Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 13 of 91
Found at i:3889269 original size:17 final size:17
Alignment explanation
Indices: 3889247--3889290 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
3889237 AGTTGTTCAT
3889247 TCTCTCTCTCTCTCTCC
1 TCTCTCTCTCTCTCTCC
*
3889264 TCTCTCTCTCTCTCTCT
1 TCTCTCTCTCTCTCTCC
3889281 TCTCTCTCTC
1 TCTCTCTCTC
3889291 CGTCAGCGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (17 bp):
TCTCTCTCTCTCTCTCC
Found at i:3889309 original size:2 final size:2
Alignment explanation
Indices: 3889247--3889290 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
3889237 AGTTGTTCAT
3889247 TC TC TC TC TC TC TC TC -C TC TC TC TC TC TC TC TC T- TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3889287 TC TC
1 TC TC
3889291 CGTCAGCGTC
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3889452 original size:2 final size:2
Alignment explanation
Indices: 3889441--3889503 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
3889431 CCCCTTTCAN
3889441 CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3889482 CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT
3889504 TCTAGCTTGG
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 59 0.98
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:3899217 original size:28 final size:28
Alignment explanation
Indices: 3899186--3899252 Score: 116
Period size: 28 Copynumber: 2.4 Consensus size: 28
3899176 ATTATGGGTG
3899186 TTTGTGTTCTTGAATATTATTATGAATA
1 TTTGTGTTCTTGAATATTATTATGAATA
*
3899214 TTTGTGTTCTTGAATATTATTATGGATA
1 TTTGTGTTCTTGAATATTATTATGAATA
*
3899242 TTTGAGTTCTT
1 TTTGTGTTCTT
3899253 CATTAATATC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.24, C:0.04, G:0.16, T:0.55
Consensus pattern (28 bp):
TTTGTGTTCTTGAATATTATTATGAATA
Found at i:3911066 original size:253 final size:252
Alignment explanation
Indices: 3910490--3911408 Score: 1069
Period size: 253 Copynumber: 3.7 Consensus size: 252
3910480 TTAATAAAAA
** * * ** ** *
3910490 TTAACCATTTACAAATGTTAA--CGTAAATGTATAATAATAAAGATAAAAATTCTTACAGTGAAA
1 TTAACCATTTACAAATGTTAATTTATAAATGTATAAAAATAAAAATAAAAACACTTGTAATGAAA
* * * * * * * *
3910553 GTTATCCATTTAAACATCTTGGTGTAGATTTATAAGAATAAATGTTAAAATTCATAAAATTGAAA
66 ATTAGCCATTTAAAAATCTTGATGTAAATTTATAAGAATAAATGTAAAAAATCATAAAGTTGAAA
* * * * * * *
3910618 TAAACATTATAAAAAAATTAATGTAAATGTGTAAGAATTATCGTAACAAGTCAATTTAGATAAAA
131 TAAGCATTATTAAAATATTAACGTAAATGTGTAAGAGTTACCGTAACAAGTCAATTTAGACAAAA
* ** * * * * *
3910683 TAAACATATTTTTTCTTAAA-TAA--ATTT-CATTCATATTCTTGAGCAAAAACTAA
196 TAAACATACTTTTAGTAAAATTAATCATTTACATTTATATTCTTGAGAAAAAAATAT
* * *
3910736 TTAACCATTTACAAAGGTTAATTTATAAATGTATAAAAATAAAAATAAAAACACTTTTAATTAAA
1 TTAACCATTTACAAATGTTAATTTATAAATGTATAAAAATAAAAATAAAAACACTTGTAATGAAA
* * * * *
3910801 ATTAGTCATTTAAAAATCTTGATGTAAATTTATAATAATGAATGTAAATAATCATGAAGTTGAAA
66 ATTAGCCATTTAAAAATCTTGATGTAAATTTATAAGAATAAATGTAAAAAATCATAAAGTTGAAA
* * * *
3910866 TAAGCATTGTTAAGATATTGACATAAATGTGTAAGAGTTACCGTAACAAGTCAATTTAGACAAAA
131 TAAGCATTATTAAAATATTAACGTAAATGTGTAAGAGTTACCGTAACAAGTCAATTTAGACAAAA
* * *
3910931 CAAACATACTTTTAGTAAAAATTAATCATTTACATTTATATTAC-CGAGTAAAAAATAT
196 TAAACATACTTTTAGT-AAAATTAATCATTTACATTTATATT-CTTGAGAAAAAAATAT
* * *
3910989 TTAACTATTTACAAATGTTAATTTATAAATGTATAAAAATAAAAATAAAAATACTTGTAATAAAA
1 TTAACCATTTACAAATGTTAATTTATAAATGTATAAAAATAAAAATAAAAACACTTGTAATGAAA
* * * * *
3911054 ATTAACCATTTAAAACTCTTGATGTATATTTATAAGAATGAATATAAAAAATCATAAAGTTGAAA
66 ATTAGCCATTTAAAAATCTTGATGTAAATTTATAAGAATAAATGTAAAAAATCATAAAGTTGAAA
* * * * * * * * *
3911119 TAAGCATTGTTAAAATGTTAACGTAAATATGTAAGAGTTGCCATAACAATTCAACTTAAACAAAG
131 TAAGCATTATTAAAATATTAACGTAAATGTGTAAGAGTTACCGTAACAAGTCAATTTAGACAAAA
3911184 TAAACATACTTTTAGTGAAAATTAATCATTTACATTTATATTCTTGAGCAAAAAAATAT
196 TAAACATACTTTTAGT-AAAATTAATCATTTACATTTATATTCTTGAG-AAAAAAATAT
* ** * * * *
3911243 TTTATAATTTACTAATGTTAATTTATAAATGTATAAAACTAAAAATTAAAACACCTGTAATGAAA
1 TTAACCATTTACAAATGTTAATTTATAAATGTATAAAAATAAAAATAAAAACACTTGTAATGAAA
* * *
3911308 ATTAGCCATTTAAAAATCTTGATGTAAATTTATAAAAATAAATTTAAAAAATTATAAAGTTGAAA
66 ATTAGCCATTTAAAAATCTTGATGTAAATTTATAAGAATAAATGTAAAAAATCATAAAGTTGAAA
* *
3911373 TAAGCATTATTAAAATATTGACGTAAATGTATAAGA
131 TAAGCATTATTAAAATATTAACGTAAATGTGTAAGA
3911409 TTTATCGTTT
Statistics
Matches: 569, Mismatches: 94, Indels: 12
0.84 0.14 0.02
Matches are distributed among these distances:
246 20 0.04
248 150 0.26
249 3 0.01
250 3 0.01
252 5 0.01
253 233 0.41
254 155 0.27
ACGTcount: A:0.48, C:0.08, G:0.09, T:0.35
Consensus pattern (252 bp):
TTAACCATTTACAAATGTTAATTTATAAATGTATAAAAATAAAAATAAAAACACTTGTAATGAAA
ATTAGCCATTTAAAAATCTTGATGTAAATTTATAAGAATAAATGTAAAAAATCATAAAGTTGAAA
TAAGCATTATTAAAATATTAACGTAAATGTGTAAGAGTTACCGTAACAAGTCAATTTAGACAAAA
TAAACATACTTTTAGTAAAATTAATCATTTACATTTATATTCTTGAGAAAAAAATAT
Found at i:3912416 original size:19 final size:19
Alignment explanation
Indices: 3912392--3912429 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3912382 CCATTTGACT
3912392 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
3912411 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
3912430 ATTTAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:3915174 original size:15 final size:15
Alignment explanation
Indices: 3915149--3915190 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
3915139 GATCAGAGAT
3915149 TTTGG-TTTTAAAGC
1 TTTGGATTTTAAAGC
*
3915163 TTTGGATTTTAAAGT
1 TTTGGATTTTAAAGC
*
3915178 TTTTGATTTTAAA
1 TTTGGATTTTAAA
3915191 ATTGTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 5 0.20
15 20 0.80
ACGTcount: A:0.26, C:0.02, G:0.17, T:0.55
Consensus pattern (15 bp):
TTTGGATTTTAAAGC
Found at i:3919364 original size:21 final size:20
Alignment explanation
Indices: 3919335--3919391 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
3919325 AGAATAACAT
*
3919335 AAAATTAAAATAACTCACTAA
1 AAAAATAAAATAACTCA-TAA
* *
3919356 AAAAATAAACTAA-TTATAA
1 AAAAATAAAATAACTCATAA
3919375 AAAAACTATAAATAACT
1 AAAAA-TA-AAATAACT
3919392 AAATTATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
19 8 0.28
20 4 0.14
21 16 0.55
22 1 0.03
ACGTcount: A:0.65, C:0.11, G:0.00, T:0.25
Consensus pattern (20 bp):
AAAAATAAAATAACTCATAA
Found at i:3919959 original size:248 final size:247
Alignment explanation
Indices: 3919498--3920140 Score: 683
Period size: 248 Copynumber: 2.6 Consensus size: 247
3919488 CTCAAGCAAA
* * * * *
3919498 AAAATATTTAACCAATTAT-AAATATTAATTTATAATGTATAAAAATAAAAATAAAAACACTTGT
1 AAAATATTTAACC-ATTTTCAAATATTAATTTATAA---ATGAAAAGAAAAATAGAAACACCTGT
* * * *
3919562 AATGAAAATTAGCCATTTAAAAATCTTGACATACATTTATAAGAATGAATGT-AAAAA-TCATAA
62 AATGAAAATTAGCCTTTTAAAAATCTTGACGTAAATTTATAAGAATAAATGTAAAAAATTCATAA
* * * * *
3919625 ATTTGAAATAAACATTTTTAAAATATAGATCTAAATATGTAAGAGTTATAGTAACAAGTCAATTT
127 AATTGAAATAAACACTATTAAAATATAGATATAAATATGTAAGAGTTACAGTAACAAGTCAATTT
* * * *
3919690 AGACAAAATAAACATACTTTTAGTGAAAATTATTCATTTATATTTATATTCTCGAGTAT
192 AAACAAAATAAACATACTTTTAGTGAAAATTAATCATTTACATTTATATTCTC-A--AC
* * *
3919749 AAAATATTTAACCATTTTCAAATTTTAATTTATAAATGAATA-AAAAATAGAAACACCAGTAATG
1 AAAATATTTAACCATTTTCAAATATTAATTTATAAATGAAAAGAAAAATAGAAACACCTGTAATG
*
3919813 AAAATTAGCCTTTTAAAAATCTTGACGTAAATTTATAAGAAT-AATGTAAAAAATTCATAAAGTT
66 AAAATTAGCCTTTTAAAAATCTTGACGTAAATTTATAAGAATAAATGTAAAAAATTCATAAAATT
* * * * ** *
3919877 GAAATAAATACTATTACAATATTGATATAAATGTGTAAGAGTTACCA-TAGTAATTCAATTTAAA
131 GAAATAAACACTATTAAAATATAGATATAAATATGTAAGAGTTA-CAGTAACAAGTCAATTTAAA
* *
3919941 TAAAGTAAACATACTTTTAGTGAAAATTAATCATTTACATTTATATTCTCAAC
195 CAAAATAAACATACTTTTAGTGAAAATTAATCATTTACATTTATATTCTCAAC
* * ** * * *
3919994 AAAAAAATTAATTATTTACAAATGTTAATGTATAAATGTAAAAAAAAGAAAAATAAAAATGATAA
1 AAAATATTTAACCATTTTCAAATATTAATTTATAAATG-----AAAAGAAAAAT----A-GA-AA
*
3920059 CA-CTGCTAATGAAAATTAG-CTATTTAAAAATATTGACGTAAATTTATAAGAATAAATGTAAAA
55 CACCTG-TAATGAAAATTAGCCT-TTTAAAAATCTTGACGTAAATTTATAAGAATAAATGTAAAA
3920122 AATT-ATAAAATTGAAATAA
118 AATTCATAAAATTGAAATAA
3920141 GTGTCGTTAA
Statistics
Matches: 334, Mismatches: 39, Indels: 32
0.82 0.10 0.08
Matches are distributed among these distances:
245 32 0.10
246 5 0.01
247 64 0.19
248 110 0.33
249 1 0.00
250 7 0.02
251 34 0.10
255 1 0.00
256 6 0.02
257 61 0.18
258 13 0.04
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34
Consensus pattern (247 bp):
AAAATATTTAACCATTTTCAAATATTAATTTATAAATGAAAAGAAAAATAGAAACACCTGTAATG
AAAATTAGCCTTTTAAAAATCTTGACGTAAATTTATAAGAATAAATGTAAAAAATTCATAAAATT
GAAATAAACACTATTAAAATATAGATATAAATATGTAAGAGTTACAGTAACAAGTCAATTTAAAC
AAAATAAACATACTTTTAGTGAAAATTAATCATTTACATTTATATTCTCAAC
Found at i:3921714 original size:246 final size:244
Alignment explanation
Indices: 3920278--3922021 Score: 983
Period size: 259 Copynumber: 6.9 Consensus size: 244
3920268 AGTATTAGCA
* *
3920278 AAAAAATATTTAACCATTTACAATTGTTAATTTATAAATG-T-ATAAAAATAAAAATACTTGTAA
1 AAAAAATATTTAACCATTTTCAATT-TTAATTTATAAATGATAATAAAAATAAAAACACTTGTAA
* * * * *
3920341 TGAAAATTAGCCATTTAAAAATCTTGACATAAATTTATAAGAGTAAATGT-AAAAATCAGAAATT
65 TGAAAATTAGCCATTTAAAAAT-TTGACGTAAATTTATAAGAATAAACGTAAAAAATCATAAAGT
* * * * * **
3920405 TGAAATAAACATTGTTAAAATATTGATATAAATATGTAAGAGTTACAGTAACAAGTTAATTTAAC
129 TGAAATAAATATTGTTAAAATATTGACAT-AATGTGTAAGAGTTACTGTAACAAGTCAATTTAGT
** * * *
3920470 AAAGTAAACATACTTTTAGTGAAAATTATTCATTTATATTTATATGGTC-GAGC
193 AAAAAAAACATACTTTTAGTGAAAATTAATCATTTGTATTTAT-T-TTCTGAGC
*
3920523 AAAAAATATTTAACCATTTTCAATTTTAATTTATAAATGTATAAAAATACAAATAAAAACACTTG
1 AAAAAATATTTAACCATTTTCAATTTTAATTTATAAATG-AT---AATAAAAATAAAAACACTTG
** * * * *
3920588 TAATGAAAATTAATCATTTTCAAAAATGTTGACGTATATTTATAACAATAAAAGAAAAAATATCA
62 TAATGAAAATTAGCCA-TTT-AAAAAT-TTGACGTAAATTTATAAGAATAAACGTAAAAA-ATCA
