Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024621.1 Corchorus olitorius cultivar O-4 contig24654, 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: 135215
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:121 original size:60 final size:59
Alignment explanation
Indices: 1--210 Score: 266
Period size: 60 Copynumber: 3.5 Consensus size: 59
* * *
1 CAATTCAAAATCATATCTCGTTTTTAAAATCCTGATAGAGGTCTCTGATAGAGAGTTTT
1 CAATTCAAAATCATATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGATAGAGAGTTTT
* * *
60 CAATTCAAAAT-ATTATCTTGTTTTTAAAAATCTTGTTCGAGGTCTCTGGTAGAGAGATTT
1 CAATTCAAAATCA-TATCTTGTTTTT-AAAATCCTGTTCGAGGTCTCTGATAGAGAGTTTT
* *
120 CAATTCAAAATCATATCTTGTTTTTAAAATCCTGTTCGAAGTCTCTAATAGAGAGTTTTT
1 CAATTCAAAATCATATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGATAGAGAG-TTTT
180 CAATATC-AAATC-T-TGCTTTGTTTTTAAAATC
1 CAAT-TCAAAATCATAT-C-TTGTTTTTAAAATC
211 TTATCTTGTT
Statistics
Matches: 133, Mismatches: 11, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
58 2 0.02
59 50 0.38
60 78 0.59
61 3 0.02
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.41
Consensus pattern (59 bp):
CAATTCAAAATCATATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGATAGAGAGTTTT
Found at i:223 original size:79 final size:78
Alignment explanation
Indices: 126--288 Score: 233
Period size: 79 Copynumber: 2.1 Consensus size: 78
116 ATTTCAATTC
126 AAAATCATATCTTGTTTTTAAAATCCTGTTCGAAGTCTCTAATAGAGAGTTTTTCAATATC-AAA
1 AAAATCATATCTTGTTTTTAAAATCCTGTTCGAAGTCTCTAATAGAGAG-TTTTCAAT-TCAAAA
190 TC-T-TGCTTTGTTTTT
64 TCATAT-C-TTGTTTTT
* * **
205 AAAATCTTATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATC
1 AAAATCATATCTTGTTTTTAAAATCCTGTTCGAAGTCTCTAATAGAGAGTTTTCAATTCAAAATC
270 ATATCTTGTTTTT
66 ATATCTTGTTTTT
283 AAAATC
1 AAAATC
289 CTGATAGAGG
Statistics
Matches: 77, Mismatches: 4, Indels: 7
0.88 0.05 0.08
Matches are distributed among these distances:
77 2 0.03
78 27 0.35
79 47 0.61
80 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.44
Consensus pattern (78 bp):
AAAATCATATCTTGTTTTTAAAATCCTGTTCGAAGTCTCTAATAGAGAGTTTTCAATTCAAAATC
ATATCTTGTTTTT
Found at i:259 original size:138 final size:138
Alignment explanation
Indices: 66--349 Score: 439
Period size: 138 Copynumber: 2.1 Consensus size: 138
56 TTTTCAATTC
* *
66 AAAATATTATCTTGTTTTTAAAAATCTTGTTCGAGGTCTCTGGTAGAGAGATTTCAATTCAAAAT
1 AAAATCTTATCTTGTTTTTAAAAATCCTGTTCGAGGTCTCTGGTAGAGAGATTTCAATTCAAAAT
* * *
131 CATATCTTGTTTTTAAAATCCTGTTCGAAGTCTCTAATAGAGAGTTTTTCAATATC-AAATCTT-
66 CATATCTTGTTTTTAAAATCCTGATAGAAGTCTCTAATAGAGAG-TTTTCAAT-TCAAAATATTA
*
194 GCTTTGTTTTT
129 TC-TTGTTTTT
*
205 AAAATCTTATCTTGTTTTT-AAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAAT
1 AAAATCTTATCTTGTTTTTAAAAATCCTGTTCGAGGTCTCTGGTAGAGAGATTTCAATTCAAAAT
* *
269 CATATCTTGTTTTTAAAATCCTGATAGAGGTCTCTGATAGAGAGTTTTCAATTCAAAATATTATC
66 CATATCTTGTTTTTAAAATCCTGATAGAAGTCTCTAATAGAGAGTTTTCAATTCAAAATATTATC
334 TTGTTTTT
131 TTGTTTTT
342 AAAATCTT
1 AAAATCTT
350 GTTCGAGGTC
Statistics
Matches: 134, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
136 2 0.01
137 30 0.22
138 84 0.63
139 18 0.13
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (138 bp):
AAAATCTTATCTTGTTTTTAAAAATCCTGTTCGAGGTCTCTGGTAGAGAGATTTCAATTCAAAAT
CATATCTTGTTTTTAAAATCCTGATAGAAGTCTCTAATAGAGAGTTTTCAATTCAAAATATTATC
TTGTTTTT
Found at i:299 original size:59 final size:59
Alignment explanation
Indices: 205--465 Score: 377
Period size: 59 Copynumber: 4.4 Consensus size: 59
195 CTTTGTTTTT
* *
205 AAAATCTTATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATTC
1 AAAATCATATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGATAGAGAGTTTTCAATTC
* *
264 AAAATCATATCTTGTTTTTAAAATCCTGATAGAGGTCTCTGATAGAGAGTTTTCAATTC
1 AAAATCATATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGATAGAGAGTTTTCAATTC
* * *
323 AAAAT-ATTATCTTGTTTTTAAAATCTTGTTCGAGGTCTCTGGTAGAGAGATTTCAATTC
1 AAAATCA-TATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGATAGAGAGTTTTCAATTC
* *
382 AAAATCATATCTTGTTTTTAAAATCCTGTTCGAAGTCTCTAATAGAGAGGTTTTCAATATC
1 AAAATCATATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGATAGAGA-GTTTTCAAT-TC
443 -AAATC-T-TGCTTGTTTTTAAAATC
1 AAAATCATAT-CTTGTTTTTAAAATC
466 TTATCTTGTT
Statistics
Matches: 183, Mismatches: 14, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
58 2 0.01
59 165 0.90
60 14 0.08
61 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (59 bp):
AAAATCATATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGATAGAGAGTTTTCAATTC
Found at i:420 original size:118 final size:119
Alignment explanation
Indices: 205--700 Score: 421
Period size: 118 Copynumber: 4.0 Consensus size: 119
195 CTTTGTTTTT
* * *
205 AAAATCTTATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATC
1 AAAATATTATCTTGTTTTTAAAATCTTGTTCGAGGTCTCTGGTAGAGAGATTTCAATTCAAAATC
* * *
270 ATATCTTGTTTTTAAAATCCTGATAGAGGTCTCTGATAGAGAGTTTTCAAT-TC
66 ATATCTTGTTTTTAAAATCCTGTTCGAAGTCTCTGATAGAGAGTTTTCAATATC
323 AAAATATTATCTTGTTTTTAAAATCTTGTTCGAGGTCTCTGGTAGAGAGATTTCAATTCAAAATC
1 AAAATATTATCTTGTTTTTAAAATCTTGTTCGAGGTCTCTGGTAGAGAGATTTCAATTCAAAATC
*
388 ATATCTTGTTTTTAAAATCCTGTTCGAAGTCTCTAATAGAGAGGTTTTCAATATC
66 ATATCTTGTTTTTAAAATCCTGTTCGAAGTCTCTGATAGAGA-GTTTTCAATATC
* * ** ** * * *
443 -AAATCTT-GCTTGTTTTTAAAATCTTATCTTGTTTTTAAAATC-CTGTTCGAG-GTCTCTGGTA
1 AAAATATTATCTTGTTTTT-AAA----ATCTTG--TTCGAGGTCTCTGGTAGAGAG-AT-T--T-
* * * * * * ***** **** * **
504 GAGAGTTTTC-AATTCAAAATCATATCTTGTTTTTAAAATCCTGATAGAGGTCTCTGATAGAGAG
54 CA-A---TTCAAAATC-ATATCTTGTTTTTAAAATCCTGTTCGAA-----GTCTCTGATAGAGAG
568 TTTTCAAT-TC
109 TTTTCAATATC
578 AAAATATTATCTTGTTTTTAAAATCTTGTTCGAGGTCTCTGGTAGAGAGATTTCAATTCAAAATC
1 AAAATATTATCTTGTTTTTAAAATCTTGTTCGAGGTCTCTGGTAGAGAGATTTCAATTCAAAATC
643 ATATCTTGTTTTTAAAATCCTGTTCGAAGTCTCTGATAGAGAGTTTTTCAATATC
66 ATATCTTGTTTTTAAAATCCTGTTCGAAGTCTCTGATAGAGAG-TTTTCAATATC
698 AAA
1 AAA
701 TCTTGGTCTC
Statistics
Matches: 285, Mismatches: 62, Indels: 60
0.70 0.15 0.15
Matches are distributed among these distances:
118 124 0.44
119 26 0.09
120 7 0.02
123 22 0.08
124 12 0.04
125 6 0.02
126 1 0.00
127 2 0.01
128 2 0.01
129 1 0.00
130 6 0.02
131 12 0.04
132 22 0.08
135 2 0.01
136 18 0.06
137 22 0.08
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (119 bp):
AAAATATTATCTTGTTTTTAAAATCTTGTTCGAGGTCTCTGGTAGAGAGATTTCAATTCAAAATC
ATATCTTGTTTTTAAAATCCTGTTCGAAGTCTCTGATAGAGAGTTTTCAATATC
Found at i:466 original size:18 final size:19
Alignment explanation
Indices: 443--484 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
433 TTTCAATATC
443 AAATCTT-GCTTGTTTTTA
