Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008420.1 Hibiscus syriacus cultivar Beakdansim tig00111200_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: 1020524
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:201885 original size:20 final size:20
Alignment explanation
Indices: 201860--201899 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
201850 ATTGAGTCCT
201860 ATACTCTCTGAAGGAATAGG
1 ATACTCTCTGAAGGAATAGG
201880 ATACTCTCTGAAGGAATAGG
1 ATACTCTCTGAAGGAATAGG
201900 GAGCGGACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (20 bp):
ATACTCTCTGAAGGAATAGG
Found at i:201893 original size:71 final size:71
Alignment explanation
Indices: 201809--201950 Score: 248
Period size: 71 Copynumber: 2.0 Consensus size: 71
201799 ATTGAGTCCT
* *
201809 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCATTGAAGATTGAGTCCTATACTCTCTGAAGG
1 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCATTGAAGATTGAGTCCTATACTCCCTGAACG
201874 AATAGG
66 AATAGG
* *
201880 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTTCTATACTCCCTGAACG
1 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCATTGAAGATTGAGTCCTATACTCCCTGAACG
201945 AATAGG
66 AATAGG
201951 GAGCGGACTC
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.25
Consensus pattern (71 bp):
ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCATTGAAGATTGAGTCCTATACTCCCTGAACG
AATAGG
Found at i:201942 original size:51 final size:52
Alignment explanation
Indices: 201880--202013 Score: 162
Period size: 51 Copynumber: 2.5 Consensus size: 52
201870 AAGGAATAGG
*
201880 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGA-TTGAGTTCT
1 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCATTGAAGATTTGAGTTCT
* * ** *
201931 ATACTCCCTGAACGAATAGGGAGCGGACTCGTTTATTGAAGATTTTTTGAGTTCT
1 ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCATTGAAGA---TTTGAGTTCT
* *
201986 ATACTCTCTGAAGGAAGAGAGAGCGGAC
1 ATACTCTCTGAAGGAATAGGGAGCGGAC
202014 CCGTTTTATT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
51 36 0.52
55 33 0.48
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (52 bp):
ATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCATTGAAGATTTGAGTTCT
Found at i:202046 original size:56 final size:56
Alignment explanation
Indices: 201880--202120 Score: 223
Period size: 55 Copynumber: 4.4 Consensus size: 56
201870 AAGGAATAGG
* * **
201880 ATACTCTCTGAAGGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-GAGT-TCT
1 ATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATTGAAGATTGTTCGAGTCT-T
* * * * * *
201931 ATACTCCCTGAACGAATAGGGAGCGGACTCG-TTTATTGAAGATTTTTTGAGT-TCT
1 ATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATTGAAGATTGTTCGAGTCT-T
* * * *
201986 ATACTCTCTGAAGGAAGAGAGAGCGGACCCGTTTTATTAAAGATTGTTCAAGTCTT
1 ATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATTGAAGATTGTTCGAGTCTT
* * *
202042 ATACTCTCTGAATGAATAGAGAGCAGATACGTTTTA-TGAAGATTGTTCGAGTCTT
1 ATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATTGAAGATTGTTCGAGTCTT
*
202097 ATACT-TCCTGAAGGAATAGGGAGC
1 ATACTCT-CTGAAGGAATAGAGAGC
202121 AGGCTCGTCA
Statistics
Matches: 159, Mismatches: 24, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
51 36 0.23
54 3 0.02
55 70 0.44
56 49 0.31
57 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (56 bp):
ATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATTGAAGATTGTTCGAGTCTT
Found at i:202647 original size:45 final size:45
Alignment explanation
Indices: 202583--202673 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
202573 CAAAAAGGGG
202583 TACTTATTTCTATGTTTCCATTCTCAATTGTTTTTGTAATTTGCT
1 TACTTATTTCTATGTTTCCATTCTCAATTGTTTTTGTAATTTGCT
*
202628 TACTTATTTCTATGTTTCCATTTTCAATTGTTTTTGTAATTTGCT
1 TACTTATTTCTATGTTTCCATTCTCAATTGTTTTTGTAATTTGCT
202673 T
1 T
202674 GTACATGCAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.18, C:0.14, G:0.09, T:0.59
Consensus pattern (45 bp):
TACTTATTTCTATGTTTCCATTCTCAATTGTTTTTGTAATTTGCT
Found at i:212119 original size:141 final size:139
Alignment explanation
Indices: 211872--212152 Score: 512
Period size: 141 Copynumber: 2.0 Consensus size: 139
211862 CTCCCGATAT
211872 TGGGCCTTCTTAAAGCAAGTGCTTCATCACAGATGGATGCTGCAATAGTGGCCTTATCGAGGGAG
1 TGGGCCTTCTTAAAGCAAGTGCTTCATCACAGATGGATGCTGCAATAGTGGCCTTATCGAGGGAG
211937 TTAGCCAAATTGAGAACAGGAAGAGCATCTGCTGGTAATTTCTGGTTTAATTG-ATTTATTTGCA
66 TTAGCCAAATTGAGAACAGGAAGAGCATCTGCTGGTAATTTCTGGTTTAATTGAATTTATTTGCA
212001 TTTTATAAAA
131 -TTTATAAAA
212011 TGGGCCTTCTGTTAAAGCAAGTGCTTCATCACAGATGGATGCTGCAATAGTGGCCTTATCGAGGG
1 TGGGCCTTC--TTAAAGCAAGTGCTTCATCACAGATGGATGCTGCAATAGTGGCCTTATCGAGGG
212076 AGTTAGCCAAATTGAG-ACAGGAAGAGCATCTGCTGGTATATTTCTGGTTTAATTGAATTTATTT
64 AGTTAGCCAAATTGAGAACAGGAAGAGCATCTGCTGGTA-ATTTCTGGTTTAATTGAATTTATTT
212140 GCATTTATAAAA
128 GCATTTATAAAA
212152 T
1 T
212153 TTTATTTTAT
Statistics
Matches: 138, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
139 9 0.07
140 22 0.16
141 96 0.70
142 11 0.08
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (139 bp):
TGGGCCTTCTTAAAGCAAGTGCTTCATCACAGATGGATGCTGCAATAGTGGCCTTATCGAGGGAG
TTAGCCAAATTGAGAACAGGAAGAGCATCTGCTGGTAATTTCTGGTTTAATTGAATTTATTTGCA
TTTATAAAA
Found at i:215170 original size:2 final size:2
Alignment explanation
Indices: 215163--215213 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
215153 GTTGATCAAT
215163 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
215205 TA TA TA TA T
1 TA TA TA TA T
215214 GTGTGTGTGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:218895 original size:25 final size:25
Alignment explanation
Indices: 218867--218916 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
218857 TATATATATT
** *
218867 TTAATTTTTTAATTATATTTAAAAA
1 TTAATTTAATAATTATATGTAAAAA
218892 TTAATTTAATAATTATATGTAAAAA
1 TTAATTTAATAATTATATGTAAAAA
218917 ATATAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
TTAATTTAATAATTATATGTAAAAA
Found at i:218900 original size:12 final size:13
Alignment explanation
Indices: 218877--218921 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
218867 TTAATTTTTT
218877 AATTATATTTAAA
1 AATTATATTTAAA
*
218890 AATTA-ATTTAAT
1 AATTATATTTAAA
*
218902 AATTATATGTAAA
1 AATTATATTTAAA
*
218915 AAATATA
1 AATTATA
218922 AAAATAAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 11 0.41
13 16 0.59
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (13 bp):
AATTATATTTAAA
Found at i:219370 original size:92 final size:92
Alignment explanation
Indices: 219213--219380 Score: 318
Period size: 92 Copynumber: 1.8 Consensus size: 92
219203 CACAAGTTAA
*
219213 ATGATAGTAACACATGCTATCATTTAATTGGAGATTAAATTTATTAAATTAAATGAAAATTGTGA
1 ATGATAGTAACACATGCTATCATTTAATTGGAGATAAAATTTATTAAATTAAATGAAAATTGTGA
*
219278 CCAAAGTAATAAATTTTTTTTTCTAAT
66 CCAAACTAATAAATTTTTTTTTCTAAT
219305 ATGATAGTAACACATGCTATCATTTAATTGGAGATAAAATTTATTAAATTAAATGAAAATTGTGA
1 ATGATAGTAACACATGCTATCATTTAATTGGAGATAAAATTTATTAAATTAAATGAAAATTGTGA
219370 CCAAACTAATA
66 CCAAACTAATA
219381 TAAATTATAA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 74 1.00
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.37
Consensus pattern (92 bp):
ATGATAGTAACACATGCTATCATTTAATTGGAGATAAAATTTATTAAATTAAATGAAAATTGTGA
CCAAACTAATAAATTTTTTTTTCTAAT
Found at i:219904 original size:28 final size:28
Alignment explanation
Indices: 219872--219927 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
219862 GCATTGGCAA
219872 ACAAATCACAATAGGAGATAAAATTATT
1 ACAAATCACAATAGGAGATAAAATTATT
219900 ACAAATCACAATAGGAGATAAAATTATT
1 ACAAATCACAATAGGAGATAAAATTATT
219928 GAGTGATCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.25
Consensus pattern (28 bp):
ACAAATCACAATAGGAGATAAAATTATT
Found at i:222173 original size:22 final size:23
Alignment explanation
Indices: 222129--222173 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
222119 GTTTACGCAA
*
222129 TTTACCTTATAATTGTTAATAAC
1 TTTACCTTATAATTATTAATAAC
* *
222152 TTTA-CTTATTATTATTATTAAC
1 TTTACCTTATAATTATTAATAAC
222174 CTAATTACAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.33, C:0.11, G:0.02, T:0.53
Consensus pattern (23 bp):
TTTACCTTATAATTATTAATAAC
Found at i:225496 original size:14 final size:14
Alignment explanation
Indices: 225473--225510 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
225463 TCTGTCTATA
*
225473 TGCAGAGATTT-TT
1 TGCAGGGATTTATT
225486 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
225501 TGCAGGGATT
1 TGCAGGGATT
225511 ACTTCCCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 3 0.14
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:229482 original size:20 final size:20
Alignment explanation
Indices: 229457--229505 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
229447 AACGAACTAG
229457 CATTCAAGTGGTACCTATGC
1 CATTCAAGTGGTACCTATGC
229477 CATTCAAGTGGTACCTATGC
1 CATTCAAGTGGTACCTATGC
229497 CATTCAAGT
1 CATTCAAGT
229506 AATGATATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (20 bp):
CATTCAAGTGGTACCTATGC
