Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 71 of 89
Found at i:16968919 original size:42 final size:41
Alignment explanation
Indices: 16968862--16968952 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 41
16968852 TAAGTCATTT
*
16968862 GGGCCATC-AGTAAGTCTTTCGAGCATGATGATTAAATCCTTC
1 GGGCCATCTA-TAAGTCTTTCGAGCAAGATGA-TAAATCCTTC
* *
16968904 GGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTC
1 GGGCCATCTATAAGTCTTTCGAGCAAGATGATAAATCCTTC
16968945 GGGCCATC
1 GGGCCATC
16968953 CAAAAGACCT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
41 16 0.36
42 27 0.61
43 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (41 bp):
GGGCCATCTATAAGTCTTTCGAGCAAGATGATAAATCCTTC
Found at i:16969324 original size:15 final size:16
Alignment explanation
Indices: 16969298--16969327 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
16969288 AAACCAGTGC
16969298 CCAAACCCAACCAGAT
1 CCAAACCCAACCAGAT
16969314 CCAAA-CCAACCAGA
1 CCAAACCCAACCAGA
16969328 ACCCAGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.43, G:0.07, T:0.03
Consensus pattern (16 bp):
CCAAACCCAACCAGAT
Found at i:16973435 original size:24 final size:20
Alignment explanation
Indices: 16973380--16973454 Score: 64
Period size: 24 Copynumber: 3.6 Consensus size: 20
16973370 CCCCTTGAAC
*
16973380 TGCATCGATGCATTCTACAG
1 TGCATCGATGCATCCTACAG
*
16973400 TGTATCGATGCATCCCTTAACATG
1 TGCATCGATGCAT-CC-T-ACA-G
*
16973424 TGCATCGATGCACTCCT-TA-
1 TGCATCGATGCA-TCCTACAG
16973443 TGCATCGATGCA
1 TGCATCGATGCA
16973455 CTTCCTGTGC
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
19 12 0.26
20 12 0.26
21 2 0.04
22 1 0.02
23 4 0.09
24 14 0.30
25 1 0.02
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.31
Consensus pattern (20 bp):
TGCATCGATGCATCCTACAG
Found at i:16973448 original size:19 final size:19
Alignment explanation
Indices: 16973424--16973470 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
16973414 CCTTAACATG
16973424 TGCATCGATGCAC-TCCTTA
1 TGCATCGATGCACTTCC-TA
*
16973443 TGCATCGATGCACTTCCTG
1 TGCATCGATGCACTTCCTA
16973462 TGCATCGAT
1 TGCATCGAT
16973471 ATACACTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 23 0.88
20 3 0.12
ACGTcount: A:0.19, C:0.30, G:0.19, T:0.32
Consensus pattern (19 bp):
TGCATCGATGCACTTCCTA
Found at i:16977606 original size:20 final size:23
Alignment explanation
Indices: 16977581--16977638 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 23
16977571 TTCCCCTTGA
*
16977581 AGTGCATCGATGCAT-TC-T-AC
1 AGTGCATCGATGCATCCCTTAAC
16977601 AGTGCATCGATGCATCCCTTAAC
1 AGTGCATCGATGCATCCCTTAAC
16977624 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
16977639 CTAATTGCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 15 0.45
21 1 0.03
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (23 bp):
AGTGCATCGATGCATCCCTTAAC
Found at i:16979992 original size:481 final size:483
Alignment explanation
Indices: 16979033--16980000 Score: 1559
Period size: 481 Copynumber: 2.0 Consensus size: 483
16979023 TTATAATGAC
16979033 TGTTATGATAATATGATGCATGTATATATATATAATGTACATTACACATATATACTTATACTTTA
1 TGTTATGATAATATGATGCATG---ATATATATAATGTACATTACACATATATACTTATACTTTA
* *
16979098 TAGTTTACATATGTATATAAAGTTCCAAATTGAACAAACATGAAATTGGAAATAAAAAAAATTGA
63 TAGTCTACATATGTATATAAAGTACCAAATTGAACAAACATGAAATTGGAAAT-AAAAAAATTGA
16979163 ATAAATTAAGCAATACACAATGATGAGGGATGAAATTGAATTAATTATAAAATGTGAAGCTAAAA
127 ATAAATTAAGCAATACACAATGATGAGGGATGAAATTGAATTAATTATAAAATGTGAAGCTAAAA
* *
16979228 TTATTATAAAAATGGATTAAATTGCATACATTTAAAAAGTTGGTGAACATAATTTGAAAATAAAT
192 TTAATATAAAAATGGACTAAATTGCATACATTTAAAAAGTTGGTGAACATAATTTGAAAATAAAT
* * *
16979293 TTATTATATGATTTACATTTTTATAGGGTTTGTTTTAAGTAAATTACAAAAATATAAATAAGTAT
257 TTATTATATGATTTACAATTTTATAGGGTTTGTTTTAAGTAAATTACAAAAAAATAAATAAATAT
* *
16979358 GGGTCAATTTCAGATACGAATATAATTTGAAGGACAAAATTGAACAAATATGAAATTAAAATTTA
322 GGGTCAATTTCAGATACGAATATAATTTGAAGGACAAAATTGAACAAATATAAAATTAAAATTAA
*
16979423 AAATTTAAATACAATAAACAATATAAAAGGATCAAATCAAAAAAATGTAAAATGTGAGGAAAATT
387 AAATTTAAATACAATAAACAACATAAAAGGATCAAATCAAAAAAATGTAAAATGTGAGGAAAATT
16979488 TCTAAAATGGATTGAAATGCATTAATTTCAAA
452 TCTAAAATGGATTGAAATGCATTAATTTCAAA
* *
16979520 TGTTATGATAATATGATGCATG-TATATATAATGTATATTATACATATATACTTATACTTTATAG
1 TGTTATGATAATATGATGCATGATATATATAATGTACATTACACATATATACTTATACTTTATAG
* *
16979584 TCTATATATGTATATAAAGTACCAAATTGAACAAACATTAAATTGGAAAT-AAAAAATTGAATAA
66 TCTACATATGTATATAAAGTACCAAATTGAACAAACATGAAATTGGAAATAAAAAAATTGAATAA
* ** * * *
16979648 ATTAAGCGATATGCATTGATGAGGTATGAAATTGAATTAATTATAAAATGTGAAGCTAATATTAA
131 ATTAAGCAATACACAATGATGAGGGATGAAATTGAATTAATTATAAAATGTGAAGCTAAAATTAA
* *
16979713 TATAAAAAATGGACTAAATTGCATATATTTATAAAGTTGGTGAACATAATTTGAAAATAAATTTA
196 TAT-AAAAATGGACTAAATTGCATACATTTAAAAAGTTGGTGAACATAATTTGAAAATAAATTTA
*
16979778 TTATGTGATTTACAATTTTATAGGGTTTGTTTTAAGTAAATTACAAAAAAATAAATAAATATGGG
260 TTATATGATTTACAATTTTATAGGGTTTGTTTTAAGTAAATTACAAAAAAATAAATAAATATGGG
* * * *
16979843 TCAATTTCAGATACGATTATAATTTGAAGGACTAAATTGGACAATTA-AAAATTACAAA-TAAAA
325 TCAATTTCAGATACGAATATAATTTGAAGGACAAAATTGAACAAATATAAAATTA-AAATTAAAA
16979906 ATTTAAATACAATAAACAACATAAAAGGATCAAATCAAAAAAATGTAAAGA-GTGAGGAAAATTT
389 ATTTAAATACAATAAACAACATAAAAGGATCAAATCAAAAAAATGTAAA-ATGTGAGGAAAATTT
* * * *
16979970 GTGAAATTGATTGAATTGCATTAATTTCAAA
453 CTAAAATGGATTGAAATGCATTAATTTCAAA
16980001 AGTTGGGGGA
Statistics
Matches: 447, Mismatches: 31, Indels: 12
0.91 0.06 0.02
Matches are distributed among these distances:
481 173 0.39
482 166 0.37
483 86 0.19
487 22 0.05
ACGTcount: A:0.47, C:0.06, G:0.13, T:0.34
Consensus pattern (483 bp):
TGTTATGATAATATGATGCATGATATATATAATGTACATTACACATATATACTTATACTTTATAG
TCTACATATGTATATAAAGTACCAAATTGAACAAACATGAAATTGGAAATAAAAAAATTGAATAA
ATTAAGCAATACACAATGATGAGGGATGAAATTGAATTAATTATAAAATGTGAAGCTAAAATTAA
TATAAAAATGGACTAAATTGCATACATTTAAAAAGTTGGTGAACATAATTTGAAAATAAATTTAT
TATATGATTTACAATTTTATAGGGTTTGTTTTAAGTAAATTACAAAAAAATAAATAAATATGGGT
CAATTTCAGATACGAATATAATTTGAAGGACAAAATTGAACAAATATAAAATTAAAATTAAAAAT
TTAAATACAATAAACAACATAAAAGGATCAAATCAAAAAAATGTAAAATGTGAGGAAAATTTCTA
AAATGGATTGAAATGCATTAATTTCAAA
Found at i:16980090 original size:15 final size:16
Alignment explanation
Indices: 16980037--16980096 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 16
16980027 AATATATATA
*
16980037 TATATATGTATGTATG
1 TATATATGAATGTATG
16980053 TATA-ATGAATGTTATG
1 TATATATGAATG-TATG
*
16980069 -ATAATATG-ATGCATG
1 TAT-ATATGAATGTATG
16980084 TATATAT-AATGTA
1 TATATATGAATGTA
16980097 CATTATACTT
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
15 19 0.53
16 14 0.39
17 3 0.08
ACGTcount: A:0.38, C:0.02, G:0.17, T:0.43
Consensus pattern (16 bp):
TATATATGAATGTATG
Found at i:16980141 original size:14 final size:14
Alignment explanation
Indices: 16980111--16980155 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
16980101 ATACTTTATA
*
16980111 TATATATATATAC-
1 TATATACATATACT
16980124 -ATATACATATACT
1 TATATACATATACT
*
16980137 TATATACTTATACT
1 TATATACATATACT
16980151 T-TATA
1 TATATA
16980156 GTTTATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 11 0.39
13 4 0.14
14 13 0.46
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (14 bp):
TATATACATATACT
Found at i:16980790 original size:2 final size:2
Alignment explanation
Indices: 16980592--16980779 Score: 103
Period size: 2 Copynumber: 97.0 Consensus size: 2
16980582 TTAAAACAAT
*
16980592 TA TA -A TA TA TA TA TA TA TA TA TA TA T- TA -A TA TA -A AA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
16980629 TA TA TA CA TA TA -A GTA TA TA AA TA TA TG TA CA CT- TA TT TA AA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * *
16980671 TA TA CA TA TA TA -A AA AA GTA TA -A GTA 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 TA
* * * * *
16980713 AA GTG CA AA CTA TA -A AA TA TA -A 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 TA
16980755 TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
16980780 AGGTATATAT
Statistics
Matches: 144, Mismatches: 24, Indels: 36
0.71 0.12 0.18
Matches are distributed among these distances:
1 12 0.08
2 128 0.89
3 4 0.03
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (2 bp):
TA
Found at i:16980801 original size:16 final size:16
Alignment explanation
Indices: 16980699--16980802 Score: 61
Period size: 16 Copynumber: 6.2 Consensus size: 16
16980689 TATAAGTATA
16980699 TATATATATATATAAAG
1 TATATATA-ATATAAAG
* *
16980716 TGCAAACTATAAAATATAA-
1 T--ATA-TATAATATA-AAG
*
16980735 TATATATATATATATA-
1 TATATATA-ATATAAAG
*
16980751 TATATATATATATATA-
1 TATATATA-ATATAAAG
*
16980767 TATATATAATATAAGG
1 TATATATAATATAAAG
* *
16980783 TATATATACTTTAAAG
1 TATATATAATATAAAG
16980799 TATA
1 TATA
16980803 AAGTGTGTAT
Statistics
Matches: 71, Mismatches: 10, Indels: 13
0.76 0.11 0.14
Matches are distributed among these distances:
15 5 0.07
16 46 0.65
17 7 0.10
19 7 0.10
20 6 0.08
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (16 bp):
TATATATAATATAAAG
Found at i:16981216 original size:64 final size:65
Alignment explanation
Indices: 16981140--16981273 Score: 175
Period size: 65 Copynumber: 2.1 Consensus size: 65
16981130 CACACCCATT
* *
16981140 TCGAATGCATTTTATTCACTGATGCACAA-CCATGCATCGATGCACTCAGGAT-TTTATTGAAAC
1 TCGAATGCATTTTATGCACTGATGCACAAGCCATGCATCGATGCACCCAGGATATTT-TTGAAAC
16981203 A
65 A
* * * *
16981204 TCGAATTG-ATTTTGTGCACTGATGCACAAGTCATGCATCGATGCACCCCGGCTATTTTTGAAAC
1 TCGAA-TGCATTTTATGCACTGATGCACAAGCCATGCATCGATGCACCCAGGATATTTTTGAAAC
16981268 A
65 A
16981269 TCGAA
1 TCGAA
16981274 GTAAATTTGT
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
64 24 0.39
65 34 0.56
66 3 0.05
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (65 bp):
TCGAATGCATTTTATGCACTGATGCACAAGCCATGCATCGATGCACCCAGGATATTTTTGAAACA
Found at i:16981269 original size:65 final size:64
Alignment explanation
Indices: 16981156--16981315 Score: 187
Period size: 65 Copynumber: 2.5 Consensus size: 64
16981146 GCATTTTATT
* * * *
16981156 CACTGATGCACAACCATGCATCGATGCACTCAGGATTTTATTGAAACATCGAATTGATTTTGTG
1 CACTGATGCACAACCATGCATCGATGCACCCAGGATTTTATTGAAACATCGAAGTAAATTTGTG
* * *
16981220 CACTGATGCACAAGTCATGCATCGATGCACCCCGGCTATTT-TTGAAACATCGAAGTAAATTTGT
1 CACTGATGCACAA-CCATGCATCGATGCACCCAGGAT-TTTATTGAAACATCGAAGTAAATTTGT
16981284 G
64 G
* * *
16981285 CACCGATGCACACCCTAGTGCACCGATGCAC
1 CACTGATGCACAACC-A-TGCATCGATGCAC
16981316 TAAGTCTTCC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
64 14 0.17
65 52 0.64
66 15 0.19
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (64 bp):
CACTGATGCACAACCATGCATCGATGCACCCAGGATTTTATTGAAACATCGAAGTAAATTTGTG
Found at i:16986912 original size:23 final size:22
Alignment explanation
Indices: 16986882--16986958 Score: 68
Period size: 23 Copynumber: 3.5 Consensus size: 22
16986872 ACACTAGTTA