1 AAATCTTAGCTTGTTTTTA
*
461 AAATCTTATCTTGTTTTTA
1 AAATCTTAGCTTGTTTTTA
480 AAATC
1 AAATC
485 CTGTTCGAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.29, C:0.12, G:0.07, T:0.52
Consensus pattern (19 bp):
AAATCTTAGCTTGTTTTTA
Found at i:470 original size:137 final size:137
Alignment explanation
Indices: 323--604 Score: 451
Period size: 137 Copynumber: 2.1 Consensus size: 137
313 TTTTCAATTC
* *
323 AAAATATTATCTTGTTTTTAAAATCTTGTTCGAGGTCTCTGGTAGAGAGATTTCAATTCAAAATC
1 AAAATCTTATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGATTTCAATTCAAAATC
* * *
388 ATATCTTGTTTTTAAAATCCTGTTCGAAGTCTCTAATAGAGAGGTTTTCAATATC-AAATCTT-G
66 ATATCTTGTTTTTAAAATCCTGATAGAAGTCTCTAATAGAGA-GTTTTCAAT-TCAAAATATTAG
451 CTTGTTTTT
129 CTTGTTTTT
*
460 AAAATCTTATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATC
1 AAAATCTTATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGATTTCAATTCAAAATC
* * *
525 ATATCTTGTTTTTAAAATCCTGATAGAGGTCTCTGATAGAGAGTTTTCAATTCAAAATATTATCT
66 ATATCTTGTTTTTAAAATCCTGATAGAAGTCTCTAATAGAGAGTTTTCAATTCAAAATATTAGCT
590 TGTTTTT
131 TGTTTTT
597 AAAATCTT
1 AAAATCTT
605 GTTCGAGGTC
Statistics
Matches: 134, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
135 2 0.01
136 15 0.11
137 117 0.87
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (137 bp):
AAAATCTTATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGATTTCAATTCAAAATC
ATATCTTGTTTTTAAAATCCTGATAGAAGTCTCTAATAGAGAGTTTTCAATTCAAAATATTAGCT
TGTTTTT
Found at i:473 original size:78 final size:78
Alignment explanation
Indices: 382--543 Score: 240
Period size: 78 Copynumber: 2.1 Consensus size: 78
372 ATTTCAATTC
382 AAAATCATATCTTGTTTTTAAAATCCTGTTCGAAGTCTCTAATAGAGAGGTTTTCAATATC-AAA
1 AAAATCATATCTTGTTTTTAAAATCCTGTTCGAAGTCTCTAATAGAGA-GTTTTCAAT-TCAAAA
446 TC-T-TGCTTGTTTTT
64 TCATAT-CTTGTTTTT
* * **
460 AAAATCTTATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATC
1 AAAATCATATCTTGTTTTTAAAATCCTGTTCGAAGTCTCTAATAGAGAGTTTTCAATTCAAAATC
525 ATATCTTGTTTTT
66 ATATCTTGTTTTT
538 AAAATC
1 AAAATC
544 CTGATAGAGG
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
76 2 0.03
77 14 0.18
78 60 0.78
79 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (78 bp):
AAAATCATATCTTGTTTTTAAAATCCTGTTCGAAGTCTCTAATAGAGAGTTTTCAATTCAAAATC
ATATCTTGTTTTT
Found at i:508 original size:196 final size:196
Alignment explanation
Indices: 264--661 Score: 590
Period size: 196 Copynumber: 2.0 Consensus size: 196
254 TTTTCAATTC
264 AAAATCATATCTTGTTTTTAAAATCCTGATAGAGGTCTCTGATAGAGAGTTTTCAATTCAAAAT-
1 AAAATCATATCTTGTTTTTAAAATCCTGATAGAGGTCTCTGATAGAGAGTTTTCAATTCAAAATC
* * * *
328 ATTATCTTGTTTTTAAAATCTTGTTCGAGGTCTCTGGTAGAGAGATTTCAATTCAAAATCA-TAT
66 A-TATCTTGTTTTTAAAATCCTGATAGAGGTCTCTGATAGAGAGATTTCAATTCAAAAT-ATTAT
*
392 CTTGTTTTTAAAATCCTGTTCGAAGTCTCTAATAGAGAGGTTTTCAATATC-AAATC-T-TGCTT
129 CTTGTTTTTAAAATCCTGTTCGAAGTCTCTAATAGAGA-GATTTCAAT-TCAAAATCATAT-CTT
454 GTTTTT
191 GTTTTT
* * * *
460 AAAATCTTATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATC
1 AAAATCATATCTTGTTTTTAAAATCCTGATAGAGGTCTCTGATAGAGAGTTTTCAATTCAAAATC
*
525 ATATCTTGTTTTTAAAATCCTGATAGAGGTCTCTGATAGAGAGTTTTCAATTCAAAATATTATCT
66 ATATCTTGTTTTTAAAATCCTGATAGAGGTCTCTGATAGAGAGATTTCAATTCAAAATATTATCT
* * **
590 TGTTTTTAAAATCTTGTTCGAGGTCTCTGGTAGAGAGATTTCAATTCAAAATCATATCTTGTTTT
131 TGTTTTTAAAATCCTGTTCGAAGTCTCTAATAGAGAGATTTCAATTCAAAATCATATCTTGTTTT
655 T
196 T
656 AAAATC
1 AAAATC
662 CTGTTCGAAG
Statistics
Matches: 183, Mismatches: 14, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
194 2 0.01
195 14 0.08
196 165 0.90
197 2 0.01
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (196 bp):
AAAATCATATCTTGTTTTTAAAATCCTGATAGAGGTCTCTGATAGAGAGTTTTCAATTCAAAATC
ATATCTTGTTTTTAAAATCCTGATAGAGGTCTCTGATAGAGAGATTTCAATTCAAAATATTATCT
TGTTTTTAAAATCCTGTTCGAAGTCTCTAATAGAGAGATTTCAATTCAAAATCATATCTTGTTTT
T
Found at i:523 original size:59 final size:59
Alignment explanation
Indices: 460--704 Score: 375
Period size: 59 Copynumber: 4.1 Consensus size: 59
450 GCTTGTTTTT
*
460 AAAATCTTATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATTC
1 AAAATCTTATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGATAGAGAGTTTTCAATTC
* * *
519 AAAATCATATCTTGTTTTTAAAATCCTGATAGAGGTCTCTGATAGAGAGTTTTCAATTC
1 AAAATCTTATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGATAGAGAGTTTTCAATTC
* * * *
578 AAAATATTATCTTGTTTTTAAAATCTTGTTCGAGGTCTCTGGTAGAGAGATTTCAATTC
1 AAAATCTTATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGATAGAGAGTTTTCAATTC
* *
637 AAAATCATATCTTGTTTTTAAAATCCTGTTCGAAGTCTCTGATAGAGAGTTTTTCAATATC
1 AAAATCTTATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGATAGAGAG-TTTTCAAT-TC
698 -AAATCTT
1 AAAATCTT
705 GGTCTCTGAT
Statistics
Matches: 166, Mismatches: 18, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
59 151 0.91
60 13 0.08
61 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (59 bp):
AAAATCTTATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGATAGAGAGTTTTCAATTC
Found at i:562 original size:255 final size:255
Alignment explanation
Indices: 1--1179 Score: 1641
Period size: 255 Copynumber: 4.6 Consensus size: 255
*
1 CAATTCAAAATCATATCTCGTTTTTAAAATCCTGATAGAGGTCTCTGATAGAGAGTTTTCAATTC
1 CAATTCAAAATCATATCTTGTTTTTAAAATCCTGATAGAGGTCTCTGATAGAGAGTTTTCAATTC
66 AAAATATTATCTTGTTTTTAAAAATCTTGTTCGAGGTCTCTGGTAGAGAGATTTCAATTCAAAAT
66 AAAATATTATCTTGTTTTT-AAAATCTTGTTCGAGGTCTCTGGTAGAGAGATTTCAATTCAAAAT
*
131 CATATCTTGTTTTTAAAATCCTGTTCGAAGTCTCTAATAGAGAGTTTTTCAATATCAAATCTTGC
130 CATATCTTGTTTTTAAAATCCTGTTCGAAGTCTCTAATAGAGAGGTTTTCAATATCAAATCTTGC
196 TTTGTTTTTAAAATCTTATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTT
195 -TTGTTTTTAAAATCTTATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTT
258 CAATTCAAAATCATATCTTGTTTTTAAAATCCTGATAGAGGTCTCTGATAGAGAGTTTTCAATTC
1 CAATTCAAAATCATATCTTGTTTTTAAAATCCTGATAGAGGTCTCTGATAGAGAGTTTTCAATTC
323 AAAATATTATCTTGTTTTTAAAATCTTGTTCGAGGTCTCTGGTAGAGAGATTTCAATTCAAAATC
66 AAAATATTATCTTGTTTTTAAAATCTTGTTCGAGGTCTCTGGTAGAGAGATTTCAATTCAAAATC
388 ATATCTTGTTTTTAAAATCCTGTTCGAAGTCTCTAATAGAGAGGTTTTCAATATCAAATCTTGCT
131 ATATCTTGTTTTTAAAATCCTGTTCGAAGTCTCTAATAGAGAGGTTTTCAATATCAAATCTTGCT
453 TGTTTTTAAAATCTTATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTT
196 TGTTTTTAAAATCTTATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTT
513 CAATTCAAAATCATATCTTGTTTTTAAAATCCTGATAGAGGTCTCTGATAGAGAGTTTTCAATTC
1 CAATTCAAAATCATATCTTGTTTTTAAAATCCTGATAGAGGTCTCTGATAGAGAGTTTTCAATTC
578 AAAATATTATCTTGTTTTTAAAATCTTGTTCGAGGTCTCTGGTAGAGAGATTTCAATTCAAAATC
66 AAAATATTATCTTGTTTTTAAAATCTTGTTCGAGGTCTCTGGTAGAGAGATTTCAATTCAAAATC
