Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002881.1 Hibiscus syriacus cultivar Beakdansim tig00005939_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: 1746118
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 9
Found at i:398426 original size:59 final size:59
Alignment explanation
Indices: 398354--398474 Score: 242
Period size: 59 Copynumber: 2.1 Consensus size: 59
398344 AAATAGCAAT
398354 TTTACCATTATTGTGTTGTAGAACAGTATGATCAGACTGGGTCTGAGTGTAACATGTTG
1 TTTACCATTATTGTGTTGTAGAACAGTATGATCAGACTGGGTCTGAGTGTAACATGTTG
398413 TTTACCATTATTGTGTTGTAGAACAGTATGATCAGACTGGGTCTGAGTGTAACATGTTG
1 TTTACCATTATTGTGTTGTAGAACAGTATGATCAGACTGGGTCTGAGTGTAACATGTTG
398472 TTT
1 TTT
398475 CAGCTCTCGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.39
Consensus pattern (59 bp):
TTTACCATTATTGTGTTGTAGAACAGTATGATCAGACTGGGTCTGAGTGTAACATGTTG
Found at i:401892 original size:20 final size:21
Alignment explanation
Indices: 401862--401902 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
401852 ACTAATAGAA
*
401862 TAAAAACTGATTCTATCTAAT
1 TAAAAACTGATCCTATCTAAT
401883 TAAAAA-TGATCCTATCTAAT
1 TAAAAACTGATCCTATCTAAT
401903 ATTTAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.37
Consensus pattern (21 bp):
TAAAAACTGATCCTATCTAAT
Found at i:409802 original size:40 final size:40
Alignment explanation
Indices: 409742--409827 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
409732 TGTAAAGAAG
* *
409742 TTTGAAGGATTGAATGTTATGCTTTCACTCTTGATAGTAT
1 TTTGATGGATTGAATGTTATGCTTTCACTCTTCATAGTAT
* * * *
409782 TTTGATGGATTGGATTTTATGCTTTCCCTCTTCATGGTAT
1 TTTGATGGATTGAATGTTATGCTTTCACTCTTCATAGTAT
409822 TTTGAT
1 TTTGAT
409828 CCAACCTTAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.49
Consensus pattern (40 bp):
TTTGATGGATTGAATGTTATGCTTTCACTCTTCATAGTAT
Found at i:416090 original size:16 final size:16
Alignment explanation
Indices: 416069--416100 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
416059 CATATACAGT
416069 AGAACATGTAATAGAA
1 AGAACATGTAATAGAA
416085 AGAACATGTAATAGAA
1 AGAACATGTAATAGAA
416101 GAGTTGATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.19, T:0.19
Consensus pattern (16 bp):
AGAACATGTAATAGAA
Found at i:417041 original size:21 final size:21
Alignment explanation
Indices: 417017--417096 Score: 83
Period size: 21 Copynumber: 3.9 Consensus size: 21
417007 CTTTGTAATG
*
417017 AACCTTAAATCCTAAACCCTA
1 AACCTTAAATCATAAACCCTA
***
417038 AACCTTAAA-CATAAATAATA
1 AACCTTAAATCATAAACCCTA
*
417058 AACCTTAAATTATAAACCCTA
1 AACCTTAAATCATAAACCCTA
*
417079 AACCCTAAATTC-TAAACC
1 AACCTTAAA-TCATAAACC
417097 ATTAATCCGA
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 16 0.34
21 30 0.64
22 1 0.02
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.25
Consensus pattern (21 bp):
AACCTTAAATCATAAACCCTA
Found at i:417417 original size:13 final size:14
Alignment explanation
Indices: 417401--417429 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
417391 AACTAAAAAG
417401 AAGAA-GTAAATAT
1 AAGAACGTAAATAT
417414 AAGAACGTAAATAT
1 AAGAACGTAAATAT
417428 AA
1 AA
417430 TTAACATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.62, C:0.03, G:0.14, T:0.21
Consensus pattern (14 bp):
AAGAACGTAAATAT
Found at i:418699 original size:23 final size:23
Alignment explanation
Indices: 418673--418720 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
418663 TGAATAAAGC
*
418673 TTAAAATCGAGCTTGAAACGAGT
1 TTAAAATCGAGCTTCAAACGAGT
* *
418696 TTAAAATTGAGCTTCAATCGAGT
1 TTAAAATCGAGCTTCAAACGAGT
418719 TT
1 TT
418721 GAGTATTGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
TTAAAATCGAGCTTCAAACGAGT
Found at i:421106 original size:20 final size:22
Alignment explanation
Indices: 421055--421103 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
421045 AAACAAGTAA
421055 GAAAAAATATTGAATTTAGTTT
1 GAAAAAATATTGAATTTAGTTT
421077 GAAAAAATATTGAATTTA-TTT
1 GAAAAAATATTGAATTTAGTTT
*
421098 TAAAAA
1 GAAAAA
421104 TATAGAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (22 bp):
GAAAAAATATTGAATTTAGTTT
Found at i:421805 original size:198 final size:200
Alignment explanation
Indices: 421465--421862 Score: 782
Period size: 198 Copynumber: 2.0 Consensus size: 200
421455 TTATCAGCAT
421465 TCAGAAATAAAACAAACTTTCAGACTCGTATATAAAAAAAATACAATTACATGCCCCCTAATCAC
1 TCAGAAATAAAACAAACTTTCAGACTCGTATATAAAAAAAATACAATTACATGCCCCCTAATCAC
421530 ATGTACTATACTCTGCAAGCAATGAGGAAAGAACTCCCTTACTGAAATCGATAGCTACACTGGTA
66 ATGTACTATACTCTGCAAGCAATGAGGAAAGAACTCCCTTACTGAAATCGATAGCTACACTGGTA
421595 CAATCCTTTTAACCTGTCATGGTGAGTAATAGAATGAGCTTTGGAAAGCTCAGTAATACAAAACT
131 CAATCCTTTTAACCTGTCATGGTGAGTAATAGAATGAGCTTTGGAAAGCTCAGTAATACAAAACT
421660 ACCAG
196 ACCAG
421665 TCAGAAATAAAACAAACTTTCAGACTCGTATA-AAAAAAAATACAATTACATGCCCCCTAA-CAC
1 TCAGAAATAAAACAAACTTTCAGACTCGTATATAAAAAAAATACAATTACATGCCCCCTAATCAC
421728 ATGTACTATACTCTGCAAGCAATGAGGAAAGAACTCCCTTACTGAAATCGATAGCTACACTGGTA
66 ATGTACTATACTCTGCAAGCAATGAGGAAAGAACTCCCTTACTGAAATCGATAGCTACACTGGTA
421793 CAATCCTTTTAACCTGTCATGGTGAGTAATAGAATGAGCTTTGGAAAGCTCAGTAATACAAAACT
131 CAATCCTTTTAACCTGTCATGGTGAGTAATAGAATGAGCTTTGGAAAGCTCAGTAATACAAAACT
421858 ACCAG
196 ACCAG
421863 ATGATGCTAC
Statistics
Matches: 198, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
198 138 0.70
199 28 0.14
200 32 0.16
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (200 bp):
TCAGAAATAAAACAAACTTTCAGACTCGTATATAAAAAAAATACAATTACATGCCCCCTAATCAC
ATGTACTATACTCTGCAAGCAATGAGGAAAGAACTCCCTTACTGAAATCGATAGCTACACTGGTA
CAATCCTTTTAACCTGTCATGGTGAGTAATAGAATGAGCTTTGGAAAGCTCAGTAATACAAAACT
ACCAG
Found at i:428288 original size:83 final size:83
Alignment explanation
Indices: 428149--428315 Score: 334
Period size: 83 Copynumber: 2.0 Consensus size: 83
428139 CTAAGGATAC
428149 AACCGTAAACTAGTGAAGAACAAAGTTTCTTATTTGGCACTAGGTTAACTGTTTCAACAATCTCA
1 AACCGTAAACTAGTGAAGAACAAAGTTTCTTATTTGGCACTAGGTTAACTGTTTCAACAATCTCA
428214 GAAAAGATAATCTCGGAA
66 GAAAAGATAATCTCGGAA
428232 AACCGTAAACTAGTGAAGAACAAAGTTTCTTATTTGGCACTAGGTTAACTGTTTCAACAATCTCA
1 AACCGTAAACTAGTGAAGAACAAAGTTTCTTATTTGGCACTAGGTTAACTGTTTCAACAATCTCA
428297 GAAAAGATAATCTCGGAA
66 GAAAAGATAATCTCGGAA
428315 A
1 A
428316 GGTTTATTTT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 84 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.28
Consensus pattern (83 bp):
AACCGTAAACTAGTGAAGAACAAAGTTTCTTATTTGGCACTAGGTTAACTGTTTCAACAATCTCA
GAAAAGATAATCTCGGAA
Found at i:429684 original size:21 final size:21
Alignment explanation
Indices: 429602--429685 Score: 64
Period size: 21 Copynumber: 3.9 Consensus size: 21
429592 CAGAACCCCA
*
429602 GGGGGGTATCGATTCCC-C-T
1 GGGGGGGATCGATTCCCTCAT
* *
429621 GTGGGGGGAATCGGTTCCCCTTCAA
1 G-GGGGGG-ATCGATT-CCC-TCAT
* * *
429646 AGGGGGAATCGGTTCCCTCAT
1 GGGGGGGATCGATTCCCTCAT
429667 GGGGGGGATCGATTCCCTC
1 GGGGGGGATCGATTCCCTC
429686 TGCACCAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
19 1 0.02
20 5 0.10
21 25 0.50
22 6 0.12
23 7 0.14
24 6 0.12
ACGTcount: A:0.14, C:0.25, G:0.37, T:0.24
Consensus pattern (21 bp):
GGGGGGGATCGATTCCCTCAT
Found at i:443292 original size:32 final size:32
Alignment explanation
Indices: 443222--443344 Score: 126
Period size: 32 Copynumber: 3.9 Consensus size: 32
443212 TCGACAACTA
* * * *
443222 TCCATAGGTCCCAAAGAACCTAGGTAA-ATTG
1 TCCATATGTCCCGAAGAACATAGGTAACACTG
* **
443253 TCCATATGTTCCTTAGAACATAGGTAATCA-TG
1 TCCATATGTCCCGAAGAACATAGGTAA-CACTG
*
443285 TCCATATGTCCCGAAGGACATAGGTAACACTG
1 TCCATATGTCCCGAAGAACATAGGTAACACTG
*
443317 TCCATATGTCTCGAA-AGACATAGGTAAC
1 TCCATATGTCCCGAAGA-ACATAGGTAAC
443345 CCTCAACTCT
Statistics
Matches: 77, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
31 24 0.31
32 52 0.68
33 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (32 bp):
TCCATATGTCCCGAAGAACATAGGTAACACTG
Found at i:443340 original size:64 final size:63
Alignment explanation
Indices: 443222--443343 Score: 147
Period size: 63 Copynumber: 1.9 Consensus size: 63
443212 TCGACAACTA
* * **
443222 TCCATAGGTCCCAAAGAACCTAGGTAAATTGTCCATATGTTCCTTAGAACATAGGTAATCATG
1 TCCATAGGTCCCAAAGAACATAGGTAAACTGTCCATATGTTCCAAAGAACATAGGTAATCATG
* * * *
443285 TCCATATGTCCCGAAGGACATAGGTAACACTGTCCATATGTCTCGAAAG-ACATAGGTAA
1 TCCATAGGTCCCAAAGAACATAGGTAA-ACTGTCCATATGT-TCCAAAGAACATAGGTAA
443344 CCCTCAACTC
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
63 23 0.47
64 22 0.45
65 4 0.08
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (63 bp):
TCCATAGGTCCCAAAGAACATAGGTAAACTGTCCATATGTTCCAAAGAACATAGGTAATCATG
Found at i:447449 original size:68 final size:68
Alignment explanation
Indices: 447364--447502 Score: 278
Period size: 68 Copynumber: 2.0 Consensus size: 68
447354 GTGTGATTGC
447364 TTCGGCAACCGCAAGACGGCCGATGATAAGCGACGGCTCCAATGGTACTACTGCCGTCGGTTTCA
1 TTCGGCAACCGCAAGACGGCCGATGATAAGCGACGGCTCCAATGGTACTACTGCCGTCGGTTTCA
447429 CGT
66 CGT
447432 TTCGGCAACCGCAAGACGGCCGATGATAAGCGACGGCTCCAATGGTACTACTGCCGTCGGTTTCA
1 TTCGGCAACCGCAAGACGGCCGATGATAAGCGACGGCTCCAATGGTACTACTGCCGTCGGTTTCA
447497 CGT
66 CGT
447500 TTC
1 TTC
447503 CAATACTCAA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 71 1.00
ACGTcount: A:0.22, C:0.29, G:0.27, T:0.22
Consensus pattern (68 bp):
TTCGGCAACCGCAAGACGGCCGATGATAAGCGACGGCTCCAATGGTACTACTGCCGTCGGTTTCA
CGT
Found at i:449986 original size:35 final size:35
Alignment explanation
Indices: 449947--450016 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
449937 TTTTGGATAT
449947 TTGAATTTTGTGTTTGGATATTTTATTAACTAATA
1 TTGAATTTTGTGTTTGGATATTTTATTAACTAATA
449982 TTGAATTTTGTGTTTGGATATTTTATTAACTAATA
1 TTGAATTTTGTGTTTGGATATTTTATTAACTAATA
450017 AAATAAAGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.03, G:0.14, T:0.54
Consensus pattern (35 bp):
TTGAATTTTGTGTTTGGATATTTTATTAACTAATA
Found at i:451664 original size:17 final size:16
Alignment explanation
Indices: 451642--451675 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
451632 TAAAAACAGT
451642 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
451659 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
451675 A
1 A
451676 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:455516 original size:19 final size:20
Alignment explanation
Indices: 455494--455537 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
455484 GAGAAAAGGT
455494 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
455513 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
455533 AAAAG
1 AAAAG
455538 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Found at i:461902 original size:17 final size:16
Alignment explanation
Indices: 461880--461913 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
461870 TAAAAACAGT
461880 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
461897 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
461913 A
1 A
461914 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:466384 original size:16 final size:16
Alignment explanation
Indices: 466363--466398 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
466353 TATGTTTGGC
*
466363 TTGAAAGTTGGTAAAG
1 TTGAAAGTTGGAAAAG
466379 TTGAAAGTTGGAAAAG
1 TTGAAAGTTGGAAAAG
466395 TTGA
1 TTGA
466399 CATCTTTGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.31
Consensus pattern (16 bp):
