Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007853.1 Hibiscus syriacus cultivar Beakdansim tig00110213_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: 2309479
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 8
Found at i:987326 original size:21 final size:23
Alignment explanation
Indices: 987302--987351 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
987292 TAAAGTGAAC
*
987302 TATCATACCAATA-CTTTA-AAT
1 TATCATACCAATATCTTAATAAT
* *
987323 TATCACATCAATATCTTAATAAT
1 TATCATACCAATATCTTAATAAT
987346 TATCAT
1 TATCAT
987352 CAATTTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 11 0.48
22 4 0.17
23 8 0.35
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.40
Consensus pattern (23 bp):
TATCATACCAATATCTTAATAAT
Found at i:995693 original size:21 final size:21
Alignment explanation
Indices: 995625--995684 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
995615 TAAATCGCAT
995625 TGCGATTTTCCAAATTCGCGA
1 TGCGATTTTCCAAATTCGCGA
**
995646 TGCGATTTTTTAAATTCGCGA
1 TGCGATTTTCCAAATTCGCGA
995667 TGCGATTTTCCAAATTCG
1 TGCGATTTTCCAAATTCG
995685 AAACGCGATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.38
Consensus pattern (21 bp):
TGCGATTTTCCAAATTCGCGA
Found at i:995702 original size:20 final size:20
Alignment explanation
Indices: 995677--995771 Score: 122
Period size: 20 Copynumber: 4.8 Consensus size: 20
995667 TGCGATTTTC
*
995677 CAAATTCGAAACGCGATAGT
1 CAAATTCGCAACGCGATAGT
* *
995697 CAAATTCTCAACGCGAAAGT
1 CAAATTCGCAACGCGATAGT
995717 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGATAGT
* *
995737 CAAATTCGCAAC-TGA-ATTT
1 CAAATTCGCAACGCGATA-GT
995756 CAAATTCGCAACGCGA
1 CAAATTCGCAACGCGA
995772 ATTTAATTTC
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
18 1 0.02
19 15 0.23
20 49 0.75
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (20 bp):
CAAATTCGCAACGCGATAGT
Found at i:995770 original size:39 final size:40
Alignment explanation
Indices: 995677--995771 Score: 138
Period size: 40 Copynumber: 2.4 Consensus size: 40
995667 TGCGATTTTC
* *
995677 CAAATTCGAAACGCGATAGTCAAATTCTCAACGCGAAAGT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAAAGT
* **
995717 CAAATTCGCAACGCGATAGTCAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAAAGT
995756 CAAATTCGCAACGCGA
1 CAAATTCGCAACGCGA
995772 ATTTAATTTC
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 20 0.40
40 30 0.60
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (40 bp):
CAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAAAGT
Found at i:995775 original size:20 final size:20
Alignment explanation
Indices: 995554--995786 Score: 111
Period size: 20 Copynumber: 11.6 Consensus size: 20
995544 AAATGACCAA
* *
995554 CAAATTCTCAACGCGAATTC
1 CAAATTCGCAACGCGAATTT
* * *
995574 CAATTTCGCAAC-CCAGTTTT
1 CAAATTCGCAACGCGA-ATTT
* * *
995594 CAATTTTGCAACGGGAATATGT
1 CAAATTCGCAACGCGAAT-T-T
** *
995616 -AAA-TCGCATTGCGATTTT
1 CAAATTCGCAACGCGAATTT
* * *
995634 CCAAATTCGCGATGCGATTTTT
1 -CAAATTCGCAACGCGA-ATTT
* * * *
995656 TAAATTCGCGATGCGATTTT
1 CAAATTCGCAACGCGAATTT
* *
995676 CCAAATTCGAAACGCG-ATAGT
1 -CAAATTCGCAACGCGAAT-TT
* **
995697 CAAATTCTCAACGCGAAAGT
1 CAAATTCGCAACGCGAATTT
*
995717 CAAATTCGCAACGCG-ATAGT
1 CAAATTCGCAACGCGAAT-TT
*
995737 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATTT
995756 CAAATTCGCAACGCGAATTT
1 CAAATTCGCAACGCGAATTT
*
995776 -AATTTCGCAAC
1 CAAATTCGCAAC
995787 AGGTTTTAGT
Statistics
Matches: 166, Mismatches: 33, Indels: 29
0.73 0.14 0.13
Matches are distributed among these distances:
18 1 0.01
19 28 0.17
20 91 0.55
21 41 0.25
22 5 0.03
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:996722 original size:24 final size:24
Alignment explanation
Indices: 996695--996748 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
996685 GTATTCGAAA
*
996695 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
996719 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
996743 TTTGAT
1 TTTGAT
996749 GATGTGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:999036 original size:18 final size:18
Alignment explanation
Indices: 999013--999051 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
999003 AACCAAAAGG
**
999013 AAATCAAAATCGTAATCA
1 AAATCAAAATCCCAATCA
999031 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
999049 AAA
1 AAA
999052 CTGGCTTCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.59, C:0.21, G:0.03, T:0.18
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:999365 original size:20 final size:20
Alignment explanation
Indices: 999316--999358 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
999306 ATGTTGTGAT
*
999316 CAACGTGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
999336 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
999356 CAA
1 CAA
999359 ACCGAAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCG
Found at i:999592 original size:61 final size:64
Alignment explanation
Indices: 999461--999601 Score: 173
Period size: 61 Copynumber: 2.2 Consensus size: 64
999451 TTTTAGAAAC
*
999461 AACAAATCAACTTTTACAAATAAATTAAATAAGCAAAAAAATAATTCTTATTTACAAATCAAATT
1 AACAAATCAACTTTTACAAATAAATTAAAT-A-CAAAAAAATAAATCTTATTTACAAATCAAATT
999526 A
64 A
* * ** *
999527 AACAAATCAACTTTTACAAATCAATT-AAT-C-AAAAAATAAATCTTATTTCCTCATC-AATTGT
1 AACAAATCAACTTTTACAAATAAATTAAATACAAAAAAATAAATCTTATTTACAAATCAAATT-A
999588 AACAAATCAACTTT
1 AACAAATCAACTTT
999602 CAATGTAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
60 4 0.06
61 35 0.51
62 1 0.01
65 3 0.04
66 25 0.37
ACGTcount: A:0.51, C:0.16, G:0.01, T:0.32
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATAAATTAAATACAAAAAAATAAATCTTATTTACAAATCAAATTA
Found at i:1000995 original size:21 final size:21
Alignment explanation
Indices: 1000971--1001060 Score: 83
Period size: 21 Copynumber: 4.3 Consensus size: 21
1000961 GGCAGGACCA
* *
1000971 CTTGAACGATGACAGTGGCCT
1 CTTGAACGATGAGAGGGGCCT
* * *
1000992 CTTGAACGGTGGGAGGGGCTT
1 CTTGAACGATGAGAGGGGCCT
* *
1001013 CTTCG-ATGATGATAGGGGCCT
1 CTT-GAACGATGAGAGGGGCCT
* *
1001034 CTTGAACGATAAGAGGCGCCT
1 CTTGAACGATGAGAGGGGCCT
1001055 CTTGAA
1 CTTGAA
1001061 TGATTATAGG
Statistics
Matches: 53, Mismatches: 14, Indels: 4
0.75 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 51 0.96
22 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.33, T:0.24
Consensus pattern (21 bp):
CTTGAACGATGAGAGGGGCCT
Found at i:1001064 original size:42 final size:42
Alignment explanation
Indices: 1000971--1001070 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 42
1000961 GGCAGGACCA
* * * * ** * *
1000971 CTTGAACGATGACAGTGGCCTCTTGAACGGTGGGAGGGGCTT
1 CTTGAATGATGATAGGGGCCTCTTGAACGATAAGAGGCGCCT
1001013 CTTCG-ATGATGATAGGGGCCTCTTGAACGATAAGAGGCGCCT
1 CTT-GAATGATGATAGGGGCCTCTTGAACGATAAGAGGCGCCT
*
1001055 CTTGAATGATTATAGG
1 CTTGAATGATGATAGG
1001071 TGCATCGGGA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
41 1 0.02
42 45 0.96
43 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26
Consensus pattern (42 bp):
CTTGAATGATGATAGGGGCCTCTTGAACGATAAGAGGCGCCT
Found at i:1001491 original size:21 final size:21
Alignment explanation
Indices: 1001467--1001519 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1001457 TGCACTATTA
*
1001467 TCTTCACGTAAAGTACCGACC
1 TCTTCACGTAAAGCACCGACC
* *
1001488 TCTTGACGCAAAGCACCGACC
1 TCTTCACGTAAAGCACCGACC
*
1001509 TCATCACGTAA
1 TCTTCACGTAA
1001520 TTCCCCTAAC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.30, C:0.34, G:0.15, T:0.21
Consensus pattern (21 bp):
TCTTCACGTAAAGCACCGACC
Found at i:1003436 original size:22 final size:22
Alignment explanation
Indices: 1003405--1003455 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1003395 GATGGAGATA
*
1003405 GACGGATTTCGTCGGAAATGGG
1 GACGGATTTCATCGGAAATGGG
* *
1003427 GATGGATTTCATCGGAGATGGG
1 GACGGATTTCATCGGAAATGGG
1003449 GACGGAT
1 GACGGAT
1003456 GTCACCGTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.41, T:0.24
Consensus pattern (22 bp):
GACGGATTTCATCGGAAATGGG
Found at i:1003608 original size:20 final size:20
Alignment explanation
Indices: 1003583--1003627 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1003573 GCGTAAAAAC
*
1003583 ATTTGACTTTCGCGTTGAGA
1 ATTTGACTATCGCGTTGAGA
*
1003603 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGAGA
1003623 ATTTG
1 ATTTG
1003628 GAAAATCGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (20 bp):
ATTTGACTATCGCGTTGAGA
Found at i:1003990 original size:13 final size:13
Alignment explanation
Indices: 1003974--1004008 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1003964 AAGACCAAAT
1003974 TTAAATATATAAA
1 TTAAATATATAAA
*
1003987 TTAAATATATAAC
1 TTAAATATATAAA
*
1004000 TTATATATA
1 TTAAATATA
1004009 GTACAAGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (13 bp):
TTAAATATATAAA
Found at i:1004404 original size:18 final size:18
Alignment explanation
Indices: 1004381--1004415 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1004371 AAGTATAAGG
*
1004381 ATTTATTTAAAATTAATC
1 ATTTATTAAAAATTAATC
1004399 ATTTATTAAAAATTAAT
1 ATTTATTAAAAATTAAT
1004416 TATAACTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTATTAAAAATTAATC
Found at i:1017685 original size:16 final size:17
Alignment explanation
Indices: 1017664--1017695 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1017654 TTTATCAAAA
1017664 GAAACTA-AAATTAATT
1 GAAACTATAAATTAATT
1017680 GAAACTATAAATTAAT
1 GAAACTATAAATTAAT
1017696 ATAAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.31
Consensus pattern (17 bp):
GAAACTATAAATTAATT
Found at i:1020458 original size:509 final size:512
Alignment explanation
Indices: 1019170--1020718 Score: 2889
Period size: 519 Copynumber: 3.0 Consensus size: 512
1019160 TGTTAAATTG
1019170 TAATGTTCCTTTATGGTTTGTTAGTGACTATCCTCAATGTATCTCGAATGTTGTTATTTTGGACG
1 TAATGTTCCTTTATGGTTTGTTAGTGACTATCCTCAATGTATCTCGAATGTTGTTATTTTGGACG
1019235 CAATTGGAATCGAATGAATGCAAATCATTTTTATTCTAAAAAAAAAATATGCTCTTAAACGACAT
