 TGTATCGATACATGAACAGTGA
1 TGTATCGATACATGAACAGTGA
* * *
930927 TATATTGATAGATGAACAGTGA
1 TGTATCGATACATGAACAGTGA
930949 TG
1 TG
930951 AATAGTGATG
Statistics
Matches: 77, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
20 2 0.03
21 2 0.03
22 35 0.45
24 13 0.17
25 2 0.03
26 23 0.30
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (22 bp):
TGTATCGATACATGAACAGTGA
Found at i:930952 original size:10 final size:10
Alignment explanation
Indices: 930937--930968 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
930927 TATATTGATA
930937 GATGAACAGT
1 GATGAACAGT
*
930947 GATGAATAGT
1 GATGAACAGT
930957 GATGAACAGT
1 GATGAACAGT
930967 GA
1 GA
930969 AAATGAGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.41, C:0.06, G:0.31, T:0.22
Consensus pattern (10 bp):
GATGAACAGT
Found at i:931108 original size:21 final size:21
Alignment explanation
Indices: 931068--931108 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
931058 GTCAACCTTG
*
931068 TGTATTGATATCAATAGTATA
1 TGTATTGATATCAACAGTATA
931089 TGTATTGATA-CAACACGTAT
1 TGTATTGATATCAACA-GTAT
931109 TTTTATTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.39
Consensus pattern (21 bp):
TGTATTGATATCAACAGTATA
Found at i:932472 original size:13 final size:13
Alignment explanation
Indices: 932454--932478 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
932444 ACTGAAGCAA
932454 TGTATCGATACAT
1 TGTATCGATACAT
932467 TGTATCGATACA
1 TGTATCGATACA
932479 ATCTGGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:934261 original size:21 final size:21
Alignment explanation
Indices: 934235--934310 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
934225 ACATGTTGCA
934235 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
934256 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
934276 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
934297 ATGTATCGATACAT
1 ATGTATCGATACAT
934311 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:934268 original size:41 final size:41
Alignment explanation
Indices: 934217--934310 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
934207 ACAGTTCAAA
*
934217 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
934258 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
934299 GTATCGATACAT
1 GTATCGATACAT
934311 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:934289 original size:20 final size:20
Alignment explanation
Indices: 934197--934289 Score: 107
Period size: 20 Copynumber: 4.6 Consensus size: 20
934187 ACCCCTAAAA
* *
934197 GTATCGATACACAGTT-CAAA
1 GTATCGATACA-TGTTGCAAT
934217 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
934237 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
934258 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
934278 GTATCGATACAT
1 GTATCGATACAT
934290 AAAAAAGATG
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
19 3 0.05
20 42 0.69
21 16 0.26
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:934367 original size:13 final size:13
Alignment explanation
Indices: 934349--934374 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
934339 TACAGCAAGT
934349 ATGTATCGATACA
1 ATGTATCGATACA
934362 ATGTATCGATACA
1 ATGTATCGATACA
934375 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:938456 original size:15 final size:15
Alignment explanation
Indices: 938436--938466 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
938426 TAAAAATGTC
*
938436 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
938451 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
938466 C
1 C
938467 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:940560 original size:20 final size:21
Alignment explanation
Indices: 940481--940559 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
940471 AATGTCCAAA
*
940481 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
940501 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
