Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007984.1 Hibiscus syriacus cultivar Beakdansim tig00110429_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: 12923621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 65
Found at i:4050663 original size:54 final size:54
Alignment explanation
Indices: 4050574--4051034 Score: 638
Period size: 54 Copynumber: 8.5 Consensus size: 54
4050564 CTATGTGTAC
* * * * *
4050574 TATAGGTACTAAGTGTGCAAGCCACATAATTCATCATATGTTGATGAACAATCA
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCG
* * ** *
4050628 TATAGGCACTAAGTGTGCAAGCAACAGAACGCATCATATGTTGATGAACAACCA
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCG
*
4050682 TATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACAACCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCG
* *
4050736 TATAGGCACTAAGTGTACAACCTACAGAATTCATCATATGTTGATGAACAACCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCG
* * * *
4050790 TATAGGCACTAAGTGTGCAACCAACGGAATTCATCATATGTTGATGAAAAATCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCG
* *
4050844 TATAGTCACTAAGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCG
* *
4050898 TATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATGTCGATGAACAACCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCG
* * * **
4050952 TATATGCACTAAGTGTGCAACCCAC-GAAATTCATAATATGTTTATGAATGACCG
1 TATAGGCACTAAGTGTGCAACCCACAG-AATTCATCATATGTTGATGAACAACCG
* *
4051006 TATCA-GCACTACGTGTGCAACCCAGAGAA
1 TAT-AGGCACTAAGTGTGCAACCCACAGAA
4051035 CTGATAATGT
Statistics
Matches: 366, Mismatches: 38, Indels: 6
0.89 0.09 0.01
Matches are distributed among these distances:
53 1 0.00
54 363 0.99
55 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (54 bp):
TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCG
Found at i:4052207 original size:22 final size:22
Alignment explanation
Indices: 4052178--4052234 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
4052168 TTCAAAGATC
4052178 CTAGGATGAATTTGGATATTTT
1 CTAGGATGAATTTGGATATTTT
*
4052200 CTATGATGAATTTGGATATTTT
1 CTAGGATGAATTTGGATATTTT
*
4052222 CTAGGTTGAATTT
1 CTAGGATGAATTT
4052235 AGACTCATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.26, C:0.05, G:0.21, T:0.47
Consensus pattern (22 bp):
CTAGGATGAATTTGGATATTTT
Found at i:4058951 original size:20 final size:20
Alignment explanation
Indices: 4058926--4058975 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
4058916 GATTGAAGTA
* *
4058926 GTATCGATACAGATATGG-AG
1 GTATCGATACAAAGA-GGAAG
4058946 GTATCGATACAAAGAGGAAG
1 GTATCGATACAAAGAGGAAG
4058966 GTATCGATAC
1 GTATCGATAC
4058976 TCTAATTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.22
Consensus pattern (20 bp):
GTATCGATACAAAGAGGAAG
Found at i:4059453 original size:15 final size:15
Alignment explanation
Indices: 4059433--4059518 Score: 100
Period size: 15 Copynumber: 5.7 Consensus size: 15
4059423 ATTTTATTGG
*
4059433 TATGTGAAAATGTTA
1 TATGTGAAAATGTTC
* *
4059448 TATGTGAATATGTTT
1 TATGTGAAAATGTTC
*
4059463 TATATGAAAATGTTC
1 TATGTGAAAATGTTC
*
4059478 TATGTGAAAATGTGC
1 TATGTGAAAATGTTC
** *
4059493 TAAATGAAAATGTTT
1 TATGTGAAAATGTTC
4059508 TATGTGAAAAT
1 TATGTGAAAAT
4059519 ACCCTATGTG
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 58 1.00
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.41
Consensus pattern (15 bp):
TATGTGAAAATGTTC
Found at i:4059483 original size:45 final size:45
Alignment explanation
Indices: 4059433--4059518 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 45
4059423 ATTTTATTGG
* ** *
4059433 TATGTGAAAATGTTATATGTGAATATGTTTTATATGAAAATGTTC
1 TATGTGAAAATGTGATAAATGAAAATGTTTTATATGAAAATGTTC
* *
4059478 TATGTGAAAATGTGCTAAATGAAAATGTTTTATGTGAAAAT
1 TATGTGAAAATGTGATAAATGAAAATGTTTTATATGAAAAT
4059519 ACCCTATGTG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.41
Consensus pattern (45 bp):
TATGTGAAAATGTGATAAATGAAAATGTTTTATATGAAAATGTTC
Found at i:4059526 original size:45 final size:45
Alignment explanation
Indices: 4059433--4059530 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 45
4059423 ATTTTATTGG
* ** * ***
4059433 TATGTGAAAATGTTATATGTGAATATGTTTTATATGAAAATGTTC
1 TATGTGAAAATGTGATAAATGAAAATGTTTTATATGAAAATACCC
* *
4059478 TATGTGAAAATGTGCTAAATGAAAATGTTTTATGTGAAAATACCC
1 TATGTGAAAATGTGATAAATGAAAATGTTTTATATGAAAATACCC
4059523 TATGTGAA
1 TATGTGAA
4059531 TGTACTCTAC
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.39
Consensus pattern (45 bp):
TATGTGAAAATGTGATAAATGAAAATGTTTTATATGAAAATACCC
Found at i:4059683 original size:23 final size:23
Alignment explanation
Indices: 4059650--4059722 Score: 69
Period size: 23 Copynumber: 3.1 Consensus size: 23
4059640 AGTAGAGGGT
* *
4059650 TCTACGAGGTCTTTCGAGACAAA
1 TCTACGCGGTCATTCGAGACAAA
4059673 TCTACGCGGTCATTC-AGGACAAA
1 TCTACGCGGTCATTCGA-GACAAA
*
4059696 TTTCTACGCGGTCCTTCG-GAACAAA
1 --TCTACGCGGTCATTCGAG-ACAAA
4059721 TC
1 TC
4059723 GACGTGGCAC
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
22 1 0.02
23 21 0.50
24 1 0.02
25 19 0.45
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (23 bp):
TCTACGCGGTCATTCGAGACAAA
Found at i:4059706 original size:25 final size:24
Alignment explanation
Indices: 4059649--4059721 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 24
4059639 GAGTAGAGGG
* *
4059649 TTCTACGAGGTCTTTCGAGACAAA-
1 TTCTACGCGGTCATTCG-GACAAAT
4059673 -TCTACGCGGTCATTCAGGACAAAT
1 TTCTACGCGGTCATTC-GGACAAAT
*
4059697 TTCTACGCGGTCCTTCGGAACAAAT
1 TTCTACGCGGTCATTCGG-ACAAAT
4059722 CGACGTGGCA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
23 19 0.45
24 3 0.07
25 20 0.48
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (24 bp):
TTCTACGCGGTCATTCGGACAAAT
Found at i:4059737 original size:48 final size:48
Alignment explanation
Indices: 4059649--4059746 Score: 112
Period size: 48 Copynumber: 2.0 Consensus size: 48
4059639 GAGTAGAGGG
* *
4059649 TTCTACGAGGTCTTTCGAGACAAATCTACGCGGTCATTCAG-GACAAAT
1 TTCTACGAGGTCCTTCGAGACAAATCGACGCGGTCATTCAGTG-CAAAT
* *
4059697 TTCTACGCGGTCCTTCG-GAACAAATCGACGTGG-CACTTCAGTGCAAAT
1 TTCTACGAGGTCCTTCGAG-ACAAATCGACGCGGTCA-TTCAGTGCAAAT
4059745 TT
1 TT
4059747 ATGAGCAGTG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
47 3 0.07
48 39 0.91
49 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (48 bp):
TTCTACGAGGTCCTTCGAGACAAATCGACGCGGTCATTCAGTGCAAAT
Found at i:4066807 original size:2 final size:2
Alignment explanation
Indices: 4066800--4066845 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
4066790 TTTGAGAAAC
4066800 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4066842 AT AT
1 AT AT
4066846 TTATCATAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4067368 original size:20 final size:20
Alignment explanation
Indices: 4067290--4067376 Score: 61
Period size: 20 Copynumber: 4.2 Consensus size: 20
4067280 TTTAACAGAA
*
4067290 CCTCA-GGGGGTATCGATTC
1 CCTCATGGGGGAATCGATTC
* *
4067309 CC-CTGTGGGAGGAATCGGTTCC
1 CCTC-ATGGG-GGAATCGATT-C
* *
4067331 CCTTCAAAGGGGGAATCGGTTC
1 CC-TC-ATGGGGGAATCGATTC
*
4067353 CCTCATGGGGGGATCGATTC
1 CCTCATGGGGGAATCGATTC
4067373 CCTC
1 CCTC
4067377 TGCACCAAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
18 1 0.02
19 2 0.04
20 20 0.38
21 10 0.19
22 6 0.11
23 10 0.19
24 4 0.08
ACGTcount: A:0.16, C:0.28, G:0.32, T:0.24
Consensus pattern (20 bp):
CCTCATGGGGGAATCGATTC
Found at i:4076053 original size:30 final size:30
Alignment explanation
Indices: 4076018--4076088 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 30
4076008 AATTTATTGG
** * *
4076018 TATGTGAAAATGTTTTATATTAAAATGTTC
1 TATGTGAAAATGTGCTAAATGAAAATGTTC
*
4076048 TATGTGAAAATGTGCTAAATGAAAATGTTT
1 TATGTGAAAATGTGCTAAATGAAAATGTTC
*
4076078 TACGTGAAAAT
1 TATGTGAAAAT
4076089 ACCCTATGTG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.39
Consensus pattern (30 bp):
TATGTGAAAATGTGCTAAATGAAAATGTTC
Found at i:4076085 original size:15 final size:15
Alignment explanation
Indices: 4076018--4076088 Score: 70
Period size: 15 Copynumber: 4.7 Consensus size: 15
4076008 AATTTATTGG
*
4076018 TATGTGAAAATGTTT
1 TATGTGAAAATGTTC
* *
4076033 TATATTAAAATGTTC
1 TATGTGAAAATGTTC
*
4076048 TATGTGAAAATGTGC
1 TATGTGAAAATGTTC
** *
4076063 TAAATGAAAATGTTT
1 TATGTGAAAATGTTC
*
4076078 TACGTGAAAAT
1 TATGTGAAAAT
4076089 ACCCTATGTG
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.39
Consensus pattern (15 bp):
TATGTGAAAATGTTC
Found at i:4076376 original size:20 final size:20
Alignment explanation
Indices: 4076351--4076392 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
4076341 CTAAGAGCTA
*
4076351 ATTTAGGACCATGTAGATGC
1 ATTTAGGACCATATAGATGC
* *
4076371 ATTTAGGAGCATATAGTTGC
1 ATTTAGGACCATATAGATGC
4076391 AT
1 AT
4076393 GTGGTAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (20 bp):
ATTTAGGACCATATAGATGC
Found at i:4095585 original size:13 final size:13
Alignment explanation
Indices: 4095563--4095598 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
4095553 CTTTTCTGAG
*
4095563 CCTTCACTTCTTT
1 CCTTCTCTTCTTT
4095576 CCTTCTCTTCTTT
1 CCTTCTCTTCTTT
4095589 CCTTCTCTTC
1 CCTTCTCTTC
4095599 ATGCACTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.03, C:0.42, G:0.00, T:0.56
Consensus pattern (13 bp):
CCTTCTCTTCTTT
Found at i:4108245 original size:13 final size:13
Alignment explanation
Indices: 4108221--4108254 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
