Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008655.1 Hibiscus syriacus cultivar Beakdansim tig00111649_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 378222
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 2 of 3
Found at i:174772 original size:49 final size:50
Alignment explanation
Indices: 174714--174812 Score: 173
Period size: 49 Copynumber: 2.0 Consensus size: 50
174704 AAAAATCATG
*
174714 TAAGTACGTGTTATTATAAATGTTTGGGTTAATAC-AAAAAGTGTTCAAA
1 TAAGTACGTGTTATTATAAATGTTTGGCTTAATACAAAAAAGTGTTCAAA
*
174763 TAAGTACGTGTTATTGTAAATGTTTGGCTTAATACAAAAAAGTGTTCAAA
1 TAAGTACGTGTTATTATAAATGTTTGGCTTAATACAAAAAAGTGTTCAAA
174813 CTATATCTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
49 33 0.70
50 14 0.30
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.36
Consensus pattern (50 bp):
TAAGTACGTGTTATTATAAATGTTTGGCTTAATACAAAAAAGTGTTCAAA
Found at i:176903 original size:81 final size:81
Alignment explanation
Indices: 176768--177117 Score: 443
Period size: 81 Copynumber: 4.3 Consensus size: 81
176758 TTTTAGGTCA
* ** * * * * *
176768 AAATGCACTGTTAAACATTTATTC-TTTCCTCTAAAGGCAGTTAACCTTTCATCTAACTTGCATT
1 AAATGCACAGTTAGGCATTTAATCTTTTACTC-AAAGGCATTTAACCTTTCATCTAACTAGCATG
*
176832 ATTGACACATTTTTGCC
65 ATTGACACATTTCTGCC
* *
176849 AAATGCACAGTTAGGCATTTAATCTTTTACCCAAAGGCATTTAATCTTTCATCTAACTAGCATGA
1 AAATGCACAGTTAGGCATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGA
176914 TT-ATCACATTTCTGCC
66 TTGA-CACATTTCTGCC
* ** * * *
176930 AATTATATAGTCAGGCATTTAATCTTTTACTCAAATGCATTTAACCTTTCATCTAACTAGCATGA
1 AAATGCACAGTTAGGCATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGA
* *
176995 TTGACATATTTCTACC
66 TTGACACATTTCTGCC
* * *
177011 AAATGCACAATTAGGCATTTAATCTTTTACTGAAAGACATTTAACCTTTCATCTAACTAGCATGA
1 AAATGCACAGTTAGGCATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGA
* *
177076 TTGGCACTTTTCTGCC
66 TTGACACATTTCTGCC
*
177092 AAATGCATAGTTAGGCATTTAATCTT
1 AAATGCACAGTTAGGCATTTAATCTT
177118 CCATTTTAAA
Statistics
Matches: 230, Mismatches: 36, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
80 1 0.00
81 223 0.97
82 6 0.03
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.38
Consensus pattern (81 bp):
AAATGCACAGTTAGGCATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGA
TTGACACATTTCTGCC
Found at i:180823 original size:21 final size:22
Alignment explanation
Indices: 180792--180840 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
180782 CTATTAAATA
180792 CCTCT-AAAAAATACTTGGA-G
1 CCTCTAAAAAAATACTTGGATG
*
180812 CCTCTAAAAAAATATTTGGATG
1 CCTCTAAAAAAATACTTGGATG
180834 CCTCTAA
1 CCTCTAA
180841 TAACTACCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 5 0.19
21 13 0.50
22 8 0.31
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (22 bp):
CCTCTAAAAAAATACTTGGATG
Found at i:184426 original size:17 final size:17
Alignment explanation
Indices: 184404--184437 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
184394 TTTTGATATA
184404 ACAAATAAAGTATTAAT
1 ACAAATAAAGTATTAAT
*
184421 ACAAATAAAGTGTTAAT
1 ACAAATAAAGTATTAAT
184438 GAATTTTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.29
Consensus pattern (17 bp):
ACAAATAAAGTATTAAT
Found at i:184972 original size:20 final size:20
Alignment explanation
Indices: 184943--184981 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
184933 CAGTTTTTTT
*
184943 AAGTTTAAAAACATACAACG
1 AAGTTGAAAAACATACAACG
184963 AAGTTGAAAAACATACAAC
1 AAGTTGAAAAACATACAAC
184982 AACGGCTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.15, G:0.10, T:0.18
Consensus pattern (20 bp):
AAGTTGAAAAACATACAACG
Found at i:191904 original size:17 final size:17
Alignment explanation
Indices: 191872--191905 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
191862 TTTCGATATA
*
191872 ACAAATAATGTATTAAT
1 ACAAATAAAGTATTAAT
*
191889 ACAAATAAAGTGTTAAT
1 ACAAATAAAGTATTAAT
191906 GAATTTTAAA
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:0.53, C:0.06, G:0.09, T:0.32
Consensus pattern (17 bp):
ACAAATAAAGTATTAAT
Found at i:194191 original size:30 final size:30
Alignment explanation
Indices: 194157--194257 Score: 89
Period size: 30 Copynumber: 3.3 Consensus size: 30
194147 GCGAACCTTA
194157 GGTAGGCTCCGAGGCCCCGAGACTTTCTTG
1 GGTAGGCTCCGAGGCCCCGAGACTTTCTTG
* * * *
194187 GGTAGGCT--TATGTCCCCGAGATCATTCTAG
1 GGTAGGCTCCGA-GGCCCCGAGA-CTTTCTTG
* *
194217 GGTAGGCCCCGTGGCCCCGAGTAACTTTCTTG
1 GGTAGGCTCCGAGGCCCCGAG--ACTTTCTTG
*
194249 CGTAGGCTC
1 GGTAGGCTC
194258 TTGGGCCCTA
Statistics
Matches: 53, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
28 1 0.02
29 9 0.17
30 21 0.40
31 8 0.15
32 13 0.25
33 1 0.02
ACGTcount: A:0.15, C:0.29, G:0.31, T:0.26
Consensus pattern (30 bp):
GGTAGGCTCCGAGGCCCCGAGACTTTCTTG
Found at i:195745 original size:3 final size:3
Alignment explanation
Indices: 195737--195774 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
195727 TTTATCCCGA
195737 TAT TAT TA- TAT TCAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TA
195775 ATTTATGTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:197970 original size:131 final size:131
Alignment explanation
Indices: 197720--198085 Score: 437
Period size: 131 Copynumber: 2.8 Consensus size: 131
197710 CTCAATATTG
* * * * * * ** *
197720 AAAATAGTCATATATTTTCATTTC-AGCTGGAGTAATAAATTATTGCTTTAAGGCATGAGAGGTT
1 AAAATAGTAATATCTCTTCATTTCGA-TTGGAGTAATAAATGACTAATTTAAGGCATGAGAGGTA
* ** * *
197784 TTTTATTCTTTATTGGAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGATTTTTAAG
65 ATTTATTCTCAATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATTGAATTTTAAG
*
197849 AT
130 AC
** * *
197851 GGAATATTAATATCTCTTCATTTCGATTGGAGTGATAAATGACTAATTTAAGGCATGAGAGGTAA
1 AAAATAGTAATATCTCTTCATTTCGATTGGAGTAATAAATGACTAATTTAAGGCATGAGAGGTAA
* * *
197916 TTTATTCTCAATTGGAAATCATTAGATATTATCATTTTCACTTGAATCAATATTGAATTTTAAGA
66 TTTATTCTCAATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATTGAATTTTAAGA
197981 C
131 C
* * * * ** *
197982 AAAATAGTGATATCTCTTTATTTCGATTGGATTAATAAATGATTGCTTTAAGGCATGAGAGGTCA
1 AAAATAGTAATATCTCTTCATTTCGATTGGAGTAATAAATGACTAATTTAAGGCATGAGAGGTAA
* *
198047 TCTATTCTCGATTGGAAATAATTAGATATTATCGTTTTC
66 TTTATTCTCAATTGGAAATAATTAGATATTATCGTTTTC
198086 TCTCTTAAAA
Statistics
Matches: 197, Mismatches: 37, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
131 196 0.99
132 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (131 bp):
AAAATAGTAATATCTCTTCATTTCGATTGGAGTAATAAATGACTAATTTAAGGCATGAGAGGTAA
TTTATTCTCAATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATTGAATTTTAAGA
C
Found at i:202532 original size:17 final size:17
Alignment explanation
Indices: 202500--202542 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
202490 TAAGAGTTAA
* *
202500 TTTAATAAATGGACTAG
1 TTTAATGAATGAACTAG
*
202517 TTTGATGAATGAACTAG
1 TTTAATGAATGAACTAG
202534 TTTAATGAA
1 TTTAATGAA
202543 CTAGATGATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.37
Consensus pattern (17 bp):
TTTAATGAATGAACTAG
Found at i:210552 original size:17 final size:17
Alignment explanation
Indices: 210530--210562 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
210520 TTTCATAAAC
*
210530 GAACTAGTTTGATGAAT
1 GAACTAGTTTAATGAAT
210547 GAACTAGTTTAATGAA
1 GAACTAGTTTAATGAA
210563 CTATTTCCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.33
Consensus pattern (17 bp):
GAACTAGTTTAATGAAT
Found at i:219505 original size:42 final size:42
Alignment explanation
Indices: 219438--219519 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
219428 AATTGGCAAG
* *
219438 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATAATTAAA
1 TCCTTCGGGCCATCAGTAAGCCTTTCGAGCAAGATAATTAAA
* *
219480 TCCTTCGGGTCATCTA-TAAGCCTTTCGAGCAAGATGATTA
1 TCCTTCGGGCCATC-AGTAAGCCTTTCGAGCAAGATAATTA
219520 GTTCTTCGGG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 34 0.97
43 1 0.03
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (42 bp):
TCCTTCGGGCCATCAGTAAGCCTTTCGAGCAAGATAATTAAA
Found at i:219713 original size:41 final size:42
Alignment explanation
Indices: 219637--219715 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
219627 ATCAATAAGT
* *
219637 CTTTCGAGCATGATGATTAATTCCTTCGGGTCATCTATTAGC
1 CTTTCAAGCAAGATGATTAATTCCTTCGGGTCATCTATTAGC
219679 CTTTCAAGCAAGATGA-TAAGTT-CTTC-GGTCCATCTAT
1 CTTTCAAGCAAGATGATTAA-TTCCTTCGGGT-CATCTAT
219716 AAGACCTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
40 3 0.09
41 14 0.42
42 16 0.48
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.37
Consensus pattern (42 bp):
CTTTCAAGCAAGATGATTAATTCCTTCGGGTCATCTATTAGC
Found at i:220485 original size:132 final size:132
Alignment explanation
Indices: 220245--220548 Score: 418
Period size: 132 Copynumber: 2.3 Consensus size: 132
220235 GCAAATCGAA
* *
220245 CTCGATTCAATATTCCCTTG-AGAACAGTGGAATAAATCAATGTCTCCAGATCTGATTTCCCTAA
1 CTCGATTCAATCTTCCC-TGAAGAACAGTGGAATGAATCAATGTCTCCAGATCTGATTTCCCTAA
* * *
220309 AGAAACAGATGAACATATCCTCTCTTTCCAGATTTGATCTTCCCTGAGTAGCAGTAGAACAAGTC
65 AGAAACAGATGAACAGATCCTCTCTTTCCAGATTTGATATTCCCTAAGTAGCAGTAGAACAAGTC
220374 TAC
130 TAC
* * * *
220377 CTTGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAATGTCTCCGGATCTTATTTCCCTGAA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAATGTCTCCAGATCTGATTTCCCTAAA
* * *
220442 GAAGCAGCAT-AACAGACGTCC-C-CTTTCCAGATTTGATATTCCCTAAGTAGTAGTGGAACAAG
66 GAAACAG-ATGAACAGA--TCCTCTCTTTCCAGATTTGATATTCCCTAAGTAGCAGTAGAACAAG
220504 TCTAC
128 TCTAC
* *
220509 CTCGATTCAATCTTCCCTAAAGAACAATGGAATGAATCAA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAA
220549 CATTTCTCGA
Statistics
Matches: 153, Mismatches: 15, Indels: 8
0.87 0.09 0.05
Matches are distributed among these distances:
131 2 0.01
132 145 0.95
133 3 0.02
134 3 0.02
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (132 bp):
CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAATGTCTCCAGATCTGATTTCCCTAAA
GAAACAGATGAACAGATCCTCTCTTTCCAGATTTGATATTCCCTAAGTAGCAGTAGAACAAGTCT
AC
Found at i:220739 original size:3 final size:3
Alignment explanation
Indices: 220733--220781 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
220723 TTATTTCATC
** * * *
220733 ATT ATT ATT ATT GGT ATT ATT ATT ATT ATT AAT GTT ATT ATT TTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
220781 A
1 A
220782 ATTTATTCAG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:220770 original size:18 final size:17
Alignment explanation
Indices: 220733--220788 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 17
220723 TTATTTCATC
**
220733 ATTATTATTATTGGTATT
1 ATTATTATTATTAAT-TT
220751 ATTATTATTATTAATGTT
1 ATTATTATTATTAAT-TT
*
220769 ATTATTTTTATTAATTT
1 ATTATTATTATTAATTT
220786 ATT
1 ATT
220789 CAGGCCAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 5 0.15
18 29 0.85
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.64
Consensus pattern (17 bp):
ATTATTATTATTAATTT
Found at i:220883 original size:16 final size:17
Alignment explanation
Indices: 220847--220883 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
220837 ATCCGGCCCA
220847 AACCCGAAGCCCAACAG
1 AACCCGAAGCCCAACAG
*
220864 -ACCC-AAGCCCAATAG
1 AACCCGAAGCCCAACAG
220879 AACCC
1 AACCC
220884 TAGGGTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.41, C:0.43, G:0.14, T:0.03
Consensus pattern (17 bp):
AACCCGAAGCCCAACAG
