Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 168 of 172
Found at i:55093467 original size:281 final size:281
Alignment explanation
Indices: 55092913--55094317 Score: 1786
Period size: 281 Copynumber: 5.0 Consensus size: 281
55092903 AAAATGTGAT
* * *
55092913 TGTTGTCATTGATGATGTTAATGACCCAGATTAGATAGATTGTATGAGTGTTAAATATTTTAGTG
1 TGTTGTCCTTGATGATATTAATGACCCAGATTAGATAGATTGTATGGGTGTTAAATATTTTAGTG
* * * *
55092978 ATGGAAGTAGAATTATTTTGACAACTCAAAATAGATAAAGATGGGTTAACTA-GGTAAAGGACTT
66 ATGGAAGTAGAATCATTGTAACATCTCAAAATAGATAAAGATGGGTTAAC-AGGGTAAAGGACTT
* *
55093042 TCTT-AGGTCTTTTGTTGTCATTGATGATGTTAATGGCCCATATTAGATAGATTGTATGGGTGTT
130 TCTTCAGGTCTTTTGTTGTCATTGATGATGTTAATGACCCAGATTAGATAGATTGTATGGGTGTT
*
55093106 AAATATTTTAGTGATGGAAGTAGAATCATTGTAACATCTAGAGATAGACAAAGATGGGTTAACAA
195 AAATATTTTAGTGATGGAAGTAGAATCATTGTAACATCTCGAGATAGACAAAGATGGGTTAACAA
55093171 GGAAAA-GAGCTTTCTTCAGGTC
260 GGAAAAGGA-CTTTCTTCAGGTC
55093193 TGTTGTCCTTGATGATATTAATGACCCAGATTAGATAGATTGTATGGGTGTTAAATATTTTAGTG
1 TGTTGTCCTTGATGATATTAATGACCCAGATTAGATAGATTGTATGGGTGTTAAATATTTTAGTG
* *
55093258 ATGGAAGTAGAACCATTATAACATCTCAAAATAGATAAAGATGGGTTAACAGGGTAAAGGACTTT
66 ATGGAAGTAGAATCATTGTAACATCTCAAAATAGATAAAGATGGGTTAACAGGGTAAAGGACTTT
* * *
55093323 CTTCAAGTCTTTTGTTGTCATTGATGATGTTAATGACCCAGATTAGATAGATTGTATGGGTATTT
131 CTTCAGGTCTTTTGTTGTCATTGATGATGTTAATGACCCAGATTAGATAGATTGTATGGGTGTTA
*
55093388 AATATTTTGGTGATGGAAGTAG-ATCCATTGTAACATCTCGAGATAGACAAAGATGGGTTAACAA
196 AATATTTTAGTGATGGAAGTAGAAT-CATTGTAACATCTCGAGATAGACAAAGATGGGTTAACAA
* *
55093452 GGAAAATGACTTTCTTTAGGTC
260 GGAAAAGGACTTTCTTCAGGTC
* * *
55093474 TGTTGTCCTTGATGATATTAATGACCCAAAATTCGATAGATTGTATGGGTATTAAATATTTTAGT
1 TGTTGTCCTTGATGATATTAATGACCC-AGATTAGATAGATTGTATGGGTGTTAAATATTTTAGT
55093539 GATGGGTTGAAGAATCTTATTAGTAGAATCATTGTAACATCTCAAAATAGATAAAGATGGGTTAA
65 GA-----TG--G------A--AGTAGAATCATTGTAACATCTCAAAATAGATAAAGATGGGTTAA
* * * *
55093604 TAAGGTAAAGGACTTTCTTCAGGTCTTTTGTTGTCATTGATGATGTTAATAACCGAGATTAGATA
115 CAGGGTAAAGGACTTTCTTCAGGTCTTTTGTTGTCATTGATGATGTTAATGACCCAGATTAGATA
* *
55093669 GATTGTATGGGTGTTAAATATTTTGGTGATGGAAGTCGAATCATTGTAACATCTCGAGATAGACA
180 GATTGTATGGGTGTTAAATATTTTAGTGATGGAAGTAGAATCATTGTAACATCTCGAGATAGACA
* * * *
55093734 AAGACGGGTTAACAGGGAAAAGGATTTTCTTCAGGCC
245 AAGATGGGTTAACAAGGAAAAGGACTTTCTTCAGGTC
* * *
55093771 TGTTGTCCTTAATGATATTAATGACCTAGATTAGATAGATTGTATGGGTGTTAAATATTCTT-CT
1 TGTTGTCCTTGATGATATTAATGACCCAGATTAGATAGATTGTATGGGTGTTAAATATT-TTAGT
* * * * *
55093835 GATGGAAGTAGAATCATTGTAACATCTCAAAATAGATAATGTTTGGTTAATAGTGTAAACGG-CT
65 GATGGAAGTAGAATCATTGTAACATCTCAAAATAGATAAAGATGGGTTAACAGGGTAAA-GGACT
* *
55093899 TTCTTCAGGTCTTTTGTTGTCATTGATGATATTAATGACTCAGATTAGATAGATTGTATGGGTGT
129 TTCTTCAGGTCTTTTGTTGTCATTGATGATGTTAATGACCCAGATTAGATAGATTGTATGGGTGT
* * * * * *
55093964 TAAATATTTTAGTGATGGAAGTAGAGTCATTATAAAATCTCAAAATAGATAAAGATGGGTTAACA
194 TAAATATTTTAGTGATGGAAGTAGAATCATTGTAACATCTCGAGATAGACAAAGATGGGTTAACA
* *
55094029 AGGTAAAGGACTTTCTTCTGGTC
259 AGGAAAAGGACTTTCTTCAGGTC
* *
55094052 TTTTGTTGTCATTGATGATGTTAATGACCCAGATT-GAATAGATTGTATGGGTGTTAAATATGTT
1 ---TGTTGTCCTTGATGATATTAATGACCCAGATTAG-ATAGATTGTATGGGTGTTAAATAT-TT
* * * * * *
55094116 AAGTGATAGAAGTAGAATCATTGTAACATCTCTAGATAGACAAAGAT--G-----AGGGAAAAGG
61 TAGTGATGGAAGTAGAATCATTGTAACATCTCAAAATAGATAAAGATGGGTTAACAGGGTAAAGG
* * * * * * *
55094174 ACTTT-TTGCAGG-C--CTGTTGTCCTTAATAATATTAATGACTCTA-ATTAGATAGATTTTATG
126 ACTTTCTT-CAGGTCTTTTGTTGTCATTGATGATGTTAATGAC-CCAGATTAGATAGATTGTATG
* * * * *
55094234 GGTGTTAAATATTTTAGAGATGGAAGTAGAATCATTGTAACTTCTCAAAATAGATAAAGATGGGT
189 GGTGTTAAATATTTTAGTGATGGAAGTAGAATCATTGTAACATCTCGAGATAGACAAAGATGGGT
* *
55094299 TAACAGGGTAAAGGACTTT
254 TAACAAGGAAAAGGACTTT
55094318 GCTTAATCTT
Statistics
Matches: 1002, Mismatches: 91, Indels: 69
0.86 0.08 0.06
Matches are distributed among these distances:
275 116 0.12
276 1 0.00
277 5 0.00
278 14 0.01
279 1 0.00
280 125 0.12
281 345 0.34
282 40 0.04
283 3 0.00
284 53 0.05
285 39 0.04
287 2 0.00
289 2 0.00
291 2 0.00
295 1 0.00
296 32 0.03
297 219 0.22
298 2 0.00
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.35
Consensus pattern (281 bp):
TGTTGTCCTTGATGATATTAATGACCCAGATTAGATAGATTGTATGGGTGTTAAATATTTTAGTG
ATGGAAGTAGAATCATTGTAACATCTCAAAATAGATAAAGATGGGTTAACAGGGTAAAGGACTTT
CTTCAGGTCTTTTGTTGTCATTGATGATGTTAATGACCCAGATTAGATAGATTGTATGGGTGTTA
AATATTTTAGTGATGGAAGTAGAATCATTGTAACATCTCGAGATAGACAAAGATGGGTTAACAAG
GAAAAGGACTTTCTTCAGGTC
Found at i:55095711 original size:75 final size:75
Alignment explanation
Indices: 55095620--55095758 Score: 224
Period size: 75 Copynumber: 1.9 Consensus size: 75
55095610 TCAAACTGAC
*
55095620 ACATGCCTTAACTTCATCACTTATCTACTCAAAGCTGTGAAAGAGGCAATGATGAAGGTCTTCTT
1 ACATGCCTTAACTTCATCACTCATCTACTCAAAGCTGTGAAAGAGGCAATGATGAAGGTCTTCTT
55095685 CTTCTTCTTT
66 CTTCTTCTTT
* * * * *
55095695 ACATGCTTTAACTTCATCACTCATCTACTCAAAGCTTTGAAAGAGGTAATTATGAATGTCTTCT
1 ACATGCCTTAACTTCATCACTCATCTACTCAAAGCTGTGAAAGAGGCAATGATGAAGGTCTTCT
55095759 CCCATGATGA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 58 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.36
Consensus pattern (75 bp):
ACATGCCTTAACTTCATCACTCATCTACTCAAAGCTGTGAAAGAGGCAATGATGAAGGTCTTCTT
CTTCTTCTTT
Found at i:55099505 original size:98 final size:99
Alignment explanation
Indices: 55099392--55099589 Score: 335
Period size: 99 Copynumber: 2.0 Consensus size: 99
55099382 TTCTAGAAAT
* * *
55099392 AGATGCAAGATG-TTTTGAAATGATTGATTTAGGTTTGATGACTTATTTTCTTAGCTTTGAAGTG
1 AGATGCAAGATGTTTTTAAAATGATTGATTTAGGTTTGATGACTTATTTTCTTAGCATGGAAGTG
55099456 AATCAAATTGAACATGGCATCCTCATAAGCCAAC
66 AATCAAATTGAACATGGCATCCTCATAAGCCAAC
*
55099490 AGATGTAAGATGTTTTTAAAATGATTGATTTAGGTTTGATGACTTATTTTCTTAGCATGGAAGTG
1 AGATGCAAGATGTTTTTAAAATGATTGATTTAGGTTTGATGACTTATTTTCTTAGCATGGAAGTG
* *
55099555 AATCAGATTGAACATGGCATCTTCATAAGCCAAC
66 AATCAAATTGAACATGGCATCCTCATAAGCCAAC
55099589 A
1 A
55099590 AGCTTTTGCA
Statistics
Matches: 93, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
98 11 0.12
99 82 0.88
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (99 bp):
AGATGCAAGATGTTTTTAAAATGATTGATTTAGGTTTGATGACTTATTTTCTTAGCATGGAAGTG
AATCAAATTGAACATGGCATCCTCATAAGCCAAC
Found at i:55100904 original size:168 final size:167
Alignment explanation
Indices: 55100613--55100948 Score: 609
Period size: 168 Copynumber: 2.0 Consensus size: 167
55100603 AATGTAATGA
55100613 AGCTATTTATGCAAATTGTATTGCTACTAATTATAGTAATGAGAGTTGTCAATTTTTCTCTCAAC
1 AGCTATTTATGCAAATTGTATTGCTACTAATTATAGTAATGAGAGTTGTCAATTTTTCTCTCAAC
**
55100678 CGATTTGTTTTTACTTCTGTTTTTCAACTTTCAAACACAAATTTTCTTTGTTTTGATCTTTGGAT
66 CGATTTGTTTTTACTTCTGGCTTTCAACTTTCAAACACAAATTTTCTTTGTTTTGATCTTTGGAT
*
55100743 GTTGATATAACTCAACAAACTGTCATGCTCTAGTCCG
131 GCTGATATAACTCAACAAACTGTCATGCTCTAGTCCG
55100780 AGCTATTTATGCAAATTGTATTGCTACTAATTATAGTAATGAGAGTTGTCAATTTTTTCTCTCAA
1 AGCTATTTATGCAAATTGTATTGCTACTAATTATAGTAATGAGAGTTGTCAA-TTTTTCTCTCAA
* *
55100845 CCGATTTGTTTTTGCTTCTGGCTTTCATCTTTCAAACACAAATTTTCTTTGTTTTGATCTTTGGA
65 CCGATTTGTTTTTACTTCTGGCTTTCAACTTTCAAACACAAATTTTCTTTGTTTTGATCTTTGGA
*
55100910 TGCTGATATAGCTCAACAAACTGTCATGCTCTAGTCCG
130 TGCTGATATAACTCAACAAACTGTCATGCTCTAGTCCG
55100948 A
1 A
55100949 AGCTTCAAGC
Statistics
Matches: 162, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
167 52 0.32
168 110 0.68
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (167 bp):
AGCTATTTATGCAAATTGTATTGCTACTAATTATAGTAATGAGAGTTGTCAATTTTTCTCTCAAC
CGATTTGTTTTTACTTCTGGCTTTCAACTTTCAAACACAAATTTTCTTTGTTTTGATCTTTGGAT
GCTGATATAACTCAACAAACTGTCATGCTCTAGTCCG
Found at i:55105222 original size:14 final size:14
Alignment explanation
Indices: 55105203--55105251 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
55105193 TACCAAGGAA
55105203 GATTTTCTTGGCCT
1 GATTTTCTTGGCCT
***
55105217 GATTTTCTT--TAA
1 GATTTTCTTGGCCT
55105229 GATTTTCTTGGCCT
1 GATTTTCTTGGCCT
55105243 GATTTTCTT
1 GATTTTCTT
55105252 TAAGCCAAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
12 9 0.33
14 18 0.67
ACGTcount: A:0.12, C:0.16, G:0.16, T:0.55
Consensus pattern (14 bp):
GATTTTCTTGGCCT
Found at i:55105237 original size:26 final size:26
Alignment explanation
Indices: 55105201--55105255 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
55105191 CATACCAAGG
55105201 AAGATTTTCTTGGCCTGATTTTCTTT
1 AAGATTTTCTTGGCCTGATTTTCTTT
55105227 AAGATTTTCTTGGCCTGATTTTCTTT
1 AAGATTTTCTTGGCCTGATTTTCTTT
55105253 AAG
1 AAG
55105256 CCAAAGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.18, C:0.15, G:0.16, T:0.51
Consensus pattern (26 bp):
AAGATTTTCTTGGCCTGATTTTCTTT
Found at i:55106356 original size:33 final size:34
Alignment explanation
Indices: 55106281--55106364 Score: 91
Period size: 33 Copynumber: 2.5 Consensus size: 34
55106271 TGGGGAAATC
* * * *
55106281 TAAGGGATTTGGGG-ATTTTGATTTGGGGAAAAAT
1 TAAGGGATTTGGGGAAATTT-ATTAGGCGAAAAAA
*
55106315 TAAAGGATTTGGGGAAATTT-TTAGGCGAAAAAA
1 TAAGGGATTTGGGGAAATTTATTAGGCGAAAAAA
*
55106348 TAAGGGATTTCGGGAAA
1 TAAGGGATTTGGGGAAA
55106365 ATGATTTGGG
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
33 25 0.60
34 13 0.31
