Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009644.1 Hibiscus syriacus cultivar Beakdansim tig00117060_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: 611714
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:151370 original size:209 final size:210
Alignment explanation
Indices: 151145--151581 Score: 583
Period size: 209 Copynumber: 2.1 Consensus size: 210
151135 TAATACGATC
* * * *
151145 CCTACGTGATGAGGACGGATGGTTATCTGGGGTTAACACGGTTCCTACGTGATGAGGAAATCAGG
1 CCTACGTGATGAGGACGGATGGTTATCT-GGGTTAACACAGCTCCTACATAATGAGGAAATCAGG
** * * * * * * *
151210 TCGGGTAATGACAC-TTTCCTATGCGATGAGGA-CAACAAGCCATCTAAGGGTTATAACATGGTT
65 TCGGGTAATGACACGACTCATACGCAATGAAGAGCAA-AAGCCATCTAAAGGTGATAACACGGTT
* **
151273 CCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAGTTCCTACATAATGAGGAGATCTGGT
129 CCTACGTGATGAGGACGGCTGATTATCTGGGTTGACACAACTCCTACATAATGAGGAGATCTGGT
*
151338 C-GGTGATGACATGGTT
194 CGGGTGATGACACGGTT
* * * * *
151354 CCTACGTGATGAGGACGGTTGTTTATCTGGGTTGACACAGCTCCTACATAATGAGGAGATCTGGT
1 CCTACGTGATGAGGACGGATGGTTATCTGGGTTAACACAGCTCCTACATAATGAGGAAATCAGGT
* ** **
151419 CGGGTGATGACACGACTCATACGCAATGAAGAGTTATGGCCATCTAAAGGTGATAACACGGTTCC
66 CGGGTAATGACACGACTCATACGCAATGAAGAGCAAAAGCCATCTAAAGGTGATAACACGGTTCC
*
151484 TACGTGATGAGGACGGCTGATTATCTGGGTTGACACAACTCCTACATATTGAGGAGATCTGGTCG
131 TACGTGATGAGGACGGCTGATTATCTGGGTTGACACAACTCCTACATAATGAGGAGATCTGGTCG
151549 GGTGATGACACGGTT
196 GGTGATGACACGGTT
151564 CCTACGTGATGAGGACGG
1 CCTACGTGATGAGGACGG
151582 CAGGCCATCC
Statistics
Matches: 197, Mismatches: 28, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
208 42 0.21
209 122 0.62
210 33 0.17
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (210 bp):
CCTACGTGATGAGGACGGATGGTTATCTGGGTTAACACAGCTCCTACATAATGAGGAAATCAGGT
CGGGTAATGACACGACTCATACGCAATGAAGAGCAAAAGCCATCTAAAGGTGATAACACGGTTCC
TACGTGATGAGGACGGCTGATTATCTGGGTTGACACAACTCCTACATAATGAGGAGATCTGGTCG
GGTGATGACACGGTT
Found at i:151426 original size:337 final size:337
Alignment explanation
Indices: 151001--151686 Score: 871
Period size: 337 Copynumber: 2.0 Consensus size: 337
150991 TTCATCTAAG
* * *
151001 GGTGATAACACGGTTCCTACATGATGAGGACGGCTGGTTATCAAAGGGTGACACGGCTCCTACGG
1 GGTGATGACACGGTTCCTACATGATGAGGACGGCTGGTTATC-AAGGGTGACACAGCTCCTACAG
** * ** * * *
151066 AATGAGGAGATCAGGTCGGGTGATGACACGGTTCTTACGTGATGAGGACGACA-GGTCATCTAAG
65 AATGAGGAGATCAGGTCGGGTGATGACACGACTCATACGCAATGAAGA-GACATGGCCATCTAAA
* * *** *
151130 GGTGATAATACGATCCCTACGTGATGAGGACGGATGGTTATCTGGGGTTAACACGGTTCCTACGT
129 GGTGATAACACGATCCCTACGTGATGAGGACGGATGATTATCT-GGGTTAACACAACTCCTACAT
* * *
151195 GA-TGAGGAAATCAGGTCGGGTAATGACAC-TTTCCTATGCGATGAGGACAACAAGCCATCTAAG
193 -ATTGAGGAAATCAGGTCGGGTAATGACACGGTTCCTACGCGATGAGGACAACAAGCCATCCAAG
*
151258 GGTTATAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAG-TTCCTACAT
257 GGTGATAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAGCTT-CTACAT
* *
151322 AATGAGGAGATCTGGTC
321 AATGAGGAAATCTAGTC
* * * * * *
151339 GGTGATGACATGGTTCCTACGTGATGAGGACGGTTGTTTATC-TGGGTTGACACAGCTCCTACAT
1 GGTGATGACACGGTTCCTACATGATGAGGACGGCTGGTTATCAAGGG-TGACACAGCTCCTACAG
* **
151403 AATGAGGAGATCTGGTCGGGTGATGACACGACTCATACGCAATGAAGAGTTATGGCCATCTAAAG
65 AATGAGGAGATCAGGTCGGGTGATGACACGACTCATACGCAATGAAGAGACATGGCCATCTAAAG
* * * *
151468 GTGATAACACGGTTCCTACGTGATGAGGACGGCTGATTATCTGGGTTGACACAACTCCTACATAT
130 GTGATAACACGATCCCTACGTGATGAGGACGGATGATTATCTGGGTTAACACAACTCCTACATAT
* * * * ** *
151533 TGAGGAGATCTGGTCGGGTGATGACACGGTTCCTACGTGATGAGGACGGCAGGCCATCCAAGGGT
195 TGAGGAAATCAGGTCGGGTAATGACACGGTTCCTACGCGATGAGGACAACAAGCCATCCAAGGGT
*
151598 GATAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAGCTTTTACATAATG
260 GATAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAGCTTCTACATAATG
151663 AGGAAATCTAGTC
325 AGGAAATCTAGTC
151676 GAG-GATGACAC
1 G-GTGATGACAC
151687 TGCTCATTCT
Statistics
Matches: 297, Mismatches: 45, Indels: 13
0.84 0.13 0.04
Matches are distributed among these distances:
335 1 0.00
336 45 0.15
337 211 0.71
338 40 0.13
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (337 bp):
GGTGATGACACGGTTCCTACATGATGAGGACGGCTGGTTATCAAGGGTGACACAGCTCCTACAGA
ATGAGGAGATCAGGTCGGGTGATGACACGACTCATACGCAATGAAGAGACATGGCCATCTAAAGG
TGATAACACGATCCCTACGTGATGAGGACGGATGATTATCTGGGTTAACACAACTCCTACATATT
GAGGAAATCAGGTCGGGTAATGACACGGTTCCTACGCGATGAGGACAACAAGCCATCCAAGGGTG
ATAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAGCTTCTACATAATGA
GGAAATCTAGTC
Found at i:151489 original size:128 final size:128
Alignment explanation
Indices: 151339--151686 Score: 475
Period size: 128 Copynumber: 2.7 Consensus size: 128
151329 AGATCTGGTC
* * *
151339 GGTGATGACATGGTTCCTACGTGATGAGGACGGTTGTTTATCTGGGTTGACACAGCTCCTACATA
1 GGTGATAACATGGTTCCTACGTGATGAGGACGGCTGATTATCTGGGTTGACACAGCTCCTACATA
** *
151404 ATGAGGAGATCTGGTCGGGTGATGACACGACTCATACGCAATGAAGA-GTTATGGCCATCTAAA
66 ATGAGGAGATCTGGTCGGGTGATGACACGACTCATACGCAATGAAGACGGCA-GGCCATCCAAA
* *
151467 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGATTATCTGGGTTGACACAACTCCTACATA
1 GGTGATAACATGGTTCCTACGTGATGAGGACGGCTGATTATCTGGGTTGACACAGCTCCTACATA
* ** * ** * *
151532 TTGAGGAGATCTGGTCGGGTGATGACACGGTTCCTACGTGATGAGGACGGCAGGCCATCCAAG
66 ATGAGGAGATCTGGTCGGGTGATGACACGACTCATACGCAATGAAGACGGCAGGCCATCCAAA
* **
151595 GGTGATAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACAGCTTTTACATA
1 GGTGATAACATGGTTCCTACGTGATGAGGACGGCTGATTATCTGGGTTGACACAGCTCCTACATA
* * *
151660 ATGAGGAAATCTAGTCGAG-GATGACAC
66 ATGAGGAGATCTGGTCGGGTGATGACAC
151687 TGCTCATTCT
Statistics
Matches: 194, Mismatches: 25, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
127 8 0.04
128 184 0.95
129 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (128 bp):
GGTGATAACATGGTTCCTACGTGATGAGGACGGCTGATTATCTGGGTTGACACAGCTCCTACATA
ATGAGGAGATCTGGTCGGGTGATGACACGACTCATACGCAATGAAGACGGCAGGCCATCCAAA
Found at i:152020 original size:32 final size:32
Alignment explanation
Indices: 151984--152070 Score: 138
Period size: 32 Copynumber: 2.7 Consensus size: 32
151974 TCGTATTAGA
* *
151984 ATGTTGAATCCCCAAAGATGCCCCAATATTTG
1 ATGTTGAATCTCCAAAGATGCCCCAACATTTG
*
152016 ATGTTGAATCTCCAAAGATGCTCCAACATTTG
1 ATGTTGAATCTCCAAAGATGCCCCAACATTTG
*
152048 ATGTTGAATCTTCAAAGATGCCC
1 ATGTTGAATCTCCAAAGATGCCC
152071 TCATTGTTCC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (32 bp):
ATGTTGAATCTCCAAAGATGCCCCAACATTTG
Found at i:160448 original size:30 final size:30
Alignment explanation
Indices: 160364--160456 Score: 71
Period size: 30 Copynumber: 3.1 Consensus size: 30
160354 TAAAAAACAT
** * * *
160364 AAACAGAAAGCTAAGAGGCTAAAATAGTAA
1 AAACAGAAATTTAAAAGACTAAAATAGCAA
* * *
160394 AAATAGAAATTTAAAAGACCAAAATAGCAC
1 AAACAGAAATTTAAAAGACTAAAATAGCAA
* * *
160424 AAACATAAATTTTAAGGACTAAAAT-GTCAA
1 AAACAGAAATTTAAAAGACTAAAATAG-CAA
160454 AAA
1 AAA
160457 TGGAATCTTA
Statistics
Matches: 48, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 47 0.98
ACGTcount: A:0.58, C:0.11, G:0.13, T:0.18
Consensus pattern (30 bp):
AAACAGAAATTTAAAAGACTAAAATAGCAA
Found at i:161736 original size:14 final size:15
Alignment explanation
Indices: 161710--161739 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
161700 TTACAACCCT
161710 AGTGGTGCTTACCAA
1 AGTGGTGCTTACCAA
161725 AGTGGT-CTTACCAA
1 AGTGGTGCTTACCAA
161739 A
1 A
161740 ATAGGATGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (15 bp):
AGTGGTGCTTACCAA
Found at i:164168 original size:20 final size:20
Alignment explanation
Indices: 164137--164209 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
164127 ATAGGTAACG
*
164137 AATTTGATAAAACCAATTGGA
1 AATTTGACAAAACCAATT-GA
*
164158 AA-TTGACAAAACCGATTGA
1 AATTTGACAAAACCAATTGA
**
164177 AATTTGACAAAACCGGTTGA
1 AATTTGACAAAACCAATTGA
*
164197 AATTTGAGAAAAC
1 AATTTGACAAAAC
164210 TAGTAAAGAG
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
19 4 0.09
20 41 0.87
21 2 0.04
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (20 bp):
AATTTGACAAAACCAATTGA
Found at i:164581 original size:196 final size:199
Alignment explanation
Indices: 164232--164747 Score: 497
Period size: 196 Copynumber: 2.6 Consensus size: 199
164222 ACCAGAATTG
* * *
164232 TTGAAATTTGTATCGATACGTGTATAAGTATATGTACCAAAGTATCGGTATTATAGGAATTTGAA
1 TTGAAATTTGCATCGATACGTGTATAAGTATATGCACCAAAGTATCGGTATTATAGGAATTTAAA
**
164297 AGAAATGAAAAAAGGAAAATGTATCGAAAGTATCGATACCTTACACACATGTATCGATACATGAC
66 AGAAATGAAAAAAGGAAAACCTATC-AAAGTATCGATACCTTACACACATGTATCGATACATGAC
* * * ** * * *
164362 AATATAACAGGTTGAAGTTTGACAAAATTGGTTTC-ATTTTACAAAACCGGTAAATAGATAGCGG
130 AATATAACAAGTTAAAATTTGACAAAACCGATTTCAATATGACAAAACCGGTAAATAGATAGCGG
164426 AATGA
195 AATGA
* * * *
164431 TTGAAATTTGCATCTATACTTTTATAAGTATATGCACCAAAGTATCGGTACTT-TATGAATTTAA
1 TTGAAATTTGCATCGATACGTGTATAAGTATATGCACCAAAGTATCGGTA-TTATAGGAATTTAA
* * * * ** * *
164495 AAGAATTGCAACAA-TAGCACCTAT-AAAGTATCGATACCTTAGACACATGTATCGATACATGAT
65 AAGAAATGAAAAAAGGAAAACCTATCAAAGTATCGATACCTTACACACATGTATCGATACATGAC
* *
164558 AATATAACAAGTTAAAATTTGACAAAACCGATTTCAATATGACAAAACCGGTAAAGT-GCTACCG
130 AATATAACAAGTTAAAATTTGACAAAACCGATTTCAATATGACAAAACCGGTAAA-TAGATAGCG
164622 GATATG-
194 GA-ATGA
* * * * * * * *
164628 TTGACGATATCGATGACGGTATCGATACTTTTATAAGTATATGTATCATAGTATCGGTACTCTAG
1 TTGA--A-AT--TTG-C---ATCGATACGTGTATAAGTATATGCACCAAAGTATCGGTATTATAG
* * ** *
164693 GAATTGAAAAGAAATG-AAAAATGAAAATGTATTGAAAGTATCGATACCTTACACA
57 GAATTTAAAAGAAATGAAAAAAGGAAAACCTA-TCAAAGTATCGATACCTTACACA
164748 AAAGTATGAG
Statistics
Matches: 257, Mismatches: 43, Indels: 25
0.79 0.13 0.08
Matches are distributed among these distances:
196 66 0.26
197 28 0.11
198 9 0.04
199 66 0.26
200 4 0.02
202 2 0.01
203 1 0.00
205 5 0.02
206 55 0.21
207 1 0.00
208 20 0.08
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (199 bp):
TTGAAATTTGCATCGATACGTGTATAAGTATATGCACCAAAGTATCGGTATTATAGGAATTTAAA
AGAAATGAAAAAAGGAAAACCTATCAAAGTATCGATACCTTACACACATGTATCGATACATGACA
ATATAACAAGTTAAAATTTGACAAAACCGATTTCAATATGACAAAACCGGTAAATAGATAGCGGA
ATGA
Found at i:171846 original size:200 final size:200
Alignment explanation
Indices: 171497--172237 Score: 1004
Period size: 200 Copynumber: 3.7 Consensus size: 200
171487 TTAACGTAAA
* * *
171497 AAAGTATCGATACACGAATAACAAAGTATCG-TACTTATAATTTCGAAACCCAATACTTTAAAGT