16986882 GTGCATCGATGCATCCCTTGAAT
1 GTGCATCGATGCAT-CCTTGAAT
* * * *
16986905 GTGCATCGATTCA-CCATAAAG
1 GTGCATCGATGCATCCTTGAAT
*
16986926 GTACA-CTGATGCATGCCTTGAAT
1 GTGCATC-GATGCAT-CCTTGAAT
16986949 GTGCATCGAT
1 GTGCATCGAT
16986959 ACACCAGTCG
Statistics
Matches: 40, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
20 1 0.03
21 14 0.35
23 24 0.60
24 1 0.03
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:16989249 original size:25 final size:25
Alignment explanation
Indices: 16989215--16989264 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
16989205 AAAAGGGGAG
16989215 AAGTATTATAGTAAGGGGGAGTAAT
1 AAGTATTATAGTAAGGGGGAGTAAT
16989240 AAGTATTATAGTAAGGGGGAGTAAT
1 AAGTATTATAGTAAGGGGGAGTAAT
16989265 TTCAAAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.32, T:0.28
Consensus pattern (25 bp):
AAGTATTATAGTAAGGGGGAGTAAT
Found at i:16990484 original size:2 final size:2
Alignment explanation
Indices: 16990477--16990640 Score: 76
Period size: 2 Copynumber: 81.5 Consensus size: 2
16990467 TTAACTCAAC
* *
16990477 AT AT AT AT AT AT AT AT ACT AT AA AGT AT AT AT ACT TT AT ACT A-
1 AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT A-T AT AT A-T AT
* * *
16990520 AA ACT TT AT AT AT AT -T AT AT ACT TT AT AT -T AT AT AT AT AT AT
1 AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
* * * * *
16990562 AT AT AT AT AT AA AGT -T TT AGT AA AA AT -T AT AT AT AC AT AT AT
1 AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
*
16990604 A- AT A- AT AT AA AGT AT AT AT -T AT AT ACT -T AT AT AT AT A
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT A
16990641 CACTTATACT
Statistics
Matches: 125, Mismatches: 18, Indels: 38
0.69 0.10 0.21
Matches are distributed among these distances:
1 9 0.07
2 105 0.84
3 11 0.09
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:16990561 original size:31 final size:32
Alignment explanation
Indices: 16990478--16990572 Score: 104
Period size: 31 Copynumber: 2.9 Consensus size: 32
16990468 TAACTCAACA
*
16990478 TATATATATATATATACTATAAAGTATATATACTT
1 TATAT-TATATATATA-TATATA-TATATATACTT
* * *
16990513 TATACTA-AAACTTTATATATAT-TATATACTT
1 TATATTATATA-TATATATATATATATATACTT
16990544 TATATTATATATATATATATATATATATA
1 TATATTATATATATATATATATATATATA
16990573 AAGTTTTAGT
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
31 25 0.50
32 9 0.18
33 7 0.14
34 5 0.10
35 4 0.08
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.48
Consensus pattern (32 bp):
TATATTATATATATATATATATATATATACTT
Found at i:16990636 original size:17 final size:17
Alignment explanation
Indices: 16990616--16990673 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
16990606 TAATATAAAG
16990616 TATATAT-TATATACTT
1 TATATATATATATACTT
*
16990632 ATATATATACACTTATACTT
1 -TATATATATA--TATACTT
* *
16990652 TATATCTATATTTACTT
1 TATATATATATATACTT
16990669 TATAT
1 TATAT
16990674 TTTATACTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 18 0.53
18 1 0.03
19 8 0.24
20 7 0.21
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATATATATACTT
Found at i:16990645 original size:14 final size:15
Alignment explanation
Indices: 16990616--16990648 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
16990606 TAATATAAAG
*
16990616 TATATATTATATACT
1 TATATATTATACACT
16990631 TATATA-TATACACT
1 TATATATTATACACT
16990645 TATA
1 TATA
16990649 CTTTATATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (15 bp):
TATATATTATACACT
Found at i:16990880 original size:45 final size:45
Alignment explanation
Indices: 16990827--16990914 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
16990817 AACATATATG
*
16990827 TATACATATGTCAGAAAACAGTATAAAACTTAAACATATCAAACA
1 TATACATATGTCAGAAAACAGTATAAAACATAAACATATCAAACA
* *
16990872 TATACATATGTCAGAAAACTGTATAAAACATATACATATCAAA
1 TATACATATGTCAGAAAACAGTATAAAACATAAACATATCAAA
16990915 ATACCACAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.52, C:0.15, G:0.07, T:0.26
Consensus pattern (45 bp):
TATACATATGTCAGAAAACAGTATAAAACATAAACATATCAAACA
Found at i:16991350 original size:39 final size:40
Alignment explanation
Indices: 16991287--16991444 Score: 200
Period size: 39 Copynumber: 4.0 Consensus size: 40
16991277 ACCTGTACAC
* *
16991287 CCAGTAA-AGACTTACCCTGTGCACAAAGCAGAGGAGCCTG
1 CCAGTAAGA-ACTTACCCTGAGCACAAAGCCGAGGAGCCTG
16991327 CCA-TAAGAACTTACCCTGAGCACAAAGCCGAGGAGCCTG
1 CCAGTAAGAACTTACCCTGAGCACAAAGCCGAGGAGCCTG
* *
16991366 -CAGTAAGGAA-TTACCATGAGCACAAAGCCGAGGAACCT-
1 CCAGTAA-GAACTTACCCTGAGCACAAAGCCGAGGAGCCTG
* * *
16991404 ACAGTAAGGACTTACCCTGAGCACAAAGCCGAGAAGCCTG
1 CCAGTAAGAACTTACCCTGAGCACAAAGCCGAGGAGCCTG
16991444 C
1 C
16991445 GAAAAACGGT
Statistics
Matches: 103, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
38 4 0.04
39 92 0.89
40 7 0.07
ACGTcount: A:0.35, C:0.28, G:0.24, T:0.13
Consensus pattern (40 bp):
CCAGTAAGAACTTACCCTGAGCACAAAGCCGAGGAGCCTG
Found at i:16997264 original size:39 final size:39
Alignment explanation
Indices: 16997210--16997362 Score: 225
Period size: 39 Copynumber: 3.9 Consensus size: 39
16997200 TTGTACACCC
* *
16997210 AGTAAGGACTTACCCTGTGCACAAAGCAGAGGAGCCTAT
1 AGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTAT
* *
16997249 AGTAAGGACTTACCCTGAGCACAAATCCGAGGAGCCTGT
1 AGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTAT
* *
16997288 AGTAAGGACTTACCCGGAGCACAAAGCTGAGGAGCCTAT
1 AGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTAT
* * *
16997327 AGTAAGGACTTAACCTAAGTACAAAGCCGAGGAGCC
1 AGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCC
16997363 CACAGAATGT
Statistics
Matches: 101, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 101 1.00
ACGTcount: A:0.34, C:0.24, G:0.26, T:0.16
Consensus pattern (39 bp):
AGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTAT
Found at i:16998973 original size:7 final size:7
Alignment explanation
Indices: 16998963--16999004 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
16998953 ATAAATTATA
16998963 TAAGTAT
1 TAAGTAT
16998970 TAAGTA-
1 TAAGTAT
16998976 TAAGTAT
1 TAAGTAT
16998983 ATAAGTAT
1 -TAAGTAT
*
16998991 TAAATAT
1 TAAGTAT
*
16998998 AAAGTAT
1 TAAGTAT
16999005 ATAACTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
6 6 0.20
7 17 0.57
8 7 0.23
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (7 bp):
TAAGTAT
Found at i:16998979 original size:13 final size:13
Alignment explanation
Indices: 16998961--16999005 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
16998951 ATATAAATTA
16998961 TATAAGTATTAAG
1 TATAAGTATTAAG
16998974 TATAAGTATATAAG
1 TATAAGTAT-TAAG
* *
16998988 TATTAAATATAAAG
1 TA-TAAGTATTAAG
16999002 TATA
1 TATA
16999006 TAACTATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 11 0.39
14 11 0.39
15 6 0.21
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (13 bp):
TATAAGTATTAAG
Found at i:16998984 original size:21 final size:22
Alignment explanation
Indices: 16998950--16999092 Score: 102
Period size: 22 Copynumber: 6.6 Consensus size: 22
16998940 GGTATATAAT
*
16998950 AATATAAATTATATAAGTATTA
1 AATATAAAGTATATAAGTATTA
*
16998972 AGTAT-AAGTATATAAGTATTA
1 AATATAAAGTATATAAGTATTA
*
16998993 AATATAAAGTATATAACTA-TA
1 AATATAAAGTATATAAGTATTA
* *
16999014 TATATAAACTATA-AAGTATATA
1 AATATAAAGTATATAAGTAT-TA
* *
16999036 TATATATA-TATATATA-TATATA
1 AATATAAAGTATATA-AGTAT-TA
* * *
16999058 TATATATA-TATATAAAGT-TTT
1 AATATAAAGTATAT-AAGTATTA
*
16999079 AGTATAAAGTATAT
1 AATATAAAGTATAT
16999093 GTACATATAT
Statistics
Matches: 101, Mismatches: 12, Indels: 16
0.78 0.09 0.12
Matches are distributed among these distances:
20 4 0.04
21 42 0.42
22 52 0.51
23 3 0.03
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.41
Consensus pattern (22 bp):
AATATAAAGTATATAAGTATTA
Found at i:16998987 original size:8 final size:8
Alignment explanation
Indices: 16998933--16999035 Score: 73
Period size: 8 Copynumber: 13.9 Consensus size: 8
16998923 AGTATAAAGT
*
16998933 GTATATAG
1 GTATATAA
16998941 GTATATAA
1 GTATATAA
16998949 -TAATATAAA
1 GT-ATAT-AA
*
16998958 TTATATAA
1 GTATATAA
16998966 GTAT-TAA
1 GTATATAA
16998973 G--TATAA
1 GTATATAA
16998979 GTATATAA
1 GTATATAA
16998987 GTAT-TAA
1 GTATATAA
*
16998994 ATATA-AA
1 GTATATAA
16999001 GTATATAA
1 GTATATAA
*
16999009 CTATAT-A
1 GTATATAA
16999016 -TATA-AA
1 GTATATAA
*
16999022 CTATA-AA
1 GTATATAA
16999029 GTATATA
1 GTATATA
16999036 TATATATATA
Statistics
Matches: 78, Mismatches: 6, Indels: 22
0.74 0.06 0.21
Matches are distributed among these distances:
5 1 0.01
6 9 0.12
7 28 0.36
8 33 0.42
9 6 0.08
10 1 0.01
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (8 bp):
GTATATAA
Found at i:16999008 original size:30 final size:29
Alignment explanation
Indices: 16998974--16999184 Score: 96
Period size: 28 Copynumber: 7.4 Consensus size: 29
16998964 AAGTATTAAG
16998974 TATAAGTATATAAGTATTAAATATAAAGTA
1 TATAAGTATATAA-TATTAAATATAAAGTA
*
16999004 TATAACTATAT-ATA-TAAACTATAAAGTA
1 TATAAGTATATAATATTAAA-TATAAAGTA
* *
16999032 TAT-A-TATATATATATATATATATATA-TA
1 TATAAGTATATA-ATAT-TAAATATAAAGTA
* *
16999060 TATATA-TATATAA-AGTTTTAGTATAAAGTA
1 TATA-AGTATATAATA--TTAAATATAAAGTA
16999090 TAT--GTACATATATATAATT-AATATAAAG--
1 TATAAGT--ATATA-AT-ATTAAATATAAAGTA
* *
16999118 TATAAGTATA-AGTA-T-ATTATAAA-TA
1 TATAAGTATATAATATTAAATATAAAGTA
* * **
16999143 TATAAAGTATA-ATTATAAAAACTAAAGTA
1 TAT-AAGTATATAATATTAAATATAAAGTA
16999172 TATAAGTATATAA
1 TATAAGTATATAA
16999185 ACTATATATA
Statistics
Matches: 140, Mismatches: 16, Indels: 51
0.68 0.08 0.25
Matches are distributed among these distances:
24 8 0.06
25 4 0.03
26 16 0.11
27 6 0.04
28 42 0.30
29 19 0.14
30 41 0.29
31 3 0.02
33 1 0.01
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (29 bp):
TATAAGTATATAATATTAAATATAAAGTA
Found at i:16999013 original size:28 final size:28
Alignment explanation
Indices: 16998991--16999073 Score: 97
Period size: 26 Copynumber: 3.1 Consensus size: 28
16998981 ATATAAGTAT
16998991 TAAA-TATAAAGTATATAACTATATATA
1 TAAACTATAAAGTATATAACTATATATA
16999018 TAAACTATAAAGTATAT-A-TATATATA
1 TAAACTATAAAGTATATAACTATATATA
* *
16999044 TATA-TATATA-TATATATA-TATATATA
1 TAAACTATAAAGTATATA-ACTATATATA
16999070 TAAA
1 TAAA
16999074 GTTTTAGTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
24 5 0.10
25 5 0.10
26 23 0.46
27 5 0.10
28 12 0.24
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (28 bp):
TAAACTATAAAGTATATAACTATATATA
Found at i:16999015 original size:2 final size:2
Alignment explanation
Indices: 16999010--16999071 Score: 88
Period size: 2 Copynumber: 30.0 Consensus size: 2
16999000 AGTATATAAC
* *
16999010 TA TA TA TA TA AA CTA TA AA GTA 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 TA
16999054 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
16999072 AAGTTTTAGT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