TTGAAAGTTGGAAAAG
Found at i:466433 original size:42 final size:40
Alignment explanation
Indices: 466399--466486 Score: 117
Period size: 39 Copynumber: 2.2 Consensus size: 40
466389 GAAAAGTTGA
* *
466399 CATCTTTGGTTGGT-GCTAACTTGTACACATTGGAAAATT
1 CATCTTTGGTAGGTGGCCAACTTGTACACATTGGAAAATT
* * *
466438 CATCTTTGGTAGGTGGCCAACTTGTGCACA-TGGGAATTT
1 CATCTTTGGTAGGTGGCCAACTTGTACACATTGGAAAATT
466477 CATCTTTGGT
1 CATCTTTGGT
466487 CCCTAAAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
39 30 0.70
40 13 0.30
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.38
Consensus pattern (40 bp):
CATCTTTGGTAGGTGGCCAACTTGTACACATTGGAAAATT
Found at i:474094 original size:17 final size:16
Alignment explanation
Indices: 474052--474150 Score: 57
Period size: 15 Copynumber: 6.3 Consensus size: 16
474042 CTGAAACAAT
474052 TATAATATATACATATA
1 TATAATATATA-ATATA
474069 TA-AACTATATAATA-A
1 TATAA-TATATAATATA
*
474084 TATAATATAT-ATAAA
1 TATAATATATAATATA
* * *
474099 CTCT-ATATATTATGTA
1 -TATAATATATAATATA
* *
474115 TA-AACTATATAGTTTA
1 TATAA-TATATAATATA
*
474131 T-TAATATAAAATATA
1 TATAATATATAATATA
474146 TATAA
1 TATAA
474151 ACTATATAGT
Statistics
Matches: 63, Mismatches: 10, Indels: 19
0.68 0.11 0.21
Matches are distributed among these distances:
14 3 0.05
15 26 0.41
16 26 0.41
17 8 0.13
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (16 bp):
TATAATATATAATATA
Found at i:474116 original size:20 final size:20
Alignment explanation
Indices: 474064--474276 Score: 79
Period size: 20 Copynumber: 11.2 Consensus size: 20
474054 TAATATATAC
474064 ATATATAA-ACTATAT-AA-T
1 ATATATAATA-TATATAAACT
474082 A-ATATAATATATATAAACT
1 ATATATAATATATATAAACT
* * *
474101 CTATATATTATGTATAAACT
1 ATATATAATATATATAAACT
474121 ATATAGT--T-TAT-T-AA-T
1 ATATA-TAATATATATAAACT
474136 ATA-A-AATATATATAAACT
1 ATATATAATATATATAAACT
* *
474154 ATATAGT-GTATATATAAAGT
1 ATATA-TAATATATATAAACT
* * *
474174 ATACATACTATGTATAAACT
1 ATATATAATATATATAAACT
* *
474194 AGAGT-T--TATATATGAACT
1 ATA-TATAATATATATAAACT
*
474212 AT-TGA-ACTATATATAAACT
1 ATAT-ATAATATATATAAACT
* * *
474231 ATATAGT-TTAAATATAAATT
1 ATATA-TAATATATATAAACT
*
474251 ATATATAAATTATATTTAAA-T
1 ATATAT-AA-TATATATAAACT
474272 ATATA
1 ATATA
474277 ATCTTATATT
Statistics
Matches: 146, Mismatches: 23, Indels: 49
0.67 0.11 0.22
Matches are distributed among these distances:
14 2 0.01
15 7 0.05
16 4 0.03
17 14 0.10
18 21 0.14
19 19 0.13
20 64 0.44
21 7 0.05
22 8 0.05
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (20 bp):
ATATATAATATATATAAACT
Found at i:474224 original size:2 final size:2
Alignment explanation
Indices: 474219--474897 Score: 71
Period size: 2 Copynumber: 340.0 Consensus size: 2
474209 ACTATTGAAC
* * * * *
474219 TA TA TA TA AA CTA TA TA GTT TA AA TA TA AA T- TA TA TA TA AA T-
1 TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
474261 TA TA TT TA AA TA TA TA -A TC T- TA TA TT TA TA TA T- TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
474300 TA -A T- TA TA AA T- TA TA TA TA CTA TG TA TA AA T- TA GA TA GTT
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA
* * * *
474340 TA TA TA GTT TA AA TA TA AA GTA TA TA -A GTA TA TA TA TA AA CTA
1 TA TA TA -TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA -TA
* * * *
474383 TA AA T- TA TA TA TA TA TA AA GCA TA TA TA CA TA TA TA -A TA -A
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* *
474423 TA TA AA GTA TA -A GTA TA T- TA TA TA TA TA AA GTA TA -A T- TA
1 TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * * * *
474462 TA AA GA -A TA AA GTA TA TA AA GTA TA TA TA CA TA TA TA -A TA -A
1 TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* *
474503 TA TA AA GGA TA -A GTA TA T- TA TA TA TA TA TA TA TA TA -A GTA
1 TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* ** * * *
474543 TA -A T- TA TA AA GGC TA AA GTA TA TA -A GCA TA TA -A TA TA AA
1 TA TA TA TA TA TA -TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA
* * *
474582 GTA TA TA -A GTA TA TA -A TA TA AA CTA TA TA AA TA TA TA AA T-
1 -TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * *
474622 TA TA TA -A TA TA -A AA GTA TA TA CA TT TA TA AA GTA TA -A GTA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA -TA
* * * *
474662 TA T- TA TA TA TA TA TA AA GTA TA -A T- TA TA AA GA CTA AA GTA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA -TA
** *
474702 TA TA GG TA TA TA -A TA TA AA GTA 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
* * *
474744 TA AA GT- TT TA GTA TA TA -A TA TA AA GTA TA -A GTA TA -A GTA TA
1 TA TA -TA TA TA -TA TA TA TA TA TA TA -TA TA TA -TA TA TA -TA TA
* * * *
474785 TA TA TA AA CTA TA AA GTA TA AA TA TA TA -A GTA TA TA TA TA AA
1 TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * *
474827 CTA TA AA GTA TA TA -A GTA TA T- TA CA TA TA AA GTA TA -A GTA TA
1 -TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA -TA TA
* *
474869 TT TA TA TA TA TA AA GTA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
474898 AGTTATAAGT
Statistics
Matches: 470, Mismatches: 118, Indels: 178
0.61 0.15 0.23
Matches are distributed among these distances:
1 45 0.10
2 381 0.81
3 44 0.09
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (2 bp):
TA
Found at i:474256 original size:11 final size:11
Alignment explanation
Indices: 474242--474276 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
474232 TATAGTTTAA
474242 ATATAAATTAT
1 ATATAAATTAT
474253 ATATAAATTAT
1 ATATAAATTAT
*
474264 ATTTAAA-TAT
1 ATATAAATTAT
474274 ATA
1 ATA
474277 ATCTTATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 5 0.23
11 17 0.77
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATATAAATTAT
Found at i:474276 original size:50 final size:50
Alignment explanation
Indices: 474220--474315 Score: 117
Period size: 50 Copynumber: 1.9 Consensus size: 50
474210 CTATTGAACT
474220 ATATATAAACTATATAGTTTAAATATAAAT-TAT-A-TATAAATTATATTTAA
1 ATATATAAACT-TATA-TTTAAATAT-AATGTATAATTATAAATTATATTTAA
* * *
474270 ATATATAATCTTATATTTATATATTATGTATAATTATAAATTATAT
1 ATATATAAACTTATATTTAAATATAATGTATAATTATAAATTATAT
474316 ATACTATGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
47 2 0.05
48 11 0.28
49 5 0.12
50 22 0.55
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (50 bp):
ATATATAAACTTATATTTAAATATAATGTATAATTATAAATTATATTTAA
Found at i:474306 original size:17 final size:17
Alignment explanation
Indices: 474254--474332 Score: 56
Period size: 17 Copynumber: 4.5 Consensus size: 17
474244 ATAAATTATA
* *
474254 TATAAATTATATTTAAA
1 TATAAATTATATATAAT
474271 TATATAATCT-TATAT--T
1 TATA-AAT-TATATATAAT
* *
474287 TATATATTATGTATAAT
1 TATAAATTATATATAAT
474304 TATAAATTATATATACTAT
1 TATAAATTATATATA--AT
474323 GTATAAATTA
1 -TATAAATTA
474333 GATAGTTTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
14 1 0.02
15 6 0.12
16 4 0.08
17 18 0.38
18 7 0.15
19 3 0.06
20 9 0.19
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (17 bp):
TATAAATTATATATAAT
Found at i:474316 original size:26 final size:26
Alignment explanation
Indices: 474254--474398 Score: 81
Period size: 25 Copynumber: 5.7 Consensus size: 26
474244 ATAAATTATA
* * *
474254 TATAAATTATATTTAAATATATAATC
1 TATAAATTATATATATATGTATAATC
*
474280 T-TATATT-TATATATTATGTATAAT-
1 TATAAATTATATATA-TATGTATAATC
*
474304 TATAAATTATATATACTATGTATAA-A
1 TATAAATTATATATA-TATGTATAATC
* * * *
474330 T-TAGA-TAGTTTATATA-GTTTAA-A
1 TATAAATTA-TATATATATGTATAATC
* * *
474353 TATAAAGTATATAAGTATATATATAAAC
1 TATAAATTATAT-A-TATATGTATAATC
474381 TATAAATTATATATATAT
1 TATAAATTATATATATAT
474399 AAAGCATATA
Statistics
Matches: 93, Mismatches: 15, Indels: 22
0.72 0.12 0.17
Matches are distributed among these distances:
23 7 0.08
24 15 0.16
25 29 0.31
26 26 0.28
27 5 0.05
28 11 0.12
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (26 bp):
TATAAATTATATATATATGTATAATC
Found at i:474384 original size:28 final size:28
Alignment explanation
Indices: 474340--475054 Score: 300
Period size: 28 Copynumber: 25.6 Consensus size: 28
474330 TTAGATAGTT
*
474340 TATATAGTTTAAATATAAAGTATATAAG
1 TATATAGTATAAATATAAAGTATATAAG
*
474368 TATATA-TATAAACTATAAATTATATATA-
1 TATATAGTATAAA-TATAAAGTATATA-AG
*
474396 TATAAAGCATATATACATATATAA-TAATATAAAG
1 TATATAG--TATA-A-ATATA-AAGT-ATAT-AAG
* *
474430 TATA-AGTAT-ATTATATA-TATA-AAG
1 TATATAGTATAAATATAAAGTATATAAG
* *
474454 TATA-ATTATAAAGAATAAAGTATATAAAG
1 TATATAGTATAAA-TATAAAGTATAT-AAG
* * *
474483 TATATA-TACATATATAATAATATA-AAG
1 TATATAGTATAAATATAA-AGTATATAAG
* * *
474510 GATA-AGTAT-ATTATATA-TATAT-A-
1 TATATAGTATAAATATAAAGTATATAAG
* **
474533 TATATAAGTATAATTATAAAGGCTA-AAG
1 TATAT-AGTATAAATATAAAGTATATAAG
*
474561 TATATAAGCATATAATATAAAGTATATAAG
1 TATAT-AGTATA-AATATAAAGTATATAAG
* *
474591 TATATAATATAAACTATATAAATATATAA-
1 TATATAGTATAAA-TATA-AAGTATATAAG
*
474620 -AT-TA-TAT-AATATAAAAGTATATACATT
1 TATATAGTATAAATAT-AAAGTATATA-A-G
* * *
474647 TATAAAGTATAAGTAT--ATTATATATA-
1 TATATAGTATAAATATAAAGTATATA-AG
* *
474673 TATAAAGTATAATTATAAAG-ACTA-AAG
1 TATATAGTATAAATATAAAGTA-TATAAG
474700 TATATAGGTATATAATATAAAGTATATATA-
1 TATATA-GTATA-AATATAAAGTATATA-AG
* *
474730 TATATA-TATATATATAAAGT-T-TTAG
1 TATATAGTATAAATATAAAGTATATAAG
*
474755 TATATAATATAAAGTAT-AAG--TATAAG
1 TATATAGTATAAA-TATAAAGTATATAAG
474781 TATATA-TATAAACTATAAAGTATA-AA-
1 TATATAGTATAAA-TATAAAGTATATAAG
* *
474807 TATATAAGTATATATATAAACTATA-AAG
1 TATAT-AGTATAAATATAAAGTATATAAG
474835 TATATAAGTATATTACATATAAAG--TATAAG
1 TATAT-AGTATA--A-ATATAAAGTATATAAG
* *
474865 TATAT-TTATATATATAAAGTATATATA-
1 TATATAGTATAAATATAAAGTATATA-AG
* * *
474892 TATATAAGTTATAAGTATTAAAATATAT-AC
1 TATAT-AG-TATAAATA-TAAAGTATATAAG
* * *
474922 TATAAAGTATTAAACTGTATA--ATATAAG
1 TATATAGTA-TAAA-TATAAAGTATATAAG
* *
474950 TAT-TAAATATAAAGTATTAAAGTATATAAA
1 TATAT-AGTATAAA-TA-TAAAGTATATAAG
*
474980 TATA-AATATTAAATATAAAGTATATAAG
1 TATATAGTA-TAAATATAAAGTATATAAG
* *
475008 TATATAAATATATAATATAAAGTAT-TAAAC
1 TATAT-AGTATA-AATATAAAGTATAT-AAG
*
475038 TATATAATATAAATATA
1 TATATAGTATAAATATA
475055 CAATATAAAA
Statistics
Matches: 539, Mismatches: 66, Indels: 164
0.70 0.09 0.21
Matches are distributed among these distances:
23 3 0.01
24 28 0.05
25 36 0.07
26 64 0.12
27 76 0.14
28 126 0.23
29 73 0.14
30 84 0.16
31 28 0.05
32 6 0.01
33 10 0.02
34 5 0.01
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (28 bp):
TATATAGTATAAATATAAAGTATATAAG
Found at i:474487 original size:40 final size:41
Alignment explanation
Indices: 474394--474567 Score: 146
Period size: 40 Copynumber: 4.2 Consensus size: 41
474384 AAATTATATA
* *
474394 TATATAAAGCATATATACATA-TATAATAATATAAAGTAT-AAG
1 TATATAAAGTATATATACA-AGTATAAT--TATAAAGGATAAAG
* *
474436 TATAT-TA-TATATATA-AAGTATAATTATAAAGAATAAAG
1 TATATAAAGTATATATACAAGTATAATTATAAAGGATAAAG
474474 TATATAAAGTATATATACATA-TATAATAATATAAAGGAT-AAG
1 TATATAAAGTATATATACA-AGTATAAT--TATAAAGGATAAAG
* * *
474516 TATATTATATATATATATATATAAGTATAATTATAAAGGCTAAAG
1 TATA-TA-A-A-GTATATATACAAGTATAATTATAAAGGATAAAG
474561 TATATAA
1 TATATAA
474568 GCATATAATA
Statistics
Matches: 110, Mismatches: 8, Indels: 27
0.76 0.06 0.19
Matches are distributed among these distances:
37 9 0.08
38 9 0.08
39 8 0.07
40 15 0.14
41 8 0.07
42 13 0.12
43 12 0.11