4108211 TAAAACCATG
4108221 TTTTGTGAAAATAA
1 TTTTG-GAAAATAA
*
4108235 TTTTGGAAAATAT
1 TTTTGGAAAATAA
4108248 TTTTGGA
1 TTTTGGA
4108255 CAGAACCCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (13 bp):
TTTTGGAAAATAA
Found at i:4118887 original size:2 final size:2
Alignment explanation
Indices: 4118880--4118917 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4118870 TTGGCTATTG
4118880 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4118918 GTTTATCTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4121001 original size:21 final size:21
Alignment explanation
Indices: 4120971--4121033 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
4120961 ATGTGAAATT
*
4120971 TGTCCCGAAGGACCTCATGTA
1 TGTCCCGAAGGACCTCATATA
* *
4120992 TGTCCAGAAGGACCTTATATA
1 TGTCCCGAAGGACCTCATATA
4121013 TGTCCCGAAGGACCTCATATA
1 TGTCCCGAAGGACCTCATATA
4121034 ATCCCTCGAC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (21 bp):
TGTCCCGAAGGACCTCATATA
Found at i:4126226 original size:10 final size:9
Alignment explanation
Indices: 4126202--4126230 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
4126192 AATCACATAG
4126202 ATATTTTTA
1 ATATTTTTA
4126211 AT-TTTTTA
1 ATATTTTTA
4126219 ATATTTTTA
1 ATATTTTTA
4126228 ATA
1 ATA
4126231 ACGATAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
ATATTTTTA
Found at i:4127468 original size:329 final size:329
Alignment explanation
Indices: 4126862--4127474 Score: 1025
Period size: 329 Copynumber: 1.9 Consensus size: 329
4126852 CCGTTACTGA
* * *
4126862 AATGTTGTATTTTGTGTCTGGTTGGTTTAGAAAAAAATGTAAGATTACCGTGTTTGGTTAAAAGA
1 AATGTTATATTTTGTGTCTGGTTAGTTTAGAAAAAAATGTAAGATTACCGTGTTTAGTTAAAAGA
*
4126927 ATAAAAGAATATTAGAATGTATATTTTACTAAATTATCTTTATTATATATTTATTTTTTAACAAG
66 ATAAAAGAATATTAGAATGTATATTTTACTAAATTATCCTTATTATATATTTATTTTTTAACAAG
4126992 TTGAATTCTACTATAATATTACTATAATTAATTTATATATTTTCTTTAAAAAATTTAAAGTCATA
131 TTGAATTCTACTATAATATTACTATAATTAATTTATATATTTTCTTTAAAAAATTTAAAGTCATA
* *
4127057 AAATTTATATAATTTTTTTACAAAATTGAAAAGATAAATAGGTTTAATAAAAAGGTAAAATTTTA
196 AAATTTATATAATTTTTTTACAAAATAGAAAAGATAAATAAGTTTAATAAAAA-GTAAAATTTTA
*
4127122 TTTTTACCCCTGAATTTCATATAAGATTACCAATGAGAATAAAAGATTACCAGGAAATATGATTA
260 TTTTAACCCCTGAATTTCATATAAGATTACCAATGAGAATAAAAGATTACCAGGAAATATGATTA
4127187 CTAAG
325 CTAAG
* * ** *
4127192 AATGTTATATTTTGTGTTTGGTTAGTTTA-ATAGGAATGTAAGATTACCGTGTTTAGTTAAAGGA
1 AATGTTATATTTTGTGTCTGGTTAGTTTAGAAAAAAATGTAAGATTACCGTGTTTAGTTAAAAGA
* *
4127256 ATAAAAGATTATTGGAATGTATATTTTACTAAATTATCCTTATTATATATTTATTTTTTAACAAG
66 ATAAAAGAATATTAGAATGTATATTTTACTAAATTATCCTTATTATATATTTATTTTTTAACAAG
4127321 TTGAATTCTACTATAATATTACTATAATTAATTTATATATTTTCTTTAAAAAAATTTAAAGTCAT
131 TTGAATTCTACTATAATATTACTATAATTAATTTATATATTTTCTTT-AAAAAATTTAAAGTCAT
*
4127386 AAAATTTATAT-TTTTTTTTACAAAATAGAAAAGATAAATAAGTTTAATGAAAGAA-TAAAATTT
195 AAAATTTATATAATTTTTTTACAAAATAGAAAAGATAAATAAGTTTAAT-AAA-AAGTAAAATTT
*
4127449 TATTTTAACCTCTGAATTTCATATAA
258 TATTTTAACCCCTGAATTTCATATAA
4127475 AAATCTAATT
Statistics
Matches: 264, Mismatches: 16, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
329 205 0.78
330 57 0.22
331 2 0.01
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.43
Consensus pattern (329 bp):
AATGTTATATTTTGTGTCTGGTTAGTTTAGAAAAAAATGTAAGATTACCGTGTTTAGTTAAAAGA
ATAAAAGAATATTAGAATGTATATTTTACTAAATTATCCTTATTATATATTTATTTTTTAACAAG
TTGAATTCTACTATAATATTACTATAATTAATTTATATATTTTCTTTAAAAAATTTAAAGTCATA
AAATTTATATAATTTTTTTACAAAATAGAAAAGATAAATAAGTTTAATAAAAAGTAAAATTTTAT
TTTAACCCCTGAATTTCATATAAGATTACCAATGAGAATAAAAGATTACCAGGAAATATGATTAC
TAAG
Found at i:4130656 original size:79 final size:79
Alignment explanation
Indices: 4130525--4130683 Score: 300
Period size: 79 Copynumber: 2.0 Consensus size: 79
4130515 AGGAAGCGGT
4130525 TAAGACATGTTCTCCCTAGTAGTTTTTAGGAACATATTTGTGAAATAACAAGGCTCTAGTGACAT
1 TAAGACATGTTCTCCCTAGTAGTTTTTAGGAACATATTTGTGAAATAACAAGGCTCTAGTGACAT
4130590 ATAAAAGATTACAA
66 ATAAAAGATTACAA
*
4130604 TAAGACATGTTCTCCCTAGTAGTTTTTAGGAACATATTTGTGAAATAACAAGGCTCTAGTGACTT
1 TAAGACATGTTCTCCCTAGTAGTTTTTAGGAACATATTTGTGAAATAACAAGGCTCTAGTGACAT
*
4130669 CTAAAAGATTACAA
66 ATAAAAGATTACAA
4130683 T
1 T
4130684 TCTTACGTTT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (79 bp):
TAAGACATGTTCTCCCTAGTAGTTTTTAGGAACATATTTGTGAAATAACAAGGCTCTAGTGACAT
ATAAAAGATTACAA
Found at i:4133727 original size:50 final size:51
Alignment explanation
Indices: 4133629--4133732 Score: 174
Period size: 50 Copynumber: 2.1 Consensus size: 51
4133619 GCAATTCGTG
* *
4133629 CGTATGTGTTTGTTCTTGTTTTTTTTTGTCTTTTCTAAGTATGCAGTTATT
1 CGTATGTATCTGTTCTTGTTTTTTTTTGTCTTTTCTAAGTATGCAGTTATT
*
4133680 CGTATGTATCTGTTCTTGTTTTTTTTT-TCTTTTCTAAGTATGGAGTTATT
1 CGTATGTATCTGTTCTTGTTTTTTTTTGTCTTTTCTAAGTATGCAGTTATT
4133730 CGT
1 CGT
4133733 GCGTATGTGT
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
50 25 0.50
51 25 0.50
ACGTcount: A:0.12, C:0.11, G:0.17, T:0.60
Consensus pattern (51 bp):
CGTATGTATCTGTTCTTGTTTTTTTTTGTCTTTTCTAAGTATGCAGTTATT
Found at i:4136498 original size:49 final size:50
Alignment explanation
Indices: 4136434--4136536 Score: 163
Period size: 51 Copynumber: 2.1 Consensus size: 50
4136424 ACACATACGC
* *
4136434 ACGAATAACTCCATACTTAGAAAAG-AAAAAAAAACAAGAACATATACAT
1 ACGAATAACTCCATACTTAGAAAAGAAAAAAAAAACAAGAACAAACACAT
*
4136483 ACGAATAACTGCATACTTAGAAAAGACAAAAAAAAACAAGAACAAACACAT
1 ACGAATAACTCCATACTTAGAAAAGA-AAAAAAAAACAAGAACAAACACAT
4136534 ACG
1 ACG
4136537 CACGAATTGC
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
49 24 0.49
51 25 0.51
ACGTcount: A:0.59, C:0.17, G:0.10, T:0.14
Consensus pattern (50 bp):
ACGAATAACTCCATACTTAGAAAAGAAAAAAAAAACAAGAACAAACACAT
Found at i:4140126 original size:2 final size:2
Alignment explanation
Indices: 4140119--4140148 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4140109 ATGAGGTCTT
4140119 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
4140149 AGTTTTAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:4141843 original size:2 final size:2
Alignment explanation
Indices: 4141836--4141863 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4141826 CTATAATTTA
4141836 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
4141864 GAAATAAATT
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:4141848 original size:106 final size:107
Alignment explanation
Indices: 4141628--4141859 Score: 269
Period size: 106 Copynumber: 2.2 Consensus size: 107
4141618 TACAATCCAG
4141628 TAATATAATTTATATATTATTATTTAAAAATAATTGTAAAAATAATTCAAATAAAAATATTAAAC
1 TAATATAATTTATATATTATTATTTAAAAATAATTGTAAAAATAATTCAAATAAAAATATTAAAC
* ** ** * *
4141693 TTATTTTTATTCTGTGATTTGGATTCTCTAAATAATTTTATTT
66 TTATTTTTATTCTGTAATTTACATTAACT-AATAATTTAATTA
*
4141736 TAATATAATTTATATATTATTATTT-AAAA-AATTGTAAAAATAATTTAAATAAAAATATTAAA-
1 TAATATAATTTATATATTATTATTTAAAAATAATTGTAAAAATAATTCAAATAAAAATATTAAAC
*
4141798 TTCA-TTTTATT-TTTAAGTCTTACATTAACT-ATAATTTAATATA
66 TT-ATTTTTATTCTGTAA-T-TTACATTAACTAATAATTTAAT-TA
*
4141841 TATATATATATATATATAT
1 TA-ATATA-ATTTATATAT
4141860 ATATGAAATA
Statistics
Matches: 108, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
104 12 0.11
105 13 0.12
106 45 0.42
107 13 0.12
108 25 0.23
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (107 bp):
TAATATAATTTATATATTATTATTTAAAAATAATTGTAAAAATAATTCAAATAAAAATATTAAAC
TTATTTTTATTCTGTAATTTACATTAACTAATAATTTAATTA
Found at i:4146848 original size:19 final size:20
Alignment explanation
Indices: 4146824--4146973 Score: 76
Period size: 20 Copynumber: 7.6 Consensus size: 20
4146814 AAATAACCAA
*
4146824 CAAATTCGCAACGTG-ATCT
1 CAAATTCGCAACGCGAATCT
* *
4146843 CAAATTTGCAACGCGAATTT
1 CAAATTCGCAACGCGAATCT
* * * *
4146863 CAATTTCGCAAC-CCAGTTTT
1 CAAATTCGCAACGCGA-ATCT
* *
4146883 CAATTTCGCAACGCGAATAT
1 CAAATTCGCAACGCGAATCT
* ** *
4146903 -ATAAATCGCAAAACG-ATAGT
1 CA-AATTCGCAACGCGAAT-CT
* **
4146923 CAAATTCTCAACGCGAAAGT
1 CAAATTCGCAACGCGAATCT
4146943 CAAATTCGCAACGCGAAT-T
1 CAAATTCGCAACGCGAATCT
* *
4146962 TAATTTCGCAAC
1 CAAATTCGCAAC
4146974 AGGTTTTAGT
Statistics
Matches: 100, Mismatches: 24, Indels: 14
0.72 0.17 0.10
Matches are distributed among these distances:
19 29 0.29
20 67 0.67
21 4 0.04
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATCT
Found at i:4146873 original size:20 final size:20
Alignment explanation
Indices: 4146845--4146973 Score: 81
Period size: 20 Copynumber: 6.5 Consensus size: 20
4146835 CGTGATCTCA
4146845 AATTT-GCAACGCGAATTTC
1 AATTTCGCAACGCGAATTTC
* *
4146864 AATTTCGCAAC-CCAGTTTTC
1 AATTTCGCAACGCGA-ATTTC
4146884 AATTTCGCAACGCGAATATAT-
1 AATTTCGCAACGCGAAT-T-TC
* ** *
4146905 AA-ATCGCAAAACG-ATAGTC
1 AATTTCGCAACGCGAAT-TTC
* * **
4146924 AAATTCTCAACGCGAAAGTC
1 AATTTCGCAACGCGAATTTC
*
4146944 AAATTCGCAACGCGAATTT-
1 AATTTCGCAACGCGAATTTC
4146963 AATTTCGCAAC
1 AATTTCGCAAC
4146974 AGGTTTTAGT
Statistics
Matches: 85, Mismatches: 17, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
18 1 0.01
19 22 0.26
20 55 0.65
21 6 0.07
22 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.26
Consensus pattern (20 bp):
AATTTCGCAACGCGAATTTC
Found at i:4147741 original size:12 final size:12
Alignment explanation
Indices: 4147720--4147753 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4147710 ACCACATTTC
*
4147720 CAATACCAAACA
1 CAATATCAAACA
4147732 CAATATCAAACA
1 CAATATCAAACA
*
4147744 CAATCTCAAA
1 CAATATCAAA
