Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 187 of 193
Found at i:58296234 original size:21 final size:21
Alignment explanation
Indices: 58296193--58296240 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
58296183 GTTGAGCTAC
58296193 GAGTTGGACTCACTACACTTG
1 GAGTTGGACTCACTACACTTG
* * * *
58296214 GTGTTGGACTGACTCCTCTTG
1 GAGTTGGACTCACTACACTTG
58296235 GAGTTG
1 GAGTTG
58296241 AGCTAACTGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.17, C:0.21, G:0.29, T:0.33
Consensus pattern (21 bp):
GAGTTGGACTCACTACACTTG
Found at i:58296394 original size:255 final size:257
Alignment explanation
Indices: 58295934--58296423 Score: 822
Period size: 255 Copynumber: 1.9 Consensus size: 257
58295924 TGTCCTCATC
*
58295934 CGAGTTGGACTCACTACCCTTGGAGTTGGACTGACTCCTCTTGGAGTTGAGCTAACCGAAGTTGA
1 CGAGTTGGACTCACTACACTTGGAGTTGGACTGACTCCTCTTGGAGTTGAGCTAACCGAAGTTGA
* * * * * *
58295999 GCTATGGGCTTGACTCAATGTGGTGGATGTCCTCATTCTAGTTGGACTGATTTCCCTTGGAGTAG
66 GCTATAGGATTGACTCAATGAGGTGGA-GTCCTCATTCGAGGTGGACTGATTACCCTTGGAGTAG
*
58296064 GACTGACCCCCGTTAAAGTTGAACTAAGAACTGGAGCTGAGCTATGGGATTGACTTGATAAGGTG
130 GACTGACCCCCGTTAAAGATGAACTAAGAACTGGAGCTGAGCTATGGGATTGACTTGATAAGGTG
* *
58296129 GATGCCCTCATCCGAGTTGGACTGACTCCTCTTGGAGTTGAACTTATACCTGAAGTTGAGCTA
195 GATACCCTCATCCGAGTTGGACTGACTACTCTTGGAGTTGAACTTATACCTGAAGTTGAGCTA
* *
58296192 CGAGTTGGACTCACTACACTTGGTGTTGGACTGACTCCTCTTGGAGTTGAGCTAACTGAAGTTGA
1 CGAGTTGGACTCACTACACTTGGAGTTGGACTGACTCCTCTTGGAGTTGAGCTAACCGAAGTTGA
58296257 GCTATAGGATTGACTCAATGAGGT-G-GTCCTCATTCGAGGTGGACTGATTACCCTTGGAGTAGG
66 GCTATAGGATTGACTCAATGAGGTGGAGTCCTCATTCGAGGTGGACTGATTACCCTTGGAGTAGG
* *
58296320 ACTGACCCCTGTTAAAGATGAACTAAGAACTGGATCTGAGCTATGGGATTGACTTGATAAGGTGG
131 ACTGACCCCCGTTAAAGATGAACTAAGAACTGGAGCTGAGCTATGGGATTGACTTGATAAGGTGG
*
58296385 ATACCCTCATCCGAGTTGGACTGACTACTGTTGGAGTTG
196 ATACCCTCATCCGAGTTGGACTGACTACTCTTGGAGTTG
58296424 GACTGACTCC
Statistics
Matches: 217, Mismatches: 15, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
255 133 0.61
257 1 0.00
258 83 0.38
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (257 bp):
CGAGTTGGACTCACTACACTTGGAGTTGGACTGACTCCTCTTGGAGTTGAGCTAACCGAAGTTGA
GCTATAGGATTGACTCAATGAGGTGGAGTCCTCATTCGAGGTGGACTGATTACCCTTGGAGTAGG
ACTGACCCCCGTTAAAGATGAACTAAGAACTGGAGCTGAGCTATGGGATTGACTTGATAAGGTGG
ATACCCTCATCCGAGTTGGACTGACTACTCTTGGAGTTGAACTTATACCTGAAGTTGAGCTA
Found at i:58296421 original size:21 final size:21
Alignment explanation
Indices: 58296397--58296444 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
58296387 ACCCTCATCC
*
58296397 GAGTTGGACTGACTACTGTTG
1 GAGTTGGACTGACTACTCTTG
*
58296418 GAGTTGGACTGACTCCTCTTG
1 GAGTTGGACTGACTACTCTTG
58296439 GAGTTG
1 GAGTTG
58296445 AACTTATAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.17, C:0.17, G:0.33, T:0.33
Consensus pattern (21 bp):
GAGTTGGACTGACTACTCTTG
Found at i:58296429 original size:105 final size:104
Alignment explanation
Indices: 58296192--58296648 Score: 435
Period size: 105 Copynumber: 4.4 Consensus size: 104
58296182 AGTTGAGCTA
* * * * *
58296192 CGAGTTGGACTCACTACACTTGGTGTTGGACTGACTCCTCTTGGAGTTGAGCT---AACTGAAGT
1 CGAGTTGGACTGACTACCCTTGGAGTTGGACTGACTCCTCTTGAAGTTGAACTAAGAACTGAA-T
* * * *
58296254 -TGAGCTATAGGATTGACTCAATGAGGT-G-GTCCTCATT
65 CTGAGCTATGGGATTGACTCGATAAGGTGGTGTCCTCATC
* * * * * * * *
58296291 CGAGGTGGACTGATTACCCTTGGAGTAGGACTGACCCCTGTTAAAGATGAACTAAGAACTGGATC
1 CGAGTTGGACTGACTACCCTTGGAGTTGGACTGACTCCTCTTGAAGTTGAACTAAGAACTGAATC
* **
58296356 TGAGCTATGGGATTGACTTGATAAGGTGGATACCCTCATC
66 TGAGCTATGGGATTGACTCGATAAGGTGG-TGTCCTCATC
** * * *
58296396 CGAGTTGGACTGACTACTGTTGGAGTTGGACTGACTCCTCTTGGAGTTGAACTTATAACTGAAGT
1 CGAGTTGGACTGACTACCCTTGGAGTTGGACTGACTCCTCTTGAAGTTGAACTAAGAACTGAA-T
* * * *
58296461 -TGAGCTATGGGATTGACTCGATAAGCTCGATGTTCTCATA
65 CTGAGCTATGGGATTGACTCGATAAGGT-GGTGTCCTCATC
* * * *
58296501 TGAGTTGGACTCACTACCCTTGGAGTTGGACTGACTCCTCTTGAAGTTGAACTGAGAACTGAAGC
1 CGAGTTGGACTGACTACCCTTGGAGTTGGACTGACTCCTCTTGAAGTTGAACTAAGAACTGAATC
* * * *
58296566 TGACCTTTGGGATTGACTTGAT-GGGATCGGTGTCCTCATC
66 TGAGCTATGGGATTGACTCGATAAGG-T-GGTGTCCTCATC
* * * *
58296606 CGAGTTGGACTGACTTCCCTTGGAGGTAGACTAACTCCTCTTG
1 CGAGTTGGACTGACTACCCTTGGAGTTGGACTGACTCCTCTTG
58296649 GAGGTGGACT
Statistics
Matches: 285, Mismatches: 62, Indels: 16
0.79 0.17 0.04
Matches are distributed among these distances:
99 41 0.14
101 1 0.00
102 29 0.10
103 1 0.00
104 1 0.00
105 210 0.74
106 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (104 bp):
CGAGTTGGACTGACTACCCTTGGAGTTGGACTGACTCCTCTTGAAGTTGAACTAAGAACTGAATC
TGAGCTATGGGATTGACTCGATAAGGTGGTGTCCTCATC
Found at i:58296528 original size:21 final size:21
Alignment explanation
Indices: 58296502--58296549 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
58296492 GTTCTCATAT
58296502 GAGTTGGACTCACTACC-CTTG
1 GAGTTGGACTCACT-CCTCTTG
*
58296523 GAGTTGGACTGACTCCTCTTG
1 GAGTTGGACTCACTCCTCTTG
*
58296544 AAGTTG
1 GAGTTG
58296550 AACTGAGAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.19, C:0.23, G:0.27, T:0.31
Consensus pattern (21 bp):
GAGTTGGACTCACTCCTCTTG
Found at i:58296582 original size:210 final size:204
Alignment explanation
Indices: 58296192--58296651 Score: 539
Period size: 210 Copynumber: 2.2 Consensus size: 204
58296182 AGTTGAGCTA
* * *
58296192 CGAGTTGGACTCACTACACTTGGTGTTGGACTGACTCCTCTTGGAGTTGAGCTAACTGAAGTTGA
1 CGAGTTGGACTGACTACACTTGGAGTTGGACTGACTCCTCTTGGAGTTGAACTAACTGAAGTTGA
* * * *
58296257 GCTATAGGATTGACTCAATGAGGTGGTCCTCATTCGAGGTGGACTGATTACCCTTGGAGTAGGAC
66 GCTATAGGATTGACTCAATAAGCTGGTCCTCATTCGAGGTGGACTCACTACCCTTGGAGTAGGAC
* * * *
58296322 TGACCCCTGTTAAAGATGAACTAAGAACTGGATCTGAGCTATGGGATTGACTTGATAAGG-T-GG
131 TGACCCCTCTTAAAGATGAACTAAGAACTGAAGCTGACCTATGGGATTGACTTGAT-AGGATCGG
58296385 ATACCCTCATC
195 -TACCCTCATC
**
58296396 CGAGTTGGACTGACTACTGTTGGAGTTGGACTGACTCCTCTTGGAGTTGAACTTATAACTGAAGT
1 CGAGTTGGACTGACTACACTTGGAGTTGGACTGACTCCTCTTGGAGTTGAAC---TAACTGAAGT
* * * *
58296461 TGAGCTATGGGATTGACTCGATAAGCTCGATGTTCTCATAT-GAGTTGGACTCACTACCCTTGGA
63 TGAGCTATAGGATTGACTCAATAAGCT-G--GTCCTCAT-TCGAGGTGGACTCACTACCCTTGGA
* * * * * * *
58296525 GTTGGACTGACTCCTCTTGAAGTTGAACTGAGAACTGAAGCTGACCTTTGGGATTGACTTGATGG
124 GTAGGACTGACCCCTCTTAAAGATGAACTAAGAACTGAAGCTGACCTATGGGATTGACTTGATAG
**
58296590 GATCGGTGTCCTCATC
189 GATCGGTACCCTCATC
* * * * *
58296606 CGAGTTGGACTGACTTCCCTTGGAGGTAGACTAACTCCTCTTGGAG
1 CGAGTTGGACTGACTACACTTGGAGTTGGACTGACTCCTCTTGGAG
58296652 GTGGACTGGA
Statistics
Matches: 215, Mismatches: 32, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
204 47 0.22
207 33 0.15
208 1 0.00
209 2 0.01
210 129 0.60
211 3 0.01
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (204 bp):
CGAGTTGGACTGACTACACTTGGAGTTGGACTGACTCCTCTTGGAGTTGAACTAACTGAAGTTGA
GCTATAGGATTGACTCAATAAGCTGGTCCTCATTCGAGGTGGACTCACTACCCTTGGAGTAGGAC
TGACCCCTCTTAAAGATGAACTAAGAACTGAAGCTGACCTATGGGATTGACTTGATAGGATCGGT
ACCCTCATC
Found at i:58297540 original size:282 final size:282
Alignment explanation
Indices: 58297030--58297593 Score: 1092
Period size: 282 Copynumber: 2.0 Consensus size: 282
58297020 AATTTCCCAC
58297030 CAATTCTACTTGGCCATCGATGATGATCTATCAATCGGCTAGGCAAATCATCAACAGGTTTTGCA
1 CAATTCTACTTGGCCATCGATGATGATCTATCAATCGGCTAGGCAAATCATCAACAGGTTTTGCA
58297095 TTTTCAGACTGATCATGTGCATTTTTCCCTTCAAGTAGATTTCTCTTTCTCTCTGGACTAGGCTT
66 TTTTCAGACTGATCATGTGCATTTTTCCCTTCAAGTAGATTTCTCTTTCTCTCTGGACTAGGCTT
*
58297160 TCGTGATAAGGTAGAGGTCTCTGATTGTTGTTTATGAACCACATTTGAAGGTGGTGTCAATGTGG
131 TCGTGATAAGGTAGAGGTCTCTGATTGTTGTTTATGAACCACATTTGAAGGTGGTGTCAATGTGC
58297225 GATCCAAGGAAACATTACTAACAGACTTTTCTTTTTCCTTTTTGCTAACAGGAATAGAAATATCA
196 GATCCAAGGAAACATTACTAACAGACTTTTCTTTTTCCTTTTTGCTAACAGGAATAGAAATATCA
58297290 TCAGACTGAAATGAAACACTAT
261 TCAGACTGAAATGAAACACTAT
*
58297312 CAATTTTACTTGGCCATCGATGATGATCTATCAATCGGCTAGGCAAATCATCAACAGGTTTTGCA
1 CAATTCTACTTGGCCATCGATGATGATCTATCAATCGGCTAGGCAAATCATCAACAGGTTTTGCA
58297377 TTTTCAGACTGATCATGTGCATTTTTCCCTTCAAGTAGATTTCTCTTTCTCTCTGGACTAGGCTT
66 TTTTCAGACTGATCATGTGCATTTTTCCCTTCAAGTAGATTTCTCTTTCTCTCTGGACTAGGCTT
* *
58297442 TTGTGATAAGGTAGAGGTCTCTGATTGTTGTTTATGAGCCACATTTGAAGGTGGTGTCAATGTGC
131 TCGTGATAAGGTAGAGGTCTCTGATTGTTGTTTATGAACCACATTTGAAGGTGGTGTCAATGTGC
58297507 GATCCAAGGAAACATTACTAACAGACTTTTCTTTTTCCTTTTTGCTAACAGGAATAGAAATATCA
196 GATCCAAGGAAACATTACTAACAGACTTTTCTTTTTCCTTTTTGCTAACAGGAATAGAAATATCA
58297572 TCAGACTGAAATGAAACACTAT
261 TCAGACTGAAATGAAACACTAT
58297594 GACTTCTCAT
Statistics
Matches: 278, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
282 278 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (282 bp):
CAATTCTACTTGGCCATCGATGATGATCTATCAATCGGCTAGGCAAATCATCAACAGGTTTTGCA
TTTTCAGACTGATCATGTGCATTTTTCCCTTCAAGTAGATTTCTCTTTCTCTCTGGACTAGGCTT
TCGTGATAAGGTAGAGGTCTCTGATTGTTGTTTATGAACCACATTTGAAGGTGGTGTCAATGTGC
GATCCAAGGAAACATTACTAACAGACTTTTCTTTTTCCTTTTTGCTAACAGGAATAGAAATATCA
TCAGACTGAAATGAAACACTAT
Found at i:58301717 original size:56 final size:55
Alignment explanation
Indices: 58301555--58301720 Score: 172
Period size: 55 Copynumber: 2.9 Consensus size: 55
58301545 AAAACGAATA
* * * *
58301555 AAAAAATATTTTATTGGGTGTTTGCCACTCAATGGGCTACACCACTTTTCTCAAATTT
1 AAAAAATATTTT-TTTGATGTTTGTCAC-CAATGGCCTACACCACTTTT-TCAAATTT
* * * *
58301613 AAAAAAATATATTTTTAATATTTGTCACCCATGGCCTACACCATCTTTTTCAAATTT
1 -AAAAAATATTTTTTTGATGTTTGTCACCAATGGCCTACACCA-CTTTTTCAAATTT
**
58301670 -AAAAATATTTTTTTGATGTTTGTCATCCAATGATCTACACCACCTTTTTCA
1 AAAAAATATTTTTTTGATGTTTGTCA-CCAATGGCCTACACCA-CTTTTTCA
58301721 TATATATATA
Statistics
Matches: 90, Mismatches: 15, Indels: 7
0.80 0.13 0.06
Matches are distributed among these distances:
55 22 0.24
56 21 0.23
57 21 0.23
58 15 0.17
59 11 0.12
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.40
Consensus pattern (55 bp):
AAAAAATATTTTTTTGATGTTTGTCACCAATGGCCTACACCACTTTTTCAAATTT
Found at i:58301808 original size:20 final size:20
Alignment explanation
Indices: 58301771--58301849 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 20
58301761 CTGCATCTCC
*