44 12 0.11
45 9 0.08
46 15 0.14
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.36
Consensus pattern (41 bp):
TATATAAAGTATATATACAAGTATAATTATAAAGGATAAAG
Found at i:474552 original size:80 final size:81
Alignment explanation
Indices: 474368--474553 Score: 265
Period size: 80 Copynumber: 2.3 Consensus size: 81
474358 AGTATATAAG
* *
474368 TATATATATA-AACTATAAATTATATA-TATATAAAGCATATATACATATATAATAATATAAAGT
1 TATATATATATAACTATAAATTATAAAGTATATAAAGCATATATACATATATAATAATATAAAGG
474431 ATAAGTATATTATATA
66 ATAAGTATATTATATA
* ** *
474447 TATA-A-AGTATAATTATAAAGAATAAAGTATATAAAGTATATATACATATATAATAATATAAAG
1 TATATATA-TATAACTATAAATTATAAAGTATATAAAGCATATATACATATATAATAATATAAAG
474510 GATAAGTATATTATATA
65 GATAAGTATATTATATA
*
474527 TATATATATATAAGTAT-AATTATAAAG
1 TATATATATATAACTATAAATTATAAAG
474554 GCTAAAGTAT
Statistics
Matches: 93, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
77 1 0.01
78 3 0.03
79 16 0.17
80 63 0.68
81 9 0.10
82 1 0.01
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (81 bp):
TATATATATATAACTATAAATTATAAAGTATATAAAGCATATATACATATATAATAATATAAAGG
ATAAGTATATTATATA
Found at i:474575 original size:30 final size:28
Alignment explanation
Indices: 474558--475054 Score: 79
Period size: 30 Copynumber: 17.7 Consensus size: 28
474548 ATAAAGGCTA
*
474558 AAGTATATAAGCATATAATATAAAGTATAT
1 AAGTATATAAG--TATAATATAAAGGATAT
474588 AAGTATATAA-TATAAACTATATAA--ATAT
1 AAGTATATAAGTAT-AA-TATA-AAGGATAT
* * *
474616 -A-TAAATTA-TATAATATAAAAGTATAT
1 AAGTATATAAGTATAATAT-AAAGGATAT
* **
474642 ACA-TTTATAAAGTATAAGTAT--ATTATAT
1 A-AGTATAT-AAGTATAA-TATAAAGGATAT
474670 -A-TATATAAAGTATAATTATAAA-GACTA-
1 AAGTATAT-AAGTATAA-TATAAAGGA-TAT
* *
474697 AAGTATATAGGTATATAATATAAAGTATAT
1 AAGTATATAAG--TATAATATAAAGGATAT
*
474727 -A-TATATATA-TATATATATAAA-G-TTT
1 AAGTATATA-AGTATA-ATATAAAGGATAT
*
474752 TAGTATATAA-TATAA-AGTATAA-G-TAT
1 AAGTATATAAGTATAATA-TA-AAGGATAT
474778 AAGTATAT-A-TATAAACTATAAA-G-TAT
1 AAGTATATAAGTAT-AA-TATAAAGGATAT
* **
474804 AAATATATAAGTATATATATAAACTATA-
1 AAGTATATAAGTATA-ATATAAAGGATAT
474832 AAGTATATAAGTATATTACATATAAA-G-TAT
1 AAGTATATAAG--TA-TA-ATATAAAGGATAT
* *
474862 AAGTATAT--TTATATATATAAAGTATAT
1 AAGTATATAAGTATA-ATATAAAGGATAT
474889 ATA-TATATAAGTTATAAGTATTAAA--ATAT
1 A-AGTATATAAG-TATAA-TA-TAAAGGATAT
* * *
474918 ATACTATA-AAGTATTAAACTGTATA--ATAT
1 A-AGTATATAAGTA-T-AA-TATAAAGGATAT
* *
474947 AAGTAT-TAAATATAAAGTATTAAAGTATAT
1 AAGTATATAAGTAT-AA-TA-TAAAGGATAT
* *
474977 AA--ATATAAATATTAAATATAAAGTATAT
1 AAGTATATAAGTA-T-AATATAAAGGATAT
* *
475005 AAGTATATAAATATATAATATAAAGTAT-T
1 AAGTATATAAGTAT--AATATAAAGGATAT
*
475034 AAACTATATAA-TATAAATATA
1 -AAGTATATAAGTAT-AATATA
475055 CAATATAAAA
Statistics
Matches: 372, Mismatches: 36, Indels: 120
0.70 0.07 0.23
Matches are distributed among these distances:
24 6 0.02
25 21 0.06
26 68 0.18
27 42 0.11
28 77 0.21
29 56 0.15
30 86 0.23
31 16 0.04
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (28 bp):
AAGTATATAAGTATAATATAAAGGATAT
Found at i:474581 original size:22 final size:22
Alignment explanation
Indices: 474351--475054 Score: 304
Period size: 22 Copynumber: 31.3 Consensus size: 22
474341 ATATAGTTTA
474351 AATATAAAGTATATAAGTATAT
1 AATATAAAGTATATAAGTATAT
* *
474373 -ATATAAACTATA-AATTATAT
1 AATATAAAGTATATAAGTATAT
*
474393 ATATATAAAGCATATATACATATATAAT
1 A-ATATAAAG--TATATA-A-GTAT-AT
*
474421 AATATAAAGTATAAGTATATTATAT
1 AATATAAAGTAT-A-TA-AGTATAT
*
474446 -ATATAAAG--TATAATTATA-
1 AATATAAAGTATATAAGTATAT
*
474464 AAGAATAAAGTATATAAAGTATAT
1 AA-TATAAAGTATAT-AAGTATAT
* *
474488 -ATACATA-TATAATAA-TATA-
1 AATATAAAGTAT-ATAAGTATAT
*
474507 AAGGAT-AAGTATATTATA-TATAT
1 AA-TATAAAGTATA-TA-AGTATAT
*
474530 ATATATATAAG--TATAATTATA-
1 A-ATATA-AAGTATATAAGTATAT
** *
474551 AAGGCTAAAGTATATAAGCATAT
1 AA-TATAAAGTATATAAGTATAT
474574 AATATAAAGTATATAAGTATAT
1 AATATAAAGTATATAAGTATAT
* *
474596 AATATAAACTATATAAATATAT
1 AATATAAAGTATATAAGTATAT
*
474618 AAATTATATAA-TATAAAAGTATAT
1 -AA-TATA-AAGTATATAAGTATAT
*
474642 ACATTTATAAAGTATAAGTATATTATAT
1 A-A--TATAAAGTAT-A-TA-AGTATAT
*
474670 ATATATAAAG--TATAATTATA-
1 A-ATATAAAGTATATAAGTATAT
* *
474690 AAGACTAAAGTATATAGGTATAT
1 AATA-TAAAGTATATAAGTATAT
*
474713 AATATAAAGTATATATATATATATAT
1 AATATAAAG--TATATA-A-GTATAT
*
474739 ATATATAAAGT-T-TTAGTATAT
1 A-ATATAAAGTATATAAGTATAT
474760 AATATAAAGTATAAGTATAAGTATAT
1 AATATAAAG--T-A-TATAAGTATAT
*
474786 -ATATAAACTATA-AAGTATA-
1 AATATAAAGTATATAAGTATAT
474805 AATATATAAGTATAT-A-TATA-
1 AATATA-AAGTATATAAGTATAT
474825 AACTATAAAGTATATAAGTATATT
1 AA-TATAAAGTATATAAGTATA-T
*
474849 ACATATAAAGTATAAGTATA-TTTAT
1 A-ATATAAAGTAT-A-TA-AGTATAT
474874 ATATATAAAGTATATATA-TATAT
1 A-ATATAAAGTATATA-AGTATAT
*
474897 AAGT-TATAAGTAT-TAAAATATAT
1 AA-TATA-AAGTATAT-AAGTATAT
* * *
474920 ACTATAAAGTAT-TAAACTGTAT
1 AATATAAAGTATAT-AAGTATAT
*
474942 AATAT-AAGTAT-TAAATATA-
1 AATATAAAGTATATAAGTATAT
*
474961 AAGTATTAAAGTATATAAATATA-
1 AA-TA-TAAAGTATATAAGTATAT
474984 AATATTAAA-TATA-AAGTATAT
1 AATA-TAAAGTATATAAGTATAT
*
475005 AAGTATATAAATATATAA-TATA-
1 AA-TATA-AAGTATATAAGTATAT
*
475027 AAGTATTAAACTATATAA-TATA-
1 AA-TA-TAAAGTATATAAGTATAT
475049 AATATA
1 AATATA
475055 CAATATAAAA
Statistics
Matches: 549, Mismatches: 51, Indels: 166
0.72 0.07 0.22
Matches are distributed among these distances:
19 11 0.02
20 81 0.15
21 71 0.13
22 155 0.28
23 68 0.12
24 53 0.10
25 43 0.08
26 32 0.06
27 24 0.04
28 11 0.02
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (22 bp):
AATATAAAGTATATAAGTATAT
Found at i:474942 original size:80 final size:80
Alignment explanation
Indices: 474876--475094 Score: 211
Period size: 79 Copynumber: 2.7 Consensus size: 80
474866 ATATTTATAT
* * * *
474876 ATATAAAGTATATATA-TATATAAGTTATAAGTATTAAAATATATACTATA-AAGTAT-TAAACT
1 ATATAAAGTAT-TAAAGTATATAA-ATATAAATATT-AAATATAAACTATATAAGTATATAAACT
474938 GTATAATATAAGTATTAA
63 GTATAATATAAGTATTAA
* *
474956 ATATAAAGTATTAAAGTATATAAATATAAATATTAAATATAAAGTATATAAGTATATAAA-TATA
1 ATATAAAGTATTAAAGTATATAAATATAAATATTAAATATAAACTATATAAGTATATAAACTGTA
475020 TAATATAAAGTATTAA
66 TAATAT-AAGTATTAA
* * * *
475036 ACTATATAA-TA-TAAA-TATA-CAATATAAAATATTAAAGTATATAAATATAGAATTATATA
1 A-TATA-AAGTATTAAAGTATATAAATAT-AAATATTAAA-TATA-AACTATATAAGTATATA
475095 TATTAAATTA
Statistics
Matches: 120, Mismatches: 10, Indels: 17
0.82 0.07 0.12
Matches are distributed among these distances:
78 17 0.14
79 41 0.34
80 40 0.33
81 20 0.17
82 2 0.02
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (80 bp):
ATATAAAGTATTAAAGTATATAAATATAAATATTAAATATAAACTATATAAGTATATAAACTGTA
TAATATAAGTATTAA
Found at i:474968 original size:35 final size:35
Alignment explanation
Indices: 474912--475084 Score: 173
Period size: 35 Copynumber: 5.0 Consensus size: 35
474902 ATAAGTATTA
* * *
474912 AAATATATACTATAAAGTATTAAACTGTATAATAT
1 AAATATACAATATAAAGTATTAAACTATATAATAT
* *
474947 AAGTATTA-AATATAAAGTATTAAAGTATATAAATAT
1 AAATA-TACAATATAAAGTATTAAACTATAT-AATAT
474983 AAATATTA-AATATAAAGTA-T--A-TA-AGT-ATAT
1 AAATA-TACAATATAAAGTATTAAACTATA-TAATAT
*
475013 AAATATATAATATAAAGTATTAAACTATATAATAT
1 AAATATACAATATAAAGTATTAAACTATATAATAT
* *
475048 AAATATACAATATAAAATATTAAAGTATATAAATAT
1 AAATATACAATATAAAGTATTAAACTATAT-AATAT
475084 A
1 A
475085 GAATTATATA
Statistics
Matches: 119, Mismatches: 8, Indels: 21
0.80 0.05 0.14
Matches are distributed among these distances:
29 2 0.02
30 20 0.17
31 2 0.02
32 3 0.03
33 2 0.02
34 3 0.03
35 56 0.47
36 31 0.26
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (35 bp):
AAATATACAATATAAAGTATTAAACTATATAATAT
Found at i:475017 original size:101 final size:101
Alignment explanation
Indices: 474556--475084 Score: 371
Period size: 101 Copynumber: 5.1 Consensus size: 101
474546 TTATAAAGGC
* *
474556 TAAAGTATATAAGCATATAATATAAAGTATATAAGTATAT-AATATA-AACTATATAAATATATA
1 TAAA-TATA-AAGTATA-AATATAAAGTATATAAGTATATAAATATATAA-TATA-AAGTAT-TA
* * * *
474619 AATTATATAATATAAAAGTATATACATTTATAAAGTATAAGTATATTATA
60 AACTATATAATAT--AAGTAT-TA-A-ATATAAAGTAT---TAAAGTATA
* * **
474669 TATATATAAAGTATAATTATAAAG-ACTA-AAGTATATAGGTATATAATATAAAGTATATATATA
1 TAAATATAAAGTATAAATATAAAGTA-TATAAGTATATAAATATATAATATAAAGTAT-TA-A-A
* * *
474732 TATATATATATATAAAGT-TTTAGTATATAA-TA-TAAAG--TA
62 -CTATATA-ATAT-AAGTATTAAATATA-AAGTATTAAAGTATA
* * * *
474771 TAAGTAT-AAGTATATATATAAACTATA-AAG--TATAAATATATAAGTATATA-TA-TAAACTA
1 TAAATATAAAGTATAAATATAAAGTATATAAGTATATAAATATATAA-TATAAAGTATTAAACTA
* *
474830 TAAAGTATATAAGTATATTACATATAAAGTA-T-AAGTATA
65 TATA--ATATAAG--TATTAAATATAAAGTATTAAAGTATA
*
474869 TTTATATATATAAAGTATATATATATATAAGT-TATAAGTAT-TAAAATATATACTATAAAGTAT
1 --TA-A-ATATAAAGTATA-A-ATATA-AAGTATATAAGTATAT-AAATATATAATATAAAGTAT
*
474932 TAAACTGTATAATATAAGTATTAAATATAAAGTATTAAAGTATA
58 TAAACTATATAATATAAGTATTAAATATAAAGTATTAAAGTATA
474976 TAAATATAAA-TATTAAATATAAAGTATATAAGTATATAAATATATAATATAAAGTATTAAACTA
1 TAAATATAAAGTA-TAAATATAAAGTATATAAGTATATAAATATATAATATAAAGTATTAAACTA
* *
475040 TATAATATAAATA-TACAATATAAAATATTAAAGTATA
65 TATAATATAAGTATTA-AATATAAAGTATTAAAGTATA
475077 TAAATATA
1 TAAATATA
475085 GAATTATATA
Statistics
Matches: 343, Mismatches: 36, Indels: 86
0.74 0.08 0.18
Matches are distributed among these distances:
94 8 0.02
95 6 0.02
96 7 0.02
97 11 0.03
98 2 0.01
99 13 0.04
100 13 0.04
101 98 0.29
102 15 0.04
103 16 0.05
104 4 0.01
105 24 0.07
106 7 0.02
107 20 0.06
108 18 0.05
109 29 0.08
110 20 0.06
111 10 0.03
112 15 0.04
113 7 0.02
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (101 bp):
TAAATATAAAGTATAAATATAAAGTATATAAGTATATAAATATATAATATAAAGTATTAAACTAT
ATAATATAAGTATTAAATATAAAGTATTAAAGTATA
Found at i:475059 original size:13 final size:12
Alignment explanation
Indices: 474349--475063 Score: 127
Period size: 13 Copynumber: 53.3 Consensus size: 12
474339 TTATATAGTT
474349 TAAATATAAAGTA
1 TAAATATAAA-TA
*
474362 TATAAGTATATATA
1 TA-AA-TATAAATA
474376 TAAACTATAAATTA
1 TAAA-TATAAA-TA
*
474390 TATATATATAAAGCA
1 TA-A-ATATAAA-TA
* * *
474405 TATATACATATA
1 TAAATATAAATA
474417 TAATAATATAAAGTA
1 T-A-AATATAAA-TA
* *
474432 TAAGTAT-ATTA
1 TAAATATAAATA
*
474443 TATATATAAAGTA
1 TAAATATAAA-TA
* *
474456 TAATTATAAAGAA
1 TAAATATAAA-TA
474469 TAAAGTATATAA-A
1 TAAA-TATA-AATA
* *
474482 GTATATATACATA
1 -TAAATATAAATA
*
474495 TATA-AT-AATA
1 TAAATATAAATA
* *
474505 TAAAGGATAAGTA
1 TAAA-TATAAATA
* *
474518 TATTATATATATA
1 TA-AATATAAATA
* *
474531 TATATATAAGTA
1 TAAATATAAATA
* **
474543 TAATTATAAAGGC
1 TAAATATAAA-TA
*
474556 TAAAGTATATAAGCA
1 TAAA-TATA-AA-TA
474571 TATAATATAAAGTA
1 TA-AATATAAA-TA
474585 TATAAGTATATAATA
1 TA-AA-TATA-AATA
474600 TAAACTAT--ATA
1 TAAA-TATAAATA
474611 -AATATATAAATTA
1 TAA-ATATAAA-TA
474624 TATAATATAAA-A
1 TA-AATATAAATA
* * **
474636 GTATATACATTTA
1 -TAAATATAAATA
*
474649 TAAAGTATAAGTA
1 TAAA-TATAAATA
* *
474662 TATTATATATATA
1 TA-AATATAAATA
*
474675 TAAAGTATAATTA
1 TAAA-TATAAATA
*
474688 TAAAGACTAAAGTA
1 TAAATA-TAAA-TA
*
474702 TATAGGTATATAATA
1 TA-A-ATATA-AATA
474717 TAAAGTATATATATA
1 TAAA-TATA-A-ATA
* *
474732 TATATATATATA
1 TAAATATAAATA
* * *
474744 TAAAGTTTTAGTA
1 TAAA-TATAAATA
474757 TATAATATAAAGTA
1 TA-AATATAAA-TA
* *
474771 TAAGTATAAGTA
1 TAAATATAAATA
*
474783 TATATATAAACTA
1 TAAATATAAA-TA
474796 TAAAGTATAAATA
1 TAAA-TATAAATA
*
474809 TATAAGTATATATA
1 TA-AA-TATAAATA
