Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold238
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: 1453955
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 499 characters in sequence are not A, C, G, or T
File 2 of 9
Found at i:162431 original size:12 final size:12
Alignment explanation
Indices: 162408--162467 Score: 75
Period size: 12 Copynumber: 4.8 Consensus size: 12
162398 CTTTTCTCTC
*
162408 TTTTTCTTTGTT
1 TTTTTTTTTGTT
*
162420 TTGTTTTTTGTT
1 TTTTTTTTTGTT
162432 TTTTTTTTTGTT
1 TTTTTTTTTGTT
162444 TTTTTTTTTGCTCT
1 TTTTTTTTTG-T-T
162458 TCTTTTTTTT
1 T-TTTTTTTT
162468 TGAAGAGAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
12 31 0.74
13 1 0.02
14 2 0.05
15 8 0.19
ACGTcount: A:0.00, C:0.07, G:0.08, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTGTT
Found at i:162451 original size:24 final size:26
Alignment explanation
Indices: 162391--162467 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 26
162381 GCTTAAGTAG
*
162391 GTTTT-TTCTTTT-CTCTCTTTTTCTTT
1 GTTTTGTT-TTTTGCTCT-TTTTTTTTT
162417 GTTTTGTTTTTTG-T-TTTTTTTTTT
1 GTTTTGTTTTTTGCTCTTTTTTTTTT
*
162441 GTTTTTTTTTTTGCTCTTCTTTTTTTT
1 GTTTTGTTTTTTGCTCTT-TTTTTTTT
162468 TGAAGAGAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
24 20 0.45
25 2 0.05
26 12 0.27
27 10 0.23
ACGTcount: A:0.00, C:0.10, G:0.08, T:0.82
Consensus pattern (26 bp):
GTTTTGTTTTTTGCTCTTTTTTTTTT
Found at i:175085 original size:51 final size:51
Alignment explanation
Indices: 174928--175098 Score: 180
Period size: 51 Copynumber: 3.3 Consensus size: 51
174918 GAAATAACGA
* * *
174928 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * * *
174980 AATTTGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * * *
175033 GGTTAGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
175084 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
175099 TCAGAAATAA
Statistics
Matches: 94, Mismatches: 23, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
51 38 0.40
52 15 0.16
53 31 0.33
54 10 0.11
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:175144 original size:27 final size:28
Alignment explanation
Indices: 175081--175156 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
175071 AAAATAAAGT
*
175081 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
175109 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
175136 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
175157 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:177650 original size:13 final size:13
Alignment explanation
Indices: 177632--177657 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
177622 ACAAAGATCC
177632 ATGTATCGATACA
1 ATGTATCGATACA
177645 ATGTATCGATACA
1 ATGTATCGATACA
177658 CAGAAAAATG
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:177653 original size:33 final size:33
Alignment explanation
Indices: 177611--177677 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
177601 AAAATTTTCA
***
177611 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
177644 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
177677 A
1 A
177678 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:177721 original size:19 final size:19
Alignment explanation
Indices: 177697--177751 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
177687 CAGTAGCTAA
*
177697 TTATGTATCGATACAATAC
1 TTATGTATCGATACAAAAC
177716 TTATGTATCGATACAAAAC
1 TTATGTATCGATACAAAAC
177735 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
177752 TCGTTGAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (19 bp):
TTATGTATCGATACAAAAC
Found at i:186452 original size:13 final size:13
Alignment explanation
Indices: 186434--186459 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
186424 CAATTTTTTG
186434 TGTATCGATACAT
1 TGTATCGATACAT
186447 TGTATCGATACAT
1 TGTATCGATACAT
186460 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:189019 original size:13 final size:13
Alignment explanation
Indices: 189001--189039 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
188991 ATAATCACCC
*
189001 TGTATCGATACAG
1 TGTATCGATACAA
189014 TGTATCGATACAA
1 TGTATCGATACAA
189027 TGTATCGATACAA
1 TGTATCGATACAA
189040 AGAAAAATGT
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:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:189050 original size:20 final size:20
Alignment explanation
Indices: 189025--189103 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
189015 GTATCGATAC
189025 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
189045 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
189070 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
189090 CATGTATCGATACA
1 AATGTATCGATACA
189104 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:191139 original size:15 final size:15
Alignment explanation
Indices: 191119--191149 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
191109 ATTTCGTTTG
*
191119 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
191134 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
191149 G
1 G
191150 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:192982 original size:21 final size:21
Alignment explanation
Indices: 192953--192997 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
192943 AAGTTTTCAT
*
192953 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
192973 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
192995 TTT
1 TTT
192998 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:195231 original size:13 final size:13
Alignment explanation
Indices: 195213--195238 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
195203 CAATTTTTTG
195213 TGTATCGATACAT
1 TGTATCGATACAT
195226 TGTATCGATACAT
1 TGTATCGATACAT
195239 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:201045 original size:54 final size:54
Alignment explanation
Indices: 200956--201119 Score: 204
Period size: 54 Copynumber: 3.1 Consensus size: 54
200946 TTCTTTTTTA
* * *
200956 TTTATTTTCAGCAACTTAATTG-TTTTTTTCGTTTCTTCTTCTTGTTGTTGCCG
1 TTTATTTTCAACAGCTTAATTGCTTTTTTTCGTTTCTTCTTCTTATTGTTGCCG
* * * * * **
201009 TTTGTTTTCAATAGCTTATTTGCTTTTTTTCATTTCTTCTTCTTATTGTTACTA
1 TTTATTTTCAACAGCTTAATTGCTTTTTTTCGTTTCTTCTTCTTATTGTTGCCG
* * *
201063 TTTATTTTCAGCAGCTTAATTGCTTTATTTCGTTTTTTCTTCTTATTGTTGCCG
1 TTTATTTTCAACAGCTTAATTGCTTTTTTTCGTTTCTTCTTCTTATTGTTGCCG
201117 TTT
1 TTT
201120 TTCAATGGCA
Statistics
Matches: 90, Mismatches: 20, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
53 17 0.19
54 73 0.81
ACGTcount: A:0.13, C:0.16, G:0.11, T:0.60
Consensus pattern (54 bp):
TTTATTTTCAACAGCTTAATTGCTTTTTTTCGTTTCTTCTTCTTATTGTTGCCG
Found at i:203558 original size:52 final size:53
Alignment explanation
Indices: 203480--203586 Score: 171
Period size: 52 Copynumber: 2.0 Consensus size: 53
203470 CCTTAGAAAT
* * *
203480 AATGGGGTTGGAGTATCCTCAATGGTG-AAAATTTTGATATTTTGGAAGTAAA
1 AATGGGGTTGGAGTATCCCCAATGGTGAAAAAATTTGATATTTTCGAAGTAAA
*
203532 AATGGGGTTGGAGTATCCCCGATGGTGAAAAAATTTGATATTTTCGAAGTAAA
1 AATGGGGTTGGAGTATCCCCAATGGTGAAAAAATTTGATATTTTCGAAGTAAA
203585 AA
1 AA
203587 CGACGTTGAG
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
52 25 0.50
53 25 0.50
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.32
Consensus pattern (53 bp):
AATGGGGTTGGAGTATCCCCAATGGTGAAAAAATTTGATATTTTCGAAGTAAA
Found at i:203693 original size:81 final size:81
Alignment explanation
Indices: 203533--203864 Score: 311
Period size: 81 Copynumber: 4.1 Consensus size: 81
203523 GGAAGTAAAA
* * * * * * *
203533 ATGGGGTTGGAGTATCCCCGATGGTGAAAAAATTTGATATTTTCGAAGTAAAAACGACGTT-GAG
1 ATGGGGTTGAAGTATCCCCGACGGTGAAAAAATTTAATATTATGGAAGTAAAAAAGAGGTTGGA-
*
203597 GTA-CTCCATCAAAAATG
65 GTATCTCC-TCGAAAATG
* *
203614 ATGGGGTTGAAGTATCCCCTACGGTGAAAAAATTCAATATTATGGAAGTAAAAATAG-GGTTGGA
1 ATGGGGTTGAAGTATCCCCGACGGTGAAAAAATTTAATATTATGGAAGTAAAAA-AGAGGTTGGA
*
203678 GTTTCTCCTCGAAAATG
65 GTATCTCCTCGAAAATG
* * * * * *
203695 ATGGGGAT-AGAGTATCCCCGATGGTAAAAAAAATTGATATT-TGGGAAGTAAAAACGAGGTTGG
1 ATGGGGTTGA-AGTATCCCCGACGGTGAAAAAATTTAATATTAT-GGAAGTAAAAAAGAGGTTGG
* *
203758 AGTATCCCCTCGAAAATA
64 AGTATCTCCTCGAAAATG
* ** * *
203776 ATGGGGTTAAAGTATCCCTAATC-ATGAAAAAATTTAATATTATGGAAGTAAAAACA-AGGTTGA
1 ATGGGGTTGAAGTATCCCCGA-CGGTGAAAAAATTTAATATTATGGAAGTAAAAA-AGAGGTTGG
203839 AGTATCTCCTC-AGAAATG
64 AGTATCTCCTCGA-AAATG
*
203857 ATGAGGTT
1 ATGGGGTT
203865 TGAGCATCCC
Statistics
Matches: 205, Mismatches: 35, Indels: 22
0.78 0.13 0.08
Matches are distributed among these distances:
80 4 0.02
81 192 0.94
82 9 0.04
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (81 bp):
ATGGGGTTGAAGTATCCCCGACGGTGAAAAAATTTAATATTATGGAAGTAAAAAAGAGGTTGGAG
TATCTCCTCGAAAATG
Found at i:203809 original size:162 final size:162
Alignment explanation
Indices: 203533--203885 Score: 437
Period size: 162 Copynumber: 2.2 Consensus size: 162
203523 GGAAGTAAAA
* * * *
203533 ATGGGGTTGGAGTATCCCCGATGGTGAAAAAATTTGATATTTTCGAAGTAAAAACGACGTTGAGG
1 ATGGGGTTAGAGTATCCCCGATGGTAAAAAAAATTGATATTTGCGAAGTAAAAACGACGTTGAGG
* * *
203598 TACTCCATCAAAAATGATGGGGTTGAAGTATCCCCTACGGTGAAAAAATTCAATATTATGGAAGT
66 TACTCCATCAAAAATAATGGGGTTAAAGTATCCCCTACGATGAAAAAATTCAATATTATGGAAGT
* * * *
203663 AAAAATAGGGTTGGAGTTTCTCCTC-GAAAATG
131 AAAAACAAGGTTGAAGTATCTCCTCAG-AAATG
* * *
203695 ATGGGGATAGAGTATCCCCGATGGTAAAAAAAATTGATATTTGGGAAGTAAAAACGAGGTTG-GA
1 ATGGGGTTAGAGTATCCCCGATGGTAAAAAAAATTGATATTTGCGAAGTAAAAACGACGTTGAG-
* * *
203759 GTA-TCCCCTCGAAAATAATGGGGTTAAAGTAT-CCCTAATC-ATGAAAAAATTTAATATTATGG
65 GTACT-CCATCAAAAATAATGGGGTTAAAGTATCCCCT-A-CGATGAAAAAATTCAATATTATGG
203821 AAGTAAAAACAAGGTTGAAGTATCTCCTCAGAAATG
127 AAGTAAAAACAAGGTTGAAGTATCTCCTCAGAAATG
* * * *
203857 ATGAGGTTTGAGCATCCCTGATGGTAAAA
1 ATGGGGTTAGAGTATCCCCGATGGTAAAA
203886 TTTTTTTGAT
Statistics
Matches: 164, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
161 6 0.04
162 156 0.95
163 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (162 bp):
ATGGGGTTAGAGTATCCCCGATGGTAAAAAAAATTGATATTTGCGAAGTAAAAACGACGTTGAGG
TACTCCATCAAAAATAATGGGGTTAAAGTATCCCCTACGATGAAAAAATTCAATATTATGGAAGT
AAAAACAAGGTTGAAGTATCTCCTCAGAAATG
Found at i:206283 original size:52 final size:51
Alignment explanation
Indices: 206227--206324 Score: 135
Period size: 52 Copynumber: 1.9 Consensus size: 51
206217 GTATGTATTG
* *
206227 ATACATTAAAAAATGTATCGATACA-TTTAGGTTAAAAACCTAGAATGTATCA