58301771 AAAATAAA-AAAAATAATTA
1 AAAATAAATTAAAATAATTA
*
58301790 AAACATAATTTAAAA-AATTA
1 AAA-ATAAATTAAAATAATTA
* *
58301810 TAATTAAATTAAAATAATTA
1 AAAATAAATTAAAATAATTA
* *
58301830 AAAAAACAATTTAAATAATT
1 AAAATA-AATTAAAATAATT
58301850 TTTAAATTAA
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
19 12 0.26
20 19 0.40
21 16 0.34
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAATAAATTAAAATAATTA
Found at i:58301816 original size:14 final size:12
Alignment explanation
Indices: 58301777--58301840 Score: 58
Period size: 14 Copynumber: 5.0 Consensus size: 12
58301767 CTCCAAAATA
58301777 AAAAAAATAATT
1 AAAAAAATAATT
*
58301789 -AAAACATAATTT
1 AAAAAAATAA-TT
58301801 AAAAAATTATAATT
1 AAAAAA--ATAATT
58301815 AAATTAAAATAATT
1 AAA--AAAATAATT
*
58301829 AAAAAAACAATT
1 AAAAAAATAATT
58301841 TAAATAATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
11 8 0.19
12 10 0.23
13 4 0.09
14 14 0.33
15 4 0.09
16 3 0.07
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (12 bp):
AAAAAAATAATT
Found at i:58301863 original size:38 final size:39
Alignment explanation
Indices: 58301780--58301863 Score: 109
Period size: 41 Copynumber: 2.2 Consensus size: 39
58301770 CAAAATAAAA
* *
58301780 AAAATAATTAAAACATAATTTAAAAAATTATAATTAAATT
1 AAAATAATTAAAAAACAATTTAAAAAATTAT-ATTAAATT
*
58301820 AAAATAATTAAAAAAACAATTTAAATAATT-T-TTAAATT
1 AAAATAATT-AAAAAACAATTTAAAAAATTATATTAAATT
58301858 AAAATA
1 AAAATA
58301864 TTACAATTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
38 13 0.32
40 10 0.25
41 17 0.43
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (39 bp):
AAAATAATTAAAAAACAATTTAAAAAATTATATTAAATT
Found at i:58302012 original size:49 final size:50
Alignment explanation
Indices: 58301951--58302047 Score: 133
Period size: 49 Copynumber: 2.0 Consensus size: 50
58301941 TCTGAAAAAG
* *** *
58301951 GTGATGTCGGTCATTAGGTGGTAAATAC-CAAAAAAATATTTTTAAATTT
1 GTGATGTAGGTCATTAGGTAACAAACACTCAAAAAAATATTTTTAAATTT
*
58302000 GTGATGTAGGTCATTGGGTAACAAACACTCAAAAAAATATTTTTAAAT
1 GTGATGTAGGTCATTAGGTAACAAACACTCAAAAAAATATTTTTAAAT
58302048 CTGGAAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
49 22 0.54
50 19 0.46
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (50 bp):
GTGATGTAGGTCATTAGGTAACAAACACTCAAAAAAATATTTTTAAATTT
Found at i:58302081 original size:57 final size:57
Alignment explanation
Indices: 58302002--58302275 Score: 247
Period size: 55 Copynumber: 4.7 Consensus size: 57
58301992 TTAAATTTGT
*
58302002 GATGTAGGTCATTGGGTAACAAACACTCAAAAAAATATTTTTAAATCTGGAAAAAATA
1 GATGTAGGTCATTGGGTGACAAACAC-CAAAAAAATATTTTTAAATCTGGAAAAAATA
* * * *
58302060 G-TGTTGGTCATTGGATGACAAACACTTAAAAAAATATTTTTAAAT-TTGAAAAATATGA
1 GATGTAGGTCATTGGGTGACAAACAC-CAAAAAAATATTTTTAAATCTGGAAAAA-AT-A
* * * * * *
58302118 TGAAAAATATTAGGCCATTGAGTAACAAACACC-AAAAAATATTTTTAAATTTGGAAAATAT-
1 -G----AT-GTAGGTCATTGGGTGACAAACACCAAAAAAATATTTTTAAATCTGGAAAAAATA
* * *
58302179 GGTGTAGGCCGTTGGGTGACAAACACC-AAAAAATATTTTTAAATCT-GAAAAAAGT-
1 GATGTAGGTCATTGGGTGACAAACACCAAAAAAATATTTTTAAATCTGGAAAAAA-TA
* *
58302234 GATGTAGGTCATTGGGTGGCAAACACCCAACAAAATATTTTT
1 GATGTAGGTCATTGGGTGACAAACA-CCAAAAAAATATTTTT
58302276 TATTCGTATT
Statistics
Matches: 177, Mismatches: 26, Indels: 27
0.77 0.11 0.12
Matches are distributed among these distances:
54 6 0.03
55 60 0.34
56 10 0.06
57 54 0.31
58 2 0.01
59 1 0.01
60 1 0.01
63 19 0.11
64 7 0.04
65 17 0.10
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (57 bp):
GATGTAGGTCATTGGGTGACAAACACCAAAAAAATATTTTTAAATCTGGAAAAAATA
Found at i:58302199 original size:120 final size:120
Alignment explanation
Indices: 58302006--58302230 Score: 319
Period size: 120 Copynumber: 1.9 Consensus size: 120
58301996 ATTTGTGATG
* * * *
58302006 TAGGTCATTGGGTAACAAACACTCAAAAAAATATTTTTAAATCTGGAAAAAATAGTGTTGGTCAT
1 TAGGCCATTGAGTAACAAACACTCAAAAAAATATTTTTAAATCTGGAAAAAATAGTGTAGGCCAT
*
58302071 TGGATGACAAACACTTAAAAAAATATTTTTAAATTTGAAAAATATGATGAAAAATAT
66 TGGATGACAAACAC--AAAAAAATATTTTTAAATCTGAAAAATATGATGAAAAATAT
* * * *
58302128 TAGGCCATTGAGTAACAAACAC-C-AAAAAATATTTTTAAATTTGGAAAATATGGTGTAGGCCGT
1 TAGGCCATTGAGTAACAAACACTCAAAAAAATATTTTTAAATCTGGAAAAAATAGTGTAGGCCAT
* *
58302191 TGGGTGACAAACACCAAAAAATATTTTTAAATCTGAAAAA
66 TGGATGACAAACACAAAAAAATATTTTTAAATCTGAAAAA
58302231 AGTGATGTAG
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
118 24 0.26
120 47 0.51
121 1 0.01
122 20 0.22
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.29
Consensus pattern (120 bp):
TAGGCCATTGAGTAACAAACACTCAAAAAAATATTTTTAAATCTGGAAAAAATAGTGTAGGCCAT
TGGATGACAAACACAAAAAAATATTTTTAAATCTGAAAAATATGATGAAAAATAT
Found at i:58304253 original size:8 final size:7
Alignment explanation
Indices: 58304229--58304268 Score: 53
Period size: 7 Copynumber: 5.3 Consensus size: 7
58304219 TTTTGGATTT
58304229 ATAAAAA
1 ATAAAAA
58304236 ATAAAAA
1 ATAAAAA
58304243 ATAAAACA
1 ATAAAA-A
58304251 ATAAAAA
1 ATAAAAA
58304258 TTATAAAAA
1 --ATAAAAA
58304267 AT
1 AT
58304269 CATTAATTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
7 16 0.53
8 7 0.23
9 7 0.23
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (7 bp):
ATAAAAA
Found at i:58304255 original size:15 final size:14
Alignment explanation
Indices: 58304229--58304268 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 14
58304219 TTTTGGATTT
58304229 ATAAAAAATAAAAA
1 ATAAAAAATAAAAA
58304243 ATAAAACAATAAAAA
1 ATAAAA-AATAAAAA
58304258 TTATAAAAAAT
1 --ATAAAAAAT
58304269 CATTAATTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 6 0.26
15 8 0.35
16 3 0.13
17 6 0.26
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (14 bp):
ATAAAAAATAAAAA
Found at i:58304311 original size:10 final size:9
Alignment explanation
Indices: 58304284--58304325 Score: 52
Period size: 8 Copynumber: 4.8 Consensus size: 9
58304274 ATTAGTACAA
*
58304284 AAAAATCAT
1 AAAAATTAT
58304293 -AAAATTAT
1 AAAAATTAT
58304301 AAAAATATAT
1 AAAAAT-TAT
58304311 AAAAATTA-
1 AAAAATTAT
58304319 AAAAATT
1 AAAAATT
58304326 TAATTAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
8 14 0.47
9 7 0.23
10 9 0.30
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (9 bp):
AAAAATTAT
Found at i:58304334 original size:19 final size:19
Alignment explanation
Indices: 58304292--58304348 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
58304282 AAAAAAATCA
58304292 TAAAATTATAAAAATATAT
1 TAAAATTATAAAAATATAT
* *
58304311 AAAAATTA-AAAAATTTAAT
1 TAAAATTATAAAAATAT-AT
*
58304330 TAAAATCATGAAAAATATA
1 TAAAATTAT-AAAAATATA
58304349 AATATATATA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
18 7 0.23
19 15 0.50
20 1 0.03
21 7 0.23
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (19 bp):
TAAAATTATAAAAATATAT
Found at i:58305252 original size:19 final size:19
Alignment explanation
Indices: 58305228--58305268 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
58305218 TAAAAGAAAT
*
58305228 TAATTTCTAATAATTTTTA
1 TAATTTCTAATAACTTTTA
*
58305247 TAATTTCTAATGACTTTTA
1 TAATTTCTAATAACTTTTA
58305266 TAA
1 TAA
58305269 ATTTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (19 bp):
TAATTTCTAATAACTTTTA
Found at i:58308120 original size:27 final size:26
Alignment explanation
Indices: 58308060--58308121 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
58308050 TACAAAAATA
* *
58308060 TTATTTTAATTTTAGAATATATATATT
1 TTATTTT-ATTTTAAAATATATATATG
*
58308087 TTGTTTT-TTTTAAAATATGATTATATG
1 TTATTTTATTTTAAAATAT-A-TATATG
58308114 TTATTTTA
1 TTATTTTA
58308122 CTAATCTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
25 10 0.36
26 1 0.04
27 17 0.61
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (26 bp):
TTATTTTATTTTAAAATATATATATG
Found at i:58308254 original size:44 final size:44
Alignment explanation
Indices: 58308198--58308282 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
58308188 TACTAAATGA
* * *
58308198 TTAACTAAATTACTTTGTATTTATTAAAAATTATTTATACTAAT
1 TTAACTAAATTACATAGTATTTATCAAAAATTATTTATACTAAT
* **
58308242 TTAATTAAATTACATAGTATTTATCATTAATTATTTATACT
1 TTAACTAAATTACATAGTATTTATCAAAAATTATTTATACT
58308283 TGATCAAGGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (44 bp):
TTAACTAAATTACATAGTATTTATCAAAAATTATTTATACTAAT
Found at i:58312729 original size:121 final size:128
Alignment explanation
Indices: 58312577--58312826 Score: 327
Period size: 126 Copynumber: 2.0 Consensus size: 128
58312567 AAAAAAGGAA
* * *
58312577 AAGCAACTGAGGGTTGGGAAGAGAGAAATAAACAGCCAACAAGTC-TCCAAAACTGTT-AAAAG-
1 AAGCAACTGAGGGTTGGGAAGAGAGAAATAAACAGCAAACAACTCTTCCAAAACTCTTAAAAAGA
* ** ** *
58312639 ACTGT-TTT-AGACATGCATT-TTGTTTCTTTATGTCTGTGGTTACATACCTGAGAATATCTTT
66 ACTGTGTTTCAGACATGC-TTCATGCATCTCAATGTCTGTGGTTACATACCTGAGAATATATTT
*
58312700 AAGCAATTGA-GGTT-GGAAGAGAGAAATAAACAGCAAACAACTCTTCCAAAACTCTTAAAAAGA
1 AAGCAACTGAGGGTTGGGAAGAGAGAAATAAACAGCAAACAACTCTTCCAAAACTCTTAAAAAGA
* *
58312763 ACTGTGTTTCAGACATGCTTCATGCATCTCAATGTCTGTGTTTACATACGTGAGAATATATTT
66 ACTGTGTTTCAGACATGCTTCATGCATCTCAATGTCTGTGGTTACATACCTGAGAATATATTT
58312826 A
1 A
58312827 CATTTTTTTT
Statistics
Matches: 109, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
121 27 0.25
122 15 0.14
123 14 0.13
124 5 0.05
125 5 0.05
126 43 0.39
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.30
Consensus pattern (128 bp):
AAGCAACTGAGGGTTGGGAAGAGAGAAATAAACAGCAAACAACTCTTCCAAAACTCTTAAAAAGA
ACTGTGTTTCAGACATGCTTCATGCATCTCAATGTCTGTGGTTACATACCTGAGAATATATTT
Found at i:58315736 original size:14 final size:13
Alignment explanation
Indices: 58315714--58315762 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 13
58315704 TCAGAGGAAT
58315714 CAATTAATCTATA
1 CAATTAATCTATA
58315727 CAAGTTAATCTATA
1 CAA-TTAATCTATA
*
58315741 CCAATTACTCTATA
1 -CAATTAATCTATA
58315755 CAAATTAA
1 C-AATTAA
58315763 AATAATTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 4 0.13
14 24 0.77
15 3 0.10
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.35
Consensus pattern (13 bp):
CAATTAATCTATA
Found at i:58316744 original size:26 final size:25
Alignment explanation