* * * ** *
3920653 TAAAGTTGAAATAAATATTATTAAAATATTGACATATATGTGTAATAGTTA-TCGCAGTAATTCA
123 TAAAGTTGAAATAAATATTGTTAAAATATTGACATA-ATGTGTAAGAGTTACT-GTAACAAGTCA
* * ** * ** * * * **
3920717 ATATAAATAAAGTAAATATACTTTTAGTGAAAATTAATCATTTACATATATATTCTCAAAT
186 AT-TTAGTAAAAAAAACATACTTTTAGTGAAAATTAATCATTTGTATTTATTTTCT-GAGC
* *
3920778 AAAAAATATTTAACCATTTACAAATGTTAATTTATAAATGTATAAAAATAAAAATAAAAATGAAA
1 AAAAAATATTTAACCATTTTC-AATTTTAATTTATAAATG-AT---AATAAAAAT----A--AAA
* * * *
3920843 AAACTTATAAT-AAAGATTAGCCATTTAAAAATGTTGACGTAAATTTATAAGTATAAACATAAAA
55 ACACTTGTAATGAAA-ATTAGCCATTTAAAAAT-TTGACGTAAATTTATAAGAATAAACGTAAAA
* * * ** * * *
3920907 AATCATAAAGTTGAAATAAATATTATTAACATATTAATGTGATTGTGTAAAAGTTACCT-TAATA
118 AATCATAAAGTTGAAATAAATATTGTTAAAATATTGACAT-AATGTGTAAGAGTTA-CTGTAACA
* * * * ** ** ** *** * **
3920971 AATCAATTT-G--GACAACATTTTTTTTTTTTGAAAAGCGTTAGA-CA--TGGGGTGA----GAG
181 AGTCAATTTAGTAAAAAAAACATACTTTTAGTGAAAA---TTA-ATCATTTGTATTTATTTTCTG
3921026 AGGC
242 A-GC
*** * * ** * *** * ** * * * *
3921030 TCGAACTCTCGACCTCAGGATCACTCTTTAAGCTAT-GA-GACCTACGCGCTAGCCAACTGCGCC
1 AAAAAATATTTAAC-CATTTTCAAT-TTTAATTTATAAATGA--TA----ATA--AAAAT-----
*** * * * * * ** * * * * *
3921093 ACCACCCCAATGGTGAT-AAGAATGAACCATTTAATAACCTTGATGTAAAATTATGAGAATGAAT
51 A--AAAACACTTGTAATGAA-AATTAGCCATTTAA-AAATTTGACGTAAATTTATAAGAATAAAC
* * * * *
3921157 GTAAAGAATAATAAAATTGAAATAAATATTGTTAAAATATTGACCTAATTGTGTTAGAGTTACTG
112 GTAAAAAATCATAAAGTTGAAATAAATATTGTTAAAATATTGACATAA-TGTGTAAGAGTTACTG
* *
3921222 TAACAAGTCAATTTAG-ACAATATAAACATACTTTTAGTAAAAATTAATCATTTGTATTTATAAT
176 TAACAAGTCAATTTAGTA-AA-AAAAACATACTTTTAGTGAAAATTAATCATTTGTATTTAT--T
3921286 TT-TGAGC
237 TTCTGAGC
* * * * *
3921293 TAAAAAA-ATTTTACCGTTTATAAAATTTAATATATAAATGTATAAGAATAAAAATAAAAACACT
1 -AAAAAATATTTAACCATTT-TCAATTTTAATTTATAAATG-AT---AATAAAAATAAAAACACT
* * *
3921357 TGTAATGAAAATTAGCCATTTAAAAATTTGGACGTAAATTTATAAGAATGATCGTAAAAAA-CAA
60 TGTAATGAAAATTAGCCATTTAAAAATTT-GACGTAAATTTATAAGAATAAACGTAAAAAATCAT
* * **
3921421 AAATTTGAAATAAATATTGTTAAAATATGGATGCA-AATGTGTAAGAGTTACAATAACAAGTCAA
124 AAAGTTGAAATAAATATTGTTAAAATATTGA--CATAATGTGTAAGAGTTACTGTAACAAGTCAA
* * *
3921485 TTTAGTAAAAAAAACATGCTTTTAGTGAAAATTAATTATTTATATTTATTTTCTCGAGC
187 TTTAGTAAAAAAAACATACTTTTAGTGAAAATTAATCATTTGTATTTATTTTCT-GAGC
3921544 AAAAAATATTTAACCATTTTCAATTTTAATTTATAAATG-T-ATAAAAATAAAAACACTTGTAAT
1 AAAAAATATTTAACCATTTTCAATTTTAATTTATAAATGATAATAAAAATAAAAACACTTGTAAT
* *
3921607 GAAAATTAGCCTTTTAAAAATGTTGACGTAAATTTATAACAATAAACGTAAAAAAATCATAAAGT
66 GAAAATTAGCCATTTAAAAAT-TTGACGTAAATTTATAAGAATAAACGT-AAAAAATCATAAAGT
* ** * * * * *
3921672 TGAAATAAACATTGTTAAAATATTGACATACATGCATAAGAGTTACTGT-AGAATTAAATATAAA
129 TGAAATAAATATTGTTAAAATATTGACATA-ATGTGTAAGAGTTACTGTAACAAGTCAAT-TTAG
* * * * * *
3921736 TAAAAGAAACATTCTTTTAGTGACAATTAATCATTTGCATTTATATTCTTGAGT
192 TAAAAAAAACATACTTTTAGTGAAAATTAATCATTTGTATTTATTTTC-TGAGC
* *
3921790 AAAAAATATTTAACCATTTACACATGTTAATTTATAAATGTATAAAAATAAAAATAAAAATGAAA
1 AAAAAATATTTAACCATTTTCA-ATTTTAATTTATAAATG-AT---AATAAAAAT----A--AAA
* * * ** *
3921855 AAACTTATAATGAAGATTAGCCATTTAAAAATATTGACAAAAATTTATAAGAATAAACATAAAAA
55 ACACTTGTAATGAAAATTAGCCATTTAAAAAT-TTGACGTAAATTTATAAGAATAAACGTAAAAA
* * ** * * *
3921920 TTCATAAAGTTGAAATAAGTATTGTTAAAATATTGATGTAAATTTGTAAGAGCTATCT-TAATAA
119 ATCATAAAGTTGAAATAAATATTGTTAAAATATTGACAT-AATGTGTAAGAGTTA-CTGTAACAA
* * *
3921984 ATCAATTTAG-ACAATATAAACATAATTTTAGTGAAAAT
182 GTCAATTTAGTA-AA-AAAAACATACTTTTAGTGAAAAT
3922022 ATATCATCTA
Statistics
Matches: 1135, Mismatches: 264, Indels: 186
0.72 0.17 0.12
Matches are distributed among these distances:
244 81 0.07
245 40 0.04
246 112 0.10
247 17 0.01
248 1 0.00
249 5 0.00
250 56 0.05
251 54 0.05
252 102 0.09
253 75 0.07
254 57 0.05
255 85 0.07
256 133 0.12
257 11 0.01
258 60 0.05
259 145 0.13
260 50 0.04
261 7 0.01
262 29 0.03
263 8 0.01
264 5 0.00
265 1 0.00
266 1 0.00
ACGTcount: A:0.47, C:0.09, G:0.10, T:0.34
Consensus pattern (244 bp):
AAAAAATATTTAACCATTTTCAATTTTAATTTATAAATGATAATAAAAATAAAAACACTTGTAAT
GAAAATTAGCCATTTAAAAATTTGACGTAAATTTATAAGAATAAACGTAAAAAATCATAAAGTTG
AAATAAATATTGTTAAAATATTGACATAATGTGTAAGAGTTACTGTAACAAGTCAATTTAGTAAA
AAAAACATACTTTTAGTGAAAATTAATCATTTGTATTTATTTTCTGAGC
Found at i:3922137 original size:21 final size:21
Alignment explanation
Indices: 3922111--3922153 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3922101 TTATCTAAAT
3922111 TTATATACTTGTAATTAATGA
1 TTATATACTTGTAATTAATGA
*
3922132 TTATATATTTGTAATTAATGA
1 TTATATACTTGTAATTAATGA
3922153 T
1 T
3922154 ATTTTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.51
Consensus pattern (21 bp):
TTATATACTTGTAATTAATGA
Found at i:3926090 original size:20 final size:20
Alignment explanation
Indices: 3926065--3926110 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
3926055 CTTCTAAACC
3926065 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
3926085 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
3926105 TCAAAT
1 TCAAAT
3926111 GGGGCCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:3926731 original size:14 final size:15
Alignment explanation
Indices: 3926691--3926733 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
3926681 TGGAAAAATC
3926691 AAAATAGTAAAATATA
1 AAAATAG-AAAATATA
3926707 AAAATAGAAAATA-A
1 AAAATAGAAAATATA
3926721 AATAA-AGAAAATA
1 AA-AATAGAAAATA
3926734 CAAAGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.42
15 8 0.31
16 7 0.27
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (15 bp):
AAAATAGAAAATATA
Found at i:3927391 original size:139 final size:139
Alignment explanation
Indices: 3927226--3927499 Score: 500
Period size: 139 Copynumber: 2.0 Consensus size: 139
3927216 AGCTAGTATA
3927226 AAGTTTTTATAAAAAATAATAATTTTTAAAATTAGATTAAAATTATTTGGTAAAATTTTTTTT-T
1 AAGTTTTTATAAAAAATAATAATTTTTAAAATTAGATTAAAATTATTTGGTAAAATTTTTTTTGT
3927290 GAAGTTATAATTTTGATTAAAATTATCATAAAAGGTA-TTTTTTTTAAGAAGATAATATGATAAT
66 -AAGTTATAATTTTGATTAAAA-TATCATAAAAGGTATTTTTTTTTAAGAAGATAATATGATAAT
3927354 TATATTTNTATG
129 TATATTT-TATG
3927366 AAGTTTTTAT-AAAAATAATAATTTTTAAAATTAGATTAAAATTATTTGGTAAAATTTTTTTTGT
1 AAGTTTTTATAAAAAATAATAATTTTTAAAATTAGATTAAAATTATTTGGTAAAATTTTTTTTGT
3927430 AAGTTATAATTTTGATTAAAATATCATAAAAGGTATTTTTTTTTAAGAAGATAATATGATAATTA
66 AAGTTATAATTTTGATTAAAATATCATAAAAGGTATTTTTTTTTAAGAAGATAATATGATAATTA
3927495 TATTT
131 TATTT
3927500 AACAGATGAG
Statistics
Matches: 132, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
138 14 0.11
139 107 0.81
140 11 0.08
ACGTcount: A:0.42, C:0.01, G:0.09, T:0.47
Consensus pattern (139 bp):
AAGTTTTTATAAAAAATAATAATTTTTAAAATTAGATTAAAATTATTTGGTAAAATTTTTTTTGT
AAGTTATAATTTTGATTAAAATATCATAAAAGGTATTTTTTTTTAAGAAGATAATATGATAATTA
TATTTTATG
Found at i:3941040 original size:19 final size:19
Alignment explanation
Indices: 3941016--3941053 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3941006 CCATTTGACT
3941016 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
3941035 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
3941054 GTTGAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:3942305 original size:13 final size:13
Alignment explanation
Indices: 3942287--3942311 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3942277 GGAGAAATTG
3942287 TGATTTTATAAAA
1 TGATTTTATAAAA
3942300 TGATTTTATAAA
1 TGATTTTATAAA
3942312 TTTTTTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:3944340 original size:40 final size:39
Alignment explanation
Indices: 3944281--3944363 Score: 103
Period size: 40 Copynumber: 2.1 Consensus size: 39
3944271 TTTTCACCAT
* * *
3944281 TGTTCACCTTAATGGGGTTTTCTAACTTTACCAAGATTGG
1 TGTTCACCTTAATGAGGTTTT-TAACCTCACCAAGATTGG
* * *
3944321 TGTTCACCTTAGTGAGGTTTTTAACCTCGCCACGATTGG
1 TGTTCACCTTAATGAGGTTTTTAACCTCACCAAGATTGG
3944360 TGTT
1 TGTT
3944364 TTCACAACTC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
39 18 0.49
40 19 0.51
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (39 bp):
TGTTCACCTTAATGAGGTTTTTAACCTCACCAAGATTGG
Found at i:3959722 original size:26 final size:26
Alignment explanation
Indices: 3959686--3959738 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
3959676 GGTAGCCAAT
3959686 GTAAGAAAACTTCTTAGACAAATTTG
1 GTAAGAAAACTTCTTAGACAAATTTG
3959712 GTAAGAAAACTTCTTAGACAAATTTG
1 GTAAGAAAACTTCTTAGACAAATTTG
3959738 G
1 G
3959739 GTCAAGAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (26 bp):
GTAAGAAAACTTCTTAGACAAATTTG
Found at i:3964282 original size:19 final size:20
Alignment explanation
Indices: 3964258--3964297 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
3964248 CCATTTGACT
3964258 TATTGGAGTATGATTT-AAG
1 TATTGGAGTATGATTTGAAG
3964277 TATTGGAGTATGATTTGAAG
1 TATTGGAGTATGATTTGAAG
3964297 T
1 T
3964298 TTAGAAGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (20 bp):
TATTGGAGTATGATTTGAAG
Found at i:3965407 original size:13 final size:13
Alignment explanation
Indices: 3965389--3965413 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3965379 GGAAAATGAG
3965389 ATTTTATAAAATA
1 ATTTTATAAAATA
3965402 ATTTTATAAAAT
1 ATTTTATAAAAT
3965414 TTTTGTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:3971148 original size:28 final size:27
Alignment explanation
Indices: 3971117--3971170 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
3971107 TTTTGGAGCA
**
3971117 TAGGGGCAAAATGGTAATTTTACCACCC
1 TAGGGGCAAAACAGTAATTTT-CCACCC
3971145 TAGGGGCAAAACAGTAATTTTCCACC
1 TAGGGGCAAAACAGTAATTTTCCACC
3971171 ACCAGGACAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.24
Consensus pattern (27 bp):
TAGGGGCAAAACAGTAATTTTCCACCC
Found at i:3975887 original size:17 final size:17
Alignment explanation