4147754 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:4147906 original size:24 final size:24
Alignment explanation
Indices: 4147879--4147932 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
4147869 ATATTCGAAA
*
4147879 TTTGATCTTGGTTAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
4147903 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
4147927 TTTGAT
1 TTTGAT
4147933 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:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:4150140 original size:17 final size:17
Alignment explanation
Indices: 4150118--4150150 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4150108 AAGAAAAAGG
*
4150118 AAATCAAAATCGCAATA
1 AAATCAAAATCCCAATA
4150135 AAATCAAAATCCCAAT
1 AAATCAAAATCCCAAT
4150151 CACAACCGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.21, G:0.03, T:0.18
Consensus pattern (17 bp):
AAATCAAAATCCCAATA
Found at i:4150539 original size:20 final size:20
Alignment explanation
Indices: 4150436--4150532 Score: 107
Period size: 20 Copynumber: 5.2 Consensus size: 20
4150426 ATGTTGCGAT
4150436 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
4150456 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
4150476 CAACGCGAAA-T--AA---G
1 CAACGCGAAAGTCAAATTCG
*** *
4150490 CGTTGCGATAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
*
4150510 CAACGTGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
4150530 CAA
1 CAA
4150533 ACCGAAAATC
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
14 7 0.11
15 1 0.02
17 4 0.06
19 1 0.02
20 49 0.79
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.18
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCG
Found at i:4150746 original size:61 final size:63
Alignment explanation
Indices: 4150615--4150755 Score: 171
Period size: 61 Copynumber: 2.2 Consensus size: 63
4150605 TTTTAGAAAC
*
4150615 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACAAATCAAATT
1 AACAAATCAACTTTTACAAATCAATT--A-AAGCAAAAAAATAAATCTTATTTACAAATCAAATT
4150680 A
63 A
* * ** *
4150681 AACAAATCAACTTTTACAAATCAATT-AATC-AAAAAATAAATCTTATTTCCTCATC-AATTGT
1 AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACAAATCAAATT-A
4150742 AACAAATCAACTTT
1 AACAAATCAACTTT
4150756 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 3 0.04
66 26 0.38
ACGTcount: A:0.50, C:0.17, G:0.01, T:0.31
Consensus pattern (63 bp):
AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACAAATCAAATTA
Found at i:4152204 original size:21 final size:21
Alignment explanation
Indices: 4152133--4152229 Score: 72
Period size: 21 Copynumber: 4.6 Consensus size: 21
4152123 GGCGAGACCA
* * *
4152133 CTTGAACGATGACAGTGGCCT
1 CTTGAATGATGATAGGGGCCT
* ** *
4152154 CTTGAACGATGGGAGGGGCTT
1 CTTGAATGATGATAGGGGCCT
*
4152175 TTTCG-ATGATGATAGGGGCCT
1 CTT-GAATGATGATAGGGGCCT
* *
4152196 CTTGAATGAT-ATGATGTGCCT
1 CTTGAATGATGAT-AGGGGCCT
4152217 CTTGAATGATGAT
1 CTTGAATGATGAT
4152230 TGGTGCATCG
Statistics
Matches: 60, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
20 3 0.05
21 54 0.90
22 3 0.05
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (21 bp):
CTTGAATGATGATAGGGGCCT
Found at i:4152235 original size:21 final size:21
Alignment explanation
Indices: 4152180--4152235 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
4152170 GGCTTTTTCG
* *
4152180 ATGATGATAGGGGCCTCTTGA
1 ATGATGATTGGTGCCTCTTGA
4152201 ATGAT-A-TGATGTGCCTCTTGA
1 ATGATGATTG--GTGCCTCTTGA
4152222 ATGATGATTGGTGC
1 ATGATGATTGGTGC
4152236 ATCGGGCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
19 1 0.03
20 1 0.03
21 24 0.83
22 1 0.03
23 2 0.07
ACGTcount: A:0.23, C:0.12, G:0.30, T:0.34
Consensus pattern (21 bp):
ATGATGATTGGTGCCTCTTGA
Found at i:4154403 original size:20 final size:20
Alignment explanation
Indices: 4154387--4154441 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
4154377 TTTGAAACTT
*
4154387 AAAATCGCAACGCGAAAATG
1 AAAATCGCAACGCGAAAATA
4154407 AAAATCGCAACGCGAAAATA
1 AAAATCGCAACGCGAAAATA
4154427 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
4154442 TTTTAGTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.51, C:0.22, G:0.18, T:0.09
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATA
Found at i:4154770 original size:22 final size:22
Alignment explanation
Indices: 4154742--4154788 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
4154732 GATGGAGATA
*
4154742 GACGGATTTCGTCGGAAATGGG
1 GACGGATTTCGTCGGAAATAGG
*
4154764 GACGGATTTCGTCGGAGATAGG
1 GACGGATTTCGTCGGAAATAGG
4154786 GAC
1 GAC
4154789 AGATGTTGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.23, C:0.15, G:0.40, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGTCGGAAATAGG
Found at i:4154962 original size:21 final size:21
Alignment explanation
Indices: 4154938--4154981 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
4154928 TTCGCGTTGA
* *
4154938 GAATTTGGAATATCGCAACGC
1 GAATTTGAAAAATCGCAACGC
*
4154959 GAATTTGAAAAATCGCAATGC
1 GAATTTGAAAAATCGCAACGC
4154980 GA
1 GA
4154982 TTTACATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.23
Consensus pattern (21 bp):
GAATTTGAAAAATCGCAACGC
Found at i:4155244 original size:2 final size:2
Alignment explanation
Indices: 4155237--4155268 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4155227 CCCCTCCTCC
4155237 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4155269 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:4155273 original size:2 final size:2
Alignment explanation
Indices: 4155268--4155298 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4155258 TCTCTCTCTC
4155268 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4155299 CCAAACAGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4161345 original size:21 final size:21
Alignment explanation
Indices: 4161319--4161363 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
4161309 AAAACGTATT
4161319 CAAGAAAAATCACACCATATC
1 CAAGAAAAATCACACCATATC
4161340 CAAGAAAAATCACACCATATC
1 CAAGAAAAATCACACCATATC
4161361 CAA
1 CAA
4161364 CACCAAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.53, C:0.29, G:0.04, T:0.13
Consensus pattern (21 bp):
CAAGAAAAATCACACCATATC
Found at i:4162214 original size:18 final size:18
Alignment explanation
Indices: 4162191--4162226 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
4162181 GAAGTAGATA
4162191 GACGAAGAACCCAACATG
1 GACGAAGAACCCAACATG
4162209 GACGAAGAACCCAACATG
1 GACGAAGAACCCAACATG
4162227 CGGCACTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.28, G:0.22, T:0.06
Consensus pattern (18 bp):
GACGAAGAACCCAACATG
Found at i:4162462 original size:6 final size:6
Alignment explanation
Indices: 4162451--4162486 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
4162441 ATTGTTTCTT
* *
4162451 TCGCTC TCGCTC TCGCTC TCGCTC CCCCTC TCGCTC
1 TCGCTC TCGCTC TCGCTC TCGCTC TCGCTC TCGCTC
4162487 CTCCTCTTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.56, G:0.14, T:0.31
Consensus pattern (6 bp):
TCGCTC
Found at i:4162487 original size:12 final size:12
Alignment explanation
Indices: 4162454--4162493 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
4162444 GTTTCTTTCG
* *
4162454 CTCTCGCTCTCG
1 CTCTCGCTCCCC
4162466 CTCTCGCTCCCC
1 CTCTCGCTCCCC
*
4162478 CTCTCGCTCCTC
1 CTCTCGCTCCCC
4162490 CTCT
1 CTCT
4162494 TTGGTCTGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.57, G:0.10, T:0.33
Consensus pattern (12 bp):
CTCTCGCTCCCC
Found at i:4171194 original size:20 final size:20
Alignment explanation
Indices: 4171157--4171216 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
4171147 TTACAGAGAA
*
4171157 AAAT-ATCCCCAAAAGGCTAG
1 AAATCATCCCC-AACGGCTAG
4171177 AAATCATCCCCAACGGCTAG
1 AAATCATCCCCAACGGCTAG
4171197 AAATCATCCCCAACGGCTAG
1 AAATCATCCCCAACGGCTAG
4171217 TAACGACCAC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
20 32 0.84
21 6 0.16
ACGTcount: A:0.38, C:0.32, G:0.15, T:0.15
Consensus pattern (20 bp):
AAATCATCCCCAACGGCTAG
Found at i:4178290 original size:17 final size:17
Alignment explanation
Indices: 4178268--4178303 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
4178258 ATATATAGAA
4178268 TCGGAAAGCACACAAAG
1 TCGGAAAGCACACAAAG
4178285 TCGGAAAGCACACAAAG
1 TCGGAAAGCACACAAAG
4178302 TC
1 TC
4178304 TAGAATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.25, G:0.22, T:0.08
Consensus pattern (17 bp):
TCGGAAAGCACACAAAG
Found at i:4179209 original size:32 final size:32
Alignment explanation
Indices: 4179168--4179246 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 32
4179158 TTTCTAGTAT
4179168 TTTATTTATTTCATTTG-CTTTTATGGAC-TTTA
1 TTTATTTATTT-ATTTGCCTTTTAT-GACTTTTA
*
4179200 TTTATTTATTT-TTATGCCTTTTATGTCTTTTA
1 TTTATTTATTTATT-TGCCTTTTATGACTTTTA
4179232 TTTATTTATTTATTT
1 TTTATTTATTTATTT
4179247 CGTTTCTTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
30 2 0.05
31 4 0.10
32 34 0.81
33 2 0.05
ACGTcount: A:0.18, C:0.08, G:0.06, T:0.68
Consensus pattern (32 bp):
TTTATTTATTTATTTGCCTTTTATGACTTTTA
Found at i:4182468 original size:13 final size:11
Alignment explanation
Indices: 4182428--4182491 Score: 67
Period size: 11 Copynumber: 5.5 Consensus size: 11
4182418 AGATTCAATC
*
4182428 AGAACAAAAAG
1 AGAAAAAAAAG
4182439 AGAAAAAAAAG
1 AGAAAAAAAAG
*
4182450 AAAAAAAGCAAAG
1 AGAAAAA--AAAG
4182463 AGAAAATAAAAAG
1 AG-AAA-AAAAAG
4182476 AGAAAAAAAAG
1 AGAAAAAAAAG
4182487 A-AAAA
1 AGAAAA
