Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008114.1 Hibiscus syriacus cultivar Beakdansim tig00110653_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: 335373
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:236162 original size:178 final size:179
Alignment explanation
Indices: 235897--236254 Score: 673
Period size: 178 Copynumber: 2.0 Consensus size: 179
235887 GGAGAATTGA
*
235897 TACTTAGAGTTCAACATTATTTCGTTTTCATTATTTTTAAAGTGTGACATTTATTCGGATTTTCT
1 TACTTAGAGTTCAACATTATTTCGTTTTCATTATTTTTAAAGTGTGACATTTATTCAGATTTTCT
*
235962 GATTATTATTTTATTAATATTTTATTTGATATACTTATTATGTTTAAATATTTTTGGGACATTGG
66 AATTATTATTTTATTAATATTTTATTTGATATACTTATTATGTTTAAATATTTTTGGGACATTGG
236027 ATATAAATTTTATTTTGAACTCTAAATTTGATGGACATTCTCTTACGTT
131 ATATAAATTTTATTTTGAACTCTAAATTTGATGGACATTCTCTTACGTT
* *
236076 TACTTAGAGTTCAACATTATTTCGTTTTCATTA-TTTTAAAGTGTGACATTTATTCATATTTTTT
1 TACTTAGAGTTCAACATTATTTCGTTTTCATTATTTTTAAAGTGTGACATTTATTCAGATTTTCT
236140 AATTATTATTTTATTAATATTTTATTTGATATACTTATTATGTTTAAATATTTTTGGGACATTGG
66 AATTATTATTTTATTAATATTTTATTTGATATACTTATTATGTTTAAATATTTTTGGGACATTGG
236205 ATATAAATTTTATTTTGAACTCTAAATTTGATGGACATTCTCTTACGTT
131 ATATAAATTTTATTTTGAACTCTAAATTTGATGGACATTCTCTTACGTT
236254 T
1 T
236255 TAATTATTGT
Statistics
Matches: 175, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
178 142 0.81
179 33 0.19
ACGTcount: A:0.28, C:0.09, G:0.11, T:0.52
Consensus pattern (179 bp):
TACTTAGAGTTCAACATTATTTCGTTTTCATTATTTTTAAAGTGTGACATTTATTCAGATTTTCT
AATTATTATTTTATTAATATTTTATTTGATATACTTATTATGTTTAAATATTTTTGGGACATTGG
ATATAAATTTTATTTTGAACTCTAAATTTGATGGACATTCTCTTACGTT
Found at i:237271 original size:71 final size:71
Alignment explanation
Indices: 237183--237325 Score: 259
Period size: 71 Copynumber: 2.0 Consensus size: 71
237173 TCAATCACTA
* *
237183 AGGTTTAATGTAAAATTAAGTGTCTAAACTATACTCAAAATTAACTTTAGGTGTCTAAAGAATTT
1 AGGTTTAATGTAAAATTAAGTGTCTAAACTATAATCAAAATTAACTTTAGGTGTCCAAAGAATTT
237248 TTCATT
66 TTCATT
*
237254 AGGTTTAATGTAAAATTAAGTGTCTAAACTATAATCAAGATTAACTTTAGGTGTCCAAAGAATTT
1 AGGTTTAATGTAAAATTAAGTGTCTAAACTATAATCAAAATTAACTTTAGGTGTCCAAAGAATTT
237319 TTCATT
66 TTCATT
237325 A
1 A
237326 AAAAGAGGAG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (71 bp):
AGGTTTAATGTAAAATTAAGTGTCTAAACTATAATCAAAATTAACTTTAGGTGTCCAAAGAATTT
TTCATT
Found at i:237682 original size:24 final size:25
Alignment explanation
Indices: 237651--237721 Score: 99
Period size: 24 Copynumber: 2.9 Consensus size: 25
237641 TGCCATATAG
*
237651 ATTTGTCTCGAATGACCGCGTAG-A
1 ATTTGTCTCGAAAGACCGCGTAGAA
* *
237675 ATTTGTCTCGAAGGACCACGTAGAA
1 ATTTGTCTCGAAAGACCGCGTAGAA
*
237700 ATTTGTCCCGAAAGACCGCGTA
1 ATTTGTCTCGAAAGACCGCGTA
237722 TAACCCTCGA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
24 21 0.51
25 20 0.49
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (25 bp):
ATTTGTCTCGAAAGACCGCGTAGAA
Found at i:237903 original size:15 final size:15
Alignment explanation
Indices: 237864--237920 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
237854 TATTTTCATG
*
237864 TAGAACATTTTCACG
1 TAGAACATTTTCACA
* *
237879 TAGCATATTTTCACA
1 TAGAACATTTTCACA
*
237894 TAGAACATTTTCATA
1 TAGAACATTTTCACA
*
237909 TA-AACATATTCA
1 TAGAACATTTTCA
237921 TACAAAAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
14 9 0.26
15 26 0.74
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.37
Consensus pattern (15 bp):
TAGAACATTTTCACA
Found at i:239917 original size:3 final size:3
Alignment explanation
Indices: 239911--239985 Score: 95
Period size: 3 Copynumber: 26.0 Consensus size: 3
239901 TCATTTGGTT
*
239911 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA TTA -TA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
239957 TT- TTAA TT- TTA ATA TTA TTA TTA TTA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
239986 CAGGCCCAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
2 8 0.13
3 53 0.84
4 2 0.03
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:241562 original size:145 final size:145
Alignment explanation
Indices: 241427--241707 Score: 335
Period size: 144 Copynumber: 2.0 Consensus size: 145
241417 TGTTTTCTAT
* *
241427 TAAATAAAAATCTTA-TTTATAAATT-TA-AT-TTTATATAAATTATTTT-TATGAAAAATAATC
1 TAAATAAAAATCTTACTTTATAAATTATATATATTAATATAAATTATTTTATATGAAAAAGAA--
*
241487 ATATTTTAATATTATTTATTTTTTAATATTAAGAAAATGATTGTCTTAAAGCAACTAGAAGTC-C
64 ATATTTTAA-ATTATTTATTTTTT-ATATTAAGAAAATGACTGTCTTAAAGCAACTAGAAGTCTC
241551 TTTCTGATA--TTTTTAAA
127 TTTCTGATATTTTTTTAAA
* * * * * *** *
241568 TAACTAAATATCTTACTTTTATAAATTATATATATTAATTTAATTTATTTTAATTTTTTAGAGAA
1 TAAATAAAAATCTTAC-TTTATAAATTATATATATTAATATAAATTATTTT-ATATGAAAAAGAA
*
241633 ATATTTTAAATTATTTATTTTTTATATTAAGAAAATGACTGTCTTAAAGCAACTAGAAGTCTTTT
64 ATATTTTAAATTATTTATTTTTTATATTAAGAAAATGACTGTCTTAAAGCAACTAGAAGTCTCTT
241698 TCTGATATTT
129 TCTGATATTT
241708 CTAAGTAAAA
Statistics
Matches: 117, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
141 13 0.11
143 10 0.09
144 39 0.33
145 25 0.21
146 23 0.20
147 1 0.01
148 6 0.05
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (145 bp):
TAAATAAAAATCTTACTTTATAAATTATATATATTAATATAAATTATTTTATATGAAAAAGAAAT
ATTTTAAATTATTTATTTTTTATATTAAGAAAATGACTGTCTTAAAGCAACTAGAAGTCTCTTTC
TGATATTTTTTTAAA
Found at i:241765 original size:144 final size:146
Alignment explanation
Indices: 241487--241765 Score: 354
Period size: 144 Copynumber: 1.9 Consensus size: 146
241477 AAAAATAATC
*
241487 ATATTTTAATATTATTTATTTTTTAATATTAAGAAAATGATTGTCTTAAAGCAACTAGAAGTCCT
1 ATATTTTAATATTATTTATTTTTTAATATTAAGAAAATGACTGTCTTAAAGCAACTAGAAGTCCT
* * * * * * ** **
241552 TTCTGATATTTTTAAATAACTAAATATCTTACTTTTATAAATTATATATATTAATTTAATTTATT
66 TTCTGATATTTCTAAATAACAAAATATCTTACTTTTATAAATAAAAAAAATTAATTTAATAAAAG
241617 TTAATTTTTTAGAGAA
131 TTAATTTTTTAGAGAA
*
241633 ATATTTTAA-ATTATTTATTTTTT-ATATTAAGAAAATGACTGTCTTAAAGCAACTAGAAGTCTT
1 ATATTTTAATATTATTTATTTTTTAATATTAAGAAAATGACTGTCTTAAAGCAACTAGAAGTC-C
* *
241696 TTTCTGATATTTCTAAGTAA-AAAATATTTTA--TTTATAAAATAAAAAAAATATATATTT-ATA
65 TTTCTGATATTTCTAAATAACAAAATATCTTACTTTTAT-AAATAAAAAAAAT-TA-ATTTAATA
241757 AAAGTTAAT
127 AAAGTTAAT
241766 ACATTTTTCT
Statistics
Matches: 115, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
142 5 0.04
143 9 0.08
144 56 0.49
145 36 0.31
146 9 0.08
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (146 bp):
ATATTTTAATATTATTTATTTTTTAATATTAAGAAAATGACTGTCTTAAAGCAACTAGAAGTCCT
