Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 44 of 167
Found at i:13512745 original size:11 final size:11
Alignment explanation
Indices: 13512731--13512769 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
13512721 TTTGCCTCTG
13512731 TTTTGCTACTA
1 TTTTGCTACTA
* *
13512742 TTTTACTATTA
1 TTTTGCTACTA
13512753 TGTTTGCTACTA
1 T-TTTGCTACTA
13512765 TTTTG
1 TTTTG
13512770 TTGTTAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.18, C:0.13, G:0.10, T:0.59
Consensus pattern (11 bp):
TTTTGCTACTA
Found at i:13524315 original size:26 final size:25
Alignment explanation
Indices: 13524275--13524337 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 25
13524265 TGGATTTTCA
* *
13524275 TGAGCTTCCCGATTAAAGGCTCTTTG
1 TGAGCTTCCCAATT-AAGGCTCTCTG
* *
13524301 TGAGCTTCCTAATTATGGCTCTCTG
1 TGAGCTTCCCAATTAAGGCTCTCTG
*
13524326 -GAGCTTCTCAAT
1 TGAGCTTCCCAAT
13524338 ATGGCTTACT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
24 10 0.32
25 9 0.29
26 12 0.39
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.37
Consensus pattern (25 bp):
TGAGCTTCCCAATTAAGGCTCTCTG
Found at i:13524489 original size:25 final size:25
Alignment explanation
Indices: 13524408--13524492 Score: 91
Period size: 25 Copynumber: 3.4 Consensus size: 25
13524398 GAGTTACCCG
13524408 TTAT-TGGCTCACATGAGCTTCCTA
1 TTATATGGCTCACATGAGCTTCCTA
** * * * **
13524432 TTATACAGCCCAGATAAGCTTCCCG
1 TTATATGGCTCACATGAGCTTCCTA
*
13524457 TTACATGGCTCACATGAGCTTCCTA
1 TTATATGGCTCACATGAGCTTCCTA
13524482 TTATATGGCTC
1 TTATATGGCTC
13524493 GAGAGAGGGC
Statistics
Matches: 44, Mismatches: 16, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
24 4 0.09
25 40 0.91
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (25 bp):
TTATATGGCTCACATGAGCTTCCTA
Found at i:13528296 original size:21 final size:21
Alignment explanation
Indices: 13528262--13528363 Score: 59
Period size: 21 Copynumber: 4.8 Consensus size: 21
13528252 ATTTCTCCTT
13528262 TTTCTTTTCT-TTTCTTCTTTA
1 TTTC-TTTCTATTTCTTCTTTA
*
13528283 TTTCTTTCTATTTCGTT-TCTTC
1 TTTCTTTCTATTTC-TTCT-TTA
* * * * *
13528305 TCTGTTTCTTTTTCTTGTTTCTC
1 TTTCTTTCTATTTCTT-CTT-TA
*
13528328 TTTCTTT-TATTTATTCTTTA
1 TTTCTTTCTATTTCTTCTTTA
13528348 TTTCATTT-TATTTCTT
1 TTTC-TTTCTATTTCTT
13528364 TCATTTACTA
Statistics
Matches: 63, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
20 10 0.16
21 23 0.37
22 22 0.35
23 8 0.13
ACGTcount: A:0.07, C:0.18, G:0.03, T:0.73
Consensus pattern (21 bp):
TTTCTTTCTATTTCTTCTTTA
Found at i:13528301 original size:26 final size:25
Alignment explanation
Indices: 13528262--13528315 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
13528252 ATTTCTCCTT
* *
13528262 TTTCTTTTCTTTTCTTCTTTATTTC
1 TTTCTTTTCGTTTCTTCTCTATTTC
*
13528287 TTTCTATTTCGTTTCTTCTCTGTTTC
1 TTTCT-TTTCGTTTCTTCTCTATTTC
13528313 TTT
1 TTT
13528316 TTCTTGTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.04, C:0.20, G:0.04, T:0.72
Consensus pattern (25 bp):
TTTCTTTTCGTTTCTTCTCTATTTC
Found at i:13535826 original size:26 final size:26
Alignment explanation
Indices: 13535797--13535904 Score: 198
Period size: 26 Copynumber: 4.2 Consensus size: 26
13535787 TGATACAAAT
13535797 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
13535823 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
13535849 TGATAATGGGTTAGGTAAATTTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
13535875 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
13535901 TGAT
1 TGAT
13535905 TGGAATTTCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:13538907 original size:26 final size:24
Alignment explanation
Indices: 13538878--13538945 Score: 66
Period size: 26 Copynumber: 2.8 Consensus size: 24
13538868 TTTCTTTTCT
13538878 TTTCTTCTTTCTTTCTTTCTATTCCG
1 TTTCTTCTTTCTTTCTTTCTATT--G
* * * *
13538904 TTTCTTCTCTGTTTCTTTTTCTTG
1 TTTCTTCTTTCTTTCTTTCTATTG
13538928 TTT-TTCTTTCTTTTCTTT
1 TTTCTTCTTTC-TTTCTTT
13538946 ATTCTTTATT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
23 5 0.14
24 11 0.31
26 19 0.54
ACGTcount: A:0.01, C:0.22, G:0.04, T:0.72
Consensus pattern (24 bp):
TTTCTTCTTTCTTTCTTTCTATTG
Found at i:13538967 original size:25 final size:24
Alignment explanation
Indices: 13538904--13538970 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 24
13538894 TTCTATTCCG
*
13538904 TTTCTTCTCTGTTTCTTTTTCTTGTT
1 TTTCTT-TCT-TTTCTTTTTCTTGTA
13538930 TTTCTTTCTTTTCTTTATTCTT-TA
1 TTTCTTTCTTTTCTTT-TTCTTGTA
13538954 TTTCATTT-TATTTCTTT
1 TTTC-TTTCT-TTTCTTT
13538971 CATTTACTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
24 13 0.35
25 18 0.49
26 6 0.16
ACGTcount: A:0.06, C:0.16, G:0.03, T:0.75
Consensus pattern (24 bp):
TTTCTTTCTTTTCTTTTTCTTGTA
Found at i:13539482 original size:53 final size:53
Alignment explanation
Indices: 13539415--13539521 Score: 178
Period size: 53 Copynumber: 2.0 Consensus size: 53
13539405 ACGAACTCAT
* * *
13539415 TTTCCTAAGTCGGAAGCCCTAAACTCACTTTTTCGGTGCCCGTAAAATATGGG
1 TTTCCTAAGACGGAAGCCCTAAACTCACTTTTCCGATGCCCGTAAAATATGGG
*
13539468 TTTCTTAAGACGGAAGCCCTAAACTCACTTTTCCGATGCCCGTAAAATATGGG
1 TTTCCTAAGACGGAAGCCCTAAACTCACTTTTCCGATGCCCGTAAAATATGGG
13539521 T
1 T
13539522 CGTTACACAG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (53 bp):
TTTCCTAAGACGGAAGCCCTAAACTCACTTTTCCGATGCCCGTAAAATATGGG
Found at i:13544013 original size:23 final size:23
Alignment explanation
Indices: 13543976--13544020 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
13543966 CATGTTTATT
*
13543976 TTATGTTTTAATTAAACTTTAAC
1 TTATGTTTTAATTAAAATTTAAC
**
13543999 TTATGTTTTCTTTAAAATTTAA
1 TTATGTTTTAATTAAAATTTAA
13544021 TTAAAATTTT
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:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (23 bp):
TTATGTTTTAATTAAAATTTAAC
Found at i:13544058 original size:33 final size:33
Alignment explanation
Indices: 13544016--13544081 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
13544006 TTCTTTAAAA
13544016 TTTAATTAAAATTTTAACTAATACTAAGCTAAG
1 TTTAATTAAAATTTTAACTAATACTAAGCTAAG
13544049 TTTAATTAAAATTTTAACTAATACTAAGCTAAG
1 TTTAATTAAAATTTTAACTAATACTAAGCTAAG
13544082 GAATGGGTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.39
Consensus pattern (33 bp):
TTTAATTAAAATTTTAACTAATACTAAGCTAAG
Found at i:13549647 original size:11 final size:11
Alignment explanation
Indices: 13549631--13549655 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
13549621 ATATCTAGAA
13549631 TTCTCTTCATT
1 TTCTCTTCATT
13549642 TTCTCTTCATT
1 TTCTCTTCATT
13549653 TTC
1 TTC
13549656 GTCAGCTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (11 bp):
TTCTCTTCATT
Found at i:13550919 original size:25 final size:25
Alignment explanation
Indices: 13550890--13550941 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
13550880 AAGAATAATT
**
13550890 TGAATATTTGATATTGCCTAATAAA
1 TGAATATCCGATATTGCCTAATAAA
* *
13550915 TGAATATCCGATATTGCTTAGTAAA
1 TGAATATCCGATATTGCCTAATAAA
13550940 TG
1 TG
13550942 TCAAGCCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (25 bp):
TGAATATCCGATATTGCCTAATAAA
Found at i:13551606 original size:33 final size:33
Alignment explanation
Indices: 13551569--13551631 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
13551559 TAATCCCAAG
13551569 ATAGTCAATCTTATTAATACCCTTAATCATGAT
1 ATAGTCAATCTTATTAATACCCTTAATCATGAT
13551602 ATAGTCAATCTTATTAATACCCTTAATCAT
1 ATAGTCAATCTTATTAATACCCTTAATCAT
13551632 AATGTTTCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.40
Consensus pattern (33 bp):
ATAGTCAATCTTATTAATACCCTTAATCATGAT
Found at i:13569859 original size:15 final size:15
Alignment explanation
Indices: 13569839--13569916 Score: 88
Period size: 15 Copynumber: 5.2 Consensus size: 15
13569829 CATAGTATCG
*
13569839 TATCTTGGGTTTCTT
1 TATCTTGGATTTCTT
*
13569854 TATCTTGGATCTCTT
1 TATCTTGGATTTCTT
13569869 TAT-TCTGGATTTCTT
1 TATCT-TGGATTTCTT
* *
13569884 TAT-TCTGGGTTTCTC
1 TATCT-TGGATTTCTT
13569899 TATCTTGGATTTCTT
1 TATCTTGGATTTCTT
13569914 TAT
1 TAT
13569917 TCGGTTTTCT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
14 1 0.02
15 52 0.96
16 1 0.02
ACGTcount: A:0.12, C:0.15, G:0.15, T:0.58
Consensus pattern (15 bp):
TATCTTGGATTTCTT
Found at i:13573741 original size:22 final size:23
Alignment explanation
Indices: 13573716--13573761 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
13573706 CAACCAAATC
13573716 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
13573738 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
13573761 A
1 A
13573762 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:13573767 original size:23 final size:23
Alignment explanation
Indices: 13573723--13573767 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
13573713 ATCAATTCAA
*
13573723 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
13573746 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
13573768 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:13577637 original size:43 final size:43
Alignment explanation
Indices: 13577573--13577756 Score: 262
Period size: 43 Copynumber: 4.3 Consensus size: 43
13577563 ATTTGAAAAC
13577573 AACGCCGCTAAAGGTCC-TGACCTTTAGCGGCGCTTTTCCCACA
1 AACGCCGCTAAAGG-CCATGACCTTTAGCGGCGCTTTTCCCACA
**
13577616 AACGCCGCTAAAGGCCATGACCTTTAGCGGCGCTTTTATCACA
1 AACGCCGCTAAAGGCCATGACCTTTAGCGGCGCTTTTCCCACA
*
13577659 AACGCCGCCAAAGGCCATGACCTTTAGCGGCGCTTTTCCCACA
1 AACGCCGCTAAAGGCCATGACCTTTAGCGGCGCTTTTCCCACA
* * * * * * *
13577702 AACGCCGCCAAAGGTCAGGACCTTTGGCGGCGCTTTTTCGAAA
1 AACGCCGCTAAAGGCCATGACCTTTAGCGGCGCTTTTCCCACA
13577745 AACGCCGCTAAA
1 AACGCCGCTAAA
13577757 TGTCATAAAA
Statistics
Matches: 128, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
42 2 0.02
43 126 0.98
ACGTcount: A:0.24, C:0.33, G:0.22, T:0.21
Consensus pattern (43 bp):
AACGCCGCTAAAGGCCATGACCTTTAGCGGCGCTTTTCCCACA
Found at i:13581953 original size:54 final size:54
Alignment explanation
Indices: 13581871--13582713 Score: 1686
Period size: 54 Copynumber: 15.6 Consensus size: 54
13581861 AACCTTGCAG
13581871 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
13581925 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
13581979 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
13582033 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