4182492 TTGAAGAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
10 4 0.09
11 23 0.50
12 3 0.07
13 11 0.24
14 3 0.07
15 2 0.04
ACGTcount: A:0.80, C:0.03, G:0.16, T:0.02
Consensus pattern (11 bp):
AGAAAAAAAAG
Found at i:4182508 original size:11 final size:11
Alignment explanation
Indices: 4182428--4182509 Score: 55
Period size: 11 Copynumber: 7.3 Consensus size: 11
4182418 AGATTCAATC
4182428 AGAACAAAAAG-
1 AGAA-AAAAAGA
4182439 AG-AAAAAA-A
1 AGAAAAAAAGA
4182448 AGAAAAAAAGCAA
1 AGAAAAAAAG--A
*
4182461 AGAGAAAATAAAA
1 AGA-AAAA-AAGA
4182474 AGAGAAAAAA-A
1 AGA-AAAAAAGA
**
4182485 AGAAAAATTGA
1 AGAAAAAAAGA
4182496 AGAAAAAAAGA
1 AGAAAAAAAGA
4182507 AGA
1 AGA
4182510 CAAGATGCAT
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
9 7 0.12
10 11 0.19
11 19 0.33
12 2 0.03
13 13 0.22
14 4 0.07
15 2 0.03
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (11 bp):
AGAAAAAAAGA
Found at i:4183635 original size:32 final size:32
Alignment explanation
Indices: 4183561--4183636 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
4183551 GCATCTTTGA
* ***
4183561 AGATTCAACATCAAATGTTGGGGCATTTTTTT
1 AGATTCAACATCAAATATTGGGGCATTTTGGG
*
4183593 AGATTTAACATCAAATATTGGGGCATATTTGGG
1 AGATTCAACATCAAATATTGGGGCAT-TTTGGG
4183626 A-ATTCAACATC
1 AGATTCAACATC
4183637 CTGATACAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
32 33 0.89
33 4 0.11
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (32 bp):
AGATTCAACATCAAATATTGGGGCATTTTGGG
Found at i:4184377 original size:106 final size:106
Alignment explanation
Indices: 4184220--4184541 Score: 448
Period size: 106 Copynumber: 3.0 Consensus size: 106
4184210 ATATCGTGCC
* *
4184220 ACTCGAGACAACACAAGTTCAACTCCACAATGAAGGGACGAG-TGGTTGTCAACAAACAATTTCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACG-GCTGGTTGTCAACAAACAATTTCC
* *
4184284 CAATTTCAGAGACAATTTCAACTTCATAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
4184326 ATTTGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
*
4184391 AATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * **
4184432 ACTCGAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCAGCTGGCTGTCAACAAACAATTTCTT
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* * * * *
4184497 AGTTCCAGAGCCAATTTTAACTTCACGGCGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
4184538 ACTC
1 ACTC
4184542 TGAACAATAC
Statistics
Matches: 192, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
105 1 0.01
106 191 0.99
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (106 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:4184863 original size:36 final size:35
Alignment explanation
Indices: 4184823--4184916 Score: 104
Period size: 32 Copynumber: 2.7 Consensus size: 35
4184813 ATTGAAAACA
* *
4184823 TTTCCATTGAAATGAATTTTATCTCGATTGAGATAG
1 TTTCCCTTGAAACGAATTTT-TCTCGATTGAGATAG
* *
4184859 TTTCCCTTGAAACGAA-ATTT-T-GTTTGAGATAG
1 TTTCCCTTGAAACGAATTTTTCTCGATTGAGATAG
4184891 TTTCCCTTGAAACGAAATTTTGTCTC
1 TTTCCCTTGAAACG-AATTTT-TCTC
4184917 TCTTGAAACA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
32 24 0.50
33 3 0.06
34 3 0.06
35 3 0.06
36 15 0.31
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (35 bp):
TTTCCCTTGAAACGAATTTTTCTCGATTGAGATAG
Found at i:4184891 original size:32 final size:32
Alignment explanation
Indices: 4184850--4184913 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
4184840 TTTATCTCGA
4184850 TTGAGATAGTTTCCCTTGAAACGAAATTTTGT
1 TTGAGATAGTTTCCCTTGAAACGAAATTTTGT
4184882 TTGAGATAGTTTCCCTTGAAACGAAATTTTGT
1 TTGAGATAGTTTCCCTTGAAACGAAATTTTGT
4184914 CTCTCTTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (32 bp):
TTGAGATAGTTTCCCTTGAAACGAAATTTTGT
Found at i:4184972 original size:36 final size:37
Alignment explanation
Indices: 4184932--4185003 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 37
4184922 AAACATAAAC
*
4184932 ATTGA-AAACATTTCCCTTGAAATG-AATTTTATCTCG
1 ATTGAGAAA-ATTTCCCTTGAAACGAAATTTTATCTCG
* * *
4184968 ATTGAGATAGTTTCCCTTGAAACGAAATTTTGTCTC
1 ATTGAGAAAATTTCCCTTGAAACGAAATTTTATCTC
4185004 CCTTGAAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
36 18 0.60
37 12 0.40
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.39
Consensus pattern (37 bp):
ATTGAGAAAATTTCCCTTGAAACGAAATTTTATCTCG
Found at i:4184991 original size:87 final size:87
Alignment explanation
Indices: 4184882--4185096 Score: 358
Period size: 87 Copynumber: 2.5 Consensus size: 87
4184872 GAAATTTTGT
*
4184882 TTGAGATAGTTTCCCTTGAAACGAAATTTTGTCTCTCTTGAAACATAAACATTGAAAACATTTCC
1 TTGAGATAGTTTCCCTTGAAACGAAATTTTGTCTCCCTTGAAACATAAACATTGAAAACATTTCC
* *
4184947 CTTGAAATGAATTTTATCTCGA
66 CTTGAAATAAATTTTATATCGA
4184969 TTGAGATAGTTTCCCTTGAAACGAAATTTTGTCTCCCTTGAAACATAAACATTGAAAACATTTCC
1 TTGAGATAGTTTCCCTTGAAACGAAATTTTGTCTCCCTTGAAACATAAACATTGAAAACATTTCC
*
4185034 CTTGAAATAAATTTTATATCGT
66 CTTGAAATAAATTTTATATCGA
* * **
4185056 TTGGGGTAGTTTCCCTTGAAAAAAAATTTTGTCTCCCTTGA
1 TTGAGATAGTTTCCCTTGAAACGAAATTTTGTCTCCCTTGA
4185097 GACAGTTTCT
Statistics
Matches: 120, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 120 1.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.37
Consensus pattern (87 bp):
TTGAGATAGTTTCCCTTGAAACGAAATTTTGTCTCCCTTGAAACATAAACATTGAAAACATTTCC
CTTGAAATAAATTTTATATCGA
Found at i:4185189 original size:101 final size:103
Alignment explanation
Indices: 4185006--4185244 Score: 342
Period size: 101 Copynumber: 2.3 Consensus size: 103
4184996 TTTGTCTCCC
* *
4185006 TTGAAACATAAACATTGAAAACATTTCCCTTGAAA-TAAATTTTATATCGTTTGGGGTAGTTTCC
1 TTGAAACATAAACATTGAAAACATTTCCCTTGAAACTAAATTTTATATCGTTTGAGATAGTTTCC
4185070 CTTGAAAAAAAATTTTGTCTCCCTTGAGACAGTTTCTA
66 CTTGAAAAAAAATTTTGTCTCCCTTGAGACAGTTTCTA
* * *
4185108 TTGAAAC-TAAACATTGAAAACATTTCCTTTGAAACT-AATTTTGTCTC-TCTTGAGATAGTTTC
1 TTGAAACATAAACATTGAAAACATTTCCCTTGAAACTAAATTTTATATCGT-TTGAGATAGTTTC
* * *
4185170 CCTTGAAACAAAATTTTGTCTCCCTTGAGATAGTTTCTC
65 CCTTGAAAAAAAATTTTGTCTCCCTTGAGACAGTTTCTA
* **
4185209 TTGAAACATAAACCTTGAAAATGTTTCCCTTGAAAC
1 TTGAAACATAAACATTGAAAACATTTCCCTTGAAAC
4185245 ACAAAATATT
Statistics
Matches: 122, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
100 1 0.01
101 89 0.73
102 32 0.26
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.37
Consensus pattern (103 bp):
TTGAAACATAAACATTGAAAACATTTCCCTTGAAACTAAATTTTATATCGTTTGAGATAGTTTCC
CTTGAAAAAAAATTTTGTCTCCCTTGAGACAGTTTCTA
Found at i:4185197 original size:37 final size:37
Alignment explanation
Indices: 4185130--4185216 Score: 131
Period size: 37 Copynumber: 2.4 Consensus size: 37
4185120 ATTGAAAACA
* * *
4185130 TTTCCTTTGAAAC-TAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
4185166 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
*
4185203 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
4185217 TAAACCTTGA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 12 0.26
37 34 0.74
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.43
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
Found at i:4185511 original size:36 final size:35
Alignment explanation
Indices: 4185281--4185514 Score: 182
Period size: 36 Copynumber: 6.7 Consensus size: 35
4185271 AAAACGAGTT
*
4185281 TTGAGACAGTTTCTCTTGAAACAAAATCTTGTCTCTC
1 TTGAGACAGTTTCTCTTGAAAC-AAAT-TTGTCCCTC
* *
4185318 TTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTC
1 TTGAGACAGTTTCTCTTGAAACAAA-TTTGTCCCTC
* *
4185354 TTGAGACAGTTTCCCTTGAAACAAA---AT--CT-
1 TTGAGACAGTTTCTCTTGAAACAAATTTGTCCCTC
* * *
4185383 TTGA-ATA-TCTTTTCCTTGAAACAAATTTCGT-CTTCC
1 TTGAGACAGT-TTCT-CTTGAAACAAATTT-GTCCCT-C
* * * *
4185419 TTGAGACAATTTCT-TTTAGAACTAAGTTTTGTCTCTC
1 TTGAGACAGTTTCTCTTGA-AAC-AA-ATTTGTCCCTC
*
4185456 TTGAGACAGTTTCTTTTGAAACAAATTCTGTCCCTC
1 TTGAGACAGTTTCTCTTGAAACAAATT-TGTCCCTC
4185492 TTGAGACAGTTTCTCTTGAAACA
1 TTGAGACAGTTTCTCTTGAAACA
4185515 CAAAAAAACC
Statistics
Matches: 161, Mismatches: 18, Indels: 37
0.75 0.08 0.17
Matches are distributed among these distances:
27 1 0.01
28 4 0.02
29 15 0.09
30 2 0.01
32 1 0.01
33 1 0.01
34 1 0.01
35 5 0.03
36 75 0.47
37 48 0.30
38 8 0.05
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (35 bp):
TTGAGACAGTTTCTCTTGAAACAAATTTGTCCCTC
Found at i:4185561 original size:40 final size:39
Alignment explanation
Indices: 4185512--4185588 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
4185502 TTCTCTTGAA
4185512 ACACA-AAAAAACC-CTCAAAATTGTTTCTCTTAAAACAC
1 ACACACAAAAAACCTCTCAAAA-TGTTTCTCTTAAAACAC
* * *
4185550 ACACACAAAAAACCTTTGAAAATGTTTCTCTTGAAACAC
1 ACACACAAAAAACCTCTCAAAATGTTTCTCTTAAAACAC
4185589 CAAACCCTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
38 5 0.15
39 24 0.71
40 5 0.15
ACGTcount: A:0.45, C:0.25, G:0.05, T:0.25
Consensus pattern (39 bp):
ACACACAAAAAACCTCTCAAAATGTTTCTCTTAAAACAC
Found at i:4186799 original size:42 final size:39
Alignment explanation
Indices: 4186747--4186843 Score: 106
Period size: 39 Copynumber: 2.4 Consensus size: 39
4186737 CACACACATA
** *
4186747 TATATATATATATATGTTAATTTTCATTATTTGTTTTA-TTAT
1 TATATATATATATATACT-ATTTT--TTATGT-TTTTATTTAT
* *
4186789 TTTATATATATATTTACTATTTTTTATGTTTTTATTTAT
1 TATATATATATATATACTATTTTTTATGTTTTTATTTAT
4186828 TATATATATATATATA
1 TATATATATATATATA
4186844 TTATCATTTC
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
38 5 0.11
39 23 0.49
41 5 0.11
42 14 0.30
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (39 bp):