Found at i:223078 original size:127 final size:130
Alignment explanation
Indices: 222760--223112 Score: 446
Period size: 131 Copynumber: 2.7 Consensus size: 130
222750 TCAATATTGA
* ** *
222760 AAATAGTAATA-TCTTTCAATTTC-AGTTGGAGTAATAAATGATTGCTTTAAGCCATGAGAGGTC
1 AAATAGTAATATTC-TTC-ATTTCGA-TTGGAGTAATAAATGACTAATTTAAGGCATGAGAGGTC
* * *
222823 ATTTATTCTCGATTGAAAATAATTAGATATTACTGTTTTCTCTCGAATCAATATTGATTTTTAAG
63 ATTTATTCTCGATTGAAAACAATTAGATATTACTGTTTTCACTCGAATCAATATTGAATTTTAAG
222888 ACG
128 ACG
* ** * * *
222891 TAATAGTAATATCTCCACATTTCGATTGGAGTGATAAACGACTAATTTAAGGCATCAGAGGTCAT
1 AAATAGTAATAT-TCTTCATTTCGATTGGAGTAATAAATGACTAATTTAAGGCATGAGAGGTCAT
* *
222956 TTATTCTCGATTGGAAACCATTAGATA-T-C-GTTTTCACTCGAATCAATATTGAATTTTAAGAC
65 TTATTCTCGATTGAAAACAATTAGATATTACTGTTTTCACTCGAATCAATATTGAATTTTAAGAC
223018 G
130 G
* * *
223019 AAATAGTGATATTCTTCATTTCGATTGGAGTAATAAATGACTATTTTAAGGCATGAGAGGTTATT
1 AAATAGTAATATTCTTCATTTCGATTGGAGTAATAAATGACTAATTTAAGGCATGAGAGGTCATT
* * *
223084 TATTCTCGATTGTAAATAATTGGATATTA
66 TATTCTCGATTGAAAACAATTAGATATTA
223113 TCATTTTCTC
Statistics
Matches: 189, Mismatches: 28, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
127 68 0.36
128 43 0.23
129 1 0.01
130 1 0.01
131 72 0.38
132 2 0.01
133 2 0.01
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (130 bp):
AAATAGTAATATTCTTCATTTCGATTGGAGTAATAAATGACTAATTTAAGGCATGAGAGGTCATT
TATTCTCGATTGAAAACAATTAGATATTACTGTTTTCACTCGAATCAATATTGAATTTTAAGACG
Found at i:224886 original size:21 final size:21
Alignment explanation
Indices: 224860--224915 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
224850 TGACACTAGG
*
224860 TACCTAGTTAGCTACCGACAC
1 TACCTAGCTAGCTACCGACAC
* **
224881 TACCTAGCTAGCTACCTATGC
1 TACCTAGCTAGCTACCGACAC
224902 TACCTAGCTAGCTA
1 TACCTAGCTAGCTA
224916 AGTGACCTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.32, G:0.14, T:0.27
Consensus pattern (21 bp):
TACCTAGCTAGCTACCGACAC
Found at i:229713 original size:37 final size:35
Alignment explanation
Indices: 229663--229768 Score: 96
Period size: 37 Copynumber: 3.0 Consensus size: 35
229653 ATATTCAAAG
*
229663 ATTTTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACA
1 ATTTTTTTTTTCAAGAGAAACTGTCTCAA--GAGACA
* *
229700 ATTTTTTTTTTCAAGGGAAACAGAT-TCAA-AG---
1 ATTTTTTTTTTCAAGAGAAACTG-TCTCAAGAGACA
*
229731 ATTTTGTTTTTCAAGAGAAACTGTCTCAAAAGAGACA
1 ATTTTTTTTTTCAAGAGAAACTGTCTC--AAGAGACA
229768 A
1 A
229769 AATTTGTTTC
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
30 1 0.02
31 22 0.40
33 2 0.04
34 4 0.07
37 25 0.45
38 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (35 bp):
ATTTTTTTTTTCAAGAGAAACTGTCTCAAGAGACA
Found at i:229810 original size:67 final size:67
Alignment explanation
Indices: 229406--230174 Score: 1000
Period size: 67 Copynumber: 11.6 Consensus size: 67
229396 GGGTATGATG
* * * * * * *
229406 GTTTCAAGATAAACCGTCTCAAGAGAGACAAAATATGTTTCAAGGGAAACAAATTCAAATA-TTG
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTT
229470 GT
66 GT
* * * *
229472 GTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAACATATTCAAAGA-TTG
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTT
229536 GT
66 GT
* * * * *
229538 GTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTTGTTTCATGGGAAACATATTCAATGATTTT
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTT
229603 GT
66 GT
* * * * * *
229605 ATATCAAGAGAAACTGTCTTAA--GAGACAACATTTGTTTCAAGGAAAACATATTCAAAGATTTT
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTT
*
229668 TT
66 GT
** *
229670 GTTTCAAGAGAAACTGTCTCAAGGGAGACAATTTTTTTTTTCAAGGGAAACAGATTCAAAGATTT
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAA-AATTTGTTTCAAGGGAAACAGATTCAAAGATTT
229735 TGT
65 TGT
* ** * *
229738 TTTTCAAGAGAAACTGTCTCAAAAGAGACAAAATTTGTTTCAAGGGAAACAAATTTAAAGATTTT
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTT
229803 GT
66 GT
* * *
229805 GTTTCAAGATAAACTGTCTCTAGGGAGACAAAATTTGTTTCAAAGGAAACAGATTCAAAGATTTT
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTT
229870 GT
66 GT
* *
229872 GTTTCAAGAGAAACTGTCTTAAGAGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTT
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTT
229937 GT
66 GT
* * *
229939 GTTTCAAGAGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGGG-AACAAATTCAAAGA-TTT
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTT
230002 -T
66 GT
* * *
230003 GTTTCAAGAGAAATTGTCTCAAGGGAGACAAACTTTGTTTCAAGGGAAACAGATTCGAAGATTTT
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTT
230068 GT
66 GT
* * ** *
230070 GTTTCAAGAGAAACTGTCTCAAGGGAGATAAAATTTTGTTTCAAGAGAAACAGCCTCCAAGA-TT
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAACAGATTCAAAGATTT
230134 T-T
65 TGT
* * *
230136 -TTTCAAGAGAAATTGTCTCAAGGGTGAAAAAATTTGTTT
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTT
230175 TGAGTAAAAT
Statistics
Matches: 623, Mismatches: 72, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
64 50 0.08
65 101 0.16
66 132 0.21
67 258 0.41
68 82 0.13
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.31
Consensus pattern (67 bp):
GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTT
GT
Found at i:229921 original size:36 final size:35
Alignment explanation
Indices: 229871--229982 Score: 99
Period size: 36 Copynumber: 3.3 Consensus size: 35
229861 AAAGATTTTG
229871 TGTTTCAAGAGAAACTGTCTTAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTTAAGAGAGA-AAAATT
* * * * **
229907 TGTTTCAAGGGAAACAG-ATTCA-A-AG--ATTTT
1 TGTTTCAAGAGAAACTGTCTTAAGAGAGAAAAATT
*
229937 GTGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAATT
1 -TGTTTCAAGAGAAACTGTCTTAAGAGAGA-AAAATT
229974 TGTTTCAAG
1 TGTTTCAAG
229983 GGAACAAATT
Statistics
Matches: 56, Mismatches: 13, Indels: 14
0.67 0.16 0.17
Matches are distributed among these distances:
30 3 0.05
31 15 0.27
32 2 0.04
33 3 0.05
34 3 0.05
35 3 0.05
36 24 0.43
37 3 0.05
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (35 bp):
TGTTTCAAGAGAAACTGTCTTAAGAGAGAAAAATT
Found at i:229946 original size:31 final size:31
Alignment explanation
Indices: 229638--229952 Score: 97
Period size: 31 Copynumber: 9.5 Consensus size: 31
229628 AGACAACATT
* *
229638 TGTTTCAAG-GAAAACATATTCAAAGATTTTT
1 TGTTTCAAGAG-AAACAGATTCAAAGATTTTG
* *
229669 TGTTTCAAGAGAAACTG-TCTCAAGGGAGACAATTTTT
1 TGTTTCAAGAGAAACAGAT-TCAA---AG---ATTTTG
* *
229706 TTTTTCAAGGGAAACAGATTCAAAGATTTTG
1 TGTTTCAAGAGAAACAGATTCAAAGATTTTG
* * **
229737 TTTTTCAAGAGAAACTG-TCTCAAAAGAGACAAAATT-
1 TGTTTCAAGAGAAACAGAT-TC--AA-AG---ATTTTG
* * *
229773 TGTTTCAAGGGAAACAAATTTAAAGATTTTG
1 TGTTTCAAGAGAAACAGATTCAAAGATTTTG
* * * **
229804 TGTTTCAAGATAAACTG-TCTCTAGGGAGACAAAATT-
1 TGTTTCAAGAGAAACAGAT-TC-A---A-A-GATTTTG
229840 TGTTTCAA-AGGAAACAGATTCAAAGATTTTG
1 TGTTTCAAGA-GAAACAGATTCAAAGATTTTG
* * * **
229871 TGTTTCAAGAGAAACTGTCTTAAGAGAGACAAAATT-
1 TGTTTCAAGAGAAACAG-ATTCA-A-AG---ATTTTG
*
229907 TGTTTCAAGGGAAACAGATTCAAAGATTTTG
1 TGTTTCAAGAGAAACAGATTCAAAGATTTTG
229938 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
229953 TGTCTCAAGA
Statistics
Matches: 206, Mismatches: 42, Indels: 72
0.64 0.13 0.22
Matches are distributed among these distances:
30 12 0.06
31 82 0.40
32 7 0.03
33 7 0.03
34 11 0.05
35 6 0.03
36 45 0.22
37 35 0.17
38 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (31 bp):
TGTTTCAAGAGAAACAGATTCAAAGATTTTG
Found at i:230204 original size:36 final size:35
Alignment explanation
Indices: 230145--230283 Score: 107
Period size: 36 Copynumber: 3.8 Consensus size: 35
230135 TTTTCAAGAG
* *
230145 AAATTGTCTCAAGGGTGAAAAAATTTGTTTTGAGTA
1 AAATTGTCTCAAGTGAGAAAAAATTTGTTTTGAG-A
* *
230181 AAATTGTCTCAAGTGAGACAAAATTCATTTTTTAGAGA
1 AAATTGTCTCAAGTGAGAAAAAATT--TGTTTT-GAGA
*** * ** * *
230219 AAACAATATCAAGTGAGATTAATTTTGTTTTAAGGA
1 AAATTGTCTCAAGTGAGAAAAAATTTGTTTTGA-GA
* *
230255 AAATTGTCTCCAGCGAGAAAAAATTTGTT
1 AAATTGTCTCAAGTGAGAAAAAATTTGTT
230284 CTTAGGAAAA
Statistics
Matches: 77, Mismatches: 22, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
35 1 0.01
36 49 0.64
38 24 0.31
39 3 0.04
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.35
Consensus pattern (35 bp):
AAATTGTCTCAAGTGAGAAAAAATTTGTTTTGAGA
Found at i:230318 original size:36 final size:34
Alignment explanation
Indices: 230210--230322 Score: 100
Period size: 36 Copynumber: 3.1 Consensus size: 34
230200 AAAATTCATT
* *
230210 TTTTAGAGAAAACAATATCAAGTGAGATTAATTTTG
1 TTTTAG-GAAAACTATCTC-AGTGAGATTAATTTTG
* * * ** *
230246 TTTTAAGGAAAATTGTCTCCAGCGAGAAAAAATTTG
1 TTTT-AGGAAAACTATCT-CAGTGAGATTAATTTTG
230282 TTCTTAGGAAAACTATCTCATGTGAGATTAATTTTG
1 TT-TTAGGAAAACTATCTCA-GTGAGATTAATTTTG
230318 TTTTA
1 TTTTA
230323 AATATTTCAA
Statistics
Matches: 59, Mismatches: 14, Indels: 9
0.72 0.17 0.11
Matches are distributed among these distances:
35 5 0.08
36 49 0.83
37 5 0.08
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (34 bp):
TTTTAGGAAAACTATCTCAGTGAGATTAATTTTG
Found at i:230321 original size:72 final size:73
Alignment explanation
Indices: 230168--230323 Score: 199
Period size: 72 Copynumber: 2.1 Consensus size: 73
230158 GGTGAAAAAA
* * * * *
230168 TTTGTTTTGAGTAAAATTGTCTCAAGTGAGACAAAATTCATTTTTTAGAGAAAACAATATCAAGT
1 TTTGTTTTAAGGAAAATTGTCTCAAGCGAGAAAAAATT-ATTTCTTAGAGAAAACAATATCAAGT
230233 GAGATTAAT
65 GAGATTAAT
* * * *
230242 TTTGTTTTAAGGAAAATTGTCTCCAGCGAGAAAAAATT-TGTTCTTAG-GAAAACTATCTCATGT
1 TTTGTTTTAAGGAAAATTGTCTCAAGCGAGAAAAAATTAT-TTCTTAGAGAAAACAATATCAAGT
230305 GAGATTAAT
65 GAGATTAAT
230314 TTTGTTTTAA
1 TTTGTTTTAA
230324 ATATTTCAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
72 33 0.46
73 6 0.08
74 33 0.46
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (73 bp):
TTTGTTTTAAGGAAAATTGTCTCAAGCGAGAAAAAATTATTTCTTAGAGAAAACAATATCAAGTG
AGATTAAT
Found at i:231740 original size:2 final size:2
Alignment explanation
Indices: 231735--231777 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
231725 TTATTGTGTG
231735 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
231777 T
1 T
231778 GGGTATACGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:234322 original size:3 final size:3
Alignment explanation
Indices: 234314--234339 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
234304 ATAACATGTA
234314 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
234340 ATATAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:235501 original size:61 final size:61
Alignment explanation
Indices: 235406--236018 Score: 897
Period size: 61 Copynumber: 10.0 Consensus size: 61
235396 TAATGCACTT
235406 TTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCGTTAGGCATTTAAC
1 TTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCGTTAGGCATTTAAC
* *
235467 TTTTCATCTAACTTGCAGTAGTGCCACCTTTCTGCCAAAAATGCACCGTTAGGCATTTAA-
1 TTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCGTTAGGCATTTAAC
* * *
235527 TTTCTCATCTAACTTGCATTAGTGGCACCTTTCAGCCAAGAATACACCGTTAGGCATTTAAC
1 TTT-TCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCGTTAGGCATTTAAC
* * * * *
235589 TTCTCATCTAACTTGTATTAGTGGCACCTTTCTTCCAGAAATGCACCGTTAGGCATATAAC
1 TTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCGTTAGGCATTTAAC
* * * *
235650 TTCTCATCGAACTTGCATTAGTGGCACCTTTCTTCCAAAAATGCACCATTAGGCATTTAAC
1 TTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCGTTAGGCATTTAAC
* * * *