1 AAAGTATCGATACACGTATAAC-AAGTATCGATACTTATAATTTCGAAACCGATTACTTTAAAGT
* * * ** ** *
171561 TATAGGTAAATTTATAATGTAAACTATAAAAATCTACATGTTTAATGATAATATTCATAAACATA
65 AATAGGTAAATTTACAATGTAAACGATAAAAATCTACCGGTTTAATGATAATAGGCGTAAACATA
* * *
171626 AAGTATTGATACTCTTTGTATAGGTATCAATACTTTTAGTCCAATATGTTTCTCAAACAACATGC
130 AAGTATTGATACTCTTTGTATAGGTATCGATACTTTTAGTCCAGTATGCTTCTCAAACAACATGC
**
171691 AAACAG
195 ACGCAG
* * * *
171697 AAAGTATTGATACACGTATCACAAGTATCAATACTTATAATTTTGAAACCGATTACTTTAAAGTA
1 AAAGTATCGATACACGTATAACAAGTATCGATACTTATAATTTCGAAACCGATTACTTTAAAGTA
* * *
171762 ATAGGTAAATTTACAATGTCAACGATAAAAGTCTACCGGTTTAATGATAATAGGCGTAAACATAT
66 ATAGGTAAATTTACAATGTAAACGATAAAAATCTACCGGTTTAATGATAATAGGCGTAAACATAA
* * * * * *
171827 AGTATCGATATTTTTTGTATTGGTATCGATACTTTTAGTCTAGTATGCTTCTAAAACAACATGCA
131 AGTATTGATACTCTTTGTATAGGTATCGATACTTTTAGTCCAGTATGCTTCTCAAACAACATGCA
171892 CGCAG
196 CGCAG
* * * *
171897 AAAGTATCGATACATGTATAACAAGTATCGATACTTATAACTTCAAAACCGATTACTTTAAAGTT
1 AAAGTATCGATACACGTATAACAAGTATCGATACTTATAATTTCGAAACCGATTACTTTAAAGTA
* * *
171962 ATAGGTAAATTTACAATGTAAAC-AGTAAAAATCTATCGATTTAATGATAATGGGCGTAAACATA
66 ATAGGTAAATTTACAATGTAAACGA-TAAAAATCTACCGGTTTAATGATAATAGGCGTAAACATA
* *
172026 AAGTATTGATACTCTTTGTATAAGTATCGATAATTTTAGTCCAGTATGCTTCTCAAACAACATGC
130 AAGTATTGATACTCTTTGTATAGGTATCGATACTTTTAGTCCAGTATGCTTCTCAAACAACATGC
*
172091 ACGTAG
195 ACGCAG
* * ** *
172097 AAAGTATCGATACACATATCACAAGTATCGATACTTATAATTTC-AAATCATATTACTTTAAAAT
1 AAAGTATCGATACACGTATAACAAGTATCGATACTTATAATTTCGAAA-CCGATTACTTTAAAGT
* *
172161 AATAGGTAAATTTACAATGTAAACGGTAAAAATCTATCGGTTTAATGATAATAGGC-TAAACATA
65 AATAGGTAAATTTACAATGTAAACGATAAAAATCTACCGGTTTAATGATAATAGGCGTAAACATA
*
172225 AACTATTGATACT
130 AAGTATTGATACT
172238 TATAATTTTG
Statistics
Matches: 473, Mismatches: 64, Indels: 9
0.87 0.12 0.02
Matches are distributed among these distances:
199 31 0.07
200 442 0.93
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (200 bp):
AAAGTATCGATACACGTATAACAAGTATCGATACTTATAATTTCGAAACCGATTACTTTAAAGTA
ATAGGTAAATTTACAATGTAAACGATAAAAATCTACCGGTTTAATGATAATAGGCGTAAACATAA
AGTATTGATACTCTTTGTATAGGTATCGATACTTTTAGTCCAGTATGCTTCTCAAACAACATGCA
CGCAG
Found at i:171937 original size:19 final size:21
Alignment explanation
Indices: 171898--171937 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
171888 TGCACGCAGA
171898 AAGTATCGATACATGTATAAC
1 AAGTATCGATACATGTATAAC
171919 AAGTATCGATAC-T-TATAAC
1 AAGTATCGATACATGTATAAC
171938 TTCAAAACCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 1 0.05
21 12 0.63
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (21 bp):
AAGTATCGATACATGTATAAC
Found at i:172311 original size:106 final size:107
Alignment explanation
Indices: 172126--172345 Score: 327
Period size: 106 Copynumber: 2.1 Consensus size: 107
172116 CACAAGTATC
* **
172126 GATACTTATAATTTCAAATCATATTACTTTAAAATAATAGGTAAATTTACAATGTAAACGGTAAA
1 GATACTTATAATTTCAAATCATATTACTTTAAAATAAAAGGTAAATTTACAAACTAAACGGTAAA
* *
172191 AATCTATCGGTTTAATGATAATAGGC-TAAACATAAACTATT
66 AATATATCAGTTTAATGATAATAGGCGTAAACATAAACTATT
* * *
172232 GATACTTATAATTTTGAAA-CTTATTACTTTAAAGTAAAAGGTAAATTTACAAACTAAACGGTAA
1 GATACTTATAA-TTTCAAATCATATTACTTTAAAATAAAAGGTAAATTTACAAACTAAACGGTAA
* *
172296 AAATATATCAGTTTAATGATAATAGGCGTAAACATAAAGTTTT
65 AAATATATCAGTTTAATGATAATAGGCGTAAACATAAACTATT
172339 GATACTT
1 GATACTT
172346 TTTGTATAGG
Statistics
Matches: 102, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
106 76 0.75
107 26 0.25
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (107 bp):
GATACTTATAATTTCAAATCATATTACTTTAAAATAAAAGGTAAATTTACAAACTAAACGGTAAA
AATATATCAGTTTAATGATAATAGGCGTAAACATAAACTATT
Found at i:173487 original size:4 final size:4
Alignment explanation
Indices: 173462--173553 Score: 56
Period size: 4 Copynumber: 25.0 Consensus size: 4
173452 TCGGGCATGG
* * * *
173462 TATA TATA TTTA AAT- TAAA TATA TATA AATA T-TA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * *
173508 T-TA -ATT TAAA T-TA AATT TAT- TA-A TAT- TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
173550 TATA
1 TATA
173554 ATAATTATTT
Statistics
Matches: 65, Mismatches: 15, Indels: 16
0.68 0.16 0.17
Matches are distributed among these distances:
3 15 0.23
4 50 0.77
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TATA
Found at i:173503 original size:6 final size:6
Alignment explanation
Indices: 173462--173553 Score: 56
Period size: 6 Copynumber: 16.7 Consensus size: 6
173452 TCGGGCATGG
* * * *
173462 TATATA TATTTA AAT-TA AATATA TATAAA TAT-TA TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * *
173508 T-TA-A TTTAAA T-TAAA TTTAT- TA-ATA T-TATA TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
173550 TATA
1 TATA
173554 ATAATTATTT
Statistics
Matches: 71, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
4 4 0.06
5 24 0.34
6 43 0.61
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATA
Found at i:173550 original size:42 final size:42
Alignment explanation
Indices: 173462--173548 Score: 137
Period size: 40 Copynumber: 2.2 Consensus size: 42
173452 TCGGGCATGG
173462 TATATA-T-ATTTAAATTAAATATATATAAATATTATATATA
1 TATATATTAATTTAAATTAAATATATATAAATATTATATATA
*
173502 TATATATTAATTTAAATTAAAT-T-TATTAATATTATATATA
1 TATATATTAATTTAAATTAAATATATATAAATATTATATATA
173542 TATATAT
1 TATATAT
173549 ATATAATAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
40 29 0.66
41 2 0.05
42 13 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (42 bp):
TATATATTAATTTAAATTAAATATATATAAATATTATATATA
Found at i:173560 original size:40 final size:40
Alignment explanation
Indices: 173462--173571 Score: 108
Period size: 40 Copynumber: 2.8 Consensus size: 40
173452 TCGGGCATGG
* *
173462 TATATATAT-TTA-AATTAAATATATATAAATATTATATATA
1 TATATATATATAATAATTAAAT-T-TATTAATATTATATATA
*
173502 TATATAT-TA-ATTTAAATTAAATTTATTAATATTATATATA
1 TATATATATATA-AT-AATTAAATTTATTAATATTATATATA
173542 TATATATATATAATAATT--ATTT-TTAATATT
1 TATATATATATAATAATTAAATTTATTAATATT
173572 TATCGGGGTA
Statistics
Matches: 60, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
37 8 0.13
38 4 0.07
39 1 0.02
40 34 0.57
41 4 0.07
42 9 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (40 bp):
TATATATATATAATAATTAAATTTATTAATATTATATATA
Found at i:175831 original size:6 final size:6
Alignment explanation
Indices: 175820--175844 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
175810 ATTATGCAGT
175820 TTTCAA TTTCAA TTTCAA TTTCAA T
1 TTTCAA TTTCAA TTTCAA TTTCAA T
175845 ATAAATATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTCAA
Found at i:176973 original size:34 final size:34
Alignment explanation
Indices: 176930--177135 Score: 143
Period size: 34 Copynumber: 5.9 Consensus size: 34
176920 CTTTGGTATC
*
176930 CTTTCATGCCAATAATGCACCCTTATGCATTATT
1 CTTTCATGCCAATAATGCACCCATATGCATTATT
* * * * * * *
176964 CTTTTATGCC-ATGCATTTCAGCTA-AGGCATCA--
1 CTTTCATGCCAAT--AATGCACCCATATGCATTATT
*
176996 -TTTCATGCTAATAATGCACCCATATGCATTATT
1 CTTTCATGCCAATAATGCACCCATATGCATTATT
* * *
177029 CTTTTATGCCGATAATGCACCCATATGCATTTTAGTCCAGGC
1 CTTTCATGCCAATAATGCACCCATATGCA--TTA-T-----T
177071 CTTTCATGCCAATAATGCACCCATATGCATTATT
1 CTTTCATGCCAATAATGCACCCATATGCATTATT
* * * *
177105 CTTTTATGCCGATACTGCACCTATATGCATT
1 CTTTCATGCCAATAATGCACCCATATGCATT
177136 TCAGCTAAGG
Statistics
Matches: 130, Mismatches: 27, Indels: 30
0.70 0.14 0.16
Matches are distributed among these distances:
30 6 0.05
31 13 0.10
32 2 0.02
33 2 0.02
34 67 0.52
35 5 0.04
36 3 0.02
37 1 0.01
39 1 0.01
40 3 0.02
42 27 0.21
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.36
Consensus pattern (34 bp):
CTTTCATGCCAATAATGCACCCATATGCATTATT
Found at i:176980 original size:65 final size:65
Alignment explanation
Indices: 176909--177038 Score: 197
Period size: 65 Copynumber: 2.0 Consensus size: 65
176899 ATGCACCCAT
** * * *
176909 ATGCATTTCAACTTTGGTATCCTTTCATGCCAATAATGCACCCTTATGCATTATTCTTTTATGCC
1 ATGCATTTCAACTAAGGCATCATTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCC
* *
176974 ATGCATTTCAGCTAAGGCATCATTTCATGCTAATAATGCACCCATATGCATTATTCTTTTATGCC
1 ATGCATTTCAACTAAGGCATCATTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCC
177039 GATAATGCAC
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
65 58 1.00
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.39
Consensus pattern (65 bp):
ATGCATTTCAACTAAGGCATCATTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCC
Found at i:177079 original size:76 final size:77
Alignment explanation
Indices: 176974--177190 Score: 303
Period size: 76 Copynumber: 2.8 Consensus size: 77
176964 CTTTTATGCC
* *
176974 ATGCATTTCAGCTAAGGCATCATTTCATGCTAATAATGCACCCATATGCATTATTCTTTTATGCC
1 ATGCATTTCAGCTAAGG-A-CCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCC
177039 GATAATGCACCCAT
64 GATAATGCACCCAT
* *
177053 ATGCATTTTAG-TCCAGG-CCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCG
1 ATGCATTTCAGCT-AAGGACCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCG
* *
177116 ATACTGCACCTAT
65 ATAATGCACCCAT
* *
177129 ATGCATTTCAGCTAAGGCATCCTTTAATGCCAATAATGCACCCATATGCATTATTCTATTAT
1 ATGCATTTCAGCTAAGG-A-CCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTAT
177191 TAATTCGTTC
Statistics
Matches: 123, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
76 68 0.55
77 1 0.01
78 1 0.01
79 53 0.43
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.35
Consensus pattern (77 bp):
ATGCATTTCAGCTAAGGACCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCGA
TAATGCACCCAT
Found at i:178075 original size:10 final size:10
Alignment explanation
Indices: 178060--178088 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
178050 TCAAATCTAC
178060 CAATAAACAT
1 CAATAAACAT
178070 CAATAAACAT
1 CAATAAACAT
178080 CAATAAACA
1 CAATAAACA
178089 CTCATATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.21, G:0.00, T:0.17
Consensus pattern (10 bp):
CAATAAACAT
Found at i:183727 original size:18 final size:18
Alignment explanation
Indices: 183704--183738 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
183694 TTCCATCTGG
*
183704 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
183722 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
183739 GTCCTTTCGA