Indices: 58316693--58316744 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
58316683 ACTATTTGAT
*
58316693 TGTAATTGATTTATCATGAAAGAATA
1 TGTAATTGA-TTATCATGAAAAAATA
58316719 TGTAATTG-TTATCATGAGATAAAATA
1 TGTAATTGATTATCATGA-A-AAAATA
58316745 AAATCATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 9 0.39
25 1 0.04
26 13 0.57
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.38
Consensus pattern (25 bp):
TGTAATTGATTATCATGAAAAAATA
Found at i:58317133 original size:15 final size:15
Alignment explanation
Indices: 58317113--58317160 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
58317103 TGATTTTTTG
58317113 AATTATTAATTAATT
1 AATTATTAATTAATT
*
58317128 AATTATTAATATAAAT
1 AATTATTAAT-TAATT
*
58317144 AGTTA-TAA-TAATT
1 AATTATTAATTAATT
58317157 AATT
1 AATT
58317161 TCGGTCAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 7 0.25
15 13 0.46
16 8 0.29
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
AATTATTAATTAATT
Found at i:58317964 original size:2 final size:2
Alignment explanation
Indices: 58317957--58317996 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
58317947 CAAGCCCAAT
58317957 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
58317997 AACCCTGTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58318758 original size:56 final size:56
Alignment explanation
Indices: 58318698--58318806 Score: 132
Period size: 56 Copynumber: 1.9 Consensus size: 56
58318688 TCATTACGGA
* * *
58318698 TACGAC-TCTTAAAGGTACAACTTTCATACTCTCC-TAAGGTTCCATTCCACTAAGAG
1 TACGACTTC-TAAAGGTACAACTCTCACACTCTCCAAAAGG-TCCATTCCACTAAGAG
* * *
58318754 TACGACTTCTAAGGGTATAGCTCTCACACTCTCCAAAAGGTCCATTCCACTAA
1 TACGACTTCTAAAGGTACAACTCTCACACTCTCCAAAAGGTCCATTCCACTAA
58318807 AAGTTCATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
56 39 0.87
57 6 0.13
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.28
Consensus pattern (56 bp):
TACGACTTCTAAAGGTACAACTCTCACACTCTCCAAAAGGTCCATTCCACTAAGAG
Found at i:58326212 original size:14 final size:14
Alignment explanation
Indices: 58326193--58326220 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
58326183 ATAGATGGTG
58326193 AAAGAAAAGAAAAA
1 AAAGAAAAGAAAAA
58326207 AAAGAAAAGAAAAA
1 AAAGAAAAGAAAAA
58326221 CTTTTTTTAA
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:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAGAAAAGAAAAA
Found at i:58327865 original size:11 final size:11
Alignment explanation
Indices: 58327849--58327873 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
58327839 GTGGCTCCAT
58327849 TCACCTCTAAG
1 TCACCTCTAAG
58327860 TCACCTCTAAG
1 TCACCTCTAAG
58327871 TCA
1 TCA
58327874 TTTAGCACAA
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:0.36, G:0.08, T:0.28
Consensus pattern (11 bp):
TCACCTCTAAG
Found at i:58332077 original size:23 final size:23
Alignment explanation
Indices: 58332051--58332106 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
58332041 TTTGGTTATG
*
58332051 GAGAAACAGTGCGAAAATGACAT
1 GAGAAACAGCGCGAAAATGACAT
58332074 GAGAAACAGCGCGAAAATGACAT
1 GAGAAACAGCGCGAAAATGACAT
58332097 GAGAAACAGC
1 GAGAAACAGC
58332107 ATTCACCTGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.48, C:0.16, G:0.27, T:0.09
Consensus pattern (23 bp):
GAGAAACAGCGCGAAAATGACAT
Found at i:58344650 original size:15 final size:17
Alignment explanation
Indices: 58344630--58344662 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
58344620 TAATTACATA
58344630 ATTAGTAT-A-AAAAAT
1 ATTAGTATGATAAAAAT
58344645 ATTAGTATGATAAAAAT
1 ATTAGTATGATAAAAAT
58344662 A
1 A
58344663 ATTTCTAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 1 0.06
17 7 0.44
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (17 bp):
ATTAGTATGATAAAAAT
Found at i:58347815 original size:6 final size:6
Alignment explanation
Indices: 58347804--58347830 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
58347794 TACCTGAGAA
58347804 GCATGG GCATGG GCATGG GCATGG GCA
1 GCATGG GCATGG GCATGG GCATGG GCA
58347831 GAGGCAGAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.48, T:0.15
Consensus pattern (6 bp):
GCATGG
Found at i:58355926 original size:19 final size:18
Alignment explanation
Indices: 58355892--58355931 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
58355882 TAGCTTTTTA
58355892 TTATATTTTATTATAATT
1 TTATATTTTATTATAATT
58355910 TTATGATTTT-TTAATAATT
1 TTAT-ATTTTATT-ATAATT
58355929 TTA
1 TTA
58355932 AAATTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
TTATATTTTATTATAATT
Found at i:58359210 original size:93 final size:93
Alignment explanation
Indices: 58359037--58359211 Score: 212
Period size: 93 Copynumber: 1.9 Consensus size: 93
58359027 AGCAGAACGC
* * * * * *
58359037 TGGCATCAAAGCATGTTATGCAGAACAAAGAAACAGTCCAACCTCCCAAAGATCCTGCAGGGTTT
1 TGGCAACAAAGCATGTTATGCAGAACAAAGAAAAAGTCCAACATCCCAAAAATCCTGCAGGATTG
* *
58359102 TTCAAGAACGGTGGAACCAGTAGAGTTG
66 GTCAAGAACAGTGGAACCAGTAGAGTTG
*
58359130 TGGCAACAAAGCATGTTATGCAGAA-ACAGGAAAAAG-CTCAACATCCCAAAAATCCT-CTAGGA
1 TGGCAACAAAGCATGTTATGCAGAACA-AAGAAAAAGTC-CAACATCCCAAAAATCCTGC-AGGA
*
58359192 TTGGTCAAGAACATTGGAAC
63 TTGGTCAAGAACAGTGGAAC
58359212 TAGTGTAACT
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
92 3 0.04
93 66 0.96
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (93 bp):
TGGCAACAAAGCATGTTATGCAGAACAAAGAAAAAGTCCAACATCCCAAAAATCCTGCAGGATTG
GTCAAGAACAGTGGAACCAGTAGAGTTG
Found at i:58370832 original size:30 final size:31
Alignment explanation
Indices: 58370796--58370858 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 31
58370786 AGTCTATATA
* *
58370796 TTTATAATTTTTAAAATATTAAATTA-AATT
1 TTTATAATTTTTAAAAGATTAAAATATAATT
*
58370826 TTTATAATTTTTTAAAGATTAAAATATAATT
1 TTTATAATTTTTAAAAGATTAAAATATAATT
58370857 TT
1 TT
58370859 ATCATTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 23 0.79
31 6 0.21
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (31 bp):
TTTATAATTTTTAAAAGATTAAAATATAATT
Found at i:58371069 original size:16 final size:16
Alignment explanation
Indices: 58371025--58371080 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
58371015 TACAAAGAAA
*
58371025 AATTGATAAAATTT-T
1 AATTTATAAAATTTAT
*
58371040 AATTT-TAATTATTTAT
1 AATTTATAA-AATTTAT
*
58371056 AATTTATAAAATTTAA
1 AATTTATAAAATTTAT
*
58371072 AATTAATAA
1 AATTTATAA
58371081 TAAAAATATA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
14 3 0.09
15 8 0.24
16 19 0.58
17 3 0.09
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
AATTTATAAAATTTAT
Found at i:58375136 original size:51 final size:51
Alignment explanation
Indices: 58375056--58375195 Score: 160
Period size: 51 Copynumber: 2.7 Consensus size: 51
58375046 TGTGTAAATG
* * *
58375056 TTGATAGAATGTGTAAATGTT-TCAAGCTAAATTTGTTAAATCAGGATCAAA
1 TTGATAGAATGTGTAAATGTTAT-AGGCTAAATTTGTTAAATCAAGACCAAA
* *
58375107 TTGATAAAATGTGTAAATGTTATTGGCTAAATTTGTTAAATCAAGACCAAA
1 TTGATAGAATGTGTAAATGTTATAGGCTAAATTTGTTAAATCAAGACCAAA
* * *
58375158 TTGACAGAATATGTAAACT-TTGA-GGGCTAAATTTGTTA
1 TTGATAGAATGTGTAAA-TGTT-ATAGGCTAAATTTGTTA
58375196 TTATATCAAT
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
51 74 0.96
52 3 0.04
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.36
Consensus pattern (51 bp):
TTGATAGAATGTGTAAATGTTATAGGCTAAATTTGTTAAATCAAGACCAAA
Found at i:58377449 original size:31 final size:31
Alignment explanation
Indices: 58377413--58377473 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
58377403 AAAGGAATTG
58377413 TTTGCTTTAGCTCCCACTGTTTTTAACTTTA
1 TTTGCTTTAGCTCCCACTGTTTTTAACTTTA
*
58377444 TTTGCTTTAGCTCCCATTGTTTTTAACTTT
1 TTTGCTTTAGCTCCCACTGTTTTTAACTTT
58377474 GAGATAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.15, C:0.21, G:0.10, T:0.54
Consensus pattern (31 bp):
TTTGCTTTAGCTCCCACTGTTTTTAACTTTA
Found at i:58390672 original size:84 final size:82
Alignment explanation
Indices: 58390581--58390736 Score: 206
Period size: 84 Copynumber: 1.9 Consensus size: 82
58390571 TTTTAAAATG
* * * * *** *
58390581 CATCAAAAAGGTCTTCAAACTTTTTT-AAAAAAAGTAATTAAGTTTTTGCTTTTATTTTGCACTC
1 CATCAAAAAAGCCCTCAAA-TTTTTTCAAAAAAAGCAATTAAGCCCTTGATTTT-TTTT-CACTC
58390645 AATTGGGTACTTTCAAAACT
63 AATTGGGTACTTTCAAAACT
58390665 CATCAAAAAAGCCCTCAAATTTTTTCAAAAAAAGCAATTAAGCCCTTGATTTTTTTTCACTCAAT
1 CATCAAAAAAGCCCTCAAATTTTTTCAAAAAAAGCAATTAAGCCCTTGATTTTTTTTCACTCAAT
58390730 TGGGTAC
66 TGGGTAC
58390737 ATGAACCGCC
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
82 15 0.24
83 10 0.16
84 38 0.60
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.37
Consensus pattern (82 bp):
CATCAAAAAAGCCCTCAAATTTTTTCAAAAAAAGCAATTAAGCCCTTGATTTTTTTTCACTCAAT
TGGGTACTTTCAAAACT
Found at i:58390865 original size:29 final size:28
Alignment explanation
Indices: 58390833--58390940 Score: 85
Period size: 29 Copynumber: 3.7 Consensus size: 28
58390823 AAAAACTATT
58390833 AAATTATTAAATTTTACTAAAAATATAGA
1 AAATTATTAAATTTTA-TAAAAATATAGA
* *
58390862 AAA-TATTAAAATTTTATTAAAAATAGAAA
1 AAATTATT-AAATTTTA-TAAAAATATAGA
* * *
58390891 AAACTTA-TAAAATATATAGAAATATAGAAA
1 AAA-TTATTAAATTTTATAAAAATATAG--A
* *
58390921 AAAATATAAAATTTTATAAA
1 AAATTATTAAATTTTATAAA
58390941 GTTGTAAGAA
Statistics
Matches: 60, Mismatches: 13, Indels: 11
0.71 0.15 0.13
Matches are distributed among these distances:
28 12 0.20
29 32 0.53
30 14 0.23
31 2 0.03
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (28 bp):
AAATTATTAAATTTTATAAAAATATAGA
Found at i:58391209 original size:9 final size:9
Alignment explanation
Indices: 58391197--58391280 Score: 66
Period size: 10 Copynumber: 9.0 Consensus size: 9
58391187 TTTTATGCAC
58391197 TTTATAATT
1 TTTATAATT
58391206 TTTAATAATTTT
1 TTT-ATAA--TT
58391218 TTTATAATTT
1 TTTATAA-TT
**
58391228 TTTATTAAAA
1 TTTA-TAATT
58391238 TTTA-AATT
1 TTTATAATT
58391246 TTTATAATT
1 TTTATAATT
*
58391255 TTTATTGATT
1 TTTA-TAATT
58391265 TTTAT--TT
1 TTTATAATT
58391272 TTTATAATT
1 TTTATAATT
58391281 CTTTTGTCAC
Statistics
Matches: 62, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
7 7 0.11
8 6 0.10