1 ATACAATAAAAAATGTATCGATA-AGTTTAGGTT-AAAACCCAGAATGTATCA
* *
206279 ATACAATGAGAAATGTATCGATAAGTTTAGGTTAAAACCCAGAATG
1 ATACAATAAAAAATGTATCGATAAGTTTAGGTTAAAACCCAGAATG
206325 ATCGAGACAT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
51 13 0.32
52 28 0.68
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (51 bp):
ATACAATAAAAAATGTATCGATAAGTTTAGGTTAAAACCCAGAATGTATCA
Found at i:206407 original size:21 final size:21
Alignment explanation
Indices: 206373--206428 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
206363 GACATGGTCT
* * *
206373 TGTATCGATGCATTTCAGACA
1 TGTATCAATACATTTCACACA
**
206394 TGTATCAATACA-TTCACTTA
1 TGTATCAATACATTTCACACA
206414 TGTATCAATACATTT
1 TGTATCAATACATTT
206429 ACTATTTGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (21 bp):
TGTATCAATACATTTCACACA
Found at i:206416 original size:20 final size:21
Alignment explanation
Indices: 206393--206446 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
206383 CATTTCAGAC
206393 ATGTATCAATACATTCACT-T
1 ATGTATCAATACATTCACTAT
*
206413 ATGTATCAATACATTTACTAT
1 ATGTATCAATACATTCACTAT
* *
206434 TTGTATCGATACA
1 ATGTATCAATACA
206447 AATTGTAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.41
Consensus pattern (21 bp):
ATGTATCAATACATTCACTAT
Found at i:211899 original size:21 final size:20
Alignment explanation
Indices: 211832--211905 Score: 67
Period size: 21 Copynumber: 3.6 Consensus size: 20
211822 CAGAGTGGTT
**
211832 TGTATCAATACATTTAAGGTA
1 TGTATCAATACATTT-ACTTA
* * *
211853 TGTATCGATATATTCACTTA
1 TGTATCAATACATTTACTTA
* *
211873 TGTATCGATACATTTACTATT
1 TGTATCAATACATTTACT-TA
211894 TGTATCAATACA
1 TGTATCAATACA
211906 AATTGTAAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
20 19 0.44
21 24 0.56
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.42
Consensus pattern (20 bp):
TGTATCAATACATTTACTTA
Found at i:213546 original size:80 final size:80
Alignment explanation
Indices: 213277--213570 Score: 235
Period size: 80 Copynumber: 3.6 Consensus size: 80
213267 CGAAGATGGC
* ** * * *
213277 AAGGTTGGAGTATCC-TTGAAGTTGGAAAA-TTTGAT-ATTTGGGGAAATAAAGACGAGGTTGAA
1 AAGGTTGGAGTATCCTTTG-AGAT-GAAAATTTTGATGA-TT-AAGAAATAAAAACGAGGCTGGA
213339 GTATCCC-CT-AAGAAATAGT
62 GTATCCCTCTCAA-AAAT-GT
* * ** *
213358 -GGGATTGGAGTATCCTTTGAGATGAAAAATTCAATGATTTAGAAATAAAAACGAGGCTGGAGTA
1 AAGG-TTGGAGTATCCTTTGAGATGAAAATTTTGATGATTAAGAAATAAAAACGAGGCTGGAGTA
* * *
213422 TCCCTTTGAAAATTGT
65 TCCCTCTCAAAAATGT
* * * * * * *
213438 GAGGTTGGAGTATCCCTTAAGATGAAAATTTTGGTGCA-TAAGAAATAAAAATGGGGTTGGAGTA
1 AAGGTTGGAGTATCCTTTGAGATGAAAATTTTGATG-ATTAAGAAATAAAAACGAGGCTGGAGTA
213502 TCCC-CTCAAAAATGAT
65 TCCCTCTCAAAAATG-T
* *
213518 AAGGTTGGAGTATCCTTTGAGATGAAAATTTTGATGTTTTAAAAAATAAAAAC
1 AAGGTTGGAGTATCCTTTGAGATGAAAATTTTGATG-ATTAAGAAATAAAAAC
213571 AAGATTGGAT
Statistics
Matches: 170, Mismatches: 33, Indels: 20
0.76 0.15 0.09
Matches are distributed among these distances:
79 7 0.04
80 118 0.69
81 39 0.23
82 6 0.04
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.30
Consensus pattern (80 bp):
AAGGTTGGAGTATCCTTTGAGATGAAAATTTTGATGATTAAGAAATAAAAACGAGGCTGGAGTAT
CCCTCTCAAAAATGT
Found at i:216026 original size:52 final size:51
Alignment explanation
Indices: 215962--216100 Score: 172
Period size: 51 Copynumber: 2.7 Consensus size: 51
215952 AATAACCTAC
* * * * *
215962 ATGTATCGATATATTGAAGAATGTATCAATACATTTGGGTGAAAAACCCATA
1 ATGTATCGATATAATGAAAAATGTATCAATACATTTGGCT-AAAAACACAGA
* *
216014 ATGTATCAATATAATGAATAAA-GTATCAATACATTTGGCTCAAAACACAGA
1 ATGTATCGATATAATGAA-AAATGTATCAATACATTTGGCTAAAAACACAGA
* *
216065 ATGTATCGATACAATGAAAAATGTATCGATACATTT
1 ATGTATCGATATAATGAAAAATGTATCAATACATTT
216101 TCCTTCCAGA
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
50 3 0.04
51 37 0.49
52 33 0.44
53 2 0.03
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.30
Consensus pattern (51 bp):
ATGTATCGATATAATGAAAAATGTATCAATACATTTGGCTAAAAACACAGA
Found at i:217324 original size:19 final size:21
Alignment explanation
Indices: 217304--217364 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
217294 TTTTAATATT
*
217304 TATTTTTTTCATATTATTTTA
1 TATTTTTATCATATTATTTTA
* *
217325 TATTTTTATCATTTTA-TATA
1 TATTTTTATCATATTATTTTA
* *
217345 TATATATATCATATTTATTT
1 TATTTTTATCATA-TTATTT
217365 AATTATATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 13 0.42
21 17 0.55
22 1 0.03
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (21 bp):
TATTTTTATCATATTATTTTA
Found at i:217690 original size:18 final size:18
Alignment explanation
Indices: 217664--217701 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
217654 TATTTTTTAC
*
217664 AAGTCAAAAGTAAAAAAA
1 AAGTAAAAAGTAAAAAAA
217682 AAGTAAAAAGTAAAAAAA
1 AAGTAAAAAGTAAAAAAA
217700 AA
1 AA
217702 AAATGCGTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.76, C:0.03, G:0.11, T:0.11
Consensus pattern (18 bp):
AAGTAAAAAGTAAAAAAA
Found at i:221504 original size:21 final size:22
Alignment explanation
Indices: 221478--221521 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
221468 AGAAAAAGAG
221478 AGAAAG-GAAAACAAAGAAAAA
1 AGAAAGAGAAAACAAAGAAAAA
**
221499 AGAAAGAGAAAAGGAAGAAAAA
1 AGAAAGAGAAAACAAAGAAAAA
221521 A
1 A
221522 AATTATGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.75, C:0.02, G:0.23, T:0.00
Consensus pattern (22 bp):
AGAAAGAGAAAACAAAGAAAAA
Found at i:222451 original size:232 final size:231
Alignment explanation
Indices: 221866--222462 Score: 607
Period size: 239 Copynumber: 2.5 Consensus size: 231
221856 ATTGTATCGT
* *
221866 GTTTTAATTATTTTCTAAG-TTTTTTTGTCTTATCTTAATTCATCTAATATTTTGGATAGTTTAT
1 GTTTTAATTATTTTCTAAGATTTTTTTGT-TTATCTTAATTCAT-TTATATTTTGAATAGTTTAT
*** * *
221930 TATAGCGATTCAATTTTTACTTTGAATTCAATTATTTAGAATATTAAAATGCAAAAAAAATATTT
64 TATAATAATTCAATTTTTACTCTGAATTCAATTATTTA-AATATTAAAAT--ATAAAAAATATTT
* * * * *
221995 ATTTATTTTCATGTTATTTTTCGTGTATTTAAAATATAAAGTATTTATTTATTTCTTCCTTTTCA
126 ATTTATTTTCACGTTATTTTTCATGTATTTAAAATATAAAGAAGTTATTTATTTCTTCATTTTCA
*
222060 TATGAACAAAAAATCATATTTATATTATTTTTCTTAACGTATA
191 TATGAACAAAAAATCATATTTATACTATTTTTCTT-A-GTATA
* * * * *
222103 TGTTTTAATTACTCTC-AAGATGTTTTTTCTTGTATCTTAATTCATTTCATAATTTTTAATAATT
1 -GTTTTAATTATTTTCTAAGAT-TTTTTTGTT-TATCTTAATTCATTT-AT-ATTTTGAATAGTT
* * *
222167 TATTATAATAATTCAATTTTTACTCCGAATTCTATTATTTAAGACATTAAAATATAAAAAATATT
61 TATTATAATAATTCAATTTTTACTCTGAATTCAATTATTTAA-ATATTAAAATATAAAAAATATT
* * * * *
222232 TATTTGTTTTCACGTTACTTTTTCATGTGTTTAAAGTATTAAGAAGTTATTTGTTTCTTCATTTT
125 TATTTATTTTCACGTTA-TTTTTCATGTATTTAAAATATAAAGAAGTTATTTATTTCTTCATTTT
** * * * * * *
222297 TTTATGAATACAAAATCGTGTTTGTGCTA-TTTT-TT-G-ATA
189 CATATGAACAAAAAATCATATTTATACTATTTTTCTTAGTATA
*
222336 -TTTTAATTATTTTCTAAAGCTATTTTTTTGTTATATC-TAATTCATATTATATTTTGCATAGTT
1 GTTTTAATTATTTTCT-AAG--ATTTTTTTGTT-TATCTTAATTCAT-TTATATTTTGAATAGTT
* * *
222399 TATTATAATAATTCAATTTTTACTCTAAATTCAAATATTTACAATGTTAAAATATTAAAAAATA
61 TATTATAATAATTCAATTTTTACTCTGAATTCAATTATTTA-AATATTAAAATA-TAAAAAATA
222463 AATAACATGT
Statistics
Matches: 298, Mismatches: 47, Indels: 33
0.79 0.12 0.09
Matches are distributed among these distances:
231 12 0.04
232 56 0.19
233 26 0.09
234 15 0.05
235 2 0.01
237 5 0.02
238 46 0.15
239 82 0.28
240 54 0.18
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (231 bp):
GTTTTAATTATTTTCTAAGATTTTTTTGTTTATCTTAATTCATTTATATTTTGAATAGTTTATTA
TAATAATTCAATTTTTACTCTGAATTCAATTATTTAAATATTAAAATATAAAAAATATTTATTTA
TTTTCACGTTATTTTTCATGTATTTAAAATATAAAGAAGTTATTTATTTCTTCATTTTCATATGA
ACAAAAAATCATATTTATACTATTTTTCTTAGTATA
Found at i:223589 original size:19 final size:18
Alignment explanation
Indices: 223564--223631 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
223554 AATTCAACGA
223564 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
223582 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
223598 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
223614 TATTGTATCGATACATAA
1 T-TTGTATCGATACATAA
223632 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
18 1 0.02
19 27 0.63
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:223602 original size:32 final size:32
Alignment explanation
Indices: 223566--223628 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
223556 TTCAACGATT
*
223566 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
223598 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
223629 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:223603 original size:13 final size:13
Alignment explanation
Indices: 223585--223609 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
223575 ACATAAGTGT
223585 TGTATCGATACAA
1 TGTATCGATACAA
223598 TGTATCGATACA
1 TGTATCGATACA
223610 TAAGTATTGT
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:223675 original size:20 final size:20
Alignment explanation
Indices: 223650--223704 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
223640 TGCCAAGGAA
223650 ATGTATCGATACATTATTTC
1 ATGTATCGATACATTATTTC
223670 ATGTATCGATACATTATTTC
1 ATGTATCGATACATTATTTC
223690 ATGTATCGATACATT
1 ATGTATCGATACATT
223705 GTATCGATAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTATTTC
Found at i:223709 original size:13 final size:13
Alignment explanation
Indices: 223691--223716 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
223681 CATTATTTCA
223691 TGTATCGATACAT
1 TGTATCGATACAT
223704 TGTATCGATACAT
1 TGTATCGATACAT
223717 GGATCTTTGT
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:226140 original size:51 final size:53
Alignment explanation
Indices: 226084--226468 Score: 167
Period size: 52 Copynumber: 7.4 Consensus size: 53
226074 CAATTCTCCG
* * * * *
226084 TAATCGGGGATATTCCATCTCTGATTTTATTTTC-AA-AACACTAA-TTTTCTA
1 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAGAACACCAATTTTTC-A
* *
226135 TAATCGAGGATACCCCAACTCCGATTTTATTTCCAAAGAACACCAATTTTTCA
1 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAGAACACCAATTTTTCA
* * * * *** *
226188 CAATCGGGGATACTCCAACCCCG--TTAATCAT-CGGGGATACTCCAACCCCGTTATTTC-
1 TAATCGGGGATACTCCAACTCCGATTTTAT-TTCCAAAGA-ACACCAA-----TT-TTTCA
** * * ** * *** *
226245 CGA--GGGGATACTCCAACCCCTG-CTTTA-TTCTTAA-AATATTGATTTCTCA
1 TAATCGGGGATACTCCAACTCC-GATTTTATTTCCAAAGAACACCAATTTTTCA
* * * * *
226294 TAATCGGGGATACTCCAACCCCGGTTTTA-TTGCTAA-AACACTAATTTTTCCA
1 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAGAACACCAATTTTT-CA
* * * * *
226346 TAATCGGGGATACTCCGAC-CCCAGTTTTATTTTC-AA-AACACCAATTTTCCTT
