Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 114 of 168
Found at i:33321800 original size:15 final size:15
Alignment explanation
Indices: 33321780--33321815 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
33321770 TATTTATTAT
33321780 AAGAAGTGAAGATAG
1 AAGAAGTGAAGATAG
*
33321795 AAGAAGTGAAGATGG
1 AAGAAGTGAAGATAG
33321810 AAGAAG
1 AAGAAG
33321816 GAGCTTTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.36, T:0.11
Consensus pattern (15 bp):
AAGAAGTGAAGATAG
Found at i:33322249 original size:20 final size:18
Alignment explanation
Indices: 33322215--33322259 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
33322205 TTTAAAAATG
*
33322215 TTTTATTAATATTTTCTGTA
1 TTTTTTTAATATTTT-T-TA
*
33322235 TTTTTTTAATTTTTTTTA
1 TTTTTTTAATATTTTTTA
33322253 TTTTTTT
1 TTTTTTT
33322260 CAAGTTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 9 0.39
19 1 0.04
20 13 0.57
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTTTTTAATATTTTTTA
Found at i:33327882 original size:18 final size:19
Alignment explanation
Indices: 33327861--33327903 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
33327851 AATTAAAAAT
33327861 ATTTTTAAAT-AAA-TTTCA
1 ATTTTT-AATGAAATTTTCA
33327879 ATTTTT-ATGAAATTTTCA
1 ATTTTTAATGAAATTTTCA
33327897 ATTTTTA
1 ATTTTTA
33327904 TTTTTACATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.09
17 3 0.14
18 17 0.77
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (19 bp):
ATTTTTAATGAAATTTTCA
Found at i:33329566 original size:19 final size:19
Alignment explanation
Indices: 33329542--33329598 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
33329532 AATGATAAAA
33329542 ATAAAAGAAATTAAAAAGG
1 ATAAAAGAAATTAAAAAGG
33329561 ATAAAATG--A-T-AAAA--
1 ATAAAA-GAAATTAAAAAGG
*
33329575 ATAAAATAAATTAAAAAGG
1 ATAAAAGAAATTAAAAAGG
33329594 ATAAA
1 ATAAA
33329599 TTGATTTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 14
0.67 0.02 0.31
Matches are distributed among these distances:
14 6 0.20
15 1 0.03
16 5 0.17
17 5 0.17
18 1 0.03
19 11 0.37
20 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.19
Consensus pattern (19 bp):
ATAAAAGAAATTAAAAAGG
Found at i:33329567 original size:33 final size:33
Alignment explanation
Indices: 33329530--33329603 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
33329520 AGCAATTCTA
33329530 AAAATGATAAAAATAAAAGAAATTAAAAAGGAT
1 AAAATGATAAAAATAAAAGAAATTAAAAAGGAT
*
33329563 AAAATGATAAAAATAAAATAAATTAAAAAGGAT
1 AAAATGATAAAAATAAAAGAAATTAAAAAGGAT
*
33329596 AAATTGAT
1 AAAATGAT
33329604 TTTTCCCTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.22
Consensus pattern (33 bp):
AAAATGATAAAAATAAAAGAAATTAAAAAGGAT
Found at i:33345717 original size:15 final size:15
Alignment explanation
Indices: 33345699--33345728 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
33345689 TAATCTATAA
33345699 TATAATAATACTTAT
1 TATAATAATACTTAT
*
33345714 TATATTAATACTTAT
1 TATAATAATACTTAT
33345729 AAAATGTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (15 bp):
TATAATAATACTTAT
Found at i:33346170 original size:203 final size:215
Alignment explanation
Indices: 33345905--33346469 Score: 586
Period size: 215 Copynumber: 2.6 Consensus size: 215
33345895 TCACATAGTG
33345905 TATAATATATTAATAGTTTATATATATGCATCAATGATTAAACGTACAATATCATATAATACTAT
1 TATAATATATTAATAGTTTATATATATGCATCAATGATTAAACGTACAATATCATATAATACTAT
33345970 ATA-TT-TT-T-AT-TATAA-ACT-AT-A-A-TATA-ATAATAGTAGTACATTATATATTAATTA
66 ATATTTATTGTAATCTATAATA-TAATAATAGTATATATAATAGTAGTACATTATATATTAATTA
*
33346024 TTATTATACTT-GTTGAAATATGCTCTAAATCCCTATACTTTTCATACATTTGAAAGTTAGCACT
130 TTATTATA-TTAGTTGAAATATGCTCTAAATCCCTATACTTTTCATACATTTGAAAGTTAACACT
*
33346088 TCTACTATATTATATAATGCTA
194 CCTACTATATTATATAATGCTA
* * * *
33346110 TATAATGTATTAATAG-TT-TATATATGCATCAAAT-ATT-AACATTATAATATCATGTAATACT
1 TATAATATATTAATAGTTTATATATATGCATC-AATGATTAAAC-GTACAATATCATATAATACT
33346171 ATATATTTTATTGTAATCTATAATATAATAATAGTTATATATAATAGTAGTACATTATATATTAA
64 ATATA-TTTATTGTAATCTATAATATAATAATAG-TATATATAATAGTAGTACATTATATATTAA
* * * * * *
33346236 TTATTATTATATTAGTTGAAATATGTTTTAAGTCCCTATATTTTTCGTACATTTGAAAGTTAACC
127 TTATTATTATATTAGTTGAAATATGCTCTAAATCCCTATACTTTTCATACATTTGAAAGTTAACA
33346301 CTCCTACTATATTATATAATGCTATATCATA
192 CTCCTACTATATTATATAATG------C-TA
* * * * *
33346332 TCATATAGTAGATAATATATTATTAGTTTATATATATGCATCGATGATTGAACATTATAATATTA
1 T-ATA-A-T--AT-AT-TA--A-TAGTTTATATATATGCATCAATGATTAAAC-GTACAATATCA
* * * * *
33346397 TACAATATTATATCTTTTATTATAATATATAATATAATAATAGTTATATATAATAGTAGTACATT
55 TATAATACTATAT-ATTTATTGTAATCTATAATATAATAATAG-TATATATAATAGTAGTACATT
33346462 ATATATTA
118 ATATATTA
33346470 TATATTACAT
Statistics
Matches: 301, Mismatches: 21, Indels: 46
0.82 0.06 0.12
Matches are distributed among these distances:
202 3 0.01
203 37 0.12
204 5 0.02
205 17 0.06
206 2 0.01
207 1 0.00
208 2 0.01
209 6 0.02
210 3 0.01
211 1 0.00
212 1 0.00
214 6 0.02
215 100 0.33
221 1 0.00
222 3 0.01
223 3 0.01
224 1 0.00
225 1 0.00
227 1 0.00
228 2 0.01
229 2 0.01
231 1 0.00
232 3 0.01
233 4 0.01
234 15 0.05
235 80 0.27
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (215 bp):
TATAATATATTAATAGTTTATATATATGCATCAATGATTAAACGTACAATATCATATAATACTAT
ATATTTATTGTAATCTATAATATAATAATAGTATATATAATAGTAGTACATTATATATTAATTAT
TATTATATTAGTTGAAATATGCTCTAAATCCCTATACTTTTCATACATTTGAAAGTTAACACTCC
TACTATATTATATAATGCTA
Found at i:33346247 original size:232 final size:236
Alignment explanation
Indices: 33346011--33346934 Score: 801
Period size: 259 Copynumber: 3.9 Consensus size: 236
33346001 AGTAGTACAT
*
33346011 TATATATTAATTATTATTATACTTGTTGAAATATGCTCTAAATCCCTATACTTTTCATACATTTG
1 TATATATTAATTATTATTATAC-TGTTGAAATATGCTCTAAGTCCCTATACTTTTCATACATTTG
* * * *
33346076 AAAGTTAGCACTTCTACTATATTATATAATGC-TAT-ATA-ATGTATTAATAG-TT-TATATATG
65 AAAGTTAACCCTCCTACTATATTATATAATGCATATCATATATATATTAATAGTTTATATATATG
*
33346136 CATCAAAT-ATT-AACATTATAATATCATGTAATACTATAT-ATTTTATTGTAATCTATAATATA
130 CATC-AATGATTAAACATTATAATATCATGTAATACTATATCA-TTTATTATAATCTATAATATA
33346198 ATAATAGTTATATATAATAGTAGTAC---AT-TA-T-A-TATTA
193 ATAATAGTTATATATAATAGTAGTACATTATATATTAATTATTA
* * * *
33346235 -AT-TATT-ATTA-TA-T-TA--GTTGAAATATGTTTTAAGTCCCTATATTTTTCGTACATTTGA
1 TATATATTAATTATTATTATACTGTTGAAATATGCTCTAAGTCCCTATACTTTTCATACATTTGA
33346292 AAGTTAACCCTCCTACTATATTATATAATGCTATATCATATCATATAGTAGATAATATATTATTA
66 AAGTTAACCCTCCTACTATATTATATAATG------CATATCATATA-T--AT-AT-TA--A-TA
* * * ** * *
33346357 GTTTATATATATGCATCGATGATTGAACATTATAATATTATACAATATTATATCTTTTATTATAA
117 GTTTATATATATGCATCAATGATTAAACATTATAATATCATGTAATACTATATCATTTATTATAA
*
33346422 TATATAATATAATAATAGTTATATATAATAGTAGTACATTATATATTATATATTACATATTA
182 TCTATAATATAATAATAGTTATATATAATAGTAGTACATTATATA-T-TA-A-T---TATTA
33346484 TTATATATTATTGTTTATTGTTTATTATTATACTGGTTGAAATATGCTCTAAGTCCCTATACTAT
1 -TATATATTA------A----TTATTATTATACT-GTTGAAATATGCTCTAAGTCCCTATACT-T
** *
33346549 TGGA-ACATTTGAAATTTAACCCTCCTACTATATTATATAATGCTATATCATATCATATATTAAT
53 TTCATACATTTGAAAGTTAACCCTCCTACTATATTATATAATGC-ATATCATAT-ATATATTAAT
* * * * *
33346613 AGTTTATATATATACGCATAAATTATTAAATATTATAATAGCATGTAATACTATCTCATTTATTA
116 AGTTTATATATAT--GCATCAATGATTAAACATTATAATATCATGTAATACTATATCATTTATTA
* * * *
33346678 TAATCTATATTATAATAATAGTTACAAATAATAGTAGTACATTATATATTACTTATTA
179 TAATCTATAATATAATAATAGTTATATATAATAGTAGTACATTATATATTAATTATTA
** * * * * *
33346736 TATATTATTGTTTATTATTATACTAATTGAAATATGCTTTAAGTCCCTATAGTTTCCGTACATTT
1 TATA-TATTAATTATTATTATACT-GTTGAAATATGCTCTAAGTCCCTATACTTTTCATACATTT
* * ** * *
33346801 AAAACTTAGTCCTCCTACTATA-T-CAT-AT-CATAT-A-ATATATATTAATAGTTTACATATAT
64 GAAAGTTAACCCTCCTACTATATTATATAATGCATATCATATATATATTAATAGTTTATATATAT
* * * * * * *
33346860 GCATCGATGACTAAACATTACAATATCAGGTAACACTATATCATTTATTATGATCTATATTATAA
129 GCATCAATGATTAAACATTATAATATCATGTAATACTATATCATTTATTATAATCTATAATATAA
33346925 TAATAGTTAT
194 TAATAGTTAT
33346935 GTATGTATTA
Statistics
Matches: 569, Mismatches: 68, Indels: 118
0.75 0.09 0.16
Matches are distributed among these distances:
215 64 0.11
218 2 0.00
219 1 0.00
220 2 0.00
221 5 0.01
222 7 0.01
223 5 0.01
224 1 0.00
225 1 0.00
227 1 0.00
228 2 0.00
229 2 0.00
231 1 0.00
232 66 0.12
233 4 0.01
234 37 0.07
235 71 0.12
236 1 0.00
237 4 0.01
238 3 0.01
239 4 0.01
240 2 0.00
241 3 0.01
242 63 0.11
244 1 0.00
249 5 0.01
251 6 0.01
252 13 0.02
255 1 0.00
257 16 0.03
258 2 0.00
259 83 0.15
260 2 0.00
261 2 0.00
262 2 0.00
263 4 0.01
264 12 0.02
265 2 0.00
266 2 0.00
269 62 0.11
270 2 0.00
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.44
Consensus pattern (236 bp):
TATATATTAATTATTATTATACTGTTGAAATATGCTCTAAGTCCCTATACTTTTCATACATTTGA
AAGTTAACCCTCCTACTATATTATATAATGCATATCATATATATATTAATAGTTTATATATATGC
ATCAATGATTAAACATTATAATATCATGTAATACTATATCATTTATTATAATCTATAATATAATA
ATAGTTATATATAATAGTAGTACATTATATATTAATTATTA
Found at i:33346471 original size:7 final size:7
Alignment explanation
Indices: 33346401--33346494 Score: 50
Period size: 7 Copynumber: 13.0 Consensus size: 7
33346391 ATATTATACA
33346401 ATATTAT
1 ATATTAT
* *
33346408 ATCTTTT
1 ATATTAT
*
33346415 ATTATAAT
1 A-TATTAT
*
33346423 ATATAAT
1 ATATTAT
*
33346430 ATAATA-
1 ATATTAT
33346436 ATAGTTAT
1 ATA-TTAT
33346444 ATA-TA-
1 ATATTAT
*
33346449 ATAGTAGT
1 ATATTA-T
*
33346457 ACATTAT
1 ATATTAT
33346464 ATATTAT
1 ATATTAT
33346471 ATATTACAT
1 ATATT--AT
33346480 ATTATTAT
1 A-TATTAT
33346488 ATATTAT
1 ATATTAT
33346495 TGTTTATTGT
Statistics
Matches: 67, Mismatches: 11, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
5 3 0.04
6 7 0.10
7 36 0.54
8 14 0.21
9 3 0.04
10 4 0.06
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (7 bp):
ATATTAT
Found at i:33346967 original size:242 final size:245
Alignment explanation
Indices: 33346322--33346980 Score: 616
Period size: 242 Copynumber: 2.7 Consensus size: 245
33346312 TTATATAATG
* *
33346322 CTATATCATATCATATAGTAGATAATATATTATTAGTTTATATATATGCATCGATGATTGAACAT
1 CTATATCATATC-TATA-TAGATAATATATTAATAGTTTATATATATGCATCGATGATTAAACAT
* ** * * * *
33346387 TATAATATTATACAATATTATATCTTTTATTATAATATATAATATAATAATAGTTA-TATATAAT
64 TATAATATCATGTAATACTATATCATTTATTATAATCTATATTATAATAATAGTTATTAT-TAAT
* * *
33346451 AGTAGTACATTATATATTATATATTACATATTATTATATATTATTGTTTATTGTTTATTATTATA
128 A--A-T--ATT-TATAGTA-ATATTATATATTATTATATATTATTGATTATTGTTTATTATTATA
** * * *
33346516 CTGGTTGAAATATGCTCTAAGTCCCTATACTATTGGAACATTTGAAATTTAACCCTCCTA
186 CTAATTGAAATATGCTCTAAGTCCCTATACTATTCGAACATTTAAAACTTAACCCTCCTA
* * * ** *
33346576 CTATATTATATAATGCTATATCATATCATATATTAATAGTTTATATATATACGCATAAATTATTA
1 CTATA-T-CAT-AT-CTATAT-AGATAATATATTAATAGTTTATATATAT--GCATCGATGATTA