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:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:185042 original size:8 final size:8
Alignment explanation
Indices: 185029--185082 Score: 57
Period size: 8 Copynumber: 7.5 Consensus size: 8
185019 GGTAAACGAC
185029 GGTCAACG
1 GGTCAACG
185037 GGTCAACG
1 GGTCAACG
185045 GGTCAACG
1 GGTCAACG
185053 GGT--A-G
1 GGTCAACG
*
185058 AGTCAACG
1 GGTCAACG
185066 GGT---CG
1 GGTCAACG
185071 GGTCAACG
1 GGTCAACG
185079 GGTC
1 GGTC
185083 GAGTAAATGG
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
5 8 0.21
6 1 0.03
7 1 0.03
8 28 0.74
ACGTcount: A:0.22, C:0.22, G:0.41, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:185072 original size:26 final size:26
Alignment explanation
Indices: 185043--185126 Score: 123
Period size: 26 Copynumber: 3.2 Consensus size: 26
185033 AACGGGTCAA
* *
185043 CGGGTCAACGGGTAGAGTCAACGGGT
1 CGGGTCAACGGGTCGAGTAAACGGGT
*
185069 CGGGTCAACGGGTCGAGTAAATGGGT
1 CGGGTCAACGGGTCGAGTAAACGGGT
**
185095 CAAGTCAACGGGTCGAGTAAACGGGT
1 CGGGTCAACGGGTCGAGTAAACGGGT
185121 CGGGTC
1 CGGGTC
185127 GGGTCAACGG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 50 1.00
ACGTcount: A:0.24, C:0.19, G:0.40, T:0.17
Consensus pattern (26 bp):
CGGGTCAACGGGTCGAGTAAACGGGT
Found at i:185126 original size:18 final size:18
Alignment explanation
Indices: 185103--185187 Score: 107
Period size: 18 Copynumber: 4.6 Consensus size: 18
185093 GTCAAGTCAA
*
185103 CGGGTCGAGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
*
185121 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTAAACGGGT
*
185139 CGGGTCGGGTAATCGGGT
1 CGGGTCGGGTAAACGGGT
*
185157 CGGGTAAACGGGTCAACGGGT
1 CGGGT---CGGGTAAACGGGT
185178 CGGGTCGGGT
1 CGGGTCGGGT
185188 TGTGACCGGT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
18 42 0.72
21 16 0.28
ACGTcount: A:0.15, C:0.19, G:0.48, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:185142 original size:13 final size:13
Alignment explanation
Indices: 185046--185122 Score: 100
Period size: 13 Copynumber: 5.9 Consensus size: 13
185036 GGGTCAACGG
*
185046 GTCAACGGGTAGA
1 GTCAACGGGTCGA
*
185059 GTCAACGGGTCGG
1 GTCAACGGGTCGA
185072 GTCAACGGGTCGA
1 GTCAACGGGTCGA
* * *
185085 GTAAATGGGTCAA
1 GTCAACGGGTCGA
185098 GTCAACGGGTCGA
1 GTCAACGGGTCGA
*
185111 GTAAACGGGTCG
1 GTCAACGGGTCG
185123 GGTCGGGTCA
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 54 1.00
ACGTcount: A:0.26, C:0.18, G:0.39, T:0.17
Consensus pattern (13 bp):
GTCAACGGGTCGA
Found at i:185183 original size:13 final size:13
Alignment explanation
Indices: 185138--185170 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
185128 GGTCAACGGG
185138 TCGGGTCGGGTAA
1 TCGGGTCGGGTAA
185151 TCGGGTCGGGTAA
1 TCGGGTCGGGTAA
*
185164 ACGGGTC
1 TCGGGTC
185171 AACGGGTCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.18, G:0.45, T:0.21
Consensus pattern (13 bp):
TCGGGTCGGGTAA
Found at i:188942 original size:18 final size:18
Alignment explanation
Indices: 188919--188953 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
188909 TTCCATCCGG
*
188919 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
188937 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
188954 GTTCTTTCGA
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:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:190247 original size:8 final size:8
Alignment explanation
Indices: 190224--190275 Score: 63
Period size: 8 Copynumber: 6.5 Consensus size: 8
190214 TCAAAGTTTT
190224 GGTCAACG
1 GGTCAACG
190232 ACGGTCAACG
1 --GGTCAACG
190242 GGTCAACG
1 GGTCAACG
190250 GGTCAAC-
1 GGTCAACG
190257 GGTCAAC-
1 GGTCAACG
*
190264 GATCAACG
1 GGTCAACG
190272 GGTC
1 GGTC
190276 GAGTCAACGG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
7 13 0.33
8 18 0.46
10 8 0.21
ACGTcount: A:0.27, C:0.27, G:0.33, T:0.13
Consensus pattern (8 bp):
GGTCAACG
Found at i:190260 original size:7 final size:7
Alignment explanation
Indices: 190232--190272 Score: 55
Period size: 7 Copynumber: 5.6 Consensus size: 7
190222 TTGGTCAACG
190232 ACGGTCA
1 ACGGTCA
190239 ACGGGTCA
1 AC-GGTCA
190247 ACGGGTCA
1 AC-GGTCA
190255 ACGGTCA
1 ACGGTCA
*
190262 ACGATCA
1 ACGGTCA
190269 ACGG
1 ACGG
190273 GTCGAGTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
7 16 0.52
8 15 0.48
ACGTcount: A:0.29, C:0.27, G:0.32, T:0.12
Consensus pattern (7 bp):
ACGGTCA
Found at i:190260 original size:15 final size:15
Alignment explanation
Indices: 190232--190288 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
190222 TTGGTCAACG
190232 ACGGTCAACGGGTCA
1 ACGGTCAACGGGTCA
190247 ACGGGTCAAC-GGTCA
1 AC-GGTCAACGGGTCA
* *
190262 ACGATCAACGGGTCG
1 ACGGTCAACGGGTCA
190277 A--GTCAACGGGTC
1 ACGGTCAACGGGTC
190289 GGGTCGGGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.27
14 6 0.16
15 14 0.38
16 7 0.19
ACGTcount: A:0.26, C:0.26, G:0.33, T:0.14
Consensus pattern (15 bp):
ACGGTCAACGGGTCA
Found at i:194519 original size:2 final size:2
Alignment explanation
Indices: 194512--194552 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
194502 AAATGTATTG
*
194512 AC AC AC AC AC AC AC AA AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
194553 TATATATATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.54, C:0.46, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:194928 original size:130 final size:127
Alignment explanation
Indices: 194701--194934 Score: 276
Period size: 130 Copynumber: 1.8 Consensus size: 127
194691 CGATACATGG
* * * *
194701 AATTTTGAAACCTATTACTTTAAGTAATAGGTAAATTAACAATGTACACAGTAAACTTTTCTACC
1 AATTTTGAAACCTATTACTTTAAGTAATAAGTAAATTAACAATATACACAGTAAACTGTTCAACC
* * **
194766 GGTATAATGAAAATAGGTGTATATGTACAAGTATCGATATTGTCATATAAGTATCTATTCTTAT
66 GGTATAAT--AAATAGGCGTAAACATACAAGTATCGATATTGTCATATAAGTATCTATTCTTAT
** *
194830 AATTTTGAAACCTATTACTTTAAAGTAATAAGTAAATTAACAATATACATGGTAATA-TGTTGAA
1 AATTTTGAAACCTATTACTTT-AAGTAATAAGTAAATTAACAATATACACAGTAA-ACTGTTCAA
194894 CCTCGGTACCTAAT-AATAGGCGTAAACATA-AAGTATCGATA
64 -C-CGGTA--TAATAAATAGGCGTAAACATACAAGTATCGATA
194935 CTCTTTGTAT
Statistics
Matches: 88, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
129 21 0.24
130 44 0.50
131 14 0.16
132 5 0.06
134 4 0.05
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (127 bp):
AATTTTGAAACCTATTACTTTAAGTAATAAGTAAATTAACAATATACACAGTAAACTGTTCAACC
GGTATAATAAATAGGCGTAAACATACAAGTATCGATATTGTCATATAAGTATCTATTCTTAT
Found at i:195340 original size:197 final size:198
Alignment explanation
Indices: 194906--195350 Score: 651
Period size: 197 Copynumber: 2.2 Consensus size: 198
194896 TCGGTACCTA
*
194906 ATAATAGGCGTAAACATAAAGTATCGATACTCTTTGTATAGGTATCGATACTTTTAGTCCAGTAT
1 ATAATAGGCGTAAACATAAAGTATCGATACTCTTTGTATAGGTATCGATACTTCTAGTCCAGTAT
** * *
194971 GCTTCTCAACAATTTGCACGCACAAAGTATCGATACATGTATAACAAGTATCGATACTTATAATT
66 GCTTCTCAACAACATGCACGCACAAAGAATCGATACACGTATAACAAGTATCGATACTTATAATT
* * * *
195036 TCAAAACCGATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGAAAAAATCTACTGATTT
131 TCAAAACCGATTACTTT-AAGTAATAGGTAAATTTACAATATAAACAGAAAAAATCTACCGATTT
195101 AATG
195 AATG
* * *
195105 ATAATAGGTGTAAACATAAAGTATCAATACTCTTTGTATAGGTATCGATACTTCTAGTCCATTAT
1 ATAATAGGCGTAAACATAAAGTATCGATACTCTTTGTATAGGTATCGATACTTCTAGTCCAGTAT
* * *
195170 GCTTCTCAAACAACATGCACGCAGAAAGAATTGATACACGTATTACAAGTATCGATACTTATAAT
66 GCTTCTC-AACAACATGCACGCACAAAGAATCGATACACGTATAACAAGTATCGATACTTATAAT
* * * *
195235 TTCAAAATCTATTAC-TT-AGTAATAGGTAAATTTACAATATAAACAGTAAAAATCTACCGGTTT
130 TTCAAAACCGATTACTTTAAGTAATAGGTAAATTTACAATATAAACAGAAAAAATCTACCGATTT
195298 AATG
195 AATG
* * * *
195302 ATAATAGGCGTTAACATAAAGTTTTGATACTTTTTGTATAGGTATCGAT
1 ATAATAGGCGTAAACATAAAGTATCGATACTCTTTGTATAGGTATCGAT
195351 GCTTTCGATC
Statistics
Matches: 220, Mismatches: 25, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
197 87 0.40
199 70 0.32
200 63 0.29
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (198 bp):
ATAATAGGCGTAAACATAAAGTATCGATACTCTTTGTATAGGTATCGATACTTCTAGTCCAGTAT
GCTTCTCAACAACATGCACGCACAAAGAATCGATACACGTATAACAAGTATCGATACTTATAATT
TCAAAACCGATTACTTTAAGTAATAGGTAAATTTACAATATAAACAGAAAAAATCTACCGATTTA
ATG
Found at i:196152 original size:225 final size:225
Alignment explanation
Indices: 195539--196227 Score: 859
Period size: 225 Copynumber: 3.0 Consensus size: 225
195529 TAACAAATCA
* * * * * *
195539 AGTAATTAACCAATTTTGTTATCGT-TGAATTTCTAAGGATCCATCATCTTTAAACGTATGGTAA
1 AGTAATTAACCTATTTTGTTATCATCAG-ATTTCTAAGGCTCCATCAGC-TTAAAC-TTTGGTAA
* *
195603 CATTTTAGGCGCTACCTAATATGTTGATCATACTGATAACAAATTAAGTAATTAACCTATTTTGT
63 CATTTTAGGCGATACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGT
* * * * * * * *
195668 TATCATCAAATTTCTAA-ACCCTATCAGCTTTAAACAAACACTACCTATTACATTAAATAAGCAC
128 TATCGTTAGATTTCTAAGGCCC-ATCAGCTTTAAACAGACGCTACCTATTACGTTAAATAAGCGC
*
195732 TACTTGTTATGTTATTATGGTTGATAATTTTTCC
192 TACTTATTATGTTATTATGGTTGATAATTTTTCC
* * * * * *
195766 AATAATTAACTTGTTTTGTTATCCTCATATTTCTAAGGCTCCATCAGGTTAAACTTTGGTAACAT
1 AGTAATTAACCTATTTTGTTATCATCAGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
*
195831 TTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTAT
66 TTTAGGCGATACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTAT
* * * * *
195896 CG-TAGAATTTCCAAGGCTTCATCGGCTTTAAACAGACGCTACCTATT-GGTTAAATAAGTGCTA
131 CGTTAG-ATTTCTAAGGC-CCATCAGCTTTAAACAGACGCTACCTATTACGTTAAATAAGCGCTA
*
195959 CTTTTTATGTTATTATGGTTGATAATTTTTCC
194 CTTATTATGTTATTATGGTTGATAATTTTTCC
*
195991 AGTAATTAACCTATTTTGTTATCATCAGATTTTTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
1 AGTAATTAACCTATTTTGTTATCATCAGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
* * *
196056 TTTAGGTGATACCTAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTAT
66 TTTAGGCGATACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTAT
* * * * * * *
196121 TGTTAGATTTCTAAGGTCCCATCAACTTTAAAAATG-TGTTACCTATTATGTTACATAAGCGCTA
131 CGTTAGATTTCTAAGG-CCCATCAGCTTTAAACA-GACGCTACCTATTACGTTAAATAAGCGCTA
* * *
196185 CATAATATATTATTATGGTTGAT-ATTGTTTCC
194 CTTATTATGTTATTATGGTTGATAATT-TTTCC
196217 AGTAATTAACC
1 AGTAATTAACC
196228 GGTTATGTTA
Statistics
Matches: 400, Mismatches: 53, Indels: 19
0.85 0.11 0.04
Matches are distributed among these distances:
224 1 0.00