1 TAATCGGGGATACTCCAACTCCGA-TTTTATTTCCAAAGAACACCAATTTTTC-A
*
226398 TAATCGGGGATACTCCAACTCCGATTTTACTTCCAAA-AACACCAATTTTTCA
1 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAGAACACCAATTTTTCA
* * *
226450 CAATTGAGGATACTCCAAC
1 TAATCGGGGATACTCCAAC
226469 CTCGTTATTT
Statistics
Matches: 255, Mismatches: 55, Indels: 47
0.71 0.15 0.13
Matches are distributed among these distances:
48 3 0.01
49 3 0.01
50 1 0.00
51 73 0.29
52 89 0.35
53 48 0.19
54 7 0.03
55 19 0.07
56 1 0.00
57 7 0.03
58 4 0.02
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (53 bp):
TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAGAACACCAATTTTTCA
Found at i:226193 original size:53 final size:51
Alignment explanation
Indices: 226106--226206 Score: 123
Period size: 53 Copynumber: 1.9 Consensus size: 51
226096 TTCCATCTCT
* * *
226106 GATTTTATTTTCAAAACACTAATTTTCTATAATCGAGGATACCCCAACTCC
1 GATTTTATTTCCAAAACACCAATTTTCTACAATCGAGGATACCCCAACTCC
* *
226157 GATTTTATTTCCAAAGAACACCAATTTT-TCACAATCGGGGATACTCCAAC
1 GATTTTATTTCC-AA-AACACCAATTTTCT-ACAATCGAGGATACCCCAAC
226207 CCCGTTAATC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
51 11 0.26
52 3 0.07
53 28 0.67
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.33
Consensus pattern (51 bp):
GATTTTATTTCCAAAACACCAATTTTCTACAATCGAGGATACCCCAACTCC
Found at i:226220 original size:27 final size:28
Alignment explanation
Indices: 226190--226264 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 28
226180 ATTTTTCACA
226190 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
226217 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
***
226245 CGAGGGGATACTCCAACCCC
1 ATCGGGGATACTCCAACCCC
226265 TGCTTTATTC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 24 0.56
28 19 0.44
ACGTcount: A:0.24, C:0.35, G:0.20, T:0.21
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:226373 original size:52 final size:49
Alignment explanation
Indices: 226248--226474 Score: 202
Period size: 52 Copynumber: 4.4 Consensus size: 49
226238 TTATTTCCGA
* * *** *
226248 GGGGATACTCCAACCCCTGCTTTATTCTTAAAATATTGATTTCTCATAATC
1 GGGGATACTCCAACCCC-GTTTTATTC-TAAAACACCAATTTTTCATAATC
*
226299 GGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTCCATAATC
1 GGGGATACTCCAACCCC-GTTTTATT-CTAAAACACCAATTTTT-CATAATC
* * * *
226351 GGGGATACTCCGACCCCAGTTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCC-GTTTTATTCT-AAAACACCAATTTTTC-ATAATC
* * * *
226403 GGGGATACTCCAACTCCGATTTTACTTCCAAAAACACCAATTTTTCACAATT
1 GGGGATACTCCAACCCCG-TTTTA-TT-CTAAAACACCAATTTTTCATAATC
* *
226455 GAGGATACTCCAACCTCGTT
1 GGGGATACTCCAACCCCGTT
226475 ATTTCATCGG
Statistics
Matches: 146, Mismatches: 23, Indels: 14
0.80 0.13 0.08
Matches are distributed among these distances:
51 41 0.28
52 88 0.60
53 17 0.12
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (49 bp):
GGGGATACTCCAACCCCGTTTTATTCTAAAACACCAATTTTTCATAATC
Found at i:228435 original size:23 final size:23
Alignment explanation
Indices: 228403--228448 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
228393 TAAACTTAAA
* *
228403 CTCATTTAAATCTAAACGAAAAG
1 CTCATCTAAACCTAAACGAAAAG
*
228426 CTCATCTAAACCTAAACTAAAAG
1 CTCATCTAAACCTAAACGAAAAG
228449 TCTAATTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.48, C:0.22, G:0.07, T:0.24
Consensus pattern (23 bp):
CTCATCTAAACCTAAACGAAAAG
Found at i:228458 original size:23 final size:22
Alignment explanation
Indices: 228408--228458 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
228398 TTAAACTCAT
* *
228408 TTAAATCTAAACGAAAAGCTCA
1 TTAAACCTAAACGAAAAGCTAA
*
228430 TCTAAACCTAAACTAAAAGTCTAA
1 T-TAAACCTAAACGAAAAG-CTAA
228454 TTAAA
1 TTAAA
228459 ACAAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 1 0.04
23 19 0.79
24 4 0.17
ACGTcount: A:0.51, C:0.18, G:0.06, T:0.25
Consensus pattern (22 bp):
TTAAACCTAAACGAAAAGCTAA
Found at i:232370 original size:19 final size:20
Alignment explanation
Indices: 232346--232385 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
232336 TTAAAAAATG
232346 TGTAAAATTA-ATTTTTCAT
1 TGTAAAATTATATTTTTCAT
*
232365 TGTAAAATTATCTTTTTCAT
1 TGTAAAATTATATTTTTCAT
232385 T
1 T
232386 AATTAATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (20 bp):
TGTAAAATTATATTTTTCAT
Found at i:232828 original size:24 final size:24
Alignment explanation
Indices: 232801--232854 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
232791 TCTGCTTCTA
** *
232801 TCGATTTGCTTCTTGTTGCTGTTG
1 TCGATTTGCTTCTAATTGCTATTG
*
232825 TCGATCTGCTTCTAATTGCTATTG
1 TCGATTTGCTTCTAATTGCTATTG
232849 TCGATT
1 TCGATT
232855 ATTGCAGTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.11, C:0.19, G:0.20, T:0.50
Consensus pattern (24 bp):
TCGATTTGCTTCTAATTGCTATTG
Found at i:233065 original size:45 final size:45
Alignment explanation
Indices: 233005--233100 Score: 183
Period size: 45 Copynumber: 2.1 Consensus size: 45
232995 TTTGTTATTT
233005 TTTTTAAATGAGTTTTAATTGGGTTTGGGTTTAAGTTTATATAGA
1 TTTTTAAATGAGTTTTAATTGGGTTTGGGTTTAAGTTTATATAGA
*
233050 TTTTTAATTGAGTTTTAATTGGGTTTGGGTTTAAGTTTATATAGA
1 TTTTTAAATGAGTTTTAATTGGGTTTGGGTTTAAGTTTATATAGA
233095 TTTTTA
1 TTTTTA
233101 GTTTGTGTTA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.25, C:0.00, G:0.21, T:0.54
Consensus pattern (45 bp):
TTTTTAAATGAGTTTTAATTGGGTTTGGGTTTAAGTTTATATAGA
Found at i:233128 original size:45 final size:45
Alignment explanation
Indices: 233005--233136 Score: 113
Period size: 45 Copynumber: 2.9 Consensus size: 45
232995 TTTGTTATTT
* * * ***
233005 TTTTTAAATGAGTTTTAATTGGGTTTGGGTTTAAGTTTATATAGA
1 TTTTTAATTGAGTGTTAAATGGGTTCACGTTTAAGTTTATATAGA
* * ***
233050 TTTTTAATTGAGTTTTAATTGGGTTTGGGTTTAAGTTTATATAGA
1 TTTTTAATTGAGTGTTAAATGGGTTCACGTTTAAGTTTATATAGA
* * * *
233095 TTTTTAGTT-TGTGTTAAATGGGCTTCACTTTTAAATTTATAT
1 TTTTTAATTGAGTGTTAAATGGG-TTCACGTTTAAGTTTATAT
233137 TTATATTTTA
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
44 10 0.13
45 66 0.87
ACGTcount: A:0.25, C:0.02, G:0.20, T:0.53
Consensus pattern (45 bp):
TTTTTAATTGAGTGTTAAATGGGTTCACGTTTAAGTTTATATAGA
Found at i:244385 original size:16 final size:16
Alignment explanation
Indices: 244356--244402 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
244346 ACACTCAAAT
*
244356 TTAAAATGAATTAAAC
1 TTAAAATGATTTAAAC
* *
244372 TTAAAGTGATTTAAAT
1 TTAAAATGATTTAAAC
*
244388 TTAAAATAATTTAAA
1 TTAAAATGATTTAAA
244403 ATTTTAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.38
Consensus pattern (16 bp):
TTAAAATGATTTAAAC
Found at i:244438 original size:25 final size:24
Alignment explanation
Indices: 244384--244431 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
244374 AAAGTGATTT
*
244384 AAATTTAAAATAATTTAAAATTTTA
1 AAATTTAAAATAATTT-AAATTTGA
244409 AAATTTAAAATAATTT-AATTTGA
1 AAATTTAAAATAATTTAAATTTGA
244432 GTTAATTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.27
25 16 0.73
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
AAATTTAAAATAATTTAAATTTGA
Found at i:246254 original size:18 final size:18
Alignment explanation
Indices: 246231--246265 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
246221 CCATTTAAAA
*
246231 ATAAAATAAAATTAATTT
1 ATAAAATAAAATAAATTT
246249 ATAAAATAAAATAAATT
1 ATAAAATAAAATAAATT
246266 CTTTTGAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAAAATAAAATAAATTT
Found at i:250407 original size:13 final size:13
Alignment explanation
Indices: 250389--250413 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
250379 ACTGTGTTCT
250389 TAGTATCGATACA
1 TAGTATCGATACA
250402 TAGTATCGATAC
1 TAGTATCGATAC
250414 TGAGTTCTTT
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):
TAGTATCGATACA
Found at i:250435 original size:33 final size:34
Alignment explanation
Indices: 250371--250440 Score: 99
Period size: 33 Copynumber: 2.1 Consensus size: 34
250361 AAACCTAGAT
*
250371 GTATCGATACTGTGTTCTTAGTATCGATACAT-A
1 GTATCGATACTGAGTTCTTAGTATCGATACATGA
*
250404 GTATCGATACTGAGTTCTTTGTATC-AGTACATGA
1 GTATCGATACTGAGTTCTTAGTATCGA-TACATGA
250438 GTA
1 GTA
250441 CTATTTAGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 1 0.03
33 28 0.85
34 4 0.12
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (34 bp):
GTATCGATACTGAGTTCTTAGTATCGATACATGA
Found at i:253065 original size:13 final size:13
Alignment explanation
Indices: 253047--253071 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
253037 ATTTTGCGTA
253047 GTATCGATACATT
1 GTATCGATACATT
253060 GTATCGATACAT
1 GTATCGATACAT
253072 GTTTATAGTA
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:253978 original size:18 final size:19
Alignment explanation
Indices: 253933--253985 Score: 72
Period size: 18 Copynumber: 2.8 Consensus size: 19
253923 TTAAATTTAT
253933 ATTTATATTAAATAATAAA
1 ATTTATATTAAATAATAAA
* *
253952 ATATATATTAAA-AATTAA
1 ATTTATATTAAATAATAAA
*
253970 GTTTATATTAAATAAT
1 ATTTATATTAAATAAT
253986 GACTATAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 15 0.52
19 14 0.48
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
ATTTATATTAAATAATAAA
Found at i:259029 original size:21 final size:21
Alignment explanation
Indices: 259000--259042 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
258990 CACTGATAAA
259000 AGTAGGATGTTCTGGGAGTTC
1 AGTAGGATGTTCTGGGAGTTC
*
259021 AGTATGATGTTCTGGGAGTTC
1 AGTAGGATGTTCTGGGAGTTC
259042 A
1 A
259043 CATGCTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.09, G:0.35, T:0.35
Consensus pattern (21 bp):
AGTAGGATGTTCTGGGAGTTC
Found at i:260928 original size:20 final size:20
Alignment explanation
Indices: 260861--260928 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 20
260851 GAAATTAAAG
260861 TAAAT-ATAAAATAATTATTA
1 TAAATAATAAAATAATT-TTA
* * *
260881 -ATAATATTAAATAAAATTTATT
1 TA-AATAATAAA-ATAATTT-TA
260903 TAAATAATAAAATAATTTTA
1 TAAATAATAAAATAATTTTA
260923 TAAATA
1 TAAATA
260929 TGATATATGA
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
19 1 0.03
20 10 0.27
21 11 0.30
22 14 0.38
23 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAATAATAAAATAATTTTA
Found at i:261728 original size:20 final size:21
Alignment explanation
Indices: 261705--261754 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
261695 TATAGTTTAG
261705 TTTAATTTAAAATAATA-ATT
1 TTTAATTTAAAATAATATATT
261725 TTTAA-TTAAAATAATATATT
1 TTTAATTTAAAATAATATATT
261745 TTT-ATTTAAA
1 TTTAATTTAAA