66 CAATTGGAATCGAATGAATGCAAATCATTTTTATTCT--AAAAAAAATATGCTCTTAAACGACAT
1019300 CAAACTGCTTACCACATGAATCAATCGTCATTGGTCAATACACTTTAAATTAATGACGGAAAGCT
129 CAAACTGCTTACCACATG-A--AATCGTCATTGGTCAATACACTTTAAATTAATGACGGAAAGCT
1019365 TAGCCTCTCAATTATAGTTTAAATTTTTTATATTATATTGCACTTAATACTTATATTACAATTAA
191 TAGCCTCTCAATTATAGTTTAAATTTTTTATATTATATTGCACTTAATACTTATATTACAATTAA
*
1019430 ATTAAAAGACTAATTTATTTAATTATCCAAATCATATTATTTATTATTTATTTAAATTAAACTGT
256 ATTAAAAGACTAATTTATTTAATTATCCAAATCATATTATTTATTATTTATTTAAATTAAATTGT
1019495 TATCGAAGTCTTTTAACTTAATAATGATATAAGTAAATATTAAGTTTGGTATAATAAAAAATAAT
321 TATCGAAGTCTTTTAACTTAATAATGATATAAGTAAATATTAAGTTTGG-ATAAT---AAATAAT
1019560 TACCTATTTAAAATATTTAAAAAATAAATAATATTATTTCAAATAAAAGAATCATAAATTTTATA
382 TACCTATTTAAAATATTTAAAAAATAAATAATATTATTTCAAATAAAAGAATCATAAATTTTATA
1019625 AAAACATATAAATTATTTAATTATTTTTTATTTCTAATAAAATGAAAAAATAGTATTTTAATTTT
447 AAAACATATAAATTATTTAATTATTTTTTATTTCTAATAAAATGAAAAAATAGTATTTTAATTTT
1019690 A
512 A
1019691 TAATGTTCCTTTATGGTTTGTTAGTGACTATCCTCAATGTATCTCGAATGTTGTTATTTTGGACG
1 TAATGTTCCTTTATGGTTTGTTAGTGACTATCCTCAATGTATCTCGAATGTTGTTATTTTGGACG
1019756 CAATTGGAATCGAATGAATGCAAATCATTTTTATTCTAAAAAAAATATGCTCTTAAACGACATCA
66 CAATTGGAATCGAATGAATGCAAATCATTTTTATTCTAAAAAAAATATGCTCTTAAACGACATCA
1019821 AACTGCTTACCACATGAATCAATCGTCATTGGTCAATACACTTTAAATTAATGACGGAAAGCTTA
131 AACTGCTTACCACATG-A--AATCGTCATTGGTCAATACACTTTAAATTAATGACGGAAAGCTTA
1019886 GCCTCTCAATTATAGTTTAAATTTTTTATATTATATTGCACTTAATACTTATATTACAATTAAAT
193 GCCTCTCAATTATAGTTTAAATTTTTTATATTATATTGCACTTAATACTTATATTACAATTAAAT
1019951 TAAAAGACTAATTTATTTAATTATCCAAATCATATTATTTATTATTTATTTAAATTAAATTGTTA
258 TAAAAGACTAATTTATTTAATTATCCAAATCATATTATTTATTATTTATTTAAATTAAATTGTTA
1020016 TCGAAGTCTTTTAACTTAATAATGATAT-AGTAAATATTAAG-TTGG-T-AT-AATAA-TACCTA
323 TCGAAGTCTTTTAACTTAATAATGATATAAGTAAATATTAAGTTTGGATAATAAATAATTACCTA
1020075 TTTAAAATATTTAAAAAATAAATAATATTATTTCAAATAAAAGAATCATAAATTTTATAAAAACA
388 TTTAAAATATTTAAAAAATAAATAATATTATTTCAAATAAAAGAATCATAAATTTTATAAAAACA
1020140 TATAAATTATTTAATTATTTTTTATTTCTAATAAAATGAAAAAATAGTATTTTAATTTTA
453 TATAAATTATTTAATTATTTTTTATTTCTAATAAAATGAAAAAATAGTATTTTAATTTTA
1020200 TAATGTTCCTTTATGGTTTGTTAGTGACTATCCTCAATGTATCTCGAATGTTGTTATTTTGGACG
1 TAATGTTCCTTTATGGTTTGTTAGTGACTATCCTCAATGTATCTCGAATGTTGTTATTTTGGACG
1020265 CAATTGGAATCGAATGAATGCAAATCATTTTTATTCTAAAAAAAA-ATGCTCTTAAACGACATCA
66 CAATTGGAATCGAATGAATGCAAATCATTTTTATTCTAAAAAAAATATGCTCTTAAACGACATCA
1020329 AACTGCTTACCACATG-AATCGTCATTGGTCAATACACTTTAAATTAATGACGGAAAGCTTAGCC
131 AACTGCTTACCACATGAAATCGTCATTGGTCAATACACTTTAAATTAATGACGGAAAGCTTAGCC
1020393 TCTCAATTATAGTTTAAATTTTTTATATTATATTGCACTTAATACTTATATTACAATTAAATTAA
196 TCTCAATTATAGTTTAAATTTTTTATATTATATTGCACTTAATACTTATATTACAATTAAATTAA
1020458 AAGACTAATTTATTTAATTATCCAAATCATATTATTTATTATTTATTTAAATTAAATTGTTATCG
261 AAGACTAATTTATTTAATTATCCAAATCATATTATTTATTATTTATTTAAATTAAATTGTTATCG
1020523 AAGTCTTTTAACTTAATAATGATATAAGTAAATATTAAGTTTGGTATAATAAAAAATAATTACCT
326 AAGTCTTTTAACTTAATAATGATATAAGTAAATATTAAGTTTGG-ATAAT---AAATAATTACCT
1020588 ATTTAAAATATTTAAAAAATAAATAATATTATTTCAAATAAAAGAATCATAAATTTTATAAAAAC
387 ATTTAAAATATTTAAAAAATAAATAATATTATTTCAAATAAAAGAATCATAAATTTTATAAAAAC
1020653 ATATAAATTATTTAATTATTTTTTATTTCTAATAAAATGAAAAAATAGTATTTTAATTTTA
452 ATATAAATTATTTAATTATTTTTTATTTCTAATAAAATGAAAAAATAGTATTTTAATTTTA
1020714 TAATG
1 TAATG
1020719 GTATAAGTAA
Statistics
Matches: 1017, Mismatches: 1, Indels: 27
0.97 0.00 0.03
Matches are distributed among these distances:
504 203 0.20
505 13 0.01
506 4 0.00
508 36 0.04
509 243 0.24
510 5 0.00
513 5 0.00
514 138 0.14
515 1 0.00
517 4 0.00
518 13 0.01
519 250 0.25
521 102 0.10
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (512 bp):
TAATGTTCCTTTATGGTTTGTTAGTGACTATCCTCAATGTATCTCGAATGTTGTTATTTTGGACG
CAATTGGAATCGAATGAATGCAAATCATTTTTATTCTAAAAAAAATATGCTCTTAAACGACATCA
AACTGCTTACCACATGAAATCGTCATTGGTCAATACACTTTAAATTAATGACGGAAAGCTTAGCC
TCTCAATTATAGTTTAAATTTTTTATATTATATTGCACTTAATACTTATATTACAATTAAATTAA
AAGACTAATTTATTTAATTATCCAAATCATATTATTTATTATTTATTTAAATTAAATTGTTATCG
AAGTCTTTTAACTTAATAATGATATAAGTAAATATTAAGTTTGGATAATAAATAATTACCTATTT
AAAATATTTAAAAAATAAATAATATTATTTCAAATAAAAGAATCATAAATTTTATAAAAACATAT
AAATTATTTAATTATTTTTTATTTCTAATAAAATGAAAAAATAGTATTTTAATTTTA
Found at i:1023318 original size:21 final size:21
Alignment explanation
Indices: 1023294--1023335 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1023284 AGTTTATTTT
1023294 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
1023315 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
1023336 AACTTGAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:1023383 original size:33 final size:33
Alignment explanation
Indices: 1023322--1023428 Score: 157
Period size: 33 Copynumber: 3.3 Consensus size: 33
1023312 TCGTAAACTT
1023322 TATTTCAA-TTATCGAACTT-GAAGTTTTTAAG
1 TATTTCAATTTATCGAACTTGGAAGTTTTTAAG
*
1023353 TATTTGAATTTATCGAACTTGGAAGTTTTTAAG
1 TATTTCAATTTATCGAACTTGGAAGTTTTTAAG
* *
1023386 TATTTGAATTTATC-ATACTTGGAAGTATTTAAG
1 TATTTCAATTTATCGA-ACTTGGAAGTTTTTAAG
1023419 TATTTCAATT
1 TATTTCAATT
1023429 ATGTTGAGTT
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
31 7 0.10
32 12 0.17
33 51 0.73
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.47
Consensus pattern (33 bp):
TATTTCAATTTATCGAACTTGGAAGTTTTTAAG
Found at i:1023457 original size:13 final size:13
Alignment explanation
Indices: 1023414--1023468 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
1023404 TTGGAAGTAT
1023414 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
1023427 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
1023441 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
1023454 TTAAGTATTTGAA
1 TTAAGTATTTCAA
1023467 TT
1 TT
1023469 TATTGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:1023690 original size:21 final size:21
Alignment explanation
Indices: 1023664--1023720 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1023654 TGGAGCGTGG
*
1023664 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
1023685 GGGAATCGGTTCCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
1023706 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
1023721 AAGTGTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.26
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:1024208 original size:18 final size:19
Alignment explanation
Indices: 1024180--1024215 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1024170 GTTTTTTTAT
1024180 AACCGGTTTTTTTTAAAAA
1 AACCGGTTTTTTTTAAAAA
1024199 AACCGG-TTTTTTTAAAA
1 AACCGGTTTTTTTTAAAA
1024216 TCGAAACCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (19 bp):
AACCGGTTTTTTTTAAAAA
Found at i:1024215 original size:15 final size:15
Alignment explanation
Indices: 1024161--1024215 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 15
1024151 TTTAATAATA
*
1024161 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
1024176 TTATAACCGGTTTTTT
1 TTAAAACCGG-TTTTT
1024192 TTAAAAAAACCGGTTTTT
1 TT---AAAACCGGTTTTT
1024210 TTAAAA
1 TTAAAA
1024216 TCGAAACCAG
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
15 12 0.36
16 7 0.21
18 7 0.21
19 7 0.21
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:1024335 original size:15 final size:17
Alignment explanation
Indices: 1024309--1024340 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1024299 TTCTATGGGA
1024309 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
1024325 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
1024341 CGGATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:1024338 original size:21 final size:21
Alignment explanation
Indices: 1024314--1024366 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
1024304 TGGGAAAAAA
1024314 CCGGATCGGATAAAAACCGAT
1 CCGGATCGGATAAAAACCGAT
1024335 CCGGATCGGATAAAAACCGAT
1 CCGGATCGGATAAAAACCGAT
1024356 CCGGATCGGAT
1 CCGGATCGGAT
1024367 TGAAATCCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.34, C:0.25, G:0.26, T:0.15
Consensus pattern (21 bp):
CCGGATCGGATAAAAACCGAT
Found at i:1024499 original size:22 final size:21
Alignment explanation
Indices: 1024457--1024499 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
1024447 AATTCCGACG
* **
1024457 GAAAAAAAAGAAATGTGATAT
1 GAAAAAAAAAAAATGACATAT
1024478 GAAAATAAAAAAAATGACATAT
1 GAAAA-AAAAAAAATGACATAT
1024500 CATGCCGCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.65, C:0.02, G:0.14, T:0.19
Consensus pattern (21 bp):
GAAAAAAAAAAAATGACATAT
Found at i:1033336 original size:27 final size:27
Alignment explanation
Indices: 1033306--1033371 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
1033296 GATCTCCGAC
1033306 TGCTACATCCTCATCCTGCTCCGGTTT
1 TGCTACATCCTCATCCTGCTCCGGTTT
* *
1033333 TGCTATATCCTCATCCTGCTCGGGTTT
1 TGCTACATCCTCATCCTGCTCCGGTTT
* *
1033360 TGCCACTTCCTC
1 TGCTACATCCTC
1033372 CTGCAAGCAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.11, C:0.36, G:0.15, T:0.38
Consensus pattern (27 bp):
TGCTACATCCTCATCCTGCTCCGGTTT
Found at i:1038424 original size:25 final size:25
Alignment explanation
Indices: 1038390--1038451 Score: 124
Period size: 25 Copynumber: 2.5 Consensus size: 25
1038380 TATGAAGTTT
1038390 TCTTTTTATTTAGTTTAGTTCATAA
1 TCTTTTTATTTAGTTTAGTTCATAA
1038415 TCTTTTTATTTAGTTTAGTTCATAA
1 TCTTTTTATTTAGTTTAGTTCATAA
1038440 TCTTTTTATTTA
1 TCTTTTTATTTA
1038452 ATCTTAAACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.23, C:0.08, G:0.06, T:0.63
Consensus pattern (25 bp):
TCTTTTTATTTAGTTTAGTTCATAA
Found at i:1040749 original size:15 final size:15
Alignment explanation
Indices: 1040729--1040761 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1040719 TGAGACATTA
*
1040729 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
1040744 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
1040759 CCC
1 CCC
1040762 ACCCAACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.70, G:0.15, T:0.06
