Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008372.1 Hibiscus syriacus cultivar Beakdansim tig00111128_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: 1214897
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:369281 original size:42 final size:41
Alignment explanation
Indices: 369222--369344 Score: 140
Period size: 42 Copynumber: 2.9 Consensus size: 41
369212 GTGAATCGGG
*
369222 CTCTTGAACGGTGGGAGGGACC-CATTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGG-CCTC-TTGAACGATGACAGGAGC
* * *
369264 CTCTTGAACGGTGGGAGGGGCCTCTTGAACAATGAGATGAGC
1 CTCTTGAACGGTGGGA-GGGCCTCTTGAACGATGACAGGAGC
* * *
369306 CTCTTAAACGATAGGAGGCGCCTCTTGAACGATGACAGG
1 CTCTTGAACGGTGGGAGG-GCCTCTTGAACGATGACAGG
369345 TGAATCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 2 0.03
42 62 0.91
43 4 0.06
ACGTcount: A:0.25, C:0.21, G:0.34, T:0.20
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGCCTCTTGAACGATGACAGGAGC
Found at i:369646 original size:21 final size:21
Alignment explanation
Indices: 369622--369671 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
369612 TAAAACAATC
*
369622 TCACGTAGAGCAGCTACCTCA
1 TCACGTAGAGCAGATACCTCA
*
369643 TCACGTAGAGTAGATACCTCA
1 TCACGTAGAGCAGATACCTCA
369664 TCACGTAG
1 TCACGTAG
369672 CACACCATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (21 bp):
TCACGTAGAGCAGATACCTCA
Found at i:372154 original size:60 final size:60
Alignment explanation
Indices: 372006--372253 Score: 231
Period size: 60 Copynumber: 4.1 Consensus size: 60
371996 AATAAAATTT
* * * *
372006 GCGTTGCAAATTTGACTTTTGTGTTGCGAATTT-GAAATTCAGTGTTGTGAATTTGAC-TA-TC
1 GCGTTGCAAATTTGACTTCTGTGTTGCG-ATTTACAAATTC-GCGTTGCG-ATTT-ACATATTC
* *
372067 GCGTTGCAAATTTGACTTCTGTATTGCGATTTACAAATTCGCGTTGCGATTTACAGATTC
1 GCGTTGCAAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGCGATTTACATATTC
* * * * * *
372127 GCATTGCCAATTTGACTTCAGTGTTGCGAATTTGAC-TA-TCGCATTGCGAATTTGACTTA-T-
1 GCGTTGCAAATTTGACTTCTGTGTTGCG-ATTT-ACAAATTCGCGTTGCG-ATTT-ACATATTC
* * * *
372187 GTGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTTGCGTTCCGATTTACATATTC
1 GCGTTGCAAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGCGATTTACATATTC
372247 GCGTTGC
1 GCGTTGC
372254 GACTTTGGAA
Statistics
Matches: 152, Mismatches: 24, Indels: 23
0.76 0.12 0.12
Matches are distributed among these distances:
58 8 0.05
59 15 0.10
60 82 0.54
61 42 0.28
62 5 0.03
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.40
Consensus pattern (60 bp):
GCGTTGCAAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGCGATTTACATATTC
Found at i:372214 original size:20 final size:19
Alignment explanation
Indices: 372008--372215 Score: 127
Period size: 20 Copynumber: 10.4 Consensus size: 19
371998 TAAAATTTGC
* *
372008 GTTGCAAATTTGACTTTTGT
1 GTTGCGAATTTGAC-TTCGT
*
372028 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTG-ACTTC-GT
* *
372049 GTTGTGAATTTGACTATCGC
1 GTTGCGAATTTGACT-TCGT
*
372069 GTTGCAAATTTGACTTCTGT
1 GTTGCGAATTTGACTTC-GT
* *
372089 ATTGCG-ATTT-ACAAATTCGC
1 GTTGCGAATTTGAC---TTCGT
*
372109 GTTGCG-ATTT-ACAGATTCGC
1 GTTGCGAATTTGAC---TTCGT
* *
372129 ATTGCCAATTTGACTTCAGT
1 GTTGCGAATTTGACTTC-GT
*
372149 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACT-TCGT
* *
372169 ATTGCGAATTTGACTTATGT
1 GTTGCGAATTTGACTT-CGT
372189 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTC-GT
372209 GTTGCGA
1 GTTGCGA
372216 TTTACAAATT
Statistics
Matches: 150, Mismatches: 25, Indels: 26
0.75 0.12 0.13
Matches are distributed among these distances:
18 2 0.01
19 10 0.07
20 111 0.74
21 25 0.17
22 2 0.01
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.40
Consensus pattern (19 bp):
GTTGCGAATTTGACTTCGT
Found at i:372238 original size:20 final size:20
Alignment explanation
Indices: 372213--372251 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
372203 TTCTGTGTTG
*
372213 CGATTTACAAATTTGCGTTC
1 CGATTTACAAATTCGCGTTC
*
372233 CGATTTACATATTCGCGTT
1 CGATTTACAAATTCGCGTT
372252 GCGACTTTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (20 bp):
CGATTTACAAATTCGCGTTC
Found at i:372295 original size:120 final size:120
Alignment explanation
Indices: 372054--372300 Score: 293
Period size: 120 Copynumber: 2.1 Consensus size: 120
372044 TCAGTGTTGT
*
372054 GAATTTGACTATCGCGTTGCAAATTTGACTTCTGTATTGCGATTTACAAATTCGCGTTGCGATTT
1 GAATTTGACTATCGCGTTGCAAATTTGACTTCTGTATTGCGATTTACAAATTCGCGTTCCGATTT
** * * *
372119 ACAGATTCGCATTGCCAATTTGACTTCAGTGTTGCGAATTTGACTATCGCATTGC
66 ACAGATTCGCATTGCCAATTTGACAACAGGGTTGCGAATTGGACTATCGCACTGC
* * * *
372174 GAATTTGACTTAT-GTGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTTGCGTTCCGATT
1 GAATTTGAC-TATCGCGTTGCAAATTTGACTTCTGTATTGCGATTTACAAATTCGCGTTCCGATT
* * * * * * *
372238 TACATATTCGCGTTGCGACTTTGGA-AACTGGGTTGCGAAATTGGAGT-TCGCGCTGC
65 TACAGATTCGCATTGCCAATTT-GACAACAGGGTTGCG-AATTGGACTATCGCACTGC
372294 GAATTTG
1 GAATTTG
372301 TTGGTCATTT
Statistics
Matches: 107, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
120 95 0.89
121 12 0.11
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (120 bp):
GAATTTGACTATCGCGTTGCAAATTTGACTTCTGTATTGCGATTTACAAATTCGCGTTCCGATTT
ACAGATTCGCATTGCCAATTTGACAACAGGGTTGCGAATTGGACTATCGCACTGC
Found at i:373751 original size:358 final size:358
Alignment explanation
Indices: 373094--373808 Score: 1394
Period size: 358 Copynumber: 2.0 Consensus size: 358
373084 CAATTACGTG
373094 GAATTAATTATTGTTGAACTTGAACTGGTTGTGATAAAAAGGTCAGTAAACTGAATAAGACTCAA
1 GAATTAATTATTGTTGAACTTGAACTGGTTGTGATAAAAAGGTCAGTAAACTGAATAAGACTCAA
373159 ATGACTCCTATAAGAAATTGGAAGATCGATAATAAATTCAAGTTCAGTGATTAATCAGTAAATCA
66 ATGACTCCTATAAGAAATTGGAAGATCGATAATAAATTCAAGTTCAGTGATTAATCAGTAAATCA
373224 ATTGACCTTAAGATTTGTAATTCTGATTACTTTTGTTAAATGCTAGATGTTGGAATGCTCGGATA
131 ATTGACCTTAAGATTTGTAATTCTGATTACTTTTGTTAAATGCTAGATGTTGGAATGCTCGGATA
373289 AAAAAATTACAAAAATATCATATGTGGTAAAATTATGAAAATGTCTTGTACTGTAAAAAAGACAA
196 AAAAAATTACAAAAATATCATATGTGGTAAAATTATGAAAATGTCTTGTACTGTAAAAAAGACAA
373354 GACTGTCCCTGAAAGTGAGAAAAACCTGAAAAGTCATACTCGATTCAATAAAACTATCGTTTCAC
261 GACTGTCCCTGAAAGTGAGAAAAACCTGAAAAGTCATACTCGATTCAATAAAACTATCGTTTCAC
373419 CTATTAAATTTTCGATCGATTTAAAGAAACCTA
326 CTATTAAATTTTCGATCGATTTAAAGAAACCTA
*
373452 GAATTAATTATTGTTGAACTTGAATTGGTTGTGATAAAAAGGTCAGTAAACTGAATAAGACTCAA
1 GAATTAATTATTGTTGAACTTGAACTGGTTGTGATAAAAAGGTCAGTAAACTGAATAAGACTCAA
373517 ATGACTCCTATAAGAAATTGGAAGATCGATAATAAATTCAAGTTCAGTGATTAATCAGTAAATCA
66 ATGACTCCTATAAGAAATTGGAAGATCGATAATAAATTCAAGTTCAGTGATTAATCAGTAAATCA
373582 ATTGACCTTAAGATTTGTAATTCTGATTACTTTTGTTAAATGCTAGATGTTGGAATGCTCGGATA
131 ATTGACCTTAAGATTTGTAATTCTGATTACTTTTGTTAAATGCTAGATGTTGGAATGCTCGGATA
*
373647 AAAAAATTACAAAAATATCATATGTGGTACAATTATGAAAATGTCTTGTACTGTAAAAAAGACAA
196 AAAAAATTACAAAAATATCATATGTGGTAAAATTATGAAAATGTCTTGTACTGTAAAAAAGACAA
* *
373712 GATTGTCCTTGAAAGTGAGAAAAACCTGAAAAGTCATACTCGATTCAATAAAACTATCGTTTCAC
261 GACTGTCCCTGAAAGTGAGAAAAACCTGAAAAGTCATACTCGATTCAATAAAACTATCGTTTCAC
373777 CTATTAAATTTTCGATCGATTTAAAGAAACCT
326 CTATTAAATTTTCGATCGATTTAAAGAAACCT
373809 TGATAATAAT
Statistics
Matches: 353, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
358 353 1.00
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (358 bp):
GAATTAATTATTGTTGAACTTGAACTGGTTGTGATAAAAAGGTCAGTAAACTGAATAAGACTCAA
ATGACTCCTATAAGAAATTGGAAGATCGATAATAAATTCAAGTTCAGTGATTAATCAGTAAATCA
ATTGACCTTAAGATTTGTAATTCTGATTACTTTTGTTAAATGCTAGATGTTGGAATGCTCGGATA
AAAAAATTACAAAAATATCATATGTGGTAAAATTATGAAAATGTCTTGTACTGTAAAAAAGACAA
GACTGTCCCTGAAAGTGAGAAAAACCTGAAAAGTCATACTCGATTCAATAAAACTATCGTTTCAC
CTATTAAATTTTCGATCGATTTAAAGAAACCTA
Found at i:379752 original size:11 final size:11
Alignment explanation
Indices: 379736--379763 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
379726 GCCTTTTCAG
379736 GCTTGGCTCAA
1 GCTTGGCTCAA
379747 GCTTGGCTCAA
1 GCTTGGCTCAA
379758 GCTTGG
1 GCTTGG
379764 AACCAGCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.14, C:0.25, G:0.32, T:0.29
Consensus pattern (11 bp):
GCTTGGCTCAA
Found at i:386320 original size:18 final size:15
Alignment explanation
Indices: 386280--386317 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
386270 TGACAACGAT
*
386280 TCCATTAACAACAAC
1 TCCAATAACAACAAC
386295 TCCAATAACAACAAC
1 TCCAATAACAACAAC
*
386310 TCCGATAA
1 TCCAATAA
386318 TAATATACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.47, C:0.32, G:0.03, T:0.18
Consensus pattern (15 bp):
TCCAATAACAACAAC
Found at i:387356 original size:23 final size:22
Alignment explanation
Indices: 387330--387393 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
387320 CAGCTCATAT
*
387330 AATTGCACCTAAGTGCCACTTAG
1 AATTGCACCT-AGTGCCACGTAG
* *
387353 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
387376 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
387394 TATAATAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.22
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:387535 original size:103 final size:103
Alignment explanation
Indices: 387409--387626 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
387399 TAATGTCCAT
* *
387409 AAGGACCACATATCATTTCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACTA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
387474 GACCTCACACATGTTCTAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
387512 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
387577 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
*
387615 AAGGGCCACATA
1 AAGGACCACATA
387627 GACCCTCAAC
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:388186 original size:64 final size:67
Alignment explanation
Indices: 388075--388202 Score: 201
Period size: 64 Copynumber: 2.0 Consensus size: 67
388065 ATTTTCATCT
388075 TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATACATAAATCCTATTCGATGTTTG
1 TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATACATAAATCCTATTCGATGTTTG
388140 TA
66 TA
* *
388142 TTTAATGG-GG-ATGCATCGATGCACT-C-CTTATGCATCGATGCATAAATCCTATTCGATGTTT
1 TTTAATGGAGGTATGCATCGATGCACTACAC-CATGCATCGATACATAAATCCTATTCGATGTTT
388203 TCTTTTTAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
63 1 0.02
64 32 0.55
65 15 0.26
66 2 0.03
67 8 0.14
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (67 bp):
TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATACATAAATCCTATTCGATGTTTG
TA
Found at i:388244 original size:64 final size:63
Alignment explanation
Indices: 388087--388247 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 63
388077 TAATGGAGGT
* * * *
388087 ATGCATCGATGCACTACACCATGCATCGATACATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACTACA-TATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGA
* * * *
388152 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT-TA
1 ATGCATCGATGCACTACATATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGA
* * *
388216 ATGCATCGATGCACTGCATGTGCGTCGATGCA