13582087 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
13582141 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
13582195 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
13582249 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
13582303 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
13582357 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
13582411 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
13582465 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
13582519 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
13582573 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
13582627 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
13582681 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAA
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGCAA
13582714 CGACAATTAC
Statistics
Matches: 789, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 789 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (54 bp):
CGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGT
Found at i:13590307 original size:354 final size:352
Alignment explanation
Indices: 13589660--13590367 Score: 1312
Period size: 354 Copynumber: 2.0 Consensus size: 352
13589650 TACCAATAAA
13589660 TGTAATACCCCTACCCGTATTCATTGCCGAAATAGGGTACGAGGCATTACCGGAGTTTACGAATT
1 TGTAATACCCCTACCCGTATTCATTGCCGAAATAGGGTACGAGGCATTACCGGAGTTTACGAATT
*
13589725 AATTTATTTTTTTCAATTCAACATATTTTCATGATAGATTCATTCATTTATATAAGATAACGTCA
66 AATTTATTTTTTTCAATTCAACATATTTTCATGATAGATTCATGCATTTATATAAGATAACGTCA
*
13589790 TCATATATCTATAACCAGGTTTGTTAACCATACTAATGGCTATACATTCATTTCACGTTAACATT
131 TCACATATCTATAACCAGGTTTGTTAACCATACTAATGGCTATACATTCATTTCACGTTAACATT
13589855 TACTTTGTTAGCTTATACATGCCATTGATTTCCAAAATAAAGTTTCTTTATATACCGAAATCCTG
196 TACTTTGTTAGCTTATACATGCCATTGATTTCCAAAATAAAGTTTCTTTATATACCGAAATCCTG
*
13589920 AGGTTGACAGTGTGATGTGTCTCCGACCAAATCCGACCTCAGAGCTCTTAACACTACAAAACAGG
261 AGGTTGACAGTGTGATGTGTCTCCGACCAAATCCGACATCAGAGCTCTTAACACTACAAAACAGG
13589985 GAAAAAGGAAACGGGGTAAGCACTTTG
326 GAAAAAGGAAACGGGGTAAGCACTTTG
*
13590012 TGTAATACCCCTACCCGTATTCATTGCCGGAATAGGGTACGAGGCATTACCGGAGTTTACGAATT
1 TGTAATACCCCTACCCGTATTCATTGCCGAAATAGGGTACGAGGCATTACCGGAGTTTACGAATT
13590077 AA-TT-TTTTTTTCAATTCAACATATTTTCATGATAGATTCATGCATTTATATAAGATAACGTCA
66 AATTTATTTTTTTCAATTCAACATATTTTCATGATAGATTCATGCATTTATATAAGATAACGTCA
13590140 TCACATATCTATAACCAGGTTTGTTAACCATACTAATGGCTAACTTTACATTCATTTCACGTTAA
131 TCACATATCTATAACCAGGTTTGTTAACCATACTAATGGCT-A---TACATTCATTTCACGTTAA
13590205 CATTTACTTTGTTAGCTTATACATGCCATTGATTTCCAAAATAAAGTTTCTTTATATACCGAAAT
192 CATTTACTTTGTTAGCTTATACATGCCATTGATTTCCAAAATAAAGTTTCTTTATATACCGAAAT
*
13590270 CCTGAGGTTGACAGTGTGATGTGTCTCCGACCAAATCCGACATCTGAGCTCTTAACACTACAAAA
257 CCTGAGGTTGACAGTGTGATGTGTCTCCGACCAAATCCGACATCAGAGCTCTTAACACTACAAAA
*
13590335 CAGGGAAAAGGGAAACGGGGTAAGCACTTTG
322 CAGGGAAAAAGGAAACGGGGTAAGCACTTTG
13590366 TG
1 TG
13590368 CTTAGTAAGC
Statistics
Matches: 346, Mismatches: 6, Indels: 6
0.97 0.02 0.02
Matches are distributed among these distances:
350 98 0.28
351 3 0.01
352 66 0.19
354 179 0.52
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (352 bp):
TGTAATACCCCTACCCGTATTCATTGCCGAAATAGGGTACGAGGCATTACCGGAGTTTACGAATT
AATTTATTTTTTTCAATTCAACATATTTTCATGATAGATTCATGCATTTATATAAGATAACGTCA
TCACATATCTATAACCAGGTTTGTTAACCATACTAATGGCTATACATTCATTTCACGTTAACATT
TACTTTGTTAGCTTATACATGCCATTGATTTCCAAAATAAAGTTTCTTTATATACCGAAATCCTG
AGGTTGACAGTGTGATGTGTCTCCGACCAAATCCGACATCAGAGCTCTTAACACTACAAAACAGG
GAAAAAGGAAACGGGGTAAGCACTTTG
Found at i:13593519 original size:109 final size:109
Alignment explanation
Indices: 13593328--13593545 Score: 418
Period size: 109 Copynumber: 2.0 Consensus size: 109
13593318 AGTGAGCTTG
* *
13593328 GATCTGAATTCCCAGTCCAGGCTAAATTCAGACCCTAATTCGGATTACCCGTCCGGGCTAAATCC
1 GATCTAAATTACCAGTCCAGGCTAAATTCAGACCCTAATTCGGATTACCCGTCCGGGCTAAATCC
13593393 ATTTTACACATATTCTTCCGGAGGGCTATATCAGGATAGGATCA
66 ATTTTACACATATTCTTCCGGAGGGCTATATCAGGATAGGATCA
13593437 GATCTAAATTACCAGTCCAGGCTAAATTCAGACCCTAATTCGGATTACCCGTCCGGGCTAAATCC
1 GATCTAAATTACCAGTCCAGGCTAAATTCAGACCCTAATTCGGATTACCCGTCCGGGCTAAATCC
13593502 ATTTTACACATATTCTTCCGGAGGGCTATATCAGGATAGGATCA
66 ATTTTACACATATTCTTCCGGAGGGCTATATCAGGATAGGATCA
13593546 CCCGTCCGGG
Statistics
Matches: 107, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
109 107 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (109 bp):
GATCTAAATTACCAGTCCAGGCTAAATTCAGACCCTAATTCGGATTACCCGTCCGGGCTAAATCC
ATTTTACACATATTCTTCCGGAGGGCTATATCAGGATAGGATCA
Found at i:13598385 original size:21 final size:21
Alignment explanation
Indices: 13598359--13598443 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 21
13598349 ACTCCTAAAC
* *
13598359 CTTAAACCCTAAACCATGTAT
1 CTTAAACCATAAACCATATAT
* *
13598380 CTTAAACCATAGTTAACTCAAAAAT
1 CTTAAACCATA---AAC-CATATAT
* *
13598405 CTTAAACCCTAAACTATATAT
1 CTTAAACCATAAACCATATAT
13598426 CTTAAACCATAAACCATA
1 CTTAAACCATAAACCATA
13598444 AACTATAATG
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
21 30 0.60
22 3 0.06
24 3 0.06
25 14 0.28
ACGTcount: A:0.45, C:0.25, G:0.02, T:0.28
Consensus pattern (21 bp):
CTTAAACCATAAACCATATAT
Found at i:13598396 original size:46 final size:46
Alignment explanation
Indices: 13598343--13598436 Score: 143
Period size: 46 Copynumber: 2.0 Consensus size: 46
13598333 CTTCAAATAC
** *
13598343 TAGTTAACTCCTAAACCTTAAACCCTAAACCATGTATCTTAAACCA
1 TAGTTAACTCAAAAACCTTAAACCCTAAACCATATATCTTAAACCA
* *
13598389 TAGTTAACTCAAAAATCTTAAACCCTAAACTATATATCTTAAACCA
1 TAGTTAACTCAAAAACCTTAAACCCTAAACCATATATCTTAAACCA
13598435 TA
1 TA
13598437 AACCATAAAC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.43, C:0.24, G:0.03, T:0.30
Consensus pattern (46 bp):
TAGTTAACTCAAAAACCTTAAACCCTAAACCATATATCTTAAACCA
Found at i:13598703 original size:40 final size:41
Alignment explanation
Indices: 13598607--13598703 Score: 142
Period size: 41 Copynumber: 2.4 Consensus size: 41
13598597 GTTATATGAC
*
13598607 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
* *
13598648 TTTTAGCGGCGTTTTTCCAAAAGCGTCGCTATTGCTCT-GT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
* *
13598688 TTTTAGTGGCATTTTT
1 TTTTAGCGGCGTTTTT
13598704 GGTAAAACAC
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 16 0.31
41 35 0.69
ACGTcount: A:0.15, C:0.21, G:0.24, T:0.40
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
Found at i:13598772 original size:12 final size:12
Alignment explanation
Indices: 13598757--13598782 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
13598747 GTTTTTTGAT
13598757 AAAACGCCGCTA
1 AAAACGCCGCTA
13598769 AAAACGCCGCTA
1 AAAACGCCGCTA
13598781 AA
1 AA
13598783 GCCCTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAACGCCGCTA
Found at i:13599462 original size:26 final size:28
Alignment explanation
Indices: 13599433--13599492 Score: 79
Period size: 26 Copynumber: 2.2 Consensus size: 28
13599423 AAATTACAAA
*
13599433 AAAAAAATTTAAAAATATAAA-AA-TAT
1 AAAAAAATTCAAAAATATAAATAATTAT
* *
13599459 AAAAAAATTCAAATATGTAAATAATTAT
1 AAAAAAATTCAAAAATATAAATAATTAT
13599487 AAAAAA
1 AAAAAA
13599493 TAATAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 18 0.62
27 2 0.07
28 9 0.31
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (28 bp):
AAAAAAATTCAAAAATATAAATAATTAT
Found at i:13600203 original size:5 final size:5
Alignment explanation
Indices: 13600193--13600217 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
13600183 ATCCCTCTCT
13600193 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
13600218 AGTTTCAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:13619499 original size:11 final size:11
Alignment explanation
Indices: 13619464--13619514 Score: 65
Period size: 10 Copynumber: 4.9 Consensus size: 11
13619454 TGAAATTCTA
13619464 AAAGATAAA-T
1 AAAGATAAATT
13619474 ACAA-ATAAA-T
1 A-AAGATAAATT
13619484 AAAGATAAATT
1 AAAGATAAATT
13619495 AAAGATAAATT
1 AAAGATAAATT
13619506 AAA-ATAAAT
1 AAAGATAAAT
13619515 CCTAGAATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
9 2 0.05
10 19 0.50
11 17 0.45
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.24
Consensus pattern (11 bp):
AAAGATAAATT
Found at i:13625303 original size:28 final size:28
Alignment explanation
Indices: 13625245--13625307 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
13625235 TTAAACCTTT
* *
13625245 AAAGTTTTAAAAATATAAAAATGATTTA
1 AAAGTTATAAAAATATAAAAATGATTAA
* *
13625273 AAAGTTATAAACATGTAAAAACTGA-TAA
1 AAAGTTATAAAAATATAAAAA-TGATTAA
13625301 AAA-TTAT
1 AAAGTTAT
13625308 TAGACAACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 4 0.13
28 23 0.77
29 3 0.10
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.32
Consensus pattern (28 bp):
AAAGTTATAAAAATATAAAAATGATTAA
Found at i:13625582 original size:21 final size:21
Alignment explanation
Indices: 13625558--13625597 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
13625548 TAAAATTATT
13625558 AAAAA-TATAGAAAAAATAAAA
1 AAAAAGTATA-AAAAAATAAAA
*
13625579 AAAAAGTATAACAAAATAA
1 AAAAAGTATAAAAAAATAA
13625598 TGAGAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.15
Consensus pattern (21 bp):
AAAAAGTATAAAAAAATAAAA
Found at i:13628434 original size:23 final size:23
Alignment explanation
Indices: 13628391--13628443 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
13628381 AAATTTGAAT
* *
13628391 TTCGAGTTAATCGAATCAAGTTA
1 TTCGAGTCAATCGAATCAAGTAA
13628414 TTCGAGTCAACTCGAAT-AAGTAA
1 TTCGAGTCAA-TCGAATCAAGTAA
*
13628437 TACGAGT
1 TTCGAGT
13628444 TCTGAGCCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (23 bp):
TTCGAGTCAATCGAATCAAGTAA
Found at i:13635705 original size:9 final size:8
Alignment explanation
Indices: 13635674--13635714 Score: 50
Period size: 7 Copynumber: 5.2 Consensus size: 8
13635664 GTTTCAATTA
13635674 ATTAATA-
1 ATTAATAT
13635681 ATTAATAT
1 ATTAATAT
*
13635689 AATAATAT
1 ATTAATAT
13635697 ATTATATAT
1 ATTA-ATAT
13635706 ATTAA-AT
1 ATTAATAT
13635713 AT
1 AT
13635715 CTTATACTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 11 0.37
8 11 0.37
9 8 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
ATTAATAT
Found at i:13637413 original size:21 final size:21