TTCTGATATTTCTAAATAACAAAATATCTTACTTTTATAAATAAAAAAAATTAATTTAATAAAAG
TTAATTTTTTAGAGAA
Found at i:247518 original size:113 final size:116
Alignment explanation
Indices: 247318--247547 Score: 423
Period size: 113 Copynumber: 2.0 Consensus size: 116
247308 TTTCTGAAAT
247318 TAATCTCCCTTTGGTTAGATATTTCAACAACTATCCTTATCTGGTATGATTGAACAAGAATTCAG
1 TAATCTCCCTTTGGTTAGATATTTCAACAACTATCCTTATCTGGTATGATTGAACAAGAATTCAG
247383 TCAAGCATAATGAATGCGGAGAATTATTG-A-AT-ATCAAGAAAAGGGACA
66 TCAAGCATAATGAATGCGGAGAATTATTGAATATCATCAAGAAAAGGGACA
247431 TAATCTCCCTTTGGTTAGATATTTCAACAACTATCCTTATCTGGTATGATTGAACAAGAATTCAA
1 TAATCTCCCTTTGGTTAGATATTTCAACAACTATCCTTATCTGGTATGATTGAACAAGAATTC-A
247496 GTCAAGCATAATGAATGC-GAGAATTATTGAATATCATCAAGAAAAGGGACA
65 GTCAAGCATAATGAATGCGGAGAATTATTGAATATCATCAAGAAAAGGGACA
247547 T
1 T
247548 GAAATTCAAC
Statistics
Matches: 113, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
113 74 0.65
114 20 0.18
115 2 0.02
116 17 0.15
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.30
Consensus pattern (116 bp):
TAATCTCCCTTTGGTTAGATATTTCAACAACTATCCTTATCTGGTATGATTGAACAAGAATTCAG
TCAAGCATAATGAATGCGGAGAATTATTGAATATCATCAAGAAAAGGGACA
Found at i:248077 original size:108 final size:108
Alignment explanation
Indices: 247888--248103 Score: 398
Period size: 108 Copynumber: 2.0 Consensus size: 108
247878 GGTGTGGATT
247888 CGACATTTGAATCAGTAAGTGAAGTCAGATTTTTTACAAGAAGTAGGAGGTGTTATTCTCCCGAG
1 CGACATTTGAATCAGTAAGTGAAGTCAGATTTTTTACAAGAAGTAGGAGGTGTTATTCTCCCGAG
*
247953 ACATCGAATGCATCAGAACA-GACAAAGCAAAGGGAAAAAGCTA
66 ACATCGAATGCATCAGAACAGGAAAAAGCAAAGGG-AAAAGCTA
247996 CGACATTTGAATCAGTAAGTGAAGTCAGATTTTTTACAAGAAGTAGGAGGTGTTATTCTCCCGAG
1 CGACATTTGAATCAGTAAGTGAAGTCAGATTTTTTACAAGAAGTAGGAGGTGTTATTCTCCCGAG
*
248061 ACATCGAATGCATCAGAACAGGAAAAAGCAGAGGGAAAAGCTA
66 ACATCGAATGCATCAGAACAGGAAAAAGCAAAGGGAAAAGCTA
248104 TAGTGATACC
Statistics
Matches: 105, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
108 93 0.89
109 12 0.11
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.22
Consensus pattern (108 bp):
CGACATTTGAATCAGTAAGTGAAGTCAGATTTTTTACAAGAAGTAGGAGGTGTTATTCTCCCGAG
ACATCGAATGCATCAGAACAGGAAAAAGCAAAGGGAAAAGCTA
Found at i:250510 original size:64 final size:64
Alignment explanation
Indices: 250373--250533 Score: 175
Period size: 64 Copynumber: 2.5 Consensus size: 64
250363 AATTATTCAG
* * *
250373 TGTGTATCGATGCA-CAGGAAGTGCATTGATGCACCCATTAAAAATAGAAACATCGAATGCAATT
1 TGTGTATCGATGCATAAGG-AGTGCATCGATGCACCCATTAAAAATAGAAACATCGAAGGCAATT
* * * **
250437 AGTGCATCGATGCATAAGGAGTGCATCGATGCACCCCCTT-AAAAT-GAAAACATCGAAGGTGAT
1 TGTGTATCGATGCATAAGGAGTGCATCGATGCA-CCCATTAAAAATAG-AAACATCGAAGGCAAT
250500 T
64 T
* * *
250501 TGTGTATCGATGAATGAGTAGTGCATCGATGCA
1 TGTGTATCGATGCATAAGGAGTGCATCGATGCA
250534 TAAGTTAAAG
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
63 1 0.01
64 72 0.89
65 8 0.10
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (64 bp):
TGTGTATCGATGCATAAGGAGTGCATCGATGCACCCATTAAAAATAGAAACATCGAAGGCAATT
Found at i:254601 original size:64 final size:65
Alignment explanation
Indices: 254492--254629 Score: 190
Period size: 64 Copynumber: 2.2 Consensus size: 65
254482 TTCAGTGTGT
* *
254492 ATCGATGCA-CCCATTAAAAGTGGAAACATCGAATGAAATTAGTGTATCGATGCATAAGGAGTGC
1 ATCGATGCACCCCATTAAAAGTGAAAACATCGAAGGAAATTAGTGTATCGATGCATAAGGAGTGC
* ** * * *
254556 ATCGATGCACCCCCTTAAAA-TGAAAACATCGAAGGTGATTTGTGTATCGATGCATGAGTAGTGC
1 ATCGATGCACCCCATTAAAAGTGAAAACATCGAAGGAAATTAGTGTATCGATGCATAAGGAGTGC
254620 ATCGATGCAC
1 ATCGATGCAC
254630 AAGTTAAAGA
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
64 56 0.86
65 9 0.14
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (65 bp):
ATCGATGCACCCCATTAAAAGTGAAAACATCGAAGGAAATTAGTGTATCGATGCATAAGGAGTGC
Found at i:254666 original size:20 final size:20
Alignment explanation
Indices: 254637--254674 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
254627 CACAAGTTAA
*
254637 AGAATGCATCGATGCACTGT
1 AGAATACATCGATGCACTGT
254657 AGAATACATCGATGCACT
1 AGAATACATCGATGCACT
254675 TTAAAGGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (20 bp):
AGAATACATCGATGCACTGT
Found at i:260024 original size:18 final size:18
Alignment explanation
Indices: 259998--260035 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
259988 CAAGTTCATC
* *
259998 TTTTTGAAATTCATTTTA
1 TTTTCGAAATTCAATTTA
260016 TTTTCGAAATTCAATTTA
1 TTTTCGAAATTCAATTTA
260034 TT
1 TT
260036 CTTTTATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.29, C:0.08, G:0.05, T:0.58
Consensus pattern (18 bp):
TTTTCGAAATTCAATTTA
Found at i:260722 original size:22 final size:22
Alignment explanation
Indices: 260660--260744 Score: 109
Period size: 22 Copynumber: 3.9 Consensus size: 22
260650 ACATCTACAT
*
260660 TCTTCAAAGATGATAGATACAT-
1 TCTTCAAAGATGATAGATTC-TC
260682 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
260704 TCTACAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* * *
260726 TTTTCAAAGAAGAAAGATT
1 TCTTCAAAGATGATAGATT
260745 TATTGGATTT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
21 1 0.02
22 55 0.98
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:261324 original size:20 final size:19
Alignment explanation
Indices: 261257--261325 Score: 52
Period size: 20 Copynumber: 3.6 Consensus size: 19
261247 AAACATTTCC
*
261257 AGAAGTGTTCATAATGAGA
1 AGAACTGTTCATAATGAGA
**
261276 AGAACTCATC-TGAA-GAGA
1 AGAACTGTTCAT-AATGAGA
**
261294 AGAAGAAGTTCATAATGAGA
1 AGAA-CTGTTCATAATGAGA
261314 AGAACTTGTTCA
1 AGAAC-TGTTCA
261326 ACCTTTTGCA
Statistics
Matches: 36, Mismatches: 9, Indels: 9
0.67 0.17 0.17
Matches are distributed among these distances:
18 9 0.25
19 13 0.36
20 14 0.39
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.23
Consensus pattern (19 bp):
AGAACTGTTCATAATGAGA
Found at i:261447 original size:20 final size:20
Alignment explanation
Indices: 261384--261448 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
261374 TTCCAGAGAA
261384 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
* **
261404 CG-TC-TGAA-GAGGAAGAAGA
1 AGTTCAT-AATGA-GAAGAACT
261423 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
*
261443 TGTTCA
1 AGTTCA
261449 ACCTTTTGCA
Statistics
Matches: 33, Mismatches: 7, Indels: 10
0.66 0.14 0.20
Matches are distributed among these distances:
18 3 0.09
19 11 0.33
20 16 0.48
21 3 0.09
ACGTcount: A:0.42, C:0.11, G:0.25, T:0.23