* * * *
33346641 AATATTATAATAGCATGTAATACTATCTCATTTATTATAATCTATATTATAATAATAGTTA-CA-
59 AACATTATAATATCATGTAATACTATATCATTTATTATAATCTATATTATAATAATAGTTATTAT
* *
33346704 -AATAATA---GTAGT-ACATTATATATTACTTAT-TA-TA-T-ATTATTGTTTATTATTATACT
124 TAATAATATTTATAGTAATATTATATATTA-TTATATATTATTGATTATTGTTTATTATTATACT
* * * **
33346760 AATTGAAATATGCTTTAAGTCCCTATAGT-TTCCGTACATTTAAAACTTAGTCCTCCTA
188 AATTGAAATATGCTCTAAGTCCCTATACTATT-CGAACATTTAAAACTTAACCCTCCTA
* *
33346818 CTATATCATATC-ATATA-AT-ATATATTAATAGTTTACATATATGCATCGATGACTAAACATTA
1 CTATATCATATCTATATAGATAATATATTAATAGTTTATATATATGCATCGATGATTAAACATTA
* * * * *
33346880 CAATATCAGGTAACACTATATCATTTATTATGATCTATATTATAATAATAGTTATGTATGTATTA
66 TAATATCATGTAATACTATATCATTTATTATAATCTATATTATAATAATAGTTAT-TAT-TAATA
*
33346945 ATATTTTTAGTAATAGTTATATATTA-TA-ATATTATT
129 ATATTTATAGTAATA-TTATATATTATTATATATTATT
33346981 TTATGCAATA
Statistics
Matches: 332, Mismatches: 51, Indels: 56
0.76 0.12 0.13
Matches are distributed among these distances:
232 63 0.19
234 23 0.07
235 2 0.01
236 1 0.00
237 10 0.03
238 1 0.00
239 2 0.01
240 10 0.03
241 7 0.02
242 81 0.24
243 1 0.00
244 2 0.01
245 13 0.04
246 4 0.01
247 3 0.01
251 1 0.00
253 1 0.00
254 6 0.02
255 1 0.00
256 7 0.02
257 31 0.09
258 1 0.00
259 61 0.18
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.45
Consensus pattern (245 bp):
CTATATCATATCTATATAGATAATATATTAATAGTTTATATATATGCATCGATGATTAAACATTA
TAATATCATGTAATACTATATCATTTATTATAATCTATATTATAATAATAGTTATTATTAATAAT
ATTTATAGTAATATTATATATTATTATATATTATTGATTATTGTTTATTATTATACTAATTGAAA
TATGCTCTAAGTCCCTATACTATTCGAACATTTAAAACTTAACCCTCCTA
Found at i:33346983 original size:30 final size:31
Alignment explanation
Indices: 33346925--33346997 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 31
33346915 TATATTATAA
*
33346925 TAATAGTTATGTATGTATTAATATTTTTA-G
1 TAATAGTTATATATGTATTAATATTTTTATG
33346955 TAATAGTTATATAT-TA-TAATATTATTTTATG
1 TAATAGTTATATATGTATTAATA-T-TTTTATG
* *
33346986 CAATAGTAATAT
1 TAATAGTTATAT
33346998 TCTAATTTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 5 0.14
29 3 0.08
30 18 0.49
31 11 0.30
ACGTcount: A:0.38, C:0.01, G:0.10, T:0.51
Consensus pattern (31 bp):
TAATAGTTATATATGTATTAATATTTTTATG
Found at i:33354462 original size:28 final size:28
Alignment explanation
Indices: 33354407--33354473 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
33354397 TCCCCTATCT
*
33354407 TTCAGATTTTATAGTATTGCTCATGTTC
1 TTCAAATTTTATAGTATTGCTCATGTTC
* * *
33354435 TTTAAATTTTATAGTTTTGCT-TTCGTTC
1 TTCAAATTTTATAGTATTGCTCAT-GTTC
*
33354463 TTCAGATTTTA
1 TTCAAATTTTA
33354474 CAATTTTCCC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
27 1 0.03
28 31 0.97
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.55
Consensus pattern (28 bp):
TTCAAATTTTATAGTATTGCTCATGTTC
Found at i:33354480 original size:28 final size:27
Alignment explanation
Indices: 33354430--33354591 Score: 114
Period size: 28 Copynumber: 5.9 Consensus size: 27
33354420 GTATTGCTCA
* * * *
33354430 TGTTCTTTAAATTTTATAGTTTTGCTT
1 TGTTCTTTAGATTTTACAATTTTCCTT
* *
33354457 TCGTTCTTCAGATTTTACAATTTTCCCCT
1 T-GTTCTTTAGATTTTACAATTTT-CCTT
* *
33354486 AGTT-TTTAGATTATACAATTTTACCTT
1 TGTTCTTTAGATTTTACAATTTT-CCTT
**
33354513 TGTTCTTTAGATTTTACAATTTTGCCCC
1 TGTTCTTTAGATTTTACAATTTT-CCTT
* *
33354541 TATT-TTAAGATTTTACAATTTTGCCTAT
1 TGTTCTTTAGATTTTACAATTTT-CCT-T
* *
33354569 AT-TTTTTTATATTTTACAATTTT
1 -TGTTCTTTAGATTTTACAATTTT
33354592 GCCCTTATTT
Statistics
Matches: 107, Mismatches: 22, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
27 43 0.40
28 45 0.42
29 19 0.18
ACGTcount: A:0.23, C:0.14, G:0.07, T:0.56
Consensus pattern (27 bp):
TGTTCTTTAGATTTTACAATTTTCCTT
Found at i:33354502 original size:27 final size:27
Alignment explanation
Indices: 33354466--33354596 Score: 129
Period size: 27 Copynumber: 4.7 Consensus size: 27
33354456 TTCGTTCTTC
33354466 AGATTTTACAATTTTCCCCTAGTTTTT
1 AGATTTTACAATTTTCCCCTAGTTTTT
* * * *
33354493 AGATTATACAATTTTACCTTTGTTCTTT
1 AGATTTTACAATTTTCCCCTAGTT-TTT
*
33354521 AGATTTTACAATTTTGCCCCTA-TTTTA
1 AGATTTTACAATTTT-CCCCTAGTTTTT
** *
33354548 AGATTTTACAATTTTGCCTATATTTTTTT
1 AGATTTTACAATTTT-CCCCTA-GTTTTT
* *
33354577 ATATTTTACAATTTTGCCCT
1 AGATTTTACAATTTTCCCCT
33354597 TATTTATAGA
Statistics
Matches: 84, Mismatches: 16, Indels: 7
0.79 0.15 0.07
Matches are distributed among these distances:
27 42 0.50
28 21 0.25
29 21 0.25
ACGTcount: A:0.24, C:0.16, G:0.07, T:0.53
Consensus pattern (27 bp):
AGATTTTACAATTTTCCCCTAGTTTTT
Found at i:33354589 original size:56 final size:55
Alignment explanation
Indices: 33354454--33354601 Score: 183
Period size: 55 Copynumber: 2.7 Consensus size: 55
33354444 TATAGTTTTG
* *
33354454 CTTTCGTTCTTCAGATTTTACAATTTT-CCCCTAGTTTTTAGATTATACAATTTTAC
1 CTTT-GTTCTTTAGATTTTACAATTTTGCCCCTA-TTTTAAGATTATACAATTTTAC
* *
33354510 CTTTGTTCTTTAGATTTTACAATTTTGCCCCTATTTTAAGATTTTACAATTTTGC
1 CTTTGTTCTTTAGATTTTACAATTTTGCCCCTATTTTAAGATTATACAATTTTAC
* * *
33354565 CTATAT-TTTTTTATATTTTACAATTTTGCCCTTATTT
1 CT-T-TGTTCTTTAGATTTTACAATTTTGCCCCTATTT
33354602 ATAGATTGAA
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
55 42 0.51
56 39 0.48
57 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.07, T:0.54
Consensus pattern (55 bp):
CTTTGTTCTTTAGATTTTACAATTTTGCCCCTATTTTAAGATTATACAATTTTAC
Found at i:33354608 original size:56 final size:54
Alignment explanation
Indices: 33354454--33354608 Score: 179
Period size: 56 Copynumber: 2.8 Consensus size: 54
33354444 TATAGTTTTG
*
33354454 CTTTCGTTCTTCAGATTTTACAATTTT-CCCCTAGTTTTTAGATTATACAATTTTAC
1 CTTT-GTTCTTTAGATTTTACAATTTTGCCCCTA--TTTTAGATTATACAATTTTAC
* *
33354510 CTTTGTTCTTTAGATTTTACAATTTTGCCCCTATTTTAAGATTTTACAATTTTGC
1 CTTTGTTCTTTAGATTTTACAATTTTGCCCCTATTTT-AGATTATACAATTTTAC
* * *
33354565 CTATAT-TTTTTTATATTTTACAATTTTGCCCTTATTTATAGATT
1 CT-T-TGTTCTTTAGATTTTACAATTTTGCCCCTATTT-TAGATT
33354609 GAAAAACCTT
Statistics
Matches: 88, Mismatches: 6, Indels: 10
0.85 0.06 0.10
Matches are distributed among these distances:
54 4 0.05
55 38 0.43
56 44 0.50
57 2 0.02
ACGTcount: A:0.23, C:0.16, G:0.07, T:0.54
Consensus pattern (54 bp):
CTTTGTTCTTTAGATTTTACAATTTTGCCCCTATTTTAGATTATACAATTTTAC
Found at i:33356053 original size:53 final size:54
Alignment explanation
Indices: 33355974--33356083 Score: 141
Period size: 53 Copynumber: 2.0 Consensus size: 54
33355964 TTATAAAACT
* ** *
33355974 TATATATATAAAATACATATTAATGCATTTATGAAAACAATGAAAAATATAAATA
1 TATACATATAAAATA-ATATTAATGCATTTACAAAAAAAATGAAAAATATAAATA
* * *
33356029 TATACATATAAAAT-ATATTCATGCATTTACAAAAAAAATGAAATATATAAGTA
1 TATACATATAAAATAATATTAATGCATTTACAAAAAAAATGAAAAATATAAATA
33356082 TA
1 TA
33356084 ATATAAAAAC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
53 35 0.73
55 13 0.27
ACGTcount: A:0.55, C:0.06, G:0.05, T:0.33
Consensus pattern (54 bp):
TATACATATAAAATAATATTAATGCATTTACAAAAAAAATGAAAAATATAAATA
Found at i:33356368 original size:3 final size:3
Alignment explanation
Indices: 33356360--33356405 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
33356350 ACATATAGGT
* *
33356360 ATA ATA ATA ATA ATA ATA TATA AT- ATA ATA ATA AAA ATA AAA ATA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA
33356405 A
1 A
33356406 CAAAATTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:33356662 original size:19 final size:21
Alignment explanation
Indices: 33356624--33356662 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
33356614 CCTTTTTTAA
*
33356624 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
33356645 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
33356663 AAAGAAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:33356872 original size:23 final size:22
Alignment explanation
Indices: 33356843--33356885 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
33356833 AAATTAAATC
33356843 TCTAAGATTACAAAATCATATAT
1 TCTAAGATTAC-AAATCATATAT
*
33356866 TCTAAGATTACATATCATAT
1 TCTAAGATTACAAATCATAT
33356886 CTAAGATTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.44, C:0.14, G:0.05, T:0.37
Consensus pattern (22 bp):
TCTAAGATTACAAATCATATAT
Found at i:33356890 original size:19 final size:19
Alignment explanation
Indices: 33356843--33356940 Score: 97
Period size: 19 Copynumber: 4.8 Consensus size: 19
33356833 AAATTAAATC
*
33356843 TCTAAGATTACAAAATCATATA
1 TCTAAGATTAC-ATATC--ATA
33356865 TTCTAAGATTACATATCATA
1 -TCTAAGATTACATATCATA
*
33356885 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
**
33356906 TCTAAGATTGTATATCATA
1 TCTAAGATTACATATCATA
*
33356925 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
33356941 CTCGAAGATT
Statistics
Matches: 69, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
19 33 0.48
20 3 0.04
21 18 0.26
22 4 0.06
23 11 0.16
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:33356903 original size:21 final size:21
Alignment explanation
Indices: 33356877--33356939 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
33356867 CTAAGATTAC
33356877 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
33356898 ATATCATATCTAAGATTG--T
1 ATATCATATCTAAGATTGCAT
33356917 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
33356938 AT
1 AT
33356940 CCTCGAAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
19 19 0.47
21 21 0.52
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.40
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:33359751 original size:20 final size:22
Alignment explanation
Indices: 33359701--33359762 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
33359691 TTTTTAAAAA
33359701 AAAAATATTAATTTAGTTTTTC
1 AAAAATATTAATTTAGTTTTTC
33359723 AAAAA-ATTAA-TTA-TTTTT-
1 AAAAATATTAATTTAGTTTTTC
33359741 AATAAATATT-ATTTAGATTTTT
1 AA-AAATATTAATTTAG-TTTTT
33359763 TTTTTGACCT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
18 2 0.06
19 9 0.26
20 9 0.26
21 5 0.14
22 10 0.29
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (22 bp):
AAAAATATTAATTTAGTTTTTC
Found at i:33360211 original size:2 final size:2
Alignment explanation
Indices: 33360204--33360236 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
33360194 CAAGTGCCAA
33360204 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33360237 ATAAAAAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33378725 original size:32 final size:31
Alignment explanation
Indices: 33378683--33378807 Score: 232
Period size: 31 Copynumber: 4.0 Consensus size: 31
33378673 AGATAATTTT
*
33378683 AAAGAGTTTTATTAGGATTCAATTACTCTTT
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