* *
643 ATATCTTGTTTTTAAAATCCTGTTCGAAGTCTCTGATAGAGAGTTTTTCAATATCAAATCTTGGT
131 ATATCTTGTTTTTAAAATCCTGTTCGAAGTCTCTAATAGAGAGGTTTTCAATATCAAATCTT-G-
* * *
708 CTCTGATAGAGAGTTTTCAATTCAAAATATTATCTTGTTTTTAAAATCCTGTTTGAGGTCTCTGA
194 --CT--T-----G-TTT---TT-AAAATCTTATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGG
773 TAGAGAGTTTT
245 TAGAGAGTTTT
* * * *
784 CAATTC-AAATCTTGTCTTGTTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTC
1 CAATTCAAAATCATATCTTGTTTTTAAAATCCTGATAGAGGTCTCTGATAGAGAGTTTTCAATTC
* * * * * * * *
848 AAAATCTTGTCTTGTTTTTAAAATCCTGCTCGAGGTCTCTGATAGAGAGTTTTCAATTCAAATTT
66 AAAATATTATCTTGTTTTTAAAATCTTGTTCGAGGTCTCTGGTAGAGAGATTTCAATTCAAAATC
* * * *
913 TTGTCTTG-TTTTAAAATCCTGTTCGAGGTCTCTGATAGAGA-GTTTTCAAT-TCAAA---T-CT
131 ATATCTTGTTTTTAAAATCCTGTTCGAAGTCTCTAATAGAGAGGTTTTCAATATCAAATCTTGCT
* * *
971 TG--------------TCTTGTTTTAAAAATCCTGATCGAGGTCTCTGGAAGAGAGTTTT
196 TGTTTTTAAAATCTTATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTT
* * * * *
1017 CGATTCAAAACCATGTCTTGTTTTTAAAATCCTGTTTGAGGTCTCTGATAGAGAGTTTTCAATTC
1 CAATTCAAAATCATATCTTGTTTTTAAAATCCTGATAGAGGTCTCTGATAGAGAGTTTTCAATTC
* * * * * *
1082 AAAAATTTTGTCTTGTTTTT-AAATCCTGTTAGAGGTCTCTGGTAGAGAGTTTTCATTTCAAAAT
66 -AAAATATTATCTTGTTTTTAAAATCTTGTTCGAGGTCTCTGGTAGAGAGATTTCAATTCAAAAT
* * * * *
1146 CTTGTCTTG-TTTTAAAATCCCGGTCGAGGTCTCT
130 CATATCTTGTTTTTAAAATCCTGTTCGAAGTCTCT
1180 GATTGAAGGT
Statistics
Matches: 861, Mismatches: 43, Indels: 59
0.89 0.04 0.06
Matches are distributed among these distances:
233 44 0.05
234 123 0.14
235 18 0.02
252 1 0.00
255 251 0.29
256 110 0.13
257 84 0.10
259 4 0.00
261 1 0.00
264 1 0.00
266 1 0.00
267 8 0.01
268 8 0.01
269 32 0.04
270 119 0.14
271 56 0.07
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (255 bp):
CAATTCAAAATCATATCTTGTTTTTAAAATCCTGATAGAGGTCTCTGATAGAGAGTTTTCAATTC
AAAATATTATCTTGTTTTTAAAATCTTGTTCGAGGTCTCTGGTAGAGAGATTTCAATTCAAAATC
ATATCTTGTTTTTAAAATCCTGTTCGAAGTCTCTAATAGAGAGGTTTTCAATATCAAATCTTGCT
TGTTTTTAAAATCTTATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTT
Found at i:733 original size:94 final size:92
Alignment explanation
Indices: 611--797 Score: 304
Period size: 94 Copynumber: 2.0 Consensus size: 92
601 TCTTGTTCGA
*
611 GGTCTCTGGTAGAGAGATTTCAATTCAAAATCA-TATCTTGTTTTTAAAATCCTGTTCGAAGTCT
1 GGTCTCTGATAGAGAGATTTCAATTCAAAAT-ATTATCTTGTTTTTAAAATCCTGTTCGAAGTCT
675 CTGATAGAGAGTTTTTCAATATCAAATCTT
65 CTGATAGAGAG-TTTTCAAT-TCAAATCTT
* * *
705 GGTCTCTGATAGAGAGTTTTCAATTCAAAATATTATCTTGTTTTTAAAATCCTGTTTGAGGTCTC
1 GGTCTCTGATAGAGAGATTTCAATTCAAAATATTATCTTGTTTTTAAAATCCTGTTCGAAGTCTC
770 TGATAGAGAGTTTTCAATTCAAATCTT
66 TGATAGAGAGTTTTCAATTCAAATCTT
797 G
1 G
798 TCTTGTTTTT
Statistics
Matches: 88, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
92 10 0.11
93 9 0.10
94 69 0.78
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.41
Consensus pattern (92 bp):
GGTCTCTGATAGAGAGATTTCAATTCAAAATATTATCTTGTTTTTAAAATCCTGTTCGAAGTCTC
TGATAGAGAGTTTTCAATTCAAATCTT
Found at i:893 original size:211 final size:210
Alignment explanation
Indices: 493--910 Score: 687
Period size: 211 Copynumber: 2.0 Consensus size: 210
483 TCCTGTTCGA
*
493 GGTCTCTGGTAGAGAGTTTTCAATTCAAAATCATATCTTGTTTTTAAAATCCTGATAGAGGTCTC
1 GGTCTCTGATAGAGAGTTTTCAATTCAAAATCATATCTTGTTTTTAAAATCCTGATAGAGGTCTC
* *
558 TGATAGAGAGTTTTCAATTCAAAATATTATCTTGTTTTTAAAATCTTGTTCGAGGTCTCTGGTAG
66 TGATAGAGAGTTTTCAATTCAAAATATTATCTTGTTTTTAAAATCCTGATCGAGGTCTCTGGTAG
*
623 AGAGATTTCAATTCAAAATCATATCTTGTTTTTAAAATCCTGTTCGAAGTCTCTGATAGAGAGTT
131 AGAGATTTCAATTCAAAATCATATCTTGTTTTTAAAATCCTGCTCGAAGTCTCTGATAGAGAG-T
688 TTTCAATATCAAATCTT
195 TTTCAAT-TCAAATCTT
* *
705 GGTCTCTGATAGAGAGTTTTCAATTCAAAAT-ATTATCTTGTTTTTAAAATCCTGTTTGAGGTCT
1 GGTCTCTGATAGAGAGTTTTCAATTCAAAATCA-TATCTTGTTTTTAAAATCCTGATAGAGGTCT
* *
769 CTGATAGAGAGTTTTCAATTC-AAATCTTGTCTTGTTTTTAAAATCCTGATCGAGGTCTCTGGTA
65 CTGATAGAGAGTTTTCAATTCAAAATATTATCTTGTTTTTAAAATCCTGATCGAGGTCTCTGGTA
* * * *
833 GAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCCTGCTCGAGGTCTCTGATAGAGAGT
130 GAGAGATTTCAATTCAAAATCATATCTTGTTTTTAAAATCCTGCTCGAAGTCTCTGATAGAGAGT
898 TTTCAATTCAAAT
195 TTTCAATTCAAAT
911 TTTTGTCTTG
Statistics
Matches: 193, Mismatches: 12, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
209 6 0.03
210 8 0.04
211 99 0.51
212 80 0.41
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (210 bp):
GGTCTCTGATAGAGAGTTTTCAATTCAAAATCATATCTTGTTTTTAAAATCCTGATAGAGGTCTC
TGATAGAGAGTTTTCAATTCAAAATATTATCTTGTTTTTAAAATCCTGATCGAGGTCTCTGGTAG
AGAGATTTCAATTCAAAATCATATCTTGTTTTTAAAATCCTGCTCGAAGTCTCTGATAGAGAGTT
TTCAATTCAAATCTT
Found at i:1200 original size:117 final size:118
Alignment explanation
Indices: 705--1182 Score: 716
Period size: 117 Copynumber: 4.1 Consensus size: 118
695 ATCAAATCTT
* * *
705 GGTCTCTGATAGAGAGTTTTCAATTCAAAATATTATCTTGTTTTTAAAATCCTGTTTGAGGTCTC
1 GGTCTCTGATAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCCTGTTCGAGGTCTC
*
770 TGATAGAGAGTTTTCAATTC-AAATCTTGTCTTGTTTTTAAAATCCTGATCGA
66 TGATAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCCTGTTCGA
* *
822 GGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCCTGCTCGAGGTCTC
1 GGTCTCTGATAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCCTGTTCGAGGTCTC
* *
887 TGATAGAGAGTTTTCAATTCAAATTTTTGTCTTG-TTTTAAAATCCTGTTCGA
66 TGATAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCCTGTTCGA
* *
939 GGTCTCTGATAGAGAGTTTTCAATTC-AAATCTTGTCTTGTTTTAAAAATCCTGATCGAGGTCTC
1 GGTCTCTGATAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCCTGTTCGAGGTCTC
* * * *
1003 TGGA-AGAGAGTTTTCGATTCAAAACCATGTCTTGTTTTTAAAATCCTGTTTGA
66 T-GATAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCCTGTTCGA
* *
1056 GGTCTCTGATAGAGAGTTTTCAATTCAAAAATTTTGTCTTGTTTTT-AAATCCTGTTAGAGGTCT
1 GGTCTCTGATAGAGAGTTTTCAATTC-AAAATCTTGTCTTGTTTTTAAAATCCTGTTCGAGGTCT
* * * *
1120 CTGGTAGAGAGTTTTCATTTCAAAATCTTGTCTTG-TTTTAAAATCCCGGTCGA
65 CTGATAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCCTGTTCGA
1173 GGTCTCTGAT
1 GGTCTCTGAT
1183 TGAAGGTTTA
Statistics
Matches: 326, Mismatches: 29, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
116 62 0.19
117 193 0.59
118 55 0.17
119 16 0.05
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42
Consensus pattern (118 bp):
GGTCTCTGATAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCCTGTTCGAGGTCTC
TGATAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCCTGTTCGA
Found at i:1201 original size:58 final size:59
Alignment explanation
Indices: 705--1182 Score: 716
Period size: 59 Copynumber: 8.2 Consensus size: 59
695 ATCAAATCTT