TATATATATATATATACTATTTTTTATGTTTTTATTTAT
Found at i:4186999 original size:4 final size:4
Alignment explanation
Indices: 4186990--4187035 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
4186980 TTTTATGGAC
* *
4186990 TTTA TTTA TTTA -TT- TTTA TATC TTTA TTTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTT
4187036 CGTTTCTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
3 4 0.11
4 27 0.77
5 4 0.11
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:4187006 original size:23 final size:22
Alignment explanation
Indices: 4186989--4187052 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
4186979 CTTTTATGGA
4186989 CTTTATTTATTTATTTTTATAT
1 CTTTATTTATTTATTTTTATAT
4187011 CTTTATTTTATTTATTTATT-TAT
1 CTTTA-TTTATTTATTT-TTATAT
** *
4187034 -TTCGTTTCTTTATTTTTAT
1 CTTTATTTATTTATTTTTAT
4187053 TTAATTTACT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
20 2 0.06
21 11 0.31
22 7 0.19
23 14 0.39
24 2 0.06
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.73
Consensus pattern (22 bp):
CTTTATTTATTTATTTTTATAT
Found at i:4187025 original size:31 final size:31
Alignment explanation
Indices: 4186990--4187060 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
4186980 TTTTATGGAC
*
4186990 TTTATTTATTTATTT-TTATATCTTTA-TTTTA
1 TTTATTTATTTATTTCGT-T-TCTTTATTTTTA
4187021 TTTATTTATTTATTTCGTTTCTTTATTTTTA
1 TTTATTTATTTATTTCGTTTCTTTATTTTTA
4187052 TTTAATTTA
1 TTT-ATTTA
4187061 CTTGTTATCG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
30 6 0.17
31 24 0.67
32 6 0.17
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.73
Consensus pattern (31 bp):
TTTATTTATTTATTTCGTTTCTTTATTTTTA
Found at i:4188536 original size:139 final size:138
Alignment explanation
Indices: 4188355--4188618 Score: 316
Period size: 139 Copynumber: 1.9 Consensus size: 138
4188345 GAACATCGGA
* * * * * *
4188355 CATAAAAGAGAGGACCAAATTAAAAATTCTCCTGAATTAAGGACTAAATATGAAATTAATC-TAA
1 CATAAAAGAGA-GACCAAATTAAAAATTCACCTAAATTAAGGAAT-AAGATGAAAATAAACTTAA
* * * * * *
4188419 AATGAAGGCTCTAATATTAAGACCTAATAAATTTTAGCAATTTATTGGATCAAATAATTAATATG
64 AAGGAAGGCTCTAATATTAAAACATAACAAATTTTAGCAATTTATTGAAACAAATAATTAATATG
4188484 GAATCTTAGG
129 GAATCTTAGG
*
4188494 CATAAAAGAGA-ACCAAATTAAAAAGTTCACCTAAATTAAAGGAATAAGGTGAAAATAAACTTAA
1 CATAAAAGAGAGACCAAATTAAAAA-TTCACCTAAATT-AAGGAATAAGATGAAAATAAACTTAA
** * * *
4188558 GGGGAAGGCTCTAATATTAAAACATAACCAATTTTAGCCATTTATTGAAACGAATAATTAA
64 AAGGAAGGCTCTAATATTAAAACATAACAAATTTTAGCAATTTATTGAAACAAATAATTAA
4188619 AACGGAACCT
Statistics
Matches: 104, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
137 13 0.12
138 21 0.20
139 70 0.67
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.28
Consensus pattern (138 bp):
CATAAAAGAGAGACCAAATTAAAAATTCACCTAAATTAAGGAATAAGATGAAAATAAACTTAAAA
GGAAGGCTCTAATATTAAAACATAACAAATTTTAGCAATTTATTGAAACAAATAATTAATATGGA
ATCTTAGG
Found at i:4189862 original size:36 final size:36
Alignment explanation
Indices: 4189821--4189900 Score: 142
Period size: 36 Copynumber: 2.2 Consensus size: 36
4189811 AATTATATAC
4189821 TTTTGAATAATTCAAATTAAAATAATATCTATTTAA
1 TTTTGAATAATTCAAATTAAAATAATATCTATTTAA
*
4189857 TTTTGAGTAATTCAAATTAAAATAATATCTATTTAA
1 TTTTGAATAATTCAAATTAAAATAATATCTATTTAA
*
4189893 GTTTGAAT
1 TTTTGAAT
4189901 GGTCAAGGGA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (36 bp):
TTTTGAATAATTCAAATTAAAATAATATCTATTTAA
Found at i:4190099 original size:19 final size:21
Alignment explanation
Indices: 4190071--4190112 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
4190061 ATTGAAGAAC
4190071 TTTTCTTCTC-TT-GAAAAATA
1 TTTTCTTCTCATTCG-AAAATA
4190091 TTTTC-TCTCATTCGAAAATA
1 TTTTCTTCTCATTCGAAAATA
4190111 TT
1 TT
4190113 CTTTTCCTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.20
20 15 0.75
21 1 0.05
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.50
Consensus pattern (21 bp):
TTTTCTTCTCATTCGAAAATA
Found at i:4194621 original size:2 final size:2
Alignment explanation
Indices: 4194614--4194660 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
4194604 TAATTAAAAT
4194614 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4194656 TA TA T
1 TA TA T
4194661 TAATCTTAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4195020 original size:2 final size:2
Alignment explanation
Indices: 4195013--4195080 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
4195003 GAAAATTGAC
4195013 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4195055 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
4195081 CTTAATTACG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4195140 original size:398 final size:396
Alignment explanation
Indices: 4194614--4195409 Score: 1233
Period size: 398 Copynumber: 2.0 Consensus size: 396
4194604 TAATTAAAAT
*
4194614 TATATATATATATATATATATATATATATATATATATATATATATATTAATCTTAATTATGCACT
1 TATATATATATATATATATATATATATATATATATATATATATATATTAATATTAATTAT-CACT
*
4194679 TTAATCATGTCCAATAAAATCATTCAATATATGCTCATCTCAACCTTGGGTTTCACCTTGTAGGT
65 TTAATCACG-CC-A-AAAATCATTCAATATATGCTCATCTCAACCTTGGGTTTCACCTTGTAGGT
4194744 TCCTACAACTGTCGAAACTA-TTTTTTCAGATTAAAAAAAAACCACACCAAGTTTAATTTTTTTA
127 TCCTACAACTGTCGAAACTATTTTTTTCAGATT-AAAAAAAACCACACCAAGTTTAATTTTTTTA
* * *
4194808 ATTTTTAATTATAGAGTTGTGATTAAAAAATTTATCGCTTCGAAAAATTTGGGATTTCATTTTTT
191 ATTTTTAATTAAAGAGTTGTGATTAAAAAAATTATCGCTTCGAAAAATTTGGGATTTCATTTTTA
* * *
4194873 AAGTAAAACACATATAGTTCGAGGAGTCGCAACCAATCCTTGATTAGGGTGTGATTTGGCACCCA
256 AAGTAAAAAACATATAGTTCGAGGAGTCGCAACCAATCCTTGATTAAGGTGTGATTGGGCACCCA
* *
4194938 AAATACGTTTTGTCATTTTAATAAGGTTTAATTATTAAAGCAACATTTTAAGGTCTATGTAACTA
321 AAATACGTTTTGTCATTTTAATAAGGTTTAATTATTAAAACAACATTTTAAGGTCTACGTAACTA
4195003 GAAAATTGACA
386 GAAAATTGACA
4195014 TATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATAT
1 TATATATATATATATATATATATATATATATATATATATATATATAT-TA-ATAT-TA-AT-TAT
* * * * *
4195079 -A-TCTTAATTACG-C-AAAATCATTCAATATTTGCTCATCTTAATCTTGGGTTTGACCTTGTAG
61 CACT-TTAATCACGCCAAAAATCATTCAATATATGCTCATCTCAACCTTGGGTTTCACCTTGTAG
* ** *
4195140 GTTCCTACAACTGTCGAAACTATTTTTTTCGGATTAAAAAAAACCACACCGGGTTTATTTTTTTT
125 GTTCCTACAACTGTCGAAACTATTTTTTTCAGATTAAAAAAAACCACACCAAGTTTAATTTTTTT
* * * *
4195205 ATTTTTTAATTAAAGAGTTGTGATTAAAAAAATTCTCGCTTCGAAAATTTTGGGATTTCCTTTTT
190 AATTTTTAATTAAAGAGTTGTGATTAAAAAAATTATCGCTTCGAAAAATTTGGGATTTCATTTTT
* *
4195270 AAAGTAAAAAACGTATAGTTCGAGGAGTCGCCACCAATCCTTGATTAAGGTGTGATTGGGCACCC
255 AAAGTAAAAAACATATAGTTCGAGGAGTCGCAACCAATCCTTGATTAAGGTGTGATTGGGCACCC
4195335 AAAATACGTTTTGTCATTTTAATAAGGTTTAATTATTAAAACAACATTTTAAGGTCTACGTAACT
320 AAAATACGTTTTGTCATTTTAATAAGGTTTAATTATTAAAACAACATTTTAAGGTCTACGTAACT
4195400 AGAAAATTGA
385 AGAAAATTGA
4195410 GTTCAGGAGT
Statistics
Matches: 364, Mismatches: 25, Indels: 16
0.90 0.06 0.04
Matches are distributed among these distances:
398 284 0.78
399 11 0.03
400 47 0.13
401 3 0.01
402 4 0.01
403 10 0.03
404 2 0.01
405 3 0.01
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (396 bp):
TATATATATATATATATATATATATATATATATATATATATATATATTAATATTAATTATCACTT
TAATCACGCCAAAAATCATTCAATATATGCTCATCTCAACCTTGGGTTTCACCTTGTAGGTTCCT
ACAACTGTCGAAACTATTTTTTTCAGATTAAAAAAAACCACACCAAGTTTAATTTTTTTAATTTT
TAATTAAAGAGTTGTGATTAAAAAAATTATCGCTTCGAAAAATTTGGGATTTCATTTTTAAAGTA
AAAAACATATAGTTCGAGGAGTCGCAACCAATCCTTGATTAAGGTGTGATTGGGCACCCAAAATA
CGTTTTGTCATTTTAATAAGGTTTAATTATTAAAACAACATTTTAAGGTCTACGTAACTAGAAAA
TTGACA
Found at i:4205626 original size:21 final size:21
Alignment explanation
Indices: 4205581--4205626 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
4205571 CTGAAGGAAT
* *
4205581 AGTATCGGTACTACAATTCAT
1 AGTATCGGTACTACAACTCAA
* *
4205602 AGTATCGGTCCTACTACTCAA
1 AGTATCGGTACTACAACTCAA
4205623 AGTA
1 AGTA
4205627 GTATCAGTAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (21 bp):
AGTATCGGTACTACAACTCAA
Found at i:4208014 original size:5 final size:5
Alignment explanation
Indices: 4208004--4208033 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
4207994 ATAATAACAA
4208004 AAATT AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT AAATT
4208034 TAAAAAGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:4208179 original size:28 final size:30
Alignment explanation
Indices: 4208132--4208187 Score: 82
Period size: 28 Copynumber: 1.9 Consensus size: 30
4208122 ATTTTAAAAA
4208132 TATTACTTAAAATCTATATA-TAATATATAC
1 TATTACTTAAAATCTATATACT-ATATATAC
4208162 TATT-CTTAAAA-CTATATACTATATAT
1 TATTACTTAAAATCTATATACTATATAT
4208188 TTTTCAAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 13 0.52
29 8 0.32
30 4 0.16
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.45
Consensus pattern (30 bp):
TATTACTTAAAATCTATATACTATATATAC
Found at i:4208272 original size:26 final size:28
Alignment explanation
Indices: 4208202--4208278 Score: 106
Period size: 30 Copynumber: 2.8 Consensus size: 28
4208192 CAAAACCATT
4208202 TTTTTTCAAAACTATATATATATACTGTA
1 TTTTTTCAAAACTATATATATATAC-GTA
4208231 TTATTTTCAAAACTATATA-ATATAC-TA
1 TT-TTTTCAAAACTATATATATATACGTA
4208258 -TTTTTCAAAACCTATATATAT
1 TTTTTTCAAAA-CTATATATAT
4208279 TATTTTATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
25 9 0.20
26 8 0.18
27 4 0.09
29 8 0.18
30 16 0.36
ACGTcount: A:0.40, C:0.12, G:0.01, T:0.47
Consensus pattern (28 bp):
TTTTTTCAAAACTATATATATATACGTA
Found at i:4208287 original size:28 final size:27
Alignment explanation
Indices: 4208203--4208288 Score: 88