235711 TTTCCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAGAAGGCACCGTTATGCATTTAAC
1 TTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCGTTAGGCATTTAAC
* * *
235772 TTCTT-ATATAACTTGCATTAGTGGCACCTTTCTGCCAAGAATGCACTGTTAGGCATTTAAC
1 TT-TTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCGTTAGGCATTTAAC
* * * * * * *
235833 TTCTCATCTAACTTGCATTAGTGACACCTTTCTACAAAAAATGAACTGTTAGGCATTTTAC
1 TTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCGTTAGGCATTTAAC
* *
235894 TTTTCATCTAACTTGCATTAGTGGTACCTTTCTGCCAAAAATACACCGTTAGGCATTTAAC
1 TTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCGTTAGGCATTTAAC
* * *
235955 TTCTCATTTAACTTGCATTAGTGGCACCTTTCTGCCAATAATGCACCGTTAGGCATTTAAC
1 TTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCGTTAGGCATTTAAC
236016 TTT
1 TTT
236019 CATTTTAGAG
Statistics
Matches: 492, Mismatches: 56, Indels: 8
0.88 0.10 0.01
Matches are distributed among these distances:
60 4 0.01
61 485 0.99
62 3 0.01
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (61 bp):
TTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCGTTAGGCATTTAAC
Found at i:239047 original size:18 final size:18
Alignment explanation
Indices: 239024--239066 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
239014 CACCCCTACA
239024 CTTAAGCTATTTATTATC
1 CTTAAGCTATTTATTATC
239042 CTTAAGCTATTTATTATC
1 CTTAAGCTATTTATTATC
239060 CTTAAGC
1 CTTAAGC
239067 AATGGATAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.28, C:0.19, G:0.07, T:0.47
Consensus pattern (18 bp):
CTTAAGCTATTTATTATC
Found at i:240476 original size:21 final size:21
Alignment explanation
Indices: 240450--240491 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
240440 ATGTTGTGAG
* *
240450 TAATATAAAATTATACGCAAT
1 TAATATAAAAGTATACACAAT
*
240471 TAATATGAAAGTATACACAAT
1 TAATATAAAAGTATACACAAT
240492 CGGAAAAGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.31
Consensus pattern (21 bp):
TAATATAAAAGTATACACAAT
Found at i:240683 original size:23 final size:21
Alignment explanation
Indices: 240648--240690 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
240638 GGTGGGGATG
240648 AAATGATAGTGTAATGTGGTAAT
1 AAATGATAGTGT-A-GTGGTAAT
240671 AAATGAATA-TGTAGTGGTAA
1 AAATG-ATAGTGTAGTGGTAA
240691 AAAGGATGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 7 0.37
22 1 0.05
23 8 0.42
24 3 0.16
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.33
Consensus pattern (21 bp):
AAATGATAGTGTAGTGGTAAT
Found at i:242444 original size:22 final size:24
Alignment explanation
Indices: 242390--242459 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 24
242380 TAGGATTAAT
242390 TATAATATTTATATTTATATATTAG
1 TATAAT-TTTATATTTATATATTAG
*
242415 GATAATTTTATATTT-TA-ATCTA-
1 TATAATTTTATATTTATATAT-TAG
*
242437 TATAATTTTA-ATATTAAATATTA
1 TATAATTTTATAT-TTATATATTA
242460 CAATAGGCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
21 2 0.05
22 13 0.34
23 7 0.18
24 11 0.29
25 5 0.13
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (24 bp):
TATAATTTTATATTTATATATTAG
Found at i:250088 original size:36 final size:36
Alignment explanation
Indices: 250048--250178 Score: 219
Period size: 36 Copynumber: 3.6 Consensus size: 36
250038 AAATCCAACA
*
250048 TTCACAAAAGAGTAGTGAAGAAATGCAAATCAAGCC
1 TTCACAAAAGAGTAGTGAAGCAATGCAAATCAAGCC
250084 TTCACAAAAGAGTAGTGAAGCAATGCAAATCAAGCC
1 TTCACAAAAGAGTAGTGAAGCAATGCAAATCAAGCC
*
250120 TTCACAAAAGAGTAGTGAAGCAATGGAAATCCAA-CC
1 TTCACAAAAGAGTAGTGAAGCAATGCAAAT-CAAGCC
*
250156 ATCACAAAAGAGTAGTGAAGCAA
1 TTCACAAAAGAGTAGTGAAGCAA
250179 GATTAGATCA
Statistics
Matches: 91, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
36 88 0.97
37 3 0.03
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.16
Consensus pattern (36 bp):
TTCACAAAAGAGTAGTGAAGCAATGCAAATCAAGCC
Found at i:255803 original size:18 final size:19
Alignment explanation
Indices: 255772--255816 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
255762 GCATAGAAAG
*
255772 AAATAAAATTAAGGAAATA
1 AAATAAAATGAAGGAAATA
255791 AAATAAAA-GAAGGAAATA
1 AAATAAAATGAAGGAAATA
*
255809 AAGTAAAA
1 AAATAAAA
255817 CAAAATATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.16
Consensus pattern (19 bp):
AAATAAAATGAAGGAAATA
Found at i:264349 original size:2 final size:2
Alignment explanation
Indices: 264338--265155 Score: 222
Period size: 2 Copynumber: 408.0 Consensus size: 2
264328 TTGAAACAAT
264338 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
264378 TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
264419 TA TA TA TA AA CTA TA TA GT- TA TA TA TA CTA TA TA TA T- TA TA
1 TA TA TA TA TA -TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA
* * * * *
264460 CTT TA TA CA TA TA TA TA T- TT TA CA TA GTA GTA -A GTA CA -A CTA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA -TA TA -TA TA TA -TA
* * * *
264502 TA -A GTT TA TA TA GTT TA TA T- TA -A TA AA CTA TA TA -A TT TA
1 TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * * *
264541 TA -A T- TA TA CA TA GTA CA TA TA TA AA TA TA TA T- TA TA TA GTT
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * *
264582 TA TA TA TA AA T- TA TA TA TA T- TA TA TA TA TA AA CTA TA TA GTT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
* ** * *
264624 TA TA TT TA TA TA TA TA CTA CG TA TA -A T- TA TA AA TA -A AA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
264664 TA CTA TG TA TA AA T- TA TA TA GTC TA GTT TA TA CT- TA TA TA T-
1 TA -TA TA TA TA TA TA TA TA TA -TA TA -TA TA TA -TA TA TA TA TA
* * * * * * *
264705 TA CTA TG TA TA AA CTA TA TA GTT TA TA CA TA TA GTG TA TA TGG TT
1 TA -TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA TA T-A TA
** * * * *
264750 TA GGG T- TA -A TT TA TA TA -A T- TA TA TA TA GTT TG TA TA TA AA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * * * * *
264790 CTA -A TA GTT TA TA CA TA GTA -A CA TA TA AA CTA TA TA TA AA CCA
1 -TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA -TA
* * * *
264833 TA TA TA CTA TA TA TA AA CTA CA TA TA TA AA CTA AA TCA -A T- TA
1 TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA -TA TA T-A TA TA TA
* * *
264875 TA TA GTT TA CA TA TGA -A CTA TA TA TA TA AA CTA -A TA TA CTA TA
1 TA TA -TA TA TA TA T-A TA -TA TA TA TA TA TA -TA TA TA TA -TA TA
* * * *
264918 TA AA T- TT TA TA TA -A CTA TA TA TGA -A CTA TA TA TA AA T- TG
1 TA TA TA TA TA TA TA TA -TA TA TA T-A TA -TA TA TA TA TA TA TA
*
264957 TA TA GTT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
264999 TA TA TA TA TA TA TA CA TA TA TA -A TA TA -A GTA TA CA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* *
265039 -A GTA TA TA CA TA TA TA TA TA TA TA TA -A GTA TA TA TA T- TT TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * * *
265080 AA TG TA TA TA T- TG TA TA TA TA TG TA AA CT- TA TA TA TA CT- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA
* *
265121 TA TA CA TA TA TA -A TA TA -A GTA TG TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
265156 AGTATACATT
Statistics
Matches: 593, Mismatches: 124, Indels: 198
0.65 0.14 0.22
Matches are distributed among these distances:
1 49 0.08
2 485 0.82
3 59 0.10
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:264427 original size:85 final size:85
Alignment explanation
Indices: 264338--265155 Score: 230
Period size: 89 Copynumber: 9.3 Consensus size: 85
264328 TTGAAACAAT
264338 TATAATATATATATATATATATATATATATTATATATATATATATATATATATTATATATATATA
1 TATAATATATATATATATATATATATATATTATATATATATATATATATATATTATATATATATA
264403 TATATATATATATATATATA
66 TATATATATATATATATATA
* * * *
264423 TATAA-ACTATATAGTTATATATACTATATATATTATACTTTATACATATATATATTTTACATAG
1 TATAATA-TATATA--TATATATA-TATATATATTATA-TATATATATATATATATATTATATA-
* * *
264487 TAGTA-AGTACA-ACTATAAGTTTATATAGTT
60 TA-TATA-TATATA-TAT-A-TATATATA-TA
* * * * *
264517 TATATTA-ATAAACTATATA-ATTTATA-ATTATACATAGTACATATATA-A-A-TATATAT-TA
1 TATAATATATATA-TATATATATATATATATTATATATA-TATATATATATATATTATATATATA
* *
264575 TATAGTTTATATATAAAT-TATA
64 TATA-TATATATATATATATATA
* * * ** *
264597 TATATTATATATATAAACTATATAGTTTATATT-TATATATATACTACGTATA-ATTATAAATA-
1 TATAATATATATATATA-TATATA-TATATATTATATATATATA-TATATATATATTATATATAT
* * *
264659 AAATATACTATGTATAAATTATATA
63 ATATATA-TATATATATA-TATATA
* * * * * * * * *
264684 GTCTAGTTTATACT-TATATAT-TACTATGTA-TAAACTATATAGTTTATACATATAGTGTATAT
1 -TATAATATATA-TATATATATATA-TATATATTATA-TATATA-TATATATATATATTATATAT
* * ** *
264746 GGTTTAGGGT-TA-ATTTATATA-AT-
61 -ATATA-TATATATATATATATATATA
* * * * * * *
264769 TAT-ATATAGTTTGTATATAAACTA-ATAGT-TTATACATAGTA-ACATATAAACTA-TATATAA
1 TATAATATA-TATATATATATA-TATATA-TATTATATATA-TATATATATATA-TATTATATAT
* * *
264829 ACCATATATACTATATATAAACTACATA
61 A-TATATATA-TATATATATA-TATATA
* * * * * *
264857 TATAA-ACTAAATCA-ATTATATAGTTTACATATGA-ACTATATATATAAACTAATATACTATAT
1 TATAATA-TATAT-ATA-TATATA-TATATATATTATA-TATATATATATA-T-ATATATTATAT
* *
264919 AAAT-TTTATATA-ACTATATATGAACTATA
59 ATATATATATATATA-TATATAT--A-TATA
* *
264948 TATAA-AT-TGTATAGTTTATATATATATA-TATATATATATATATATATATATTATATATATAT
1 TATAATATATATATA-TATATATATATATATTATATATATATATATATATATATTATATATATAT
* *
265010 ATACATATATAATATAAGTATACA
65 ATATATATAT-ATAT-A-TATATA
* * * * *
265034 TTATAAGTATATACATATATATATATATATAAGTATATATATTTTAAATGTATATATTGTATATA
1 -TATAA-TATATATATATATATATATATAT-ATTATATATA-TATATATATATATA-T-TATATA
* * *
265099 TATGTAAACTTATATATACTTATATACATA
60 TATATATA--TATATATA--TATATATATA
*
265129 TATAATATA-AGTATGTATATATATATA
1 TATAATATATA-TATATATATATATATA
265156 AGTATACATT
Statistics
Matches: 526, Mismatches: 118, Indels: 170
0.65 0.14 0.21
Matches are distributed among these distances:
80 11 0.02
81 8 0.02
82 9 0.02
83 33 0.06
84 29 0.06
85 57 0.11
86 30 0.06
87 53 0.10
88 55 0.10
89 82 0.16
90 32 0.06
91 30 0.06
92 29 0.06
93 30 0.06
94 22 0.04
95 6 0.01
96 7 0.01
97 3 0.01
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (85 bp):
TATAATATATATATATATATATATATATATTATATATATATATATATATATATTATATATATATA
TATATATATATATATATATA
Found at i:264960 original size:11 final size:11
Alignment explanation
Indices: 264812--264953 Score: 74
Period size: 11 Copynumber: 13.6 Consensus size: 11
264802 ACATAGTAAC
264812 ATATAAACTAT
1 ATATAAACTAT
*
264823 ATATAAACCAT
1 ATATAAACTAT
264834 ATAT--ACTAT
1 ATATAAACTAT
264843 ATATAAACTACAT
1 ATATAAACT--AT
264856 ATATAAACTA-
1 ATATAAACTAT
*
264866 A-ATCAA-T-T
1 ATATAAACTAT
*** *
264874 ATATAGTTTAC
1 ATATAAACTAT
*
264885 ATATGAACTATAT
1 ATATAAAC--TAT
264898 ATATAAACTA-
1 ATATAAACTAT
264908 ATAT--AC--T
1 ATATAAACTAT
* *
264915 ATATAAATTTT
1 ATATAAACTAT
264926 ATAT-AACTAT
1 ATATAAACTAT
*
264936 ATATGAACTAT
1 ATATAAACTAT
264947 ATATAAA
1 ATATAAA
264954 TTGTATAGTT
Statistics
Matches: 98, Mismatches: 17, Indels: 32
0.67 0.12 0.22
Matches are distributed among these distances:
7 4 0.04
8 4 0.04
9 15 0.15
10 14 0.14
11 41 0.42
13 20 0.20
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (11 bp):
ATATAAACTAT
Found at i:265292 original size:2 final size:2
Alignment explanation
Indices: 265285--265351 Score: 50
Period size: 2 Copynumber: 33.5 Consensus size: 2
265275 AATATTAGTG
* *
265285 TA TA TA TA TA TA AA T- TA TA GA GTA TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* *
265326 -A GTA TA AA GTA TA TA TA TA TG TA TA T
1 TA -TA TA TA -TA TA TA TA TA TA TA TA T