2 52 0.96
3 2 0.04
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:16999159 original size:26 final size:23
Alignment explanation
Indices: 16999012--16999159 Score: 72
Period size: 26 Copynumber: 6.2 Consensus size: 23
16999002 TATATAACTA
*
16999012 TATATATAAACTATAAAGTATATAT
1 TATATATAAAATAT-AAGTATA-AT
*
16999037 ATATATATATATATATATA-TATATAT
1 -TATATATA-AAATATA-AGTATA-AT
* * * *
16999063 ATATATATAAAGTTTTAGTATAAAG
1 -TATATATAAAATATAAGTAT-AAT
* *
16999088 TATATGT-ACATAT-A-TATAAT
1 TATATATAAAATATAAGTATAAT
* *
16999108 TA-ATATAAAGTATAAGTATAAG
1 TATATATAAAATATAAGTATAAT
16999130 TATATTATAAATATATAAAGTATAAT
1 TATA-TATAAA-ATAT-AAGTATAAT
16999156 TATA
1 TATA
16999160 AAAACTAAAG
Statistics
Matches: 93, Mismatches: 18, Indels: 22
0.70 0.14 0.17
Matches are distributed among these distances:
19 3 0.03
20 8 0.09
21 4 0.04
22 8 0.09
23 4 0.04
24 13 0.14
25 10 0.11
26 38 0.41
27 5 0.05
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.42
Consensus pattern (23 bp):
TATATATAAAATATAAGTATAAT
Found at i:17002827 original size:22 final size:24
Alignment explanation
Indices: 17002766--17002893 Score: 80
Period size: 22 Copynumber: 5.6 Consensus size: 24
17002756 GTGTGACATA
*
17002766 TTATATAC-TTATATACTTT-TGT
1 TTATATACATTATATACTTTATAT
17002788 CTT-TATA-A-T-TATACTTTATAT
1 -TTATATACATTATATACTTTATAT
*
17002809 TTA-ATAC-TTATATAATTTATATT
1 TTATATACATTATATACTTTATA-T
*
17002832 ATTATATTCATATATATACTTTATAT
1 -TTATATACAT-TATATACTTTATAT
* * *
17002858 TTA-ATA-TTTATATATTTTACA-
1 TTATATACATTATATACTTTATAT
*
17002879 TTATATACTTTATAT
1 TTATATACATTATAT
17002894 TATATGCTTA
Statistics
Matches: 84, Mismatches: 8, Indels: 26
0.71 0.07 0.22
Matches are distributed among these distances:
20 13 0.15
21 7 0.08
22 28 0.33
23 11 0.13
24 5 0.06
25 6 0.07
26 2 0.02
27 12 0.14
ACGTcount: A:0.35, C:0.07, G:0.01, T:0.57
Consensus pattern (24 bp):
TTATATACATTATATACTTTATAT
Found at i:17002833 original size:27 final size:26
Alignment explanation
Indices: 17002791--17002872 Score: 71
Period size: 27 Copynumber: 3.0 Consensus size: 26
17002781 CTTTTGTCTT
17002791 TATAA-TTATACTTTATATTTAATACTTA
1 TATAATTTATA-TTTATATTTAATA--TA
*
17002819 TATAATTTATA-TTATTATATTCATATA
1 TATAATTTATATTTA-TAT-TTAATATA
*
17002846 TATACTTTATATTTAATATTT-ATATA
1 TATAATTTATATTT-ATATTTAATATA
17002872 T
1 T
17002873 TTTACATTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
26 6 0.13
27 17 0.36
28 13 0.28
29 11 0.23
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (26 bp):
TATAATTTATATTTATATTTAATATA
Found at i:17002852 original size:49 final size:48
Alignment explanation
Indices: 17002797--17002955 Score: 166
Period size: 49 Copynumber: 3.3 Consensus size: 48
17002787 TCTTTATAAT
17002797 TATACTTTATATTTAATACTTATATAATTTATATTATTATATTCATATA
1 TATACTTTATATTTAATACTTATATAATTTATATTATTATATT-ATATA
* * *
17002846 TATACTTTATATTTAATATTTATATATTTTACATTA-TATACTTTATATTA
1 TATACTTTATATTTAATACTTATATAATTTATATTATTATA--TTATA-TA
* * *
17002896 TATGCTTATATACTTTAGT-CTT-TATAA-TTATACT-TTATATATATATA
1 TATACTT-TATA-TTTAATACTTATATAATTTATATTATTATAT-TATATA
17002943 TATACTTTATATT
1 TATACTTTATATT
17002956 ATTATTATTA
Statistics
Matches: 93, Mismatches: 10, Indels: 18
0.77 0.08 0.15
Matches are distributed among these distances:
45 2 0.02
46 4 0.04
47 9 0.10
48 8 0.09
49 45 0.48
50 14 0.15
51 6 0.06
52 5 0.05
ACGTcount: A:0.36, C:0.07, G:0.01, T:0.56
Consensus pattern (48 bp):
TATACTTTATATTTAATACTTATATAATTTATATTATTATATTATATA
Found at i:17002884 original size:14 final size:14
Alignment explanation
Indices: 17002865--17002898 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
17002855 TATTTAATAT
*
17002865 TTATATATTTTACA
1 TTATATACTTTACA
*
17002879 TTATATACTTTATA
1 TTATATACTTTACA
17002893 TTATAT
1 TTATAT
17002899 GCTTATATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATATACTTTACA
Found at i:17002905 original size:36 final size:36
Alignment explanation
Indices: 17002844--17002912 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
17002834 TATATTCATA
*
17002844 TATATACTTTATATTTAATATTTATATATTTTACAT
1 TATATACTTTATATTTAATATTTATATACTTTACAT
17002880 TATATACTTTATA-TT-ATATGCTTATATACTTTA
1 TATATACTTTATATTTAATAT--TTATATACTTTA
17002913 GTCTTTATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 4 0.13
35 2 0.07
36 24 0.80
ACGTcount: A:0.35, C:0.07, G:0.01, T:0.57
Consensus pattern (36 bp):
TATATACTTTATATTTAATATTTATATACTTTACAT
Found at i:17002907 original size:22 final size:20
Alignment explanation
Indices: 17002841--17002957 Score: 95
Period size: 19 Copynumber: 6.0 Consensus size: 20
17002831 TATTATATTC
17002841 ATATATATACTTTATATT-T
1 ATATATATACTTTATATTAT
* * * *
17002860 A-ATATTTA-TATATTTTAC
1 ATATATATACTTTATATTAT
17002878 AT-TATATACTTTATATTAT
1 ATATATATACTTTATATTAT
* *
17002897 ATGCTTATATACTTTAGTCTT-T
1 AT--ATATATACTTTA-TATTAT
17002919 ATA-ATTATACTTTATA-TAT
1 ATATA-TATACTTTATATTAT
17002938 ATATATATACTTTATATTAT
1 ATATATATACTTTATATTAT
17002958 TATTATTATA
Statistics
Matches: 76, Mismatches: 11, Indels: 21
0.70 0.10 0.19
Matches are distributed among these distances:
17 6 0.08
18 13 0.17
19 27 0.36
20 13 0.17
22 14 0.18
23 3 0.04
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.56
Consensus pattern (20 bp):
ATATATATACTTTATATTAT
Found at i:17004786 original size:2 final size:2
Alignment explanation
Indices: 17004779--17005131 Score: 96
Period size: 2 Copynumber: 176.0 Consensus size: 2
17004769 ACTAAAACTT
* * *
17004779 TA TA TA TA TA TA TA TA TA T- TA TA GTT TA TA TA TA CA GTG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA
* * * *
17004822 GTT TA TA TA TA GTT TA TA T- TA -A TA AA CTA TA TA -A TT TA TA
1 -TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * *
17004862 CA CA -A TA TA TA TA GTT TA TA TA TA GTA TA TA -A TA -A TA TA AA
1 TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * *
17004903 TA TA AA CTA TA TA GTT TA TA TA CA TA GTT TA TA TA TA TA -A TA
1 TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * * *
17004945 TA TA TA T- TT TA TA TA TA CA T- TA TA TA GTT TA TA TA TA GTG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA
* * ** *
17004987 TA T- TA -A TA AA CTA TA TA GTT TA TA CG TA -A TA TA TA TA GTT
1 TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA
* * * * *
17005027 TA TA TA TA TA GTT TT TT TA TA TA TA -A TA TA TA TG T- TT TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
17005068 TA TA AA CTA TA -A TT TA TA CA TA -A TA TA TA TA GT- TCA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA T-A TA TA
*
17005108 TA GTA TA CA TA TA TA TA TA T- TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA
17005132 ATTGTTTCAG
Statistics
Matches: 256, Mismatches: 56, Indels: 78
0.66 0.14 0.20
Matches are distributed among these distances:
1 19 0.07
2 216 0.84
3 21 0.08
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (2 bp):
TA
Found at i:17005138 original size:75 final size:77
Alignment explanation
Indices: 17004825--17005131 Score: 207
Period size: 75 Copynumber: 4.1 Consensus size: 77
17004815 GTGTATAGTT
* *
17004825 TATATATAG-TTTATATTAATAAACTATATAATTTATACACAATATATATAGTT--TATATATAG
1 TATATAT-GTTTTATA-T-ATAAACTATATAGTTTATACATAATATATATAGTTCATATATATAG
*
17004887 TATATA-ATAATATAA
63 TACATATAT-ATATAA
*** * * * * *
17004902 -ATATAAACTATATAGTTTATA-TACATAGTTTATATATATAATATATATA-TT--T-TATATA-
1 TATATATGTTTTATA-TATAAACTATATAG-TT-TATACATAATATATATAGTTCATATATATAG
*
17004960 TACAT-TATATAGT-T
63 TACATATATATA-TAA
* * *
17004974 TATATATAG-TGTATATTAATAAACTATATAGTTTATACGTAATATATATAGTTTATATATATAG
1 TATATAT-GTTTTATA-T-ATAAACTATATAGTTTATACATAATATATATAGTTCATATATATAG
*** *
17005038 TTTTTTTATATATAA
63 TACATATATATATAA
17005053 TATATATGTTTTATATATAAACTATA-A-TTTATACATAATATATATAGTTCATATATAGTA-TA
1 TATATATGTTTTATATATAAACTATATAGTTTATACATAATATATATAGTTCATATATA-TAGTA
*
17005115 CATATATATATAT
65 CATATATATATAA
17005128 TATA
1 TATA
17005132 ATTGTTTCAG
Statistics
Matches: 179, Mismatches: 33, Indels: 38
0.72 0.13 0.15
Matches are distributed among these distances:
72 3 0.02
73 33 0.18
74 18 0.10
75 56 0.31
76 30 0.17
77 16 0.09
78 5 0.03
79 18 0.10
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (77 bp):
TATATATGTTTTATATATAAACTATATAGTTTATACATAATATATATAGTTCATATATATAGTAC
ATATATATATAA
Found at i:17006209 original size:27 final size:27
Alignment explanation
Indices: 17006173--17006230 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
17006163 CTCTAATGGA
* *
17006173 GAAAATAGTCAAGAGAGATGTTAGTTG
1 GAAAATAGTCAAGAGAAATATTAGTTG
17006200 GAAAATAGTCAAGAGAAATATTAGTTG
1 GAAAATAGTCAAGAGAAATATTAGTTG
17006227 GAAA
1 GAAA
17006231 TTAAAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.47, C:0.03, G:0.26, T:0.24
Consensus pattern (27 bp):
GAAAATAGTCAAGAGAAATATTAGTTG
Found at i:17008708 original size:40 final size:40
Alignment explanation
Indices: 17008646--17008725 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
17008636 ACATAAATGT
* * * *
17008646 AAATGTGTAACAATATTTAAGGCATTATGACCACTTTACC
1 AAATGAGTAACAATAATCAAGGCATTACGACCACTTTACC
* *
17008686 AAATGAGTATCAATAATCAAGGCATTACGATCACTTTACC
1 AAATGAGTAACAATAATCAAGGCATTACGACCACTTTACC
17008726 TAATATTTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (40 bp):
AAATGAGTAACAATAATCAAGGCATTACGACCACTTTACC
Found at i:17010500 original size:19 final size:20
Alignment explanation
Indices: 17010476--17010521 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
17010466 CAAAATAATC
17010476 CAATTTC-ACATTCTAACAT
1 CAATTTCAACATTCTAACAT
17010495 CAATTTCAACATTCTAACAT
1 CAATTTCAACATTCTAACAT
*
17010515 TAATTTC
1 CAATTTC
17010522 TAGCATAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.37, C:0.24, G:0.00, T:0.39
Consensus pattern (20 bp):
CAATTTCAACATTCTAACAT
Found at i:17023498 original size:17 final size:17
Alignment explanation
Indices: 17023476--17023510 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
17023466 ATGTAAAATC
17023476 AAATTAAGATTTAATAT
1 AAATTAAGATTTAATAT
**
17023493 AAATTATTATTTAATAT
1 AAATTAAGATTTAATAT
17023510 A
1 A
17023511 TATATTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
AAATTAAGATTTAATAT
Found at i:17023579 original size:25 final size:23
Alignment explanation
Indices: 17023530--17023594 Score: 67
Period size: 25 Copynumber: 2.7 Consensus size: 23
17023520 ATGACTATAT
**
17023530 AATAATAATAAAAATAATATTTA
1 AATAATAATAAAAATAATACATA
*
17023553 AATATATAAGTAAAATTAATACATA
1 AATA-ATAA-TAAAAATAATACATA
*
17023578 AATAAACAATAAAAATA
1 AAT-AATAATAAAAATA
17023595 TGATTAGAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
23 4 0.12
24 11 0.32
25 18 0.53
26 1 0.03
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (23 bp):
AATAATAATAAAAATAATACATA
Found at i:17024896 original size:3 final size:3