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:261459 original size:123 final size:123
Alignment explanation
Indices: 261125--261978 Score: 1066
Period size: 123 Copynumber: 6.9 Consensus size: 123
261115 TCAACATTTC
*
261125 CAACATTTCCAGA-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAAT
1 CAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAAT
**
261189 GAGAAGAACTTGTTCAACCTTTTGCATGAAGCTATCACAGAAGGAGATAGATCAACAT
66 GAGAAGAACTTGTTCAACCTTTTGCATGATTCTATCACAGAAGGAGATAGATCAACAT
* ** *
261247 AAACATTTCCAGA-AGTGTTCATAATGAGAAGAACTCATCTGAAG-AGAAGAAGAAGTTCATAAT
1 CAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAAT
* *
261310 GAGAAGAACTTGTTCAACCTTTTGCATGATTCTATCATAGAAAGAGATAGATCAACAT
66 GAGAAGAACTTGTTCAACCTTTTGCATGATTCTATCACAGAAGGAGATAGATCAACAT
* *
261368 CAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCGTCTGAAG-AGGAAGAAGAAGTTCATAA
1 CAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCATAA
*
261432 TGAGAAGAACTTGTTCAACCTTTTGCATGATTCTATCACAGAAGGAGATAGATCAGCAT
65 TGAGAAGAACTTGTTCAACCTTTTGCATGATTCTATCACAGAAGGAGATAGATCAACAT
* * *
261491 CAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATTTGAAGAAGGAGAATAAGTTCATAAT
1 CAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAAT
*
261556 GAGAAGAACTTGTTCAACCATTTGCATGATTCTATCACAGAAGGAGATAGATCAACAT
66 GAGAAGAACTTGTTCAACCTTTTGCATGATTCTATCACAGAAGGAGATAGATCAACAT
*
261614 CAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAAT
1 CAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAAT
* * * * *
261679 GAGAAGAATTTGCTCAACCTTTTGCTTGACTCTATCACAGAAAGAGATAGATCAACA-
66 GAGAAGAACTTGTTCAACCTTTTGCATGATTCTATCACAGAAGGAGATAGATCAACAT
* * * ** *
261736 CTAACATTTCCAGATAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAATAAGAAGTTTGTG
1 C-AACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCATA
* * * ** * * * * *
261800 ATGAGAAGAACTTGTTCGACC-TTAGCTTGATTC-ATCACCTATGGAG-TTGAATTAAAGAA
64 ATGAGAAGAACTTGTTCAACCTTTTGCATGATTCTATCACAGAAGGAGATAG-A-TCAACAT
* * * * * *
261859 GAAC-CTCCCTTGAGAATCAACGTTTTCATAATGAGAAGAACTCATCTGAAGATGAAGAAGAAGT
1 CAACATTTCC-AGAG-A--AA-G--TTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGT
* * * *
261923 TCATAATAAGAAGAACTTATTCAACTTTTTG-ATAGATTAC-ATCACAAAAGGAGATA
59 TCATAATGAGAAGAACTTGTTCAACCTTTTGCAT-GATT-CTATCACAGAAGGAGATA
261979 AATTGTCATC
Statistics
Matches: 642, Mismatches: 70, Indels: 31
0.86 0.09 0.04
Matches are distributed among these distances:
120 2 0.00
121 96 0.15
122 95 0.15
123 369 0.57
124 3 0.00
125 2 0.00
126 1 0.00
128 54 0.08
129 8 0.01
130 11 0.02
131 1 0.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (123 bp):
CAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAAT
GAGAAGAACTTGTTCAACCTTTTGCATGATTCTATCACAGAAGGAGATAGATCAACAT
Found at i:262180 original size:3 final size:3
Alignment explanation
Indices: 262174--262273 Score: 100
Period size: 3 Copynumber: 34.0 Consensus size: 3
262164 TCATTTGGTT
262174 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
* * * * * *
262219 TTA TT- TTA TAA TT- TTAA TTA -TA ATA ATA ATA ATA ATA TTA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
262262 TTA TTA TTA TTA
1 TTA TTA TTA TTA
262274 CAGGCCCAAA
Statistics
Matches: 88, Mismatches: 3, Indels: 12
0.85 0.03 0.12
Matches are distributed among these distances:
2 8 0.09
3 75 0.85
4 5 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:263645 original size:3 final size:3
Alignment explanation
Indices: 263637--263666 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
263627 AATATATTTA
263637 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
263667 TAGTCATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:264058 original size:154 final size:151
Alignment explanation
Indices: 263795--264075 Score: 422
Period size: 154 Copynumber: 1.8 Consensus size: 151
263785 TAATCATATT
*
263795 TTAATATTTATTTATTTTTTAATATTAAGAAAATGAGTGTCTTAAAGCAACTAGAAGTCATTTTC
1 TTAATATTTATTTATATTTTAATATTAAGAAAATGAGTGTCTTAAAGCAACTAGAAGTCATTTTC
* * *
263860 TGATATTTTTAAATAACTAAATATCTTACTTTTATAAATTATATATATATTAATTTAATTTATTT
66 TGATATTTTTAAATAAATAAATATCTTACTTTTAAAAATAATATATATA-T-ATTT-ATTTATTT
263925 TAATATTTTTAGAGAAATGTTTTA
128 TAATATTTTTAGAGAAATGTTTTA
* * *
263949 TTAATATTTATTTATATTTTAATATT-AGAAAAATGATTGTCTTAAAGCAACTATAAGTCTTTTT
1 TTAATATTTATTTATATTTTAATATTAAG-AAAATGAGTGTCTTAAAGCAACTAGAAGTCATTTT
* *
264013 CTGATATTTTTAAGTAAATAAATATTTTA-TTTATAAAAATAATATATATATATTTATTTATTT
65 CTGATATTTTTAAATAAATAAATATCTTACTTT-TAAAAATAATATATATATATTTATTTATTT
264076 ATTTATAAAA
Statistics
Matches: 116, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
151 8 0.07
152 4 0.03
153 6 0.05
154 98 0.84
ACGTcount: A:0.39, C:0.05, G:0.06, T:0.50
Consensus pattern (151 bp):
TTAATATTTATTTATATTTTAATATTAAGAAAATGAGTGTCTTAAAGCAACTAGAAGTCATTTTC
TGATATTTTTAAATAAATAAATATCTTACTTTTAAAAATAATATATATATATTTATTTATTTTAA
TATTTTTAGAGAAATGTTTTA
Found at i:265386 original size:18 final size:18
Alignment explanation
Indices: 265363--265399 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
265353 GTTATGGCTT
265363 GATGAATTTTATTGATGA
1 GATGAATTTTATTGATGA
265381 GATGAATTTTATTGATGA
1 GATGAATTTTATTGATGA
265399 G
1 G
265400 GAATATTGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.43
Consensus pattern (18 bp):
GATGAATTTTATTGATGA
Found at i:269587 original size:23 final size:22
Alignment explanation
Indices: 269548--269590 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
269538 AAATTTGATT
269548 AAAATGAACTTAAAATGAAAAA
1 AAAATGAACTTAAAATGAAAAA
269570 AAAATTGAA-TTAATAATGAAA
1 AAAA-TGAACTTAA-AATGAAA
269591 TCAAAGCCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.23
Consensus pattern (22 bp):
AAAATGAACTTAAAATGAAAAA
Found at i:287137 original size:21 final size:21
Alignment explanation
Indices: 287111--287155 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
287101 GATTTCTGGG
* *
287111 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
287132 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
287153 CAA
1 CAA
287156 ACGATAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:287994 original size:31 final size:31
Alignment explanation
Indices: 287956--288204 Score: 446
Period size: 31 Copynumber: 8.0 Consensus size: 31
287946 AGGGTCGAGG
287956 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
287987 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
288018 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