265352 GTATGACTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
1 3 0.06
2 45 0.88
3 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.43
Consensus pattern (2 bp):
TA
Found at i:265296 original size:21 final size:21
Alignment explanation
Indices: 265272--265342 Score: 54
Period size: 23 Copynumber: 3.2 Consensus size: 21
265262 AGTATTAAAG
265272 TATAATATTAGTGTATATATA
1 TATAATATTAGTGTATATATA
*
265293 TATAA-ATTATAGAGTATAATATA
1 TATAATA-T-TAGTGTAT-ATATA
* * *
265316 TATATATATAAGTATAAAGTATA
1 TATA-ATATTAGTGTATA-TATA
265339 TATA
1 TATA
265343 TATGTATATG
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
20 1 0.03
21 6 0.15
22 8 0.21
23 21 0.54
24 2 0.05
25 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.42
Consensus pattern (21 bp):
TATAATATTAGTGTATATATA
Found at i:265324 original size:35 final size:35
Alignment explanation
Indices: 265232--265338 Score: 128
Period size: 35 Copynumber: 3.0 Consensus size: 35
265222 TAAATTAAAT
*
265232 AAGTATAAAATATATATATATAAAGTATAAAGTATTA
1 AAGTATAATATATATATATAT-AAGTATAAAGTA-TA
* *
265269 AAGTATAATAT-TAGTGTATATATA-TATAAATTATA
1 AAGTATAATATATA-TATATATA-AGTATAAAGTATA
*
265304 GAGTATAATATATATATATATAAGTATAAAGTATA
1 AAGTATAATATATATATATATAAGTATAAAGTATA
265339 TATATATGTA
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
34 1 0.02
35 29 0.48
36 13 0.22
37 17 0.28
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.38
Consensus pattern (35 bp):
AAGTATAATATATATATATATAAGTATAAAGTATA
Found at i:265343 original size:23 final size:22
Alignment explanation
Indices: 264964--265345 Score: 103
Period size: 21 Copynumber: 17.5 Consensus size: 22
264954 TTGTATAGTT
*
264964 TATATATATATATA-TAT-ATA
1 TATATATATATAGAGTATAATA
* *
264984 TATATATATATATATTATATATA
1 TATATATATATAGAGTATA-ATA
* * * *
265007 TATATACATATATAATATAA-G
1 TATATATATATAGAGTATAATA
*
265028 TATACAT-TATA-AGTAT-ATA
1 TATATATATATAGAGTATAATA
* *
265047 CATATATATATATA-TATAAGTA
1 TATATATATATAGAGTATAA-TA
* *
265069 TATATAT-TTTAAATGTAT-ATA
1 TATATATATATAGA-GTATAATA
* *
265090 T-TGTATATATA-TGTA-AACTTA
1 TATATATATATAGAGTATAA--TA
* *
265111 TATATACTTATATACATATATAATA
1 TATATA--TATATAGA-GTATAATA
* *
265136 TAAGTATGTATATATA-TATAAGTA
1 T-A-TATATATATAGAGTATAA-TA
* *
265160 TACATTATACTTATAAGTGTATAATA
1 TATA-TATA--TAT-AGAGTATAATA
* *
265186 TATA-ACATATA-AGTATAAAA
1 TATATATATATAGAGTATAATA
* * *
265206 TACATATACATAGGATTA-AAT-
1 TATATATATATA-GAGTATAATA
* * *
265227 TAAATA-AGTATAAAATAT-ATA
1 TATATATA-TATAGAGTATAATA
* *
265248 TATATAAAGTATAAAGTATTAA-A
1 TATATATA-TATAGAGTAT-AATA
*
265271 GTATA-ATAT-TAGTGTAT-ATA
1 -TATATATATATAGAGTATAATA
*
265291 TATATAAATTATAGAGTATAATA
1 TATATATA-TATAGAGTATAATA
265314 TATATATATATA-AGTATAA-A
1 TATATATATATAGAGTATAATA
265334 GTATATATATAT
1 -TATATATATAT
265346 GTATATGTAT
Statistics
Matches: 273, Mismatches: 45, Indels: 87
0.67 0.11 0.21
Matches are distributed among these distances:
18 1 0.00
19 18 0.07
20 49 0.18
21 67 0.25
22 42 0.15
23 48 0.18
24 16 0.06
25 13 0.05
26 9 0.03
27 10 0.04
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (22 bp):
TATATATATATAGAGTATAATA
Found at i:265345 original size:21 final size:21
Alignment explanation
Indices: 265126--265340 Score: 77
Period size: 22 Copynumber: 10.5 Consensus size: 21
265116 ACTTATATAC
265126 ATATATAATATAAGTAT---GT
1 ATATAT-ATATAAGTATAAAGT
*
265145 ATATATATATAAGTATACA-T
1 ATATATATATAAGTATAAAGT
*
265165 -TATACT-TATAAGTGTATAA-T
1 ATATA-TATATAAGTATA-AAGT
* *
265185 ATATAACATATAAGTATAAAAT
1 ATAT-ATATATAAGTATAAAGT
* * * *
265207 ACATATACAT-AGGATTAA--
1 ATATATATATAAGTATAAAGT
*
265225 AT-TA-A-ATAAGTATAAAAT
1 ATATATATATAAGTATAAAGT
265243 ATATATATATAAAGTATAAAGT
1 ATATATATAT-AAGTATAAAGT
* **
265265 AT-TAAAGTATAA-TATTAGTGT
1 ATATATA-TATAAGTA-TAAAGT
* *
265286 ATATATATATAAATTATAGAGT
1 ATATATATAT-AAGTATAAAGT
265308 ATA-ATATATATA-TATATAAGT
1 ATATATATATA-AGTATA-AAGT
*
265329 ATAAAGTATATA
1 ATATA-TATATA
265341 TATATGTATA
Statistics
Matches: 152, Mismatches: 19, Indels: 46
0.70 0.09 0.21
Matches are distributed among these distances:
15 2 0.01
16 7 0.05
17 2 0.01
18 13 0.09
19 21 0.14
20 18 0.12
21 38 0.25
22 43 0.28
23 8 0.05
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.38
Consensus pattern (21 bp):
ATATATATATAAGTATAAAGT
Found at i:266019 original size:16 final size:16
Alignment explanation
Indices: 265994--266028 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
265984 AATGCTCCAC
*
265994 CTTCTCGACTCCTCAT
1 CTTCTCGACTCATCAT
*
266010 CTTCTTGACTCATCAT
1 CTTCTCGACTCATCAT
266026 CTT
1 CTT
266029 TTATAGTCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.14, C:0.37, G:0.06, T:0.43
Consensus pattern (16 bp):
CTTCTCGACTCATCAT
Found at i:266435 original size:2 final size:2
Alignment explanation
Indices: 266430--266495 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
266420 TTTTCCACAC
266430 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
266472 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
266496 TTTTTTATAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:266528 original size:7 final size:7
Alignment explanation
Indices: 266513--266558 Score: 67
Period size: 7 Copynumber: 6.6 Consensus size: 7
266503 TATTTGTTTG
*
266513 TATTGTT
1 TATTATT
266520 TATTATT
1 TATTATT
266527 TATTTATT
1 TA-TTATT
266535 TATT-TT
1 TATTATT
266541 TATTATT
1 TATTATT
266548 TATTATT
1 TATTATT
266555 TATT
1 TATT
266559 TCTTTTCCTT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
6 6 0.17
7 23 0.64
8 7 0.19
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (7 bp):
TATTATT
Found at i:266529 original size:4 final size:4
Alignment explanation
Indices: 266518--266559 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
266508 GTTTGTATTG
*
266518 TTTA -TTA TTTA TTTA TTTA TTTT TATTA TTTA -TTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTT
266560 CTTTTCCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
3 6 0.18
4 24 0.73
5 3 0.09
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:266544 original size:28 final size:28
Alignment explanation
Indices: 266503--266559 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
266493 TATTTTTTTA
* *
266503 TATTTGTTTGTATTGTTTATTATTTATT
1 TATTTATTTGTATTATTTATTATTTATT
*
266531 TATTTATTTTTATTATTTATTATTTATT
1 TATTTATTTGTATTATTTATTATTTATT
266559 T
1 T
266560 CTTTTCCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (28 bp):
TATTTATTTGTATTATTTATTATTTATT
Found at i:266638 original size:21 final size:21
Alignment explanation
Indices: 266598--266639 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
266588 TTTTGCTTTG
*
266598 TATTATATGTTTTCTGTTATT
1 TATTATATGTTTTCTATTATT
* *
266619 TATTATTTGTTTTGTATTATT
1 TATTATATGTTTTCTATTATT
266640 CGTTTGTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.02, G:0.10, T:0.69
Consensus pattern (21 bp):
TATTATATGTTTTCTATTATT
Found at i:267450 original size:36 final size:36
Alignment explanation
Indices: 267410--267482 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
267400 TATTTGCTAA
** *
267410 TTGTTTTCTGTTTTATATATTTTTTATTTTCTGTTT
1 TTGTTTTCAATTTTATATATTTTTTATTTTATGTTT
* *
267446 TTGTTTTGAATTTTATATGTTTTTTATTTTATGTTT
1 TTGTTTTCAATTTTATATATTTTTTATTTTATGTTT
267482 T
1 T
267483 CTTTTTGTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.14, C:0.03, G:0.10, T:0.74
Consensus pattern (36 bp):
TTGTTTTCAATTTTATATATTTTTTATTTTATGTTT
Found at i:267553 original size:22 final size:22
Alignment explanation
Indices: 267527--267568 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
267517 ACATTATATG
* *
267527 TTTTTATTTTTTTTCTATTTAT
1 TTTTTATTTGTTTTCAATTTAT
267549 TTTTTATTTGTTTTCAATTT
1 TTTTTATTTGTTTTCAATTT
267569 TTTATTAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (22 bp):
TTTTTATTTGTTTTCAATTTAT
Found at i:267569 original size:17 final size:17
Alignment explanation
Indices: 267486--267643 Score: 60
Period size: 17 Copynumber: 9.2 Consensus size: 17
267476 ATGTTTTCTT
*
267486 TTTGTTTTCTGTTTTTA
1 TTTGTTTTCTATTTTTA
* **
267503 TTTGTTGTTTGTATACATTA
1 TTTG-T-TTTCTAT-TTTTA
*
267523 TATGTTTT-TATTTTT-
1 TTTGTTTTCTATTTTTA
* *
267538 TTTCTATT-TATTTTTTA
1 TTTGTTTTCTA-TTTTTA
*
267555 TTTGTTTTCAATTTTTTA
1 TTTGTTTTCTA-TTTTTA
* *
267573 TTAG--TTCAATCTTATT-
1 TTTGTTTTCTAT-TT-TTA
* *
267589 TTCTGTTTTTTTACTTTT-
1 TT-TG-TTTTCTATTTTTA
* *
267607 TTTGTTTTTTGTTTTTA
1 TTTGTTTTCTATTTTTA
267624 TTTGTTTTCTATTTTTA
1 TTTGTTTTCTATTTTTA
267641 TTT
1 TTT
267644 TTATTTTATT
Statistics
Matches: 106, Mismatches: 22, Indels: 26
0.69 0.14 0.17
Matches are distributed among these distances:
15 8 0.08
16 26 0.25
17 36 0.34
18 19 0.18
19 8 0.08
20 9 0.08
ACGTcount: A:0.13, C:0.06, G:0.08, T:0.73
Consensus pattern (17 bp):
TTTGTTTTCTATTTTTA
Found at i:267631 original size:23 final size:22
Alignment explanation
Indices: 267596--267650 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
267586 ATTTTCTGTT
* *
267596 TTTTTACTTTTTTTGT-TTTTTG
1 TTTTTA-TTTTTTTCTATTTTTA
267618 TTTTTATTTGTTTTCTATTTTTA
1 TTTTTATTT-TTTTCTATTTTTA
267641 TTTTTATTTT
1 TTTTTATTTT
267651 ATTAGTTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 3 0.10
22 12 0.41
23 14 0.48
ACGTcount: A:0.09, C:0.04, G:0.05, T:0.82
Consensus pattern (22 bp):
TTTTTATTTTTTTCTATTTTTA
Found at i:267653 original size:17 final size:17
Alignment explanation
Indices: 267595--267653 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
267585 TATTTTCTGT
*
267595 TTTTTTACTTTT-TTTG
1 TTTTTTATTTTTATTTG
*
267611 TTTTTTGTTTTTATTTG
1 TTTTTTATTTTTATTTG
*
267628 TTTTCTATTTTTATTT-
1 TTTTTTATTTTTATTTG
267644 TTATTTTATT
1 TT-TTTTATT
267654 AGTTGATTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
16 12 0.33
17 24 0.67
ACGTcount: A:0.10, C:0.03, G:0.05, T:0.81
Consensus pattern (17 bp):
TTTTTTATTTTTATTTG
Found at i:267762 original size:31 final size:31
Alignment explanation
Indices: 267722--267784 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
267712 TATTTTTATT
* *
267722 TGTTGATGTGAATGATATTAGTTGATTCTTA
1 TGTTAATGTGAAGGATATTAGTTGATTCTTA
267753 TGTTAATGTGAAGGATATTAGTTGATTCTTA
1 TGTTAATGTGAAGGATATTAGTTGATTCTTA
267784 T
1 T
267785 ATTGTTTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.03, G:0.22, T:0.48
Consensus pattern (31 bp):
TGTTAATGTGAAGGATATTAGTTGATTCTTA
Found at i:267801 original size:82 final size:82
Alignment explanation
Indices: 267650--267867 Score: 328
Period size: 82 Copynumber: 2.6 Consensus size: 82
267640 ATTTTTATTT
*
267650 TATTAGTTGATTCTTATGTTAATGTGAATGACTTTGAATTAGTTGATTCTTATAATGGTTTCTAT
1 TATTAGTTGATTCTTATGTTAATGTGAAGGA---T--ATTAGTTGATTCTTATAATGGTTTCTAT
*
267715 TTTTATTTGTTGATGTGAATGA
61 TTTTATTTGTTGATGTGAAGGA
* * *
267737 TATTAGTTGATTCTTATGTTAATGTGAAGGATATTAGTTGATTCTTATATTGTTTTCTGTTTTTA
1 TATTAGTTGATTCTTATGTTAATGTGAAGGATATTAGTTGATTCTTATAATGGTTTCTATTTTTA
*
267802 TTTGTTGATGTGTAGGA
66 TTTGTTGATGTGAAGGA
267819 TATTAGTTGATTCTTAATGTTAATGTGAAGGATATTAGTTGATTCTTAT
1 TATTAGTTGATTCTT-ATGTTAATGTGAAGGATATTAGTTGATTCTTAT
267868 GTTAATGTGA
Statistics
Matches: 124, Mismatches: 6, Indels: 6
0.91 0.04 0.04
Matches are distributed among these distances:
82 60 0.48
83 33 0.27
84 1 0.01
87 30 0.24
ACGTcount: A:0.25, C:0.04, G:0.19, T:0.52
Consensus pattern (82 bp):
TATTAGTTGATTCTTATGTTAATGTGAAGGATATTAGTTGATTCTTATAATGGTTTCTATTTTTA