* * *
705 GGTCTCTGATAGAGAGTTTTCAATTCAAAATATTATCTTGTTTTTAAAATCCTGTTTGA
1 GGTCTCTGATAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCCTGTTCGA
*
764 GGTCTCTGATAGAGAGTTTTCAATTC-AAATCTTGTCTTGTTTTTAAAATCCTGATCGA
1 GGTCTCTGATAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCCTGTTCGA
* *
822 GGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCCTGCTCGA
1 GGTCTCTGATAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCCTGTTCGA
* *
881 GGTCTCTGATAGAGAGTTTTCAATTCAAATTTTTGTCTTG-TTTTAAAATCCTGTTCGA
1 GGTCTCTGATAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCCTGTTCGA
* *
939 GGTCTCTGATAGAGAGTTTTCAATTC-AAATCTTGTCTTGTTTTAAAAATCCTGATCGA
1 GGTCTCTGATAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCCTGTTCGA
* * * *
997 GGTCTCTGGA-AGAGAGTTTTCGATTCAAAACCATGTCTTGTTTTTAAAATCCTGTTTGA
1 GGTCTCT-GATAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCCTGTTCGA
* *
1056 GGTCTCTGATAGAGAGTTTTCAATTCAAAAATTTTGTCTTGTTTTT-AAATCCTGTTAGA
1 GGTCTCTGATAGAGAGTTTTCAATTC-AAAATCTTGTCTTGTTTTTAAAATCCTGTTCGA
* * * *
1115 GGTCTCTGGTAGAGAGTTTTCATTTCAAAATCTTGTCTTG-TTTTAAAATCCCGGTCGA
1 GGTCTCTGATAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCCTGTTCGA
1173 GGTCTCTGAT
1 GGTCTCTGAT
1183 TGAAGGTTTA
Statistics
Matches: 380, Mismatches: 32, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
57 15 0.04
58 168 0.44
59 181 0.48
60 16 0.04
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42
Consensus pattern (59 bp):
GGTCTCTGATAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCCTGTTCGA
Found at i:1474 original size:29 final size:27
Alignment explanation
Indices: 1419--1492 Score: 96
Period size: 29 Copynumber: 2.7 Consensus size: 27
1409 CTTGTCTCTT
* *
1419 ATTTTGGTCATTTGTGCATTCAGGGGC
1 ATTTTGGTCATTTTTGCATTCAAGGGC
*
1446 ATTTTGGTCATTTTTGCACATTTAAGGGC
1 ATTTTGGTCATTTTTG--CATTCAAGGGC
1475 ATTTTGGTCA-TTTTGCAT
1 ATTTTGGTCATTTTTGCAT
1493 ACCCAGGGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 3 0.07
27 15 0.36
28 5 0.12
29 19 0.45
ACGTcount: A:0.18, C:0.14, G:0.23, T:0.46
Consensus pattern (27 bp):
ATTTTGGTCATTTTTGCATTCAAGGGC
Found at i:7013 original size:53 final size:52
Alignment explanation
Indices: 6905--7025 Score: 140
Period size: 53 Copynumber: 2.3 Consensus size: 52
6895 GTTGGTAGTG
* *
6905 GAAAGACTTTCCATGGTTTGGTTGAATTAAAACATGTGGGAAAGTAAAGGATA
1 GAAA-ACTTTCCATGGTTTGGTTAAATTAAAACAGGTGGGAAAGTAAAGGATA
*
6958 GAAATACTTTCCATGGTTTTGGTTAAATTAAATTA-AGGTGGG-AAGT-AAGGGTA
1 GAAA-ACTTTCCATGG-TTTGGTTAAATTAAA--ACAGGTGGGAAAGTAAAGGATA
*
7011 GAAAACTTCCCATGG
1 GAAAACTTTCCATGG
7026 AGGAGTAGGG
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
52 10 0.17
53 25 0.42
54 18 0.30
55 6 0.10
56 1 0.02
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.30
Consensus pattern (52 bp):
GAAAACTTTCCATGGTTTGGTTAAATTAAAACAGGTGGGAAAGTAAAGGATA
Found at i:7614 original size:54 final size:54
Alignment explanation
Indices: 7532--7634 Score: 206
Period size: 54 Copynumber: 1.9 Consensus size: 54
7522 AGTTTCAATC
7532 ATAAACCGAAAAACCCGACGCGAATGCGCGAGGATAATATATATATATATATAT
1 ATAAACCGAAAAACCCGACGCGAATGCGCGAGGATAATATATATATATATATAT
7586 ATAAACCGAAAAACCCGACGCGAATGCGCGAGGATAATATATATATATA
1 ATAAACCGAAAAACCCGACGCGAATGCGCGAGGATAATATATATATATA
7635 ATAGGTATAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.20
Consensus pattern (54 bp):
ATAAACCGAAAAACCCGACGCGAATGCGCGAGGATAATATATATATATATATAT
Found at i:8944 original size:118 final size:117
Alignment explanation
Indices: 8759--8992 Score: 387
Period size: 118 Copynumber: 2.0 Consensus size: 117
8749 GGAGTGAGTC
* *
8759 ATAGAGGTGAATCCGTATATATAGTCATATATAAAGTATAACGGAAATTACAATAATTATCGTCA
1 ATAGAAGTGAATCCATATATATAGTCATATATAAAGTATAACGGAAATTACAATAATTATCGTCA
* * *
8824 TTTAGTATCATTGATATTTGATATTAAGATAAAAAAACAAACCAATAATTATT
66 TTTAGTATCATTAATATCTAATATTAAGAT-AAAAAACAAACCAATAATTATT
*
8877 ATAGAAGTGAATCCATATATATAGTCATATATAAAGTATAACGGAAATTACAATAATTATTGTCA
1 ATAGAAGTGAATCCATATATATAGTCATATATAAAGTATAACGGAAATTACAATAATTATCGTCA
* *
8942 TTTATTATCATTAATATCTAATATTAAGATAAAAAACAAATCAATAATTAT
66 TTTAGTATCATTAATATCTAATATTAAGATAAAAAACAAACCAATAATTAT
8993 AAGAATTAAT
Statistics
Matches: 108, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
117 20 0.19
118 88 0.81
ACGTcount: A:0.47, C:0.09, G:0.10, T:0.35
Consensus pattern (117 bp):
ATAGAAGTGAATCCATATATATAGTCATATATAAAGTATAACGGAAATTACAATAATTATCGTCA
TTTAGTATCATTAATATCTAATATTAAGATAAAAAACAAACCAATAATTATT
Found at i:11079 original size:2 final size:2
Alignment explanation
Indices: 11074--11149 Score: 61
Period size: 2 Copynumber: 39.5 Consensus size: 2
11064 ATTGTGATGT
* * * *
11074 TA TA TA TA TA TA TA TA T- TA TA TA TA TT TA GA AA TA -A TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
11114 GGA TA TG TA T- TA TA TA -A TA TA TA TA TA TA TA TA TA T
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11150 TATGTAAAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 10
0.75 0.13 0.13
Matches are distributed among these distances:
1 4 0.07
2 54 0.92
3 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (2 bp):
TA
Found at i:11080 original size:17 final size:16
Alignment explanation
Indices: 11058--11100 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
11048 ATATAGTATA
* *
11058 ATATATATTGTGATGTT
1 ATATATATTAT-ATATT
11075 ATATATATATATATATT
1 ATATATAT-TATATATT
11092 ATATATATT
1 ATATATATT
11101 TAGAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 1 0.04
17 20 0.87
18 2 0.09
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (16 bp):
ATATATATTATATATT
Found at i:11726 original size:1 final size:1
Alignment explanation
Indices: 11720--11762 Score: 77
Period size: 1 Copynumber: 43.0 Consensus size: 1
11710 TAATGTTGTC
*
11720 AAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11763 CCTTAATTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.98, C:0.02, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:32528 original size:22 final size:22
Alignment explanation
Indices: 32502--32550 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
32492 TCGAACTCAT
*
32502 GCCTTTTGAATGAACTTTTGAG
1 GCCTTTCGAATGAACTTTTGAG
* *
32524 GCCTTTCGGATGAATTTTTGAG
1 GCCTTTCGAATGAACTTTTGAG
32546 GCCTT
1 GCCTT
32551 GACCATTAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.18, C:0.16, G:0.24, T:0.41
Consensus pattern (22 bp):
GCCTTTCGAATGAACTTTTGAG
Found at i:33330 original size:37 final size:35
Alignment explanation
Indices: 33252--33418 Score: 237
Period size: 37 Copynumber: 4.7 Consensus size: 35
33242 ATGTTTTATA
*