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:1046635 original size:23 final size:23
Alignment explanation
Indices: 1046609--1046653 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1046599 CACCACAGCT
*
1046609 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
1046632 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1046654 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:1046974 original size:145 final size:146
Alignment explanation
Indices: 1046632--1047067 Score: 707
Period size: 145 Copynumber: 3.0 Consensus size: 146
1046622 CGAAGTGCCC
1046632 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACGTAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACGTAGAATTCTTTAAGAAT
1046697 CATATAC-TATGCTAGGGATC-AGTATGTGTCTTTCCAGACTTCACATGTTCCAAAGAATATACA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACATGTTCCAAAGAATATACA
1046760 TATGTCCCGAAGAACCG
131 -ATGTCCCGAAGAACCG
1046777 CGTAG-A----A----AGTGCCATATAATGATGTCCATAAGGACCACGTAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACGTAGAATTCTTTAAGAAT
1046833 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACATGTTCCAAAGAATATAC-
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACATGTTCCAAAGAATATACA
1046897 ATGTCCCGAAGAACCG
131 ATGTCCCGAAGAACCG
* *
1046913 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACGTAGAATTCTTTAAGAAT
* *
1046978 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATATTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTT--CACATGTTCCAAAGAATATA
*
1047043 CATATGTCTCGAAGAACCG
129 CA-ATGTCCCGAAGAACCG
1047062 CGTAGA
1 CGTAGA
1047068 CCCTCGACTC
Statistics
Matches: 271, Mismatches: 5, Indels: 26
0.90 0.02 0.09
Matches are distributed among these distances:
136 77 0.28
137 14 0.05
138 42 0.15
140 1 0.00
141 1 0.00
144 1 0.00
145 94 0.35
147 20 0.07
149 21 0.08
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (146 bp):
CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACGTAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACATGTTCCAAAGAATATACA
ATGTCCCGAAGAACCG
Found at i:1047708 original size:2 final size:2
Alignment explanation
Indices: 1047701--1047732 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1047691 TCTCTTAGAC
1047701 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
1047733 TCACATGTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1048698 original size:20 final size:21
Alignment explanation
Indices: 1048658--1048701 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1048648 ATTCTGTCGT
*
1048658 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
1048679 TTGAATGGGTA-CGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
1048699 TTG
1 TTG
1048702 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.16, C:0.23, G:0.30, T:0.32
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:1061406 original size:20 final size:20
Alignment explanation
Indices: 1061381--1061473 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
1061371 TTTTCCCAAT
1061381 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
1061401 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
1061421 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* * *
1061442 TCGCAACGCGAATTGAGAAAA
1 TCGCAATGCGAA-TAAGTAAA
1061463 TCGCAATGCGA
1 TCGCAATGCGA
1061474 TACTGACTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 27 0.46
21 32 0.54
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:1061423 original size:41 final size:41
Alignment explanation
Indices: 1061378--1061473 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
1061368 CGATTTTCCC
*
1061378 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
1061419 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
*
1061460 AAATCGCAATGCGA
1 AATTCGCAATGCGA
1061474 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
Found at i:1061486 original size:41 final size:41
Alignment explanation
Indices: 1061400--1061530 Score: 115
Period size: 41 Copynumber: 3.2 Consensus size: 41
1061390 GAATAAGTAA
* * * *
1061400 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCG-ATACTG-ACT
1061441 ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
* * * * * *
1061482 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGAGAAAATCGCAATGCGATACTGACT
*
1061523 TTCGCAAC
1 ATCGCAAC
1061531 ACGATACTGA
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
40 4 0.05
41 69 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
Found at i:1061487 original size:20 final size:20
Alignment explanation
Indices: 1061462--1061556 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
1061452 AATTGAGAAA
*
1061462 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1061482 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
1061503 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
1061523 TTCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1061543 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1061557 ATACATAATC
Statistics
Matches: 59, Mismatches: 15, Indels: 2
0.78 0.20 0.03
Matches are distributed among these distances:
20 45 0.76
21 14 0.24
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1061772 original size:22 final size:22
Alignment explanation
Indices: 1061744--1061787 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1061734 CACTCTCTCA
1061744 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1061766 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1061788 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1062076 original size:20 final size:20
Alignment explanation
Indices: 1062051--1062088 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1062041 CGGTTCTCTC
1062051 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
1062071 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
1062089 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:1063428 original size:18 final size:18
Alignment explanation
Indices: 1063407--1063451 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1063397 TCCACTTCGG
*
1063407 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
1063425 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
1063443 GAGCCATCA
1 GAGCCATCA
1063452 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1063969 original size:19 final size:20
Alignment explanation
Indices: 1063915--1063970 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
1063905 TAGTTTACTT
* *
1063915 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1063935 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
*
1063955 TCGCAATGC-GAAATGA
1 TCGCAACGCGGAAATGA
1063971 AAATCACAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1063989 original size:14 final size:14
Alignment explanation
Indices: 1063970--1064027 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1063960 ATGCGAAATG
*
1063970 AAAATCACAACGAC
1 AAAATCGCAACGAC
*
1063984 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
1064000 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1064016 AAAATCGCAACG
1 AAAATCGCAACG
1064028 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.50, C:0.26, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1064013 original size:32 final size:33
Alignment explanation
Indices: 1063954--1064044 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1063944 GGAAATGGCT
* *
1063954 ATCGCAATGCGAAATGAAAATCACAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1063987 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1064019 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
1064045 TGTGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:1064080 original size:14 final size:14
Alignment explanation
Indices: 1064061--1064149 Score: 88
Period size: 14 Copynumber: 5.8 Consensus size: 14
1064051 TTGTGTTTCG
1064061 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1064075 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1064091 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
1064107 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1064123 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1064139 CGTTGCGATTT
1 CGTTGCGATTT
1064150 CATTTCGCAT
Statistics
Matches: 63, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
14 33 0.52
16 8 0.13
18 22 0.35
ACGTcount: A:0.09, C:0.18, G:0.26, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1064092 original size:32 final size:32
Alignment explanation
Indices: 1064056--1064165 Score: 211
Period size: 32 Copynumber: 3.4 Consensus size: 32
1064046 GTGATTTGTG
1064056 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1064088 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1064120 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
*
1064152 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
1064166 AGCCATTTCC
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 77 1.00
ACGTcount: A:0.10, C:0.19, G:0.25, T:0.46
Consensus pattern (32 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
Found at i:1064184 original size:20 final size:19
Alignment explanation
Indices: 1064150--1064204 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
1064140 GTTGCGATTT
*
1064150 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1064169 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
1064189 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
1064205 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1066092 original size:14 final size:14
Alignment explanation
Indices: 1066073--1066108 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1066063 ATTGTTTAAT
1066073 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1066087 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1066101 TGATTTGT
1 TGATTTGT
1066109 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1066234 original size:14 final size:14
Alignment explanation
