Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold71
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: 5741892
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 121862 characters in sequence are not A, C, G, or T
File 20 of 33
Found at i:3152998 original size:16 final size:16
Alignment explanation
Indices: 3152977--3153008 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3152967 AAATGAAAGC
3152977 TAGATCCTCTCATTGT
1 TAGATCCTCTCATTGT
*
3152993 TAGATCTTCTCATTGT
1 TAGATCCTCTCATTGT
3153009 GACAATCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.22, G:0.12, T:0.47
Consensus pattern (16 bp):
TAGATCCTCTCATTGT
Found at i:3153654 original size:27 final size:27
Alignment explanation
Indices: 3153619--3153712 Score: 79
Period size: 28 Copynumber: 3.5 Consensus size: 27
3153609 AATATATAAT
3153619 TTATAATTAAATTTAATAATTTATATAA
1 TTATAATTAAATTTAATAATTTATAT-A
* * *
3153647 TTAT-ATTATATTTATGTATTTTATATA
1 TTATAATTAAATTTA-ATAATTTATATA
** *
3153674 TTATAATTGTATTTAAGATATTT-TATA
1 TTATAATTAAATTTAATA-ATTTATATA
3153701 TTAT-A-TAAATTT
1 TTATAATTAAATTT
3153713 TGATATATTA
Statistics
Matches: 54, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
25 5 0.09
26 1 0.02
27 23 0.43
28 25 0.46
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.56
Consensus pattern (27 bp):
TTATAATTAAATTTAATAATTTATATA
Found at i:3153894 original size:2 final size:2
Alignment explanation
Indices: 3153887--3153911 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3153877 CTCTTAAGAC
3153887 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3153912 TCGAATAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3154450 original size:27 final size:27
Alignment explanation
Indices: 3154420--3154475 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
3154410 ATTAAAATTT
3154420 TAAAAATAAATAA-ATATTTTATTAATA
1 TAAAAATAAATAATA-ATTTTATTAATA
* * *
3154447 TAAAATTATATAATAATTTTATTTATA
1 TAAAAATAAATAATAATTTTATTAATA
3154474 TA
1 TA
3154476 TTTAGTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
TAAAAATAAATAATAATTTTATTAATA
Found at i:3155719 original size:22 final size:22
Alignment explanation
Indices: 3155694--3155736 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3155684 TTCACACTTT
*
3155694 AACTTAAATTTTTTAAATTAAA
1 AACTTAAACTTTTTAAATTAAA
* *
3155716 AACTTTAACTTTTTAACTTAA
1 AACTTAAACTTTTTAAATTAA
3155737 TTCAGATACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (22 bp):
AACTTAAACTTTTTAAATTAAA
Found at i:3160329 original size:17 final size:18
Alignment explanation
Indices: 3160289--3160330 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
3160279 CTATAATCTA
* *
3160289 ATAATTATAAAAAGTTATT
1 ATAA-TATAAAAAATCATT
3160308 ATAATATAAAAAATCATT
1 ATAATATAAAAAATCATT
3160326 -TAATA
1 ATAATA
3160331 AATCATTGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 5 0.24
18 12 0.57
19 4 0.19
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (18 bp):
ATAATATAAAAAATCATT
Found at i:3162916 original size:16 final size:18
Alignment explanation
Indices: 3162895--3162950 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 18
3162885 ATTAATTAAA
3162895 TATATTAA-T-TAAAATT
1 TATATTAACTGTAAAATT
3162911 TATATTAACTTGTAAAATT
1 TATATTAAC-TGTAAAATT
* *
3162930 TATTTTATA-TGTAAATTT
1 TATATTA-ACTGTAAAATT
3162948 TAT
1 TAT
3162951 CAAATATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 8 0.24
18 12 0.35
19 13 0.38
20 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.54
Consensus pattern (18 bp):
TATATTAACTGTAAAATT
Found at i:3164571 original size:219 final size:217
Alignment explanation
Indices: 3164142--3166220 Score: 1747
Period size: 218 Copynumber: 9.8 Consensus size: 217
3164132 AACCTTAAAA
* * ** * * *
3164142 TTAACAAACTATAATAAATACGATACGATACTACAACAATAAGAAAAACTCAATTAGCATAAAAA
1 TTAACAAACTATAATAAACACGACACGGCACTATAACAATAA-AAAAACTCGATTACCATAAAAA
* * *
3164207 AATTAACTCCATACCACACTTGAACTTTGTAGGTCCATC----------ATGAAACTCAAGTTTT
65 AATTAACTCTATACCACACTTAAATTTTGTAGGTCCATCAAGTTATTATATGAAACTCAAGTTTT
* * *
3164262 TAAGTCATGAATTTTTATATAATTTTATATTATTATTGAACTATTAATAAATAATCATAAGCTTA
130 TAAGTAATGAATTTTTATATAATTTTGTATTATGATTGAACTATTAATAAATAATCATAAGCTTA
* **
3164327 CAAAATTTAAACTAACTTCAAAG
195 CAAAATTCAAACTAACCCCAAAG
* *
3164350 TTAACAAACTATAATAAACACAACACGGCACTATAATAATAAGAAAAACTCGATTACCATAAAAA
1 TTAACAAACTATAATAAACACGACACGGCACTATAACAATAA-AAAAACTCGATTACCAT-AAAA
* * * *
3164415 AAAATAACTCCATACCACACTTAAATTTTGTAGGTCCATCAACTTATTATATAAAACTCAAGTTT
64 AAATTAACTCTATACCACACTTAAATTTTGTAGGTCCATCAAGTTATTATATGAAACTCAAGTTT
* * *
3164480 TTAAGTAATGAATTTCTATATAATTTTGTATTGTGATTGAACTATTAATAAATAATCATAAGTTT
129 TTAAGTAATGAATTTTTATATAATTTTGTATTATGATTGAACTATTAATAAATAATCATAAGCTT
* * * **
3164545 ACAAAATTTAAAATGACCTTAAAG
194 ACAAAATTCAAACTAACCCCAAAG
* * * * * *
3164569 TTAATAAACAATAATAAGCACGACACGACACTACAACAATAAAAAAAACTTGATTACCATAAAAA
1 TTAACAAACTATAATAAACACGACACGGCACTATAACAAT-AAAAAAACTCGATTACCATAAAAA
* *
3164634 AATTAACTTTATACCACACTTAAATTTTGTAGGTCCATTAAGTTATTATATGAAACTCAAGTTTT
65 AATTAACTCTATACCACACTTAAATTTTGTAGGTCCATCAAGTTATTATATGAAACTCAAGTTTT
*
3164699 TAAGTAATGAATTTTTATATAATTTTGTATTATGATTGAACTATTAATAAATAATCATAAGCTCA
130 TAAGTAATGAATTTTTATATAATTTTGTATTATGATTGAACTATTAATAAATAATCATAAGCTTA
3164764 CAAAATTCAAACTAACCCCAAAG
195 CAAAATTCAAACTAACCCCAAAG
* * * *
3164787 TTAACAAATTATAATAAACACGACAAGGCACTATAACAATAAAAAAAGCTCGGTTATCATAAAAA
1 TTAACAAACTATAATAAACACGACACGGCACTATAACAATAAAAAAA-CTCGATTACCATAAAAA
* * * *
3164852 AATTAACTCTATACCACATTTAAATTTTGTAGATCTATCAAGTTATTAAATGAAACTCAAGTTTT
65 AATTAACTCTATACCACACTTAAATTTTGTAGGTCCATCAAGTTATTATATGAAACTCAAGTTTT
* * *
3164917 GAAGTCATGAATTTTTATATAATTTTGTATTATTATTGAACTATTAATAAATAATCATAAGCTTA
130 TAAGTAATGAATTTTTATATAATTTTGTATTATGATTGAACTATTAATAAATAATCATAAGCTTA
*
3164982 CAAAATTCAAACTAACCCCAAAA
195 CAAAATTCAAACTAACCCCAAAG
* * * ** * * * ** ** * *
3165005 TCAATAAACTATAATAAACATGACACAACACTACAACCACACTTAAATTTTGTAGGT-CCAT---
1 TTAACAAACTATAATAAACACGACACGGCACTATAACAATA-AAAAAACTCG-A-TTACCATAAA
* ** * * * * *
3165066 TAAATT-A-T-TATATAAAACTCAAGTTTT-TAAGT-CATGAA-TT-TT-TAT---A-T-AA-TT
63 AAAATTAACTCTATACCACACTTAAATTTTGTAGGTCCATCAAGTTATTATATGAAACTCAAGTT
* * * * * * * * * ** * *
3165117 TTGTATTGTGATTGAACTATTA-ATAA--AT-AATCATAAGTT-TAC-AAAAATCAAAATAACCC
128 TT-TA-AGT-AATGAATTTTTATATAATTTTGTATTATGA-TTGAACTATTAAT--AAATAATCA
* * * * *
3165176 TAAAG-TTA-ATAAACTATAATAAATACGACACGACA-
187 T-AAGCTTACA-AAA-T-TCA-AACTA--ACCCCAAAG
* * * * * ** ** * * ***
3165211 CT-AC-AACAATAAGAAAAAC-TCAC-TTA-TCATAA-AA-AAATTAACTCCA-TACCACATCTA
1 TTAACAAACTATAATAAACACGACACGGCACT-ATAACAATAAAAAAACTCGATTACCATAAAAA
* * *** * * * * ** * ** *
3165268 AATT--TTGTAGGTC-CA-TCAAGTTATTATATG-AAACTCAAGTT-TT-TAAGTCA-T-AAATT
65 AATTAACTCTATACCACACTTAAATT-TTGTAGGTCCA-TCAAGTTATTATATGAAACTCAAGTT
3165324 TTT-A-T-AT-AA----T-T------TTGTATTATGATTGAACTATTAATAAATAATCATAAGCT
128 TTTAAGTAATGAATTTTTATATAATTTTGTATTATGATTGAACTATTAATAAATAATCATAAGCT
* * *
3165374 CACAAAAATCAAATTAACCCCAAAG
193 TACAAAATTCAAACTAACCCCAAAG
* * * **
3165399 TTAACAAACTATAATAAACATGACACGGCACTACAACAATAAGAAAAACTCGGTTATTATAAAAA
1 TTAACAAACTATAATAAACACGACACGGCACTATAACAATAA-AAAAACTCGATTACCATAAAAA
* * * *
3165464 AATTAACTCCATACCATATTTAAATTTTGTAAGTCCATCAAGTTATTATATGAAACTCAAGTTTT
65 AATTAACTCTATACCACACTTAAATTTTGTAGGTCCATCAAGTTATTATATGAAACTCAAGTTTT
* * *
3165529 TAAGTCATAAATTTTTATATAATTTTGCATTATGATTGAACTATTAAT-AA-AATCATAAGCTTA
130 TAAGTAATGAATTTTTATATAATTTTGTATTATGATTGAACTATTAATAAATAATCATAAGCTTA
3165592 CAAAATTCAAACTAACCCCAAAG
195 CAAAATTCAAACTAACCCCAAAG
* * * * * *
3165615 TTAATC-AATTATAATAAACACGACACGACACTACAATAATAAAAAAAACTC-AGTTATCATAAG
1 TTAA-CAAACTATAATAAACACGACACGGCACTATAACAAT-AAAAAAACTCGA-TTACCATAAA
*
3165678 AAAATTAACTCCATACCACACTTAAATTTTGTAGGTCCATCAAGTTATTATATGAAACTCAAGTT
63 AAAATTAACTCTATACCACACTTAAATTTTGTAGGTCCATCAAGTTATTATATGAAACTCAAGTT
** *
3165743 TTTAAGCCATGAATTTTTATATAATTTTGTATTATATATGGTTGAACTATTAATAAATAATCATA
128 TTTAAGTAATGAATTTTTATATAATTTTG---TAT-TATGATTGAACTATTAATAAATAATCATA
3165808 AGCTTACAAAATTCAAACTAACCCCAAAG
189 AGCTTACAAAATTCAAACTAACCCCAAAG
* * * ** * * ** *
3165837 TTAACAAACTATATTAAGCACGATACAACACTACAACAATAGGAAAATTTTGATTACCATAAAAA
1 TTAACAAACTATAATAAACACGACACGGCACTATAACAATA-AAAAAACTCGATTACCATAAAAA
* *
3165902 AATTAACTCTATACCACACTTAAATTTTGTAGGTCCATTAACTTATTATATGAAACTCAAGTTTT