TTTGTTGATGTGAAGGA
Found at i:267873 original size:31 final size:32
Alignment explanation
Indices: 267804--267881 Score: 131
Period size: 32 Copynumber: 2.5 Consensus size: 32
267794 TGTTTTTATT
* *
267804 TGTTGATGTGTAGGATATTAGTTGATTCTTAA
1 TGTTAATGTGAAGGATATTAGTTGATTCTTAA
267836 TGTTAATGTGAAGGATATTAGTTGATTCTT-A
1 TGTTAATGTGAAGGATATTAGTTGATTCTTAA
267867 TGTTAATGTGAAGGA
1 TGTTAATGTGAAGGA
267882 CTTTGAATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
31 16 0.36
32 28 0.64
ACGTcount: A:0.28, C:0.03, G:0.26, T:0.44
Consensus pattern (32 bp):
TGTTAATGTGAAGGATATTAGTTGATTCTTAA
Found at i:267957 original size:31 final size:30
Alignment explanation
Indices: 267922--267980 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
267912 CTATTTTTTA
267922 TTTTATTTCTTTTTTATTATTTAGTTTATGT
1 TTTTATTTCTTTTTTATTATTTA-TTTATGT
* *
267953 TTTTATTTGTTTTTTGTTATTTATTTAT
1 TTTTATTTCTTTTTTATTATTTATTTAT
267981 TTTCTCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.15, C:0.02, G:0.07, T:0.76
Consensus pattern (30 bp):
TTTTATTTCTTTTTTATTATTTATTTATGT
Found at i:267960 original size:17 final size:19
Alignment explanation
Indices: 267938--267983 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
267928 TTCTTTTTTA
267938 TTATTTAG-TTTATGTT-T
1 TTATTTAGTTTTATGTTAT
*
267955 TTATTT-GTTTTTTGTTAT
1 TTATTTAGTTTTATGTTAT
267973 TTATTTA-TTTT
1 TTATTTAGTTTT
267984 CTCTTTTCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 1 0.04
17 13 0.52
18 11 0.44
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76
Consensus pattern (19 bp):
TTATTTAGTTTTATGTTAT
Found at i:268010 original size:54 final size:54
Alignment explanation
Indices: 267900--268020 Score: 122
Period size: 54 Copynumber: 2.2 Consensus size: 54
267890 TAGTTGATTC
* * *
267900 TTATATTATTTTCTATTTTTTATTTTATTTCTTTTTTATTATTTAGTTTATGTTT
1 TTAT-TTATTTTTTGTTATTTATTTTATTTCTTTTTTATTATTTAGTTTATGTTT
* * *
267955 TTATTTGTTTTTTGTTATTTA-TTTATTTTCTCTTTTCTGTTATTTA-TTTGT-TTT
1 TTATTTATTTTTTGTTATTTATTTTA-TTTCT-TTTT-TATTATTTAGTTTATGTTT
*
268009 TTGTTTATTTTT
1 TTATTTATTTTT
268021 ACTGTTCTAA
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
53 4 0.07
54 31 0.56
55 12 0.22
56 8 0.15
ACGTcount: A:0.14, C:0.04, G:0.06, T:0.76
Consensus pattern (54 bp):
TTATTTATTTTTTGTTATTTATTTTATTTCTTTTTTATTATTTAGTTTATGTTT
Found at i:268013 original size:18 final size:17
Alignment explanation
Indices: 267916--268020 Score: 70
Period size: 18 Copynumber: 5.9 Consensus size: 17
267906 TATTTTCTAT
267916 TTTTTATTTTATTTCTTT-
1 TTTTTA-TTTATTT-TTTG
* *
267934 TTTATTATTTAGTTTATG
1 TTT-TTATTTATTTTTTG
*
267952 TTTTTATTTGTTTTTTG
1 TTTTTATTTATTTTTTG
* *
267969 TTATTTATTTATTTTCTC
1 TT-TTTATTTATTTTTTG
*
267987 TTTTCT-GTTATTTATTTG
1 TTTT-TATTTATTT-TTTG
*
268005 TTTTTTGTTTATTTTT
1 -TTTTTATTTATTTTT
268021 ACTGTTCTAA
Statistics
Matches: 68, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
17 23 0.34
18 32 0.47
19 13 0.19
ACGTcount: A:0.12, C:0.04, G:0.07, T:0.77
Consensus pattern (17 bp):
TTTTTATTTATTTTTTG
Found at i:270378 original size:56 final size:57
Alignment explanation
Indices: 270312--270419 Score: 164
Period size: 57 Copynumber: 1.9 Consensus size: 57
270302 AGGGTGTAAC
** * *
270312 TGCTTTTACATTTA-TTGTTTTTCATTAATTTTCATGAATTTTAGCAAGCATTCTAT
1 TGCTTTTACATTTACTACTTTTTCATTAATTTTCATAAATTTCAGCAAGCATTCTAT
*
270368 TGCTTTTACATTTACTACTTTTTGATTAATTTTCATAAATTTCAGCAAGCAT
1 TGCTTTTACATTTACTACTTTTTCATTAATTTTCATAAATTTCAGCAAGCAT
270420 ATAAATGAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
56 14 0.30
57 32 0.70
ACGTcount: A:0.27, C:0.14, G:0.08, T:0.51
Consensus pattern (57 bp):
TGCTTTTACATTTACTACTTTTTCATTAATTTTCATAAATTTCAGCAAGCATTCTAT
Found at i:270608 original size:22 final size:22
Alignment explanation
Indices: 270518--270609 Score: 114
Period size: 22 Copynumber: 4.2 Consensus size: 22
270508 GCTTTACCAT
270518 TGATTGG-ATTGGTATGAATGC
1 TGATTGGAATTGGTATGAATGC
*
270539 TGACTGGAATTGGTATGAATGC
1 TGATTGGAATTGGTATGAATGC
* * *
270561 TGACTGGACTTGGTCTGAATGC
1 TGATTGGAATTGGTATGAATGC
* * *
270583 TGATTGGAATTCGTCTGAATGT
1 TGATTGGAATTGGTATGAATGC
270605 TGATT
1 TGATT
270610 AGAAATCATT
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
21 6 0.10
22 57 0.90
ACGTcount: A:0.23, C:0.10, G:0.30, T:0.37
Consensus pattern (22 bp):
TGATTGGAATTGGTATGAATGC
Found at i:271244 original size:19 final size:19
Alignment explanation
Indices: 271220--271256 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
271210 AGTAAATATA
*
271220 TAAAGTCAATTTAGTAATT
1 TAAAGTAAATTTAGTAATT
271239 TAAAGTAAATTTAGTAAT
1 TAAAGTAAATTTAGTAAT
271257 ATAATGATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.41
Consensus pattern (19 bp):
TAAAGTAAATTTAGTAATT
Found at i:277756 original size:31 final size:31
Alignment explanation
Indices: 277685--277759 Score: 107
Period size: 32 Copynumber: 2.4 Consensus size: 31
277675 GGGGCCTGAG
277685 AGCCTACCCAAGAAAGATCTCGGGGCCACAA
1 AGCCTACCCAAGAAAGATCTCGGGGCCACAA
* *
277716 AGGCCTACCCAAGAAA-AGTCTCGGGGTCGCAA
1 A-GCCTACCCAAGAAAGA-TCTCGGGGCCACAA
277748 AGCCTACCCAAG
1 AGCCTACCCAAG
277760 GGTTGTCTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
31 13 0.32
32 27 0.68
ACGTcount: A:0.33, C:0.32, G:0.24, T:0.11
Consensus pattern (31 bp):
AGCCTACCCAAGAAAGATCTCGGGGCCACAA
Found at i:278896 original size:18 final size:18
Alignment explanation
Indices: 278870--278904 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
278860 ACAAAGTAAC
*
278870 TGAATTTAAGTTAGAAAT
1 TGAACTTAAGTTAGAAAT
*
278888 TGAACTTAATTTAGAAA
1 TGAACTTAAGTTAGAAA
278905 CCATATTGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.03, G:0.14, T:0.37
Consensus pattern (18 bp):
TGAACTTAAGTTAGAAAT
Found at i:285064 original size:17 final size:17
Alignment explanation
Indices: 285042--285087 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
285032 CAGACCAACT
285042 TTTGTCTTAAAAAATGA
1 TTTGTCTTAAAAAATGA
285059 TTTGTCTTAAAAAATGA
1 TTTGTCTTAAAAAATGA
*
285076 TTTTTCTTAAAA
1 TTTGTCTTAAAA
285088 TTGTTTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.46
Consensus pattern (17 bp):
TTTGTCTTAAAAAATGA
Found at i:285087 original size:16 final size:16
Alignment explanation
Indices: 285041--285107 Score: 61
Period size: 17 Copynumber: 4.2 Consensus size: 16
285031 GCAGACCAAC
285041 TTTTGTCTTAAAAAATG
1 TTTT-TCTTAAAAAATG
*
285058 ATTTGTCTTAAAAAATG
1 -TTTTTCTTAAAAAATG
*
285075 ATTTTTCTT-AAAATTG
1 -TTTTTCTTAAAAAATG
285091 -TTTT-TT-AAAAATG
1 TTTTTCTTAAAAAATG
285104 TTTT
1 TTTT
285108 AGGTATTCGA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
13 8 0.18
14 7 0.16
16 6 0.14
17 20 0.45
18 3 0.07
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.52
Consensus pattern (16 bp):
TTTTTCTTAAAAAATG
Found at i:286679 original size:6 final size:6
Alignment explanation
Indices: 286670--286723 Score: 56
Period size: 6 Copynumber: 8.7 Consensus size: 6
286660 CTTTTTCATT
* *
286670 TTTGCA TTTGCA TTTGCA TTTGCA TCTTTGCA TTTTACA TCTGCA TTTGC-
1 TTTGCA TTTGCA TTTGCA TTTGCA --TTTGCA -TTTGCA TTTGCA TTTGCA
286720 TTTG
1 TTTG
286724 TCGCATTCTA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
5 4 0.10
6 26 0.63
7 5 0.12
8 6 0.15
ACGTcount: A:0.15, C:0.19, G:0.15, T:0.52
Consensus pattern (6 bp):
TTTGCA
Found at i:288931 original size:12 final size:11
Alignment explanation
Indices: 288898--288932 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
288888 AAAGACCAAC
288898 AAGAAACAAAA
1 AAGAAACAAAA
288909 AAGAAACAAAA
1 AAGAAACAAAA
*
288920 AAGCAAAGAAAA
1 AAG-AAACAAAA
288932 A
1 A
288933 TAAGAAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 14 0.64
12 8 0.36
ACGTcount: A:0.80, C:0.09, G:0.11, T:0.00
Consensus pattern (11 bp):
AAGAAACAAAA
Found at i:288939 original size:25 final size:24
Alignment explanation
Indices: 288905--288957 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
288895 AACAAGAAAC
*
288905 AAAAAAGAAACAA-AAAAGCAAAGA
1 AAAAAAGAAA-AAGAAAAACAAAGA
288929 AAAATAAGAAAAAGAAAAACAAAGA
1 AAAA-AAGAAAAAGAAAAACAAAGA
288954 AAAA
1 AAAA
288958 GGAGATTGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 6 0.23
25 20 0.77
ACGTcount: A:0.81, C:0.06, G:0.11, T:0.02
Consensus pattern (24 bp):
AAAAAAGAAAAAGAAAAACAAAGA
Found at i:288944 original size:15 final size:16
Alignment explanation
Indices: 288906--288958 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
288896 ACAAGAAACA
*
288906 AAAAAGAAACAAAAAAG
1 AAAAAGAAA-AACAAAG
* *
288923 -CAAAGAAAAA-TAAG
1 AAAAAGAAAAACAAAG
288937 AAAAAGAAAAACAAAG
1 AAAAAGAAAAACAAAG
288953 AAAAAG
1 AAAAAG
288959 GAGATTGATG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
14 3 0.10
15 11 0.37
16 16 0.53
ACGTcount: A:0.79, C:0.06, G:0.13, T:0.02
Consensus pattern (16 bp):
AAAAAGAAAAACAAAG
Found at i:290151 original size:36 final size:36
Alignment explanation
Indices: 290064--290169 Score: 117
Period size: 36 Copynumber: 2.9 Consensus size: 36
290054 AAACAAAGGG
* * *
290064 TCGTCTCGCTCAAGACGAGTTTTCGTAAGAACAAATT
1 TCGTCTCGCTCGAGAC-AGTTTTCTTAAAAACAAATT
*
290101 T-GTCTCGCTTGAGACAGTTTTCTTAAAAACAAATT
1 TCGTCTCGCTCGAGACAGTTTTCTTAAAAACAAATT
* * *
290136 TCGTCTCGCTGGAGACAATCTTCCTT-AAAACAAA
1 TCGTCTCGCTCGAGACAGT-TTTCTTAAAAACAAA
290170 ATTAATCTCA
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
35 19 0.32
36 35 0.58
37 6 0.10
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (36 bp):
TCGTCTCGCTCGAGACAGTTTTCTTAAAAACAAATT
Found at i:290590 original size:36 final size:36
Alignment explanation
Indices: 290422--291000 Score: 409
Period size: 36 Copynumber: 16.1 Consensus size: 36
290412 TTAAAATAAG
* * *
290422 ATTTTCTCTCGCTTGAGATA-GTTTCCCTCGAAACATAA
1 ATTTTGTCTCTCTTGAGA-ACGTTTCCCTTGAAAC--AA
* *
290460 GATTTTATCTCGT-TTGAGATA-GTTTCCCTCGAAACATAA
1 -ATTTTGTCTC-TCTTGAGA-ACGTTTCCCTTGAAAC--AA
* * *
290499 TATTTTATCTCGCTTGAGATA-GTTTCCCTCGAAACATAA
1 -ATTTTGTCTCTCTTGAGA-ACGTTTCCCTTGAAAC--AA
* * *
290538 GATTTTATCTCACTTGAGAACGTTTCCCTTGAAACGA
1 -ATTTTGTCTCTCTTGAGAACGTTTCCCTTGAAACAA
* *
290575 ATTTTGTCTCTCTTGAG-TCAGTTTCCCTTAAAACAA
1 ATTTTGTCTCTCTTGAGAAC-GTTTCCCTTGAAACAA
* *
290611 ATTTTGTCTCACTTGAG-ACAGTTTCCCTTGAAACGA
1 ATTTTGTCTCTCTTGAGAAC-GTTTCCCTTGAAACAA
*
290647 ATTTTGTCTCCCTTGAG-ACAGTTTCCCTTGAAACAA
1 ATTTTGTCTCTCTTGAGAAC-GTTTCCCTTGAAACAA
290683 ATTTTGTCTCTCTTGAGATA-GTTTCCCTTGAAACAA
1 ATTTTGTCTCTCTTGAGA-ACGTTTCCCTTGAAACAA
*
290719 ATTTTGTCTCCCTTGAGATA-GTTTCCCTTGAAACAA
1 ATTTTGTCTCTCTTGAGA-ACGTTTCCCTTGAAACAA
*
290755 ATTTTATCTCTCTTGAG-ACAGTTTCCCTTGAAACAA
1 ATTTTGTCTCTCTTGAGAAC-GTTTCCCTTGAAACAA
* * *
290791 ATTTTGTCTCCCTTGAGATA-GTTTCTCTTGAAACAC
1 ATTTTGTCTCTCTTGAGA-ACGTTTCCCTTGAAACAA
** * *
290827 A----G-AACT-TTGAAAATGTTTCCCTTGAAACAA
1 ATTTTGTCTCTCTTGAGAACGTTTCCCTTGAAACAA
* * *
290857 ATTCTGTCTCTCTTAAG-ACAATTTCCCCTTGAAACAA
1 ATTTTGTCTCTCTTGAGAAC-GTTT-CCCTTGAAACAA
* ** *
290894 ATTTTGTCTCCCTTGAGATA-GTTTATCTTGAAACAC
1 ATTTTGTCTCTCTTGAGA-ACGTTTCCCTTGAAACAA
** * *
290930 A----G-AACT-TTGAGAACGTTTCCCTTTAAACGA
1 ATTTTGTCTCTCTTGAGAACGTTTCCCTTGAAACAA
* *
290960 ATTTTGTCTCCCTTGAG-ACAGTTTCTCTTGAAACAA
1 ATTTTGTCTCTCTTGAGAAC-GTTTCCCTTGAAACAA
*
290996 GTTTT
1 ATTTT
291001 TGAGACAGTT
Statistics
Matches: 450, Mismatches: 61, Indels: 61
0.79 0.11 0.11
Matches are distributed among these distances:
29 2 0.00
30 38 0.08
31 2 0.00
32 2 0.00
34 3 0.01
35 7 0.02
36 261 0.58
37 30 0.07
38 3 0.01
39 102 0.23
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (36 bp):
ATTTTGTCTCTCTTGAGAACGTTTCCCTTGAAACAA
Found at i:290638 original size:72 final size:72
Alignment explanation
Indices: 290422--291102 Score: 530
Period size: 72 Copynumber: 9.6 Consensus size: 72
290412 TTAAAATAAG
* * * ** *
290422 ATTTTCTCTCGCTTGAGATAGTTTCCCTCGAAACATAAGATTTTATCTCGTTTGAGATAGTTTCC
1 ATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAAC--AA-ATTTTATCTCACTTGAGACAGTTTCC
*
290487 CTCGAAACATAA
63 CTTGAAAC--AA
* * *
290499 TATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACATAAGATTTTATCTCACTTGAGA-ACGTTT
1 -ATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAAC--AA-ATTTTATCTCACTTGAGACA-GTTT
*
290563 CCCTTGAAACGA
61 CCCTTGAAACAA
* * *
290575 ATTTTGTCTCTCTTGAG-TCAGTTTCCCTTAAAACAAATTTTGTCTCACTTGAGACAGTTTCCCT
1 ATTTTGTCTCCCTTGAGAT-AGTTTCCCTTGAAACAAATTTTATCTCACTTGAGACAGTTTCCCT
*
290639 TGAAACGA
65 TGAAACAA
* * * *
290647 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTT
1 ATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAAATTTTATCTCACTTGAGACAGTTTCCCTT
290712 GAAACAA
66 GAAACAA
*
290719 ATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTT
1 ATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAAATTTTATCTCACTTGAGACAGTTTCCCTT
290784 GAAACAA
66 GAAACAA
* * * * *
290791 ATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACACA---GAACT---TTGA-AAATGTTTCCCT
1 ATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAAATTTTATCTCACTTGAGACA-GTTTCCCT
290849 TGAAACAA
65 TGAAACAA
* * * * * * * * **
290857 ATTCTGTCTCTCTTAAGACAATTTCCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTTTATCT
1 ATTTTGTCTCCCTTGAGATAGTTT-CCCTTGAAACAAATTTTATCTCACTTGAGACAGTTTCCCT
*
290922 TGAAACAC
65 TGAAACAA
* * * * * *
290930 A----GAACT---TTGAGA-ACGTTTCCCTTTAAACGAATTTTGTCTCCCTTGAGACAGTTTCTC
1 ATTTTG-TCTCCCTTGAGATA-GTTTCCCTTGAAACAAATTTTATCTCACTTGAGACAGTTTCCC
290987 TTGAAAC-A
64 TTGAAACAA
* * * * ** **
290995 A----GT-T--TTTGAGACAGTTTTCCCTTGAAACAAAATGTATCTCACTTGAGATGGTTTTTCT
1 ATTTTGTCTCCCTTGAGATAG-TTTCCCTTGAAACAAATTTTATCTCACTTGAGACAGTTTCCCT
* *
291053 TAAAACCA
65 TGAAACAA
* * * *
291061 ACTTCGTCTCGCTTGAGATAGTTTTCCCTTGAAACAAGTTTT
1 ATTTTGTCTCCCTTGAGATAG-TTTCCCTTGAAACAAATTTT
291103 TGAGACAGTT
Statistics
Matches: 515, Mismatches: 62, Indels: 57
0.81 0.10 0.09
Matches are distributed among these distances:
63 1 0.00
64 7 0.01
65 44 0.09
66 84 0.16
67 19 0.04
69 4 0.01
70 6 0.01
71 1 0.00
72 202 0.39
73 47 0.09
74 3 0.01
75 28 0.05
76 1 0.00
77 1 0.00
78 67 0.13
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (72 bp):
ATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAAATTTTATCTCACTTGAGACAGTTTCCCTT
GAAACAA
Found at i:290680 original size:108 final size:108
Alignment explanation
Indices: 290422--290825 Score: 508
Period size: 108 Copynumber: 3.7 Consensus size: 108
290412 TTAAAATAAG
* * * * *
290422 ATTTTCTCTCGCTTGAGATAGTTTCCCTCGAAACATAAGATTTTATCTCGT-TTGAGATAGTTTC
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAAC--AA-ATTTTGTCTC-TCTTGAGATAGTTTC
* * * *
290486 CCTCGAAACATAATATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACATAA
62 CCTTGAAAC--AA-ATTTTGTCTCACTTGAGATAGTTTCCCTTGAAAC--AA
*
290538 GATTTTATCTCACTTGAGA-ACGTTTCCCTTGAAACGAATTTTGTCTCTCTTGAG-TCAGTTTCC
1 -ATTTTATCTCACTTGAGACA-GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGAT-AGTTTCC
* * *
290601 CTTAAAACAAATTTTGTCTCACTTGAGACAGTTTCCCTTGAAACGA
63 CTTGAAACAAATTTTGTCTCACTTGAGATAGTTTCCCTTGAAACAA
* *
290647 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTT
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTT
*
290712 GAAACAAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAA
66 GAAACAAATTTTGTCTCACTTGAGATAGTTTCCCTTGAAACAA
* * *
290755 ATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTTTCTCTT
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTT
290820 GAAACA
66 GAAACA
290826 CAGAACTTTG
Statistics
Matches: 259, Mismatches: 23, Indels: 19
0.86 0.08 0.06
Matches are distributed among these distances:
108 164 0.63
109 3 0.01
111 30 0.12
112 2 0.01
113 2 0.01
114 27 0.10
115 1 0.00
116 1 0.00
117 29 0.11
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.39
Consensus pattern (108 bp):
ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTT
GAAACAAATTTTGTCTCACTTGAGATAGTTTCCCTTGAAACAA
Found at i:290907 original size:21 final size:21
Alignment explanation
Indices: 290844--290909 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
290834 TGAAAATGTT
*
290844 TCCCTTGAAACAAATTCTGTC
1 TCCCTTGAAACAAATTTTGTC
*
290865 TCTCTT-AAGAC-AA--TT-TC
1 TCCCTTGAA-ACAAATTTTGTC
290882 -CCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
290902 TCCCTTGA
1 TCCCTTGA
290910 GATAGTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 14
0.67 0.06 0.27
Matches are distributed among these distances:
16 6 0.17
17 6 0.17
18 1 0.03
19 2 0.06
20 6 0.17
21 14 0.40
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.36
Consensus pattern (21 bp):
TCCCTTGAAACAAATTTTGTC
Found at i:291002 original size:103 final size:102
Alignment explanation
Indices: 290623--291000 Score: 483
Period size: 103 Copynumber: 3.6 Consensus size: 102
290613 TTTGTCTCAC
*
290623 TTGAG-ACAGTTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTT
1 TTGAGAAC-GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTT
* * * *
290687 TGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTG-TCT
65 TGTCTCCCTTGAGATAGTTTCTCTTGAAACACA----GAACT
* *
290728 CCCTTGAGATA-GTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 ---TTGAGA-ACGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAA
290792 TTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACACAGAACT
62 TTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACACAGAACT
* * * * * *
290833 TTGAAAATGTTTCCCTTGAAACAAATTCTGTCTCTCTTAAGACAATTTCCCCTTGAAACAAATTT
1 TTGAGAACGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTT-CCCTTGAAACAAATTT
*
290898 TGTCTCCCTTGAGATAGTTTATCTTGAAACACAGAACT
65 TGTCTCCCTTGAGATAGTTTCTCTTGAAACACAGAACT
* * * *
290936 TTGAGAACGTTTCCCTTTAAACGAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAGTTTT
1 TTGAGAACGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
291001 TGAGACAGTT
Statistics
Matches: 242, Mismatches: 23, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
101 1 0.00
102 56 0.23
103 93 0.38
104 1 0.00
105 2 0.01
108 88 0.36
110 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (102 bp):
TTGAGAACGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
GTCTCCCTTGAGATAGTTTCTCTTGAAACACAGAACT
Found at i:291102 original size:17 final size:17
Alignment explanation
Indices: 291080--291127 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 17
291070 CGCTTGAGAT
291080 AGTTTTCCCTTGAAACA
1 AGTTTTCCCTTGAAACA
*
291097 AG-TTT---TTGAGAC-
1 AGTTTTCCCTTGAAACA
291109 AGTTTTCCCTTGAAACA
1 AGTTTTCCCTTGAAACA
291126 AG
1 AG
291128 AAATTGAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 10
0.67 0.06 0.28
Matches are distributed among these distances:
12 2 0.08
13 9 0.38
16 9 0.38
17 4 0.17
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (17 bp):
AGTTTTCCCTTGAAACA
Found at i:291110 original size:102 final size:105
Alignment explanation
Indices: 290965--291202 Score: 358
Period size: 105 Copynumber: 2.3 Consensus size: 105
290955 AACGAATTTT
*
290965 GTCTCCCTTGAGACAG-TTTCTCTTGAAACAAGTTTTTGAGACAGTTTTCCCTTGAAAC-A-AAA
1 GTCTCGCTTGAGACAGTTTTCTCTTGAAACAAGTTTTTGAGACAGTTTTCCCTTGAAACAAGAAA
* *
291027 -TGTATCTCACTTGAGATGGTTTTTCTTAAAACCAACTTC
66 TTGAATCTCACTTGAGATGGTTTTTCTGAAAACCAACTTC
* *
291066 GTCTCGCTTGAGATAGTTTTCCCTTGAAACAAGTTTTTGAGACAGTTTTCCCTTGAAACAAGAAA
1 GTCTCGCTTGAGACAGTTTTCTCTTGAAACAAGTTTTTGAGACAGTTTTCCCTTGAAACAAGAAA
* *
291131 TTGAATCTCACTTGAGATGGTTTTTCTGAAAATCTACTTC
66 TTGAATCTCACTTGAGATGGTTTTTCTGAAAACCAACTTC
* * *
291171 GTCTTGCTTGAGACAATTTTCTTTTGAAACAA
1 GTCTCGCTTGAGACAGTTTTCTCTTGAAACAA
291203 AATTTATCTC
Statistics
Matches: 121, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
101 14 0.12
102 41 0.34
103 1 0.01
104 3 0.02
105 62 0.51
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (105 bp):
GTCTCGCTTGAGACAGTTTTCTCTTGAAACAAGTTTTTGAGACAGTTTTCCCTTGAAACAAGAAA
TTGAATCTCACTTGAGATGGTTTTTCTGAAAACCAACTTC
Found at i:291134 original size:29 final size:29
Alignment explanation
Indices: 291073--291134 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
291063 TTCGTCTCGC
* ***
291073 TTGAGATAGTTTTCCCTTGAAACAAGTTT
1 TTGAGACAGTTTTCCCTTGAAACAAGAAA
291102 TTGAGACAGTTTTCCCTTGAAACAAGAAA
1 TTGAGACAGTTTTCCCTTGAAACAAGAAA
291131 TTGA
1 TTGA
291135 ATCTCACTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (29 bp):
TTGAGACAGTTTTCCCTTGAAACAAGAAA
Found at i:291297 original size:61 final size:61
Alignment explanation
Indices: 291177--291297 Score: 190
Period size: 61 Copynumber: 2.0 Consensus size: 61
291167 CTTCGTCTTG
* * * *
291177 CTTGAGACAATTTTCTTTTGAAACAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACC
1 CTTGAGACAATTTTCCTTTGAAACAAAATTTATCTCACTTGAGATGGCTTATCTAAAAACC
291238 CTTGAGACAATTTTCCTTTGAAACAAAATTTATCTCACTTGAGA-GAGCTTATCTAAAAAC
1 CTTGAGACAATTTTCCTTTGAAACAAAATTTATCTCACTTGAGATG-GCTTATCTAAAAAC
291298 AAGTTTCTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
60 1 0.02
61 54 0.98
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (61 bp):
CTTGAGACAATTTTCCTTTGAAACAAAATTTATCTCACTTGAGATGGCTTATCTAAAAACC
Found at i:291912 original size:19 final size:19
Alignment explanation
Indices: 291888--291951 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
291878 TTCATAATGA
291888 GAAGAACTCATCTAACAAG
1 GAAGAACTCATCTAACAAG
**
291907 GAAGAA-GAAGT-TCATA-AAG
1 GAAGAACTCA-TCT-A-ACAAG
291926 AGAAGAACTCATCTAACAAG
1 -GAAGAACTCATCTAACAAG
291946 GAAGAA
1 GAAGAA
291952 GAAGTTCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
18 2 0.06
19 18 0.53
20 12 0.35
21 2 0.06
ACGTcount: A:0.52, C:0.14, G:0.20, T:0.14
Consensus pattern (19 bp):
GAAGAACTCATCTAACAAG
Found at i:291914 original size:22 final size:22
Alignment explanation
Indices: 291887--291954 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 22
291877 GTTCATAATG
291887 AGAAGAACTCATCTAACAAGGA
1 AGAAGAACTCATCTAACAAGGA
*
291909 AGAAGAAGT--TC-ATA-AA-G-
1 AGAAGAACTCATCTA-ACAAGGA
291926 AGAAGAACTCATCTAACAAGGA
1 AGAAGAACTCATCTAACAAGGA
291948 AGAAGAA
1 AGAAGAA
291955 GTTCATAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
17 8 0.22
18 1 0.03
19 6 0.16
20 6 0.16
21 1 0.03
22 15 0.41
ACGTcount: A:0.53, C:0.13, G:0.21, T:0.13
Consensus pattern (22 bp):
AGAAGAACTCATCTAACAAGGA
Found at i:291930 original size:39 final size:39
Alignment explanation
Indices: 291876--291973 Score: 187
Period size: 39 Copynumber: 2.5 Consensus size: 39
291866 CCAAGTGGAG
291876 AGTTCATAATGAGAAGAACTCATCTAACAAGGAAGAAGA
1 AGTTCATAATGAGAAGAACTCATCTAACAAGGAAGAAGA
*
291915 AGTTCATAAAGAGAAGAACTCATCTAACAAGGAAGAAGA
1 AGTTCATAATGAGAAGAACTCATCTAACAAGGAAGAAGA
291954 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
291974 TGTTCAACTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.49, C:0.12, G:0.20, T:0.18
Consensus pattern (39 bp):
AGTTCATAATGAGAAGAACTCATCTAACAAGGAAGAAGA