Alignment explanation
Indices: 17024879--17024927 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
17024869 TAATTTTTAT
*
17024879 TAA TGA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
17024923 TAA TA
1 TAA TA
17024928 TTTAAATGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 4 0.10
3 35 0.85
4 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:17025207 original size:40 final size:39
Alignment explanation
Indices: 17025162--17025262 Score: 175
Period size: 39 Copynumber: 2.6 Consensus size: 39
17025152 AGGGTTGAAC
17025162 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAAT
1 AAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAAAT
* *
17025202 GAGTTCTTCTCATTATGAATTTCTTCTTCCTCTTCAAAT
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAAAT
17025241 AAGTTCTTCTCATTATGAACTT
1 AAGTTCTTCTCATTATGAACTT
17025263 TCTGGAAAAG
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
39 29 0.51
40 28 0.49
ACGTcount: A:0.23, C:0.23, G:0.07, T:0.48
Consensus pattern (39 bp):
AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAAAT
Found at i:17025265 original size:40 final size:41
Alignment explanation
Indices: 17025162--17025265 Score: 178
Period size: 40 Copynumber: 2.6 Consensus size: 41
17025152 AGGGTTGAAC
17025162 AAGTTCTTCTCATTATGAAC-TTCTTCTTCCTTCTTCAAAT
1 AAGTTCTTCTCATTATGAACTTTCTTCTTCCTTCTTCAAAT
*
17025202 GAGTTCTTCTCATTATGAA-TTTCTTCTTCC-TCTTCAAAT
1 AAGTTCTTCTCATTATGAACTTTCTTCTTCCTTCTTCAAAT
17025241 AAGTTCTTCTCATTATGAACTTTCT
1 AAGTTCTTCTCATTATGAACTTTCT
17025266 GGAAAAGTTG
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
39 27 0.45
40 33 0.55
ACGTcount: A:0.22, C:0.23, G:0.07, T:0.48
Consensus pattern (41 bp):
AAGTTCTTCTCATTATGAACTTTCTTCTTCCTTCTTCAAAT
Found at i:17025645 original size:113 final size:111
Alignment explanation
Indices: 17025205--17026075 Score: 1163
Period size: 113 Copynumber: 7.8 Consensus size: 111
17025195 TTCAAATGAG
* * *
17025205 TTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAAATAAGTTCTTCTCATTATGAACTTTCTGGA
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTGGA
*
17025269 AAAGTTGATCCATCGAGTGATGAATTCAAACAAAAAGTTGAACAAA
66 AAAGTTGATCCATCGAGTGATGAATTCAAACAAAAGGTTGAACAAA
* * *
17025315 TTCTTCTCATTATGAATTTCTTCTTTC-TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTGGA
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTGGA
* *
17025379 AAAGTTGATCAATCGAGTGATGAATTCAAACAAAAAGTTGAACAAA
66 AAAGTTGATCCATCGAGTGATGAATTCAAACAAAAGGTTGAACAAA
* * * *
17025425 TACTTCTCATTATGAATTTCTTATTCC-TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTGGA
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTGGA
*
17025489 AAAGTTGATCCATCGAGTGATGAATTCAAACAAAAAGTTGAACAAA
66 AAAGTTGATCCATCGAGTGATGAATTCAAACAAAAGGTTGAACAAA
*
17025535 TTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-T-CCTG
* * * *
17025600 GCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAA
64 GAAAAGTTGATCCATCGAGTGATGAATTCAAACAAAAGGTTGAACAAA
*
17025648 TTCTTCTTATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTC-CTG
* * * * ** * *
17025713 GAAATGTTGATCCATCAAGTAATGGATTTGAGCAAAAGGTTGAACAAG
64 GAAAAGTTGATCCATCGAGTGATGAATTCAAACAAAAGGTTGAACAAA
** * **
17025761 CACTTCTCATTATGAACTTCTTCTTATTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-T-CCTG
* * * *
17025826 GTAATGATGATCCATCGAATGATGAATTCAAACAAAAGGTTGAACAAA
64 GAAAAGTTGATCCATCGAGTGATGAATTCAAACAAAAGGTTGAACAAA
*
17025874 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTATCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TC-CTG
* * * * ** * *
17025939 GAAATGTTGATCCATCAAGTAATGGATTTGAGCAAAAGGTTGAACAAG
64 GAAAAGTTGATCCATCGAGTGATGAATTCAAACAAAAGGTTGAACAAA
* * * *
17025987 CTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTC-CTG
* *
17026052 GAAAAGTTGATCCATTGAATGATG
64 GAAAAGTTGATCCATCGAGTGATG
17026076 GATTTGAACT
Statistics
Matches: 686, Mismatches: 66, Indels: 15
0.89 0.09 0.02
Matches are distributed among these distances:
110 237 0.35
111 29 0.04
112 4 0.01
113 413 0.60
114 3 0.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.38
Consensus pattern (111 bp):
TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTGGA
AAAGTTGATCCATCGAGTGATGAATTCAAACAAAAGGTTGAACAAA
Found at i:17026562 original size:22 final size:22
Alignment explanation
Indices: 17026483--17026559 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
17026473 GATAAAGTTT
17026483 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
17026505 TCATCTTTAAAAAGAGAATTTA
1 TCATCTTTGAAAAGAGAATCTA
*
17026527 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
17026549 TTATCTTTGAA
1 TCATCTTTGAA
17026560 GAGTGTAGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:17028624 original size:3 final size:3
Alignment explanation
Indices: 17028616--17028662 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
17028606 ATTAATTATT
*
17028616 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA -AA CAA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
17028660 TAA
1 TAA
17028663 ATAAAACAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 8 0.20
3 32 0.80
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:17028639 original size:13 final size:13
Alignment explanation
Indices: 17028603--17028666 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
17028593 TGTATGAAAA
*
17028603 ATAAT-TAATTAT
1 ATAATATAATAAT
*
17028615 TTAATAATAATAAT
1 ATAAT-ATAATAAT
17028629 ATAATATAATAAT
1 ATAATATAATAAT
* * *
17028642 AAAACAAAATAAT
1 ATAATATAATAAT
17028655 AATAATA-AATAA
1 -ATAATATAATAA
17028667 AACAAATGAA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
12 4 0.10
13 23 0.56
14 14 0.34
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (13 bp):
ATAATATAATAAT
Found at i:17028639 original size:16 final size:15
Alignment explanation
Indices: 17028618--17028665 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
17028608 TAATTATTTA
17028618 ATAATAATAATATAAT
1 ATAATAATAATA-AAT
* *
17028634 ATAATAATAAAACAAA
1 ATAATAATAATA-AAT
17028650 ATAATAATAATAAAT
1 ATAATAATAATAAAT
17028665 A
1 A
17028666 AAACAAATGA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 3 0.11
16 24 0.89
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (15 bp):
ATAATAATAATAAAT
Found at i:17029053 original size:54 final size:53
Alignment explanation
Indices: 17028971--17029126 Score: 258
Period size: 54 Copynumber: 2.9 Consensus size: 53
17028961 ATAATCACTG
17028971 GTTCGTAAAACGTTTGACAACACATTCATCATTTCATGTGGTTTCTGCTCAGAT
1 GTTCGTAAAACGTTTGACAACACATTCATCATTTC-TGTGGTTTCTGCTCAGAT
*
17029025 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGTTTCTGCTCAGAT
1 GTTCGTAAAACGTTTGACAACACATTCATCATTT-CTGTGGTTTCTGCTCAGAT
* *
17029079 GTTCGTAAAGCGTTTGACAACACATTCATCCTTTTCTGTGGTTTCTGC
1 GTTCGTAAAACGTTTGACAACACATTCAT-CATTTCTGTGGTTTCTGC
17029127 CAAAATTTCT
Statistics
Matches: 96, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
54 91 0.95
55 5 0.05
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.38
Consensus pattern (53 bp):
GTTCGTAAAACGTTTGACAACACATTCATCATTTCTGTGGTTTCTGCTCAGAT
Found at i:17031384 original size:114 final size:114
Alignment explanation
Indices: 17031184--17031403 Score: 377
Period size: 114 Copynumber: 1.9 Consensus size: 114
17031174 AATCATGTAG
* ** *
17031184 TTCATCTTTCAAATCCAATGATTGGTTATGGGGTTCCTACTGAACCAGATCAGATAACTCACAGA
1 TTCATCTTTCAAATCCAATGATTGGTTATGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
17031249 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
* *
17031298 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTATGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
17031363 ACACTTCCAGAAGATGCTATTGGGTCTCTTTATTTCTACTA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
17031404 CGAGAACATG
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 99 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTATGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:17037505 original size:13 final size:13
Alignment explanation
Indices: 17037487--17037544 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
17037477 TTAATTCTTG
17037487 AATAAAATAAATA
1 AATAAAATAAATA
17037500 AATAAAATAAA-A
1 AATAAAATAAATA
*
17037512 AATAATAATATATA
1 AATAA-AATAAATA
*
17037526 AA-AATAATAAGT-
1 AATAA-AATAAATA
17037538 AATAAAA
1 AATAAAA
17037545 AATTTGAAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
12 10 0.26
13 26 0.67
14 3 0.08
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (13 bp):
AATAAAATAAATA
Found at i:17037516 original size:16 final size:15
Alignment explanation
Indices: 17037487--17037547 Score: 63
Period size: 16 Copynumber: 4.0 Consensus size: 15
17037477 TTAATTCTTG
*
17037487 AATAAAAT-AAATA-
1 AATAAAATAAAAAAT
17037500 AATAAAATAAAAAAT
1 AATAAAATAAAAAAT
*
17037515 AATAATATATAAAAAT
1 AATAAAATA-AAAAAT
17037531 AATAAGTAATAAAAAAT
1 AATAA--AATAAAAAAT
17037548 TTGAAAGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
13 8 0.20
14 4 0.10
15 8 0.20
16 11 0.28
17 6 0.15
18 3 0.08
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (15 bp):
AATAAAATAAAAAAT
Found at i:17038323 original size:17 final size:17
Alignment explanation
Indices: 17038301--17038335 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
17038291 ATGTAAAATC
17038301 AAATTAAGATTTAATAT
1 AAATTAAGATTTAATAT
**
17038318 AAATTATTATTTAATAT
1 AAATTAAGATTTAATAT
17038335 A
1 A
17038336 TATATTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
AAATTAAGATTTAATAT
Found at i:17039721 original size:3 final size:3
Alignment explanation
Indices: 17039704--17039767 Score: 69
Period size: 3 Copynumber: 21.7 Consensus size: 3
17039694 TAATTTTTAT
* * * *
17039704 TAA TGA TAA -AA TAA TAA TAA TAA TTA TTA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
17039751 TAA TAA T-A TAAA TAA TA
1 TAA TAA TAA T-AA TAA TA
17039768 TTTAAATGAA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
2 4 0.08
3 46 0.88
4 2 0.04
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:17039724 original size:27 final size:29
Alignment explanation
Indices: 17039691--17039755 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
17039681 TTTGGGCCTG
17039691 TAATAAT-TT-TTATTAATGATAA-AATAA
1 TAATAATATTATTA-TAATGATAATAATAA
*
17039718 TAATAATAATTATTATAATTATAATAATAA
1 TAATAAT-ATTATTATAATGATAATAATAA
17039748 TAATAATA
1 TAATAATA
17039756 ATATAAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 7 0.21
29 11 0.33
30 15 0.45
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (29 bp):
TAATAATATTATTATAATGATAATAATAA
Found at i:17040356 original size:85 final size:84
Alignment explanation
Indices: 17040251--17040416 Score: 199
Period size: 85 Copynumber: 2.0 Consensus size: 84
17040241 ATACAATCAA
* * * * * * *