Indices: 1066215--1066268 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
1066205 CGAAATGGCT
1066215 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
1066229 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
1066248 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
1066262 ATCGCAA
1 ATCGCAA
1066269 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:1066286 original size:33 final size:33
Alignment explanation
Indices: 1066196--1066273 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
1066186 AAAACAGACT
* ***
1066196 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1066229 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1066262 ATCGCAATGCGA
1 ATCGCAATGCGA
1066274 TTTTCATTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:1066317 original size:20 final size:20
Alignment explanation
Indices: 1066292--1066348 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
1066282 TCGCATTGCG
*
1066292 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAACC
1066312 ATTTTCGCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAACC
*
1066332 ATTTTCGCATTGCGATA
1 ATTTTCGCGTTGCGATA
1066349 GTCAAATGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAACC
Found at i:1066735 original size:14 final size:14
Alignment explanation
Indices: 1066716--1066751 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1066706 ATTGTTTAAT
1066716 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1066730 TGATTTGTAAATGC
1 TGATTTGTAAAAGA
1066744 TGATTTGT
1 TGATTTGT
1066752 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.03, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1067325 original size:14 final size:14
Alignment explanation
Indices: 1067306--1067341 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1067296 ATTGTTTAAT
1067306 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1067320 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1067334 TGATTTGT
1 TGATTTGT
1067342 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1067687 original size:589 final size:590
Alignment explanation
Indices: 1066312--1067716 Score: 2731
Period size: 590 Copynumber: 2.4 Consensus size: 590
1066302 TGCGATAACC
*
1066312 ATTTTCGCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
1 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
* * *
1066377 AACTGAACAGATAATAGCAATGTTCAAACTCAAGTTATTAATACATGCCTAACTGAAAAAGTTAA
66 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
1066442 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
131 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
1066507 ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
196 ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
1066572 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
261 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
1066637 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
326 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
1066702 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGCTGATTTGTTTAATTGATGTGTAC
391 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGCTGATTTGTTTAATTGATGTGTAC
1066767 ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
456 ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
1066832 ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCA
521 ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCA
1066897 TTGCA
586 TTGCA
1066902 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
1 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
1066967 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
66 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
1067032 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
131 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
1067097 ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
196 ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
1067162 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
261 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
1067227 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
326 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
*
1067292 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAC
391 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGCTGATTTGTTTAATTGATGTGTAC
1067357 -TAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
456 ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
1067421 ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCA
521 ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCA
*
1067486 TTGCG
586 TTGCA
1067491 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
1 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
1067556 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
66 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
*
1067621 AAGTGCATACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
131 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
*
1067686 ATATTTGGTTAAGTACCTAGAATTCAATAAT
196 ATGTTTGGTTAAGTACCTAGAATTCAATAAT
1067717 AATTGTTAAA
Statistics
Matches: 807, Mismatches: 8, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
589 357 0.44
590 450 0.56
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.36
Consensus pattern (590 bp):
ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGCTGATTTGTTTAATTGATGTGTAC
ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCA
TTGCA
Found at i:1068641 original size:24 final size:24
Alignment explanation
Indices: 1068585--1068643 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
1068575 AGTCAGTATT
* *
1068585 CGAAATTTGATCTTAGTCAATACC
1 CGAAATTTGATATTAGTCAATACA
* * *
1068609 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTAGTCAATACA
*
1068633 CGAATTTTGAT
1 CGAAATTTGAT
1068644 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTAGTCAATACA
Found at i:1068835 original size:12 final size:12
Alignment explanation
Indices: 1068818--1068842 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1068808 ATATAATCCT
1068818 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1068830 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1068842 G
1 G
1068843 TCACCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1071158 original size:19 final size:19
Alignment explanation
Indices: 1071136--1071233 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
1071126 GGAAATTACT
1071136 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1071155 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1071169 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
1071188 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
1071202 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1071221 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1071234 TTTAATTTCG
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.50
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1071178 original size:33 final size:33
Alignment explanation
Indices: 1071136--1071229 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
1071126 GGAAATTACT
1071136 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1071169 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1071202 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1071230 CGAATTTAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1071251 original size:19 final size:20
Alignment explanation
Indices: 1071229--1071271 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1071219 AAATCGCAAC
1071229 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
1071248 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
1071268 GCGA
1 GCGA
1071272 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:1071256 original size:14 final size:14
Alignment explanation
Indices: 1071257--1071290 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1071247 TGCGATTTTC
1071257 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
1071271 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
1071285 ATTTTC
1 ATTTTC
1071291 ATTCGCATTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:1071430 original size:14 final size:14
Alignment explanation
Indices: 1071411--1071447 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1071401 CATCAATTAA
1071411 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1071425 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1071439 ACAAATCAA
1 ACAAATCAA
1071448 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1072870 original size:21 final size:21
Alignment explanation
Indices: 1072804--1072870 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1072794 GTGAATCGGG
*
1072804 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1072824 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1072846 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1072867 CTCT
1 CTCT
1072871 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1072889 original size:42 final size:41
Alignment explanation
Indices: 1072804--1072926 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1072794 GTGAATCGGG
* * * * *
1072804 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
1072846 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
1072888 CTCTTCAACGATAGGAGTGGACTCTTGATGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
1072927 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.24
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:1074970 original size:20 final size:19
Alignment explanation
Indices: 1074925--1075046 Score: 57
Period size: 20 Copynumber: 6.8 Consensus size: 19
1074915 TCTTTTGGTT
1074925 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* * *
1074944 GATAATGAGAATTGCAACGCG
1 GA-AATGAAAATCGCAACG-A
** *
1074965 GAAATGACTATCGCAATGA
1 GAAATGAAAATCGCAACGA
*
1074984 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** *
1074998 GAAATGACTATCGCGACGA
1 GAAATGAAAATCGCAACGA
*