1 ATGCATCGATGCACTACATATGCATCGATGCA
388248 CCTTAAACAA
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 56 0.68
65 23 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTACATATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGA
Found at i:392351 original size:24 final size:25
Alignment explanation
Indices: 392278--392358 Score: 73
Period size: 24 Copynumber: 3.4 Consensus size: 25
392268 ACTACGGTGT
392278 ATTTCTACGTGGCACTTCGGTGC--
1 ATTTCTACGTGGCACTTCGGTGCAA
** *
392301 ATTTCTACACGGTC-CTTCGG-GAAAA
1 ATTTCTACGTGG-CACTTCGGTG-CAA
392326 ATTT-TACGTGGCACTTCGGTGCAA
1 ATTTCTACGTGGCACTTCGGTGCAA
*
392350 ATTTATACG
1 ATTTCTACG
392359 AGCTGTGGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
22 1 0.02
23 17 0.38
24 18 0.40
25 9 0.20
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (25 bp):
ATTTCTACGTGGCACTTCGGTGCAA
Found at i:393420 original size:18 final size:18
Alignment explanation
Indices: 393375--393424 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
393365 ATAAACTTGA
*
393375 AAATAAGATATGAATATG
1 AAATAAGTTATGAATATG
*
393393 AAATTAAGTTATGAATCTG
1 AAA-TAAGTTATGAATATG
393412 AAATAAGTTATGA
1 AAATAAGTTATGA
393425 GTTCGGAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 13 0.45
19 16 0.55
ACGTcount: A:0.50, C:0.02, G:0.16, T:0.32
Consensus pattern (18 bp):
AAATAAGTTATGAATATG
Found at i:393433 original size:19 final size:18
Alignment explanation
Indices: 393375--393439 Score: 58
Period size: 19 Copynumber: 3.5 Consensus size: 18
393365 ATAAACTTGA
* **
393375 AAATAAGATATGAATATG
1 AAATAAGTTATGAATCGG
*
393393 AAATTAAGTTATGAATCTG
1 AAA-TAAGTTATGAATCGG
*
393412 AAATAAGTTATGAGTTCGG
1 AAATAAGTTATGA-ATCGG
*
393431 AAACAAGTT
1 AAATAAGTT
393440 CTAAAATGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
18 13 0.32
19 27 0.68
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.31
Consensus pattern (18 bp):
AAATAAGTTATGAATCGG
Found at i:393485 original size:13 final size:13
Alignment explanation
Indices: 393461--393520 Score: 68
Period size: 13 Copynumber: 4.7 Consensus size: 13
393451 AAGTACAGAT
*
393461 TATGAAAATGAAA
1 TATGAAAGTGAAA
*
393474 TGTGAAAGTG-AA
1 TATGAAAGTGAAA
393486 TATGAAAGTGAAA
1 TATGAAAGTGAAA
* * *
393499 GATGAAAATGAGA
1 TATGAAAGTGAAA
393512 TATGAAAGT
1 TATGAAAGT
393521 TTTGTATTGT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
12 11 0.29
13 27 0.71
ACGTcount: A:0.52, C:0.00, G:0.25, T:0.23
Consensus pattern (13 bp):
TATGAAAGTGAAA
Found at i:393497 original size:25 final size:25
Alignment explanation
Indices: 393443--393520 Score: 77
Period size: 25 Copynumber: 3.0 Consensus size: 25
393433 ACAAGTTCTA
* *
393443 AAATGTGAAAGTACAGATTATGAAAATG
1 AAATGTGAAAGT---GAATATGAAAGTG
393471 AAATGTGAAAGTGAATATGAAAGTG
1 AAATGTGAAAGTGAATATGAAAGTG
*
393496 AAA-GATGAAAATGAGATATGAAAGT
1 AAATG-TGAAAGTGA-ATATGAAAGT
393521 TTTGTATTGT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
24 1 0.02
25 22 0.49
26 10 0.22
28 12 0.27
ACGTcount: A:0.51, C:0.01, G:0.24, T:0.23
Consensus pattern (25 bp):
AAATGTGAAAGTGAATATGAAAGTG
Found at i:393598 original size:39 final size:39
Alignment explanation
Indices: 393550--393632 Score: 130
Period size: 39 Copynumber: 2.1 Consensus size: 39
393540 AAAAAGAATA
* * *
393550 TGATGTGACTGTTATGTATGATATTGTTTATCTTGGCTT
1 TGATATGACTATTATGTATGATATTGTTTATCATGGCTT
*
393589 TGATATGACTATTATGTATGATATTGTTTATCATGGTTT
1 TGATATGACTATTATGTATGATATTGTTTATCATGGCTT
393628 TGATA
1 TGATA
393633 AAATCATGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.23, C:0.06, G:0.20, T:0.51
Consensus pattern (39 bp):
TGATATGACTATTATGTATGATATTGTTTATCATGGCTT
Found at i:395874 original size:25 final size:25
Alignment explanation
Indices: 395840--395914 Score: 114
Period size: 25 Copynumber: 3.0 Consensus size: 25
395830 GAGTCGAGGG
*
395840 TTCTACGTGGACCTTCGGGACAAAT
1 TTCTACGTGGTCCTTCGGGACAAAT
*
395865 TTCTACGTGGTCCTTTGGGACAAAT
1 TTCTACGTGGTCCTTCGGGACAAAT
* *
395890 TTCTACATGGTCCTTCAGGACAAAT
1 TTCTACGTGGTCCTTCGGGACAAAT
395915 CTATGTGGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (25 bp):
TTCTACGTGGTCCTTCGGGACAAAT
Found at i:399206 original size:13 final size:13
Alignment explanation
Indices: 399188--399234 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
399178 TATAAATAAA
399188 TAAATATTTATTT
1 TAAATATTTATTT
*
399201 TAAATAAATTATTT
1 TAAAT-ATTTATTT
399215 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
399228 TCAATAT
1 TAAATAT
399235 CAAAGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:399933 original size:14 final size:14
Alignment explanation
Indices: 399916--399952 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
399906 TTATATGTTT
399916 TATTTTATTTGCAA
1 TATTTTATTTGCAA
*
399930 TATTTTATTT-CAT
1 TATTTTATTTGCAA
399943 TA-TTTATTTG
1 TATTTTATTTG
399953 TCAAGGTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 7 0.33
13 4 0.19
14 10 0.48
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.65
Consensus pattern (14 bp):
TATTTTATTTGCAA
Found at i:403203 original size:15 final size:15
Alignment explanation
Indices: 403180--403211 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
403170 TTTGGGATCA
*
403180 ATACCTTTTGCATAC
1 ATACATTTTGCATAC
403195 ATACATTTTGCATAC
1 ATACATTTTGCATAC
403210 AT
1 AT
403212 TCATCATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.41
Consensus pattern (15 bp):
ATACATTTTGCATAC
Found at i:410577 original size:21 final size:21
Alignment explanation
Indices: 410552--410592 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
410542 ATGCTTGAAG
* * *
410552 AAAAAGTGAAGAAGGAAAAAA
1 AAAAAGAGAAAAAAGAAAAAA
410573 AAAAAGAGAAAAAAGAAAAA
1 AAAAAGAGAAAAAAGAAAAA
410593 GGGGGGGGTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (21 bp):
AAAAAGAGAAAAAAGAAAAAA
Found at i:410933 original size:16 final size:16
Alignment explanation
Indices: 410907--410951 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
410897 TTTGAATACA
*
410907 ATTCTATTTATTTCAAG
1 ATTCAATTTATTT-AAG
*
410924 -TTCAATTTATTTGAG
1 ATTCAATTTATTTAAG
410939 ATTCAATTTATTT
1 ATTCAATTTATTT
410952 TTGAAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTCAATTTATTTAAG
Found at i:411892 original size:83 final size:83
Alignment explanation
Indices: 411753--412376 Score: 1024
Period size: 83 Copynumber: 7.5 Consensus size: 83
411743 TAATGTGCTC
*
411753 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTTAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATT
411818 TAGAAGATGAATTTGCCA
66 TAGAAGATGAATTTGCCA
411836 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATT
* *
411901 TGGAAGATGAATGTGCTC-
66 TAGAAGATGAATTTGC-CA
*
411919 ATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATT
* *
411984 TGGAAGATGAATGTGCTC-
66 TAGAAGATGAATTTGC-CA
* * *
412002 ATAGCATCTTTTGGAAATGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTTAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATT
412067 TAGAAGATGAATTTGCCA
66 TAGAAGATGAATTTGCCA
*
412085 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-TAGAACCAATCATTGAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAACCAATCATTGAAT
412149 TTAGAAGATGAATTTGCCA
65 TTAGAAGATGAATTTGCCA
412168 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATT
412233 TAGAAGATGAATTTGCCA
66 TAGAAGATGAATTTGCCA
* * *
412251 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATAAAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATT
* * *
412316 GAGAAGAAT-AATGTGTTC-
66 TAGAAG-ATGAATTTG-CCA
412334 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
412377 TGGTAGGAAC
Statistics
Matches: 516, Mismatches: 19, Indels: 12
0.94 0.03 0.02
Matches are distributed among these distances:
82 5 0.01
83 503 0.97
84 8 0.02
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.37
Consensus pattern (83 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATT
TAGAAGATGAATTTGCCA
Found at i:413303 original size:116 final size:116
Alignment explanation
Indices: 413094--413770 Score: 1155
Period size: 116 Copynumber: 5.9 Consensus size: 116
413084 ATTCAAATCT
** * *
413094 ATCATTTGATGGATTGACATTGCCAGAGAAG-GTTCATAATGAGAAGAA--C-TCATCTGAAGAA
1 ATCATTTGATGGATCAACGTTGCCA-AGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
* * *
413155 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
65 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTC
* * * * *
413207 ATCACTTGATGGATTATCGTTGCCATGTAGAGTTCATAATAAGAAGAACTCGTCATCTGAAGAAG
1 ATCATTTGATGGATCAACGTTGCCAAGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
413272 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTC
66 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTC
* *
413323 ATCATTTGATGGATCAACGTTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAT
1 ATCATTTGATGGATCAACGTTGCCAAGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
413388 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTC
66 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTC
*
413439 ATCATTTGATGGATCAACGTTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
1 ATCATTTGATGGATCAACGTTGCCAAGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
413504 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTC
66 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTC
*
413555 ATCATTTGATGGATCAACATTGCCAAGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
1 ATCATTTGATGGATCAACGTTGCCAAGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
413620 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTC
66 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTC
*
413671 ATCATTTGATGGATCAACATTGCCAAGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
1 ATCATTTGATGGATCAACGTTGCCAAGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
*
413736 GAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAA
66 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
413771 TAATTCTATC
Statistics
Matches: 540, Mismatches: 20, Indels: 5
0.96 0.04 0.01
Matches are distributed among these distances:
112 3 0.01
113 37 0.07
115 1 0.00
116 499 0.92
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (116 bp):
ATCATTTGATGGATCAACGTTGCCAAGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTC
Found at i:414095 original size:3 final size:3
Alignment explanation
Indices: 414087--414145 Score: 100
Period size: 3 Copynumber: 19.7 Consensus size: 3
414077 TTTTTACCCA
* *
414087 TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
414135 TAT TAT TAT TA
1 TAT TAT TAT TA
414146 AATATATATT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:414320 original size:16 final size:16
Alignment explanation
Indices: 414299--414337 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
414289 TAATCCCATG
414299 CCAGCCGCCTCTGCCT
1 CCAGCCGCCTCTGCCT
414315 CCAGCCGCCTCTGCCT
1 CCAGCCGCCTCTGCCT
414331 CCA-CCGC