225 277 0.69
226 84 0.21
227 38 0.09
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.40
Consensus pattern (225 bp):
AGTAATTAACCTATTTTGTTATCATCAGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
TTTAGGCGATACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTAT
CGTTAGATTTCTAAGGCCCATCAGCTTTAAACAGACGCTACCTATTACGTTAAATAAGCGCTACT
TATTATGTTATTATGGTTGATAATTTTTCC
Found at i:197531 original size:15 final size:14
Alignment explanation
Indices: 197488--197534 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
197478 TATATTAGTA
197488 ATTTAA-TTTTTAT
1 ATTTAATTTTTTAT
* *
197501 TTTTAGTATTTTTAT
1 ATTTAAT-TTTTTAT
197516 ATTTAATTTTTCTAT
1 ATTTAATTTTT-TAT
197531 ATTT
1 ATTT
197535 GTATAGTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 4 0.15
14 4 0.15
15 19 0.70
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (14 bp):
ATTTAATTTTTTAT
Found at i:201267 original size:19 final size:18
Alignment explanation
Indices: 201243--201287 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
201233 GGTCAAAGTT
*
201243 AACGGTTAACGGCCAGGTC
1 AACGGTCAACGGCCA-GTC
* *
201262 AACGGTCAATGGGCAGTC
1 AACGGTCAACGGCCAGTC
201280 AACGGTCA
1 AACGGTCA
201288 GGTCAAAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.29, C:0.24, G:0.31, T:0.16
Consensus pattern (18 bp):
AACGGTCAACGGCCAGTC
Found at i:202943 original size:20 final size:19
Alignment explanation
Indices: 202899--202960 Score: 115
Period size: 19 Copynumber: 3.2 Consensus size: 19
202889 TAAAAATTAT
202899 TTTTAAAATATTTATTTAA
1 TTTTAAAATATTTATTTAA
202918 TTTTAAAATATTTATTTAA
1 TTTTAAAATATTTATTTAA
202937 CTTTTAAAATATTTATTTAA
1 -TTTTAAAATATTTATTTAA
202957 TTTT
1 TTTT
202961 TATTATACTA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 23 0.55
20 19 0.45
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTAAAATATTTATTTAA
Found at i:202961 original size:20 final size:20
Alignment explanation
Indices: 202897--202962 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
202887 TCTAAAAATT
202897 ATTTTTAAAATATTTATTTA
1 ATTTTTAAAATATTTATTTA
202917 A-TTTTAAAATATTTATTTA
1 ATTTTTAAAATATTTATTTA
*
202936 ACTTTTAAAATATTTATTTA
1 ATTTTTAAAATATTTATTTA
202956 ATTTTTA
1 ATTTTTA
202963 TTATACTAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 19 0.43
20 25 0.57
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTTTAAAATATTTATTTA
Found at i:210650 original size:88 final size:88
Alignment explanation
Indices: 210500--210666 Score: 241
Period size: 88 Copynumber: 1.9 Consensus size: 88
210490 GAGTCTCTAA
* **
210500 ACTATTAAAAATTACAAAATTATCATTCGATTATAGGGTGTTGCTTTGTTGAGTCCTAGACTATT
1 ACTATTAAAAATTACAAAATGATCATTAAATTATAGGGTGTTGCTTTGTTGAGTCCTAGACTATT
210565 AAAAGTTACAAAATGGTCACCTG
66 AAAAGTTACAAAATGGTCACCTG
* *
210588 ACTATTAAAAATTAC-AAATGAT-ATCTAAATTATATGGTGTTGCTTTGTTGAGACTTCT-GACT
1 ACTATTAAAAATTACAAAATGATCAT-TAAATTATAGGGTGTTGCTTTGTTGAG--TCCTAGACT
210650 ATTAAAAGTTACAAAAT
63 ATTAAAAGTTACAAAAT
210667 ATATTCTAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
86 2 0.03
87 30 0.42
88 36 0.51
89 3 0.04
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (88 bp):
ACTATTAAAAATTACAAAATGATCATTAAATTATAGGGTGTTGCTTTGTTGAGTCCTAGACTATT
AAAAGTTACAAAATGGTCACCTG
Found at i:213969 original size:21 final size:21
Alignment explanation
Indices: 213936--213989 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
213926 GTTTCCAGAT
*
213936 TCGCAACGCGAACTTCGACTA
1 TCGCAAAGCGAACTTCGACTA
* *
213957 TCTCAAAGCGAACTTGGACTA
1 TCGCAAAGCGAACTTCGACTA
*
213978 TCGCAATGCGAA
1 TCGCAAAGCGAA
213990 TATGTAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.20
Consensus pattern (21 bp):
TCGCAAAGCGAACTTCGACTA
Found at i:214420 original size:11 final size:11
Alignment explanation
Indices: 214388--214420 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
214378 TATCGGATTG
*
214388 AAAATATTTAG
1 AAAATATTTAA
214399 AAAATATTTAA
1 AAAATATTTAA
214410 AAAATATTTAA
1 AAAATATTTAA
214421 TCTAATGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (11 bp):
AAAATATTTAA
Found at i:215131 original size:59 final size:59
Alignment explanation
Indices: 215039--215182 Score: 243
Period size: 59 Copynumber: 2.4 Consensus size: 59
215029 TCAGGTTACC
* *
215039 ATTTTGTAACTTTTAGTAGTCGAGAAGCTAAAAAAACAACATTTTATAGTCAAGAGATT
1 ATTTTGTAACTTTTAATAGTCGAGAGGCTAAAAAAACAACATTTTATAGTCAAGAGATT
* *
215098 ATTTTGTAACTTTTAATAGTCGAGAGGCTAAAAAAACAATATTTTATAGTCAATAGATT
1 ATTTTGTAACTTTTAATAGTCGAGAGGCTAAAAAAACAACATTTTATAGTCAAGAGATT
*
215157 ATTTTATAACTTTTAATAGTCGAGAG
1 ATTTTGTAACTTTTAATAGTCGAGAG
215183 ACTCAATAAA
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 80 1.00
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.37
Consensus pattern (59 bp):
ATTTTGTAACTTTTAATAGTCGAGAGGCTAAAAAAACAACATTTTATAGTCAAGAGATT
Found at i:218887 original size:14 final size:14
Alignment explanation
Indices: 218868--218897 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
218858 GTTCTCTAAA
218868 AATTATAATTAATT
1 AATTATAATTAATT
*
218882 AATTATAATTTATT
1 AATTATAATTAATT
218896 AA
1 AA
218898 CGGTTAACCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTATAATTAATT
Found at i:220143 original size:32 final size:31
Alignment explanation
Indices: 220106--220192 Score: 104
Period size: 35 Copynumber: 2.7 Consensus size: 31
220096 TTGAATAGTG
220106 TGTTAAGCATTAATATTAGAATATAGAGAGTT
1 TGTTAAGCATTAATATTAGAATATAGAGAG-T
*
220138 TGTTAAGCATTAATATTAACAAAATATAGAGAGT
1 TGTTAAGCATTAATATT---AGAATATAGAGAGT
*
220172 TGCTAGAGCATTAAT-TTAGAA
1 TGTTA-AGCATTAATATTAGAA
220193 GGATCTAGAG
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
31 3 0.06
32 17 0.35
34 7 0.15
35 21 0.44
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.34
Consensus pattern (31 bp):
TGTTAAGCATTAATATTAGAATATAGAGAGT
Found at i:223047 original size:26 final size:26
Alignment explanation
Indices: 222986--223039 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
222976 CTTACTAGAT
222986 GGTGATGAACCCATCACGGTTCATCA
1 GGTGATGAACCCATCACGGTTCATCA
223012 GGTGATGAACCCATCACGGTTCATCA
1 GGTGATGAACCCATCACGGTTCATCA
223038 GG
1 GG
223040 CTTTGAACTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.22
Consensus pattern (26 bp):
GGTGATGAACCCATCACGGTTCATCA
Found at i:239464 original size:15 final size:15
Alignment explanation
Indices: 239433--239462 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
239423 ACACTAAATC
239433 GGTTTCGGTTTTTTT
1 GGTTTCGGTTTTTTT
239448 GGTTATCGGTTTTTT
1 GGTT-TCGGTTTTTT
239463 GGATCGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.03, C:0.07, G:0.27, T:0.63
Consensus pattern (15 bp):
GGTTTCGGTTTTTTT
Found at i:239726 original size:43 final size:43
Alignment explanation
Indices: 239679--239765 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
239669 ACATATGTAA
239679 TGACTATTTCATGAATATACAAAAATAGTGACACTACAACAAT
1 TGACTATTTCATGAATATACAAAAATAGTGACACTACAACAAT
239722 TGACTATTTCATGAATATACAAAAATAGTGACACTACAACAAT
1 TGACTATTTCATGAATATACAAAAATAGTGACACTACAACAAT
239765 T
1 T
239766 TATCAATTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.29
Consensus pattern (43 bp):
TGACTATTTCATGAATATACAAAAATAGTGACACTACAACAAT
Found at i:240701 original size:19 final size:19
Alignment explanation
Indices: 240650--240693 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
240640 AGTTAACCCA
240650 ACCCGACCCATTGACTTTG
1 ACCCGACCCATTGACTTTG
* * *
240669 ACCCAACCCTTTGATTTTG
1 ACCCGACCCATTGACTTTG
240688 ACCCGA
1 ACCCGA
240694 TCCGTTGACC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.23, C:0.36, G:0.14, T:0.27
Consensus pattern (19 bp):
ACCCGACCCATTGACTTTG
Found at i:241341 original size:27 final size:27
Alignment explanation
Indices: 241282--241343 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
241272 TACTTCGATT
* *
241282 GTGTAAAATTTTGAAAATATCCTTTTG
1 GTGTAAAATTATGAAAATATCCTTATG
*
241309 GGGTAAAATTATGAAAATA-CTCTTATG
1 GTGTAAAATTATGAAAATATC-CTTATG
*
241336 TTGTAAAA
1 GTGTAAAA
241344 AGCCAAGAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 1 0.03
27 28 0.97
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (27 bp):
GTGTAAAATTATGAAAATATCCTTATG
Found at i:242476 original size:35 final size:35
Alignment explanation
Indices: 242425--242543 Score: 109
Period size: 35 Copynumber: 3.4 Consensus size: 35
242415 GATCCAGCTC
* *
242425 GATCAAACTGATAATTCCTTATATAGGTTCAGACA
1 GATCGAACTGGTAATTCCTTATATAGGTTCAGACA
** *
242460 GATCGAACTGGTAATTCCTTACGGTATGTTCA-ACTA
1 GATCGAACTGGTAATTCCTTA-TATAGGTTCAGAC-A
* * *
242496 -AGT-GAAATTGTAATTCCTTATATAGGTTCAGACT
1 GA-TCGAACTGGTAATTCCTTATATAGGTTCAGACA
*
242530 GATCGAGCTGGTAA
1 GATCGAACTGGTAA
242544 AACCTTACGG
Statistics
Matches: 64, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
34 8 0.12
35 47 0.73
36 9 0.14
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (35 bp):
GATCGAACTGGTAATTCCTTATATAGGTTCAGACA
Found at i:242910 original size:21 final size:22
Alignment explanation
Indices: 242884--242943 Score: 86
Period size: 21 Copynumber: 2.8 Consensus size: 22
242874 AATATTAAGA
* *
242884 GGTATCGATACCCCTATGAAT-
1 GGTATCAATACCCCTATAAATG
242905 GGTATCAATACCCCTATAAATG
1 GGTATCAATACCCCTATAAATG
*
242927 GGTACCAATACCCCTAT
1 GGTATCAATACCCCTAT
242944 CAATACCTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
21 19 0.54
22 16 0.46
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.27
Consensus pattern (22 bp):
GGTATCAATACCCCTATAAATG
Found at i:242935 original size:22 final size:21
Alignment explanation
Indices: 242891--242943 Score: 79
Period size: 22 Copynumber: 2.5 Consensus size: 21
242881 AGAGGTATCG
* *
242891 ATACCCCTATGAATGGTATCA
1 ATACCCCTATAAATGGTACCA
242912 ATACCCCTATAAATGGGTACCA
1 ATACCCCTATAAAT-GGTACCA
242934 ATACCCCTAT
1 ATACCCCTAT
242944 CAATACCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.34, C:0.28, G:0.11, T:0.26
Consensus pattern (21 bp):
ATACCCCTATAAATGGTACCA
Found at i:242950 original size:34 final size:35
Alignment explanation
Indices: 242907--242978 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 35
242897 CTATGAATGG
*
242907 TATCAATACC-CCTATAAATGGGTACCAATACCCC
1 TATCAATACCTCCTATAAACGGGTACCAATACCCC
** * *
242941 TATCAATACCTTTTATGAACGGGTACCGATACCCC