940526 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
940546 TTGTATCGATACAT
1 ATGTATCGATACAT
940560 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:940564 original size:13 final size:13
Alignment explanation
Indices: 940546--940584 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
940536 ACATTTTTCT
940546 TTGTATCGATACA
1 TTGTATCGATACA
940559 TTGTATCGATACA
1 TTGTATCGATACA
*
940572 CTGTATCGATACA
1 TTGTATCGATACA
940585 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:943049 original size:20 final size:20
Alignment explanation
Indices: 943026--943098 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
943016 ACAATTCAAA
943026 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
943046 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
943067 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
943087 GTATCGATACAT
1 GTATCGATACAT
943099 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:943070 original size:21 final size:21
Alignment explanation
Indices: 943044--943119 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
943034 ACATGTTGCA
943044 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
943065 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
943085 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
943106 ATGTATCGATACAT
1 ATGTATCGATACAT
943120 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:943077 original size:41 final size:41
Alignment explanation
Indices: 943026--943119 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
943016 ACAATTCAAA
*
943026 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
943067 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
943108 GTATCGATACAT
1 GTATCGATACAT
943120 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:943176 original size:13 final size:13
Alignment explanation
Indices: 943158--943183 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
943148 TACAGCAAGT
943158 ATGTATCGATACA
1 ATGTATCGATACA
943171 ATGTATCGATACA
1 ATGTATCGATACA
943184 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:945722 original size:34 final size:35
Alignment explanation
Indices: 945684--945750 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
945674 CCTTACAACA
*
945684 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGACTAAGATAG-AACCTCTCTCT
945718 CTATCTTTTTCAAAGACTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGACTAAGATAGAACCTCTC
945751 AATCACTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.41
37 12 0.41
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGACTAAGATAGAACCTCTCTCT
Found at i:946239 original size:13 final size:13
Alignment explanation
Indices: 946221--946245 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
946211 CTATTCACAA
946221 TGTATCGATACAC
1 TGTATCGATACAC
946234 TGTATCGATACA
1 TGTATCGATACA
946246 TGAGTAGTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:946331 original size:22 final size:22
Alignment explanation
Indices: 946303--946359 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
946293 GTGAACAGTT
946303 ATGAACAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
* **
946325 ATGAACAGTGATATATCGATTG
1 ATGAACAGTGATGTATCGATAC
946347 ATGAACAGTGATG
1 ATGAACAGTGATG
946360 AATAGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.28
Consensus pattern (22 bp):
ATGAACAGTGATGTATCGATAC
Found at i:946360 original size:10 final size:10
Alignment explanation
Indices: 946345--946377 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
946335 ATATATCGAT
946345 TGATGAACAG
1 TGATGAACAG
*
946355 TGATGAATAG
1 TGATGAACAG
946365 TGATGAACAG
1 TGATGAACAG
946375 TGA
1 TGA
946378 AAATGAGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.39, C:0.06, G:0.30, T:0.24
Consensus pattern (10 bp):
TGATGAACAG
Found at i:946550 original size:21 final size:21
Alignment explanation