288049 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
288080 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
288111 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
288142 GTTTACCTATGTTCTTCGGGACATATAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
288173 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
288204 G
1 G
288205 GTCCTTCGGG
Statistics
Matches: 212, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
31 211 1.00
32 1 0.00
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:293715 original size:22 final size:21
Alignment explanation
Indices: 293654--293715 Score: 56
Period size: 22 Copynumber: 3.0 Consensus size: 21
293644 ACGAATTTGA
*
293654 AAATCCTTCGGGTCATCTG-T
1 AAATCCTTCGGGTCATATGTT
* * *
293674 AAGTCCTACGAG-CATGATGTTT
1 AAATCCTTCGGGTCAT-ATG-TT
293696 AAATCCTTCGGGTCATATGT
1 AAATCCTTCGGGTCATATGT
293716 CAGTCTTTCA
Statistics
Matches: 31, Mismatches: 7, Indels: 7
0.69 0.16 0.16
Matches are distributed among these distances:
19 3 0.10
20 11 0.35
21 1 0.03
22 13 0.42
23 3 0.10
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (21 bp):
AAATCCTTCGGGTCATATGTT
Found at i:293882 original size:20 final size:20
Alignment explanation
Indices: 293857--293944 Score: 117
Period size: 20 Copynumber: 4.4 Consensus size: 20
293847 TTCCCAGTAC
*
293857 TTTGTAAAGCCTCTGGGTTA
1 TTTGTAAAGCCTCTGGGTAA
*
293877 TTTGTAAAGCCTCTGGGTCA
1 TTTGTAAAGCCTCTGGGTAA
293897 TTTGTAAAGCCT-TCGGGTAA
1 TTTGTAAAGCCTCT-GGGTAA
*
293917 TTTGTAAAGCCT-TAAGGTAA
1 TTTGTAAAGCCTCT-GGGTAA
293937 TTTGTAAA
1 TTTGTAAA
293945 TCCTTCGGGT
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
19 1 0.02
20 62 0.98
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.38
Consensus pattern (20 bp):
TTTGTAAAGCCTCTGGGTAA
Found at i:293920 original size:40 final size:40
Alignment explanation
Indices: 293857--293954 Score: 128
Period size: 40 Copynumber: 2.5 Consensus size: 40
293847 TTCCCAGTAC
* * *
293857 TTTGTAAAGCC-TCTGGGTTATTTGTAAAGCCTCT-GGGTCA
1 TTTGTAAAGCCTTC-GGGTAATTTGTAAAGCCT-TAAGGTAA
293897 TTTGTAAAGCCTTCGGGTAATTTGTAAAGCCTTAAGGTAA
1 TTTGTAAAGCCTTCGGGTAATTTGTAAAGCCTTAAGGTAA
*
293937 TTTGTAAATCCTTCGGGT
1 TTTGTAAAGCCTTCGGGT
293955 CATCTGTTAG
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
39 1 0.02
40 49 0.94
41 2 0.04
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (40 bp):
TTTGTAAAGCCTTCGGGTAATTTGTAAAGCCTTAAGGTAA
Found at i:298773 original size:25 final size:26
Alignment explanation
Indices: 298752--298802 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
298742 ATTTATTATT
298752 TTTAGAATT-TAATAAAAATATTAAA
1 TTTAGAATTGTAATAAAAATATTAAA
* *
298777 TTTATAATTGGTAATAAAAAAATTAA
1 TTTAGAATT-GTAATAAAAATATTAA
298803 TAAAATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 8 0.36
27 14 0.64
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (26 bp):
TTTAGAATTGTAATAAAAATATTAAA
Found at i:299216 original size:11 final size:11
Alignment explanation
Indices: 299200--299224 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
299190 CTATTAACCC
299200 GACCCGATATT
1 GACCCGATATT
299211 GACCCGATATT
1 GACCCGATATT
299222 GAC
1 GAC
299225 ACAATCCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (11 bp):
GACCCGATATT
Found at i:299601 original size:9 final size:10
Alignment explanation
Indices: 299587--299628 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
299577 TCGGGTTTTA
299587 ATTA-TTATT
1 ATTATTTATT
299596 ATTA-TTATT
1 ATTATTTATT
* *
299605 ACTATTTAGT
1 ATTATTTATT
299615 ATTATTTATT
1 ATTATTTATT
299625 ATTA
1 ATTA
299629 ATATATTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
9 12 0.43
10 16 0.57
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (10 bp):
ATTATTTATT
Found at i:302003 original size:16 final size:15
Alignment explanation
Indices: 301982--302013 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
301972 ATATGTTATC
301982 TTTTTTCTTTTTCTTT
1 TTTTTTCTTTTT-TTT
301998 TTTTTTCTTTTTTTT
1 TTTTTTCTTTTTTTT
302013 T
1 T
302014 GTATTTGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (15 bp):
TTTTTTCTTTTTTTT
Found at i:302008 original size:9 final size:10
Alignment explanation
Indices: 301984--302013 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
301974 ATGTTATCTT
301984 TTTTCTTTTTC
1 TTTT-TTTTTC
301995 TTTTTTTTTC
1 TTTTTTTTTC
302005 TTTTTTTTT
1 TTTTTTTTT
302014 GTATTTGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:303414 original size:16 final size:16
Alignment explanation
Indices: 303395--303453 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
303385 TGAACTGAAA
303395 TCAACCCGAACCGAAG
1 TCAACCCGAACCGAAG
* *
303411 TCAACCCTAATCGAAAG
1 TCAACCCGAACCG-AAG
* *
303428 -CAACTCGAACCAAAAG
1 TCAACCCGAACC-GAAG
303444 T-AACCCGAAC
1 TCAACCCGAAC
303454 TAAAATCAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
16 30 0.91
17 3 0.09
ACGTcount: A:0.42, C:0.34, G:0.14, T:0.10
Consensus pattern (16 bp):
TCAACCCGAACCGAAG
Found at i:304211 original size:46 final size:45
Alignment explanation
Indices: 304159--304268 Score: 148
Period size: 46 Copynumber: 2.4 Consensus size: 45
304149 ATGGTTGAAA
*
304159 CAAACCAAAATCAACTTGAATTGACTCAAAAATCTAAAGGTTGACC
1 CAAACCAAAA-CAACTTGAATTGACCCAAAAATCTAAAGGTTGACC
* * * *
304205 CGAACCAAAACCGACCTGAATTGACCCGAAAATCTAAAGGTTGACC
1 CAAACCAAAA-CAACTTGAATTGACCCAAAAATCTAAAGGTTGACC
*
304251 CAAACCAAAACAAATTGA
1 CAAACCAAAACAACTTGA
304269 CCGATACTAA
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
45 5 0.09
46 49 0.91
ACGTcount: A:0.45, C:0.25, G:0.13, T:0.17
Consensus pattern (45 bp):
CAAACCAAAACAACTTGAATTGACCCAAAAATCTAAAGGTTGACC
Found at i:304326 original size:32 final size:32
Alignment explanation
Indices: 304288--304378 Score: 121
Period size: 32 Copynumber: 2.8 Consensus size: 32
304278 ACCCAACTCG
* * *
304288 AAACCAACCGATCTGATATTAACCCGA-CTGAA
1 AAACCAATCGATCCGATTTTAACCCGACCT-AA
* *
304320 AAACCAATTGATCCGATTTTAACTCGACCTAA
1 AAACCAATCGATCCGATTTTAACCCGACCTAA
304352 AAACCAATCGATCCGATTTTAACCCGA
1 AAACCAATCGATCCGATTTTAACCCGA
304379 ACCCGAACCC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
32 49 0.96
33 2 0.04
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.23
Consensus pattern (32 bp):
AAACCAATCGATCCGATTTTAACCCGACCTAA
Found at i:304726 original size:15 final size:15
Alignment explanation
Indices: 304706--304737 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