35 4 0.10
ACGTcount: A:0.36, C:0.02, G:0.32, T:0.30
Consensus pattern (34 bp):
TAAGGGATTTGGGGAAATTTATTAGGCGAAAAAA
Found at i:55106846 original size:13 final size:15
Alignment explanation
Indices: 55106793--55106843 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
55106783 ATAAATTAAA
* *
55106793 TTTAACATTTAATAT
1 TTTAACACTTAATTT
*
55106808 TTTAATA-TATAATTT
1 TTTAACACT-TAATTT
55106823 TTTAACACTTAATTT
1 TTTAACACTTAATTT
55106838 TTTAAC
1 TTTAAC
55106844 TTATCATACA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
14 1 0.03
15 29 0.94
16 1 0.03
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTAACACTTAATTT
Found at i:55109162 original size:17 final size:16
Alignment explanation
Indices: 55109132--55109165 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55109122 GTGTAAATTT
*
55109132 TTTTTAATAATTTAAA
1 TTTTTAAAAATTTAAA
55109148 TTTTTAAAAAGTTTAAA
1 TTTTTAAAAA-TTTAAA
55109165 T
1 T
55109166 GAAAAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTTTAAAAATTTAAA
Found at i:55113715 original size:189 final size:189
Alignment explanation
Indices: 55113383--55113871 Score: 653
Period size: 189 Copynumber: 2.6 Consensus size: 189
55113373 GTTGGAATCA
* * * *
55113383 CTTCATGATCTGGATCTTAGTCATTGCCCAATAGCCGAATTCCCAAAAATCCCAAGAAGCTTGAC
1 CTTCGTGATCTGAATCTTAGTCATTGCCCAATAGCCGAATTCCCAGAAATCCCAAGAAGCTTAAC
* * *
55113448 AGAATTAAACTTATCTGAAACTCAAATTGAAGATGTGTGCTTGTCTAGCGACACTCCAAGCAATC
66 AGAATTAAACTTATCTGGAACTCAAATTGAAGAAGTGTCCTTGTCTAGCGACACTCCAAGCAATC
* * **
55113513 TTCAGAAGTTAGATATGAGTGGCTCAAGGGTGAAA-AATGTATCCATCAAGATGGATTCC
131 TTCAGAAGTTAGATATGAGGGGCTCAAGAGT-AAAGAATGTATCCATCAAGATGGAAGCC
* * *
55113572 CTTCGTGATCTGAATCTTAGTCATTGCCCAATAGTCAAATTTCCC-GAAATCCCAAGAACCTTAA
1 CTTCGTGATCTGAATCTTAGTCATTGCCCAATAGCCGAA-TTCCCAGAAATCCCAAGAAGCTTAA
* * ** * ** *
55113636 CAAAATTAAACTTATCTGGAACTCAAATTGAAGAGGTGTCCTTGTCTCTCGACTCTGTAGGCAAT
65 CAGAATTAAACTTATCTGGAACTCAAATTGAAGAAGTGTCCTTGTCTAGCGACACTCCAAGCAAT
*
55113701 CTTCA-AACGTTAGATATGAGGGGCTCAAGAGTAAAGAATGTATCGATCAAGATGGAAGCC
130 CTTCAGAA-GTTAGATATGAGGGGCTCAAGAGTAAAGAATGTATCCATCAAGATGGAAGCC
* * *
55113761 CTCCGTGATCTGAATCTTAGTCATTGCCCAATAACCGAATTCCCAGAAATCCCAAGAAGCTTAAG
1 CTTCGTGATCTGAATCTTAGTCATTGCCCAATAGCCGAATTCCCAGAAATCCCAAGAAGCTTAAC
* * *
55113826 AGAATTAAATTTATCTGGGACTCAAATT-AAGGAAGTGACCTTGTCT
66 AGAATTAAACTTATCTGGAACTCAAATTGAA-GAAGTGTCCTTGTCT
55113872 TTAGACTCCC
Statistics
Matches: 262, Mismatches: 33, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
188 12 0.05
189 245 0.94
190 5 0.02
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (189 bp):
CTTCGTGATCTGAATCTTAGTCATTGCCCAATAGCCGAATTCCCAGAAATCCCAAGAAGCTTAAC
AGAATTAAACTTATCTGGAACTCAAATTGAAGAAGTGTCCTTGTCTAGCGACACTCCAAGCAATC
TTCAGAAGTTAGATATGAGGGGCTCAAGAGTAAAGAATGTATCCATCAAGATGGAAGCC
Found at i:55116840 original size:23 final size:21
Alignment explanation
Indices: 55116782--55116840 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 21
55116772 AAATAATATG
*
55116782 GTATTAAAGGTATATACATAA
1 GTATTAAAGATATATACATAA
55116803 -TATATATAAGAATATATACATAAA
1 GTAT-TA-AAG-ATATATACAT-AA
55116827 GTATTAAAG-TATAT
1 GTATTAAAGATATAT
55116841 GTGTAAGATG
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
20 3 0.09
21 7 0.22
22 3 0.09
23 12 0.38
24 4 0.12
25 3 0.09
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (21 bp):
GTATTAAAGATATATACATAA
Found at i:55117098 original size:3 final size:3
Alignment explanation
Indices: 55117090--55117140 Score: 77
Period size: 3 Copynumber: 17.0 Consensus size: 3
55117080 AAGGATACTG
*
55117090 ATA ATA ATA ATA ATA ATA ACA ATA A-A TATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA
55117135 ATA ATA
1 ATA ATA
55117141 GGCAAAGTGA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 1 0.02
3 42 0.95
4 1 0.02
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:55124840 original size:3 final size:3
Alignment explanation
Indices: 55124832--55124866 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
55124822 TCTTTCATGG
* *
55124832 CTT CTT CTT CTT CTT CTT CTT CCT CTT CCT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
55124867 CCTCAAACAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (3 bp):
CTT
Found at i:55126831 original size:44 final size:44
Alignment explanation
Indices: 55126768--55126854 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
55126758 TATCACTGTG
55126768 AATGAGCATTGTCTTAGGATACATAACATGAGATTTTCACAATT
1 AATGAGCATTGTCTTAGGATACATAACATGAGATTTTCACAATT
*
55126812 AATGAGCATTGTCTTAGGATATATAACATGAGATTTTCACAAT
1 AATGAGCATTGTCTTAGGATACATAACATGAGATTTTCACAAT
55126855 GATTTATTGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (44 bp):
AATGAGCATTGTCTTAGGATACATAACATGAGATTTTCACAATT
Found at i:55128269 original size:189 final size:187
Alignment explanation
Indices: 55127773--55128316 Score: 648
Period size: 189 Copynumber: 2.9 Consensus size: 187
55127763 ATTTCAAAGT
* * * * *
55127773 TGGAATCACTTCGTGATATGGATCTTAGTCATTGTCCAATGGTCGAATTCCCAGAAATTCCC-AG
1 TGGAATCCCTTCGTGATCTGAATCTTAGTCATTGCCCAATGATCGAATTCCCAGAAA-TCCCAAG
* * * * * * *
55127837 AAGCTTGACAGATTTAAACTTATCTGAAACTCAAATTGAAGAGGTGTGCTTGTCTCTTGCCACTC
65 AAGCTT-AGAGAATTAAACTTATCTGGAACTCAAATTGAAGAGGTGTACTTGTCTCTAGACTCTC
* * * *
55127902 CAAGTAATCTTCAGAGCTTAAATATGAGTGGCTCAAGGGTCAAAATTGTATCGATCAAGA
129 TAAATAATCTTCAGAG-TTAAATATGAGTTGCTCAAGGGTAAAAATTGTATCGATCAAGA
*
55127962 TGGAATCCCTTCGTGATCTGAATCTTAGTCATTGCCCAAT-AGTCAAATTTCCC-GAAATCCCAA
1 TGGAATCCCTTCGTGATCTGAATCTTAGTCATTGCCCAATGA-TCGAA-TTCCCAGAAATCCCAA
* * * *
55128025 GAAGCTTAGCAAAATTAAACTTATCCGGAACTCAAATTGAAGAGGTGTCCTTGTCTCTCGACTCT
64 GAAGCTTAG-AGAATTAAACTTATCTGGAACTCAAATTGAAGAGGTGTACTTGTCTCTAGACTCT
* ** *
55128090 TTATTTAATCTTCAGACGTTAGATATGAGTTGCTCAAGGGTAAAAAGTT-TATCGATCAAGA
128 CTAAATAATCTTCAGA-GTTAAATATGAGTTGCTCAAGGGTAAAAA-TTGTATCGATCAAGA
*
55128151 TGGAATCCCTTTGTGATCTGAATCTTAGTCATTGCCCAATGATCGAATTCCCAGAAATCCCAAGA
1 TGGAATCCCTTCGTGATCTGAATCTTAGTCATTGCCCAATGATCGAATTCCCAGAAATCCCAAGA
* * * * * *
55128216 AGCTTAAGAGAATTAAATTTATCTGGGACTCAAATT-AAGGAAGCGAACTTGTCTTTAGACTCTC
66 AGCTT-AGAGAATTAAACTTATCTGGAACTCAAATTGAA-GAGGTGTACTTGTCTCTAGACTCTC
* *
55128280 TAAATAATCTTCAGAAGTTAAAGATGAGCTGCTCAAG
129 TAAATAATCTTCAG-AGTTAAATATGAGTTGCTCAAG
55128317 TATTCAAAAG
Statistics
Matches: 304, Mismatches: 40, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
188 12 0.04
189 280 0.92
190 12 0.04
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (187 bp):
TGGAATCCCTTCGTGATCTGAATCTTAGTCATTGCCCAATGATCGAATTCCCAGAAATCCCAAGA
AGCTTAGAGAATTAAACTTATCTGGAACTCAAATTGAAGAGGTGTACTTGTCTCTAGACTCTCTA
AATAATCTTCAGAGTTAAATATGAGTTGCTCAAGGGTAAAAATTGTATCGATCAAGA
Found at i:55130500 original size:25 final size:25
Alignment explanation
Indices: 55130472--55130551 Score: 78
Period size: 25 Copynumber: 3.3 Consensus size: 25
55130462 AATTGTTCAT
55130472 AATAAATACAAATTTATTTACACAA
1 AATAAATACAAATTTATTTACACAA
* * * *
55130497 AATAAATA-TAA-TAATTGT--TCAT
1 AATAAATACAAATTTATT-TACACAA
*
55130519 AATAAATACAAATTTATTTACATAA
1 AATAAATACAAATTTATTTACACAA
55130544 AATAAATA
1 AATAAATA
55130552 AACATATTTA
Statistics
Matches: 41, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
22 10 0.24
23 7 0.17
24 7 0.17
25 17 0.41
ACGTcount: A:0.56, C:0.07, G:0.01, T:0.35
Consensus pattern (25 bp):
AATAAATACAAATTTATTTACACAA
Found at i:55130517 original size:47 final size:47
Alignment explanation
Indices: 55130460--55130551 Score: 175
Period size: 47 Copynumber: 2.0 Consensus size: 47
55130450 TGCAACAATT
55130460 ATAATTGTTCATAATAAATACAAATTTATTTACACAAAATAAATATA
1 ATAATTGTTCATAATAAATACAAATTTATTTACACAAAATAAATATA
*
55130507 ATAATTGTTCATAATAAATACAAATTTATTTACATAAAATAAATA
1 ATAATTGTTCATAATAAATACAAATTTATTTACACAAAATAAATA
55130552 AACATATTTA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.37
Consensus pattern (47 bp):
ATAATTGTTCATAATAAATACAAATTTATTTACACAAAATAAATATA
Found at i:55135636 original size:41 final size:39
Alignment explanation
Indices: 55135573--55135861 Score: 312
Period size: 41 Copynumber: 7.0 Consensus size: 39
55135563 GTGATTGAAT
* * *
55135573 ATAATACAGACGTTACGTCTAGCAGGCTTAATGCCGGTG
1 ATAATTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG
*
55135612 AAGTAATTCAGACTTTAAGTCTAGCAGGCTAAATGCCGGTG
1 -A-TAATTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG
55135653 ATACATTTCAGACTTTAATACGTCTAGCAGGCTTAATGCCGGTG
1 ATA-A-TTCAGACTTT-A-A-GTCTAGCAGGCTTAATGCCGGTG
*
55135697 AAGTAATTCAGACTTTAAGTCTAGCAGGCTAAATGCCGGTG
1 -A-TAATTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG
55135738 ATACATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG
1 ATA-A-TTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG
* *
55135779 ATACATTTCAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG
1 ATA-A-TTCAGACTTTAAGTCTAGCAGGCTTAA-TGCCGGTG
* * **
55135820 TACTGAA-TCAGGCTTTAAGCCTAGCAGGCAAAATGCCGGTG
1 -A-T-AATTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG
55135861 A
1 A
55135862 ATCTGTTTAA
Statistics
Matches: 220, Mismatches: 14, Indels: 30
0.83 0.05 0.11