Alignment explanation
Indices: 13637375--13637414 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
13637365 CTATTGTGTC
*
13637375 TAGTTTGATTTTTATTGAAAT
1 TAGTTTGAATTTTATTGAAAT
13637396 TAGTTT-AATTTTAGTTGAA
1 TAGTTTGAATTTTA-TTGAA
13637415 TAATAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (21 bp):
TAGTTTGAATTTTATTGAAAT
Found at i:13646442 original size:19 final size:19
Alignment explanation
Indices: 13646418--13646469 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
13646408 GAAGTTGTTG
13646418 GACCAAATATGGCCATTGA
1 GACCAAATATGGCCATTGA
13646437 GACCAAATATGGCCATTGA
1 GACCAAATATGGCCATTGA
*
13646456 GATCAAATATGGCC
1 GACCAAATATGGCC
13646470 GATGACCTGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (19 bp):
GACCAAATATGGCCATTGA
Found at i:13650184 original size:26 final size:26
Alignment explanation
Indices: 13650154--13650216 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
13650144 GATTAGGCAC
13650154 AAAGGCTTTTCCAAATGACATGCCAA
1 AAAGGCTTTTCCAAATGACATGCCAA
* * * *
13650180 AAAGGTTTTTTCAAGTGACATGCCAC
1 AAAGGCTTTTCCAAATGACATGCCAA
13650206 AAAGGCTTTTC
1 AAAGGCTTTTC
13650217 AAAAGATTAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (26 bp):
AAAGGCTTTTCCAAATGACATGCCAA
Found at i:13651575 original size:8 final size:8
Alignment explanation
Indices: 13651562--13651587 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
13651552 ATTTATCAGC
13651562 TTTTATTA
1 TTTTATTA
13651570 TTTTATTA
1 TTTTATTA
13651578 TTTTATTA
1 TTTTATTA
13651586 TT
1 TT
13651588 CTGAAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTATTA
Found at i:13652682 original size:16 final size:17
Alignment explanation
Indices: 13652651--13652683 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
13652641 GATTCTAGCA
*
13652651 TTAGGTTTTCTTTTATT
1 TTAGCTTTTCTTTTATT
13652668 TTAGCTTTT-TTTTATT
1 TTAGCTTTTCTTTTATT
13652684 CTATTACGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.12, C:0.06, G:0.09, T:0.73
Consensus pattern (17 bp):
TTAGCTTTTCTTTTATT
Found at i:13653931 original size:14 final size:14
Alignment explanation
Indices: 13653912--13653949 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
13653902 GTTTGCCAGT
*
13653912 AAAATGTTTTCCGG
1 AAAATGATTTCCGG
*
13653926 AAAATGATTTCTGG
1 AAAATGATTTCCGG
13653940 AAAATGATTT
1 AAAATGATTT
13653950 ACTTTTCTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (14 bp):
AAAATGATTTCCGG
Found at i:13654066 original size:20 final size:20
Alignment explanation
Indices: 13654041--13654080 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
13654031 CTGTTTTTAC
13654041 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
13654061 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
13654081 TTTAAATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATATTAATAAATTTATAT
Found at i:13654085 original size:16 final size:18
Alignment explanation
Indices: 13654036--13654080 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
13654026 AAAAGCTGTT
* *
13654036 TTTACATATATTAATAAA
1 TTTATATATTTTAATAAA
13654054 TTTATATATATATTAATAAA
1 TTTATATAT-T-TTAATAAA
13654074 TTTATAT
1 TTTATAT
13654081 TTTAAATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
20 15 0.65
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTATATATTTTAATAAA
Found at i:13656353 original size:4 final size:4
Alignment explanation
Indices: 13656344--13656368 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
13656334 GAAAAGCAGG
13656344 GAAA GAAA GAAA GAAA GAAA GAAA G
1 GAAA GAAA GAAA GAAA GAAA GAAA G
13656369 GAGAAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:13656376 original size:20 final size:18
Alignment explanation
Indices: 13656353--13656393 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
13656343 GGAAAGAAAG
13656353 AAAGAAAGAAAGAAAGGAGA
1 AAAGAAAGAAA-AAAGG-GA
*
13656373 AAAGAAGGAAAAAAGGGA
1 AAAGAAAGAAAAAAGGGA
13656391 AAA
1 AAA
13656394 TTCAAGGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 5 0.25
20 10 0.50
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (18 bp):
AAAGAAAGAAAAAAGGGA
Found at i:13657568 original size:53 final size:53
Alignment explanation
Indices: 13657503--13657621 Score: 184
Period size: 53 Copynumber: 2.2 Consensus size: 53
13657493 CTGTTACCGT
* * * *
13657503 TACTATTACTGTTTCAGATTTGTTCTGATGAGGTACTCTGTGTACCGTAATGT
1 TACTGTTACTGTTTCAGATTTGTTCCGATGAGGTACTCTGTATACCGTAATGC
* *
13657556 TATTGTTACTGTTTCAGATTTGTTCCGATGAGGTACTCTGTATACCGTACTGC
1 TACTGTTACTGTTTCAGATTTGTTCCGATGAGGTACTCTGTATACCGTAATGC
13657609 TACTGTTACTGTT
1 TACTGTTACTGTT
13657622 ACTGTTTCGG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 59 1.00
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.44
Consensus pattern (53 bp):
TACTGTTACTGTTTCAGATTTGTTCCGATGAGGTACTCTGTATACCGTAATGC
Found at i:13657765 original size:19 final size:19
Alignment explanation
Indices: 13657743--13657794 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
13657733 AAAGATCGAC
13657743 TGTTACTGAATAATTTAAT
1 TGTTACTGAATAATTTAAT
* *
13657762 TGTTACTGTAT-ATCTAAT
1 TGTTACTGAATAATTTAAT
* *
13657780 TTTTACTAAATAATT
1 TGTTACTGAATAATT
13657795 GACTGTTACT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
18 14 0.54
19 12 0.46
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.50
Consensus pattern (19 bp):
TGTTACTGAATAATTTAAT
Found at i:13657890 original size:18 final size:18
Alignment explanation
Indices: 13657828--13657891 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 18
13657818 GTTGATTTGA
*
13657828 TACTGAATAACTGATTAT
1 TACTGAATAATTGATTAT
* *
13657846 TATTGAATAATTGATTGT
1 TACTGAATAATTGATTAT
* *
13657864 TACCGAATAATTGACTAT
1 TACTGAATAATTGATTAT
*
13657882 TACTAAATAA
1 TACTGAATAA
13657892 ATAATTGTTC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (18 bp):
TACTGAATAATTGATTAT
Found at i:13657891 original size:36 final size:36
Alignment explanation
Indices: 13657832--13657900 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 36
13657822 ATTTGATACT
* * * * *
13657832 GAATAACTGATTATTATTGAATAATTGATTGTTACC
1 GAATAACTGACTATTACTAAATAAATAATTGTTACC
*
13657868 GAATAATTGACTATTACTAAATAAATAATTGTT
1 GAATAACTGACTATTACTAAATAAATAATTGTT
13657901 CTGATTGGCT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 27 1.00
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.41
Consensus pattern (36 bp):
GAATAACTGACTATTACTAAATAAATAATTGTTACC
Found at i:13662494 original size:17 final size:19
Alignment explanation
Indices: 13662474--13662508 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
13662464 GATGAAGAAT
13662474 GGAAGAA-GGAA-AAGGAA
1 GGAAGAACGGAAGAAGGAA
13662491 GGAAGAACGGAAGAAGGA
1 GGAAGAACGGAAGAAGGA
13662509 GAAAGACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.54, C:0.03, G:0.43, T:0.00
Consensus pattern (19 bp):
GGAAGAACGGAAGAAGGAA
Found at i:13666112 original size:6 final size:6
Alignment explanation
Indices: 13666096--13666126 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
13666086 GTAGGTTTCC
*
13666096 AAAATG GAAATG AAAATG AAAATG AAAATG A
1 AAAATG AAAATG AAAATG AAAATG AAAATG A
13666127 TTCATTTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.19, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:13666297 original size:27 final size:26
Alignment explanation
Indices: 13666263--13666339 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 26
13666253 ACATATTTTC
13666263 TCAAAATTTTAATAGAGGTAAAATCA
1 TCAAAATTTTAATAGAGGTAAAATCA
*
13666289 TCAAAAATTTTACCA-AGA-GTAAAATCG
1 TC-AAAATTTTA--ATAGAGGTAAAATCA
*
13666316 TCAAAATTTT-ATTGAAGGTAAAAT
1 TCAAAATTTTAATAG-AGGTAAAAT
13666340 AGAGATGAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
23 1 0.02
24 1 0.02
25 1 0.02
26 17 0.40
27 19 0.44
28 3 0.07
29 1 0.02
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.31
Consensus pattern (26 bp):
TCAAAATTTTAATAGAGGTAAAATCA
Found at i:13670921 original size:14 final size:14
Alignment explanation
Indices: 13670902--13670928 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13670892 CATTTTTTAT
13670902 TTTTAACTTTACTC
1 TTTTAACTTTACTC
13670916 TTTTAACTTTACT
1 TTTTAACTTTACT
13670929 TATATTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.19, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTTAACTTTACTC
Found at i:13671305 original size:23 final size:20
Alignment explanation
Indices: 13671279--13671328 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
13671269 TTCTTCTTCT
*
13671279 TCTTCTTCTTTACTGCTGCA
1 TCTTCTTCTTCACTGCTGCA
13671299 TCTTCTTCTTCACTGCTGCA
1 TCTTCTTCTTCACTGCTGCA
13671319 TCTTCTTCTT
1 TCTTCTTCTT
13671329 GCAGGTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.08, C:0.32, G:0.08, T:0.52
Consensus pattern (20 bp):
TCTTCTTCTTCACTGCTGCA
Found at i:13674813 original size:9 final size:9
Alignment explanation
Indices: 13674795--13674843 Score: 62
Period size: 9 Copynumber: 5.4 Consensus size: 9
13674785 TTGCAAGAAT
*
13674795 GATGATGAC
1 GATGAGGAC
*
13674804 GATGAAGAC
1 GATGAGGAC
*
13674813 GATGAGGAT
1 GATGAGGAC
13674822 GATGAGGAC
1 GATGAGGAC
*
13674831 GATGAGGAT
1 GATGAGGAC
13674840 GATG
1 GATG
13674844 TTTCTTCAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.35, C:0.06, G:0.41, T:0.18
Consensus pattern (9 bp):
GATGAGGAC
Found at i:13674825 original size:18 final size:18
Alignment explanation
Indices: 13674804--13674843 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
13674794 TGATGATGAC
13674804 GATGAAGACGATGAGGAT
1 GATGAAGACGATGAGGAT
*
13674822 GATGAGGACGATGAGGAT
1 GATGAAGACGATGAGGAT
13674840 GATG
1 GATG
13674844 TTTCTTCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.35, C:0.05, G:0.42, T:0.17
Consensus pattern (18 bp):
GATGAAGACGATGAGGAT
Found at i:13675068 original size:11 final size:10
Alignment explanation
Indices: 13675049--13675121 Score: 56
Period size: 11 Copynumber: 6.7 Consensus size: 10
13675039 AGTGCTGTTT
13675049 TTTTGTGCTA
1 TTTTGTGCTA
*
13675059 TTTTGTTGCTG
1 TTTTG-TGCTA
* * *
13675070 TTTCGGAGCTG
1 TTT-TGTGCTA
13675081 TTTTGATGCTA
1 TTTTG-TGCTA
13675092 TTTTGGTGCTA
1 TTTT-GTGCTA
13675103 TTTTAGTGCTA
1 TTTT-GTGCTA
13675114 CTTTTGTG
1 -TTTTGTG
13675122 GTGTTTTATT
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