33252 ATGGGAACTTTCCCAATTTGGAAACTG-AAACTTG
1 ATGGGAACTTTCCCAATTTGAAAACTGAAAACTTG
33286 ATGGGAACTTTCCCAATTTGAAAACTTTGAAAACTTG
1 ATGGGAACTTTCCCAATTTGAAAAC--TGAAAACTTG
* *
33323 ATAGGAACTTTCCCAATTCGAAAACTGAAAACTTG
1 ATGGGAACTTTCCCAATTTGAAAACTGAAAACTTG
* *
33358 GTGGGAACTTTCCCATTTTGAAAACTTTGAAAACTTG
1 ATGGGAACTTTCCCAATTTGAAAAC--TGAAAACTTG
*
33395 ATGAGAACTTTCCCAATTTGAAAA
1 ATGGGAACTTTCCCAATTTGAAAA
33419 GAGCTAAAAG
Statistics
Matches: 118, Mismatches: 10, Indels: 7
0.87 0.07 0.05
Matches are distributed among these distances:
34 24 0.20
35 31 0.26
36 2 0.02
37 61 0.52
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (35 bp):
ATGGGAACTTTCCCAATTTGAAAACTGAAAACTTG
Found at i:33336 original size:71 final size:71
Alignment explanation
Indices: 33255--33418 Score: 267
Period size: 72 Copynumber: 2.3 Consensus size: 71
33245 TTTTATAATG
*
33255 GGAACTTTCCCAATTTGGAAACTG-AAACTTGATGGGAACTTTCCCAATTTGAAAACTTTGAAAA
1 GGAACTTTCCCAATTTGAAAACTGAAAACTTGATGGGAACTTTCCCAATTTGAAAACTTTGAAAA
33319 CTTGAT
66 CTTGAT
* * *
33325 AGGAACTTTCCCAATTCGAAAACTGAAAACTTGGTGGGAACTTTCCCATTTTGAAAACTTTGAAA
1 -GGAACTTTCCCAATTTGAAAACTGAAAACTTGATGGGAACTTTCCCAATTTGAAAACTTTGAAA
33390 ACTTGAT
65 ACTTGAT
33397 GAGAACTTTCCCAATTTGAAAA
1 G-GAACTTTCCCAATTTGAAAA
33419 GAGCTAAAAG
Statistics
Matches: 86, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
71 23 0.27
72 63 0.73
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30
Consensus pattern (71 bp):
GGAACTTTCCCAATTTGAAAACTGAAAACTTGATGGGAACTTTCCCAATTTGAAAACTTTGAAAA
CTTGAT
Found at i:35439 original size:2 final size:2
Alignment explanation
Indices: 35432--35463 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
35422 ATTTTGAAAG
35432 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
35464 ATGATAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41843 original size:18 final size:18
Alignment explanation
Indices: 41820--41854 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41810 TCATAACAGA
41820 AAAAAGGAAAAATTAAGG
1 AAAAAGGAAAAATTAAGG
*
41838 AAAAAGGGAAAATTAAG
1 AAAAAGGAAAAATTAAG
41855 AAGACGTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.23, T:0.11
Consensus pattern (18 bp):
AAAAAGGAAAAATTAAGG
Found at i:51941 original size:20 final size:18
Alignment explanation
Indices: 51902--51937 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
51892 CTAGCCCTTA
*
51902 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAAATAG
51920 AACTAGAAGAGAAAAATA
1 AACTAGAAGA-AAAAATA
51938 AGAAGAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (18 bp):
AACTAGAAGAAAAAATAG
Found at i:52570 original size:19 final size:18
Alignment explanation
Indices: 52537--52572 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
52527 TGGAAATAAT
52537 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
52555 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
52573 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:58771 original size:2 final size:2
Alignment explanation
Indices: 58764--58788 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
58754 GTACATAAAG
58764 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
58789 GACACACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:65618 original size:18 final size:18
Alignment explanation
Indices: 65583--65618 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
65573 AAATAAGTGG
*
65583 GAAGGAAGAAAAAGAAAA
1 GAAGGAAGAAAAAAAAAA
*
65601 GAAGGGAGAAAAAAAAAA
1 GAAGGAAGAAAAAAAAAA
65619 AAAAAACACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (18 bp):
GAAGGAAGAAAAAAAAAA
Found at i:66774 original size:12 final size:12
Alignment explanation
Indices: 66759--66798 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
66749 CGGCAGCTGC
66759 TGCTGCTACTGG
1 TGCTGCTACTGG
66771 TGCTGCTACTGCG
1 TGCTGCTACTG-G
*
66784 -GCTGCTTCTGG
1 TGCTGCTACTGG
66795 TGCT
1 TGCT
66799 TCCACTGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 1 0.04
12 23 0.92
13 1 0.04
ACGTcount: A:0.05, C:0.28, G:0.33, T:0.35
Consensus pattern (12 bp):
TGCTGCTACTGG
Found at i:66805 original size:24 final size:24
Alignment explanation
Indices: 66755--66805 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
66745 GCTCCGGCAG
* *
66755 CTGCTGCTGCTACTGGTGCTGCTA
1 CTGCGGCTGCTACTGGTGCTGCCA
* *
66779 CTGCGGCTGCTTCTGGTGCTTCCA
1 CTGCGGCTGCTACTGGTGCTGCCA
66803 CTG
1 CTG
66806 TTCATGGTGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.06, C:0.31, G:0.29, T:0.33
Consensus pattern (24 bp):
CTGCGGCTGCTACTGGTGCTGCCA
Found at i:69812 original size:16 final size:16
Alignment explanation
Indices: 69793--69836 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
69783 ACCCGTTCGA
*
69793 ACCCAAACCCGAAAAT
1 ACCCGAACCCGAAAAT
* *
69809 ACCCGAGCCCCAAAAT
1 ACCCGAACCCGAAAAT
69825 ACCCGAACCCGA
1 ACCCGAACCCGA
69837 GGCAGCCCGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.41, C:0.43, G:0.11, T:0.05
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:71897 original size:13 final size:12
Alignment explanation
Indices: 71861--71907 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
71851 TCAATCTTTA
*
71861 TATATATTGATAA
1 TATATATT-ATAT
*
71874 TA-ATGTTATAT
1 TATATATTATAT
71885 TATATTATTATAT
1 TATA-TATTATAT
71898 TATATATTAT
1 TATATATTAT
71908 CAATAAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:72088 original size:16 final size:16
Alignment explanation
Indices: 72050--72111 Score: 81
Period size: 16 Copynumber: 3.8 Consensus size: 16
72040 CCCGAATCGA
72050 ACCCGAACCCCGAAAAT
1 ACCCGAA-CCCGAAAAT
*
72067 ACCCGAACCC-AACAT
1 ACCCGAACCCGAAAAT
*
72082 AACCCGAGCCCGAAAAT
1 -ACCCGAACCCGAAAAT
72099 ACCCGAACCCGAA
1 ACCCGAACCCGAA
72112 CCCGCCCGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
15 4 0.10
16 24 0.62
17 11 0.28
ACGTcount: A:0.40, C:0.42, G:0.13, T:0.05
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:72556 original size:21 final size:22
Alignment explanation
Indices: 72530--72573 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
72520 ATATTGTTAT
72530 TCAATTCA-TTTTTTAACTAAA
1 TCAATTCATTTTTTTAACTAAA
72551 TCAATTCATTTTTTTAACTAAA
1 TCAATTCATTTTTTTAACTAAA
72573 T
1 T
72574 TATTGCTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (22 bp):
TCAATTCATTTTTTTAACTAAA
Found at i:76818 original size:17 final size:17
Alignment explanation
Indices: 76785--76819 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
76775 CTCCTCTTGC
*
76785 ATGAAAACACTTCTTTT
1 ATGAAAACAATTCTTTT
*
76802 ATGAAAACAATTTTTTT
1 ATGAAAACAATTCTTTT
76819 A
1 A