33378714 AAAGAGTTTTTATTAGGATTCAATTACTCTTG
1 AAAGAG-TTTTATTAGGATTCAATTACTCTTG
33378746 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
33378777 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
33378808 TAATTTGCCT
Statistics
Matches: 92, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
31 62 0.67
32 30 0.33
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:33378755 original size:63 final size:62
Alignment explanation
Indices: 33378683--33378807 Score: 232
Period size: 63 Copynumber: 2.0 Consensus size: 62
33378673 AGATAATTTT
*
33378683 AAAGAGTTTTATTAGGATTCAATTACTCTTTAAAGAGTTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTGAAAGAG-TTTTATTAGGATTCAATTACTCTTG
33378746 AAAGAGTTTTATTAGGATTCAATTACTCTTGAAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTGAAAGAGTTTTATTAGGATTCAATTACTCTTG
33378808 TAATTTGCCT
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
62 25 0.41
63 36 0.59
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (62 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTGAAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:33379159 original size:29 final size:27
Alignment explanation
Indices: 33379110--33379168 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 27
33379100 ATCTATCCTT
*
33379110 TTTTATTTATTTATTTATTATTTAACTAA
1 TTTTATTTATTTAGTTATTATTT--CTAA
*
33379139 TTTTATTTATTCTCGTT-TTATTTCTAA
1 TTTTATTTATT-TAGTTATTATTTCTAA
33379166 TTT
1 TTT
33379169 GTGTTTCTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 7 0.26
29 17 0.63
30 3 0.11
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.68
Consensus pattern (27 bp):
TTTTATTTATTTAGTTATTATTTCTAA
Found at i:33379256 original size:21 final size:21
Alignment explanation
Indices: 33379232--33379272 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
33379222 ACGTTGTCAA
33379232 TGAGATTAG-TCATTGTAACAG
1 TGAGATTAGAT-ATTGTAACAG
*
33379253 TGAGATTGGATATTGTAACA
1 TGAGATTAGATATTGTAACA
33379273 ATAAGTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.34
Consensus pattern (21 bp):
TGAGATTAGATATTGTAACAG
Found at i:33379580 original size:15 final size:15
Alignment explanation
Indices: 33379560--33379590 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
33379550 ATTGTGTAAG
*
33379560 ATAAATTATTTAATA
1 ATAAATTATCTAATA
33379575 ATAAATTATCTAATA
1 ATAAATTATCTAATA
33379590 A
1 A
33379591 ATTTATAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAAATTATCTAATA
Found at i:33379588 original size:12 final size:12
Alignment explanation
Indices: 33379572--33379610 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
33379562 AAATTATTTA
33379572 ATAATAAATTAT
1 ATAATAAATTAT
*
33379584 CTAATAAATT-T
1 ATAATAAATTAT
*
33379595 ATAAGAAATTAT
1 ATAATAAATTAT
33379607 ATAA
1 ATAA
33379611 ATACTAAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (12 bp):
ATAATAAATTAT
Found at i:33385291 original size:88 final size:89
Alignment explanation
Indices: 33385178--33385352 Score: 228
Period size: 88 Copynumber: 2.0 Consensus size: 89
33385168 TTTTTTTAAA
* * * * *
33385178 AAATTATATTTTGACCTCTAAACTTT-TCTAAAAATATATTTTGACCCCTAAACTTTTTCAAAAT
1 AAATTACATTTTGACCCCTAAACTTTCT-TAAAAATACATTTTGACCACTAAACTTTCTCAAAAT
*
33385242 TACATTTCAACCCCTAAACTTTTCT
65 TACATTTCAACCCCAAAACTTTTCT
* *
33385267 AAATTACA-TTTGACCCCTAAACTTTCTTTAAATTACATTTTGACCACTAAACTTTCTCAAAATT
1 AAATTACATTTTGACCCCTAAACTTTCTTAAAAATACATTTTGACCACTAAACTTTCTCAAAATT
** *
33385331 ATGTTTCAGCCCCAAAACTTTT
66 ACATTTCAACCCCAAAACTTTT
33385353 GCTGCATTTA
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
88 66 0.89
89 8 0.11
ACGTcount: A:0.34, C:0.22, G:0.03, T:0.40
Consensus pattern (89 bp):
AAATTACATTTTGACCCCTAAACTTTCTTAAAAATACATTTTGACCACTAAACTTTCTCAAAATT
ACATTTCAACCCCAAAACTTTTCT
Found at i:33385300 original size:58 final size:59
Alignment explanation
Indices: 33385177--33385331 Score: 170
Period size: 58 Copynumber: 2.6 Consensus size: 59
33385167 ATTTTTTTAA
* ** * * *
33385177 AAAATTATATTTTGACCTCTAAACTTTTCTAAAAATATATTTTGACCCCTAAACTTTTTC
1 AAAATTACATTTCAACCACTAAACTTTTCT-AAATTACATTTTGACCCCTAAACTTTTTC
*
33385237 AAAATTACATTTCAACCCCTAAACTTTTCTAAATTACA-TTTGACCCCTAAACTTTCTT-
1 AAAATTACATTTCAACCACTAAACTTTTCTAAATTACATTTTGACCCCTAAACTTT-TTC
* ** *
33385295 TAAATTACATTTTGACCACTAAACTTTCTCAAAATTA
1 AAAATTACATTTCAACCACTAAACTTT-TCTAAATTA
33385332 TGTTTCAGCC
Statistics
Matches: 82, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
58 40 0.49
59 16 0.20
60 26 0.32
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.40
Consensus pattern (59 bp):
AAAATTACATTTCAACCACTAAACTTTTCTAAATTACATTTTGACCCCTAAACTTTTTC
Found at i:33385330 original size:30 final size:29
Alignment explanation
Indices: 33385177--33385331 Score: 177
Period size: 30 Copynumber: 5.2 Consensus size: 29
33385167 ATTTTTTTAA
* *
33385177 AAAATTATATTTTGACCTCTAAACTTTTC
1 AAAATTACATTTTGACCCCTAAACTTTTC
* *
33385206 TAAAAATATATTTTGACCCCTAAACTTTTTC
1 -AAAATTACATTTTGACCCCTAAAC-TTTTC
**
33385237 AAAATTACATTTCAACCCCTAAACTTTTC
1 AAAATTACATTTTGACCCCTAAACTTTTC
* *
33385266 TAAATTACA-TTTGACCCCTAAACTTTCTT
1 AAAATTACATTTTGACCCCTAAACTTT-TC
* *
33385295 TAAATTACATTTTGACCACTAAACTTTCTC
1 AAAATTACATTTTGACCCCTAAACTTT-TC
33385325 AAAATTA
1 AAAATTA
33385332 TGTTTCAGCC
Statistics
Matches: 109, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
28 15 0.14
29 23 0.21
30 66 0.61
31 5 0.05
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.40
Consensus pattern (29 bp):
AAAATTACATTTTGACCCCTAAACTTTTC
Found at i:33385831 original size:7 final size:7
Alignment explanation
Indices: 33385806--33385862 Score: 53
Period size: 7 Copynumber: 8.0 Consensus size: 7
33385796 GCTGATCAGG
33385806 GAAGAAA
1 GAAGAAA
*
33385813 GAAAGGAA
1 G-AAGAAA
33385821 GAAGAAA
1 GAAGAAA
33385828 GAAGAAA
1 GAAGAAA
* *
33385835 -ATGGGAA
1 GA-AGAAA
33385842 GAAGAAA
1 GAAGAAA
33385849 GAAGAAA
1 GAAGAAA
*
33385856 AAAGAAA
1 GAAGAAA
33385863 ATAAATTTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
6 1 0.03
7 32 0.80
8 7 0.17
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (7 bp):
GAAGAAA
Found at i:33385843 original size:21 final size:21
Alignment explanation
Indices: 33385817--33385856 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
33385807 AAGAAAGAAA
33385817 GGAAGAAGAAAGAAGAAAATG
1 GGAAGAAGAAAGAAGAAAATG
33385838 GGAAGAAGAAAGAAGAAAA
1 GGAAGAAGAAAGAAGAAAA
33385857 AAGAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.03
Consensus pattern (21 bp):
GGAAGAAGAAAGAAGAAAATG
Found at i:33386527 original size:38 final size:40
Alignment explanation
Indices: 33386474--33386577 Score: 115
Period size: 38 Copynumber: 2.6 Consensus size: 40
33386464 AATCGAAATA
* *
33386474 TTCAAAAAAAATCGTGTTTTCAAAAAAAAATTCCT-GTGT
1 TTCAAAAATATTCGTGTTTTCAAAAAAAAATTCCTCGTGT
* * * * *
33386513 TTC-GAAATTTTCGTGTCTTC-AAAAAAATTTTCTCGTGT
1 TTCAAAAATATTCGTGTTTTCAAAAAAAAATTCCTCGTGT
33386551 TTCAAAAAATATTCGTGTTTTCAAAAA
1 TTC-AAAAATATTCGTGTTTTCAAAAA
33386578 TAAGGCAACG
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
37 11 0.22
38 19 0.37
39 3 0.06
40 14 0.27
41 4 0.08
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (40 bp):
TTCAAAAATATTCGTGTTTTCAAAAAAAAATTCCTCGTGT
Found at i:33386566 original size:18 final size:18
Alignment explanation
Indices: 33386474--33386577 Score: 61
Period size: 19 Copynumber: 5.4 Consensus size: 18
33386464 AATCGAAATA
*
33386474 TTCAAAAAA-AATCGTGTT
1 TTCAAAAAATATTCGTG-T
*
33386492 TTCAAAAAAAAATTCCTGTGT
1 TTC-AAAAAATATT-C-GTGT
* *
33386513 TTC--GAAATTTTCGTGT
1 TTCAAAAAATATTCGTGT
*
33386529 CTTCAAAAAAATTTTCTCGTGT
1 -TTC-AAAAAA-TAT-TCGTGT
33386551 TTCAAAAAATATTCGTGTT
1 TTCAAAAAATATTCGTG-T
33386570 TTCAAAAA
1 TTCAAAAA
33386578 TAAGGCAACG
Statistics
Matches: 69, Mismatches: 6, Indels: 21
0.72 0.06 0.22
Matches are distributed among these distances:
16 4 0.06
17 4 0.06
18 13 0.19
19 17 0.25
20 11 0.16
21 11 0.16
22 9 0.13
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (18 bp):
TTCAAAAAATATTCGTGT
Found at i:33386579 original size:18 final size:19
Alignment explanation
Indices: 33386474--33386577 Score: 72
Period size: 20 Copynumber: 5.4 Consensus size: 19
33386464 AATCGAAATA
*
33386474 TTCAAAAAA-AATCGTGTT
1 TTCAAAAAATATTCGTGTT
* *
33386492 TTCAAAAAAAAATTCCTGTGT
1 TTC-AAAAAATATTCGTGT-T
* * *
33386513 TTC--GAAATTTTCGTGTC
1 TTCAAAAAATATTCGTGTT
*
33386530 TTCAAAAAAATTTTC-TCGTGT
1 TTC-AAAAAATATTCGT-GT-T
33386551 TTCAAAAAATATTCGTGTT
1 TTCAAAAAATATTCGTGTT
33386570 TTCAAAAA
1 TTCAAAAA
33386578 TAAGGCAACG
Statistics
Matches: 67, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
17 3 0.04
18 12 0.18
19 16 0.24
20 28 0.42
21 8 0.12
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (19 bp):
TTCAAAAAATATTCGTGTT
Found at i:33386822 original size:18 final size:17
Alignment explanation
Indices: 33386801--33386897 Score: 92
Period size: 18 Copynumber: 5.5 Consensus size: 17
33386791 AAAATTCTAT
33386801 TTTTCAAAATTTTTCGTG
1 TTTTCAAAA-TTTTCGTG
*
33386819 TTTTCAACAATTCTCGTG
1 TTTTCAA-AATTTTCGTG
33386837 -TTTCAAAAATTTTCGTG
1 TTTTC-AAAATTTTCGTG
* *
33386854 -TCTCTAAAATTATCGTG
1 TTTTC-AAAATTTTCGTG
33386871 TTTT-AAAATTTTTTCGTG
1 TTTTCAAAA--TTTTCGTG
33386889 TTTTCAAAA
1 TTTTCAAAA
33386898 AAAATCGTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
16 4 0.06
17 27 0.41
18 29 0.44
19 6 0.09
ACGTcount: A:0.27, C:0.13, G:0.10, T:0.49
Consensus pattern (17 bp):
TTTTCAAAATTTTCGTG
Found at i:33386841 original size:35 final size:34
Alignment explanation
Indices: 33386802--33386897 Score: 122
Period size: 35 Copynumber: 2.8 Consensus size: 34
33386792 AAATTCTATT
*
33386802 TTTCAAAATTTTTCGTGTTTTCAACAATTCTCGTG
1 TTTCAAAATTTTTCGTGTTTTCAA-AATTATCGTG
* *
33386837 TTTCAAAAATTTTCGTG-TCTCTAAAATTATCGTG
1 TTTCAAAATTTTTCGTGTTTTC-AAAATTATCGTG
*
33386871 TTTTAAAATTTTTTCGTGTTTTCAAAA
1 TTTCAAAA-TTTTTCGTGTTTTCAAAA
33386898 AAAATCGTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
34 19 0.37
35 30 0.58
36 3 0.06
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (34 bp):
TTTCAAAATTTTTCGTGTTTTCAAAATTATCGTG
Found at i:33386847 original size:17 final size:17
Alignment explanation
Indices: 33386767--33386898 Score: 79
Period size: 17 Copynumber: 7.5 Consensus size: 17
33386757 AGAATCCGTT
*
33386767 TTTC-AAAATTCTCATG
1 TTTCAAAAATTCTCGTG
* *
33386783 TTTTCAGAAAAATTCT-ATT
1 -TTTC--AAAAATTCTCGTG
* *
33386802 TTTCAAAATTTTTCGTG
1 TTTCAAAAATTCTCGTG
*
33386819 TTTTCAACAATTCTCGTG
1 -TTTCAAAAATTCTCGTG
*
33386837 TTTCAAAAATTTTCGTG
1 TTTCAAAAATTCTCGTG
* * *
33386854 TCTCTAAAATTATCGTG
1 TTTCAAAAATTCTCGTG
* * *