9 14 0.23
10 23 0.37
11 7 0.11
12 5 0.08
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (9 bp):
TTTATAATT
Found at i:58391224 original size:11 final size:11
Alignment explanation
Indices: 58391197--58391230 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
58391187 TTTTATGCAC
58391197 TTTATAA-TTT
1 TTTATAATTTT
*
58391207 TTAATAATTTT
1 TTTATAATTTT
58391218 TTTATAATTTT
1 TTTATAATTTT
58391229 TT
1 TT
58391231 ATTAAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 6 0.29
11 15 0.71
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTATAATTTT
Found at i:58391646 original size:89 final size:89
Alignment explanation
Indices: 58391486--58391653 Score: 198
Period size: 89 Copynumber: 1.9 Consensus size: 89
58391476 GAGCTTTTTT
* * * * * * **
58391486 TTTTTTTATGCATTTTGAAAGTTCAAGTATCCAATTGAGTGCAAAATAAAAGTAGAGGCTTAATT
1 TTTTTTGATACATTTTAAAAGTTCAAGTATCCAAATGAGTGAAAAAAAAAACAAGAGGCTTAATT
*
58391551 GCTTTTTTGAAAAAGTTTGAGTGC
66 GCTTTTTTAAAAAAGTTTGAGTGC
58391575 TTTTTTGATACATTTTAAAAGTTCAAGTA-CTCAAATGAGTGAAAAAAAAAAAACAAGA-GCTTA
1 TTTTTTGATACATTTTAAAAGTTCAAGTATC-CAAATGAGTG--AAAAAAAAAACAAGAGGCTTA
*
58391638 ATT-TTTTTTTAAAAAA
63 ATTGCTTTTTTAAAAAA
58391654 AAATTGAGGG
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
88 1 0.02
89 46 0.70
90 8 0.12
91 11 0.17
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (89 bp):
TTTTTTGATACATTTTAAAAGTTCAAGTATCCAAATGAGTGAAAAAAAAAACAAGAGGCTTAATT
GCTTTTTTAAAAAAGTTTGAGTGC
Found at i:58395947 original size:16 final size:16
Alignment explanation
Indices: 58395913--58395953 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
58395903 ATTACAGTTT
* *
58395913 TATTTCATTACATCTC
1 TATTTCATTACAACCC
58395929 TATTTCATTACAACCC
1 TATTTCATTACAACCC
*
58395945 TATTCCATT
1 TATTTCATT
58395954 TACCTCAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.46
Consensus pattern (16 bp):
TATTTCATTACAACCC
Found at i:58396100 original size:16 final size:15
Alignment explanation
Indices: 58396076--58396126 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
58396066 TCAAACTTTT
*
58396076 AAAACCTCGAACTCA
1 AAAAACTCGAACTCA
*
58396091 AAAAGACTCGAACTTA
1 AAAA-ACTCGAACTCA
* *
58396107 AAAAACTTGAACCCA
1 AAAAACTCGAACTCA
58396122 AAAAA
1 AAAAA
58396127 ACCCAAACCT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
15 17 0.57
16 13 0.43
ACGTcount: A:0.55, C:0.24, G:0.08, T:0.14
Consensus pattern (15 bp):
AAAAACTCGAACTCA
Found at i:58396112 original size:32 final size:30
Alignment explanation
Indices: 58396059--58396126 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
58396049 ATCAAAAATT
* * *
58396059 AAAAAACTCAAACTTTTAAAACCTCGAACTC
1 AAAAAACTCAAAC-TTAAAAAACTCGAACCC
* *
58396090 AAAAAGACTCGAACTTAAAAAACTTGAACCC
1 AAAAA-ACTCAAACTTAAAAAACTCGAACCC
58396121 AAAAAA
1 AAAAAA
58396127 ACCCAAACCT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
30 1 0.03
31 23 0.74
32 7 0.23
ACGTcount: A:0.54, C:0.22, G:0.06, T:0.18
Consensus pattern (30 bp):
AAAAAACTCAAACTTAAAAAACTCGAACCC
Found at i:58397239 original size:21 final size:19
Alignment explanation
Indices: 58397213--58397254 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
58397203 TATTTTAGAA
58397213 TTTAAAGTAATATATTATATT
1 TTTAAA-TAAT-TATTATATT
*
58397234 TTTAAATTATTATTATATT
1 TTTAAATAATTATTATATT
58397253 TT
1 TT
58397255 AGTATTTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 11 0.55
20 3 0.15
21 6 0.30
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTAAATAATTATTATATT
Found at i:58397457 original size:30 final size:31
Alignment explanation
Indices: 58397421--58397492 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
58397411 TATAGTGAAT
* *
58397421 AAATACGAAAAATTTGAA-CCAAAAA-ATCTC
1 AAATACGAAAAACTTAAACCCAAAAAGA-CTC
58397451 AAATACGAAAAACTTAAACCCAAAAAGACTC
1 AAATACGAAAAACTTAAACCCAAAAAGACTC
*
58397482 AAATTCGAAAA
1 AAATACGAAAA
58397493 GATAATTATA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 16 0.43
31 20 0.54
32 1 0.03
ACGTcount: A:0.58, C:0.18, G:0.07, T:0.17
Consensus pattern (31 bp):
AAATACGAAAAACTTAAACCCAAAAAGACTC
Found at i:58398004 original size:21 final size:23
Alignment explanation
Indices: 58397947--58398006 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 23
58397937 TTAAATGTCG
58397947 AAATTAAATTATAATTATTACAAT
1 AAATTAAATTATAATT-TTACAAT
58397971 AAA--AAA-TATAATTTTA-AA-
1 AAATTAAATTATAATTTTACAAT
*
58397989 AAATTAAATTAAAATTTT
1 AAATTAAATTATAATTTT
58398007 TATTATTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
18 3 0.09
19 2 0.06
20 6 0.19
21 15 0.47
22 3 0.09
24 3 0.09
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATTAAATTATAATTTTACAAT
Found at i:58398017 original size:31 final size:33
Alignment explanation
Indices: 58397982--58398046 Score: 91
Period size: 32 Copynumber: 2.0 Consensus size: 33
58397972 AAAAATATAA
*
58397982 TTTT-AAAAAATTAAATTA-AAATTT-TTATTAT
1 TTTTAAAAAAATTAAAGTATAAATTTATT-TTAT
58398013 TTTTAAAAAAATTAAAGTATAAATTTATTTTAT
1 TTTTAAAAAAATTAAAGTATAAATTTATTTTAT
58398046 T
1 T
58398047 AAATTAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 4 0.13
32 13 0.43
33 11 0.37
34 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (33 bp):
TTTTAAAAAAATTAAAGTATAAATTTATTTTAT
Found at i:58398788 original size:21 final size:21
Alignment explanation
Indices: 58398762--58398806 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
58398752 TTAGGGTCCA
*
58398762 ATTGCCCT-GGAGGAGTAGAGT
1 ATTG-CCTGGGAGGAGTAAAGT
58398783 ATTGCCTGGGAGGAGTAAAGT
1 ATTGCCTGGGAGGAGTAAAGT
58398804 ATT
1 ATT
58398807 ACGGTGGCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.27, C:0.11, G:0.36, T:0.27
Consensus pattern (21 bp):
ATTGCCTGGGAGGAGTAAAGT
Found at i:58400837 original size:16 final size:16
Alignment explanation
Indices: 58400816--58400864 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
58400806 TGATTGGGGT
58400816 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
58400832 ATTATTTTTAT-ATT-
1 ATTATTTTGATAATTA
58400846 A-TATTTTGATAATTA
1 ATTATTTTGATAATTA
58400861 ATTA
1 ATTA
58400865 GCTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 8 0.29
14 4 0.14
15 4 0.14
16 12 0.43
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:58401229 original size:94 final size:94
Alignment explanation
Indices: 58401055--58401405 Score: 534
Period size: 93 Copynumber: 3.8 Consensus size: 94
58401045 ATTATATTAT
* *
58401055 TTTTAAATCAATAAATATGAACAATGTTTTTTACTTACTACTATTACTAACAAC-AAATAAAATT
1 TTTTAAATCAATAAATATAAACAATGTTTTTTACTTACTACTACTACTAACAACAAAATAAAATT
58401119 ACTAACTAAATTTTTTAAAAAATATTAAA
66 ACTAACTAAATTTTTTAAAAAATATTAAA
58401148 TTTTAAATCAATAAATATAAACAATGTTTTTTACTTACTACTACTACTAACAACAAAATAAAATT
1 TTTTAAATCAATAAATATAAACAATGTTTTTTACTTACTACTACTACTAACAACAAAATAAAATT
* * *
58401213 GCTAACTAAATTTTTTAAACATTATTAAA
66 ACTAACTAAATTTTTTAAAAAATATTAAA
58401242 -TTTAAATCAATAAATATAAACAATGTTTTTTACTTACTACTACTACTAACAACAAAATAAAATT
1 TTTTAAATCAATAAATATAAACAATGTTTTTTACTTACTACTACTACTAACAACAAAATAAAATT
*** *
58401306 ACTAACTAACAAAATTT-AAACATATTAAA
66 ACTAACTAA-ATTTTTTAAAAAATATTAAA
* * *
58401335 CTTTAAATCAATAAATATGAACAATATTTTTTAC-T--TACTACTACTAACAACAAAATAAAATT
1 TTTTAAATCAATAAATATAAACAATGTTTTTTACTTACTACTACTACTAACAACAAAATAAAATT
*
58401397 ATTAACTAA
66 ACTAACTAA
58401406 CAAAATTAAA
Statistics
Matches: 240, Mismatches: 15, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
91 35 0.15
93 134 0.56
94 71 0.30
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (94 bp):
TTTTAAATCAATAAATATAAACAATGTTTTTTACTTACTACTACTACTAACAACAAAATAAAATT
ACTAACTAAATTTTTTAAAAAATATTAAA
Found at i:58401370 original size:187 final size:183
Alignment explanation
Indices: 58401056--58401405 Score: 549
Period size: 187 Copynumber: 1.9 Consensus size: 183
58401046 TTATATTATT
* *
58401056 TTTAAATCAATAAATATGAACAATGTTTTTTACTTACTACTATTACTAACAACAAATAAAATTAC
1 TTTAAATCAATAAATATAAACAATGTTTTTTACTTACTACTACTACTAACAACAAATAAAATTAC
*** * *
58401121 TAACTAAATTTTTTAAAAAATATTAAATTTTAAATCAATAAATATAAACAATGTTTTTTACTTAC
66 TAACTAAAAAATTTAAAAAATATTAAACTTTAAATCAATAAATATAAACAATATTTTTTAC-T--
*
58401186 TACTACTACTAACAACAAAATAAAATTGCTAACTAAATTTTTTAAACATTATTAAA
128 TACTACTACTAACAACAAAATAAAATTACTAACTAAATTTTTTAAACATTATTAAA
58401242 TTTAAATCAATAAATATAAACAATGTTTTTTACTTACTACTACTACTAACAACAAAATAAAATTA
1 TTTAAATCAATAAATATAAACAATGTTTTTTACTTACTACTACTACTAACAAC-AAATAAAATTA
* *
58401307 CTAACTAACAAAATTT-AAACATATTAAACTTTAAATCAATAAATATGAACAATATTTTTTACTT
65 CTAACTAA-AAAATTTAAAAAATATTAAACTTTAAATCAATAAATATAAACAATATTTTTTACTT
*
58401371 ACTACTACTAACAACAAAATAAAATTATTAACTAA
129 ACTACTACTAACAACAAAATAAAATTACTAACTAA
58401406 CAAAATTAAA
Statistics
Matches: 151, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
184 34 0.23
186 52 0.34
187 61 0.40
188 4 0.03
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (183 bp):
TTTAAATCAATAAATATAAACAATGTTTTTTACTTACTACTACTACTAACAACAAATAAAATTAC
TAACTAAAAAATTTAAAAAATATTAAACTTTAAATCAATAAATATAAACAATATTTTTTACTTAC
TACTACTAACAACAAAATAAAATTACTAACTAAATTTTTTAAACATTATTAAA
Found at i:58401409 original size:21 final size:20
Alignment explanation
Indices: 58401379--58401418 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
58401369 TTACTACTAC
58401379 TAACAACAAAATAAAATTAT
1 TAACAACAAAATAAAATTAT
*
58401399 TAACTAACAAAATTAAATTA
1 TAAC-AACAAAATAAAATTA
58401419 AAATAAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (20 bp):
TAACAACAAAATAAAATTAT
Found at i:58401560 original size:19 final size:19
Alignment explanation
Indices: 58401514--58401560 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
58401504 AATCAATTAA
*
58401514 AAATTAAATTAAAGAAAAC
1 AAATTAACTTAAAGAAAAC
**
58401533 AAAAAAACTTAAA-ATAAAC
1 AAATTAACTTAAAGA-AAAC
58401552 AAATTAACT
1 AAATTAACT
58401561 AACCATTAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 1 0.05
19 21 0.95
ACGTcount: A:0.68, C:0.09, G:0.02, T:0.21
Consensus pattern (19 bp):
AAATTAACTTAAAGAAAAC
Found at i:58402625 original size:78 final size:78
Alignment explanation