Indices: 946510--946550 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
946500 GTCAACCTTG
*
946510 TGTATTGATACCAATAGTATA
1 TGTATTGATACCAACAGTATA
946531 TGTATTGATA-CAACACGTAT
1 TGTATTGATACCAACA-GTAT
946551 TTTTATTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (21 bp):
TGTATTGATACCAACAGTATA
Found at i:953132 original size:21 final size:20
Alignment explanation
Indices: 953107--953145 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
953097 ATAGACATGC
*
953107 TAAAAAGCTTGGAACATGGCA
1 TAAAAAGCAT-GAACATGGCA
*
953128 TAAAATGCATGAACATGG
1 TAAAAAGCATGAACATGG
953146 GGTGTTAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.21
Consensus pattern (20 bp):
TAAAAAGCATGAACATGGCA
Found at i:954119 original size:21 final size:21
Alignment explanation
Indices: 954095--954146 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
954085 ATGAATATTG
*
954095 TATCGATACACTCCAAGCATA
1 TATCGATACACTACAAGCATA
* *
954116 TATCAATACACTACAAGCATG
1 TATCGATACACTACAAGCATA
954137 TATCGATACA
1 TATCGATACA
954147 TTCACTTATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (21 bp):
TATCGATACACTACAAGCATA
Found at i:954230 original size:20 final size:21
Alignment explanation
Indices: 954205--954254 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
954195 ATGGTCCAGC
* *
954205 ATCGATGCATTCACTT-ATGT
1 ATCGATACATTAACTTGATGT
*
954225 ATCGATACATTAACTTGTTGT
1 ATCGATACATTAACTTGATGT
954246 ATCGATACA
1 ATCGATACA
954255 AATTGTAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (21 bp):
ATCGATACATTAACTTGATGT
Found at i:955284 original size:15 final size:15
Alignment explanation
Indices: 955264--955293 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
955254 TTCCGTTGGA
955264 GATGAAATGATGATG
1 GATGAAATGATGATG
955279 GATGAAATGATGATG
1 GATGAAATGATGATG
955294 TAATGTATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.33, T:0.27
Consensus pattern (15 bp):
GATGAAATGATGATG
Found at i:957908 original size:32 final size:34
Alignment explanation
Indices: 957863--957953 Score: 109
Period size: 36 Copynumber: 2.7 Consensus size: 34
957853 CAACACTATC
957863 TTTC-AAGGCTAAGATAGAAACCTC-C-CTATC-T
1 TTTCAAAGGCTAAGATAG-AACCTCTCTCTATCTT
**
957894 TTTCACGGGCTAAGATAGAACCTTTCTCTCTATCTT
1 TTTCAAAGGCTAAGATAGAACC--TCTCTCTATCTT
957930 TTTCAAAGGCTAAGATAGAACCTC
1 TTTCAAAGGCTAAGATAGAACCTC
957954 ACAATCACTT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
31 8 0.16
32 11 0.22
33 2 0.04
34 3 0.06
35 5 0.10
36 21 0.42
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (34 bp):
TTTCAAAGGCTAAGATAGAACCTCTCTCTATCTT
Found at i:961639 original size:21 final size:21
Alignment explanation
Indices: 961615--961658 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
961605 TCTTTTCTCC
* *
961615 TCTAATTCATTTATTTTCCTT
1 TCTAATTCACTTAATTTCCTT
*
961636 TCTAATTCACTTAATTTCTTT
1 TCTAATTCACTTAATTTCCTT
961657 TC
1 TC
961659 AAGAATATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.59
Consensus pattern (21 bp):
TCTAATTCACTTAATTTCCTT
Found at i:963238 original size:36 final size:32
Alignment explanation
Indices: 963155--963249 Score: 97
Period size: 36 Copynumber: 2.9 Consensus size: 32
963145 CCTTACAACA
963155 CTATC-TTTC-AAGGCTAAGATAGAAACC-TCC
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTTCC
**
963185 CTATCTTTTCACGGGCTAAGATAGAACCTTTCTC
1 CTATCTTTTCAAAGGCTAAGATAGAACC-TTC-C
*
963219 TCTATCTTTTTCAAAGGCTAAGATTGAACCT
1 -CTATC-TTTTCAAAGGCTAAGATAGAACCT
963250 CACAATCACT
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
30 5 0.09
31 8 0.15
32 11 0.21
33 2 0.04
34 1 0.02
35 6 0.11
36 20 0.38
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (32 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTTCC
Found at i:963756 original size:10 final size:10
Alignment explanation
Indices: 963741--963771 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
963731 TTTGAACAGT
963741 ATGAATAGTG
1 ATGAATAGTG