10 6 0.12
11 39 0.76
12 6 0.12
ACGTcount: A:0.10, C:0.11, G:0.25, T:0.55
Consensus pattern (10 bp):
TTTTGTGCTA
Found at i:13675106 original size:22 final size:22
Alignment explanation
Indices: 13675048--13675119 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
13675038 TAGTGCTGTT
* * *
13675048 TTTTTGTGCTATTTTGTTGCTG
1 TTTTGGTGCTATTTTGATGCTA
* * *
13675070 TTTCGGAGCTGTTTTGATGCTA
1 TTTTGGTGCTATTTTGATGCTA
13675092 TTTTGGTGCTATTTT-AGTGCTA
1 TTTTGGTGCTATTTTGA-TGCTA
13675114 CTTTTG
1 -TTTTG
13675120 TGGTGTTTTA
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
21 1 0.03
22 33 0.85
23 5 0.13
ACGTcount: A:0.10, C:0.11, G:0.24, T:0.56
Consensus pattern (22 bp):
TTTTGGTGCTATTTTGATGCTA
Found at i:13675690 original size:47 final size:47
Alignment explanation
Indices: 13675636--13675730 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 47
13675626 TAGTGCCTAG
* * *
13675636 TGATTGAAATAAAAACTTCTAAATAGTTGAGTGACTTGATGAAAACT
1 TGATTGAAATAAAAACTTCTAAATAATTGAGTGAATTAATGAAAACT
*
13675683 TGATTGAAATAAAAACTTCTAAATAATTTAGTGAATTAATGAAAACT
1 TGATTGAAATAAAAACTTCTAAATAATTGAGTGAATTAATGAAAACT
13675730 T
1 T
13675731 TCGAATAGCT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (47 bp):
TGATTGAAATAAAAACTTCTAAATAATTGAGTGAATTAATGAAAACT
Found at i:13684418 original size:41 final size:41
Alignment explanation
Indices: 13684354--13684435 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
13684344 AATTATTAAG
* * *
13684354 ATGGGATGCCATTTTTTATATATAACAAGGAAACACTAACT
1 ATGGGATGACATTCTTTAGATATAACAAGGAAACACTAACT
*
13684395 ATGGGATGACATTCTTTAGATATAACGAGGAAACACTAACT
1 ATGGGATGACATTCTTTAGATATAACAAGGAAACACTAACT
13684436 TTGCCTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (41 bp):
ATGGGATGACATTCTTTAGATATAACAAGGAAACACTAACT
Found at i:13688629 original size:15 final size:15
Alignment explanation
Indices: 13688611--13688730 Score: 61
Period size: 16 Copynumber: 7.5 Consensus size: 15
13688601 TGAAGTACAT
13688611 AATAAAATAAAATAA
1 AATAAAATAAAATAA
**
13688626 AATAAAATATATAAGTCT
1 AATAAAATA-A-AA-TAA
13688644 AA-AAAATAAAA-AA
1 AATAAAATAAAATAA
*
13688657 AATAATAACAAGAA-AA
1 AATAA-AATAA-AATAA
13688673 AATACAAATAGAAATAGA
1 AATA-AAATA-AAATA-A
*
13688691 AATAAAAGAAAA-ATA
1 AATAAAATAAAATA-A
13688706 AATAAAACATAAAACT-A
1 AAT-AAA-ATAAAA-TAA
13688723 AATAAAAT
1 AATAAAAT
13688731 TTAAATAATT
Statistics
Matches: 82, Mismatches: 9, Indels: 28
0.69 0.08 0.24
Matches are distributed among these distances:
13 2 0.02
14 2 0.02
15 22 0.27
16 24 0.29
17 24 0.29
18 8 0.10
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.18
Consensus pattern (15 bp):
AATAAAATAAAATAA
Found at i:13698913 original size:37 final size:37
Alignment explanation
Indices: 13698863--13698935 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
13698853 GATAATATCC
13698863 TACTAATTTACATTTTTAGATACCATACTTAGCATCG
1 TACTAATTTACATTTTTAGATACCATACTTAGCATCG
13698900 TACTAATTTACATTTTTAGATACCATACTTAGCATC
1 TACTAATTTACATTTTTAGATACCATACTTAGCATC
13698936 ATCAGTCTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (37 bp):
TACTAATTTACATTTTTAGATACCATACTTAGCATCG
Found at i:13699368 original size:20 final size:19
Alignment explanation
Indices: 13699313--13699369 Score: 53
Period size: 20 Copynumber: 3.0 Consensus size: 19
13699303 ACATAGCAAA
*
13699313 CTGGCAC-CAGAGTGCATC
1 CTGGCACACAAAGTGCATC
* ** *
13699331 CTGGCATACAAAACGCATAT
1 CTGGCACACAAAGTGCAT-C
13699351 CTGGCACACAAAGTGCATC
1 CTGGCACACAAAGTGCATC
13699370 TTCGCATATA
Statistics
Matches: 28, Mismatches: 9, Indels: 3
0.70 0.22 0.08
Matches are distributed among these distances:
18 6 0.21
19 7 0.25
20 15 0.54
ACGTcount: A:0.32, C:0.30, G:0.21, T:0.18
Consensus pattern (19 bp):
CTGGCACACAAAGTGCATC
Found at i:13701327 original size:30 final size:31
Alignment explanation
Indices: 13701271--13701330 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
13701261 TTTAACAAGA
13701271 AAATGCCTCTAAAATAAATAAAAAAATTAAC
1 AAATGCCTCTAAAATAAATAAAAAAATTAAC
* * *
13701302 AAATTCCTTTAAAAT-AATAACAAAATTAA
1 AAATGCCTCTAAAATAAATAAAAAAATTAA
13701331 TAATAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.27
Consensus pattern (31 bp):
AAATGCCTCTAAAATAAATAAAAAAATTAAC
Found at i:13703741 original size:95 final size:95
Alignment explanation
Indices: 13703625--13703818 Score: 388
Period size: 95 Copynumber: 2.0 Consensus size: 95
13703615 TATGTCCACT
13703625 CACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCATGTTACATGTATC
1 CACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCATGTTACATGTATC
13703690 AATATGTGTAATCGTGGTATATCCACTTAG
66 AATATGTGTAATCGTGGTATATCCACTTAG
13703720 CACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCATGTTACATGTATC
1 CACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCATGTTACATGTATC
13703785 AATATGTGTAATCGTGGTATATCCACTTAG
66 AATATGTGTAATCGTGGTATATCCACTTAG
13703815 CACC
1 CACC
13703819 TCATTACATG
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 99 1.00
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.31
Consensus pattern (95 bp):
CACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCATGTTACATGTATC
AATATGTGTAATCGTGGTATATCCACTTAG
Found at i:13703759 original size:47 final size:48
Alignment explanation
Indices: 13703625--13703828 Score: 286
Period size: 48 Copynumber: 4.3 Consensus size: 48
13703615 TATGTCCACT
13703625 CACCACGTTA-ATGAATCAATATATGTAACCGTGGCATATCCACTTAG
1 CACCACGTTACATGAATCAATATATGTAACCGTGGCATATCCACTTAG
* * * * *
13703672 CACCATGTTACATGTATCAATATGTGTAATCGTGGTATATCCACTTAG
1 CACCACGTTACATGAATCAATATATGTAACCGTGGCATATCCACTTAG
13703720 CACCACGTTA-ATGAATCAATATATGTAACCGTGGCATATCCACTTAG
1 CACCACGTTACATGAATCAATATATGTAACCGTGGCATATCCACTTAG
* * * * *
13703767 CACCATGTTACATGTATCAATATGTGTAATCGTGGTATATCCACTTAG
1 CACCACGTTACATGAATCAATATATGTAACCGTGGCATATCCACTTAG
* *
13703815 CACCTCATTACATG
1 CACCACGTTACATG
13703829 TATAACCGTG
Statistics
Matches: 137, Mismatches: 18, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
47 51 0.37
48 86 0.63
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.31
Consensus pattern (48 bp):
CACCACGTTACATGAATCAATATATGTAACCGTGGCATATCCACTTAG
Found at i:13714027 original size:93 final size:93
Alignment explanation
Indices: 13713915--13714086 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
13713905 TGCCCATAAG
*
13713915 CGAACTCGGACTCAACTCAACGAGCTCGGGCATTCACATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCA
13713980 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
13714008 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCA
13714073 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
13714087 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:13714083 original size:46 final size:46
Alignment explanation
Indices: 13713908--13714083 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
13713898 TGTAACCTGC
* *
13713908 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCATTCACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
*
13713954 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCACAT
* *
13714004 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
*
13714047 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
13714084 TGCTCAACCA
Statistics
Matches: 113, Mismatches: 8, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.56
47 29 0.26
48 2 0.02
49 2 0.02
50 5 0.04
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
Found at i:13717207 original size:136 final size:136
Alignment explanation
Indices: 13716963--13717236 Score: 539
Period size: 136 Copynumber: 2.0 Consensus size: 136
13716953 ATCTCATTTC
*
13716963 ACATTTTTCTTCTATTTCTTATCCATTTTCCATCTCAATATCGAATACCACATCTTACGTTCAAT
1 ACATTTTTCTTCTATTTCTTATCCATTTGCCATCTCAATATCGAATACCACATCTTACGTTCAAT
13717028 TTTAAATTTTCATGGATTTCAAATGCTTATTCATTATCATCATTTTTATCCTTTATCTCCCTATT
66 TTTAAATTTTCATGGATTTCAAATGCTTATTCATTATCATCATTTTTATCCTTTATCTCCCTATT
13717093 AACACG
131 AACACG
13717099 ACATTTTTCTTCTATTTCTTATCCATTTGCCATCTCAATATCGAATACCACATCTTACGTTCAAT
1 ACATTTTTCTTCTATTTCTTATCCATTTGCCATCTCAATATCGAATACCACATCTTACGTTCAAT
13717164 TTTAAATTTTCATGGATTTCAAATGCTTATTCATTATCATCATTTTTATCCTTTATCTCCCTATT
66 TTTAAATTTTCATGGATTTCAAATGCTTATTCATTATCATCATTTTTATCCTTTATCTCCCTATT
13717229 AACACG
131 AACACG
13717235 AC
1 AC
13717237 TTGGACTCGA
Statistics
Matches: 137, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
136 137 1.00
ACGTcount: A:0.27, C:0.23, G:0.05, T:0.46
Consensus pattern (136 bp):
ACATTTTTCTTCTATTTCTTATCCATTTGCCATCTCAATATCGAATACCACATCTTACGTTCAAT
TTTAAATTTTCATGGATTTCAAATGCTTATTCATTATCATCATTTTTATCCTTTATCTCCCTATT
AACACG
Found at i:13720482 original size:17 final size:19
Alignment explanation
Indices: 13720462--13720498 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
13720452 TAAATTAAAA
13720462 TTTATT-AAA-TAATATTT
1 TTTATTCAAATTAATATTT
13720479 TTTATTCAAATTAATATTT
1 TTTATTCAAATTAATATTT
13720498 T
1 T
13720499 GAAATATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTATTCAAATTAATATTT
Found at i:13729818 original size:42 final size:46
Alignment explanation
Indices: 13729755--13729966 Score: 159
Period size: 49 Copynumber: 4.6 Consensus size: 46
13729745 CTTCGTTTAC
** * *
13729755 TCGATGTCATAGTTCAACTATGGTCTTACAC-AT-C-T-TCATATA
1 TCGATGTCATAGCCCAGCTATGGTCTTACACAATACATATCACATA
13729797 TCGATGTCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATA
1 TCGATGTCATAGCCCAGCTATGGTCTTACAC--AAT-ACATATCACATA
* * *
13729846 TCGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCA-C
1 TCGATGTCATAGCCCAGCTATGGTCTTACAC-AAT-ACATATCACATA
* * * * * *
13729893 T-GATGCCATATCCCAGATATGGTCTTATACAGTAGCATAT-ATCACA
1 TCGATGTCATAGCCCAGCTATGGTCTTACACAATA-CATATCA-CATA
* * * *
13729939 CCGATGCCATATCCCAGATATGGTCTTA
1 TCGATGTCATAGCCCAGCTATGGTCTTA
13729967 TACGGAAATT
Statistics
Matches: 144, Mismatches: 15, Indels: 17
0.82 0.09 0.10
Matches are distributed among these distances:
42 28 0.19
44 1 0.01
45 11 0.08
46 26 0.18
47 28 0.19
48 14 0.10
49 36 0.25
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (46 bp):
TCGATGTCATAGCCCAGCTATGGTCTTACACAATACATATCACATA
Found at i:13729857 original size:49 final size:48
Alignment explanation
Indices: 13729796--13729966 Score: 197