261755 TTAAATTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTAATTTAAAATAATATATT
Found at i:261755 original size:19 final size:19
Alignment explanation
Indices: 261705--261755 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
261695 TATAGTTTAG
261705 TTTAATTTAAAATAATAATT
1 TTTAATTT-AAATAATAATT
*
261725 TTTAATTAAAATAATATATT
1 TTTAATTTAAATAATA-ATT
261745 TTT-ATTTAAAT
1 TTTAATTTAAAT
261756 TAAATTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTAATTTAAATAATAATT
Found at i:261792 original size:18 final size:18
Alignment explanation
Indices: 261771--261823 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
261761 TATAAAATAT
261771 ATAAATATTAATATAAAA
1 ATAAATATTAATATAAAA
* *
261789 ATAATTTTTTAA-ATAAAA
1 ATAA-ATATTAATATAAAA
* *
261807 ATAAATAATAATTTAAA
1 ATAAATATTAATATAAA
261824 TTTATAAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
17 4 0.15
18 18 0.67
19 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAATATTAATATAAAA
Found at i:261849 original size:29 final size:31
Alignment explanation
Indices: 261798--261862 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
261788 AATAATTTTT
* *
261798 TAAATAAAAATAAATAATAATTT-AAATTTA
1 TAAATTAAAATAAATAACAATTTAAAATTTA
*
261828 TAAATTAAATTAAAT-ACAATTTAAAATTTA
1 TAAATTAAAATAAATAACAATTTAAAATTTA
261858 -AAATT
1 TAAATT
261863 TTTTAAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 11 0.35
30 20 0.65
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAATTAAAATAAATAACAATTTAAAATTTA
Found at i:261877 original size:29 final size:31
Alignment explanation
Indices: 261798--261879 Score: 82
Period size: 29 Copynumber: 2.8 Consensus size: 31
261788 AATAATTTTT
* * *
261798 TAAATAAAAATAAATAATAATTT-AAATTTA
1 TAAATTAAATTAAATTATAATTTAAAATTTA
*
261828 TAAATTAAATTAAA-TACAATTTAAAATTTA
1 TAAATTAAATTAAATTATAATTTAAAATTTA
**
261858 -AAATT-TTTTAAATTATAATTTA
1 TAAATTAAATTAAATTATAATTTA
261880 CTTTAAATCA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
28 5 0.12
29 19 0.44
30 19 0.44
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (31 bp):
TAAATTAAATTAAATTATAATTTAAAATTTA
Found at i:262215 original size:23 final size:23
Alignment explanation
Indices: 262188--262232 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
262178 AAAATATTTA
* *
262188 TATATTTATTTTATTTTATATTG
1 TATATTTATATTATTTAATATTG
262211 TATATTTATATTATTTAATATT
1 TATATTTATATTATTTAATATT
262233 ATTACTATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TATATTTATATTATTTAATATTG
Found at i:262218 original size:18 final size:16
Alignment explanation
Indices: 262182--262224 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 16
262172 AAGTTAAAAA
262182 TATTTATATATTTATTT
1 TATTT-TATATTTATTT
262199 TATTTTATATTGTATATT
1 TATTTTATATT-TAT-TT
*
262217 TATATTAT
1 TATTTTAT
262225 TTAATATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 6 0.26
17 8 0.35
18 9 0.39
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
TATTTTATATTTATTT
Found at i:262383 original size:18 final size:18
Alignment explanation
Indices: 262342--262390 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
262332 TTTTTAAAAA
262342 TTATAT-AATA-TAAATT
1 TTATATAAATATTAAATT
*
262358 AT-TA-AAATATTAAATT
1 TTATATAAATATTAAATT
*
262374 TTATATAAATATAAAAT
1 TTATATAAATATTAAAT
262391 ATTTTTAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
15 6 0.23
16 8 0.31
17 2 0.08
18 10 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TTATATAAATATTAAATT
Found at i:262400 original size:27 final size:25
Alignment explanation
Indices: 262347--262439 Score: 80
Period size: 27 Copynumber: 3.4 Consensus size: 25
262337 AAAAATTATA
262347 TAATATAAATTATTAAAATATTAAATT
1 TAATATAAA-TA-TAAAATATTAAATT
* *
262374 TTATATAAATATAAAATATTTTTAATT
1 TAATATAAATATAAAATA--TTAAATT
*
262401 TAAT-TATAATATAATAAATATATAAATA
1 TAATATA-AATAT-A-AAATAT-TAAATT
262429 TAATATAAATA
1 TAATATAAATA
262440 ATTATCATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
25 7 0.13
26 4 0.07
27 23 0.43
28 13 0.24
29 7 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
TAATATAAATATAAAATATTAAATT
Found at i:267204 original size:24 final size:24
Alignment explanation
Indices: 267177--267231 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
267167 TCTTCATAAT
*
267177 TAATTTTTTTGTTAAT-ATTAAATA
1 TAATTTTTTT-ATAATAATTAAATA
** *
267201 TAATAATTTTATAATAATTTAATA
1 TAATTTTTTTATAATAATTAAATA
267225 TAATTTT
1 TAATTTT
267232 CCTATAAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
TAATTTTTTTATAATAATTAAATA
Found at i:267215 original size:11 final size:11
Alignment explanation
Indices: 267199--267231 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
267189 TAATATTAAA
267199 TATAATAATTT
1 TATAATAATTT
267210 TATAATAATTT
1 TATAATAATTT
*
267221 AAT-ATAATTT
1 TATAATAATTT
267231 T
1 T
267232 CCTATAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 7 0.35
11 13 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TATAATAATTT
Found at i:267361 original size:2 final size:2
Alignment explanation
Indices: 267356--267380 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
267346 TGATATATTC
267356 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
267381 ACATATACAC
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:268618 original size:24 final size:24
Alignment explanation
Indices: 268591--268656 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 24
268581 TATTATATTC
*
268591 ATATTATTTTTATAATTTTTTTAT
1 ATATTATTTTTATAATTTATTTAT
* *
268615 ATATAAATTTTGATATATTTATTTAT
1 ATAT-TATTTTTATA-ATTTATTTAT
*
268641 TTATTATTTATTATAA
1 ATATTATTT-TTATAA
268657 AATAATGATT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
24 4 0.12
25 13 0.39
26 16 0.48
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (24 bp):
ATATTATTTTTATAATTTATTTAT
Found at i:269672 original size:22 final size:21
Alignment explanation
Indices: 269623--269665 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
269613 AAGTATCAAA
269623 TATATATAAATTTGGACACAT
1 TATATATAAATTTGGACACAT
*
269644 TATATATAAATTTTGACACAT
1 TATATATAAATTTGGACACAT
269665 T
1 T
269666 CGTATATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (21 bp):
TATATATAAATTTGGACACAT
Found at i:277506 original size:27 final size:27
Alignment explanation
Indices: 277445--277519 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 27
277435 AAAACCACCA
*
277445 TTTATTTGTAAAAAATAGTGGTTACTT
1 TTTATTTGTAAAAAATGGTGGTTACTT
** * * *
277472 AGTGTTTGTTAAAAATGGTGGTTTCTT
1 TTTATTTGTAAAAAATGGTGGTTACTT
*
277499 TTTATTTGTCAAAAATGGTGG
1 TTTATTTGTAAAAAATGGTGG
277520 CATGTTGTTT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.28, C:0.04, G:0.21, T:0.47
Consensus pattern (27 bp):
TTTATTTGTAAAAAATGGTGGTTACTT
Found at i:278570 original size:16 final size:16
Alignment explanation
Indices: 278545--278604 Score: 75
Period size: 16 Copynumber: 3.7 Consensus size: 16
278535 GACCTATCCG
*
278545 ACTCGAAAATAATCCAA
1 ACTCG-AAATGATCCAA
*
278562 ACTCGAAATGATCAAA
1 ACTCGAAATGATCCAA
* *
278578 ACTTGAAATGATCCGA
1 ACTCGAAATGATCCAA
278594 ACTCGAAATGA
1 ACTCGAAATGA
278605 CCCGAATAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
16 32 0.86
17 5 0.14
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (16 bp):
ACTCGAAATGATCCAA
Found at i:278609 original size:16 final size:16
Alignment explanation
Indices: 278540--278610 Score: 72
Period size: 16 Copynumber: 4.4 Consensus size: 16
278530 AACCCGACCT
*
278540 ATCCG-ACTCGAAAATA
1 ATCCGAACTCG-AAATG
*
278556 ATCCAAACTCGAAATG
1 ATCCGAACTCGAAATG
** *
278572 ATCAAAACTTGAAATG
1 ATCCGAACTCGAAATG
278588 ATCCGAACTCGAAATG
1 ATCCGAACTCGAAATG
*
278604 ACCCGAA
1 ATCCGAA
278611 TAATTAACCC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
16 41 0.89
17 5 0.11
ACGTcount: A:0.44, C:0.24, G:0.14, T:0.18
Consensus pattern (16 bp):
ATCCGAACTCGAAATG
Found at i:281081 original size:22 final size:23
Alignment explanation
Indices: 281053--281108 Score: 105
Period size: 22 Copynumber: 2.5 Consensus size: 23
281043 TGGACATGTT
281053 AAAAATGCATGAAACATAAT-AA
1 AAAAATGCATGAAACATAATAAA
281075 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
281098 AAAAATGCATG
1 AAAAATGCATG
281109 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 20 0.61
23 13 0.39
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:282066 original size:20 final size:20
Alignment explanation
Indices: 282019--282093 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
282009 AAAAAGACAT
*
282019 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
282038 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
282059 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
*
282079 AATGCATCGATACAT
1 AATGTATCGATACAT
282094 CAGGGTATGA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:282088 original size:40 final size:39
Alignment explanation
Indices: 282016--282093 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
282006 GGTAAAAAGA
* * *
282016 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATACATCGATACATT
* *
282055 CATACATGTATCGATATATTGAAAAATGCATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATACATCGATACAT
282094 CAGGGTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATACATCGATACATT
Found at i:282962 original size:29 final size:29
Alignment explanation
Indices: 282569--284266 Score: 2387
Period size: 29 Copynumber: 59.2 Consensus size: 29
282559 ACAGTGGTGA
* *
282569 TTTGAAAAGGGTTGCCATTGACTTGCATGGGC
1 TTTGAAAAGAG-TGCCACTGACTTG--TGGGC
* *
282601 TTT-AAAAGGGTGCCACTGACGTGCGTGGGC
1 TTTGAAAAGAGTGCCACTGAC-T-TGTGGGC
* * *
282631 TTTG-AAAGAATGCCACTAACTCGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
282659 TTTGAAAGGA-TGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
282687 TTTG-AAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
282715 TTTGAAAAG-GTACCACTGACTTGCGTGAGC
1 TTTGAAAAGAGTGCCACTGACTT--GTGGGC
282745 TTT-AAAAGGAGTGCCACTGACTTGTGTGAGC
1 TTTGAAAA-GAGTGCCACTGACTTGTG-G-GC
*
282776 TTT-AAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
282804 TTTG-AAAGAGTGCCACTGAATTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
282832 TTCGCAATG-GTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
282860 -TTCAAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
282888 TCTG-AAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
282916 TTTG-AAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