963751 ATGAATAGTG
1 ATGAATAGTG
*
963761 ATGAACAGTG
1 ATGAATAGTG
963771 A
1 A
963772 AAAATGAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.42, C:0.03, G:0.29, T:0.26
Consensus pattern (10 bp):
ATGAATAGTG
Found at i:966101 original size:12 final size:13
Alignment explanation
Indices: 966084--966162 Score: 51
Period size: 12 Copynumber: 6.2 Consensus size: 13
966074 AAGAAGAGAG
966084 AGGAGG-GATGAT
1 AGGAGGAGATGAT
*
966096 AGGAGGAGA-GAC
1 AGGAGGAGATGAT
*
966108 AGGAGAGATAGTAGAAT
1 AGGAG-GAGA-T-G-AT
966125 AGGAGG-GATGAT
1 AGGAGGAGATGAT
*
966137 AGGAGGAGA-GAC
1 AGGAGGAGATGAT
*
966149 AGGA-GAGATAAT
1 AGGAGGAGATGAT
966161 AG
1 AG
966163 AGAGAGGATG
Statistics
Matches: 52, Mismatches: 7, Indels: 16
0.69 0.09 0.21
Matches are distributed among these distances:
11 4 0.08
12 30 0.58
13 8 0.15
14 1 0.02
15 1 0.02
16 2 0.04
17 6 0.12
ACGTcount: A:0.42, C:0.03, G:0.44, T:0.11
Consensus pattern (13 bp):
AGGAGGAGATGAT
Found at i:966111 original size:24 final size:24
Alignment explanation
Indices: 966078--966162 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 24
966068 AAGAGAAAGA
*
966078 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
966102 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
966120 AGA-ATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
966143 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
966163 AGAGAGGATG
Statistics
Matches: 47, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
17 5 0.11
18 5 0.11
19 2 0.04
20 3 0.06
21 3 0.06
22 2 0.04
23 5 0.11
24 22 0.47
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.11
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:966129 original size:41 final size:42
Alignment explanation
Indices: 966078--966177 Score: 166
Period size: 41 Copynumber: 2.4 Consensus size: 42
966068 AAGAGAAAGA
*
966078 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAGT
1 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
*
966120 AGA-ATAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
1 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
*
966161 AGAGAGAGGATGGATGA
1 AGAGAGAGGAGGGATGA
966178 CAGAGGGAGG
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
41 39 0.74
42 14 0.26
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.11
Consensus pattern (42 bp):
AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
Found at i:969016 original size:110 final size:110
Alignment explanation
Indices: 968823--969044 Score: 426
Period size: 110 Copynumber: 2.0 Consensus size: 110
968813 TGATTTTGCT
*
968823 AATCATTTGAATTGGAATGTGATGCATCTAATGTAGGGATAGGGGTTGTTTTGATGCAAGGAGGG
1 AATCATTTGAATTGGAATGTGATGCATCTAATGTAGGGATAGGGGCTGTTTTGATGCAAGGAGGG
*
968888 CATCCCATTTCCTACTTTAGTGAAAAGCTTAATGGGGCTAGTTTG
66 CATCCCATTGCCTACTTTAGTGAAAAGCTTAATGGGGCTAGTTTG
968933 AATCATTTGAATTGGAATGTGATGCATCTAATGTAGGGATAGGGGCTGTTTTGATGCAAGGAGGG
1 AATCATTTGAATTGGAATGTGATGCATCTAATGTAGGGATAGGGGCTGTTTTGATGCAAGGAGGG
968998 CATCCCATTGCCTACTTTAGTGAAAAGCTTAATGGGGCTAGTTTG
66 CATCCCATTGCCTACTTTAGTGAAAAGCTTAATGGGGCTAGTTTG
969043 AA
1 AA
969045 GTATCCTACT
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
110 110 1.00
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.32
Consensus pattern (110 bp):
AATCATTTGAATTGGAATGTGATGCATCTAATGTAGGGATAGGGGCTGTTTTGATGCAAGGAGGG
CATCCCATTGCCTACTTTAGTGAAAAGCTTAATGGGGCTAGTTTG
Found at i:974663 original size:31 final size:31
Alignment explanation
Indices: 974626--974687 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
974616 CATAGAAATG
974626 AGAGATAATCAGAATGTATTTTATAATTGCC
1 AGAGATAATCAGAATGTATTTTATAATTGCC
974657 AGAGATAATCAGAATGTATTTTATAATTGCC
1 AGAGATAATCAGAATGTATTTTATAATTGCC
974688 TTCAATCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (31 bp):
AGAGATAATCAGAATGTATTTTATAATTGCC
Found at i:975421 original size:13 final size:13
Alignment explanation