Indices: 58402496--58402653 Score: 316
Period size: 78 Copynumber: 2.0 Consensus size: 78
58402486 TCCGACTTCA
58402496 ATTTAATTCTGTTCTCACGGGCTATTTATTGCTAAAGGTTTTTCATCGTATTTTACCATTTCTTT
1 ATTTAATTCTGTTCTCACGGGCTATTTATTGCTAAAGGTTTTTCATCGTATTTTACCATTTCTTT
58402561 TTTGTAATTTTAT
66 TTTGTAATTTTAT
58402574 ATTTAATTCTGTTCTCACGGGCTATTTATTGCTAAAGGTTTTTCATCGTATTTTACCATTTCTTT
1 ATTTAATTCTGTTCTCACGGGCTATTTATTGCTAAAGGTTTTTCATCGTATTTTACCATTTCTTT
58402639 TTTGTAATTTTAT
66 TTTGTAATTTTAT
58402652 AT
1 AT
58402654 ATTTATTTGA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.21, C:0.14, G:0.11, T:0.54
Consensus pattern (78 bp):
ATTTAATTCTGTTCTCACGGGCTATTTATTGCTAAAGGTTTTTCATCGTATTTTACCATTTCTTT
TTTGTAATTTTAT
Found at i:58403659 original size:10 final size:10
Alignment explanation
Indices: 58403644--58403707 Score: 76
Period size: 10 Copynumber: 6.1 Consensus size: 10
58403634 ACATTTCTCA
58403644 AAACAATGTT
1 AAACAATGTT
58403654 AAACAATGTT
1 AAACAATGTT
*
58403664 AAAC-ATTTCT
1 AAACAATGT-T
58403674 CAAAAACAATGTT
1 ---AAACAATGTT
58403687 AAACAATGTT
1 AAACAATGTT
58403697 AAACAATGTT
1 AAACAATGTT
58403707 A
1 A
58403708 TAAAAATTGA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
9 3 0.06
10 36 0.77
13 5 0.11
14 3 0.06
ACGTcount: A:0.50, C:0.12, G:0.08, T:0.30
Consensus pattern (10 bp):
AAACAATGTT
Found at i:58403680 original size:33 final size:32
Alignment explanation
Indices: 58403632--58403701 Score: 131
Period size: 33 Copynumber: 2.2 Consensus size: 32
58403622 GTACTTTTTA
58403632 AAACATTTCTCAAAACAATGTTAAACAATGTT
1 AAACATTTCTCAAAACAATGTTAAACAATGTT
58403664 AAACATTTCTCAAAAACAATGTTAAACAATGTT
1 AAACATTTCTC-AAAACAATGTTAAACAATGTT
58403697 AAACA
1 AAACA
58403702 ATGTTATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 11 0.30
33 26 0.70
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.29
Consensus pattern (32 bp):
AAACATTTCTCAAAACAATGTTAAACAATGTT
Found at i:58409118 original size:18 final size:18
Alignment explanation
Indices: 58409095--58409137 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
58409085 GAATAATTTT
58409095 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
58409113 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
58409131 TTAATTA
1 TTAATTA
58409138 CAACTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:58415539 original size:21 final size:21
Alignment explanation
Indices: 58415515--58415554 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
58415505 TTCTAAATTA
58415515 TTTA-AATATTTTAAAAAATAT
1 TTTATAATA-TTTAAAAAATAT
58415536 TTTATAATATTTAAAAAAT
1 TTTATAATATTTAAAAAAT
58415555 TATACAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTATAATATTTAAAAAATAT
Found at i:58417636 original size:6 final size:6
Alignment explanation
Indices: 58417625--58417664 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
58417615 TGTGACAAGG
58417625 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
58417665 TGTGTGTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTCT
Found at i:58417795 original size:11 final size:14
Alignment explanation
Indices: 58417756--58417798 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
58417746 AAATGAGTCT
*
58417756 TTCTCTTCTTCTTC
1 TTCTCTCCTTCTTC
58417770 TTCTCTCCTTCTTC
1 TTCTCTCCTTCTTC
58417784 TTC-CTCCTTTCTTC
1 TTCTCTCC-TTCTTC
58417798 T
1 T
58417799 GCTACTGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 4 0.15
14 23 0.85
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (14 bp):
TTCTCTCCTTCTTC
Found at i:58421570 original size:6 final size:6
Alignment explanation
Indices: 58421559--58421592 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
58421549 AACTCTGGGC
58421559 CAGGGA CAGGGA CAGGGA CAGGGA CAGGGA CAGG
1 CAGGGA CAGGGA CAGGGA CAGGGA CAGGGA CAGG
58421593 CTCAAACTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.18, G:0.50, T:0.00
Consensus pattern (6 bp):
CAGGGA
Found at i:58422183 original size:17 final size:17
Alignment explanation
Indices: 58422146--58422188 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
58422136 AAAATAATAG
* * *
58422146 AATTTAATAAATTTAAC
1 AATTTAAAAAATATAAA
58422163 AATTTAAAAAATATAAA
1 AATTTAAAAAATATAAA
58422180 AA-TTAAAAA
1 AATTTAAAAA
58422189 TGATCAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 7 0.30
17 16 0.70
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
AATTTAAAAAATATAAA
Found at i:58445587 original size:36 final size:36
Alignment explanation
Indices: 58445540--58445615 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
58445530 TAAGATGTTA
*
58445540 ATGTACTTTGGCATTTGAATTAATTCCTAGAATGGG
1 ATGTACTTTGGCATTTGAATTAATGCCTAGAATGGG
*
58445576 ATGTAGTTTGGCATTTGAATTAATGCCTAGAATGGG
1 ATGTACTTTGGCATTTGAATTAATGCCTAGAATGGG
58445612 ATGT
1 ATGT
58445616 GTTGATATTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.28, C:0.09, G:0.25, T:0.38
Consensus pattern (36 bp):
ATGTACTTTGGCATTTGAATTAATGCCTAGAATGGG
Found at i:58446923 original size:24 final size:24
Alignment explanation
Indices: 58446890--58446940 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
58446880 AGAAATAATC
*
58446890 TTTCAGTTAAACTCTGATTATTTG
1 TTTCAATTAAACTCTGATTATTTG
*
58446914 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGATTATTTG
58446938 TTT
1 TTT
58446941 GAGTCAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGATTATTTG
Found at i:58446949 original size:24 final size:24
Alignment explanation
Indices: 58446898--58446957 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
58446888 TCTTTCAGTT
*
58446898 AAACTCTGATTATTTGTTTCAATT
1 AAACTCTGATTATTTGTTTCAATC
* * *
58446922 AAACTCTGTTTATTTGTTTGAGTC
1 AAACTCTGATTATTTGTTTCAATC
*
58446946 AAACTCTTATTA
1 AAACTCTGATTA
58446958 CTCTAGATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.48
Consensus pattern (24 bp):
AAACTCTGATTATTTGTTTCAATC
Found at i:58450621 original size:23 final size:23
Alignment explanation
Indices: 58450595--58450760 Score: 123
Period size: 23 Copynumber: 7.4 Consensus size: 23
58450585 AGTGTTGGGC
58450595 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
58450618 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
*
58450637 -AC--TGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
58450657 ATCAGAGAGCACACGAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* * * *
58450680 ATCGGAGAGCACACACAGAGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
* *
58450704 TAACAGAGAGCACGA-GACGTGCTA
1 -AACAGAGAGCAC-ACAAAGTGCTA
* *
58450728 AACAGAGAGCACATACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
58450751 ATCAAAGAGC
1 AACAGAGAGC
58450761 GCGCTAGTGT
Statistics
Matches: 111, Mismatches: 21, Indels: 22
0.72 0.14 0.14
Matches are distributed among these distances:
16 10 0.09
18 3 0.03
19 1 0.01
20 1 0.01
21 2 0.02
22 1 0.01
23 76 0.68
24 2 0.02
25 14 0.13
26 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:58450655 original size:39 final size:39
Alignment explanation
Indices: 58450601--58450675 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
58450591 GGGCAACAGA
*
58450601 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
* *
58450640 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
58450676 GCTAATCGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Found at i:58450714 original size:48 final size:46
Alignment explanation
Indices: 58450640--58450760 Score: 145
Period size: 48 Copynumber: 2.6 Consensus size: 46
58450630 ACAAAGTACT
* * *
58450640 GAGCACACAAAGTGCTAATCAGAGAGCAC-ACGAAGTGCTAATCGGA
1 GAGCACACACAGTGCTAATCAGAGAGCACGA-GAAGTGCTAAACAGA
* *
58450686 GAGCACACACAGAGCTAATAACAGAGAGCACGAGACGTGCTAAACAGA
1 GAGCACACACAGTGCTAAT--CAGAGAGCACGAGAAGTGCTAAACAGA
* *
58450734 GAGCACATACAGTGCTAATCAAAGAGC
1 GAGCACACACAGTGCTAATCAGAGAGC
58450761 GCGCTAGTGT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
46 24 0.38
48 39 0.61
49 1 0.02
ACGTcount: A:0.41, C:0.22, G:0.25, T:0.12
Consensus pattern (46 bp):
GAGCACACACAGTGCTAATCAGAGAGCACGAGAAGTGCTAAACAGA
Found at i:58452794 original size:21 final size:22
Alignment explanation
Indices: 58452770--58452821 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
58452760 GTCCATGAAG
*
58452770 TTAAAAAAAAT-AACT-CTTAAT
1 TTAAAAAAAATAAACTAATT-AT
*
58452791 TTAAAGAAAATAAACTAATTAT
1 TTAAAAAAAATAAACTAATTAT
58452813 TTAAAAAAA
1 TTAAAAAAA
58452822 GTTTCAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 10 0.38
22 14 0.54
23 2 0.08
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.31
Consensus pattern (22 bp):
TTAAAAAAAATAAACTAATTAT
Found at i:58460103 original size:18 final size:19
Alignment explanation
Indices: 58460080--58460115 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
58460070 ACTTTATATA
58460080 TATTTTGAA-TTTTGAATT
1 TATTTTGAATTTTTGAATT
*
58460098 TATTTTTAATTTTTGAAT
1 TATTTTGAATTTTTGAAT
58460116 ATTTTTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (19 bp):
TATTTTGAATTTTTGAATT
Found at i:58460111 original size:19 final size:18
Alignment explanation
Indices: 58460080--58460141 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 18
58460070 ACTTTATATA
*
58460080 TATTTTGAATTTTGAATT
1 TATTTTTAATTTTGAATT
58460098 TATTTTTAATTTTTGAATAT
1 TATTTTTAA-TTTTGAAT-T
* *
58460118 T-TTTATAAATTTT-AAAT
1 TATTT-TTAATTTTGAATT
58460135 TATTTTT
1 TATTTTT
58460142 TGACGTGATA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
17 3 0.08
18 13 0.36
19 15 0.42
20 5 0.14
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.65
Consensus pattern (18 bp):
TATTTTTAATTTTGAATT
Found at i:58460328 original size:15 final size:14
Alignment explanation
Indices: 58460304--58460352 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
58460294 AAATTTAACT
58460304 ATAAAA-AATAAAA
1 ATAAAATAATAAAA
58460317 ATAAAATTAATAAAA
1 ATAAAA-TAATAAAA
*
58460332 ATATAAATATTAAAA
1 ATA-AAATAATAAAA
58460347 ACTAAA
1 A-TAAA
58460353 TTTATTATTG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
13 6 0.19
15 20 0.65
16 5 0.16