282944 TTTAAAAAGAGCGCCACTGATTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
282973 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
283002 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
283031 TTTG-AAAGGGTGCCATTGACTTGTGGTC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
283059 TTTGAAAAGAGTGCCACTGATTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
283088 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
283117 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
283146 TTTG-AAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
283174 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
283203 TTTGAAAAG-GTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
283231 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
283260 TTTG-AAAGGGTGCCACTAACTTATGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
283288 TTTGAAAAGAGTGCCACTGATTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
283317 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
283346 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
283375 TTTG-AAAGGGTGCCACTGAGTTGTCGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
283403 TTTG-AAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
283431 TTTGAAAAGAGTGCCACTGATTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
283460 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
283489 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
283518 TTTG-AAAGGGTGCCAC-GAACTTATGGGC
1 TTTGAAAAGAGTGCCACTG-ACTTGTGGGC
*
283546 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
283575 TTTGAAAAG-GTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
283603 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
283632 TTTG-AAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
283660 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
283689 TTTG-AAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
283717 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
283746 TTTG-AAGGGGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
283774 TTTG-AAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
283802 TTTGAAAAGAGTGCCACAGATTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
283831 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
283860 TTTGAAAGGAGTGCCATTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
283889 TTTG-AAAGGGTGCCACTAAGTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
283917 TTTG-AAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
283945 TTTGAAAAGAGTGCCACTGATTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
283974 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
284003 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
284032 TTTG-AAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
284060 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
284089 TTTGAAAAG-GTGCCACTGACTTGCGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
284117 TTTGAAAAGAGTGCCATTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
284146 TTTG-AAAGGGTGGCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
284174 TTTG-AAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
284202 TTTGAAAAGAGTGCCATTGATTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
284231 TTTGAAAAGAGTGCCACTGACTGGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
284260 TTTGAAA
1 TTTGAAA
284267 GGGATGAACA
Statistics
Matches: 1501, Mismatches: 132, Indels: 69
0.88 0.08 0.04
Matches are distributed among these distances:
27 9 0.01
28 642 0.43
29 760 0.51
30 57 0.04
31 29 0.02
32 4 0.00
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.28
Consensus pattern (29 bp):
TTTGAAAAGAGTGCCACTGACTTGTGGGC
Found at i:283053 original size:143 final size:143
Alignment explanation
Indices: 282581--284266 Score: 2477
Period size: 143 Copynumber: 11.8 Consensus size: 143
282571 TGAAAAGGGT
* * * **
282581 TGCCATTGACTTGCATGGGCTTTAAAAGGGTGCCACTGACGTGCGTGGGCTTTGAAAGAATGCCA
1 TGCCACTGACTTG--TGGGCTTTGAAAGGGTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCA
* * *
282646 CTAACTCGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTT
62 CTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTT
*
282709 GTGGGCTTTGAAAAG-G
127 GTGGGCTTTGAAAGGAG
* * * *
282725 TACCACTGACTTGCGTGAGCTTTAAAAGGAGTGCCACTGACTTGTGTGAGCTTTAAAAGGGTGCC
1 TGCCACTGACTT--GTGGGCTTTGAAAGG-GTGCCACTGACTTGTG-G-GCTTTGAAAGGGTGCC
* * * *
282790 ACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGAATTGTGGGCTTCGCAATG-GTGCCACTGACT
61 ACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
**
282853 TGTGGGCTTCAAAAGG-G
126 TGTGGGCTTTGAAAGGAG
* *
282870 TGCCACTGACTTGTGGGCTCTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGA
* * *
282935 CTTGTGGGCTTTAAAAAGAGCGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGG
66 CTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGG
283000 GCTTTGAAAGGAG
131 GCTTTGAAAGGAG
* * *
283013 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCATTGACTTGTGGTCTTTGAAAAGAGTGCCACTG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTG
* *
283078 ATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTG
65 ACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTG
283143 GGCTTTGAAAGG-G
130 GGCTTTGAAAGGAG
* *
283156 TGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTG
1 TGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG
* * *
283221 ACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTAACTTATG
65 ACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTG
*
283285 GGCTTTGAAAAGAG
130 GGCTTTGAAAGGAG
* *
283299 TGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACT
1 TGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACT
* * * *
283364 GACTTGTGGGCTTTG-AAAGGGTGCCACTGAGTTGTCGGCTTTG-AAAGGGTGCCACTGACTTGT
64 GACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGT
*
283427 GGGCTTTGAAAAGAG
129 GGGCTTTGAAAGGAG
* *
283442 TGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACT
1 TGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACT
* * *
283507 GACTTGTGGGCTTTG-AAAGGGTGCCAC-GAACTTATGGGCTTTGAAAGGAGTGCCACTGACTTG
64 GACTTGTGGGCTTTGAAAAGAGTGCCACTG-ACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
*
283570 TGGGCTTTGAAAAG-G
128 TGGGCTTTGAAAGGAG
*
283585 TGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTA
1 TGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG
* *
283650 ACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTG
65 ACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTG
*
283714 GGCTTTGAAAAGAG
130 GGCTTTGAAAGGAG
* *
283728 TGCCACTGACTTGTGGGCTTTGAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAA
1 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGA
* *
283793 CTTGTGGGCTTTGAAAAGAGTGCCACAGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGG
66 CTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGG
283858 GCTTTGAAAGGAG
131 GCTTTGAAAGGAG
* * *
283871 TGCCATTGACTTGTGGGCTTTGAAAGGGTGCCACTAAGTTGTGGGCTTTGAAAGGGTGCCACTGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGA
*
283936 CTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGG
66 CTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGG
284001 GCTTTGAAAGGAG
131 GCTTTGAAAGGAG
*
284014 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTG
* *
284079 ACTTGTGGGCTTTGAAAAG-GTGCCACTGACTTGCGGGCTTTGAAAAGAGTGCCATTGACTTGTG
65 ACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTG
284143 GGCTTTGAAAGG-G
130 GGCTTTGAAAGGAG
* * *
284156 TGGCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCATTG
1 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTG
* *
284221 ATTTGTGGGCTTTGAAAAGAGTGCCACTGACTGGTGGGCTTTGAAA
65 ACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
284267 GGGATGAACA
Statistics
Matches: 1420, Mismatches: 97, Indels: 51
0.91 0.06 0.03
Matches are distributed among these distances:
140 32 0.02
141 29 0.02
142 279 0.20
143 757 0.53
144 222 0.16
145 97 0.07
146 4 0.00
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.28
Consensus pattern (143 bp):
TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGA
CTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGG
GCTTTGAAAGGAG
Found at i:283064 original size:57 final size:56
Alignment explanation
Indices: 282569--284269 Score: 2378
Period size: 57 Copynumber: 29.7 Consensus size: 56
282559 ACAGTGGTGA
* * *
282569 TTTGAAAAGGGTTGCCATTGACTTGCATGGGCTTTAAAAGGGTGCCACTGACGTGCGTGGGC
1 TTTG-AAAGGG-TGCCACTGACTTG--TGGGCTTTGAAAGGGTGCCACTGAC-T-TGTGGGC
** * * *
282631 TTTGAAAGAATGCCACTAACTCGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
* * * *
282687 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTACCACTGACTTGCGTGAGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTT--GTGGGC
* *
282745 TTTAAAAGGAGTGCCACTGACTTGTGTGAGCTTTAAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGG-GTGCCACTGACTTGTG-G-GCTTTGAAAGGGTGCCACTGACTTGTGGGC
* * * * *
282804 TTTGAAAGAGTGCCACTGAATTGTGGGCTTCGCAATGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
** * *
282860 TTCAAAAGGGTGCCACTGACTTGTGGGCTCTGAAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
* * * *
282916 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTAAAAAGAGCGCCACTGATTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTT-GAAAGGGTGCCACTGACTTGTGGGC
*
282973 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGC
* * * *
283031 TTTGAAAGGGTGCCATTGACTTGTGGTCTTTGAAAAGAGTGCCACTGATTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGC
*
283088 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGC
*
283146 TTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGC
* *
283203 TTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGC
* * * *
283260 TTTGAAAGGGTGCCACTAACTTATGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGC
*
283317 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGC
* *
283375 TTTGAAAGGGTGCCACTGAGTTGTCGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
* * *
283431 TTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTG-AAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGC
*
283489 TTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCAC-GAACTTATGGGC
1 TTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG-ACTTGTGGGC
*
283546 TTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGC
1 TTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
*
283603 TTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
283660 TTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
* *
283717 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAGGGGTGCCACTGACTTGTGGGC
1 TTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
* * * *
283774 TTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACAGATTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGC
* *
283831 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCATTGACTTGTGGGC
1 TTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGC
* *
283889 TTTGAAAGGGTGCCACTAAGTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
* * *
283945 TTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTG-AAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGC
*
284003 TTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
* *
284060 TTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGCGGGC
1 TTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
* * *
284117 TTTGAAAAGAGTGCCATTGACTTGTGGGCTTTGAAAGGGTGGCACTGACTTGTGGGC
1 TTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
* * *
284174 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCATTGATTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGC
* *
284231 TTTGAAAAGAGTGCCACTGACTGGTGGGCTTTGAAAGGG
1 TTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGG
284270 ATGAACATTC
Statistics
Matches: 1477, Mismatches: 133, Indels: 63
0.88 0.08 0.04
Matches are distributed among these distances:
56 249 0.17
57 782 0.53
58 378 0.26
59 28 0.02
60 11 0.01
61 25 0.02
62 4 0.00
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.28
Consensus pattern (56 bp):
TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
Found at i:285508 original size:1 final size:1
Alignment explanation
Indices: 285504--285566 Score: 63
Period size: 1 Copynumber: 63.0 Consensus size: 1
285494 TTTTGTGCTA
* * * * * * *
285504 TTTTTTCTTTTTTTTTGTTTTTTTGTTTTGTTTTTTTTTGTGTTTTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
285567 GGTGTAAAGG
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.89
Consensus pattern (1 bp):
T
Found at i:285527 original size:13 final size:13
Alignment explanation
Indices: 285504--285566 Score: 74
Period size: 13 Copynumber: 4.8 Consensus size: 13
285494 TTTTGTGCTA
*
285504 TTTTTTCTTTTT-
1 TTTTTTTTTTTTG
*
285516 TTTTGTTTTTTTG
1 TTTTTTTTTTTTG
285529 TTTTGTTTTTTTTTG
1 -TTT-TTTTTTTTTG
*
285544 TGTTTTTTTTTTG
1 TTTTTTTTTTTTG
285557 TTTTTTTTTT
1 TTTTTTTTTT
285567 GGTGTAAAGG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
12 10 0.23
13 19 0.44
14 5 0.12
15 9 0.21
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.89
Consensus pattern (13 bp):
TTTTTTTTTTTTG
Found at i:285571 original size:25 final size:24
Alignment explanation
Indices: 285490--285565 Score: 97
Period size: 23 Copynumber: 3.3 Consensus size: 24
285480 GACCCTTATA
* * *
285490 TTTTTTTTGTG-CTATT-TTTTCT
1 TTTTTTTTGTGTTTTTTGTTTTGT
285512 TTTTTTTTGT-TTTTTTGTTTTGT
1 TTTTTTTTGTGTTTTTTGTTTTGT
285535 TTTTTTTTGTGTTTTTT-TTTTGT
1 TTTTTTTTGTGTTTTTTGTTTTGT
285558 TTTTTTTT
1 TTTTTTTT
285566 TGGTGTAAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.27
23 29 0.60
24 6 0.12
ACGTcount: A:0.01, C:0.03, G:0.11, T:0.86
Consensus pattern (24 bp):
TTTTTTTTGTGTTTTTTGTTTTGT
Found at i:298635 original size:22 final size:23
Alignment explanation
Indices: 298607--298662 Score: 105
Period size: 22 Copynumber: 2.5 Consensus size: 23
298597 TGGACATGTT
298607 AAAAATGCATGAAACATAAT-AA
1 AAAAATGCATGAAACATAATAAA
298629 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
298652 AAAAATGCATG
1 AAAAATGCATG
298663 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 20 0.61
23 13 0.39
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:299620 original size:20 final size:20
Alignment explanation
Indices: 299573--299647 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
299563 AAAAAGACAT
*
299573 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
299592 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
299613 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
*
299633 AATGCATCGATACAT
1 AATGTATCGATACAT
299648 CAGGGTATGA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:299642 original size:40 final size:39
Alignment explanation
Indices: 299570--299647 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
299560 GGTAAAAAGA
* * *
299570 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATACATCGATACATT
* *
299609 CATACATGTATCGATATATTGAAAAATGCATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATACATCGATACAT
299648 CAGGGTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATACATCGATACATT
Found at i:302242 original size:13 final size:13
Alignment explanation
Indices: 302224--302248 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
302214 CAATTTTTTG
302224 TGTATCGATACAC
1 TGTATCGATACAC
302237 TGTATCGATACA
1 TGTATCGATACA
302249 TACTTTGTGT
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:302261 original size:32 final size:33
Alignment explanation
Indices: 302204--302267 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
302194 TACAAGCCAA
**
302204 TGTATCGATACAATTTTTTGTGTATCGATACAC
1 TGTATCGATACAATACTTTGTGTATCGATACAC
302237 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
302268 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAC
Found at i:309424 original size:154 final size:155
Alignment explanation
Indices: 309096--309433 Score: 355
Period size: 154 Copynumber: 2.2 Consensus size: 155
309086 TTCTTTCATA
* * * *
309096 TTTTTTCTGTTTTCAAAATATGAAGTTTTTGACTTCATAAATTTCTTTAGTAATATTTTTCTGAG
1 TTTTTTC-G-TTTCAAAATATGAAATTTTTGACTCCATAAAATTCTTTAGTAAAATTTTTCTGAG
* * *
309161 CTTATGATTTTCAAAATTCTTCAAATATTATTTTTTTAATTTATATTAAATGACTATTGAAAAAT
64 CTTATAATTTTCAAAATTCTTCAAATATTATTTTTTTAATTCATATTAAATGACTATTAAAAAAT
* *
309226 TTAATTTATTTTATAAGTATTAGAATT
129 TAAACTTATTTTATAAGTATTAGAATT
** * ** * * *
309253 TTTCCT-ATTATTGAAATA-GAGAATTTTTTACTCCGTAAAATT-TTTGGTAAAATTTTTCT-AT
1 TTTTTTCGTT-TCAAAATATGA-AATTTTTGACTCCATAAAATTCTTTAGTAAAATTTTTCTGA-
* * * *
309314 GCTTATAATTTTTAAAATTCTTCAAATATTA-TTTTTTAATTCCTATTAAATTG-GTTTTAAAAA
63 GCTTATAATTTTCAAAATTCTTCAAATATTATTTTTTTAATTCATATTAAA-TGACTATTAAAAA
* *
309377 ATTAAACTTATTTTATCAGTTTTAGAATT
127 ATTAAACTTATTTTATAAGTATTAGAATT
309406 TTTTTTCGTTTCCAAAATATGGAAATTT
1 TTTTTTCGTTT-CAAAATAT-GAAATTT
309434 CTATTCTGTA
Statistics
Matches: 145, Mismatches: 28, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
153 55 0.38
154 57 0.39
155 27 0.19
156 2 0.01
157 4 0.03
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.51
Consensus pattern (155 bp):
TTTTTTCGTTTCAAAATATGAAATTTTTGACTCCATAAAATTCTTTAGTAAAATTTTTCTGAGCT
TATAATTTTCAAAATTCTTCAAATATTATTTTTTTAATTCATATTAAATGACTATTAAAAAATTA
AACTTATTTTATAAGTATTAGAATT
Found at i:315135 original size:19 final size:19
Alignment explanation
Indices: 315111--315210 Score: 107
Period size: 19 Copynumber: 5.9 Consensus size: 19
315101 AATTCAACAA
315111 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
315130 TTTGTATCGAT--ATAA--
1 TTTGTATCGATACATAAGT
315145 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
315162 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
315177 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
315194 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
315211 TTAGCTACTG
Statistics
Matches: 69, Mismatches: 0, Indels: 24
0.74 0.00 0.26
Matches are distributed among these distances:
13 20 0.29
15 6 0.09
17 6 0.09
19 37 0.54
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:315149 original size:32 final size:32
Alignment explanation
Indices: 315113--315207 Score: 172
Period size: 32 Copynumber: 3.0 Consensus size: 32
315103 TTCAACAATT
*
315113 TGTATCGATACATAAGTTTTGTATCGATATAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
315145 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
*
315177 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTTTTGTATCGATACA
315208 TAATTAGCTA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTTTTGTATCGATACAA
Found at i:315187 original size:13 final size:13
Alignment explanation
Indices: 315132--315188 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
315122 ACATAAGTTT
*
315132 TGTATCGATATAA
1 TGTATCGATACAA
315145 TGTATCGATACATAA
1 TGTATCGATAC--AA
315160 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
315177 TGTATCGATACA
1 TGTATCGATACA
315189 TAAGTATTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 22 0.59
15 2 0.05
17 2 0.05
19 11 0.30
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:315268 original size:13 final size:13
Alignment explanation
Indices: 315250--315275 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
315240 CATTTTTCTG
315250 TGTATCGATACAT
1 TGTATCGATACAT
315263 TGTATCGATACAT
1 TGTATCGATACAT
315276 GGATCTTTGT
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:315272 original size:33 final size:33
Alignment explanation
Indices: 315230--315296 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
315220 GCCAAGGAAA
***
315230 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
315263 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
315296 T
1 T
315297 TAGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:315827 original size:17 final size:17
Alignment explanation
Indices: 315807--315840 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
315797 AATCCTTTAG
315807 CAAAAAAAAAAAAAAAC
1 CAAAAAAAAAAAAAAAC
* *
315824 CAAAAACAAAGAAAAAC
1 CAAAAAAAAAAAAAAAC
315841 ACTATTCCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.82, C:0.15, G:0.03, T:0.00
Consensus pattern (17 bp):
CAAAAAAAAAAAAAAAC
Found at i:317884 original size:52 final size:53
Alignment explanation
Indices: 317799--317968 Score: 181
Period size: 52 Copynumber: 3.3 Consensus size: 53
317789 TTATTTTCGA
* * *
317799 GGGGATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAATTTTTCCACAATT
1 GGGGATACTCCAACTCCGGTTTTATTTC-CAAAAACACCAATTTTTCCACAATC
* * **
317851 GGGGATACTCCAA-TCCTGGTTTTATTTTC-AAAACGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACTCC-GGTTTTATTTCCAAAAACACCAATTTTTCC-ACAATC
* *
317903 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACTCCGGTTTTATTTCCAAAAACACCAATTTTTCCACAATC
*