1 CCAGCCGC
414338 TGCCACGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.08, C:0.59, G:0.18, T:0.15
Consensus pattern (16 bp):
CCAGCCGCCTCTGCCT
Found at i:414533 original size:19 final size:20
Alignment explanation
Indices: 414504--414542 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
414494 ACCTGCAAAC
414504 AAAAAAGGAGAGAGACAGAG
1 AAAAAAGGAGAGAGACAGAG
414524 AAAAAA-GAGAGAGACAGAG
1 AAAAAAGGAGAGAGACAGAG
414543 CCGGAGAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.62, C:0.05, G:0.33, T:0.00
Consensus pattern (20 bp):
AAAAAAGGAGAGAGACAGAG
Found at i:415518 original size:13 final size:13
Alignment explanation
Indices: 415502--415548 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
415492 ATATAATAAA
415502 TAAATATTTATTT
1 TAAATATTTATTT
*
415515 TAAATAAATTATTT
1 TAAAT-ATTTATTT
415529 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
415542 TCAATAT
1 TAAATAT
415549 CAAAGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:416966 original size:2 final size:2
Alignment explanation
Indices: 416959--416989 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
416949 ATATAAAATT
*
416959 TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
416990 GATAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:418037 original size:17 final size:16
Alignment explanation
Indices: 418015--418096 Score: 58
Period size: 17 Copynumber: 4.8 Consensus size: 16
418005 ATTGGCTTGA
*
418015 AATATTTTCTTAATAAT
1 AATATTTT-TTAAAAAT
418032 AATATTTTTTAAAACAT
1 AATATTTTTTAAAA-AT
* *
418049 AATATATTATTAAGAA-
1 AATAT-TTTTTAAAAAT
*
418065 AATATTTATTGAAAATATT
1 AATATTT-TTTAAAA-A-T
418084 AATATATTTTTAA
1 AATAT-TTTTTAA
418097 TATTTTTGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
15 2 0.04
16 14 0.27
17 17 0.33
18 7 0.14
19 9 0.18
20 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (16 bp):
AATATTTTTTAAAAAT
Found at i:418069 original size:33 final size:35
Alignment explanation
Indices: 418032--418096 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
418022 TCTTAATAAT
*
418032 AATATTT-TTTAAAACA-TAATATATTATTAAGAA
1 AATATTTATTGAAAACATTAATATATTATTAAGAA
* *
418065 AATATTTATTGAAAATATTAATATATTTTTAA
1 AATATTTATTGAAAACATTAATATATTATTAA
418097 TATTTTTGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 7 0.26
34 7 0.26
35 13 0.48
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (35 bp):
AATATTTATTGAAAACATTAATATATTATTAAGAA
Found at i:419958 original size:2 final size:2
Alignment explanation
Indices: 419951--419982 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
419941 GAAATTCAGG
419951 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
419983 CACACAAGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:425369 original size:15 final size:15
Alignment explanation
Indices: 425345--425378 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
425335 TCGTAGGAGC
425345 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
*
425360 ACTACGTCCCGAAGG
1 ACTACATCCCGAAGG
425375 ACTA
1 ACTA
425379 TTATACTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:426057 original size:64 final size:64
Alignment explanation
Indices: 425905--426061 Score: 162
Period size: 64 Copynumber: 2.5 Consensus size: 64
425895 TAATGAAGGT
** * * *
425905 ATGCATCGATGCAC-AAGTAGTGCATCGGTGCATAAAATGCATTCGATGTTTTATTATTAATGGG
1 ATGCATCGATGCACTACCT-GTGCATCGATGCATAAAATGCATTCGATGTTTTATTATTAAAGAG
* * *
425969 ATGCATCGATGCA-TGCCTTATGCATCGATGCACT-AATTGCATTCGATGTTTTTATT-TTAAA-
1 ATGCATCGATGCACTACC-TGTGCATCGATGCA-TAAAATGCATTCGATG-TTTTATTATTAAAG
426030 AG
63 AG
426032 AGTGCATCGATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACCTGTGCATCGAT
426062 ACACCTTCAA
Statistics
Matches: 77, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
63 2 0.03
64 63 0.82
65 12 0.16
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTGTGCATCGATGCATAAAATGCATTCGATGTTTTATTATTAAAGAG
Found at i:433602 original size:15 final size:15
Alignment explanation
Indices: 433574--433607 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
433564 CCGTAGGACC
*
433574 ACTACATCCTGAAGG
1 ACTACATCCCGAAGG
*
433589 ACTACGTCCCGAAGG
1 ACTACATCCCGAAGG
433604 ACTA
1 ACTA
433608 TTATACTCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.18
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:434286 original size:64 final size:64
Alignment explanation
Indices: 434134--434290 Score: 162
Period size: 64 Copynumber: 2.5 Consensus size: 64
434124 TAATGAAGGT
** * * *
434134 ATGCATCGATGCAC-AAGTAGTGCATCGGTGCATAAAATGCATTCGATGTTTTATTATTAATGGG
1 ATGCATCGATGCACTACCT-GTGCATCGATGCATAAAATGCATTCGATGTTTTATTATTAAAGAG
* * *
434198 ATGCATCGATGCA-TGCCTTATGCATCGATGCACT-AATTGCATTCGATGTTTTTATT-TTAAA-
1 ATGCATCGATGCACTACC-TGTGCATCGATGCA-TAAAATGCATTCGATG-TTTTATTATTAAAG
434259 AG
63 AG
434261 AGTGCATCGATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACCTGTGCATCGAT
434291 ACACCTTCAA
Statistics
Matches: 77, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
63 2 0.03
64 63 0.82
65 12 0.16
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTGTGCATCGATGCATAAAATGCATTCGATGTTTTATTATTAAAGAG
Found at i:436372 original size:13 final size:13
Alignment explanation
Indices: 436354--436378 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
436344 ATGAATGTTG
436354 GAATCTGTTATGA
1 GAATCTGTTATGA
436367 GAATCTGTTATG
1 GAATCTGTTATG
436379 TAGTCAGTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (13 bp):
GAATCTGTTATGA
Found at i:436404 original size:12 final size:11
Alignment explanation
Indices: 436357--436400 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 11
436347 AATGTTGGAA
436357 TCTGTTATGAG
1 TCTGTTATGAG
436368 AATCTGTTATGTAG
1 --TCTGTTATG-AG
*
436382 TCAGTTATGAG
1 TCTGTTATGAG
436393 TCTGTTAT
1 TCTGTTAT
436401 TGAGGTAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 9 0.32
12 8 0.29
13 9 0.32
14 2 0.07
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.45
Consensus pattern (11 bp):
TCTGTTATGAG
Found at i:436520 original size:26 final size:26
Alignment explanation
Indices: 436484--436535 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
436474 AAAATTACAG
436484 AGCATTATTCATTGAGTTTTAAACTT
1 AGCATTATTCATTGAGTTTTAAACTT
436510 AGCATTATTCATTGAGTTTTAAACTT
1 AGCATTATTCATTGAGTTTTAAACTT
436536 CTCAGCAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.46
Consensus pattern (26 bp):
AGCATTATTCATTGAGTTTTAAACTT
Found at i:441475 original size:24 final size:24
Alignment explanation
Indices: 441415--441476 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
441405 CAATCTTATA
*
441415 TGGCACTACGGTGC-ATTTCTACG
1 TGGCACTACGGTGCAAATTCTACG
* * *
441438 CGGCACTTCAGTGCAAATTCTACG
1 TGGCACTACGGTGCAAATTCTACG
441462 TGGCACTACGGTGCA
1 TGGCACTACGGTGCA
441477 TATTTTTACG
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 11 0.35
24 20 0.65
ACGTcount: A:0.21, C:0.27, G:0.26, T:0.26
Consensus pattern (24 bp):
TGGCACTACGGTGCAAATTCTACG
Found at i:442181 original size:11 final size:11
Alignment explanation
Indices: 442167--442201 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
442157 ATTTTACGAA
*
442167 AGTATTGTAGC
1 AGTACTGTAGC
*
442178 AGTACTGTAGT
1 AGTACTGTAGC
442189 AGTACTGTAGC
1 AGTACTGTAGC
442200 AG
1 AG
442202 GGAATCGGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.31
Consensus pattern (11 bp):
AGTACTGTAGC
Found at i:442289 original size:12 final size:12
Alignment explanation
Indices: 442272--442324 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
442262 CATTCGAAAA
*
442272 TGTTCATGGTAC
1 TGTTCATGGTAT
*
442284 TGTTCA--CTAT
1 TGTTCATGGTAT
442294 TGTTCATGGTAT
1 TGTTCATGGTAT
442306 TGTTCATGGTAT
1 TGTTCATGGTAT
442318 TGTTCAT
1 TGTTCAT
442325 TACTGTTCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
10 8 0.22
12 28 0.78
ACGTcount: A:0.17, C:0.13, G:0.21, T:0.49
Consensus pattern (12 bp):
TGTTCATGGTAT
Found at i:442300 original size:22 final size:23
Alignment explanation
Indices: 442272--442333 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 23
442262 CATTCGAAAA
442272 TGTTCATGGTACTGTTCA-CTAT
1 TGTTCATGGTACTGTTCAGCTAT
* *
442294 TGTTCATGGTATTGTTCATGGTAT
1 TGTTCATGGTACTGTTCA-GCTAT
442318 TGTTCAT--TACTGTTCA
1 TGTTCATGGTACTGTTCA
442334 TACGGTACTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 25 0.71
24 10 0.29
ACGTcount: A:0.18, C:0.15, G:0.19, T:0.48
Consensus pattern (23 bp):
TGTTCATGGTACTGTTCAGCTAT
Found at i:443322 original size:32 final size:32
Alignment explanation
Indices: 443299--443371 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
443289 AAGGGTCTGG
*
443299 TTAACGGGTCAACGATTGGGTCAACGGCCAGA
1 TTAACGGGTCAACGATTAGGTCAACGGCCAGA
*
443331 TTAACGGGTCAACGATTAGGTCAATGGCCAGA
1 TTAACGGGTCAACGATTAGGTCAACGGCCAGA
443363 TTAACGGGT
1 TTAACGGGT
443372 TGATGGTCTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.22
Consensus pattern (32 bp):
TTAACGGGTCAACGATTAGGTCAACGGCCAGA
Found at i:446100 original size:21 final size:21
Alignment explanation
Indices: 446075--446132 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
446065 GCGACGGCCA
446075 CAATAGCACCCACGACAGTCG
1 CAATAGCACCCACGACAGTCG
* **
446096 TAATAGTGCCCACGACAGTCG
1 CAATAGCACCCACGACAGTCG
*
446117 CAATAGCACCCGCGAC
1 CAATAGCACCCACGAC
446133 GACTGCAGTC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.36, G:0.21, T:0.12
Consensus pattern (21 bp):
CAATAGCACCCACGACAGTCG
Found at i:457851 original size:21 final size:19
Alignment explanation
Indices: 457822--457873 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 19
457812 TTATGGAACT
*
457822 TGGAGAGGAAGAAGAAAGAAA
1 TGGAAAGGAAGAAG--AGAAA
457843 TGGAAAGGAAG-AG-GAAA
1 TGGAAAGGAAGAAGAGAAA
457860 T-GAAAGGAAGAAGA
1 TGGAAAGGAAGAAGA
457874 TGAATGGAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 9 0.32
17 7 0.25
20 2 0.07
21 10 0.36
ACGTcount: A:0.56, C:0.00, G:0.38, T:0.06
Consensus pattern (19 bp):
TGGAAAGGAAGAAGAGAAA
Found at i:457864 original size:16 final size:17
Alignment explanation
Indices: 457839--457870 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
457829 GAAGAAGAAA
457839 GAAATGGAAAGGAAGAG
1 GAAATGGAAAGGAAGAG
457856 GAAAT-GAAAGGAAGA
1 GAAATGGAAAGGAAGA
457871 AGATGAATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.56, C:0.00, G:0.38, T:0.06
Consensus pattern (17 bp):
GAAATGGAAAGGAAGAG
Found at i:462217 original size:9 final size:9
Alignment explanation
Indices: 462205--462519 Score: 118
Period size: 9 Copynumber: 35.4 Consensus size: 9
462195 TTAAAACAAT
462205 TATAATATA
1 TATAATATA
*
462214 TATAGTATA
1 TATAATATA
462223 TACTAATATA
1 TA-TAATATA
*
462233 TATATAAACTA
1 TATA-ATA-TA
*
462244 TATAGTTATA
1 TATA-ATATA
*
462254 TATACTATA
1 TATAATATA
*
462263 TCTAA-ACTA
1 TATAATA-TA
* *
462272 TATAGTATG
1 TATAATATA
462281 TA-AACTATA
1 TATAA-TATA
*
462290 TATATAAACTA
1 TATA-ATA-TA
*