Indices: 3975865--3975906 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
3975855 GTTTTATGAG
3975865 AAATAAATGGAATTATA
1 AAATAAATGGAATTATA
3975882 AAATAAATGGAATTATA
1 AAATAAATGGAATTATA
3975899 AAATAAAT
1 AAATAAAT
3975907 TGAAATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.29
Consensus pattern (17 bp):
AAATAAATGGAATTATA
Found at i:3978811 original size:11 final size:12
Alignment explanation
Indices: 3978795--3978858 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
3978785 TTTTAGGGAT
3978795 AAAAAAGAAA-A
1 AAAAAAGAAAGA
3978806 AAAAAAGAAAGA
1 AAAAAAGAAAGA
* *
3978818 AAAAGAGTAAAGC
1 AAAAAAG-AAAGA
*
3978831 AAAGAAGAAA-A
1 AAAAAAGAAAGA
3978842 TAGATAAAAGAAAGA
1 -A-A-AAAAGAAAGA
3978857 AA
1 AA
3978859 TAATTAAAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
11 10 0.24
12 11 0.27
13 11 0.27
14 8 0.20
15 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.05
Consensus pattern (12 bp):
AAAAAAGAAAGA
Found at i:3978820 original size:21 final size:21
Alignment explanation
Indices: 3978796--3978858 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
3978786 TTTAGGGATA
*
3978796 AAAAAGAAAAAAAAAAGAAAG
1 AAAAAGATAAAAAAAAGAAAG
**
3978817 AAAAAGAGTAAAGCAAAG-AAG
1 AAAAAGA-TAAAAAAAAGAAAG
*
3978838 AAAATAGATAAAAGAAAGAAA
1 AAAA-AGATAAAAAAAAGAAA
3978859 TAATTAAAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
21 22 0.65
22 12 0.35
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.05
Consensus pattern (21 bp):
AAAAAGATAAAAAAAAGAAAG
Found at i:3980319 original size:13 final size:13
Alignment explanation
Indices: 3980301--3980325 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3980291 TTCCAAAAAA
3980301 TTTATAAAATCAT
1 TTTATAAAATCAT
3980314 TTTATAAAATCA
1 TTTATAAAATCA
3980326 CAATTTCTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:3983118 original size:27 final size:27
Alignment explanation
Indices: 3983058--3983120 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 27
3983048 TATATATCAT
* * *
3983058 GTTGAAAAAAAAGTTATTGCATCTTAT
1 GTTGAAAAAAAAGTTACTCCATCTTAC
* *
3983085 GTT-AAAAAAAAGTTGCTCCATGTTAC
1 GTTGAAAAAAAAGTTACTCCATCTTAC
3983111 GTTGAAAAAA
1 GTTGAAAAAA
3983121 TATTGTTGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 21 0.70
27 9 0.30
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.32
Consensus pattern (27 bp):
GTTGAAAAAAAAGTTACTCCATCTTAC
Found at i:3983212 original size:26 final size:26
Alignment explanation
Indices: 3983167--3983245 Score: 117
Period size: 26 Copynumber: 3.1 Consensus size: 26
3983157 ATTGTATGCG
*
3983167 ATGTTG-AAACAAGTTATTACACATC
1 ATGTTGAAAAAAAGTTATTACACATC
*
3983192 ATGTTTTAAAAAAA-TTATTACACATC
1 ATG-TTGAAAAAAAGTTATTACACATC
3983218 ATGTTGAAAAAAAGTTATTACACATC
1 ATGTTGAAAAAAAGTTATTACACATC
3983244 AT
1 AT
3983246 ACTAAAAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
25 12 0.25
26 31 0.65
27 5 0.10
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.34
Consensus pattern (26 bp):
ATGTTGAAAAAAAGTTATTACACATC
Found at i:3983253 original size:26 final size:26
Alignment explanation
Indices: 3983177--3983256 Score: 99
Period size: 26 Copynumber: 3.1 Consensus size: 26
3983167 ATGTTGAAAC
* *
3983177 AAGTTATTACACATCATGTTTTAAAAA
1 AAGTTATTACACATCAT-ATTAAAAAA
* *
3983204 AA-TTATTACACATCATGTTGAAAAA
1 AAGTTATTACACATCATATTAAAAAA
*
3983229 AAGTTATTACACATCATACTAAAAAA
1 AAGTTATTACACATCATATTAAAAAA
3983255 AA
1 AA
3983257 TTGTTATACG
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
25 9 0.19
26 36 0.77
27 2 0.04
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.31
Consensus pattern (26 bp):
AAGTTATTACACATCATATTAAAAAA
Found at i:3983358 original size:26 final size:28
Alignment explanation
Indices: 3983311--3983388 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 28
3983301 TTCAAAATGT
** *
3983311 TATTACATGCCAGGTT-GAAAAAA-AAA
1 TATTACATGCCATATTGGAAAAAATAGA
*
3983337 TATTACATGCCATATTGGAAAAAATAGT
1 TATTACATGCCATATTGGAAAAAATAGA
* *
3983365 TGTTACATACCATATT-GAAAAAAT
1 TATTACATGCCATATTGGAAAAAAT
3983389 GTTACAATCA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
26 14 0.32
27 15 0.34
28 15 0.34
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (28 bp):
TATTACATGCCATATTGGAAAAAATAGA
Found at i:3983360 original size:28 final size:27
Alignment explanation
Indices: 3983311--3983387 Score: 75
Period size: 28 Copynumber: 2.9 Consensus size: 27
3983301 TTCAAAATGT
**
3983311 TATTACATGCCAGGTTG-AAAAAAAAA
1 TATTACATGCCATATTGAAAAAAAAAA
* **
3983337 TATTACATGCCATATTGGAAAAAATAGT
1 TATTACATGCCATATT-GAAAAAAAAAA
* *
3983365 TGTTACATACCATATTGAAAAAA
1 TATTACATGCCATATTGAAAAAA
3983388 TGTTACAATC
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
26 14 0.33
27 8 0.19
28 20 0.48
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.29
Consensus pattern (27 bp):
TATTACATGCCATATTGAAAAAAAAAA
Found at i:3983391 original size:23 final size:25
Alignment explanation
Indices: 3983330--3983394 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 25
3983320 CCAGGTTGAA
* *
3983330 AAAAAAATATTACATGCCATATTGG
1 AAAAAAATGTTACATACCATATTGG
3983355 AAAAAATAGTTGTTACATACCATATT-G
1 AAAAAA-A--TGTTACATACCATATTGG
3983382 -AAAAAATGTTACA
1 AAAAAAATGTTACA
3983395 ATCATCTCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
23 7 0.20
25 7 0.20
26 6 0.17
27 1 0.03
28 14 0.40
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (25 bp):
AAAAAAATGTTACATACCATATTGG
Found at i:3984378 original size:22 final size:22
Alignment explanation
Indices: 3984353--3984397 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3984343 TAACTAAATG
*
3984353 AAATATATAATTTATTATAATA
1 AAATATATAATTTATCATAATA
* *
3984375 AAATTTATATTTTATCATAATA
1 AAATATATAATTTATCATAATA
3984397 A
1 A
3984398 TATGTACATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
AAATATATAATTTATCATAATA
Found at i:3984408 original size:22 final size:22
Alignment explanation
Indices: 3984363--3984409 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3984353 AAATATATAA
* * *
3984363 TTTATTATAATAAAATTTATAT
1 TTTATCATAATAAAATGTACAT
*
3984385 TTTATCATAATAATATGTACAT
1 TTTATCATAATAAAATGTACAT
3984407 TTT
1 TTT
3984410 CATTACATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTATCATAATAAAATGTACAT
Found at i:3995316 original size:6 final size:5
Alignment explanation
Indices: 3995257--3995326 Score: 56
Period size: 5 Copynumber: 13.8 Consensus size: 5
3995247 AAAGTAAAGT
* *
3995257 TTTTA TTTAA TTTT- TTCTA TTTATA TTATTA TTATTA TTATTA -TTTA
1 TTTTA TTTTA TTTTA TTTTA TTT-TA TT-TTA TT-TTA TT-TTA TTTTA
*
3995304 TTTT- TTTAA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTT
3995327 TTCATATATT
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
4 9 0.17
5 26 0.48
6 18 0.33
7 1 0.02
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:3999181 original size:21 final size:19
Alignment explanation
Indices: 3999140--3999183 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
3999130 TCATAAATTT
*
3999140 TATAATTTTATAATAATAA
1 TATAATTTTATAATAAAAA
*
3999159 TATAATTAATTATATTAAAAA
1 TATAATT--TTATAATAAAAA
3999180 TATA
1 TATA
3999184 CAAAAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.33
21 14 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TATAATTTTATAATAAAAA
Found at i:4002437 original size:19 final size:20
Alignment explanation
Indices: 4002402--4002440 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
4002392 AAAAACTAAT
*
4002402 AAATAACAATCAAATTAAAA
1 AAATAACAATAAAATTAAAA
4002422 AAATAAC-ATAAAATTAAAA
1 AAATAACAATAAAATTAAAA
4002441 TAACTCACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (20 bp):
AAATAACAATAAAATTAAAA
Found at i:4003771 original size:19 final size:20
Alignment explanation
Indices: 4003737--4003781 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
4003727 TTTTTTTTAG
*
4003737 AACATAGATAAAACATGCAA
1 AACATAAATAAAACATGCAA
4003757 AACATAAAT-AAACATGCAA
1 AACATAAATAAAACATGCAA
*
4003776 GACATA
1 AACATA
4003782 TCTTAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.60, C:0.16, G:0.09, T:0.16
Consensus pattern (20 bp):
AACATAAATAAAACATGCAA
Found at i:4012582 original size:15 final size:15
Alignment explanation
Indices: 4012558--4012595 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
4012548 CGTTATGCAC
*
4012558 AAAAAGAAAAAAAAT
1 AAAAATAAAAAAAAT
*
4012573 AAAAATAAAATAAAT
1 AAAAATAAAAAAAAT
4012588 -AAAATAAA
1 AAAAATAAA
4012596 GACGCTGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (15 bp):
AAAAATAAAAAAAAT
Found at i:4013463 original size:23 final size:23
Alignment explanation
Indices: 4013415--4013489 Score: 68
Period size: 23 Copynumber: 3.3 Consensus size: 23
4013405 AAATGGTAGT
4013415 ATATAATTATATTAAATA-TAACATA
1 ATATAATTATA--AAATATTAA-ATA
4013440 ATATAATTATAAAATATTAAATA
1 ATATAATTATAAAATATTAAATA
* *
4013463 AT-TCAA-TATAAAA-GTTAATTA
1 ATAT-AATTATAAAATATTAAATA
4013484 ATATAA
1 ATATAA
4013490 AAATTTACTA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
21 10 0.22
22 9 0.20
23 12 0.27
24 3 0.07
25 11 0.24
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (23 bp):
ATATAATTATAAAATATTAAATA
Found at i:4014091 original size:28 final size:28
Alignment explanation
Indices: 4014060--4014131 Score: 67
Period size: 28 Copynumber: 2.5 Consensus size: 28
4014050 GGTTAGAAAA
*
4014060 TTAATTTTTTAATTAAATTTAA-TATTAT
1 TTAATTTTTTAATTAAATTAAATTATT-T
* * *
4014088 TTAACTTTATAAAGT-AATTAAATTATTT
1 TTAA-TTTTTTAATTAAATTAAATTATTT
4014116 TATAATTTTTTAATTA
1 T-TAATTTTTTAATTA
4014132 TAAAGTAATG
Statistics
Matches: 33, Mismatches: 7, Indels: 7
0.70 0.15 0.15
Matches are distributed among these distances:
28 19 0.58
29 14 0.42
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (28 bp):