Indices: 975403--975428 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
975393 TACACCAAGT
975403 ATGTATCGATACA
1 ATGTATCGATACA
975416 ATGTATCGATACA
1 ATGTATCGATACA
975429 CCAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:975426 original size:32 final size:33
Alignment explanation
Indices: 975385--975448 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
975375 TAGCCAAACT
**
975385 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
975417 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
975449 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:977680 original size:21 final size:21
Alignment explanation
Indices: 977647--977696 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
977637 TTGCAAGTTG
*
977647 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
977669 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
977690 AAATAAA
1 AAATAAA
977697 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:981623 original size:13 final size:13
Alignment explanation
Indices: 981605--981630 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
981595 ACATTTTTCT
981605 TTGTATCGATACA
1 TTGTATCGATACA
981618 TTGTATCGATACA
1 TTGTATCGATACA
981631 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:981794 original size:20 final size:20
Alignment explanation
Indices: 981751--981796 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
981741 AAATCTTTTG
981751 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
981772 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
981792 CAAAA
1 CAAAA
981797 CCAACATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:984204 original size:13 final size:13
Alignment explanation
Indices: 984186--984211 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
984176 TACACCAAGT
984186 ATGTATCGATACA
1 ATGTATCGATACA
984199 ATGTATCGATACA
1 ATGTATCGATACA
984212 CCAAACATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:984209 original size:32 final size:33
Alignment explanation
Indices: 984168--984231 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
984158 TAGCCAAACT
**
984168 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAACATTGTATCGATACAA
984200 TGTATCGATACACCAAACATTGTATCGATACA
1 TGTATCGATACACCAAACATTGTATCGATACA
984232 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAACATTGTATCGATACAA
Found at i:985155 original size:83 final size:82
Alignment explanation
Indices: 985065--985290 Score: 208
Period size: 83 Copynumber: 2.7 Consensus size: 82
985055 AAATTTTGAA
* * * **
985065 TTTTTGAAGAATGGGGTTAGAGTGTCCCCTTAAAAGAGTAGGATGGAGTTTCCCTAAAGGTTATA
1 TTTTTGAAGAATGGGGTTAGAGTATCCCCTTAAAAGAATAGGATAGAGTTTCCCTAAAAATTATA
985130 CGAAGGAAAAA-TTTAAGT
66 CGAA--AAAAAGTTTAAGT
** *** * * *
985148 TTTTTGAA-AATCACGGTTAGAGTATCCCCTCGGAGGAATGGGTATAGAGTTTTTCC-AAAAATT
1 TTTTTGAAGAAT-GGGGTTAGAGTATCCCCTTAAAAGAATAGG-ATAGAG-TTTCCCTAAAAATT
985211 ATACGAAAAAAAGTTTAAGT
63 ATACGAAAAAAAGTTTAAGT
* * **
985231 TTTTTGACGATTGGGGTTAGAGTATCCTTTTAAAA-AACTAGGGATAGAGTTTCCCTAAAA
1 TTTTTGAAGAATGGGGTTAGAGTATCCCCTTAAAAGAA-TA-GGATAGAGTTTCCCTAAAA
985291 TTGAAAATTT
Statistics
Matches: 110, Mismatches: 25, Indels: 16
0.73 0.17 0.11
Matches are distributed among these distances:
82 15 0.14
83 69 0.63
84 21 0.19
85 5 0.05
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (82 bp):
TTTTTGAAGAATGGGGTTAGAGTATCCCCTTAAAAGAATAGGATAGAGTTTCCCTAAAAATTATA
CGAAAAAAAGTTTAAGT
Found at i:985334 original size:19 final size:19
Alignment explanation
Indices: 985307--985346 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
985297 ATTTGTAATG
985307 TTTTAATAGAGAA-ATTTTT
1 TTTTAATAGA-AAGATTTTT
*
985326 TTTTCATAGAAAGATTTTT
1 TTTTAATAGAAAGATTTTT
985345 TT
1 TT
985347 AAAAAAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.55
Consensus pattern (19 bp):
TTTTAATAGAAAGATTTTT
Found at i:994761 original size:28 final size:28
Alignment explanation