462301 TATAGAAACTA
1 TATA-ATA-TA
462312 TATAATATA
1 TATAATATA
462321 TA-AATATA
1 TATAATATA
*
462329 TATATTATA
1 TATAATATA
462338 TAT-ATATA
1 TATAATATA
462346 TA-AACTATA
1 TATAA-TATA
462355 TAT-ATATA
1 TATAATATA
462363 TA-AAT-TA
1 TATAATATA
*
462370 TAT-ATATG
1 TATAATATA
462378 TATAA-ACTA
1 TATAATA-TA
* *
462387 -ATAGTTTA
1 TATAATATA
462395 TAT-ATATA
1 TATAATATA
462403 TATAA-ATA
1 TATAATATA
462411 TA-AACTATA
1 TATAA-TATA
**
462420 TAGTTTTATA
1 TA-TAATATA
462430 TA-AACTATA
1 TATAA-TATA
462439 TATAA-A-A
1 TATAATATA
*
462446 TAT-ATGTA
1 TATAATATA
462454 CTAT-ATATA
1 -TATAATATA
462463 TATAA-AGTA
1 TATAATA-TA
*
462472 TATAGT-T-
1 TATAATATA
*
462479 TAT-ATTTA
1 TATAATATA
*
462487 TATACTATA
1 TATAATATA
462496 TATAAACTATA
1 TAT-AA-TATA
*
462507 TATACTATA
1 TATAATATA
462516 TATA
1 TATA
462520 TAAACTATGT
Statistics
Matches: 231, Mismatches: 37, Indels: 76
0.67 0.11 0.22
Matches are distributed among these distances:
6 2 0.01
7 16 0.07
8 56 0.24
9 95 0.41
10 31 0.13
11 31 0.13
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (9 bp):
TATAATATA
Found at i:462247 original size:11 final size:10
Alignment explanation
Indices: 462208--462523 Score: 80
Period size: 11 Copynumber: 30.2 Consensus size: 10
462198 AAACAATTAT
462208 AATATATAT-
1 AATATATATA
*
462217 AGTATATACTA
1 AATATATA-TA
462228 ATATATATATA
1 A-ATATATATA
462239 AACTATATAGT-
1 AA-TATATA-TA
*
462250 TATATATACTA
1 AATATATA-TA
* * *
462261 TATCTAAACTA
1 AATATATA-TA
* *
462272 TATAGTATGTA
1 AATA-TATATA
462283 AACTATATATA
1 AA-TATATATA
462294 TAA-ACTATATA
1 -AATA-TATATA
462305 GAA-ACTATAT-
1 -AATA-TATATA
462315 AATA--TATA
1 AATATATATA
462323 AATATATATA
1 AATATATATA
*
462333 TTATATATATA
1 -AATATATATA
* *
462344 TATAAACTATA
1 AATATA-TATA
*
462355 TATATATATA
1 AATATATATA
462365 AAT-TATAT-
1 AATATATATA
*
462373 -ATATGTATA
1 AATATATATA
*
462382 AACTA-ATAGTT
1 AA-TATATA-TA
*
462393 TATATATATA
1 AATATATATA
* *
462403 TATAAATATA
1 AATATATATA
*
462413 AA-CTATATA
1 AATATATATA
** *
462422 GTTTTATATA
1 AATATATATA
462432 AACTATATATAA
1 AA-TATATAT-A
462444 AATATATGTACTA
1 AATATA--TA-TA
*
462457 TATATATATA
1 AATATATATA
*
462467 AAGTATATAGTT
1 AA-TATATA-TA
* *
462479 TATATTTATA
1 AATATATATA
*
462489 TACTATATATA
1 -AATATATATA
462500 AACTATATATA
1 AA-TATATATA
*
462511 CTATATATATA
1 -AATATATATA
462522 AA
1 AA
462524 CTATGTAGTT
Statistics
Matches: 231, Mismatches: 43, Indels: 65
0.68 0.13 0.19
Matches are distributed among these distances:
7 5 0.02
8 8 0.03
9 19 0.08
10 54 0.23
11 117 0.51
12 19 0.08
13 8 0.03
14 1 0.00
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.42
Consensus pattern (10 bp):
AATATATATA
Found at i:462247 original size:13 final size:13
Alignment explanation
Indices: 462229--462527 Score: 123
Period size: 13 Copynumber: 23.2 Consensus size: 13
462219 TATATACTAA
462229 TATATATATAAAC
1 TATATATATAAAC
*
462242 TATATAGTTATATA-
1 TATATA--TATAAAC
*
462256 TACTATATCTAAAC
1 TA-TATATATAAAC
462270 TATATAGTATGTAAAC
1 TATATA-TA--TAAAC
462286 TATATATATAAAC
1 TATATATATAAAC
*
462299 --TATATAGAAAC
1 TATATATATAAAC
*
462310 TATATAATATATAAA
1 TATAT-ATATA-AAC
*
462325 TATATATATTATA-
1 TATATATA-TAAAC
462338 TATATATATAAAC
1 TATATATATAAAC
462351 TATATATAT--A-
1 TATATATATAAAC
* *
462361 TATAAAT-TATA-
1 TATATATATAAAC
*
462372 TATATGTATAAAC
1 TATATATATAAAC
* *
462385 TA-ATAGTTTATA-
1 TATATA-TATAAAC
462397 TATATATATAAA-
1 TATATATATAAAC
* * *
462409 TATAAACTATATAG
1 TATATA-TATAAAC
*
462423 T-TTTATATAAAC
1 TATATATATAAAC
462435 TATATATA-AAA-
1 TATATATATAAAC
*
462446 TATATGTACT--A-
1 TATATATA-TAAAC
*
462457 TATATATATAAAG
1 TATATATATAAAC
* **
462470 TATATAGTTTATATT
1 TATATA-TATA-AAC
*
462485 TATATACTATATA-
1 TATATA-TATAAAC
* *
462498 TAAACTATATATAC
1 TATA-TATATAAAC
462512 TATATATATAAAC
1 TATATATATAAAC
462525 TAT
1 TAT
462528 GTAGTTTATA
Statistics
Matches: 218, Mismatches: 37, Indels: 62
0.69 0.12 0.20
Matches are distributed among these distances:
9 1 0.00
10 7 0.03
11 32 0.15
12 29 0.13
13 86 0.39
14 22 0.10
15 30 0.14
16 11 0.05
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.42
Consensus pattern (13 bp):
TATATATATAAAC
Found at i:462275 original size:18 final size:17
Alignment explanation
Indices: 462252--462442 Score: 78
Period size: 17 Copynumber: 11.5 Consensus size: 17
462242 TATATAGTTA
462252 TATATACTATATCTAAAC
1 TATATA-TATATCTAAAC
* *
462270 TATATA-GTATGTAAAC
1 TATATATATATCTAAAC
462286 --TATATATA--TAAAC
1 TATATATATATCTAAAC
* * *
462299 TATATAGA-AACTATATAA
1 TATATATATATCTA-A-AC
* * * *
462317 TATATAAATATATATAT
1 TATATATATATCTAAAC
*
462334 TATATATATATATAAAC
1 TATATATATATCTAAAC
* *
462351 TATATATATATATAAAT
1 TATATATATATCTAAAC
* *
462368 TATATATATGTATAAAC
1 TATATATATATCTAAAC
* *
462385 TA-ATAGT-T-TATATA-
1 TATATA-TATATCTAAAC
* *
462399 TATATATAAATATAAAC
1 TATATATATATCTAAAC
* *
462416 TATATAGTTTTATATAAAC
1 TATATA--TATATCTAAAC
462435 TATATATA
1 TATATATA
462443 AAATATATGT
Statistics
Matches: 136, Mismatches: 22, Indels: 31
0.72 0.12 0.16
Matches are distributed among these distances:
13 5 0.04
14 8 0.06
15 15 0.11
16 19 0.14
17 57 0.42
18 14 0.10
19 18 0.13
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (17 bp):
TATATATATATCTAAAC
Found at i:462563 original size:2 final size:2
Alignment explanation
Indices: 462205--462544 Score: 158
Period size: 2 Copynumber: 162.5 Consensus size: 2
462195 TTAAAACAAT
*
462205 TA TA -A TA TA TA TA GTA TA TA CTA -A TA TA TA TA TA AA CTA TA
1 TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA -TA TA
* * * *
462246 TA GT- TA TA TA TA CTA TA TC TA AA CTA TA TA GTA TG TA AA CTA TA
1 TA -TA TA TA TA TA -TA TA TA TA TA -TA TA TA -TA TA TA TA -TA TA
* * * *
462290 TA TA TA AA CTA TA TA GA AA CTA TA TA -A TA TA TA AA 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
* *
462333 T- TA TA TA TA TA TA TA AA CTA TA TA TA TA TA TA AA T- 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
* * * * *
462374 TA TG TA TA AA CTA -A TA GTT TA TA TA TA TA TA TA AA TA TA AA CTA
1 TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * * *
462418 TA TA GT- TT TA TA TA AA CTA TA TA TA -A AA TA TA TG TA CTA TA
1 TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA
* * * *
462459 TA TA TA TA AA GTA TA TA GTT TA TA TT TA TA TA CTA 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
* * *
462502 CTA TA TA TA CTA TA TA TA TA AA CTA TG TA GTT 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 T
462545 TGTATATGAA
Statistics
Matches: 254, Mismatches: 51, Indels: 66
0.68 0.14 0.18
Matches are distributed among these distances:
1 9 0.04
2 214 0.84
3 31 0.12
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (2 bp):
TA
Found at i:462581 original size:22 final size:22
Alignment explanation
Indices: 462492--462581 Score: 62
Period size: 22 Copynumber: 4.2 Consensus size: 22
462482 ATTTATATAC
* *
462492 TATATATAAACTATATATACTA
1 TATATATAAACTATATAAACTT
* *
462514 TATATATAAACTATGT--AGTT
1 TATATATAAACTATATAAACTT
** *
462534 TATATATATATTGTATATGAAC--
1 TATATATA-A-ACTATATAAACTT
*
462556 TATATATAGACTATATAAACTT
1 TATATATAAACTATATAAACTT
462578 TATA
1 TATA
462582 GTTTATATTT
Statistics
Matches: 51, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
20 18 0.35
21 1 0.02
22 31 0.61
24 1 0.02
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (22 bp):
TATATATAAACTATATAAACTT
Found at i:462653 original size:20 final size:20
Alignment explanation
Indices: 462630--462725 Score: 61
Period size: 22 Copynumber: 4.6 Consensus size: 20
462620 TTTTATATAC
462630 TATATAATTTATATATAAAA
1 TATATAATTTATATATAAAA
* *
462650 TATATATACTCTATATATAAAT
1 TATATA-A-TTTATATATAAAA
* * *
462672 TGTATAGTTTAT-TA-ATATA
1 TATATAATTTATATATA-AAA
*
462691 TACTATAATTTATTAATATAAAT
1 TA-TATAATTTA-T-ATATAAAA
*
462714 TATATAGTTTAT
1 TATATAATTTAT
462726 TAATATAATA
Statistics
Matches: 56, Mismatches: 12, Indels: 15
0.67 0.14 0.18
Matches are distributed among these distances:
18 1 0.02
19 4 0.07
20 18 0.32
21 3 0.05
22 24 0.43
23 5 0.09
24 1 0.02
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (20 bp):
TATATAATTTATATATAAAA
Found at i:462689 original size:22 final size:22
Alignment explanation
Indices: 462664--462738 Score: 100
Period size: 22 Copynumber: 3.5 Consensus size: 22
462654 TATACTCTAT
*
462664 ATATAAATTGTATAGTTTATTA
1 ATATAAATTATATAGTTTATTA
* *
462686 ATATATACTATA-A-TTTATTA
1 ATATAAATTATATAGTTTATTA
462706 ATATAAATTATATAGTTTATTA
1 ATATAAATTATATAGTTTATTA
462728 ATATAATATTA
1 ATATAA-ATTA
462739 ATTGAAAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
20 17 0.38
21 2 0.04
22 22 0.49
23 4 0.09
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (22 bp):
ATATAAATTATATAGTTTATTA
Found at i:464985 original size:22 final size:20
Alignment explanation
Indices: 464958--465014 Score: 71
Period size: 19 Copynumber: 2.8 Consensus size: 20
464948 TACCACCTGA
464958 GGGTATCGGTACCATTTCATGG
1 GGGTATCGGTACCATTT-A-GG
* *
464980 GGGTATCGATACC-TATAGG
1 GGGTATCGGTACCATTTAGG
464999 GGGTATCGGTACCATT
1 GGGTATCGGTACCATT
465015 CGAGCATTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 14 0.47
20 2 0.07
21 2 0.07
22 12 0.40
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.30
Consensus pattern (20 bp):
GGGTATCGGTACCATTTAGG
Found at i:471341 original size:21 final size:19
Alignment explanation
Indices: 471312--471363 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 19
471302 TTATGGAACT
*
471312 TGGAGAGGAAGAAGAAAGAAA
1 TGGAAAGGAAGAAG--AGAAA
471333 TGGAAAGGAAG-AG-GAAA
1 TGGAAAGGAAGAAGAGAAA
471350 T-GAAAGGAAGAAGA
1 TGGAAAGGAAGAAGA
471364 TGAATGGAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 9 0.32
17 7 0.25
20 2 0.07
21 10 0.36
ACGTcount: A:0.56, C:0.00, G:0.38, T:0.06
Consensus pattern (19 bp):
TGGAAAGGAAGAAGAGAAA
Found at i:471354 original size:16 final size:17
Alignment explanation
Indices: 471329--471360 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
471319 GAAGAAGAAA
471329 GAAATGGAAAGGAAGAG
1 GAAATGGAAAGGAAGAG
471346 GAAAT-GAAAGGAAGA
1 GAAATGGAAAGGAAGA
471361 AGATGAATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.56, C:0.00, G:0.38, T:0.06
Consensus pattern (17 bp):
GAAATGGAAAGGAAGAG
Found at i:475707 original size:9 final size:9
Alignment explanation
Indices: 475695--476036 Score: 74
Period size: 9 Copynumber: 38.4 Consensus size: 9
475685 TTAAAACAAT
475695 TATAATATA
1 TATAATATA
*
475704 TATAGTATA
1 TATAATATA
475713 TACTAATATA
1 TA-TAATATA
475723 -AT-ATATA
1 TATAATATA
475730 TA-AACTATA
1 TATAA-TATA
*
475739 TAGTTTATATTTA
1 TA---TA-ATATA
*
475752 TATACTATA
1 TATAATATA
*
475761 TCTAA-ACTA
1 TATAATA-TA
* *
475770 TATAGTATG
1 TATAATATA
475779 TA-AACTATA
1 TATAA-TATA
475788 TAT-AT-TA
1 TATAATATA
475795 TA-AACTATA
1 TATAA-TATA
*
475804 TAGAA-ACTA
1 TATAATA-TA
475813 TATAATATA
1 TATAATATA
*
475822 TA-AA-CTA
1 TATAATATA