1 TATCAATACCTCCTATAAACGGGTACCAATACCCC
242976 TAT
1 TAT
242979 GAATGTGTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
34 10 0.31
35 22 0.69
ACGTcount: A:0.32, C:0.29, G:0.11, T:0.28
Consensus pattern (35 bp):
TATCAATACCTCCTATAAACGGGTACCAATACCCC
Found at i:243456 original size:33 final size:33
Alignment explanation
Indices: 243419--243488 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
243409 TTTTGTACAG
* *
243419 GGGAAAGGTTCTAATTGAACCCGTGAAAAGCTA
1 GGGAAAAGTTCTAATTGAACCCGTGAAAAACTA
* * * *
243452 GGGAAAAGTTCTAGTTTAGCCTGTGAAAAACTA
1 GGGAAAAGTTCTAATTGAACCCGTGAAAAACTA
243485 GGGA
1 GGGA
243489 GTTTGTAAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.36, C:0.13, G:0.29, T:0.23
Consensus pattern (33 bp):
GGGAAAAGTTCTAATTGAACCCGTGAAAAACTA
Found at i:244491 original size:15 final size:14
Alignment explanation
Indices: 244464--244503 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
244454 ATGTTGAAGG
*
244464 AAGATGAAGAAAATA
1 AAGA-GAAGAAAAAA
244479 AAGAGAAGAAAAAA
1 AAGAGAAGAAAAAA
244493 AAGAAGAAGAA
1 AAG-AGAAGAA
244504 TGAGGTAGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (14 bp):
AAGAGAAGAAAAAA
Found at i:246175 original size:18 final size:19
Alignment explanation
Indices: 246152--246208 Score: 89
Period size: 18 Copynumber: 2.9 Consensus size: 19
246142 TATATTTTCC
246152 AACAATTGGTATCTTTTT-
1 AACAATTGGTATCTTTTTA
246170 AACAATTGGTATACTTTTGTA
1 AACAATTGGTAT-CTTTT-TA
246191 AACAATTGGTATCTTTTT
1 AACAATTGGTATCTTTTT
246209 CATTAAACAT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
18 12 0.33
19 6 0.17
20 6 0.17
21 12 0.33
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.47
Consensus pattern (19 bp):
AACAATTGGTATCTTTTTA
Found at i:246467 original size:22 final size:22
Alignment explanation
Indices: 246437--246541 Score: 86
Period size: 22 Copynumber: 4.7 Consensus size: 22
246427 ATACCCCTAT
246437 CAATACCCCTATGAATGGGTAC
1 CAATACCCCTATGAATGGGTAC
* * *** *
246459 CGATACCCCTATCAATACCCCTAT
1 CAATACCCCTATGAAT--GGGTAC
* *
246483 CAATACCTCTTATGAACGGGTAC
1 CAATACC-CCTATGAATGGGTAC
* *
246506 CGATACCCCTATGAATGGGTAT
1 CAATACCCCTATGAATGGGTAC
246528 CAATACCCC-ATGAA
1 CAATACCCCTATGAA
246542 GGCTCAAATT
Statistics
Matches: 61, Mismatches: 19, Indels: 7
0.70 0.22 0.08
Matches are distributed among these distances:
21 5 0.08
22 34 0.56
23 8 0.13
24 8 0.13
25 6 0.10
ACGTcount: A:0.31, C:0.30, G:0.14, T:0.24
Consensus pattern (22 bp):
CAATACCCCTATGAATGGGTAC
Found at i:246478 original size:12 final size:12
Alignment explanation
Indices: 246461--246489 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
246451 ATGGGTACCG
246461 ATACCCCTATCA
1 ATACCCCTATCA
246473 ATACCCCTATCA
1 ATACCCCTATCA
246485 ATACC
1 ATACC
246490 TCTTATGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.41, G:0.00, T:0.24
Consensus pattern (12 bp):
ATACCCCTATCA
Found at i:246999 original size:33 final size:34
Alignment explanation
Indices: 246955--247018 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 34
246945 TCTTTTGTAA
*
246955 AGGGAAAAGGTTATAGTTGATCCTGTGAAAAGCT
1 AGGGAAAAGGTTATAGTTGAGCCTGTGAAAAGCT
* * *
246989 AGGG-AAAGGTTCTTGTTTAGCCTGTGAAAA
1 AGGGAAAAGGTTATAGTTGAGCCTGTGAAAA
247019 AATATGGAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 22 0.85
34 4 0.15
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (34 bp):
AGGGAAAAGGTTATAGTTGAGCCTGTGAAAAGCT
Found at i:254446 original size:30 final size:31
Alignment explanation
Indices: 254410--254523 Score: 115
Period size: 31 Copynumber: 3.7 Consensus size: 31
254400 GGGCATGAGA
*
254410 GCCTACCCAAGAAAGTTCTC-GGGCCAGGAG
1 GCCTACCCAAGAAAGATCTCAGGGCCAGGAG
* * * *
254440 GCCTACCCAAGAAAGCTCTCGGGGCTACGAG
1 GCCTACCCAAGAAAGATCTCAGGGCCAGGAG
* * * *
254471 GCTTACCCAATAAAGATCTCAAGGCC-GTAGG
1 GCCTACCCAAGAAAGATCTCAGGGCCAGGA-G
*
254502 GCCTACCTAAGAAAGATCTCAG
1 GCCTACCCAAGAAAGATCTCAG
254524 TGTTGTAGAG
Statistics
Matches: 67, Mismatches: 15, Indels: 3
0.79 0.18 0.04
Matches are distributed among these distances:
30 20 0.30
31 47 0.70
ACGTcount: A:0.30, C:0.29, G:0.25, T:0.16
Consensus pattern (31 bp):
GCCTACCCAAGAAAGATCTCAGGGCCAGGAG
Found at i:255317 original size:22 final size:22
Alignment explanation
Indices: 255252--255317 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
255242 TTTCGATCAG
* *
255252 AGTCAACGATCATACCGGTCAA
1 AGTCAATGGTCATACCGGTCAA
*
255274 AGTCAATGGTC-TAATCGGTCAA
1 AGTCAATGGTCAT-ACCGGTCAA
* *
255296 GGTCAATGGTCATACCGATCAA
1 AGTCAATGGTCATACCGGTCAA
255318 TGGTTCAAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 1 0.03
22 34 0.94
23 1 0.03
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (22 bp):
AGTCAATGGTCATACCGGTCAA
Found at i:257740 original size:19 final size:19
Alignment explanation
Indices: 257716--257753 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
257706 TTATTAAGCC
*
257716 TATGTTAGTATAGAAATTT
1 TATGTTAATATAGAAATTT
257735 TATGTTAATATAGAAATTT
1 TATGTTAATATAGAAATTT
257754 GAGATGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.47
Consensus pattern (19 bp):
TATGTTAATATAGAAATTT
Found at i:258872 original size:23 final size:23
Alignment explanation
Indices: 258806--258885 Score: 82
Period size: 23 Copynumber: 3.7 Consensus size: 23
258796 AATAAATTGT
258806 CTTTATGATACATTTTTCTCTGC
1 CTTTATGATACATTTTTCTCTGC
* *
258829 C-TTATG-T--ATTCTTCTAT--
1 CTTTATGATACATTTTTCTCTGC
*
258846 CTTTATGATACGTTTTTCTCTGC
1 CTTTATGATACATTTTTCTCTGC
*
258869 CTTTATGACACATTTTT
1 CTTTATGATACATTTTT
258886 AGTCGTTTGA
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
17 1 0.02
18 5 0.11
19 9 0.20
21 8 0.18
22 5 0.11
23 16 0.36
ACGTcount: A:0.17, C:0.20, G:0.09, T:0.54
Consensus pattern (23 bp):
CTTTATGATACATTTTTCTCTGC
Found at i:259498 original size:25 final size:25
Alignment explanation
Indices: 259429--259502 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 25
259419 ATCTAAGTCC
* *
259429 AACTTTCCAAAATCAATTTTT-ACCA
1 AACTTTTCAAAATCAATTTTTGA-AA
* * * *
259454 CACTTTTTAAAATTATTTTTTGAAA
1 AACTTTTCAAAATCAATTTTTGAAA
*
259479 AACTTTTCAAAATC-ACTTTTGAAA
1 AACTTTTCAAAATCAATTTTTGAAA
259503 GTAATGCAAA
Statistics
Matches: 37, Mismatches: 11, Indels: 3
0.73 0.22 0.06
Matches are distributed among these distances:
24 8 0.22
25 28 0.76
26 1 0.03
ACGTcount: A:0.39, C:0.16, G:0.03, T:0.42
Consensus pattern (25 bp):
AACTTTTCAAAATCAATTTTTGAAA
Found at i:259759 original size:17 final size:18
Alignment explanation
Indices: 259716--259760 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
259706 ATTTTAGATT
259716 TTATATATTTCATAAAAA
1 TTATATATTTCATAAAAA
* *
259734 ATATATATTT-ATTAAAA
1 TTATATATTTCATAAAAA
*
259751 TTATTTATTT
1 TTATATATTT
259761 TCAGTAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
TTATATATTTCATAAAAA
Found at i:259792 original size:15 final size:16
Alignment explanation
Indices: 259774--259816 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
259764 GTAAATATTT
259774 TTTATTATATTTTA-A
1 TTTATTATATTTTATA
*
259789 TTTAATATATTTTATA
1 TTTATTATATTTTATA
*
259805 TGTTATAATATT
1 T-TTATTATATT
259817 AAAGAATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 13 0.57
16 2 0.09
17 8 0.35
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TTTATTATATTTTATA
Found at i:259818 original size:25 final size:25
Alignment explanation
Indices: 259767--259818 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
259757 ATTTTCAGTA
* *
259767 AATATTTTTTATTATATTTTAATTT
1 AATATATTTTATTATATTATAATTT
*
259792 AATATATTTTA-TATGTTATAATATT
1 AATATATTTTATTATATTATAAT-TT
259817 AA
1 AA
259819 AGAATTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (25 bp):
AATATATTTTATTATATTATAATTT
Found at i:260251 original size:18 final size:15
Alignment explanation
Indices: 260209--260246 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
260199 TAATAAGGTT
*
260209 ATTTATTTTAAAATA
1 ATTTATTATAAAATA
260224 ATTTATTATAAAATA
1 ATTTATTATAAAATA
260239 ATTTATTA
1 ATTTATTA
260247 GTATAGATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTATTATAAAATA
Found at i:260264 original size:22 final size:22
Alignment explanation
Indices: 260248--260454 Score: 81
Period size: 22 Copynumber: 8.0 Consensus size: 22
260238 AATTTATTAG
260248 TATAGATTGATTTATTTTAAAA
1 TATAGATTGATTTATTTTAAAA
*
260270 TATGGATTGATTTATTTTAAATAA
1 TATAGATTGATTTATTTT-AA-AA
*
260294 TTTATTAGTATAGATTGATTTATTTTAAAA
1 --TA-TAG-ATTGA-T---TTATTTTAAAA
*
260324 TATGGATTGATTTATTTTAAATTTTA
1 TATAGATTGATTTATTTTAAA----A
260350 TTAGTATGATTGATTTATTTTAAATAA
1 -TA-TA-GATTGATTTATTTT-AA-AA
*
260377 TTTATTAGTATGGATTGATTTATTTTAAAA
1 --TA-TAG-ATTGA-T---TTATTTTAAAA
*
260407 TATGGATTGATTTATTTTAAATAA
1 TATAGATTGATTTATTTT-AA-AA
260431 TTGTATAGATTGATTTATTTTAAA
1 ---TATAGATTGATTTATTTTAAA
260455 TAATTTATTT
Statistics
Matches: 144, Mismatches: 11, Indels: 57
0.68 0.05 0.27
Matches are distributed among these distances:
22 34 0.24
23 4 0.03
24 4 0.03
25 3 0.02
26 13 0.09
27 27 0.19
28 18 0.12
29 16 0.11
30 6 0.04
31 5 0.03
32 14 0.10
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
TATAGATTGATTTATTTTAAAA
Found at i:260295 original size:54 final size:54
Alignment explanation
Indices: 260224--260681 Score: 458
Period size: 54 Copynumber: 8.4 Consensus size: 54
260214 TTTTAAAATA
* *
260224 ATTTATTATAAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATT-TTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
260279 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
**
260333 ATTTATTTTAAAT--TTTATTAGTAT-GATTGATTTATTTT-AAATAATTTATTAG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAT-ATGGATT-G
** * ** * * * *
260385 TATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTTTAAATAATTGTATAGATTG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AA---TATGGATTG
*
260443 ATTTATTTTAAATAATTTATTTGTATGGATTGATTT-TTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
260496 ATTTATTTTAAATAATTTATTAGTATGGA-TGATTTATTTTAAATAATTTATTTGTATGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AA--TA--TG---GATTG
* * * * ***
260558 ATTTATTTT-AA-AA--TA-TAG-ATTGATTTATTAAATTTATTGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
260606 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