Found at i:232621 original size:26 final size:26
Alignment explanation
Indices: 232581--232634 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
232571 AATGTACTCT
*
232581 GGTTATCAAATTGTAAAGAAATCGTG
1 GGTTATCAAACTGTAAAGAAATCGTG
232607 GGTTATCAAACTGTAAAGAAATCGTG
1 GGTTATCAAACTGTAAAGAAATCGTG
232633 GG
1 GG
232635 AGGCATTGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.37, C:0.09, G:0.26, T:0.28
Consensus pattern (26 bp):
GGTTATCAAACTGTAAAGAAATCGTG
Found at i:233740 original size:23 final size:23
Alignment explanation
Indices: 233676--233750 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 23
233666 TCAAAGCTGA
233676 GTTGACTGTTGATCGTTGATCGAC
1 GTTGACT-TTGATCGTTGATCGAC
* * ** *
233700 GTTTACTTTAATTATTGACCGAC
1 GTTGACTTTGATCGTTGATCGAC
*
233723 GTTGACTTTGACCGTTGATCGAC
1 GTTGACTTTGATCGTTGATCGAC
*
233746 ATTGA
1 GTTGA
233751 TTTTTTCGAA
Statistics
Matches: 39, Mismatches: 12, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
23 33 0.85
24 6 0.15
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.39
Consensus pattern (23 bp):
GTTGACTTTGATCGTTGATCGAC
Found at i:237060 original size:4 final size:4
Alignment explanation
Indices: 237051--237138 Score: 90
Period size: 4 Copynumber: 24.5 Consensus size: 4
237041 TTTAAAAATA
237051 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA- TTA- TTA- TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
237096 TTAT TTA- TTA- TTA- TTA- TTA- TTA- TTA- TTAT TATAT TT-T TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT T-TAT TTAT TTAT
237137 TT
1 TT
237139 TTATAAACCC
Statistics
Matches: 80, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
3 33 0.41
4 43 0.54
5 4 0.05
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TTAT
Found at i:237091 original size:3 final size:3
Alignment explanation
Indices: 237083--237127 Score: 72
Period size: 3 Copynumber: 14.3 Consensus size: 3
237073 ATTTATTTAT
237083 TTA TTA TTA TTA TTTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA T
237128 ATTTTTTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.83
4 7 0.17
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:239407 original size:2 final size:2
Alignment explanation
Indices: 239400--239446 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
239390 TTATTATTAT
239400 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
239442 TA TA T
1 TA TA T
239447 GTTACGGAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:247157 original size:44 final size:43
Alignment explanation
Indices: 247068--247231 Score: 247
Period size: 44 Copynumber: 3.7 Consensus size: 43
247058 ACAATTAAAT
* *
247068 AATAAAAAATTAAGAAACAAAATAAATAAATAAATCCATAATTA
1 AATAAAAAATTAAGAAACAAAATAAATAAA-AAGTACATAATTA
* * *
247112 AATAAAAACATTAATAAACAAAATAAATAAAAAGTTCATAGTTA
1 AATAAAAA-ATTAAGAAACAAAATAAATAAAAAGTACATAATTA
*
247156 AATAAAAACATTAAGTAACAAAATAAATAAAAAGTACATAATTA
1 AATAAAAA-ATTAAGAAACAAAATAAATAAAAAGTACATAATTA
247200 AATAAAAAATTAAGAAACAAAATAAATAAAAA
1 AATAAAAAATTAAGAAACAAAATAAATAAAAA
247232 CAAGTCTATT
Statistics
Matches: 110, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
43 23 0.21
44 66 0.60
45 21 0.19
ACGTcount: A:0.68, C:0.06, G:0.04, T:0.22
Consensus pattern (43 bp):
AATAAAAAATTAAGAAACAAAATAAATAAAAAGTACATAATTA
Found at i:247304 original size:47 final size:47
Alignment explanation
Indices: 247251--247344 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
247241 TGATGTCTGC
* *
247251 GTCTTGAATGTGTTCCACAGGGCGGTGGTTGTCTATTTCGATGATGA
1 GTCTTGAATGTGTTCCACAGGGAGGTGGCTGTCTATTTCGATGATGA
247298 GTCTTGAATGTGTTCCACAGGGAGGTGGCTGTCTATTTCGATGATGA
1 GTCTTGAATGTGTTCCACAGGGAGGTGGCTGTCTATTTCGATGATGA
247345 TTTATTCGTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.18, C:0.15, G:0.32, T:0.35
Consensus pattern (47 bp):
GTCTTGAATGTGTTCCACAGGGAGGTGGCTGTCTATTTCGATGATGA
Found at i:251491 original size:20 final size:21
Alignment explanation
Indices: 251466--251517 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
251456 TTTTCCCAAT
*
251466 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
251486 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
251507 TCGCAATGCGA
1 TCGCAATGCGA
251518 TACTTACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:251584 original size:20 final size:20
Alignment explanation
Indices: 251548--251600 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
251538 TAATACAAAA
* *
251548 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
*
251568 TCGTAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
251588 TCGCAACGCGATT
1 TCGCAACGCGATT
251601 TACATAGCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:252241 original size:20 final size:19
Alignment explanation
Indices: 252176--252260 Score: 143
Period size: 19 Copynumber: 4.4 Consensus size: 19
252166 GAAACCAAAA
*
252176 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
252195 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
252214 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
252233 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
252253 TCGCGTTG
1 TCGCGTTG
252261 TCTGGTCGCG
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
19 44 0.71
20 18 0.29
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:252253 original size:39 final size:38
Alignment explanation
Indices: 252176--252354 Score: 143
Period size: 38 Copynumber: 4.6 Consensus size: 38
252166 GAAACCAAAA
*
252176 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
252214 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
**
252253 TCGCGTTGTCTGGTCGCGATAGTCATTTCGCGTTGCGA--TTC---
1 TCGC---G--T--T-GCGATTTTCATTTCGCGTTGCGATTTTCATT
* ** *
252294 TCTCGTTGCGATAGTCATTTCCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTT-CGCGTTGCGATTTTCATT
*
252333 ATCTCGTTGCGATTTTCATTTC
1 -TCGCGTTGCGATTTTCATTTC
252355 AACCAAAAGA
Statistics
Matches: 116, Mismatches: 9, Indels: 31
0.74 0.06 0.20
Matches are distributed among these distances:
33 13 0.11
34 11 0.09
36 3 0.03
38 22 0.19
39 20 0.17
40 18 0.16
41 3 0.03
42 1 0.01
44 4 0.03
46 8 0.07
47 13 0.11
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:252331 original size:20 final size:20
Alignment explanation
Indices: 252297--252354 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
252287 GCGATTCTCT
**
252297 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
252317 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
252337 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
252355 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:253682 original size:21 final size:20
Alignment explanation
Indices: 253611--253683 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
253601 CTCCACTTCG
253611 AGAGCCATCACCTCAC--CC
1 AGAGCCATCACCTCACAACC
*
253629 AGAGCCATCACCTGATCAACC
1 AGAGCCATCACCTCA-CAACC
* * *
253650 CGA-CTATACACCTCTACAACG
1 AGAGCCAT-CACCTC-ACAACC
253671 AGAGCCATCACCT
1 AGAGCCATCACCT
253684 ATCCCGTCAC
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
18 14 0.33
19 1 0.02
20 3 0.07
21 20 0.48
22 4 0.10
ACGTcount: A:0.32, C:0.41, G:0.12, T:0.15
Consensus pattern (20 bp):
AGAGCCATCACCTCACAACC
Found at i:254408 original size:42 final size:41
Alignment explanation
Indices: 254348--254439 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 41
254338 GCCCGACTCG
* *
254348 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCA-CGTTCAAGAGGCC
* * *
254390 CCTATCATTCCTCGAGAGTCCCCTCCCACGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACGTTCAAGAGGCC
* *
254431 ACTGTCATC
1 CCTATCATC
254440 GTTGAAGAGG
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 18 0.43
42 24 0.57
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.24
Consensus pattern (41 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACGTTCAAGAGGCC
Found at i:255637 original size:14 final size:14
Alignment explanation
Indices: 255618--255653 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
255608 ATTGTTTAAT
255618 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
255632 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
255646 TGATTTGT
1 TGATTTGT
255654 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:255822 original size:19 final size:19
Alignment explanation
Indices: 255760--255813 Score: 81
Period size: 20 Copynumber: 2.8 Consensus size: 19
255750 AAAAAGTACT
*
255760 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
255779 ATCGCAGCGCGAAAATGAAA
1 ATCGCAACGCG-AAATGAAA
255799 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
255814 TAAATTCGCG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 13 0.42
20 18 0.58
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:255840 original size:19 final size:19
Alignment explanation
Indices: 255818--255968 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
255808 CGAAATTAAA
255818 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
255837 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