Period size: 47 Copynumber: 3.6 Consensus size: 48
13729786 ATCTTCATAT
* *
13729796 ATCGATGTCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACA
1 ATCGATGCCATAGCCCAGATATGGTCTTACACGTAATCACATATCACA
* *
13729844 TATCGATGCCATAGCCCAGCTATGGTCTTACACG-AATCACATATCTCA
1 -ATCGATGCCATAGCCCAGATATGGTCTTACACGTAATCACATATCACA
* * * * *
13729892 CT-GATGCCATATCCCAGATATGGTCTTATACAGT-AGCATATATCAC-
1 ATCGATGCCATAGCCCAGATATGGTCTTACAC-GTAATCACATATCACA
* *
13729938 ACCGATGCCATATCCCAGATATGGTCTTA
1 ATCGATGCCATAGCCCAGATATGGTCTTA
13729967 TACGGAAATT
Statistics
Matches: 108, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
46 26 0.24
47 37 0.34
48 13 0.12
49 32 0.30
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (48 bp):
ATCGATGCCATAGCCCAGATATGGTCTTACACGTAATCACATATCACA
Found at i:13730031 original size:31 final size:31
Alignment explanation
Indices: 13729988--13730198 Score: 305
Period size: 31 Copynumber: 6.8 Consensus size: 31
13729978 CTTGTCACTT
*
13729988 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* * *
13730019 GTAGCCGGAGCTACCATTTTTCATTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* * *
13730050 GTAGTCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
13730081 GTAGCAGAAGCTACCACTTTTCACTTATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* **
13730112 GCAGTAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
13730143 GTAGCCGAAGCTACCACTTTTCACTAATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
13730174 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
13730199 TGTCATTTGT
Statistics
Matches: 162, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 162 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:13730276 original size:50 final size:51
Alignment explanation
Indices: 13730174--13730302 Score: 206
Period size: 50 Copynumber: 2.5 Consensus size: 51
13730164 CACTAATCAG
* * * *
13730174 GTAGCCGAAGCTACCACTTTTCACTTGTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTATCCTTGATCAGATAAGT
*
13730225 GTAGCCGAAGCTATTACTTATCACTT-TCACTTATCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTATCCTTGATCAGATAAGT
13730275 GTAGCCGAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
13730303 TGCCATGGTC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
50 47 0.66
51 24 0.34
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCACTTATCCTTGATCAGATAAGT
Found at i:13744990 original size:15 final size:15
Alignment explanation
Indices: 13744967--13744997 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13744957 TTAAACTCAT
*
13744967 TTTATTTTTATTTTC
1 TTTACTTTTATTTTC
13744982 TTTACTTTTATTTTC
1 TTTACTTTTATTTTC
13744997 T
1 T
13744998 ATTTATTTTT
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:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTACTTTTATTTTC
Found at i:13755989 original size:22 final size:22
Alignment explanation
Indices: 13755963--13756011 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
13755953 TCAAATACAC
*
13755963 TTATTTTA-TTTTATTCGTTTTA
1 TTATTTTACTTATATTC-TTTTA
13755985 TTA-TTTACTTATATTCTTTTA
1 TTATTTTACTTATATTCTTTTA
*
13756006 TAATTT
1 TTATTT
13756012 CAAACTTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.69
Consensus pattern (22 bp):
TTATTTTACTTATATTCTTTTA
Found at i:13759206 original size:36 final size:36
Alignment explanation
Indices: 13759159--13759232 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 36
13759149 TCTGAGCTAT
* *
13759159 AGATCATCAAACAGGATTTTGAGGGAAAGANG-TTAG
1 AGATCATCAAACAAGATTTTGAGAGAAAGA-GTTTAG
13759195 AGATCATCAAACAAGATTTTGAGAGAAAGAGTTTAG
1 AGATCATCAAACAAGATTTTGAGAGAAAGAGTTTAG
13759231 AG
1 AG
13759233 CTAGAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 1 0.03
36 34 0.97
ACGTcount: A:0.42, C:0.08, G:0.26, T:0.23
Consensus pattern (36 bp):
AGATCATCAAACAAGATTTTGAGAGAAAGAGTTTAG
Found at i:13760944 original size:16 final size:17
Alignment explanation
Indices: 13760920--13760952 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
13760910 CATAGGCCTT
13760920 CATGAAACA-ATATGGC
1 CATGAAACAGATATGGC
*
13760936 CATGTAACAGATATGGC
1 CATGAAACAGATATGGC
13760953 ACACTGCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (17 bp):
CATGAAACAGATATGGC
Found at i:13765313 original size:40 final size:40
Alignment explanation
Indices: 13765258--13765339 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
13765248 TCAATCGAGT
* *
13765258 TTTCCCAAAAGCTTTTTCTCAATTTTCTCTCTGTGCACCC
1 TTTCCCAAAAGCTTTTTCCCAATTTTCTCTCTGTACACCC
13765298 TTTCCCAAAAGCTTTTTCCCAATTTTCTCTCTGTACACCC
1 TTTCCCAAAAGCTTTTTCCCAATTTTCTCTCTGTACACCC
13765338 TT
1 TT
13765340 AGTTTAGTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.18, C:0.33, G:0.06, T:0.43
Consensus pattern (40 bp):
TTTCCCAAAAGCTTTTTCCCAATTTTCTCTCTGTACACCC
Found at i:13769614 original size:13 final size:13
Alignment explanation
Indices: 13769598--13769630 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
13769588 TTTAATTAAA
*
13769598 TTAGTTAATTAGT
1 TTAGATAATTAGT
13769611 TTAGATAATTAGT
1 TTAGATAATTAGT
13769624 TTA-ATAA
1 TTAGATAA
13769631 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:13778529 original size:133 final size:133
Alignment explanation
Indices: 13778302--13778553 Score: 312
Period size: 133 Copynumber: 1.9 Consensus size: 133
13778292 AAGCCATAGA
*
13778302 TCTTATCTCCCTGAAGTTGCAATGGAGTAGATCAAAGATAGCAAATCTTATCTCTCTAAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAATGGAGTAGATCAAAGATAGCAAATCTTATCTCCCTAAAGTTGC
* * * * *
13778367 AGTAGAGCAGATTAAAGCTATAAAACTTATCTATCTGAAGTTGCAGTAGAGCAGGTTGAAATTAC
66 AGTAGAGCAGATGAAAGATACAAAACTTATCTACCTAAAGTTGCAGTAGAGCAGGTTGAAATTAC
13778432 GAG
131 GAG
* * * *
13778435 TCTTATCTCCCTGAAGTTGTAGTGGAGTAGATCGAAA-ATTA-CAAGTCTTATCTCCCTGAAGTT
1 TCTTATCTCCCTGAAGTTGCAATGGAGTAGATC-AAAGA-TAGCAAATCTTATCTCCCTAAAGTT
* * * * * *
13778498 GCAGTGGAGCATACTGAAA-ATACCAATCTTATCTCCCTAAAGTTGCAGTGGAGCAG
64 GCAGTAGAGCAGA-TGAAAGATACAAAACTTATCTACCTAAAGTTGCAGTAGAGCAG
13778554 ATTAAAGCTA
Statistics
Matches: 100, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
133 91 0.91
134 9 0.09
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (133 bp):
TCTTATCTCCCTGAAGTTGCAATGGAGTAGATCAAAGATAGCAAATCTTATCTCCCTAAAGTTGC
AGTAGAGCAGATGAAAGATACAAAACTTATCTACCTAAAGTTGCAGTAGAGCAGGTTGAAATTAC
GAG
Found at i:13778655 original size:128 final size:131
Alignment explanation
Indices: 13778482--13778833 Score: 371
Period size: 128 Copynumber: 2.7 Consensus size: 131
13778472 ATTACAAGTC
* * *
13778482 TTATCTCCCTGAAGTTGCAGTGGAGCATACTGAAA-ATACCAATCTTATCTCCCTAAAGTTGCAG
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAGACA-CAATCTTATCTCCCTAAAGTTGCAG
* * *
13778546 TGGAGCAGATTAAAGCTACTAATTCTATTTC-CT-TGAATTTGCAG-AGAAGCAGGTTAAA-A-A
64 TGGAGCAGATTAAAGCTACTAATTCTATATCTCTCTGAAGTTGCAGTAG-AGCAGATTAAACATA
13778606 AACA
128 AACA
* * *
13778610 TTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCCACAGATCTTATCTCCCTGAAGTTGCAGT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGACACA-ATCTTATCTCCCTAAAGTTGCAGT
* *
13778675 GAAGCAGATTAAAGCTAC-AAATCT-TATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATA
65 GGAGCAGATTAAAGCTACTAATTCTATATCTCTCTGAAGTTGCAGTAGAGCAGATTAAA-C-ATA
*
13778738 AACC
128 AACA
* * * ** * *
13778742 TTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAGATGTCAATCTTATAC-CTCTAAAGTTACAG
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGA-CACAATCTTAT-CTCCCTAAAGTTGCAG
* * *
13778806 TAGAGCAGATTGAAGCTACTAATCCTAT
64 TGGAGCAGATTAAAGCTACTAATTCTAT
13778834 CTCCCTAAAA
Statistics
Matches: 184, Mismatches: 27, Indels: 20
0.80 0.12 0.09
Matches are distributed among these distances:
126 3 0.02
127 13 0.07
128 88 0.48
129 2 0.01
131 1 0.01
132 69 0.38
133 7 0.04
134 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (131 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGACACAATCTTATCTCCCTAAAGTTGCAGTG
GAGCAGATTAAAGCTACTAATTCTATATCTCTCTGAAGTTGCAGTAGAGCAGATTAAACATAAAC
A
Found at i:13778729 original size:88 final size:86
Alignment explanation
Indices: 13778254--13778865 Score: 497
Period size: 88 Copynumber: 7.0 Consensus size: 86
13778244 GTCATTATGG
** * * *
13778254 CAAATCTTATCTCTCTGAAGTTATAGTGGAGCAAATTAAAGCCATAGATCTTATCTCCCTGAAGT
1 CAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA-ATCTTATCTCCCTGAAGT
* * * *
13778319 TGCAATGGAGTAGATCAAAGATA
65 TGCAGTGAAGCAGATTAAA-ATA
* * * * **
13778342 GCAAATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATTAAAGCTATAAAACTTATCTATCTGAAG
1 -CAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCTA-CAATCTTATCTCCCTGAAG
* *
13778407 TTGCAGT-AGAGCAGGTTGAAATTA
64 TTGCAGTGA-AGCAGATT-AAAATA
* * * * * * **
13778431 CGAGTCTTATCTCCCTGAAGTTGTAGTGGAGTAGATCGAAAATTACAAGTCTTATCTCCCTGAAG
1 CAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGAT-TAAAGCTACAA-TCTTATCTCCCTGAAG
* * *
13778496 TTGCAGTGGAGCATACTGAAAATA
64 TTGCAGTGAAGCAGA-TTAAAATA
* * * * * *
13778520 CCAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACTAAT-TCTATTTCCTTGAAT
1 CAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC-AATCT-TATCTCCCTGAAG
* *
13778584 TTGCAGAGAAGCAGGTT-AAA-A
64 TTGCAGTGAAGCAGATTAAAATA
*
13778605 -AAA-CATTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCCACAGATCTTATCTCCCTGAAG
1 CAAATC-TTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA-ATCTTATCTCCCTGAAG
*
13778668 TTGCAGTGAAGCAGATTAAAGCTA
64 TTGCAGTGAAGCAGATTAAA-ATA
* * *
13778692 CAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATAAACCTTATCTCCCTGAAGT
1 CAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCTA-CAATCTTATCTCCCTGAAGT
* * *
13778757 TGCAGT-AGAGCAGGTTGAAGATGT
65 TGCAGTGA-AGCAGATT-AAAAT-A
* * * * * * *
13778781 C-AATCTTATAC-CTCTAAAGTTACAGTAGAGCAGATTGAAGCTACTAATCCTATCTCCCTAAAA
1 CAAATCTTAT-CTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC-AATCTTATCTCCCTGAAG
*
13778844 TTACAGTGAAGC-GAATTAAAAT
64 TTGCAGTGAAGCAG-ATTAAAAT
13778866 GATGAATCCT
Statistics
Matches: 418, Mismatches: 80, Indels: 52
0.76 0.15 0.09
Matches are distributed among these distances:
83 2 0.00
84 65 0.16
85 4 0.01
86 3 0.01
87 9 0.02
88 191 0.46
89 139 0.33
90 5 0.01
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (86 bp):
CAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAATCTTATCTCCCTGAAGTT
GCAGTGAAGCAGATTAAAATA
Found at i:13778850 original size:44 final size:44
Alignment explanation
Indices: 13778256--13778839 Score: 428
Period size: 44 Copynumber: 13.3 Consensus size: 44
13778246 CATTATGGCA
* ** * * *
13778256 AATCTTATCTCTCTGAAGTTATAGTGGAGCAAATTAAAGCCA-T
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCTACT
* * * * * *
13778299 AGATCTTATCTCCCTGAAGTTGCAATGGAGTAGATCAAAGATAGCA
1 A-ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCTA-CT
* *
13778345 AATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATTAAAGCTA-T
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCTACT
* ** * * *
13778388 AAAACTTATCTATCTGAAGTTGCAGTAGAGCAGGTTGAAA-TTACG
1 -AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATT-AAAGCTACT
* * * * * **
13778433 AGTCTTATCTCCCTGAAGTTGTAGTGGAGTAGATCGAAAATTAC-
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGAT-TAAAGCTACT
* * * * *
13778477 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCATACTGAAA-ATACC
1 AA-TCTTATCTCCCTGAAGTTGCAGTAGAGCAGA-TTAAAGCTACT
* *
13778522 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACT
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCTACT
* * * *
13778566 AAT-TCTATTTCCTTGAATTTGCAG-AGAAGCAGGTTAAA---A--
1 AATCT-TATCTCCCTGAAGTTGCAGTAG-AGCAGATTAAAGCTACT
* * * *
13778605 AAACATTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCCAC-
1 AATC-TTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCTACT
*
13778649 AGATCTTATCTCCCTGAAGTTGCAGT-GAAGCAGATTAAAGCTACA
1 A-ATCTTATCTCCCTGAAGTTGCAGTAG-AGCAGATTAAAGCTACT
*
13778694 AATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTA-T
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCTACT
* * * * *
13778737 AAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAGAT-GT
1 -AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCTACT
* * * *
13778781 CAATCTTATAC-CTCTAAAGTTACAGTAGAGCAGATTGAAGCTACT
1 -AATCTTAT-CTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCTACT
*
13778826 AATCCTATCTCCCT
1 AATCTTATCTCCCT
13778840 AAAATTACAG
Statistics
Matches: 435, Mismatches: 76, Indels: 59
0.76 0.13 0.10
Matches are distributed among these distances:
39 2 0.00
40 25 0.06
41 3 0.01
43 10 0.02
44 312 0.72
45 81 0.19
46 2 0.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCTACT
Found at i:13778879 original size:88 final size:88
Alignment explanation
Indices: 13778616--13778896 Score: 229
Period size: 88 Copynumber: 3.2 Consensus size: 88
13778606 AACATTATCT
* * * * * * * * *
13778616 CTCTGAAGTTGCAGTGGAGCAGATTAAAGCCACAGATCTTATCTCCCTGAAGTTGCAGT-GAAGC
1 CTCTAAAGTTGCAGTAGAGCAGATTAAAGCTATAAACCTTATCTCCCTAAAATTACAGTAG-AGC
*
13778680 AGATT--AAA-GCTACAAATCTTAT-C
65 AGATTGAAAATG-T-C-AATCCTATAC
* * * *
13778703 TCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATAAACCTTATCTCCCTGAAGTTGCAGTAGAGC
1 -CTCTAAAGTTGCAGTAGAGCAGATTAAAGCTATAAACCTTATCTCCCTAAAATTACAGTAGAGC
* * *
13778768 AGGTTGAAGATGTCAATCTTATAC
65 AGATTGAAAATGTCAATCCTATAC
* * *
13778792 CTCTAAAGTTACAGTAGAGCAGATTGAAGCTACTAATCC-TATCTCCCTAAAATTACAGT-GAAG
1 CTCTAAAGTTGCAGTAGAGCAGATTAAAGCTA-TAAACCTTATCTCCCTAAAATTACAGTAG-AG
*
13778855 C-GAATT-AAAATGATGAATCCTATAC
64 CAG-ATTGAAAATG-TCAATCCTATAC
13778880 CTCTAAAGTTGCAGTAG
1 CTCTAAAGTTGCAGTAG
13778897 GTCGGATTAA
Statistics
Matches: 165, Mismatches: 19, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
87 7 0.04
88 146 0.88
89 8 0.05
90 3 0.02
91 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (88 bp):
CTCTAAAGTTGCAGTAGAGCAGATTAAAGCTATAAACCTTATCTCCCTAAAATTACAGTAGAGCA
GATTGAAAATGTCAATCCTATAC
Found at i:13780486 original size:22 final size:22
Alignment explanation
Indices: 13780461--13780509 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
13780451 TCAAATACAC
*
13780461 TTATTTTA-TTTTATTCGTTTTA
1 TTATTTTACTTATATTC-TTTTA
13780483 TTA-TTTACTTATATTCTTTTA
1 TTATTTTACTTATATTCTTTTA
*
13780504 TAATTT
1 TTATTT
13780510 CAAACTTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.69
Consensus pattern (22 bp):
TTATTTTACTTATATTCTTTTA
Found at i:13782678 original size:24 final size:24
Alignment explanation
Indices: 13782651--13782722 Score: 62
Period size: 24 Copynumber: 3.2 Consensus size: 24
13782641 TAGTTTTACT
13782651 TTATGTAATTAATACAAAAAAATA
1 TTATGTAATTAATACAAAAAAATA
* * ****
13782675 TTATTTAA--AATA-ATAGGTCT-
1 TTATGTAATTAATACAAAAAAATA
13782695 TTATGTAATTAATACAAAAAAATA
1 TTATGTAATTAATACAAAAAAATA
13782719 TTAT
1 TTAT
13782723 TTAAAATAAT
Statistics
Matches: 32, Mismatches: 12, Indels: 8
0.62 0.23 0.15
Matches are distributed among these distances:
20 7 0.22
21 3 0.09
22 8 0.25
23 3 0.09
24 11 0.34
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (24 bp):
TTATGTAATTAATACAAAAAAATA
Found at i:13782699 original size:44 final size:44
Alignment explanation
Indices: 13782649--13782736 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
13782639 TATAGTTTTA
13782649 CTTTATGTAATTAATACAAAAAAATATTATTTAAAATAATAGGT
1 CTTTATGTAATTAATACAAAAAAATATTATTTAAAATAATAGGT
13782693 CTTTATGTAATTAATACAAAAAAATATTATTTAAAATAATAGGT
1 CTTTATGTAATTAATACAAAAAAATATTATTTAAAATAATAGGT
13782737 AATTAACATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.39
Consensus pattern (44 bp):
CTTTATGTAATTAATACAAAAAAATATTATTTAAAATAATAGGT
Found at i:13783992 original size:19 final size:20
Alignment explanation
Indices: 13783956--13783994 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
13783946 TTTTAATTTC
* *
13783956 AAAATTTTAAGAGTTTAAAA
1 AAAATTTAAAGAGGTTAAAA
13783976 AAAATTTAAAG-GGTTAAAA
1 AAAATTTAAAGAGGTTAAAA
13783995 TTGATATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (20 bp):
AAAATTTAAAGAGGTTAAAA
Found at i:13790383 original size:43 final size:43
Alignment explanation
Indices: 13790329--13790483 Score: 258
Period size: 43 Copynumber: 3.6 Consensus size: 43
13790319 CCGGCATTAC
13790329 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
13790372 GCCTG-TCAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCT-AGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* *
13790415 GCCTGCTAGGCACAAAGGCCCGAATACACATCACCAGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* *
13790458 GCCTGCTAGGCACGATGGCCCAAATA
1 GCCTGCTAGGCACGAAGGCCCGAATA
13790484 TAATACCAGC
Statistics
Matches: 105, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
42 1 0.01
43 103 0.98
44 1 0.01
ACGTcount: A:0.31, C:0.34, G:0.25, T:0.10
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
Found at i:13790567 original size:38 final size:38
Alignment explanation
Indices: 13790481--13790599 Score: 139
Period size: 38 Copynumber: 3.1 Consensus size: 38
13790471 GATGGCCCAA
* * * * * *
13790481 ATATAATACCAGCACTAGGCCTGCAGGATTTATCTCGA
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
13790519 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
** *
13790557 ATATTTTACCAGCACGAAGCCTGCGGGTTTTTAAGCCCGG
1 ATATAATACCAGCACGAAGCCTGCGGG-ATTTAA-CCCGG
13790597 ATA
1 ATA
13790600 CACATCAAAT
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
38 57 0.81
39 5 0.07
40 8 0.11
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (38 bp):
ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
Found at i:13803833 original size:42 final size:42
Alignment explanation
Indices: 13803787--13803929 Score: 103
Period size: 42 Copynumber: 3.2 Consensus size: 42
13803777 CATAGCTCAC
13803787 GTGAGCAGCATCGTGTAGCTTACATTCTGATCCACAGCTCGT
1 GTGAGCAGCATCGTGTAGCTTACATTCTGATCCACAGCTCGT
* * * * **
13803829 GTGAGCAGGCCCA-CTTCATAGC-T-CATGTGATGTAAATTCTCCATAGCTCAC
1 GTGAGCA-G--CATCGT-GTAGCTTACAT-T-CTG---A---TCCACAGCTCGT
13803880 GTGAGCAGCATCGTGTAGCTTACATTCTGATCCACAGCTCGT
1 GTGAGCAGCATCGTGTAGCTTACATTCTGATCCACAGCTCGT
13803922 GTGAGCAG
1 GTGAGCAG
13803930 GCCCACTTCA
Statistics
Matches: 74, Mismatches: 12, Indels: 30
0.64 0.10 0.26
Matches are distributed among these distances:
42 24 0.32
43 4 0.05
44 4 0.05
45 9 0.12
48 9 0.12
49 4 0.05
50 4 0.05
51 16 0.22
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (42 bp):
GTGAGCAGCATCGTGTAGCTTACATTCTGATCCACAGCTCGT
Found at i:13803925 original size:93 final size:93
Alignment explanation
Indices: 13803766--13803951 Score: 372
Period size: 93 Copynumber: 2.0 Consensus size: 93
13803756 TTGTATTTGT
13803766 TGTAAATTCTCCATAGCTCACGTGAGCAGCATCGTGTAGCTTACATTCTGATCCACAGCTCGTGT
1 TGTAAATTCTCCATAGCTCACGTGAGCAGCATCGTGTAGCTTACATTCTGATCCACAGCTCGTGT
13803831 GAGCAGGCCCACTTCATAGCTCATGTGA
66 GAGCAGGCCCACTTCATAGCTCATGTGA
13803859 TGTAAATTCTCCATAGCTCACGTGAGCAGCATCGTGTAGCTTACATTCTGATCCACAGCTCGTGT
1 TGTAAATTCTCCATAGCTCACGTGAGCAGCATCGTGTAGCTTACATTCTGATCCACAGCTCGTGT
13803924 GAGCAGGCCCACTTCATAGCTCATGTGA
66 GAGCAGGCCCACTTCATAGCTCATGTGA
13803952 GCATTGTTGA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 93 1.00
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.28
Consensus pattern (93 bp):
TGTAAATTCTCCATAGCTCACGTGAGCAGCATCGTGTAGCTTACATTCTGATCCACAGCTCGTGT
GAGCAGGCCCACTTCATAGCTCATGTGA
Found at i:13814137 original size:13 final size:13
Alignment explanation
Indices: 13814115--13814145 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
13814105 TTATAGATAC
13814115 TTTCTATTTTCTT
1 TTTCTATTTTCTT
*
13814128 TTTCTTTTTTCTT
1 TTTCTATTTTCTT
13814141 TTTCT
1 TTTCT
13814146 CTCATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTCTATTTTCTT
Found at i:13821324 original size:29 final size:30
Alignment explanation
Indices: 13821277--13821344 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
13821267 GTGGCCAAGA
* * * *
13821277 GTAAATACTCAAAATTTGAGGGATTAA-AAT
1 GTAAATA-TAAAAAGTTGAAGGACTAATAAT
*
13821307 GTAAATATAAAAAGTTGAAGGACTAATAGT
1 GTAAATATAAAAAGTTGAAGGACTAATAAT
13821337 GTAAATAT
1 GTAAATAT
13821345 TTTAAGGGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.49, C:0.04, G:0.18, T:0.29
Consensus pattern (30 bp):
GTAAATATAAAAAGTTGAAGGACTAATAAT
Found at i:13824335 original size:91 final size:91
Alignment explanation
Indices: 13823785--13824304 Score: 986
Period size: 91 Copynumber: 5.7 Consensus size: 91
13823775 ATGAAATGTG
*
13823785 TAAGACCATGGTTGAAAGATACCATGGCAACATGATATAAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGATCATGGTTGAAAGATACCATGGCAACATGATATAAAATGTGTAAGACCATGGTTGAAAGA