304696 TTCAGTTTGA
*
304706 AAAAAAACCGATTAT
1 AAAAAAACCAATTAT
304721 AAAAAAACCAATTAT
1 AAAAAAACCAATTAT
304736 AA
1 AA
304738 TATTATTAAA
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:0.66, C:0.12, G:0.03, T:0.19
Consensus pattern (15 bp):
AAAAAAACCAATTAT
Found at i:304815 original size:32 final size:32
Alignment explanation
Indices: 304779--304855 Score: 127
Period size: 33 Copynumber: 2.4 Consensus size: 32
304769 ACAAAGTTTA
*
304779 CGATAATTGAAATACTTAAATACTTCCAAGTT
1 CGATAATTGAAATACTTAAAAACTTCCAAGTT
*
304811 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGAT-AATTGAAATACTTAAAAACTTCCAAGTT
304844 CGATAATTGAAA
1 CGATAATTGAAA
304856 CAAAGTTTAC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 11 0.27
33 30 0.73
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (32 bp):
CGATAATTGAAATACTTAAAAACTTCCAAGTT
Found at i:304869 original size:21 final size:21
Alignment explanation
Indices: 304844--304885 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
304834 CTTCCAAGTT
304844 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
304865 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
304886 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:314614 original size:112 final size:113
Alignment explanation
Indices: 314210--314678 Score: 674
Period size: 114 Copynumber: 4.2 Consensus size: 113
314200 TACATGTACA
** * * *
314210 AAAAGTATATATACTTTCAATATATCAGGTAGCTCTTTACCGGTTTTGTCATAATAAAACTGGTT
1 AAAAGTATCGATACTTTCAACATATCAGGTAACTCTTTACCGGTTTTGTCATAATGAAACTGGTT
* *
314275 TTGTCATATTTTTA-CTTGTTATATTATAAAGTATCGATACATTTTAAT
66 TTGTCATATTTTTATC-TGTTATATTGTAAAGTATCGATACATTTTTAT
* * * * * *
314323 AAAAATGATCGATACTTTCAACATGTCATGTCACTCTTTACCGGTTTTGTCATAATGAAATTTGT
1 AAAAGT-ATCGATACTTTCAACATATCAGGTAACTCTTTACCGGTTTTGTCATAATGAAACTGGT
* *
314388 TTTGTCATATTTTTACCTTTTATATTGTAAAGTATCGATACATTTTTAT
65 TTTGTCATATTTTTATCTGTTATATTGTAAAGTATCGATACATTTTTAT
* * *
314437 AAAAATTATCTATACTTTCAACATATCAGGTAGCTCTTTACCGGTTTTGTCATAATGAAACTGGT
1 -AAAAGTATCGATACTTTCAACATATCAGGTAACTCTTTACCGGTTTTGTCATAATGAAACTGGT
*
314502 TTTGTCATATGTTTATCTGTTATATTGTAAAGTATCGATACATTTTTAT
65 TTTGTCATATTTTTATCTGTTATATTGTAAAGTATCGATACATTTTTAT
* * ** *
314551 -AAAGTATCGATACTTTCAACATATCATGTAATTCTTTATTGATTTTGTCATAATGAAACTGGTT
1 AAAAGTATCGATACTTTCAACATATCAGGTAACTCTTTACCGGTTTTGTCATAATGAAACTGGTT
314615 TTGTCATATTTTTATCTGTTATATTGTAAAGTATCGATACATTTTTAT
66 TTGTCATATTTTTATCTGTTATATTGTAAAGTATCGATACATTTTTAT
314663 -AAAGTATCGATACTTT
1 AAAAGTATCGATACTTT
314679 ATAAGTGCTA
Statistics
Matches: 319, Mismatches: 34, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
112 119 0.37
113 5 0.02
114 189 0.59
115 6 0.02
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (113 bp):
AAAAGTATCGATACTTTCAACATATCAGGTAACTCTTTACCGGTTTTGTCATAATGAAACTGGTT
TTGTCATATTTTTATCTGTTATATTGTAAAGTATCGATACATTTTTAT
Found at i:314681 original size:18 final size:19
Alignment explanation
Indices: 314641--314682 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
314631 TGTTATATTG
314641 TAAAGTATCGATACATTTTTA
1 TAAAGTATCGATAC--TTTTA
314662 TAAAGTATCGATAC-TTTA
1 TAAAGTATCGATACTTTTA
314680 TAA
1 TAA
314683 GTGCTATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.33
21 14 0.67
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (19 bp):
TAAAGTATCGATACTTTTA
Found at i:314996 original size:72 final size:71
Alignment explanation
Indices: 314762--315001 Score: 345
Period size: 73 Copynumber: 3.3 Consensus size: 71
314752 ACATATCTGA
* * *
314762 TAGGTATTTTAATGTAATAGATAGCACTTATTTTTTTACCGTTTATATTATTAGCAACATTCAAA
1 TAGGTATTTTAATGTAATAGGTAGCAC-TATTTTTTTACCGTTTATATTATTAACAACCTTCAAA
314827 AAAACTAG
65 AAAAC-AG
* * * * *
314835 TAGGTATTTTAATGTAATAGGTAACACTATTTTTTTTACCGTTTACATTATTAACCATCTTAAAA
1 TAGGTATTTTAATGTAATAGGTAGCACTA-TTTTTTTACCGTTTATATTATTAACAACCTTCAAA
314900 AAAACATG
65 AAAACA-G
*
314908 TAGGTATTTTAATGTAATAGGTAGCGCATATTTTTTTACCGTTTATATTATTAACAACCTTCAAA
1 TAGGTATTTTAATGTAATAGGTAGCAC-TATTTTTTTACCGTTTATATTATTAACAACCTTCAAA
314973 AAAACAG
65 AAAACAG
*
314980 TAGATATTTTAATGTAATAGGT
1 TAGGTATTTTAATGTAATAGGT
315002 TGTTTAAATT
Statistics
Matches: 149, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
72 25 0.17
73 122 0.82
74 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.41
Consensus pattern (71 bp):
TAGGTATTTTAATGTAATAGGTAGCACTATTTTTTTACCGTTTATATTATTAACAACCTTCAAAA
AAACAG
Found at i:315309 original size:23 final size:23
Alignment explanation
Indices: 315214--315297 Score: 141
Period size: 23 Copynumber: 3.7 Consensus size: 23
315204 ACATATTTTA
315214 TTATATAAGCGCTACCTATTACG
1 TTATATAAGCGCTACCTATTACG
* * *
315237 TTATATAAGTGTTACCTACTACG
1 TTATATAAGCGCTACCTATTACG
315260 TTATATAAGCGCTACCTATTACG
1 TTATATAAGCGCTACCTATTACG
315283 TTATATAAGCGCTAC
1 TTATATAAGCGCTAC
315298 ATAATATGTT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (23 bp):
TTATATAAGCGCTACCTATTACG
Found at i:315309 original size:46 final size:46
Alignment explanation
Indices: 315214--315309 Score: 147
Period size: 46 Copynumber: 2.1 Consensus size: 46
315204 ACATATTTTA
* * * *
315214 TTATATAAGCGCTACCTATTACGTTATATAAGTGTTACCTACTACG
1 TTATATAAGCGCTACCTATTACGTTATATAAGCGCTACATAATACG
*
315260 TTATATAAGCGCTACCTATTACGTTATATAAGCGCTACATAATATG
1 TTATATAAGCGCTACCTATTACGTTATATAAGCGCTACATAATACG
315306 TTAT
1 TTAT
315310 TCTGCCTAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (46 bp):
TTATATAAGCGCTACCTATTACGTTATATAAGCGCTACATAATACG
Found at i:315418 original size:204 final size:204
Alignment explanation
Indices: 315068--315449 Score: 595
Period size: 204 Copynumber: 1.9 Consensus size: 204
315058 ATTAAGCAAT
** * * * *
315068 TACCTATTTTGTTACATAAGCGCTACCTAATATGTTATTATGCTTTATAATGTTTCGAGTAATTA
1 TACCTATTACGTTACATAAGCGCTACATAATATGTTATTATGCCTAATAATGTTTCAAGTAATTA
* * *
315133 ACCAGTTATATTATCTTTGGTAACATTTTAAGCGTTTACATAATATGTTGTAATAACAAATTAAG
66 ACCAGTTATATTATCATTGGTAACATTTTAAGCATTTACATAATATGTTGTAATAACAAATTAAA
*
315198 TAATTAACATATTTTATTATATAAGCGCTACCTATTACGTTATATAAGTGTTACCTACTACGTTA
131 TAATTAACATATTTTATTATATAAGCACTACCTATTACGTTATATAAGTGTTACCTACTACGTTA
315263 TATAAGCGC
196 TATAAGCGC
* *
315272 TACCTATTACGTTATATAAGCGCTACATAATATGTTATTCTGCCTAATAATGTTTCAAGTAATTA
1 TACCTATTACGTTACATAAGCGCTACATAATATGTTATTATGCCTAATAATGTTTCAAGTAATTA
* * *
315337 ACCGGTTATGTTATCATTGGTAACATTTT-AGTCATTTACCTAATATGTTGTAATAACAAATTAA
66 ACCAGTTATATTATCATTGGTAACATTTTAAG-CATTTACATAATATGTTGTAATAACAAATTAA