255852 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
255870 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
255884 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
255903 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
255918 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
255936 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
255955 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
255969 GGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 45 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:255864 original size:33 final size:32
Alignment explanation
Indices: 255822--255948 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
255812 ATTAAATTCG
255822 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
255855 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
255888 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
255921 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
255949 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:255911 original size:66 final size:66
Alignment explanation
Indices: 255815--255947 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
255805 ACGCGAAATT
*
255815 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
255880 G
66 G
*
255881 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
255946 G
66 G
255947 A
1 A
255948 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:258253 original size:12 final size:12
Alignment explanation
Indices: 258236--258260 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
258226 TCTTCGGGGA
258236 CTTTTTCTTCTT
1 CTTTTTCTTCTT
258248 CTTTTTCTTCTT
1 CTTTTTCTTCTT
258260 C
1 C
258261 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:258469 original size:24 final size:24
Alignment explanation
Indices: 258435--258488 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
258425 CTGAAACATC
* *
258435 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
258459 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
258483 ATCAAA
1 ATCAAA
258489 TTTCAAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:259531 original size:19 final size:19
Alignment explanation
Indices: 259488--259555 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
259478 GAAATGAAAA
259488 TCGCATTGCGA-TTT--TT
1 TCGCATTGCGATTTTCATT
259504 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
259521 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
259540 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
259556 TCATTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 6 0.13
15 3 0.06
16 3 0.06
17 5 0.11
19 30 0.64
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:259692 original size:14 final size:14
Alignment explanation
Indices: 259673--259709 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
259663 CATCAATTAA
259673 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
259687 ACAAATCATCTTTT
1 ACAAATCAACATTT
259701 ACAAATCAA
1 ACAAATCAA
259710 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:261600 original size:19 final size:19
Alignment explanation
Indices: 261557--261673 Score: 75
Period size: 20 Copynumber: 6.4 Consensus size: 19
261547 TAGTTTACTT
*
261557 TCGCAACACGAAACTTAAAA
1 TCGCAACACGAAA-TGAAAA
**
261577 TCGCAACACGAAATGACTA
1 TCGCAACACGAAATGAAAA
* ***
261596 TCGCAACGCGAAAATGGCTA
1 TCGCAACACG-AAATGAAAA
**
261616 TCGCAATGCGAAATGAAAA
1 TCGCAACACGAAATGAAAA
*
261635 TCGC-A-ACG--A-CAAAA
1 TCGCAACACGAAATGAAAA
*
261649 TCGCAACGCGAAATG-AAA
1 TCGCAACACGAAATGAAAA
261667 TCGCAAC
1 TCGCAAC
261674 GACAAAATCG
Statistics
Matches: 78, Mismatches: 13, Indels: 14
0.74 0.12 0.13
Matches are distributed among these distances:
14 8 0.10
15 2 0.03
16 2 0.03
17 2 0.03
18 12 0.15
19 22 0.28
20 30 0.38
ACGTcount: A:0.44, C:0.25, G:0.18, T:0.14
Consensus pattern (19 bp):
TCGCAACACGAAATGAAAA
Found at i:261616 original size:20 final size:20
Alignment explanation
Indices: 261576--261642 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 20
261566 GAAACTTAAA
*
261576 ATCGCAACACG-AAATGACT
1 ATCGCAACGCGAAAATGACT
*
261595 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGACT
* **
261615 ATCGCAATGCG-AAATGAAA
1 ATCGCAACGCGAAAATGACT
261634 ATCGCAACG
1 ATCGCAACG
261643 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 23 0.57
20 17 0.43
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:261650 original size:14 final size:14
Alignment explanation
Indices: 261631--261688 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
261621 ATGCGAAATG
261631 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
261645 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
261661 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
261677 AAAATCGCAACG
1 AAAATCGCAACG
261689 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:261673 original size:32 final size:33
Alignment explanation
Indices: 261615--261693 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
261605 GAAAATGGCT
*
261615 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
261648 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
261680 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
261694 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:261771 original size:19 final size:20
Alignment explanation
Indices: 261749--261791 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
261739 TACGATTTTT
261749 ATTT-CGCATTGCGATAGCC
1 ATTTCCGCATTGCGATAGCC
* *
261768 ATTTCCGCGTTGCGATAGTC
1 ATTTCCGCATTGCGATAGCC
261788 ATTT
1 ATTT
261792 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTTCCGCATTGCGATAGCC
Found at i:261782 original size:20 final size:20
Alignment explanation
Indices: 261757--261802 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
261747 TTATTTCGCA
261757 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
261777 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
261797 TTGCGA
1 TTGCGA
261803 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:262310 original size:18 final size:18
Alignment explanation
Indices: 262284--262328 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
262274 GTCGATCAGA
*
262284 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
262302 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
262320 TGATGGCTC
1 TGATGGCTC
262329 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:263671 original size:20 final size:20
Alignment explanation
Indices: 263646--263698 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
263636 AATAGTTTCT
263646 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
263666 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
*
263686 GAAACT-AAAATCG
1 GAAAATGAAAATCG
263699 TGTTGCGATT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.49, C:0.21, G:0.17, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:263940 original size:22 final size:22
Alignment explanation
Indices: 263913--263956 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
263903 AGATGGAGAT
263913 AGACGGATTTCGCCGGAGATGG
1 AGACGGATTTCGCCGGAGATGG
*
263935 AGACGGATTTCGTCGGAGATGG
1 AGACGGATTTCGCCGGAGATGG
263957 GTGAGAGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.16, G:0.41, T:0.20
Consensus pattern (22 bp):
AGACGGATTTCGCCGGAGATGG
Found at i:264170 original size:20 final size:20
Alignment explanation
Indices: 264145--264238 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
264135 GATTATGTAT
264145 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
264165 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
264185 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
264206 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
264226 TATCGCATTGCGA
1 TATCGCGTTGCGA
264239 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:264239 original size:20 final size:20
Alignment explanation
Indices: 264125--264239 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
264115 CGCTTTGAAA
*
264125 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
264146 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
264166 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
264186 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
264207 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
264227 ATCGCATTGCGAT
1 ATCGCATTGCGAT
264240 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:264257 original size:21 final size:21
Alignment explanation
Indices: 264228--264320 Score: 91
Period size: 20 Copynumber: 4.5 Consensus size: 21
264218 ATAGTCAGTA
264228 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
264249 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
*
264269 TCGTATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
264290 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
264310 TCGCATTGCGA
1 TCGCATTGCGA
264321 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:264258 original size:41 final size:41