65 AATTAACTCTATACCACACTTAAATTTTGTAGGTCCATCAAGTTATTATATGAAACTCAAGTTTT
* * *
3165967 TAAGTCATGAATTTTTATATAATTCTGTATTATGGTTGAACTATTAATAAATAATCATAAGCTTA
130 TAAGTAATGAATTTTTATATAATTTTGTATTATGATTGAACTATTAATAAATAATCATAAGCTTA
*
3166032 CAAAATTCAAACTAACCTCAAAG
195 CAAAATTCAAACTAACCCCAAAG
* * * ** *
3166055 TT----AACTATAATAAACACGACACAGCACTACAACAATAAAAAAATTTTAATTATCATAAAAA
1 TTAACAAACTATAATAAACACGACACGGCACTATAACAATAAAAAAA-CTCGATTACCATAAAAA
* * *
3166116 AATTAACTCCATACCACACTTAAATTTTATAGGTCCATCAAGTTATTATATGAAACTCAAATTTT
65 AATTAACTCTATACCACACTTAAATTTTGTAGGTCCATCAAGTTATTATATGAAACTCAAGTTTT
* * * *
3166181 TAAATCATAAATTTTTATATAATTTTATATTATGATTGAA
130 TAAGTAATGAATTTTTATATAATTTTGTATTATGATTGAA
3166221 TAATTGTAGC
Statistics
Matches: 1519, Mismatches: 254, Indels: 190
0.77 0.13 0.10
Matches are distributed among these distances:
187 5 0.00
188 1 0.00
189 6 0.00
190 13 0.01
191 6 0.00
192 20 0.01
193 11 0.01
194 6 0.00
195 6 0.00
196 11 0.01
197 3 0.00
198 4 0.00
199 22 0.01
200 25 0.02
201 22 0.01
202 29 0.02
203 24 0.02
204 21 0.01
205 15 0.01
206 7 0.00
207 11 0.01
208 53 0.03
209 43 0.03
210 2 0.00
211 5 0.00
212 4 0.00
213 17 0.01
214 142 0.09
215 1 0.00
216 177 0.12
217 12 0.01
218 447 0.29
219 153 0.10
220 20 0.01
221 4 0.00
222 170 0.11
223 1 0.00
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (217 bp):
TTAACAAACTATAATAAACACGACACGGCACTATAACAATAAAAAAACTCGATTACCATAAAAAA
ATTAACTCTATACCACACTTAAATTTTGTAGGTCCATCAAGTTATTATATGAAACTCAAGTTTTT
AAGTAATGAATTTTTATATAATTTTGTATTATGATTGAACTATTAATAAATAATCATAAGCTTAC
AAAATTCAAACTAACCCCAAAG
Found at i:3165189 original size:176 final size:176
Alignment explanation
Indices: 3164864--3165217 Score: 537
Period size: 176 Copynumber: 2.0 Consensus size: 176
3164854 TTAACTCTAT
* * * *
3164864 ACCACATTTAAATTTTGTAGATCTATCAAGTTATTAAATGAAACTCAAGTTTTGAAGTCATGAAT
1 ACCACACTTAAATTTTGTAGATCCATCAAATTATTAAATAAAACTCAAGTTTTGAAGTCATGAAT
* * *
3164929 TTTTATATAATTTTGTATTATTATTGAACTATTAATAAATAATCATAAGCTTACAAAATTCAAAC
66 TTTTATATAATTTTGTATTATGATTGAACTATTAATAAATAATCATAAGCTTACAAAAATCAAAA
*
3164994 TAACCCCAAAATCAATAAACTATAATAAACATGACACAACACTACA
131 TAACCCCAAAATCAATAAACTATAATAAACACGACACAACACTACA
* * * *
3165040 ACCACACTTAAATTTTGTAGGTCCATTAAATTATTATATAAAACTCAAGTTTTTAAGTCATGAAT
1 ACCACACTTAAATTTTGTAGATCCATCAAATTATTAAATAAAACTCAAGTTTTGAAGTCATGAAT
* *
3165105 TTTTATATAATTTTGTATTGTGATTGAACTATTAATAAATAATCATAAGTTTACAAAAATCAAAA
66 TTTTATATAATTTTGTATTATGATTGAACTATTAATAAATAATCATAAGCTTACAAAAATCAAAA
* * * * *
3165170 TAACCCTAAAGTTAATAAACTATAATAAATACGACACGACACTACA
131 TAACCCCAAAATCAATAAACTATAATAAACACGACACAACACTACA
3165216 AC
1 AC
3165218 AATAAGAAAA
Statistics
Matches: 159, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
176 159 1.00
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.34
Consensus pattern (176 bp):
ACCACACTTAAATTTTGTAGATCCATCAAATTATTAAATAAAACTCAAGTTTTGAAGTCATGAAT
TTTTATATAATTTTGTATTATGATTGAACTATTAATAAATAATCATAAGCTTACAAAAATCAAAA
TAACCCCAAAATCAATAAACTATAATAAACACGACACAACACTACA
Found at i:3165394 original size:394 final size:394
Alignment explanation
Indices: 3164646--3165435 Score: 1267
Period size: 394 Copynumber: 2.0 Consensus size: 394
3164636 TTAACTTTAT
* *
3164646 ACCACACTTAAATTTTGTAGGTCCATTAAGTTATTATATGAAACTCAAGTTTTTAAGTAATGAAT
1 ACCACACTTAAATTTTGTAGGTCCATTAAATTATTATATAAAACTCAAGTTTTTAAGTAATGAAT
* *
3164711 TTTTATATAATTTTGTATTATGATTGAACTATTAATAAATAATCATAAGCTCACAAAATTCAAAC
66 TTTTATATAATTTTGTATTATGATTGAACTATTAATAAATAATCATAAGCTCACAAAAATCAAAA
* * * **
3164776 TAACCCCAAAGTTAACAAATTATAATAAACACGACAAGGCACTATAACAATAAAAAAAGCTCGGT
131 TAACCCCAAAGTTAACAAACTATAATAAACACGACAAGACACTACAACAATAAAAAAAGCTCACT
* * *
3164841 TATCATAAAAAAATTAACTCTATACCACATTTAAATTTTGTAGATCTATCAAGTTATTAAATGAA
196 TATCATAAAAAAATTAACTCCATACCACATCTAAATTTTGTAGATCCATCAAGTTATTAAATGAA
* *
3164906 ACTCAAGTTTTGAAGTCATGAATTTTTATATAATTTTGTATTATTATTGAACTATTAATAAATAA
261 ACTCAAGTTTTGAAGTCATAAATTTTTATATAATTTTGTATTATGATTGAACTATTAATAAATAA
* * *
3164971 TCATAAGCTTACAAAATTCAAACTAACCCCAAAATCAATAAACTATAATAAACATGACACAACAC
326 TCATAAGCTCACAAAAATCAAACTAACCCCAAAATCAACAAACTATAATAAACATGACACAACAC
3165036 TACA
391 TACA
*
3165040 ACCACACTTAAATTTTGTAGGTCCATTAAATTATTATATAAAACTCAAGTTTTTAAGTCATGAAT
1 ACCACACTTAAATTTTGTAGGTCCATTAAATTATTATATAAAACTCAAGTTTTTAAGTAATGAAT
* * *
3165105 TTTTATATAATTTTGTATTGTGATTGAACTATTAATAAATAATCATAAGTTTACAAAAATCAAAA
66 TTTTATATAATTTTGTATTATGATTGAACTATTAATAAATAATCATAAGCTCACAAAAATCAAAA
* * * *
3165170 TAACCCTAAAGTTAATAAACTATAATAAATACGACACGACACTACAACAATAAGAAAAA-CTCAC
131 TAACCCCAAAGTTAACAAACTATAATAAACACGACAAGACACTACAACAATAA-AAAAAGCTCAC
* *
3165234 TTATCATAAAAAAATTAACTCCATACCACATCTAAATTTTGTAGGTCCATCAAGTTATTATATGA
195 TTATCATAAAAAAATTAACTCCATACCACATCTAAATTTTGTAGATCCATCAAGTTATTAAATGA
*
3165299 AACTCAAGTTTTTAAGTCATAAATTTTTATATAATTTTGTATTATGATTGAACTATTAATAAATA
260 AACTCAAGTTTTGAAGTCATAAATTTTTATATAATTTTGTATTATGATTGAACTATTAATAAATA
* * * **
3165364 ATCATAAGCTCACAAAAATCAAATTAACCCCAAAGTTAACAAACTATAATAAACATGACACGGCA
325 ATCATAAGCTCACAAAAATCAAACTAACCCCAAAATCAACAAACTATAATAAACATGACACAACA
3165429 CTACA
390 CTACA
3165434 AC
1 AC
3165436 AATAAGAAAA
Statistics
Matches: 362, Mismatches: 33, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
394 357 0.99
395 5 0.01
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (394 bp):
ACCACACTTAAATTTTGTAGGTCCATTAAATTATTATATAAAACTCAAGTTTTTAAGTAATGAAT
TTTTATATAATTTTGTATTATGATTGAACTATTAATAAATAATCATAAGCTCACAAAAATCAAAA
TAACCCCAAAGTTAACAAACTATAATAAACACGACAAGACACTACAACAATAAAAAAAGCTCACT
TATCATAAAAAAATTAACTCCATACCACATCTAAATTTTGTAGATCCATCAAGTTATTAAATGAA
ACTCAAGTTTTGAAGTCATAAATTTTTATATAATTTTGTATTATGATTGAACTATTAATAAATAA
TCATAAGCTCACAAAAATCAAACTAACCCCAAAATCAACAAACTATAATAAACATGACACAACAC
TACA
Found at i:3166545 original size:22 final size:23
Alignment explanation
Indices: 3166500--3166546 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
3166490 AGTATAAGAT
**
3166500 ATTATTTATTTTAAAAATTTTAA
1 ATTATTTATTTTAAAAATAATAA
*
3166523 ATTATTTTTTTTAAAAA-AATAA
1 ATTATTTATTTTAAAAATAATAA
3166545 AT
1 AT
3166547 ATGACTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTATTTATTTTAAAAATAATAA
Found at i:3168096 original size:17 final size:17
Alignment explanation
Indices: 3168058--3168102 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
3168048 TTTTAACATT
3168058 AATAAATATTAGATATAA
1 AATAAATATTA-ATATAA
3168076 AATAAATACTTAATA-AA
1 AATAAATA-TTAATATAA
*
3168093 AATATATATT
1 AATAAATATT
3168103 TAATTTAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 2 0.08
17 9 0.36
18 11 0.44
19 3 0.12
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (17 bp):
AATAAATATTAATATAA
Found at i:3168105 original size:17 final size:17
Alignment explanation
Indices: 3168058--3168106 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
3168048 TTTTAACATT
3168058 AATAAATA-TTAGATATAA
1 AATAAATACTTA-ATA-AA
3168076 AATAAATACTTAATAAA
1 AATAAATACTTAATAAA
* *
3168093 AATATATATTTAAT
1 AATAAATACTTAAT
3168107 TTAATGATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 14 0.50
18 11 0.39
19 3 0.11
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (17 bp):
AATAAATACTTAATAAA
Found at i:3169054 original size:19 final size:18
Alignment explanation
Indices: 3169004--3169057 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
3168994 TGATGTTTTA
3169004 TATAATAATAATTATAATT
1 TATAATAATAATTATAA-T
3169023 TATTTAA-AA-AATTATAAT
1 TA--TAATAATAATTATAAT
3169041 TATAATAATCAATTATA
1 TATAATAAT-AATTATA
3169058 TAAACTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
16 3 0.10
17 2 0.07
18 3 0.10
19 17 0.57
20 2 0.07
21 3 0.10
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
TATAATAATAATTATAAT
Found at i:3172178 original size:20 final size:21
Alignment explanation
Indices: 3172140--3172180 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
3172130 ATTGCTGAAA
* *
3172140 TATTAAATTATTAATTTCATT
1 TATTAAAATATTAAATTCATT
3172161 TATTAAAAT-TTAAATTCATT
1 TATTAAAATATTAAATTCATT
3172181 CAATCTCGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (21 bp):
TATTAAAATATTAAATTCATT
Found at i:3173923 original size:2 final size:2
Alignment explanation
Indices: 3173916--3173953 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3173906 AATTCATACA
*