Matches are distributed among these distances:
39 4 0.02
40 9 0.04
41 161 0.73
42 5 0.02
43 4 0.02
44 33 0.15
45 2 0.01
46 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (39 bp):
ATAATTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG
Found at i:55135685 original size:85 final size:84
Alignment explanation
Indices: 55135586--55135819 Score: 386
Period size: 85 Copynumber: 2.8 Consensus size: 84
55135576 ATACAGACGT
55135586 TACGTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTTTAAGTCTAGCAGGCTAAATGCCGG
1 TACGTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTTTAAGTCTAGCAGGCTAAATGCCGG
55135651 TGATACATTTCAGACTTTAA
66 TGATACATTTCAGACTTT-A
55135671 TACGTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTTTAAGTCTAGCAGGCTAAATGCCGG
1 TACGTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTTTAAGTCTAGCAGGCTAAATGCCGG
55135736 TGATACATTTCAGACTTTA
66 TGATACATTTCAGACTTTA
* * *
55135755 -A-GTCTAGCAGGCTTAATGCCGGTG-A-TACATTTCAGACTATATGTCTAGCAGGCTAAGTGCC
1 TACGTCTAGCAGGCTTAATGCCGGTGAAGTA-A-TTCAGACTTTAAGTCTAGCAGGCTAAATGCC
55135816 GGTG
64 GGTG
55135820 TACTGAATCA
Statistics
Matches: 144, Mismatches: 3, Indels: 7
0.94 0.02 0.05
Matches are distributed among these distances:
80 2 0.01
81 2 0.01
82 55 0.38
83 1 0.01
84 1 0.01
85 83 0.58
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (84 bp):
TACGTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTTTAAGTCTAGCAGGCTAAATGCCGG
TGATACATTTCAGACTTTA
Found at i:55135816 original size:82 final size:82
Alignment explanation
Indices: 55135579--55135862 Score: 387
Period size: 82 Copynumber: 3.4 Consensus size: 82
55135569 GAATATAATA
* *
55135579 CAGACGTTACGTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTTTAAGTCTAGCAGGCTAA
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTTTAAGTCTAGCAGGCTAA
55135644 ATGCCGGTGATACATTT
66 ATGCCGGTGATACATTT
55135661 CAGACTTTAATACGTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTTTAAGTCTAGCAGGC
1 CAGACTTT-A-A-GTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTTTAAGTCTAGCAGGC
55135726 TAAATGCCGGTGATACATTT
63 TAAATGCCGGTGATACATTT
* *
55135746 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG-A-TACATTTCAGACTATATGTCTAGCAGGCT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGAAGTA-A-TTCAGACTTTAAGTCTAGCAGGCT
* *
55135809 AAGTGCCGGTG-TAC-TGAAT
64 AAATGCCGGTGATACAT--TT
* * **
55135828 CAGGCTTTAAGCCTAGCAGGCAAAATGCCGGTGAA
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGAA
55135863 TCTGTTTAAA
Statistics
Matches: 184, Mismatches: 10, Indels: 15
0.88 0.05 0.07
Matches are distributed among these distances:
80 3 0.02
81 5 0.03
82 92 0.50
83 3 0.02
84 1 0.01
85 80 0.43
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (82 bp):
CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTTTAAGTCTAGCAGGCTAA
ATGCCGGTGATACATTT
Found at i:55144099 original size:24 final size:24
Alignment explanation
Indices: 55144067--55144116 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
55144057 TTACGAGAGG
55144067 TTTGGGGAATATTTAAGGAAGCAC
1 TTTGGGGAATATTTAAGGAAGCAC
55144091 TTTGGGGAATATTTAAGGAAGCAC
1 TTTGGGGAATATTTAAGGAAGCAC
55144115 TT
1 TT
55144117 AATGTGTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (24 bp):
TTTGGGGAATATTTAAGGAAGCAC
Found at i:55146460 original size:2 final size:2
Alignment explanation
Indices: 55146453--55146480 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
55146443 TGCTTTTGCG
55146453 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
55146481 ATTCTCCCAA
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:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:55149174 original size:22 final size:19
Alignment explanation
Indices: 55149148--55149187 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 19
55149138 TGTATTCTAT
55149148 ATTTTATCTTTAATTTCTAAAC
1 ATTTTA-CTTT-A-TTCTAAAC
55149170 ATTTTACTTTATTCTAAA
1 ATTTTACTTTATTCTAAA
55149188 TAAAAGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 1 0.06
21 4 0.22
22 6 0.33
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTTACTTTATTCTAAAC
Found at i:55158379 original size:21 final size:22
Alignment explanation
Indices: 55158344--55158384 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
55158334 AACATTTTTT
55158344 TATAAAATTACAA-TTAAATCA
1 TATAAAATTACAATTTAAATCA
55158365 TATAAAATTTA-AATTTAAAT
1 TATAAAA-TTACAATTTAAAT
55158385 TGATATATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (22 bp):
TATAAAATTACAATTTAAATCA
Found at i:55161675 original size:9 final size:9
Alignment explanation
Indices: 55161661--55161685 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
55161651 TATAACAATC
55161661 TCAAAATTA
1 TCAAAATTA
55161670 TCAAAATTA
1 TCAAAATTA
55161679 TCAAAAT
1 TCAAAAT
55161686 CGGACAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (9 bp):
TCAAAATTA
Found at i:55164029 original size:15 final size:16
Alignment explanation
Indices: 55164004--55164034 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
55163994 AAATTGTGAG
55164004 AATTATTATTTTAAAT
1 AATTATTATTTTAAAT
55164020 AATT-TTATTTTAAAT
1 AATTATTATTTTAAAT
55164035 TTTAATGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AATTATTATTTTAAAT
Found at i:55167362 original size:20 final size:20
Alignment explanation
Indices: 55167334--55167375 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
55167324 TAATGCATTC
* *
55167334 AAAAGAAAAGGAAAAGGAAGA
1 AAAAAAAAAAGAAAA-GAAGA
55167355 AAAAAAAAAAGAAAAGAAGA
1 AAAAAAAAAAGAAAAGAAGA
55167375 A
1 A
55167376 GAAGCTGCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAGAAAAGAAGA
Found at i:55179604 original size:19 final size:21
Alignment explanation
Indices: 55179553--55179604 Score: 51
Period size: 19 Copynumber: 2.7 Consensus size: 21
55179543 AGAAAATATA
*
55179553 ATATAATTATATACTTGTATC
1 ATATAATTATATAATTGTATC
55179574 A-A-AATTGA-ATAATT-TAT-
1 ATATAATT-ATATAATTGTATC
55179591 ATATAATTATATAA
1 ATATAATTATATAA
55179605 ATATTTAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 10
0.70 0.03 0.27
Matches are distributed among these distances:
17 1 0.04
18 5 0.19
19 17 0.65
20 2 0.08
21 1 0.04
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (21 bp):
ATATAATTATATAATTGTATC
Found at i:55181584 original size:19 final size:19
Alignment explanation
Indices: 55181545--55181581 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
55181535 ATTTTTCAAA
55181545 ATCATATAACTTAAATTTT
1 ATCATATAACTTAAATTTT
*
55181564 ATCATA-AACTTTAATTTT
1 ATCATATAACTTAAATTTT
55181582 TATGTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.49
Consensus pattern (19 bp):
ATCATATAACTTAAATTTT
Found at i:55182215 original size:31 final size:31
Alignment explanation
Indices: 55182180--55182238 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
55182170 TAGCCTATTG
* *
55182180 ACTTAAATAAAAAATTTTGAGTAGTTTAACA
1 ACTTAAATAAAAAATTTCGAATAGTTTAACA
* *
55182211 ACTTAAATGAAAACTTTCGAATAGTTTA
1 ACTTAAATAAAAAATTTCGAATAGTTTA
55182239 GTGACCAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (31 bp):
ACTTAAATAAAAAATTTCGAATAGTTTAACA
Found at i:55196737 original size:48 final size:48
Alignment explanation
Indices: 55196682--55196773 Score: 184
Period size: 48 Copynumber: 1.9 Consensus size: 48
55196672 ACATCTATTT
55196682 ATTCAAACATATTCCATAATTTTTATGGTCAGATGTAATTATTAATAA
1 ATTCAAACATATTCCATAATTTTTATGGTCAGATGTAATTATTAATAA
55196730 ATTCAAACATATTCCATAATTTTTATGGTCAGATGTAATTATTA
1 ATTCAAACATATTCCATAATTTTTATGGTCAGATGTAATTATTA
55196774 CAACCTTAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (48 bp):
ATTCAAACATATTCCATAATTTTTATGGTCAGATGTAATTATTAATAA
Found at i:55198059 original size:21 final size:21
Alignment explanation
Indices: 55198033--55198077 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
55198023 ATGAATGGTT
*
55198033 CTTTCATTGATGCTAATTTTC
1 CTTTCATTGATACTAATTTTC
55198054 CTTTCATTGATACTAATTTTC
1 CTTTCATTGATACTAATTTTC
55198075 CTT
1 CTT
55198078 ACGGATCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.53
Consensus pattern (21 bp):
CTTTCATTGATACTAATTTTC
Found at i:55205348 original size:14 final size:14
Alignment explanation
Indices: 55205329--55205358 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
55205319 TATTTTCAAG
55205329 ATAGATTAACGCAT
1 ATAGATTAACGCAT
*
55205343 ATAGATTTACGCAT
1 ATAGATTAACGCAT
55205357 AT
1 AT
55205359 TTATAAAAAA
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:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (14 bp):
ATAGATTAACGCAT
Found at i:55207540 original size:32 final size:32
Alignment explanation
Indices: 55207495--55207565 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
55207485 TTACAAGAAA
**
55207495 TAGGAAAGGATTAACTCACTTGGTGCAAAAAT
1 TAGGAAAAAATTAACTCACTTGGTGCAAAAAT
55207527 TAGGAAAAAATTAACTCACTTGGTGCAAAAAT
1 TAGGAAAAAATTAACTCACTTGGTGCAAAAAT
*
55207559 TATGAAA
1 TAGGAAA
55207566 TACCAGCTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.25
Consensus pattern (32 bp):
TAGGAAAAAATTAACTCACTTGGTGCAAAAAT
Found at i:55208874 original size:18 final size:18