Alignment explanation
Indices: 264167--264301 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
264157 AAAGTCAGTA
* * * ** *
264167 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
264207 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
264249 TCGCGTTGCGAT-TTACTTATTCGTATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
264290 TCGCGTTGCGAT
1 TCGCGTTGCGAT
264302 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:264302 original size:41 final size:41
Alignment explanation
Indices: 264228--264320 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
264218 ATAGTCAGTA
264228 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
*
264269 TCGTATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
264310 TCGCATTGCGA
1 TCGCATTGCGA
264321 ATTGGGAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:265281 original size:43 final size:43
Alignment explanation
Indices: 265219--265326 Score: 121
Period size: 43 Copynumber: 2.5 Consensus size: 43
265209 ATGCCCTCCA
* ** *
265219 TAGAGGATCCTATATAGAATCATGATAAG-GATGATG-CATTGCG
1 TAGAGGATCCCATGCAGAATCAGGA-AAGTGATGATGCCATT-CG
* * *
265262 TAGAGGATCCCATGCAGAATCAGGACAGTGATGTTGCCCTTCG
1 TAGAGGATCCCATGCAGAATCAGGAAAGTGATGATGCCATTCG
265305 TAGAGGATCCCATGCAGAATCA
1 TAGAGGATCCCATGCAGAATCA
265327 AGACGAGGAT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
42 2 0.04
43 51 0.91
44 3 0.05
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (43 bp):
TAGAGGATCCCATGCAGAATCAGGAAAGTGATGATGCCATTCG
Found at i:265357 original size:43 final size:43
Alignment explanation
Indices: 265267--265375 Score: 123
Period size: 43 Copynumber: 2.5 Consensus size: 43
265257 TTGCGTAGAG
* * * * *
265267 GATCCCATGCAGAATCAGGACAGTGATGTTGCCCTTCGTAGAG
1 GATCCCATGCAGAATCAAGACAGTGATGATACCCTTCGTAAAA
265310 GATCCCATGCAGAATCAAGACGAG-GATGATACCCTAT-GTAAAA
1 GATCCCATGCAGAATCAAGAC-AGTGATGATACCCT-TCGTAAAA
* *
265353 GATCCCATGTAAAATCAAGACAG
1 GATCCCATGCAGAATCAAGACAG
265376 AGATATAATC
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
42 2 0.04
43 52 0.91
44 3 0.05
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (43 bp):
GATCCCATGCAGAATCAAGACAGTGATGATACCCTTCGTAAAA
Found at i:266010 original size:13 final size:14
Alignment explanation
Indices: 265986--266017 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
265976 CTTAAAAAAA
265986 TCAATGGGTCAAAG
1 TCAATGGGTCAAAG
266000 TCAAT-GGTCAAAG
1 TCAATGGGTCAAAG
266013 TCAAT
1 TCAAT
266018 TATCGACGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.25
Consensus pattern (14 bp):
TCAATGGGTCAAAG
Found at i:266052 original size:23 final size:23
Alignment explanation
Indices: 266026--266087 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
266016 ATTATCGACG
* *
266026 GTCAACAGGTCGGGTCGATAAAA
1 GTCAACAGGTCGAGTCAATAAAA
* * *
266049 GTCAACTGGTTGAGTCAATCAAA
1 GTCAACAGGTCGAGTCAATAAAA
* *
266072 GTCAACGGGTAGAGTC
1 GTCAACAGGTCGAGTC
266088 TGATTAAATT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (23 bp):
GTCAACAGGTCGAGTCAATAAAA
Found at i:269646 original size:42 final size:42
Alignment explanation
Indices: 269599--269701 Score: 109
Period size: 43 Copynumber: 2.4 Consensus size: 42
269589 GTTCTTATTT
* * *
269599 TGCATGTGATCCTCTATGAAGG-CATCATCCCCGTCCTGATTC
1 TGCATG-GATCCTCTATAAAGGCCAACATCCCCATCCTGATTC
* *
269641 TGCATGGAATCCTCTATAAAGGCCAACATCTCCATCTTGATTC
1 TGCATGG-ATCCTCTATAAAGGCCAACATCCCCATCCTGATTC
* *
269684 TACATGAGATCTTCTATA
1 TGCATG-GATCCTCTATA
269702 CATCCACGTC
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
41 1 0.02
42 19 0.37
43 30 0.59
44 1 0.02
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (42 bp):
TGCATGGATCCTCTATAAAGGCCAACATCCCCATCCTGATTC
Found at i:271478 original size:3 final size:3
Alignment explanation
Indices: 271472--271498 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
271462 AAAATTTAAA
271472 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
271499 TATTATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:272789 original size:14 final size:14
Alignment explanation
Indices: 272750--272803 Score: 76
Period size: 14 Copynumber: 4.0 Consensus size: 14
272740 ACTATATAAT
272750 ATATGTTTTC-AAA
1 ATATGTTTTCAAAA
* *
272763 AT-TATTTTAAAAA
1 ATATGTTTTCAAAA
272776 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
272790 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
272804 CTATATAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
12 5 0.14
13 7 0.20
14 23 0.66
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (14 bp):
ATATGTTTTCAAAA
Found at i:272836 original size:95 final size:92
Alignment explanation
Indices: 272733--272912 Score: 254
Period size: 95 Copynumber: 1.9 Consensus size: 92
272723 TCAAAAACCA
*
272733 TTTTAAAACTATATAATATATGTTTTC-AAAATTATTTTAAAAAATATGTTTTCAAAAATATGTT
1 TTTTAAAACTATATAATATATGTTTTCAAAAATTATATT-AAAAATATGTTTTCAAAAATA--TT
* *
272797 TTCAAAACTATATAATATATATTATATATG
63 TTAAAAACCATATAATATATATTATATATG
* * *
272827 TTTTCAAAACTATATACTATATGTTTTCAAAAATTATATTATATATATGTTTTCAAAAATATTTT
1 TTTT-AAAACTATATAATATATGTTTTCAAAAATTATATTAAAAATATGTTTTCAAAAATATTTT
*
272892 AAAAACCATATATTATATATT
65 AAAAACCATATAATATATATT
272913 TTAAAACGTG
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
93 22 0.29
94 4 0.05
95 41 0.53
96 10 0.13
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (92 bp):
TTTTAAAACTATATAATATATGTTTTCAAAAATTATATTAAAAATATGTTTTCAAAAATATTTTA
AAAACCATATAATATATATTATATATG
Found at i:272840 original size:23 final size:23
Alignment explanation
Indices: 272814--272884 Score: 90
Period size: 23 Copynumber: 3.0 Consensus size: 23
272804 CTATATAATA
272814 TATATTATATATGTTTTCAAAAC
1 TATATTATATATGTTTTCAAAAC
*
272837 TATA-TACTATATGTTTTCAAAAAT
1 TATATTA-TATATGTTTTC-AAAAC
272861 TATATTATATATATGTTTTCAAAA
1 TATA-T-TATATATGTTTTCAAAA
272885 ATATTTTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
22 2 0.05
23 15 0.36
24 8 0.19
25 4 0.10
26 11 0.26
27 2 0.05
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (23 bp):
TATATTATATATGTTTTCAAAAC
Found at i:272993 original size:43 final size:38
Alignment explanation
Indices: 272940--273035 Score: 102
Period size: 38 Copynumber: 2.4 Consensus size: 38
272930 AACCATATTA
*
272940 TATATATTTTCGAAAATCAATTTTTATAAAAAAATATATATAT
1 TATATGTTTTC-AAAATCAA-TTTTAT--AAAAA-ATATATAT
* * * *
272983 TATATGTTTTCAAAAACCATTTTCTAAAAACTATATAT
1 TATATGTTTTCAAAATCAATTTTATAAAAAATATATAT
273021 TATATGTTTTCAAAA
1 TATATGTTTTCAAAA
273036 ATATTTTCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
38 22 0.46
39 5 0.10
41 5 0.10
42 6 0.12
43 10 0.21
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (38 bp):
TATATGTTTTCAAAATCAATTTTATAAAAAATATATAT
Found at i:273018 original size:36 final size:35
Alignment explanation
Indices: 272977--273059 Score: 114
Period size: 38 Copynumber: 2.3 Consensus size: 35
272967 AAAAAAATAT
272977 ATATATTATATGTTTTCAAAAACCATTTTCTAAAAAC
1 ATATATTATATGTTTTCAAAAA-CATTTTC-AAAAAC
*
273014 TATATATTATATGTTTTCAAAAATATTTTCAAAAAC
1 -ATATATTATATGTTTTCAAAAACATTTTCAAAAAC
*
273050 -TATACTATAT
1 ATATATTATAT
273060 TGTTATATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
34 9 0.21
36 6 0.14
37 6 0.14
38 22 0.51
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.43
Consensus pattern (35 bp):
ATATATTATATGTTTTCAAAAACATTTTCAAAAAC
Found at i:273018 original size:38 final size:37
Alignment explanation
Indices: 272866--273053 Score: 140
Period size: 35 Copynumber: 5.1 Consensus size: 37
272856 AAAATTATAT
* *
272866 TATA-TATATGTTTTCAAAAATA-TTT-TAAAAACCA
1 TATATTATATGTTTTCAAAAACATTTTCTAAAAACTA
* * * *
272900 TATATTATATATTTT--AAAACGTGTTT-TTAAAACCA
1 TATATTATATGTTTTCAAAAACAT-TTTCTAAAAACTA
* * * *
272935 TAT-TATATATATTTTCGAAAATCAATTTTTATAAAAAAATATA
1 TATAT-TATATGTTTTC-AAAAAC-A-TTTTCT--AAAAA-CTA
272978 TATATTATATGTTTTCAAAAACCATTTTCTAAAAACTA
1 TATATTATATGTTTTCAAAAA-CATTTTCTAAAAACTA
*
273016 TATATTATATGTTTTCAAAAATATTTTC-AAAAACTA
1 TATATTATATGTTTTCAAAAACATTTTCTAAAAACTA
273052 TA
1 TA
273054 CTATATTGTT
Statistics
Matches: 125, Mismatches: 14, Indels: 28
0.75 0.08 0.17
Matches are distributed among these distances:
33 4 0.03
34 5 0.04
35 33 0.26
36 10 0.08
37 6 0.05
38 27 0.22
39 8 0.06
40 2 0.02
41 5 0.04
42 9 0.07
43 15 0.12
44 1 0.01
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.44
Consensus pattern (37 bp):
TATATTATATGTTTTCAAAAACATTTTCTAAAAACTA
Found at i:273782 original size:200 final size:199
Alignment explanation
Indices: 273415--273782 Score: 441
Period size: 200 Copynumber: 1.8 Consensus size: 199
273405 TCAAAAGTTT
* *
273415 ATTTTGTTGACAGACAACTTTTCTCGACTTAAGCTATGCCATAAATTAGGCTGGGAGATAGTTCC
1 ATTTTGTTGACAGACAACTTTTCTCGACTTAAGATATGCCATAAATTAGGCTGGGAGATAGTTCA
* *** * *
273480 TTGTTGCTAAATCAAATCCAACCTAGGTCTTCTTCTTGGTTTAAAGACCTCGGTTTAAAATTCAT
66 TTGTTGCTAAATCAAAGCCAACCTAGGTCTTCTTCTTAACTTAAAGACCTCAGTTTAAAATTCAA
* *
273545 CTGGAAAGTAGTTCATCGATGCTACCCTACAGTTGATATGCCCTCGAGATGAATATAATCGAACT