3173916 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3173954 TCAAATAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3174737 original size:2 final size:2
Alignment explanation
Indices: 3174730--3174762 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3174720 AATGAAGTGG
3174730 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
3174763 GAAAATGGCA
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:3176213 original size:16 final size:15
Alignment explanation
Indices: 3176194--3176261 Score: 55
Period size: 16 Copynumber: 4.3 Consensus size: 15
3176184 ATCATTTCAA
3176194 ATTCGGATAATTTCGG
1 ATTCGGATAATTTC-G
* * *
3176210 ATTCTGATCATTTTG
1 ATTCGGATAATTTCG
**
3176225 ATTCGGACCATTTCG
1 ATTCGGATAATTTCG
*
3176240 AGTTCAGATAATTTCAG
1 A-TTCGGATAATTTC-G
3176257 ATTCG
1 ATTCG
3176262 AATCAATTAG
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
15 14 0.35
16 24 0.60
17 2 0.05
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (15 bp):
ATTCGGATAATTTCG
Found at i:3178824 original size:19 final size:18
Alignment explanation
Indices: 3178798--3178842 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
3178788 TTTTATTTTT
*
3178798 ATAATTATA-ATTATAATA
1 ATAATTATATA-TAAAATA
3178816 ATCAATTATATATAAAATA
1 AT-AATTATATATAAAATA
3178835 ATAATTAT
1 ATAATTAT
3178843 TTTGTAAGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 8 0.33
19 15 0.62
20 1 0.04
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAATTATATATAAAATA
Found at i:3181784 original size:22 final size:23
Alignment explanation
Indices: 3181759--3181814 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
3181749 AGTGAGATTT
3181759 ATTTATTTATTATTA-TTCAACC
1 ATTTATTTATTATTACTTCAACC
*
3181781 ATTTATTTAGTATTACTTCAACC
1 ATTTATTTATTATTACTTCAACC
3181804 ATTTATTTATT
1 ATTTATTTATT
3181815 TAGCCATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 14 0.45
23 17 0.55
ACGTcount: A:0.30, C:0.12, G:0.02, T:0.55
Consensus pattern (23 bp):
ATTTATTTATTATTACTTCAACC
Found at i:3181821 original size:16 final size:16
Alignment explanation
Indices: 3181802--3181832 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3181792 ATTACTTCAA
3181802 CCATTTATTTATTTAG
1 CCATTTATTTATTTAG
3181818 CCATTTATTTATTTA
1 CCATTTATTTATTTA
3181833 TTTTGGTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.13, G:0.03, T:0.58
Consensus pattern (16 bp):
CCATTTATTTATTTAG
Found at i:3182666 original size:28 final size:25
Alignment explanation
Indices: 3182625--3182726 Score: 105
Period size: 26 Copynumber: 3.9 Consensus size: 25
3182615 TTAGTTACTA
*
3182625 ATTTTTTTTATTTATAAAAAATAAT
1 ATTTTTTTTGTTTATAAAAAATAAT
*
3182650 GATTTTTTTTTGGTTTATAAAAAATAGT
1 -A-TTTTTTTT-GTTTATAAAAAATAAT
* * *
3182678 AATTTTTTTGTTTGTAAAAAATGAT
1 ATTTTTTTTGTTTATAAAAAATAAT
* *
3182703 AGTTCTTTTTGTTTGTAAAAAATA
1 A-TTTTTTTTGTTTATAAAAAATA
3182727 GTGACTTATT
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
25 14 0.22
26 27 0.42
27 9 0.14
28 14 0.22
ACGTcount: A:0.36, C:0.01, G:0.10, T:0.53
Consensus pattern (25 bp):
ATTTTTTTTGTTTATAAAAAATAAT
Found at i:3187231 original size:28 final size:28
Alignment explanation
Indices: 3187195--3187268 Score: 139
Period size: 28 Copynumber: 2.6 Consensus size: 28
3187185 AAAGCCACCC
*
3187195 TTTTTGTTTGTCAAAAATGGTAGTTCCT
1 TTTTTGTTTGTAAAAAATGGTAGTTCCT
3187223 TTTTTGTTTGTAAAAAATGGTAGTTCCT
1 TTTTTGTTTGTAAAAAATGGTAGTTCCT
3187251 TTTTTGTTTGTAAAAAAT
1 TTTTTGTTTGTAAAAAAT
3187269 AGTAACTTGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.26, C:0.07, G:0.16, T:0.51
Consensus pattern (28 bp):
TTTTTGTTTGTAAAAAATGGTAGTTCCT
Found at i:3189589 original size:27 final size:27
Alignment explanation
Indices: 3189559--3189610 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
3189549 ATGTATTCGT
*
3189559 ATCATGTTTATA-TATTTTTATATTATA
1 ATCATGTTTAAATTA-TTTTATATTATA
3189586 ATCATGTTTAAATTATTTTATATTA
1 ATCATGTTTAAATTATTTTATATTA
3189611 ATGCAAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (27 bp):
ATCATGTTTAAATTATTTTATATTATA
Found at i:3191895 original size:2 final size:2
Alignment explanation
Indices: 3191884--3191933 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
3191874 AAACCAATTC
* * * *
3191884 AT AT -T AT AT AT AT AT AT AT AT AC AC AT AT AT AT AA AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3191925 AT AT A- AT AT
1 AT AT AT AT AT
3191934 TAAAAGAGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3193788 original size:6 final size:6
Alignment explanation
Indices: 3193777--3193854 Score: 75
Period size: 6 Copynumber: 12.5 Consensus size: 6
3193767 TTTTTACTCG
* * *
3193777 TTTATA TTTATA TTTATA TTTATA TTCATA TCTATA TTTATA TATATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
* * *
3193825 TATATA TGTTTTGA TTAATTA TTTATA TTT
1 TTTATA T-TTAT-A TTTA-TA TTTATA TTT
3193855 TGCTGATTAC
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
6 49 0.83
7 7 0.12
8 3 0.05
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (6 bp):
TTTATA
Found at i:3194502 original size:24 final size:22
Alignment explanation
Indices: 3194451--3194507 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
3194441 TAATAAATTT
3194451 AAAAGATAAAAATAAAAAAGAG
1 AAAAGATAAAAATAAAAAAGAG
*
3194473 CAAAGATAAAAATAATAAAAG-G
1 AAAAGATAAAAATAA-AAAAGAG
3194495 AAATAAGATAAAA
1 -AA-AAGATAAAA
3194508 CACTATCCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 15 0.50
23 6 0.20
24 9 0.30
ACGTcount: A:0.74, C:0.02, G:0.12, T:0.12
Consensus pattern (22 bp):
AAAAGATAAAAATAAAAAAGAG
Found at i:3195795 original size:25 final size:27
Alignment explanation
Indices: 3195767--3195820 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 27
3195757 GGATTATTCT
3195767 TTTGAATTGAAATAAATT-TT-TTTAA
1 TTTGAATTGAAATAAATTATTATTTAA
* **
3195792 TTTGATTTGATTTAAATTATTATTTAA
1 TTTGAATTGAAATAAATTATTATTTAA
3195819 TT
1 TT
3195821 ATTATTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 15 0.62
26 2 0.08
27 7 0.29
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (27 bp):
TTTGAATTGAAATAAATTATTATTTAA
Found at i:3196462 original size:27 final size:26
Alignment explanation
Indices: 3196432--3196515 Score: 70
Period size: 27 Copynumber: 3.2 Consensus size: 26
3196422 TGATCGTTTT
3196432 TTTTTGGGCTATGTCATGCTTTAATTA
1 TTTTT-GGCTATGTCATGCTTTAATTA
*
3196459 TTTTT--CTTATGTTATG-TGATT-ATT-
1 TTTTTGGC-TATGTCATGCT--TTAATTA
3196483 TTTCTTGGACTATGTCATGCTTTAATTA
1 TTT-TTGG-CTATGTCATGCTTTAATTA
3196511 TTTTT
1 TTTTT
3196516 CTCATATTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 20
0.67 0.03 0.30
Matches are distributed among these distances:
24 5 0.11
25 13 0.29
26 4 0.09
27 18 0.40
28 5 0.11
ACGTcount: A:0.18, C:0.10, G:0.14, T:0.58
Consensus pattern (26 bp):
TTTTTGGCTATGTCATGCTTTAATTA
Found at i:3205719 original size:19 final size:19
Alignment explanation
Indices: 3205692--3205743 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
3205682 TTAAAATTTT
*
3205692 TTTATATTTATTATTTAAA
1 TTTAAATTTATTATTTAAA
*
3205711 TTTAAATTTAATT-TATAAA
1 TTTAAATTT-ATTATTTAAA
*
3205730 CTTAAATTT-TTATT
1 TTTAAATTTATTATT
3205744 AAAAATATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
17 2 0.07
18 1 0.04
19 21 0.78
20 3 0.11
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTAAATTTATTATTTAAA
Found at i:3206757 original size:2 final size:2
Alignment explanation
Indices: 3206750--3206789 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
3206740 TCAAAATCAA
* *
3206750 TC TC TC TC TC TC TC TC TC TC TG TC TC TC TC TC TC GC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3206790 GTCTTGGTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.47, G:0.05, T:0.47
Consensus pattern (2 bp):
TC
Found at i:3209945 original size:2 final size:2
Alignment explanation
Indices: 3209940--3209968 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3209930 TATATATATA
3209940 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
3209969 ATTACTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3212803 original size:6 final size:6
Alignment explanation
Indices: 3212796--3212830 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
3212786 CTACAACAGG
*
3212796 AGCAGG AGCAGT AGCAGT AGCAGT AGCAGT AGCAG
1 AGCAGT AGCAGT AGCAGT AGCAGT AGCAGT AGCAG