* *
315401 ATAATTAACCTATTTTATTATATTAGCACTACCTATTACGTTATATAAG
130 ATAATTAACATATTTTATTATATAAGCACTACCTATTACGTTATATAAG
315450 CACTACCTAA
Statistics
Matches: 160, Mismatches: 17, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
203 2 0.01
204 158 0.99
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (204 bp):
TACCTATTACGTTACATAAGCGCTACATAATATGTTATTATGCCTAATAATGTTTCAAGTAATTA
ACCAGTTATATTATCATTGGTAACATTTTAAGCATTTACATAATATGTTGTAATAACAAATTAAA
TAATTAACATATTTTATTATATAAGCACTACCTATTACGTTATATAAGTGTTACCTACTACGTTA
TATAAGCGC
Found at i:315434 original size:23 final size:23
Alignment explanation
Indices: 315408--315458 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
315398 TAAATAATTA
** *
315408 ACCTATTTTATTATATTAGCACT
1 ACCTATTACATTATATAAGCACT
*
315431 ACCTATTACGTTATATAAGCACT
1 ACCTATTACATTATATAAGCACT
315454 ACCTA
1 ACCTA
315459 ATATGTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCACT
Found at i:315466 original size:23 final size:23
Alignment explanation
Indices: 315418--315467 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
315408 ACCTATTTTA
* *
315418 TTATATTAGCACTACCTATTACG
1 TTATATAAGCACTACCTAATACG
*
315441 TTATATAAGCACTACCTAATATG
1 TTATATAAGCACTACCTAATACG
315464 TTAT
1 TTAT
315468 TGTGCTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.40
Consensus pattern (23 bp):
TTATATAAGCACTACCTAATACG
Found at i:315538 original size:158 final size:158
Alignment explanation
Indices: 315260--315644 Score: 592
Period size: 158 Copynumber: 2.4 Consensus size: 158
315250 ACCTACTACG
* * * *
315260 TTATATAAGCGCTACCTATTACGTTATATAAGCGCTACATAATATGTTATTCTGCCTAATAATGT
1 TTATATAAGCGCTACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTAATAATAT
*
315325 TTCAAGTAATTAACCGGTTATGTTATCATTGGTAACATTTTAGTCATTTACCTAATATGTTGTAA
66 TTCTAGTAATTAACCGGTTATGTTATCATTGGTAACATTTTAGTCATTTACCTAATATGTTGTAA
315390 TAACAAATTAAATAATTAACCTATTTTA
131 TAACAAATTAAATAATTAACCTATTTTA
* * *
315418 TTATATTAGCACTACCTATTACGTTATATAAGCACTACCTAATATGTTATTGTGCTTAATAATAT
1 TTATATAAGCGCTACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTAATAATAT
* * *
315483 TTCTAGTAATTAACCGGTTATGTTATCCTTGGTAACATTTTAGGT-GTTTCCCTAATATGTTGTA
66 TTCTAGTAATTAACCGGTTATGTTATCATTGGTAACATTTTA-GTCATTTACCTAATATGTTGTA
* *
315547 ATAACAAATTAAGTAATTAATCTATTTTA
130 ATAACAAATTAAATAATTAACCTATTTTA
* * ** *
315576 TTATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTATTTGATAATAT
1 TTATATAAGCGCTACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTAATAATAT
315641 TTCT
66 TTCT
315645 GTTTAAATGA
Statistics
Matches: 205, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
158 203 0.99
159 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.42
Consensus pattern (158 bp):
TTATATAAGCGCTACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTAATAATAT
TTCTAGTAATTAACCGGTTATGTTATCATTGGTAACATTTTAGTCATTTACCTAATATGTTGTAA
TAACAAATTAAATAATTAACCTATTTTA
Found at i:315625 original size:23 final size:23
Alignment explanation
Indices: 315575--315619 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
315565 AATCTATTTT
* *
315575 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAACGCTACCTAATAC
315598 ATTATATAAACGCTACCTAATA
1 ATTATATAAACGCTACCTAATA
315620 TGTTATTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (23 bp):
ATTATATAAACGCTACCTAATAC
Found at i:317945 original size:6 final size:6
Alignment explanation
Indices: 317934--318015 Score: 107
Period size: 6 Copynumber: 13.8 Consensus size: 6
317924 ACTATGAAAG
317934 GGGGAA GGGGAA GGGGAA GGGGAA GGGGAAA GGGGAA GGGGAA GGGGAA
1 GGGGAA GGGGAA GGGGAA GGGGAA GGGG-AA GGGGAA GGGGAA GGGGAA
* *
317983 GGGGAAA GGGAAA AGGG-A GGGG-A GGGG-A GGGGA
1 GGGG-AA GGGGAA GGGGAA GGGGAA GGGGAA GGGGA
318016 GAATGGACTG
Statistics
Matches: 69, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
5 14 0.20
6 44 0.64
7 11 0.16
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (6 bp):
GGGGAA
Found at i:317966 original size:25 final size:25
Alignment explanation
Indices: 317931--318010 Score: 119
Period size: 25 Copynumber: 3.3 Consensus size: 25
317921 TAGACTATGA
*
317931 AAGGGGGAAGGGGAAGGGGAAGGGG
1 AAGGGGAAAGGGGAAGGGGAAGGGG
317956 AAGGGGAAAGGGGAAGGGGAAGGGG
1 AAGGGGAAAGGGGAAGGGGAAGGGG
* *
317981 AAGGGGAAAGGGAAAAGGG-AGGGG
1 AAGGGGAAAGGGGAAGGGGAAGGGG
318005 -AGGGGA
1 AAGGGGA
318011 GGGGAGAATG
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
23 6 0.12
24 5 0.10
25 41 0.79
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (25 bp):
AAGGGGAAAGGGGAAGGGGAAGGGG
Found at i:318054 original size:17 final size:17
Alignment explanation
Indices: 318032--318064 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
318022 ACTGTTTGAT
*
318032 TTTTTAATTTTTTTTAC
1 TTTTTAAATTTTTTTAC
318049 TTTTTAAATTTTTTTA
1 TTTTTAAATTTTTTTA
318065 AATAAAATTT
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:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTAAATTTTTTTAC
Found at i:321908 original size:22 final size:23
Alignment explanation
Indices: 321883--321929 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
321873 TTAAAGTACA
*
321883 ATAACATACTA-GTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
321905 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
321928 AT
1 AT
321930 TTACCTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:322376 original size:23 final size:23
Alignment explanation
Indices: 322340--322412 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
322330 ACACTTTACA
*
322340 ATATAACCACTACCTATTACATT
1 ATATAAACACTACCTATTACATT
*
322363 ATATAAACAATACCTATTACATT
1 ATATAAACACTACCTATTACATT
* * *
322386 ATATAAGCGCTACCTATTACATC
1 ATATAAACACTACCTATTACATT
322409 ATAT
1 ATAT
322413 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.34
Consensus pattern (23 bp):
ATATAAACACTACCTATTACATT
Found at i:322785 original size:425 final size:427
Alignment explanation
Indices: 321996--323038 Score: 1933
Period size: 425 Copynumber: 2.5 Consensus size: 427
321986 TATTACATTA
321996 TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
322061 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAA-TTAATAATTTC
66 TTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
322125 ATTTGCACAAAAAATTATTTGATT-TTTGAT-TTTTAT-AAATATTATTTAGAATTTTTAATTTA
130 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
*
322187 ATAATAATATATATCGTAACGTAAAAATAAATCATTAGACCCTATAATTACTAAATTAATATCTT