131 CTGGAAAGTAGTTCATCGATGATACCATACAGTTGATATGCCCTCGAGATGAATATAATCGAACT
273610 AAAA
196 AAAA
* ** * *** * * *
273614 ATTTTCGTTGACAGATAGTTTTTCTTGACTTAAGATATGTTGTAACTTAGGCTGTGATATAGTTC
1 ATTTT-GTTGACAGACAACTTTTCTCGACTTAAGATATGCCATAAATTAGGCTGGGAGATAGTTC
** * * * * *
273679 ATTGTTGCTAAATCGCAGCCAACAC-ATGTCTTTTTCTTAACTTAAAGACCTTAGTTTGAACTTC
65 ATTGTTGCTAAATCAAAGCCAAC-CTAGGTCTTCTTCTTAACTTAAAGACCTCAGTTTAAAATTC
* * *
273743 AACTGGAAAGTAGTTCATCGTTGATTCCATACGGTTGATA
129 AACTGGAAAGTAGTTCATCGATGATACCATACAGTTGATA
273783 CGTCATCGAG
Statistics
Matches: 137, Mismatches: 30, Indels: 3
0.81 0.18 0.02
Matches are distributed among these distances:
199 5 0.04
200 131 0.96
201 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (199 bp):
ATTTTGTTGACAGACAACTTTTCTCGACTTAAGATATGCCATAAATTAGGCTGGGAGATAGTTCA
TTGTTGCTAAATCAAAGCCAACCTAGGTCTTCTTCTTAACTTAAAGACCTCAGTTTAAAATTCAA
CTGGAAAGTAGTTCATCGATGATACCATACAGTTGATATGCCCTCGAGATGAATATAATCGAACT
AAAA
Found at i:273807 original size:200 final size:200
Alignment explanation
Indices: 273415--273832 Score: 437
Period size: 200 Copynumber: 2.1 Consensus size: 200
273405 TCAAAAGTTT
* *
273415 ATTTT-GTTGACAGACAACTTTTCTCGACTTAAGCTATGCCATAAATTAGGCTGGGAGATAGTTC
1 ATTTTCGTTGACAGATAACTTTTCTCGACTTAAGATATGCCATAAATTAGGCTGGGAGATAGTTC
* * *** *
273479 CTTGTTGCTAAATCAAATCCAACCTAGGTCTTCTTCTTGGTTTAAAGACCTCGGTTTAAAATTCA
66 ATTGTTGCTAAATCAAAGCCAACCTAGGTCTTCTTCTTAACTTAAAGACCTCAGTTTAAAATTCA
* * * * * *
273544 TCTGGAAAGTAGTTCATCGATGCTACCCTACAGTTGATATGCCCTCGAGATGAATATAATCGAAC
131 ACTGGAAAGTAGTTCATCGATGATACCATACAGTTGATACGCCATCGAGATGAATAGAATCGAAC
273609 TA-AAA
196 -ACAAA
** * *** * * *
273614 ATTTTCGTTGACAGATAGTTTTTCTTGACTTAAGATATGTTGTAACTTAGGCTGTGATATAGTTC
1 ATTTTCGTTGACAGATAACTTTTCTCGACTTAAGATATGCCATAAATTAGGCTGGGAGATAGTTC
** * * * * *
273679 ATTGTTGCTAAATCGCAGCCAACAC-ATGTCTTTTTCTTAACTTAAAGACCTTAGTTTGAACTTC
66 ATTGTTGCTAAATCAAAGCCAAC-CTAGGTCTTCTTCTTAACTTAAAGACCTCAGTTTAAAATTC
* * * * * * *
273743 AACTGGAAAGTAGTTCATCGTTGATTCCATACGGTTGATACGTCATCGAGCTGAGTGGAATCGAA
130 AACTGGAAAGTAGTTCATCGATGATACCATACAGTTGATACGCCATCGAGATGAATAGAATCGAA
273808 CACGAAA
195 CAC-AAA
* *
273815 GTTTTCATTGACAGATAA
1 ATTTTCGTTGACAGATAA
273833 TCCTTCTCTC
Statistics
Matches: 175, Mismatches: 40, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
199 6 0.03
200 150 0.86
201 19 0.11
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (200 bp):
ATTTTCGTTGACAGATAACTTTTCTCGACTTAAGATATGCCATAAATTAGGCTGGGAGATAGTTC
ATTGTTGCTAAATCAAAGCCAACCTAGGTCTTCTTCTTAACTTAAAGACCTCAGTTTAAAATTCA
ACTGGAAAGTAGTTCATCGATGATACCATACAGTTGATACGCCATCGAGATGAATAGAATCGAAC
ACAAA
Found at i:276464 original size:103 final size:103
Alignment explanation
Indices: 276239--276456 Score: 436
Period size: 103 Copynumber: 2.1 Consensus size: 103
276229 GTCGAGGGTC
276239 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
276304 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
276342 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
276407 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
276445 TATGTGGTCCTT
1 TATGTGGTCCTT
276457 ATGGACATTA
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 115 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:276540 original size:23 final size:23
Alignment explanation
Indices: 276472--276532 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
276462 CATTATTATA
*
276472 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTATG
*
276495 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
276518 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
276533 TTTATATGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTATG
Found at i:280266 original size:2 final size:2
Alignment explanation
Indices: 280259--280289 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
280249 ATGATCTTTG
280259 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
280290 ATGAAATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:281534 original size:103 final size:103
Alignment explanation
Indices: 281309--281526 Score: 418
Period size: 103 Copynumber: 2.1 Consensus size: 103
281299 GTCGAGGGTC
* *
281309 TATGTGGTCCATCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTTTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
281374 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
281412 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
281477 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
281515 TATGTGGTCCTT
1 TATGTGGTCCTT
281527 ATGGACATTA
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 113 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:281610 original size:23 final size:23
Alignment explanation
Indices: 281542--281602 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
281532 CATTATTATA
*
281542 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTATG
*
281565 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
281588 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
281603 TTTATATGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTATG
Found at i:285196 original size:167 final size:167
Alignment explanation
Indices: 284920--285252 Score: 621
Period size: 167 Copynumber: 2.0 Consensus size: 167
284910 ATATGGATCT
*
284920 TTTTTTTATTAAAGGAATTTGATCTCGGCATATATCAAAAGGCTATAACCTTATTTCCCAAAATG
1 TTTTTTTATTAAAGGAATTTGATCTCGGCATATATCAAAAGGCTATAACCTCATTTCCCAAAATG
*
284985 TGCATTTCATTATACTTGATATTCACTGAATTTCAAACAATTCTTTATTACTTAAAGAAATGTTA
66 TGCATTTCATTATACTTGATATTCACTGAATTTCAAACAATTCTTTATTACTCAAAGAAATGTTA
*
285050 TTTTAAAAGAAATGTTCAAATATATAAAAGATAAATA
131 TTTTAAAAGAAATGTTCAAACATATAAAAGATAAATA
*
285087 TTTTTTTATTAAAGGAATTTGATCTCGGCATATGTCAAAAGGCTATAACCTCATTTCCCAAAATG
1 TTTTTTTATTAAAGGAATTTGATCTCGGCATATATCAAAAGGCTATAACCTCATTTCCCAAAATG
*
285152 TGCATTTCATTATACTTGATATTCATTGAATTTCAAACAATTCTTTATTACTCAAAGAAATGTTA
66 TGCATTTCATTATACTTGATATTCACTGAATTTCAAACAATTCTTTATTACTCAAAGAAATGTTA
285217 TTTTAAAAGAAATGTTCAAACATATAAAAGATAAAT
131 TTTTAAAAGAAATGTTCAAACATATAAAAGATAAAT
285253 TCAAATAAGA
Statistics
Matches: 161, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
167 161 1.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (167 bp):
TTTTTTTATTAAAGGAATTTGATCTCGGCATATATCAAAAGGCTATAACCTCATTTCCCAAAATG
TGCATTTCATTATACTTGATATTCACTGAATTTCAAACAATTCTTTATTACTCAAAGAAATGTTA
TTTTAAAAGAAATGTTCAAACATATAAAAGATAAATA
Found at i:288930 original size:14 final size:14
Alignment explanation
Indices: 288911--288938 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
288901 TACTTGTCCC
288911 CAGTGGAGTTGCCA
1 CAGTGGAGTTGCCA
288925 CAGTGGAGTTGCCA
1 CAGTGGAGTTGCCA
288939 ATCTGTCGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.36, T:0.21
Consensus pattern (14 bp):
CAGTGGAGTTGCCA
Found at i:289293 original size:3 final size:3
Alignment explanation
Indices: 289287--289335 Score: 89
Period size: 3 Copynumber: 16.0 Consensus size: 3
289277 TTTTTTTAAA
289287 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
289333 AAT
1 AAT
289336 TAAAAATATA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:290482 original size:3 final size:3
Alignment explanation
Indices: 290474--290566 Score: 109
Period size: 3 Copynumber: 30.7 Consensus size: 3
290464 GGACCCCTAA
290474 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
* * * *
290522 AAT AGT AAC AA- CAT AAT -AT AAT ATT ATAT AAT AAAT AAAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT -AAT -AAT AAT AA
290567 ACAATACATA
Statistics
Matches: 79, Mismatches: 7, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
2 3 0.04
3 67 0.85
4 9 0.11
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:290693 original size:37 final size:36
Alignment explanation
Indices: 290620--290939 Score: 208
Period size: 35 Copynumber: 8.9 Consensus size: 36
290610 ATACATTATA
* *
290620 TTTTCAAAAACCATTTTAAAAACTATATA-CTATATG
1 TTTTCAAAAA-TATTTTAAAAACTATATATATATATG
290656 TTTTCAAAAATATTTTAAAAACTATATATTATATATG
1 TTTTCAAAAATATTTTAAAAACTATATA-TATATATG
* *
290693 TTTTCATAAATATGTTTTCAAAACTATATAT-TATATG
1 TTTTCA-AAA-ATATTTTAAAAACTATATATATATATG
* *
290730 TTTTC-AAAA-A--CT----A-TAT-TATATATACG
1 TTTTCAAAAATATTTTAAAAACTATATATATATATG
*
290756 TTTTCAAAAATATTTTAAAAACCATATAT-TATATG
1 TTTTCAAAAATATTTTAAAAACTATATATATATATG
* * * * *
290791 TTTT-AAAACGTGTTTTCAAAACCATAT-TATATATA
1 TTTTCAAAA-ATATTTTAAAAACTATATATATATATG
*
290826 TTTTCAAAAACTAATTTTTTTTTAAAAA-TATATATATTATTTG
1 TTTTCAAAAA-T-A-----TTTTAAAAACTATATATA-TATATG
*
290869 TTTTCAAAAACCGT-TTTCTAAAAACTATATA-ATATATT
1 TTTTCAAAAA---TATTT-TAAAAACTATATATATATATG
*
290907 TTTTCAAAAATAATTTCAAAAACTATACTATAT
1 TTTTCAAAAAT-ATTTTAAAAACTATA-TATAT
290940 TATTATATAT
Statistics
Matches: 225, Mismatches: 24, Indels: 68
0.71 0.08 0.21
Matches are distributed among these distances:
25 3 0.01
26 13 0.06
27 5 0.02
28 1 0.00
30 1 0.00
31 1 0.00
34 7 0.03
35 56 0.25
36 28 0.12
37 28 0.12
38 23 0.10
39 24 0.11
40 6 0.03
41 4 0.02
42 10 0.04
43 14 0.06
45 1 0.00