Found at i:293654 original size:2 final size:2
Alignment explanation
Indices: 293647--293676 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
293637 CGTGTTTCCC
293647 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
293677 GCACTGAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:295734 original size:61 final size:59
Alignment explanation
Indices: 295604--295721 Score: 188
Period size: 61 Copynumber: 2.0 Consensus size: 59
295594 TTATGTACCG
295604 AAATTAATTTGATTTTTGTAATTTACTCCTTAAAATTAATCTTTTGAAATTAACATTGTTT
1 AAATTAATTTGATTTTTGTAATTTA--CCTTAAAATTAATCTTTTGAAATTAACATTGTTT
295665 AAATTAATTTGATTTTTGTAATTTA-C-T-AAATTAATCTTTTTGAAATTAACATTGTTT
1 AAATTAATTTGATTTTTGTAATTTACCTTAAAATTAATC-TTTTGAAATTAACATTGTTT
295722 TAGAATCCTA
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
56 9 0.16
57 21 0.38
58 1 0.02
61 25 0.45
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.52
Consensus pattern (59 bp):
AAATTAATTTGATTTTTGTAATTTACCTTAAAATTAATCTTTTGAAATTAACATTGTTT
Found at i:296422 original size:23 final size:23
Alignment explanation
Indices: 296382--296455 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 23
296372 AAACAACCGA
296382 AAAGGAAGACGAAAAATGTGCCAC
1 AAAGGAAGA-GAAAAATGTGCCAC
* *
296406 AAAGGAAGAGAAAAATGTACCAT
1 AAAGGAAGAGAAAAATGTGCCAC
* * *
296429 AAAGGCAA-AGATAAACGTGCCGC
1 AAAGG-AAGAGAAAAATGTGCCAC
296452 AAAG
1 AAAG
296456 ACAGATTATT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
23 31 0.74
24 11 0.26
ACGTcount: A:0.51, C:0.15, G:0.24, T:0.09
Consensus pattern (23 bp):
AAAGGAAGAGAAAAATGTGCCAC
Found at i:299255 original size:20 final size:21
Alignment explanation
Indices: 299214--299264 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
299204 AAAAAAAAAA
* *
299214 TTGGAT-TCGGATCCGGATAT
1 TTGGATATCCGATCCGGAAAT
299234 TTGGATATCCGATCC-GAAAT
1 TTGGATATCCGATCCGGAAAT
299254 TTCGGATATCC
1 TT-GGATATCC
299265 AAATTTTCGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (21 bp):
TTGGATATCCGATCCGGAAAT
Found at i:299270 original size:15 final size:17
Alignment explanation
Indices: 299245--299293 Score: 66
Period size: 16 Copynumber: 3.0 Consensus size: 17
299235 TGGATATCCG
299245 ATCCGAAA-TTTCGGAT
1 ATCCGAAATTTTCGGAT
299261 ATCC-AAATTTTCGGAT
1 ATCCGAAATTTTCGGAT
**
299277 ATCCGATTTTTTCGGAT
1 ATCCGAAATTTTCGGAT
299294 CGGATAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 3 0.10
16 16 0.55
17 10 0.34
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (17 bp):
ATCCGAAATTTTCGGAT
Found at i:299941 original size:23 final size:23
Alignment explanation
Indices: 299907--300030 Score: 137
Period size: 23 Copynumber: 5.3 Consensus size: 23
299897 GAGTCGAGGG
* *
299907 TTCTACGCGGTCTTTCGGGACAA
1 TTCTACGTGGTCCTTCGGGACAA
*
299930 TTCTACGTGGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGACAA
*
299953 TTCTACGTGATCCTTCGGGAC-A
1 TTCTACGTGGTCCTTCGGGACAA
*
299975 TATCTATGTGGTCCTTCGGGACAA
1 T-TCTACGTGGTCCTTCGGGACAA
299999 TTTCTACGTGG-CACTTCGGTG-CATA
1 -TTCTACGTGGTC-CTTCGG-GACA-A
300024 TTCTACG
1 TTCTACG
300031 CGGCACTAAG
Statistics
Matches: 87, Mismatches: 8, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
22 1 0.01
23 59 0.68
24 24 0.28
25 3 0.03
ACGTcount: A:0.17, C:0.25, G:0.24, T:0.34
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAA
Found at i:300043 original size:24 final size:24
Alignment explanation
Indices: 300000--300045 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
299990 TCGGGACAAT
* **
300000 TTCTACGTGGCACTTCGGTGCATA
1 TTCTACGCGGCACTAAGGTGCATA
300024 TTCTACGCGGCACTAAGGTGCA
1 TTCTACGCGGCACTAAGGTGCA
300046 ATTTATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (24 bp):
TTCTACGCGGCACTAAGGTGCATA
Found at i:301143 original size:180 final size:180
Alignment explanation
Indices: 300841--301201 Score: 713
Period size: 180 Copynumber: 2.0 Consensus size: 180
300831 ATAGAGAAGC
*
300841 TAAATAGGAGGGAGGCCCGATGGCGGCATGCCTCGATGGACAACATTAAGGCCGTTGTCGACGTC
1 TAAATAGGAGGGAGGCCCGATGGAGGCATGCCTCGATGGACAACATTAAGGCCGTTGTCGACGTC
300906 GGGAGAAAAGAGTGGGGATGAAAAAATAGGGTAAACTACAGATTTGGTCACTTTTATTTGAGTTT
66 GGGAGAAAAGAGTGGGGATGAAAAAATAGGGTAAACTACAGATTTGGTCACTTTTATTTGAGTTT
300971 TATAACTTATGGTCACTAGATTCAAAAAAACATAATACAATCACTTTCGT
131 TATAACTTATGGTCACTAGATTCAAAAAAACATAATACAATCACTTTCGT
301021 TAAATAGGAGGGAGGCCCGATGGAGGCATGCCTCGATGGACAACATTAAGGCCGTTGTCGACGTC
1 TAAATAGGAGGGAGGCCCGATGGAGGCATGCCTCGATGGACAACATTAAGGCCGTTGTCGACGTC
301086 GGGAGAAAAGAGTGGGGATGAAAAAATAGGGTAAACTACAGATTTGGTCACTTTTATTTGAGTTT
66 GGGAGAAAAGAGTGGGGATGAAAAAATAGGGTAAACTACAGATTTGGTCACTTTTATTTGAGTTT
301151 TATAACTTATGGTCACTAGATTCAAAAAAACATAATACAATCACTTTCGT
131 TATAACTTATGGTCACTAGATTCAAAAAAACATAATACAATCACTTTCGT
301201 T
1 T
301202 TTATTTCAAT
Statistics
Matches: 180, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
180 180 1.00
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (180 bp):
TAAATAGGAGGGAGGCCCGATGGAGGCATGCCTCGATGGACAACATTAAGGCCGTTGTCGACGTC
GGGAGAAAAGAGTGGGGATGAAAAAATAGGGTAAACTACAGATTTGGTCACTTTTATTTGAGTTT
TATAACTTATGGTCACTAGATTCAAAAAAACATAATACAATCACTTTCGT
Found at i:304946 original size:59 final size:59
Alignment explanation
Indices: 304767--304953 Score: 178
Period size: 60 Copynumber: 3.1 Consensus size: 59
304757 GCACCATATG
* * * * * *
304767 TCCCCAAACTATGACTCTTATTTTAAATTTGTCCTTAAACTTTTGAATATTTTAATTTTA
1 TCCCCAAACTATGAC-CCTAATTTAAATTAGTCCTTAAACTTTTGAATCTTCTAATTTCA
* * * * * *
304827 TCCCCAAATTATGACTCTCACTCTAAATTAGTCCTTAAACTTTTG-ATCATTCCAAATTCA
1 TCCCCAAACTATGACCCT-AATTTAAATTAGTCCTTAAACTTTTGAATC-TTCTAATTTCA
* * * **
304887 TCCCTAAACTATGACCCTAATTTAGATTGGTCCCCAAACTTTTGAATCTTCTAATTTCA
1 TCCCCAAACTATGACCCTAATTTAAATTAGTCCTTAAACTTTTGAATCTTCTAATTTCA
*
304946 TCTCCAAA
1 TCCCCAAA
304954 TTCATCCAAA
Statistics
Matches: 100, Mismatches: 24, Indels: 7
0.76 0.18 0.05
Matches are distributed among these distances:
59 38 0.38
60 62 0.62
ACGTcount: A:0.30, C:0.24, G:0.06, T:0.40
Consensus pattern (59 bp):
TCCCCAAACTATGACCCTAATTTAAATTAGTCCTTAAACTTTTGAATCTTCTAATTTCA
Found at i:305512 original size:2 final size:2
Alignment explanation
Indices: 305505--305534 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
305495 AGTAGTTTTA
305505 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
305535 TAATTATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:309527 original size:43 final size:46
Alignment explanation
Indices: 309427--309538 Score: 167
Period size: 46 Copynumber: 2.5 Consensus size: 46
309417 TACATACATA
*
309427 ATAAATGACTTTCTCTATTTAAGACTTCATCATAATAATATTTATT
1 ATAAATGACTTTCTCTATTTAAGACTTCATCATAATAATATATATT
*
309473 ATAAATGACTTTCTCTATTTAAGGCTTCATCATAATAA-A-AT-TT
1 ATAAATGACTTTCTCTATTTAAGACTTCATCATAATAATATATATT
* *
309516 ATAAATTACTTTTTCTATTTAAG
1 ATAAATGACTTTCTCTATTTAAG
309539 TGCAATTATA
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
43 23 0.37
44 1 0.02
45 1 0.02
46 37 0.60
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.46
Consensus pattern (46 bp):
ATAAATGACTTTCTCTATTTAAGACTTCATCATAATAATATATATT
Found at i:309966 original size:28 final size:28
Alignment explanation
Indices: 309934--309988 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
309924 TAGATGGACT
*
309934 AAATT-ATTTTTTGTCGAGTTCAAGGGTC
1 AAATTAATTTTTT-TCAAGTTCAAGGGTC
*
309962 AAATTAATTTTTTTTAAGTTCAAGGGT
1 AAATTAATTTTTTTCAAGTTCAAGGGT
309989 TTTTTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.29, C:0.07, G:0.18, T:0.45
Consensus pattern (28 bp):
AAATTAATTTTTTTCAAGTTCAAGGGTC
Found at i:310063 original size:15 final size:14
Alignment explanation
Indices: 310045--310109 Score: 53
Period size: 15 Copynumber: 4.4 Consensus size: 14
310035 TAAAATTTAA
310045 AAATATTAAAAAATT
1 AAATATT-AAAAATT
310060 AAATA-TAAAAATACT
1 AAATATTAAAAAT--T
*
310075 AAA-AATAAAAATT
1 AAATATTAAAAATT
*
310088 AAATTACTAAAAATGT
1 AAA-TATTAAAAAT-T
310104 AAATAT
1 AAATAT
310110 ATATTAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
13 10 0.24
14 2 0.05
15 26 0.62
16 4 0.10
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (14 bp):
AAATATTAAAAATT
Found at i:310083 original size:21 final size:22
Alignment explanation
Indices: 310028--310110 Score: 78
Period size: 23 Copynumber: 3.7 Consensus size: 22
310018 TTTTAGAATT
* * *
310028 TAAAATTTAAAATTTAAAAATAT
1 TAAAAATT-AAATATAAAAATAC
310051 TAAAAAATTAAATATAAAAATAC
1 T-AAAAATTAAATATAAAAATAC
* * *
310074 TAAAAA-TAAAAATTAAATTAC
1 TAAAAATTAAATATAAAAATAC
310095 TAAAAATGTAAATATA
1 TAAAAAT-TAAATATA
310111 TATTAAAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
21 18 0.37
22 5 0.10
23 20 0.41
24 6 0.12
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.31
Consensus pattern (22 bp):
TAAAAATTAAATATAAAAATAC
Found at i:310154 original size:21 final size:21
Alignment explanation
Indices: 310042--310154 Score: 74
Period size: 21 Copynumber: 5.4 Consensus size: 21
310032 ATTTAAAATT
310042 TAAAAATATTAAAAAATTAAATA
1 TAAAAATATTAAAAAATT-AA-A
* *
310065 TAAAAATACT-AAAAATAAAAA
1 TAAAAATATTAAAAAAT-TAAA
* * *
310086 TTAAATTACT-AAAAATGTAAA
1 TAAAAATATTAAAAAAT-TAAA
* *
310107 T--ATATATTAAAAATACTAAA
1 TAAAAATATTAAAAA-ATTAAA
*
310127 -AACAATATTAAAAAATTAAA
1 TAAAAATATTAAAAAATTAAA
310147 TAAAAATA
1 TAAAAATA
310155 CATTACAAAA
Statistics
Matches: 70, Mismatches: 14, Indels: 14
0.71 0.14 0.14
Matches are distributed among these distances:
19 4 0.06
20 13 0.19
21 36 0.51
22 8 0.11
23 9 0.13
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.28
Consensus pattern (21 bp):
TAAAAATATTAAAAAATTAAA
Found at i:312915 original size:20 final size:20
Alignment explanation
Indices: 312740--312913 Score: 233
Period size: 20 Copynumber: 8.7 Consensus size: 20
312730 TTTTCCTAAT
312740 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * ** *
312760 TCGCAACGCAAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
* *
312781 TCGCAATGCTATTACGTAAA
1 TCGCAATGCGAATACGTAAA
312801 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
312821 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
312841 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
312861 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
312881 TCGCAACGCGAAT-CTATAAA
1 TCGCAATGCGAATAC-GTAAA
*
312901 TCGCAACGCGAAT
1 TCGCAATGCGAAT
312914 CTGACTATCG
Statistics
Matches: 137, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
19 1 0.01
20 122 0.89
21 14 0.10
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:312923 original size:20 final size:20
Alignment explanation
Indices: 312880--312942 Score: 76
Period size: 20 Copynumber: 3.1 Consensus size: 20
312870 GAATACGTAA
312880 ATCGCAACGCGAATCT-A-T
1 ATCGCAACGCGAATCTGACT
312898 AAATCGCAACGCGAATCTGACT
1 --ATCGCAACGCGAATCTGACT
* *
312920 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGAATCTGACT
312940 ATC
1 ATC
312943 ACAATACTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
20 37 0.95
21 1 0.03
22 1 0.03
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGAATCTGACT
Found at i:314137 original size:20 final size:20
Alignment explanation
Indices: 314114--314203 Score: 92
Period size: 20 Copynumber: 4.5 Consensus size: 20
314104 TCTGAAACTT
314114 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
314134 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** ** **