474823 TAAACTATAAAGTA
1 TAAA-TATAAA-TA
474837 TATAAGTATATTACATA
1 TA-AA-TATA--A-ATA
*
474854 TAAAGTATAAGTA
1 TAAA-TATAAATA
** *
474867 TATTTATATATA
1 TAAATATAAATA
474879 TAAAGTAT--ATA
1 TAAA-TATAAATA
* *
474890 TATATATAAGTTA
1 TAAATATAA-ATA
*
474903 TAAGTATTAAAATA
1 TAAATA-T-AAATA
*
474917 TATACTATAAAGTA
1 TA-AATATAAA-TA
*
474931 TTAAACTGTATAATA
1 -TAAA-TATA-AATA
*
474946 TAAGTATTAAATA
1 TAAATA-TAAATA
474959 TAAAGTATTAAAGTATA
1 TAAA-TA-T-AA--ATA
474976 TAAATATAAATA
1 TAAATATAAATA
474988 TTAAATATAAAGTATA
1 -TAAATAT-AA--ATA
475004 TAAGTATATAAATA
1 TAA--ATATAAATA
475018 TATAATATAAAGTA
1 TA-AATATAAA-TA
475032 TTAAACTATATAATA
1 -TAAA-TATA-AATA
475047 TAAATATACAATA
1 TAAATATA-AATA
475060 TAAA
1 TAAA
475064 ATATTAAAGT
Statistics
Matches: 522, Mismatches: 100, Indels: 160
0.67 0.13 0.20
Matches are distributed among these distances:
10 14 0.03
11 19 0.04
12 63 0.12
13 169 0.32
14 130 0.25
15 84 0.16
16 26 0.05
17 16 0.03
18 1 0.00
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.37
Consensus pattern (12 bp):
TAAATATAAATA
Found at i:475080 original size:30 final size:28
Alignment explanation
Indices: 474576--475110 Score: 214
Period size: 28 Copynumber: 19.0 Consensus size: 28
474566 AAGCATATAA
*
474576 TATAAAGTATATAAGTATATAATATAAACTA
1 TATAAAGTATATAAATATA-AATATAAA--A
474607 TATAAA-TATATAAATTATATAATATAAAA
1 TATAAAGTATATAAA-TATA-AATATAAAA
* * *
474636 GTATATACA-TTTATAAAGTATAAGTAT--AT
1 -TATA-A-AGTATATAAA-TATAAATATAAAA
* *
474665 TATATA-TATATAAAGTATAATTATAAAGA
1 TATAAAGTATATAAA-TATAAATATAAA-A
* ** *
474694 -CTAAAGTATATAGGTATATAATATAAAG
1 TATAAAGTATATAAATATA-AATATAAAA
* * * *
474722 TATATA-TATATATATATATATATAAAG
1 TATAAAGTATATAAATATAAATATAAAA
** *
474749 T-TTTAGTATAT-AATATAAAGTAT-AAG
1 TATAAAGTATATAAATATAAA-TATAAAA
*
474775 TAT-AAGTATAT--ATATAAACTATAAAG
1 TATAAAGTATATAAATATAAA-TATAAAA
* * *
474801 TATAAA-TATATAAGTATATATATAAAC
1 TATAAAGTATATAAATATAAATATAAAA
* *
474828 TATAAAGTATATAAGTATATTACATATAAAG
1 TATAAAGTATATAA--ATA-TAAATATAAAA
* *
474859 TAT-AAGTATAT--TTATATATATAAAGTA
1 TATAAAGTATATAAATATAAATATAAA--A
* * *
474886 TATATA-TATATAAGTTATAAGTATTAAAA
1 TATAAAGTATATAA-ATATAAATA-TAAAA
* * * * *
474915 TATATACTATA-AAGTATTAAACTGTATAA
1 TATAAAGTATATAAATA-TAAA-TATAAAA
*
474944 TAT-AAGTAT-TAAATATAAA-GT---A
1 TATAAAGTATATAAATATAAATATAAAA
*
474966 T-TAAAGTATATAAATATAAATATTAAA
1 TATAAAGTATATAAATATAAATATAAAA
*
474993 TATAAAGTATATAAGTATATAAATATATAA
1 TATAAAGTATATAA--ATATAAATATAAAA
475023 TATAAAGTAT-TAAACTATATAATAT-AAA
1 TATAAAGTATATAAA-TATA-AATATAAAA
475051 TATACAA-TATA-AAATATTAAAGTATATAAA
1 TATA-AAGTATATAAATA-TAAA-TATA-AAA
* *
475081 TATAGAATTATATATAT-TAAATTATAAAA
1 TATA-AAGTATATAAATATAAA-TATAAAA
475110 T
1 T
475111 TCGTATGAAC
Statistics
Matches: 402, Mismatches: 51, Indels: 104
0.72 0.09 0.19
Matches are distributed among these distances:
21 1 0.00
22 8 0.02
23 10 0.02
24 1 0.00
25 21 0.05
26 50 0.12
27 51 0.13
28 78 0.19
29 51 0.13
30 72 0.18
31 44 0.11
32 15 0.04
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (28 bp):
TATAAAGTATATAAATATAAATATAAAA
Found at i:475083 original size:58 final size:56
Alignment explanation
Indices: 474521--475084 Score: 240
Period size: 58 Copynumber: 9.9 Consensus size: 56
474511 ATAAGTATAT
* * * **
474521 TATATATATATATATATAAGTAT-AATTATAAAG-GCTAAAGTATATAAGCATAT-AA-
1 TATAAATATATA-ATATAAATATAAAGTATAAAGTATTAAAGTATATAA--ATATAAAG
* * *
474576 TATAAAGTATATAAGTATATAATATAAACTATATAAATATATAAATTATAT-AATATAAAAG
1 TATAAA-TATATAA-TATA-AATATAAAGTATA-AAGTAT-TAAAGTATATAAATAT-AAAG
* * * * *
474637 TATATACATTTATAAAGTATAAGTAT--ATTATATA-TATATAAAG--TATAATTATAAAG
1 TATA-A-ATATAT-AA-TATAAATATAAAGTATAAAGTAT-TAAAGTATATAAATATAAAG
* * * *
474693 -ACTAAAGTATATAGGTATATAATATAAAGTATATA-TA-TATA-TATATATATATAAAG
1 TA-TAAA-TATATA-ATATA-AATATAAAGTATAAAGTATTAAAGTATATAAATATAAAG
* * *
474749 TTTTAGTATATAATATAAAGTAT-AAGTAT-AAGTA-T--A-TATATAAACTATAAAG
1 TATAAATATATAATATAAA-TATAAAGTATAAAGTATTAAAGTATATAAA-TATAAAG
* * *
474801 TATAAATATATAAGTATATATATAAACTATAAAGTA-TATAAGTATATTACATATAAAG
1 TATAAATATATAA-TATAAATATAAAGTATAAAGTATTA-AAGTATA-TAAATATAAAG
* * * * * *
474859 TATAAGTATAT-TTATATATATAAAGTATATA-TATATATAAGT-TATAAGTATTAAAA
1 TATAAATATATAATATAAATATAAAGTATAAAGTAT-TA-AAGTATATAAATA-TAAAG
* * *
474915 TATATACTATA-AAGTATTAAACTGTATAA-TAT-AAGTATTAAA-TATA-AAGTATTAAAG
1 TATA-AATATATAA-TA-TAAA-TATA-AAGTATAAAGTATTAAAGTATATAAATA-TAAAG
474972 TATATAA-ATATAAATATTAAATATAAAGTATATAAGTATATAAA-TATAT-AATATAAAG
1 TATA-AATATAT-AATA-TAAATATAAAGTATA-AAGTAT-TAAAGTATATAAATATAAAG
*
475030 TATTAAACTATATAATATAAATATACAA-TATAAAATATTAAAGTATATAAATATA
1 TA-TAAA-TATATAATATAAATATA-AAGTATAAAGTATTAAAGTATATAAATATA
475085 GAATTATATA
Statistics
Matches: 402, Mismatches: 49, Indels: 113
0.71 0.09 0.20
Matches are distributed among these distances:
51 8 0.02
52 21 0.05
53 21 0.05
54 19 0.05
55 33 0.08
56 72 0.18
57 64 0.16
58 80 0.20
59 31 0.08
60 21 0.05
61 15 0.04
62 9 0.02
63 8 0.02
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (56 bp):
TATAAATATATAATATAAATATAAAGTATAAAGTATTAAAGTATATAAATATAAAG
Found at i:475097 original size:14 final size:14
Alignment explanation
Indices: 474944--475108 Score: 73
Period size: 14 Copynumber: 11.4 Consensus size: 14
474934 AACTGTATAA
*
474944 TATAAGTATTAAA-
1 TATAAATATTAAAT
474957 TATAAAGTATTAAAGT
1 TATAAA-TATTAAA-T
474973 ATATAAATA-TAAA-
1 -TATAAATATTAAAT
474986 TATTAAATA-TAAAGT
1 TA-TAAATATTAAA-T
*
475001 ATATAAGTATATAAA-
1 -TATAAATAT-TAAAT
*
475016 TATATAATA-TAAAG
1 TATA-AATATTAAAT
475030 TATTAAACTA-TATAA-
1 TA-TAAA-TATTA-AAT
475045 TATAAATA-TACAA-
1 TATAAATATTA-AAT
475058 TATAAAATATTAAAGT
1 TAT-AAATATTAAA-T
475074 ATATAAATA-TAGAAT
1 -TATAAATATTA-AAT
*
475089 TATATATATTAAAT
1 TATAAATATTAAAT
475103 TATAAA
1 TATAAA
475109 ATTCGTATGA
Statistics
Matches: 124, Mismatches: 6, Indels: 43
0.72 0.03 0.25
Matches are distributed among these distances:
12 2 0.02
13 28 0.23
14 41 0.33
15 27 0.22
16 13 0.10
17 13 0.10
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.37
Consensus pattern (14 bp):
TATAAATATTAAAT
Found at i:475099 original size:65 final size:66
Alignment explanation
Indices: 474955--475110 Score: 205
Period size: 65 Copynumber: 2.4 Consensus size: 66
474945 ATAAGTATTA
* *
474955 AATATAAAGTATTAAAGTATATAAATATAAATATTAAATATAAAGTATATAAGTATATAAATATA
1 AATATAAAGTATTAAACTATATAAATATAAATATTAAATATAAAATATATAAGTATATAAATATA
*
475020 T
66 G
475021 AATATAAAGTATTAAACTATAT-AATATAAATA-TACAATATAAAATAT-TAAAGTATATAAATA
1 AATATAAAGTATTAAACTATATAAATATAAATATTA-AATATAAAATATAT-AAGTATATAAATA
475083 TAG
64 TAG
* *
475086 AATTATATA-TATTAAATTATA-AAAT
1 AA-TATAAAGTATTAAACTATATAAAT
475111 TCGTATGAAC
Statistics
Matches: 81, Mismatches: 5, Indels: 9
0.85 0.05 0.09
Matches are distributed among these distances:
64 3 0.04
65 52 0.64
66 26 0.32
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (66 bp):
AATATAAAGTATTAAACTATATAAATATAAATATTAAATATAAAATATATAAGTATATAAATATA
G
Found at i:475111 original size:22 final size:21
Alignment explanation
Indices: 474954--475110 Score: 151
Period size: 22 Copynumber: 7.2 Consensus size: 21
474944 TATAAGTATT
474954 AAATATAAAGTATTAAAGTATA
1 AAATATAAAGTATTAAA-TATA
474976 TAAATATAAA-TATTAAATATA
1 -AAATATAAAGTATTAAATATA
*
474997 AAGTATATAAGTATATAAATATA
1 AAATATA-AAGTAT-TAAATATA
*
475020 TAATATAAAGTATTAAACTATA
1 AAATATAAAGTATTAAA-TATA
*
475042 TAATATAAA-TA-TACAATATA
1 AAATATAAAGTATTA-AATATA
475062 AAATATTAAAGTATATAAATATA
1 AAATA-TAAAGTAT-TAAATATA
* *
475085 GAATTATATA-TATTAAATTATA
1 -AAATATAAAGTATTAAA-TATA
475107 AAAT
1 AAAT
475111 TCGTATGAAC
Statistics
Matches: 116, Mismatches: 7, Indels: 24
0.79 0.05 0.16
Matches are distributed among these distances:
20 16 0.14
21 25 0.22
22 38 0.33
23 31 0.27
24 6 0.05
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.36
Consensus pattern (21 bp):
AAATATAAAGTATTAAATATA
Found at i:475719 original size:17 final size:17
Alignment explanation
Indices: 475697--475730 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
475687 ACTATTTAAC
475697 ATGCAATGCAACATGAA
1 ATGCAATGCAACATGAA
*
475714 ATGCAATTCAACATGAA
1 ATGCAATGCAACATGAA
475731 TTAATATGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.21
Consensus pattern (17 bp):
ATGCAATGCAACATGAA
Found at i:476314 original size:3 final size:3
Alignment explanation
Indices: 476303--476360 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
476293 TTTTTTCCCG
** *
476303 TTA TT- TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
476348 TTA TTTA TTA TTA
1 TTA -TTA TTA TTA
476361 CAATTTTTGC
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 5 0.11
3 37 0.82
4 3 0.07
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:476508 original size:25 final size:25
Alignment explanation
Indices: 476479--476577 Score: 159
Period size: 25 Copynumber: 4.0 Consensus size: 25
476469 GAACCAACCC
476479 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
476504 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
476529 ATCAGATTAGGGTTTCAAACCCTAAA
1 ATCAGATTAGGGTTTCAAACCCT-AA
476555 AT-A-ATTTAGGGTTTC-AACCCTAA
1 ATCAGA-TTAGGGTTTCAAACCCTAA
476578 TCCCCTAACT
Statistics
Matches: 72, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
23 2 0.03
24 7 0.10
25 59 0.82
26 4 0.06
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.29
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:491411 original size:87 final size:89
Alignment explanation
Indices: 491249--491413 Score: 280
Period size: 87 Copynumber: 1.9 Consensus size: 89
491239 ATCCCCCGGA
*
491249 CCAGATCTCTTCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGG
1 CCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGG
*
491314 AACCGTGTTATCACCTTTAGATGG
66 AACCGAGTTATCACCTTTAGATGG
* *
491338 CCAGATCTCTTCATCACGTAAGAGCCGTGTCAACC-T-GATAACCAGTCGTCCTCATTACGTAGG
1 CCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGG
491401 AACCGAGTTATCA
66 AACCGAGTTATCA
491414 TCCCTAAAGA
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
87 37 0.51
88 1 0.01
89 34 0.47
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (89 bp):
CCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGG
AACCGAGTTATCACCTTTAGATGG
Found at i:491457 original size:3 final size:3
Alignment explanation
Indices: 491451--491554 Score: 156
Period size: 3 Copynumber: 34.7 Consensus size: 3
491441 TTTTTATCCA
* * *
491451 TAT TAT TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT CAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
491499 TAT TAT TAT TAT TAT TAT TATT TAT TTT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
491545 T-T TAT TAT TA
1 TAT TAT TAT TA
491555 AATATATTAA
Statistics
Matches: 91, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.02
3 86 0.95
4 3 0.03
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:503813 original size:6 final size:6
Alignment explanation
Indices: 503789--503886 Score: 80
Period size: 6 Copynumber: 16.5 Consensus size: 6
503779 ATGCTTGAAG
*
503789 AAAAGA AAGAAG- AAGAGA AAAAGA AAAAGA AAAAGA AAAAG- -AAAGA
1 AAAAGA AA-AAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
* * * *
503835 AAAA-A AAAGGGG AAAAGA AAAAAA AAGAAGA AAAA-A TAATAGA AAAAGA