33386871 TTTTAAAATTTTTTCGTG
1 TTTCAAAA-ATTCTCGTG
33386889 TTTTCAAAAA
1 -TTTCAAAAA
33386899 AAATCGTTTC
Statistics
Matches: 88, Mismatches: 20, Indels: 13
0.73 0.17 0.11
Matches are distributed among these distances:
16 7 0.08
17 39 0.44
18 25 0.28
19 9 0.10
20 8 0.09
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.48
Consensus pattern (17 bp):
TTTCAAAAATTCTCGTG
Found at i:33392564 original size:10 final size:11
Alignment explanation
Indices: 33392550--33392586 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
33392540 ATTATGCCTA
33392550 AAAAACAAAA-
1 AAAAACAAAAC
33392560 AAAAACAAAAC
1 AAAAACAAAAC
*
33392571 AAAAACAAAAG
1 AAAAACAAAAC
33392582 AAAAA
1 AAAAA
33392587 AGAAGGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 10 0.40
11 15 0.60
ACGTcount: A:0.86, C:0.11, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAC
Found at i:33393604 original size:77 final size:76
Alignment explanation
Indices: 33393438--33393615 Score: 261
Period size: 77 Copynumber: 2.3 Consensus size: 76
33393428 TTTCACAAAT
* *
33393438 TATTTTTCAATTTCTGTTTTTGAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGC
1 TATTTCTCAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGC
*
33393503 ACATGCCGAAG
66 ACAAGCCGAAG
*
33393514 TATTTTTCAATTTCTGTTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
1 TATTTCTCAATTTCTG-TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
*
33393579 TCGCAAGCCG-AG
65 -CACAAGCCGAAG
*
33393591 CTA-TTCTCGATTTCTGTTTTTCAAA
1 -TATTTCTCAATTTCTGTTTTTCAAA
33393616 TAAAAAGAAT
Statistics
Matches: 94, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
76 25 0.27
77 60 0.64
78 9 0.10
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (76 bp):
TATTTCTCAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGC
ACAAGCCGAAG
Found at i:33393804 original size:30 final size:30
Alignment explanation
Indices: 33393769--33393926 Score: 187
Period size: 30 Copynumber: 5.2 Consensus size: 30
33393759 ATTTTTTAAA
* * *
33393769 AAAATTGCATTTTGACCCTTAAACTTTTCT
1 AAAATTACATTTTAACCCCTAAACTTTTCT
*
33393799 AAAATTACATTTTAACCCCTAAACTTTTTT
1 AAAATTACATTTTAACCCCTAAACTTTTCT
*
33393829 CAAAATTATATTTTAACCCCTAAACTTTCTCT
1 -AAAATTACATTTTAACCCCTAAACTTT-TCT
*
33393861 -AAATTACATTTTAACCCCTGAACTTTCTCT
1 AAAATTACATTTTAACCCCTAAACTTT-TCT
* *
33393891 -AAATTACATTTTGACCACTAAAC-TTTCT
1 AAAATTACATTTTAACCCCTAAACTTTTCT
33393919 CAAAATTA
1 -AAAATTA
33393927 TGTTTCAGCC
Statistics
Matches: 113, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.03
29 2 0.02
30 80 0.71
31 26 0.23
32 2 0.02
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.41
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCTAAACTTTTCT
Found at i:33393912 original size:60 final size:60
Alignment explanation
Indices: 33393769--33393926 Score: 203
Period size: 61 Copynumber: 2.6 Consensus size: 60
33393759 ATTTTTTAAA
* *
33393769 AAAATTGCATTTTGACCCTTAAACTTT-TCTAAAATTACATTTTAACCCCTAAACTTTTTTC
1 AAAATTACATTTTGACCC-TAAACTTTCTCT-AAATTACATTTTAACCCCTAAACTTTTCTC
* * *
33393830 AAAATTATATTTTAACCCCTAAACTTTCTCTAAATTACATTTTAACCCCTGAAC-TTTCTC
1 AAAATTACATTTTGA-CCCTAAACTTTCTCTAAATTACATTTTAACCCCTAAACTTTTCTC
* *
33393890 TAAATTACATTTTGACCACTAAACTTTCTCAAAATTA
1 AAAATTACATTTTGACC-CTAAACTTTCTCTAAATTA
33393927 TGTTTCAGCC
Statistics
Matches: 85, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
59 2 0.02
60 35 0.41
61 42 0.49
62 6 0.07
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.41
Consensus pattern (60 bp):
AAAATTACATTTTGACCCTAAACTTTCTCTAAATTACATTTTAACCCCTAAACTTTTCTC
Found at i:33394283 original size:9 final size:9
Alignment explanation
Indices: 33394269--33394316 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
33394259 AACCGCAAGC
33394269 AAAAAGAAG
1 AAAAAGAAG
33394278 AAAAAGAAG
1 AAAAAGAAG
33394287 AAAAA-AAG
1 AAAAAGAAG
*
33394295 -CAAAGAAG
1 AAAAAGAAG
33394303 AAAAA-AGAG
1 AAAAAGA-AG
33394312 AAAAA
1 AAAAA
33394317 AGGGGGAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
7 3 0.09
8 7 0.21
9 24 0.71
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:33394438 original size:7 final size:7
Alignment explanation
Indices: 33394414--33394471 Score: 64
Period size: 7 Copynumber: 8.0 Consensus size: 7
33394404 CTGATCGGGG
33394414 AAGAAAGA
1 AAGAAA-A
33394422 AAGGAAGAA
1 AA-GAA-AA
*
33394431 AA-AAGA
1 AAGAAAA
*
33394437 AAGAAGA
1 AAGAAAA
33394444 AAGAAAA
1 AAGAAAA
33394451 AAGAAAA
1 AAGAAAA
33394458 AAGAAAA
1 AAGAAAA
33394465 AAGAAAA
1 AAGAAAA
33394472 TAATTTTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
6 3 0.07
7 33 0.73
8 2 0.04
9 6 0.13
10 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:33394449 original size:18 final size:18
Alignment explanation
Indices: 33394414--33394463 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
33394404 CTGATCGGGG
*
33394414 AAGAAAGAAAGGAAGAAAA
1 AAGAAAG-AAGAAAGAAAA
33394433 AAGAAAGAAGAAAGAAAA
1 AAGAAAGAAGAAAGAAAA
*
33394451 AAGAAAAAAGAAA
1 AAGAAAGAAGAAA
33394464 AAAGAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 22 0.76
19 7 0.24
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (18 bp):
AAGAAAGAAGAAAGAAAA
Found at i:33394599 original size:16 final size:16
Alignment explanation
Indices: 33394576--33394616 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
33394566 CAGATCAACC
33394576 CAAAAAAATAGCAGCAG
1 CAAAAAAA-AGCAGCAG
*
33394593 CAAAAAAAAGCAGTAG
1 CAAAAAAAAGCAGCAG
*
33394609 TAAAAAAA
1 CAAAAAAA
33394617 CAGTAGGCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.66, C:0.12, G:0.15, T:0.07
Consensus pattern (16 bp):
CAAAAAAAAGCAGCAG
Found at i:33395199 original size:20 final size:20
Alignment explanation
Indices: 33395139--33395199 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
33395129 CCGTGTTTCG
*
33395139 AAATTTTCGTGTCTTCAAAA
1 AAATTTTCGTGTTTTCAAAA
*
33395159 AATTTTTC-TCGTGTTTC-AAA
1 AAATTTTCGT-GT-TTTCAAAA
*
33395179 AAATATTCGTGTTTTCAAAA
1 AAATTTTCGTGTTTTCAAAA
33395199 A
1 A
33395200 TAAGGCAACG
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
19 5 0.15
20 24 0.73
21 4 0.12
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (20 bp):
AAATTTTCGTGTTTTCAAAA
Found at i:33395201 original size:18 final size:18
Alignment explanation
Indices: 33395096--33395199 Score: 61
Period size: 19 Copynumber: 5.4 Consensus size: 18
33395086 AATCAAAATA
* *
33395096 TTCAAAAACAAATTCGTATT
1 TTCAAAAA-ATATTCGT-GT
33395116 TTCAAAAAA-ATTCCCGTGT
1 TTCAAAAAATATT--CGTGT
* *
33395135 TTC--GAAATTTTCGTGT
1 TTCAAAAAATATTCGTGT
*
33395151 CTTCAAAAAATTTTTCTCGTGT
1 -TTCAAAAAA--TAT-TCGTGT
33395173 TTCAAAAAATATTCGTGTT
1 TTCAAAAAATATTCGTG-T
33395192 TTCAAAAA
1 TTCAAAAA
33395200 TAAGGCAACG
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
16 5 0.07
17 6 0.09
18 10 0.14
19 19 0.28
20 11 0.16
21 12 0.17
22 6 0.09
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (18 bp):
TTCAAAAAATATTCGTGT
Found at i:33395411 original size:18 final size:18
Alignment explanation
Indices: 33395385--33395466 Score: 64
Period size: 18 Copynumber: 4.7 Consensus size: 18
33395375 AAGAATCCGT
33395385 TTTTC-AAAATTCTCATG
1 TTTTCAAAAATTCTCATG
33395402 TTTTCAAAAAAATTCT-AT-
1 TTTTC--AAAAATTCTCATG
* * **
33395420 TTTTCAAAATTTTTTGTG
1 TTTTCAAAAATTCTCATG
* *
33395438 TTTTCAACAATTCTCGTG
1 TTTTCAAAAATTCTCATG
33395456 -TTTCAAAAATT
1 TTTTCAAAAATT
33395467 TTCGTGTCTC
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
16 7 0.13
17 16 0.31
18 19 0.37
19 2 0.04
20 8 0.15
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.49
Consensus pattern (18 bp):
TTTTCAAAAATTCTCATG
Found at i:33395460 original size:35 final size:34
Alignment explanation
Indices: 33395421--33395516 Score: 113
Period size: 35 Copynumber: 2.8 Consensus size: 34
33395411 AAATTCTATT
*
33395421 TTTCAAAATTTTTTGTGTTTTCAACAATTCTCGTG
1 TTTCAAAATTTTTTGTGTTTTCAA-AATTATCGTG
* * *
33395456 TTTCAAAAATTTTCGTG-TCTCTAAAATTATCGTG
1 TTTCAAAATTTTTTGTGTTTTC-AAAATTATCGTG
*
33395490 TTTTAAAATTTTTTCGTGTTTTCAAAA
1 TTTCAAAATTTTTT-GTGTTTTCAAAA
33395517 AAAATCGTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
34 23 0.46
35 24 0.48
36 3 0.06
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.50
Consensus pattern (34 bp):
TTTCAAAATTTTTTGTGTTTTCAAAATTATCGTG
Found at i:33395466 original size:17 final size:17
Alignment explanation
Indices: 33395386--33395517 Score: 70
Period size: 17 Copynumber: 7.5 Consensus size: 17
33395376 AGAATCCGTT
*
33395386 TTTC-AAAATTCTCATG
1 TTTCAAAAATTCTCGTG
* *
33395402 TTTTCAAAAAAATTCT-ATT
1 -TTTC--AAAAATTCTCGTG
* * *
33395421 TTTCAAAATTTTTTGTG
1 TTTCAAAAATTCTCGTG
*
33395438 TTTTCAACAATTCTCGTG
1 -TTTCAAAAATTCTCGTG
*
33395456 TTTCAAAAATTTTCGTG
1 TTTCAAAAATTCTCGTG
* * *
33395473 TCTCTAAAATTATCGTG
1 TTTCAAAAATTCTCGTG
* * *
33395490 TTTTAAAATTTTTTCGTG
1 TTTCAAAA-ATTCTCGTG
33395508 TTTTCAAAAA
1 -TTTCAAAAA
33395518 AAATCGTTTT
Statistics
Matches: 87, Mismatches: 21, Indels: 13
0.72 0.17 0.11
Matches are distributed among these distances:
16 7 0.08
17 39 0.45
18 24 0.28
19 9 0.10
20 8 0.09
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.48
Consensus pattern (17 bp):
TTTCAAAAATTCTCGTG
Found at i:33395508 original size:18 final size:17
Alignment explanation
Indices: 33395420--33395516 Score: 83
Period size: 18 Copynumber: 5.5 Consensus size: 17
33395410 AAAATTCTAT
*
33395420 TTTTCAAAATTTTTTGTG
1 TTTTCAAAA-TTTTCGTG
*
33395438 TTTTCAACAATTCTCGTG
1 TTTTCAA-AATTTTCGTG
33395456 -TTTCAAAAATTTTCGTG
1 TTTTC-AAAATTTTCGTG
* *
33395473 -TCTCTAAAATTATCGTG
1 TTTTC-AAAATTTTCGTG
33395490 TTTT-AAAATTTTTTCGTG
1 TTTTCAAAA--TTTTCGTG
33395508 TTTTCAAAA
1 TTTTCAAAA
33395517 AAAATCGTTT
Statistics
Matches: 65, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
16 4 0.06
17 27 0.42
18 28 0.43
19 6 0.09
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.51
Consensus pattern (17 bp):
TTTTCAAAATTTTCGTG
Found at i:33397140 original size:6 final size:7
Alignment explanation
Indices: 33397124--33397148 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
33397114 TCAACTTTTA
33397124 TTTTGAT
1 TTTTGAT
33397131 TTTTGAT
1 TTTTGAT
33397138 TTTTGAT
1 TTTTGAT
33397145 TTTT
1 TTTT
33397149 ACTTTTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (7 bp):
TTTTGAT
Found at i:33401802 original size:4 final size:4
Alignment explanation
Indices: 33401795--33401898 Score: 52
Period size: 4 Copynumber: 25.2 Consensus size: 4
33401785 AAATAAGCCC
* * *
33401795 ATAA ATAA TATAA ATAA ATAA CATAA AAAA ACTAA TATAA ACTAG ATTA
1 ATAA ATAA -ATAA ATAA ATAA -ATAA ATAA A-TAA -ATAA A-TAA ATAA
* * * * * *