13823850 TACCATGACAACATGACGAGAATGAA
66 TACCATGACAACATGACGAGAATGAA
13823876 TAAGATCATGGTTGAAAGATACCATGGCAACATGATATAAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGATCATGGTTGAAAGATACCATGGCAACATGATATAAAATGTGTAAGACCATGGTTGAAAGA
13823941 TACCATGACAACATGACGAGAATGAA
66 TACCATGACAACATGACGAGAATGAA
13823967 TAAGATCATGGTTGAAAGATACCATGGCAACATGATATAAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGATCATGGTTGAAAGATACCATGGCAACATGATATAAAATGTGTAAGACCATGGTTGAAAGA
13824032 TACCATGACAACATGACGAGAATGAA
66 TACCATGACAACATGACGAGAATGAA
13824058 TAAGATCATGGTTGAAAGATACCATGGCAACATGATATAAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGATCATGGTTGAAAGATACCATGGCAACATGATATAAAATGTGTAAGACCATGGTTGAAAGA
13824123 TACCATGACAACATGACGAGAATGAA
66 TACCATGACAACATGACGAGAATGAA
13824149 TAAGATCATGGTTGAAAGATACCATGGCAACATGATATAAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGATCATGGTTGAAAGATACCATGGCAACATGATATAAAATGTGTAAGACCATGGTTGAAAGA
13824214 TACCATGACAACATGACGAGAATGAA
66 TACCATGACAACATGACGAGAATGAA
* * * * *
13824240 TAAGATCATGGTTGAAAGATACCATGGCAACCTGACAGAAAATGAGTAAGACCATAGTTGAAAGA
1 TAAGATCATGGTTGAAAGATACCATGGCAACATGATATAAAATGTGTAAGACCATGGTTGAAAGA
13824305 CACTATGGCA
Statistics
Matches: 423, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 423 1.00
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (91 bp):
TAAGATCATGGTTGAAAGATACCATGGCAACATGATATAAAATGTGTAAGACCATGGTTGAAAGA
TACCATGACAACATGACGAGAATGAA
Found at i:13824621 original size:16 final size:17
Alignment explanation
Indices: 13824600--13824632 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
13824590 ATGATGGAGC
13824600 ATGAAA-CATTGATATA
1 ATGAAATCATTGATATA
*
13824616 ATGAAATGATTGATATA
1 ATGAAATCATTGATATA
13824633 TACTTATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.48, C:0.03, G:0.15, T:0.33
Consensus pattern (17 bp):
ATGAAATCATTGATATA
Found at i:13828704 original size:19 final size:19
Alignment explanation
Indices: 13828680--13828719 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
13828670 ATTGATTTTG
13828680 ATCAAATAAAATTAAA-TTA
1 ATCAAAT-AAATTAAAGTTA
*
13828699 ATCAAATCAATTAAAGTTA
1 ATCAAATAAATTAAAGTTA
13828718 AT
1 AT
13828720 ATGATAGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (19 bp):
ATCAAATAAATTAAAGTTA
Found at i:13829156 original size:17 final size:17
Alignment explanation
Indices: 13829134--13829224 Score: 59
Period size: 17 Copynumber: 5.4 Consensus size: 17
13829124 ATTTTAATAG
13829134 TTTAATATTAAATTTAA
1 TTTAATATTAAATTTAA
**
13829151 TTTAATACTT-ACCTTAA
1 TTTAATA-TTAAATTTAA
*
13829168 TTGT-AT-TT-CA-TTAA
1 TT-TAATATTAAATTTAA
13829182 TTTAATATTAAAGTGATT-A
1 TTTAATATTAAA-T--TTAA
13829201 TCTTAATATTAAATTTAA
1 T-TTAATATTAAATTTAA
13829219 TTTAAT
1 TTTAAT
13829225 GTTTATCTTG
Statistics
Matches: 58, Mismatches: 5, Indels: 22
0.68 0.06 0.26
Matches are distributed among these distances:
13 1 0.02
14 8 0.14
15 4 0.07
16 1 0.02
17 23 0.40
18 5 0.09
19 3 0.05
20 13 0.22
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (17 bp):
TTTAATATTAAATTTAA
Found at i:13829272 original size:62 final size:59
Alignment explanation
Indices: 13829203--13829319 Score: 171
Period size: 62 Copynumber: 1.9 Consensus size: 59
13829193 AGTGATTATC
* * *
13829203 TTAATATTAAATTTAATTTAATGTTTATCTTGTAGATAAATATTCTATTAACTTAATAAGAT
1 TTAATATTAAATTTAATCTAATATTTATC-T-T-GATAAATATTATATTAACTTAATAAGAT
*
13829265 TTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATA
1 TTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAACTTAATA
13829320 TTAATATGAT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 22 0.43
60 1 0.02
61 1 0.02
62 27 0.53
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (59 bp):
TTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAACTTAATAAGAT
Found at i:13830711 original size:37 final size:36
Alignment explanation
Indices: 13830629--13830702 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
13830619 TTATCTAGCC
13830629 TAAGAATTAAAGGATATTTTTTAAACTAAAACTAAT
1 TAAGAATTAAAGGATATTTTTTAAACTAAAACTAAT
13830665 TAAGAATTAAAGGATATTTTTTAAACTAAAACTAAT
1 TAAGAATTAAAGGATATTTTTTAAACTAAAACTAAT
13830701 TA
1 TA
13830703 TCTAATTAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.36
Consensus pattern (36 bp):
TAAGAATTAAAGGATATTTTTTAAACTAAAACTAAT
Found at i:13834873 original size:24 final size:24
Alignment explanation
Indices: 13834839--13834903 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
13834829 ATGTAAGCAT
**
13834839 ATAAGCGGGAAGTTCATGTGAGCCA
1 ATAA-CGGGAAGTTCATACGAGCCA
* *
13834864 TTAACGGGAAGCTCATACGAGCCA
1 ATAACGGGAAGTTCATACGAGCCA
*
13834888 ATATCGGGAAGGTTCA
1 ATAACGGGAA-GTTCA
13834904 AGCGAGCTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
24 25 0.78
25 7 0.22
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.20
Consensus pattern (24 bp):
ATAACGGGAAGTTCATACGAGCCA
Found at i:13838313 original size:27 final size:27
Alignment explanation
Indices: 13838176--13838303 Score: 84
Period size: 27 Copynumber: 4.7 Consensus size: 27
13838166 AAGGATACTC
* * *
13838176 TTTCATATTGCGCCACAAAGGCGTTAC-
1 TTTCATATTACGCCACAAATGTGTT-CT
* *
13838203 TTTCATATTGCGCCATACAAA--CGTTCT
1 TTTCATATTACGCC--ACAAATGTGTTCT
* * * *
13838230 TTTCATATTACACCATAAAAG-GAATTCC
1 TTTCATATTACGCCACAAATGTG--TTCT
*
13838258 ATTCATATTACGCCACAAATGTGTTCT
1 TTTCATATTACGCCACAAATGTGTTCT
*
13838285 TTTCATATTATGCCACAAA
1 TTTCATATTACGCCACAAA
13838304 GGCTATCTTT
Statistics
Matches: 82, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
25 4 0.05
26 2 0.02
27 50 0.61
28 20 0.24
29 6 0.07
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.34
Consensus pattern (27 bp):
TTTCATATTACGCCACAAATGTGTTCT
Found at i:13840039 original size:21 final size:21
Alignment explanation
Indices: 13840014--13840059 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
13840004 ATTAGTGTTA
13840014 AAATTTTGGTCACAAAAAATT
1 AAATTTTGGTCACAAAAAATT
*
13840035 AAATTTTGGTCATAAAAAATT
1 AAATTTTGGTCACAAAAAATT
13840056 AAAT
1 AAAT
13840060 AATATTTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.35
Consensus pattern (21 bp):
AAATTTTGGTCACAAAAAATT
Found at i:13840171 original size:17 final size:18
Alignment explanation
Indices: 13840140--13840174 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
13840130 TCTTTAAGAG
*
13840140 TATTTAAATATTTATTTT
1 TATTAAAATATTTATTTT
13840158 TATTAAAATA-TTATTTT
1 TATTAAAATATTTATTTT
13840175 AATTCTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTAAAATATTTATTTT
Found at i:13841842 original size:9 final size:9
Alignment explanation
Indices: 13841828--13841903 Score: 50
Period size: 9 Copynumber: 8.2 Consensus size: 9
13841818 TTTCCTTTCC
13841828 TCTTCTTTT
1 TCTTCTTTT
13841837 TCTTCTTTTT
1 TCTTC-TTTT
13841847 TCTT-TTTT
1 TCTTCTTTT
13841855 TCTT-TCTTT
1 TCTTCT-TTT
* *
13841864 TATTCTCTT
1 TCTTCTTTT
*
13841873 TCTTTGTTGTT
1 TC-TTCTT-TT
*
13841884 TCTAT-TGTT
1 TCT-TCTTTT
13841893 TCTTCTTTT
1 TCTTCTTTT
13841902 TC
1 TC
13841904 GGTCGATTGT
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
8 10 0.19
9 24 0.45
10 14 0.26
11 5 0.09
ACGTcount: A:0.03, C:0.18, G:0.04, T:0.75
Consensus pattern (9 bp):
TCTTCTTTT
Found at i:13841857 original size:15 final size:16
Alignment explanation
Indices: 13841830--13841859 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13841820 TCCTTTCCTC
13841830 TTCTTTTTCTTCTTTT
1 TTCTTTTTCTTCTTTT
13841846 TTCTTTTT-TTCTTT
1 TTCTTTTTCTTCTTT
13841860 CTTTTATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
TTCTTTTTCTTCTTTT
Found at i:13841860 original size:12 final size:14
Alignment explanation
Indices: 13841845--13841877 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
13841835 TTTCTTCTTT
13841845 TTTCTTTT-TT-TC
1 TTTCTTTTATTCTC
13841857 TTTCTTTTATTCTC
1 TTTCTTTTATTCTC
13841871 TTTCTTT
1 TTTCTTT
13841878 GTTGTTTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
13 2 0.11
14 9 0.47
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTCTTTTATTCTC
Found at i:13850263 original size:24 final size:22
Alignment explanation
Indices: 13850216--13850263 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
13850206 TGATATTTTA
* *
13850216 AACTTAACTTTTAAATTTTTTT
1 AACTTAACTTTTAAAATTTATT
13850238 AACTTAAACATTTTAAAATTTATT
1 AACTT-AAC-TTTTAAAATTTATT
13850262 AA
1 AA
13850264 ATTGAACTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 5 0.23
23 3 0.14
24 14 0.64
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (22 bp):
AACTTAACTTTTAAAATTTATT
Found at i:13850327 original size:19 final size:19
Alignment explanation
Indices: 13850257--13850330 Score: 58
Period size: 19 Copynumber: 3.6 Consensus size: 19
13850247 ATTTTAAAAT
*
13850257 TTATTAAATTGAACTATAA
1 TTATTAAATTAAACTATAA
** * *
13850276 TTATTAAAAAAAATTAGAA
1 TTATTAAATTAAACTATAA
13850295 TTACATTTAAAAATTAAACTATAA
1 TT--A-TT--AAATTAAACTATAA
13850319 TTATTAAATTAA
1 TTATTAAATTAA
13850331 GTAATTCAAC
Statistics
Matches: 41, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
19 23 0.56
21 3 0.07
22 3 0.07
24 12 0.29
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (19 bp):
TTATTAAATTAAACTATAA
Found at i:13854046 original size:145 final size:146
Alignment explanation
Indices: 13853850--13854176 Score: 613
Period size: 145 Copynumber: 2.2 Consensus size: 146
13853840 TTGATGGAAA
*
13853850 GAAACAATTATATGAGCCAAAATCTAGGGAAAGCAAAATCCAGAAACAACCAGAGGAAGTAATTT
1 GAAACAATTAGAT-AGCCAAAATCTAGGGAAAGCAAAATCCAGAAACAACCAGAGGAAGTAATTT
13853915 CCATGTTAGATCCAGCTCCAGCATACAACAATCAAAACTAAACTCGAAATTTCACC-AAAAAAAA
65 CCATGTTAGATCCAGCTCCAGCATACAACAATCAAAACTAAACTCGAAATTTCACCAAAAAAAAA
*
13853979 AAACTAAACTTGAAAAG
130 AAACTAAACTCGAAAAG
13853996 GAAACAATTAGATAGCCAAAATCTAGGGAAAGCAAAATCCAGAAACAACCAGAGGAAGTAATTTC
1 GAAACAATTAGATAGCCAAAATCTAGGGAAAGCAAAATCCAGAAACAACCAGAGGAAGTAATTTC
13854061 CATGTTAGATCCAGCTCCAGCATACAACAATCAAAACTAAACTCGAAATTTCACCAAAAAAAAAA
66 CATGTTAGATCCAGCTCCAGCATACAACAATCAAAACTAAACTCGAAATTTCACCAAAAAAAAAA
13854126 AACTAAACTCGAAAAG
131 AACTAAACTCGAAAAG
13854142 GAAACAATTAGATAGCCAAAATCTA-GGAAAGCAAA
1 GAAACAATTAGATAGCCAAAATCTAGGGAAAGCAAA
13854177 TGTGAGAAAC
Statistics
Matches: 178, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