475829 TATAAT-T-
1 TATAATATA
*
475836 TAT-ATTTA
1 TATAATATA
*
475844 TATACTATA
1 TATAATATA
475853 TATAAACTATA
1 TAT-AA-TATA
*
475864 TATATTATA
1 TATAATATA
475873 TATAAATTATA
1 TAT-AA-TATA
* *
475884 TATATTATG
1 TATAATATA
475893 TATAA-ACTA
1 TATAATA-TA
*
475902 -ATAGTTTATA
1 TATA--ATATA
475912 TATAATATA
1 TATAATATA
475921 TA-AATATA
1 TATAATATA
*
475929 -A-ACTATA
1 TATAATATA
* *
475936 TAGT-TTTTA
1 TA-TAATATA
475945 TATAAACTATA
1 TAT-AA-TATA
475956 TATAA-A-A
1 TATAATATA
*
475963 TAT-ATGTA
1 TATAATATA
475971 CTAT-ATATA
1 -TATAATATA
475980 TATAA-AGTA
1 TATAATA-TA
*
475989 TATAGT-T-
1 TATAATATA
*
475996 TAT-ATTTA
1 TATAATATA
*
476004 TATACTATA
1 TATAATATA
476013 TATAAACTATA
1 TAT-AA-TATA
*
476024 TATACTATA
1 TATAATATA
476033 TATA
1 TATA
476037 TAAACTATGT
Statistics
Matches: 245, Mismatches: 38, Indels: 100
0.64 0.10 0.26
Matches are distributed among these distances:
6 4 0.02
7 32 0.13
8 38 0.16
9 111 0.45
10 22 0.09
11 31 0.13
13 6 0.02
14 1 0.00
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (9 bp):
TATAATATA
Found at i:475721 original size:19 final size:17
Alignment explanation
Indices: 475697--475731 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
475687 AAAACAATTA
475697 TAATATATATAGTATATAC
1 TAATATA-ATA-TATATAC
475716 TAATATAATATATATA
1 TAATATAATATATATA
475732 AACTATATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 3 0.19
19 7 0.44
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (17 bp):
TAATATAATATATATAC
Found at i:475740 original size:11 final size:11
Alignment explanation
Indices: 475704--476044 Score: 79
Period size: 11 Copynumber: 32.3 Consensus size: 11
475694 TTATAATATA
*
475704 TATAGTATATAC
1 TATA-TATAAAC
475716 TA-ATAT-AA-
1 TATATATAAAC
475724 TATATATAAAC
1 TATATATAAAC
**
475735 TATATAGTTTA-
1 TATATA-TAAAC
* *
475746 TATTTATATAC
1 TATATATAAAC
*
475757 TATATCTAAAC
1 TATATATAAAC
**
475768 TATATAGT-ATG
1 TATATA-TAAAC
* *
475779 TAAACTATATA-
1 TATA-TATAAAC
475790 TAT-TATAAAC
1 TATATATAAAC
*
475800 TATATAGAAAC
1 TATATATAAAC
475811 --TATAT-AA-
1 TATATATAAAC
475818 --TATATAAAC
1 TATATATAAAC
**
475827 TATATAATTTA-
1 TATAT-ATAAAC
* *
475838 TATTTATATAC
1 TATATATAAAC
475849 TATATATAAAC
1 TATATATAAAC
*
475860 TATATAT--AT
1 TATATATAAAC
475869 TATATATAAA-
1 TATATATAAAC
* *
475879 T-TATATATAT
1 TATATATAAAC
*
475889 TATGTATAAAC
1 TATATATAAAC
**
475900 TA-ATAGTTTA-
1 TATATA-TAAAC
*
475910 TATATAATATA-
1 TATAT-ATAAAC
*
475921 TAAATATAAAC
1 TATATATAAAC
*
475932 TATATAGT---T
1 TATATA-TAAAC
*
475941 TTTATATAAAC
1 TATATATAAAC
*
475952 TATATATAAAA
1 TATATATAAAC
*
475963 TATATGTACTATA-
1 TATA--TA-TAAAC
*
475976 TATATATAAAG
1 TATATATAAAC
**
475987 TATATAGTTTA-
1 TATATA-TAAAC
* *
475998 TATTTATATAC
1 TATATATAAAC
476009 TATATATAAAC
1 TATATATAAAC
*
476020 TATATATACTA-
1 TATATATA-AAC
476031 TATATATAAAC
1 TATATATAAAC
476042 TAT
1 TAT
476045 GTAGTTTATA
Statistics
Matches: 242, Mismatches: 51, Indels: 73
0.66 0.14 0.20
Matches are distributed among these distances:
7 5 0.02
8 7 0.03
9 34 0.14
10 32 0.13
11 140 0.58
12 15 0.06
13 6 0.02
14 3 0.01
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.44
Consensus pattern (11 bp):
TATATATAAAC
Found at i:475804 original size:43 final size:42
Alignment explanation
Indices: 475744--475839 Score: 129
Period size: 43 Copynumber: 2.2 Consensus size: 42
475734 CTATATAGTT
* ** * *
475744 TATATTTATATACTATATCTAAACTATATAGTATGTAAACTA
1 TATATTTATAAACTATATAGAAACTATATAATATATAAACTA
475786 TATATATTATAAACTATATAGAAACTATATAATATATAAACTA
1 TATAT-TTATAAACTATATAGAAACTATATAATATATAAACTA
475829 TATAATTTATA
1 TAT-ATTTATA
475840 TTTATATACT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
42 5 0.11
43 40 0.85
44 2 0.04
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (42 bp):
TATATTTATAAACTATATAGAAACTATATAATATATAAACTA
Found at i:476033 original size:33 final size:31
Alignment explanation
Indices: 475702--476038 Score: 203
Period size: 33 Copynumber: 10.6 Consensus size: 31
475692 AATTATAATA
* *
475702 TATATAGTATATACTAATATAATATATATAAAC
1 TATATA-TATATATTTATAT-ATATATATAAAC
* *
475735 TATATAGTTTATATTTATATACTATATCTAAAC
1 TATATA-TATATATTTATATA-TATATATAAAC
* **
475768 TATATAGTATGTAAACTATATATAT-TATAAAC
1 TATATA-TATAT-ATTTATATATATATATAAAC
* *
475800 TATATAGA-A-A-CTATATA-ATATATAAAC
1 TATATATATATATTTATATATATATATAAAC
*
475827 TATATAATTTATATTTATATACTATATATAAAC
1 TATAT-ATATATATTTATATA-TATATATAAAC
* * * **
475860 TATATATATTATATATAAATTATATATATTATG
1 TATATATA-TATATTTATA-TATATATATAAAC
*
475893 TATAAACTA-ATAGTTTATATATAATATATAAA-
1 TATATA-TATATA-TTTATATAT-ATATATAAAC
* *
475925 TATAAACTATATA-GT-T-T-T-TATATAAAC
1 TATATA-TATATATTTATATATATATATAAAC
* *
475952 TATATATAAAATATATGTACTATATATATATAAAG
1 TATATAT---ATATATTTA-TATATATATATAAAC
*
475987 TATATAGTTTATATTTATATACTATATATAAAC
1 TATATA-TATATATTTATATA-TATATATAAAC
*
476020 TATATATACTATATATATA
1 TATATATA-TATATTTATA
476039 AACTATGTAG
Statistics
Matches: 243, Mismatches: 33, Indels: 56
0.73 0.10 0.17
Matches are distributed among these distances:
26 11 0.05
27 24 0.10
28 3 0.01
29 7 0.03
30 4 0.02
31 8 0.03
32 36 0.15
33 123 0.51
34 12 0.05
35 14 0.06
36 1 0.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (31 bp):
TATATATATATATTTATATATATATATAAAC
Found at i:476080 original size:2 final size:2
Alignment explanation
Indices: 475695--476061 Score: 128
Period size: 2 Copynumber: 176.5 Consensus size: 2
475685 TTAAAACAAT
*
475695 TA TA -A TA TA TA TA GTA TA TA CTA -A TA TA -A TA TA TA TA AA CTA
1 TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA
* * * * *
475737 TA TA GTT TA TA TT TA TA TA CTA TA TC TA AA CTA TA TA GTA TG TA
1 TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA -TA TA TA
* * * *
475781 AA CTA TA TA TA T- TA TA AA CTA TA TA GA AA CTA TA TA -A TA TA
1 TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA
* * * *
475822 TA AA CTA TA TA -A TT TA TA TT TA TA TA CTA TA TA TA AA CTA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA
* * *
475864 TA TA T- TA TA TA TA AA T- TA TA TA TA T- TA TG TA TA AA CTA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * * *
475903 TA GTT TA TA TA TA -A TA TA TA AA TA TA AA CTA TA TA GTT TT TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
* * * *
475945 TA TA AA CTA TA TA TA -A AA TA TA TG TA CTA TA TA TA TA TA AA GTA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA
* * *
475989 TA TA GTT TA TA TT TA TA TA CTA TA TA TA AA CTA TA TA TA CTA TA
1 TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA -TA TA
* * *
476033 TA TA TA AA CTA TG TA GTT TA TA TA TA TA T
1 TA TA TA TA -TA TA TA -TA TA TA TA TA TA T
476062 TGTATATGAA
Statistics
Matches: 267, Mismatches: 60, Indels: 76
0.66 0.15 0.19
Matches are distributed among these distances:
1 12 0.04
2 221 0.83
3 34 0.13
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:476098 original size:22 final size:22
Alignment explanation
Indices: 476009--476098 Score: 62
Period size: 22 Copynumber: 4.2 Consensus size: 22
475999 ATTTATATAC
* *
476009 TATATATAAACTATATATACTA
1 TATATATAAACTATATAAACTT
* *
476031 TATATATAAACTATGT--AGTT
1 TATATATAAACTATATAAACTT
** *
476051 TATATATATATTGTATATGAAC--
1 TATATATA-A-ACTATATAAACTT
*
476073 TATATATAGACTATATAAACTT
1 TATATATAAACTATATAAACTT
476095 TATA
1 TATA
476099 GTTTATATTT
Statistics
Matches: 51, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
20 18 0.35
21 1 0.02
22 31 0.61
24 1 0.02
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (22 bp):
TATATATAAACTATATAAACTT
Found at i:476173 original size:22 final size:22
Alignment explanation
Indices: 476147--476236 Score: 64
Period size: 22 Copynumber: 4.2 Consensus size: 22
476137 TTTTATATAC
476147 TATATAATTTATATATAAAATA
1 TATATAATTTATATATAAAATA
* *
476169 TATATACTATATATAT-AAAT-
1 TATATAATTTATATATAAAATA
* * *
476189 TGTAT-AGTT-TAT-TAATATA
1 TATATAATTTATATATAAAATA
*
476208 TACTATAATTTATTAATATAAATTA
1 TA-TATAATTTA-T-ATATAAAATA
476233 TATA
1 TATA
476237 GTTTATTAAT
Statistics
Matches: 49, Mismatches: 11, Indels: 14
0.66 0.15 0.19
Matches are distributed among these distances:
17 1 0.02
18 6 0.12
19 2 0.04
20 7 0.14
21 7 0.14
22 14 0.29
23 1 0.02
24 4 0.08
25 7 0.14
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TATATAATTTATATATAAAATA
Found at i:476219 original size:20 final size:20
Alignment explanation
Indices: 476191--476250 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
476181 ATATAAATTG
* *
476191 TATAGTTTATTAATATATAC
1 TATAATTTATTAATATAAAC
*
476211 TATAATTTATTAATATAAAT
1 TATAATTTATTAATATAAAC
476231 TATATAGTTTATTAATATAA
1 TATA-A-TTTATTAATATAA
476251 TATTAATTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
20 21 0.60
21 1 0.03
22 13 0.37
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (20 bp):
TATAATTTATTAATATAAAC
Found at i:476241 original size:22 final size:22
Alignment explanation
Indices: 476181--476255 Score: 100
Period size: 22 Copynumber: 3.5 Consensus size: 22
476171 TATACTATAT
*
476181 ATATAAATTGTATAGTTTATTA
1 ATATAAATTATATAGTTTATTA
* *
476203 ATATATACTATA-A-TTTATTA
1 ATATAAATTATATAGTTTATTA
476223 ATATAAATTATATAGTTTATTA
1 ATATAAATTATATAGTTTATTA
476245 ATATAATATTA
1 ATATAA-ATTA
476256 ATTGAAAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
20 17 0.38
21 2 0.04
22 22 0.49
23 4 0.09
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (22 bp):
ATATAAATTATATAGTTTATTA
Found at i:478498 original size:22 final size:20
Alignment explanation
Indices: 478471--478527 Score: 71
Period size: 19 Copynumber: 2.8 Consensus size: 20
478461 TACCACCTGA
478471 GGGTATCGGTACCATTTCATGG
1 GGGTATCGGTACCATTT-A-GG
* *
478493 GGGTATCGATACC-TATAGG
1 GGGTATCGGTACCATTTAGG
478512 GGGTATCGGTACCATT
1 GGGTATCGGTACCATT
478528 CGAGCATTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 14 0.47
20 2 0.07
21 2 0.07
22 12 0.40
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.30
Consensus pattern (20 bp):
GGGTATCGGTACCATTTAGG
Found at i:481317 original size:44 final size:44
Alignment explanation
Indices: 481244--481340 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
481234 CATCAGGGGG
*
481244 TATCGATACCCATTCAAAGATGGTATCGATACCTA-T-TGTAGGGC
1 TATCGATACCCATTCAAAGAGGGTATCGATA-CTAGTCT-TAGGGC
* * * *
481288 TATCGATACCTATTCAAAGGGGGTTTCGATACTAGTCTTAGGGG
1 TATCGATACCCATTCAAAGAGGGTATCGATACTAGTCTTAGGGC
481332 TATCGATAC
1 TATCGATAC
481341 TTTATTCACA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
43 3 0.07
44 42 0.91
45 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.31
Consensus pattern (44 bp):
TATCGATACCCATTCAAAGAGGGTATCGATACTAGTCTTAGGGC
Found at i:487042 original size:19 final size:19
Alignment explanation
Indices: 487018--487069 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
487008 ACCATTACAT
*
487018 GGGGTATCGATACCTATGG
1 GGGGTATCGATACCTATAG
487037 GGGGTATCGATACCTATAG