33401844 A-AA GT-T ACAA ATAA GTAA AGAA ATAA ATAA A-ATA TTAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA-A ATAA ATAA ATAA
33401890 ATAA ATAA A
1 ATAA ATAA A
33401899 ACCCCTTCTC
Statistics
Matches: 73, Mismatches: 18, Indels: 18
0.67 0.17 0.17
Matches are distributed among these distances:
3 2 0.03
4 53 0.73
5 17 0.23
6 1 0.01
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:33401813 original size:13 final size:13
Alignment explanation
Indices: 33401795--33401835 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
33401785 AAATAAGCCC
33401795 ATAAATAATATAA
1 ATAAATAATATAA
*
33401808 ATAAATAACATAA
1 ATAAATAATATAA
*
33401821 AAAAACTAATATAA
1 ATAAA-TAATATAA
33401835 A
1 A
33401836 CTAGATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
13 16 0.67
14 8 0.33
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (13 bp):
ATAAATAATATAA
Found at i:33406585 original size:22 final size:22
Alignment explanation
Indices: 33406560--33406601 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
33406550 TATTTTCCTT
33406560 TTTTACATTATTTC-TCTTTTTC
1 TTTTACATT-TTTCTTCTTTTTC
*
33406582 TTTTTCATTTTTCTTCTTTT
1 TTTTACATTTTTCTTCTTTT
33406602 ATAATATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTTACATTTTTCTTCTTTTTC
Found at i:33407424 original size:30 final size:29
Alignment explanation
Indices: 33407353--33407437 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 29
33407343 ATATTTTATA
* *
33407353 TATCATTATATTAAATAATATAAATATCATT
1 TATCATTATATTAAA-ATTTTAAA-ATCATT
33407384 TATCATTATATTAAAATTTTAAAATCATAT
1 TATCATTATATTAAAATTTTAAAATCAT-T
* * * *
33407414 TTTTATTATATTTAATTTTTAAAA
1 TATCATTATATTAAAATTTTAAAA
33407438 AATATATATA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
29 5 0.11
30 27 0.57
31 15 0.32
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.51
Consensus pattern (29 bp):
TATCATTATATTAAAATTTTAAAATCATT
Found at i:33410711 original size:7 final size:7
Alignment explanation
Indices: 33410691--33410730 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
33410681 ATTTATTAAA
33410691 AATTTAT
1 AATTTAT
33410698 AAATTTAT
1 -AATTTAT
33410706 AATTTAT
1 AATTTAT
33410713 AA-TT-T
1 AATTTAT
33410718 AATTTAT
1 AATTTAT
33410725 AATTTA
1 AATTTA
33410731 ATTGACAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 3 0.10
6 4 0.13
7 16 0.53
8 7 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
AATTTAT
Found at i:33410722 original size:12 final size:12
Alignment explanation
Indices: 33410691--33410733 Score: 59
Period size: 12 Copynumber: 3.3 Consensus size: 12
33410681 ATTTATTAAA
33410691 AATTTATAAATTTAT
1 AATTTAT-AA-TT-T
33410706 AATTTATAATTT
1 AATTTATAATTT
33410718 AATTTATAATTT
1 AATTTATAATTT
33410730 AATT
1 AATT
33410734 GACAAACCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 17 0.61
13 2 0.07
14 2 0.07
15 7 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AATTTATAATTT
Found at i:33410805 original size:21 final size:22
Alignment explanation
Indices: 33410762--33410851 Score: 139
Period size: 22 Copynumber: 4.2 Consensus size: 22
33410752 CCCTAACCCT
* *
33410762 AACCCT-AACACTAAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
*
33410783 AACCATAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
33410805 AACCCTAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
33410827 AACCCT-AACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
33410848 AACC
1 AACC
33410852 GTAACCTAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
21 24 0.38
22 40 0.62
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.21
Consensus pattern (22 bp):
AACCCTAAACCCTTAACTTAAA
Found at i:33410811 original size:43 final size:41
Alignment explanation
Indices: 33410762--33410860 Score: 135
Period size: 43 Copynumber: 2.3 Consensus size: 41
33410752 CCCTAACCCT
33410762 AACCCTAACACTAAACTTAAAAACCATAAACCCTTAACTTAAA
1 AACCCTAAC-CTAAACTTAAAAACCAT-AACCCTTAACTTAAA
* *
33410805 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
1 AACCCT-AA-CCTAAACTTAAAAACCATAACCCTTAACTTAAA
*
33410848 AACCGTAACCTAA
1 AACCCTAACCTAA
33410861 TTTATTAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
41 4 0.08
42 2 0.04
43 26 0.52
44 17 0.34
45 1 0.02
ACGTcount: A:0.47, C:0.30, G:0.01, T:0.21
Consensus pattern (41 bp):
AACCCTAACCTAAACTTAAAAACCATAACCCTTAACTTAAA
Found at i:33410900 original size:12 final size:12
Alignment explanation
Indices: 33410883--33410912 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
33410873 TTATAAATTA
33410883 TAAATTTATAAT
1 TAAATTTATAAT
33410895 TAAATTTATAAT
1 TAAATTTATAAT
*
33410907 TTAATT
1 TAAATT
33410913 GACAAACCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TAAATTTATAAT
Found at i:33411012 original size:21 final size:21
Alignment explanation
Indices: 33410935--33411052 Score: 173
Period size: 21 Copynumber: 5.5 Consensus size: 21
33410925 TAAAAATCCT
*
33410935 AAACCCTAACCCTAAACTTAA
1 AAACCCTAACCCTTAACTTAA
* **
33410956 AAACCATAAACATTTAACTTAA
1 AAACCCT-AACCCTTAACTTAA
33410978 AAACCCTAAGCCCTTAACTTAA
1 AAACCCTAA-CCCTTAACTTAA
33411000 AAACCCTAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
*
33411021 AAACTCTAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
33411042 AAACCCTAACC
1 AAACCCTAACC
33411053 TAATTTATTA
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
21 50 0.58
22 36 0.42
ACGTcount: A:0.46, C:0.31, G:0.01, T:0.23
Consensus pattern (21 bp):
AAACCCTAACCCTTAACTTAA
Found at i:33411013 original size:174 final size:176
Alignment explanation
Indices: 33410662--33411029 Score: 580
Period size: 174 Copynumber: 2.1 Consensus size: 176
33410652 TTGAGTTATT
* *
33410662 ACTTAAAAACCCTAAACTAATTTATTAAAAATTTATAAATTTATAATTTATAATTTAATTTATAA
1 ACTTAAAAACCCTAAACTAATTTATTAAAAAATTATAAATTTATAATTTATAATTAAATTTATAA
33410727 TTTAATTGACAAACCCTAACAAAAACCCTAACCCTAACCCTAACACTAAACTTAAAAACCATAAA
66 TTTAATTGACAAACCCTAACAAAAACCCTAA--C-AACCCTAACACTAAACTTAAAAACCATAAA
*
33410792 CCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTA
128 CACTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTA
* *
33410841 ACTTAAAAACCGTAACCTAATTTATTAAAAAATTATAAA-TTATAAATTTATAATTAAATTTATA
1 ACTTAAAAACCCTAAACTAATTTATTAAAAAATTATAAATTTAT-AATTTATAATTAAATTTATA
* * *
33410905 ATTTAATTGACAAACCCTAATAAAAATCCT-A-AACCCTAACCCTAAACTTAAAAACCATAAACA
65 ATTTAATTGACAAACCCTAACAAAAACCCTAACAACCCTAACACTAAACTTAAAAACCATAAACA
* *
33410968 TTTAACTTAAAAACCCTAAGCCCTTAACTTAAAAACCCTAACCCTTA
130 CTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTA
*
33411015 ACTTAAAAACTCTAA
1 ACTTAAAAACCCTAA
33411030 CCCTTAACTT
Statistics
Matches: 176, Mismatches: 12, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
174 88 0.50
178 5 0.03
179 83 0.47
ACGTcount: A:0.48, C:0.21, G:0.01, T:0.30
Consensus pattern (176 bp):
ACTTAAAAACCCTAAACTAATTTATTAAAAAATTATAAATTTATAATTTATAATTAAATTTATAA
TTTAATTGACAAACCCTAACAAAAACCCTAACAACCCTAACACTAAACTTAAAAACCATAAACAC
TTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTA
Found at i:33411045 original size:195 final size:196
Alignment explanation
Indices: 33410775--33411131 Score: 619
Period size: 195 Copynumber: 1.8 Consensus size: 196
33410765 CCTAACACTA
33410775 AACTTAAAAACCATAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTT
1 AACTTAAAAACCATAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTT
* *
33410840 AACTTAAAAACCGTAACCTAATTTATTAAAAAATTATAAA-TTATAAATTTATAATTAAATTTAT
66 AACTTAAAAACCCTAACCTAATTTATTAAAAAATTAAAAATTTA-AAATTTATAATTAAATTTAT
* *
33410904 AATTTAATTGACAAACCCTAATAAAAATCCTAAACCCTAACCCTAAACTTAAAAACCATAAACAT
130 AATTTAATTGACAAACCCTAACAAAAACCCTAAACCCTAACCCTAAACTTAAAAACCATAAACAT
33410969 TT
195 TT
* * *
33410971 AACTTAAAAACCCTAAGCCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACTCTAACCCTT
1 AACTTAAAAACCATAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTT
*
33411035 AACTTAAAAACCCTAACCTAATTTATTAAAAATTTAAAAATTTAAAATTTATAATTAAATTTATA
66 AACTTAAAAACCCTAACCTAATTTATTAAAAAATTAAAAATTTAAAATTTATAATTAAATTTATA
33411100 ATTTAATTGACAAACCCTAACAAAAACCCTAA
131 ATTTAATTGACAAACCCTAACAAAAACCCTAA
33411132 CCGGATCAAC
Statistics
Matches: 152, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
195 115 0.76
196 37 0.24
ACGTcount: A:0.48, C:0.21, G:0.01, T:0.29
Consensus pattern (196 bp):
AACTTAAAAACCATAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTT
AACTTAAAAACCCTAACCTAATTTATTAAAAAATTAAAAATTTAAAATTTATAATTAAATTTATA
ATTTAATTGACAAACCCTAACAAAAACCCTAAACCCTAACCCTAAACTTAAAAACCATAAACATT
T
Found at i:33411064 original size:43 final size:42
Alignment explanation
Indices: 33410935--33411066 Score: 167
Period size: 43 Copynumber: 3.1 Consensus size: 42
33410925 TAAAAATCCT
* * *
33410935 AAACCCTAACCCTAAACTTAAAAACCATAAACATTTAACTTAA
1 AAACCCTAACCCTTAACTTAAAAACCCTAACCATTT-ACTTAA
* *
33410978 AAACCCTAAGCCCTTAACTTAAAAACCCTAACCCTTAACTTAA
1 AAACCCTAA-CCCTTAACTTAAAAACCCTAACCATTTACTTAA
*
33411021 AAACTCTAACCCTTAACTTAAAAACCCTAACCTAATTTA-TTAA
1 AAACCCTAACCCTTAACTTAAAAACCCTAACC--ATTTACTTAA
33411064 AAA
1 AAA
33411067 TTTAAAAATT
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
42 23 0.29
43 30 0.38
44 25 0.32
ACGTcount: A:0.47, C:0.27, G:0.01, T:0.25
Consensus pattern (42 bp):
AAACCCTAACCCTTAACTTAAAAACCCTAACCATTTACTTAA
Found at i:33412194 original size:2 final size:2
Alignment explanation
Indices: 33412187--33412217 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
33412177 TAAAGTACAA
33412187 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33412218 AAATAACACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33417881 original size:47 final size:47
Alignment explanation
Indices: 33417827--33418048 Score: 246
Period size: 47 Copynumber: 4.7 Consensus size: 47
33417817 AAAAGCTGCT
* * * *
33417827 AATACGTTGTGGATGAATCACTGGTCGAGTAGATGACTGCCGACTGA
1 AATACGTTGTGGATAAACCACTGGTCGAGCAGATGACTGCCGACTAA
* * * * *
33417874 AATACGTTGTGGATAAATCATTGGTCAAACAGATGACTGCTGACTAA
1 AATACGTTGTGGATAAACCACTGGTCGAGCAGATGACTGCCGACTAA
* * * ** *
33417921 AATACGTTATAGATAAACTACTGGTCGAGCAGATGTTTGTCGACTAA
1 AATACGTTGTGGATAAACCACTGGTCGAGCAGATGACTGCCGACTAA
* * * * *
33417968 AATACGTTATGGATAAACCATTGGTCGAGTAGATGTCTGCCGATTAA
1 AATACGTTGTGGATAAACCACTGGTCGAGCAGATGACTGCCGACTAA
* *
33418015 AATATGTTGTGGATAAACCACTGGTCGAGAAGAT
1 AATACGTTGTGGATAAACCACTGGTCGAGCAGAT
33418049 AAACTGCTGA
Statistics
Matches: 146, Mismatches: 29, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 146 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (47 bp):
AATACGTTGTGGATAAACCACTGGTCGAGCAGATGACTGCCGACTAA
Found at i:33418209 original size:34 final size:35