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (14 bp):
ATAAAATAATAAAA
Found at i:58466484 original size:6 final size:6
Alignment explanation
Indices: 58466473--58466498 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
58466463 GCCCTGACTC
58466473 TCCCTT TCCCTT TCCCTT TCCCTT TC
1 TCCCTT TCCCTT TCCCTT TCCCTT TC
58466499 GTGTGTAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (6 bp):
TCCCTT
Found at i:58494633 original size:29 final size:29
Alignment explanation
Indices: 58494600--58494853 Score: 237
Period size: 29 Copynumber: 8.8 Consensus size: 29
58494590 GACGTCTTTT
*
58494600 ACAGAATCAGCCATAAAGGCTCACATTTA
1 ACAGAATCAGCCACAAAGGCTCACATTTA
* ** *
58494629 GCAGAATCAATCACAAAGACTCACATTTA
1 ACAGAATCAGCCACAAAGGCTCACATTTA
* * * * *
58494658 ATAGATTCAGACACAAAGGTTCACATCTA
1 ACAGAATCAGCCACAAAGGCTCACATTTA
* *
58494687 ATA-AGTTCAAG-CACAAAGGCTCACATTTA
1 ACAGA-ATC-AGCCACAAAGGCTCACATTTA
* * * *
58494716 ATAGATTCAGCCATAAAGACTCACATTTA
1 ACAGAATCAGCCACAAAGGCTCACATTTA
*
58494745 ATAGAATCAGCCACAAAGGCTCAC-TTTA
1 ACAGAATCAGCCACAAAGGCTCACATTTA
* ** *
58494773 ACAGATTCAATCACAAAGGCTCACATTCA
1 ACAGAATCAGCCACAAAGGCTCACATTTA
* *
58494802 ATAGAATCAGCCACAAATGCTCAC-TTTA
1 ACAGAATCAGCCACAAAGGCTCACATTTA
* *
58494830 ACATATTCAGCCACAAAGGCTCAC
1 ACAGAATCAGCCACAAAGGCTCAC
58494854 TTTTCAGTAA
Statistics
Matches: 185, Mismatches: 35, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
28 50 0.27
29 132 0.71
30 3 0.02
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.22
Consensus pattern (29 bp):
ACAGAATCAGCCACAAAGGCTCACATTTA
Found at i:58494682 original size:58 final size:57
Alignment explanation
Indices: 58494595--58494853 Score: 261
Period size: 58 Copynumber: 4.5 Consensus size: 57
58494585 ACAAAGACGT
* * * * ** * *
58494595 CTTTTACAGAATCAGCCATAAAGGCTCACATTTAGCAGAATCAATCACAAAGACTCA
1 CTTTAACAGATTCAGACACAAAGGCTCACATTTAATAGAATCAACCACAAAGGCTCA
* * * * *
58494652 CATTTAATAGATTCAGACACAAAGGTTCACATCTAATA-AGTTCAAGCACAAAGGCTCA
1 C-TTTAACAGATTCAGACACAAAGGCTCACATTTAATAGA-ATCAACCACAAAGGCTCA
* * * * *
58494710 CATTTAATAGATTCAGCCATAAAGACTCACATTTAATAGAATCAGCCACAAAGGCTCA
1 C-TTTAACAGATTCAGACACAAAGGCTCACATTTAATAGAATCAACCACAAAGGCTCA
* * *
58494768 CTTTAACAGATTCA-ATCACAAAGGCTCACATTCAATAGAATCAGCCACAAATGCTCA
1 CTTTAACAGATTCAGA-CACAAAGGCTCACATTTAATAGAATCAACCACAAAGGCTCA
* *
58494825 CTTTAACATATTCAGCCACAAAGGCTCAC
1 CTTTAACAGATTCAGACACAAAGGCTCAC
58494854 TTTTCAGTAA
Statistics
Matches: 169, Mismatches: 28, Indels: 10
0.82 0.14 0.05
Matches are distributed among these distances:
57 77 0.46
58 91 0.54
59 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (57 bp):
CTTTAACAGATTCAGACACAAAGGCTCACATTTAATAGAATCAACCACAAAGGCTCA
Found at i:58495215 original size:15 final size:16
Alignment explanation
Indices: 58495195--58495236 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
58495185 CACTAAAACT
58495195 TCATGCACAGAC-TCC
1 TCATGCACAGACTTCC
* *
58495210 TCATGCAGAGACTTTC
1 TCATGCACAGACTTCC
58495226 TCATG-ACAGAC
1 TCATGCACAGAC
58495237 CACAATCATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.24
Consensus pattern (16 bp):
TCATGCACAGACTTCC
Found at i:58504321 original size:16 final size:15
Alignment explanation
Indices: 58504287--58504317 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
58504277 TGATTTAATT
58504287 ATTTTATGATTACAA
1 ATTTTATGATTACAA
58504302 ATTTTATGATTACAA
1 ATTTTATGATTACAA
58504317 A
1 A
58504318 ATTTGTTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (15 bp):
ATTTTATGATTACAA
Found at i:58505326 original size:18 final size:19
Alignment explanation
Indices: 58505305--58505342 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
58505295 TTGTAACACA
58505305 TTATTAATAAT-ATTTATT
1 TTATTAATAATAATTTATT
*
58505323 TTATTTATAATAATTTATT
1 TTATTAATAATAATTTATT
58505342 T
1 T
58505343 GTTAACGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTATTAATAATAATTTATT
Found at i:58506836 original size:22 final size:22
Alignment explanation
Indices: 58506810--58506854 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
58506800 CGAAAATTTG
* *
58506810 AATATAAAAATTAAATTAAAAA
1 AATATAAAAATAAAAATAAAAA
*
58506832 AATATTAAAATAAAAATAAAAA
1 AATATAAAAATAAAAATAAAAA
58506854 A
1 A
58506855 TGGTTAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (22 bp):
AATATAAAAATAAAAATAAAAA
Found at i:58508884 original size:24 final size:24
Alignment explanation
Indices: 58508848--58508893 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
58508838 AAATTTAATA
* *
58508848 TTTATTAGCATAATATATTTTATT
1 TTTATTAACATAAAATATTTTATT
* *
58508872 TTTATTAATATAAAATCTTTTA
1 TTTATTAACATAAAATATTTTA
58508894 ATATTTCATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (24 bp):
TTTATTAACATAAAATATTTTATT
Found at i:58512685 original size:30 final size:29
Alignment explanation
Indices: 58512627--58512686 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 29
58512617 GATAGAAGGA
*
58512627 AAGTAAAAGTTTTGAGGGAAAGTGAAAAG
1 AAGTAAAAGTTTTGAGGGAAAGTAAAAAG
58512656 AAGTAAAAGTTTTG-GGGAAAAAGTAAAAAG
1 AAGTAAAAGTTTTGAGGG--AAAGTAAAAAG
58512686 A
1 A
58512687 TTTATGAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 3 0.11
29 14 0.50
30 11 0.39
ACGTcount: A:0.52, C:0.00, G:0.28, T:0.20
Consensus pattern (29 bp):
AAGTAAAAGTTTTGAGGGAAAGTAAAAAG
Found at i:58518484 original size:112 final size:111
Alignment explanation
Indices: 58518355--58518632 Score: 296
Period size: 112 Copynumber: 2.5 Consensus size: 111
58518345 TTTGGAGTTG
* *
58518355 GCCATGCATTGGCCGACACCAGCATGTTTTATTAGATAAAAAAGTATTTTTTGGTGTTGGCCAAT
1 GCCATGCATTGGTCGACACCA-CAT-TTTTATCAGATAAAAAA-TATTTTTTGGTGTTGGCCAAT
*
58518420 GCTCGG-TCAACACCACCTTTTCGACCAG-AAAA-AATTTTTTGGTGCTA
63 GCTCGGCT-AACACCACCTTTTCAACCAGAAAAATAATTTTTTGGTGCTA
* **
58518467 GCCATGCATTGGTCGACAACAACATTTTTATCAGATAAAAAA-A-AATTTGGTGTTGGCCAATGC
1 GCCATGCATTGGTCGAC-ACCACATTTTTATCAGATAAAAAATATTTTTTGGTGTTGGCCAATGC
* * * ** * *
58518530 TTGGCTGACACCACCTTTTTAATTAGATAAAAATAATTTTTTGGTGTTG
65 TCGGCTAACACCACCTTTTCAACCAG--AAAAATAATTTTTTGGTGCTA
* * *
58518579 GGCATACATTGGTCGACACCACCTTTTTAATCAGATAAAAAATAATTTTTTGGT
1 GCCATGCATTGGTCGACACCACATTTTT-ATCAGATAAAAAAT-ATTTTTTGGT
58518633 ATTGACCATG
Statistics
Matches: 137, Mismatches: 19, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
108 36 0.26
109 2 0.01
111 29 0.21
112 60 0.44
113 3 0.02
114 1 0.01
115 6 0.04
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (111 bp):
GCCATGCATTGGTCGACACCACATTTTTATCAGATAAAAAATATTTTTTGGTGTTGGCCAATGCT
CGGCTAACACCACCTTTTCAACCAGAAAAATAATTTTTTGGTGCTA
Found at i:58518597 original size:57 final size:58
Alignment explanation
Indices: 58518345--58518833 Score: 445
Period size: 58 Copynumber: 8.5 Consensus size: 58
58518335 AAAAAAAAAA
* * * *
58518345 TTTGGAGTTGGCCATGCATTGGCCGACACCAGCATGTTTT-ATTAGATAAAAAAGT-ATTT
1 TTTGGTGTTGGCCATGCATTGGTCGACACCA-CCT-TTTTAATCAGATAAAAAA-TAATTT
* * ** *
58518404 TTTGGTGTTGGCCAATGC-TCGGTCAACACCACCTTTTCGACCAG----AAAA-AATTT
1 TTTGGTGTTGGCC-ATGCATTGGTCGACACCACCTTTTTAATCAGATAAAAAATAATTT
* * * * *
58518457 TTTGGTGCTAGCCATGCATTGGTCGACAACAACATTTTT-ATCAGATAAAAAA-AA--A
1 TTTGGTGTTGGCCATGCATTGGTCGAC-ACCACCTTTTTAATCAGATAAAAAATAATTT
*
58518512 TTTGGTGTTGGCCAATGC-TTGG-CTGACACCACCTTTTTAATTAGAT-AAAAATAATTT
1 TTTGGTGTTGGCC-ATGCATTGGTC-GACACCACCTTTTTAATCAGATAAAAAATAATTT
* *
58518569 TTTGGTGTTGGGCATACATTGGTCGACACCACCTTTTTAATCAGATAAAAAATAATTT
1 TTTGGTGTTGGCCATGCATTGGTCGACACCACCTTTTTAATCAGATAAAAAATAATTT
* * * ** *
58518627 TTTGGTATTGACCATGAATTTATCGACACCACCTTTTTAATTAGATAAAAAATAATTT
1 TTTGGTGTTGGCCATGCATTGGTCGACACCACCTTTTTAATCAGATAAAAAATAATTT
* * ** *
58518685 TTTTGTGTTGGACATGCATTGACCGACACTACCTTTTTAATCCA-ATAAAAAATAATATT
1 TTTGGTGTTGGCCATGCATTGGTCGACACCACCTTTTTAAT-CAGATAAAAAATAAT-TT
* * * * * *
58518744 TTTTGTGTTGACCATGCATTTGCCGACACCATCTTTTTTATCAGATAAAAAATAATTTT
1 TTTGGTGTTGGCCATGCATTGGTCGACACCACCTTTTTAATCAGATAAAAAATAA-TTT
*
58518803 TTTGGTGTTAGCCATGCATTGG-CTGACACCA
1 TTTGGTGTTGGCCATGCATTGGTC-GACACCA
58518834 TACGTTGGGA
Statistics
Matches: 353, Mismatches: 54, Indels: 46
0.78 0.12 0.10
Matches are distributed among these distances:
52 4 0.01
53 26 0.07
54 27 0.08
55 26 0.07
56 7 0.02
57 46 0.13
58 115 0.33
59 97 0.27
60 5 0.01
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (58 bp):
TTTGGTGTTGGCCATGCATTGGTCGACACCACCTTTTTAATCAGATAAAAAATAATTT
Found at i:58519406 original size:29 final size:30
Alignment explanation
Indices: 58519358--58519447 Score: 130
Period size: 29 Copynumber: 3.1 Consensus size: 30
58519348 AAAAAATAAT
*
58519358 AATTAGAAATGAAATTTAAAATATAAACGA
1 AATTAGAAATAAAATTTAAAATATAAACGA
58519388 AATTAGAAA-AAAATTTAAAATATAAACGA
1 AATTAGAAATAAAATTTAAAATATAAACGA
* * *
58519417 AATTACAAATTAAATTTTAAA-ATAAACGA
1 AATTAGAAATAAAATTTAAAATATAAACGA
58519446 AA
1 AA
58519448 AAAAATCAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
29 37 0.67
30 18 0.33
ACGTcount: A:0.62, C:0.04, G:0.07, T:0.27
Consensus pattern (30 bp):
AATTAGAAATAAAATTTAAAATATAAACGA
Found at i:58520589 original size:36 final size:36
Alignment explanation
Indices: 58520533--58520604 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
58520523 ATTTTTTAAT
58520533 ATTTCGAAAATATAAAAAAT-ATATGTAAAAAAATTC
1 ATTTCGAAAATATAAAAAATAAT-TGTAAAAAAATTC
* * *
58520569 ATTTTGAAGATATAAAAAATAATTTTAAAAAAATTC
1 ATTTCGAAAATATAAAAAATAATTGTAAAAAAATTC
58520605 GAAAAGCTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
36 30 0.94
37 2 0.06
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (36 bp):
ATTTCGAAAATATAAAAAATAATTGTAAAAAAATTC
Found at i:58520667 original size:88 final size:87
Alignment explanation
Indices: 58520530--58520739 Score: 332
Period size: 88 Copynumber: 2.4 Consensus size: 87
58520520 AATATTTTTT
* ** *
58520530 AATATTTCGAAAATATAAAAAATATATGTAAAAAAATTCATTTTGAAGATATAAAAAATAATTTT
1 AATATTTTGAAAATATAAAAAATATATGTAAAAAAATTCATTTCAAAGATATAAAAAATAATTTG
58520595 AAAAAAATTCGAAAAGCTAAAA
66 AAAAAAATTCGAAAAGCTAAAA
*
58520617 AATATTTTGAAAATATAAAATAATATATGTAAAAAATTTCATTTCAAAGATATAAAAAATAATTT