317955 GAGGATACTCCAAC
1 GGGGATACTCCAAC
317969 CTCGTTATTT
Statistics
Matches: 98, Mismatches: 13, Indels: 14
0.78 0.10 0.11
Matches are distributed among these distances:
51 9 0.09
52 71 0.72
53 13 0.13
54 5 0.05
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (53 bp):
GGGGATACTCCAACTCCGGTTTTATTTCCAAAAACACCAATTTTTCCACAATC
Found at i:317988 original size:28 final size:28
Alignment explanation
Indices: 317952--318028 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
317942 ATTTTTCACA
* * *
317952 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
317980 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
318008 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
318029 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:318014 original size:212 final size:212
Alignment explanation
Indices: 317685--318074 Score: 597
Period size: 212 Copynumber: 1.8 Consensus size: 212
317675 TTCAAAACAC
* *
317685 TAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGAT
1 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGAT
* * *
317750 ACTCCAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACTC
66 ACTCCAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCC
* * *
317815 CGGTTTTA-TCGCTAAAACACTAATTTTTCCACAATTGGGGATACTCCAATCCTGGTTTTATTTT
131 CGGCTTTATTC-CCAAAACACTAATTTCT-CACAATTGGGGATACTCCAATCCTGGTTTTATTTT
317879 CAAAACGCCAATTTTCCTT
194 CAAAACGCCAATTTTCCTT
*
317898 TAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGAT
1 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGAT
* *
317961 ACTCCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACC
66 ACTCCAACCCCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACC
* * * *
318026 CCGGCTTTATTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAA
130 CCGGCTTTATTCCCAAAACACTAATTTCTCACAATTGGGGATACTCCAA
318075 CCCCGTTATT
Statistics
Matches: 160, Mismatches: 15, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
211 47 0.29
212 78 0.49
213 35 0.22
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (212 bp):
TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGAT
ACTCCAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCC
CGGCTTTATTCCCAAAACACTAATTTCTCACAATTGGGGATACTCCAATCCTGGTTTTATTTTCA
AAACGCCAATTTTCCTT
Found at i:318095 original size:107 final size:107
Alignment explanation
Indices: 317690--318107 Score: 287
Period size: 107 Copynumber: 3.9 Consensus size: 107
317680 AACACTAATC
* * * * *
317690 GGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCC
1 GGGGATACTCCAACCCCGACTTTATTTCC-AAAAATACCAATTTC-TCACAATCGAGGATACTCC
* * * *
317755 AACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTTCGA
64 AACCCCGTTATTTATCGGGGATACTCCAACCCCGTTACTTCCGA
* * * * * * * * *
317799 GGGGATACTCCAACTCCG-GTTT-TATCGCTAAAACACTAATTTTTCCACAATTGGGGATACTCC
1 GGGGATACTCCAACCCCGACTTTATTTC-CAAAAATACCAATTTCT-CACAATCGAGGATACTCC
* * * ***** * * ** * *
317862 AATCCTGGT-TTTATTTTCAAAACGCCAATTTTCCTTTA-AT-C--
64 AACCCCGTTATTTATCGGGGATACTCCAA--CCCCGTTACTTCCGA
* * *
317903 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
317968 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
66 CCCCGTTATTT-ATCGGGGATACTCCAACCCCGTTACTTCCGA
* * *** * * *
318011 GGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
318075 CCCCGTTATTT-TCGAAGGGATACTCCAATCCCG
66 CCCCGTTATTTATCG--GGGATACTCCAACCCCG
318108 ATTTTTTTTT
Statistics
Matches: 237, Mismatches: 58, Indels: 30
0.73 0.18 0.09
Matches are distributed among these distances:
104 44 0.19
105 24 0.10
106 25 0.11
107 97 0.41
108 30 0.13
109 17 0.07
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
CCCCGTTATTTATCGGGGATACTCCAACCCCGTTACTTCCGA
Found at i:318132 original size:79 final size:79
Alignment explanation
Indices: 317982--318184 Score: 221
Period size: 79 Copynumber: 2.6 Consensus size: 79
317972 GTTATTTCAT
* * * *
317982 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
** * *
318047 TGATTTCTCATAAT
66 CAATTTCTCACAAC
* * * * ** *
318061 TGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCCGATTTTTTTTTC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAAT-A
318125 TCAATTTCTCACAAC
65 TCAATTTCTCACAAC
* *
318140 CGGGGATACTCCAGCCCCGTTATTTTC-AAGGGAACACTCCAACCC
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGG-ATACTCCAACCC
318185 TGTTATTATC
Statistics
Matches: 103, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
78 8 0.08
79 95 0.92
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
CAATTTCTCACAAC
Found at i:321015 original size:13 final size:13
Alignment explanation
Indices: 320997--321023 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
320987 ACATTATGCT
320997 TTGTATCGATACA
1 TTGTATCGATACA
321010 TTGTATCGATACA
1 TTGTATCGATACA
321023 T
1 T
321024 GCTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:321032 original size:19 final size:19
Alignment explanation
Indices: 321008--321064 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
320998 TGTATCGATA
321008 CATTGTATCGATACATG-C
1 CATTGTATCGATACATGAC
321026 TCATTGTATCGATACATAGAC
1 -CATTGTATCGATACAT-GAC
*
321047 AATTGTATCGATACATGA
1 CATTGTATCGATACATGA
321065 GAGTGACAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
19 18 0.51
20 16 0.46
21 1 0.03
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (19 bp):
CATTGTATCGATACATGAC
Found at i:321139 original size:21 final size:21
Alignment explanation
Indices: 321092--321144 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
321082 CTACCACTGT
321092 TTGTATCAATACATGGGACAA
1 TTGTATCAATACATGGGACAA
* *
321113 -TGTATCCATACATGATGA-AA
1 TTGTATCAATACATG-GGACAA
*
321133 TTGTATCGATAC
1 TTGTATCAATAC
321145 TGAAAGCTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (21 bp):
TTGTATCAATACATGGGACAA
Found at i:321915 original size:13 final size:13
Alignment explanation
Indices: 321897--321922 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
321887 ACATTTGGTC
321897 ATGTATCGATACA
1 ATGTATCGATACA
321910 ATGTATCGATACA
1 ATGTATCGATACA
321923 TCTTGTATGT
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:321938 original size:32 final size:33
Alignment explanation
Indices: 321875--321942 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
321865 CGTTACAAGC
321875 CAATATATCGATACATTTGGTCATGTATCGATA
1 CAATATATCGATACATTTGGTCATGTATCGATA
*
321908 CAATGTATCGATACATCTT-GT-ATGTATCGATA
1 CAATATATCGATACAT-TTGGTCATGTATCGATA
321940 CAA
1 CAA
321943 ACAGTTAAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 14 0.42
33 17 0.52
34 2 0.06
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (33 bp):
CAATATATCGATACATTTGGTCATGTATCGATA
Found at i:322019 original size:20 final size:21
Alignment explanation
Indices: 321972--322024 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
321962 GCCAATCACC
*
321972 TGTATCGATACATTCTTTGTA
1 TGTATCGATACATTCTTGGTA
*
321993 AGTATCGATACA-T-TTGGTCA
1 TGTATCGATACATTCTTGGT-A
322013 TGTATCGATACA
1 TGTATCGATACA
322025 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 4 0.14
20 13 0.46
21 11 0.39
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTTGGTA
Found at i:322030 original size:13 final size:13
Alignment explanation
Indices: 322012--322036 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
322002 ACATTTGGTC
322012 ATGTATCGATACA
1 ATGTATCGATACA
322025 ATGTATCGATAC
1 ATGTATCGATAC
322037 TGTGCATTAT
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):
ATGTATCGATACA
Found at i:324520 original size:28 final size:28
Alignment explanation
Indices: 324464--324530 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
324454 GGAATAAAGC
** *
324464 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
324492 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
324520 CGAGGTTGGAG
1 CGGGGTTGGAG
324531 CATACTCGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.21
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:324593 original size:52 final size:52
Alignment explanation
Indices: 324537--324861 Score: 161
Period size: 52 Copynumber: 6.2 Consensus size: 52
324527 GGAGCATACT
324537 CGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCC
1 CGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCC
** * ** * *
324589 CGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACCAGGA-TTGGAGTATCCC
1 CGATT-GTGAAAAATTGGTATTTTTGGAAATAAAATC-GGAGTTGGAGTATCCC
* * * *
324641 CGATTGTGAAAAAATTAGTGTTTTAGCG--ATAAAACCGGAGTTGGAGTATCCC
1 CGATTGTG-AAAAATTGGTATTTTTG-GAAATAAAATCGGAGTTGGAGTATCCC
** **** * * *
324693 C---TCAGAAATAACGGGGTTAGAGTA-TCCCCGATGAT-TAA-CGGGGTTGGAGTATCCC
1 CGATTGTGAAA-AA-----TT-G-GTATTTTTGGA-AATAAAATCGGAGTTGGAGTATCCC
* *
324748 CGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTAGAGTATCCC
1 CGATTGTGAA-AAATT-G-GTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCC
* * * * * *
324803 CGATTAT-AGAAAATTAGT-GTTTTGAAAATAAAATCGGAGTTGGAATATCCT
1 CGATTGTGA-AAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCC
324854 CGATTGTG
1 CGATTGTG
324862 GAGAATTGAT
Statistics
Matches: 201, Mismatches: 46, Indels: 52
0.67 0.15 0.17
Matches are distributed among these distances:
48 3 0.01
49 4 0.02
51 38 0.19
52 66 0.33
53 23 0.11
54 14 0.07
55 40 0.20
56 4 0.02
57 2 0.01
58 6 0.03
59 1 0.00
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (52 bp):
CGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCC
Found at i:324798 original size:55 final size:51
Alignment explanation
Indices: 324739--324866 Score: 141
Period size: 51 Copynumber: 2.4 Consensus size: 51
324729 AACGGGGTTG
* *
324739 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTGTG-AGAAATTAGTG---TTTTGAAAATAAAATCGGAGTTA
* *
324794 GAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTGTGAG-AAATTAGTGTTTTGAAAATAAAATCGGAGTTA
* *
324845 GAATATCCTCGATTGTGGAGAA
1 GAGTATCCCCGATTGT-GAGAA
324867 TTGATAAACT
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
51 34 0.54
52 2 0.03
53 4 0.06
54 8 0.13
55 15 0.24
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (51 bp):
GAGTATCCCCGATTGTGAGAAATTAGTGTTTTGAAAATAAAATCGGAGTTA
Found at i:326479 original size:13 final size:13
Alignment explanation
Indices: 326461--326486 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
326451 ACAAAGATCC
326461 ATGTATCGATACA
1 ATGTATCGATACA
326474 ATGTATCGATACA
1 ATGTATCGATACA
326487 CAGAAAAATG