Alignment explanation
Indices: 55208851--55208886 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
55208841 TTATTATTTT
55208851 TAAAATTATAAAAATATA
1 TAAAATTATAAAAATATA
* *
55208869 TAAAATTGTTAAAATATA
1 TAAAATTATAAAAATATA
55208887 CACTTTCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
TAAAATTATAAAAATATA
Found at i:55208969 original size:16 final size:16
Alignment explanation
Indices: 55208947--55209015 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
55208937 TTTGGTTCGC
55208947 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
55208963 CGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
55208979 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
55208996 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
55209012 TGTA
1 TGTA
55209016 ATAGCTAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:55208993 original size:33 final size:32
Alignment explanation
Indices: 55208947--55209015 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
55208937 TTTGGTTCGC
55208947 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
*
55208979 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGCGTATTGGATTAGAGG
55209012 TGTA
1 TGTA
55209016 ATAGCTAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 6 0.17
33 29 0.83
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (32 bp):
TGTATTGGATTAGAGGCGTATTGGATTAGAGG
Found at i:55209080 original size:44 final size:45
Alignment explanation
Indices: 55208996--55209086 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
55208986 GGATTAGAGG
* * *
55208996 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
55209041 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
55209085 TG
1 TG
55209087 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:55209272 original size:18 final size:17
Alignment explanation
Indices: 55209251--55209285 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
55209241 TTATTATTAA
*
55209251 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
55209269 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
55209286 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:55209392 original size:18 final size:17
Alignment explanation
Indices: 55209371--55209405 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
55209361 TTATTATTAA
*
55209371 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
55209389 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
55209406 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:55209447 original size:120 final size:120
Alignment explanation
Indices: 55209234--55209455 Score: 435
Period size: 120 Copynumber: 1.9 Consensus size: 120
55209224 ATCATATTTA
55209234 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
55209299 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTGACTCAAATCATAATATATGATACTGTAAAATATAAATT
55209354 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
55209419 TATTCTTATATTAATTGACTCAAATCATAATATATGA
66 TATTCTTATATTAATTGACTCAAATCATAATATATGA
55209456 ATTGGACCAA
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 101 1.00
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTGACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:55212718 original size:11 final size:11
Alignment explanation
Indices: 55212702--55212740 Score: 78
Period size: 11 Copynumber: 3.5 Consensus size: 11
55212692 AATCGGGAGG
55212702 CGAAGGTAGAA
1 CGAAGGTAGAA
55212713 CGAAGGTAGAA
1 CGAAGGTAGAA
55212724 CGAAGGTAGAA
1 CGAAGGTAGAA
55212735 CGAAGG
1 CGAAGG
55212741 AAGAGGCGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.44, C:0.10, G:0.38, T:0.08
Consensus pattern (11 bp):
CGAAGGTAGAA
Found at i:55213706 original size:27 final size:27
Alignment explanation
Indices: 55213675--55213734 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
55213665 GACGCCAATG
* **
55213675 AAAAATTTAAATTTTATAAAAAT-ATAA
1 AAAAAATTAAATTCAAT-AAAATCATAA
55213702 AAAAAATTAAATTCAATAAAATCATAA
1 AAAAAATTAAATTCAATAAAATCATAA
55213729 AAAAAA
1 AAAAAA
55213735 GAAGTTCATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 5 0.17
27 24 0.83
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.28
Consensus pattern (27 bp):
AAAAAATTAAATTCAATAAAATCATAA
Found at i:55213748 original size:26 final size:26
Alignment explanation
Indices: 55213690--55213749 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
55213680 TTTAAATTTT
*
55213690 ATAAAAATATAAAAAAAATTAAATTC
1 ATAAAAATATAAAAAAAATGAAATTC
*
55213716 A-ATAAAATCATAAAAAAAA-GAAGTTC
1 ATA-AAAAT-ATAAAAAAAATGAAATTC
55213742 ATAAAAAT
1 ATAAAAAT
55213750 TCAAAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
25 1 0.03
26 17 0.59
27 11 0.38
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.23
Consensus pattern (26 bp):
ATAAAAATATAAAAAAAATGAAATTC
Found at i:55214223 original size:29 final size:30
Alignment explanation
Indices: 55214168--55214228 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
55214158 AATTTAGTTA
* *
55214168 TTAATATTTTCATTTTTAATTAATTTT-TT
1 TTAATATTTTCATGTTAAATTAATTTTATT
55214197 TTAATATTTTC-TGTTAAATTAACTTTTATT
1 TTAATATTTTCATGTTAAATTAA-TTTTATT
55214227 TT
1 TT
55214229 TTATTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 9 0.32
29 15 0.54
30 4 0.14
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (30 bp):
TTAATATTTTCATGTTAAATTAATTTTATT
Found at i:55219230 original size:13 final size:13
Alignment explanation
Indices: 55219212--55219237 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55219202 AATAACATAA
55219212 CATAGTGAAATGT
1 CATAGTGAAATGT
55219225 CATAGTGAAATGT
1 CATAGTGAAATGT
55219238 ACTAACCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (13 bp):
CATAGTGAAATGT
Found at i:55222021 original size:21 final size:21
Alignment explanation
Indices: 55221992--55222031 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
55221982 AAAATATTAA
*
55221992 ATTTGTTAAACAATAAATGAT
1 ATTTGTTAAACAAGAAATGAT
*
55222013 ATTTTTTAAACAAGAAATG
1 ATTTGTTAAACAAGAAATG
55222032 TTAGCTTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.38
Consensus pattern (21 bp):
ATTTGTTAAACAAGAAATGAT
Found at i:55227725 original size:38 final size:38
Alignment explanation
Indices: 55227643--55227837 Score: 230
Period size: 38 Copynumber: 5.0 Consensus size: 38
55227633 AAACCCAAAC
* * * ***
55227643 ATAACACCAGCACGAAGCCTACGAGACTTTAAACTTAGAT
1 ATAATACCAGCACGAAGCCTGCGGGA-TTT-AACCCGGAT
* *
55227683 ATAATACCAGCACTAGGCCTGCGGGATTTAACCCGGAT
1 ATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGAT
55227721 ATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGAT
1 ATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGAT
*
55227759 ATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGAT
1 ATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGAT
* * *
55227797 ATAATTCCAGCA-TATAGCCTGCGGGTCTTTAAGCCCGGAT
1 ATAATACCAGCACGA-AGCCTGCGGG-ATTTAA-CCCGGAT
55227837 A
1 A
55227838 CACATCAAAT
Statistics
Matches: 137, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
37 1 0.01
38 99 0.72
39 8 0.06
40 29 0.21
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.22
Consensus pattern (38 bp):
ATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGAT
Found at i:55230327 original size:23 final size:23
Alignment explanation
Indices: 55230293--55230340 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
55230283 GGGCTGTCAC
*
55230293 ATTAATAGTGTTATGAAAATTTG
1 ATTAATAGTGTTAAGAAAATTTG
55230316 ATTAAT-GATGTTAAGAAAATTTG
1 ATTAATAG-TGTTAAGAAAATTTG
55230339 AT
1 AT
55230341 GTGTCCCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.42
Consensus pattern (23 bp):
ATTAATAGTGTTAAGAAAATTTG
Found at i:55235251 original size:28 final size:28
Alignment explanation
Indices: 55235220--55235274 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
55235210 TTAATATAAT
* *
55235220 ATTTGGTATTTAAATTTGATTTTTTTTA
1 ATTTGATATTTAAATTTAATTTTTTTTA
*
55235248 ATTTGATGTTTAAATTTAATTTTTTTT
1 ATTTGATATTTAAATTTAATTTTTTTT
55235275 CTTAATTTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.65
Consensus pattern (28 bp):
ATTTGATATTTAAATTTAATTTTTTTTA
Found at i:55241270 original size:10 final size:9
Alignment explanation
Indices: 55241257--55241354 Score: 76
Period size: 10 Copynumber: 10.4 Consensus size: 9
55241247 GACATGTGGC
55241257 AAAAGATTAT
1 AAAA-ATTAT
55241267 AAAAA-T-T
1 AAAAATTAT
*
55241274 AAAAATCAAT
1 AAAAAT-TAT
55241284 AAAAATTAT
1 AAAAATTAT
*
55241293 AAAAAATATT
1 AAAAATTA-T
*
55241303 AAATATTAAT
1 AAAAATT-AT
*
55241313 AAAAATATTT
1 AAAAAT-TAT
55241323 AAAAATTAT
1 AAAAATTAT
55241332 AAAAATCGTA-
1 AAAAAT--TAT
55241342 AAAAATTAT
1 AAAAATTAT
55241351 AAAA
1 AAAA
55241355 TATATAGAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 19
0.72 0.08 0.19
Matches are distributed among these distances:
7 6 0.08
8 3 0.04
9 22 0.31
10 36 0.51
11 4 0.06
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:55241297 original size:19 final size:18
Alignment explanation
Indices: 55241265--55241354 Score: 76
Period size: 19 Copynumber: 4.8 Consensus size: 18