TTAATTTTTTAATTAAATTAAATTATTT
Found at i:4016716 original size:21 final size:20
Alignment explanation
Indices: 4016692--4016758 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
4016682 GACATTTCAT
*
4016692 AAAGTTTTAATACTTGGATTC
1 AAAGTCTTAATACTT-GATTC
* * *
4016713 AAAGTCTTGATACCTAGTTTC
1 AAAGTCTTAATA-CTTGATTC
*
4016734 AAAGCCTTAATACTTGACTTC
1 AAAGTCTTAATACTTGA-TTC
4016755 AAAG
1 AAAG
4016759 GCTTGATACC
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 3 0.08
21 31 0.86
22 2 0.06
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.36
Consensus pattern (20 bp):
AAAGTCTTAATACTTGATTC
Found at i:4016767 original size:21 final size:20
Alignment explanation
Indices: 4016701--4016767 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
4016691 TAAAGTTTTA
*
4016701 ATACTTGGATTCAAAGTCTTG
1 ATACTT-GATTCAAAGCCTTG
* * *
4016722 ATACCTAGTTTCAAAGCCTTA
1 ATA-CTTGATTCAAAGCCTTG
*
4016743 ATACTTGACTTCAAAGGCTTG
1 ATACTTGA-TTCAAAGCCTTG
4016764 ATAC
1 ATAC
4016768 CTAACACAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 3 0.08
21 31 0.86
22 2 0.06
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.34
Consensus pattern (20 bp):
ATACTTGATTCAAAGCCTTG
Found at i:4017297 original size:28 final size:28
Alignment explanation
Indices: 4017248--4017364 Score: 137
Period size: 28 Copynumber: 4.2 Consensus size: 28
4017238 AATGATGTAA
* *
4017248 AGGTTTTATCT-AACCTTAGAAAAGGCTG
1 AGGTTTTACCTGATCCTT-GAAAAGGCTG
* *
4017276 AGGTTTTGCCTGATCCTTGAAAAGGCTA
1 AGGTTTTACCTGATCCTTGAAAAGGCTG
* * *
4017304 AGGTTTAACTTGATCCTTGACAAGGCTG
1 AGGTTTTACCTGATCCTTGAAAAGGCTG
**
4017332 AGGTTTTTTCTGATCCTTGAAAAGGCTG
1 AGGTTTTACCTGATCCTTGAAAAGGCTG
4017360 AGGTT
1 AGGTT
4017365 ATGTTTGCTC
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
28 69 0.93
29 5 0.07
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (28 bp):
AGGTTTTACCTGATCCTTGAAAAGGCTG
Found at i:4017308 original size:56 final size:57
Alignment explanation
Indices: 4017247--4017364 Score: 152
Period size: 56 Copynumber: 2.1 Consensus size: 57
4017237 CAATGATGTA
*
4017247 AAGGTTTTATC-T-AACCTTAGAAAAGGCTGAGGTTTTGCCTGATCCTTGAAAAGGCT
1 AAGGTTTTAACTTGAACCTT-GAAAAGGCTGAGGTTTTGCCTGATCCTTGAAAAGGCT
* * **
4017303 AAGG-TTTAACTTGATCCTTGACAAGGCTGAGGTTTTTTCTGATCCTTGAAAAGGCT
1 AAGGTTTTAACTTGAACCTTGAAAAGGCTGAGGTTTTGCCTGATCCTTGAAAAGGCT
*
4017359 GAGGTT
1 AAGGTT
4017365 ATGTTTGCTC
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
55 5 0.09
56 42 0.79
57 6 0.11
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (57 bp):
AAGGTTTTAACTTGAACCTTGAAAAGGCTGAGGTTTTGCCTGATCCTTGAAAAGGCT
Found at i:4017376 original size:28 final size:27
Alignment explanation
Indices: 4017261--4017385 Score: 124
Period size: 28 Copynumber: 4.4 Consensus size: 27
4017251 TTTTATCTAA
*
4017261 CCTTAGAAAAGGCTGAGGTTTTGCCTGAT
1 CCTT-GAAAAGGCTGAGG-TTTGCTTGAT
* *
4017290 CCTTGAAAAGGCTAAGGTTTAACTTGAT
1 CCTTGAAAAGGCTGAGGTTT-GCTTGAT
* **
4017318 CCTTGACAAGGCTGAGGTTTTTTCTGAT
1 CCTTGAAAAGGCTGAGGTTTGCT-TGAT
* *
4017346 CCTTGAAAAGGCTGAGGTTATGTTTGCT
1 CCTTGAAAAGGCTGAGGTT-TGCTTGAT
*
4017374 CCTCGAAAAGGC
1 CCTTGAAAAGGC
4017386 ATTGTGTGGG
Statistics
Matches: 82, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
27 4 0.05
28 71 0.87
29 7 0.09
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.32
Consensus pattern (27 bp):
CCTTGAAAAGGCTGAGGTTTGCTTGAT
Found at i:4017490 original size:34 final size:32
Alignment explanation
Indices: 4017413--4017491 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 32
4017403 TGCTTCCGTG
* *
4017413 AAAAGACAGTGTGGATTATGCTTAATCCTTTAA
1 AAAAG-CAATGTGGATTATGCTTAATCCTTCAA
* * *
4017446 AAAGGTAATGTGAGATTATGCTTGATCCTCTCAA
1 AAAAGCAATGTG-GATTATGCTTAATCCT-TCAA
4017480 AAAAGCAATGTG
1 AAAAGCAATGTG
4017492 TAAAGGTTAC
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
32 5 0.14
33 19 0.51
34 13 0.35
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (32 bp):
AAAAGCAATGTGGATTATGCTTAATCCTTCAA
Found at i:4022462 original size:12 final size:12
Alignment explanation
Indices: 4022445--4022505 Score: 58
Period size: 12 Copynumber: 5.1 Consensus size: 12
4022435 TTAAGTGAAG
4022445 TAATAATTAAAA
1 TAATAATTAAAA
4022457 TAATAA-T--AA
1 TAATAATTAAAA
4022466 TAATAATTAAAA
1 TAATAATTAAAA
4022478 -ATATATATTAAAA
1 TA-ATA-ATTAAAA
4022491 TAGATAAGTTAAAA
1 TA-ATAA-TTAAAA
4022505 T
1 T
4022506 TTTTAATATT
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
9 8 0.20
10 1 0.02
11 2 0.05
12 11 0.27
13 8 0.20
14 11 0.27
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (12 bp):
TAATAATTAAAA
Found at i:4023278 original size:33 final size:35
Alignment explanation
Indices: 4023241--4023309 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
4023231 AATAGATGTG
* * *
4023241 ATAATTAATATAAACAAACAAATAATAACAATAATA
1 ATAAATAATAGAAAC-AACAAATAATAAAAATAATA
4023277 ATAAATGAATAGAAACAACAAATAATAAAAATA
1 ATAAAT-AATAGAAACAACAAATAATAAAAATA
4023310 TAAACTAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
36 21 0.72
37 8 0.28
ACGTcount: A:0.68, C:0.07, G:0.03, T:0.22
Consensus pattern (35 bp):
ATAAATAATAGAAACAACAAATAATAAAAATAATA
Found at i:4023711 original size:15 final size:16
Alignment explanation
Indices: 4023691--4023725 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4023681 AATTAAAAGA
4023691 AATTTA-AATATTTTG
1 AATTTAGAATATTTTG
*
4023706 AATTTAGATTATTTTG
1 AATTTAGAATATTTTG
4023722 AATT
1 AATT
4023726 CAGATCAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (16 bp):
AATTTAGAATATTTTG
Found at i:4023718 original size:16 final size:16
Alignment explanation
Indices: 4023699--4023742 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
4023689 GAAATTTAAA
4023699 TATTTTGAATTTAGAT
1 TATTTTGAATTTAGAT
*
4023715 TATTTTGAATTCAGAT
1 TATTTTGAATTTAGAT
* *
4023731 CAATTTGAATTT
1 TATTTTGAATTT
4023743 CAATCATCTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.52
Consensus pattern (16 bp):
TATTTTGAATTTAGAT
Found at i:4060859 original size:25 final size:26
Alignment explanation
Indices: 4060824--4060880 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
4060814 TTAATAATTA
4060824 AAAAATAAAAGAAGTT-ATATTTTATT
1 AAAAATAAAAG-AGTTAATATTTTATT
* *
4060850 AAAAAT-AAAGATTTAATTTTTTATT
1 AAAAATAAAAGAGTTAATATTTTATT
4060875 AAAAAT
1 AAAAAT
4060881 TAAATTTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 3 0.11
25 19 0.68
26 6 0.21
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.40
Consensus pattern (26 bp):
AAAAATAAAAGAGTTAATATTTTATT
Found at i:4060887 original size:24 final size:25
Alignment explanation
Indices: 4060843--4060889 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
4060833 AGAAGTTATA
4060843 TTTTATTAAAAATAAAGATTTAATT
1 TTTTATTAAAAATAAAGATTTAATT
*
4060868 TTTTATTAAAAATTAA-ATTTAA
1 TTTTATTAAAAATAAAGATTTAA
4060890 CTAAAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
TTTTATTAAAAATAAAGATTTAATT
Found at i:4063254 original size:4 final size:4
Alignment explanation
Indices: 4063245--4063385 Score: 129
Period size: 4 Copynumber: 35.2 Consensus size: 4
4063235 TCACAAGAAC
* * * *
4063245 ATAT ATAT ATAT ATAT ATAT TTAT ATAT GTAT GTAT ATGT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * * * * *
4063293 ACAT ATTT ATAT ATGT ATAT ATTT ATAC AAAT TTAT ATAT GTAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * *
4063341 ATAC ATAT ATAA ATAT GTAT ATAT ATAT TTAT ATAT ATGT ATAT A
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT A
4063386 ATCAATGTTC
Statistics
Matches: 105, Mismatches: 32, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
4 105 1.00
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:4063260 original size:10 final size:10
Alignment explanation
Indices: 4063245--4063385 Score: 129
Period size: 10 Copynumber: 14.1 Consensus size: 10
4063235 TCACAAGAAC
4063245 ATATATATAT
1 ATATATATAT
4063255 ATATATATAT
1 ATATATATAT
* *
4063265 TTATATATGT
1 ATATATATAT
* *
4063275 ATGTATATGT
1 ATATATATAT
*
4063285 ATATATATAC
1 ATATATATAT
*
4063295 ATATTTATAT
1 ATATATATAT
*
4063305 ATGTATATAT
1 ATATATATAT
* * *
4063315 TTATACAAAT
1 ATATATATAT
* *
4063325 TTATATATGT
1 ATATATATAT
*
4063335 ATATATATAC
1 ATATATATAT
*
4063345 ATATATAAAT
1 ATATATATAT
*
4063355 ATGTATATAT
1 ATATATATAT
*
4063365 ATATTTATAT
1 ATATATATAT
*
4063375 ATATGTATAT
1 ATATATATAT
4063385 A
1 A
4063386 ATCAATGTTC
Statistics
Matches: 103, Mismatches: 28, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 103 1.00
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (10 bp):
ATATATATAT
Found at i:4063288 original size:26 final size:25
Alignment explanation
Indices: 4063247--4063384 Score: 95
Period size: 26 Copynumber: 5.4 Consensus size: 25
4063237 ACAAGAACAT
* *
4063247 ATATATATATATATATATTTATATA
1 ATATGTATATGTATATATTTATATA
* * *
4063272 TGTATGTATATGTATATATATACAT-
1 -ATATGTATATGTATATATTTATATA
* * *
4063297 ATTTATATATGTATATATTTATACAA
1 ATATGTATATGTATATATTTATA-TA
* *
4063323 ATTTATATATGTATATATATACATATATAA
1 ATATGTATATGTATATAT-T---TATAT-A
4063353 ATATGTATA--TATATATTTATAT-
1 ATATGTATATGTATATATTTATATA
4063375 ATATGTATAT
1 ATATGTATAT
4063385 AATCAATGTT
Statistics
Matches: 90, Mismatches: 14, Indels: 19
0.73 0.11 0.15
Matches are distributed among these distances:
22 9 0.10
24 23 0.26
26 37 0.41
27 2 0.02
28 7 0.08
30 12 0.13
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (25 bp):
ATATGTATATGTATATATTTATATA
Found at i:4068625 original size:14 final size:15
Alignment explanation
Indices: 4068606--4068637 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
4068596 ACCTCTAGCC
4068606 TAACA-TTTTTTTAT
1 TAACATTTTTTTTAT
4068620 TAACATTTTTTTTAT