1 AATATTTTGAAAATATAAAA-AATATATGTAAAAAAATTCATTTCAAAGATATAAAAAATAATTT
58520682 GAAAAAAATTCGAAAAGCTAAAA
65 GAAAAAAATTCGAAAAGCTAAAA
* *
58520705 AAT-GTTTCAAAACTATAAAAAATATATGTAAAAAA
1 AATATTTTGAAAA-TATAAAAAATATATGTAAAAAA
58520740 GTATTTCGAA
Statistics
Matches: 114, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
87 41 0.36
88 73 0.64
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.30
Consensus pattern (87 bp):
AATATTTTGAAAATATAAAAAATATATGTAAAAAAATTCATTTCAAAGATATAAAAAATAATTTG
AAAAAAATTCGAAAAGCTAAAA
Found at i:58520813 original size:20 final size:20
Alignment explanation
Indices: 58520766--58520813 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
58520756 ATTTAAAAAA
58520766 TTTAAAAATAAAAAAAATAT
1 TTTAAAAATAAAAAAAATAT
** *
58520786 TTCGAAAATAGAAAAAATAT
1 TTTAAAAATAAAAAAAATAT
58520806 TTTAAAAA
1 TTTAAAAA
58520814 ATTCGAAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (20 bp):
TTTAAAAATAAAAAAAATAT
Found at i:58520814 original size:21 final size:20
Alignment explanation
Indices: 58520760--58520815 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
58520750 AATATTATTT
58520760 AAAAA-ATTT-AAAAATAAA
1 AAAAATATTTAAAAAATAAA
** *
58520778 AAAAATATTTCGAAAATAGA
1 AAAAATATTTAAAAAATAAA
58520798 AAAAATATTTTAAAAAAT
1 AAAAATA-TTTAAAAAAT
58520816 TCGAAAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 5 0.16
19 4 0.13
20 14 0.45
21 8 0.26
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (20 bp):
AAAAATATTTAAAAAATAAA
Found at i:58522447 original size:91 final size:92
Alignment explanation
Indices: 58522053--58522490 Score: 675
Period size: 93 Copynumber: 4.7 Consensus size: 92
58522043 AATTAAGGGT
* * *
58522053 AATTTGGTAAATAATGTATTGTAAAATTAACACATTTTTTGATATAAATTGAAATCTTATAATAA
1 AATTTGGTAAATAATGTATTGT-AAATCAACACATTATTTGATATAAATTGAAATATTATAAT-A
58522118 TCATTTTTAATTTAAATAATTTTAATATTTG
64 --ATTTTTAATTTAAATAATTTTAATATTTG
* *
58522149 AATTTGGTAAATAATGTATTGTCAAATCAATACATTATTTGATATAAATTAAAATATTATAATAA
1 AATTTGGTAAATAATGTATTGT-AAATCAACACATTATTTGATATAAATTGAAATATTATAATAA
58522214 TTTTTAATTTAAATAATTTTAATATTTG
65 TTTTTAATTTAAATAATTTTAATATTTG
*
58522242 AATTTGGTAAATAATGTA--GTCAAATCAACAAATTATTTGATATAAATTGAAATATTATAATAA
1 AATTTGGTAAATAATGTATTGT-AAATCAACACATTATTTGATATAAATTGAAATA-T-T-ATAA
58522305 TAATTTTTAATTTAAATAATTTTAATATTTG
62 TAATTTTTAATTTAAATAATTTTAATATTTG
* *
58522336 AATTTGGTAAATAATGTATTG-AAATGAACACATTATTTGATATAAATTGAAATATTATAATAGT
1 AATTTGGTAAATAATGTATTGTAAATCAACACATTATTTGATATAAATTGAAATATTATAATAAT
58522400 TTTTAATTTAAATAATTTTAATATTTG
66 TTTTAATTTAAATAATTTTAATATTTG
* *
58522427 AATTTGGTAAATAATTTATTGTCAAATCAACATATTATTTGATATAAATTGAAATATTATAATA
1 AATTTGGTAAATAATGTATTGT-AAATCAACACATTATTTGATATAAATTGAAATATTATAATA
58522491 TATTGTCAAA
Statistics
Matches: 320, Mismatches: 15, Indels: 17
0.91 0.04 0.05
Matches are distributed among these distances:
91 87 0.27
92 2 0.01
93 88 0.28
94 84 0.26
95 1 0.00
96 58 0.18
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (92 bp):
AATTTGGTAAATAATGTATTGTAAATCAACACATTATTTGATATAAATTGAAATATTATAATAAT
TTTTAATTTAAATAATTTTAATATTTG
Found at i:58522453 original size:187 final size:188
Alignment explanation
Indices: 58522053--58522490 Score: 738
Period size: 187 Copynumber: 2.3 Consensus size: 188
58522043 AATTAAGGGT
* * * * *
58522053 AATTTGGTAAATAATGTATTGTAAAATTAACACATTTTTTGATATAAATTGAAATCTTATAATAA
1 AATTTGGTAAATAATGTATTGTCAAATCAACAAATTATTTGATATAAATTGAAATATTATAATAA
* *
58522118 TCATTTTTAATTTAAATAATTTTAATATTTGAATTTGGTAAATAATGTATTGTCAAATCAATACA
66 TAATTTTTAATTTAAATAATTTTAATATTTGAATTTGGTAAATAATGTATTG-CAAATCAACACA
58522183 TTATTTGATATAAATTAAAATATTATAATAATTTTTAATTTAAATAATTTTAATATTTG
130 TTATTTGATATAAATTAAAATATTATAATAATTTTTAATTTAAATAATTTTAATATTTG
58522242 AATTTGGTAAATAATGTA--GTCAAATCAACAAATTATTTGATATAAATTGAAATATTATAATAA
1 AATTTGGTAAATAATGTATTGTCAAATCAACAAATTATTTGATATAAATTGAAATATTATAATAA
*
58522305 TAATTTTTAATTTAAATAATTTTAATATTTGAATTTGGTAAATAATGTATTG-AAATGAACACAT
66 TAATTTTTAATTTAAATAATTTTAATATTTGAATTTGGTAAATAATGTATTGCAAATCAACACAT
* *
58522369 TATTTGATATAAATTGAAATATTATAATAGTTTTTAATTTAAATAATTTTAATATTTG
131 TATTTGATATAAATTAAAATATTATAATAATTTTTAATTTAAATAATTTTAATATTTG
* *
58522427 AATTTGGTAAATAATTTATTGTCAAATCAACATATTATTTGATATAAATTGAAATATTATAATA
1 AATTTGGTAAATAATGTATTGTCAAATCAACAAATTATTTGATATAAATTGAAATATTATAATA
58522491 TATTGTCAAA
Statistics
Matches: 235, Mismatches: 12, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
185 83 0.35
187 134 0.57
189 18 0.08
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (188 bp):
AATTTGGTAAATAATGTATTGTCAAATCAACAAATTATTTGATATAAATTGAAATATTATAATAA
TAATTTTTAATTTAAATAATTTTAATATTTGAATTTGGTAAATAATGTATTGCAAATCAACACAT
TATTTGATATAAATTAAAATATTATAATAATTTTTAATTTAAATAATTTTAATATTTG
Found at i:58522498 original size:48 final size:48
Alignment explanation
Indices: 58522437--58522538 Score: 179
Period size: 48 Copynumber: 2.1 Consensus size: 48
58522427 AATTTGGTAA
*
58522437 ATAATTTATTGTCAAATCAACA-TATTATTTGATATAAATTGAAATATT
1 ATAATATATTGTCAAATCAACACT-TTATTTGATATAAATTGAAATATT
58522485 ATAATATATTGTCAAATCAACACTTTATTTGATATAAATTGAAATATT
1 ATAATATATTGTCAAATCAACACTTTATTTGATATAAATTGAAATATT
58522533 ATAATA
1 ATAATA
58522539 ATCATTTTTA
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
48 51 0.98
49 1 0.02
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.42
Consensus pattern (48 bp):
ATAATATATTGTCAAATCAACACTTTATTTGATATAAATTGAAATATT
Found at i:58535549 original size:11 final size:12
Alignment explanation
Indices: 58535525--58535554 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
58535515 CAACCCAAAT
58535525 TTTATTATTTTA
1 TTTATTATTTTA
58535537 TTTATTA-TTTA
1 TTTATTATTTTA
58535548 TTTATTA
1 TTTATTA
58535555 AATAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:58536574 original size:30 final size:30
Alignment explanation
Indices: 58536535--58536681 Score: 118
Period size: 30 Copynumber: 4.8 Consensus size: 30
58536525 GATCCTCAAT
* *
58536535 TTTTTCAAAAATTCTAATTTGACCCCAAAA
1 TTTTCCAAAAATTCAAATTTGACCCCAAAA
* *
58536565 TTTTCCAAAAAAATT-AAATTCGACCCCTAAA
1 TTTTCC--AAAAATTCAAATTTGACCCCAAAA
* * *
58536596 TTTTCCAAAAAATTCCAATTTGACCTCTAAA
1 TTTTCC-AAAAATTCAAATTTGACCCCAAAA
* * * * * *
58536627 CTTTCTAGAACTTCCAATTTGGCCCCTAAAA
1 TTTTCCAAAAATTCAAATTTGACCCC-AAAA
*
58536658 GTTT-CAAAAATTCAAATTTGACCC
1 TTTTCCAAAAATTCAAATTTGACCC
58536682 GGTTTTAATT
Statistics
Matches: 93, Mismatches: 20, Indels: 8
0.77 0.17 0.07
Matches are distributed among these distances:
30 44 0.47
31 42 0.45
32 7 0.08
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.33
Consensus pattern (30 bp):
TTTTCCAAAAATTCAAATTTGACCCCAAAA
Found at i:58536576 original size:31 final size:30
Alignment explanation
Indices: 58536536--58536681 Score: 118
Period size: 31 Copynumber: 4.8 Consensus size: 30
58536526 ATCCTCAATT
*
58536536 TTTTC-AAAAATTCTAATTTGACCCCAAAA
1 TTTTCAAAAAATTCAAATTTGACCCCAAAA
* *
58536565 TTTTCCAAAAAAATT-AAATTCGACCCCTAAA
1 TTTT-C-AAAAAATTCAAATTTGACCCCAAAA
* * *
58536596 TTTTCCAAAAAATTCCAATTTGACCTCTAAA
1 TTTT-CAAAAAATTCAAATTTGACCCCAAAA
* * * * * *
58536627 CTTTCTAGAACTTCCAATTTGGCCCCTAAAA
1 TTTTCAAAAAATTCAAATTTGACCCC-AAAA
*
58536658 GTTTC-AAAAATTCAAATTTGACCC
1 TTTTCAAAAAATTCAAATTTGACCC
58536682 GGTTTTAATT
Statistics
Matches: 94, Mismatches: 18, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
29 4 0.04
30 41 0.44
31 42 0.45
32 7 0.07
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.33
Consensus pattern (30 bp):
TTTTCAAAAAATTCAAATTTGACCCCAAAA
Found at i:58540608 original size:26 final size:26
Alignment explanation
Indices: 58540556--58540608 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
58540546 CTTATCATAT
* * *
58540556 TTATATTAAAATTATACATTTTCATA
1 TTATATTAAAATTATAAATATTAATA
* *
58540582 TTATTTTAATATTATAAATATTAATA
1 TTATATTAAAATTATAAATATTAATA
58540608 T
1 T
58540609 AAAATTATAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (26 bp):
TTATATTAAAATTATAAATATTAATA
Found at i:58542348 original size:24 final size:24
Alignment explanation
Indices: 58542321--58542366 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
58542311 GCTTCGATTC
*
58542321 ATCTCTTTTAGACTTCTCTAATGA
1 ATCTCCTTTAGACTTCTCTAATGA
58542345 ATCTCCTTTAGACTTCTCTAAT
1 ATCTCCTTTAGACTTCTCTAAT
58542367 TGGGCTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.07, T:0.46
Consensus pattern (24 bp):
ATCTCCTTTAGACTTCTCTAATGA
Found at i:58544182 original size:20 final size:21
Alignment explanation
Indices: 58544157--58544197 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
58544147 ATTATCAAAT
58544157 AACATATATTAAGAA-AAAAA
1 AACATATATTAAGAAGAAAAA
* *
58544177 AACATATTTTATGAAGAAAAA
1 AACATATATTAAGAAGAAAAA
58544198 TATAATTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.63, C:0.05, G:0.07, T:0.24
Consensus pattern (21 bp):
AACATATATTAAGAAGAAAAA
Found at i:58561519 original size:158 final size:157
Alignment explanation
Indices: 58561192--58561504 Score: 488
Period size: 158 Copynumber: 2.0 Consensus size: 157
58561182 TTAATCCACT
* * * *
58561192 AAATAAAATTT-AGATTTTTGAAATCTGAAAATTTTTAAAAATCAACTTAAAAATCTGTGTGTTA
1 AAATAAAATTTGAG-TTTTTGAAATCTAAAAAATTTTAAAAATAAACTTAAAAATCTGGGTGTTA
*
58561256 CAAATATTCTTCTTTCTCATTGTTCCATACTTTTGTTCATCTGTAAGCCTTTAGAAACACTAATT
65 CAAATATTCTTCTTCCTCATTGTTCCATACTTTTGTTCATCTGTAAGCCTTTAGAAACACTAATT
*
58561321 TTCAAATTTCAAAAATCCAAATTTTTAA
130 TTCAAATTTCAAAAACCCAAATTTTTAA
58561349 AAATAAAATTTGAGTTTTTGAAATCTAAAAAATTTTAAAAATTAAACTTAAAAA-CTTGGGTGTT
1 AAATAAAATTTGAGTTTTTGAAATCTAAAAAATTTTAAAAA-TAAACTTAAAAATC-TGGGTGTT
* * *
58561413 ACAAATATTTTTCTTCCTTATTGTTCCATACTTTTGTTCATCTGTAAGCCTTTAGAAACACTACT
64 ACAAATATTCTTCTTCCTCATTGTTCCATACTTTTGTTCATCTGTAAGCCTTTAGAAACACTAAT
*
58561478 TTTCAAATTT-TAAAACCCAAATTTTTA
129 TTTCAAATTTCAAAAACCCAAATTTTTA
58561505 GTGGATTAAG
Statistics
Matches: 143, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
157 52 0.36
158 91 0.64
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (157 bp):