55241255 GCAAAAGATT
55241265 ATAAAAA-T-TAAAAATCA
1 ATAAAAATTATAAAAAT-A
55241282 ATAAAAATTATAAAAAATA
1 ATAAAAATTAT-AAAAATA
* *
55241301 TTAAATATTAATAAAAATA
1 ATAAAAATT-ATAAAAATA
* *
55241320 TTTAAAAATTATAAAAATC
1 -ATAAAAATTATAAAAATA
*
55241339 GTAAAAAATTATAAAA
1 AT-AAAAATTATAAAA
55241355 TATATAGAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
17 7 0.11
18 2 0.03
19 37 0.60
20 16 0.26
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.30
Consensus pattern (18 bp):
ATAAAAATTATAAAAATA
Found at i:55241328 original size:29 final size:29
Alignment explanation
Indices: 55241267--55241359 Score: 93
Period size: 29 Copynumber: 3.2 Consensus size: 29
55241257 AAAAGATTAT
55241267 AAAA-ATTAAAAATCAATAAAAATTATAA
1 AAAATATTAAAAATCAATAAAAATTATAA
* * *
55241295 AAAATATTAAATATTAATAAAAATATTTAA
1 AAAATATTAAAAATCAATAAAAAT-TATAA
* *
55241325 AAATTA-TAAAAATC-GTAAAAAATTATAA
1 AAAATATTAAAAATCAAT-AAAAATTATAA
*
55241353 AATATAT
1 AAAATAT
55241360 AGAAATATAG
Statistics
Matches: 51, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
28 13 0.25
29 29 0.57
30 9 0.18
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.31
Consensus pattern (29 bp):
AAAATATTAAAAATCAATAAAAATTATAA
Found at i:55241384 original size:10 final size:10
Alignment explanation
Indices: 55241282--55241393 Score: 58
Period size: 10 Copynumber: 11.5 Consensus size: 10
55241272 TTAAAAATCA
55241282 ATAAAAA-TT
1 ATAAAAATTT
*
55241291 ATAAAAA-AT
1 ATAAAAATTT
* *
55241300 ATTAAATATTA
1 A-TAAAAATTT
55241311 ATAAAAATATT
1 ATAAAAAT-TT
55241322 -TAAAAA-TT
1 ATAAAAATTT
*
55241330 ATAAAAATCGT
1 ATAAAAAT-TT
55241341 A-AAAAA-TT
1 ATAAAAATTT
*
55241349 AT-AAAATAT
1 ATAAAAATTT
* *
55241358 ATAGAAATAT
1 ATAAAAATTT
*
55241368 AGAAAAAATTT
1 A-TAAAAATTT
*
55241379 ATAAAATTTT
1 ATAAAAATTT
55241389 ATAAA
1 ATAAA
55241394 GTCGTAAGAA
Statistics
Matches: 78, Mismatches: 15, Indels: 19
0.70 0.13 0.17
Matches are distributed among these distances:
8 8 0.10
9 18 0.23
10 41 0.53
11 11 0.14
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (10 bp):
ATAAAAATTT
Found at i:55241663 original size:9 final size:9
Alignment explanation
Indices: 55241649--55241724 Score: 50
Period size: 9 Copynumber: 8.1 Consensus size: 9
55241639 TTTCATAATT
55241649 TTTTTATAA
1 TTTTTATAA
55241658 TTTTTATAAA
1 TTTTTAT-AA
* *
55241668 ATTTTACAA
1 TTTTTATAA
55241677 TTTTTTTATATA
1 --TTTTTATA-A
55241689 TTTTTA-AA
1 TTTTTATAA
*
55241697 TTTTAAT-A
1 TTTTTATAA
55241705 TTTTTA-ATA
1 TTTTTATA-A
55241714 TTTTTACTAA
1 TTTTTA-TAA
55241724 T
1 T
55241725 ATTCAATTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 17
0.69 0.08 0.23
Matches are distributed among these distances:
8 12 0.23
9 17 0.33
10 15 0.29
11 7 0.13
12 1 0.02
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:55241682 original size:21 final size:20
Alignment explanation
Indices: 55241658--55241700 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
55241648 TTTTTTATAA
55241658 TTTTTATAAAATTTTACAATT
1 TTTTTATAAAATTTTA-AATT
* *
55241679 TTTTTATATATTTTTAAATT
1 TTTTTATAAAATTTTAAATT
55241699 TT
1 TT
55241701 AATATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTTATAAAATTTTAAATT
Found at i:55241699 original size:8 final size:9
Alignment explanation
Indices: 55241679--55241719 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
55241669 TTTTACAATT
55241679 TTTTTATATA
1 TTTTTA-ATA
55241689 TTTTTAA-A
1 TTTTTAATA
55241697 -TTTTAATA
1 TTTTTAATA
55241705 TTTTTAATA
1 TTTTTAATA
55241714 TTTTTA
1 TTTTTA
55241720 CTAATATTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 6 0.21
8 2 0.07
9 15 0.52
10 6 0.21
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTTAATA
Found at i:55241707 original size:16 final size:18
Alignment explanation
Indices: 55241680--55241717 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
55241670 TTTACAATTT
55241680 TTTTATATATTTTTAA-A
1 TTTTATATATTTTTAATA
55241697 TTTTA-ATATTTTTAATA
1 TTTTATATATTTTTAATA
55241714 TTTT
1 TTTT
55241718 TACTAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTATATATTTTTAATA
Found at i:55241735 original size:27 final size:25
Alignment explanation
Indices: 55241678--55241736 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 25
55241668 ATTTTACAAT
*
55241678 TTTTTTATATATTTTTAAATTTTAA
1 TTTTTTATATATTTTTAAATTTCAA
55241703 TATTTTTA-ATATTTTTACTAATATTCAA
1 T-TTTTTATATATTTTTA--AAT-TTCAA
55241731 TTTTTT
1 TTTTTT
55241737 TAAACTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
25 10 0.34
26 6 0.21
27 8 0.28
28 5 0.17
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (25 bp):
TTTTTTATATATTTTTAAATTTCAA
Found at i:55241736 original size:28 final size:25
Alignment explanation
Indices: 55241648--55241739 Score: 78
Period size: 28 Copynumber: 3.4 Consensus size: 25
55241638 ATTTCATAAT
55241648 TTTTTTATAAT-TTTTATAAAATTTTACAA
1 TTTTTT-TAATATTTT-T-AAA-TTT-CAA
*
55241677 TTTTTTTATATATTTTTAAATTTTAA
1 TTTTTTTA-ATATTTTTAAATTTCAA
*
55241703 TATTTTTAATATTTTTACTAATATTCAA
1 TTTTTTTAATATTTTTA--AAT-TTCAA
55241731 TTTTTTTAA
1 TTTTTTTAA
55241740 ACTTTTATTA
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
25 9 0.17
26 9 0.17
27 6 0.11
28 17 0.31
29 9 0.17
30 4 0.07
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (25 bp):
TTTTTTTAATATTTTTAAATTTCAA
Found at i:55242017 original size:9 final size:9
Alignment explanation
Indices: 55242003--55242028 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
55241993 TATTTGACCG
55242003 TTTCTCCTC
1 TTTCTCCTC
55242012 TTTCTCCTC
1 TTTCTCCTC
55242021 TTTCTCCT
1 TTTCTCCT
55242029 TCACTCCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (9 bp):
TTTCTCCTC
Found at i:55242625 original size:6 final size:6
Alignment explanation
Indices: 55242611--55242711 Score: 121
Period size: 6 Copynumber: 16.8 Consensus size: 6
55242601 CCGGCTTCGA
* * * *
55242611 CTCCGG CTCCTG CTCGTG CTCCTG CTCCTG CTCCTG CACCTG CACCTG
1 CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG
* * * * *
55242659 CTCCTG CTCCTG CTCCTG CTCCTA CTCGTG CTCCTA CTCCTA CTCCTA
1 CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG
55242707 CTCCT
1 CTCCT
55242712 ACTACCACTT
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 85 1.00
ACGTcount: A:0.06, C:0.49, G:0.15, T:0.31
Consensus pattern (6 bp):
CTCCTG
Found at i:55246039 original size:27 final size:27
Alignment explanation
Indices: 55245982--55246056 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 27
55245972 ACTCATTAAT
*
55245982 ATTATAAATATTATTAACAAGATGTAAAA
1 ATTATAAATATTATT-A-AAGATATAAAA
*
55246011 ATTATAAATGATTATTAAA-ATATACAA
1 ATTATAAAT-ATTATTAAAGATATAAAA
55246038 ATTATAGAATAATTATTAA
1 ATTATA-AAT-ATTATTAA
55246057 TTATTAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 12 0.29
28 13 0.32
29 10 0.24
30 6 0.15
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (27 bp):
ATTATAAATATTATTAAAGATATAAAA
Found at i:55263507 original size:8 final size:8
Alignment explanation
Indices: 55263494--55263521 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
55263484 ATAAATCTCT
55263494 TTTTTTTC
1 TTTTTTTC
55263502 TTTTTTTC
1 TTTTTTTC
55263510 TTTTTTTC
1 TTTTTTTC
55263518 TTTT
1 TTTT
55263522 ACTTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTTC
Found at i:55270287 original size:57 final size:57
Alignment explanation
Indices: 55270199--55270316 Score: 209
Period size: 57 Copynumber: 2.1 Consensus size: 57
55270189 ATATATTATC
* *
55270199 ATTACCAATATATACATACACCCCAAAATGCATGTGGATCGAGTAATAAATAATTTA
1 ATTACCAATATATACATACACACCAAAATGCATGTGGATCGAGCAATAAATAATTTA
*
55270256 ATTACCAATATATACATACACACCAAAATGCATGTGGGTCGAGCAATAAATAATTTA
1 ATTACCAATATATACATACACACCAAAATGCATGTGGATCGAGCAATAAATAATTTA
55270313 ATTA
1 ATTA
55270317 TTTTTAAATA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (57 bp):
ATTACCAATATATACATACACACCAAAATGCATGTGGATCGAGCAATAAATAATTTA
Found at i:55272497 original size:1 final size:1
Alignment explanation
Indices: 55272491--55272522 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
55272481 TGGTTGCGGC
55272491 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
55272523 CTGGACCACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:55278766 original size:29 final size:31
Alignment explanation
Indices: 55278729--55278798 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 31
55278719 AACGATAACG
* *
55278729 TAAGTGACTAAAACGTAA-C-ATTTCAAACA
1 TAAGTGACTAAAACGTAATCAAATGCAAACA
*
55278758 TAAGTGACTAAAATGTAATCAAATGCAAACA
1 TAAGTGACTAAAACGTAATCAAATGCAAACA
*
55278789 AAAGTGACTA
1 TAAGTGACTA
55278799 TTTTTGCACT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 17 0.49
30 1 0.03
31 17 0.49
ACGTcount: A:0.50, C:0.14, G:0.13, T:0.23
Consensus pattern (31 bp):
TAAGTGACTAAAACGTAATCAAATGCAAACA
Found at i:55278794 original size:31 final size:29
Alignment explanation
Indices: 55278730--55278798 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 29
55278720 ACGATAACGT
* * *
55278730 AAGTGACTAAAACGTAACATTTCAAACAT
1 AAGTGACTAAAACGTAACAATGCAAACAA
*
55278759 AAGTGACTAAAATGTAATCAAATGCAAACAA