1075017 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
1075031 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1075047 TGCGATTTTG
Statistics
Matches: 74, Mismatches: 17, Indels: 24
0.64 0.15 0.21
Matches are distributed among these distances:
14 18 0.24
16 4 0.05
17 4 0.05
19 20 0.27
20 26 0.35
21 2 0.03
ACGTcount: A:0.43, C:0.19, G:0.25, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1075007 original size:33 final size:33
Alignment explanation
Indices: 1074950--1075048 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
1074940 ACGAGATAAT
*
1074950 GAGAATTGCAACGCGGAAATGACTATCGCAATGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAATGA
* *
1074984 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAATGA
**
1075017 GAGAATCGCAACGCGAAATGAAAATCGCAATG
1 GAGAATCGCAACGCGAAATGACTATCGCAATG
1075049 CGATTTTGGT
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 45 0.78
34 13 0.22
ACGTcount: A:0.39, C:0.20, G:0.26, T:0.14
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAATGA
Found at i:1075080 original size:19 final size:19
Alignment explanation
Indices: 1075047--1075113 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
1075037 AAAATCGCAA
**
1075047 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
1075066 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
** *
1075085 TGCGATAGTTATTTCCGCTT
1 TGCGATTTTTATTT-CGCGT
1075105 TGCGATTTT
1 TGCGATTTT
1075114 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 29 0.73
20 11 0.28
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.49
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:1075661 original size:20 final size:20
Alignment explanation
Indices: 1075636--1075687 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1075626 CGCTAAGTAA
*
1075636 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTAAGT
1075656 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGAAAGTAAGT
*
1075676 ATCTCGTTGCGA
1 ATCGCGTTGCGA
1075688 TTTTTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTAAGT
Found at i:1075707 original size:41 final size:41
Alignment explanation
Indices: 1075655--1075732 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
1075645 CGAAAGTCAG
* * *
1075655 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCACATTGCGATTTTTTAT
* *
1075696 TATCGCATTGCGATAGTCAGTATCACATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCACATTGCGATTTT
1075733 CCCAATTCGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCACATTGCGATTTTTTAT
Found at i:1075748 original size:41 final size:41
Alignment explanation
Indices: 1075655--1075750 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 41
1075645 CGAAAGTCAG
* * * ** *
1075655 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGATAGTAAGTATCACATTGCGATTTTCCAA
* *
1075696 TATCGCATTGCGATAGTCAGTATCACATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGTATCACATTGCGATTTT-CCAA
1075738 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
1075751 TTACTTATTC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 43 0.96
42 2 0.04
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.38
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCACATTGCGATTTTCCAA
Found at i:1077221 original size:5 final size:5
Alignment explanation
Indices: 1077211--1077245 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
1077201 CAAAAATCCG
*
1077211 ACCCA ACCCA ACCCA ACCCA ACCCA ATCCA ACCCA
1 ACCCA ACCCA ACCCA ACCCA ACCCA ACCCA ACCCA
1077246 TGACCATCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.40, C:0.57, G:0.00, T:0.03
Consensus pattern (5 bp):
ACCCA
Found at i:1094564 original size:18 final size:19
Alignment explanation
Indices: 1094525--1094574 Score: 77
Period size: 18 Copynumber: 2.7 Consensus size: 19
1094515 GAAATATACA
1094525 TTAAATATTAAATAACTAT
1 TTAAATATTAAATAACTAT
1094544 TTAAATATATAAA-AA-TAT
1 TTAAATAT-TAAATAACTAT
1094562 TTAAATATTAAAT
1 TTAAATATTAAAT
1094575 TAATATGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.14
18 11 0.38
19 10 0.34
20 4 0.14
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
TTAAATATTAAATAACTAT
Found at i:1097204 original size:9 final size:10
Alignment explanation
Indices: 1097182--1097207 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1097172 CGGACCGGCT
1097182 AAAAACCGGA
1 AAAAACCGGA
1097192 AAAAACCGGA
1 AAAAACCGGA
1097202 AAAAAC
1 AAAAAC
1097208 TGGGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.65, C:0.19, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAACCGGA
Found at i:1098168 original size:19 final size:20
Alignment explanation
Indices: 1098081--1098169 Score: 101
Period size: 19 Copynumber: 4.3 Consensus size: 20
1098071 CGCGATTTTA
1098081 AAAAATGTGTTGCGATAGT-
1 AAAAATGTGTTGCGATAGTG
* *
1098100 TAAAATGTGTTGCGAGAGTTTG
1 AAAAATGTGTTGCGATAG--TG
1098122 AAAAACGTGTTGTTGCGATAGTG
1 AAAAA--TG-TGTTGCGATAGTG
1098145 AAAAA-GTGTTGCGATAGTG
1 AAAAATGTGTTGCGATAGTG
1098164 AAAAAT
1 AAAAAT
1098170 CCAAAATAAG
Statistics
Matches: 59, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
19 34 0.58
20 1 0.02
21 1 0.02
22 4 0.07
23 7 0.12
24 2 0.03
25 10 0.17
ACGTcount: A:0.36, C:0.06, G:0.28, T:0.30
Consensus pattern (20 bp):
AAAAATGTGTTGCGATAGTG
Found at i:1098583 original size:21 final size:21
Alignment explanation
Indices: 1098557--1098607 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
1098547 GATAATTTGA
1098557 ACTATCGCAACGCGAACTTCG
1 ACTATCGCAACGCGAACTTCG
* *
1098578 ACTATCGCAACGTGAACTTGG
1 ACTATCGCAACGCGAACTTCG
1098599 ACTATCGCA
1 ACTATCGCA
1098608 TTGCGATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (21 bp):
ACTATCGCAACGCGAACTTCG
Found at i:1098650 original size:20 final size:20
Alignment explanation
Indices: 1098625--1098675 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1098615 TTTGTATTAT
1098625 CGCGTTGCGATAGTCAGAAC
1 CGCGTTGCGATAGTCAGAAC
* * *
1098645 CGCGTTACAATAGTTAGAAC
1 CGCGTTGCGATAGTCAGAAC
1098665 CGCGTTGCGAT
1 CGCGTTGCGAT
1098676 TTTGTATTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (20 bp):
CGCGTTGCGATAGTCAGAAC
Found at i:1098755 original size:20 final size:20
Alignment explanation
Indices: 1098623--1098756 Score: 56
Period size: 20 Copynumber: 6.6 Consensus size: 20
1098613 ATTTTGTATT
*
1098623 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAAA
* * * * *
1098643 ACCGCGTTACAATAGTTAGA
1 ATCGCGTTGCGATAGTCAAA
* * **
1098663 ACCGCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--TAGTCAAA
* *
1098684 ATCGCGTTGCGAT-TTACATA
1 ATCGCGTTGCGATAGT-CAAA
* * **
1098704 TTCGCATTGCGATTTTCTAAA
1 ATCGCGTTGCGATAGTC-AAA
**
1098725 ATCGCAATGCGATAGTCAAA
1 ATCGCGTTGCGATAGTCAAA
1098745 ATCGCGTTGCGA
1 ATCGCGTTGCGA
1098757 ATCTGGAAAT
Statistics
Matches: 87, Mismatches: 21, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
18 1 0.01
19 1 0.01
20 53 0.61
21 29 0.33
22 3 0.03
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.31
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAAA
Found at i:1098766 original size:20 final size:21
Alignment explanation
Indices: 1098743--1098796 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
1098733 GCGATAGTCA
1098743 AAATCGCGTTGCGAAT-CTGG
1 AAATCGCGTTGCGAATACTGG
* **
1098763 AAATTGATTTGCG-ATACTGG
1 AAATCGCGTTGCGAATACTGG
*
1098783 AGATCGCGTTGCGA
1 AAATCGCGTTGCGA
1098797 TTTAGAGATC
Statistics
Matches: 25, Mismatches: 7, Indels: 3
0.71 0.20 0.09
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (21 bp):
AAATCGCGTTGCGAATACTGG
Found at i:1098797 original size:20 final size:19
Alignment explanation
Indices: 1098771--1098816 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1098761 GGAAATTGAT
* *
1098771 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
1098791 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
1098810 TTGCGAT
1 TTGCGAT
1098817 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:1098806 original size:19 final size:19
Alignment explanation
Indices: 1098782--1098818 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1098772 TGCGATACTG
*
1098782 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
1098801 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
1098819 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:1100215 original size:31 final size:31
Alignment explanation
Indices: 1100164--1100226 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
1100154 AACAAGAATT
1100164 TAACAAGCCTAGTGTGAACACA-ATAATTGAA
1 TAACAAGCCTAGTGTGAACACAGA-AATTGAA
* * *
1100195 TAACAATCCTGGTGTTAACACAGAAATTGAA
1 TAACAAGCCTAGTGTGAACACAGAAATTGAA
1100226 T
1 T
1100227 TTACAACGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (31 bp):
TAACAAGCCTAGTGTGAACACAGAAATTGAA
Found at i:1109077 original size:34 final size:29
Alignment explanation
Indices: 1109040--1109098 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1109030 GAATACGTCA
1109040 TTCGATTCGGATCACTTAAGAAAAACATG
1 TTCGATTCGGATCACTTAAGAAAAACATG
1109069 TTCGATTCGGATCACTTAAGAAAAACATG
1 TTCGATTCGGATCACTTAAGAAAAACATG
1109098 T
1 T
1109099 CATTCTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (29 bp):
TTCGATTCGGATCACTTAAGAAAAACATG
Found at i:1109657 original size:31 final size:31
Alignment explanation
Indices: 1109592--1109658 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
1109582 ATAATTATAT
* * *
1109592 ATTTAGTCCATATTATTTATATATTATATCA
1 ATTTAGTCCATATTATTTATAAATTAAATAA
1109623 ATTTAGT-CATA-TATTTAATAAATTAAAATAA
1 ATTTAGTCCATATTATTT-ATAAATT-AAATAA
1109654 ATTTA
1 ATTTA
1109659 ATATTTGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 5 0.16
30 10 0.32
31 16 0.52
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (31 bp):
ATTTAGTCCATATTATTTATAAATTAAATAA
Found at i:1109974 original size:30 final size:29
Alignment explanation
Indices: 1109939--1110135 Score: 99
Period size: 30 Copynumber: 6.8 Consensus size: 29
1109929 TTTATGTATT
* *
1109939 TTAACTTTAAAAATATATTTAATTTTTATC