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:326482 original size:33 final size:33
Alignment explanation
Indices: 326440--326506 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
326430 AAAATTTCCA
***
326440 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
326473 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
326506 A
1 A
326507 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:326550 original size:19 final size:18
Alignment explanation
Indices: 326526--326593 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
326516 CAGTAGCTAA
326526 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
*
326545 TTATGTTTCGATAC--A-
1 TTATGTATCGATACAAAC
326560 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
326577 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
326594 TTGTTGAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
13 10 0.24
14 1 0.02
16 2 0.05
18 4 0.10
19 24 0.59
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:326570 original size:32 final size:32
Alignment explanation
Indices: 326529--326591 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
326519 TAGCTAATTA
* *
326529 TGTATCGATACAATACTTATGTTTCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
326561 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
326592 AATTGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:327374 original size:55 final size:55
Alignment explanation
Indices: 327290--327967 Score: 1062
Period size: 55 Copynumber: 12.3 Consensus size: 55
327280 ATAAACTGTA
* * * * * * *
327290 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGGTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
327345 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
327400 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
327455 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* * *
327510 TCCTGTTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGGTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
327565 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
327620 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
327675 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
327730 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
327785 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
327840 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
327895 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
327950 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
327968 AAAAAGCGGA
Statistics
Matches: 585, Mismatches: 29, Indels: 18
0.93 0.05 0.03
Matches are distributed among these distances:
54 13 0.02
55 560 0.96
56 12 0.02
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:327454 original size:29 final size:29
Alignment explanation
Indices: 327366--327454 Score: 87
Period size: 29 Copynumber: 3.2 Consensus size: 29
327356 GAGGACTAAA
327366 AGGTGCCACCAACTTGTGTGGGCTTTAAG
1 AGGTGCCACCAACTTGTGTGGGCTTTAAG
** * ** *
327395 AGGTGTCCTGC-TCTT-TG-GGGAATGAA-
1 AGGTG-CCACCAACTTGTGTGGGCTTTAAG
327421 AGGTGCCACCAACTTGTGTGGGCTTTAAG
1 AGGTGCCACCAACTTGTGTGGGCTTTAAG
327450 AGGTG
1 AGGTG
327455 TCCTGCTCTT
Statistics
Matches: 43, Mismatches: 12, Indels: 10
0.66 0.18 0.15
Matches are distributed among these distances:
25 3 0.07
26 8 0.19
27 8 0.19
28 8 0.19
29 13 0.30
30 3 0.07
ACGTcount: A:0.20, C:0.18, G:0.34, T:0.28
Consensus pattern (29 bp):
AGGTGCCACCAACTTGTGTGGGCTTTAAG
Found at i:341530 original size:28 final size:27
Alignment explanation
Indices: 341497--341563 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 27
341487 GGAATAAAGC
341497 CGGGGTTGGAGTATCCCC-TCGAAAGTAA
1 CGGGGTTGGAGTATCCCCAT-GAAA-TAA
341525 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCC-ATGAAATAA
*
341553 CGAGGTTGGAG
1 CGGGGTTGGAG
341564 CATACTCGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
28 31 0.86
29 4 0.11
30 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.36, T:0.21
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCATGAAATAA
Found at i:341573 original size:28 final size:29
Alignment explanation
Indices: 341517--341573 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
341507 GTATCCCCTC
* * *
341517 GAAAGTAACGGGGTTGGAGTATCCCCGAT
1 GAAAGTAACGAGGTTGGAGCATACCCGAT
*
341546 GAAA-TAACGAGGTTGGAGCATACTCGAT
1 GAAAGTAACGAGGTTGGAGCATACCCGAT
341574 TGTGAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.32, C:0.16, G:0.32, T:0.21
Consensus pattern (29 bp):
GAAAGTAACGAGGTTGGAGCATACCCGAT
Found at i:341626 original size:52 final size:52
Alignment explanation
Indices: 341570--341894 Score: 170
Period size: 52 Copynumber: 6.2 Consensus size: 52
341560 GGAGCATACT
341570 CGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCC
1 CGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCC
** * ** * *
341622 CGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACCAGGA-TTGGAGTATCCC
1 CGATT-GTGAAAAATTGGTATTTTTGGAAATAAAATC-GGAGTTGGAGTATCCC
* * * *
341674 CGATTGTGAAAAAATTAGTGTTTTAGCG--ATAAAACCGGAGTTGGAGTATCCC
1 CGATTGTG-AAAAATTGGTATTTTTG-GAAATAAAATCGGAGTTGGAGTATCCC
* **** * * *
341726 C--TCG-GAAATAACGGGGTTGG-AGTATCCCCGATGAT-TAA-CGGGGTTGGAGTATCCC
1 CGATTGTGAAA-AA-----TTGGTA-T-TTTTGGA-AATAAAATCGGAGTTGGAGTATCCC
* *
341781 CGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTAGAGTATCCC
1 CGATTGTGAA-AAATT-G-GTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCC
* * * * * *
341836 CGATTAT-AGAAAATTAGT-GTTTTGAAAATAAAATCGGAGTTGGAATATCCT
1 CGATTGTGA-AAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCC
341887 CGATTGTG
1 CGATTGTG
341895 GAGAATTGAT
Statistics
Matches: 203, Mismatches: 42, Indels: 56
0.67 0.14 0.19
Matches are distributed among these distances:
48 3 0.01
49 3 0.01
50 2 0.01
51 38 0.19
52 66 0.33
53 20 0.10
54 17 0.08
55 42 0.21
56 2 0.01
57 4 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (52 bp):
CGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCC
Found at i:341753 original size:28 final size:27
Alignment explanation
Indices: 341713--341783 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
341703 TAAAACCGGA
**
341713 GTTGGAGTATCCCCTCGGAAATAACGGG
1 GTTGGAGTATCCCCGAGG-AATAACGGG
* *
341741 GTTGGAGTATCCCCGATGATTAACGGG
1 GTTGGAGTATCCCCGAGGAATAACGGG
341768 GTTGGAGTATCCCCGA
1 GTTGGAGTATCCCCGA
341784 TTGTGAAGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 24 0.62
28 15 0.38
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (27 bp):
GTTGGAGTATCCCCGAGGAATAACGGG
Found at i:341796 original size:107 final size:105
Alignment explanation
Indices: 341443--341836 Score: 302
Period size: 107 Copynumber: 3.7 Consensus size: 105
341433 CCTTCGAAAA
* * * * * *
341443 TAACGGGGTTGGAGTATCCCCAATTATG-AGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGA
1 TAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTAGTATTTT-GGAATAAAACCGGAGTTGGA
*
341507 GTATCCCCTCGAAAGTAACGGGGTTGGAGTATCCCCGATGAAA
65 GTATCCCCTCGAAA-TAACGGGGTTGGAGTATCCCCGATG-AT
* * * * * *
341550 TAACGAGGTTGGAGCATACTCGATTGTGAA-AAATTGGTATTTTTGGAAATAAAATCGGAGTTGG
1 TAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTAGTA-TTTTGG-AATAAAACCGGAGTTGG
* * ** * ** **
341614 AGTAT-CCC-CG-ATTAAAGGAAAATTGGCGT-T--TTGAAAAT
64 AGTATCCCCTCGAAATAACGG--GGTTGGAGTATCCCCGATGAT
* * * * *
341652 AAAACCAGGATTGGAGTATCCCCGATTGTGAAAAAATTAGTGTTTTAGCG-ATAAAACCGGAGTT
1 -TAA-CGGGGTTGGAGTATCCCCGATTGTGAAGAAATTAGTATTTT-G-GAATAAAACCGGAGTT
341716 GGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAT
62 GGAGTATCCCCTC-GAAATAACGGGGTTGGAGTATCCCCGATGAT
* * *
341761 TAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTT
1 TAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATT--AG-TATTTTGG-AATAAAACCGGAGTT
*
341826 AGAGTATCCCC
62 GGAGTATCCCC
341837 GATTATAGAA
Statistics
Matches: 216, Mismatches: 49, Indels: 41
0.71 0.16 0.13
Matches are distributed among these distances:
102 1 0.00
103 4 0.02
104 50 0.23
105 13 0.06
106 16 0.07
107 65 0.30
108 33 0.15
109 6 0.03
110 28 0.13
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.27
Consensus pattern (105 bp):
TAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTAGTATTTTGGAATAAAACCGGAGTTGGAG
TATCCCCTCGAAATAACGGGGTTGGAGTATCCCCGATGAT
Found at i:341831 original size:55 final size:51
Alignment explanation
Indices: 341772--341899 Score: 141
Period size: 51 Copynumber: 2.4 Consensus size: 51
341762 AACGGGGTTG
* *
341772 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTGTG-AGAAATTAGTG---TTTTGAAAATAAAATCGGAGTTA
* *
341827 GAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTGTGAG-AAATTAGTGTTTTGAAAATAAAATCGGAGTTA
* *
341878 GAATATCCTCGATTGTGGAGAA
1 GAGTATCCCCGATTGT-GAGAA
341900 TTGATAAACT
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
51 34 0.54
52 2 0.03
53 4 0.06
54 8 0.13
55 15 0.24
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (51 bp):
GAGTATCCCCGATTGTGAGAAATTAGTGTTTTGAAAATAAAATCGGAGTTA
Found at i:344275 original size:13 final size:13
Alignment explanation
Indices: 344257--344282 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
344247 ACAAAGATCC
344257 ATGTATCGATACA
1 ATGTATCGATACA
344270 ATGTATCGATACA
1 ATGTATCGATACA
344283 CAGAAAAATG
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:344278 original size:33 final size:33
Alignment explanation
Indices: 344236--344302 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
344226 AAAATTTCCA
***
344236 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
344269 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
344302 A
1 A
344303 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:344346 original size:19 final size:18
Alignment explanation
Indices: 344322--344389 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
344312 CAGTAGCTAA
344322 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
344341 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
344356 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
344373 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
344390 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:344362 original size:13 final size:13
Alignment explanation
Indices: 344344--344368 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
344334 ACAATACTTA
344344 TGTATCGATACAT
1 TGTATCGATACAT
344357 TGTATCGATACA
1 TGTATCGATACA
344369 AAACTTATGT
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.