1 AAGTGACTAAAACGTAA-C-AATGCAAACAA
55278790 AAGTGACTA
1 AAGTGACTA
55278799 TTTTTGCACT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.47
30 1 0.03
31 17 0.50
ACGTcount: A:0.51, C:0.14, G:0.13, T:0.22
Consensus pattern (29 bp):
AAGTGACTAAAACGTAACAATGCAAACAA
Found at i:55279405 original size:16 final size:16
Alignment explanation
Indices: 55279380--55279413 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55279370 TTGAATTTGA
* *
55279380 ATTATTTCAAGTTTAG
1 ATTATGTCAAGCTTAG
55279396 ATTATGTCAAGCTTAG
1 ATTATGTCAAGCTTAG
55279412 AT
1 AT
55279414 CAACTTGTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (16 bp):
ATTATGTCAAGCTTAG
Found at i:55284407 original size:19 final size:20
Alignment explanation
Indices: 55284374--55284423 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 20
55284364 CGAGTAAGGC
*
55284374 TTCTTTTTTACTATTTTTTGCTT
1 TTCTTTTTTA-T-TTTCTTG-TT
55284397 TT-TTTTTTATTTTCTTGTT
1 TTCTTTTTTATTTTCTTGTT
55284416 TTCTTTTT
1 TTCTTTTT
55284424 CAGTATTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.16
20 11 0.44
21 1 0.04
22 7 0.28
23 2 0.08
ACGTcount: A:0.06, C:0.10, G:0.04, T:0.80
Consensus pattern (20 bp):
TTCTTTTTTATTTTCTTGTT
Found at i:55286373 original size:18 final size:19
Alignment explanation
Indices: 55286350--55286386 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
55286340 CAAATTTAAA
*
55286350 AAAAATTA-ATATATTTAT
1 AAAAATTATATAAATTTAT
55286368 AAAAATTATATAAATTTAT
1 AAAAATTATATAAATTTAT
55286387 GTACAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAAATTATATAAATTTAT
Found at i:55292651 original size:13 final size:14
Alignment explanation
Indices: 55292623--55292657 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
55292613 TTTAGGTTGG
55292623 AAAATTTAAAGAAA
1 AAAATTTAAAGAAA
55292637 AAAATTTAAAGAAA
1 AAAATTTAAAGAAA
*
55292651 AACATTT
1 AAAATTT
55292658 TTATGTAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.26
Consensus pattern (14 bp):
AAAATTTAAAGAAA
Found at i:55300002 original size:23 final size:23
Alignment explanation
Indices: 55299972--55300018 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
55299962 CTTTTGTTCA
55299972 TACATAACACTTCTAAAGGAATT
1 TACATAACACTTCTAAAGGAATT
55299995 TACATAACACTTCTAAAGGAATT
1 TACATAACACTTCTAAAGGAATT
55300018 T
1 T
55300019 CAGTAAGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.32
Consensus pattern (23 bp):
TACATAACACTTCTAAAGGAATT
Found at i:55303326 original size:13 final size:14
Alignment explanation
Indices: 55303310--55303342 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
55303300 GCAAAACAAC
55303310 TTAATAAG-CTTAA
1 TTAATAAGACTTAA
55303323 TTAAT-AGACTTAA
1 TTAATAAGACTTAA
55303336 TTAATAA
1 TTAATAA
55303343 ACACATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 15 0.83
14 1 0.06
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (14 bp):
TTAATAAGACTTAA
Found at i:55310082 original size:18 final size:18
Alignment explanation
Indices: 55310038--55310082 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
55310028 TAATGTGCAT
* *
55310038 TTAATCGAATTATTCAAA
1 TTAATCGAACTATCCAAA
*
55310056 TTATTCGAACTATCCAAA
1 TTAATCGAACTATCCAAA
*
55310074 TTAACCGAA
1 TTAATCGAA
55310083 TTAACATGTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (18 bp):
TTAATCGAACTATCCAAA
Found at i:55311487 original size:16 final size:18
Alignment explanation
Indices: 55311455--55311487 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55311445 GTTAATAAAG
55311455 TAAATTTAGTGTTAATTA
1 TAAATTTAGTGTTAATTA
55311473 TAAATTT-GT-TTAATT
1 TAAATTTAGTGTTAATT
55311488 TGTCAAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (18 bp):
TAAATTTAGTGTTAATTA
Found at i:55315976 original size:14 final size:14
Alignment explanation
Indices: 55315957--55315997 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
55315947 TCCTTAGATT
55315957 AAATTATTAAATTA
1 AAATTATTAAATTA
55315971 AAATTATTAAA-T-
1 AAATTATTAAATTA
55315983 AAATTA--AAATTA
1 AAATTATTAAATTA
55315995 AAA
1 AAA
55315998 AATTTAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 3 0.12
11 1 0.04
12 9 0.36
13 1 0.04
14 11 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATTATTAAATTA
Found at i:55315996 original size:15 final size:16
Alignment explanation
Indices: 55315976--55316012 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
55315966 AATTAAAATT
55315976 ATTAAATAAA-TTAA-A
1 ATTAAA-AAATTTAAGA
55315991 ATTAAAAAATTTAAGA
1 ATTAAAAAATTTAAGA
55316007 ATTAAA
1 ATTAAA
55316013 GGGGTCAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 3 0.15
15 10 0.50
16 7 0.35
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
ATTAAAAAATTTAAGA
Found at i:55316000 original size:18 final size:18
Alignment explanation
Indices: 55315964--55316000 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
55315954 ATTAAATTAT
**
55315964 TAAATTAAAATTATTAAA
1 TAAATTAAAATTAAAAAA
55315982 TAAATTAAAATTAAAAAA
1 TAAATTAAAATTAAAAAA
55316000 T
1 T
55316001 TTAAGAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAATTAAAATTAAAAAA
Found at i:55326563 original size:21 final size:19
Alignment explanation
Indices: 55326533--55326585 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
55326523 TTGATATTTT
55326533 TATTTAAAAATATTAAAAA
1 TATTTAAAAATATTAAAAA
55326552 TATTATAGAAAATCA-TAAAAA
1 TATT-TA-AAAAT-ATTAAAAA
*
55326573 TGTTTAAAAATAT
1 TATTTAAAAATAT
55326586 AATGCGTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
18 1 0.03
19 9 0.31
20 4 0.14
21 14 0.48
22 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (19 bp):
TATTTAAAAATATTAAAAA
Found at i:55326697 original size:26 final size:26
Alignment explanation
Indices: 55326621--55326698 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 26
55326611 ATAAATGACA
* * *
55326621 AAAAATTCTATAAATTATAAAATTTATT
1 AAAAATTTTATAAATTACAAAA--AATT
* * * *
55326649 AAAAATTTGAAAAAATACTAAAAATT
1 AAAAATTTTATAAATTACAAAAAATT
55326675 AAAAATTTTATAAATTACAAAAAA
1 AAAAATTTTATAAATTACAAAAAA
55326699 AATATGAAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
26 23 0.59
28 16 0.41
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (26 bp):
AAAAATTTTATAAATTACAAAAAATT
Found at i:55326699 original size:37 final size:36
Alignment explanation
Indices: 55326592--55326728 Score: 125
Period size: 38 Copynumber: 3.7 Consensus size: 36
55326582 ATATAATGCG
* * *
55326592 TAAAAATTAAAAAATTATTATAAATGACAAAAAATTC
1 TAAAAATT-AAAAATTATTAAAAATTACAAAAAATAC
* **
55326629 TATAAATTATAAAATTTATTAAAAATTTGAAAAAATAC
1 TAAAAATTA-AAAA-TTATTAAAAATTACAAAAAATAC
*
55326667 TAAAAATTAAAAATT-TTATAAATTACAAAAAAAATA-
1 TAAAAATTAAAAATTATTAAAAATTAC--AAAAAATAC
*
55326703 TGAAAATTGTAAAAATTATTAAAAAT
1 T-AAAAAT-TAAAAATTATTAAAAAT
55326729 ATTAATGAAA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
35 8 0.10
36 4 0.05
37 28 0.35
38 34 0.42
39 7 0.09
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (36 bp):
TAAAAATTAAAAATTATTAAAAATTACAAAAAATAC
Found at i:55326727 original size:19 final size:18
Alignment explanation
Indices: 55326592--55326733 Score: 65
Period size: 19 Copynumber: 7.6 Consensus size: 18
55326582 ATATAATGCG
*
55326592 TAAAAATTAAAAAATTAT
1 TAAAAATTTAAAAATTAT
* ** *
55326610 TATAAATGACAAAAAATT-C
1 TAAAAAT--TTAAAAATTAT
* *
55326629 TATAAATTATAAAATTTAT
1 TAAAAATT-TAAAAATTAT
* *
55326648 TAAAAATTTGAAAAAATAC
1 TAAAAATTT-AAAAATTAT
55326667 TAAAAA-TTAAAAATT-T
1 TAAAAATTTAAAAATTAT
* * **
55326683 TATAAATTACAAAAAAAAT
1 TAAAAATT-TAAAAATTAT
*
55326702 ATGAAAATTGTAAAAATTAT
1 -TAAAAATT-TAAAAATTAT
55326722 TAAAAATATTAA
1 TAAAAAT-TTAA
55326734 TGAAATTAAC
Statistics
Matches: 90, Mismatches: 24, Indels: 19
0.68 0.18 0.14
Matches are distributed among these distances:
16 5 0.06
17 7 0.08
18 20 0.22
19 36 0.40
20 22 0.24
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (18 bp):
TAAAAATTTAAAAATTAT
Found at i:55326772 original size:18 final size:17
Alignment explanation
Indices: 55326744--55326804 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 17
55326734 TGAAATTAAC
*
55326744 AAAATATTATAAAACACAT
1 AAAA-ATTATAAAA-AAAT
55326763 AAAAATTATAAAAAAAT
1 AAAAATTATAAAAAAAT
*
55326780 AAAATTATATGAAAAAAAT
1 AAAAAT-TAT-AAAAAAAT
55326799 ATAAAA
1 A-AAAA
55326805 CTAACCCTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
17 8 0.22
18 12 0.33
19 13 0.36
20 3 0.08
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.25
Consensus pattern (17 bp):
AAAAATTATAAAAAAAT
Found at i:55326773 original size:9 final size:9
Alignment explanation
Indices: 55326592--55326788 Score: 68
Period size: 9 Copynumber: 21.2 Consensus size: 9
55326582 ATATAATGCG
55326592 TAAAAATTA
1 TAAAAATTA
55326601 -AAAAATTA
1 TAAAAATTA
* *
55326609 TTATAAATGA
1 -TAAAAATTA
* *
55326619 CAAAAAATTC
1 -TAAAAATTA
*
55326629 TATAAATTA
1 TAAAAATTA
*
55326638 TAAAATTTA
1 TAAAAATTA
55326647 TTAAAAATT-
1 -TAAAAATTA
*
55326656 TGAAAAAATA
1 T-AAAAATTA
55326666 CTAAAAA-T-
1 -TAAAAATTA
*
55326674 TAAAAATTT
1 TAAAAATTA
*
55326683 TATAAATTACA
1 TAAAAATT--A
* *
55326694 AAAAAAATA
1 TAAAAATTA
* *
55326703 TGAAAATTG
1 TAAAAATTA