Alignment explanation
Indices: 33418163--33418237 Score: 93
Period size: 34 Copynumber: 2.2 Consensus size: 35
33418153 GAACATATGG
33418163 TAGC-AATCAATATGCTTATAACAGT-TCAATACAA
1 TAGCAAATCAATATGCTTATAACA-TATCAATACAA
* * *
33418197 TAGCAAAT-AATATGTTTATAACATATCGATTCAA
1 TAGCAAATCAATATGCTTATAACATATCAATACAA
33418231 TAGCAAA
1 TAGCAAA
33418238 AGTCATGCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 1 0.03
34 32 0.89
35 3 0.08
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (35 bp):
TAGCAAATCAATATGCTTATAACATATCAATACAA
Found at i:33420674 original size:27 final size:27
Alignment explanation
Indices: 33420636--33420696 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
33420626 AGTGGGCCCC
* * *
33420636 ACTATTCGCGCCTCTGAGTTAGGCACA
1 ACTAGTCGCGCCTCCGAGATAGGCACA
*
33420663 ACTAGTCGCGCCTCCGAGATAGGCTCA
1 ACTAGTCGCGCCTCCGAGATAGGCACA
33420690 ACTAGTC
1 ACTAGTC
33420697 AACCTGTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.23, C:0.31, G:0.23, T:0.23
Consensus pattern (27 bp):
ACTAGTCGCGCCTCCGAGATAGGCACA
Found at i:33439306 original size:49 final size:49
Alignment explanation
Indices: 33439252--33439419 Score: 291
Period size: 49 Copynumber: 3.4 Consensus size: 49
33439242 GTTTATATTA
* *
33439252 ATGTAATAAAATACAAAATAGTTTATTTTGAATAATTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
33439301 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
* *
33439350 ATTTAATAAAATATAAAATAGTTTATTTTGAATATTTTGATATTATTTC
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
*
33439399 ATTTAATAAAATACAAAATAG
1 ATGTAATAAAATACAAAATAG
33439420 CTAATATTTT
Statistics
Matches: 114, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 114 1.00
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (49 bp):
ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
Found at i:33442096 original size:124 final size:123
Alignment explanation
Indices: 33441855--33442264 Score: 642
Period size: 124 Copynumber: 3.3 Consensus size: 123
33441845 CCCAAACATG
* ** *
33441855 CTACTGTAGCAAAAACTTGTCCATGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
* * * *
33441920 TTGAAGCGTTTTTTATACTATTTTCTTAGAAACGTCAACTCGAAATTATTTTTTAGGAC
66 TTGAAGC-ATTTTTATACTATTTACTCAGAAACGTCAACTCGAAATTATTTTTCAGGAC
*
33441979 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGAGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
* *
33442044 TTCAAGCATTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
66 TTGAAGCATTTTTATACTATTTACTCAGAAACGTCAACTCGAAATTA-TTTTTCAGGAC
* *
33442103 CTACTGTAGCAAAAGCACGTCCTCGTGGGAGCGATTAT-AGAAATTCTTCTGATAAAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATT-TCAGAAATTCTTCTGATAAAGCATCCTG
33442167 CTTGAAGCATTTTTTATACTATTTACTCAGAAACGTCAACTCGAAATTATTTTTCAGGAC
65 CTTGAAGCA-TTTTTATACTATTTACTCAGAAACGTCAACTCGAAATTATTTTTCAGGAC
* *
33442227 CTACTGTAGCAAAAGCGCATCTACGTGGGAGCGATTTC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTC
33442265 CTTAATAAAT
Statistics
Matches: 263, Mismatches: 19, Indels: 8
0.91 0.07 0.03
Matches are distributed among these distances:
123 38 0.14
124 186 0.71
125 39 0.15
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (123 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
TTGAAGCATTTTTATACTATTTACTCAGAAACGTCAACTCGAAATTATTTTTCAGGAC
Found at i:33442462 original size:6 final size:6
Alignment explanation
Indices: 33442451--33442476 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
33442441 AAATCCTAAA
33442451 AACCCT AACCCT AACCCT AACCCT AA
1 AACCCT AACCCT AACCCT AACCCT AA
33442477 AAACCCAAAA
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:0.38, C:0.46, G:0.00, T:0.15
Consensus pattern (6 bp):
AACCCT
Found at i:33442592 original size:40 final size:40
Alignment explanation
Indices: 33442543--33442619 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
33442533 TACGTGGCAA
**
33442543 CAAAACGCGCCCTTGAGGGA-GTGATTTTCAT-CCACGTAAG
1 CAAAACGCGCCC-CCAGGGACGTGATTTTC-TGCCACGTAAG
*
33442583 CAAAGCGCGCCCCCAGGGACGTGATTTTCTGCCACGT
1 CAAAACGCGCCCCCAGGGACGTGATTTTCTGCCACGT
33442620 CCCCTGACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 6 0.19
40 26 0.81
ACGTcount: A:0.23, C:0.30, G:0.26, T:0.21
Consensus pattern (40 bp):
CAAAACGCGCCCCCAGGGACGTGATTTTCTGCCACGTAAG
Found at i:33444432 original size:25 final size:25
Alignment explanation
Indices: 33444404--33444451 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
33444394 TTAGAATTTT
33444404 ATTTTAAAATTTTTAAAAAATATAA
1 ATTTTAAAATTTTTAAAAAATATAA
* * *
33444429 ATTTTAAAGTTTTTTATAAATAT
1 ATTTTAAAATTTTTAAAAAATAT
33444452 TTTGAATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
ATTTTAAAATTTTTAAAAAATATAA
Found at i:33444461 original size:19 final size:19
Alignment explanation
Indices: 33444440--33444500 Score: 70
Period size: 20 Copynumber: 3.2 Consensus size: 19
33444430 TTTTAAAGTT
*
33444440 TTTTATAAA-TATTTTGAA
1 TTTTAAAAATTATTTTGAA
33444458 TTTTAAAAATTATTTTGAAA
1 TTTTAAAAATTATTTTG-AA
* * *
33444478 ATTTGAAAGTTATTTTGAA
1 TTTTAAAAATTATTTTGAA
33444497 TTTT
1 TTTT
33444501 TTTTTTTGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
18 8 0.22
19 12 0.33
20 16 0.44
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (19 bp):
TTTTAAAAATTATTTTGAA
Found at i:33446734 original size:21 final size:21
Alignment explanation
Indices: 33446704--33446744 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
33446694 TCACCTGCAA
* *
33446704 CAAAATGTATCGATACTTTTT
1 CAAAAAGTATCGATAATTTTT
33446725 CAAAAAGTATCGATAATTTT
1 CAAAAAGTATCGATAATTTT
33446745 AACATTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
CAAAAAGTATCGATAATTTTT
Found at i:33448293 original size:229 final size:226
Alignment explanation
Indices: 33447934--33448488 Score: 592
Period size: 229 Copynumber: 2.4 Consensus size: 226
33447924 AATCATTCCC
* * * * * *
33447934 GGCGTTTT-TGAGAAAGCGCTGTAAAAAACCTAGCGCAACGACGCCGTTTCCCCAGCATTC-GGT
1 GGCGTTTTCTG-GAAAGCGCCGCAAAAAAACTAGCGCAACGACGTCGTTTCCCGAGCTTTCAGG-
* **
33447997 GATTTAGCGGCGTTTTTCAGTAAGCGCCGCTAATGCTCAAGGCTTTAGCGGCGTTTCTAGGAAAG
64 GATTTAGCGGCGTTTTACAAAAAGCGCCGCTAATGCTCAAGGCTTTAGCGGCGTTTCTAGGAAAG
* * * *
33448062 CGCCGCAAAAATAA-CTAAGCTCAACGATGTCGTTTCCCGAGCTTTCAGGGA-TTTAGCGGCGCT
129 CGCCGCAAAAAAAACCTAAGCCCAACGACGCCGTTTCCCG-GCTTTCAGGGATTTTAGCGGCG-T
33448125 TTCT-ATAAAGCGCCGCTAATGGTT-AGGTCTTTAGCA
192 TTCTGATAAAGCGCCGCTAAT-GTTCA-GTCTTTAG-A
**
33448161 -GCG-TTTCTGGAAAAGCGCCGCTACGTAAAACTAGCGCAACGACGTC-TTCTCCCGAGCTTTCA
1 GGCGTTTTCTGG-AAAGCGCCGC-A-AAAAAACTAGCGCAACGACGTCGTT-TCCCGAGCTTTCA
* * * *
33448223 GGGATTTAGCGGCGCTTTTACAAAAAGCGCCGCTAATGCTGAAGTCTTTAGCGGCGTTT-TTGTT
62 GGGATTTAGCGGCG-TTTTACAAAAAGCGCCGCTAATGCTCAAGGCTTTAGCGGCGTTTCTAG-G
* * * *
33448287 AAAGCGCCGCAAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGGCTTTCGGGGATTTTATCGGC
125 AAAGCGCCGCAAAAAAAACCTAAGCCCAACGACGCCGTTTCCCGGCTTTCAGGGATTTTAGCGGC
* *
33448352 GTTTTTGTTAAAGCGCCGCTAATGTTCAGTCTTTAGA
190 GTTTCTGATAAAGCGCCGCTAATGTTCAGTCTTTAGA
* * * * * * *
33448389 GGCGTTTTTTGGAAAGCGCCGCAAAAAAACTAAGTGCAACGTCGTCGTTTTCTGTGCTTTTGAGG
1 GGCGTTTTCTGGAAAGCGCCGCAAAAAAACT-AGCGCAACGACGTCGTTTCCCGAGC-TTTCAGG
*
33448454 GATTTAGCGGCGTTTTTA-GAAAAGCGCCGCTAATG
64 GATTTAGCGGCG-TTTTACAAAAAGCGCCGCTAATG
33448489 ATAAGGGATT
Statistics
Matches: 275, Mismatches: 36, Indels: 33
0.80 0.10 0.10
Matches are distributed among these distances:
225 4 0.01
226 13 0.05
227 9 0.03
228 77 0.28
229 121 0.44
230 51 0.19
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (226 bp):
GGCGTTTTCTGGAAAGCGCCGCAAAAAAACTAGCGCAACGACGTCGTTTCCCGAGCTTTCAGGGA
TTTAGCGGCGTTTTACAAAAAGCGCCGCTAATGCTCAAGGCTTTAGCGGCGTTTCTAGGAAAGCG
CCGCAAAAAAAACCTAAGCCCAACGACGCCGTTTCCCGGCTTTCAGGGATTTTAGCGGCGTTTCT
GATAAAGCGCCGCTAATGTTCAGTCTTTAGA
Found at i:33448335 original size:115 final size:114
Alignment explanation
Indices: 33447933--33448488 Score: 499
Period size: 114 Copynumber: 4.9 Consensus size: 114
33447923 TAATCATTCC
* * * * * * *
33447933 CGGCGTTTTTGAGAAAGCGCTG-TAAAAAACCT-AGCGCAACGACGCCGTTTCCCCAGCATTC-G
1 CGGCGTTTTTGTGAAAGCGCCGCAAAAAAAACTAAGCGCAACGACGTCGTTTCCCGAGCTTTCAG
* ** * *
33447995 GTGATTTAGCGGCGTTTTTCAGTAAGCGCCGCTAATGCTCAAGGCTTTAG
66 G-GATTTAGCGGCGTTTTACAAAAAGCGCCGCTAATGCTTAAGTCTTTAG
* * * *
33448045 CGGCGTTTCTAG-GAAAGCGCCGCAAAAATAACTAAGCTCAACGATGTCGTTTCCCGAGCTTTCA
1 CGGCGTTT-TTGTGAAAGCGCCGCAAAAAAAACTAAGCGCAACGACGTCGTTTCCCGAGCTTTCA
* * * *
33448109 GGGATTTAGCGGCGCTTT-CTATAAAGCGCCGCTAATGGTTAGGTCTTTAG
65 GGGATTTAGCGGCGTTTTAC-AAAAAGCGCCGCTAATGCTTAAGTCTTTAG
* * ***
33448159 CAGCGTTTCTG-GAAAAGCGCCGCTACGTAAAACT-AGCGCAACGACGTC-TTCTCCCGAGCTTT
1 CGGCGTTTTTGTG-AAAGCGCCGC-AAAAAAAACTAAGCGCAACGACGTCGTT-TCCCGAGCTTT
*
33448221 CAGGGATTTAGCGGCGCTTTTACAAAAAGCGCCGCTAATGCTGAAGTCTTTAG
63 CAGGGATTTAGCGGCG-TTTTACAAAAAGCGCCGCTAATGCTTAAGTCTTTAG
* * * * * *
33448274 CGGCGTTTTTGTTAAAGCGCCGCAAAAAAAACCTAAGCCCAACGACGCCGTTTTCTG-GCTTTCG
1 CGGCGTTTTTGTGAAAGCGCCGCAAAAAAAA-CTAAGCGCAACGACGTCGTTTCCCGAGCTTTCA
* **** *
33448338 GGGATTTTATCGGCGTTTTTGTTAAAGCGCCGCTAATG-TTCAGTCTTTAG
65 GGGA-TTTAGCGGCGTTTTACAAAAAGCGCCGCTAATGCTTAAGTCTTTAG
* * * * * * *
33448388 AGGCGTTTTT-TGGAAAGCGCCGC-AAAAAAACTAAGTGCAACGTCGTCGTTTTCTGTGCTTTTG
1 CGGCGTTTTTGT-GAAAGCGCCGCAAAAAAAACTAAGCGCAACGACGTCGTTTCCCGAGC-TTTC
*
33448451 AGGGATTTAGCGGCGTTTTTA-GAAAAGCGCCGCTAATG
64 AGGGATTTAGCGGCG-TTTTACAAAAAGCGCCGCTAATG
33448489 ATAAGGGATT
Statistics
Matches: 364, Mismatches: 61, Indels: 37
0.79 0.13 0.08
Matches are distributed among these distances:
112 38 0.10
113 48 0.13
114 164 0.45
115 87 0.24
116 25 0.07
117 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (114 bp):
CGGCGTTTTTGTGAAAGCGCCGCAAAAAAAACTAAGCGCAACGACGTCGTTTCCCGAGCTTTCAG
GGATTTAGCGGCGTTTTACAAAAAGCGCCGCTAATGCTTAAGTCTTTAG
Found at i:33448785 original size:7 final size:7
Alignment explanation
Indices: 33448775--33448823 Score: 62
Period size: 7 Copynumber: 6.7 Consensus size: 7
33448765 GAGTACTTAA
33448775 GGTTTAG
1 GGTTTAG
33448782 GGTTTATG
1 GGTTTA-G
33448790 GGTTTAG
1 GGTTTAG
33448797 GGTTTAG
1 GGTTTAG
**
33448804 GGATTTTT
1 GG-TTTAG
33448812 GGTTTAG
1 GGTTTAG
33448819 GGTTT
1 GGTTT
33448824 GAACGGTAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
7 24 0.67
8 12 0.33
ACGTcount: A:0.12, C:0.00, G:0.39, T:0.49
Consensus pattern (7 bp):
GGTTTAG
Found at i:33448795 original size:15 final size:14
Alignment explanation
Indices: 33448775--33448823 Score: 62
Period size: 15 Copynumber: 3.4 Consensus size: 14
33448765 GAGTACTTAA
33448775 GGTTTAGGGTTTATG
1 GGTTTAGGGTTTA-G
33448790 GGTTTAGGGTTTAG
1 GGTTTAGGGTTTAG