195 ATAATAATATATATCGTAACATAAAAATAAATCATTAGACCCTATAATTACTAAATTAATATCTT
* * *
322252 AGAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTT
260 AAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAATGAAAAAAATATGGACACTTTT
322317 ATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACAATACCTATTA
325 ATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACAATACCTATTA
322382 CATTATATAAGCGCTACCTATTACATCATATTTTTACC
390 CATTATATAAGCGCTACCTATTACATCATATTTTTACC
*
322420 TATTATATTGAAAGTGTCCATACTTTTTAT-AAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
322484 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
66 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
322549 TTTGCACAAAAAATTA-TTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
131 TTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
322613 TAAT-A-ATATATCGTAACATAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCT
196 TAATAATATATATCGTAACAT-AAAAATAAATCATTAGAC-CCTATAATTACTAAATTAATATCT
322676 TAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAATGAAAAAAATATGGACACTTT
259 TAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAATGAAAAAAATATGGACACTTT
322741 TATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACAATACCTATT
324 TATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACAATACCTATT
322806 ACATTATATAAGCGCTACCTATTACATCATATTTTTACC
389 ACATTATATAAGCGCTACCTATTACATCATATTTTTACC
322845 TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
322910 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
66 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
* *
322975 TTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTATAA-TTTCAATTTAA
131 TTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
323039 CAACATTAAC
Statistics
Matches: 603, Mismatches: 8, Indels: 14
0.96 0.01 0.02
Matches are distributed among these distances:
422 47 0.08
423 91 0.15
424 55 0.09
425 251 0.42
426 124 0.21
427 35 0.06
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (427 bp):
TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
TTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
TAATAATATATATCGTAACATAAAAATAAATCATTAGACCCTATAATTACTAAATTAATATCTTA
AAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAATGAAAAAAATATGGACACTTTTA
TAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACAATACCTATTAC
ATTATATAAGCGCTACCTATTACATCATATTTTTACC
Found at i:322801 original size:23 final size:23
Alignment explanation
Indices: 322765--322837 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
322755 ACACTTTACA
*
322765 ATATAACCACTACCTATTACATT
1 ATATAAACACTACCTATTACATT
*
322788 ATATAAACAATACCTATTACATT
1 ATATAAACACTACCTATTACATT
* * *
322811 ATATAAGCGCTACCTATTACATC
1 ATATAAACACTACCTATTACATT
322834 ATAT
1 ATAT
322838 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.34
Consensus pattern (23 bp):
ATATAAACACTACCTATTACATT
Found at i:326213 original size:183 final size:183
Alignment explanation
Indices: 325706--326196 Score: 882
Period size: 183 Copynumber: 2.7 Consensus size: 183
325696 TTAAAATTAC
*
325706 CGACACTTTTT---AATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
1 CGACACTTTTTAACAAT-GTATCGACACATTTTTTTTCCAATCTGGACATAAAGTACCGACACAA
* * *
325768 TATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGT
65 GATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGT
325833 TATATTACAAATTTATCTATTACATTATAATTATGGGTTCTGATGTGTAAATGT
130 TATATTACAAATTTATCTATTACATTATAATTATGGGTTCTGATGTGTAAATGT
325887 CGACACTTTTTAACAATGTATCGACACATTTTTTTTCCAATCTGGACATAAAGTACCGACACAAG
1 CGACACTTTTTAACAATGTATCGACACATTTTTTTTCCAATCTGGACATAAAGTACCGACACAAG
*
325952 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCAGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
326017 ATATTACAAATTTATCTATTACATTATAATTATGGGTTAC-GATGTGTAAATGT
131 ATATTACAAATTTATCTATTACATTATAATTATGGGTT-CTGATGTGTAAATGT
*
326070 CGACACTTTTTAACAATGTATCGAAACATTTTTTTTCCAATCTGGACATAAAGTACCGACACAAG
1 CGACACTTTTTAACAATGTATCGACACATTTTTTTTCCAATCTGGACATAAAGTACCGACACAAG
326135 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
326197 ATAGCATTGC
Statistics
Matches: 299, Mismatches: 7, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
181 11 0.04
183 284 0.95
184 4 0.01
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (183 bp):
CGACACTTTTTAACAATGTATCGACACATTTTTTTTCCAATCTGGACATAAAGTACCGACACAAG
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAATTTATCTATTACATTATAATTATGGGTTCTGATGTGTAAATGT
Found at i:327383 original size:88 final size:91
Alignment explanation
Indices: 327215--327383 Score: 317
Period size: 88 Copynumber: 1.9 Consensus size: 91
327205 TACCCACACC
327215 AACATCATTGAGATCTTTACAGTAGGTAACAGAATCGTATGTTTGCATTTTTTTTGATCCTGTTC
1 AACATCATTGAGATCTTTACAGTAGGTAACAGAATCGTATGTTTGCATTTTTTTTGATCCTGTTC
327280 ACAAACAGTCGAACATGGACGTTCCA
66 ACAAACAGTCGAACATGGACGTTCCA
327306 AACATCATTGAGATCTTTACAGTAGGT-ACAG-ATCGTATGTTTGCA-TTTTTTTGATCCTGTTC
1 AACATCATTGAGATCTTTACAGTAGGTAACAGAATCGTATGTTTGCATTTTTTTTGATCCTGTTC
327368 ACAAACAGTCGAACAT
66 ACAAACAGTCGAACAT
327384 AAATATGTAG
Statistics
Matches: 78, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
88 33 0.42
89 14 0.18
90 4 0.05
91 27 0.35
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (91 bp):
AACATCATTGAGATCTTTACAGTAGGTAACAGAATCGTATGTTTGCATTTTTTTTGATCCTGTTC
ACAAACAGTCGAACATGGACGTTCCA
Found at i:327855 original size:3 final size:3
Alignment explanation
Indices: 327847--327924 Score: 66
Period size: 3 Copynumber: 26.0 Consensus size: 3
327837 ACTTGTTTGG
* * * ** *
327847 ATC ATC ATC TTC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC AGC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * *
327895 TTC ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
327925 GTCAGCTTCA
Statistics
Matches: 56, Mismatches: 19, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.23, C:0.35, G:0.06, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:327864 original size:12 final size:12
Alignment explanation
Indices: 327851--327936 Score: 91
Period size: 12 Copynumber: 6.9 Consensus size: 12
327841 GTTTGGATCA
*
327851 TCATCTTCATCA
1 TCATCTTCATCG
*
327863 TCATCATCATCG
1 TCATCTTCATCG
327875 TCATCATCTTCATCG
1 ---TCATCTTCATCG
* *
327890 CCAGCTTCATCG
1 TCATCTTCATCG
*
327902 TCATCATCATCG
1 TCATCTTCATCG
327914 TCATCTTCATCG
1 TCATCTTCATCG
*
327926 TCAGCTTCATC
1 TCATCTTCATC
327937 TTCTGCGACC