3212831 AAACTCCTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.34, C:0.17, G:0.37, T:0.11
Consensus pattern (6 bp):
AGCAGT
Found at i:3215032 original size:12 final size:12
Alignment explanation
Indices: 3215015--3215041 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3215005 TCCAAGCTTT
3215015 TAATGTGAGATA
1 TAATGTGAGATA
3215027 TAATGTGAGATA
1 TAATGTGAGATA
3215039 TAA
1 TAA
3215042 GTAGATTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (12 bp):
TAATGTGAGATA
Found at i:3215681 original size:2 final size:2
Alignment explanation
Indices: 3215674--3215705 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3215664 ATGATCAGAT
3215674 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
3215706 AACAAAGTTT
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:3220168 original size:2 final size:2
Alignment explanation
Indices: 3220156--3220195 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
3220146 AAAACAAACC
*
3220156 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3220196 AGTATCAACT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3220381 original size:14 final size:14
Alignment explanation
Indices: 3220357--3220397 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3220347 TATATCTTTC
*
3220357 ATTAATATTAAATA
1 ATTATTATTAAATA
* *
3220371 ATTTTTATTAAAAA
1 ATTATTATTAAATA
3220385 ATTATTATTAAAT
1 ATTATTATTAAAT
3220398 TAAAATATTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTATTATTAAATA
Found at i:3222519 original size:23 final size:23
Alignment explanation
Indices: 3222493--3222552 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
3222483 TTGTTTATCA
3222493 ATTAAAGAAATTAATTTATTCTT
1 ATTAAAGAAATTAATTTATTCTT
3222516 ATTAAAGAAATTAATTTATTCTT
1 ATTAAAGAAATTAATTTATTCTT
*
3222539 ATTAAAAAAATTAA
1 ATTAAAGAAATTAA
3222553 AAACAAAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (23 bp):
ATTAAAGAAATTAATTTATTCTT
Found at i:3227640 original size:101 final size:102
Alignment explanation
Indices: 3227467--3227652 Score: 320
Period size: 101 Copynumber: 1.8 Consensus size: 102
3227457 AACGGACCCC
* *
3227467 TTTCATATATCCACTGCACGTTAAGAAAAGTCTTCGTGCATTCTTTTGGACTTGGTCCAACTAAT
1 TTTCATATATCCACTACACGTTAAGAAAAGTCTTCGTGCATTCTTTTGGACTTGGTCCAACAAAT
3227532 GGAGCCTTATTTCATTTAAGTCTCTCAGAGGACTCCT
66 GGAGCCTTATTTCATTTAAGTCTCTCAGAGGACTCCT
* * *
3227569 TTTC-TATATCCACTACGCGTTAAGAAAAGTCTTTGTGCATTCTTTTGGACTTGGTTCAACAAAT
1 TTTCATATATCCACTACACGTTAAGAAAAGTCTTCGTGCATTCTTTTGGACTTGGTCCAACAAAT
3227633 GGAGCCTTATTTCATTTAAG
66 GGAGCCTTATTTCATTTAAG
3227653 GCTTTAAGTT
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
101 75 0.95
102 4 0.05
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (102 bp):
TTTCATATATCCACTACACGTTAAGAAAAGTCTTCGTGCATTCTTTTGGACTTGGTCCAACAAAT
GGAGCCTTATTTCATTTAAGTCTCTCAGAGGACTCCT
Found at i:3228345 original size:27 final size:28
Alignment explanation
Indices: 3228310--3228377 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 28
3228300 TGTGTTGGAT
3228310 ATATATTTAAATATAAATATAAAAAAT-A
1 ATAT-TTTAAATATAAATATAAAAAATAA
*
3228338 ATATTTTAAATAT--ATATAAAAATTAA
1 ATATTTTAAATATAAATATAAAAAATAA
*
3228364 AAATTTTAAA-ATAA
1 ATATTTTAAATATAA
3228378 TAGTATCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
25 12 0.34
26 10 0.29
27 9 0.26
28 4 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
ATATTTTAAATATAAATATAAAAAATAA
Found at i:3230492 original size:2 final size:2
Alignment explanation
Indices: 3230487--3230513 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3230477 TTTGATTAAT
3230487 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3230514 TAGAAATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3231843 original size:2 final size:2
Alignment explanation
Indices: 3231836--3231862 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3231826 GTGGAAGGTG
3231836 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3231863 TATGTGCAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3235041 original size:21 final size:21
Alignment explanation
Indices: 3235017--3235062 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
3235007 TAAAACATAT
*
3235017 TATTCTAAATATTTATTTAAA
1 TATTCTAAATATTTAATTAAA
* * *
3235038 TATTTTAATTATTTAATTAAT
1 TATTCTAAATATTTAATTAAA
3235059 TATT
1 TATT
3235063 GTATAATTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTCTAAATATTTAATTAAA
Found at i:3235052 original size:8 final size:8
Alignment explanation
Indices: 3235029--3235087 Score: 50
Period size: 8 Copynumber: 7.5 Consensus size: 8
3235019 TTCTAAATAT
3235029 TTATTTAA
1 TTATTTAA
*
3235037 ATATTTTAA
1 TTA-TTTAA
3235046 TTATTTAA
1 TTATTTAA
*
3235054 TTAATT-A
1 TTATTTAA
* *
3235061 TTGTATAA
1 TTATTTAA
*
3235069 TTATATAA
1 TTATTTAA
3235077 TT-TTTAA
1 TTATTTAA
3235084 TTAT
1 TTAT
3235088 ATTATATTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
7 10 0.25
8 23 0.57
9 7 0.17
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (8 bp):
TTATTTAA
Found at i:3235084 original size:15 final size:16
Alignment explanation
Indices: 3235029--3235089 Score: 54
Period size: 15 Copynumber: 3.9 Consensus size: 16
3235019 TTCTAAATAT
* *
3235029 TTATTTAAATATTTTAA
1 TTATTTAATTA-TATAA
*
3235046 TTATTTAATTA-ATTA
1 TTATTTAATTATATAA
* *
3235061 TTGTATAATTATATAA
1 TTATTTAATTATATAA
3235077 TT-TTTAATTATAT
1 TTATTTAATTATAT
3235090 TATATTAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
15 21 0.58
16 5 0.14
17 10 0.28
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (16 bp):
TTATTTAATTATATAA
Found at i:3236499 original size:14 final size:14
Alignment explanation
Indices: 3236477--3236506 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3236467 ATCCTTAATC
*
3236477 TTCTTTCTCTCTCT
1 TTCTCTCTCTCTCT
3236491 TTCTCTCTCTCTCT
1 TTCTCTCTCTCTCT
3236505 TT
1 TT
3236507 TATAAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (14 bp):
TTCTCTCTCTCTCT
Found at i:3238751 original size:28 final size:28
Alignment explanation
Indices: 3238671--3238753 Score: 130
Period size: 28 Copynumber: 3.0 Consensus size: 28
3238661 CAAATGTCAC
*
3238671 CCTTTGTATTTGTCAAATATGGTAGTTT
1 CCTTTGTATTTGTCAAATATGGTGGTTT
*
3238699 TCTTTGTATTTGTCAAATATGGTGGTTT
1 CCTTTGTATTTGTCAAATATGGTGGTTT
* *
3238727 CCTTTATATTTGTCAAATATAGTGGTT
1 CCTTTGTATTTGTCAAATATGGTGGTT
3238754 ATTTTTGTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.22, C:0.10, G:0.18, T:0.51
Consensus pattern (28 bp):
CCTTTGTATTTGTCAAATATGGTGGTTT
Found at i:3238797 original size:24 final size:23
Alignment explanation
Indices: 3238758--3238802 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
3238748 GTGGTTATTT
3238758 TTGTTTGAAAAATTGGTGGCTTG
1 TTGTTTGAAAAATTGGTGGCTTG
*
3238781 TTGTTTGTCAAAATTGGTGGCT
1 TTGTTTG-AAAAATTGGTGGCT
3238803 AATTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.20, C:0.07, G:0.29, T:0.44
Consensus pattern (23 bp):
TTGTTTGAAAAATTGGTGGCTTG
Found at i:3243392 original size:24 final size:24
Alignment explanation
Indices: 3243356--3243401 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
3243346 GTGGTTATTT
3243356 TTGTTTGTAAAAATTGGTGGCTTG
1 TTGTTTGTAAAAATTGGTGGCTTG
*
3243380 TTGTTTGTCAAAATTGGTGGCT
1 TTGTTTGTAAAAATTGGTGGCT
3243402 AATTTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.20, C:0.07, G:0.28, T:0.46
Consensus pattern (24 bp):
TTGTTTGTAAAAATTGGTGGCTTG
Found at i:3245162 original size:14 final size:13
Alignment explanation
Indices: 3245136--3245166 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
3245126 AAGAATTATC
3245136 TTAAAATTAAAAT
1 TTAAAATTAAAAT
3245149 TTAAAATATAAAAT
1 TTAAAAT-TAAAAT
3245163 TTAA
1 TTAA
3245167 TTCAATTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TTAAAATTAAAAT
Found at i:3246929 original size:89 final size:87
Alignment explanation
Indices: 3246750--3246935 Score: 282
Period size: 89 Copynumber: 2.1 Consensus size: 87
3246740 ATAAATTGAT
* *
3246750 ATAAAAATAAAAATAATAAATTAATACGATCCATAGCAACTTCATTTTTTTAATATTTAATATAT
1 ATAAAATTAAAAATAATAAATTAATACGATCCATAGCAACTTCATTTTTTTAATATTTAATATAC
3246815 ATATTTACTTTAATTCGTTAAA
66 ATATTTACTTTAATTCGTTAAA
* * * *
3246837 ATAAAATTAAAAATAATGAATTAATACGATCCATAAGTAATTTTATTTTTTTTAATATTTAATAT
1 ATAAAATTAAAAATAATAAATTAATACGATCCAT-AGCAACTTCA-TTTTTTTAATATTTAATAT
* *
3246902 ACATATTTACTTTAATTGGTTAGA
64 ACATATTTACTTTAATTCGTTAAA