1 TAACATTTTTTTTAT
4068635 TAA
1 TAA
4068638 TTCTTAGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (15 bp):
TAACATTTTTTTTAT
Found at i:4077141 original size:18 final size:19
Alignment explanation
Indices: 4077111--4077153 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
4077101 GATCCTTTCC
4077111 TTTT-CTTTACCATCT-TCT
1 TTTTACTTTACCATCTAT-T
4077129 TTTTACTTT-CCATCTATT
1 TTTTACTTTACCATCTATT
4077147 TTTTACT
1 TTTTACT
4077154 CTCTTTCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.14, C:0.23, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTACTTTACCATCTATT
Found at i:4077891 original size:18 final size:18
Alignment explanation
Indices: 4077857--4077891 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4077847 TTTATTCAAG
*
4077857 TAATTAAAATAAGAATTC
1 TAATTAAAATAAAAATTC
*
4077875 TAATTAAACTAAAAATT
1 TAATTAAAATAAAAATT
4077892 ATTCAACTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (18 bp):
TAATTAAAATAAAAATTC
Found at i:4077901 original size:15 final size:15
Alignment explanation
Indices: 4077881--4077922 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
4077871 ATTCTAATTA
4077881 AACTAAAAATTATTC
1 AACTAAAAATTATTC
* *
4077896 AACTAAAAATAATTT
1 AACTAAAAATTATTC
*
4077911 AATTAAAAATTA
1 AACTAAAAATTA
4077923 AAGCAACAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (15 bp):
AACTAAAAATTATTC
Found at i:4085552 original size:19 final size:19
Alignment explanation
Indices: 4085528--4085565 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
4085518 CCATTTGACT
4085528 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
4085547 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
4085566 GTTAAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:4086260 original size:10 final size:10
Alignment explanation
Indices: 4086228--4086263 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
4086218 GTGGCTGAAA
4086228 TTGATGATAT
1 TTGATGATAT
*
4086238 TTCATGATAT
1 TTGATGATAT
*
4086248 TTGGTGATAT
1 TTGATGATAT
4086258 TTGATG
1 TTGATG
4086264 TTTGGTGAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.25, C:0.03, G:0.22, T:0.50
Consensus pattern (10 bp):
TTGATGATAT
Found at i:4090970 original size:77 final size:76
Alignment explanation
Indices: 4090887--4091050 Score: 231
Period size: 77 Copynumber: 2.1 Consensus size: 76
4090877 TGAATTTCTC
* * *
4090887 AAATTAAAATACTATCCTTAATTTTAGGAATTTCTTTTAAAATAGGAAACAATTTCCTATTCTTT
1 AAATTAAAATACTATCCTTAATTTTAGGAATTACTTTTAAAACAGAAAACAATTT-CTATTCTTT
4090952 ATAAATCAGC-CA
65 ATAAATCA-CTCA
* * * *
4090964 AAATTAAAATTCTATCCTTAATTTTAGGAATTACTTTTAAAGCAGAAAATAATTTCTATTTTTTA
1 AAATTAAAATACTATCCTTAATTTTAGGAATTACTTTTAAAACAGAAAACAATTTCTATTCTTTA
*
4091029 TGAATCACTCA
66 TAAATCACTCA
4091040 AAATTAAAATA
1 AAATTAAAATA
4091051 TATGGCATAT
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
75 1 0.01
76 27 0.35
77 49 0.64
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.40
Consensus pattern (76 bp):
AAATTAAAATACTATCCTTAATTTTAGGAATTACTTTTAAAACAGAAAACAATTTCTATTCTTTA
TAAATCACTCA
Found at i:4114438 original size:16 final size:16
Alignment explanation
Indices: 4114417--4114449 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
4114407 TTTTAACTGC
4114417 TATTGATAAAAGTCTG
1 TATTGATAAAAGTCTG
4114433 TATTGATAAAAGTCTG
1 TATTGATAAAAGTCTG
4114449 T
1 T
4114450 CACTGTGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.39
Consensus pattern (16 bp):
TATTGATAAAAGTCTG
Found at i:4121284 original size:109 final size:109
Alignment explanation
Indices: 4121126--4121328 Score: 316
Period size: 109 Copynumber: 1.9 Consensus size: 109
4121116 TTGGAGGATT
* *
4121126 AAGGGACTAATGGAGAAAAAAAGAAAAAGAAGAAGAAATAATCCGTGCCACGTGGCATTGCAAGT
1 AAGGGACTAATGGAGAAAAAAAGAAAAAGAAGAAGAAATAATCCGTGCCACGTAGCATTGCAAGA
* *
4121191 GAAAAAGAAATAATCTATGCCATGTGGCATCGCACATTCTTTCG
66 GAAAAAGAAATAATCTATCCCACGTGGCATCGCACATTCTTTCG
** * *
4121235 AAGGGACTAATGGAGAAAGGAAGGAAGAGAAGAAGAAATAATCCGTGCCACGTAGCATTGCAAGA
1 AAGGGACTAATGGAGAAAAAAAGAAAAAGAAGAAGAAATAATCCGTGCCACGTAGCATTGCAAGA
* *
4121300 GAAGAAGAAATAATTTATCCCACGTGGCA
66 GAAAAAGAAATAATCTATCCCACGTGGCA
4121329 GCTGTCGTGA
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
109 84 1.00
ACGTcount: A:0.43, C:0.15, G:0.25, T:0.17
Consensus pattern (109 bp):
AAGGGACTAATGGAGAAAAAAAGAAAAAGAAGAAGAAATAATCCGTGCCACGTAGCATTGCAAGA
GAAAAAGAAATAATCTATCCCACGTGGCATCGCACATTCTTTCG
Found at i:4137324 original size:2 final size:2
Alignment explanation
Indices: 4137317--4137368 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
4137307 AAAACACAAC
4137317 AT 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 AT
4137359 AT AT AT AT AT
1 AT AT AT AT AT
4137369 CAACATAATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4138130 original size:18 final size:20
Alignment explanation
Indices: 4138107--4138143 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
4138097 AAGAAAAGAA
4138107 AAGG-AAAGAAAAT-AAAAC
1 AAGGAAAAGAAAATGAAAAC
4138125 AAGGAAAAGAAAATGAAAA
1 AAGGAAAAGAAAATGAAAA
4138144 TCTTGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 9 0.53
20 4 0.24
ACGTcount: A:0.73, C:0.03, G:0.19, T:0.05
Consensus pattern (20 bp):
AAGGAAAAGAAAATGAAAAC
Found at i:4156464 original size:28 final size:29
Alignment explanation
Indices: 4156407--4156466 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
4156397 TTTTTGAAAT
* *
4156407 TTACACTTTTACCCCAAAAAAAGTCAAAAA
1 TTACACTTTTACCCC-AAAAAACTAAAAAA
*
4156437 TTACATTTTTACCCC-AAAAACTAAAAAA
1 TTACACTTTTACCCCAAAAAACTAAAAAA
4156465 TT
1 TT
4156467 GCCCATAGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 13 0.48
30 14 0.52
ACGTcount: A:0.48, C:0.22, G:0.02, T:0.28
Consensus pattern (29 bp):
TTACACTTTTACCCCAAAAAACTAAAAAA
Found at i:4166816 original size:2 final size:2
Alignment explanation
Indices: 4166809--4166852 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
4166799 ATGTCTTAAC
4166809 AT 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 AT
4166851 AT
1 AT
4166853 CCCTATGCCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4186809 original size:9 final size:10
Alignment explanation
Indices: 4186788--4186816 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
4186778 CTAAGGTAGT
4186788 TTTTATGAAA
1 TTTTATGAAA
4186798 TTTTAT-AAA
1 TTTTATGAAA
4186807 TTTTATGAAA
1 TTTTATGAAA
4186817 AATGGATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (10 bp):
TTTTATGAAA
Found at i:4188275 original size:17 final size:17
Alignment explanation
Indices: 4188243--4188274 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
4188233 CAAAGCATGA
4188243 TTTTAAAGTTTTTTTTG
1 TTTTAAAGTTTTTTTTG
4188260 TTTTAAA-TTTTTTTT
1 TTTTAAAGTTTTTTTT
4188275 TAAAAGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (17 bp):
TTTTAAAGTTTTTTTTG
Found at i:4194043 original size:13 final size:13
Alignment explanation
Indices: 4194025--4194049 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4194015 TTTCAAAAAA
4194025 TTTATAAAATCAT
1 TTTATAAAATCAT
4194038 TTTATAAAATCA
1 TTTATAAAATCA
4194050 CAATTTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:4196731 original size:98 final size:97
Alignment explanation
Indices: 4196546--4196743 Score: 303
Period size: 98 Copynumber: 2.0 Consensus size: 97
4196536 AAGAACTCTG
*
4196546 TAAATTTTCAGAAAAAGAAGAAGATGAACAGAGCAAAGGATTAACAACTTTGGAAGAAAAAACTC
1 TAAATTTTCAGAAAAAGAAGAAGATGAACAAAGCAAAGGATTAACAACTTTGGAAGAAAAAAC-C
* *
4196611 TCTCACCTTCATTTAGAGTTTTATATATATATA
65 TCTCACCTTCATTCAGAGTTTTAGATATATATA
4196644 TAAACTTTT-AGAAAAAGAAGAAGATGAACAAAGC-AAGAGATTAACAACTTTGGAAGAAAAAA-
1 TAAA-TTTTCAGAAAAAGAAGAAGATGAACAAAGCAAAG-GATTAACAACTTTGGAAGAAAAAAC
4196706 CTCTCACCTTCATTCAGAGTTTTTTAGATATATATA
64 CTCTCACCTTCATTCAGAG--TTTTAGATATATATA
4196742 TA
1 TA
4196744 TATATATATA
Statistics
Matches: 93, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
96 18 0.19
97 3 0.03
98 68 0.73
99 4 0.04
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.28
Consensus pattern (97 bp):
TAAATTTTCAGAAAAAGAAGAAGATGAACAAAGCAAAGGATTAACAACTTTGGAAGAAAAAACCT
CTCACCTTCATTCAGAGTTTTAGATATATATA
Found at i:4196903 original size:34 final size:34
Alignment explanation
Indices: 4196865--4196947 Score: 103
Period size: 34 Copynumber: 2.4 Consensus size: 34
4196855 ACACACCAAT
* *
4196865 GCTTCAGCATCAGATGTTATACACCAAGGTCAAA
1 GCTTCAGCACCAGATGTTATACACCAAAGTCAAA
* * * *
4196899 GCTTCAACACCTGATGTTATACGCCAAAGTTAAA
1 GCTTCAGCACCAGATGTTATACACCAAAGTCAAA
*
4196933 GCTTTAGCACCAGAT
1 GCTTCAGCACCAGAT
4196948 ATTACATGCC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (34 bp):
GCTTCAGCACCAGATGTTATACACCAAAGTCAAA
Found at i:4197335 original size:17 final size:17
Alignment explanation
Indices: 4197313--4197346 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4197303 GAGAGCAAAT
* *
4197313 TGGGGAGCATAATAGAA
1 TGGGGAACATAACAGAA
4197330 TGGGGAACATAACAGAA
1 TGGGGAACATAACAGAA
4197347 GAATGGTGGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.09, G:0.32, T:0.15
Consensus pattern (17 bp):
TGGGGAACATAACAGAA
Found at i:4210987 original size:30 final size:31
Alignment explanation
Indices: 4210946--4211010 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
4210936 CGTTTAGTTA
*
4210946 TTTATACTTTTAA-ATAATAATCT-ATTGATC
1 TTTATACTTTTAATATAATAA-CTAAATGATC
* *
4210976 TTTATATTTTTAATATCATAACTAAATGATC
1 TTTATACTTTTAATATAATAACTAAATGATC
4211007 TTTA
1 TTTA
4211011 CGTCAACATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 14 0.47
31 16 0.53
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (31 bp):
TTTATACTTTTAATATAATAACTAAATGATC
Found at i:4215649 original size:38 final size:37
Alignment explanation