1 AAAAGA AAA-AGA AAAAGA AAAAGA AA-AAGA AAAAGA -AAAAGA AAAAGA
503884 AAA
1 AAA
503887 GGGTCAAGGT
Statistics
Matches: 73, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
4 4 0.05
5 7 0.10
6 50 0.68
7 12 0.16
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (6 bp):
AAAAGA
Found at i:504240 original size:18 final size:16
Alignment explanation
Indices: 504202--504242 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
504192 CTATTTCAAG
*
504202 TTCAATTTATTTGAGA
1 TTCAATTTATTTGAAA
504218 TTCAATTTATTTTGGAAA
1 TTCAATTTA-TTT-GAAA
504236 TTCAATT
1 TTCAATT
504243 ATTCTTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.41
17 3 0.14
18 10 0.45
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (16 bp):
TTCAATTTATTTGAAA
Found at i:505175 original size:99 final size:99
Alignment explanation
Indices: 504999--505190 Score: 368
Period size: 99 Copynumber: 1.9 Consensus size: 99
504989 GAAAGAGACT
504999 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAATAGCATCTTCTGG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAATAGCATCTTCTGG
505064 AAGTGTTCTTGAGTTATCTGATCTGGTTAGACAG
66 AAGTGTTCTTGAGTTATCTGATCTGGTTAGACAG
505098 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GACAGAATAGCATCTTCTGG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAATAGCATCTTCTGG
505162 AAGTGTTCTTTGAGTTATCTGATCTGGTT
66 AAGTGTTC-TTGAGTTATCTGATCTGGTT
505191 GGCAGAACCA
Statistics
Matches: 92, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
98 28 0.30
99 64 0.70
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.39
Consensus pattern (99 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAATAGCATCTTCTGG
AAGTGTTCTTGAGTTATCTGATCTGGTTAGACAG
Found at i:505197 original size:49 final size:50
Alignment explanation
Indices: 504999--505190 Score: 370
Period size: 49 Copynumber: 3.9 Consensus size: 50
504989 GAAAGAGACT
504999 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
505049 AATAGCATCTTCTGGAAGTGTTC-TTGAGTTATCTGATCTGGTTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
505098 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
505147 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
505191 GGCAGAACCA
Statistics
Matches: 141, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
49 98 0.70
50 43 0.30
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.39
Consensus pattern (50 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
Found at i:506358 original size:119 final size:118
Alignment explanation
Indices: 505906--506433 Score: 837
Period size: 119 Copynumber: 4.5 Consensus size: 118
505896 TAGCAAAGAT
* *
505906 TTGAATCCATCACTTGATGGATCATTCTTTTCCAGA-GAA-AGTTCATAATGAGAAGAA--C-TC
1 TTGAATTCATCACTTGATGGATCA-TCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCATC
*
505966 ATCTGAAGAAGGAAGAGGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
65 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
*
506020 TTGAATTCATCACTTGATGGATCA--ATTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
1 TTGAATTCATCACTTGATGGATCATCA-TTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCATC
506083 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
65 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
*
506137 TTGAA-T--TCACTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCA
1 TTGAATTCATCACTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCATCA
506199 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
66 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
*
506252 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCATC
1 TTGAATTCATC-ACTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCATC
506317 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
65 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * ** *
506371 TTGAATTCATCATTTGATGGAACATCATCCCCAGCA-GAA-AGTTCGTAATGAGAAGAACTCATC
1 TTGAATTCATCACTTGATGGATCATCATTTCCAG-AGGAAGAGTTCATAATGAGAAGAACTCATC
506434 TGGAGAAAAA
Statistics
Matches: 391, Mismatches: 10, Indels: 23
0.92 0.02 0.05
Matches are distributed among these distances:
112 8 0.02
113 3 0.01
114 56 0.14
115 96 0.25
116 4 0.01
117 83 0.21
118 24 0.06
119 117 0.30
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (118 bp):
TTGAATTCATCACTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCATCA
TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:506592 original size:3 final size:3
Alignment explanation
Indices: 506584--506667 Score: 107
Period size: 3 Copynumber: 27.7 Consensus size: 3
506574 TTTTTATCCA
* * *
506584 TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT CAT TAT TAA TAT TATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
*
506630 TAT TAT T-T TAT TTT TATT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TA
506668 AATATATTAA
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
2 2 0.03
3 62 0.89
4 6 0.09
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:507149 original size:14 final size:14
Alignment explanation
Indices: 507130--507156 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
507120 AAAAAAGAGA
507130 GACAGAGACAGAAG
1 GACAGAGACAGAAG
507144 GACAGAGACAGAA
1 GACAGAGACAGAA
507157 CCAAAAGAAA
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:0.52, C:0.15, G:0.33, T:0.00
Consensus pattern (14 bp):
GACAGAGACAGAAG
Found at i:507459 original size:13 final size:13
Alignment explanation
Indices: 507443--507468 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
507433 GCCACCGGAA
507443 ACGGTGGCCGGCG
1 ACGGTGGCCGGCG
507456 ACGGTGGCCGGCG
1 ACGGTGGCCGGCG
507469 GCAGAAATCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.31, G:0.54, T:0.08
Consensus pattern (13 bp):
ACGGTGGCCGGCG
Found at i:508927 original size:3 final size:3
Alignment explanation
Indices: 508916--508973 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
508906 TTTTTTTCCG
** *
508916 TTA TT- TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
508961 TTA TTTA TTA TTA
1 TTA -TTA TTA TTA
508974 CAATTTTTGC
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 5 0.11
3 37 0.82
4 3 0.07
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:509121 original size:25 final size:25
Alignment explanation
Indices: 509092--509240 Score: 257
Period size: 25 Copynumber: 6.0 Consensus size: 25
509082 GAACCAACCC
509092 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
509117 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
509142 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
509167 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
*
509192 TTCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
*
509217 AACA-ATTTAGGGTTTC-AACCCTAA
1 ATCAGA-TTAGGGTTTCAAACCCTAA
509241 TCCCCTAACT
Statistics
Matches: 120, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
24 9 0.08
25 111 0.93
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:516459 original size:165 final size:165
Alignment explanation
Indices: 516176--516672 Score: 763
Period size: 165 Copynumber: 3.0 Consensus size: 165
516166 ACGGTTCCTC
* *
516176 AAATAATCTTGAACCTACTCTTTCTTGTTATAGATCGATGCGAAAACTTAATAATCTTCATCTTT
1 AAATTATCTTGAACCTACTCTTTCTTGTTATAGATCGATGTGAAAACTTAATAATCTTCATCTTT
*
516241 TAGGATAACCCATG-TATGATTTT-ACAGGTGTCTTAGGGTTTGTGACTAGAAATTGAAGCTATA
66 TAGGATAACCCA-GATATGATTTTCA-AGGTGTCTTAGGGTTTGTGGCTAGAAATTGAAGCTATA
* *
516304 CTTGAATTTGGTAGTATTAGTGTTCAGGCTTGAATTA
129 CTTGAATTTGGTAGTATTGGTGTTCAGGTTTGAATTA
* * *
516341 AAATTATCTTCAACCTACTCTTTCTTGGTATAGATCGATGTGAGAACTTAATAATCTTCATCTTT
1 AAATTATCTTGAACCTACTCTTTCTTGTTATAGATCGATGTGAAAACTTAATAATCTTCATCTTT
* *
516406 TGGGATAACCCAGATATGATTTTCAAGATGTCTTAGGGTTTGTGGCTAGAAATTGAAGCTATACT
66 TAGGATAACCCAGATATGATTTTCAAGGTGTCTTAGGGTTTGTGGCTAGAAATTGAAGCTATACT
516471 TGAATTTGGTAGTATTGGTGTTCAGGTTTGAATTA
131 TGAATTTGGTAGTATTGGTGTTCAGGTTTGAATTA
* *
516506 AAATCATCTTGAACCTACACTTT-TCTGTTATAGATCGATGTGAAAAC-T--TAATCTTCATCTT
1 AAATTATCTTGAACCTACTCTTTCT-TGTTATAGATCGATGTGAAAACTTAATAATCTTCATCTT
* * * *
516567 TTAGGATAATCAAGATATGATTTTCAAGGTGTCTTGGGGTTGGTGGCTAGAAATTGAAGCTATAC
65 TTAGGATAACCCAGATATGATTTTCAAGGTGTCTTAGGGTTTGTGGCTAGAAATTGAAGCTATAC
* *
516632 TTGAATTTGGTAGCATTGGTGTTCAGATTTGAATTA
130 TTGAATTTGGTAGTATTGGTGTTCAGGTTTGAATTA
516668 AAATT
1 AAATT
516673 TGTTGCCTTT
Statistics
Matches: 305, Mismatches: 24, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
162 110 0.36
164 3 0.01
165 191 0.63
166 1 0.00
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (165 bp):
AAATTATCTTGAACCTACTCTTTCTTGTTATAGATCGATGTGAAAACTTAATAATCTTCATCTTT
TAGGATAACCCAGATATGATTTTCAAGGTGTCTTAGGGTTTGTGGCTAGAAATTGAAGCTATACT
TGAATTTGGTAGTATTGGTGTTCAGGTTTGAATTA
Found at i:517506 original size:21 final size:20
Alignment explanation
Indices: 517473--517512 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
517463 CACCAGAGAA
*
517473 AATGAATCTTTAAAGAAAGAG
1 AATGAATCCTTAAA-AAAGAG
*
517494 AATGTATCCTTAAAAAAGA
1 AATGAATCCTTAAAAAAGA
517513 ACGATGGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.53, C:0.07, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGAATCCTTAAAAAAGAG
Found at i:517873 original size:23 final size:23
Alignment explanation
Indices: 517819--517873 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
517809 GTGAATATGC
*
517819 TAAATGAACATGTTCATGAACAA
1 TAAATGAACATGTTCACGAACAA
** **
517842 TAAGCGAACATGTTCACGAACGT
1 TAAATGAACATGTTCACGAACAA
517865 TAAATGAAC
1 TAAATGAAC
517874 GTATTTATAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (23 bp):
TAAATGAACATGTTCACGAACAA
Found at i:534058 original size:162 final size:165
Alignment explanation
Indices: 533877--534204 Score: 610
Period size: 162 Copynumber: 2.0 Consensus size: 165
533867 TTAGATTTGA
533877 TATTCAAATACAGATACTCCTGCTTGTGGCTCTCGTCTTTTCAGTATTTACTTTGTTTCTTACAT
1 TATTCAAATACAGATACTCCTGCTTGTGGCTCTCGTCTTTTCAGTATTTACTTTGTTTCTTACAT
533942 TTCTCTCTCACCAGTTACTCAATTTCAGCCTTTTCTGTCTTATATTTG-CTA-TCTCTATTCCAT
66 TTCTCTCTCACCAGTTACTCAATTTCAGCCTTTTCTGTCTTATATTTGTCTATTCTCTATTCCAT
534005 TC-TTTTTTCCTTCC-TTTATTCAACCCTCAGCTAC
131 TCTTTTTTTCCTTCCTTTTATTC-ACCCTCAGCTAC
534039 TATTCAAATACAGATACTCCTGCTTGTGGCTCTCGTCTTTTCAGTATTTACTTTGTTTCTTACAT
1 TATTCAAATACAGATACTCCTGCTTGTGGCTCTCGTCTTTTCAGTATTTACTTTGTTTCTTACAT
534104 TTCTCTCTCACCAGTTACTCAATTTCAGCCTTTTCTGTCTTATATTTGTCTATTCTCTATTCCAT
66 TTCTCTCTCACCAGTTACTCAATTTCAGCCTTTTCTGTCTTATATTTGTCTATTCTCTATTCCAT
534169 TCTTTTTTTTCCTTCCTTTTATTCACCCTCAGCTAC
131 TC-TTTTTTTCCTTCCTTTTATTCACCCTCAGCTAC
534205 ATAACCGAGC
Statistics
Matches: 161, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
162 113 0.70
163 3 0.02
164 14 0.09
166 24 0.15
167 7 0.04
ACGTcount: A:0.17, C:0.27, G:0.08, T:0.48
Consensus pattern (165 bp):
TATTCAAATACAGATACTCCTGCTTGTGGCTCTCGTCTTTTCAGTATTTACTTTGTTTCTTACAT
TTCTCTCTCACCAGTTACTCAATTTCAGCCTTTTCTGTCTTATATTTGTCTATTCTCTATTCCAT
TCTTTTTTTCCTTCCTTTTATTCACCCTCAGCTAC
Found at i:537571 original size:16 final size:16
Alignment explanation
Indices: 537550--537582 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
537540 AATTAGTTAC
537550 TTTCCT-AGTTTAAGAT
1 TTTCCTAAG-TTAAGAT
537566 TTTCCTAAGTTAAGAT
1 TTTCCTAAGTTAAGAT
537582 T
1 T
537583 ACAGCTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.48