3246926 ATAAAATTAA
1 ATAAAATTAA
3246936 GGATTGAGAA
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
87 32 0.36
88 7 0.08
89 50 0.56
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (87 bp):
ATAAAATTAAAAATAATAAATTAATACGATCCATAGCAACTTCATTTTTTTAATATTTAATATAC
ATATTTACTTTAATTCGTTAAA
Found at i:3250154 original size:22 final size:21
Alignment explanation
Indices: 3250104--3250154 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
3250094 GTTTTTGATT
3250104 AAAA-AAT-TAAAAAATTAAA
1 AAAATAATATAAAAAATTAAA
*
3250123 AATATAATATAAAAAATATAAA
1 AAAATAATATAAAAAAT-TAAA
*
3250145 AAAATTATAT
1 AAAATAATAT
3250155 CACAATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 3 0.12
20 3 0.12
21 8 0.31
22 12 0.46
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAATAATATAAAAAATTAAA
Found at i:3253876 original size:28 final size:29
Alignment explanation
Indices: 3253823--3253877 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
3253813 AATTCATAGA
* *
3253823 ATATATATTTTATAAAATAGTTAATTATG
1 ATATATATTTTACAAAATAGTGAATTATG
3253852 ATAT-TATTTTACAAAATTA-TGAATTA
1 ATATATATTTTACAAAA-TAGTGAATTA
3253878 CTCGTTCAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.47
Consensus pattern (29 bp):
ATATATATTTTACAAAATAGTGAATTATG
Found at i:3254308 original size:34 final size:36
Alignment explanation
Indices: 3254242--3254314 Score: 96
Period size: 34 Copynumber: 2.1 Consensus size: 36
3254232 TTATTATATA
** *
3254242 ATTTATTATTTTTATTTAAATGTTTTTAAATTATTT
1 ATTTATTATTTTTATTTAAATAATTTTAAATTATGT
*
3254278 ATTTTTTA-TTTTATTTAAA-AATTTTAAATTATGT
1 ATTTATTATTTTTATTTAAATAATTTTAAATTATGT
3254312 ATT
1 ATT
3254315 AATTTCACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 15 0.45
35 11 0.33
36 7 0.21
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (36 bp):
ATTTATTATTTTTATTTAAATAATTTTAAATTATGT
Found at i:3254405 original size:15 final size:15
Alignment explanation
Indices: 3254375--3254420 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
3254365 AAAATATTTA
3254375 AATAAATATATAAAAT
1 AATAAATAT-TAAAAT
*
3254391 AATAATTATTAAAAT
1 AATAAATATTAAAAT
**
3254406 TTTAAATATTAAAAT
1 AATAAATATTAAAAT
3254421 GTTATTGTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
15 18 0.69
16 8 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AATAAATATTAAAAT
Found at i:3254894 original size:37 final size:36
Alignment explanation
Indices: 3254842--3254939 Score: 106
Period size: 37 Copynumber: 2.6 Consensus size: 36
3254832 ATAAAATTTA
* **
3254842 TAAATAATTAAAATTTTATTTTATTATTTTATTATAT
1 TAAATAATTATAATTTTA-TTTATTACATTATTATAT
* *
3254879 TAAATAATGATAATTTTCATTTATTACATTATTTTAT
1 TAAATAATTATAATTTT-ATTTATTACATTATTATAT
* *
3254916 TATATAATTATAAATTTTAATTAT
1 TAAATAATTAT-AATTTTATTTAT
3254940 AATAAATTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
37 44 0.86
38 7 0.14
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (36 bp):
TAAATAATTATAATTTTATTTATTACATTATTATAT
Found at i:3254938 original size:21 final size:22
Alignment explanation
Indices: 3254909--3254949 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
3254899 TTATTACATT
3254909 ATTTTATTAT-AT-AATTATAA
1 ATTTTATTATAATAAATTATAA
3254929 ATTTTAATTATAATAAATTAT
1 ATTTT-ATTATAATAAATTAT
3254950 CAAAGTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 5 0.28
22 2 0.11
23 6 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTTTATTATAATAAATTATAA
Found at i:3255803 original size:23 final size:23
Alignment explanation
Indices: 3255735--3255805 Score: 76
Period size: 23 Copynumber: 3.1 Consensus size: 23
3255725 TTAATAAATA
* *
3255735 AAAATAATATTTAAATTTAATTAT
1 AAAATAATATTTATA-TTATTTAT
*
3255759 AAAAT-ATATTTATATT-TATAT
1 AAAATAATATTTATATTATTTAT
3255780 AAAATTAATATTT-TATTATTTAT
1 AAAA-TAATATTTATATTATTTAT
3255803 AAA
1 AAA
3255806 TAAAAAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 7 0.17
22 7 0.17
23 21 0.52
24 5 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AAAATAATATTTATATTATTTAT
Found at i:3256257 original size:19 final size:22
Alignment explanation
Indices: 3256235--3256280 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
3256225 ATAAAATATA
3256235 AAATTAT-TTT-T-AAAGATTT
1 AAATTATGTTTGTCAAAGATTT
*
3256254 AAATAATGTTTGTCAAAGATTT
1 AAATTATGTTTGTCAAAGATTT
*
3256276 GAATT
1 AAATT
3256281 TAAAATGCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
19 6 0.29
20 3 0.14
21 1 0.05
22 11 0.52
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (22 bp):
AAATTATGTTTGTCAAAGATTT
Found at i:3257991 original size:2 final size:2
Alignment explanation
Indices: 3257984--3258097 Score: 228
Period size: 2 Copynumber: 57.0 Consensus size: 2
3257974 TTCACTGCCA
3257984 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 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
3258026 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 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
3258068 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3258098 GGAAAATTTT
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 112 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3259828 original size:22 final size:22
Alignment explanation
Indices: 3259800--3259841 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
3259790 TTAAGATATT
3259800 AATTTAAGTTTAAATTAAAAAA
1 AATTTAAGTTTAAATTAAAAAA
*
3259822 AATTTAAGTTTAATTTAAAA
1 AATTTAAGTTTAAATTAAAA
3259842 TTTTTATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (22 bp):
AATTTAAGTTTAAATTAAAAAA
Found at i:3259847 original size:20 final size:20
Alignment explanation
Indices: 3259824--3259865 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
3259814 TTAAAAAAAA
3259824 TTTAAGTTTAATTTAAAATT
1 TTTAAGTTTAATTTAAAATT
* *
3259844 TTTATGTTTAATTTTAAATT
1 TTTAAGTTTAATTTAAAATT
3259864 TT
1 TT
3259866 AATATTTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (20 bp):
TTTAAGTTTAATTTAAAATT
Found at i:3261174 original size:18 final size:18
Alignment explanation
Indices: 3261153--3261195 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
3261143 AGTCACGAGT
*
3261153 ATATTTATAAAAATATTA
1 ATATTTATAAAAAAATTA
*
3261171 ATATTTTTAAAAAAATTA
1 ATATTTATAAAAAAATTA
*
3261189 AAATTTA
1 ATATTTA
3261196 ATATTTAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATTTATAAAAAAATTA
Found at i:3261710 original size:16 final size:16
Alignment explanation
Indices: 3261684--3261720 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
3261674 AATATTATAT
*
3261684 ATTTAATTTTTTAAAA
1 ATTTAAATTTTTAAAA
*
3261700 TTTTAAATTTTTAAAA
1 ATTTAAATTTTTAAAA
3261716 ATTTA
1 ATTTA
3261721 TCATTAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTAAATTTTTAAAA
Found at i:3262066 original size:15 final size:16
Alignment explanation
Indices: 3262048--3262080 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3262038 TACGATTATA
3262048 ATTATAA-TAAATATT
1 ATTATAATTAAATATT
*
3262063 ATTATAATTAATTATT
1 ATTATAATTAAATATT
3262079 AT
1 AT
3262081 AAATATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTATAATTAAATATT
Found at i:3262078 original size:13 final size:13
Alignment explanation
Indices: 3262045--3262085 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
3262035 TATTACGATT
*
3262045 ATAATTATAATAA
1 ATAATTATTATAA
3262058 AT-ATTATTATAA
1 ATAATTATTATAA
*
3262070 TTAATTATTATAA
1 ATAATTATTATAA
3262083 ATA
1 ATA
3262086 TAAATCATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATAATTATTATAA
Found at i:3262881 original size:20 final size:20
Alignment explanation
Indices: 3262856--3262999 Score: 69
Period size: 22 Copynumber: 6.8 Consensus size: 20
3262846 TACGATATTA
3262856 TTATATTTATATTTTAAATT
1 TTATATTTATATTTTAAATT
* *
3262876 TTATATATT-TATATAAAATT
1 TTATAT-TTATATTTTAAATT
* *
3262896 TAATATATATAAATTATTAATATAT
1 T--TATATTTATATT-TTAA-AT-T
* *
3262921 TTATA-TTATTTTTTTATATT
1 TTATATTTA-TATTTTAAATT
*
3262941 TTATTATATATATTTTATAATT
1 TTA-TATTTATATTTTA-AATT
* *
3262963 TTTTATTATATTATATTT-AATA
1 TTATATT-TA-TAT-TTTAAATT
*
3262985 TTATATTTAAATTTT
1 TTATATTTATATTTT
3263000 TTTCGTATAA
Statistics
Matches: 92, Mismatches: 18, Indels: 29
0.66 0.13 0.21
Matches are distributed among these distances:
19 3 0.03
20 22 0.24
21 18 0.20
22 30 0.33
23 12 0.13
24 5 0.05
25 2 0.02
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATATTTATATTTTAAATT
Found at i:3262906 original size:18 final size:19
Alignment explanation
Indices: 3262856--3262906 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
3262846 TACGATATTA
* * *
3262856 TTATATTTATATTTTAAATT
1 TTATATATATA-TATAAAAT
*
3262876 TTATATATTTATATAAAAT
1 TTATATATATATATAAAAT
3262895 TTA-ATATATATA
1 TTATATATATATA
3262907 AATTATTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 8 0.31
19 9 0.35
20 9 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATATATATATATAAAAT
Found at i:3262917 original size:17 final size:17
Alignment explanation
Indices: 3262885--3262930 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
3262875 TTTATATATT
*
3262885 TATATAAAAT-TTAATA
1 TATATAAATTATTAATA
3262901 TATATAAATTATTAATA
1 TATATAAATTATTAATA
* *
3262918 TATTTATATTATT
1 TATATAAATTATT
3262931 TTTTTATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 9 0.35
17 17 0.65
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATAAATTATTAATA
Found at i:3262945 original size:32 final size:33
Alignment explanation
Indices: 3262909--3263001 Score: 102
Period size: 34 Copynumber: 2.8 Consensus size: 33
3262899 TATATATAAA
*
3262909 TTATTAATATA-TTTAT-ATTATTTTTTTATATT
1 TTATTAATATATTTTATAATT-TTTTATTATATT
3262941 TTATTATATATATTTTATAATTTTTTATTATATT
1 TTATTA-ATATATTTTATAATTTTTTATTATATT
*
3262975 ATATTTAATATTATATTTA-AATTTTTT
1 TTA-TTAATA-TAT-TTTATAATTTTTT
3263002 TCGTATAATA
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
32 6 0.11
33 5 0.09
34 21 0.40
35 17 0.32
36 4 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (33 bp):
TTATTAATATATTTTATAATTTTTTATTATATT
Found at i:3262958 original size:29 final size:29
Alignment explanation
Indices: 3262909--3262989 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
3262899 TATATATAAA
* *
3262909 TTATTA-A-TATATTTATATTAT-TTTTT
1 TTATTATATTATATATATATTATAATTTT
* *
3262935 TATATTTTATTATATATATTTTATAATTTT
1 T-TATTATATTATATATATATTATAATTTT
*
3262965 TTATTATATTATATTTAATATTATA
1 TTATTATATTATATAT-ATATTATA
3262990 TTTAAATTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
26 1 0.02
27 4 0.09
28 1 0.02
29 25 0.58
30 12 0.28
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (29 bp):
TTATTATATTATATATATATTATAATTTT
Found at i:3262981 original size:24 final size:24
Alignment explanation
Indices: 3262921--3262981 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
3262911 ATTAATATAT
* *
3262921 TTATATTAT-TTTTTTATATTTTA
1 TTATATTATATTTATAATATTTTA
*
3262944 TTATA-TATATTTTATAATTTTTTA
1 TTATATTATA-TTTATAATATTTTA
3262968 TTATATTATATTTA
1 TTATATTATATTTA
3262982 ATATTATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
22 3 0.09
23 5 0.16
24 20 0.62
25 4 0.12
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (24 bp):
TTATATTATATTTATAATATTTTA
Found at i:3263000 original size:34 final size:33
Alignment explanation
Indices: 3262877--3263002 Score: 87
Period size: 34 Copynumber: 3.7 Consensus size: 33
3262867 TTTTAAATTT
* ** *
3262877 TATATATTTATATAAAATTTAATATATATAAATTA
1 TATATATTT-TATAAATTTTTTTATAT-TATATTA
* *
3262912 T-TAATATATTTATATTATTTTTTTATATTTTATTA
1 TAT-ATAT-TTTATA-AATTTTTTTATATTATATTA
*
3262947 TATATATTTTATAATTTTTTATTATATTATATT-
1 TATATATTTTATAAATTTTT-TTATATTATATTA
*
3262980 TA-ATATTATATTTAAATTTTTTT
1 TATATATT-T-TATAAATTTTTTT
3263003 CGTATAATAT
Statistics
Matches: 73, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
32 5 0.07
33 10 0.14
34 27 0.37
35 19 0.26
36 12 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (33 bp):
TATATATTTTATAAATTTTTTTATATTATATTA
Found at i:3263456 original size:21 final size:20
Alignment explanation
Indices: 3263432--3263471 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3263422 TATTTAATAA
3263432 ATTTAATACTTATAATTTTTT
1 ATTTAATA-TTATAATTTTTT
*
3263453 ATTTTATATTAT-ATTTTTT
1 ATTTAATATTATAATTTTTT
3263472 TTAATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 4 0.22
21 7 0.39
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (20 bp):
ATTTAATATTATAATTTTTT
Found at i:3274225 original size:2 final size:2
Alignment explanation
Indices: 3274218--3274250 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3274208 AATCTCATAC
3274218 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3274251 TTCAATCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3274303 original size:2 final size:2
Alignment explanation
Indices: 3274296--3274329 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3274286 GGAAAAAGAA
*
3274296 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3274330 GTTACCATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3276694 original size:18 final size:18
Alignment explanation
Indices: 3276655--3276690 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3276645 AAAATACAAT
3276655 ATAAAATAAATAATTAAA
1 ATAAAATAAATAATTAAA
*
3276673 ATAAAATATAT-ATTAAA
1 ATAAAATAAATAATTAAA
3276690 A
1 A
3276691 ATAACAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAAAATAAATAATTAAA
Found at i:3277970 original size:21 final size:21
Alignment explanation
Indices: 3277937--3277977 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
3277927 TTTTAAGCAT
3277937 TATAATGCCTCTTTTGCAAGTAC
1 TATAATG-CTCTTTT-CAAGTAC
3277960 TATAATG-TCTTTTCAAGT
1 TATAATGCTCTTTTCAAGT
3277978 TCTTAACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
23 7 0.39
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.44
Consensus pattern (21 bp):
TATAATGCTCTTTTCAAGTAC
Found at i:3278069 original size:16 final size:17
Alignment explanation
Indices: 3278041--3278079 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
3278031 TTTTTCAAGC
3278041 ATTTAACCTCTTTCAAA
1 ATTTAACCTCTTTCAAA
*
3278058 GTTTAA-CTCTTTCAAA
1 ATTTAACCTCTTTCAAA
3278074 ATTTAA
1 ATTTAA
3278080 ATTATGACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.36, C:0.18, G:0.03, T:0.44
Consensus pattern (17 bp):
ATTTAACCTCTTTCAAA
Found at i:3278273 original size:17 final size:18
Alignment explanation
Indices: 3278229--3278273 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
3278219 CATCATTTTG
*
3278229 CCTTTTCGAGCATCTAAT
1 CCTTTTCAAGCATCTAAT
3278247 CCTTTT-AAGCATCTAA-
1 CCTTTTCAAGCATCTAAT
*
3278263 CTTTTTCAAGC
1 CCTTTTCAAGC
3278274 TCTGACACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 5 0.21
17 13 0.54
18 6 0.25
ACGTcount: A:0.24, C:0.27, G:0.09, T:0.40
Consensus pattern (18 bp):
CCTTTTCAAGCATCTAAT
Found at i:3278298 original size:38 final size:36
Alignment explanation
Indices: 3278256--3278345 Score: 92
Period size: 37 Copynumber: 2.4 Consensus size: 36
3278246 TCCTTTTAAG
*
3278256 CATCTAACTTTTTCAAGC-TCTGACACATTTTCACATAT
1 CATCTAAC-TTTTCAAGCTTC-AACACA-TTTCACATAT
**
3278294 CATCTAGACCCTTCAAGCTTCAACACATTTCACATAT
1 CATCTA-ACTTTTCAAGCTTCAACACATTTCACATAT
*
3278331 CATCTAGCCTTTTCA
1 CATCTA-ACTTTTCA
3278346 GACATCAAGC
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
37 22 0.50
38 18 0.41
39 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.06, T:0.36
Consensus pattern (36 bp):
CATCTAACTTTTCAAGCTTCAACACATTTCACATAT
Found at i:3279346 original size:2 final size:2
Alignment explanation
Indices: 3279335--3279366 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3279325 ACTTTACACC
3279335 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3279367 GCAGTACAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3279475 original size:2 final size:2
Alignment explanation
Indices: 3279470--3279497 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3279460 TTGGTTGTCC
3279470 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
3279498 GGGTTTAGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3281751 original size:28 final size:28
Alignment explanation
Indices: 3281720--3281773 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
3281710 ATAATTAAAA
3281720 CATGACACAATATGAAAAATAATATGGG
1 CATGACACAATATGAAAAATAATATGGG
** *
3281748 CATGACATTATATGAAAAGTAATATG
1 CATGACACAATATGAAAAATAATATG
3281774 AATATGATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.48, C:0.09, G:0.17, T:0.26
Consensus pattern (28 bp):
CATGACACAATATGAAAAATAATATGGG
Found at i:3282243 original size:23 final size:23
Alignment explanation
Indices: 3282200--3282260 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 23