1 GGGGTATCGATACCTATAG
*
487056 GGGGTATCGGTACC
1 GGGGTATCGATACC
487070 ATTCGAGCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.21, C:0.17, G:0.37, T:0.25
Consensus pattern (19 bp):
GGGGTATCGATACCTATAG
Found at i:488525 original size:20 final size:20
Alignment explanation
Indices: 488500--488537 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
488490 CACATGTTAA
488500 AGAATGCATCAATGCACTGT
1 AGAATGCATCAATGCACTGT
* *
488520 AGAATGTATCGATGCACT
1 AGAATGCATCAATGCACT
488538 TCAAAGGGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
AGAATGCATCAATGCACTGT
Found at i:490109 original size:23 final size:23
Alignment explanation
Indices: 490083--490146 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
490073 GGACATTATA
* *
490083 TGGCACTACGGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTAAG
490106 TGGCACTTCGGTGCATTTCTAAG
1 TGGCACTTCGGTGCATTTCTAAG
*
490129 CGGCACTTCGGTGCATTT
1 TGGCACTTCGGTGCATTT
490147 ACATGAGCTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.33
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTAAG
Found at i:491373 original size:18 final size:18
Alignment explanation
Indices: 491350--491385 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
491340 TGTGTTTTAT
491350 GTGGTCCTTCGAGACATA
1 GTGGTCCTTCGAGACATA
*
491368 GTGGTCGTTCGAGACATA
1 GTGGTCCTTCGAGACATA
491386 ATTGTCCTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (18 bp):
GTGGTCCTTCGAGACATA
Found at i:492407 original size:102 final size:103
Alignment explanation
Indices: 492276--492462 Score: 256
Period size: 102 Copynumber: 1.8 Consensus size: 103
492266 CATCCAAAAA
* *
492276 CCCTCATTTGATATTTATAAACACTAAAACCC-AAACCCTATCCTA-TTTTTT-GATCAAACACC
1 CCCTCATTTGATATTTAAAAACACTAAAACCCAAAACCC-AACCTATTTTTTTCGATCAAACACC
*
492338 TAAAAATTCAACCTTTGTTCATCCGTTTTCATCCCCAAAC
65 -AAAAATTCAACCCTTGTTCATCCGTTTTCATCCCCAAAC
* *
492378 CCCTCATTTGATCTTTAAAAACA-TCAAAACCCAAAACCCAACCTATTTTTTTCGATCAAACGCC
1 CCCTCATTTGATATTTAAAAACACT-AAAACCCAAAACCCAACCTATTTTTTTCGATCAAACACC
**
492442 CCAAATTCAACCCTTGTTCAT
65 AAAAATTCAACCCTTGTTCAT
492463 TCTAGTTTAT
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
101 1 0.01
102 33 0.45
103 30 0.41
104 10 0.14
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (103 bp):
CCCTCATTTGATATTTAAAAACACTAAAACCCAAAACCCAACCTATTTTTTTCGATCAAACACCA
AAAATTCAACCCTTGTTCATCCGTTTTCATCCCCAAAC
Found at i:492489 original size:102 final size:96
Alignment explanation
Indices: 492264--492713 Score: 315
Period size: 98 Copynumber: 4.6 Consensus size: 96
492254 TTTATTTGTG
** * ** * * *
492264 TTCATCCAAAAACCCTCATTTGATATTTATAAACACTAAAACCCAAACCCTATCCTATTTTTTGA
1 TTCATCCTCAAACCCTTATTTGATCCTTAAAAACAC-AAAACCAAAACCC-AACCTATTTTTTGA
** *
492329 TCAAACACCTAAAAATTCAACCTTTGTTCATCCGT-T
64 TCAAA-ACC-CCAAATTCAACCCTTGTTCAT-C-TAT
* * *
492365 TTCATCCCCAAACCCCTCATTTGATCTTTAAAAACATCAAAACCCAAAACCCAACCTATTTTTTT
1 TTCATCCTCAAA-CCCTTATTTGATCCTTAAAAACA-CAAAA-CCAAAACCCAACCTA-TTTTTT
*
492430 CGATCAAACGCCCCAAATTCAACCCTTGTTCATTCTAGT
62 -GATCAAA-ACCCCAAATTCAACCCTTGTTCA-TCTA-T
* * * * ** *
492469 TT-ATCCTTAAACCCTTATTTGATCCTT----ACA-AACACCTAAATCCAAATTTTTTTTTGATC
1 TTCATCCTCAAACCCTTATTTGATCCTTAAAAACACAAAACCAAAACCCAACCTATTTTTTGATC
* * *
492528 AAAACCCCAAATTCAACCTTTGTTTATCCAT
66 AAAACCCCAAATTCAACCCTTGTTCATCTAT
* ** *
492559 ATTCATCCAT-AAACCCTTATTCGATCCTTAAAAACACCCAAAATAAAAACCCAACCTATATTTT
1 -TTCATCC-TCAAACCCTTATTTGATCCTTAAAAACA--CAAAACCAAAACCCAACCTATTTTTT
* * * * *
492623 GAT-TAAACCCTACATTTAACCCTTATTCATCTAT
62 GATCAAAACCCCAAATTCAACCCTTGTTCATCTAT
* * *
492657 ATTCATCCTCAAACCCTTATTTGATCCTTACAAACACCCAAAATCAAAACTCAACCT
1 -TTCATCCTCAAACCCTTATTTGATCCTTA-AAA-ACACAAAACCAAAACCCAACCT
492714 GGTTTTCTAG
Statistics
Matches: 282, Mismatches: 46, Indels: 45
0.76 0.12 0.12
Matches are distributed among these distances:
90 1 0.00
91 5 0.02
92 42 0.15
93 8 0.03
94 6 0.02
95 10 0.04
96 6 0.02
97 1 0.00
98 70 0.25
99 22 0.08
100 2 0.01
101 10 0.04
102 45 0.16
103 40 0.14
104 14 0.05
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.32
Consensus pattern (96 bp):
TTCATCCTCAAACCCTTATTTGATCCTTAAAAACACAAAACCAAAACCCAACCTATTTTTTGATC
AAAACCCCAAATTCAACCCTTGTTCATCTAT
Found at i:492542 original size:92 final size:93
Alignment explanation
Indices: 492423--492596 Score: 244
Period size: 92 Copynumber: 1.9 Consensus size: 93
492413 ACCCAACCTA
* * * *
492423 TTTTTTTCGATCAAACGCCCCAAATTCAACCCTTGTTCATTC-TAGTTTATCCTTAAACCCTTAT
1 TTTTTTTCGATCAAACACCCCAAATTCAACCCTTGTTCATCCATA-TTCATCCATAAACCCTTAT
* *
492487 TTGATCCTTACAAACACCTAAATCCAAAT
65 TCGATCCTTAAAAACACCTAAATCCAAAT
* * *
492516 TTTTTTTTGATCAAA-ACCCCAAATTCAACCTTTGTTTATCCATATTCATCCATAAACCCTTATT
1 TTTTTTTCGATCAAACACCCCAAATTCAACCCTTGTTCATCCATATTCATCCATAAACCCTTATT
492580 CGATCCTTAAAAACACC
66 CGATCCTTAAAAACACC
492597 CAAAATAAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
92 55 0.77
93 16 0.23
ACGTcount: A:0.31, C:0.28, G:0.05, T:0.37
Consensus pattern (93 bp):
TTTTTTTCGATCAAACACCCCAAATTCAACCCTTGTTCATCCATATTCATCCATAAACCCTTATT
CGATCCTTAAAAACACCTAAATCCAAAT
Found at i:493217 original size:2 final size:2
Alignment explanation
Indices: 493212--493246 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
493202 TTTAAATTTT
493212 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 T
493247 TGACCCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:495840 original size:29 final size:30
Alignment explanation
Indices: 495765--495850 Score: 90
Period size: 29 Copynumber: 2.9 Consensus size: 30
495755 ATTAACTTTT
*
495765 TAATGATTATAATTAATTTTATTAATCATG
1 TAATCATTATAATTAATTTTATTAATCATG
* *
495795 T--TCAATATCAATAAATTATT-TTAA-CATG
1 TAATCATTAT-AATTAATT-TTATTAATCATG
*
495823 TAATCATTATAATTAATTTAATTAATCA
1 TAATCATTATAATTAATTTTATTAATCA
495851 CGTTCAATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
28 11 0.25
29 22 0.50
30 11 0.25
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (30 bp):
TAATCATTATAATTAATTTTATTAATCATG
Found at i:504628 original size:18 final size:18
Alignment explanation
Indices: 504605--504640 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
504595 CAGCAGCACA
504605 GATAGAAGAAAGAAGCAG
1 GATAGAAGAAAGAAGCAG
*
504623 GATAGAAGAAAGATGCAG
1 GATAGAAGAAAGAAGCAG
504641 CACTCTATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.33, T:0.08
Consensus pattern (18 bp):
GATAGAAGAAAGAAGCAG
Found at i:512057 original size:92 final size:92
Alignment explanation
Indices: 511900--512083 Score: 368
Period size: 92 Copynumber: 2.0 Consensus size: 92
511890 ATACTTTAAA
511900 AAATATGTACGAAATATTTTATTTATAAATATTATATCAACAAATAATTATAAATAGAGTGATAA
1 AAATATGTACGAAATATTTTATTTATAAATATTATATCAACAAATAATTATAAATAGAGTGATAA
511965 AAAAAACTTGTATACAATAGTTATTAG
66 AAAAAACTTGTATACAATAGTTATTAG
511992 AAATATGTACGAAATATTTTATTTATAAATATTATATCAACAAATAATTATAAATAGAGTGATAA
1 AAATATGTACGAAATATTTTATTTATAAATATTATATCAACAAATAATTATAAATAGAGTGATAA
512057 AAAAAACTTGTATACAATAGTTATTAG
66 AAAAAACTTGTATACAATAGTTATTAG
512084 TCTCTTAGGT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (92 bp):
AAATATGTACGAAATATTTTATTTATAAATATTATATCAACAAATAATTATAAATAGAGTGATAA
AAAAAACTTGTATACAATAGTTATTAG
Found at i:517498 original size:17 final size:17
Alignment explanation
Indices: 517476--517508 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
517466 TTTCGGTTTG
517476 AAAAAAACCAGTTTTTT
1 AAAAAAACCAGTTTTTT
*
517493 AAAAAAACCGGTTTTT
1 AAAAAAACCAGTTTTT
517509 AATCCGGTAA
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:0.45, C:0.12, G:0.09, T:0.33
Consensus pattern (17 bp):
AAAAAAACCAGTTTTTT
Found at i:517581 original size:21 final size:21
Alignment explanation
Indices: 517535--517582 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
517525 CGGTCATCCA
*** *
517535 ATTTTTTAAACCTTGGACCGG
1 ATTTTTTAAACCCCAGACCAG
517556 A-TTTTTAAACCCCAGACCAG
1 ATTTTTTAAACCCCAGACCAG
517576 ATTTTTT
1 ATTTTTT
517583 TCAAACCGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (21 bp):
ATTTTTTAAACCCCAGACCAG
Found at i:524319 original size:41 final size:41
Alignment explanation
Indices: 524255--524442 Score: 168
Period size: 41 Copynumber: 4.6 Consensus size: 41
524245 TTTTGCGTAA
* * *
524255 TTTGTTTCAAAAACGCCACTAAAGAATGATTCCTTTGCGGCA
1 TTTGTTT-AGAAACGCCACTAAAGAATGATTCCTTTGCGACG
**
524297 TTTGTTTAGAAACGCCACTAAAG--T-ATTAGGTTGTAGCGACG
1 TTTGTTTAGAAACGCCACTAAAGAATGATT-CCTT-T-GCGACG
* * * *
524338 TTTGTTTAAAAATGCCACTAAAGAATGATTCTTTTGCGGCG
1 TTTGTTTAGAAACGCCACTAAAGAATGATTCCTTTGCGACG
* * * * *
524379 TTTGTTTAGAAACACCACTAAAGTAGGATT-CTGTGATGACG
1 TTTGTTTAGAAACGCCACTAAAGAATGATTCCTTTG-CGACG
*
524420 TTTGTTTAGAAACACCACTAAAG
1 TTTGTTTAGAAACGCCACTAAAG
524443 TAGGATTTTG
Statistics
Matches: 120, Mismatches: 19, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
38 3 0.03
39 3 0.03
40 4 0.03
41 96 0.80
42 8 0.07
43 3 0.03
44 3 0.03
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Consensus pattern (41 bp):
TTTGTTTAGAAACGCCACTAAAGAATGATTCCTTTGCGACG
Found at i:524420 original size:82 final size:82
Alignment explanation
Indices: 524255--524485 Score: 252
Period size: 82 Copynumber: 2.8 Consensus size: 82
524245 TTTTGCGTAA
* * *
524255 TTTGTTTCAAAAACGCCACTAAAGAATGATTCCTTTGCGGCATTTGTTTAGAAACGCCACTAAAG
1 TTTGTTT-AAAAACGCCACTAAAGAATGATTCTTTTGCGGCGTTTGTTTAGAAACACCACTAAAG
**
524320 TATTAGGTTGTAGCGACG
65 TAGGAGGTTGTAGCGACG
*
524338 TTTGTTTAAAAATGCCACTAAAGAATGATTCTTTTGCGGCGTTTGTTTAGAAACACCACTAAAGT
1 TTTGTTTAAAAACGCCACTAAAGAATGATTCTTTTGCGGCGTTTGTTTAGAAACACCACTAAAGT
* *
524403 AGGA-TTCTGT-GATGACG
66 AGGAGGT-TGTAG-CGACG
* * * * * * ** *
524420 TTTGTTTAGAAACACCACTAAAGTAGGATT-TTGTGATGAAGTTTGTTTAAAAACACCACTAAAG
1 TTTGTTTAAAAACGCCACTAAAGAATGATTCTTTTG-CGGCGTTTGTTTAGAAACACCACTAAAG
524484 TA
65 TA
524486 ATTATATGTA
Statistics
Matches: 127, Mismatches: 18, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
81 6 0.05
82 114 0.90
83 7 0.06
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.33
Consensus pattern (82 bp):
TTTGTTTAAAAACGCCACTAAAGAATGATTCTTTTGCGGCGTTTGTTTAGAAACACCACTAAAGT
AGGAGGTTGTAGCGACG
Found at i:524443 original size:41 final size:41
Alignment explanation
Indices: 524377--524485 Score: 191
Period size: 41 Copynumber: 2.7 Consensus size: 41
524367 TCTTTTGCGG
524377 CGTTTGTTTAGAAACACCACTAAAGTAGGATTCTGTGATGA
1 CGTTTGTTTAGAAACACCACTAAAGTAGGATTCTGTGATGA
*
524418 CGTTTGTTTAGAAACACCACTAAAGTAGGATTTTGTGATGA
1 CGTTTGTTTAGAAACACCACTAAAGTAGGATTCTGTGATGA
* *
524459 AGTTTGTTTAAAAACACCACTAAAGTA
1 CGTTTGTTTAGAAACACCACTAAAGTA
524486 ATTATATGTA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 65 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (41 bp):
CGTTTGTTTAGAAACACCACTAAAGTAGGATTCTGTGATGA
Found at i:524504 original size:82 final size:81
Alignment explanation
Indices: 524255--524525 Score: 221
Period size: 82 Copynumber: 3.3 Consensus size: 81