**
33448804 GGATTTTTGGTTTAG
1 GG-TTTAGGGTTTAG
33448819 GGTTT
1 GGTTT
33448824 GAACGGTAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
14 6 0.19
15 25 0.81
ACGTcount: A:0.12, C:0.00, G:0.39, T:0.49
Consensus pattern (14 bp):
GGTTTAGGGTTTAG
Found at i:33452800 original size:7 final size:7
Alignment explanation
Indices: 33452788--33452831 Score: 56
Period size: 7 Copynumber: 6.4 Consensus size: 7
33452778 TCATGTTATC
*
33452788 ATAAAAG
1 ATAAAAT
33452795 AT-AAA-
1 ATAAAAT
33452800 ATAAAAT
1 ATAAAAT
33452807 ATAAAAT
1 ATAAAAT
33452814 ATAAAAT
1 ATAAAAT
33452821 ATAAAAAT
1 AT-AAAAT
33452829 ATA
1 ATA
33452832 TGTTTTCTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 2 0.06
6 6 0.18
7 19 0.56
8 7 0.21
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (7 bp):
ATAAAAT
Found at i:33453228 original size:9 final size:9
Alignment explanation
Indices: 33453198--33453231 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
33453188 ACTCAAAACT
33453198 TACATAACC
1 TACATAACC
*
33453207 TAAATAACC
1 TACATAACC
*
33453216 TACATAACT
1 TACATAACC
33453225 TACATAA
1 TACATAA
33453232 TACAAAACTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (9 bp):
TACATAACC
Found at i:33455747 original size:66 final size:65
Alignment explanation
Indices: 33455639--33455809 Score: 202
Period size: 66 Copynumber: 2.6 Consensus size: 65
33455629 GAGCAAATTA
* * * *
33455639 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTG-GTGTTCAAAG-AAGATATGAAGAACTCC
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAG-GTTCAAAGAAAG-TATGAAGAACTCC
33455702 AG
64 AG
*
33455704 CTACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAAGAAAGTATGAAGAACTCCA
33455769 G
65 G
* * * * *
33455770 CAGCAGCTTAGAGCAGATGCGGCAGCAAGAGAAGCAGAGG
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
33455810 CGGCAGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
65 2 0.02
66 86 0.93
67 4 0.04
ACGTcount: A:0.39, C:0.19, G:0.29, T:0.13
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAAGAAAGTATGAAGAACTCCAG
Found at i:33455807 original size:21 final size:21
Alignment explanation
Indices: 33455781--33455824 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
33455771 AGCAGCTTAG
*
33455781 AGCAGATGCGGCAGCAAGAGA
1 AGCAGAGGCGGCAGCAAGAGA
*
33455802 AGCAGAGGCGGCAGCGAGAGA
1 AGCAGAGGCGGCAGCAAGAGA
33455823 AG
1 AG
33455825 TACAGGCTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.18, G:0.43, T:0.02
Consensus pattern (21 bp):
AGCAGAGGCGGCAGCAAGAGA
Found at i:33455831 original size:21 final size:21
Alignment explanation
Indices: 33455788--33455831 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
33455778 TAGAGCAGAT
*
33455788 GCGGCAGCAAGAGAAGCAGAG
1 GCGGCAGCAAGAGAAGCACAG
* *
33455809 GCGGCAGCGAGAGAAGTACAG
1 GCGGCAGCAAGAGAAGCACAG
33455830 GC
1 GC
33455832 TGCTAAGAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.43, T:0.02
Consensus pattern (21 bp):
GCGGCAGCAAGAGAAGCACAG
Found at i:33455851 original size:42 final size:42
Alignment explanation
Indices: 33455800--33455892 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
33455790 GGCAGCAAGA
**
33455800 GAAGCAGAGGCGGCAGCGAGAGAAGTACAGGCTGCTA-AGAGG
1 GAAGCAGAGGCGAAAGCGAGAGAAGTACAGGCTGC-AGAGAGG
* * * * *
33455842 GAAGCAGAGGCTAAAGCGAGGGAAGTAGAGGTTGCAGCGAGG
1 GAAGCAGAGGCGAAAGCGAGAGAAGTACAGGCTGCAGAGAGG
33455884 GAAGCAGAG
1 GAAGCAGAG
33455893 CAGCGTCAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 1 0.02
42 42 0.98
ACGTcount: A:0.34, C:0.14, G:0.44, T:0.08
Consensus pattern (42 bp):
GAAGCAGAGGCGAAAGCGAGAGAAGTACAGGCTGCAGAGAGG
Found at i:33455862 original size:21 final size:21
Alignment explanation
Indices: 33455838--33455892 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
33455828 AGGCTGCTAA
33455838 GAGGGAAGCAGAGGCTAAAGC
1 GAGGGAAGCAGAGGCTAAAGC
* * **
33455859 GAGGGAAGTAGAGGTTGCAGC
1 GAGGGAAGCAGAGGCTAAAGC
33455880 GAGGGAAGCAGAG
1 GAGGGAAGCAGAG
33455893 CAGCGTCAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.35, C:0.11, G:0.47, T:0.07
Consensus pattern (21 bp):
GAGGGAAGCAGAGGCTAAAGC
Found at i:33456316 original size:43 final size:43
Alignment explanation
Indices: 33456241--33456377 Score: 188
Period size: 43 Copynumber: 3.2 Consensus size: 43
33456231 AAAGGTATTA
*
33456241 GTCTTTAGCGGCGTTTTTTGGTATAAGCGCCGCTATAGAAT-AGG
1 GTCTTTAGCGGCG-TTTTTGGTAAAAGCGCCGCTATAG-ATCAGG
33456285 GTCTTTAGCGGCGTTTTTGGTAAAAGCGCCGCTATAGATCAGG
1 GTCTTTAGCGGCGTTTTTGGTAAAAGCGCCGCTATAGATCAGG
* * **
33456328 GTCTTTAGTGGCGTTTGTGACCAAAA-CGCCGCTATAGATCAGG
1 GTCTTTAGCGGCGTTTTTG-GTAAAAGCGCCGCTATAGATCAGG
33456371 GTCTTTA
1 GTCTTTA
33456378 AAGCTCTTAC
Statistics
Matches: 86, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
42 2 0.02
43 67 0.78
44 17 0.20
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.32
Consensus pattern (43 bp):
GTCTTTAGCGGCGTTTTTGGTAAAAGCGCCGCTATAGATCAGG
Found at i:33462579 original size:18 final size:18
Alignment explanation
Indices: 33462553--33462594 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
33462543 GACTAGAAAA
* * *
33462553 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
33462571 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
33462589 AGGATA
1 AGGATA
33462595 TGCACCTGGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.45, C:0.07, G:0.29, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:33474948 original size:10 final size:10
Alignment explanation
Indices: 33474922--33474958 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
33474912 GTTTCCTATT
33474922 TATTCATTTC
1 TATTCATTTC
33474932 -A-TCATTTC
1 TATTCATTTC
33474940 TATTCATTTC
1 TATTCATTTC
*
33474950 TGTTCATTT
1 TATTCATTT
33474959 GATTCAACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
8 7 0.29
9 2 0.08
10 15 0.62
ACGTcount: A:0.19, C:0.19, G:0.03, T:0.59
Consensus pattern (10 bp):
TATTCATTTC
Found at i:33480522 original size:38 final size:37
Alignment explanation
Indices: 33480475--33480547 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 37
33480465 AAAAATAATA
33480475 TTATATTAATAG-ATTTAATATTTAATTTAAT-TTAAAAC
1 TTATATTAATAGTATTT--TA-TTAATTTAATATTAAAAC
*
33480513 TTATCTTAATAGTATTTTATTAATTTAATATTAAA
1 TTATATTAATAGTATTTTATTAATTTAATATTAAA
33480548 GTGATTATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 10 0.31
37 7 0.22
38 11 0.34
39 4 0.12
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (37 bp):
TTATATTAATAGTATTTTATTAATTTAATATTAAAAC
Found at i:33480560 original size:68 final size:72
Alignment explanation
Indices: 33480488--33480623 Score: 190
Period size: 68 Copynumber: 1.9 Consensus size: 72
33480478 TATTAATAGA
* * *
33480488 TTTAATATTTAATTTAATTTAAAACTTATC-T-TA-AT-AGTATTTTATTAATTTAATATTAAAG
1 TTTAATATTAAATTTAATTTAAAACTTATCTTGTAGATAAATATTATATTAATTTAATATTAAAG
33480549 TGATTAT
66 TGATTAT
* * *
33480556 TTTAATATTAAATTTAATTTAATATTTATCTTGTAGATAAATATTATGTTAATTTAATATTAAAG
1 TTTAATATTAAATTTAATTTAAAACTTATCTTGTAGATAAATATTATATTAATTTAATATTAAAG
33480621 TGA
66 TGA
33480624 CTAAGTTTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
68 27 0.47
69 1 0.02
70 2 0.03
71 2 0.03
72 26 0.45
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.51
Consensus pattern (72 bp):
TTTAATATTAAATTTAATTTAAAACTTATCTTGTAGATAAATATTATATTAATTTAATATTAAAG
TGATTAT
Found at i:33483491 original size:20 final size:20
Alignment explanation
Indices: 33483466--33483504 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
33483456 AATATAAGTG
*
33483466 ATAATGATGATAATAATAAT
1 ATAATGATGACAATAATAAT
33483486 ATAATGATGACAATAATAA
1 ATAATGATGACAATAATAA
33483505 GGAACAGCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.03, G:0.10, T:0.31
Consensus pattern (20 bp):
ATAATGATGACAATAATAAT
Found at i:33484756 original size:25 final size:25
Alignment explanation
Indices: 33484722--33484771 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
33484712 ACAGCCTGCA
33484722 AAAGAGAAAAAACAGGTTATGTGAT
1 AAAGAGAAAAAACAGGTTATGTGAT
33484747 AAAGAGAAAAAACAGGTTATGTGAT
1 AAAGAGAAAAAACAGGTTATGTGAT
33484772 TCATTGACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.04, G:0.24, T:0.20
Consensus pattern (25 bp):
AAAGAGAAAAAACAGGTTATGTGAT
Found at i:33493509 original size:40 final size:40
Alignment explanation
Indices: 33493465--33493544 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
33493455 TCATACAATC
* **
33493465 TTTGAAAATAAATTATTACGAACTTGATAACTATACCGTA
1 TTTGAAAATAAATCATTACGAACTCAATAACTATACCGTA
*
33493505 TTTGAAAATAAATCATTATGAACTCAATAACTATACCGTA
1 TTTGAAAATAAATCATTACGAACTCAATAACTATACCGTA
33493545 GAATAAGTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.34
Consensus pattern (40 bp):
TTTGAAAATAAATCATTACGAACTCAATAACTATACCGTA
Found at i:33496799 original size:28 final size:28
Alignment explanation
Indices: 33496764--33496829 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
33496754 ATAAAAAATA
*
33496764 ACCAAAATATTATAACTTTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTTATTT
33496792 ACCAAAATATTATAAATTTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTTATTT
33496820 ACCAAAATAT
1 ACCAAAATAT
33496830 ACCAAAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (28 bp):
ACCAAAATATTATAAATTTTTTTTATTT
Found at i:33497267 original size:19 final size:19
Alignment explanation
Indices: 33497243--33497308 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
33497233 ATTAAAAAAG
33497243 TTTAATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
* *
33497262 TTTAATGTAATAA-ACTAT
1 TTTAATTTAATAACTCTAT
* *
33497280 TCTCATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
33497299 TTTAATTTAA
1 TTTAATTTAA
33497309 AAAAATTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
18 14 0.37
19 24 0.63
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (19 bp):
TTTAATTTAATAACTCTAT
Found at i:33497561 original size:18 final size:19
Alignment explanation
Indices: 33497522--33497580 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 19
33497512 ATTTTATATT
33497522 TTAAATGAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
* *
33497541 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
33497559 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
33497578 TTA
1 TTA
33497581 CTTAATTAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 15 0.44
19 19 0.56
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (19 bp):
TTAAATGAAAATAGAGTTA
Found at i:33506293 original size:41 final size:41
Alignment explanation
Indices: 33506238--33506317 Score: 151
Period size: 41 Copynumber: 2.0 Consensus size: 41
33506228 CCTAATTGGA