17040251 GACACACGAATTTGTGTCATCTT-TTTTAATGATGTGTGCTTCAATAACACGCAATGTAAGTCAT
1 GACACACAAATGTGTGTCATCTTCATTT-ATGACGGGGGCTTCAATAACACGCAATGCAAGTCAT
*
17040315 GAATATGTGTCATAAATTTAT
65 -AATACGTGTCATAAATTTAT
* * *
17040336 GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACGCGCAATGCATGTCATA
1 GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATAACACGCAATGCAAGTCATA
*
17040401 ATGCGTGTCATAAATT
66 ATACGTGTCATAAATT
17040417 AGCATCATAA
Statistics
Matches: 68, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
84 15 0.22
85 50 0.74
86 3 0.04
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (84 bp):
GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATAACACGCAATGCAAGTCATA
ATACGTGTCATAAATTTAT
Found at i:17042530 original size:45 final size:44
Alignment explanation
Indices: 17042465--17042559 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 44
17042455 GAAAATATGA
*
17042465 TGAATCAAAAGTTTTTATCCTTAGTACTTAAAAACAGAACCCATG
1 TGAATCAAAAGTTTTCATCCTTAGTACTT-AAAACAGAACCCATG
* *
17042510 TGAATCAAAAGTTTTCATCCTTAGTACTTAAAATATAACCCATG
1 TGAATCAAAAGTTTTCATCCTTAGTACTTAAAACAGAACCCATG
17042554 TGAATC
1 TGAATC
17042560 TAGAGTAATC
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
44 19 0.40
45 28 0.60
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.33
Consensus pattern (44 bp):
TGAATCAAAAGTTTTCATCCTTAGTACTTAAAACAGAACCCATG
Found at i:17042572 original size:44 final size:45
Alignment explanation
Indices: 17042465--17042572 Score: 128
Period size: 44 Copynumber: 2.4 Consensus size: 45
17042455 GAAAATATGA
** *
17042465 TGAATCAAAAGTTTTTATCCTTAGTACTTAAAAACAGAACCCATG
1 TGAATCAAAAGTAATCATCCTTAGTACTTAAAAACAGAACCCATG
** * *
17042510 TGAATCAAAAGTTTTCATCCTTAGTACTT-AAAATATAACCCATG
1 TGAATCAAAAGTAATCATCCTTAGTACTTAAAAACAGAACCCATG
* *
17042554 TGAATCTAGAGTAATCATC
1 TGAATCAAAAGTAATCATC
17042573 AACTAACATA
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
44 28 0.50
45 28 0.50
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (45 bp):
TGAATCAAAAGTAATCATCCTTAGTACTTAAAAACAGAACCCATG
Found at i:17046962 original size:18 final size:18
Alignment explanation
Indices: 17046939--17047011 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
17046929 GTTCTTAAGG
17046939 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
17046957 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
17046976 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
*
17046995 AGTTGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
17047012 AATATTCAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 30 0.62
19 4 0.08
20 14 0.29
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:17046990 original size:38 final size:38
Alignment explanation
Indices: 17046939--17047012 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
17046929 GTTCTTAAGG
*
17046939 AGTGGTCCTTCGGGACATAGTGGTTCTTCGGAACAATC
1 AGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACAATC
* *
17046977 AGTGGTCCTTCGGGACATAGTTGTCCTTCGGGACAA
1 AGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACAA
17047013 ATATTCAGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (38 bp):
AGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACAATC
Found at i:17050478 original size:20 final size:23
Alignment explanation
Indices: 17050414--17050478 Score: 64
Period size: 24 Copynumber: 2.9 Consensus size: 23
17050404 CATCGATGCA
*
17050414 TAAGGAGTGCATCGATGCACATGT
1 TAAGGAATGCATCGATGCAC-TGT
* * *
17050438 TAAGGGATGCATCGGTACACTG-
1 TAAGGAATGCATCGATGCACTGT
17050460 T-A-GAATGCATCGATGCACT
1 TAAGGAATGCATCGATGCACT
17050479 TCAAGGGAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
20 14 0.41
21 1 0.03
22 1 0.03
23 2 0.06
24 16 0.47
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (23 bp):
TAAGGAATGCATCGATGCACTGT
Found at i:17051854 original size:23 final size:23
Alignment explanation
Indices: 17051821--17051864 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
17051811 GAGTCGAGGG
17051821 TCTACGCGGTCCTTCGGGACAAT
1 TCTACGCGGTCCTTCGGGACAAT
* *
17051844 TCTACGTGGTCTTTCGGGACA
1 TCTACGCGGTCCTTCGGGACA
17051865 TATATATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (23 bp):
TCTACGCGGTCCTTCGGGACAAT
Found at i:17051974 original size:18 final size:18
Alignment explanation
Indices: 17051946--17052018 Score: 92
Period size: 18 Copynumber: 3.9 Consensus size: 18
17051936 TTTCTTAAGG
* *
17051946 AGTGATCCTTCGAGACAT
1 AGTGGTCCTTCGGGACAT
* *
17051964 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
17051983 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
17052002 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
17052019 AATATTCAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 29 0.62
19 4 0.09
20 14 0.30
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:17052002 original size:38 final size:38
Alignment explanation
Indices: 17051946--17052019 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
17051936 TTTCTTAAGG
*
17051946 AGTGATCCTTCGAGACATAGTGGTTCTTCGGAACAATC
1 AGTGATCCTTCGAGACATAGTGGTCCTTCGGAACAATC
* * *
17051984 AGTGGTCCTTCGGGACATAGTGGTCCTTCGGGACAA
1 AGTGATCCTTCGAGACATAGTGGTCCTTCGGAACAA
17052020 ATATTCAGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (38 bp):
AGTGATCCTTCGAGACATAGTGGTCCTTCGGAACAATC
Found at i:17062802 original size:21 final size:21
Alignment explanation
Indices: 17062778--17062827 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
17062768 ACGCTTTAAG
17062778 TATCGATACTCGGGCTTGTAT
1 TATCGATACTCGGGCTTGTAT
17062799 TATCGATACTCGGGCTTGTAT
1 TATCGATACTCGGGCTTGTAT
17062820 TATCGATA
1 TATCGATA
17062828 TTACCTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (21 bp):
TATCGATACTCGGGCTTGTAT
Found at i:17064108 original size:20 final size:20
Alignment explanation
Indices: 17064083--17064199 Score: 87
Period size: 20 Copynumber: 5.8 Consensus size: 20
17064073 AATGACCAAC
17064083 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGAATATG
* *
17064103 AAAATCGCAATGCGAA-ATA
1 AAAATCGCAACGCGAATATG
*
17064122 AAAATCGCAATGCG-ATA-G
1 AAAATCGCAACGCGAATATG
* ** * * *
17064140 TACAAATTTGCATTGCGATTTTCC
1 -A-AAA-TCGCAACGCGAATAT-G
*
17064164 AGAATCGCAACGCGAATATG
1 AAAATCGCAACGCGAATATG
17064184 AAAATCGCAACGCGAA
1 AAAATCGCAACGCGAA
17064200 CGTATAAATC
Statistics
Matches: 74, Mismatches: 16, Indels: 14
0.71 0.15 0.13
Matches are distributed among these distances:
18 1 0.01
19 18 0.24
20 33 0.45
21 18 0.24
22 3 0.04
23 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.20
Consensus pattern (20 bp):
AAAATCGCAACGCGAATATG
Found at i:17064208 original size:20 final size:19
Alignment explanation
Indices: 17064083--17064218 Score: 80
Period size: 20 Copynumber: 6.8 Consensus size: 19
17064073 AATGACCAAC
17064083 AAAATCGCAACGCGAATAT
1 AAAATCGCAACGCGAATAT
*
17064102 GAAAATCGCAATGCGAA-AT
1 -AAAATCGCAACGCGAATAT
*
17064121 AAAAATCGCAATGCG-ATAGT
1 -AAAATCGCAACGCGAATA-T
* ** * *
17064141 ACAAATTTGCATTGCGATTTT
1 A-AAA-TCGCAACGCGAATAT
*
17064162 CCAGAATCGCAACGCGAATAT
1 --AAAATCGCAACGCGAATAT
17064183 GAAAATCGCAACGCGAACGTAT
1 -AAAATCGCAACGCGAA--TAT
*
17064205 -AAATCTCAACGCGA
1 AAAATCGCAACGCGA
17064219 TTCTTACTAT
Statistics
Matches: 92, Mismatches: 15, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
18 1 0.01
19 18 0.20
20 47 0.51
21 19 0.21
22 6 0.07
23 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.20
Consensus pattern (19 bp):
AAAATCGCAACGCGAATAT
Found at i:17064219 original size:61 final size:61
Alignment explanation
Indices: 17064105--17064220 Score: 137
Period size: 62 Copynumber: 1.9 Consensus size: 61
17064095 CGAATATGAA
* * * **
17064105 AATCGCAATGCGAAATAAAAATCGCAATGCGATAGTACAAATTTGCATTGCGATTTTCCAG
1 AATCGCAACGCGAAATAAAAATCGCAACGCGATAGTACAAATCTGCAACGCGATTTTCCAG
* *
17064166 AATCGCAACGCGAATATGAAAATCGCAACGCGA-ACGTATAAATCT-CAACGCGATT
1 AATCGCAACGCGAA-ATAAAAATCGCAACGCGATA-GTACAAATCTGCAACGCGATT
17064221 CTTACTATCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
61 22 0.48
62 24 0.52
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (61 bp):
AATCGCAACGCGAAATAAAAATCGCAACGCGATAGTACAAATCTGCAACGCGATTTTCCAG
Found at i:17064272 original size:20 final size:21
Alignment explanation
Indices: 17064166--17064320 Score: 108
Period size: 20 Copynumber: 7.6 Consensus size: 21
17064156 GATTTTCCAG
* **
17064166 AATCGCAACGCGAATATG-AA
1 AATCGCAACGCGTATCCGTAA
*
17064186 AATCGCAACGCG-A-ACGTATA
1 AATCGCAACGCGTATCCGTA-A
* * * *
17064206 AATCTCAACGCG-ATTCTTAC
1 AATCGCAACGCGTATCCGTAA
* * *
17064226 TATCGCAACGAGTATCCATAAA
1 AATCGCAACGCGTATCCGT-AA
17064248 AATCGCAACGCGTATCCGT-A
1 AATCGCAACGCGTATCCGTAA
* * *
17064268 AATCGCAATGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGTAA
17064289 AATCGCAACGCGTATCCGT-A
1 AATCGCAACGCGTATCCGTAA
17064309 AATCGCAACGCG
1 AATCGCAACGCG
17064321 ATTTTTAAAG
Statistics
Matches: 107, Mismatches: 20, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
18 2 0.02
19 2 0.02
20 63 0.59
21 23 0.21
22 17 0.16
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.19
Consensus pattern (21 bp):
AATCGCAACGCGTATCCGTAA
Found at i:17066693 original size:82 final size:81
Alignment explanation
Indices: 17066556--17066711 Score: 267
Period size: 82 Copynumber: 1.9 Consensus size: 81
17066546 TAGATTGCTT
* *
17066556 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTGTATTCTTTAACACTGTGAA-ATAGT
17066621 ATTTGTCTTTTGGTTGA
65 ATTTGTCTTTTGGTTGA
* *
17066638 AGTAAATTTATTCGGTTGCTTCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
17066703 TTTGTCTTT
66 TTTGTCTTT
17066712 GTTTTGTCTT
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
81 14 0.20
82 56 0.80
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (81 bp):
AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTTGGTTGA
Found at i:17066767 original size:63 final size:63
Alignment explanation
Indices: 17066668--17066793 Score: 209
Period size: 63 Copynumber: 2.0 Consensus size: 63
17066658 TCCAATTCTG
*
17066668 CTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1 CTAAACTGTGTATTCTTTAACACTCTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
17066731 CTAAACTGTGTATTC-TTAATACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1 CTAAACTGTGTATTCTTTAACACTCTGAA-ATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
17066794 GTAATGCAAT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 11 0.19
63 48 0.81
ACGTcount: A:0.21, C:0.11, G:0.17, T:0.50
Consensus pattern (63 bp):
CTAAACTGTGTATTCTTTAACACTCTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:17066925 original size:14 final size:14
Alignment explanation
Indices: 17066903--17066967 Score: 67
Period size: 14 Copynumber: 4.3 Consensus size: 14
17066893 GCGAAATGAA
17066903 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