Indices: 4215544--4215820 Score: 285
Period size: 38 Copynumber: 7.5 Consensus size: 37
4215534 GACTCAAAAT
* * * * **
4215544 TGAGGCAATGTAATTTTAAAAATAAACTCCTCAAAAT
1 TGAGGCAACGAAACTTTAAAAATGAACTCCTCAAAGC
* * * *
4215581 TAAGGTAATGAAACTTGAAAAATGAACTCCTCAAAGC
1 TGAGGCAACGAAACTTTAAAAATGAACTCCTCAAAGC
4215618 TGAGGCAACGAAACTTCTAAAAATGAACTCCTCAAAGC
1 TGAGGCAACGAAACTT-TAAAAATGAACTCCTCAAAGC
* * *
4215656 TGTGGCAACG-AACTTTTAAAACGAACTCCTCAAAGC
1 TGAGGCAACGAAACTTTAAAAATGAACTCCTCAAAGC
* *
4215692 TGAGGCAATGAAACTTTTAAAAATGATCTCCTCAAAGC
1 TGAGGCAACGAAAC-TTTAAAAATGAACTCCTCAAAGC
* * *
4215730 TAAGGCAAC-ATGACTTTAAAAAAGTG-GCTCCTCAAAGC
1 TGAGGCAACGA-AACTTT-AAAAA-TGAACTCCTCAAAGC
*
4215768 TGAGGCAAC-ATAACTTT-AAAATGAACTCCTCAAAAC
1 TGAGGCAACGA-AACTTTAAAAATGAACTCCTCAAAGC
*
4215804 TGAGGCAAAGAAACTTT
1 TGAGGCAACGAAACTTT
4215821 TTTTAAAAAT
Statistics
Matches: 203, Mismatches: 29, Indels: 17
0.82 0.12 0.07
Matches are distributed among these distances:
35 2 0.01
36 55 0.27
37 55 0.27
38 89 0.44
39 2 0.01
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (37 bp):
TGAGGCAACGAAACTTTAAAAATGAACTCCTCAAAGC
Found at i:4215670 original size:74 final size:72
Alignment explanation
Indices: 4215592--4215811 Score: 257
Period size: 74 Copynumber: 3.0 Consensus size: 72
4215582 AAGGTAATGA
*
4215592 AACTTGAAAAATGAACTCCTCAAAGCTGAGGCAACGAAACTTCTAAAAATGAACTCCTCAAAGCT
1 AACTTAAAAAATGAACTCCTCAAAGCTGAGGCAACGAAACTT-TAAAAATGAACTCCTCAAAGCT
*
4215657 GTGGCAAC
65 GAGGCAAC
** * * *
4215665 GAACTTTTAAAACGAACTCCTCAAAGCTGAGGCAATGAAACTTTTAAAAATGATCTCCTCAAAGC
1 -AACTTAAAAAATGAACTCCTCAAAGCTGAGGCAACGAAAC-TTTAAAAATGAACTCCTCAAAGC
*
4215730 TAAGGCAAC
64 TGAGGCAAC
*
4215739 ATGACTTTAAAAAAGTG-GCTCCTCAAAGCTGAGGCAAC-ATAACTTT-AAAATGAACTCCTCAA
1 A--AC-TTAAAAAA-TGAACTCCTCAAAGCTGAGGCAACGA-AACTTTAAAAATGAACTCCTCAA
*
4215801 AACTGAGGCAA
61 AGCTGAGGCAA
4215812 AGAAACTTTT
Statistics
Matches: 125, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
73 1 0.01
74 87 0.70
75 8 0.06
76 28 0.22
77 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.21
Consensus pattern (72 bp):
AACTTAAAAAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTAAAAATGAACTCCTCAAAGCTG
AGGCAAC
Found at i:4215736 original size:112 final size:112
Alignment explanation
Indices: 4215568--4215821 Score: 320
Period size: 112 Copynumber: 2.3 Consensus size: 112
4215558 TTTAAAAATA
* * * * *
4215568 AACTCCTCAAAATTAAGGTAATGAAAC-TTGAAAAATGAACTCCTCAAAGCTGAGGCAACGA-AA
1 AACTCCTCAAAACTGAGGCAATGAAACTTTTAAAAATGAACTCCTCAAAGCTAAGGCAAC-ATAA
*
4215631 CTTCT-AAAAA-TGAACTCCTCAAAGCTGTGGCAAC-GAACTTTTAAAACG
65 CTT-TAAAAAAGTG-ACTCCTCAAAGCTGAGGCAACAGAAC-TTTAAAACG
* * *
4215679 AACTCCTCAAAGCTGAGGCAATGAAACTTTTAAAAATGATCTCCTCAAAGCTAAGGCAACATGAC
1 AACTCCTCAAAACTGAGGCAATGAAACTTTTAAAAATGAACTCCTCAAAGCTAAGGCAACATAAC
* * *
4215744 TTTAAAAAAGTGGCTCCTCAAAGCTGAGGCAACATAACTTTAAAATG
66 TTTAAAAAAGTGACTCCTCAAAGCTGAGGCAACAGAACTTTAAAACG
*
4215791 AACTCCTCAAAACTGAGGCAAAGAAACTTTT
1 AACTCCTCAAAACTGAGGCAATGAAACTTTT
4215822 TTTAAAAATG
Statistics
Matches: 124, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
111 25 0.20
112 94 0.76
113 5 0.04
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.22
Consensus pattern (112 bp):
AACTCCTCAAAACTGAGGCAATGAAACTTTTAAAAATGAACTCCTCAAAGCTAAGGCAACATAAC
TTTAAAAAAGTGACTCCTCAAAGCTGAGGCAACAGAACTTTAAAACG
Found at i:4215820 original size:74 final size:73
Alignment explanation
Indices: 4215558--4215820 Score: 248
Period size: 74 Copynumber: 3.5 Consensus size: 73
4215548 GCAATGTAAT
* * * * *
4215558 TTTAAAAATAAACTCCTCAAAATTAAGGTAATGAAAC-TTGAAAAA-TGAACTCCTCAAAGCTGA
1 TTTAAAAATGAACTCCTCAAAACTAAGGCAAAG-AACTTTAAAAAAGTG-ACTCCTCAAAGCTGA
4215621 GGCAACGAAAC
64 GGCAAC-AAAC
* ** * * * *
4215632 TTCTAAAAATGAACTCCTCAAAGCTGTGGCAACGAACTTTTAAAACG-AACTCCTCAAAGCTGAG
1 TT-TAAAAATGAACTCCTCAAAACTAAGGCAAAGAACTTTAAAAAAGTGACTCCTCAAAGCTGAG
*
4215696 GCAATGAAAC
65 GCAA-CAAAC
* * *
4215706 TTTTAAAAATGATCTCCTCAAAGCTAAGGCAACATG-ACTTTAAAAAAGTGGCTCCTCAAAGCTG
1 -TTTAAAAATGAACTCCTCAAAACTAAGGCAA-A-GAACTTTAAAAAAGTGACTCCTCAAAGCTG
4215770 AGGCAACATAAC
63 AGGCAACA-AAC
*
4215782 TTT-AAAATGAACTCCTCAAAACTGAGGCAAAGAAACTTT
1 TTTAAAAATGAACTCCTCAAAACTAAGGCAAAG-AACTTT
4215821 TTTTAAAAAT
Statistics
Matches: 155, Mismatches: 23, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
72 1 0.01
73 1 0.01
74 84 0.54
75 46 0.30
76 23 0.15
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (73 bp):
TTTAAAAATGAACTCCTCAAAACTAAGGCAAAGAACTTTAAAAAAGTGACTCCTCAAAGCTGAGG
CAACAAAC
Found at i:4215849 original size:41 final size:41
Alignment explanation
Indices: 4215785--4215866 Score: 94
Period size: 41 Copynumber: 2.0 Consensus size: 41
4215775 ACATAACTTT
* * *
4215785 AAAATGAACTCCTCAAAACTGAGGCAA-AGAAACTTTTTTTA
1 AAAATGAACTCCTAAAAAATGAGGCAACA-AAACCTTTTTTA
* * *
4215826 AAAATGAATTCTTAAAAAATGAGGTAACAAAACCTTTTTTA
1 AAAATGAACTCCTAAAAAATGAGGCAACAAAACCTTTTTTA
4215867 TTTTTTGAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
41 33 0.97
42 1 0.03
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.29
Consensus pattern (41 bp):
AAAATGAACTCCTAAAAAATGAGGCAACAAAACCTTTTTTA
Found at i:4228206 original size:15 final size:15
Alignment explanation
Indices: 4228188--4228243 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
4228178 TATATTCGAA
4228188 TTATTATTATTATTT
1 TTATTATTATTATTT
* * *
4228203 TTATCATCATTTTTT
1 TTATTATTATTATTT
*
4228218 TTATCTATTGTTATTT
1 TTAT-TATTATTATTT
*
4228234 AT-TTATTATT
1 TTATTATTATT
4228244 TTTGTTGAGT
Statistics
Matches: 31, Mismatches: 9, Indels: 3
0.72 0.21 0.07
Matches are distributed among these distances:
14 6 0.19
15 17 0.55
16 8 0.26
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (15 bp):
TTATTATTATTATTT
Found at i:4228594 original size:3 final size:3
Alignment explanation
Indices: 4228586--4228620 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
4228576 TTAACTTACA
4228586 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT T
4228621 TGTTTTCCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:4229147 original size:20 final size:19
Alignment explanation
Indices: 4229108--4229148 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
4229098 TATAAAACCC
*
4229108 TCATTTTCTCCTTTCCTTT
1 TCATTTTCTCCTTTCATTT
*
4229127 TCATTTTCTCTCTTTTATTT
1 TCATTTTCTC-CTTTCATTT
4229147 TC
1 TC
4229149 TCTCTCTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (19 bp):
TCATTTTCTCCTTTCATTT
Found at i:4229148 original size:14 final size:15
Alignment explanation
Indices: 4229123--4229153 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
4229113 TTCTCCTTTC
4229123 CTTTTCATTTTCTCT
1 CTTTTCATTTTCTCT
4229138 CTTTT-ATTTTCTCT
1 CTTTTCATTTTCTCT
4229152 CT
1 CT
4229154 CTAACCCGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.06, C:0.26, G:0.00, T:0.68
Consensus pattern (15 bp):
CTTTTCATTTTCTCT
Found at i:4232849 original size:22 final size:22
Alignment explanation
Indices: 4232807--4232866 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 22
4232797 AGACACCTAA
*
4232807 AAAATAAATAAAAAATTTAAATT
1 AAAATAAATAAAAAA-TTAAAAT
*
4232830 ATAATAAAATAAAAAA-TAAAAT
1 AAAAT-AAATAAAAAATTAAAAT
*
4232852 AAAATAATTAAAAAA
1 AAAATAAATAAAAAA
4232867 AAAAAGAGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 9 0.28
22 9 0.28
23 4 0.12
24 10 0.31
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (22 bp):
AAAATAAATAAAAAATTAAAAT
Found at i:4232867 original size:17 final size:17
Alignment explanation
Indices: 4232804--4232858 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
4232794 TGTAGACACC
*
4232804 TAAAAAATAAATAAAAAA
1 TAAAAAATAAA-ATAAAA
** * *
4232822 TTTAAATTATAATAAAA
1 TAAAAAATAAAATAAAA
4232839 TAAAAAATAAAATAAAA
1 TAAAAAATAAAATAAAA
4232856 TAA
1 TAA
4232859 TTAAAAAAAA
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
17 21 0.75
18 7 0.25
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
TAAAAAATAAAATAAAA
Found at i:4235477 original size:31 final size:29
Alignment explanation
Indices: 4235442--4235512 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
4235432 CTAGTTATTA
*
4235442 TGGATATTTAATATATCTTGCTTAGCTACTG
1 TGGATA-TT-ATACATCTTGCTTAGCTACTG
* *
4235473 TGGATATTGTACATCTTGTTTAGCTACTG
1 TGGATATTATACATCTTGCTTAGCTACTG
*
4235502 TGGATGTTATA
1 TGGATATTATA
4235513 AATATTTTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 27 0.77
30 2 0.06
31 6 0.17
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.45
Consensus pattern (29 bp):
TGGATATTATACATCTTGCTTAGCTACTG
Found at i:4238309 original size:22 final size:24
Alignment explanation
Indices: 4238283--4238330 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
4238273 TCTTTGTCAC
4238283 TTTCTTCCTC-ATTT-TCTTTATT
1 TTTCTTCCTCTATTTCTCTTTATT
* *
4238305 TTTCTTCTTCTATTTCTTTTTATT
1 TTTCTTCCTCTATTTCTCTTTATT
4238329 TT
1 TT
4238331 CTCAACTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 9 0.41
23 4 0.18
24 9 0.41
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTCTTCCTCTATTTCTCTTTATT
Found at i:4238882 original size:34 final size:34
Alignment explanation
Indices: 4238844--4238916 Score: 146
Period size: 34 Copynumber: 2.1 Consensus size: 34
4238834 AAATTGTTCC
4238844 TCTTTTGTTTAACTAGGTAGTGTTTAATTTCTAT
1 TCTTTTGTTTAACTAGGTAGTGTTTAATTTCTAT
4238878 TCTTTTGTTTAACTAGGTAGTGTTTAATTTCTAT
1 TCTTTTGTTTAACTAGGTAGTGTTTAATTTCTAT
4238912 TCTTT
1 TCTTT
4238917 CGGTGTTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.19, C:0.10, G:0.14, T:0.58
Consensus pattern (34 bp):
TCTTTTGTTTAACTAGGTAGTGTTTAATTTCTAT
Found at i:4239181 original size:25 final size:25
Alignment explanation
Indices: 4239153--4239206 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