524245 TTTTGCGTAA
* * * *
524255 TTTGTTTCAAAAACGCCACTAAAGAATGATTCCTT-TGCGGCA-TTTGTTTAGAAACGCCACTAA
1 TTTGTTT-AAAAACACCACTAAAGAAGGATT-CTTGTGC-GAAGTTTGTTTAGAAACACCACTAA
524318 AGT-ATTAGGTTGTAGCGACG
63 AGTAATTA--TTGTAGCGACG
** * * **
524338 TTTGTTTAAAAATGCCACTAAAGAATGATTCTTTTGCGGCGTTTGTTTAGAAACACCACTAAAGT
1 TTTGTTTAAAAACACCACTAAAGAAGGATTCTTGTGCGAAGTTTGTTTAGAAACACCACTAAAGT
* *
524403 AGGATT-CTGT-GATGACG
66 A--ATTATTGTAG-CGACG
* * * *
524420 TTTGTTTAGAAACACCACTAAAGTAGGATT-TTGTGATGAAGTTTGTTTAAAAACACCACTAAAG
1 TTTGTTTAAAAACACCACTAAAGAAGGATTCTTGTG-CGAAGTTTGTTTAGAAACACCACTAAAG
*
524484 TAATTATATGTAGCGGCG
65 TAATTAT-TGTAGCGACG
** *
524502 TTTGTGAAATAAACGCCACTAAAG
1 TTTGTTTAA-AAACACCACTAAAG
524526 TACAAGTTTT
Statistics
Matches: 154, Mismatches: 23, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
80 3 0.02
81 9 0.06
82 118 0.77
83 21 0.14
85 3 0.02
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (81 bp):
TTTGTTTAAAAACACCACTAAAGAAGGATTCTTGTGCGAAGTTTGTTTAGAAACACCACTAAAGT
AATTATTGTAGCGACG
Found at i:524505 original size:41 final size:40
Alignment explanation
Indices: 524297--524527 Score: 150
Period size: 41 Copynumber: 5.6 Consensus size: 40
524287 CTTTGCGGCA
* *
524297 TTTGTTTAGAAACGCCACTAAAGT-ATTAGGTTGTAGCGACG
1 TTTGTTTAAAAACACCACTAAAGTAATTA--TTGTAGCGACG
** * * * *
524338 TTTGTTTAAAAATGCCACTAAAG-AATGATTCTTTTGCGGCG
1 TTTGTTTAAAAACACCACTAAAGTAATTA-T-TGTAGCGACG
* * *
524379 TTTGTTTAGAAACACCACTAAAGTAGGATT-CTGT-GATGACG
1 TTTGTTTAAAAACACCACTAAAGTA--ATTATTGTAG-CGACG
* * *
524420 TTTGTTTAGAAACACCACTAAAGTAGGATT-TTGT-GATGAAG
1 TTTGTTTAAAAACACCACTAAAGTA--ATTATTGTAG-CGACG
*
524461 TTTGTTTAAAAACACCACTAAAGTAATTATATGTAGCGGCG
1 TTTGTTTAAAAACACCACTAAAGTAATTAT-TGTAGCGACG
** *
524502 TTTGTGAAATAAACGCCACTAAAGTA
1 TTTGTTTAA-AAACACCACTAAAGTA
524528 CAAGTTTTAG
Statistics
Matches: 156, Mismatches: 24, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
39 3 0.02
40 3 0.02
41 131 0.84
42 17 0.11
44 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.32
Consensus pattern (40 bp):
TTTGTTTAAAAACACCACTAAAGTAATTATTGTAGCGACG
Found at i:534264 original size:3 final size:3
Alignment explanation
Indices: 534258--534353 Score: 124
Period size: 3 Copynumber: 32.0 Consensus size: 3
534248 CCATTCGGTT
*
534258 TTA TTA TTA TTA TTA TTA TTA ATA TTA TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
* * *
534304 TTA TTTA TTA TTA -TA TTA TAA TTA -TA ATA TTA TTA ATA TTA TTA
1 TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
534348 TTA TTA
1 TTA TTA
534354 CAGGCCCAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
2 4 0.05
3 72 0.88
4 6 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:535546 original size:13 final size:13
Alignment explanation
Indices: 535528--535555 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
535518 ATTTATTTTA
535528 ATTTTAATTTGAT
1 ATTTTAATTTGAT
535541 ATTTTAATTTGAT
1 ATTTTAATTTGAT
535554 AT
1 AT
535556 AAATTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (13 bp):
ATTTTAATTTGAT
Found at i:535800 original size:15 final size:14
Alignment explanation
Indices: 535762--535812 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
535752 CATTGTTTAG
535762 TTATAT-TTTAATT
1 TTATATATTTAATT
* *
535775 TTATATGTTTATTT
1 TTATATATTTAATT
535789 TTAATATATTTAATT
1 TT-ATATATTTAATT
535804 ATTAT-TATT
1 -TTATATATT
535813 ATTATTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 6 0.19
14 12 0.38
15 12 0.38
16 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TTATATATTTAATT
Found at i:536745 original size:13 final size:13
Alignment explanation
Indices: 536727--536765 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
536717 TTTCATAATA
536727 TTTATTATATTTT
1 TTTATTATATTTT
*
536740 TTTATTA-ATGTT
1 TTTATTATATTTT
*
536752 TTTATTTTATTTT
1 TTTATTATATTTT
536765 T
1 T
536766 AGATATTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (13 bp):
TTTATTATATTTT
Found at i:539615 original size:12 final size:12
Alignment explanation
Indices: 539598--539622 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
539588 CTAATTTCTA
539598 TGAAGAAAGAAG
1 TGAAGAAAGAAG
539610 TGAAGAAAGAAG
1 TGAAGAAAGAAG
539622 T
1 T
539623 AATATGGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.32, T:0.12
Consensus pattern (12 bp):
TGAAGAAAGAAG
Found at i:547627 original size:17 final size:17
Alignment explanation
Indices: 547605--547640 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
547595 AAGTTTATCT
547605 TTTTGAAATTCAATTTA
1 TTTTGAAATTCAATTTA
547622 TTTTGAAATTCAATTTA
1 TTTTGAAATTCAATTTA
547639 TT
1 TT
547641 CTTTTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (17 bp):
TTTTGAAATTCAATTTA
Found at i:548290 original size:22 final size:22
Alignment explanation
Indices: 548260--548344 Score: 116
Period size: 22 Copynumber: 3.9 Consensus size: 22
548250 ACATCTACAT
* *
548260 TCTTTAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAAATTCTC
*
548282 TCTTAAAAGATGATAAATTCTC
1 TCTTCAAAGATGATAAATTCTC
*
548304 TCTTCAAAGATGATATATTCTC
1 TCTTCAAAGATGATAAATTCTC
* *
548326 TCTTCAAAGAAGAAAAATT
1 TCTTCAAAGATGATAAATT
548345 TATTGGATTT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 56 1.00
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (22 bp):
TCTTCAAAGATGATAAATTCTC
Found at i:548908 original size:20 final size:20
Alignment explanation
Indices: 548846--548909 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
548836 TCTTGAGAAA
548846 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* ***
548866 -ATC-TGAA-GAGGAAGAAGAA
1 GTTCAT-AATGA-GAAGAACTT
548885 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
548905 GTTCA
1 GTTCA
548910 ACTTTTTGCT
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
18 3 0.10
19 10 0.32
20 15 0.48
21 3 0.10
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:548985 original size:122 final size:122
Alignment explanation
Indices: 548841--549281 Score: 656
Period size: 122 Copynumber: 3.6 Consensus size: 122
548831 AATTTTCTTG
*
548841 AGAA-AGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACT
1 AGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAACT
* * * * * *
548904 TGTTCAACTTTTTGCTTGATTCTATCACATAAGGACATAGATCAGCATCAATATTTCC
65 TGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCATCATCAATATTTCC
* * * *
548962 AGAAGTGTTCATAATGAGAAGAACTCCTCTGAAGAAGGAGAAGAAATTCATAATGAGAAGAATTT
1 AGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAACTT
549027 GTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCATCATCAACT-TTTCC
66 GTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCATCATCAA-TATTTCC
* *
549084 AGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAAC
1 AGA-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAAC
* * * *
549148 TTGTTCAACCTTTTGCATGACTATATCATAGAAGGAGATAGATCATCATTAACATTTCC
64 TTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCATCATCAATATTTCC
*
549207 AGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAATTT
1 AGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAACTT
549272 GTTCAACCTT
66 GTTCAACCTT
549282 GCCTTAATTC
Statistics
Matches: 289, Mismatches: 24, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
121 4 0.01
122 171 0.59
123 114 0.39
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.27
Consensus pattern (122 bp):
AGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAACTT
GTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCATCATCAATATTTCC
Found at i:549153 original size:20 final size:20
Alignment explanation
Indices: 549091--549154 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
549081 TCCAGAGAAA
549091 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* ***
549111 -ATC-TGAA-GAGGAAGAAGAA
1 GTTCAT-AATGA-GAAGAACTT
549130 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
549150 GTTCA
1 GTTCA
549155 ACCTTTTGCA
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
18 3 0.10
19 10 0.32
20 15 0.48
21 3 0.10
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:549153 original size:245 final size:234
Alignment explanation
Indices: 548715--549281 Score: 794
Period size: 245 Copynumber: 2.4 Consensus size: 234
548705 CATTCAATGG
* *
548715 ATCAACATTTCCGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCATA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCATA
* * * ** * **
548780 ATGAGAAAAATTTGTTCAACCTTTTGCTTTAATTCATCACTCGATGGATCAAATTTTCTTGAGAA
65 ATGAGAAGAATTTGTTCAACCTTTTGCATGAATTCATCACGAGATGCATCAAATTTTCCAGAGAA
548845 AGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
130 AGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * * * *
548910 ACTTTTTGCTTGATTCTATCACATAAGGACATAGATCAGC
195 ACCTTTTGCATGACTATATCACAGAAGGACATAGATCAGC
* * * *
548950 ATCAATATTTCCAGAAGTGTTCATAATGAGAAGAACTCCTCTGAAGAAGGAGAAGAAATTCATAA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAA
*
549015 TGAGAAGAATTTGTTCAACCTTTTGCATG-ACTCTATCACAGAAGGAGATAGATCATCATCAACT
66 TGAGAAGAATTTGTTCAACCTTTTGCATGAATTC-ATCAC-----GAGAT-G--CATCA--AA-T
549079 TTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
119 TTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
* * *
549144 GAACTTGTTCAACCTTTTGCATGACTATATCATAGAAGGAGATAGATCATC
184 GAACTTGTTCAACCTTTTGCATGACTATATCACAGAAGGACATAGATCAGC
*
549195 ATTAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAA
549260 TGAGAAGAATTTGTTCAACCTT
66 TGAGAAGAATTTGTTCAACCTT
549282 GCCTTAATTC
Statistics
Matches: 292, Mismatches: 28, Indels: 14
0.87 0.08 0.04
Matches are distributed among these distances:
233 3 0.01
234 44 0.15
235 46 0.16
239 3 0.01
240 1 0.00
242 4 0.01
244 2 0.01
245 189 0.65
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (234 bp):
ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAA
TGAGAAGAATTTGTTCAACCTTTTGCATGAATTCATCACGAGATGCATCAAATTTTCCAGAGAAA
GTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
CCTTTTGCATGACTATATCACAGAAGGACATAGATCAGC
Found at i:549649 original size:3 final size:3
Alignment explanation
Indices: 549643--549739 Score: 92
Period size: 3 Copynumber: 32.0 Consensus size: 3
549633 CCATTCGGTT
* *
549643 TTA TTA TTA ATA TTA TTA TTA TTA TTA TGGA TTTA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA -TTA -TTA TTA TTA TTA
* * *
549691 TTA TTA TTA TTA -TA TTA TAA TT- TTAA TTA -TA ATA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
549734 TTA TTA
1 TTA TTA
549740 CAGGCCTAAA
Statistics
Matches: 81, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
2 6 0.07
3 66 0.81
4 8 0.10
5 1 0.01
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:549719 original size:23 final size:23
Alignment explanation
Indices: 549643--549739 Score: 81
Period size: 23 Copynumber: 4.1 Consensus size: 23
549633 CCATTCGGTT
* *
549643 TTATTATTAATATTATTATTATTA
1 TTATTATTATTA-TATTATAATTA
* *
549667 TTATGGATTTATT-TATTATTATTA
1 TTAT-TA-TTATTATATTATAATTA