260660 ATTTATTTTAAATAATTTATTA
1 ATTTATTTTAAATAATTTATTA
260682 TTGTAGTTGT
Statistics
Matches: 335, Mismatches: 37, Indels: 63
0.77 0.09 0.14
Matches are distributed among these distances:
48 14 0.04
49 2 0.01
50 6 0.02
51 21 0.06
52 24 0.07
53 52 0.16
54 124 0.37
55 9 0.03
56 8 0.02
57 20 0.06
58 16 0.05
59 20 0.06
60 3 0.01
61 2 0.01
62 14 0.04
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:260312 original size:32 final size:30
Alignment explanation
Indices: 260274--260569 Score: 269
Period size: 31 Copynumber: 10.6 Consensus size: 30
260264 TTAAAATATG
260274 GATTGATTTATTTTAAATAATTTATTAGTAT
1 GATTGATTTATTTTAAATAATTTATT-GTAT
260305 AGATTGATTTATTTT-AA-AA--TA-TG---
1 -GATTGATTTATTTTAAATAATTTATTGTAT
260328 GATTGATTTATTTTAAAT--TTTATTAGTAT
1 GATTGATTTATTTTAAATAATTTATT-GTAT
260357 GATTGATTTATTTTAAATAATTTATTAGTAT
1 GATTGATTTATTTTAAATAATTTATT-GTAT
260388 GGATTGATTTATTTT-AA-AA--TA-TG---
1 -GATTGATTTATTTTAAATAATTTATTGTAT
260411 GATTGATTTATTTTAAAT-A---ATTGTAT
1 GATTGATTTATTTTAAATAATTTATTGTAT
260437 AGATTGATTTATTTTAAATAATTTATTTGTAT
1 -GATTGATTTATTTTAAATAATTTA-TTGTAT
260469 GGATTGATTT-TTTT-AA-AA--TA-TG---
1 -GATTGATTTATTTTAAATAATTTATTGTAT
260491 GATTGATTTATTTTAAATAATTTATTAGTAT
1 GATTGATTTATTTTAAATAATTTATT-GTAT
260522 GGA-TGATTTATTTTAAATAATTTATTTGTAT
1 -GATTGATTTATTTTAAATAATTTA-TTGTAT
260553 GATTGATTTATTTTAAA
1 GATTGATTTATTTTAAA
260570 ATATAGATTG
Statistics
Matches: 226, Mismatches: 1, Indels: 75
0.75 0.00 0.25
Matches are distributed among these distances:
21 9 0.04
22 33 0.15
23 9 0.04
24 4 0.02
25 3 0.01
26 5 0.02
27 23 0.10
28 6 0.03
29 20 0.09
30 8 0.04
31 59 0.26
32 47 0.21
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (30 bp):
GATTGATTTATTTTAAATAATTTATTGTAT
Found at i:260457 original size:164 final size:164
Alignment explanation
Indices: 260248--260681 Score: 699
Period size: 164 Copynumber: 2.7 Consensus size: 164
260238 AATTTATTAG
*
260248 TATAGATTGATTTATTTT-AA-AA---TATGGATTGATTTATTTTAAATAATTTATTAGTATAGA
1 TATAGATTGATTTATTTTAAATAATTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGA
260308 TTGATTTATTTTAAAATATGGATTGATTTATTTTAAAT-TTTATTAGTAT-GATTGATTTATTTT
66 TTGATTTATTTTAAAATATGGATTGATTTATTTTAAATATTTATTAGTATGGA-TGATTTATTTT
260371 AAATAATTTATTAGTATGGATTGATTTATTTTAAAA
130 AAATAATTTATTAGTAT-GATTGATTTATTTTAAAA
* * *
260407 TATGGATTGATTTATTTTAAATAATTGTATAGATTGATTTATTTTAAATAATTTATTTGTATGGA
1 TATAGATTGATTTATTTTAAATAATTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGA
260472 TTGATTT-TTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATGATTTATTTT
66 TTGATTTATTTTAAAATATGGATTGATTTATTTTAAAT-ATTTATTAGTATGGATGATTTATTTT
*
260536 AAATAATTTATTTGTATGATTGATTTATTTTAAAA
130 AAATAATTTATTAGTATGATTGATTTATTTTAAAA
*
260571 TATAGATTGATTTA--TTAAATTTATTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGG
1 TATAGATTGATTTATTTTAAA-TAATTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGG
260634 ATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
65 ATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAT-ATTTATTA
260682 TTGTAGTTGT
Statistics
Matches: 256, Mismatches: 9, Indels: 15
0.91 0.03 0.05
Matches are distributed among these distances:
159 17 0.07
160 2 0.01
161 2 0.01
162 5 0.02
163 78 0.30
164 112 0.44
165 38 0.15
166 2 0.01
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (164 bp):
TATAGATTGATTTATTTTAAATAATTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGA
TTGATTTATTTTAAAATATGGATTGATTTATTTTAAATATTTATTAGTATGGATGATTTATTTTA
AATAATTTATTAGTATGATTGATTTATTTTAAAA
Found at i:260490 original size:21 final size:22
Alignment explanation
Indices: 260466--260507 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
260456 AATTTATTTG
260466 TATGGATTGATTT-TTTTAAAA
1 TATGGATTGATTTATTTTAAAA
260487 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
260508 TAATTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.52
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:260515 original size:14 final size:14
Alignment explanation
Indices: 260496--260548 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
260486 ATATGGATTG
260496 ATTTATTTTAAATA
1 ATTTATTTTAAATA
** *
260510 ATTTATTAGTATGGATG
1 ATTTATT--T-TAAATA
260527 ATTTATTTTAAATA
1 ATTTATTTTAAATA
260541 ATTTATTT
1 ATTTATTT
260549 GTATGATTGA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
14 18 0.60
15 1 0.03
16 1 0.03
17 10 0.33
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:260615 original size:22 final size:21
Alignment explanation
Indices: 260542--260615 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 21
260532 TTTTAAATAA
260542 TTTATTTGTATGATTGATTTAT
1 TTTA-TTGTATGATTGATTTAT
***
260564 TTTAAAATATAGATTGATTTATT
1 TTTATTGTAT-GATTGATTTA-T
260587 AAATTTATTGTATGGATTGATTTAT
1 ---TTTATTGTAT-GATTGATTTAT
260612 TTTA
1 TTTA
260616 AATAATTTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
21 3 0.08
22 18 0.45
23 1 0.03
25 1 0.03
26 17 0.43
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.57
Consensus pattern (21 bp):
TTTATTGTATGATTGATTTAT
Found at i:260635 original size:32 final size:31
Alignment explanation
Indices: 260588--260649 Score: 115
Period size: 32 Copynumber: 2.0 Consensus size: 31
260578 TGATTTATTA
260588 AATTTATTGTATGGATTGATTTATTTTAAAT
1 AATTTATTGTATGGATTGATTTATTTTAAAT
260619 AATTTATTAGTATGGATTGATTTATTTTAAA
1 AATTTATT-GTATGGATTGATTTATTTTAAA
260650 ATATGGATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 8 0.27
32 22 0.73
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (31 bp):
AATTTATTGTATGGATTGATTTATTTTAAAT
Found at i:260654 original size:22 final size:22
Alignment explanation
Indices: 260629--260671 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
260619 AATTTATTAG
260629 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
260651 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
260672 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:262177 original size:2 final size:2
Alignment explanation
Indices: 262170--262197 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
262160 AAGATAAGTT
262170 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
262198 CCCCACTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:271598 original size:26 final size:26
Alignment explanation
Indices: 271562--271623 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
271552 TTTAACACGG
271562 AGGTGAATTTTTTGCAAGGGAAAAGA
1 AGGTGAATTTTTTGCAAGGGAAAAGA
271588 AGGTGAATTTTTTGCAAGGGAAAAGA
1 AGGTGAATTTTTTGCAAGGGAAAAGA
*
271614 AGTTGAATTT
1 AGGTGAATTT
271624 ATATGTATCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.37, C:0.03, G:0.29, T:0.31
Consensus pattern (26 bp):
AGGTGAATTTTTTGCAAGGGAAAAGA
Found at i:275888 original size:60 final size:59
Alignment explanation
Indices: 275806--275961 Score: 176
Period size: 60 Copynumber: 2.6 Consensus size: 59
275796 ATCGGTCCCT
275806 AAACTTTT-AA-ATGTTCTAATTTCATCCCTAAACTATGA-TTATAATTCTAAATTAGTCCTC
1 AAACTTTTGAACAT-TTC-AATTTCATCCC-AAACTATGACTT-TAATTCTAAATTAGTCCTC
** * * *
275866 AAACTTTTGAACATTTCAATTTCATCTCCAAGTTATGACTTTCATTCTAAATTGGTTCTC
1 AAACTTTTGAACATTTCAATTTCATC-CCAAACTATGACTTTAATTCTAAATTAGTCCTC
275926 AAACTTTTTGAAC-TTTCCAATTTCATCCCAAACTAT
1 AAAC-TTTTGAACATTT-CAATTTCATCCCAAACTAT
275962 AAGCATATAC
Statistics
Matches: 83, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
60 54 0.65
61 27 0.33
62 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.42
Consensus pattern (59 bp):
AAACTTTTGAACATTTCAATTTCATCCCAAACTATGACTTTAATTCTAAATTAGTCCTC
Found at i:281660 original size:24 final size:23
Alignment explanation
Indices: 281628--281681 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
281618 TAGTTTAAAA
* *
281628 TAAAAAT-AATTATATTTATATTT
1 TAAAAATAAATAATAATT-TATTT
281651 TATAAAATAAATAATAATTTATTT
1 TA-AAAATAAATAATAATTTATTT
281675 TAAAAAT
1 TAAAAAT
281682 TTAATTCATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 7 0.26
24 12 0.44
25 8 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TAAAAATAAATAATAATTTATTT
Found at i:281883 original size:12 final size:13
Alignment explanation
Indices: 281865--281895 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
281855 TACTTATTTA
281865 ATAATTAAAAATT
1 ATAATTAAAAATT
281878 -TAATTAAAAATT
1 ATAATTAAAAATT
281890 ATAATT
1 ATAATT
281896 TGTAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATAATTAAAAATT
Found at i:282331 original size:23 final size:21
Alignment explanation
Indices: 282292--282340 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 21
282282 TTGGTTGAAT
*
282292 AAAATTAATTAAATAATAATTTA
1 AAAATTAATGAAATAAT--TTTA
282315 AAAATTAA-GAAACTAATTTTA
1 AAAATTAATGAAA-TAATTTTA
282336 AAAAT
1 AAAAT
282341 GTCACGTCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 9 0.38
22 3 0.12
23 12 0.50
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
AAAATTAATGAAATAATTTTA
Found at i:282690 original size:18 final size:19
Alignment explanation
Indices: 282648--282695 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
282638 TATCATGATG
*
282648 ATCGAAAGAGTGGGTTGGG
1 ATCGAAAGAGTGGGTTGGA
282667 ATCGAAAGAGTGGGTT-GA
1 ATCGAAAGAGTGGGTTGGA
282685 ATCGAAAGAGT
1 ATCGAAAGAGT
282696 TTAAGTACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 12 0.43
19 16 0.57
ACGTcount: A:0.33, C:0.06, G:0.40, T:0.21
Consensus pattern (19 bp):
ATCGAAAGAGTGGGTTGGA
Found at i:285689 original size:29 final size:29
Alignment explanation
Indices: 285657--285720 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
285647 TTTCCAAAAA
285657 GTCACCTTTTTCAAAATAATTCCCAGAAT
1 GTCACCTTTTTCAAAATAATTCCCAGAAT
* *
285686 GTCACATTTTTCAAAATATTTCCCAGAAT
1 GTCACCTTTTTCAAAATAATTCCCAGAAT
285715 GTCACC
1 GTCACC
285721 GTTTCGGACG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.33, C:0.25, G:0.08, T:0.34
Consensus pattern (29 bp):
GTCACCTTTTTCAAAATAATTCCCAGAAT
Found at i:290831 original size:18 final size:18
Alignment explanation
Indices: 290808--290855 Score: 71
Period size: 19 Copynumber: 2.7 Consensus size: 18
290798 GTTTCGACCG
290808 GTTTTGACCGTTTGAACC
1 GTTTTGACCGTTTGAACC
*
290826 GTTTTGACCGGTCTGAACC
1 GTTTTGACC-GTTTGAACC
290845 GTTTT-ACCGTT
1 GTTTTGACCGTT