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (36 bp):
TTTTCAAAAATATTTTAAAAACTATATATATATATG
Found at i:290744 original size:24 final size:26
Alignment explanation
Indices: 290702--290765 Score: 98
Period size: 26 Copynumber: 2.6 Consensus size: 26
290692 GTTTTCATAA
290702 ATATGTTTTC-AAAACTATA-TAT-T
1 ATATGTTTTCAAAAACTATATTATAT
290725 ATATGTTTTCAAAAACTATATTATAT
1 ATATGTTTTCAAAAACTATATTATAT
*
290751 ATACGTTTTCAAAAA
1 ATATGTTTTCAAAAA
290766 TATTTTAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
23 10 0.27
24 9 0.24
25 3 0.08
26 15 0.41
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (26 bp):
ATATGTTTTCAAAAACTATATTATAT
Found at i:290783 original size:61 final size:62
Alignment explanation
Indices: 290668--290798 Score: 187
Period size: 61 Copynumber: 2.1 Consensus size: 62
290658 TTCAAAAATA
* * * *
290668 TTTTAAAAACTATATATTATATATGTTTTCATAAATATGTTTTCAAAACTATATATTATATG
1 TTTTAAAAACTATATATTATATACGTTTTCATAAATATATTTTAAAAACCATATATTATATG
290730 TTTTCAAAAACTATAT-TATATATACGTTTTCA-AAA-ATATTTTAAAAACCATATATTATATG
1 TTTT-AAAAACTATATAT-TATATACGTTTTCATAAATATATTTTAAAAACCATATATTATATG
290791 TTTTAAAA
1 TTTTAAAA
290799 CGTGTTTTCA
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
60 4 0.06
61 27 0.43
62 8 0.13
63 24 0.38
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.46
Consensus pattern (62 bp):
TTTTAAAAACTATATATTATATACGTTTTCATAAATATATTTTAAAAACCATATATTATATG
Found at i:290858 original size:135 final size:137
Alignment explanation
Indices: 290620--290879 Score: 300
Period size: 135 Copynumber: 1.9 Consensus size: 137
290610 ATACATTATA
* *
290620 TTTTCAAAAACCATTTTAAAAACTATATACTATATGTTTTCAAAAATATTTTAAAAACTATATAT
1 TTTTCAAAAACCATTTTAAAAACCATATACTATATGTTTTCAAAAATATTTTAAAAAC-ACATAT
* *
290685 TATATATGTTTTCATAAATATGTTTTCAAAAC---TATATATTATATGTTTTCAAAAACTATATT
65 TATATATATTTTCAAAAATATGTTTTCAAAACATATATATATTAT-TGTTTTCAAAAACTATATT
290747 ATATATACG
129 ATATATACG
* * * * *
290756 TTTTCAAAAA-TATTTTAAAAACCATATATTATATGTTTT-AAAACGTGTTTTCAAAAC-CATAT
1 TTTTCAAAAACCATTTTAAAAACCATATACTATATGTTTTCAAAA-ATATTTTAAAAACACATAT
* *
290818 TATATATATTTTCAAAAACTAATTTTTTTTTAAAA-ATATATATATTATTTGTTTTCAAAAAC
65 TATATATATTTTCAAAAA-T-A--TGTTTTCAAAACATATATATATTA-TTGTTTTCAAAAAC
290880 CGTTTTCTAA
Statistics
Matches: 104, Mismatches: 11, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
133 20 0.19
134 5 0.05
135 37 0.36
136 10 0.10
137 9 0.09
139 22 0.21
140 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.45
Consensus pattern (137 bp):
TTTTCAAAAACCATTTTAAAAACCATATACTATATGTTTTCAAAAATATTTTAAAAACACATATT
ATATATATTTTCAAAAATATGTTTTCAAAACATATATATATTATTGTTTTCAAAAACTATATTAT
ATATACG
Found at i:291313 original size:13 final size:12
Alignment explanation
Indices: 291290--291321 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
291280 TTTGGTAAAG
291290 TTTTAAAATCTT
1 TTTTAAAATCTT
291302 TTTTATAAATCTT
1 TTTTA-AAATCTT
291315 TTTTAAA
1 TTTTAAA
291322 TAAATAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTTAAAATCTT
Found at i:296914 original size:29 final size:29
Alignment explanation
Indices: 296853--296914 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
296843 GTTATTATAT
* *
296853 TTTATTTTAATCATTCTATTTTCAAATAC
1 TTTATTTTAATCATTCTATTATCAAATAA
* *
296882 TTTATTTTCATCATT-TATTCATCAATTAA
1 TTTATTTTAATCATTCTATT-ATCAAATAA
296911 TTTA
1 TTTA
296915 AAAATAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 4 0.14
29 24 0.86
ACGTcount: A:0.31, C:0.13, G:0.00, T:0.56
Consensus pattern (29 bp):
TTTATTTTAATCATTCTATTATCAAATAA
Found at i:298772 original size:20 final size:21
Alignment explanation
Indices: 298747--298798 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
298737 TTTTCCCAAT
*
298747 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
298767 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
298788 TCGCAATGCGA
1 TCGCAATGCGA
298799 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:298812 original size:20 final size:20
Alignment explanation
Indices: 298787--298900 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
298777 AATTGGGAAA
*
298787 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
298807 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
298827 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
298848 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
298868 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
298888 TTCGCAACGCGAT
1 ATCGCAACGCGAT
298901 TTACATAGCG
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.02
20 65 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:298831 original size:61 final size:61
Alignment explanation
Indices: 298784--298900 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
298774 GCGAATTGGG
* * * *
298784 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
298845 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
298901 TTACATAGCG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:299528 original size:20 final size:19
Alignment explanation
Indices: 299487--299647 Score: 126
Period size: 20 Copynumber: 8.8 Consensus size: 19
299477 CAATGCGATT
299487 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
299506 TTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGC-G
299526 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
299545 TTGCGATTGTC---T-G-G
1 TTGCGATTTTCATTTCGCG
* **
299559 TCGCGATAGTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
299578 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
** *
299592 TTGCGATAGTCATTTCCGTG
1 TTGCGATTTTCATTT-CGCG
* *
299612 TTGCGATTCTCATTATCTCG
1 TTGCGATTTTCATT-TCGCG
299632 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
299648 AACCAAAAGA
Statistics
Matches: 113, Mismatches: 16, Indels: 26
0.73 0.10 0.17
Matches are distributed among these distances:
14 20 0.18
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 37 0.33
20 47 0.42
21 1 0.01
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:299563 original size:39 final size:39
Alignment explanation
Indices: 299487--299563 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
299477 CAATGCGATT
* **
299487 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
299526 TTGCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
299564 ATAGTCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.45
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
Found at i:299572 original size:33 final size:33
Alignment explanation
Indices: 299535--299622 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
299525 GTTGCGATTT
* *
299535 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
299568 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
299601 TCATTTCCGTGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
299623 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 36 0.72
34 14 0.28
ACGTcount: A:0.11, C:0.24, G:0.25, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:301627 original size:40 final size:40
Alignment explanation
Indices: 301572--301650 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 40
301562 CGACTCGCCT
* * *
301572 ATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCC
1 ATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCC
* * *
301612 ATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 ATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
301651 ACTGTCATCG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.23, C:0.38, G:0.18, T:0.22
Consensus pattern (40 bp):
ATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCC
Found at i:301647 original size:21 final size:21
Alignment explanation
Indices: 301623--301689 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
301613 TCATTCCTCG
301623 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
301644 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
301665 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
301686 AGAG
1 AGAG
301690 CCGATTCACA
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:302923 original size:14 final size:14
Alignment explanation
Indices: 302904--302939 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
302894 ATTGTTTAAT
302904 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
302918 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
302932 TGATTTGT
1 TGATTTGT
302940 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:303162 original size:33 final size:31
Alignment explanation
Indices: 303115--303245 Score: 163
Period size: 33 Copynumber: 4.1 Consensus size: 31
303105 GCGAAATTAA
* *
303115 ATTCGCGTTGCGATTTTCATTTCGCATTGTG
1 ATTCTCGTTGCGATTTTCATTTCGCATTGCG
303146 ATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
1 ATT--CTCGTTGCGATTTTCATTTCGCATTGCG
** *
303179 AAATTAGCGTTGCGATTTTCATTTTCGCATTACG
1 --ATTCTCGTTGCGATTTTCA-TTTCGCATTGCG
*
303213 ATTCTCGTTGCGATTTTAATTTCGCATTGCG
1 ATTCTCGTTGCGATTTTCATTTCGCATTGCG
303244 AT
1 AT