Indices: 994721--994774 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
994711 TACTGCCAAA
994721 AACTTGTATTTTTGTTATTTTTTCTTAG
1 AACTTGTATTTTTGTTATTTTTTCTTAG
994749 AACTTGTATTTTTGTTATTTTTTCTT
1 AACTTGTATTTTTGTTATTTTTTCTT
994775 GTTATAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.17, C:0.07, G:0.09, T:0.67
Consensus pattern (28 bp):
AACTTGTATTTTTGTTATTTTTTCTTAG
Found at i:994896 original size:21 final size:20
Alignment explanation
Indices: 994854--994896 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
994844 TTTGTATTGT
* *
994854 ATTTTTATATTATATTTTAA
1 ATTTTTATATTAGATTTAAA
*
994874 ATTTTCTATATTAGGTTTAAA
1 ATTTT-TATATTAGATTTAAA
994895 AT
1 AT
994897 CGTCCGATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (20 bp):
ATTTTTATATTAGATTTAAA
Found at i:997351 original size:17 final size:17
Alignment explanation
Indices: 997329--997395 Score: 66
Period size: 17 Copynumber: 4.1 Consensus size: 17
997319 TTAATTAATT
**
997329 CGAATTTAAATTTGATC
1 CGAATTTAAAAATGATC
997346 CGAATTTAAAAATGATC
1 CGAATTTAAAAATGATC
* * *
997363 CGAACTT-AAAATAATT
1 CGAATTTAAAAATGATC
*
997379 CGAATCT-AAAATGATC
1 CGAATTTAAAAATGATC
997395 C
1 C
997396 AAACCCAAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
16 20 0.49
17 21 0.51
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.31
Consensus pattern (17 bp):
CGAATTTAAAAATGATC
Found at i:997414 original size:32 final size:32
Alignment explanation
Indices: 997354--997414 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
997344 TCCGAATTTA
* ** *
997354 AAAATGATCCGAACTTAAAATAATTCGAATCT
1 AAAATGATCCAAACCCAAAATAACTCGAATCT
*
997386 AAAATGATCCAAACCCAAAATGACTCGAA
1 AAAATGATCCAAACCCAAAATAACTCGAA
997415 CAATCAATCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.49, C:0.20, G:0.10, T:0.21
Consensus pattern (32 bp):
AAAATGATCCAAACCCAAAATAACTCGAATCT
Found at i:1000011 original size:31 final size:31
Alignment explanation
Indices: 999974--1000045 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
999964 AATTGACTAC
*
999974 AATCCAATTTTAAAAGCCATTTTAATGCCCA
1 AATCCAATTTTAAAACCCATTTTAATGCCCA
* *
1000005 AATCCAATTTTAAGACCCATTTTAATGCCTA
1 AATCCAATTTTAAAACCCATTTTAATGCCCA
1000036 AATCCAATTT
1 AATCCAATTT
1000046 AATGCATGCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.35
Consensus pattern (31 bp):
AATCCAATTTTAAAACCCATTTTAATGCCCA
Found at i:1000756 original size:36 final size:36
Alignment explanation
Indices: 1000709--1000778 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
1000699 ATGATCACAT
*
1000709 TTGTAAAGGTGATTAACGAAAGTAAAATTGAGATAC
1 TTGTAAAGGTGATTAACGAAACTAAAATTGAGATAC
1000745 TTGTAAAGGTGATTAACGAAACTAAAATTGAGAT
1 TTGTAAAGGTGATTAACGAAACTAAAATTGAGAT
1000779 TAAGCTTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (36 bp):
TTGTAAAGGTGATTAACGAAACTAAAATTGAGATAC
Found at i:1002854 original size:13 final size:14
Alignment explanation
Indices: 1002829--1002857 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1002819 TCCTCGAACA
1002829 AAAAAATGTTTCAT
1 AAAAAATGTTTCAT
1002843 AAAAAATG-TTCAT
1 AAAAAATGTTTCAT
1002856 AA
1 AA
1002858 CTCACAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31
Consensus pattern (14 bp):
AAAAAATGTTTCAT
Found at i:1003473 original size:2 final size:2
Alignment explanation
Indices: 1003466--1003491 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1003456 TGGTCCTCCA
1003466 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
1003492 TTATTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1003636 original size:2 final size:2
Alignment explanation
Indices: 1003629--1003666 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1003619 TGTAAATTGA
1003629 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
1003667 TTCAGAAGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1006717 original size:27 final size:28
Alignment explanation
Indices: 1006687--1006763 Score: 88