76820 ACTACCCTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (17 bp):
ATGAAAACAATTCTTTT
Found at i:82470 original size:22 final size:22
Alignment explanation
Indices: 82445--82570 Score: 71
Period size: 22 Copynumber: 5.7 Consensus size: 22
82435 GTAACCACAT
*
82445 TATGAAATTTTGATAACCTCCA
1 TATGAAATTTTGATAAACTCCA
* * * * *
82467 TATGAGAGTTTGGT-AATTGCA
1 TATGAAATTTTGATAAACTCCA
*
82488 CTATGAAATTTGGATAAACTCC-
1 -TATGAAATTTTGATAAACTCCA
* * *
82510 TCATGAAATTATAATAAACTTC-
1 T-ATGAAATTTTGATAAACTCCA
*
82532 TAATGAAATTTTGATAATCT-CA
1 T-ATGAAATTTTGATAAACTCCA
* *
82554 TTTTGAAAATTTGATAA
1 -TATGAAATTTTGATAA
82571 TCACACAAAG
Statistics
Matches: 77, Mismatches: 22, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
21 6 0.08
22 66 0.86
23 5 0.06
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAAACTCCA
Found at i:84487 original size:47 final size:42
Alignment explanation
Indices: 84376--84510 Score: 171
Period size: 43 Copynumber: 3.0 Consensus size: 42
84366 ATATGATAGG
*
84376 ATTTATATGCTAAAAAATTTAAAGTTGTAAGTTGAAAAACGTT
1 ATTTATATGCTAAAAAA-TTAAAGTTGTAAGTTGAAAAAAGTT
*
84419 ATTTATATGCTAAAAAAATTAAAGTTGTAAGTTGAAATCTAGAATTT
1 ATTTATATGCT-AAAAAATTAAAGTTGTAAGTTGAAA---A-AAGTT
* *
84466 ATTTATATGCTAAAAACATTAAAATTGTAAGTTGACAAAAGTT
1 ATTTATATGCTAAAAA-ATTAAAGTTGTAAGTTGAAAAAAGTT
84509 AT
1 AT
84511 GTACTATAAT
Statistics
Matches: 81, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
43 36 0.44
44 7 0.09
46 6 0.07
47 32 0.40
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (42 bp):
ATTTATATGCTAAAAAATTAAAGTTGTAAGTTGAAAAAAGTT
Found at i:84820 original size:27 final size:26
Alignment explanation
Indices: 84782--84832 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 26
84772 TTTTAATGTT
84782 TAAATTTTATTTT-TCTTTTAAAAAAA
1 TAAATTTTATTTTAT-TTTTAAAAAAA
84808 TAAATTATTATTTTATTTTTAAAAA
1 TAAATT-TTATTTTATTTTTAAAAA
84833 TAAACATGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 6 0.26
27 16 0.70
28 1 0.04
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (26 bp):
TAAATTTTATTTTATTTTTAAAAAAA
Found at i:84821 original size:26 final size:25
Alignment explanation
Indices: 84782--84836 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
84772 TTTTAATGTT
*
84782 TAAATTTTATTTTTCTTTTAAAAAAA
1 TAAATTTTATTTTTATTTT-AAAAAA
*
84808 TAAATTATTA-TTTTATTTTTAAAAA
1 TAAATT-TTATTTTTATTTTAAAAAA
84833 TAAA
1 TAAA
84837 CATGGGTAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 9 0.35
26 14 0.54
27 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (25 bp):
TAAATTTTATTTTTATTTTAAAAAA
Found at i:86737 original size:2 final size:2
Alignment explanation
Indices: 86730--86758 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
86720 TGGTAAACAA
86730 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
86759 AGGATTTTTT
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:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:91355 original size:30 final size:30
Alignment explanation
Indices: 91319--91376 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
91309 AGTTCATGAT
*
91319 TGAAGATTTATTGAAG-ATAATTTCAAGACA
1 TGAAGA-TCATTGAAGAATAATTTCAAGACA
*
91349 TGAAGATCATTGAAGAATTATTTCAAGA
1 TGAAGATCATTGAAGAATAATTTCAAGA
91377 AGCAAGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (30 bp):
TGAAGATCATTGAAGAATAATTTCAAGACA
Found at i:95403 original size:41 final size:40
Alignment explanation
Indices: 95304--95408 Score: 106
Period size: 41 Copynumber: 2.5 Consensus size: 40
95294 CATAAATCAA
* *
95304 AAATAAAATCCTAAATCAGGGACAAAATTGCATCATACAAT
1 AAATAATA-CCTAAATCAGGGACAAAATTGAATCATACAAT
* * *
95345 AAATATTACCCTTAATCAGGGACAAAATTGAATCA-ATTAAT
1 AAATAATA-CCTAAATCAGGGACAAAATTGAATCATA-CAAT
95386 AAATGAGATA-CTAAATCAGGGAC
1 AAAT-A-ATACCTAAATCAGGGAC
95409 TAAGGTGAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
40 1 0.02
41 49 0.92
42 1 0.02
43 2 0.04
ACGTcount: A:0.49, C:0.15, G:0.12, T:0.24
Consensus pattern (40 bp):
AAATAATACCTAAATCAGGGACAAAATTGAATCATACAAT
Found at i:98571 original size:11 final size:11
Alignment explanation
Indices: 98555--98581 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
98545 GGGTTTAGGG
98555 TTTGACCATTT
1 TTTGACCATTT
98566 TTTGACCATTT
1 TTTGACCATTT
98577 TTTGA
1 TTTGA
98582 TAACTTTGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.19, C:0.15, G:0.11, T:0.56
Consensus pattern (11 bp):
TTTGACCATTT
Found at i:102758 original size:24 final size:24
Alignment explanation
Indices: 102726--102778 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
102716 GAGTTGAGTA
*
102726 GGAGAGAGAGCTTGATCCTAAGAG
1 GGAGAGAGAGCTTGATCATAAGAG
*
102750 GGAGAGAGAGCTTGATGATAAGAG
1 GGAGAGAGAGCTTGATCATAAGAG
102774 GGAGA
1 GGAGA
102779 TGATCAGTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.36, C:0.08, G:0.42, T:0.15
Consensus pattern (24 bp):
GGAGAGAGAGCTTGATCATAAGAG
Found at i:106544 original size:29 final size:30
Alignment explanation
Indices: 106510--106575 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
106500 ATGGCGCGGA
106510 GGATGGCACGGATGACC-GGCAGGCGGCGC
1 GGATGGCACGGATGACCGGGCAGGCGGCGC
106539 GGATGGCACGGATGACCGGGCAGGCGGCGC
1 GGATGGCACGGATGACCGGGCAGGCGGCGC
106569 GGATGGC
1 GGATGGC
106576 CGGGCAGGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 17 0.47
30 19 0.53
ACGTcount: A:0.17, C:0.26, G:0.50, T:0.08
Consensus pattern (30 bp):
GGATGGCACGGATGACCGGGCAGGCGGCGC
Found at i:106599 original size:21 final size:21
Alignment explanation
Indices: 106547--106600 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
106537 GCGGATGGCA
*
106547 CGGATGACCGGGCAGGCGGCG
1 CGGATGACCGGGCAGGCGACG
* * *
106568 CGGATGGCCGGGCAGGTGACT
1 CGGATGACCGGGCAGGCGACG
*
106589 CGGCTGACCGGG
1 CGGATGACCGGG
106601 GCATGGCCGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.13, C:0.28, G:0.50, T:0.09
Consensus pattern (21 bp):
CGGATGACCGGGCAGGCGACG
Found at i:110728 original size:11 final size:12
Alignment explanation
Indices: 110701--110728 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
110691 ACCCTTGCCT
110701 AAAAACTAGAAG
1 AAAAACTAGAAG
110713 AAAAACTAGAAG
1 AAAAACTAGAAG
110725 AAAA
1 AAAA
110729 GATCTTAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.71, C:0.07, G:0.14, T:0.07
Consensus pattern (12 bp):
AAAAACTAGAAG
Found at i:113337 original size:25 final size:25
Alignment explanation
Indices: 113303--113351 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
113293 CAAATCTCTA
*
113303 ATCTACCATGTAGTATAACAATGCC
1 ATCTACCATGAAGTATAACAATGCC
113328 ATCTACCATGAAGTATAACAATGC
1 ATCTACCATGAAGTATAACAATGC