549691 TTATTATTATTATATTATAATT-
1 TTATTATTATTATATTATAATTA
* * *
549713 TTAATTATAATAATATTATTATTA
1 TT-ATTATTATTATATTATAATTA
549737 TTA
1 TTA
549740 CAGGCCTAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
22 7 0.11
23 28 0.46
24 21 0.34
25 1 0.02
26 4 0.07
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (23 bp):
TTATTATTATTATATTATAATTA
Found at i:551089 original size:14 final size:13
Alignment explanation
Indices: 551017--551107 Score: 51
Period size: 14 Copynumber: 6.5 Consensus size: 13
551007 TTTTATTGCT
551017 TTTTATATTTTAA
1 TTTTATATTTTAA
* *
551030 ATATATAGTTTTAA
1 TTTTATA-TTTTAA
551044 TTTTATTCACTGTTT-A
1 TTTTA-T-A-T-TTTAA
*
551060 -GTTATATTTTAA
1 TTTTATATTTTAA
*
551072 TTTTATATGTTTAT
1 TTTTATAT-TTTAA
551086 TTTTAATATATTTAA
1 TTTT-ATAT-TTTAA
551101 TTATTAT
1 TT-TTAT
551108 TATTATTATT
Statistics
Matches: 59, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
11 3 0.05
12 2 0.03
13 12 0.20
14 18 0.31
15 16 0.27
16 5 0.08
17 3 0.05
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (13 bp):
TTTTATATTTTAA
Found at i:551099 original size:15 final size:14
Alignment explanation
Indices: 551061--551111 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
551051 CACTGTTTAG
551061 TTATAT-TTTAATT
1 TTATATATTTAATT
* *
551074 TTATATGTTTATTT
1 TTATATATTTAATT
551088 TTAATATATTTAATT
1 TT-ATATATTTAATT
551103 ATTAT-TATT
1 -TTATATATT
551112 ATTATTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 6 0.19
14 12 0.38
15 12 0.38
16 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TTATATATTTAATT
Found at i:557008 original size:16 final size:16
Alignment explanation
Indices: 556973--557035 Score: 67
Period size: 16 Copynumber: 4.0 Consensus size: 16
556963 GTTTACTTCA
556973 GAATGATT--AAGCGCT
1 GAATGATTCAAAG-GCT
* *
556988 GAATGATTCAAATGTT
1 GAATGATTCAAAGGCT
*
557004 GAATGATTCAGAGGCT
1 GAATGATTCAAAGGCT
*
557020 GAATGATTCAGAGGCT
1 GAATGATTCAAAGGCT
557036 CTGAATGGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
15 8 0.20
16 31 0.76
17 2 0.05
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.29
Consensus pattern (16 bp):
GAATGATTCAAAGGCT
Found at i:557172 original size:23 final size:23
Alignment explanation
Indices: 557107--557172 Score: 114
Period size: 23 Copynumber: 2.9 Consensus size: 23
557097 TGTACTTCTG
* *
557107 TGCTGAATCATTCAGCACTTTTT
1 TGCTGAATCAGTCAGCACTGTTT
557130 TGCTGAATCAGTCAGCACTGTTT
1 TGCTGAATCAGTCAGCACTGTTT
557153 TGCTGAATCAGTCAGCACTG
1 TGCTGAATCAGTCAGCACTG
557173 AATCATTCAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.35
Consensus pattern (23 bp):
TGCTGAATCAGTCAGCACTGTTT
Found at i:566671 original size:3 final size:3
Alignment explanation
Indices: 566663--566715 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
566653 TGTTTCCATA
566663 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
566711 AAT AA
1 AAT AA
566716 AAGAGAAGCC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:567578 original size:28 final size:28
Alignment explanation
Indices: 567547--567600 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
567537 TGAGGACTCT
* *
567547 TGCAACACAACTAGAGAAAACCAACACC
1 TGCAACACAACAAAAGAAAACCAACACC
* *
567575 TGCATCACAGCAAAAGAAAACCAACA
1 TGCAACACAACAAAAGAAAACCAACA
567601 AAAACAAGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.52, C:0.30, G:0.11, T:0.07
Consensus pattern (28 bp):
TGCAACACAACAAAAGAAAACCAACACC
Found at i:570480 original size:21 final size:21
Alignment explanation
Indices: 570456--570496 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
570446 GTGTTGTGAG
570456 TAATATAAAAGTATACACAAA
1 TAATATAAAAGTATACACAAA
* **
570477 TAATGTGCAAGTATACACAA
1 TAATATAAAAGTATACACAA
570497 TCGCTCAAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.12, G:0.10, T:0.24
Consensus pattern (21 bp):
TAATATAAAAGTATACACAAA
Found at i:574719 original size:18 final size:19
Alignment explanation
Indices: 574687--574726 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
574677 ATGGAGAGAG
*
574687 AAAAGTAAAATAAAGAAAT
1 AAAAGTAAAAGAAAGAAAT
*
574706 AAAA-TAAAAGAAAGGAAT
1 AAAAGTAAAAGAAAGAAAT
574724 AAA
1 AAA
574727 TCAAAAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (19 bp):
AAAAGTAAAAGAAAGAAAT
Found at i:578657 original size:16 final size:17
Alignment explanation
Indices: 578636--578670 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
578626 TCATAGGACT
578636 AAAATAAAATG-AATAA
1 AAAATAAAATGAAATAA
*
578652 AAAATAAAGTGAAATAA
1 AAAATAAAATGAAATAA
578669 AA
1 AA
578671 GTATTGCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (17 bp):
AAAATAAAATGAAATAA
Found at i:580354 original size:47 final size:46
Alignment explanation
Indices: 580286--580427 Score: 212
Period size: 47 Copynumber: 3.0 Consensus size: 46
580276 TAAAATCTCA
580286 TTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCGAAGGTTT
1 TTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCGAAGGTTT
*
580332 TTTGAAAAACATCCTGCACTGAAGGTCTTATGGATGACCGGAAGGCTT
1 TTTG-AAAACATCCTGCACTGAAGGTCTTATGGATGACC-GAAGGTTT
* * * *
580380 TTTGAAAATATCTTACACTGAAGGTCTTATGGATGACCCAAAGGTTT
1 TTTGAAAACATCCTGCACTGAAGGTCTTATGGATGA-CCGAAGGTTT
580427 T
1 T
580428 ACAACTTACC
Statistics
Matches: 87, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
46 4 0.05
47 70 0.80
48 13 0.15
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.31
Consensus pattern (46 bp):
TTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCGAAGGTTT
Found at i:581124 original size:42 final size:41
Alignment explanation
Indices: 581056--581136 Score: 126
Period size: 42 Copynumber: 2.0 Consensus size: 41
581046 AAGGACTTAT
* * *
581056 CATCTTGCTCGAAAACTGACAGATGACCCGAAGGTTTTAAG
1 CATCATGCTCGAAAACTAACAGATGACCCGAAGGATTTAAG
581097 CATCATGCTCGAAAGACTAACAGATGACCCGAAGGATTTA
1 CATCATGCTCGAAA-ACTAACAGATGACCCGAAGGATTTA
581137 CAAATTTGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
41 13 0.36
42 23 0.64
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (41 bp):
CATCATGCTCGAAAACTAACAGATGACCCGAAGGATTTAAG
Found at i:581439 original size:249 final size:249
Alignment explanation
Indices: 580449--581449 Score: 1675
Period size: 248 Copynumber: 4.0 Consensus size: 249
580439 GGAGGTTTTA
*** * * *
580449 ATTTTCTAGAACATTAAATGAGAAACTTTGGTAATCGGTTTCTCATTTTCATGTGAAAATCATAT
1 ATTTTCTAGAACATTAAATGAGAAACTTTAAAAATCGCTATCTCATTTTCATGCGAAAATCATAT
580514 GTGAACAT-CTACCCAAAGGCTTTACGGATGACCCTAAGGACTTATCATCTTGCTCGAAAGACTG
66 GTGAACATCCTACCCAAAGGCTTTACGGATGACCCTAAGGACTTATCATCTTGCTCGAAAGACTG
* * *
580578 ACAGATGACCCGGAGGTTTTAAGCATCATGCTCGAAAGACTAATAGATGACTCGAAGGATTTACA
131 ACAGATGACCCGAAGGTTTTAAGCATCATGCTCGAAAGACTAACAGATGACCCGAAGGATTTACA
*
580643 AATTTGTGGAAAATACTTTACTAGGTAAGAAACTTCTTACTTTTCAAGAATTTG
196 AATTTGTGGGAAATACTTTACTAGGTAAGAAACTTCTTACTTTTCAAGAATTTG
*
580697 ATTTTCTAGAACATTAAATGAGAAACTTTAAAAATCGCTATCTCATTTTCATGCGAAAATAATAT
1 ATTTTCTAGAACATTAAATGAGAAACTTTAAAAATCGCTATCTCATTTTCATGCGAAAATCATAT
* * * *
580762 GTGAACATCCTACCCTAAGGCTTTACGGATAATCCTAAGGACTTATCATCTTGCT-GAAAGCCTG
66 GTGAACATCCTACCCAAAGGCTTTACGGATGACCCTAAGGACTTATCATCTTGCTCGAAAGACTG
* *
580826 ACAGATGACCCGAAGGTTTTAAGCATCATGCTCAAAAGACTAACAGATGACCCGAAAGATTTACA
131 ACAGATGACCCGAAGGTTTTAAGCATCATGCTCGAAAGACTAACAGATGACCCGAAGGATTTACA
580891 AATTTGTGGGAAATACTTTACTAGGTAAGAAACTTCTTACTTTTCAAGAATTTG
196 AATTTGTGGGAAATACTTTACTAGGTAAGAAACTTCTTACTTTTCAAGAATTTG
* ** *
580945 ATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCATTATCTCATTTTCATGCGAAAAGCATAT
1 ATTTTCTAGAACATTAAATGAGAAACTTTAAAAATCGCTATCTCATTTTCATGCGAAAATCATAT
* *
581010 GTGAACATCCTACCTAAAGGCTTTACGGATGGCCCTAAGGACTTATCATCTTGCTCGAAA-ACTG
66 GTGAACATCCTACCCAAAGGCTTTACGGATGACCCTAAGGACTTATCATCTTGCTCGAAAGACTG
581074 ACAGATGACCCGAAGGTTTTAAGCATCATGCTCGAAAGACTAACAGATGACCCGAAGGATTTACA
131 ACAGATGACCCGAAGGTTTTAAGCATCATGCTCGAAAGACTAACAGATGACCCGAAGGATTTACA
*
581139 AATTTGTGGGAAATACTTTACTAGGTAAGAAACTTCTTACTTTTGAAGAATTTG
196 AATTTGTGGGAAATACTTTACTAGGTAAGAAACTTCTTACTTTTCAAGAATTTG
* * *
581193 ATTTTCTAGAACATTAAATGAGAAACTTTAAAAATTGCTATCTCATTTTCATGCAAAAATCACAT
1 ATTTTCTAGAACATTAAATGAGAAACTTTAAAAATCGCTATCTCATTTTCATGCGAAAATCATAT
* *
581258 GTGAACATCCTACCCAAAGGCTTTACGGATGGCTCTAAGGACTTATCATCTTGCTCGAAAGACTG
66 GTGAACATCCTACCCAAAGGCTTTACGGATGACCCTAAGGACTTATCATCTTGCTCGAAAGACTG
* * *
581323 ACAGATGACCCAAAGGTTTTAAGCATCATACTCGAAAGACTAACAGATTACCCGAAGGATTTACA
131 ACAGATGACCCGAAGGTTTTAAGCATCATGCTCGAAAGACTAACAGATGACCCGAAGGATTTACA
* *
581388 AATTTGTGGGAAATACTTTACTGGGTAAGAAACTTCTTACTTTTCAAGAATTTC
196 AATTTGTGGGAAATACTTTACTAGGTAAGAAACTTCTTACTTTTCAAGAATTTG
581442 ATTTTCTA
1 ATTTTCTA
581450 AAAAAGATTA
Statistics
Matches: 704, Mismatches: 46, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
248 532 0.76
249 172 0.24
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (249 bp):
ATTTTCTAGAACATTAAATGAGAAACTTTAAAAATCGCTATCTCATTTTCATGCGAAAATCATAT
GTGAACATCCTACCCAAAGGCTTTACGGATGACCCTAAGGACTTATCATCTTGCTCGAAAGACTG
ACAGATGACCCGAAGGTTTTAAGCATCATGCTCGAAAGACTAACAGATGACCCGAAGGATTTACA
AATTTGTGGGAAATACTTTACTAGGTAAGAAACTTCTTACTTTTCAAGAATTTG
Found at i:581936 original size:25 final size:25
Alignment explanation
Indices: 581902--581951 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
581892 TTTCATTTAC
581902 GGAGCTCTTGTTACAGTCAGAATTA
1 GGAGCTCTTGTTACAGTCAGAATTA
581927 GGAGCTCTTGTTACAGTCAGAATTA
1 GGAGCTCTTGTTACAGTCAGAATTA
581952 TGCCTCAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (25 bp):
GGAGCTCTTGTTACAGTCAGAATTA
Found at i:584150 original size:9 final size:9
Alignment explanation
Indices: 584138--584174 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
584128 ATTTAATTTA
*
584138 TTTTTTTCC
1 TTTTTTTCT
584147 TTTTTTTCT
1 TTTTTTTCT
*
584156 TTTTTTTTT
1 TTTTTTTCT
584165 TTTTTTTCT
1 TTTTTTTCT
584174 T
1 T
584175 ATGGATGAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:590208 original size:20 final size:20
Alignment explanation
Indices: 590183--590239 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
590173 ATTAATGACT
590183 AAAATAATAATAAAATAAAG
1 AAAATAATAATAAAATAAAG
590203 AAAAT-AT-ATCAAAATAAAAG
1 AAAATAATAAT-AAAAT-AAAG
* *
590223 AAAATAAAAATATAATA
1 AAAATAATAATAAAATA
590240 GCTAATTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 2 0.06
19 7 0.23
20 15 0.48
21 5 0.16
22 2 0.06
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.21
Consensus pattern (20 bp):
AAAATAATAATAAAATAAAG
Found at i:593540 original size:23 final size:23
Alignment explanation
Indices: 593473--593540 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
593463 CATTTTATAT
* * *
593473 GGCACTTCGGTGTAATCCTACGT
1 GGCACTTCGGTGCAATTCTACGC
* *
593496 GGCACTACGGTGCATTTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
*
593519 GGCACTTCGGTGCAATTATACG
1 GGCACTTCGGTGCAATTCTACG
593541 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Done.