33506238 AAAATAATTCTCTTATTCTAATAAAGTACTAAAAGATAAGG
1 AAAATAATTCTCTTATTCTAATAAAGTACTAAAAGATAAGG
*
33506279 AAAATAATTCTCTTATTCTAATAAATTACTAAAAGATAA
1 AAAATAATTCTCTTATTCTAATAAAGTACTAAAAGATAA
33506318 AATAAAATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.34
Consensus pattern (41 bp):
AAAATAATTCTCTTATTCTAATAAAGTACTAAAAGATAAGG
Found at i:33510231 original size:18 final size:19
Alignment explanation
Indices: 33510208--33510247 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
33510198 TAATTTATTC
33510208 TAAGATTTATCTA-CTAAA
1 TAAGATTTATCTACCTAAA
33510226 TAAGATTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
33510245 TAA
1 TAA
33510248 CTTTAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (19 bp):
TAAGATTTATCTACCTAAA
Found at i:33516652 original size:6 final size:6
Alignment explanation
Indices: 33516643--33516672 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
33516633 ATATAAAAAA
33516643 TTATAT TTATAT TTATAT TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT
33516673 ATTTTTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTATAT
Found at i:33516979 original size:19 final size:20
Alignment explanation
Indices: 33516943--33516980 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
33516933 ACTTTGATAA
*
33516943 AATTTGTAATTTTATATATC
1 AATTTGTAATTTGATATATC
*
33516963 AATTT-TAATTTGGTATAT
1 AATTTGTAATTTGATATAT
33516981 TTGTATACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (20 bp):
AATTTGTAATTTGATATATC
Found at i:33533912 original size:16 final size:16
Alignment explanation
Indices: 33533872--33533929 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 16
33533862 ATTTTAATCA
33533872 TAATTAAACATA-ATTAT
1 TAATTAAA-ATATATT-T
33533889 T-ATT-AAATATATTT
1 TAATTAAAATATATTT
33533903 TAATTAAAATATATAATT
1 TAATTAAAATATAT--TT
33533921 TAA-TAAAAT
1 TAATTAAAAT
33533930 TCTTATAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 5 0.14
15 8 0.22
16 11 0.31
17 7 0.19
18 5 0.14
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATTAAAATATATTT
Found at i:33533916 original size:18 final size:17
Alignment explanation
Indices: 33533895--33533929 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
33533885 TTATTATTAA
*
33533895 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
33533913 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
33533930 TCTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:33534069 original size:155 final size:157
Alignment explanation
Indices: 33533782--33534096 Score: 535
Period size: 155 Copynumber: 2.0 Consensus size: 157
33533772 TAGAATACCC
* *
33533782 TTAGCATAAATTTGTTTTGGTAAATGATTATTATTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGATAAATGATTATTATTATTGTTATTTAAATTTTAATAAGATTATTA
* * * *
33533847 TTATCAGTAATAAATATTTTAATCATAATTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAACCATAATTAAACATAATTATTATTAAATATATTTTAATTAAAA
33533912 TATATAATTTAATAAAATTCTT-ATAA
131 TATATAATTTAATAAAATTCTTAATAA
* *
33533938 TTAGCAGAAATTTGTTTTGATAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTA-TA
1 TTAGCAGAAATTTGTTTTGATAAATGATTATTATTATTGTTATTTAAATTTTAATAAGATTATTA
*
33534002 ATATCAATAATAAATAATTTAACCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAACCATAATTAAACATAATTATTATTAAATATATTTTAATTAAAA
33534067 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
33534094 TTA
1 TTA
33534097 ATATTCTTAT
Statistics
Matches: 149, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
155 84 0.56
156 65 0.44
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGATAAATGATTATTATTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAACCATAATTAAACATAATTATTATTAAATATATTTTAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:33534071 original size:18 final size:17
Alignment explanation
Indices: 33534050--33534084 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
33534040 TTATTATTAA
*
33534050 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
33534068 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
33534085 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:33534149 original size:39 final size:38
Alignment explanation
Indices: 33534105--33534383 Score: 111
Period size: 39 Copynumber: 7.0 Consensus size: 38
33534095 TAATATTCTT
33534105 ATATAAATTTACTCAAATCATAATATATGATACTGTAAA
1 ATATAAATTTACTCAAATCATAATATATGATACT-TAAA
* * ** *
33534144 ATATAAATTAACAT-AATTATTATTAAATATATTTTAATTAAA
1 ATATAAATTTAC-TCAA--ATCA-T-AATATATGATACTTAAA
* * * * ***
33534186 ATATATAATTTAATAAAATTCTTAATA-ATTAATA-TTCTT
1 ATATA-AATTTACTCAAA-TCATAATATA-TGATACTTAAA
*
33534225 ATATGAATTTACTCAAATCATAATATATGATACTGTAAA
1 ATATAAATTTACTCAAATCATAATATATGATACT-TAAA
* * ** *
33534264 ATATAAATTAACAT-AATTATTATTAAATATATTTTAATTAAA
1 ATATAAATTTAC-TCAA--ATCA-T-AATATATGATACTTAAA
* * * * ***
33534306 ATATATAATTTAATAAAATTCTTAATA-ATTAATA-TTCTT
1 ATATA-AATTTACTCAAA-TCATAATATA-TGATACTTAAA
*
33534345 ATATGAATTTACTCAAATCATAATATATGATACTATAAA
1 ATATAAATTTACTCAAATCATAATATATGATACT-TAAA
33534384 TGAAAATTTG
Statistics
Matches: 171, Mismatches: 45, Indels: 48
0.65 0.17 0.18
Matches are distributed among these distances:
37 22 0.13
38 24 0.14
39 41 0.24
40 16 0.09
41 10 0.06
42 24 0.14
43 34 0.20
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (38 bp):
ATATAAATTTACTCAAATCATAATATATGATACTTAAA
Found at i:33534191 original size:18 final size:17
Alignment explanation
Indices: 33534170--33534204 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
33534160 TTATTATTAA
*
33534170 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
33534188 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
33534205 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:33534311 original size:18 final size:17
Alignment explanation
Indices: 33534290--33534324 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
33534280 TTATTATTAA
*
33534290 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
33534308 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
33534325 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:33534456 original size:120 final size:120
Alignment explanation
Indices: 33534033--33534438 Score: 719
Period size: 120 Copynumber: 3.4 Consensus size: 120
33534023 ACCATATTTA
33534033 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
33534098 TATTCTTATATAAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
33534153 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
33534218 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
33534273 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
33534338 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTAT-AAATGA-AAATTT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAAT-ATAAA-TT
* * *
33534393 GAA-ATAATTAATATTAAATATATTTTAATTATAATATATGATTTAA
1 -AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAA
33534439 AATAATTTAA
Statistics
Matches: 278, Mismatches: 5, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
119 7 0.03
120 269 0.97
121 2 0.01
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:33534538 original size:92 final size:91
Alignment explanation
Indices: 33534461--33534669 Score: 217
Period size: 92 Copynumber: 2.3 Consensus size: 91
33534451 TAATTATAAC
* * * *
33534461 TAATAAATTATATTTTATGAATTTGTATAATCTAAAATAA-TAATTATTACATATAATTTAATAA
1 TAATAAATTATATTATATGAATTTATACAATCTAAAATAATTAA-TATTAAATATAATTTAATAA
* *
33534525 TTAATATTAAATTTCATAAAATACTTGA
65 TTAATATTAAATTTCAAAAAATAC-TAA
* * * *
33534553 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAAT-AG
1 TAATAAATTATATTATATGAATTTATACAATCTAAAATAATTAATATTAAATATAATTTAATAAT
* * *
33534617 TGATA-TATAATTTCATAAAATTCTCAA
66 TAATATTA-AATTTCAAAAAATACT-AA
* *
33534644 TAATAAATTGTTCTTATATGAATTTA
1 TAATAAATT-ATATTATATGAATTTA
33534670 CTAAAATCAA
Statistics
Matches: 102, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
90 3 0.03
91 29 0.28
92 67 0.66
93 3 0.03
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (91 bp):
TAATAAATTATATTATATGAATTTATACAATCTAAAATAATTAATATTAAATATAATTTAATAAT
TAATATTAAATTTCAAAAAATACTAA
Found at i:33548057 original size:20 final size:19
Alignment explanation
Indices: 33548020--33548059 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
33548010 AATTTCGAGG
* *
33548020 GTTTTTTTTTTTATTTGAA
1 GTTTTTTCTTTTACTTGAA
33548039 GTTTTTTCTTTTAGCTTGAA
1 GTTTTTTCTTTTA-CTTGAA
33548059 G
1 G
33548060 AAGGGGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.15, C:0.05, G:0.15, T:0.65
Consensus pattern (19 bp):
GTTTTTTCTTTTACTTGAA
Found at i:33550365 original size:54 final size:54
Alignment explanation
Indices: 33550262--33550365 Score: 127
Period size: 54 Copynumber: 1.9 Consensus size: 54
33550252 GCCATATCCC
* * **
33550262 ACCCGTGTCTCTACCTGTATAACTTACTGACTTGAGACACATGGTCGTGTTACA
1 ACCCGTGTCTCTACCCGTATAACTCACTGACTTGAGACACATGACCGTGTTACA
* * * * *
33550316 ACCCGTGTCTCTGCCCGTGTAACTCATTGACTTGGGTCACATGACCGTGT
1 ACCCGTGTCTCTACCCGTATAACTCACTGACTTGAGACACATGACCGTGT
33550366 AATCCAATTC
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 41 1.00
ACGTcount: A:0.20, C:0.28, G:0.21, T:0.31
Consensus pattern (54 bp):
ACCCGTGTCTCTACCCGTATAACTCACTGACTTGAGACACATGACCGTGTTACA
Found at i:33551027 original size:28 final size:29
Alignment explanation
Indices: 33550959--33551028 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
33550949 TTACAATTTA
*
33550959 AACTTATTTAATTTTTTATAATAATATAG
1 AACTAATTTAATTTTTTATAATAATATAG
* *
33550988 AGACAAAATTAATTTTTTAATAATAA-A-AG
1 A-ACTAATTTAATTTTTT-ATAATAATATAG
33551017 AACTAATTTAAT
1 AACTAATTTAAT
33551029 GTAGTCTCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
28 9 0.26
29 4 0.12
30 14 0.41
31 7 0.21
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (29 bp):
AACTAATTTAATTTTTTATAATAATATAG
Found at i:33576706 original size:2 final size:2
Alignment explanation
Indices: 33576699--33576738 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
33576689 NNNNNNNNNA
33576699 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33576739 TTCCTTACCC
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):
AT
Found at i:33583862 original size:30 final size:30
Alignment explanation
Indices: 33583819--33583877 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
33583809 AAACAGTTAA
* *
33583819 ACTTTAATCAGTATTCAAGCAAGCCCTTAT
1 ACTTTAATCAGTATCCAAACAAGCCCTTAT
* * *
33583849 ACTTTATTTAGTATCCAAATAAGCCCTTA
1 ACTTTAATCAGTATCCAAACAAGCCCTTA
33583878 ATTTTTAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (30 bp):
ACTTTAATCAGTATCCAAACAAGCCCTTAT
Done.