3282190 CACAAAAAAT
3282200 AACATAATATAGAAAAAATAAT-TAA
1 AACATAATAT-G-AAAAATAATAT-A
*
3282225 AACATAATATGAAAAATAATATG
1 AACATAATATGAAAAATAATATA
3282248 AACATAATATGAA
1 AACATAATATGAA
3282261 TACACAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
23 22 0.65
24 2 0.06
25 10 0.29
ACGTcount: A:0.64, C:0.05, G:0.07, T:0.25
Consensus pattern (23 bp):
AACATAATATGAAAAATAATATA
Found at i:3282256 original size:11 final size:11
Alignment explanation
Indices: 3282225--3282260 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
3282215 AAATAATTAA
3282225 AACATAATATG
1 AACATAATATG
*
3282236 AAAAATAATATG
1 -AACATAATATG
3282248 AACATAATATG
1 AACATAATATG
3282259 AA
1 AA
3282261 TACACAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.61, C:0.06, G:0.08, T:0.25
Consensus pattern (11 bp):
AACATAATATG
Found at i:3283564 original size:12 final size:13
Alignment explanation
Indices: 3283549--3283598 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
3283539 ACTGTGCAGC
3283549 CAATTTTG-AATT
1 CAATTTTGAAATT
3283561 CAA-TTTGAAATAGT
1 CAATTTTGAAAT--T
*
3283575 TAATTTTGAAATT
1 CAATTTTGAAATT
3283588 CAA-TTTGAAAT
1 CAATTTTGAAAT
3283599 AGTAAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
11 4 0.12
12 14 0.44
13 3 0.09
14 3 0.09
15 8 0.25
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (13 bp):
CAATTTTGAAATT
Found at i:3283592 original size:27 final size:26
Alignment explanation
Indices: 3283550--3283601 Score: 95
Period size: 27 Copynumber: 2.0 Consensus size: 26
3283540 CTGTGCAGCC
3283550 AATTTTGAATTCAATTTGAAATAGTT
1 AATTTTGAATTCAATTTGAAATAGTT
3283576 AATTTTGAAATTCAATTTGAAATAGT
1 AATTTTG-AATTCAATTTGAAATAGT
3283602 AAAAGTTGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (26 bp):
AATTTTGAATTCAATTTGAAATAGTT
Found at i:3288342 original size:12 final size:13
Alignment explanation
Indices: 3288327--3288376 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
3288317 ACTGTGCAGC
3288327 CAATTTTG-AATT
1 CAATTTTGAAATT
3288339 CAA-TTTGAAATAGT
1 CAATTTTGAAAT--T
*
3288353 TAATTTTGAAATT
1 CAATTTTGAAATT
3288366 CAA-TTTGAAAT
1 CAATTTTGAAAT
3288377 AGTAAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
11 4 0.12
12 14 0.44
13 3 0.09
14 3 0.09
15 8 0.25
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (13 bp):
CAATTTTGAAATT
Found at i:3288370 original size:27 final size:26
Alignment explanation
Indices: 3288328--3288379 Score: 95
Period size: 27 Copynumber: 2.0 Consensus size: 26
3288318 CTGTGCAGCC
3288328 AATTTTGAATTCAATTTGAAATAGTT
1 AATTTTGAATTCAATTTGAAATAGTT
3288354 AATTTTGAAATTCAATTTGAAATAGT
1 AATTTTG-AATTCAATTTGAAATAGT
3288380 AAAAGTTGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (26 bp):
AATTTTGAATTCAATTTGAAATAGTT
Found at i:3289471 original size:37 final size:39
Alignment explanation
Indices: 3289419--3289492 Score: 116
Period size: 37 Copynumber: 1.9 Consensus size: 39
3289409 TCTATGATTT
*
3289419 AAATTTAAAATTTAAAAATTAATCT-TTAAATACATATA
1 AAATTTAAAATTTAAAAATTAATCTAATAAATACATATA
*
3289457 AAATTT-AAATTTAAAAATTTATCTAATAAATACATA
1 AAATTTAAAATTTAAAAATTAATCTAATAAATACATA
3289493 CATGAACTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 17 0.52
38 16 0.48
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (39 bp):
AAATTTAAAATTTAAAAATTAATCTAATAAATACATATA
Found at i:3289833 original size:13 final size:12
Alignment explanation
Indices: 3289815--3289854 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
3289805 TCACATCATA
3289815 AAAAATTAAGATT
1 AAAAATTAA-ATT
*
3289828 AAAAATTCAAATA
1 AAAAATT-AAATT
3289841 AAAAATTAAATT
1 AAAAATTAAATT
3289853 AA
1 AA
3289855 TATGATCTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 6 0.25
13 16 0.67
14 2 0.08
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28
Consensus pattern (12 bp):
AAAAATTAAATT
Found at i:3290131 original size:20 final size:21
Alignment explanation
Indices: 3290089--3290133 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
3290079 ATAAAAAAGT
* **
3290089 TTTTTTCTTGATTTTATCTAA
1 TTTTTTATTGATTGAATCTAA
3290110 TTTTTTATTGATTGAATC-AA
1 TTTTTTATTGATTGAATCTAA
3290130 TTTT
1 TTTT
3290134 AGACTAGTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.64
Consensus pattern (21 bp):
TTTTTTATTGATTGAATCTAA
Found at i:3290545 original size:14 final size:14
Alignment explanation
Indices: 3290528--3290571 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
3290518 TTTTAAAATA
*
3290528 ATTTTAATTAATTT
1 ATTTTAATAAATTT
*
3290542 ATTTTAAATAAATAT
1 ATTTT-AATAAATTT
*
3290557 AATTTAATAAATTT
1 ATTTTAATAAATTT
3290571 A
1 A
3290572 CCTCAAAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTTTAATAAATTT
Found at i:3290564 original size:25 final size:23
Alignment explanation
Indices: 3290514--3290560 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
3290504 TTTATCAATA
* *
3290514 AATTTTTTAAAATAATTTTAATT
1 AATTTTTTAAAATAAATATAATT
*
3290537 AATTTATTTTAAATAAATATAATT
1 AATTT-TTTAAAATAAATATAATT
3290561 TAATAAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
AATTTTTTAAAATAAATATAATT
Found at i:3291014 original size:12 final size:12
Alignment explanation
Indices: 3290999--3291025 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3290989 TTAATTGTAA
3290999 TTAAAATTAATT
1 TTAAAATTAATT
3291011 TTAAAATTAATT
1 TTAAAATTAATT
3291023 TTA
1 TTA
3291026 TTTTATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAAAATTAATT
Found at i:3292070 original size:17 final size:19
Alignment explanation
Indices: 3292048--3292082 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
3292038 TGATTTCAAA
3292048 CATATTT-TTA-ATTATAT
1 CATATTTATTATATTATAT
3292065 CATATTTATTATATTATA
1 CATATTTATTATATTATA
3292083 AATATAATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (19 bp):
CATATTTATTATATTATAT
Found at i:3292111 original size:12 final size:12
Alignment explanation
Indices: 3292094--3292128 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
3292084 ATATAATAGA
3292094 TATTATTATAAT
1 TATTATTATAAT
*
3292106 TATTATTATCAT
1 TATTATTATAAT
*
3292118 TATAATTATAA
1 TATTATTATAA
3292129 ATTTTTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (12 bp):
TATTATTATAAT
Found at i:3295003 original size:3 final size:3
Alignment explanation
Indices: 3294988--3295025 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
3294978 TAAGTTAGAA
*
3294988 ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3295026 ATATGGGGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3295731 original size:2 final size:2
Alignment explanation
Indices: 3295724--3295751 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3295714 TGAACTTTCA
3295724 GT 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 GT
3295752 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:3311863 original size:112 final size:110
Alignment explanation
Indices: 3311662--3311875 Score: 313
Period size: 112 Copynumber: 1.9 Consensus size: 110
3311652 AGGTTGATGT
*
3311662 TCATAGTAACACATTTAGACATGGTAAAAAATACAAATAACTAGCTGAAATAGTAAACATAATGT
1 TCATAGTAACACATTTAGACATGGCAAAAAATACAAATAACTAGCTGAAATAGTAAACATAATGT
*
3311727 AATACAAATTGTTTGAAGAGATTGGTCATAATTGATATAAGAATG
66 AATACAAATTGTTTGAAGAAATTGGTCATAATTGATATAAGAATG
* * * * *
3311772 TCATAGTAACGCATTTAGAGATGGCACAAAAATACAAATATCTAGCTATAAATAGTAATCATAAT
1 TCATAGTAACACATTTAGACATGGCA-AAAAATACAAATAACTAGCT-GAAATAGTAAACATAAT
* *
3311837 GTAATATAAATTTTTTGACA-AAATTGGTCATAATTGATA
64 GTAATACAAATTGTTTGA-AGAAATTGGTCATAATTGATA
3311876 GAAATATTAA
Statistics
Matches: 92, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
110 23 0.25
111 19 0.21
112 49 0.53
113 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (110 bp):
TCATAGTAACACATTTAGACATGGCAAAAAATACAAATAACTAGCTGAAATAGTAAACATAATGT
AATACAAATTGTTTGAAGAAATTGGTCATAATTGATATAAGAATG
Found at i:3317550 original size:6 final size:6
Alignment explanation
Indices: 3317541--3317567 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3317531 TCTGAATCTG
3317541 ACTCGC ACTCGC ACTCGC ACTCGC ACT
1 ACTCGC ACTCGC ACTCGC ACTCGC ACT
3317568 TCCACTTGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.48, G:0.15, T:0.19
Consensus pattern (6 bp):
ACTCGC
Found at i:3318375 original size:17 final size:18
Alignment explanation
Indices: 3318349--3318386 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