Period size: 30 Copynumber: 3.1 Consensus size: 27
4208193 AAAACCATTT
4208203 TTTTTCAAAACTATATATATATACTGTATTA
1 TTTTTCAAAACTATATATAT-TA-T-T-TTA
**
4208234 -TTTTCAAAACTATATA-A-TATACTA
1 TTTTTCAAAACTATATATATTATTTTA
4208258 TTTTTCAAAACCTATATATATTATTTTA
1 TTTTTCAAAA-CTATATATATTATTTTA
4208286 TTT
1 TTT
4208289 ATATTATACT
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
24 2 0.04
25 9 0.19
26 8 0.17
27 3 0.06
28 8 0.17
29 1 0.02
30 16 0.34
ACGTcount: A:0.38, C:0.10, G:0.01, T:0.50
Consensus pattern (27 bp):
TTTTTCAAAACTATATATATTATTTTA
Found at i:4216572 original size:17 final size:17
Alignment explanation
Indices: 4216550--4216589 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
4216540 GATTACAGTG
4216550 TGGCTCTCTAAGAATTT
1 TGGCTCTCTAAGAATTT
4216567 TGGCTCTCTAAGAATTT
1 TGGCTCTCTAAGAATTT
4216584 TGGCTC
1 TGGCTC
4216590 GTAATTCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (17 bp):
TGGCTCTCTAAGAATTT
Found at i:4219686 original size:22 final size:22
Alignment explanation
Indices: 4219658--4219702 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
4219648 GGGTCAAGAG
4219658 AAAAACTCTCTAAGAGTAAATC
1 AAAAACTCTCTAAGAGTAAATC
4219680 AAAAACTCTCTAAGAGTAAATC
1 AAAAACTCTCTAAGAGTAAATC
4219702 A
1 A
4219703 GGGCAAGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.51, C:0.18, G:0.09, T:0.22
Consensus pattern (22 bp):
AAAAACTCTCTAAGAGTAAATC
Found at i:4221101 original size:2 final size:2
Alignment explanation
Indices: 4221096--4221125 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4221086 ACTGTGTGTG
*
4221096 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4221126 CATCAGCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4222941 original size:24 final size:24
Alignment explanation
Indices: 4222908--4222968 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
4222898 TCAAATAGAT
*
4222908 TTGTCCCGAATGACCGCGTAGAATA
1 TTGTCCCGAATGACCACGTAGAA-A
* *
4222933 TT-TCTCGAAGGACCACGTAGAAA
1 TTGTCCCGAATGACCACGTAGAAA
4222956 TTGTCCCGAATGA
1 TTGTCCCGAATGA
4222969 TATTGTAGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 3 0.10
24 25 0.83
25 2 0.07
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (24 bp):
TTGTCCCGAATGACCACGTAGAAA
Found at i:4223127 original size:15 final size:15
Alignment explanation
Indices: 4223109--4223146 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
4223099 CACATAGGGT
4223109 ATTTTCAC-GTGCAAC
1 ATTTTCACTGTGC-AC
*
4223124 ATTTTCACTTTGCAC
1 ATTTTCACTGTGCAC
4223139 ATTTTCAC
1 ATTTTCAC
4223147 ATAGAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 18 0.86
16 3 0.14
ACGTcount: A:0.24, C:0.26, G:0.08, T:0.42
Consensus pattern (15 bp):
ATTTTCACTGTGCAC
Found at i:4223671 original size:20 final size:20
Alignment explanation
Indices: 4223642--4223694 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
4223632 TTTCAATTAC
*
4223642 AGTATCGATACCTTACTCCT
1 AGTATTGATACCTTACTCCT
*
4223662 AGTATTGATATCTTACTCCT
1 AGTATTGATACCTTACTCCT
4223682 AGTATTGATACCT
1 AGTATTGATACCT
4223695 CCATATCAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.40
Consensus pattern (20 bp):
AGTATTGATACCTTACTCCT
Found at i:4229020 original size:24 final size:24
Alignment explanation
Indices: 4228992--4229053 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 24
4228982 TCCATTTTCA
4228992 ACTTTAAAATCTTTTCTTTATT-TT
1 ACTTTAAAATCTTTT-TTTATTATT
*
4229016 ACTTT-AAATC-ATTTTTATTATT
1 ACTTTAAAATCTTTTTTTATTATT
4229038 A-TTTAAATATCTTTTT
1 ACTTTAAA-ATCTTTTT
4229054 ACCAACCCCC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
21 9 0.28
22 7 0.22
23 8 0.25
24 8 0.25
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (24 bp):
ACTTTAAAATCTTTTTTTATTATT
Found at i:4237165 original size:26 final size:26
Alignment explanation
Indices: 4237116--4237167 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
4237106 GTCTGACGTA
* *
4237116 GTAGTTTCTAGAAGGTCCAGTCAGCG
1 GTAGTTTCTAGAAGATCCACTCAGCG
*
4237142 GTAGTTTCTAGAAGATCTACTCAGCG
1 GTAGTTTCTAGAAGATCCACTCAGCG
4237168 CGCCTTCTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (26 bp):
GTAGTTTCTAGAAGATCCACTCAGCG
Found at i:4237573 original size:28 final size:28
Alignment explanation
Indices: 4237542--4237600 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
4237532 CCCTTAATAA
4237542 CTTCAGAATATCTCTCTCAATTTCTGCG
1 CTTCAGAATATCTCTCTCAATTTCTGCG
4237570 CTTCAGAATATCTCTCTCAATTTCTGCG
1 CTTCAGAATATCTCTCTCAATTTCTGCG
4237598 CTT
1 CTT
4237601 ACTTTTCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.20, C:0.29, G:0.10, T:0.41
Consensus pattern (28 bp):
CTTCAGAATATCTCTCTCAATTTCTGCG
Found at i:4240048 original size:24 final size:24
Alignment explanation
Indices: 4239995--4240048 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
4239985 CAACACTGCT
* * *
4239995 CATATAATTTGCATCGAAGTGCCA
1 CATAGAATATGCACCGAAGTGCCA
**
4240019 TGTAGAATATGCACCGAAGTGCCA
1 CATAGAATATGCACCGAAGTGCCA
4240043 CATAGA
1 CATAGA
4240049 TTTGTCCTGA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (24 bp):
CATAGAATATGCACCGAAGTGCCA
Found at i:4240085 original size:24 final size:24
Alignment explanation
Indices: 4240042--4240109 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
4240032 CCGAAGTGCC
** *
4240042 ACATAG-ATTTGTCCTGAAGGATA
1 ACATAGAATTTGTCCCAAAGGACA
*
4240065 ACATAGAATTTGTCCCAAAGGACC
1 ACATAGAATTTGTCCCAAAGGACA
* *
4240089 ACGTAGAAATTGTCCCGAAAG
1 ACATAGAATTTGTCCC-AAAG
4240110 ACTGCGTAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
23 6 0.16
24 27 0.73
25 4 0.11
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.24
Consensus pattern (24 bp):
ACATAGAATTTGTCCCAAAGGACA
Found at i:4240269 original size:15 final size:15
Alignment explanation
Indices: 4240251--4240302 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
4240241 CACATAGGGT
*
4240251 ATTTTCACGTACAAC
1 ATTTTCACATACAAC
4240266 ATTTTCA-ATTAGC-AC
1 ATTTTCACA-TA-CAAC
*
4240281 ATTTTCACATAGAAC
1 ATTTTCACATACAAC
4240296 ATTTTCA
1 ATTTTCA
4240303 TAAAAAAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 29 0.94
16 2 0.06
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.38
Consensus pattern (15 bp):
ATTTTCACATACAAC
Found at i:4250948 original size:30 final size:31
Alignment explanation
Indices: 4250893--4250954 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
4250883 ACATGTTAGA
* *
4250893 TTACATGTGTTTGGTTGATTTTTTTTTTCTT
1 TTACACGTATTTGGTTGATTTTTTTTTTCTT
4250924 TTACACGTATTTGGTTGA-TTTTTTTTTCTT
1 TTACACGTATTTGGTTGATTTTTTTTTTCTT
4250954 T
1 T
4250955 CTTTTTCAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 13 0.45
31 16 0.55
ACGTcount: A:0.11, C:0.08, G:0.15, T:0.66
Consensus pattern (31 bp):
TTACACGTATTTGGTTGATTTTTTTTTTCTT
Found at i:4251012 original size:17 final size:17
Alignment explanation
Indices: 4250992--4251063 Score: 74
Period size: 17 Copynumber: 4.1 Consensus size: 17
4250982 GAGCTCAAAA
4250992 TTGAGCTTCAATCGAGC
1 TTGAGCTTCAATCGAGC
*
4251009 TTGAG-TCTCGAGCTCGAGTC
1 TTGAGCT-TC-A-ATCGAG-C
4251029 TTGAGCTTCAATCGAGC
1 TTGAGCTTCAATCGAGC
* *
4251046 TCGAGCTTCAACCGAGC
1 TTGAGCTTCAATCGAGC
4251063 T
1 T
4251064 CCTGAGATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
16 1 0.02
17 24 0.52
18 6 0.13
19 6 0.13
20 8 0.17
21 1 0.02
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.28
Consensus pattern (17 bp):
TTGAGCTTCAATCGAGC
Found at i:4251019 original size:13 final size:13
Alignment explanation
Indices: 4251003--4251036 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
4250993 TGAGCTTCAA
4251003 TCGAGCTTGAGTC
1 TCGAGCTTGAGTC
*
4251016 TCGAGCTCGAGTC
1 TCGAGCTTGAGTC
*
4251029 TTGAGCTT
1 TCGAGCTT
4251037 CAATCGAGCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.15, C:0.24, G:0.29, T:0.32
Consensus pattern (13 bp):
TCGAGCTTGAGTC
Found at i:4251357 original size:55 final size:55
Alignment explanation
Indices: 4251271--4251378 Score: 207
Period size: 55 Copynumber: 2.0 Consensus size: 55
4251261 CGTATTTTTT
*
4251271 ATGGATTAGGGGTGTATTATTTGTCCGATATAAATATAAAGAGCATAAATATACG
1 ATGGATTAGGGGTGTATTATTTGTCCAATATAAATATAAAGAGCATAAATATACG
4251326 ATGGATTAGGGGTGTATTATTTGTCCAATATAAATATAAAGAGCATAAATATA
1 ATGGATTAGGGGTGTATTATTTGTCCAATATAAATATAAAGAGCATAAATATA
4251379 TGAAATTATC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.33
Consensus pattern (55 bp):
ATGGATTAGGGGTGTATTATTTGTCCAATATAAATATAAAGAGCATAAATATACG
Found at i:4255050 original size:2 final size:2
Alignment explanation
Indices: 4255043--4255094 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
4255033 ATAAAATAGG
* * *
4255043 GA GA GA GA AA GA GA GA GA GA GA GA GA GG GA GA GA GA GA GG GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4255085 GA GA GA GA GA
1 GA GA GA GA GA
4255095 AAGAAGAAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4255297 original size:29 final size:29
Alignment explanation
Indices: 4255263--4255321 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
4255253 CCTAAATTAA
4255263 TTTGATGCCATTGCTTACATCAATTTAGT
1 TTTGATGCCATTGCTTACATCAATTTAGT
*
4255292 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGCCATTGCTTACATCAATTTAGT
4255321 T
1 T
4255322 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.15, G:0.14, T:0.47
Consensus pattern (29 bp):
TTTGATGCCATTGCTTACATCAATTTAGT
Found at i:4259987 original size:29 final size:29