113352 TATGCAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (25 bp):
ATCTACCATGAAGTATAACAATGCC
Found at i:113650 original size:27 final size:27
Alignment explanation
Indices: 113590--113665 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 27
113580 TTATGGACTA
113590 AAATGACCAAAATGCCCCCGTAAATGCAC
1 AAATGACCAAAATG-CCCC-TAAATGCAC
* **
113619 AAATGACCAAAATGCCCCTGAATGTGC
1 AAATGACCAAAATGCCCCTAAATGCAC
113646 AAATGACCAAAATGCCCCTA
1 AAATGACCAAAATGCCCCTA
113666 GGTGATCCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 25 0.58
28 4 0.09
29 14 0.33
ACGTcount: A:0.41, C:0.29, G:0.14, T:0.16
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTAAATGCAC
Found at i:116705 original size:142 final size:143
Alignment explanation
Indices: 116438--116722 Score: 466
Period size: 142 Copynumber: 2.0 Consensus size: 143
116428 AGCCTCTAAG
116438 AAGTGTCTTTATTCCTCTTGAAGGCTACCATTGTGGTGGTAACTCCAACTAGGGTGGTCACCATT
1 AAGTGTCTTTATTCCTCTTGAAGGCTACCATTGTGGTGGTAACTCCAACTAGGGTGGTCACCATT
* * *
116503 TGATTATAAAGAACCCATATATTAAGAGGTAGCTTGAATCATGGTGGCCGGCCTACAATGGTAAA
66 TGATTATAAAGAACCCATATATCAAGAGGTAGCTTAAATCATGGTGACCGGCCTACAATGGTAAA
116568 TCCCCCATGGTTT
131 TCCCCCATGGTTT
* *
116581 AAGTGTCTTTATTCTTCTTGAAGGCTACCATTGTGGTGGTAACTCCAAC-ATGGTGGTCACCATT
1 AAGTGTCTTTATTCCTCTTGAAGGCTACCATTGTGGTGGTAACTCCAACTAGGGTGGTCACCATT
* * * *
116645 TGATTATAAAGAACTCA-ACTATCAAGAGGTAGCTTAAATCATGGTGATCGGCTTAGAATGGTAA
66 TGATTATAAAGAACCCATA-TATCAAGAGGTAGCTTAAATCATGGTGACCGGCCTACAATGGTAA
116709 ATCCCCCATGGTTT
130 ATCCCCCATGGTTT
116723 CCTTCCCCTT
Statistics
Matches: 132, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
141 1 0.01
142 83 0.63
143 48 0.36
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (143 bp):
AAGTGTCTTTATTCCTCTTGAAGGCTACCATTGTGGTGGTAACTCCAACTAGGGTGGTCACCATT
TGATTATAAAGAACCCATATATCAAGAGGTAGCTTAAATCATGGTGACCGGCCTACAATGGTAAA
TCCCCCATGGTTT
Found at i:116909 original size:72 final size:72
Alignment explanation
Indices: 116792--117075 Score: 507
Period size: 72 Copynumber: 3.9 Consensus size: 72
116782 GGTTCATCTC
116792 AAGGTCCACTATGTGGCAAGGCATTGGTGATTGTAGCAATCTATAGCTCTCACCTTATCTTTATT
1 AAGGTCCACTATGTGGCAAGGCATTGGTGATTGTAGCAATCTATAGCTCTCACCTTATCTTTATT
116857 ATTTACA
66 ATTTACA
*
116864 AAGGTCCACTATGTGGCAAGGCATTGGTGATTGTAGCAATCTATAGCTCTCACCTTGTCTTTATT
1 AAGGTCCACTATGTGGCAAGGCATTGGTGATTGTAGCAATCTATAGCTCTCACCTTATCTTTATT
*
116929 ATTTATA
66 ATTTACA
*
116936 AAGGTCCACTATGTGGCAAGGCATTGGTGATTGTAGCAATCTATAGCTCTCACCTTGTCTTTATT
1 AAGGTCCACTATGTGGCAAGGCATTGGTGATTGTAGCAATCTATAGCTCTCACCTTATCTTTATT
117001 ATTTACA
66 ATTTACA
* *
117008 AAGGTCCACTATGTGGCAAGGCATTGGTGATTGTAGCAACCTATAGCTCTCACC-TAGTCTTCAT
1 AAGGTCCACTATGTGGCAAGGCATTGGTGATTGTAGCAATCTATAGCTCTCACCTTA-TCTTTAT
117072 TATT
65 TATT
117076 ATGGCATTTT
Statistics
Matches: 205, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
71 1 0.00
72 204 1.00
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (72 bp):
AAGGTCCACTATGTGGCAAGGCATTGGTGATTGTAGCAATCTATAGCTCTCACCTTATCTTTATT
ATTTACA
Found at i:117435 original size:147 final size:147
Alignment explanation
Indices: 117241--117543 Score: 473
Period size: 147 Copynumber: 2.1 Consensus size: 147
117231 CAGGAGAGCT
*
117241 ACTGTTCATGACCTCTGCTGGGATGTCGGACCCACTGTCAAGCACTGTTGGGACCCACAGCAAGC
1 ACTGTTCATGACCTCTGCTGGGATGTCGGACCCACTATCAAGCACTGTTGGGACCCACAGCAAGC
* * * *
117306 TGACGTGGCAACACCGGAGACATGCTGATCGTGGGGCTCACTAATAGATGGGTTTATTGTTTTCT
66 TAACGTGGCAACACCCGAGACATGCTGATAGTGGGGCTCACTAATAGATGAGTTTATTGTTTTC-
*
117371 A-CCCCTGCTGGAAGGTC
130 AGCCCCTGCTGGAAGATC
* *
117388 ACTGTTCATGACCTCTGCTGGGATGTCGGACCCACTATCAGGCACTGTTGGGACCCACGGCAAGC
1 ACTGTTCATGACCTCTGCTGGGATGTCGGACCCACTATCAAGCACTGTTGGGACCCACAGCAAGC
* *
117453 TAACGTGGCAACACCCGAGACATGCTGATAGTGGGGCTCACTAGTAGGTGAGTTTATTGTTTTCA
66 TAACGTGGCAACACCCGAGACATGCTGATAGTGGGGCTCACTAATAGATGAGTTTATTGTTTTCA
* * *
117518 GCCTCTGTTGGAAGATT
131 GCCCCTGCTGGAAGATC
117535 ACTGTTCAT
1 ACTGTTCAT
117544 CGGCCTCTAT
Statistics
Matches: 142, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
146 1 0.01
147 141 0.99
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.26
Consensus pattern (147 bp):
ACTGTTCATGACCTCTGCTGGGATGTCGGACCCACTATCAAGCACTGTTGGGACCCACAGCAAGC
TAACGTGGCAACACCCGAGACATGCTGATAGTGGGGCTCACTAATAGATGAGTTTATTGTTTTCA
GCCCCTGCTGGAAGATC
Found at i:119651 original size:15 final size:15
Alignment explanation
Indices: 119631--119668 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
119621 TCTTTAACAA
119631 CTTTCTTTGAAATCC
1 CTTTCTTTGAAATCC
119646 CTTTCTTTGAAATCC
1 CTTTCTTTGAAATCC
119661 CTTTCTTT
1 CTTTCTTT
119669 TCACCCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.16, C:0.26, G:0.05, T:0.53
Consensus pattern (15 bp):
CTTTCTTTGAAATCC
Found at i:120498 original size:11 final size:11
Alignment explanation
Indices: 120482--120543 Score: 63
Period size: 11 Copynumber: 5.6 Consensus size: 11
120472 AAATAATTTA
120482 TTATATATATT
1 TTATATATATT
*
120493 TTATATATATC
1 TTATATATATT
* *
120504 ATAAATATATT
1 TTATATATATT
120515 TTATATAT-TT
1 TTATATATATT
* *
120525 CATAAATATATT
1 -TTATATATATT
120537 TTATATA
1 TTATATA
120544 ATACCATAAT
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
10 2 0.05
11 35 0.90
12 2 0.05
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (11 bp):
TTATATATATT
Found at i:120514 original size:22 final size:22
Alignment explanation
Indices: 120486--120552 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
120476 AATTTATTAT
120486 ATATATTTTATATATATCATAA
1 ATATATTTTATATATATCATAA
*
120508 ATATATTTTATATATTTCATAA
1 ATATATTTTATATATATCATAA
*
120530 ATATATTTTATATAATACCATAA
1 ATATATTTTATAT-ATATCATAA
120553 TCGGTCGGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 34 0.83
23 7 0.17
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (22 bp):
ATATATTTTATATATATCATAA
Found at i:122108 original size:622 final size:622
Alignment explanation
Indices: 120730--122414 Score: 2903
Period size: 622 Copynumber: 2.7 Consensus size: 622
120720 CACACTAGTC
* *
120730 ATCA-CACACATGGACCTTACTGACTTGACCATCGGAGAGGGTACCCTCGGGATACACCCGGGGG
1 ATCATCACGCATGGACCCTACTGACTTGACCATCGGAGAGGGTACCCTCGGGATACACCCGGGGG
120794 TCCTTCCTC-CATGGTTCTCTATTGTGCAGGCCACTCAAAGCTCTTTCTATCTCGATGTTGGACC
66 TCCTTCCTCTCATGGTTCTCTATTGTGCAGGCCACTCAAAGCTCTTTCTATCTCGATGTTGGACC
120858 ACGACACATTTTAACACCAACAAAGAAAAAGTAGAGACGGTTAATTTATTCATAACTTTTTATAT
131 ACGACACATTTTAACACCAACAAAGAAAAAGTAGAGACGGTTAATTTATTCATAACTTTTTATAT
*
120923 ATGAGCGATGTTCCATTAATCCAGATGTTCAATTTCATACTCTAATCACACCATATTTCTTGCTT