303246 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
31 16 0.19
32 16 0.19
33 40 0.47
34 11 0.13
35 3 0.03
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.44
Consensus pattern (31 bp):
ATTCTCGTTGCGATTTTCATTTCGCATTGCG
Found at i:303179 original size:19 final size:19
Alignment explanation
Indices: 303116--303179 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 19
303106 CGAAATTAAA
*
303116 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
303135 TTCGCATTGTGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
303151 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
303168 TTCGCATTGCGA
1 TTCGCATTGCGA
303180 AATTAGCGTT
Statistics
Matches: 33, Mismatches: 7, Indels: 10
0.66 0.14 0.20
Matches are distributed among these distances:
14 5 0.15
16 6 0.18
17 6 0.18
19 16 0.48
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:303239 original size:65 final size:65
Alignment explanation
Indices: 303113--303244 Score: 203
Period size: 65 Copynumber: 2.0 Consensus size: 65
303103 ACGCGAAATT
* ** *
303113 AAATTCGCGTTGCGATTTTCATTTCGCATTGTGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTACGATT-CCTCGTTGCGATTTTAATTTCGCATTGC
303178 G
65 G
303179 AAATTAGCGTTGCGATTTTCATTTTCGCATTACGATT-CTCGTTGCGATTTTAATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCA-TTTCGCATTACGATTCCTCGTTGCGATTTTAATTTCGCATTGC
303243 G
65 G
303244 A
1 A
303245 TAGTAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
65 28 0.46
66 20 0.33
67 13 0.21
ACGTcount: A:0.18, C:0.20, G:0.19, T:0.42
Consensus pattern (65 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTACGATTCCTCGTTGCGATTTTAATTTCGCATTGCG
Found at i:303244 original size:19 final size:20
Alignment explanation
Indices: 303229--303267 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
303219 GTTGCGATTT
303229 TAATTT-CGCATTGCGATAG
1 TAATTTCCGCATTGCGATAG
*
303248 TAATTTCCGCGTTGCGATAG
1 TAATTTCCGCATTGCGATAG
303268 ACATTAAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (20 bp):
TAATTTCCGCATTGCGATAG
Found at i:303264 original size:20 final size:19
Alignment explanation
Indices: 303218--303267 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
303208 TTACGATTCT
**
303218 CGTTGCGATTTTAATTTCG
1 CGTTGCGATAGTAATTTCG
*
303237 CATTGCGATAGTAATTTCCG
1 CGTTGCGATAGTAATTT-CG
303257 CGTTGCGATAG
1 CGTTGCGATAG
303268 ACATTAAGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTAATTTCG
Found at i:306710 original size:20 final size:20
Alignment explanation
Indices: 306685--306740 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
306675 ATTCATTTGA
306685 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
306705 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
306725 CTATCGCAATGCGAAA
1 CTATCGCAACGCGAAA
306741 TGAAAATTGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.36, C:0.25, G:0.23, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:306771 original size:14 final size:14
Alignment explanation
Indices: 306752--306805 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
306742 GAAAATTGCA
306752 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
306766 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
306783 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
306799 TTGCGAT
1 TTGCGAT
306806 AGCCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:306786 original size:33 final size:33
Alignment explanation
Indices: 306749--306824 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
306739 AATGAAAATT
***
306749 GCATTGCGATTTTCTCGTTGCGATTTTCATTTC
1 GCATTGCGATTTTCTCGTTGCGATAGCCATTTC
306782 GCATTGCGATTTTCTCGTTGCGATAGCCATTTC
1 GCATTGCGATTTTCTCGTTGCGATAGCCATTTC
*
306815 GCGTTGCGAT
1 GCATTGCGAT
306825 AGTCTGTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.42
Consensus pattern (33 bp):
GCATTGCGATTTTCTCGTTGCGATAGCCATTTC
Found at i:308724 original size:20 final size:19
Alignment explanation
Indices: 308684--308750 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
308674 GAAACTTAAA
308684 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
* *
308703 ATCGCAACGTGAAAATGGCT
1 ATCGCAACGCG-AAATGACT
* **
308723 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
308742 ATCGCAACG
1 ATCGCAACG
308751 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 23 0.59
20 16 0.41
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:308757 original size:39 final size:35
Alignment explanation
Indices: 308684--308801 Score: 120
Period size: 32 Copynumber: 3.4 Consensus size: 35
308674 GAAACTTAAA
** **
308684 ATCGCAACGCGAAATGACTATCGCAACGTGAAAATGGCT
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAAA----T
*
308723 ATCGCAATGCGAAATGAAAATCGCAACGAC-AAA-
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAAAT
308756 ATCGCAACGCGAAATG-AAATCGCAACGAC-AAA-
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAAAT
308788 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
308802 CACAAATCGC
Statistics
Matches: 73, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
32 30 0.41
33 15 0.21
38 3 0.04
39 25 0.34
ACGTcount: A:0.43, C:0.24, G:0.20, T:0.13
Consensus pattern (35 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAAAT
Found at i:308758 original size:14 final size:14
Alignment explanation
Indices: 308739--308796 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
308729 ATGCGAAATG
308739 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
308753 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
308769 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
308785 AAAATCGCAACG
1 AAAATCGCAACG
308797 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:308781 original size:32 final size:33
Alignment explanation
Indices: 308723--308801 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
308713 GAAAATGGCT
*
308723 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
308756 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
308788 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
308802 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:308849 original size:14 final size:14
Alignment explanation
Indices: 308830--308887 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
308820 TTTCATTTCG
308830 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
308844 CGTTGCGATTTCATTGCG
1 CGTTGCGA-TT--TTG-T
308862 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
308876 CGTTGGGATTTT
1 CGTTGCGATTTT
308888 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 19 0.51
15 5 0.14
17 5 0.14
18 8 0.22
ACGTcount: A:0.09, C:0.16, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:308901 original size:33 final size:33
Alignment explanation
Indices: 308813--308903 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
308803 ACAAATCGCA
308813 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
308846 TTGCGA-TTTCATTGCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
* *
308878 TTGGGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
308904 AGCCATTTCC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 30 0.57
33 23 0.43
ACGTcount: A:0.11, C:0.18, G:0.25, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:309449 original size:18 final size:18
Alignment explanation
Indices: 309423--309467 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
309413 GTCGATCAGA
*
309423 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
309441 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
309459 TGATGGCTC
1 TGATGGCTC
309468 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:310812 original size:20 final size:20
Alignment explanation
Indices: 310787--310829 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
310777 AATAGTTTCT
310787 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
310807 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
310827 GAA
1 GAA
310830 TTCGACTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.19, G:0.19, T:0.09
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:311364 original size:20 final size:20
Alignment explanation
Indices: 311339--311432 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
311329 GATTATGTAT
311339 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
311359 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
311379 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
311400 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
311420 TATCGCATTGCGA
1 TATCGCGTTGCGA
311433 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:311433 original size:20 final size:20
Alignment explanation
Indices: 311319--311433 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
311309 CTCTTTGAAA
*
311319 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
311340 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
311360 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
311380 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