17066917 AATCACAACGAGAAATG
1 AATCGCAACGAG--A-G
*
17066934 AAAATCGCAACGATAG
1 --AATCGCAACGAGAG
17066950 AATCGCAACGAGAG
1 AATCGCAACGAGAG
17066964 AATC
1 AATC
17066968 AAAATCGCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
14 28 0.67
16 2 0.05
17 2 0.05
19 10 0.24
ACGTcount: A:0.48, C:0.20, G:0.22, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:17066932 original size:33 final size:33
Alignment explanation
Indices: 17066889--17066980 Score: 139
Period size: 33 Copynumber: 2.8 Consensus size: 33
17066879 ATGACTATCG
*
17066889 CAACGCGAAATGAAAATCGCAACGAGAGAATCA
1 CAACGAGAAATGAAAATCGCAACGAGAGAATCA
* *
17066922 CAACGAGAAATGAAAATCGCAACGATAGAATCG
1 CAACGAGAAATGAAAATCGCAACGAGAGAATCA
*
17066955 CAACGAGAGAATCAAAATCGCAACGA
1 CAACGAGA-AATGAAAATCGCAACGA
17066981 CAAAATCGTA
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
33 38 0.70
34 16 0.30
ACGTcount: A:0.49, C:0.21, G:0.21, T:0.10
Consensus pattern (33 bp):
CAACGAGAAATGAAAATCGCAACGAGAGAATCA
Found at i:17066987 original size:20 final size:20
Alignment explanation
Indices: 17066950--17066987 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
17066940 GCAACGATAG
* *
17066950 AATCGCAACGAGAGAATCAA
1 AATCGCAACGACAAAATCAA
17066970 AATCGCAACGACAAAATC
1 AATCGCAACGACAAAATC
17066988 GTAACGCGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.24, G:0.16, T:0.11
Consensus pattern (20 bp):
AATCGCAACGACAAAATCAA
Found at i:17067005 original size:19 final size:19
Alignment explanation
Indices: 17066981--17067018 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
17066971 ATCGCAACGA
*
17066981 CAAAATCGTAACGCGAAAC
1 CAAAATCGCAACGCGAAAC
*
17067000 CAAAATTGCAACGCGAAAC
1 CAAAATCGCAACGCGAAAC
17067019 TATAATCGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.26, G:0.16, T:0.11
Consensus pattern (19 bp):
CAAAATCGCAACGCGAAAC
Found at i:17067005 original size:67 final size:66
Alignment explanation
Indices: 17066885--17067012 Score: 157
Period size: 67 Copynumber: 1.9 Consensus size: 66
17066875 AAAAATGACT
* * * * **
17066885 ATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCACAACGAGAAATGAAAATCGCAACGATAG
1 ATCGCAACGAGAAATCAAAATCGCAACGACAAAATCACAACGAGAAACCAAAATCGCAACGATAG
17066950 A
66 A
** * *
17066951 ATCGCAACGAGAGAATCAAAATCGCAACGACAAAATCGTAACGCGAAACCAAAATTGCAACG
1 ATCGCAACGAGA-AATCAAAATCGCAACGACAAAATCACAACGAGAAACCAAAATCGCAACG
17067013 CGAAACTATA
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
66 11 0.22
67 40 0.78
ACGTcount: A:0.48, C:0.22, G:0.20, T:0.11
Consensus pattern (66 bp):
ATCGCAACGAGAAATCAAAATCGCAACGACAAAATCACAACGAGAAACCAAAATCGCAACGATAG
A
Found at i:17067077 original size:33 final size:33
Alignment explanation
Indices: 17067035--17067098 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
17067025 CGCGTTTTCG
**
17067035 CGTTGCGATTTTGGTTTCACGTTGCGATTTTGT
1 CGTTGCGATTTTCATTTCACGTTGCGATTTTGT
*
17067068 CGTTGCGATTTTCATTTCGCGTTGCGATTTT
1 CGTTGCGATTTTCATTTCACGTTGCGATTTT
17067099 CATTTCTCGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.09, C:0.17, G:0.25, T:0.48
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCACGTTGCGATTTTGT
Found at i:17067099 original size:19 final size:19
Alignment explanation
Indices: 17067030--17067187 Score: 111
Period size: 19 Copynumber: 8.7 Consensus size: 19
17067020 ATAATCGCGT
**
17067030 TTTCGCGTTGCGATTTTGG
1 TTTCGCGTTGCGATTTTCA
*
17067049 TTTCACGTTGCGA-TTT--
1 TTTCGCGTTGCGATTTTCA
*
17067065 TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
17067082 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* *
17067101 TTTCTCGTTGTGA--TTC-
1 TTTCGCGTTGCGATTTTCA
*
17067117 --TCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
**
17067134 TTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATTTTCA
* *
17067153 TTTTTCACGTTGCGATTTTAA
1 --TTTCGCGTTGCGATTTTCA
*
17067174 GTTTCGTGTTGCGA
1 -TTTCGCGTTGCGA
17067188 AAGTAAACTA
Statistics
Matches: 111, Mismatches: 16, Indels: 23
0.74 0.11 0.15
Matches are distributed among these distances:
14 18 0.16
15 3 0.03
16 5 0.05
17 5 0.05
18 3 0.03
19 51 0.46
20 11 0.10
21 15 0.14
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.47
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:17067110 original size:52 final size:52
Alignment explanation
Indices: 17067030--17067171 Score: 194
Period size: 52 Copynumber: 2.7 Consensus size: 52
17067020 ATAATCGCGT
** *
17067030 TTTCGCGTTGCGATTTTGGTTTCACGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCATTTCACGTTGCGATTTTCTCGTTGCGATTTTCA
* * *
17067082 TTTCGCGTTGCGATTTTCATTTCTCGTTGTGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCATTTCACGTTGCGATTTTCTCGTTGCGATTTTCA
**
17067134 TTTCGCGTTGCGATAGTCATTTTTCACGTTGCGATTTT
1 TTTCGCGTTGCGATTTTCA--TTTCACGTTGCGATTTT
17067172 AAGTTTCGTG
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
52 63 0.82
54 14 0.18
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.49
Consensus pattern (52 bp):
TTTCGCGTTGCGATTTTCATTTCACGTTGCGATTTTCTCGTTGCGATTTTCA
Found at i:17069139 original size:14 final size:14
Alignment explanation
Indices: 17069120--17069155 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
17069110 ATTGTTTAAT
17069120 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
17069134 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
17069148 TGATTTGT
1 TGATTTGT
17069156 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:17069334 original size:33 final size:33
Alignment explanation
Indices: 17069292--17069569 Score: 439
Period size: 33 Copynumber: 8.2 Consensus size: 33
17069282 TCGCAACGAG
* *
17069292 TGCGATTCTCTCGTTGCCATTTTCATTTCGTAT
1 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
17069325 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
17069358 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
*
17069391 TGTGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
17069424 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
17069457 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
17069490 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
* * *
17069523 TGTGATAGTCATTTCTACGTTGCGATATTCATATTCGCGT
1 TGCGAT--TC---TCT-CGTTGCGATTTTCAT-TTCGCAT
17069563 TGCGATT
1 TGCGATT
17069570 TTCATTTCGC
Statistics
Matches: 230, Mismatches: 8, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
33 199 0.87
35 2 0.01
38 4 0.02
39 14 0.06
40 11 0.05
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
Found at i:17069554 original size:20 final size:19
Alignment explanation
Indices: 17069402--17069587 Score: 105
Period size: 19 Copynumber: 10.5 Consensus size: 19
17069392 GTGATTCTCT
*
17069402 CGTTGCGATTTTCATTTCG
1 CGTTGCGATATTCATTTCG
* *
17069421 CATTGCG--ATTC---TCT
1 CGTTGCGATATTCATTTCG
*
17069435 CGTTGCGATTTTCATTTCG
1 CGTTGCGATATTCATTTCG
* *
17069454 CATTGCG--ATTC---TCT
1 CGTTGCGATATTCATTTCG
*
17069468 CGTTGCGATTTTCATTTCG
1 CGTTGCGATATTCATTTCG
* *
17069487 CATTGCG--ATTC---TCT
1 CGTTGCGATATTCATTTCG
*
17069501 CGTTGCGATTTTCATTTCG
1 CGTTGCGATATTCATTTCG
* * * *
17069520 CATTGTGATAGTCATTTCTA
1 CGTTGCGATATTCATTTC-G
17069540 CGTTGCGATATTCATATTCG
1 CGTTGCGATATTCAT-TTCG
*
17069560 CGTTGCGATTTTCATTTCG
1 CGTTGCGATATTCATTTCG
*
17069579 CATTGCGAT
1 CGTTGCGAT
17069588 TCTCTCGTTG
Statistics
Matches: 121, Mismatches: 29, Indels: 34
0.66 0.16 0.18
Matches are distributed among these distances:
14 24 0.20
16 9 0.07
17 9 0.07
19 50 0.41
20 26 0.21
21 3 0.02
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.45
Consensus pattern (19 bp):
CGTTGCGATATTCATTTCG
Found at i:17072161 original size:24 final size:24
Alignment explanation
Indices: 17072094--17072153 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
17072084 CTGAAACATC
17072094 ATCAAAATTCGAGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
* * *
17072118 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
*
17072142 ATCAAATTTCGA
1 ATCAAAATTCGA
17072154 ATACTGACTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (24 bp):
ATCAAAATTCGAGTATTGACCAAG
Found at i:17072294 original size:12 final size:12
Alignment explanation
Indices: 17072273--17072306 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
17072263 GGTTGTAGGT
*
17072273 TTTGAGATTGTG
1 TTTGATATTGTG
17072285 TTTGATATTGTG
1 TTTGATATTGTG
*
17072297 TTTGGTATTG
1 TTTGATATTG
17072307 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:17072993 original size:20 final size:19
Alignment explanation
Indices: 17072968--17073200 Score: 155
Period size: 20 Copynumber: 11.5 Consensus size: 19
17072958 AAATTTAAGT
17072968 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTAC-GATTCTC
* *
17072988 GTTGCGATTAACGTATTCTG
1 GTTGCGATTTACG-ATTCTC
* * *
17073008 GTTGCGA-TAATCAGAATCGC
1 GTTGCGATTTA-C-GATTCTC
17073028 GTTGCGATTTTACGTATTCTC
1 GTTGCGA-TTTACG-ATTCTC
** * *
17073049 GTTAAGATTTACGGATACGC
1 GTTGCGATTTAC-GATTCTC
17073069 GTTGCGATTTTACGTATTCTC
1 GTTGCGA-TTTACG-ATTCTC
* *
17073090 GTTGCGATTTACGGATACGC
1 GTTGCGATTTAC-GATTCTC
*
17073110 GTTGCGATTTTACGAATACTC
1 GTTGCGA-TTTACG-ATTCTC
* * *
17073131 GTTGCGATAGT-CAGAATCGC
1 GTTGCGAT-TTAC-GATTCTC
17073151 GTTGCGATTTACGTATTCTC
1 GTTGCGATTTACG-ATTCTC
* *
17073171 GTTGCGATTTACGGATACGC
1 GTTGCGATTTAC-GATTCTC
17073191 GTTGCGATTT
1 GTTGCGATTT
17073201 TTACGAATAC
Statistics
Matches: 168, Mismatches: 28, Indels: 34
0.73 0.12 0.15
Matches are distributed among these distances:
19 6 0.04
20 111 0.66
21 49 0.29
22 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (19 bp):
GTTGCGATTTACGATTCTC
Found at i:17073070 original size:41 final size:41
Alignment explanation
Indices: 17072968--17073261 Score: 289
Period size: 41 Copynumber: 7.2 Consensus size: 41
17072958 AAATTTAAGT
* * * * *
17072968 GTTGCGATTTACAGATTCTCGTTGCGA-TTAACGTATTCTG
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
* *
17073008 GTTGCGA-TAATCAGA-ATCGCGTTGCGATTTTACGTATTCTC
1 GTTGCGATTTA-CGGATA-CGCGTTGCGATTTTACGTATTCTC
**
17073049 GTTAAGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
* *
17073090 GTTGCGATTTACGGATACGCGTTGCGATTTTACGAATACTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
* *
17073131 GTTGCGATAGT-CAGA-ATCGCGTTGCGA-TTTACGTATTCTC
1 GTTGCGAT-TTACGGATA-CGCGTTGCGATTTTACGTATTCTC
* *
17073171 GTTGCGATTTACGGATACGCGTTGCGATTTTTACGAATACTC
1 GTTGCGATTTACGGATACGCGTTGCGA-TTTTACGTATTCTC
* * * * * *
17073213 ATTGCGATAGTAAGAAT-CGCGTTGCGATTTT-CATATTCGC
1 GTTGCGAT-TTACGGATACGCGTTGCGATTTTACGTATTCTC
17073253 GTTGCGATT
1 GTTGCGATT
17073262 CTGGAAAATC
Statistics
Matches: 211, Mismatches: 31, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
39 3 0.01
40 65 0.31
41 106 0.50
42 32 0.15
43 5 0.02
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (41 bp):
GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