Consensus pattern (16 bp):
TTTCCTAAGTTAAGAT
Found at i:539037 original size:12 final size:12
Alignment explanation
Indices: 539020--539044 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
539010 TTTTATATAT
539020 CCAGAAAATTAC
1 CCAGAAAATTAC
539032 CCAGAAAATTAC
1 CCAGAAAATTAC
539044 C
1 C
539045 AAAGACACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.28, G:0.08, T:0.16
Consensus pattern (12 bp):
CCAGAAAATTAC
Found at i:544295 original size:11 final size:10
Alignment explanation
Indices: 544249--544332 Score: 57
Period size: 11 Copynumber: 8.1 Consensus size: 10
544239 CGATAATATA
544249 ATAATTATTTT
1 ATAA-TATTTT
* *
544260 ATAGTATTTAG
1 ATAATATTT-T
544271 ATAA-A-TTT
1 ATAATATTTT
544279 ATTAATAATTTT
1 A-TAAT-ATTTT
*
544291 ATAATCTTTT
1 ATAATATTTT
*
544301 AATAA-ATTTA
1 -ATAATATTTT
544311 ATAAGTATTTT
1 ATAA-TATTTT
544322 ATAATATTTT
1 ATAATATTTT
544332 A
1 A
544333 AACTTTATTT
Statistics
Matches: 57, Mismatches: 8, Indels: 17
0.70 0.10 0.21
Matches are distributed among these distances:
8 1 0.02
9 9 0.16
10 20 0.35
11 23 0.40
12 4 0.07
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.54
Consensus pattern (10 bp):
ATAATATTTT
Found at i:544308 original size:20 final size:21
Alignment explanation
Indices: 544280--544332 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
544270 GATAAATTTA
*
544280 TTAAT-AATTTTATAA-TCTT
1 TTAATAAATTTTATAAGTATT
*
544299 TTAATAAATTTAATAAGTATT
1 TTAATAAATTTTATAAGTATT
544320 TT-ATAATATTTTA
1 TTAATAA-ATTTTA
544333 AACTTTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 5 0.18
20 13 0.46
21 10 0.36
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (21 bp):
TTAATAAATTTTATAAGTATT
Found at i:544332 original size:31 final size:30
Alignment explanation
Indices: 544247--544333 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 30
544237 TTCGATAATA
*
544247 TAATAATTATTTTATAGTA-TTTAGATAAATT
1 TAATAA-TATTTTATAATATTTTA-ATAAATT
* *
544278 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATATTTTAATAAATT
544309 TAATAAGTATTTTATAATATTTTAA
1 TAATAA-TATTTTATAATATTTTAA
544334 ACTTTATTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 42 0.88
32 5 0.10
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (30 bp):
TAATAATATTTTATAATATTTTAATAAATT
Found at i:545120 original size:31 final size:30
Alignment explanation
Indices: 545085--545171 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
545075 TCAATAAAGT
545085 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAAATTATAAAATA-TTATTAAATTTA
* *
545116 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAA-TATTATTAAATTTA
* *
545147 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAAT-ATTATTA
545172 TATTATTGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 44 0.92
32 3 0.06
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (30 bp):
TTAAAAAATTATAAAATATTATTAAATTTA
Found at i:545147 original size:20 final size:20
Alignment explanation
Indices: 545080--545147 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 20
545070 TTTCGTCAAT
*
545080 AAAG-TTTAAAAAATTA-TA
1 AAAGATTTATAAAATTATTA
* * *
545098 AAATACTTATTAAATTTATTA
1 AAAGATTTA-TAAAATTATTA
545119 AAAGA-TTATAAAATTATTA
1 AAAGATTTATAAAATTATTA
545138 ATAA-ATTTAT
1 A-AAGATTTAT
545148 CTAAATACTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 3 0.08
19 15 0.38
20 15 0.38
21 6 0.15
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (20 bp):
AAAGATTTATAAAATTATTA
Found at i:554287 original size:24 final size:24
Alignment explanation
Indices: 554255--554304 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
554245 TTCGTTTTTA
*
554255 TTTAGTTAAGATGAACCTCACGAG
1 TTTAGTTAAGATGAACATCACGAG
*
554279 TTTAGTTAAGATGATCATCACGAG
1 TTTAGTTAAGATGAACATCACGAG
554303 TT
1 TT
554305 AATTATCGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (24 bp):
TTTAGTTAAGATGAACATCACGAG
Found at i:556436 original size:21 final size:21
Alignment explanation
Indices: 556409--556478 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
556399 GACCATTATG
*
556409 GTACTAACGTGATAATTCATT
1 GTACTAACATGATAATTCATT
* * * * **
556430 ATACTAACTTG-CAATCCACG
1 GTACTAACATGATAATTCATT
556450 GTACTAACATGATAATTCATT
1 GTACTAACATGATAATTCATT
556471 GTACTAAC
1 GTACTAAC
556479 TTGCAATCCA
Statistics
Matches: 36, Mismatches: 12, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
20 14 0.39
21 22 0.61
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (21 bp):
GTACTAACATGATAATTCATT
Found at i:556456 original size:20 final size:20
Alignment explanation
Indices: 556431--556492 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
556421 TAATTCATTA
556431 TACTAACTTGCAATCCACGG
1 TACTAACTTGCAATCCACGG
* * * **
556451 TACTAACATGATAATTCATTG
1 TACTAACTTG-CAATCCACGG
556472 TACTAACTTGCAATCCACGG
1 TACTAACTTGCAATCCACGG
556492 T
1 T
556493 GCTGACGTGA
Statistics
Matches: 31, Mismatches: 10, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.31
Consensus pattern (20 bp):
TACTAACTTGCAATCCACGG
Found at i:556508 original size:41 final size:41
Alignment explanation
Indices: 556408--556509 Score: 159
Period size: 41 Copynumber: 2.5 Consensus size: 41
556398 TGACCATTAT
556408 GGTACTAACGTGATAATTCATTATACTAACTTGCAATCCAC
1 GGTACTAACGTGATAATTCATTATACTAACTTGCAATCCAC
* *
556449 GGTACTAACATGATAATTCATTGTACTAACTTGCAATCCAC
1 GGTACTAACGTGATAATTCATTATACTAACTTGCAATCCAC
* * *
556490 GGTGCTGACGTGACAATTCA
1 GGTACTAACGTGATAATTCA
556510 AAAGATGGTA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (41 bp):
GGTACTAACGTGATAATTCATTATACTAACTTGCAATCCAC
Found at i:558180 original size:3 final size:3
Alignment explanation
Indices: 558172--558225 Score: 74
Period size: 3 Copynumber: 18.0 Consensus size: 3
558162 ATTAAATCGT
* *
558172 TTA TTA TTA TTA TTA TTA TTAA ATA GT- TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
558217 TTA TTA TTA
1 TTA TTA TTA
558226 AGTAAGAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
2 1 0.02
3 43 0.93
4 2 0.04
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:558192 original size:27 final size:27
Alignment explanation
Indices: 558160--558219 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
558150 TTGTTAATTG
*
558160 TTATTAAATCGTTTATTATTATTATTA
1 TTATTAAATAGTTTATTATTATTATTA
558187 TTATTAAATAGTTTATTATTATTATTA
1 TTATTAAATAGTTTATTATTATTATTA
558214 TTATTA
1 TTATTA
558220 TTATTAAGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (27 bp):
TTATTAAATAGTTTATTATTATTATTA
Found at i:561970 original size:18 final size:18
Alignment explanation
Indices: 561944--562029 Score: 77
Period size: 18 Copynumber: 4.8 Consensus size: 18
561934 TTAATCTAAG
561944 TCTGATAACTGTAAAACA
1 TCTGATAACTGTAAAACA
* *
561962 TCTGCTAACTG-AAAATCG
1 TCTGATAACTGTAAAA-CA
* *
561980 TCTGATAACTAT-AAATA
1 TCTGATAACTGTAAAACA
* **
561997 TCTGATAACTGTGAAATG
1 TCTGATAACTGTAAAACA
*
562015 TCTGATAACCGTAAA
1 TCTGATAACTGTAAA
562030 CATTTAGAAT
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
17 15 0.27
18 40 0.73
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (18 bp):
TCTGATAACTGTAAAACA
Found at i:562007 original size:35 final size:36
Alignment explanation
Indices: 561943--562023 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 36
561933 ATTAATCTAA
* *
561943 GTCTGATAACTGTAAAACATCTGCTAACTG-AAAAT
1 GTCTGATAACTATAAAACATCTGATAACTGTAAAAT
* *
561978 CGTCTGATAACTAT-AAATATCTGATAACTGTGAAAT
1 -GTCTGATAACTATAAAACATCTGATAACTGTAAAAT
562014 GTCTGATAAC
1 GTCTGATAAC
562024 CGTAAACATT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
35 24 0.60
36 16 0.40
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (36 bp):
GTCTGATAACTATAAAACATCTGATAACTGTAAAAT
Found at i:563606 original size:22 final size:22
Alignment explanation
Indices: 563580--563625 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
563570 TCCAATCAAC
*
563580 TTTCTAA-CTTAAAATTCCAGCA
1 TTTCTAATATTAAAATT-CAGCA
563602 TTTCTAATATTAAAATTCAGCA
1 TTTCTAATATTAAAATTCAGCA
563624 TT
1 TT
563626 AACACTCCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.37, C:0.17, G:0.04, T:0.41
Consensus pattern (22 bp):
TTTCTAATATTAAAATTCAGCA
Found at i:564855 original size:29 final size:29
Alignment explanation
Indices: 564773--564857 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 29
564763 ATAAAATATA
564773 TAACTTTTCAAAATTATATTTTAGTACCT
1 TAACTTTTCAAAATTATATTTTAGTACCT
* * * *
564802 AAACGTTTTCAAAGTTTATACTTTAG-CCCTT
1 TAAC-TTTTCAAA-ATTATATTTTAGTACC-T
564833 TAACTTTT-AAAACTTATATTTTAGT
1 TAACTTTTCAAAA-TTATATTTTAGT
564858 CACTAGTCAA
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
29 16 0.36
30 14 0.32
31 14 0.32
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (29 bp):
TAACTTTTCAAAATTATATTTTAGTACCT
Found at i:565888 original size:26 final size:26
Alignment explanation
Indices: 565859--565908 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
565849 CTATTTGCAC
*
565859 TTGCATC-CTGTATTTCATCTTTGCTT
1 TTGCATCTC-GTATTGCATCTTTGCTT
*
565885 TTGCATCTCGTATTGCGTCTTTGC
1 TTGCATCTCGTATTGCATCTTTGC
565909 ATTTACATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 20 0.95
27 1 0.05
ACGTcount: A:0.10, C:0.24, G:0.16, T:0.50
Consensus pattern (26 bp):
TTGCATCTCGTATTGCATCTTTGCTT
Found at i:567918 original size:20 final size:20
Alignment explanation
Indices: 567893--567935 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
567883 TCTTAAGGCA
567893 CATTTAGGACCATATAGATG
1 CATTTAGGACCATATAGATG
* * *
567913 CATTTAGGATCATGTAGTTG
1 CATTTAGGACCATATAGATG
567933 CAT
1 CAT
567936 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:574452 original size:60 final size:61
Alignment explanation
Indices: 574346--574500 Score: 149
Period size: 60 Copynumber: 2.6 Consensus size: 61
574336 TTAGAAGATG
* * * * * * *
574346 CAAAAGTTTAGGGACTGA-TTAGAATGATATTCAT-AGTTTAGGGATGAAATTGAAAT-ATT
1 CAAAAGTTTAAGGACTAATTTAGAATGA-AGTCATAAATCTAGGGATGAAACTAAAATGATT
*
574405 CAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAAATCTA-GGATGAAACTAAAATGTTT
1 CAAAAGTTTAAGGACTAATTTAGAATGA-AGTCATAAATCTAGGGATGAAACTAAAATGATT
* * *
574466 GAAAA-TTTAAAGACTAATTTAAAATGAAGGTCATA
1 CAAAAGTTTAAGGACTAATTTAGAATGAA-GTCATA
574501 GTTTAAGTAC
Statistics
Matches: 80, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
59 17 0.21
60 53 0.66
61 10 0.12
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (61 bp):
CAAAAGTTTAAGGACTAATTTAGAATGAAGTCATAAATCTAGGGATGAAACTAAAATGATT
Found at i:576076 original size:32 final size:32
Alignment explanation
Indices: 576040--576101 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
576030 AGAGAGAAAA
576040 GGTAGACCATGTTAAATTGAACCAGATTTTAT
1 GGTAGACCATGTTAAATTGAACCAGATTTTAT
* *
576072 GGTAGACCATGTTAAATTGAATCGGATTTT
1 GGTAGACCATGTTAAATTGAACCAGATTTT
576102 CCCAATGTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.35
Consensus pattern (32 bp):
GGTAGACCATGTTAAATTGAACCAGATTTTAT
Found at i:577213 original size:27 final size:27
Alignment explanation
Indices: 577178--577229 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
577168 ACTAAAACAG
*
577178 AAAGCAAATTTTACAAACCAAAAAAAGA
1 AAAGCAAA-TTGACAAACCAAAAAAAGA
*
577206 AAAG-AAATTGATAAACCAAAAAAA
1 AAAGCAAATTGACAAACCAAAAAAA