145 117 0.66
146 61 0.34
ACGTcount: A:0.50, C:0.20, G:0.13, T:0.17
Consensus pattern (146 bp):
GAAACAATTAGATAGCCAAAATCTAGGGAAAGCAAAATCCAGAAACAACCAGAGGAAGTAATTTC
CATGTTAGATCCAGCTCCAGCATACAACAATCAAAACTAAACTCGAAATTTCACCAAAAAAAAAA
AACTAAACTCGAAAAG
Found at i:13854221 original size:145 final size:145
Alignment explanation
Indices: 13853850--13854249 Score: 540
Period size: 145 Copynumber: 2.8 Consensus size: 145
13853840 TTGATGGAAA
* * **
13853850 GAAACAATTATATGAGCCAAAATCTAGGGAAAGCAAAATCCAGAAACAACCAGAGGAAGTAATTT
1 GAAACAATTAGAT-AGCCAAAATCTAGGGAAAGCAAAATCCAGAAACAACCAGAGGAAGCAACAT
*
13853915 CCATGTTAGATCCAGCTCCAGCATACAACAATCAAAACTAAACTCGAAATTTCACCAAAAAAAAA
65 CCATGTAAGATCCAGCTCCAGCATACAACAATCAAAACTAAACTCGAAATTTCACCAAAAAAAAA
*
13853980 AACTAAACTTGAAAAG
130 AACTAAACTCGAAAAG
* **
13853996 GAAACAATTAGATAGCCAAAATCTAGGGAAAGCAAAATCCAGAAACAACCAGAGGAAGTAATTTC
1 GAAACAATTAGATAGCCAAAATCTAGGGAAAGCAAAATCCAGAAACAACCAGAGGAAGCAACATC
*
13854061 CATGTTAGATCCAGCTCCAGCATACAACAATCAAAACTAAACTCGAAATTTCACCAAAAAAAAAA
66 CATGTAAGATCCAGCTCCAGCATACAACAATCAAAACTAAACTCGAAATTTCACC-AAAAAAAAA
13854126 AACTAAACTCGAAAAG
130 AACTAAACTCGAAAAG
** *
13854142 GAAACAATTAGATAGCCAAAATCTA-GGAAAGC-AAATGTGAGAAACAGCCTA-AGGAAGCAACA
1 GAAACAATTAGATAGCCAAAATCTAGGGAAAGCAAAAT-CCAGAAACAACC-AGAGGAAGCAACA
* * * * * *
13854204 T-CACTGTAA-AGTGCAGCTCTAGCATATAACAACCAGAACTGAACTC
64 TCCA-TGTAAGA-TCCAGCTCCAGCATACAACAATCAAAACTAAACTC
13854250 CAAAACTCTT
Statistics
Matches: 234, Mismatches: 15, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
144 7 0.03
145 165 0.71
146 62 0.26
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.17
Consensus pattern (145 bp):
GAAACAATTAGATAGCCAAAATCTAGGGAAAGCAAAATCCAGAAACAACCAGAGGAAGCAACATC
CATGTAAGATCCAGCTCCAGCATACAACAATCAAAACTAAACTCGAAATTTCACCAAAAAAAAAA
ACTAAACTCGAAAAG
Found at i:13856299 original size:29 final size:31
Alignment explanation
Indices: 13856233--13856299 Score: 77
Period size: 29 Copynumber: 2.2 Consensus size: 31
13856223 TATTATTTGG
* *
13856233 TACTTATATTTTTATAATATGTTCAATGTGA
1 TACTTATACTTTTATAATATGTTCAATATGA
*
13856264 TACTTATACTTTTA-AA-ATGTTTAATATGTA
1 TACTTATACTTTTATAATATGTTCAATATG-A
13856294 TA-TTAT
1 TACTTAT
13856300 TATGTACATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 14 0.44
30 5 0.16
31 13 0.41
ACGTcount: A:0.34, C:0.06, G:0.07, T:0.52
Consensus pattern (31 bp):
TACTTATACTTTTATAATATGTTCAATATGA
Found at i:13860124 original size:44 final size:44
Alignment explanation
Indices: 13860061--13860145 Score: 161
Period size: 44 Copynumber: 1.9 Consensus size: 44
13860051 ATCCTTTGAG
13860061 TCTGTTTCTATTTTTATTTTGTGGGAAATGCCTCTCTAGTCATA
1 TCTGTTTCTATTTTTATTTTGTGGGAAATGCCTCTCTAGTCATA
*
13860105 TCTGTTTCTATTTTTATTTTGTGGGAAATTCCTCTCTAGTC
1 TCTGTTTCTATTTTTATTTTGTGGGAAATGCCTCTCTAGTC
13860146 TTATGACGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.16, C:0.16, G:0.15, T:0.52
Consensus pattern (44 bp):
TCTGTTTCTATTTTTATTTTGTGGGAAATGCCTCTCTAGTCATA
Found at i:13862775 original size:15 final size:15
Alignment explanation
Indices: 13862712--13862776 Score: 62
Period size: 15 Copynumber: 4.3 Consensus size: 15
13862702 GGTTGATAAA
*
13862712 TTGAAAAATCAAGTG
1 TTGAAAAATTAAGTG
* *
13862727 TCGAGAAAA-TAAATG
1 TTGA-AAAATTAAGTG
*
13862742 TTGAAAAAATT-AGTA
1 TTG-AAAAATTAAGTG
13862757 TTGAAAAATTAAGTG
1 TTGAAAAATTAAGTG
13862772 TTGAA
1 TTGAA
13862777 TTTAAGTTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
14 7 0.18
15 26 0.67
16 6 0.15
ACGTcount: A:0.49, C:0.03, G:0.18, T:0.29
Consensus pattern (15 bp):
TTGAAAAATTAAGTG
Found at i:13862876 original size:5 final size:5
Alignment explanation
Indices: 13862863--13862892 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
13862853 ATAAAATCCT
*
13862863 AAATG AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA AAATA
13862893 GAAAACCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:13865855 original size:35 final size:35
Alignment explanation
Indices: 13865809--13865876 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
13865799 ACACAGATGA
13865809 CACATTATATTTTAAACAGCATCTGAAAGTTAACT
1 CACATTATATTTTAAACAGCATCTGAAAGTTAACT
* *
13865844 CACATTGTATTTTAAACGGCATCTGAAAGTTAA
1 CACATTATATTTTAAACAGCATCTGAAAGTTAA
13865877 TTCTCAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (35 bp):
CACATTATATTTTAAACAGCATCTGAAAGTTAACT
Found at i:13869647 original size:93 final size:92
Alignment explanation
Indices: 13869542--13869756 Score: 253
Period size: 87 Copynumber: 2.4 Consensus size: 92
13869532 TACAATTTTG
* * *
13869542 TATTTAAGTCAAAATGGAATTTGAAATTTATACATTATCATGGTTATCCTGTTAAAATTTTACAA
1 TATTTAAATCAAAATGAAATTTGAAATTTATACA-TA-CATGGTTATCCAGTTAAAATTTTACAA
* * *
13869607 TTTAAAAATAACTAAAT-G-AATATTCTTT
64 TTTAAAAATAACTAAATAGTAAAATT-GTA
* *
13869635 TATTTAAATCAAAATGAAATTT-AAATTT-T--ATACATTGTTATCCAGTTAAAATTTTATAATT
1 TATTTAAATCAAAATGAAATTTGAAATTTATACATACATGGTTATCCAGTTAAAATTTTACAATT
* *
13869696 TAAAATTAATTAAATAAGTAAAATTGTA
66 TAAAAATAACTAAAT-AGTAAAATTGTA
*
13869724 TATTTAAATCAAAATAAAATTTGAAATTTATAC
1 TATTTAAATCAAAATGAAATTTGAAATTTATAC
13869757 TATTTTACAG
Statistics
Matches: 104, Mismatches: 11, Indels: 14
0.81 0.09 0.11
Matches are distributed among these distances:
87 39 0.38
88 2 0.02
89 24 0.23
90 11 0.11
91 2 0.02
92 6 0.06
93 20 0.19
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.42
Consensus pattern (92 bp):
TATTTAAATCAAAATGAAATTTGAAATTTATACATACATGGTTATCCAGTTAAAATTTTACAATT
TAAAAATAACTAAATAGTAAAATTGTA
Found at i:13869915 original size:20 final size:22
Alignment explanation
Indices: 13869867--13869922 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 22
13869857 TAAATTAAAC
* *
13869867 AATTTTTAAAATAAAGTTTTGA
1 AATTCTTAAAATATAGTTTTGA
*
13869889 TATTCTTAAAATATA-TTTT-A
1 AATTCTTAAAATATAGTTTTGA
13869909 AATTCTTAAAATAT
1 AATTCTTAAAATAT
13869923 TTTCTTAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 14 0.47
21 4 0.13
22 12 0.40
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.48
Consensus pattern (22 bp):
AATTCTTAAAATATAGTTTTGA
Found at i:13871299 original size:78 final size:77
Alignment explanation
Indices: 13871205--13871353 Score: 194
Period size: 77 Copynumber: 1.9 Consensus size: 77
13871195 GGGTTAATTT
* ** *
13871205 TTTTAGTATTTCTATAGAA-ATTTCTTTGTATTTAATTTTATTTATTTTT-GCTTCTTTTCTTGG
1 TTTTAGAATTTCTATAGAATATTTCTTTGTA-CGAA-TTTATTTATTTTTAG-TTCTTTTCTTGA
13871268 ATTAAATTATTGTCC
63 ATTAAATTATTGTCC
* * *
13871283 TTTTAGAATTTTTATAGAATTTTTGTTTGTACGAATTTATTTATTTTTAGTTCTTTTCTTGAATT
1 TTTTAGAATTTCTATAGAATATTTCTTTGTACGAATTTATTTATTTTTAGTTCTTTTCTTGAATT
13871348 AAATTA
66 AAATTA
13871354 CTGTGGTTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
77 33 0.53
78 20 0.32
79 9 0.15
ACGTcount: A:0.24, C:0.07, G:0.09, T:0.60
Consensus pattern (77 bp):
TTTTAGAATTTCTATAGAATATTTCTTTGTACGAATTTATTTATTTTTAGTTCTTTTCTTGAATT
AAATTATTGTCC
Found at i:13874145 original size:44 final size:44
Alignment explanation
Indices: 13874053--13874718 Score: 858
Period size: 44 Copynumber: 15.1 Consensus size: 44
13874043 CGAATGTCAG
* * * *
13874053 ATCTGCTATCTTCGATCTGCTCCCCGGCTAATACAGAGATGCCAA
1 ATCTGCTATCTTCGATCTGCTCTCTGTC-AATACAGAGACGCCAA
13874098 ATCTG-TCATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
1 ATCTGCT-ATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
* *
13874142 ATCTG-TCATCTTCGATCTGCCCTCTGTCAATACAGAGACACCAA
1 ATCTGCT-ATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
* * * **
13874186 ATCTGCTATCTTTGATCTGCTCCCCGTTGATACAGAGACGCCAA
1 ATCTGCTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
* *
13874230 ATCTACTATCTTCGATCTGCTCTCTGTCAATATAGAGACGCCAA
1 ATCTGCTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
* * * *
13874274 ATCTGTTATCTTCGATCTGCCCTCTTGTCAATACAGAGATGTCAA
1 ATCTGCTATCTTCGATCTGCTCTC-TGTCAATACAGAGACGCCAA
* * * * *
13874319 ATCTG-TCATCTTCGATCTGCTCCCTATCGATACAGAAATGCCAA
1 ATCTGCT-ATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
* *
13874363 ATCTGCTATCTTCGATCAGCTCTCTGTCAATACAGAAACGCCAA
1 ATCTGCTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
* *
13874407 ATCTG-TCATCTTCAATCTGCTCTCTGTCAATACAGAGACACCAA
1 ATCTGCT-ATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
* *
13874451 ATCTG-TCATCTTCGATCTGCTCCCTGTCGATACAGAGACGCCAA
1 ATCTGCT-ATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
13874495 ATCTGCTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
1 ATCTGCTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
* *
13874539 ATCTGCTATCTTCGATCCGC-CTTCTATCAATACAGAGACGCCAA
1 ATCTGCTATCTTCGATCTGCTC-TCTGTCAATACAGAGACGCCAA
* *
13874583 ATCTGCTATCTTCGATCTGCTCTCTATCAATACAGAGACACCAA
1 ATCTGCTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
* * *
13874627 ATCTGCTATCTTTGATCTGCTCTCCGTCGATACAGAGACGCCAA
1 ATCTGCTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
* * * * *
13874671 ATCTACTATATTTGATCTGCTCCCTGTCAATACAGAGACACCAA
1 ATCTGCTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
13874715 ATCT
1 ATCT
13874719 ACTTTCTAGA
Statistics
Matches: 550, Mismatches: 62, Indels: 19
0.87 0.10 0.03
Matches are distributed among these distances:
43 2 0.00
44 484 0.88
45 64 0.12
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.29
Consensus pattern (44 bp):
ATCTGCTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
Found at i:13880072 original size:26 final size:25
Alignment explanation
Indices: 13880036--13880086 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
13880026 TCCCAACAAG
13880036 CAATTATAAGAGAGCTTAATGTCCA
1 CAATTATAAGAGAGCTTAATGTCCA
* *
13880061 NCAATTATAAGAGGGCTTGATGTCCA
1 -CAATTATAAGAGAGCTTAATGTCCA
13880087 TCACTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.27
Consensus pattern (25 bp):
CAATTATAAGAGAGCTTAATGTCCA
Found at i:13882863 original size:14 final size:16
Alignment explanation
Indices: 13882833--13882864 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
13882823 GAATGCATAT
13882833 AATGCGATGAGATGCA
1 AATGCGATGAGATGCA
13882849 AATGC-ATGA-ATGCA
1 AATGCGATGAGATGCA
13882863 AA
1 AA
13882865 AAGATATCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 4 0.25
16 5 0.31
ACGTcount: A:0.44, C:0.12, G:0.25, T:0.19
Consensus pattern (16 bp):
AATGCGATGAGATGCA
Done.