Found at i:17073073 original size:61 final size:60
Alignment explanation
Indices: 17072968--17073198 Score: 252
Period size: 61 Copynumber: 3.8 Consensus size: 60
17072958 AAATTTAAGT
* * *
17072968 GTTGCGATTTACAG-ATTCTCGTTGCGATTAACGTATTCTG-GTTGCGATAATCAGAATCGC
1 GTTGCGATTTAC-GTATTCTCGTTGCGATTTACGGATAC-GCGTTGCGATAATCAGAATCGC
** * * * *
17073028 GTTGCGATTTTACGTATTCTCGTTAAGATTTACGGATACGCGTTGCGAT-TTTACGTATTCTC
1 GTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATAATCA-G-AATCGC
* * * * * *
17073090 GTTGCGATTTACGGATACGCGTTGCGATTTTACGAATACTCGTTGCGATAGTCAGAATCGC
1 GTTGCGATTTACGTATTCTCGTTGCGA-TTTACGGATACGCGTTGCGATAATCAGAATCGC
17073151 GTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGAT
1 GTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGAT
17073199 TTTTACGAAT
Statistics
Matches: 139, Mismatches: 25, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
60 30 0.22
61 76 0.55
62 31 0.22
63 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (60 bp):
GTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATAATCAGAATCGC
Found at i:17073203 original size:82 final size:81
Alignment explanation
Indices: 17072987--17073261 Score: 331
Period size: 82 Copynumber: 3.4 Consensus size: 81
17072977 TACAGATTCT
* * * * * * *
17072987 CGTTGCGATTAACGTATTCTGGTTGCGA-TAATCAGA-ATCGCGTTGCGATTTTACGTATTCTCG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTA-CGGATA-CGCGTTGCGATTTTACGAATACTCA
** * * *
17073050 TTAAGAT-TTACGGATACG
64 TTGCGATAGTAAGAAT-CG
*
17073068 CGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGAATACTCGT
1 CGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGAATACTCAT
*
17073133 TGCGATAGTCAGAATCG
65 TGCGATAGTAAGAATCG
17073150 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTTACGAATACTCAT
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGA-TTTTACGAATACTCAT
17073215 TGCGATAGTAAGAATCG
65 TGCGATAGTAAGAATCG
* * *
17073232 CGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGTTGCGATTTACGTATTCTCGTTGCGATT
17073262 CTGGAAAATC
Statistics
Matches: 172, Mismatches: 17, Indels: 9
0.87 0.09 0.05
Matches are distributed among these distances:
81 48 0.28
82 117 0.68
83 7 0.04
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (81 bp):
CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGAATACTCATT
GCGATAGTAAGAATCG
Found at i:17073239 original size:20 final size:20
Alignment explanation
Indices: 17073021--17073261 Score: 168
Period size: 20 Copynumber: 11.8 Consensus size: 20
17073011 GCGATAATCA
17073021 GAAT-CGCGTTGCGATTTTAC
1 GAATACGCGTTGCGA-TTTAC
* * * **
17073041 GTATTCTCGTTAAGATTTAC
1 GAATACGCGTTGCGATTTAC
*
17073061 GGATACGCGTTGCGATTTTAC
1 GAATACGCGTTGCGA-TTTAC
* * *
17073082 GTATTCTCGTTGCGATTTAC
1 GAATACGCGTTGCGATTTAC
*
17073102 GGATACGCGTTGCGATTTTAC
1 GAATACGCGTTGCGA-TTTAC
* *
17073123 GAATACTCGTTGCGATAGT-C
1 GAATACGCGTTGCGAT-TTAC
17073143 AGAAT-CGCGTTGCGATTTAC
1 -GAATACGCGTTGCGATTTAC
* * *
17073163 GTATTCTCGTTGCGATTTAC
1 GAATACGCGTTGCGATTTAC
*
17073183 GGATACGCGTTGCGATTTTTAC
1 GAATACGCGTTGCGA--TTTAC
* * * *
17073205 GAATACTCATTGCGATAGTAA
1 GAATACGCGTTGCGAT-TTAC
*
17073226 GAAT-CGCGTTGCGATTTTC
1 GAATACGCGTTGCGATTTAC
*
17073245 -ATATTCGCGTTGCGATT
1 GA-ATACGCGTTGCGATT
17073262 CTGGAAAATC
Statistics
Matches: 174, Mismatches: 35, Indels: 24
0.75 0.15 0.10
Matches are distributed among these distances:
18 1 0.01
19 7 0.04
20 96 0.55
21 53 0.30
22 17 0.10
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.37
Consensus pattern (20 bp):
GAATACGCGTTGCGATTTAC
Found at i:17080149 original size:20 final size:20
Alignment explanation
Indices: 17080124--17080165 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
17080114 TAAAGAGCTA
*
17080124 TGAGAGAATATT-AGAGTATT
1 TGAGAGAA-ATTGAGAGGATT
17080144 TGAGAGAAATTGAGAGGATT
1 TGAGAGAAATTGAGAGGATT
17080164 TG
1 TG
17080166 GTGTGATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (20 bp):
TGAGAGAAATTGAGAGGATT
Found at i:17081020 original size:19 final size:19
Alignment explanation
Indices: 17080996--17081041 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
17080986 AGCAGCTTGA
* *
17080996 AACCGGTTTGAACGGTCTG
1 AACCGGTTTGAACGATCCG
* *
17081015 AACCGGGTTGACCGATCCG
1 AACCGGTTTGAACGATCCG
17081034 AACCGGTT
1 AACCGGTT
17081042 CGACCCGACC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.22, C:0.26, G:0.30, T:0.22
Consensus pattern (19 bp):
AACCGGTTTGAACGATCCG
Found at i:17081066 original size:13 final size:13
Alignment explanation
Indices: 17081048--17081075 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
17081038 GGTTCGACCC
17081048 GACCCGACCCGTT
1 GACCCGACCCGTT
17081061 GACCCGACCCGTT
1 GACCCGACCCGTT
17081074 GA
1 GA
17081076 TCGTTAACCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.18, C:0.43, G:0.25, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:17081066 original size:18 final size:19
Alignment explanation
Indices: 17081021--17081071 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
17081011 TCTGAACCGG
* *
17081021 GTTGA-CCGATCCGAACCG
1 GTTGACCCGACCCGAACCC
17081039 GTTCGACCCGACCCG-ACCC
1 GTT-GACCCGACCCGAACCC
17081058 GTTGACCCGACCCG
1 GTTGACCCGACCCG
17081072 TTGATCGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 14 0.48
19 8 0.28
20 7 0.24
ACGTcount: A:0.18, C:0.43, G:0.25, T:0.14
Consensus pattern (19 bp):
GTTGACCCGACCCGAACCC
Found at i:17082425 original size:17 final size:19
Alignment explanation
Indices: 17082398--17082436 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
17082388 ATATCTGTAT
17082398 TATTAATATTT-TGTTCTA
1 TATTAATATTTATGTTCTA
17082416 TATT-ATATTTAATGTTCTA
1 TATTAATATTT-ATGTTCTA
17082435 TA
1 TA
17082437 AGTTATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTAATATTTATGTTCTA
Found at i:17088220 original size:13 final size:13
Alignment explanation
Indices: 17088202--17088227 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17088192 CGAACTGGTT
17088202 CGACCCGTTGACC
1 CGACCCGTTGACC
17088215 CGACCCGTTGACC
1 CGACCCGTTGACC
17088228 GTCGACTTCC
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:0.15, C:0.46, G:0.23, T:0.15
Consensus pattern (13 bp):
CGACCCGTTGACC
Found at i:17090732 original size:65 final size:65
Alignment explanation
Indices: 17090590--17090750 Score: 211
Period size: 65 Copynumber: 2.5 Consensus size: 65
17090580 TGCACTAAGA
* * *
17090590 GTGCATCGATGCATCAAGTGCATTTGATGTT-TCAAAATAGCCAGAGTGCATCAATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTCTCAAAATAGCCACAGTGCATCAATGCATGGCTG
* * **
17090654 GTGCATCGATGCATCAAATGCATTCGATGTTCTCATAAA-ATCCTCAGTGCATCGGTGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGATGTTCTCA-AAATAGCCACAGTGCATCAATGCATGGCT
17090717 G
65 G
*
17090718 TGTGCATCGATGCATGAAATGCATTCGATGTTC
1 -GTGCATCGATGCATCAAATGCATTCGATGTTC
17090751 AATTTAATTC
Statistics
Matches: 86, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
64 31 0.36
65 52 0.60
66 3 0.03
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTCTCAAAATAGCCACAGTGCATCAATGCATGGCTG
Found at i:17090788 original size:65 final size:63
Alignment explanation
Indices: 17090590--17090799 Score: 187
Period size: 65 Copynumber: 3.3 Consensus size: 63
17090580 TGCACTAAGA
* * * * *
17090590 GTGCATCGATGCATCAAGTGCATTTGATGTT-TCAA-AATAGC-CAGAGTGCATCAATGCATGGC
1 GTGCATCGATGCATCAAATGCATTCGATGTTCT-AATAAAATCTC--AGTGCATCGATGCATGG-
17090652 TG
62 TG
* *
17090654 GTGCATCGATGCATCAAATGCATTCGATGTTCTCATAAAATCCTCAGTGCATCGGTGCATGGTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTCTAATAAAAT-CTCAGTGCATCGATGCATGGTG
* ** *
17090718 TGTGCATCGATGCATGAAATGCATTCGATGTTC-AATTTAAT-TCATGGTGCATCGATGCGTGGA
1 -GTGCATCGATGCATCAAATGCATTCGATGTTCTAATAAAATCTCA--GTGCATCGATGCATGG-
17090781 TTG
62 -TG
*
17090784 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
17090800 CTCTGAAAAA
Statistics
Matches: 122, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
62 3 0.02
64 51 0.42
65 64 0.52
66 3 0.02
67 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTCTAATAAAATCTCAGTGCATCGATGCATGGTG
Found at i:17091852 original size:58 final size:60
Alignment explanation
Indices: 17091722--17091856 Score: 149
Period size: 58 Copynumber: 2.3 Consensus size: 60
17091712 AAATTATTTT
*
17091722 TGAGCTTTAGTTTTTC--TCTCAATTACAGAGAAGGGGGTGAGTTTTATTTTAAAAGAAAA
1 TGAGCTTTAGTTTTTCTGTTTCAATTACAGAGAAGGGGGTGAGTTTTA-TTTAAAAGAAAA
* * * **
17091781 TG-G-TTTAGCTTTTCTGTTTC-TTTACAGAGAAGGGGGTGAGTTTTA-TT-CAAGCCAA
1 TGAGCTTTAGTTTTTCTGTTTCAATTACAGAGAAGGGGGTGAGTTTTATTTAAAAGAAAA
17091836 TAGAGCTTTAGTTTTTCTGTT
1 T-GAGCTTTAGTTTTTCTGTT
17091857 AAGAAAATGG
Statistics
Matches: 64, Mismatches: 7, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
55 6 0.09
56 3 0.05
57 11 0.17
58 39 0.61
59 5 0.08
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.41
Consensus pattern (60 bp):
TGAGCTTTAGTTTTTCTGTTTCAATTACAGAGAAGGGGGTGAGTTTTATTTAAAAGAAAA
Found at i:17092609 original size:10 final size:10
Alignment explanation
Indices: 17092539--17092576 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
17092529 CATGTTTAAT
17092539 TATATAC-TA
1 TATATACTTA
17092548 TATATACTTA
1 TATATACTTA
17092558 TATATA-TATA
1 TATATACT-TA
17092568 TATATACTT
1 TATATACTT
17092577 GTGTACATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 8 0.31
10 17 0.65
11 1 0.04
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (10 bp):
TATATACTTA
Found at i:17092622 original size:7 final size:8
Alignment explanation
Indices: 17092538--17092629 Score: 61
Period size: 8 Copynumber: 11.8 Consensus size: 8
17092528 TCATGTTTAA
17092538 TTATATAC
1 TTATATAC
17092546 TATATATAC
1 T-TATATAC
17092555 TTATATA-
1 TTATATAC
17092562 -TATATA-
1 TTATATAC
17092568 -TATATAC
1 TTATATAC
* *
17092575 TTGTGTAC
1 TTATATAC
* *
17092583 ATACATTAC
1 TTATA-TAC
17092592 ATATATATAC
1 -T-TATATAC
17092602 TTATATA-
1 TTATATAC
*
17092609 TTGTATAC
1 TTATATAC
17092617 TT-TATAC
1 TTATATAC
17092624 TTATAT
1 TTATAT
17092630 GTAAATACAC
Statistics
Matches: 67, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
6 12 0.18
7 13 0.19
8 24 0.36
9 12 0.18
10 3 0.04
11 3 0.04
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (8 bp):
TTATATAC
Found at i:17092790 original size:2 final size:2
Alignment explanation
Indices: 17092783--17092824 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
17092773 AAATTATGAC
17092783 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17092824 A
1 A
17092825 AGTATATTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17093134 original size:23 final size:23
Alignment explanation
Indices: 17093104--17093156 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
17093094 TTGTGTTGCA
*
17093104 CATTTTCATACGCCTTTATGGTT
1 CATTTTCATACGCCTTTATGGCT
17093127 CATTTTCATACGCCTTTATGGCT