577230 AAGATAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 15 0.68
27 3 0.14
28 4 0.18
ACGTcount: A:0.67, C:0.12, G:0.08, T:0.13
Consensus pattern (27 bp):
AAAGCAAATTGACAAACCAAAAAAAGA
Found at i:578543 original size:60 final size:59
Alignment explanation
Indices: 578470--578603 Score: 153
Period size: 60 Copynumber: 2.2 Consensus size: 59
578460 ATCGGGTGAT
* * *
578470 CATTTTGTTACTTTTAATAG-TGAATGAACTCAATAAAGTAATGTCATATAGTCAGGAGAC
1 CATTTTG-TACTTTTAATAGTTGAAAG-ACTCAACAAAGTAATGTCATATAATCAGGAGAC
** * *
578530 CATTTTGTAACTTTTAATAGTTGAAAGACTCGGCAAAGTAATGTCCTATAATCAGGGGAC
1 CATTTTGT-ACTTTTAATAGTTGAAAGACTCAACAAAGTAATGTCATATAATCAGGAGAC
*
578590 AATTTGTGTACTTT
1 CATTT-TGTACTTT
578604 GCCATATATA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
59 1 0.02
60 54 0.86
61 8 0.13
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.36
Consensus pattern (59 bp):
CATTTTGTACTTTTAATAGTTGAAAGACTCAACAAAGTAATGTCATATAATCAGGAGAC
Found at i:583206 original size:59 final size:59
Alignment explanation
Indices: 583143--583254 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 59
583133 ATGGTCTCTT
*
583143 GACTATATGACACTGCTTTGTTGAGTCCC-CTGACTATTAAAAGTTACAAAATGATCCAC
1 GACTATAGGACACTGCTTTGTTGAGTCCCTC-GACTATTAAAAGTTACAAAATGATCCAC
*** * *
583202 GACTATAGGATGTTGCTTTGTTGAGTTCTTCGACTATTAAAAGTTACAAAATG
1 GACTATAGGACACTGCTTTGTTGAGTCCCTCGACTATTAAAAGTTACAAAATG
583255 GTCAACCAAC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 45 0.98
60 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (59 bp):
GACTATAGGACACTGCTTTGTTGAGTCCCTCGACTATTAAAAGTTACAAAATGATCCAC
Found at i:583544 original size:60 final size:60
Alignment explanation
Indices: 583480--583611 Score: 155
Period size: 59 Copynumber: 2.2 Consensus size: 60
583470 TCGGGTGATT
* *
583480 ATTTTGTAACTTTTAG-TAGTAAGGGGACTCAACAAAGCAACATCTTATAGTTAGGG-GACC
1 ATTTTGTAACTTTTAGATAGTAA-GGGACTCAACAAAACAACATCATATAG-TAGGGAGACC
* * * *
583540 ATTTTGTAA-TTTTTGATAGTTAGTGACTCAACAAAACAACATCATATAGTAGGGAGATC
1 ATTTTGTAACTTTTAGATAGTAAGGGACTCAACAAAACAACATCATATAGTAGGGAGACC
583599 A-TTTGTATACTTT
1 ATTTTGTA-ACTTT
583612 ACCCTAAAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
58 11 0.18
59 34 0.55
60 17 0.27
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (60 bp):
ATTTTGTAACTTTTAGATAGTAAGGGACTCAACAAAACAACATCATATAGTAGGGAGACC
Found at i:584173 original size:11 final size:12
Alignment explanation
Indices: 584141--584167 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
584131 GCAAGGTACT
584141 AAAATGAAACAA
1 AAAATGAAACAA
584153 AAAATGAAACAA
1 AAAATGAAACAA
584165 AAA
1 AAA
584168 CTAAACTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.78, C:0.07, G:0.07, T:0.07
Consensus pattern (12 bp):
AAAATGAAACAA
Found at i:584766 original size:24 final size:23
Alignment explanation
Indices: 584726--584774 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
584716 CTCCTAACTT
* *
584726 AAAACCTTAAATTATAAACCTTA
1 AAAACCTTAAATCATAAACCCTA
584749 AAAACCTCTAAATCATAAACCCTA
1 AAAACCT-TAAATCATAAACCCTA
584773 AA
1 AA
584775 TTCTAACTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.53, C:0.22, G:0.00, T:0.24
Consensus pattern (23 bp):
AAAACCTTAAATCATAAACCCTA
Found at i:586883 original size:31 final size:30
Alignment explanation
Indices: 586848--586922 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
586838 CGTTAACCTT
* *
586848 AAGTGACCACATTTTAAATAAAACAAAACGA
1 AAGTGACCA-AATCTAAATAAAACAAAACGA
**
586879 AAGTGACCAAATCTAGTTAAAACAAAACGA
1 AAGTGACCAAATCTAAATAAAACAAAACGA
586909 AAGTGACCAAATCT
1 AAGTGACCAAATCT
586923 TATGTTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 31 0.77
31 9 0.22
ACGTcount: A:0.52, C:0.17, G:0.12, T:0.19
Consensus pattern (30 bp):
AAGTGACCAAATCTAAATAAAACAAAACGA
Found at i:586902 original size:30 final size:30
Alignment explanation
Indices: 586866--586922 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
586856 ACATTTTAAA
586866 TAAAACAAAACGAAAGTGACCAAATCTAGT
1 TAAAACAAAACGAAAGTGACCAAATCTAGT
586896 TAAAACAAAACGAAAGTGACCAAATCT
1 TAAAACAAAACGAAAGTGACCAAATCT
586923 TATGTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.54, C:0.18, G:0.12, T:0.16
Consensus pattern (30 bp):
TAAAACAAAACGAAAGTGACCAAATCTAGT
Found at i:588202 original size:2 final size:2
Alignment explanation
Indices: 588195--588260 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
588185 CAATAAATTA
588195 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
588237 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
588261 GTGTCATACG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:588431 original size:2 final size:2
Alignment explanation
Indices: 588424--588452 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
588414 AATCAAGAAT
588424 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 T
588453 TTGAGTCGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:592838 original size:15 final size:15
Alignment explanation
Indices: 592805--592847 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
592795 AAAATAATAT
* *
592805 TAAAATTAAAACTAA
1 TAAAAATAAAACAAA
592820 -AAAAATAAAACAAA
1 TAAAAATAAAACAAA
592834 TAAAAAT-AAACAAA
1 TAAAAATAAAACAAA
592848 CAAACACTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 19 0.76
15 6 0.24
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.16
Consensus pattern (15 bp):
TAAAAATAAAACAAA
Found at i:596111 original size:23 final size:23
Alignment explanation
Indices: 596067--596115 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
596057 ATAAAGAACC
*
596067 AAAATAAACTTAAATATACCATT
1 AAAATAAACTTAAACATACCATT
*
596090 AAAATAAAGTTAAAACAT-CCATT
1 AAAATAAACTT-AAACATACCATT
596113 AAA
1 AAA
596116 CCAACACCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTTAAACATACCATT
Found at i:597577 original size:19 final size:19
Alignment explanation
Indices: 597541--597578 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
597531 TTCATTTTAC
*
597541 TATTATTATTCTATATTAT
1 TATTATTATTCTAAATTAT
*
597560 TATTATTATTTTAAATTAT
1 TATTATTATTCTAAATTAT
597579 AAAAAAATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (19 bp):
TATTATTATTCTAAATTAT
Found at i:602600 original size:16 final size:17
Alignment explanation
Indices: 602579--602611 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
602569 GTTCTTGATG
*
602579 GTTAGTTTG-TTGTTGT
1 GTTAGTTAGTTTGTTGT
602595 GTTAGTTAGTTTGTTGT
1 GTTAGTTAGTTTGTTGT
602612 TTAAGGTTGT
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:0.09, C:0.00, G:0.30, T:0.61
Consensus pattern (17 bp):
GTTAGTTAGTTTGTTGT
Found at i:603760 original size:85 final size:85
Alignment explanation
Indices: 603621--603811 Score: 210
Period size: 85 Copynumber: 2.2 Consensus size: 85
603611 ATATATCTCT
* * * * * *
603621 GATGACACGCAATTGTGTGTCATAAATCTATTACTCGCATTTATGACTCGCATTGCACT-TCATT
1 GATGACACACATTTGTGTGTCATAAATCTATGACACACATTTATGACTCACATTGC-CTGTCATT
* *
603685 G-AA-GC-CTCCATTATAAATGAA
65 GAAACACACGCCATTA-AAA--AA
* * *
603706 GATGACACACATTTGTGTGTCATAAATTTATGACACACATTTATGACTTACATTGCGTGTCATTG
1 GATGACACACATTTGTGTGTCATAAATCTATGACACACATTTATGACTCACATTGCCTGTCATTG
603771 AAACACACGCCATTAAAAAA
66 AAACACACGCCATTAAAAAA
*
603791 GATGACACACATTCGTGTGTC
1 GATGACACACATTTGTGTGTC
603812 GTGATTGTAT
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
84 1 0.01
85 76 0.84
86 2 0.02
87 4 0.04
88 7 0.08
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Consensus pattern (85 bp):
GATGACACACATTTGTGTGTCATAAATCTATGACACACATTTATGACTCACATTGCCTGTCATTG
AAACACACGCCATTAAAAAA
Found at i:603838 original size:2 final size:2
Alignment explanation
Indices: 603831--603859 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
603821 TGTCGTAAAT
603831 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 T
603860 TGTAGATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:605787 original size:22 final size:22
Alignment explanation
Indices: 605759--605804 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
605749 TCTTTAACCT
*
605759 TGTAAATGAACTTCTCATCTAG
1 TGTAAATGAACTACTCATCTAG
*
605781 TGTAAATGAACTAGTCATCTAG
1 TGTAAATGAACTACTCATCTAG
605803 TG
1 TG
605805 GAAACGGTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (22 bp):
TGTAAATGAACTACTCATCTAG
Found at i:606139 original size:26 final size:26
Alignment explanation
Indices: 606109--606200 Score: 75
Period size: 26 Copynumber: 3.6 Consensus size: 26
606099 TTGTTGGAAA
606109 CGAAGAGGAGAAAAGAGAAGGGACAC
1 CGAAGAGGAGAAAAGAGAAGGGACAC
* * * * * *
606135 CGAAGACGAAAAAAAAGAA-AGAAAA
1 CGAAGAGGAGAAAAGAGAAGGGACAC
*
606160 TGAAGAGG-GAAAAGGAGAAGGGACAC
1 CGAAGAGGAGAAAA-GAGAAGGGACAC
606186 CGCAA-AGGA-AAAAGA
1 CG-AAGAGGAGAAAAGA
606201 AAGAGGAGAA
Statistics
Matches: 48, Mismatches: 14, Indels: 9
0.68 0.20 0.13
Matches are distributed among these distances:
24 4 0.08
25 15 0.31
26 27 0.56
27 2 0.04
ACGTcount: A:0.57, C:0.10, G:0.33, T:0.01
Consensus pattern (26 bp):
CGAAGAGGAGAAAAGAGAAGGGACAC
Found at i:607991 original size:20 final size:20
Alignment explanation
Indices: 607966--608003 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
607956 TTCCCATTAA
607966 AGTGCATCGATACATTCTAC
1 AGTGCATCGATACATTCTAC
*
607986 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
608004 TTAATATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:608019 original size:24 final size:24
Alignment explanation
Indices: 607987--608049 Score: 108
Period size: 24 Copynumber: 2.6 Consensus size: 24
607977 ACATTCTACA
* *
607987 GTGCATCGATGCATTCTTTAATAT
1 GTGCATCGATGCACTCTTTAACAT
608011 GTGCATCGATGCACTCTTTAACAT
1 GTGCATCGATGCACTCTTTAACAT
608035 GTGCATCGATGCACT
1 GTGCATCGATGCACT
608050 ACCCATGCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (24 bp):
GTGCATCGATGCACTCTTTAACAT
Found at i:608127 original size:47 final size:45
Alignment explanation
Indices: 608054--608158 Score: 131
Period size: 47 Copynumber: 2.3 Consensus size: 45
608044 TGCACTACCC
* * *
608054 ATGCATCGATACACAAATTACCTTCGATGTTTTCATTTTTTAAAGGG
1 ATGCATCGATACACAAATTACATTCGATG-TTTC-TTCTTTAAAGAG
* * *
608101 ATGCATCGATGCACTAATTGCATTCGATGTTTCTTCTTTAAAGAG
1 ATGCATCGATACACAAATTACATTCGATGTTTCTTCTTTAAAGAG
608146 -TGCATCGATACAC
1 ATGCATCGATACAC
608159 CTTGCCCATA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
44 12 0.24
45 10 0.20
46 4 0.08
47 25 0.49
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (45 bp):
ATGCATCGATACACAAATTACATTCGATGTTTCTTCTTTAAAGAG
Found at i:610356 original size:2 final size:2
Alignment explanation
Indices: 610349--610400 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
610339 TCAATCTACA
610349 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
610391 AT AT AT AT AT
1 AT AT AT AT AT
610401 TTTATGACAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:613953 original size:79 final size:78
Alignment explanation
Indices: 613712--613953 Score: 281
Period size: 79 Copynumber: 3.1 Consensus size: 78
613702 TTGTTATCCC
** **
613712 TTGAGGTC-CTGGATTCATGCTCCATGTATGTAGAGGTGTATAAGCGTTCAATGTCAAATAATTG
1 TTGAGGTCTC-GGATTTGTGCTCCATGTATGTAG-GGTGTATAAGCGTTCAATGTCAAATGTTTG
*
613776 AGAATATTTTAT-TCT
64 AGAATCTTTTATCT-T
* * * ** *
613791 TTGAGGTTTCGAATTTGAGAACCATGTATGTAGGGATGTATAAGTGTTCAATGTCAAATGTTTGA