1 TTAAC-TTAAAAATATATTTTATTTTCATC
** * **
1109969 TTAACTTATTCAATATA-TTT-TTATCAAA
1 TTAACTTA-AAAATATATTTTATTTTCATC
* * * *
1109997 TTAAATTAAAATATATATTTTATACTT-GTT
1 TTAACTTAAAA-ATATATTTTAT-TTTCATC
1110027 TTAA-TTAAAAA-A-A-TTTATTCTT-ATC
1 TTAACTTAAAAATATATTTTATT-TTCATC
1110052 -TAACTTAAAAATATATTTTA-TTTCATC
1 TTAACTTAAAAATATATTTTATTTTCATC
* *
1110079 TTTACTTTTAAAAATATAATTTTATTTTCATT
1 TTAAC--TTAAAAATAT-ATTTTATTTTCATC
* *
1110111 TTAACTTTTAAAAATGTATTGTATT
1 TTAAC--TTAAAAATATATTTTATT
1110136 CCTACTTTAA
Statistics
Matches: 128, Mismatches: 23, Indels: 31
0.70 0.13 0.17
Matches are distributed among these distances:
24 3 0.02
25 15 0.12
26 4 0.03
27 7 0.05
28 24 0.19
29 14 0.11
30 26 0.20
31 14 0.11
32 21 0.16
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (29 bp):
TTAACTTAAAAATATATTTTATTTTCATC
Found at i:1110104 original size:31 final size:31
Alignment explanation
Indices: 1110056--1110135 Score: 110
Period size: 32 Copynumber: 2.6 Consensus size: 31
1110046 CTTATCTAAC
1110056 TTAAAAATATATTTTA-TTTCATCTTT-ACTT
1 TTAAAAATATATTTTATTTTCAT-TTTAACTT
1110086 TTAAAAATATAATTTTATTTTCATTTTAACTT
1 TTAAAAATAT-ATTTTATTTTCATTTTAACTT
* *
1110118 TTAAAAATGTATTGTATT
1 TTAAAAATATATTTTATT
1110136 CCTACTTTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
30 10 0.22
31 16 0.36
32 19 0.42
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (31 bp):
TTAAAAATATATTTTATTTTCATTTTAACTT
Found at i:1110263 original size:76 final size:79
Alignment explanation
Indices: 1110183--1110330 Score: 187
Period size: 76 Copynumber: 1.9 Consensus size: 79
1110173 TAACACAAAA
* * * * * *
1110183 ATATTTTAATCTTATTTTAGCT-TAAACAATATACTTTATTTT-GTGTTAAC-TT-AAAATGTAT
1 ATATTTTAATCTTATCTT-GATATAAAAAATATACTTTATTTTAATCTTAACTTTAAAAATATAT
1110244 ATTTTATTCTAATAT
65 ATTTTATTCTAATAT
* *
1110259 ATATTTTATTCTTATCTTGATATAAAAAATATATTTTATTTTAATCTTAACTTTAAAAATATATA
1 ATATTTTAATCTTATCTTGATATAAAAAATATACTTTATTTTAATCTTAACTTTAAAAATATATA
1110324 TTTTATT
66 TTTTATT
1110331 TTTATCTTAA
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
75 2 0.03
76 34 0.57
77 6 0.10
78 2 0.03
79 16 0.27
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.53
Consensus pattern (79 bp):
ATATTTTAATCTTATCTTGATATAAAAAATATACTTTATTTTAATCTTAACTTTAAAAATATATA
TTTTATTCTAATAT
Found at i:1110292 original size:30 final size:28
Alignment explanation
Indices: 1110257--1110356 Score: 112
Period size: 30 Copynumber: 3.4 Consensus size: 28
1110247 TTATTCTAAT
*
1110257 ATATATTTTATTCTTATCTTGATATAAAAA
1 ATATATTTTATT-TTATCTTAAT-TAAAAA
1110287 ATATATTTTATTTTAATCTTAACTTTAAAAA
1 ATATATTTTATTTT-ATCTTAA--TTAAAAA
*
1110318 TATATATTTTATTTTTATCTTAATTTAAAA
1 -ATATATTTTA-TTTTATCTTAATTAAAAA
1110348 ATAT-TTTTA
1 ATATATTTTA
1110357 ACATATATTT
Statistics
Matches: 63, Mismatches: 2, Indels: 12
0.82 0.03 0.16
Matches are distributed among these distances:
28 5 0.08
29 6 0.10
30 24 0.38
31 6 0.10
32 18 0.29
33 4 0.06
ACGTcount: A:0.39, C:0.05, G:0.01, T:0.55
Consensus pattern (28 bp):
ATATATTTTATTTTATCTTAATTAAAAA
Found at i:1110323 original size:32 final size:30
Alignment explanation
Indices: 1110254--1110351 Score: 135
Period size: 31 Copynumber: 3.2 Consensus size: 30
1110244 ATTTTATTCT
* *
1110254 AATATATATTTTATTCTTATCTTGATATAAA
1 AATATATATTTTATT-TTATCTTAATTTAAA
1110285 AA-ATATATTTTATTTTAATCTTAACTTTAAA
1 AATATATATTTTATTTT-ATCTTAA-TTTAAA
1110316 AATATATATTTTATTTTTATCTTAATTTAAA
1 AATATATATTTTA-TTTTATCTTAATTTAAA
1110347 AATAT
1 AATAT
1110352 TTTTAACATA
Statistics
Matches: 61, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
29 2 0.03
30 18 0.30
31 20 0.33
32 17 0.28
33 4 0.07
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.53
Consensus pattern (30 bp):
AATATATATTTTATTTTATCTTAATTTAAA
Found at i:1110481 original size:29 final size:29
Alignment explanation
Indices: 1110423--1110555 Score: 122
Period size: 31 Copynumber: 4.3 Consensus size: 29
1110413 ATTAATAAAA
* *
1110423 AATAAAATATATTTTTAAAATTTAAGATAAG
1 AATAAAATATATTTTT--AAGTTAAAATAAG
* * *
1110454 AACAAAATATATTTTTCAGTTAAAATAAAAA
1 AATAAAATATATTTTTAAGTTAAAAT--AAG
**
1110485 AATAAAATATATTTTTAAGTTAAGCTAAG
1 AATAAAATATATTTTTAAGTTAAAATAAG
* *
1110514 AATAAAATAAATATTTTTAAATTAAAAATAAT
1 AATAAAAT--ATATTTTTAAGTT-AAAATAAG
1110546 AATAAAATAT
1 AATAAAATAT
1110556 TTAAAAAAAT
Statistics
Matches: 83, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
29 17 0.20
30 2 0.02
31 51 0.61
32 13 0.16
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (29 bp):
AATAAAATATATTTTTAAGTTAAAATAAG
Found at i:1110495 original size:62 final size:60
Alignment explanation
Indices: 1110402--1110555 Score: 170
Period size: 62 Copynumber: 2.5 Consensus size: 60
1110392 ATATATATGG
* * *
1110402 AATATATTTAAATT--AATAAAAAATAAAATATATTTTTAAAATTTAAGATAAGAACAAAAT
1 AATATTTTTAAATTAAAAAAAAAAATAAAATATATTTTT--AAGTTAAGATAAGAACAAAAT
* * * *
1110462 -ATATTTTTCAGTTAAAATAAAAAAATAAAATATATTTTTAAGTTAAGCTAAGAATAAAAT
1 AATATTTTTAAATTAAAA-AAAAAAATAAAATATATTTTTAAGTTAAGATAAGAACAAAAT
* *
1110522 AAATATTTTTAAATTAAAAATAATAATAAAATAT
1 -AATATTTTTAAATTAAAAAAAAAAATAAAATAT
1110556 TTAAAAAAAT
Statistics
Matches: 78, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
59 10 0.13
60 18 0.23
61 15 0.19
62 35 0.45
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (60 bp):
AATATTTTTAAATTAAAAAAAAAAATAAAATATATTTTTAAGTTAAGATAAGAACAAAAT
Found at i:1111503 original size:24 final size:23
Alignment explanation
Indices: 1111460--1111508 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
1111450 ATTTAAATTC
*
1111460 TTATATATTTTAGATAATTTTTT
1 TTATATATTTTAGATAATTTATT
1111483 TTATAT-TTTTATTGATAATTTATT
1 TTATATATTTTA--GATAATTTATT
1111507 TT
1 TT
1111509 GTCCCATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 5 0.22
23 6 0.26
24 12 0.52
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (23 bp):
TTATATATTTTAGATAATTTATT
Found at i:1114057 original size:32 final size:31
Alignment explanation
Indices: 1114015--1114075 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
1114005 AACAATTACA
*
1114015 AAATAATCATTATATTTCAT-CAAAATATTATG
1 AAATAATCATTAAATTT-ATCCAAAA-ATTATG
*
1114047 AAATTATCATTAAATTTATCCAAAAATTA
1 AAATAATCATTAAATTTATCCAAAAATTA
1114076 CAATTAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 6 0.23
32 20 0.77
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (31 bp):
AAATAATCATTAAATTTATCCAAAAATTATG
Found at i:1119640 original size:2 final size:2
Alignment explanation
Indices: 1119633--1119660 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1119623 GTCAAATACG
1119633 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
1119661 TTCTTCATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1122521 original size:6 final size:6
Alignment explanation
Indices: 1122498--1122561 Score: 110
Period size: 6 Copynumber: 10.7 Consensus size: 6
1122488 ACCATGATTT
* *
1122498 CTGAGC CTGTGT CTGAGC CTGAGC CTGAGC CTGAGC CTGAGC CTGAGC
1 CTGAGC CTGAGC CTGAGC CTGAGC CTGAGC CTGAGC CTGAGC CTGAGC
1122546 CTGAGC CTGAGC CTGA
1 CTGAGC CTGAGC CTGA
1122562 AGCATCAATT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.16, C:0.31, G:0.33, T:0.20
Consensus pattern (6 bp):
CTGAGC
Found at i:1123721 original size:72 final size:72
Alignment explanation
Indices: 1123640--1123779 Score: 192
Period size: 72 Copynumber: 1.9 Consensus size: 72
1123630 CTGCACTATT
* * * * *
1123640 AACAGCAGCAACAGCCTCGTTG-CCGTCTTTGTTATTTTCACTTTCATCACCCCTTGCATCATTT
1 AACAACAGCAACAGCCTCCTTGTCC-TCATTGTTATTTTCACTTTCATCACCCCATGCATCATTA
1123704 GCACAAAA
65 GCACAAAA
* * *
1123712 AACAACAGCAACAGCCTCCTTGTTCTCATTGTTCTTTTCACTTTCATCACTCCATGCATCATTAG
1 AACAACAGCAACAGCCTCCTTGTCCTCATTGTTATTTTCACTTTCATCACCCCATGCATCATTAG
1123777 CAC
66 CAC
1123780 TAACATTATC
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
72 58 0.98
73 1 0.02
ACGTcount: A:0.25, C:0.31, G:0.11, T:0.33
Consensus pattern (72 bp):
AACAACAGCAACAGCCTCCTTGTCCTCATTGTTATTTTCACTTTCATCACCCCATGCATCATTAG
CACAAAA
Found at i:1123904 original size:87 final size:87
Alignment explanation
Indices: 1123806--1123971 Score: 255
Period size: 87 Copynumber: 1.9 Consensus size: 87
1123796 AATAGCATCA
*
1123806 TCACTCTCTTTGTCCTTCTTCTTCTTTTTCTTCTTTTCACTTTCATC-ACCCCTTACATCA-TCT
1 TCACTCTCTTTGTCCTTCTTCTTCTTTTTCCTCTTTTCACTTTCATCAACCCC-TACATCAGT-T
*
1123869 GCAGTATCAACAACAGTAGTCTCC
64 GCACTATCAACAACAGTAGTCTCC
** *
1123893 TCACTCTCTTTGTTGTTCTTCTTCTTTTTCCTCTTTTCACTTTCATCAACCCCTGCATCAGTTGC
1 TCACTCTCTTTGTCCTTCTTCTTCTTTTTCCTCTTTTCACTTTCATCAACCCCTACATCAGTTGC
1123958 ACTATCAACAACAG
66 ACTATCAACAACAG
1123972 CAAAAGCCTC
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
87 66 0.92
88 6 0.08
ACGTcount: A:0.17, C:0.33, G:0.07, T:0.43
Consensus pattern (87 bp):
TCACTCTCTTTGTCCTTCTTCTTCTTTTTCCTCTTTTCACTTTCATCAACCCCTACATCAGTTGC
ACTATCAACAACAGTAGTCTCC
Found at i:1124005 original size:72 final size:71
Alignment explanation
Indices: 1123924--1124133 Score: 264
Period size: 72 Copynumber: 2.9 Consensus size: 71
1123914 TTCTTTTTCC
* * * *
1123924 TCTTTTCACTTTCATCAACCCCTGCATCAGTT-GCACTATCAACAACAGCAAAAGCCTCCTTGCT
1 TCTTTTCACTTTCATCAGCCCCTGCATCA-TTAGCACTATTAACAACAGCAATAGCCTCCTCGCT
1123988 CGCTTT-GT
65 --CTTTAGT
* * *
1123996 TCTTTTCACTTTCATCAGCTCCTACATCATTAGCACTATTAGCAACAGCAATAGCCTCCTCGCTC
1 TCTTTTCACTTTCATCAGCCCCTGCATCATTAGCACTATTAACAACAGCAATAGCCTCCTCGCTC
1124061 TTTACGT
66 TTTA-GT
* * *
1124068 TCTTTTCACTTTCATCAGCTCCC-GCATCATTAGCACTATTATCAACAACAATAGCCTCCTCACT
1 TCTTTTCACTTTCATCAGC-CCCTGCATCATTAGCACTATTAACAACAGCAATAGCCTCCTCGCT
1124132 CT
65 CT
1124134 CTTTGCCTTT
Statistics
Matches: 122, Mismatches: 12, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
70 4 0.03
71 2 0.02
72 114 0.93
73 2 0.02
ACGTcount: A:0.24, C:0.33, G:0.09, T:0.33
Consensus pattern (71 bp):
TCTTTTCACTTTCATCAGCCCCTGCATCATTAGCACTATTAACAACAGCAATAGCCTCCTCGCTC
TTTAGT
Found at i:1124336 original size:66 final size:66
Alignment explanation