AAATAAAATTTGAGTTTTTGAAATCTAAAAAATTTTAAAAATAAACTTAAAAATCTGGGTGTTAC
AAATATTCTTCTTCCTCATTGTTCCATACTTTTGTTCATCTGTAAGCCTTTAGAAACACTAATTT
TCAAATTTCAAAAACCCAAATTTTTAA
Found at i:58561655 original size:30 final size:32
Alignment explanation
Indices: 58561601--58561671 Score: 101
Period size: 30 Copynumber: 2.2 Consensus size: 32
58561591 AATAATTATT
*
58561601 TAATTATTATTATTTTAAAAAAAATAATTTTAG
1 TAATT-TTATTATTTTAAAAAAAATAATTTTAA
*
58561634 TAATTTTA-TATTTT-TAAAAAATAATTTTAA
1 TAATTTTATTATTTTAAAAAAAATAATTTTAA
58561664 TAATTTTA
1 TAATTTTA
58561672 AAATCATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 22 0.61
31 6 0.17
32 3 0.08
33 5 0.14
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (32 bp):
TAATTTTATTATTTTAAAAAAAATAATTTTAA
Found at i:58561660 original size:21 final size:22
Alignment explanation
Indices: 58561634--58561674 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
58561624 ATAATTTTAG
*
58561634 TAATTTT-ATATTTTTAAAAAA
1 TAATTTTAATAATTTTAAAAAA
58561655 TAATTTTAATAATTTTAAAA
1 TAATTTTAATAATTTTAAAA
58561675 TCATTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TAATTTTAATAATTTTAAAAAA
Found at i:58561680 original size:20 final size:21
Alignment explanation
Indices: 58561651--58561690 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
58561641 ATATTTTTAA
*
58561651 AAAATAATTTTAATA-ATTTT
1 AAAATAATTTAAATACATTTT
*
58561671 AAAATCATTTAAATACATTT
1 AAAATAATTTAAATACATTT
58561691 GGACTGTCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (21 bp):
AAAATAATTTAAATACATTTT
Found at i:58561931 original size:17 final size:18
Alignment explanation
Indices: 58561909--58561946 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
58561899 AAGATGCATG
* *
58561909 AATTAATTATA-TATATA
1 AATTAAATATACTAAATA
58561926 AATTAAATATACTAAATA
1 AATTAAATATACTAAATA
58561944 AAT
1 AAT
58561947 ATTTAGGCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
AATTAAATATACTAAATA
Found at i:58565072 original size:5 final size:5
Alignment explanation
Indices: 58565046--58565089 Score: 52
Period size: 5 Copynumber: 8.2 Consensus size: 5
58565036 CTTTTATCCA
*
58565046 TCTTT TCTATT TCTTATT TCTTT TCTTT TCTTT TCTCT TCTTT T
1 TCTTT TCT-TT TC-T-TT TCTTT TCTTT TCTTT TCTTT TCTTT T
58565090 ACATCAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 24 0.69
6 5 0.14
7 6 0.17
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (5 bp):
TCTTT
Found at i:58567627 original size:21 final size:23
Alignment explanation
Indices: 58567586--58567634 Score: 75
Period size: 21 Copynumber: 2.2 Consensus size: 23
58567576 TTTGAGTTTG
58567586 TTTAAAATTTTACATAAATATCTT
1 TTTAAAATTTTA-ATAAATATCTT
58567610 TTTAAAATTTT-A-AAATATCTT
1 TTTAAAATTTTAATAAATATCTT
58567631 TTTA
1 TTTA
58567635 CAGTTTGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 13 0.52
22 1 0.04
24 11 0.44
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTAAAATTTTAATAAATATCTT
Found at i:58567699 original size:29 final size:29
Alignment explanation
Indices: 58567660--58567716 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
58567650 AAAATGTTTA
58567660 GAAAACTATGTTGTTTTCCTGAAAATTTG
1 GAAAACTATGTTGTTTTCCTGAAAATTTG
* * *
58567689 GAAAATTATGTTGTTTTCTTTAAAATTT
1 GAAAACTATGTTGTTTTCCTGAAAATTT
58567717 ACCGATCTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.47
Consensus pattern (29 bp):
GAAAACTATGTTGTTTTCCTGAAAATTTG
Found at i:58570192 original size:2 final size:2
Alignment explanation
Indices: 58570185--58570213 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
58570175 CTTTTGGAGT
58570185 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
58570214 TATTTGGGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:58581298 original size:34 final size:34
Alignment explanation
Indices: 58581252--58581321 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
58581242 TTATTATTCG
58581252 TATTATAAAAGAAAGGATTGTAGTTGTACAGGTT
1 TATTATAAAAGAAAGGATTGTAGTTGTACAGGTT
*
58581286 TATTATAGAAGAAAGGATTGTAGTTGTACAGGTT
1 TATTATAAAAGAAAGGATTGTAGTTGTACAGGTT
58581320 TA
1 TA
58581322 CATATATAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (34 bp):
TATTATAAAAGAAAGGATTGTAGTTGTACAGGTT
Found at i:58596254 original size:17 final size:17
Alignment explanation
Indices: 58596232--58596270 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
58596222 CTCCACATTG
*
58596232 ACAAGAATTCTCT-ACGA
1 ACAAGAACTCT-TAACGA
58596249 ACAAGAACTCTTAACGA
1 ACAAGAACTCTTAACGA
58596266 ACAAG
1 ACAAG
58596271 TTTTCCACCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.46, C:0.23, G:0.13, T:0.18
Consensus pattern (17 bp):
ACAAGAACTCTTAACGA
Found at i:58600614 original size:27 final size:27
Alignment explanation
Indices: 58600560--58600615 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
58600550 ACCTTATTCT
** *
58600560 AATTAAAATAAAATAATAATCTATTCC
1 AATTAAAATAAAATAATAATAAAGTCC
58600587 AATTAAAATAAAATAA-AAGTAAAGTCC
1 AATTAAAATAAAATAATAA-TAAAGTCC
58600614 AA
1 AA
58600616 AATAAAAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.61, C:0.09, G:0.04, T:0.27
Consensus pattern (27 bp):
AATTAAAATAAAATAATAATAAAGTCC
Found at i:58607957 original size:61 final size:63
Alignment explanation
Indices: 58607856--58607987 Score: 171
Period size: 61 Copynumber: 2.1 Consensus size: 63
58607846 GGTCTAAATG
* * * *
58607856 TAAATTTAGTCATCTAATGTTTACATATTTTATCAATTTAATTTTAAATAT-AAAAAATTCAA
1 TAAATTTAGTCATCTAATGCTTACAAAATTTATCAATTTAATTTAAAATATAAAAAAATTCAA
* * *
58607918 TAAATTTAG-CA-CTCAATGCTTACAAAATTTATCATTTTAATTTAAAATCTAAAAAAATTTAA
1 TAAATTTAGTCATCT-AATGCTTACAAAATTTATCAATTTAATTTAAAATATAAAAAAATTCAA
58607980 TAAATTTA
1 TAAATTTA
58607988 TCCTTCAATA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
60 2 0.03
61 32 0.52
62 27 0.44
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.42
Consensus pattern (63 bp):
TAAATTTAGTCATCTAATGCTTACAAAATTTATCAATTTAATTTAAAATATAAAAAAATTCAA
Found at i:58608003 original size:62 final size:61
Alignment explanation
Indices: 58607856--58608007 Score: 164
Period size: 62 Copynumber: 2.5 Consensus size: 61
58607846 GGTCTAAATG
* * * *
58607856 TAAATTTAGTCA-TCTAATGTTTACATATTTTATCAATTTAATTTTAAATATAAAAAATTCAA
1 TAAATTTAG-CACTC-AATATTTACAAAATTTATCAATTTAATTTAAAATATAAAAAATTCAA
** * * *
58607918 TAAATTTAGCACTCAATGCTTACAAAATTTATCATTTTAATTTAAAATCTAAAAAAATTTAA
1 TAAATTTAGCACTCAATATTTACAAAATTTATCAATTTAATTTAAAATAT-AAAAAATTCAA
*
58607980 TAAATTTATC-CTTCAATATTTACAAAAT
1 TAAATTTAGCAC-TCAATATTTACAAAAT
58608008 ATGTTATTTT
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
61 33 0.43
62 44 0.57
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.42
Consensus pattern (61 bp):
TAAATTTAGCACTCAATATTTACAAAATTTATCAATTTAATTTAAAATATAAAAAATTCAA
Found at i:58609276 original size:16 final size:16
Alignment explanation
Indices: 58609217--58609276 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
58609207 GAGCTAGATA
* *
58609217 AAATAATTCGAGCTTG
1 AAATAATTCAAACTTG
* *
58609233 AAAAAATTCGAACTT-
1 AAATAATTCAAACTTG
*
58609248 AAATAGATCCAAACTTG
1 AAATA-ATTCAAACTTG
58609265 AAATAATTCAAA
1 AAATAATTCAAA
58609277 TCTGAGATTG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
15 4 0.11
16 27 0.75
17 5 0.14
ACGTcount: A:0.50, C:0.13, G:0.10, T:0.27
Consensus pattern (16 bp):
AAATAATTCAAACTTG
Found at i:58610614 original size:25 final size:25
Alignment explanation
Indices: 58610586--58610634 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
58610576 AAGATTACCC
*
58610586 AATAAGATA-ATTACATGTGAAAAAT
1 AATAAGATACATTAAAT-TGAAAAAT
*
58610611 AATAATATACATTAAATTGAAAAA
1 AATAAGATACATTAAATTGAAAAA
58610635 ATAACTCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.59, C:0.04, G:0.08, T:0.29
Consensus pattern (25 bp):
AATAAGATACATTAAATTGAAAAAT
Found at i:58612529 original size:60 final size:57
Alignment explanation
Indices: 58612440--58612571 Score: 165
Period size: 59 Copynumber: 2.2 Consensus size: 57
58612430 GACTCCCACC
* * *
58612440 ACTATGATTAAATTTAATCACTTTAATATTAAATTAATATAATACTTATCAAGATAAAT
1 ACTA-GATTAAATTTAATCACATTAATATTAAATTAATAAAATA-TTATCAAAATAAAT
* * *
58612499 ATTAGATTAAATTTAATATCACATTAATATTAAATTAATAAAATATTATTAAAATAATT
1 ACTAGATTAAATTT-A-ATCACATTAATATTAAATTAATAAAATATTATCAAAATAAAT
*
58612558 ACTAAATTAAATTT
1 ACTAGATTAAATTT
58612572 TTATAAATAT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
58 10 0.16
59 27 0.43
60 26 0.41
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (57 bp):
ACTAGATTAAATTTAATCACATTAATATTAAATTAATAAAATATTATCAAAATAAAT
Found at i:58612546 original size:22 final size:23
Alignment explanation
Indices: 58612495--58612546 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
58612485 TTATCAAGAT
58612495 AAATATT-AGATTAAATTTAATA
1 AAATATTAAGATTAAATTTAATA
** * *
58612517 TCACATTAATATTAAA-TTAATA
1 AAATATTAAGATTAAATTTAATA
58612539 AAATATTA
1 AAATATTA
58612547 TTAAAATAAT
Statistics
Matches: 22, Mismatches: 7, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (23 bp):
AAATATTAAGATTAAATTTAATA
Found at i:58639573 original size:29 final size:30
Alignment explanation
Indices: 58639541--58639609 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
58639531 AAAAACTTGG
* *
58639541 TTTTATTTTATTTTAT-TTTAAAATATTAT
1 TTTTATTTGATTTAATATTTAAAATATTAT
* *
58639570 TTTTATTAGGATTTAATATTTAAGATATTAT
1 TTTTATT-TGATTTAATATTTAAAATATTAT
58639601 TTATTATTT
1 TT-TTATTT
58639610 AAATTTGTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
29 7 0.22
30 6 0.19
31 14 0.44
32 5 0.16
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (30 bp):
TTTTATTTGATTTAATATTTAAAATATTAT
Found at i:58639602 original size:19 final size:19
Alignment explanation
Indices: 58639580--58639624 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
58639570 TTTTATTAGG
58639580 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
58639599 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
58639618 ATTTAAT
1 ATTTAAT
58639625 TCATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Done.