Alignment explanation
Indices: 4259953--4260011 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
4259943 CCTAAATTAA
4259953 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
4259982 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
4260011 T
1 T
4260012 ATGTGAAAAT
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:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:4261897 original size:82 final size:82
Alignment explanation
Indices: 4261806--4262048 Score: 206
Period size: 82 Copynumber: 3.0 Consensus size: 82
4261796 GCATTTGTTT
* * * *
4261806 ACAAACGCCGCAAAAGACTAGGA-ATTTTGTGGCGTTTTTCT-GTAAACGCCGCGATAGAGTATA
1 ACAAACGCCGCAAAAGACTAGGATA-GTAGTGGCGTTTTT-TAGTAAACACCGCGATAGAGTAGA
4261869 ACTATAGAGGCGTTTTCAA
64 ACTATAGAGGCGTTTTCAA
* * * * *
4261888 ACAATCGCCGTAAAAGATTTGGATAGTAGTGGCGTTTTTTAGTAAACATCGCGATAGAGTAGAAC
1 ACAAACGCCGCAAAAGACTAGGATAGTAGTGGCGTTTTTTAGTAAACACCGCGATAGAGTAGAAC
*
4261953 TATAGAGGCGTTATT-AG
66 TATAGAGGCGTT-TTCAA
* * * ** * * * * * * *
4261970 ATAAATGTCGGTATAGACGT-GGATAGTAGTGTCATTTTTTTGGTAAACATCGCTATAGAGTAGC
1 ACAAACGCCGCAAAAGAC-TAGGATAGTAGTGGC-GTTTTTTAGTAAACACCGCGATAGAGTAGA
*
4262034 ACTACAGAGGCGTTT
64 ACTATAGAGGCGTTT
4262049 GGTTTACAAA
Statistics
Matches: 132, Mismatches: 24, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
81 1 0.01
82 88 0.67
83 43 0.33
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (82 bp):
ACAAACGCCGCAAAAGACTAGGATAGTAGTGGCGTTTTTTAGTAAACACCGCGATAGAGTAGAAC
TATAGAGGCGTTTTCAA
Found at i:4270163 original size:21 final size:21
Alignment explanation
Indices: 4270139--4270196 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
4270129 CATTAACAAA
* *
4270139 AGCACAGAGAGAAGTAGCGGC
1 AGCACAGAGAGAAGCAGCGAC
* *
4270160 AGCACAAAGAGAAGCAGTGAC
1 AGCACAGAGAGAAGCAGCGAC
4270181 AGCACAGAGAGAAGCA
1 AGCACAGAGAGAAGCA
4270197 ACGTATCAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.45, C:0.19, G:0.33, T:0.03
Consensus pattern (21 bp):
AGCACAGAGAGAAGCAGCGAC
Found at i:4270660 original size:44 final size:42
Alignment explanation
Indices: 4270610--4270764 Score: 143
Period size: 44 Copynumber: 3.6 Consensus size: 42
4270600 TTGCGGTTGT
* ** *
4270610 GGCGTTTGTATCCTAAAAACGCCATTATATACCAAACATTTTAC
1 GGCGTTTGTATCCGAAAAACGCCGCTATATACCAGAC-TTTT-C
* * *
4270654 GGCGTTTATAT--GAAAAACGCTGCTATATACCAGACCTTTC
1 GGCGTTTGTATCCGAAAAACGCCGCTATATACCAGACTTTTC
* * *
4270694 GTGACGTTTGTATCCAAAAAACGTCGCTATATACCAGACCTTTTGT
1 G-G-CGTTTGTATCCGAAAAACGCCGCTATATACCAGA-CTTTT-C
*
4270740 GGTGTTTGTATCCGAAAAACGCCGC
1 GGCGTTTGTATCCGAAAAACGCCGC
4270765 AAAATATAAC
Statistics
Matches: 89, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
40 2 0.02
41 4 0.04
42 27 0.30
44 50 0.56
45 5 0.06
46 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (42 bp):
GGCGTTTGTATCCGAAAAACGCCGCTATATACCAGACTTTTC
Found at i:4270915 original size:43 final size:43
Alignment explanation
Indices: 4270822--4270958 Score: 123
Period size: 43 Copynumber: 3.2 Consensus size: 43
4270812 TGCATTTTTT
* * * * * *
4270822 CGGCGTTTTTGGGGAAAACGCCGCTAAATCTCAACACCAATTT
1 CGGCGTTTATGAGAAAAACGCCGCTAAATCTCAATACCTATTG
* * * * * *
4270865 TGTCGTTTGTGAGACAAGCGTCGCTAAATCTCAATACCTATTG
1 CGGCGTTTATGAGAAAAACGCCGCTAAATCTCAATACCTATTG
* * *
4270908 CGGCGTTTATGGGAAAAACGCCGCTATATCTC-GTCACCTATTG
1 CGGCGTTTATGAGAAAAACGCCGCTAAATCTCAAT-ACCTATTG
4270951 CGGCGTTT
1 CGGCGTTT
4270959 TTTGTTATCA
Statistics
Matches: 73, Mismatches: 20, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
42 1 0.01
43 72 0.99
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (43 bp):
CGGCGTTTATGAGAAAAACGCCGCTAAATCTCAATACCTATTG
Found at i:4281865 original size:13 final size:13
Alignment explanation
Indices: 4281847--4281871 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4281837 ACACTCAAGA
4281847 CAAGAAAAATGAG
1 CAAGAAAAATGAG
4281860 CAAGAAAAATGA
1 CAAGAAAAATGA
4281872 CCAAAAGGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.08, G:0.20, T:0.08
Consensus pattern (13 bp):
CAAGAAAAATGAG
Found at i:4282363 original size:10 final size:10
Alignment explanation
Indices: 4282348--4282387 Score: 62
Period size: 10 Copynumber: 3.8 Consensus size: 10
4282338 CATGGGTACC
4282348 TAAAAAAAAA
1 TAAAAAAAAA
4282358 TAAAAAAAAA
1 TAAAAAAAAA
4282368 TACAAAAAATAA
1 TA-AAAAAA-AA
4282380 TAAAAAAA
1 TAAAAAAA
4282388 TGGACAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 12 0.43
11 12 0.43
12 4 0.14
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (10 bp):
TAAAAAAAAA
Found at i:4282396 original size:21 final size:20
Alignment explanation
Indices: 4282352--4282406 Score: 69
Period size: 19 Copynumber: 2.7 Consensus size: 20
4282342 GGTACCTAAA
4282352 AAAAAATAA-AAAAAAATAC
1 AAAAAATAATAAAAAAATAC
4282371 AAAAAATAATAAAAAAATGGAC
1 AAAAAATAATAAAAAAAT--AC
4282393 -AAAAATAATTAAAA
1 AAAAAATAA-TAAAA
4282407 CGGGTTGCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.28
20 8 0.25
21 8 0.25
22 7 0.22
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.15
Consensus pattern (20 bp):
AAAAAATAATAAAAAAATAC
Found at i:4289853 original size:20 final size:20
Alignment explanation
Indices: 4289830--4289940 Score: 159
Period size: 20 Copynumber: 5.5 Consensus size: 20
4289820 TATGTAAATA
* *
4289830 GCAATGCGATTATGACTATC
1 GCAACGCGATTCTGACTATC
*
4289850 GCAACGCGATTTTGACTATC
1 GCAACGCGATTCTGACTATC
*
4289870 GCAACGAGATTCTGACTATC
1 GCAACGCGATTCTGACTATC
*
4289890 GCAACGCGATTCTGACTGTC
1 GCAACGCGATTCTGACTATC
*
4289910 GCAACGCGATGCTGACTATC
1 GCAACGCGATTCTGACTATC
*
4289930 GCAATGCGATT
1 GCAACGCGATT
4289941 TTCAAAGCGC
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 81 1.00
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (20 bp):
GCAACGCGATTCTGACTATC
Found at i:4289873 original size:60 final size:60
Alignment explanation
Indices: 4289793--4289938 Score: 159
Period size: 60 Copynumber: 2.4 Consensus size: 60
4289783 AATTCGCGTT
*
4289793 GCGATTTTCCGACTATCGCAATGCGAATATGTA-AATAGCAATGCGATTATGACTATCGCAAC
1 GCGATTTT--GACTATCGCAATGCGAATATG-ACAATAGCAACGCGATTATGACTATCGCAAC
* * * * * * * *
4289855 GCGATTTTGACTATCGCAACGAGATTCTGACTATCGCAACGCGATTCTGACTGTCGCAAC
1 GCGATTTTGACTATCGCAATGCGAATATGACAATAGCAACGCGATTATGACTATCGCAAC
**
4289915 GCGATGCTGACTATCGCAATGCGA
1 GCGATTTTGACTATCGCAATGCGA
4289939 TTTTCAAAGC
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
59 1 0.01
60 61 0.87
62 8 0.11
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (60 bp):
GCGATTTTGACTATCGCAATGCGAATATGACAATAGCAACGCGATTATGACTATCGCAAC
Found at i:4290156 original size:22 final size:22
Alignment explanation
Indices: 4290106--4290157 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
4290096 CACTCTCTAA
* *
4290106 GGCGACATCTGTCCCCATCTCC
1 GGCGAAATCAGTCCCCATCTCC
**
4290128 GATGAAATCAGTCCCCATCTCC
1 GGCGAAATCAGTCCCCATCTCC
4290150 GGCGAAAT
1 GGCGAAAT
4290158 ACGTCTATCT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.21
Consensus pattern (22 bp):
GGCGAAATCAGTCCCCATCTCC
Found at i:4290633 original size:20 final size:20
Alignment explanation
Indices: 4290527--4290633 Score: 110
Period size: 20 Copynumber: 5.5 Consensus size: 20
4290517 AGAATCGCAA
*
4290527 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCATTTTCGCGT
4290546 TGCGATTTTCA-TTTCGCGT
1 TGCGATTTTCATTTTCGCGT
** **
4290565 TGCGATAGTCAAATTCGCGT
1 TGCGATTTTCATTTTCGCGT
** *
4290585 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
* *
4290605 TGCGGTTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
4290625 TGCGATTTT
1 TGCGATTTT
4290634 AAGTTTCAGA
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
19 26 0.34
20 50 0.66
ACGTcount: A:0.13, C:0.17, G:0.24, T:0.46
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:4292257 original size:21 final size:21
Alignment explanation
Indices: 4292228--4292273 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
4292218 TGGTGCATGG
* *
4292228 CGTGTTGAGGT-GTCTACTTTA
1 CGTGGTGAGGTAG-CTACTCTA
4292249 CGTGGTGAGGTAGCTACTCTA
1 CGTGGTGAGGTAGCTACTCTA
4292270 CGTG
1 CGTG
4292274 AGATGGTAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.15, C:0.17, G:0.33, T:0.35
Consensus pattern (21 bp):
CGTGGTGAGGTAGCTACTCTA
Found at i:4292568 original size:20 final size:20
Alignment explanation
Indices: 4292537--4292604 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
4292527 TAGTTTACTT
*
4292537 TCGCAACACGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
4292557 TTGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
** *
4292577 TCGCAACGCGAATTTGATTA
1 TCGCAACGCGAAAATGACTA
4292597 TCGCAACG
1 TCGCAACG
4292605 AAAGAATCGC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:4294726 original size:13 final size:14
Alignment explanation
Indices: 4294678--4294716 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
4294668 TTGCTTGTTT
*
4294678 AATTGATTTATAAA
1 AATTGATTTGTAAA
4294692 AATTGATTTGTAAA
1 AATTGATTTGTAAA
4294706 AATTGATTTGT
1 AATTGATTTGT
4294717 TTAATTGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:4294825 original size:20 final size:20
Alignment explanation
Indices: 4294800--4294852 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
4294790 AGGTACACTT
* *
4294800 TCGCAATGCTAAACTCAAAA
1 TCGCAATGCGAAACACAAAA
*
4294820 TCGCAATGCGAAAGACAAAA
1 TCGCAATGCGAAACACAAAA
*
4294840 TCGCAACGCGAAA
1 TCGCAATGCGAAA