55326712 TAAAAATTA
1 TAAAAATTA
55326721 TTAAAAA-TA
1 -TAAAAATTA
55326730 TTAATGAAATTAA
1 -TAA--AAATT-A
*
55326743 CAAAATATTA
1 TAAAA-ATTA
*
55326753 TAAAACA-CA
1 TAAAA-ATTA
55326762 TAAAAATTA
1 TAAAAATTA
*
55326771 TAAAAA-AA
1 TAAAAATTA
55326779 T-AAAATTA
1 TAAAAATTA
55326787 TA
1 TA
55326789 TGAAAAAAAT
Statistics
Matches: 137, Mismatches: 32, Indels: 38
0.66 0.15 0.18
Matches are distributed among these distances:
7 10 0.07
8 15 0.11
9 59 0.43
10 37 0.27
11 12 0.09
12 3 0.02
13 1 0.01
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.31
Consensus pattern (9 bp):
TAAAAATTA
Found at i:55326785 original size:16 final size:18
Alignment explanation
Indices: 55326744--55326788 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
55326734 TGAAATTAAC
*
55326744 AAAATATTATAAAACACAT
1 AAAA-ATTATAAAACAAAT
55326763 AAAAATTATAAAA-AAAT
1 AAAAATTATAAAACAAAT
55326780 -AAAATTATA
1 AAAAATTATA
55326789 TGAAAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 9 0.36
17 3 0.12
18 9 0.36
19 4 0.16
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAAATTATAAAACAAAT
Found at i:55327080 original size:9 final size:9
Alignment explanation
Indices: 55327066--55327209 Score: 59
Period size: 9 Copynumber: 15.4 Consensus size: 9
55327056 TGTAATTTCC
55327066 ATTTTTATA
1 ATTTTTATA
*
55327075 ATTTTTTTCA
1 ATTTTTAT-A
*
55327085 CATTTCTAT-
1 -ATTTTTATA
55327094 ATTTTTATAA
1 ATTTTTAT-A
55327104 TATTTTTAATA
1 -ATTTTT-ATA
*
55327115 ATATTCTAT-
1 AT-TTTTATA
55327124 ATTTTTA-A
1 ATTTTTATA
55327132 ATATATTCT-TA
1 AT-T-TT-TATA
55327143 A--TTTATA
1 ATTTTTATA
*
55327150 ATTTTTATT
1 ATTTTTATA
* *
55327159 ATGTTCATA
1 ATTTTTATA
*
55327168 ATTTATATA
1 ATTTTTATA
55327177 ATTTTTA-A
1 ATTTTTATA
*
55327185 ACTTTTTTTA
1 A-TTTTTATA
55327195 ATATTTTAATA
1 AT-TTTT-ATA
55327206 ATTT
1 ATTT
55327210 CTGATTTTTA
Statistics
Matches: 100, Mismatches: 16, Indels: 37
0.65 0.10 0.24
Matches are distributed among these distances:
6 1 0.01
7 5 0.05
8 15 0.15
9 39 0.39
10 15 0.15
11 23 0.23
12 2 0.02
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (9 bp):
ATTTTTATA
Found at i:55327097 original size:19 final size:19
Alignment explanation
Indices: 55327061--55327099 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
55327051 ACTTTTGTAA
*
55327061 TTTCCATTTTTATAATTTT
1 TTTCCATTTCTATAATTTT
55327080 TTTCACATTTCTAT-ATTTT
1 TTTC-CATTTCTATAATTTT
55327099 T
1 T
55327100 ATAATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.21, C:0.13, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTCCATTTCTATAATTTT
Found at i:55327102 original size:28 final size:30
Alignment explanation
Indices: 55327066--55327144 Score: 92
Period size: 28 Copynumber: 2.7 Consensus size: 30
55327056 TGTAATTTCC
* * *
55327066 ATTTTTATAATTTTTTTCA-CAT-TTCTAT
1 ATTTTTATAATATTTTTAATAATATTCTAT
55327094 ATTTTTATAATATTTTTAATAATATTCTAT
1 ATTTTTATAATATTTTTAATAATATTCTAT
55327124 ATTTTTA-AATATATTCTTAAT
1 ATTTTTATAATAT-TT-TTAAT
55327145 TTATAATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
28 17 0.39
29 7 0.16
30 15 0.34
31 5 0.11
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (30 bp):
ATTTTTATAATATTTTTAATAATATTCTAT
Found at i:55327146 original size:19 final size:19
Alignment explanation
Indices: 55327103--55327140 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
55327093 TATTTTTATA
55327103 ATATTTTTAATAATATTCT
1 ATATTTTTAATAATATTCT
55327122 ATATTTTTAA-ATATATTCT
1 ATATTTTTAATA-ATATTCT
55327141 TAATTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 1 0.06
19 17 0.94
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (19 bp):
ATATTTTTAATAATATTCT
Found at i:55327154 original size:25 final size:25
Alignment explanation
Indices: 55327121--55327174 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
55327111 AATAATATTC
* *
55327121 TATATTTTTAAATATATTCTTAATT
1 TATAATTTTAAATATATTCATAATT
* * *
55327146 TATAATTTTTATTATGTTCATAATT
1 TATAATTTTAAATATATTCATAATT
55327171 TATA
1 TATA
55327175 TAATTTTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (25 bp):
TATAATTTTAAATATATTCATAATT
Found at i:55327220 original size:17 final size:16
Alignment explanation
Indices: 55327198--55327243 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
55327188 TTTTTTAATA
55327198 TTTTAA-TAATTTCTGAT
1 TTTTAATTAATTT-T-AT
55327215 TTTTAATTAATTTTAT
1 TTTTAATTAATTTTAT
55327231 TTTT-ATT-ATTTTA
1 TTTTAATTAATTTTA
55327244 ATAATTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 6 0.21
15 3 0.11
16 6 0.21
17 7 0.25
18 6 0.21
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (16 bp):
TTTTAATTAATTTTAT
Found at i:55328117 original size:15 final size:15
Alignment explanation
Indices: 55328086--55328116 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
55328076 TATTAATTAA
55328086 TTAATTAAAATAATT
1 TTAATTAAAATAATT
55328101 TTAATT-AAATAATT
1 TTAATTAAAATAATT
55328115 TT
1 TT
55328117 TCTCAACTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTAATTAAAATAATT
Found at i:55333585 original size:6 final size:6
Alignment explanation
Indices: 55333574--55333601 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
55333564 AGATTGTTTG
55333574 TTTCTT TTTCTT TTTCTT TTTCTT TTTC
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTC
55333602 ACACCTCACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTCTT
Found at i:55344690 original size:3 final size:3
Alignment explanation
Indices: 55344682--55344714 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
55344672 AGTCACAATT
55344682 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
55344715 GGGGTAGACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:55348476 original size:13 final size:14
Alignment explanation
Indices: 55348460--55348488 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
55348450 TTTTGAACAA
55348460 TTTATTT-TTTATT
1 TTTATTTCTTTATT
55348473 TTTATTTCTTTATT
1 TTTATTTCTTTATT
55348487 TT
1 TT
55348489 CCTTTTCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTATTTCTTTATT
Found at i:55353884 original size:19 final size:18
Alignment explanation
Indices: 55353843--55353886 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
55353833 CGGTTAATTA
* *
55353843 ATTAA-TTTTAATTGATT
1 ATTAATTTTTAATTAATG
55353860 ATTAATTTTTAATTTAATG
1 ATTAATTTTTAA-TTAATG
55353879 ATTAATTT
1 ATTAATTT
55353887 ATATTATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 6 0.26
19 12 0.52
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (18 bp):
ATTAATTTTTAATTAATG
Found at i:55354518 original size:29 final size:30
Alignment explanation
Indices: 55354486--55354556 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
55354476 AAATAAAAAA
*
55354486 TTCATGTATAAAATTGCACA-AAATCAAAG
1 TTCATGTATAAAATTGCACATAAACCAAAG
* * *
55354515 TTCATATATATAATTGCACATTAAACCATAG
1 TTCATGTATAAAATTGCACA-TAAACCAAAG
55354546 TTCATGTATAA
1 TTCATGTATAA
55354557 TCTTGGGATT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 18 0.53
31 16 0.47
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (30 bp):
TTCATGTATAAAATTGCACATAAACCAAAG
Found at i:55362150 original size:30 final size:30
Alignment explanation
Indices: 55362116--55362174 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
55362106 TATAAAACTT
*
55362116 ATTTTCTTATTATTTTAAAGGCATTTGTTA
1 ATTTTCTTATTATTTTAAAGACATTTGTTA
* *
55362146 ATTTTTTTATTATTTTAGAGACATTTGTT
1 ATTTTCTTATTATTTTAAAGACATTTGTT
55362175 TGTTAAGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.25, C:0.05, G:0.10, T:0.59
Consensus pattern (30 bp):
ATTTTCTTATTATTTTAAAGACATTTGTTA
Found at i:55370685 original size:19 final size:19
Alignment explanation
Indices: 55370647--55370686 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
55370637 TCATTATAAT
* * *
55370647 ATCTTATTCGAGATAGCAA
1 ATCTTATTCCACATAACAA
55370666 ATCTTATTCCACATAACAA
1 ATCTTATTCCACATAACAA
55370685 AT
1 AT
55370687 TTTTCATGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (19 bp):
ATCTTATTCCACATAACAA
Found at i:55371518 original size:39 final size:39
Alignment explanation
Indices: 55371464--55371546 Score: 121
Period size: 39 Copynumber: 2.1 Consensus size: 39
55371454 GAGATTGACG
* *
55371464 GGTGGACCGATGGTGACTACCTGACTGGTGAACAATGAT
1 GGTGGACCGATGGTGACTACCTGACTGATGAACAACGAT
* * *
55371503 GGTGGACCGGTGGTGACTGCCTGACTGATGAACGACGAT
1 GGTGGACCGATGGTGACTACCTGACTGATGAACAACGAT
55371542 GGTGG
1 GGTGG
55371547 TGGCTGGTGG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.22, C:0.18, G:0.39, T:0.22
Consensus pattern (39 bp):
GGTGGACCGATGGTGACTACCTGACTGATGAACAACGAT
Found at i:55372396 original size:29 final size:30
Alignment explanation
Indices: 55372340--55372407 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 30
55372330 AATTTGTGAG
* *
55372340 AATTAGATCAAATCATAATTTCATGTATAA
1 AATTATATAAAATCATAATTTCATGTATAA
*
55372370 AATTATATAAAATCA-AATTTTATGTATAA
1 AATTATATAAAATCATAATTTCATGTATAA
*
55372399 AATTGTATA
1 AATTATATA
55372408 TTTGAACAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 21 0.62
30 13 0.38
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (30 bp):