4239143 TATTTTAAAT
4239153 CAAACAAATCC-TAATTACTATTAAC
1 CAAACAAA-CCTTAATTACTATTAAC
* * *
4239178 CAAATAAACCTTAATTATTATTAAT
1 CAAACAAACCTTAATTACTATTAAC
4239203 CAAA
1 CAAA
4239207 ATATCTCTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 2 0.08
25 23 0.92
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (25 bp):
CAAACAAACCTTAATTACTATTAAC
Found at i:4240323 original size:19 final size:19
Alignment explanation
Indices: 4240299--4240342 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
4240289 CATTCACCAA
4240299 ACATCTAATTCCCACCTAG
1 ACATCTAATTCCCACCTAG
4240318 ACATCTAATTCCCACCTAG
1 ACATCTAATTCCCACCTAG
4240337 ACATCT
1 ACATCT
4240343 CTTCATTGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.32, C:0.36, G:0.05, T:0.27
Consensus pattern (19 bp):
ACATCTAATTCCCACCTAG
Found at i:4244879 original size:2 final size:2
Alignment explanation
Indices: 4244872--4244897 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4244862 AGATGTGTAA
4244872 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
4244898 TAGAGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:4248612 original size:19 final size:19
Alignment explanation
Indices: 4248585--4248631 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
4248575 AACCAAAAAG
*
4248585 ATAAGATAAAATTTT-TAAA
1 ATAAAATAAAATTTTAT-AA
* *
4248604 ATAAAATAATATTTTATTA
1 ATAAAATAAAATTTTATAA
4248623 ATAAAATAA
1 ATAAAATAA
4248632 TATTAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 23 0.96
20 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
ATAAAATAAAATTTTATAA
Found at i:4251720 original size:22 final size:22
Alignment explanation
Indices: 4251692--4251759 Score: 127
Period size: 22 Copynumber: 3.1 Consensus size: 22
4251682 TTGGTGTCAG
4251692 AGCTTTTGGTTTTAAAGATCAA
1 AGCTTTTGGTTTTAAAGATCAA
4251714 AGCTTTTGGTTTTAAAGATCAA
1 AGCTTTTGGTTTTAAAGATCAA
*
4251736 AGCCTTTGGTTTTAAAGATCAA
1 AGCTTTTGGTTTTAAAGATCAA
4251758 AG
1 AG
4251760 TACAAAGCTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.38
Consensus pattern (22 bp):
AGCTTTTGGTTTTAAAGATCAA
Found at i:4253519 original size:24 final size:23
Alignment explanation
Indices: 4253487--4253533 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 23
4253477 AAATTCATTT
4253487 TCTCCCATTACCCATCATTGGCNC
1 TCTCCCATTACCCATCATTGGC-C
4253511 TCTCCCATTACCCATCATTGGCC
1 TCTCCCATTACCCATCATTGGCC
4253534 GAATTTTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.17, C:0.43, G:0.09, T:0.30
Consensus pattern (23 bp):
TCTCCCATTACCCATCATTGGCC
Found at i:4255526 original size:13 final size:13
Alignment explanation
Indices: 4255508--4255532 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4255498 TTTCCAAAAA
4255508 TTTATAAAATCAT
1 TTTATAAAATCAT
4255521 TTTATAAAATCA
1 TTTATAAAATCA
4255533 CAATTTCTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:4273110 original size:19 final size:20
Alignment explanation
Indices: 4273081--4273120 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
4273071 TCACTTCTAA
4273081 ACTTCAAATCATACTCCAAT
1 ACTTCAAATCATACTCCAAT
4273101 ACTT-AAATCATACTCCAAT
1 ACTTCAAATCATACTCCAAT
4273120 A
1 A
4273121 AGTCAAATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (20 bp):
ACTTCAAATCATACTCCAAT
Found at i:4282294 original size:28 final size:29
Alignment explanation
Indices: 4282253--4282312 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
4282243 GTCTATGGGC
*
4282253 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
4282281 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
4282311 AA
1 AA
4282313 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:4290474 original size:28 final size:29
Alignment explanation
Indices: 4290433--4290492 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
4290423 GTCTATGGGC
*
4290433 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
4290461 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
4290491 AA
1 AA
4290493 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:4304703 original size:41 final size:41
Alignment explanation
Indices: 4304640--4304722 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 41
4304630 CATATTGAGT
*
4304640 TATTAGATTGAACTATTGAGATATAATAT-ATTATGATAGGC
1 TATTAGATTGAACTATTAAGATATAATATGA-TATGATAGGC
* * *
4304681 TATTAGGTTGGACTGTTAAGATATAATATGATATGATAGGC
1 TATTAGATTGAACTATTAAGATATAATATGATATGATAGGC
4304722 T
1 T
4304723 TAGATTTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 36 0.97
42 1 0.03
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (41 bp):
TATTAGATTGAACTATTAAGATATAATATGATATGATAGGC
Found at i:4311135 original size:35 final size:35
Alignment explanation
Indices: 4311096--4311163 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
4311086 TTGTTCTATG
* * *
4311096 TGAAGTAGTGTTTTACTTGTTCTAATTGTTTTCCA
1 TGAAGTAATGCTTCACTTGTTCTAATTGTTTTCCA
*
4311131 TGAAGTAATGCTTCACTTGTTCTAGTTGTTTTC
1 TGAAGTAATGCTTCACTTGTTCTAATTGTTTTC
4311164 ATCATTCTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.19, C:0.13, G:0.18, T:0.50
Consensus pattern (35 bp):
TGAAGTAATGCTTCACTTGTTCTAATTGTTTTCCA
Found at i:4332833 original size:23 final size:23
Alignment explanation
Indices: 4332804--4332847 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
4332794 TTCATAATAT
4332804 TAATTTAAATATTAATATTTTTA
1 TAATTTAAATATTAATATTTTTA
*
4332827 TAATTTAATTATTAATATTTT
1 TAATTTAAATATTAATATTTT
4332848 AAAATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TAATTTAAATATTAATATTTTTA
Found at i:4332857 original size:23 final size:23
Alignment explanation
Indices: 4332805--4332858 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
4332795 TCATAATATT
* *
4332805 AATTTAAATATTAATATTTTTAT
1 AATTTAATTATTAATATTTTTAA
4332828 AATTTAATTATTAATA-TTTTAA
1 AATTTAATTATTAATATTTTTAA
4332850 AATATTAAT
1 AAT-TTAAT
4332859 ATTTTATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 8 0.29
23 20 0.71
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AATTTAATTATTAATATTTTTAA
Found at i:4332897 original size:24 final size:23
Alignment explanation
Indices: 4332849--4333118 Score: 63
Period size: 24 Copynumber: 11.7 Consensus size: 23
4332839 TAATATTTTA
* *
4332849 AAATATTAATATTTTATTTAATTT
1 AAATATTAATATATTA-TTATTTT
*
4332873 AAATATTATTATGATTATTATTTT
1 AAATATTAATAT-ATTATTATTTT
* * *
4332897 -AAT-TTATTTTATTTTTTAGCTTATT
1 AAATATTAATATA-TTATTA--TT-TT
4332922 AAA-ATTTAATA-A-T-TTA-TTT
1 AAATA-TTAATATATTATTATTTT
* *
4332941 ATAATACTAATA-ATTGATCA-TTT
1 A-AATATTAATATATT-ATTATTTT
* *
4332964 AAATATTAATATTTTATTTAATTT
1 AAATATTAATATATTA-TTATTTT
* *
4332988 AAATATTATTATGATCAATTATTTT
1 AAATATTAATAT-AT-TATTATTTT
*
4333013 --AT-TT--TATTTTA-T-TTTT
1 AAATATTAATATATTATTATTTT
* * *
4333029 AAATGTTAATAATAGATAATTTATTTA
1 AAATATTAAT-AT--ATTA-TTATTTT
*
4333056 AAATATTAATA-ATTGA-TAATTT
1 AAATATTAATATATT-ATTATTTT
* *
4333078 AAATGTTAATATTTTATTTATTTT
1 AAATATTAATATATTA-TTATTTT
*
4333102 AAATATTATTATGATTA
1 AAATATTAATAT-ATTA
4333119 ATGTTTTATT
Statistics
Matches: 181, Mismatches: 31, Indels: 67
0.65 0.11 0.24
Matches are distributed among these distances:
16 4 0.02
17 1 0.01
18 3 0.02
19 6 0.03
20 12 0.07
21 4 0.02
22 40 0.22
23 22 0.12
24 52 0.29
25 15 0.08
26 6 0.03
27 16 0.09
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (23 bp):
AAATATTAATATATTATTATTTT
Found at i:4333064 original size:27 final size:28
Alignment explanation
Indices: 4333020--4333078 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
4333010 TTTATTTTAT
* *
4333020 TTTATTTTTAAATGTTAATAATAGATAA
1 TTTATTTTAAAATATTAATAATAGATAA
*
4333048 TTTA-TTTAAAATATTAATAATTGATAA
1 TTTATTTTAAAATATTAATAATAGATAA
4333075 TTTA
1 TTTA
4333079 AATGTTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 24 0.86
28 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (28 bp):
TTTATTTTAAAATATTAATAATAGATAA
Found at i:4333096 original size:114 final size:113
Alignment explanation
Indices: 4332823--4333210 Score: 480
Period size: 113 Copynumber: 3.4 Consensus size: 113
4332813 TATTAATATT
* * * *
4332823 TTTATAAT-TTAATTATTAATATTTTAAAATATTAATATTTTATTTAATTTAAATATTATTATGA
1 TTTAAAATATTAATAATTGATAATTT-AAATATTAATATTTTATTTAATTTAAATATTATTATGA
* * **
4332887 TTATTATTTTAATTTATTTTATTTTTTAGCTTATTAA-AATTTA-ATAATTTA
65 TAATTATTTTATTTTATTTTA-TTTTTA-AATATTAATAA--TAGATAATTTA
* * *
4332938 TTTATAATACTAATAATTGATCATTTAAATATTAATATTTTATTTAATTTAAATATTATTATGAT
1 TTTAAAATATTAATAATTGATAATTTAAATATTAATATTTTATTTAATTTAAATATTATTATGAT
*
4333003 CAATTATTTTATTTTATTTTATTTTTAAATGTTAATAATAGATAATTTA
66 -AATTATTTTATTTTATTTTATTTTTAAATATTAATAATAGATAATTTA
* *
4333052 TTTAAAATATTAATAATTGATAATTTAAATGTTAATATTTTATTTATTTTAAATATTATTATGAT
1 TTTAAAATATTAATAATTGATAATTTAAATATTAATATTTTATTTAATTTAAATATTATTATGA-
* *
4333117 TAA-TGTTTTATTTTA-TTTATTTTTAAAATATTAATAATTGATAATTTA
65 TAATTATTTTATTTTATTTTATTTTT-AAATATTAATAATAGATAATTTA
* * * * *
4333165 TTTAAAATATTGATAATTGATAAGTTAATTATCAACATTTTATTTA
1 TTTAAAATATTAATAATTGATAATTTAAATATTAATATTTTATTTA
4333211 TAATTTAATC
Statistics
Matches: 243, Mismatches: 24, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
112 9 0.04
113 74 0.30
114 74 0.30
115 56 0.23
116 30 0.12
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (113 bp):
TTTAAAATATTAATAATTGATAATTTAAATATTAATATTTTATTTAATTTAAATATTATTATGAT
AATTATTTTATTTTATTTTATTTTTAAATATTAATAATAGATAATTTA
Found at i:4333106 original size:46 final size:45
Alignment explanation
Indices: 4333047--4333164 Score: 133
Period size: 46 Copynumber: 2.7 Consensus size: 45
4333037 ATAATAGATA
*
4333047 ATTTATTTAAAATATTAATAATTGATAATTTAAATGTTAATATTTT
1 ATTTATTTTAAATATTAATAATTGATAATTTAAATGTT-ATATTTT
* *