290856 CTGACCCGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 2 0.07
18 12 0.44
19 13 0.48
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.40
Consensus pattern (18 bp):
GTTTTGACCGTTTGAACC
Found at i:290858 original size:18 final size:19
Alignment explanation
Indices: 290808--290859 Score: 81
Period size: 18 Copynumber: 2.8 Consensus size: 19
290798 GTTTCGACCG
290808 GTTTTGACCGTT-TGAACC
1 GTTTTGACCGTTCTGAACC
*
290826 GTTTTGACCGGTCTGAACC
1 GTTTTGACCGTTCTGAACC
290845 GTTTT-ACCGTTCTGA
1 GTTTTGACCGTTCTGA
290860 CCCGACTCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 20 0.65
19 11 0.35
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (19 bp):
GTTTTGACCGTTCTGAACC
Found at i:290881 original size:9 final size:9
Alignment explanation
Indices: 290858--290887 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
290848 TTACCGTTCT
290858 GACCCGACTC
1 GACCCGAC-C
290868 GACCCGACC
1 GACCCGACC
290877 GACCCGACC
1 GACCCGACC
290886 GA
1 GA
290888 TCGTTGACTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.60
10 8 0.40
ACGTcount: A:0.23, C:0.50, G:0.23, T:0.03
Consensus pattern (9 bp):
GACCCGACC
Found at i:292114 original size:23 final size:23
Alignment explanation
Indices: 292087--292133 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
292077 CTTTCGAAAA
292087 TGTTTTCCCTCTTTCAGATACTG
1 TGTTTTCCCTCTTTCAGATACTG
292110 TGTTTTCCCTCTTTCAGATACTG
1 TGTTTTCCCTCTTTCAGATACTG
292133 T
1 T
292134 TGGTTAGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.13, C:0.26, G:0.13, T:0.49
Consensus pattern (23 bp):
TGTTTTCCCTCTTTCAGATACTG
Found at i:298163 original size:9 final size:9
Alignment explanation
Indices: 298149--298237 Score: 61
Period size: 9 Copynumber: 9.3 Consensus size: 9
298139 GCTGCTGAAA
298149 ACCGGTTTG
1 ACCGGTTTG
*
298158 ACCGGTTTTCA
1 ACCGG-TTT-G
298169 ACCGGTTTG
1 ACCGGTTTG
298178 ACCGGTTTTG
1 ACCGG-TTTG
* *
298188 ATCGGTTCG
1 ACCGGTTTG
* *
298197 AACCGTTTTA
1 -ACCGGTTTG
* *
298207 ACCGATCTG
1 ACCGGTTTG
298216 AACCGGTTTG
1 -ACCGGTTTG
*
298226 ACCGGTCTG
1 ACCGGTTTG
298235 ACC
1 ACC
298238 CGACCCGACC
Statistics
Matches: 61, Mismatches: 14, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
9 30 0.49
10 26 0.43
11 5 0.08
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.31
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:298173 original size:20 final size:20
Alignment explanation
Indices: 298148--298186 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
298138 TGCTGCTGAA
298148 AACCGGTTTGACCGGTTTTC
1 AACCGGTTTGACCGGTTTTC
298168 AACCGGTTTGACCGGTTTT
1 AACCGGTTTGACCGGTTTT
298187 GATCGGTTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.23, G:0.26, T:0.36
Consensus pattern (20 bp):
AACCGGTTTGACCGGTTTTC
Found at i:298193 original size:10 final size:10
Alignment explanation
Indices: 298149--298194 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
298139 GCTGCTGAAA
298149 ACCGG-TTTG
1 ACCGGTTTTG
*
298158 ACCGGTTTTCA
1 ACCGGTTTT-G
298169 ACCGG-TTTG
1 ACCGGTTTTG
298178 ACCGGTTTTG
1 ACCGGTTTTG
*
298188 ATCGGTT
1 ACCGGTT
298195 CGAACCGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
9 10 0.32
10 16 0.52
11 5 0.16
ACGTcount: A:0.13, C:0.22, G:0.28, T:0.37
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:298218 original size:19 final size:19
Alignment explanation
Indices: 298196--298235 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
298186 TGATCGGTTC
*
298196 GAACCGTTTTAACCGATCT
1 GAACCGGTTTAACCGATCT
* *
298215 GAACCGGTTTGACCGGTCT
1 GAACCGGTTTAACCGATCT
298234 GA
1 GA
298236 CCCGACCCGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (19 bp):
GAACCGGTTTAACCGATCT
Found at i:298264 original size:7 final size:7
Alignment explanation
Indices: 298252--298287 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
298242 CCGACCCGAT
298252 CGTTGAC
1 CGTTGAC
298259 CGTTGAC
1 CGTTGAC
*
298266 TGTTGAC
1 CGTTGAC
*
298273 TGTTGAC
1 CGTTGAC
298280 CGTTGAC
1 CGTTGAC
298287 C
1 C
298288 AAAACTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.14, C:0.25, G:0.28, T:0.33
Consensus pattern (7 bp):
CGTTGAC
Found at i:301544 original size:32 final size:31
Alignment explanation
Indices: 301506--301582 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
301496 CGGGGCTATG
*
301506 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** ** *
301538 GGGCCTACCCGAGAATGATCTCAGGGCCGTA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
301569 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
301583 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:302497 original size:29 final size:29
Alignment explanation
Indices: 302456--302560 Score: 147
Period size: 29 Copynumber: 3.6 Consensus size: 29
302446 CACATTCGAA
*
302456 AATTCCTAAAATGTCACCTTTTTTAAAAT
1 AATTCCTAGAATGTCACCTTTTTTAAAAT
*
302485 AATTCCTAGAATGTCACCTTTTTCAAAAT
1 AATTCCTAGAATGTCACCTTTTTTAAAAT
* *
302514 ATTTCCTAGATTGTCACCTTTTTTAAAAT
1 AATTCCTAGAATGTCACCTTTTTTAAAAT
* * *
302543 ATTTCCCAGAATATCACC
1 AATTCCTAGAATGTCACC
302561 CAGTCAGGTC
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 68 1.00
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.40
Consensus pattern (29 bp):
AATTCCTAGAATGTCACCTTTTTTAAAAT
Found at i:307615 original size:47 final size:47
Alignment explanation
Indices: 307564--307872 Score: 516
Period size: 47 Copynumber: 6.6 Consensus size: 47
307554 TGTATTAACA
*
307564 CATCCATTT-ATGCATTTT-AATTTATGTCATCCTTTCATGCCTTAATG
1 CATCC-TTTCATGCATTTTCAA-TTATGGCATCCTTTCATGCCTTAATG
307611 CATCCTTTCATGCATTTTCAATTATGGCATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCTTTCATGCCTTAATG
* *
307658 CATCCTTTCATGCATTTTCAAATATTGCATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCTTTCATGCCTTAATG
307705 CATCCTTTCATGCATTTTCAATTATGGCATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCTTTCATGCCTTAATG
*
307752 CATCCTTTCATGCATTTTCAATTACGGCATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCTTTCATGCCTTAATG
* *
307799 CATCCTTTCATGCATTGTCAATTATGACATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCTTTCATGCCTTAATG
307846 CATCCTTTCATGCATTTT-AATTTATGG
1 CATCCTTTCATGCATTTTCAA-TTATGG
307873 ATTCGATTTG
Statistics
Matches: 248, Mismatches: 11, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
46 5 0.02
47 241 0.97
48 2 0.01
ACGTcount: A:0.22, C:0.25, G:0.10, T:0.43
Consensus pattern (47 bp):
CATCCTTTCATGCATTTTCAATTATGGCATCCTTTCATGCCTTAATG
Found at i:310507 original size:8 final size:8
Alignment explanation
Indices: 310491--310524 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
310481 TACAGATAAG
310491 TAATTAAA
1 TAATTAAA
*
310499 TAGTTAAA
1 TAATTAAA
310507 TAATTAAA
1 TAATTAAA
310515 TAATTAAA
1 TAATTAAA
310523 TA
1 TA
310525 TATAAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (8 bp):
TAATTAAA
Found at i:311326 original size:19 final size:20
Alignment explanation
Indices: 311299--311336 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
311289 TTAGGGTTGA
311299 GAGACGGGAGA-GCAGAGAG
1 GAGACGGGAGAGGCAGAGAG
*
311318 GAGATGGGAGAGGCAGAGA
1 GAGACGGGAGAGGCAGAGA
311337 ACGGCGAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.37, C:0.08, G:0.53, T:0.03
Consensus pattern (20 bp):
GAGACGGGAGAGGCAGAGAG
Found at i:313799 original size:16 final size:16
Alignment explanation
Indices: 313773--313810 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
313763 TCTACTAAAG
313773 CATGATTGGGTAGATAT
1 CATG-TTGGGTAGATAT
313790 CATGTTGGGTAGATAT
1 CATGTTGGGTAGATAT
313806 CATGT
1 CATGT
313811 GAATAAGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.26, C:0.08, G:0.29, T:0.37
Consensus pattern (16 bp):
CATGTTGGGTAGATAT
Found at i:323799 original size:8 final size:8
Alignment explanation
Indices: 323786--323838 Score: 67
Period size: 8 Copynumber: 6.9 Consensus size: 8
323776 AAAATGAGTG
323786 AAAAAATA
1 AAAAAATA
323794 AAAAAATA
1 AAAAAATA
323802 AAAAAAT-
1 AAAAAATA
323809 -AAAAAT-
1 AAAAAATA
323815 AAAAAATGA
1 AAAAAAT-A
*
323824 AAAAAATG
1 AAAAAATA
323832 AAAAAAT
1 AAAAAAT
323839 GAGGGTTCAA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
6 6 0.15
7 6 0.15
8 22 0.54
9 7 0.17
ACGTcount: A:0.83, C:0.00, G:0.04, T:0.13
Consensus pattern (8 bp):
AAAAAATA
Found at i:323812 original size:22 final size:23
Alignment explanation
Indices: 323787--323836 Score: 77
Period size: 22 Copynumber: 2.2 Consensus size: 23
323777 AAATGAGTGA
323787 AAAAATAAAAAAAT-AAAAAAAT-
1 AAAAATAAAA-AATGAAAAAAATG
323809 AAAAATAAAAAATGAAAAAAATG
1 AAAAATAAAAAATGAAAAAAATG
323832 AAAAA
1 AAAAA
323837 ATGAGGGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 3 0.12
22 18 0.69
23 5 0.19
ACGTcount: A:0.84, C:0.00, G:0.04, T:0.12
Consensus pattern (23 bp):
AAAAATAAAAAATGAAAAAAATG
Found at i:325230 original size:221 final size:220
Alignment explanation
Indices: 324844--325427 Score: 1012
Period size: 221 Copynumber: 2.6 Consensus size: 220
324834 CAACGATTGT
324844 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAAGGGGGCAGACACGATTGTTGAAGATTG
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAAT-AGGGGGCAGACACGATTGTTGAAGATTG
* * *
324909 TTCGAGTCTTATACTCTCTGAAGAAATAAGGGGCAGACGCAATCAGTGAAGATTGTTCGAGTCTT
65 TTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCAGTAAAGATTGTTCGAGTCTT
324974 ATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTG
130 ATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTG
325039 AAGAAATAGGGGGCAGACGCGATCAG
195 AAGAAATAGGGGGCAGACGCGATCAG
325065 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGGCAGACACGATTGTTGAA-AGTT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATA-GGGGGCAGACACGATTGTTGAAGA-TT
325129 GTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCAGTAAAGATTGTTCGAGTCT
64 GTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCAGTAAAGATTGTTCGAGTCT
*
325194 TATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGAAGATTGTTCGAGTCTTATACTCTCT
129 TATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCT
325259 GAAGAAATAGGGGGCAGACGCGATCAG
194 GAAGAAATAGGGGGCAGACGCGATCAG
* *
325286 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCAG-TGAAGATTG
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGAT-TGTTGAAGATTG
* * * *