Indices: 1124207--1124347 Score: 174
Period size: 66 Copynumber: 2.1 Consensus size: 66
1124197 TATCAACAAC
* * * * *
1124207 AGCAATAGCCTTCTTGCTCGCTTTGTTCTTTTCTCTTCCATCAGCTCCTACATCAGTAACACTAT
1 AGCAACAGCCTTCTCGCTCGCTTTGTTCTTTTCACTTACATCAGCACCTACATCAGTAACACTAT
1124272 T
66 T
* * * * * *
1124273 GGCAACAGCCTTCTCGCTCTCTTTGTTCTTTTCACTTACATCAGCACCTGCTTCATTAGCACTAT
1 AGCAACAGCCTTCTCGCTCGCTTTGTTCTTTTCACTTACATCAGCACCTACATCAGTAACACTAT
1124338 T
66 T
*
1124339 ATCAACAGC
1 AGCAACAGC
1124348 AATAACCGCC
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.21, C:0.31, G:0.11, T:0.37
Consensus pattern (66 bp):
AGCAACAGCCTTCTCGCTCGCTTTGTTCTTTTCACTTACATCAGCACCTACATCAGTAACACTAT
T
Found at i:1124608 original size:243 final size:243
Alignment explanation
Indices: 1123908--1125177 Score: 1732
Period size: 243 Copynumber: 5.3 Consensus size: 243
1123898 CTCTTTGTTG
* * *
1123908 TTCTTCTTCTTTTTCCTCTTTTCACTTTCATCAACCCCTGCATCAGTTGCACTATCAACAACAGC
1 TTCTTCTTCTTTTTCCTCATTTCACTTTCATCCACCCCTGCATCATTTGCACTATCAACAACAGC
*
1123973 AAAAGCCTCCTTGCTCGCTTTGTTCTTTTCACTTTCATCAGCTCCTACATCATTAGCACTATTAG
66 AATAGCCTCCTTGCTCGCTTTGTTCTTTTCACTTTCATCAGCTCCTACATCATTAGCACTATTAG
* * * *
1124038 CAACAGCAATAGCCTCCTCGCTCT-TTACGTTCTTTTCACTTTCATCAGCTCCCGCATCATTAGC
131 CAACAGCAACAGCCTTCTCGCTCTCTT-TGTTCTTTTCACTTTCATCAGCTCCTGCATCATTAGC
*
1124102 ACTATTATCAACAACAATAGCCTCCTCACTCTCTTTGCCTTT-C-C-TC
195 ACTATTATCAACAGCAATAGCCTCCTCACTCTCTTTGCCTTTCCTCTTC
* * *
1124148 TTCTTC--C-TTTTCCTCTTTTCACTTTCATCGACCCTTGCATCATTTGCACTATCAACAACAGC
1 TTCTTCTTCTTTTTCCTCATTTCACTTTCATCCACCCCTGCATCATTTGCACTATCAACAACAGC
* * * * *
1124210 AATAGCCTTCTTGCTCGCTTTGTTCTTTTCTCTTCCATCAGCTCCTACATCAGTAACACTATT-G
66 AATAGCCTCCTTGCTCGCTTTGTTCTTTTCACTTTCATCAGCTCCTACATCATTAGCACTATTAG
* * *
1124274 -----GCAACAGCCTTCTCGCTCTCTTTGTTCTTTTCACTTACATCAGCACCTGCTTCATTAGCA
131 CAACAGCAACAGCCTTCTCGCTCTCTTTGTTCTTTTCACTTTCATCAGCTCCTGCATCATTAGCA
* * * *
1124334 CTATTATCAACAGCAATAACCGCCGCACTCTCTTTGCATTTCCTCTTC
196 CTATTATCAACAGCAATAGCCTCCTCACTCTCTTTGCCTTTCCTCTTC
* * * * *
1124382 TTCTTCTTCGTTTTCTTCATTTCATTTTCA-CCACCCCCTGCTTCATTTGCACCATCAACAACAG
1 TTCTTCTTCTTTTTCCTCATTTCACTTTCATCCA-CCCCTGCATCATTTGCACTATCAACAACAG
*
1124446 CAATAGCTTCCTTTG-TCGCTTTGTTCTTTTCACTTTCATCAGCTCCTACATCATTAGCACTATT
65 CAATAGCCTCC-TTGCTCGCTTTGTTCTTTTCACTTTCATCAGCTCCTACATCATTAGCACTATT
* * *
1124510 AGCAACAGCAACACCCTTCTCGTTCTCTTTATTCTTTTCACTTTCATCAGCTCCTGCATCATTAG
129 AGCAACAGCAACAGCCTTCTCGCTCTCTTTGTTCTTTTCACTTTCATCAGCTCCTGCATCATTAG
* * *
1124575 CACTATCATCAACAGCAATAGCCTCCTCACTCTCTTTGCCTTTTCTCCTC
194 CACTATTATCAACAGCAATAGCCTCCTCACTCTCTTTGCCTTTCCTCTTC
* * * * ** *
1124625 TTCTTCTTCTTTTTCTTCATTTCACTTTCATCAACCCCCGCACCATTTAAACTATCAACAACAGA
1 TTCTTCTTCTTTTTCCTCATTTCACTTTCATCCACCCCTGCATCATTTGCACTATCAACAACAGC
1124690 AATAGCCTCCTTGCTCGCTTTGTTCTTTTCACTTTCATCAGCTCCTACATCATTAGCACTATTAG
66 AATAGCCTCCTTGCTCGCTTTGTTCTTTTCACTTTCATCAGCTCCTACATCATTAGCACTATTAG
* * *
1124755 -AGCCAGCAACAGCCTCCTCGCTCACTTTGTTCTTTTCACTTTCATCAGCTCCTGCATCATTAGC
131 CA-ACAGCAACAGCCTTCTCGCTCTCTTTGTTCTTTTCACTTTCATCAGCTCCTGCATCATTAGC
*
1124819 ACTATTATCAACGGCAATAGCCTCCTCACTCTCTTTGCCTTTCCTCTTC
195 ACTATTATCAACAGCAATAGCCTCCTCACTCTCTTTGCCTTTCCTCTTC
* * * * *
1124868 TTCTTCTTCTTTTTCCTCTTTTCACTTTCATCGACCCCTGCATCATTTGAACTACCAAGAACAGC
1 TTCTTCTTCTTTTTCCTCATTTCACTTTCATCCACCCCTGCATCATTTGCACTATCAACAACAGC
* * *
1124933 AATAGCCTCCTTGCTTGCTTTGTTCTTTTCACTTTCATAAGCTCCTACATCATTAGCAATATTAG
66 AATAGCCTCCTTGCTCGCTTTGTTCTTTTCACTTTCATCAGCTCCTACATCATTAGCACTATTAG
* ** * *
1124998 CAACATCAACAGCC-TCTTCGCTAACTTCGTTCTTTTCACTTTCATCGGCTCCTGCATCATTAGC
131 CAACAGCAACAGCCTTC-TCGCTCTCTTTGTTCTTTTCACTTTCATCAGCTCCTGCATCATTAGC
* * * *
1125062 ACTATCATCAACAGCGATAGCTTCCTCACTCTCTTTTCCTTTCCTCTTC
195 ACTATTATCAACAGCAATAGCCTCCTCACTCTCTTTGCCTTTCCTCTTC
* * * *
1125111 TTCTTCTTCGTTTTCTTCATTTCACTTTCAT-CAGCCCCTGCGTCATTTGCACTAAT-AACAAGA
1 TTCTTCTTCTTTTTCCTCATTTCACTTTCATCCA-CCCCTGCATCATTTGCACT-ATCAACAACA
1125174 GCAA
64 GCAA
1125178 CGGCAACGGC
Statistics
Matches: 908, Mismatches: 100, Indels: 41
0.87 0.10 0.04
Matches are distributed among these distances:
231 86 0.09
232 3 0.00
233 1 0.00
234 8 0.01
236 4 0.00
237 207 0.23
238 5 0.01
240 6 0.01
242 6 0.01
243 578 0.64
244 4 0.00
ACGTcount: A:0.21, C:0.33, G:0.09, T:0.38
Consensus pattern (243 bp):
TTCTTCTTCTTTTTCCTCATTTCACTTTCATCCACCCCTGCATCATTTGCACTATCAACAACAGC
AATAGCCTCCTTGCTCGCTTTGTTCTTTTCACTTTCATCAGCTCCTACATCATTAGCACTATTAG
CAACAGCAACAGCCTTCTCGCTCTCTTTGTTCTTTTCACTTTCATCAGCTCCTGCATCATTAGCA
CTATTATCAACAGCAATAGCCTCCTCACTCTCTTTGCCTTTCCTCTTC
Found at i:1124609 original size:72 final size:72
Alignment explanation
Indices: 1124418--1124611 Score: 226
Period size: 72 Copynumber: 2.7 Consensus size: 72
1124408 TTCACCACCC
* * * * *** * *
1124418 CCTGCTTCATTTGCACCATCAACAACAGCAATAGCTTCCTTTGTCGCTTTGTTCTTTTCACTTTC
1 CCTGCATCATTAGCACTATCAACAACAGCAATAGCCTCCTCACTCTCTTTATTCTTTTCACTTTC
1124483 ATCAGCT
66 ATCAGCT
* * * * * * **
1124490 CCTACATCATTAGCACTATTAGCAACAGCAACACCCTTCTCGTTCTCTTTATTCTTTTCACTTTC
1 CCTGCATCATTAGCACTATCAACAACAGCAATAGCCTCCTCACTCTCTTTATTCTTTTCACTTTC
1124555 ATCAGCT
66 ATCAGCT
*
1124562 CCTGCATCATTAGCACTATCATCAACAGCAATAGCCTCCTCACTCTCTTT
1 CCTGCATCATTAGCACTATCAACAACAGCAATAGCCTCCTCACTCTCTTT
1124612 GCCTTTTCTC
Statistics
Matches: 99, Mismatches: 23, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
72 99 1.00
ACGTcount: A:0.23, C:0.32, G:0.09, T:0.36
Consensus pattern (72 bp):
CCTGCATCATTAGCACTATCAACAACAGCAATAGCCTCCTCACTCTCTTTATTCTTTTCACTTTC
ATCAGCT
Found at i:1124841 original size:72 final size:72
Alignment explanation
Indices: 1124685--1124855 Score: 236
Period size: 72 Copynumber: 2.4 Consensus size: 72
1124675 ACTATCAACA
* * *
1124685 ACAGAAATAGCCTCCTTGCTCGCTTTGTTCTTTTCACTTTCATCAGCTCCTACATCATTAGCACT
1 ACAGCAATAGCCTCCTCGCTCACTTTGTTCTTTTCACTTTCATCAGCTCCTACATCATTAGCACT
*
1124750 ATTAGAG
66 ATTACAG
* * *
1124757 CCAGCAACAGCCTCCTCGCTCACTTTGTTCTTTTCACTTTCATCAGCTCCTGCATCATTAGCACT
1 ACAGCAATAGCCTCCTCGCTCACTTTGTTCTTTTCACTTTCATCAGCTCCTACATCATTAGCACT
1124822 ATTATCA-
66 ATTA-CAG
* * *
1124829 ACGGCAATAGCCTCCTCACTCTCTTTG
1 ACAGCAATAGCCTCCTCGCTCACTTTG
1124856 CCTTTCCTCT
Statistics
Matches: 86, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
72 85 0.99
73 1 0.01
ACGTcount: A:0.22, C:0.32, G:0.12, T:0.35
Consensus pattern (72 bp):
ACAGCAATAGCCTCCTCGCTCACTTTGTTCTTTTCACTTTCATCAGCTCCTACATCATTAGCACT
ATTACAG
Found at i:1125012 original size:72 final size:72
Alignment explanation
Indices: 1124927--1125076 Score: 185
Period size: 72 Copynumber: 2.1 Consensus size: 72
1124917 AACTACCAAG
* ** *
1124927 AACAGCAATAGCCTCCTT-GCTTGCTTTGTTCTTTTCACTTTCATAAGCTCCTACATCATTAGCA
1 AACAGCAACAGCCT-CTTCGCTAACTTCGTTCTTTTCACTTTCATAAGCTCCTACATCATTAGCA
1124991 ATATTAGC
65 ATATTAGC
* ** * *
1124999 AACATCAACAGCCTCTTCGCTAACTTCGTTCTTTTCACTTTCATCGGCTCCTGCATCATTAGCAC
1 AACAGCAACAGCCTCTTCGCTAACTTCGTTCTTTTCACTTTCATAAGCTCCTACATCATTAGCAA
* *
1125064 TATCATC
66 TATTAGC
1125071 AACAGC
1 AACAGC
1125077 GATAGCTTCC
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
71 3 0.05
72 62 0.95
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.35
Consensus pattern (72 bp):
AACAGCAACAGCCTCTTCGCTAACTTCGTTCTTTTCACTTTCATAAGCTCCTACATCATTAGCAA
TATTAGC
Found at i:1125465 original size:96 final size:96
Alignment explanation
Indices: 1125295--1125482 Score: 331
Period size: 96 Copynumber: 2.0 Consensus size: 96
1125285 GAACCAGCTC
* *
1125295 CAACCATATCTTCATCCACAATTCCCTTCTCCTCCTCGGTCTTCTTTTCATTTTCAGCATCAGAA
1 CAACCATATCTTCATCCACAATCCCCTTCTCCTCCTCGGTCTTCTTTTCAGTTTCAGCATCAGAA
**
1125360 TCCTTTTTATTCTTCTTCTCAACATCACCTT
66 TCCCGTTTATTCTTCTTCTCAACATCACCTT
*
1125391 CAACCATATCTTCATCCACAATCCCCTTCTCCTCCTCGGTCTTCTTTTCAGTTTCAGCATCAGAG
1 CAACCATATCTTCATCCACAATCCCCTTCTCCTCCTCGGTCTTCTTTTCAGTTTCAGCATCAGAA
1125456 TCCCGTTTATTCTTCTTCTCAACATCA
66 TCCCGTTTATTCTTCTTCTCAACATCA
1125483 TCTTGATCTC
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
96 87 1.00
ACGTcount: A:0.20, C:0.35, G:0.06, T:0.39
Consensus pattern (96 bp):
CAACCATATCTTCATCCACAATCCCCTTCTCCTCCTCGGTCTTCTTTTCAGTTTCAGCATCAGAA
TCCCGTTTATTCTTCTTCTCAACATCACCTT
Found at i:1129644 original size:17 final size:16
Alignment explanation
Indices: 1129611--1129643 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1129601 CGTTGTAAGG
1129611 TAATTTTTTTAATATA
1 TAATTTTTTTAATATA
1129627 TAATTTTTTT-ATATA
1 TAATTTTTTTAATATA
1129642 TA
1 TA
1129644 TGATTATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TAATTTTTTTAATATA
Found at i:1130996 original size:27 final size:27
Alignment explanation
Indices: 1130943--1131004 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
1130933 TGGCGATATT
* *
1130943 TGGTATAGGAATGGCGGTAGCAACATC
1 TGGTATGGGAACGGCGGTAGCAACATC
**
1130970 TGGTATGGGAACGGCGGTAGCGGCATC
1 TGGTATGGGAACGGCGGTAGCAACATC
*
1130997 TGATATGG
1 TGGTATGG
1131005 CTGCGGACCC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.24, C:0.15, G:0.39, T:0.23
Consensus pattern (27 bp):
TGGTATGGGAACGGCGGTAGCAACATC
Found at i:1134120 original size:2 final size:2
Alignment explanation
Indices: 1134113--1134158 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
1134103 ATCATCTAAG
* * *
1134113 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1134155 AT AT
1 AT AT
1134159 GTATGTATGT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1134159 original size:14 final size:14
Alignment explanation
Indices: 1134126--1134168 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
1134116 TATATATATA
* * *
1134126 TATATATATATATA
1 TATATGTATGTATG
1134140 TATATGTATGTATG
1 TATATGTATGTATG
1134154 TATATGTATGTATG
1 TATATGTATGTATG
1134168 T
1 T
1134169 CAAGAACTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (14 bp):
TATATGTATGTATG
Found at i:1138123 original size:72 final size:72
Alignment explanation
Indices: 1138006--1138151 Score: 222
Period size: 72 Copynumber: 2.0 Consensus size: 72