AATTATATAAAATCATAATTTCATGTATAA
Found at i:55372732 original size:13 final size:13
Alignment explanation
Indices: 55372714--55372739 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55372704 TTTTTTTCAA
55372714 ATTATATATATAT
1 ATTATATATATAT
55372727 ATTATATATATAT
1 ATTATATATATAT
55372740 TTCTCATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTATATATATAT
Found at i:55376905 original size:19 final size:19
Alignment explanation
Indices: 55376883--55376919 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
55376873 GAGGATAGAT
* *
55376883 TTGAGAGAAAATAATAATA
1 TTGAAAGAAAAAAATAATA
55376902 TTGAAAGAAAAAAATAAT
1 TTGAAAGAAAAAAATAAT
55376920 TTTACTAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.14, T:0.24
Consensus pattern (19 bp):
TTGAAAGAAAAAAATAATA
Found at i:55383401 original size:20 final size:21
Alignment explanation
Indices: 55383378--55383431 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 21
55383368 TTTTTTTCTT
55383378 ATTTTTATTAAAATTTAAT-A
1 ATTTTTATTAAAATTTAATAA
*
55383398 ATTTTTA-T-AAATTTATTAA
1 ATTTTTATTAAAATTTAATAA
*
55383417 ATTTTT-TTATAATTT
1 ATTTTTATTAAAATTT
55383432 TTTTTGTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 8 0.28
19 9 0.31
20 12 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTTTTATTAAAATTTAATAA
Found at i:55383421 original size:58 final size:58
Alignment explanation
Indices: 55383302--55383411 Score: 134
Period size: 58 Copynumber: 1.9 Consensus size: 58
55383292 TTTTTTATGC
* * * *
55383302 ATTTTATAA-TTTTTTATTATTTTTATAAAAATTCACAATTTTTTTTACATTTTCATG
1 ATTTTATAATTTTTTTATTATTTTTATAAAAATTCACAAATTTTTATAAATTTTCATA
* * *
55383359 ATTTTATAATTTTTTTCTTATTTTTATTAAAATTTA-ATAATTTTTATAAATTT
1 ATTTTATAATTTTTTTATTATTTTTATAAAAATTCACA-AATTTTTATAAATTT
55383412 ATTAAATTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
57 10 0.22
58 35 0.78
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.62
Consensus pattern (58 bp):
ATTTTATAATTTTTTTATTATTTTTATAAAAATTCACAAATTTTTATAAATTTTCATA
Found at i:55383655 original size:12 final size:12
Alignment explanation
Indices: 55383626--55383654 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
55383616 TTTGAAGACC
55383626 TTTTTTATGCAT
1 TTTTTTATGCAT
55383638 TTTTTTATGC-T
1 TTTTTTATGCAT
55383649 TTTTTT
1 TTTTTT
55383655 TTTTAAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.10, C:0.07, G:0.07, T:0.76
Consensus pattern (12 bp):
TTTTTTATGCAT
Found at i:55383804 original size:14 final size:14
Alignment explanation
Indices: 55383787--55383813 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
55383777 AAAAAATTAT
55383787 AAATAAATATTAAG
1 AAATAAATATTAAG
55383801 AAATAAATATTAA
1 AAATAAATATTAA
55383814 CCCACAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (14 bp):
AAATAAATATTAAG
Found at i:55389655 original size:7 final size:6
Alignment explanation
Indices: 55389614--55389651 Score: 58
Period size: 6 Copynumber: 6.0 Consensus size: 6
55389604 TTCAATTTTC
55389614 AGAAAA TAGAAAA AGAAAA AGAAAA AGAAAA TAGAAAA
1 AGAAAA -AGAAAA AGAAAA AGAAAA AGAAAA -AGAAAA
55389652 TAGAGATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 18 0.60
7 12 0.40
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (6 bp):
AGAAAA
Found at i:55401248 original size:29 final size:30
Alignment explanation
Indices: 55401208--55401282 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 30
55401198 AGTAAATTAA
55401208 TTTAATAA-AAAATTAATA-AG-AACTTAAAT
1 TTTAA-AATAAAATTAATATAGAAAC-TAAAT
*
55401237 TTTAAAATAAAA-AAATATAGAAACTAAAT
1 TTTAAAATAAAATTAATATAGAAACTAAAT
55401266 TTCTAAAAGTAAAATTA
1 TT-TAAAA-TAAAATTA
55401283 TTAATGATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
28 6 0.16
29 18 0.47
30 8 0.21
31 5 0.13
32 1 0.03
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (30 bp):
TTTAAAATAAAATTAATATAGAAACTAAAT
Found at i:55407717 original size:14 final size:14
Alignment explanation
Indices: 55407698--55407729 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
55407688 AGGTCATTTA
55407698 GCCCAACCAAACTG
1 GCCCAACCAAACTG
55407712 GCCCAACCAAACTG
1 GCCCAACCAAACTG
55407726 GCCC
1 GCCC
55407730 GGTGATTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.47, G:0.16, T:0.06
Consensus pattern (14 bp):
GCCCAACCAAACTG
Found at i:55408548 original size:3 final size:3
Alignment explanation
Indices: 55408535--55408566 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
55408525 CAAACAAGTA
*
55408535 AAT ATT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
55408567 AAGTTACAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:55408661 original size:3 final size:3
Alignment explanation
Indices: 55408643--55408677 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
55408633 CTAACAAGTA
* *
55408643 AAT ATT AAT TAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
55408678 AAGTTACAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:55408718 original size:111 final size:111
Alignment explanation
Indices: 55408527--55408856 Score: 630
Period size: 111 Copynumber: 3.0 Consensus size: 111
55408517 TGGCATGCCA
55408527 AACAAGTAAATATT-A--ATAATAATAATAATAATAATAATAAAAGTTACAACTCAGCCCTAGCT
1 AACAAGTAAATATTAATTATAATAATAATAATAATAATAATAAAAGTTACAACTCAGCCCTAGCT
*
55408589 TCCCATCTTAATCACTCTATTTAAAAGTCAAATCCCACGATTCTCT
66 TCCCATCTTAATCACTCTATTTAAGAGTCAAATCCCACGATTCTCT
55408635 AACAAGTAAATATTAATTATAATAATAATAATAATAATAATAAAAGTTACAACTCAGCCCTAGCT
1 AACAAGTAAATATTAATTATAATAATAATAATAATAATAATAAAAGTTACAACTCAGCCCTAGCT
55408700 TCCCATCTTAATCACTCTATTTAAGAGTCAAATCCCACGATTCTCT
66 TCCCATCTTAATCACTCTATTTAAGAGTCAAATCCCACGATTCTCT
55408746 AACAAGTAAATATTAATTATAATAATAATAATAATAATAATAAAAGTTACAACTCAGCCCTAGCT
1 AACAAGTAAATATTAATTATAATAATAATAATAATAATAATAAAAGTTACAACTCAGCCCTAGCT
55408811 TCCCATCTTAATCACTCTATTTAAGAGTCAAATCCCACGATTCTCT
66 TCCCATCTTAATCACTCTATTTAAGAGTCAAATCCCACGATTCTCT
55408857 TTCTAAGCCA
Statistics
Matches: 218, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
108 14 0.06
109 1 0.00
111 203 0.93
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.31
Consensus pattern (111 bp):
AACAAGTAAATATTAATTATAATAATAATAATAATAATAATAAAAGTTACAACTCAGCCCTAGCT
TCCCATCTTAATCACTCTATTTAAGAGTCAAATCCCACGATTCTCT
Found at i:55408772 original size:3 final size:3
Alignment explanation
Indices: 55408754--55408788 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
55408744 CTAACAAGTA
* *
55408754 AAT ATT AAT TAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
55408789 AAGTTACAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:55409174 original size:12 final size:10
Alignment explanation
Indices: 55409146--55409202 Score: 62
Period size: 10 Copynumber: 5.5 Consensus size: 10
55409136 AATAATATTT
55409146 ATTTTTATAA
1 ATTTTTATAA
55409156 ATTTTTATAA
1 ATTTTTATAA
*
55409166 ATTTTTTTATA
1 ATTTTTATA-A
*
55409177 ATTTATTGT-A
1 ATTT-TTATAA
55409187 ATTTTTATAA
1 ATTTTTATAA
55409197 CATTTT
1 -ATTTT
55409203 ATATTTCTCG
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
9 3 0.08
10 24 0.60
11 10 0.25
12 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (10 bp):
ATTTTTATAA
Found at i:55409192 original size:22 final size:22
Alignment explanation
Indices: 55409142--55409192 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
55409132 ATATAATAAT
55409142 ATTTATTTTTATAAATTTTTATA
1 ATTT-TTTTTATAAATTTTTATA
* *
55409165 AATTTTTTTAT-AATTTATTGTA
1 ATTTTTTTTATAAATTT-TTATA
55409187 ATTTTT
1 ATTTTT
55409193 ATAACATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 5 0.21
22 16 0.67
23 3 0.12
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
ATTTTTTTTATAAATTTTTATA
Found at i:55414926 original size:22 final size:23
Alignment explanation
Indices: 55414875--55414933 Score: 93
Period size: 23 Copynumber: 2.5 Consensus size: 23
55414865 ATATTAAAAT
55414875 GAAAAAATTATATTTTTACCATC
1 GAAAAAATTATATTTTTACCATC
55414898 GAAAAAATTATATTTTTACCATC
1 GAAAAAATTATATTTTTACCATC
55414921 -ATAAAAATATATA
1 GA-AAAAAT-TATA
55414934 ATTTAACTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
22 1 0.03
23 29 0.85
24 4 0.12
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.37
Consensus pattern (23 bp):
GAAAAAATTATATTTTTACCATC
Found at i:55421037 original size:12 final size:12
Alignment explanation
Indices: 55421020--55421055 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
55421010 AAAAACCCGC
55421020 CCTGCCCCTGCT
1 CCTGCCCCTGCT
55421032 CCTGCCCCTGCT
1 CCTGCCCCTGCT
*
55421044 CCTGCTCCTGCT
1 CCTGCCCCTGCT
55421056 ACAACATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.00, C:0.56, G:0.17, T:0.28
Consensus pattern (12 bp):
CCTGCCCCTGCT
Found at i:55421042 original size:18 final size:18
Alignment explanation
Indices: 55421019--55421054 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
55421009 AAAAAACCCG
55421019 CCCTGCCCCTGCTCCTGC
1 CCCTGCCCCTGCTCCTGC
*
55421037 CCCTGCTCCTGCTCCTGC
1 CCCTGCCCCTGCTCCTGC
55421055 TACAACATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.58, G:0.17, T:0.25
Consensus pattern (18 bp):
CCCTGCCCCTGCTCCTGC
Done.