325350 TTCGAGTCTTATACTCTCTGAAGAAATAGGAGGCATATGCGAT-TGTTAAAGATTGTTCGAGTCT
65 TTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCAG-TAAAGATTGTTCGAGTCT
325414 TATACTCTCTGAAG
129 TATACTCTCTGAAG
325428 GACTAGAGAA
Statistics
Matches: 348, Mismatches: 10, Indels: 11
0.94 0.03 0.03
Matches are distributed among these distances:
219 1 0.00
220 95 0.27
221 252 0.72
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.28
Consensus pattern (220 bp):
TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGATTGT
TCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCAGTAAAGATTGTTCGAGTCTTA
TACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
AGAAATAGGGGGCAGACGCGATCAG
Found at i:325445 original size:55 final size:55
Alignment explanation
Indices: 324837--325427 Score: 933
Period size: 55 Copynumber: 10.7 Consensus size: 55
324827 GGTTTCCCAA
*
324837 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAAGGGGGCAGACA
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAAT-AGGGGGCAGACG
*
324893 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAAGGGGCAGACG
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * *
324948 CAATCAG-TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACA
1 CGAT-TGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
325003 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* *
325058 CGATCAG-TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGGCAGACA
1 CGAT-TGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATA-GGGGGCAGACG
325114 CGATTGTTGAA-AGTTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
1 CGATTGTTGAAGA-TTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* *
325169 CGATCAG-TAAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
1 CGAT-TGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
325224 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
*
325279 CGATCAG-TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
1 CGAT-TGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * * *
325334 CGATCAG-TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGAGGCATATG
1 CGAT-TGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
*
325389 CGATTGTTAAAGATTGTTCGAGTCTTATACTCTCTGAAG
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAG
325428 GACTAGAGAA
Statistics
Matches: 501, Mismatches: 23, Indels: 23
0.92 0.04 0.04
Matches are distributed among these distances:
54 3 0.01
55 401 0.80
56 97 0.19
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.28
Consensus pattern (55 bp):
CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
Found at i:325754 original size:2 final size:2
Alignment explanation
Indices: 325747--325786 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
325737 GTAGTTATTA
325747 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
325787 GCGGATAAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:325812 original size:8 final size:8
Alignment explanation
Indices: 325796--325829 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
325786 TGCGGATAAG
325796 TAATTAAA
1 TAATTAAA
*
325804 TAGTTAAA
1 TAATTAAA
325812 TAATTAAA
1 TAATTAAA
325820 TAATTAAA
1 TAATTAAA
325828 TA
1 TA
325830 TATAAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (8 bp):
TAATTAAA
Found at i:326860 original size:19 final size:20
Alignment explanation
Indices: 326833--326870 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
326823 TTAGGGTTGA
326833 GAGACGGGAGA-GCAGAGAG
1 GAGACGGGAGAGGCAGAGAG
*
326852 GAGATGGGAGAGGCAGAGA
1 GAGACGGGAGAGGCAGAGA
326871 ACGGCGAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.37, C:0.08, G:0.53, T:0.03
Consensus pattern (20 bp):
GAGACGGGAGAGGCAGAGAG
Found at i:327639 original size:2 final size:2
Alignment explanation
Indices: 327632--327656 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
327622 ATGTATAGAG
327632 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 T
327657 TTTATAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:328087 original size:36 final size:36
Alignment explanation
Indices: 328040--328112 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
328030 TCGAATATTC
328040 TTTATCTTTCTAATGACTTGGTAATTTTAAATTAAA
1 TTTATCTTTCTAATGACTTGGTAATTTTAAATTAAA
328076 TTTATCTTTCTAATGACTTGGTAATTTTAAATTAAA
1 TTTATCTTTCTAATGACTTGGTAATTTTAAATTAAA
328112 T
1 T
328113 CTATTTTGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.51
Consensus pattern (36 bp):
TTTATCTTTCTAATGACTTGGTAATTTTAAATTAAA
Found at i:329535 original size:2 final size:2
Alignment explanation
Indices: 329528--329573 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
329518 TACATACATG
* * * *
329528 AT AT AT AT AT AT AC AC AC AC 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
329570 AT AT
1 AT AT
329574 TGTCAGAACT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:333960 original size:24 final size:24
Alignment explanation
Indices: 333931--333976 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
333921 TTATCCTTGA
333931 ATGAAATGTTGGATTCCTTGCTGC
1 ATGAAATGTTGGATTCCTTGCTGC
333955 ATGAAATGTTGGATTCCTTGCT
1 ATGAAATGTTGGATTCCTTGCT
333977 AGATGCAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (24 bp):
ATGAAATGTTGGATTCCTTGCTGC
Found at i:338172 original size:6 final size:6
Alignment explanation
Indices: 338158--338208 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
338148 GATGTCTCAG
* ** * *
338158 AGAGAA AGAGGA AGAGGA AGAGGA AGAGTT TGAGGA AGAGGT AGAGGA
1 AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA
338206 AGA
1 AGA
338209 AATCAACTTG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.45, T:0.08
Consensus pattern (6 bp):
AGAGGA
Found at i:343311 original size:21 final size:20
Alignment explanation
Indices: 343286--343353 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
343276 AGTCGAGGGT
343286 TATATGTGGTCTTTCAGGACA
1 TATATGTGGTCTTT-AGGACA
**
343307 TATATGTAATCCTTT-GGAACA
1 TATATGTGGT-CTTTAGG-ACA
*
343328 TATATGCGGTTCTTTAGGACA
1 TATATGTGG-TCTTTAGGACA
343349 TATAT
1 TATAT
343354 TTTGGTCCTT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
20 2 0.05
21 29 0.76
22 7 0.18
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (20 bp):
TATATGTGGTCTTTAGGACA
Found at i:344320 original size:2 final size:2
Alignment explanation
Indices: 344283--344309 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
344273 AATTTTGTTA
344283 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 A
344310 GGAAATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:346701 original size:16 final size:17
Alignment explanation
Indices: 346670--346702 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
346660 GCCACCATAG
*
346670 TCTCGAATATAAATTAA
1 TCTCAAATATAAATTAA
346687 TCTCAAATA-AAATTAA
1 TCTCAAATATAAATTAA
346703 GAGAACCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.12, G:0.03, T:0.33
Consensus pattern (17 bp):
TCTCAAATATAAATTAA
Found at i:349697 original size:21 final size:21
Alignment explanation
Indices: 349673--349714 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
349663 TCAATCTTGC
*
349673 GGGATAAACGAATAGGGTTGT
1 GGGATAAACAAATAGGGTTGT
349694 GGGATAAACAAATAGGGTTGT
1 GGGATAAACAAATAGGGTTGT
349715 CAAGTAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.36, T:0.24
Consensus pattern (21 bp):
GGGATAAACAAATAGGGTTGT
Found at i:352453 original size:16 final size:16
Alignment explanation
Indices: 352404--352453 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
352394 TTTAAGGACT
*
352404 AAATTG-AATACATATA
1 AAATTGAAATAAAT-TA
* *
352420 AAAGTGAAAT-ACTTA
1 AAATTGAAATAAATTA
352435 AAATTGAAATAAATTA
1 AAATTGAAATAAATTA
352451 AAA
1 AAA
352454 ACACAAAAGG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
15 11 0.41
16 13 0.48
17 3 0.11
ACGTcount: A:0.60, C:0.04, G:0.08, T:0.28
Consensus pattern (16 bp):
AAATTGAAATAAATTA
Found at i:352560 original size:14 final size:15
Alignment explanation
Indices: 352541--352631 Score: 59
Period size: 18 Copynumber: 6.1 Consensus size: 15
352531 AAATTTAAAA
352541 AATATAA-TATATAT
1 AATATAACTATATAT
*
352555 AATATAAGT-T-TAT
1 AATATAACTATATAT
352568 -ATATAACTATATAT
1 AATATAACTATATAT
352582 -ATA-AACTATATTTAT
1 AATATAACTATA--TAT
*
352597 ATTATAAACTATATAATT
1 AATAT-AACTATAT-A-T
*
352615 ATTATAAGCTATATAT
1 AATATAA-CTATATAT
352631 A
1 A
352632 TAAATTAGGT
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
12 7 0.11
13 11 0.17
14 14 0.22
15 4 0.06
16 5 0.08
17 4 0.06
18 19 0.30
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (15 bp):
AATATAACTATATAT
Found at i:352573 original size:12 final size:12
Alignment explanation
Indices: 352550--352670 Score: 61
Period size: 13 Copynumber: 9.5 Consensus size: 12
352540 AAATATAATA
*
352550 TATATAATATAAG
1 TATAT-ATATAAC
*
352563 TTTATATATAAC
1 TATATATATAAC
352575 TATATATATAAAC
1 TATATATAT-AAC
*
352588 TATATTTATATTA-
1 TATA--TATATAAC
*
352601 TAAACTATATAA-
1 TATA-TATATAAC
352613 T-TAT-TATAAGC
1 TATATATATAA-C
*
352624 TATATATATAAAT
1 TATATATAT-AAC
*
352637 TAGGTTTATATGAAC
1 TA--TATATAT-AAC
352652 TATATATATAAAC
1 TATATATAT-AAC
352665 TATATA
1 TATATA
352671 CGTACAAACT
Statistics
Matches: 84, Mismatches: 14, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
9 5 0.06
10 1 0.01
11 2 0.02
12 24 0.29
13 34 0.40
14 3 0.04
15 15 0.18
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (12 bp):
TATATATATAAC
Found at i:352590 original size:13 final size:13
Alignment explanation
Indices: 352565--352670 Score: 71
Period size: 13 Copynumber: 8.3 Consensus size: 13
352555 AATATAAGTT
352565 TATATAT-AACTA
1 TATATATAAACTA
352577 TATATATAAACTA
1 TATATATAAACTA
* *
352590 TAT-T-TATATTA
1 TATATATAAACTA
*
352601 TAAACTATATAA-T-
1 TATA-TATA-AACTA
*
352614 TAT-TATAAGCTA
1 TATATATAAACTA
*
352626 TATATATAAATTA
1 TATATATAAACTA
* *
352639 GGTTTATATGAACTA
1 --TATATATAAACTA
352654 TATATATAAACTA
1 TATATATAAACTA
352667 TATA
1 TATA
352671 CGTACAAACT
Statistics
Matches: 71, Mismatches: 13, Indels: 19
0.69 0.13 0.18
Matches are distributed among these distances:
10 1 0.01
11 12 0.17
12 11 0.15
13 33 0.46
14 3 0.04
15 11 0.15
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (13 bp):
TATATATAAACTA
Done.