311401 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
311421 ATCGCATTGCGAT
1 ATCGCATTGCGAT
311434 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:311451 original size:21 final size:21
Alignment explanation
Indices: 311422--311514 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
311412 ATAGTCAGTA
311422 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
311443 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
311463 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
311484 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
311504 TCGCATTGCGA
1 TCGCATTGCGA
311515 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:311452 original size:41 final size:41
Alignment explanation
Indices: 311361--311495 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
311351 AAAGTCAGTA
* * * ** *
311361 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
311401 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
311443 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
311484 TCGCGTTGCGAT
1 TCGCGTTGCGAT
311496 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:311496 original size:41 final size:41
Alignment explanation
Indices: 311422--311514 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
311412 ATAGTCAGTA
311422 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
311463 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
311504 TCGCATTGCGA
1 TCGCATTGCGA
311515 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:311839 original size:11 final size:11
Alignment explanation
Indices: 311805--311853 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
311795 GTGATATGCG
311805 TTTTATAATAATA
1 TTTTATAAT--TA
* *
311818 ATTTATGATTA
1 TTTTATAATTA
311829 TTTTATAATTA
1 TTTTATAATTA
*
311840 TTTTATATTTA
1 TTTTATAATTA
311851 TTT
1 TTT
311854 ATTTATTTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
11 24 0.77
13 7 0.23
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (11 bp):
TTTTATAATTA
Found at i:323614 original size:2 final size:2
Alignment explanation
Indices: 323609--323640 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
323599 AAAAAGGAAA
323609 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
323641 CAAAGTATTA
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):
AT
Found at i:323986 original size:18 final size:17
Alignment explanation
Indices: 323963--324005 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
323953 ATATATACAT
323963 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
323981 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
323998 ATAA-AATA
1 ATAATAATA
324006 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:324412 original size:37 final size:38
Alignment explanation
Indices: 324362--324466 Score: 142
Period size: 37 Copynumber: 2.8 Consensus size: 38
324352 GTGCTTGTGG
* * * *
324362 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAAC-TCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTTCT
* *
324399 ATCCTATTTTTAGGAGTTTGAATCCTAGCA-AACTTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTTCT
324436 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
324467 GACGAAAATG
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
36 3 0.05
37 56 0.95
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (38 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTTCT
Found at i:325310 original size:105 final size:105
Alignment explanation
Indices: 325009--325640 Score: 873
Period size: 105 Copynumber: 6.0 Consensus size: 105
324999 ACATTGTTCC
* * ** * *
325009 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCT-AGAACCGGGAAATTATTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTT-GTTGTTGACA
* * * * * *
325073 ACCAGCCGTCCTTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
325115 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGA-A-T--GAAATT-TTGTTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTG-TTGACAA
* *
325175 GAAGCGGTCCCTTCGTCGTGGAGTTGAACTTGCGTTGTCTG
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
325216 GAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTTAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* *
325281 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTA
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
325321 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
325386 CAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
325426 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
325491 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
325531 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAA
* * * *
325596 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 GCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
325637 GAGT
1 GAGT
325641 GTCACGATAT
Statistics
Matches: 478, Mismatches: 39, Indels: 18
0.89 0.07 0.03
Matches are distributed among these distances:
100 3 0.01
101 77 0.16
102 7 0.01
103 1 0.00
105 301 0.63
106 87 0.18
107 2 0.00
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:325880 original size:36 final size:36
Alignment explanation
Indices: 325840--325915 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
325830 TGTTTGGAGA
* * **
325840 GAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
*
325876 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
325912 GAAA
1 GAAA
325916 TGTTTTCAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:325984 original size:39 final size:39
Alignment explanation
Indices: 325927--326003 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 39
325917 GTTTTCAATG
* * *
325927 TTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAT
1 TTTATGTTTCAAGAGAAACTATCTCAAGAGAGAAAAAAT
* *
325966 TTTATGTTTCGAGGGAAACTATCTCAAGAGAGAAAAAA
1 TTTATGTTTCAAGAGAAACTATCTCAAGAGAGAAAAAA
326004 AATCATTTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (39 bp):
TTTATGTTTCAAGAGAAACTATCTCAAGAGAGAAAAAAT
Found at i:326090 original size:39 final size:39
Alignment explanation
Indices: 326036--326110 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
326026 TCAATGTTTA
* *
326036 TGTTTCAAGAGAAACTGTCTCAAGG-GAGACAAAATTTTT
1 TGTTTCAAGAGAAACTATCTC-AGGAGAGAAAAAATTTTT
* *
326075 TGTTTCGAGGGAAACTATCTCAGGAGAGAAAAAATT
1 TGTTTCAAGAGAAACTATCTCAGGAGAGAAAAAATT
326111 AATTTCAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 3 0.10
39 28 0.90
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (39 bp):
TGTTTCAAGAGAAACTATCTCAGGAGAGAAAAAATTTTT
Found at i:326149 original size:105 final size:104
Alignment explanation
Indices: 325815--326133 Score: 518
Period size: 105 Copynumber: 3.1 Consensus size: 104
325805 TTCGTTAAAT
* ** *
325815 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA---TTTGTTTCAAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTTGTTTCGAGGG
* *
325877 AAACTATCTCAAGCGAGATAAAATTCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
*
325916 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTATGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTTGTTTCGAGGG
*
325981 AAACTATCTCAAGAGAGAAAAAAAATCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAG-AAAAAATTCATTTCAAGGGAAA
326021 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTTGTTTCGAGGG
* *
326086 AAACTATCTCAGGAGAGAAAAAATTAATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
326125 TGTTTTCAA
1 TGTTTTCAA
326134 GAGAAACTGT
Statistics
Matches: 202, Mismatches: 12, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
101 46 0.23
104 56 0.28
105 100 0.50
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (104 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTTGTTTCGAGGG
AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
Found at i:327785 original size:183 final size:183
Alignment explanation
Indices: 327477--327998 Score: 929
Period size: 183 Copynumber: 2.9 Consensus size: 183
327467 ATCAGGTTTA
* *
327477 ACTGAAGGGTTCATCTCATCATAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* **
327542 GCCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGT
66 GCCAAGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
327606 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
* * *
327660 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAACAAACACCAAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
327725 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
*
327790 TCCTCTTTAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
327843 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCATGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
327908 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCAAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
327973 TCCTCTATAACCAATTGCCTTAGTGG
131 TCCTCTATAACCAATTGCCTTAGTGG
327999 CTCAGCTTTA
Statistics
Matches: 323, Mismatches: 15, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
183 322 1.00
184 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Done.