314154 ACTATCGCAATGCGAATTTG
1 AAAATCGCAACACGAAAATG
** *
314174 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
314193 AAAATCGCAAC
1 AAAATCGCAAC
314204 GACAGAATCG
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
19 12 0.20
20 47 0.80
ACGTcount: A:0.46, C:0.22, G:0.17, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:314362 original size:22 final size:22
Alignment explanation
Indices: 314300--314365 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
314290 TGACCGTGAA
* *
314300 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
314322 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
314344 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
314366 GGATGTCGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.21, C:0.15, G:0.39, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:314586 original size:20 final size:20
Alignment explanation
Indices: 314563--314696 Score: 187
Period size: 20 Copynumber: 6.7 Consensus size: 20
314553 CGATAGTCAG
*
314563 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
314583 ATTCGCTTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
314603 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
314623 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
314643 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
* *
314664 ATTCGCGTTGCGATATACGT
1 ATTCGCATTGCGATTTACGT
314684 ATTCGCATTGCGA
1 ATTCGCATTGCGA
314697 ATTAGGAAAA
Statistics
Matches: 100, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
20 85 0.85
21 15 0.15
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:314688 original size:61 final size:60
Alignment explanation
Indices: 314545--314696 Score: 191
Period size: 60 Copynumber: 2.5 Consensus size: 60
314535 GCTATGTAAA
* * * **
314545 TCGCATTGCGATAGT-CAG-ATTCGCGTTGCGATTTACGTATTCGCTTTGCGATTTACGTAT
1 TCGCATTGCGATA-TAC-GTATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACAAAT
* *
314605 TCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATATACGTATTCGCATTGCGATTTACGTAATCGCATTGCGA-TTTACAAAT
*
314666 TCGCGTTGCGATATACGTATTCGCATTGCGA
1 TCGCATTGCGATATACGTATTCGCATTGCGA
314697 ATTAGGAAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
59 2 0.03
60 43 0.54
61 35 0.44
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (60 bp):
TCGCATTGCGATATACGTATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACAAAT
Found at i:314717 original size:41 final size:41
Alignment explanation
Indices: 314545--314719 Score: 178
Period size: 40 Copynumber: 4.3 Consensus size: 41
314535 GCTATGTAAA
* *
314545 TCGCATTGCGATAGT-CAG-ATTCGCGTTGCGATTTACG-TAT
1 TCGCATTGCGATA-TAC-GTATTCGCATTGCGATTTACGAAAT
* * *
314585 TCGCTTTGCGATTTACGTATTCGCATTGCGATTTACG-TAT
1 TCGCATTGCGATATACGTATTCGCATTGCGATTTACGAAAT
* * * *
314625 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATATACGTATTCGCATTGCGATTTACGAAAT
* * * *
314666 TCGCGTTGCGATATACGTATTCGCATTGCGAATTAGGAAAA
1 TCGCATTGCGATATACGTATTCGCATTGCGATTTACGAAAT
*
314707 TCGCAATGCGATA
1 TCGCATTGCGATA
314720 GTCAGAATCA
Statistics
Matches: 114, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
39 2 0.02
40 66 0.58
41 46 0.40
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (41 bp):
TCGCATTGCGATATACGTATTCGCATTGCGATTTACGAAAT
Found at i:314734 original size:61 final size:61
Alignment explanation
Indices: 314610--314737 Score: 152
Period size: 61 Copynumber: 2.1 Consensus size: 61
314600 CGTATTCGCA
* * * * ** *
314610 TTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTCGCG
1 TTGCGATATACGTATTCGCATTGCGAATTACGAAATCGCAATGCGATAGTCCAAATTCACG
*
314671 TTGCGATATACGTATTCGCATTGCGAATTAGGAAAATCGCAATGCGATAGT-CAGAA-TCACG
1 TTGCGATATACGTATTCGCATTGCGAATTACG-AAATCGCAATGCGATAGTCCA-AATTCACG
314732 TTGCGA
1 TTGCGA
314738 ATCTGGAAAC
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
61 41 0.72
62 16 0.28
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (61 bp):
TTGCGATATACGTATTCGCATTGCGAATTACGAAATCGCAATGCGATAGTCCAAATTCACG
Found at i:315379 original size:26 final size:27
Alignment explanation
Indices: 315336--315400 Score: 98
Period size: 26 Copynumber: 2.4 Consensus size: 27
315326 TTTAAAAATC
*
315336 AGTTTTTTAAAATTTATATATATTATAT
1 AGTTTTTGAAAA-TTATATATATTATAT
315364 AGTTTTTGAAAA-TATATATATTATAT
1 AGTTTTTGAAAATTATATATATTATAT
315390 AG-TTTTGAAAA
1 AGTTTTTGAAAA
315401 CATTTTGAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
25 9 0.25
26 16 0.44
28 11 0.31
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.51
Consensus pattern (27 bp):
AGTTTTTGAAAATTATATATATTATAT
Found at i:315409 original size:36 final size:36
Alignment explanation
Indices: 315367--315623 Score: 343
Period size: 36 Copynumber: 6.9 Consensus size: 36
315357 ATTATATAGT
*
315367 TTTTGAAAATATATATATTATATAGTTTTGAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTGAAAACA
* *
315403 TTTTGAAAATATATATAATATATAGTTTTTAAAAATA
1 TTTTGAAAATATATATAATATATAG-TTTTGAAAACA
315440 TTTTGAATATATATATATAATATATAGTTTTTGAAAACA
1 TTTTGAA-A-ATATATATAATATATAG-TTTTGAAAACA
*
315479 TTTTGAAAACATATATAATATATAGTTTTGAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTGAAAACA
* *
315515 TTTTGAAAACATATATAACATATAGTTTTGAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTGAAAACA
* *
315551 TTTTAAAAACATATATATATATATATAGTTTTGAATACA
1 TTTT-GAAA-ATATATATA-ATATATAGTTTTGAAAACA
* *
315590 TTTTAAAAACATATCTATAATATATAGTTTTGAA
1 TTTT-GAAA-ATATATATAATATATAGTTTTGAA
315624 TATATATATA
Statistics
Matches: 203, Mismatches: 12, Indels: 10
0.90 0.05 0.04
Matches are distributed among these distances:
36 74 0.36
37 35 0.17
38 25 0.12
39 69 0.34
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (36 bp):
TTTTGAAAATATATATAATATATAGTTTTGAAAACA
Found at i:315482 original size:11 final size:11
Alignment explanation
Indices: 315468--315562 Score: 59
Period size: 11 Copynumber: 8.1 Consensus size: 11
315458 AATATATAGT
315468 TTTTGAAAACA
1 TTTTGAAAACA
315479 TTTTGAAAACA
1 TTTTGAAAACA
* *
315490 TATAT-AATATATA
1 T-TTTGAA-A-ACA
315503 GTTTTGAAAACA
1 -TTTTGAAAACA
315515 TTTTGAAAACA
1 TTTTGAAAACA
* *
315526 TATAT-AACATATA
1 T-TTTGAA-A-ACA
315539 GTTTTGAAAACA
1 -TTTTGAAAACA
*
315551 TTTTAAAAACA
1 TTTTGAAAACA
315562 T
1 T
315563 ATATATATAT
Statistics
Matches: 65, Mismatches: 9, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
11 39 0.60
12 10 0.15
13 10 0.15
14 6 0.09
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.38
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:315487 original size:112 final size:111
Alignment explanation
Indices: 315367--315623 Score: 363
Period size: 112 Copynumber: 2.3 Consensus size: 111
315357 ATTATATAGT
* * *
315367 TTTTGAAAATATATATATTATATAGTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTT
1 TTTTGAAAATATATATAATATATAGTTTTGAAAACATTTTGAAAACATATATAACATATAG-TTT
* * * *
315432 TAAAAATATTTTGAATATATATATATA-ATATATAGTTTTTGAAAACA
65 TAAAAACATTTTAAAAACATATATATATATATATAG-TTTTGAAAACA
*
315479 TTTTGAAAACATATATAATATATAGTTTTGAAAACATTTTGAAAACATATATAACATATAGTTTT
1 TTTTGAAAATATATATAATATATAGTTTTGAAAACATTTTGAAAACATATATAACATATAGTTTT
* *
315544 GAAAACATTTTAAAAACATATATATATATATATAGTTTTGAATACA
66 AAAAACATTTTAAAAACATATATATATATATATAGTTTTGAAAACA
* *
315590 TTTTAAAAACATATCTATAATATATAGTTTTGAA
1 TTTT-GAAA-ATATATATAATATATAGTTTTGAA
315624 TATATATATA
Statistics
Matches: 129, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
111 39 0.30
112 68 0.53
113 22 0.17
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (111 bp):
TTTTGAAAATATATATAATATATAGTTTTGAAAACATTTTGAAAACATATATAACATATAGTTTT
AAAAACATTTTAAAAACATATATATATATATATAGTTTTGAAAACA
Found at i:315628 original size:2 final size:2
Alignment explanation
Indices: 315623--315704 Score: 157
Period size: 2 Copynumber: 41.5 Consensus size: 2
315613 ATAGTTTTGA
315623 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
315664 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT A
315705 GTTTTTGAAA
Statistics
Matches: 79, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 78 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:315759 original size:35 final size:40
Alignment explanation
Indices: 315688--315764 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 40
315678 ATATATATAT
*
315688 ATATATATATATATATAGTTTTTGAAAACAT-TTTTTTAA
1 ATATATATATATATATAGTTTTTGAAAACATGTTTTTGAA
315727 ATATATATA-ATATATAG-TTTTG-AAA-ATGTTTTTGAA
1 ATATATATATATATATAGTTTTTGAAAACATGTTTTTGAA
315763 AT
1 AT
315765 TTTGAAAACA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
35 2 0.06
36 12 0.33
37 5 0.14
38 8 0.22
39 9 0.25
ACGTcount: A:0.42, C:0.01, G:0.08, T:0.49
Consensus pattern (40 bp):
ATATATATATATATATAGTTTTTGAAAACATGTTTTTGAA
Found at i:315778 original size:20 final size:20
Alignment explanation
Indices: 315744--315783 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
315734 TAATATATAG
** *
315744 TTTTGAAAATGTTTTTGAAA
1 TTTTGAAAACATTTTAGAAA
315764 TTTTGAAAACATTTTAGAAA
1 TTTTGAAAACATTTTAGAAA
315784 ATATATATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (20 bp):
TTTTGAAAACATTTTAGAAA
Found at i:316968 original size:5 final size:5
Alignment explanation
Indices: 316958--317019 Score: 56
Period size: 5 Copynumber: 11.8 Consensus size: 5
316948 ATTCAACACT
316958 TTTTA TTTTA TTTTA TTTTA TTTTCCCA CTTTTTA TTTTA TTTTA --TTA
1 TTTTA TTTTA TTTTA TTTTA TTTT---A --TTTTA TTTTA TTTTA TTTTA
*
317006 TTTTA TATTA TTTT
1 TTTTA TTTTA TTTT
317020 TTATATTCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
3 3 0.06
5 39 0.81
7 1 0.02
8 1 0.02
10 4 0.08
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:317008 original size:13 final size:13
Alignment explanation
Indices: 316990--317026 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
316980 TTCCCACTTT
*
316990 TTATTTTATTTTA
1 TTATTTTATATTA
317003 TTATTTTATATTA
1 TTATTTTATATTA
317016 TT-TTTTATATT
1 TTATTTTATATT
317027 CTTTTTAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTATTTTATATTA
Found at i:317023 original size:12 final size:12
Alignment explanation
Indices: 316993--317032 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
316983 CCACTTTTTA
*
316993 TTTTATTTTATT
1 TTTTATATTATT
317005 ATTTTATATTATT
1 -TTTTATATTATT
*
317018 TTTTATATTCTT
1 TTTTATATTATT
317030 TTT
1 TTT
317033 AACATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTATATTATT
Found at i:317733 original size:31 final size:31
Alignment explanation
Indices: 317698--317767 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
317688 TAAGGGAAAA
* *
317698 TAGTCCCTAACGTTATCGATCTGTTCAATTT
1 TAGTCCCTAACGTTATCGATCTCTTCAATTC
* * *
317729 TAGTCTCTAATGTTATCGATCTCTTCGATTC
1 TAGTCCCTAACGTTATCGATCTCTTCAATTC
317760 TAGTCCCT
1 TAGTCCCT
317768 TAGCCGTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.43
Consensus pattern (31 bp):
TAGTCCCTAACGTTATCGATCTCTTCAATTC
Found at i:318449 original size:27 final size:26
Alignment explanation
Indices: 318419--318469 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
318409 GTTAATTGTG
318419 TACAGATTTAGCTAAAAATAACTAAAA
1 TACAGATTTAG-TAAAAATAACTAAAA
** *
318446 TACATTTTTAGTAATAATAACTAA
1 TACAGATTTAGTAAAAATAACTAA
318470 TATTATTATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.51, C:0.10, G:0.06, T:0.33
Consensus pattern (26 bp):
TACAGATTTAGTAAAAATAACTAAAA
Done.