3318339 TATACGTTAG
3318349 ATATTGAAATTTA-TTAA
1 ATATTGAAATTTATTTAA
*
3318366 ATATTTAAATTTATTTAA
1 ATATTGAAATTTATTTAA
3318384 ATA
1 ATA
3318387 ATTTTTTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
ATATTGAAATTTATTTAA
Found at i:3319193 original size:21 final size:22
Alignment explanation
Indices: 3319142--3319194 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
3319132 AAAAATGTTT
*
3319142 ATTTTAAATATGATATAATTAAA
1 ATTTAAAATATGATATAA-TAAA
*
3319165 A--TATAATATGATATAA-AAA
1 ATTTAAAATATGATATAATAAA
3319184 ATTTAAAATAT
1 ATTTAAAATAT
3319195 TAAAATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
19 4 0.16
21 20 0.80
23 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40
Consensus pattern (22 bp):
ATTTAAAATATGATATAATAAA
Found at i:3319225 original size:18 final size:18
Alignment explanation
Indices: 3319154--3319226 Score: 57
Period size: 17 Copynumber: 4.3 Consensus size: 18
3319144 TTTAAATATG
3319154 ATATAAT-TAAAATA-TA
1 ATATAATATAAAATATTA
* *
3319170 ATATGATATAAAAAATT-
1 ATATAATATAAAATATTA
* *
3319187 -TAAAATATTAAAAT-TTT
1 ATATAATA-TAAAATATTA
*
3319204 ATATAATATAAATTATTA
1 ATATAATATAAAATATTA
3319222 ATATA
1 ATATA
3319227 TCAAAATAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
16 13 0.30
17 16 0.37
18 14 0.33
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (18 bp):
ATATAATATAAAATATTA
Found at i:3319269 original size:29 final size:32
Alignment explanation
Indices: 3319203--3319275 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 32
3319193 ATTAAAATTT
*
3319203 TATAT-AATATAAATTATTAATATATCAAAATA
1 TATATAAATAT-AATTATTAATACATCAAAATA
* *
3319235 AATATAAATATAATTA-TAATACATAAAAATA
1 TATATAAATATAATTATTAATACATCAAAATA
*
3319266 TATAAAAATA
1 TATATAAATA
3319276 AAGTAAATAC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 21 0.60
32 9 0.26
33 5 0.14
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (32 bp):
TATATAAATATAATTATTAATACATCAAAATA
Found at i:3319284 original size:29 final size:31
Alignment explanation
Indices: 3319220--3319287 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
3319210 TATAAATTAT
* * * *
3319220 TAATATATCAAAATAAATATAAATATAATTA
1 TAATACATAAAAATAAATAAAAATATAAGTA
*
3319251 TAATACATAAAAATATATAAAAATA-AAGTA
1 TAATACATAAAAATAAATAAAAATATAAGTA
3319281 -AATACAT
1 TAATACAT
3319288 TAAATTTATG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 7 0.22
30 4 0.12
31 21 0.66
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.31
Consensus pattern (31 bp):
TAATACATAAAAATAAATAAAAATATAAGTA
Found at i:3326597 original size:19 final size:19
Alignment explanation
Indices: 3326564--3326603 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3326554 TTTAAATAAA
3326564 TTATTTAATATTATAAAAT
1 TTATTTAATATTATAAAAT
*
3326583 TTATATTAATA-TATAATAT
1 TTAT-TTAATATTATAAAAT
3326602 TT
1 TT
3326604 TAAATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTATTTAATATTATAAAAT
Found at i:3326605 original size:20 final size:20
Alignment explanation
Indices: 3326564--3326621 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
3326554 TTTAAATAAA
*
3326564 TTAT-TTAATATTATAA-AAT
1 TTATATTAATA-TATAATATT
3326583 TTATATTAATATATAATATT
1 TTATATTAATATATAATATT
*
3326603 TTAAATATAA-ATATAATAT
1 TTATAT-TAATATATAATAT
3326622 AAAATTAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 9 0.26
20 22 0.65
21 3 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATATTAATATATAATATT
Found at i:3326647 original size:16 final size:16
Alignment explanation
Indices: 3326604--3326650 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
3326594 TATAATATTT
3326604 TAAATATAAATATAATA
1 TAAA-ATAAATATAATA
*
3326621 TAAAATTAATATAAT-
1 TAAAATAAATATAATA
*
3326636 TAAACGTAAATATAA
1 TAAA-ATAAATATAA
3326651 GAATTATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 4 0.15
16 18 0.69
17 4 0.15
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (16 bp):
TAAAATAAATATAATA
Found at i:3327040 original size:16 final size:17
Alignment explanation
Indices: 3327001--3327044 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
3326991 AAAATATATT
*
3327001 TAAA-ATAATTAATAAA
1 TAAATATAATAAATAAA
*
3327017 TTAATATAATAAATAAA
1 TAAATATAATAAATAAA
3327034 -AAATATAATAA
1 TAAATATAATAA
3327045 TATTTTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAATATAATAAATAAA
Found at i:3327124 original size:23 final size:22
Alignment explanation
Indices: 3327097--3327144 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
3327087 AATCCAAAAT
* *
3327097 AAATAATCTTATAATTAAAATTA
1 AAATAAT-TTAGAACTAAAATTA
*
3327120 AAATAATTTAGACCTAAAATTA
1 AAATAATTTAGAACTAAAATTA
3327142 AAA
1 AAA
3327145 ATTGAATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.33
Consensus pattern (22 bp):
AAATAATTTAGAACTAAAATTA
Found at i:3328819 original size:24 final size:22
Alignment explanation
Indices: 3328761--3328823 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 22
3328751 GTCATATTTG
*
3328761 AATATATTGTGTTATTTTTATTA
1 AATATATTGT-TTATATTTATTA
*
3328784 TAT-TATT-TTTATATTTATTA
1 AATATATTGTTTATATTTATTA
3328804 AATATATTGTAATTATATTT
1 AATATATTGT--TTATATTT
3328824 TTTTATAGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 13 0.39
21 5 0.15
22 5 0.15
23 2 0.06
24 8 0.24
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (22 bp):
AATATATTGTTTATATTTATTA
Found at i:3329429 original size:2 final size:2
Alignment explanation
Indices: 3329422--3329449 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3329412 AAAGAGGTTG
3329422 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
3329450 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3330510 original size:2 final size:2
Alignment explanation
Indices: 3330497--3330530 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3330487 TTCAAATCCA
*
3330497 AT AT AT AC 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
3330531 TATTAAACCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3330716 original size:11 final size:11
Alignment explanation
Indices: 3330691--3330731 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
3330681 TCGTTCATTA
3330691 ATTTTTAAAAT
1 ATTTTTAAAAT
3330702 -TTTTTAAAAT
1 ATTTTTAAAAT
*
3330712 ATTTTT-ACAT
1 ATTTTTAAAAT
3330722 CATTTTTAAA
1 -ATTTTTAAA
3330732 TTTTTATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
10 13 0.52
11 11 0.44
12 1 0.04
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTTTTAAAAT
Found at i:3331314 original size:2 final size:2
Alignment explanation
Indices: 3331307--3331339 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
3331297 CACCTAAAAC
*
3331307 TA TA TA TA TA TA TA TA TA TG TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3331340 AAATTGAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3331677 original size:12 final size:12
Alignment explanation
Indices: 3331656--3331688 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
3331646 AAGATACAAT
*
3331656 TTTATCATTATA
1 TTTATAATTATA
3331668 TTTATAATTATA
1 TTTATAATTATA
3331680 TTTATAATT
1 TTTATAATT
3331689 TTATCGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (12 bp):
TTTATAATTATA
Found at i:3331691 original size:32 final size:34
Alignment explanation
Indices: 3331653--3331719 Score: 86
Period size: 32 Copynumber: 2.0 Consensus size: 34
3331643 ATTAAGATAC
*
3331653 AATTTTATC-ATTATATTTA-TAAT-TATATTTAT
1 AATTTTATCGATT-TATTTATTAATATATATATAT
*
3331685 AATTTTATCGATTTTTTTATTAATATATATATAT
1 AATTTTATCGATTTATTTATTAATATATATATAT
3331719 A
1 A
3331720 TGTAACAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 14 0.47
33 7 0.23
34 9 0.30
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.58
Consensus pattern (34 bp):
AATTTTATCGATTTATTTATTAATATATATATAT
Found at i:3332273 original size:15 final size:15
Alignment explanation
Indices: 3332253--3332310 Score: 61
Period size: 14 Copynumber: 4.1 Consensus size: 15
3332243 TAATTATGAT
3332253 ATAAAATATCATAT-A
1 ATAAAATAT-ATATAA
3332268 ATAAAATA-ATATAA
1 ATAAAATATATATAA
* *
3332282 ATAAAATATAAATAT
1 ATAAAATATATATAA
3332297 AT-AAATATAT-TAA
1 ATAAAATATATATAA
3332310 A
1 A
3332311 ATTTATATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
13 7 0.19
14 16 0.43
15 14 0.38
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
ATAAAATATATATAA
Done.