1 CATTTTCATACGCCTTTATGGCT
17093150 CATTTTC
1 CATTTTC
17093157 TTATGCTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.17, C:0.25, G:0.11, T:0.47
Consensus pattern (23 bp):
CATTTTCATACGCCTTTATGGCT
Found at i:17107339 original size:21 final size:20
Alignment explanation
Indices: 17107306--17107344 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
17107296 CATCAAGGTC
*
17107306 TTTGTGGAAGCCATGAAATAT
1 TTTGTCGAAGCCAT-AAATAT
*
17107327 TTTGTCGAGGCCATAAAT
1 TTTGTCGAAGCCATAAAT
17107345 TGTTGCAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (20 bp):
TTTGTCGAAGCCATAAATAT
Found at i:17116347 original size:39 final size:39
Alignment explanation
Indices: 17116303--17116399 Score: 158
Period size: 39 Copynumber: 2.5 Consensus size: 39
17116293 TTCTAATAGA
*
17116303 AAGTTCATAATGAGAAGAGCTTGTCTAAAGAGAGAGAAG
1 AAGTTCATAATGAGAAGAACTTGTCTAAAGAGAGAGAAG
* *
17116342 TAGTTCATAATGAGAATAACTTGTCTAAAGAGAGAGAAG
1 AAGTTCATAATGAGAAGAACTTGTCTAAAGAGAGAGAAG
*
17116381 AAATTCATAATGAGAAGAA
1 AAGTTCATAATGAGAAGAA
17116400 TTTATTCAAC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.46, C:0.07, G:0.24, T:0.23
Consensus pattern (39 bp):
AAGTTCATAATGAGAAGAACTTGTCTAAAGAGAGAGAAG
Found at i:17116508 original size:156 final size:153
Alignment explanation
Indices: 17116219--17116652 Score: 471
Period size: 156 Copynumber: 2.8 Consensus size: 153
17116209 GTCCGAAGGG
* *
17116219 GAGAATAAACTCATAATGAGAAGAACTTATTCAACATTGGTTCAAATACATCCCA-AAAGAAGAT
1 GAGAA-AAATTCATAATGAGAAGAACTTATTCAACATTGGTTCAAAT-CATCACAGAAAG-AGAT
* * * * * * * *
17116283 GGATCAACATTTCTAATAGAAAGTTCATAATGAGAAGAGCTTGTCTAAAGAGAGAGAAGTAGTTC
63 GGATCAACATTTCTAATAGAGAGTTCATAATGAGAAGAACTCGTCCAATGAGGGAGAAGAAGTTA
*
17116348 ATAATGAGAATAACT-TGTCTAAAGAGA-
128 ATAATAAGAATAACTAT-TC-AAAGA-AT
* *
17116375 GAGAAGAAATTCATAATGAGAAGAATTTATTCAACCA-TGGTTCAAATCTATCACAGAAAGAGGT
1 GAGAA-AAATTCATAATGAGAAGAACTTATTCAA-CATTGGTTCAAATC-ATCACAGAAAGAGAT
* * *
17116439 GGATCAACATTGCTAATAGAGAGTTCATAAGGAGAAGAACTCGTCCGATGAGGGAGAAGAAGTTA
63 GGATCAACATTTCTAATAGAGAGTTCATAATGAGAAGAACTCGTCCAATGAGGGAGAAGAAGTTA
* *
17116504 ATAATAAGAATAACTCATTCGATGAAT
128 ATAATAAGAATAACT-ATTCAAAGAAT
* * * * * *
17116531 GAGAAAAAGTTCATAATGAGAAGAGCTTGTTTAACATTGGTTCAAATCCACCACAGAATGAGATT
1 GAGAAAAA-TTCATAATGAGAAGAACTTATTCAACATTGGTTCAAAT-CATCACAGAAAGAGATG
* * * * *
17116596 GATCAACATTTCTATTTGAGAGTTCATATTGAAAAGAACTCATCCAATGAGGGAGAA
64 GATCAACATTTCTAATAGAGAGTTCATAATGAGAAGAACTCGTCCAATGAGGGAGAA
17116653 TATGTTCATA
Statistics
Matches: 234, Mismatches: 35, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
155 7 0.03
156 217 0.93
157 9 0.04
158 1 0.00
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (153 bp):
GAGAAAAATTCATAATGAGAAGAACTTATTCAACATTGGTTCAAATCATCACAGAAAGAGATGGA
TCAACATTTCTAATAGAGAGTTCATAATGAGAAGAACTCGTCCAATGAGGGAGAAGAAGTTAATA
ATAAGAATAACTATTCAAAGAAT
Found at i:17119299 original size:2 final size:2
Alignment explanation
Indices: 17119288--17119316 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
17119278 ATTATTGTAA
17119288 AT AT -T 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
17119317 TAAATATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:17119307 original size:32 final size:32
Alignment explanation
Indices: 17119262--17119326 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 32
17119252 TCGGTGAGGT
*
17119262 TATATATGCATATATGAT-TAT-TGTAAATATTA
1 TATATATACATATAT-ATATATAT-TAAATATTA
*
17119294 TATATATATATATATATATATATTAAATATTA
1 TATATATACATATATATATATATTAAATATTA
17119326 T
1 T
17119327 TAAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 2 0.07
32 26 0.90
33 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.49
Consensus pattern (32 bp):
TATATATACATATATATATATATTAAATATTA
Found at i:17127874 original size:68 final size:68
Alignment explanation
Indices: 17127765--17127909 Score: 272
Period size: 68 Copynumber: 2.1 Consensus size: 68
17127755 TTTAGGGGTT
*
17127765 AAATTTTAAGAAATTATAAAATGGTGAATTTAATTGGTATTTTGAAAGAAACGGTGGATTAAATT
1 AAATTTTAAGAAATTATAAAATGGTGAATTTAATTGGTATTTTGAAAGAAACGATGGATTAAATT
17127830 ATA
66 ATA
17127833 AAATTTTAAGAAATTATAAAATGGTGAATTTAATTGGTATTTTGAAAGAAACGATGGATTAAATT
1 AAATTTTAAGAAATTATAAAATGGTGAATTTAATTGGTATTTTGAAAGAAACGATGGATTAAATT
*
17127898 GTA
66 ATA
17127901 AAATTTTAA
1 AAATTTTAA
17127910 AGTTGGCAGA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 75 1.00
ACGTcount: A:0.45, C:0.01, G:0.17, T:0.37
Consensus pattern (68 bp):
AAATTTTAAGAAATTATAAAATGGTGAATTTAATTGGTATTTTGAAAGAAACGATGGATTAAATT
ATA
Found at i:17134114 original size:2 final size:2
Alignment explanation
Indices: 17134107--17134139 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
17134097 TAGGTCATTA
17134107 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
17134140 AAAAGAATGT
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:17138286 original size:15 final size:15
Alignment explanation
Indices: 17138266--17138296 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17138256 CAACAAATAG
17138266 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
17138281 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
17138296 A
1 A
17138297 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:17138481 original size:20 final size:20
Alignment explanation
Indices: 17138456--17138534 Score: 106
Period size: 20 Copynumber: 4.0 Consensus size: 20
17138446 TATTCCCTGG
*
17138456 TAATCTTTTATTCTCATTGA
1 TAATCTTTTATTCTCACTGA
*
17138476 TAATCTTTTATTCTCACTGG
1 TAATCTTTTATTCTCACTGA
17138496 TAATCTTTTATTCTCACT-A
1 TAATCTTTTATTCTCACTGA
* *
17138515 GTAATATTTTATTCTTACTG
1 -TAATCTTTTATTCTCACTG
17138535 GCAATCTTAC
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.24, C:0.16, G:0.06, T:0.53
Consensus pattern (20 bp):
TAATCTTTTATTCTCACTGA
Found at i:17138496 original size:40 final size:40
Alignment explanation
Indices: 17138452--17138542 Score: 130
Period size: 40 Copynumber: 2.3 Consensus size: 40
17138442 ATCCTATTCC
* *
17138452 CTGGTAATCTTTTATTCTCA-TTGATAATCTTTTATTCTCA
1 CTGGTAATCTTTTATTCTCACTAG-TAATATTTTATTCTCA
*
17138492 CTGGTAATCTTTTATTCTCACTAGTAATATTTTATTCTTA
1 CTGGTAATCTTTTATTCTCACTAGTAATATTTTATTCTCA
*
17138532 CTGGCAATCTT
1 CTGGTAATCTT
17138543 ACATTCCGTG
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 44 0.96
41 2 0.04
ACGTcount: A:0.23, C:0.18, G:0.09, T:0.51
Consensus pattern (40 bp):
CTGGTAATCTTTTATTCTCACTAGTAATATTTTATTCTCA
Found at i:17139073 original size:2 final size:2
Alignment explanation
Indices: 17139068--17139103 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
17139058 TAATACTTTA
17139068 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17139104 TTTGCATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17147012 original size:46 final size:45
Alignment explanation
Indices: 17146959--17147243 Score: 365
Period size: 46 Copynumber: 6.2 Consensus size: 45
17146949 ACTCTAAATG
**
17146959 GTGCATTATCGGCATGAAATAATGCCATAAAT-AAATATGCATAAC
1 GTGCATTATCGGCATGAAAGGATGCCATAAATGAAA-ATGCATAAC
* * *
17147004 AGTGCATTATCAGTATGAAAGGATGTCATAAATGAAAATGCATAAC
1 -GTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
*
17147050 GATGCATTATCGGCATGAAAGGATGCCATAAATGAAAAATTCATAAC
1 G-TGCATTATCGGCATGAAAGGATGCCATAAATG-AAAATGCATAAC
* *
17147097 AGTGCATTATCGACATGAAAGGATGCCAAAAATGAAAATGCATAAC
1 -GTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
* * *
17147143 GATGCATTATCGGCATGAAAGAATGCCATAAATGAAAATGTATAATG
1 G-TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAA-C
* * *
17147190 GTGGATTATCGGCATGAAAGGATGCCACAAATGAAAATGCATAATG
1 GTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAA-C
17147236 GTGCATTA
1 GTGCATTA
17147244 ACGACTTTTT
Statistics
Matches: 211, Mismatches: 22, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
45 2 0.01
46 163 0.77
47 45 0.21
48 1 0.00
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.24
Consensus pattern (45 bp):
GTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
Found at i:17147198 original size:139 final size:138
Alignment explanation
Indices: 17146959--17147248 Score: 386
Period size: 139 Copynumber: 2.1 Consensus size: 138
17146949 ACTCTAAATG
* * * *
17146959 GTGCATTATCGGCATGAAATAATGCCATAAATAAATATGCATAACAGTGCATTATCAGTATGAAA
1 GTGCATTATCGACATGAAAGAATGCCAAAAATAAATATGCATAACAGTGCATTATCAGCATGAAA
* * *
17147024 GGATGTCATAAATGAAAATGCATAACGATGCATTATCGGCATGAAAGGATGCCATAAATGAAAAA
66 GAATGCCATAAATGAAAATGCATAACGATGCATTATCGGCATGAAAGGATGCCACAAATG-AAAA
*
17147089 TTCATAACA
130 TGCATAACA
* *
17147098 GTGCATTATCGACATGAAAGGATGCCAAAAATGAAA-ATGCATAAC-GATGCATTATCGGCATGA
1 GTGCATTATCGACATGAAAGAATGCCAAAAAT-AAATATGCATAACAG-TGCATTATCAGCATGA
* * * *
17147161 AAGAATGCCATAAATGAAAATGTATAATGGTGGATTATCGGCATGAAAGGATGCCACAAATGAAA
64 AAGAATGCCATAAATGAAAATGCATAACGATGCATTATCGGCATGAAAGGATGCCACAAATGAAA
**
17147226 ATGCATAATG
129 ATGCATAACA
*
17147236 GTGCATTAACGAC
1 GTGCATTATCGAC
17147249 TTTTTGGCAC
Statistics
Matches: 132, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
138 23 0.17
139 106 0.80
140 3 0.02
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (138 bp):
GTGCATTATCGACATGAAAGAATGCCAAAAATAAATATGCATAACAGTGCATTATCAGCATGAAA
GAATGCCATAAATGAAAATGCATAACGATGCATTATCGGCATGAAAGGATGCCACAAATGAAAAT
GCATAACA
Found at i:17151579 original size:16 final size:16
Alignment explanation
Indices: 17151555--17151585 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17151545 TATATATATA
17151555 ATATAATGGATTATTT
1 ATATAATGGATTATTT
*
17151571 ATATTATGGATTATT
1 ATATAATGGATTATT
17151586 AGATTTTGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (16 bp):
ATATAATGGATTATTT
Found at i:17160589 original size:45 final size:45
Alignment explanation
Indices: 17160522--17160614 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 45
17160512 GAATAATGAC
* *
17160522 AAGTGTATTGGTAAAATAAGCTTACGAGCTTATGGTATTAAATGGT
1 AAGTATATTGGTAAAATAAGCTTACGAGCTTATGGGA-TAAATGGT
17160568 AAGTATATTGGT-AAATAAGCTTACGAGCTTATGGGATAAATGGT
1 AAGTATATTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGT
17160612 AAG
1 AAG
17160615 AGATTTTATA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 11 0.24
45 23 0.51
46 11 0.24
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.32
Consensus pattern (45 bp):
AAGTATATTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGT
Found at i:17161155 original size:22 final size:22
Alignment explanation
Indices: 17161106--17161148 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
17161096 GATGCACTAT
*
17161106 TCACTGTTCACGGGTAATGTTCA
1 TCACTGTTCA-TGGTAATGTTCA
*
17161129 TCACTGTTCATGGTACTGTT
1 TCACTGTTCATGGTAATGTT
17161149 TGTCACTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.40
Consensus pattern (22 bp):
TCACTGTTCATGGTAATGTTCA
Done.