Period size: 27 Copynumber: 2.8 Consensus size: 28
1006677 CATGTCACCG
* *
1006687 ATGGAATTTATCATTAAAT-TTTCATTT
1 ATGGAATTTATAATTAAATCTTTCATAT
*
1006714 ATGGAATTTTTAATTAAATCTTTCATAT
1 ATGGAATTTATAATTAAATCTTTCATAT
*
1006742 AT-GAATTTTTAAATTAAA-CTTT
1 ATGGAATTTAT-AATTAAATCTTT
1006764 TAAATAGGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
27 29 0.64
28 16 0.36
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.51
Consensus pattern (28 bp):
ATGGAATTTATAATTAAATCTTTCATAT
Found at i:1006751 original size:28 final size:28
Alignment explanation
Indices: 1006699--1006763 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
1006689 GGAATTTATC
* *
1006699 ATTAAAT-TTTCATTTATGGAATTTTTA
1 ATTAAATCTTTCATATATGGAATTTTAA
1006726 ATTAAATCTTTCATATAT-GAATTTTTAA
1 ATTAAATCTTTCATATATGGAA-TTTTAA
1006754 ATTAAA-CTTT
1 ATTAAATCTTT
1006764 TAAATAGGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 14 0.41
28 20 0.59
ACGTcount: A:0.37, C:0.06, G:0.05, T:0.52
Consensus pattern (28 bp):
ATTAAATCTTTCATATATGGAATTTTAA
Found at i:1006774 original size:27 final size:27
Alignment explanation
Indices: 1006689--1006774 Score: 77
Period size: 27 Copynumber: 3.2 Consensus size: 27
1006679 TGTCACCGAT
* * **
1006689 GGAATTTATCATTAAAT-TTTCATTTA
1 GGAATTTTTAATTAAATCTTTCAAATA
*
1006715 TGGAATTTTTAATTAAATCTTTCATATA
1 -GGAATTTTTAATTAAATCTTTCAAATA
* *
1006743 TGAATTTTTAAATTAAA-CTTTTAAATA
1 GGAATTTTT-AATTAAATCTTTCAAATA
1006770 GGAAT
1 GGAAT
1006775 GTAGAATATT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
27 35 0.70
28 15 0.30
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (27 bp):
GGAATTTTTAATTAAATCTTTCAAATA
Found at i:1007286 original size:19 final size:19
Alignment explanation
Indices: 1007264--1007322 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
1007254 AAATTGAGAG
1007264 GAAAAAAAAAAAAAAGAAA
1 GAAAAAAAAAAAAAAGAAA
* * *
1007283 GAAAGAAAAATAAAAGAGA
1 GAAAAAAAAAAAAAAGAAA
1007302 GAAAAAGAAAACAAAAAGAAA
1 GAAAAA-AAAA-AAAAAGAAA
1007323 TCTTGCAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
19 21 0.66
20 4 0.12
21 7 0.22
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (19 bp):
GAAAAAAAAAAAAAAGAAA
Found at i:1007319 original size:21 final size:20
Alignment explanation
Indices: 1007259--1007320 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
1007249 AGAAAAAATT
1007259 GAGAGGAAAAA-AAAAAAAAA
1 GAGA-GAAAAAGAAAAAAAAA
*
1007279 GA-A-AGAAAGAAAAATAAAA
1 GAGAGAAAAAGAAAAA-AAAA
1007298 GAGAGAAAAAGAAAACAAAAA
1 GAGAGAAAAAGAAAA-AAAAA
1007319 GA
1 GA
1007321 AATCTTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
17 4 0.11
18 5 0.14
19 7 0.20
20 3 0.09
21 15 0.43
22 1 0.03
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (20 bp):
GAGAGAAAAAGAAAAAAAAA
Found at i:1007395 original size:15 final size:13
Alignment explanation
Indices: 1007360--1007398 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
1007350 ACTACCTATT
1007360 TTTTCTTTATTCA
1 TTTTCTTTATTCA
*
1007373 TCTTCTTTATCTCCA
1 TTTTCTTTAT-T-CA
1007388 TTTTCTTTATT
1 TTTTCTTTATT
1007399 TACTTAATGC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 9 0.41
14 2 0.09
15 11 0.50
ACGTcount: A:0.13, C:0.21, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTTCTTTATTCA
Found at i:1010395 original size:13 final size:13
Alignment explanation
Indices: 1010377--1010401 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1010367 CATAAAGTGT
1010377 TGTATCGATACAA
1 TGTATCGATACAA
1010390 TGTATCGATACA
1 TGTATCGATACA
1010402 TTTTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1010482 original size:13 final size:13
Alignment explanation
Indices: 1010464--1010488 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1010454 ATCACTTAAA
1010464 TGTATCGATACAT
1 TGTATCGATACAT
1010477 TGTATCGATACA
1 TGTATCGATACA
1010489 CTAATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Done.