4294853 GTCAATTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.25, G:0.17, T:0.13
Consensus pattern (20 bp):
TCGCAATGCGAAACACAAAA
Found at i:4294906 original size:34 final size:34
Alignment explanation
Indices: 4294862--4294986 Score: 110
Period size: 34 Copynumber: 3.5 Consensus size: 34
4294852 AGTCAATTCG
* * *
4294862 CGTTGTGATAGTCTAATACGCTTTGCGATTTTCT
1 CGTTGCGATAGTCAAATACGCATTGCGATTTTCT
*
4294896 CGTTGCGATAGTCAAATACCCATTGCGATACTCAAATTCGT
1 CGTTGCGATAGTCAAATACGCATTGCGAT--T----TTC-T
*
4294937 -GTTGCGATAGTCAAAT-CTGCGTTGCGATTTTCT
1 CGTTGCGATAGTCAAATAC-GCATTGCGATTTTCT
*
4294970 CATTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
4294987 TTGCGTTACG
Statistics
Matches: 75, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
33 1 0.01
34 43 0.57
36 1 0.01
38 1 0.01
39 1 0.01
40 27 0.36
41 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATACGCATTGCGATTTTCT
Found at i:4294960 original size:20 final size:19
Alignment explanation
Indices: 4294896--4295120 Score: 121
Period size: 20 Copynumber: 11.9 Consensus size: 19
4294886 GCGATTTTCT
**
4294896 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAAT-TG
* *
4294916 CATTGCGATACTCAAATTCG
1 CGTTGCGATAGTCAAATT-G
*
4294936 TGTTGCGATAGTCAAATCTG
1 CGTTGCGATAGTCAAAT-TG
**
4294956 CGTTGCGATTTTC----T-
1 CGTTGCGATAGTCAAATTG
*
4294970 CATTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAA-TTG
* *
4294990 CGTTACGATAGACAAATTCG
1 CGTTGCGATAGTCAAATT-G
*
4295010 CGTTGCGATAGTCATATT-
1 CGTTGCGATAGTCAAATTG
4295028 CATGTTGCGATAGTCAAATTCG
1 C--GTTGCGATAGTCAAATT-G
*
4295050 CGTTGCGAT--T---TTTG
1 CGTTGCGATAGTCAAATTG
* * * *
4295064 AGTTGAGATAATCAAATTCA
1 CGTTGCGATAGTCAAATT-G
*
4295084 CGTTGTGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATT-G
*
4295104 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
4295121 GAATGTGTAA
Statistics
Matches: 155, Mismatches: 31, Indels: 38
0.69 0.14 0.17
Matches are distributed among these distances:
14 18 0.12
15 3 0.02
16 1 0.01
18 2 0.01
19 5 0.03
20 124 0.80
21 1 0.01
22 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (19 bp):
CGTTGCGATAGTCAAATTG
Found at i:4294962 original size:40 final size:40
Alignment explanation
Indices: 4294896--4295120 Score: 149
Period size: 40 Copynumber: 5.9 Consensus size: 40
4294886 GCGATTTTCT
* * *
4294896 CGTTGCGATAGTCAAATAC-CCATTGCGATACTCAAATTCG
1 CGTTGCGATAGTCAAAT-CTGCGTTGCGATAGTCAAATTCG
* *
4294936 TGTTGCGATAGTCAAATCTGCGTTGCGAT--T----TTCT
1 CGTTGCGATAGTCAAATCTGCGTTGCGATAGTCAAATTCG
* * * *
4294970 CATTGCGATAGTCAAATTTGCGTTACGATAGACAAATTCG
1 CGTTGCGATAGTCAAATCTGCGTTGCGATAGTCAAATTCG
*
4295010 CGTTGCGATAGTCATAT-T-CATGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATCTGC--GTTGCGATAGTCAAATTCG
* * * * *
4295050 CGTTGCGAT--T----TTTGAGTTGAGATAATCAAATTCA
1 CGTTGCGATAGTCAAATCTGCGTTGCGATAGTCAAATTCG
* *
4295084 CGTTGTGATAGTCAAAT-TCGCGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAATCT-GCGTTGCGATAGTCAAAT
4295121 GAATGTGTAA
Statistics
Matches: 145, Mismatches: 22, Indels: 36
0.71 0.11 0.18
Matches are distributed among these distances:
34 53 0.37
35 1 0.01
36 1 0.01
38 3 0.02
39 3 0.02
40 84 0.58
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (40 bp):
CGTTGCGATAGTCAAATCTGCGTTGCGATAGTCAAATTCG
Found at i:4294977 original size:74 final size:74
Alignment explanation
Indices: 4294856--4295023 Score: 212
Period size: 74 Copynumber: 2.3 Consensus size: 74
4294846 CGCGAAAGTC
* * * * *
4294856 AATTCGCGTTGTGATAGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAATACCCATTG
1 AATTCGCGTTGCGATAGTCAAATACGCGTTGCGATTTTCTCATTGCGATAGTCAAATACCCATTA
*
4294921 CGATACTCA
66 CGATACACA
* *** *
4294930 AATTCGTGTTGCGATAGTCAAAT-CTGCGTTGCGATTTTCTCATTGCGATAGTCAAATTTGCGTT
1 AATTCGCGTTGCGATAGTCAAATAC-GCGTTGCGATTTTCTCATTGCGATAGTCAAATACCCATT
*
4294994 ACGATAGACA
65 ACGATACACA
4295004 AATTCGCGTTGCGATAGTCA
1 AATTCGCGTTGCGATAGTCA
4295024 TATTCATGTT
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
73 1 0.01
74 79 0.99
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.35
Consensus pattern (74 bp):
AATTCGCGTTGCGATAGTCAAATACGCGTTGCGATTTTCTCATTGCGATAGTCAAATACCCATTA
CGATACACA
Found at i:4294978 original size:54 final size:54
Alignment explanation
Indices: 4294916--4295018 Score: 145
Period size: 54 Copynumber: 1.9 Consensus size: 54
4294906 GTCAAATACC
* * *
4294916 CATTGCGATACTCAAATTCGTGTTGCGATAGTCAAA-TCTGCGTTGCGATTTTCT
1 CATTGCGATACTCAAATTCGCGTTACGATAGACAAATTC-GCGTTGCGATTTTCT
* *
4294970 CATTGCGATAGTCAAATTTGCGTTACGATAGACAAATTCGCGTTGCGAT
1 CATTGCGATACTCAAATTCGCGTTACGATAGACAAATTCGCGTTGCGAT
4295019 AGTCATATTC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
54 41 0.95
55 2 0.05
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.34
Consensus pattern (54 bp):
CATTGCGATACTCAAATTCGCGTTACGATAGACAAATTCGCGTTGCGATTTTCT
Found at i:4295079 original size:94 final size:94
Alignment explanation
Indices: 4294918--4295120 Score: 266
Period size: 94 Copynumber: 2.2 Consensus size: 94
4294908 CAAATACCCA
* * *
4294918 TTGCGATACTCAAATTCGTGTTGCGATAGTCAAATCTGCGTTGCGATTTTCTCATTGCGATAGTC
1 TTGCGATACTCAAATTCATGTTGCGATAGTCAAATCTGCGTTGCGATTTTCTCATTGAGATAATC
**
4294983 AAATTTGCGTTACGATAGACAAATTCGCG
66 AAATTCACGTTACGATAGACAAATTCGCG
* * *
4295012 TTGCGATAGTCATATTCATGTTGCGATAGTCAAAT-TCGCGTTGCGATTTT-TGAGTTGAGATAA
1 TTGCGATACTCAAATTCATGTTGCGATAGTCAAATCT-GCGTTGCGATTTTCTCA-TTGAGATAA
** *
4295075 TCAAATTCACGTTGTGATAGTCAAATTCGCG
64 TCAAATTCACGTTACGATAGACAAATTCGCG
*
4295106 TTGCGATATTCAAAT
1 TTGCGATACTCAAAT
4295121 GAATGTGTAA
Statistics
Matches: 94, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
93 3 0.03
94 91 0.97
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (94 bp):
TTGCGATACTCAAATTCATGTTGCGATAGTCAAATCTGCGTTGCGATTTTCTCATTGAGATAATC
AAATTCACGTTACGATAGACAAATTCGCG
Found at i:4295437 original size:18 final size:18
Alignment explanation
Indices: 4295414--4295448 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4295404 AAGCCGGTTG
4295414 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
4295432 TGATTGCGATTTTGATT
1 TGATTGAGATTTTGATT
4295449 GCCTTTTTCT
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:0.20, C:0.03, G:0.23, T:0.54
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:4297730 original size:24 final size:24
Alignment explanation
Indices: 4297696--4297749 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
4297686 CTGAAACATC
4297696 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
4297720 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
4297744 ATCAAA
1 ATCAAA
4297750 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:4298595 original size:20 final size:20
Alignment explanation
Indices: 4298570--4298656 Score: 129
Period size: 20 Copynumber: 4.3 Consensus size: 20
4298560 GAAATTCAGT
4298570 GTTGCGACAGTCAGAATCGC
1 GTTGCGACAGTCAGAATCGC
4298590 GTTGCGACAGTCAGAATCGC
1 GTTGCGACAGTCAGAATCGC
*
4298610 GTTGCGATAGTCAGAATCGC
1 GTTGCGACAGTCAGAATCGC
* * *
4298630 ATTGCGATAGTCATAATCGC
1 GTTGCGACAGTCAGAATCGC
*
4298650 ATTGCGA
1 GTTGCGA
4298657 TTTACATATT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (20 bp):
GTTGCGACAGTCAGAATCGC
Found at i:4298657 original size:20 final size:20
Alignment explanation
Indices: 4298571--4298721 Score: 119
Period size: 20 Copynumber: 7.5 Consensus size: 20
4298561 AAATTCAGTG
* * *
4298571 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCATAATCGCA
* * *
4298591 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCATAATCGCA
*
4298611 TTGCGATAGTCAGAATCGCA
1 TTGCGATAGTCATAATCGCA
4298631 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCATAATCGCA
* * *
4298651 TTGCGAT-TTACATATTCGTA
1 TTGCGATAGT-CATAATCGCA
* * *
4298671 TTGCGAT-TTACATATTTGCA
1 TTGCGATAGT-CATAATCGCA
* *
4298691 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CATAATCGCA
4298711 TTGCGATAGTC
1 TTGCGATAGTC
4298722 GGAAAATAAC
Statistics
Matches: 119, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
19 1 0.01
20 117 0.98
21 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCATAATCGCA
Found at i:4298674 original size:40 final size:40
Alignment explanation
Indices: 4298586--4298721 Score: 141
Period size: 40 Copynumber: 3.4 Consensus size: 40
4298576 ACAGTCAGAA
* * * * * * *
4298586 TCGCGTTGCGACAGTCAGAATCGCGTTGCGATAGT-CAGAA
1 TCGCATTGCGATAGTCATAATCGCATTGCGAT-TTACATAT
4298626 TCGCATTGCGATAGTCATAATCGCATTGCGATTTACATAT
1 TCGCATTGCGATAGTCATAATCGCATTGCGATTTACATAT
* * * *
4298666 TCGTATTGCGAT-TTACATATTTGCATTGCGATTTACATAT
1 TCGCATTGCGATAGT-CATAATCGCATTGCGATTTACATAT
4298706 TCGCATTGCGATAGTC
1 TCGCATTGCGATAGTC
4298722 GGAAAATAAC
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
39 2 0.03
40 77 0.96
41 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (40 bp):
TCGCATTGCGATAGTCATAATCGCATTGCGATTTACATAT
Found at i:4299694 original size:35 final size:37
Alignment explanation
Indices: 4299653--4299723 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
4299643 TATACATGGA
4299653 TTTATTGA-TTTTT-TATATCATTATACCTTGATTCC
1 TTTATTGATTTTTTATATATCATTATACCTTGATTCC
4299688 TTTATTGATTTTTTATATATCATTATACCTTGATTC
1 TTTATTGATTTTTTATATATCATTATACCTTGATTC
4299724 GTCATCTCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
35 8 0.24
36 5 0.15
37 21 0.62
ACGTcount: A:0.24, C:0.13, G:0.06, T:0.58
Consensus pattern (37 bp):
TTTATTGATTTTTTATATATCATTATACCTTGATTCC
Done.