1137996 TATTACTAGA
** *
1138006 TGGAGTTGACCCAAACACCAAGCCGTAACTGGTGTTACCAAACACATTCTGTGATGGAGTAGCAA
1 TGGAGTTGACCCAAACACCAAGCCGTAACTGGTGTTACCAAACACAGACTGTGACGGAGTAGCAA
1138071 CTGCAGC
66 CTGCAGC
* * *
1138078 TGGAGTTGACCCAAACACCAAGCCCG-GATTGGTGTTACCAAACACAGACTGTGACGGGGTAGCA
1 TGGAGTTGACCCAAACACCAAG-CCGTAACTGGTGTTACCAAACACAGACTGTGACGGAGTAGCA
1138142 ACTGCAGC
65 ACTGCAGC
1138150 TG
1 TG
1138152 AAGTGAAAGA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
72 64 0.96
73 3 0.04
ACGTcount: A:0.29, C:0.25, G:0.26, T:0.19
Consensus pattern (72 bp):
TGGAGTTGACCCAAACACCAAGCCGTAACTGGTGTTACCAAACACAGACTGTGACGGAGTAGCAA
CTGCAGC
Found at i:1150002 original size:18 final size:18
Alignment explanation
Indices: 1149973--1150020 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
1149963 ATGCTCGTAT
*
1149973 GCATGCAATTAGTTGTTA
1 GCATGCAGTTAGTTGTTA
*
1149991 GGATGCAGTTAGTTGTTA
1 GCATGCAGTTAGTTGTTA
1150009 GCATGCAGTTAG
1 GCATGCAGTTAG
1150021 CTGGTAAACC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.25, C:0.10, G:0.29, T:0.35
Consensus pattern (18 bp):
GCATGCAGTTAGTTGTTA
Found at i:1152770 original size:24 final size:24
Alignment explanation
Indices: 1152721--1152779 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
1152711 AGCCTAATTC
1152721 ACATGTGGGAAACAACCACGACCA
1 ACATGTGGGAAACAACCACGACCA
* **
1152745 ACATATGGGAAACAACC-CTGGTCA
1 ACATGTGGGAAACAACCAC-GACCA
1152769 ACATGTGGGAA
1 ACATGTGGGAA
1152780 GCAGTACTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 1 0.03
24 29 0.97
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.14
Consensus pattern (24 bp):
ACATGTGGGAAACAACCACGACCA
Found at i:1154690 original size:18 final size:18
Alignment explanation
Indices: 1154644--1154691 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
1154634 ATGCTCGTAT
* *
1154644 GCATGCAATTAGTTGTTA
1 GCATGCAGTTAGTTATTA
1154662 GCATGCAGTTAGTTATTA
1 GCATGCAGTTAGTTATTA
*
1154680 GCATGCGGTTAG
1 GCATGCAGTTAG
1154692 CTGGTAAACC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (18 bp):
GCATGCAGTTAGTTATTA
Found at i:1156226 original size:21 final size:20
Alignment explanation
Indices: 1156140--1156297 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
1156130 AAATGACCAA
**
1156140 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1156159 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1156179 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1156199 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1156220 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1156241 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1156261 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1156282 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1156298 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1156326 original size:20 final size:20
Alignment explanation
Indices: 1156264--1156533 Score: 260
Period size: 20 Copynumber: 13.5 Consensus size: 20
1156254 CGATTTTCCA
* ** *
1156264 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1156284 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1156304 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1156324 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1156344 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
1156364 AAATCGTAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1156384 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1156404 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1156424 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1156444 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1156464 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1156484 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1156504 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1156524 AAATCACAAC
1 AAATCGCAAC
1156534 ACTGAAATTT
Statistics
Matches: 208, Mismatches: 34, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 204 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1156350 original size:40 final size:40
Alignment explanation
Indices: 1156303--1156533 Score: 288
Period size: 40 Copynumber: 5.8 Consensus size: 40
1156293 CGCGAACACA
* * *
1156303 TAAATCGCAACGCGTATCCGTAAATCGCAACG-TGTATCCG
1 TAAATCGCAACGAGAATCCGTAAATCGCAACGAT-AATCCG
* * * *
1156343 TATATCGCAACGCGTATCCGTAAATCGTAATGCG-T-ATCCG
1 TAAATCGCAACGAGAATCCGTAAATCGCAA--CGATAATCCG
* * *
1156383 TATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCG
*
1156423 TAAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCG
*
1156463 TAAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCG
* *
1156503 TAAATCGCAACGAGAATCTGTAAATCACAAC
1 TAAATCGCAACGAGAATCCGTAAATCGCAAC
1156534 ACTGAAATTT
Statistics
Matches: 179, Mismatches: 8, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
38 2 0.01
39 1 0.01
40 173 0.97
42 3 0.02
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (40 bp):
TAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCG
Found at i:1157254 original size:24 final size:24
Alignment explanation
Indices: 1157215--1157261 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1157205 AAATTTGGTC
1157215 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1157239 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1157262 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1157453 original size:12 final size:12
Alignment explanation
Indices: 1157436--1157471 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
1157426 ATATAATCCT
1157436 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1157448 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1157460 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1157472 ATCCCCGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1159803 original size:33 final size:33
Alignment explanation
Indices: 1159752--1159961 Score: 184
Period size: 33 Copynumber: 6.2 Consensus size: 33
1159742 CGGAAATTAC
*
1159752 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAAC-ATGAAAATCGCAATGCGAAATGAA
*
1159785 AATCCCAACATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACATGAAAATCGCAATGC-GAAATGAA
*
1159819 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAAC-ATGAAAATCGCAATGCGAAATGAA
* * *
1159852 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C---ATGAAAATCGCAATGCGA-AAT-GAA
1159891 AAT-GCGAA-ATGAAAATCGCAATGCGAAATG-A
1 AATCGC-AACATGAAAATCGCAATGCGAAATGAA
*
1159922 AATCGC-A-ATGAGAGAATCGCAATGCGAAATTAA
1 AATCGCAACATGA-A-AATCGCAATGCGAAATGAA
1159955 AATCGCA
1 AATCGCA
1159962 TTGCGATTCT
Statistics
Matches: 148, Mismatches: 13, Indels: 31
0.77 0.07 0.16
Matches are distributed among these distances:
30 5 0.03
31 5 0.03
32 22 0.15
33 60 0.41
34 29 0.20
35 2 0.01
37 1 0.01
38 15 0.10
39 8 0.05
40 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (33 bp):
AATCGCAACATGAAAATCGCAATGCGAAATGAA
Found at i:1159857 original size:19 final size:19
Alignment explanation
Indices: 1159766--1159967 Score: 194
Period size: 19 Copynumber: 11.7 Consensus size: 19
1159756 GCAACGAGAG
1159766 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1159785 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1159799 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1159819 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1159833 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1159852 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1159871 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1159885 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1159904 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
*
1159922 AATCGCAAT--G--A-GAG
1 AATCGCAATGCGAAATGAA
*
1159936 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
1159955 AATCGCATTGCGA
1 AATCGCAATGCGA
1159968 TTCTCCCGTT
Statistics
Matches: 151, Mismatches: 10, Indels: 44
0.74 0.05 0.21
Matches are distributed among these distances:
13 1 0.01
14 42 0.28
15 2 0.01
16 7 0.05
17 4 0.03
18 14 0.09
19 68 0.45
20 13 0.09
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1159879 original size:52 final size:52
Alignment explanation
Indices: 1159794--1159967 Score: 305
Period size: 52 Copynumber: 3.3 Consensus size: 52
1159784 AAATCCCAAC
1159794 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1159847 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
1159899 ATGAAAATCGCAATGCGAAATG-AAATCGCAATGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
1159950 ATTAAAATCGCATTGCGA
1 ATGAAAATCGCAATGCGA
1159968 TTCTCCCGTT
Statistics
Matches: 118, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
51 44 0.37
52 58 0.49
53 16 0.14
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.16
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:1160015 original size:53 final size:52
Alignment explanation
Indices: 1159957--1160073 Score: 207
Period size: 53 Copynumber: 2.2 Consensus size: 52
1159947 GAAATTAAAA
*
1159957 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGTATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
*
1160010 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1160062 TCGCATTGCGAT
1 TCGCATTGCGAT
1160074 AGTCAATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:1160019 original size:19 final size:19
Alignment explanation
Indices: 1159976--1160073 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
1159966 GATTCTCCCG
*
1159976 TTGCGATTTTCATTTCCGTA
1 TTGCGATTTTCATTT-CGCA
1159996 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1160015 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1160029 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1160048 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1160067 TTGCGAT
1 TTGCGAT
1160074 AGTCAATTTT
Statistics
Matches: 70, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 7 0.10
19 35 0.50
20 15 0.21
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Done.