196 GTGAGCGATGTTCCATTAATCCAGATGTTCAATTTCATACTCTAATCACACCATATTTCTTGCTT
*
120988 ATTCATTTAGAATAAATAAGTTAAAGAGAAAATAATATAAATAAATAAATAGTAAAAAGAAAAGG
261 ATTGATTTAGAATAAATAAGTTAAAGAGAAAATAATATAAATAAATAAATAGTAAAAAGAAAAGG
* *
121053 AAAAATTAGCTTAGTGTTCATGACCGTGCAATTATAAAAATTCATGAATGTCCATTATTGAGAAT
326 AAAAATTAGCTCAGTGTTCATGACCGTGCAATTATAACAATTCATGAATGTCCATTATTGAGAAT
121118 AATAAGCAAGTCAGTCAAGTGAGTCTTCAGCTTCAATTCAAGGGTAATATTATATACTGGTAGTG
391 AATAAGCAAGTCAGTCAAGTGAGTCTTCAG---C--TTC---------A--ATATACTGGTAGTG
121183 ATCTTAAATCATATAAATTTCTTTCTTTTTTTATATCGGTCGGTTTTGGTTCGGTTTCGGGTTAG
440 ATCTTAAATCATATAAATTTCTTTCTTTTTTTATATCGGTCGGTTTTGGTTCGGTTTCGGGTTAG
* *
121248 GAAATCTATACCTAATACCGACCGAGATGAGGCGTTTTAGAGGTTTAATCGGTTTAGACGGTTTA
505 GAAACCTATACCGAATACCGACCGAGATGAGGCGTTTTAGAGGTTTAATCGGTTTAGACGGTTTA
*
121313 AACCGCCATCGATTATGCTATTGAGAGTTGGAGAGTATTAGATATAATAAACA
570 AACCGCCACCGATTATGCTATTGAGAGTTGGAGAGTATTAGATATAATAAACA
* *
121366 ATCATCACGCATGGATCCTACTGACTTGACCATCGGAGAGGGTACCCTTGGGATACACCCGGGGG
1 ATCATCACGCATGGACCCTACTGACTTGACCATCGGAGAGGGTACCCTCGGGATACACCCGGGGG
*
121431 TCCTTCCTCTCATGGTTCTTTATTGTGCAGGCCACTCAAAGCTCTTTCTATCTCGATGTTGGACC
66 TCCTTCCTCTCATGGTTCTCTATTGTGCAGGCCACTCAAAGCTCTTTCTATCTCGATGTTGGACC
* *
121496 ACGACACATTTTAACACCAACAAGGAAAAAGTAGACA-GGTTAATTTATTCATAACTTTTTATAT
131 ACGACACATTTTAACACCAACAAAGAAAAAGTAGAGACGGTTAATTTATTCATAACTTTTTATAT
121560 GTGAGCGATGTTCCATTAATCCAGATGTTCAATTTCATACTCTAATCACACCATATTTCTTGCTT
196 GTGAGCGATGTTCCATTAATCCAGATGTTCAATTTCATACTCTAATCACACCATATTTCTTGCTT
*
121625 ATTGATTTAGAATAAATAAGTTAAAGAGAAAATAATATAAATAAATAAATAGTAAAAGGAAAAGG
261 ATTGATTTAGAATAAATAAGTTAAAGAGAAAATAATATAAATAAATAAATAGTAAAAAGAAAAGG
121690 AAAAATTAGCTCAGTGTTCATGACCGTGCAATTATAACAATTCATGAATGTCCATTATTGAGAAT
326 AAAAATTAGCTCAGTGTTCATGACCGTGCAATTATAACAATTCATGAATGTCCATTATTGAGAAT
* * *
121755 AATAAGCAAGTCAGGCAAGTGAGTCTTTAGCTTCAAT-TACTTGTAGTGATCTTAAATCATATAA
391 AATAAGCAAGTCAGTCAAGTGAGTCTTCAGCTTCAATATACTGGTAGTGATCTTAAATCATATAA
*
121819 ATTTCTTTCTTTTTTTAATAATCGGTCGGTTTTGGTTCGGTTTTGGGTTAGGAAACCTATACCGA
456 ATTTCTTTCTTTTTTT-AT-ATCGGTCGGTTTTGGTTCGGTTTCGGGTTAGGAAACCTATACCGA
* *
121884 ATACCGACCGAGATGAGGCGTTTTAGCGGTTTAATCGGTTTAGGCGGTTTAAACCGCCACCGATT
519 ATACCGACCGAGATGAGGCGTTTTAGAGGTTTAATCGGTTTAGACGGTTTAAACCGCCACCGATT
*
121949 ATGCTATTGAGAGTTGGAGAGTATTAGCTATAATAAACA
584 ATGCTATTGAGAGTTGGAGAGTATTAGATATAATAAACA
* **
121988 ATCATCACGCATGGACCCTACTGACTTGACCATCGGAGAGGGTCCCCTCGGGATACACCCATGGG
1 ATCATCACGCATGGACCCTACTGACTTGACCATCGGAGAGGGTACCCTCGGGATACACCCGGGGG
122053 TCCTTCCTCTCATGGTTCTCTATTGTGCAGGCCACTCAAAGCTCTTTCTATCTCGATGTTGGACC
66 TCCTTCCTCTCATGGTTCTCTATTGTGCAGGCCACTCAAAGCTCTTTCTATCTCGATGTTGGACC
*
122118 ACGACACATTTTAACATCAACAAAGAAAAAGTAGAGACGGTTAATTTATTCATAACTTTTTATAT
131 ACGACACATTTTAACACCAACAAAGAAAAAGTAGAGACGGTTAATTTATTCATAACTTTTTATAT
* *
122183 GTGAGCGATGTTCCATTAATCCAAATGTTCAATTTCATACTCTAATCACACCATATTTATTGCTT
196 GTGAGCGATGTTCCATTAATCCAGATGTTCAATTTCATACTCTAATCACACCATATTTCTTGCTT
122248 ATTGATTTAGAATAAATAAGTTAAAGAG-AAATAATATAAATAAATAAATAGTAAAAAGAAAAGG
261 ATTGATTTAGAATAAATAAGTTAAAGAGAAAATAATATAAATAAATAAATAGTAAAAAGAAAAGG
* *
122312 AAAAATTAGCTCAGTGTTCATGACCGTGCAATTATAACAATTCATTAATGTTCATTATTGAGAAT
326 AAAAATTAGCTCAGTGTTCATGACCGTGCAATTATAACAATTCATGAATGTCCATTATTGAGAAT
122377 AATAAGCAAGTCAGTCAAGTGAGTCTTCAGCTTCAATA
391 AATAAGCAAGTCAGTCAAGTGAGTCTTCAGCTTCAATA
122415 CAAGGGTAAT
Statistics
Matches: 1005, Mismatches: 38, Indels: 25
0.94 0.04 0.02
Matches are distributed among these distances:
620 42 0.04
621 4 0.00
622 433 0.43
623 119 0.12
632 3 0.00
634 1 0.00
636 4 0.00
637 310 0.31
638 89 0.09
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (622 bp):
ATCATCACGCATGGACCCTACTGACTTGACCATCGGAGAGGGTACCCTCGGGATACACCCGGGGG
TCCTTCCTCTCATGGTTCTCTATTGTGCAGGCCACTCAAAGCTCTTTCTATCTCGATGTTGGACC
ACGACACATTTTAACACCAACAAAGAAAAAGTAGAGACGGTTAATTTATTCATAACTTTTTATAT
GTGAGCGATGTTCCATTAATCCAGATGTTCAATTTCATACTCTAATCACACCATATTTCTTGCTT
ATTGATTTAGAATAAATAAGTTAAAGAGAAAATAATATAAATAAATAAATAGTAAAAAGAAAAGG
AAAAATTAGCTCAGTGTTCATGACCGTGCAATTATAACAATTCATGAATGTCCATTATTGAGAAT
AATAAGCAAGTCAGTCAAGTGAGTCTTCAGCTTCAATATACTGGTAGTGATCTTAAATCATATAA
ATTTCTTTCTTTTTTTATATCGGTCGGTTTTGGTTCGGTTTCGGGTTAGGAAACCTATACCGAAT
ACCGACCGAGATGAGGCGTTTTAGAGGTTTAATCGGTTTAGACGGTTTAAACCGCCACCGATTAT
GCTATTGAGAGTTGGAGAGTATTAGATATAATAAACA
Found at i:125833 original size:22 final size:22
Alignment explanation
Indices: 125805--125848 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
125795 TTTAACCGAC
125805 ACTTAATGAGTACTTCATATGG
1 ACTTAATGAGTACTTCATATGG
*
125827 ACTTAATGAGTATTTCATATGG
1 ACTTAATGAGTACTTCATATGG
125849 GATAATAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (22 bp):
ACTTAATGAGTACTTCATATGG
Found at i:131058 original size:29 final size:29
Alignment explanation
Indices: 131025--131118 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
131015 TTTAAACTAA
*
131025 AAAGATCTAACTTTCTACATATTATGAGC
1 AAAGATCTAACTTTCTACATATTATAAGC
* * * * *
131054 AAAGACCT-ATTTTTTTCGTACTT-TAAGCC
1 AAAGATCTAACTTTCTACATA-TTATAAG-C
131083 AAAAGGATCTAACTTTCTACATATTATAAGC
1 -AAA-GATCTAACTTTCTACATATTATAAGC
131114 AAAGA
1 AAAGA
131119 CCTATTTTTT
Statistics
Matches: 48, Mismatches: 11, Indels: 12
0.68 0.15 0.17
Matches are distributed among these distances:
28 11 0.23
29 12 0.25
30 6 0.12
31 7 0.15
32 12 0.25
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (29 bp):
AAAGATCTAACTTTCTACATATTATAAGC
Found at i:131087 original size:59 final size:58
Alignment explanation
Indices: 131024--131149 Score: 207
Period size: 60 Copynumber: 2.1 Consensus size: 58
131014 TTTTAAACTA
* *
131024 AAAAGATCTAACTTTCTACATATTATGAGCAAAGACCTATTTTTTTCGTACTTTAAGCC
1 AAAAGATCTAACTTTCTACATATTATAAGCAAAGACCTA-TTTTTTCATACTTTAAGCC
*
131083 AAAAGGATCTAACTTTCTACATATTATAAGCAAAGACCTATTTTTTCATACTTTAAGCT
1 AAAA-GATCTAACTTTCTACATATTATAAGCAAAGACCTATTTTTTCATACTTTAAGCC
131142 AAAAGATC
1 AAAAGATC
131150 GCATATTTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
58 4 0.06
59 25 0.40
60 34 0.54
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (58 bp):
AAAAGATCTAACTTTCTACATATTATAAGCAAAGACCTATTTTTTCATACTTTAAGCC
Found at i:131709 original size:22 final size:21
Alignment explanation
Indices: 131684--131737 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
131674 GAAGTTCGTG
131684 TTTGAAGACTTATTGAAGATAA
1 TTTGAAGA-TTATTGAAGATAA
*
131706 TTTGAAGA-T-TTGAAGATCA
1 TTTGAAGATTATTGAAGATAA
131725 -TTGAAGAATTATT
1 TTTGAAG-ATTATT
131738 TCCAAGAAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (21 bp):
TTTGAAGATTATTGAAGATAA
Done.