4333093 ATTTATTTTAAATA-T--T-ATT-ATGA-TT-AATGTTTTATTTT
1 ATTTATTTTAAATATTAATAATTGATAATTTAAATGTTATATTTT
4333131 ATTTATTTTTAAAATATTAATAATTGATAATTTA
1 ATTTA-TTTT-AAATATTAATAATTGATAATTTA
4333165 TTTAAAATAT
Statistics
Matches: 59, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
38 11 0.19
39 10 0.17
40 7 0.12
41 4 0.07
42 3 0.05
43 2 0.03
44 3 0.05
45 4 0.07
46 15 0.25
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (45 bp):
ATTTATTTTAAATATTAATAATTGATAATTTAAATGTTATATTTT
Found at i:4333165 original size:38 final size:37
Alignment explanation
Indices: 4332973--4333167 Score: 94
Period size: 38 Copynumber: 5.1 Consensus size: 37
4332963 TAAATATTAA
* * * *
4332973 TATTTTATTTAATTTAAATATTATTATGATCAATTATTT
1 TATTTTATTTATTTTAAATATTA-TATAATTAA-TAATT
*
4333012 TATTTTATTTTATTTTTAAATGTTA-ATAA-TAGATAATT
1 TATTTTA-TTTA-TTTTAAATATTATATAATTA-ATAATT
* ** * * * * * **
4333050 TATTTAAAATATTAATAATTGATAATTTAAATGTTAA--
1 TATTTTATTTATT-TTAAAT-ATTATATAATTAATAATT
* **
4333087 TATTTTATTTATTTTAAATATTATTATGATTAATGTTT
1 TATTTTATTTATTTTAAATATTA-TATAATTAATAATT
*
4333125 TATTTTATTTATTTTTAAAATATTA-ATAATTGATAATT
1 TATTTTATTTA-TTTT-AAATATTATATAATTAATAATT
4333163 TATTT
1 TATTT
4333168 AAAATATTGA
Statistics
Matches: 112, Mismatches: 32, Indels: 25
0.66 0.19 0.15
Matches are distributed among these distances:
35 3 0.03
36 11 0.10
37 16 0.14
38 38 0.34
39 21 0.19
40 13 0.12
41 10 0.09
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (37 bp):
TATTTTATTTATTTTAAATATTATATAATTAATAATT
Found at i:4333211 original size:113 final size:114
Alignment explanation
Indices: 4332823--4333210 Score: 496
Period size: 114 Copynumber: 3.4 Consensus size: 114
4332813 TATTAATATT
* * * *
4332823 TTTATAAT-TTAATTATTAATATTTTAAAATATTAATATTTTATTTAATTTAAATATTATTATGA
1 TTTAAAATATTAATAATTGATAATTT-AAATATTAATATTTTATTTAATTTAAATATTATTATGA
* * *** *
4332887 TTATTATTTTAATTTATTTTATTTTTTAGCTTATTAA-AATTTAATAATTTA
65 TTAATATTTTATTTTATTTTA-TTTTTAAAATATTAATAA-TTGATAATTTA
* * *
4332938 TTTATAATACTAATAATTGATCATTTAAATATTAATATTTTATTTAATTTAAATATTATTATGAT
1 TTTAAAATATTAATAATTGATAATTTAAATATTAATATTTTATTTAATTTAAATATTATTATGAT
* * *
4333003 CAATTATTTTATTTTATTTTATTTTT-AAATGTTAATAATAGATAATTTA
66 TAA-TATTTTATTTTATTTTATTTTTAAAATATTAATAATTGATAATTTA
* *
4333052 TTTAAAATATTAATAATTGATAATTTAAATGTTAATATTTTATTTATTTTAAATATTATTATGAT
1 TTTAAAATATTAATAATTGATAATTTAAATATTAATATTTTATTTAATTTAAATATTATTATGAT
*
4333117 TAATGTTTTATTTTA-TTTATTTTTAAAATATTAATAATTGATAATTTA
66 TAATATTTTATTTTATTTTATTTTTAAAATATTAATAATTGATAATTTA
* * * * *
4333165 TTTAAAATATTGATAATTGATAAGTTAATTATCAACATTTTATTTA
1 TTTAAAATATTAATAATTGATAATTTAAATATTAATATTTTATTTA
4333211 TAATTTAATC
Statistics
Matches: 240, Mismatches: 29, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
112 9 0.04
113 72 0.30
114 76 0.32
115 55 0.23
116 28 0.12
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (114 bp):
TTTAAAATATTAATAATTGATAATTTAAATATTAATATTTTATTTAATTTAAATATTATTATGAT
TAATATTTTATTTTATTTTATTTTTAAAATATTAATAATTGATAATTTA
Found at i:4333249 original size:113 final size:111
Alignment explanation
Indices: 4332930--4333251 Score: 270
Period size: 114 Copynumber: 2.8 Consensus size: 111
4332920 TTAAAATTTA
* * * * * * *
4332930 ATAATTTATTTATAATACTAATAATTGATCATTTAAATATTAATATTTTATTTAATTTAAATATT
1 ATAATTTATTTAAAATATTAATAATTGATAAGTTAAATATCAACATTTTATTTATTTTAAATATT
** * * * ** *
4332995 ATTATGATCAATTATTTTATTTTATTTTATTTTTAAATGTTAATAATAG
66 AACATGATTAA--A-ATAATAATATTTTATTTTTAAATATTAATAATAG
* * * *
4333044 ATAATTTATTTAAAATATTAATAATTGATAATTTAAATGTTAATATTTTATTTATTTTAAATATT
1 ATAATTTATTTAAAATATTAATAATTGATAAGTTAAATATCAACATTTTATTTATTTTAAATATT
** ** ** * * *
4333109 ATTATGATTAATGTTTTATTTTATTTATTTTTAAAATATTAATAATTG
66 AACATGATTAAAATAATAATAT-TTTATTTTT-AAATATTAATAATAG
* *
4333157 ATAATTTATTTAAAATATTGATAATTGATAAGTTAATTATCAACATTTTATTTATAATTT-AATC
1 ATAATTTATTTAAAATATTAATAATTGATAAGTTAAATATCAACATTTTATTTAT--TTTAAAT-
* *
4333221 TTTAACAT-TTTAAAATAATAATATTTTATTT
63 ATTAACATGATTAAAATAATAATATTTTATTT
4333252 ATAATTGAAA
Statistics
Matches: 174, Mismatches: 29, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
111 6 0.03
112 9 0.05
113 69 0.40
114 82 0.47
115 8 0.05
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (111 bp):
ATAATTTATTTAAAATATTAATAATTGATAAGTTAAATATCAACATTTTATTTATTTTAAATATT
AACATGATTAAAATAATAATATTTTATTTTTAAATATTAATAATAG
Found at i:4333351 original size:27 final size:28
Alignment explanation
Indices: 4333294--4333355 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
4333284 GAATTTAATT
* *
4333294 TAATTTATTTTTAAACATTAATAATTTA
1 TAATTTATTTTAAAACATTAATAATTGA
* *
4333322 TAATTTA-TTTAAAATATTACTAATTGA
1 TAATTTATTTTAAAACATTAATAATTGA
4333349 TAATTTA
1 TAATTTA
4333356 ATTATTAGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 23 0.77
28 7 0.23
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.52
Consensus pattern (28 bp):
TAATTTATTTTAAAACATTAATAATTGA
Found at i:4334150 original size:2 final size:2
Alignment explanation
Indices: 4334108--4334139 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4334098 TTATTACTAC
4334108 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
4334140 GTGGATATAT
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:4346367 original size:28 final size:28
Alignment explanation
Indices: 4346325--4346383 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
4346315 GGACAAGTGT
*
4346325 CCTGGTGGTGGAAAATTA-CTATTTTGCC
1 CCTGGTGGTGGAAAATTATC-ATTTTACC
4346353 CCTGG-GGTGGCAAAATTATCATTTTACC
1 CCTGGTGGTGG-AAAATTATCATTTTACC
4346381 CCT
1 CCT
4346384 ATGCTCCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 5 0.18
28 22 0.79
29 1 0.04
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (28 bp):
CCTGGTGGTGGAAAATTATCATTTTACC
Found at i:4367461 original size:26 final size:26
Alignment explanation
Indices: 4367405--4367461 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
4367395 AGAAGACTAC
4367405 TATATATAGTAAAATTATTAATATAT
1 TATATATAGTAAAATTATTAATATAT
* * * *
4367431 AATATAT-TTAAAATATATTAGTTTAT
1 TATATATAGTAAAAT-TATTAATATAT
4367457 TATAT
1 TATAT
4367462 GTATATAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (26 bp):
TATATATAGTAAAATTATTAATATAT
Found at i:4371303 original size:2 final size:2
Alignment explanation
Indices: 4371296--4371329 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4371286 NNNAATAATA
4371296 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
4371330 GCTTGATTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4372139 original size:104 final size:104
Alignment explanation
Indices: 4371954--4372187 Score: 414
Period size: 104 Copynumber: 2.2 Consensus size: 104
4371944 TGGTAAAGTG
* *
4371954 TTTCTAACAAAAAATTCTGTTGGAAATTACCGACAAATTTTTCGACGAAAATTTTCGTTTGTATT
1 TTTCCAACAAAAAATTATGTTGGAAATTACCGACAAATTTTTCGACGAAAATTTTCGTTTGTATT
*
4372019 GGTTTCCAACGAAAAATTCTGAAGAAAATCCATTGAAAA
66 GGTTTCCAACAAAAAATTCTGAAGAAAATCCATTGAAAA
*
4372058 TTTCCAACAAAAAATTATGTTGGAAATTACCGACAAATTTTTCGACGAAAATTTTCGTTTGTGTT
1 TTTCCAACAAAAAATTATGTTGGAAATTACCGACAAATTTTTCGACGAAAATTTTCGTTTGTATT
*
4372123 GGTTTCCAACAAAAAATTTTGAAGAAAATCCATTGAAAA
66 GGTTTCCAACAAAAAATTCTGAAGAAAATCCATTGAAAA
*
4372162 TTTCCAACAAAAAATTTTGTTGGAAA
1 TTTCCAACAAAAAATTATGTTGGAAA
4372188 CTCTGTTGGT
Statistics
Matches: 124, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
104 124 1.00
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (104 bp):
TTTCCAACAAAAAATTATGTTGGAAATTACCGACAAATTTTTCGACGAAAATTTTCGTTTGTATT
GGTTTCCAACAAAAAATTCTGAAGAAAATCCATTGAAAA
Found at i:4372251 original size:37 final size:36
Alignment explanation
Indices: 4372126--4372253 Score: 96
Period size: 37 Copynumber: 3.4 Consensus size: 36
4372116 TTGTGTTGGT
* * * **
4372126 TTCCAACAAAAAATTTTG-AAGAAAATCCATTGAAAA
1 TTCCAACGAAAAATTCTGTTAG-AAATCCATTGGTAA
* * * **
4372162 TTTCCAACAAAAAATTTTGTTGGAAACTCTGTTGGTAAA
1 -TTCCAACGAAAAATTCTGTTAGAAA-TCCATTGGT-AA
*
4372201 TTCCAATGAAAAATTCTGTTAGAAATCCATTGGTAA
1 TTCCAACGAAAAATTCTGTTAGAAATCCATTGGTAA
*
4372237 TTGCCAACGGAAAATTC
1 TT-CCAACGAAAAATTC
4372254 CTAAGCAAAA
Statistics
Matches: 73, Mismatches: 14, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
36 4 0.05
37 40 0.55
38 27 0.37
39 2 0.03
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (36 bp):
TTCCAACGAAAAATTCTGTTAGAAATCCATTGGTAA
Found at i:4375844 original size:19 final size:19
Alignment explanation
Indices: 4375820--4375857 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
4375810 CCATTTGACT
4375820 TATTAGAGTATGATTTGAG
1 TATTAGAGTATGATTTGAG
4375839 TATTAGAGTATGATTTGAG
1 TATTAGAGTATGATTTGAG
4375858 GTTAAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (19 bp):
TATTAGAGTATGATTTGAG
Found at i:4381089 original size:20 final size:20
Alignment explanation
Indices: 4381045--4381091 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
4381035 ACTTCTAAAC
* *
4381045 CTCAAATCATACTTCAATTA
1 CTCAAATCATACTCCAATAA
4381065 CTCAAATCATACTCCAATAA
1 CTCAAATCATACTCCAATAA
*
4381085 GTCAAAT
1 CTCAAAT
4381092 GGGGCAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.26, G:0.02, T:0.30
Consensus pattern (20 bp):
CTCAAATCATACTCCAATAA
Found at i:4383101 original size:36 final size:36
Alignment explanation
Indices: 4383054--4383128 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
4383044 ATGGACTAAC
* *
4383054 CATTATTATTAACTGAAAATAAATGTAATCCATAAT
1 CATTAATATTAAATGAAAATAAATGTAATCCATAAT
** *
4383090 CATTAATATTAAATGTTAATAAATGTAATGCATAAT
1 CATTAATATTAAATGAAAATAAATGTAATCCATAAT
4383126 CAT
1 CAT
4383129 AAGAAAGATG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.37
Consensus pattern (36 bp):
CATTAATATTAAATGAAAATAAATGTAATCCATAAT
Done.