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
12 50 0.82
15 11 0.18
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:327870 original size:18 final size:18
Alignment explanation
Indices: 327847--327936 Score: 81
Period size: 18 Copynumber: 4.8 Consensus size: 18
327837 ACTTGTTTGG
327847 ATCATCATCTTCATCATC
1 ATCATCATCTTCATCATC
*
327865 ATCATCATCGTCATCATC
1 ATCATCATCTTCATCATC
* * *
327883 TTCATCGCCAGCTTCATCGTC
1 ATCAT---CATCTTCATCATC
* *
327904 ATCATCATCGTCATCTTC
1 ATCATCATCTTCATCATC
* *
327922 ATCGTCAGCTTCATC
1 ATCATCATCTTCATC
327937 TTCTGCGACC
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
18 43 0.75
21 14 0.25
ACGTcount: A:0.22, C:0.34, G:0.08, T:0.36
Consensus pattern (18 bp):
ATCATCATCTTCATCATC
Found at i:327900 original size:36 final size:36
Alignment explanation
Indices: 327860--327936 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
327850 ATCATCTTCA
*
327860 TCATCATCATCATCGTCATCATCTTCATCGCCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCT
* * *
327896 TCATCGTCATCATCATCGTCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCT
327932 TCATC
1 TCATC
327937 TTCTGCGACC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.21, C:0.35, G:0.09, T:0.35
Consensus pattern (36 bp):
TCATCATCATCATCATCATCATCTTCATCGCCAGCT
Found at i:327939 original size:6 final size:6
Alignment explanation
Indices: 327851--327939 Score: 61
Period size: 6 Copynumber: 14.3 Consensus size: 6
327841 GTTTGGATCA
* * * * * *
327851 TCATCT TCATCA TCATCA TCATCGT CATCATCT TCATCG CCAGCT TCATCG
1 TCATCT TCATCT TCATCT TCATC-T --TCATCT TCATCT TCATCT TCATCT
* * * *
327902 TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
327940 TGCGACCGCT
Statistics
Matches: 64, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
6 58 0.91
8 1 0.02
9 5 0.08
ACGTcount: A:0.20, C:0.35, G:0.08, T:0.37
Consensus pattern (6 bp):
TCATCT
Found at i:329761 original size:195 final size:197
Alignment explanation
Indices: 329393--330904 Score: 2782
Period size: 194 Copynumber: 7.8 Consensus size: 197
329383 TTTAAATTAG
329393 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG--T-
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
329455 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
329520 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCA-CCTGTTTTCCATTCATTCTGGAAAA
329585 AAA
195 AAA
329588 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATA-T-TCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
329651 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
329716 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTG-TTTCCATTCATTCTGG-AAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTGTTTTCCATTCATTCTGGAAAAA
329779 AA
196 AA
329781 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
329846 ATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
329910 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTGTTTTCCATTCATTCTGG-AAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTGTTTTCCATTCATTCTGGAAAAA
329974 AA
196 AA
329976 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATA---TCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
330038 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
330103 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTGTTTTCCATTCATTCTGGAAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTGTTTTCCATTCATTCTGGAAAAA
330168 AA
196 AA
330170 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
330235 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
330300 CGACAC--TTT-TATATGGATCGACACTTTATGGGTGCACCTGTTTTCCATTCATTCTGGAAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTGTTTTCCATTCATTCTGGAAAAA
330362 AA
196 AA
330364 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
330429 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
330494 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTGTTTTCCATTCATTCTGGAAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTGTTTTCCATTCATTCTGGAAAAA
330559 AA
196 AA
330561 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATA-T-TCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
330624 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
330688 CGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCTGTTTTCCATTCATTCTGG-AAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTGTTTTCCATTCATTCTGGAAAAA
330751 AA
196 AA
330753 -ATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATA-T-TCTCATAAAA-CGGTAT-
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
330813 A-T-TACCGGTTAGATTGAAAAATT--ATATTACATTATACTTTT-GGTTCGATG-TTTT-GGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
330871 TGACACTTTTTATATATGGATCGACACTTTATGG
131 CGACACTTTTTATATATGGATCGACACTTTATGG
330905 TATTTGCCTT
Statistics
Matches: 1300, Mismatches: 1, Indels: 43
0.97 0.00 0.03
Matches are distributed among these distances:
183 9 0.01
184 31 0.02
185 23 0.02
186 3 0.00
187 21 0.02
188 1 0.00
189 1 0.00
190 6 0.00
191 54 0.04
192 42 0.03
193 223 0.17
194 377 0.29
195 213 0.16
196 108 0.08
197 188 0.14
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (197 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTGTTTTCCATTCATTCTGGAAAAA
AA
Found at i:331056 original size:19 final size:19
Alignment explanation
Indices: 331010--331058 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
331000 TTATATTCAC
*
331010 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
331029 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
331048 ATACAAAATTA
1 ATACAAAATTA
331059 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:332873 original size:33 final size:33
Alignment explanation
Indices: 332836--332901 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
332826 CATCTTAATA
*
332836 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
332869 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
332902 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:332975 original size:21 final size:21
Alignment explanation
Indices: 332935--332999 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
332925 CCCCTTATGC
* *
332935 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
332956 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
332977 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
332998 CT
1 CT
333000 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Done.