1 TTGAGGTCTCGGATTTGTGCTCCATGTATGTAGGG-TGTATAAGCGTTCAATGTCAAATGTTTGA
* **
613856 GAGTCTTTTATCCC
65 GAATCTTTTATCTT
* *
613870 TTGAGGTCTCGGATTTGTGCTCTATGTATGCAAGGGTGTATAAGCGTTCAATGTCAAATGTTTGA
1 TTGAGGTCTCGGATTTGTGCTCCATGTATG-TAGGGTGTATAAGCGTTCAATGTCAAATGTTTGA
613935 GAATCTTTTATCTT
65 GAATCTTTTATCTT
613949 TTGAG
1 TTGAG
613954 ATCTGGGGGT
Statistics
Matches: 134, Mismatches: 25, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
78 2 0.01
79 127 0.95
80 5 0.04
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.39
Consensus pattern (78 bp):
TTGAGGTCTCGGATTTGTGCTCCATGTATGTAGGGTGTATAAGCGTTCAATGTCAAATGTTTGAG
AATCTTTTATCTT
Found at i:613975 original size:79 final size:78
Alignment explanation
Indices: 613735--614079 Score: 268
Period size: 79 Copynumber: 4.4 Consensus size: 78
613725 TTCATGCTCC
* ** * *
613735 ATGTATGTAGAGGTGTATAAGCGTTCAATGTCAAATAATTGAGAATATTTTAT-TCTTTGAGGTT
1 ATGTATGCAG-GGTGTATAAGCGTTCAATGTCAAATGTTTGAGAATCTTTTATCT-TTTGAGGTC
* *
613799 TCGAATTTGAG-AACC
64 TCGGATTTGAGTAA-T
* * * **
613814 ATGTATGTAGGGATGTATAAGTGTTCAATGTCAAATGTTTGAGAGTCTTTTATCCCTTGAGGTCT
1 ATGTATGCAGGG-TGTATAAGCGTTCAATGTCAAATGTTTGAGAATCTTTTATCTTTTGAGGTCT
* *
613879 CGGATTTGTGCT-CT
65 CGGATTTGAG-TAAT
*
613893 ATGTATGCAAGGGTGTATAAGCGTTCAATGTCAAATGTTTGAGAATCTTTTATCTTTTGAGATCT
1 ATGTATGC-AGGGTGTATAAGCGTTCAATGTCAAATGTTTGAGAATCTTTTATCTTTTGAGGTCT
* ** *
613958 GGGGGTCGAGTAAT
65 CGGATTTGAGTAAT
* * * * * * * ** *
613972 ATGTTTGCAGCAGTGTATAAGTGTTCAATGTCAAATGGTTAACATTCTTTTATCCCTTGAGGTCC
1 ATGTATGCAG-GGTGTATAAGCGTTCAATGTCAAATGTTTGAGAATCTTTTATCTTTTGAGGTCT
** *
614037 CAAATTT-A-AACAT
65 CGGATTTGAGTA-AT
*
614050 CATGTATGCAAAGGTGTATAAGCGTTCAAT
1 -ATGTATGC-AGGGTGTATAAGCGTTCAAT
614080 CTTGATTGAG
Statistics
Matches: 210, Mismatches: 46, Indels: 20
0.76 0.17 0.07
Matches are distributed among these distances:
77 1 0.00
78 8 0.04
79 196 0.93
80 5 0.02
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (78 bp):
ATGTATGCAGGGTGTATAAGCGTTCAATGTCAAATGTTTGAGAATCTTTTATCTTTTGAGGTCTC
GGATTTGAGTAAT
Found at i:613993 original size:158 final size:156
Alignment explanation
Indices: 613705--614079 Score: 398
Period size: 158 Copynumber: 2.4 Consensus size: 156
613695 AGGATTGTTG
* *
613705 TTATCCCTTGAGGTCCTGGATTCATGCTCCATGTATG-TAGAGGTGTATAAGCGTTCAATGTCAA
1 TTATCCCTTGAGGTCC-GGATTTATGCT-CATGTATGCAAG-GGTGTATAAGCGTTCAATGTCAA
* * * * * *
613769 ATAATTGAGAATATTTTATTCTTTGAGGTTTCGAATTTGAGAACCATGTATGTAGGGATGTATAA
63 ATAATTGAGAATATTTTATTCTTTGAGATCTCGAAGTCGAGAACCATGTATGCAGAGATGTATAA
* * *
613834 GTGTTCAATGTCAAATGTTTGAGAGTCTT
128 GTGTTCAATGTCAAATGGTTAACAGTCTT
*
613863 TTATCCCTTGAGGTCTCGGATTTGTGCTCTATGTATGCAAGGGTGTATAAGCGTTCAATGTCAAA
1 TTATCCCTTGAGGTC-CGGATTTATGCTC-ATGTATGCAAGGGTGTATAAGCGTTCAATGTCAAA
** * * ** * *
613928 TGTTTGAGAATCTTTTA-TCTTTTGAGATCTGGGGGTCGAGTAA-TATGTTTGCAGCAG-TGTAT
64 TAATTGAGAATATTTTATTC-TTTGAGATCTCGAAGTCGAG-AACCATGTATGCAG-AGATGTAT
*
613990 AAGTGTTCAATGTCAAATGGTTAACATTCTT
126 AAGTGTTCAATGTCAAATGGTTAACAGTCTT
** ** *
614021 TTATCCCTTGAGGTCCCAAATTTAAACATCATGTATGCAAAGGTGTATAAGCGTTCAAT
1 TTATCCCTTGAGGT-CCGGATTTATGC-TCATGTATGCAAGGGTGTATAAGCGTTCAAT
614080 CTTGATTGAG
Statistics
Matches: 182, Mismatches: 27, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
157 3 0.02
158 170 0.93
159 9 0.05
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (156 bp):
TTATCCCTTGAGGTCCGGATTTATGCTCATGTATGCAAGGGTGTATAAGCGTTCAATGTCAAATA
ATTGAGAATATTTTATTCTTTGAGATCTCGAAGTCGAGAACCATGTATGCAGAGATGTATAAGTG
TTCAATGTCAAATGGTTAACAGTCTT
Found at i:617314 original size:55 final size:55
Alignment explanation
Indices: 617246--617395 Score: 237
Period size: 55 Copynumber: 2.7 Consensus size: 55
617236 CAAATGATAA
* *
617246 GTCTGCTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTTAATAAACGT
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTTAACAAACGT
* * * *
617301 GTCTGCTCCCTATTTCTTTAGAGAGTATAAGACTCAAACAATCTTTAACAATCGT
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTTAACAAACGT
*
617356 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTTGAACA
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
617396 TATTCTCTTA
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 85 1.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.32
Consensus pattern (55 bp):
GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTTAACAAACGT
Found at i:617472 original size:54 final size:54
Alignment explanation
Indices: 617391--617673 Score: 496
Period size: 54 Copynumber: 5.3 Consensus size: 54
617381 TATAAGACTT
* * * *
617391 GAACATATTC-TCTTACAGGTTCACTCCCTCTTTCTTTAGGGAGTATGGAACTC
1 GAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC
617444 GAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC
1 GAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC
*
617498 GAACATCTTCTTCTTATGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC
1 GAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC
617552 GAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC
1 GAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC
**
617606 GAACATCTTCTTCTTACGGGTTCGCTCATTCTTTCTCTAGGGAGTATGGAACTC
1 GAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC
617660 GAACATCTTCTTCT
1 GAACATCTTCTTCT
617674 GCTTTACTAC
Statistics
Matches: 221, Mismatches: 8, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
53 9 0.04
54 212 0.96
ACGTcount: A:0.18, C:0.26, G:0.19, T:0.36
Consensus pattern (54 bp):
GAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC
Found at i:617746 original size:37 final size:37
Alignment explanation
Indices: 617673--617752 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 37
617663 CATCTTCTTC
* * *
617673 TGCTTTACTACTTTCTAGTGAAGACTTCTAGATGATT
1 TGCTTCACTACTCTCTAGTGAAGACTTCAAGATGATT
* *
617710 TGCTTCACTACTCTCTCGTGAAGACTT-AAGTTTGATT
1 TGCTTCACTACTCTCTAGTGAAGACTTCAAG-ATGATT
617747 TGCTTC
1 TGCTTC
617753 GAAGGTCGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 2 0.05
37 35 0.95
ACGTcount: A:0.21, C:0.20, G:0.16, T:0.42
Consensus pattern (37 bp):
TGCTTCACTACTCTCTAGTGAAGACTTCAAGATGATT
Found at i:618091 original size:36 final size:37
Alignment explanation
Indices: 618026--618139 Score: 185
Period size: 37 Copynumber: 3.1 Consensus size: 37
618016 ACTCTTCCGA
* *
618026 GAAGGCTTAAAAAGGATATGCTTCACTACTCTTTGGT
1 GAAGGCTTAAAATGGATTTGCTTCACTACTCTTTGGT
*
618063 GAAGGCTTAAGATGG-TTTGCTTCACTACTCTTTGGT
1 GAAGGCTTAAAATGGATTTGCTTCACTACTCTTTGGT
*
618099 GAAGGCTCAAAATGGATTTGCTTCACTACTCTTTGGT
1 GAAGGCTTAAAATGGATTTGCTTCACTACTCTTTGGT
618136 GAAG
1 GAAG
618140 ACTTGGCTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 33 0.46
37 38 0.54
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (37 bp):
GAAGGCTTAAAATGGATTTGCTTCACTACTCTTTGGT
Found at i:618103 original size:73 final size:73
Alignment explanation
Indices: 618000--618139 Score: 201
Period size: 73 Copynumber: 1.9 Consensus size: 73
617990 CTGATAGTCT
*
618000 GATGGTTTGCTCCAACACTCTTCCGAGAAGGCTTAAAAAGGATATGCTTCACTACTCTTTGGTGA
1 GATGGTTTGCTCCAACACTCTTCCGAGAAGGCTCAAAAAGGATATGCTTCACTACTCTTTGGTGA
618065 AGGCTTAA
66 AGGCTTAA
* ** * * *
618073 GATGGTTTGCTTC-ACTACTCTTTGGTGAAGGCTCAAAATGGATTTGCTTCACTACTCTTTGGTG
1 GATGGTTTGCTCCAAC-ACTCTTCCGAGAAGGCTCAAAAAGGATATGCTTCACTACTCTTTGGTG
618137 AAG
65 AAG
618140 ACTTGGCTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
72 2 0.03
73 57 0.97
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (73 bp):
GATGGTTTGCTCCAACACTCTTCCGAGAAGGCTCAAAAAGGATATGCTTCACTACTCTTTGGTGA
AGGCTTAA
Found at i:623088 original size:72 final size:73
Alignment explanation
Indices: 622971--623121 Score: 261
Period size: 72 Copynumber: 2.1 Consensus size: 73
622961 CCCCTAACAG
622971 GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
1 GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
623036 TTCAT-TT
66 TTCATATT
* * *
623043 GTTCTTGATCATTTGTTATCATCACATTGGTTGCACCACTAACATTCAGATTCTCACCCGAAGTC
1 GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
623108 TTCATATT
66 TTCATATT
623116 -TTCTTG
1 GTTCTTG
623122 TGTAATAGGG
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
72 73 0.97
73 2 0.03
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (73 bp):
GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
TTCATATT
Found at i:623860 original size:55 final size:55
Alignment explanation
Indices: 623789--623896 Score: 180
Period size: 55 Copynumber: 2.0 Consensus size: 55
623779 TGTGGATTAG
* * *
623789 TCTTCAATCAGTTTCAAATTTCTTCATTCATTGGATGTCTTTCTTCATGAATCGT
1 TCTTCAATCAGATTCAAATTTCTTCATTCATCGGATGTCCTTCTTCATGAATCGT
*
623844 TCTTCAGTCAGATTCAAATTTCTTCATTCATCGGATGTCCTTCTTCATGAATC
1 TCTTCAATCAGATTCAAATTTCTTCATTCATCGGATGTCCTTCTTCATGAATC
623897 ATCTGAACGC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.44
Consensus pattern (55 bp):
TCTTCAATCAGATTCAAATTTCTTCATTCATCGGATGTCCTTCTTCATGAATCGT
Found at i:624258 original size:47 final size:47
Alignment explanation
Indices: 624202--624333 Score: 178
Period size: 45 Copynumber: 2.9 Consensus size: 47
624192 CACAAAAAAT
* * **
624202 CCTAACCGCATGATATCTAATTCATATGCTTGTTCGAGAAAAATAAA
1 CCTAACCGCATGATTTCTAGTTCGCATGCTTGTTCGAGAAAAATAAA
* * * *
624249 CCTAGCCGCATGATTTCTAGTTCGCATACATGCTC-A-AAAAATAAA
1 CCTAACCGCATGATTTCTAGTTCGCATGCTTGTTCGAGAAAAATAAA
624294 CCTAACCGCATGATTTCTAGTTCGCATGCTTGTTCGAGAA
1 CCTAACCGCATGATTTCTAGTTCGCATGCTTGTTCGAGAA
624334 GAAAAGAAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
45 40 0.56
46 2 0.03
47 29 0.41
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.30
Consensus pattern (47 bp):
CCTAACCGCATGATTTCTAGTTCGCATGCTTGTTCGAGAAAAATAAA
Found at i:627284 original size:22 final size:22
Alignment explanation
Indices: 627256--627299 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
627246 GAACCCCTTA
627256 CAATTTGCTTTTGTCCAATGCG
1 CAATTTGCTTTTGTCCAATGCG
627278 CAATTTGCTTTTGTCCAATGCG
1 CAATTTGCTTTTGTCCAATGCG
627300 AAGAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (22 bp):
CAATTTGCTTTTGTCCAATGCG
Found at i:629281 original size:50 final size:50
Alignment explanation
Indices: 629222--629369 Score: 271
Period size: 50 Copynumber: 3.0 Consensus size: 50
629212 CTATCGGACA
629222 ATTCTGCAATG-TCCTTCACTAGGCTAGGAACGCTAGTTGGTGTCATGACG
1 ATTCTGCAATGAT-CTTCACTAGGCTAGGAACGCTAGTTGGTGTCATGACG
629272 ATTCTGCAATGATCTTCACTAGGCTAGGAACGCTAGTTGGTGTCATGACG
1 ATTCTGCAATGATCTTCACTAGGCTAGGAACGCTAGTTGGTGTCATGACG
*
629322 ATTCTGCAATGATCTTCACTAGGCTAGGAACACTAGTTGGTGTCATGA
1 ATTCTGCAATGATCTTCACTAGGCTAGGAACGCTAGTTGGTGTCATGA
629370 GCTTGTACTA
Statistics
Matches: 96, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
50 95 0.99
51 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.30
Consensus pattern (50 bp):
ATTCTGCAATGATCTTCACTAGGCTAGGAACGCTAGTTGGTGTCATGACG
Found at i:629404 original size:65 final size:65
Alignment explanation
Indices: 629318--629613 Score: 470
Period size: 65 Copynumber: 4.6 Consensus size: 65
629308 TTGGTGTCAT
* * *
629318 GACGATTCTGCAATGATCTTCACTAGGCTAGGAACACTAGTTGGTGTCATGAGCTTGTACTATCG
1 GACGACTCTGCAACGACCTTCACTAGGCTAGGAACACTAGTTGGTGTCATGAGCTTGTACTATCG
*
629383 GATGACTCTGCAACGACCTTCACTAGGCTAGGAACACTAGTTGGTGTCATGAGCTTGTACTATCG
1 GACGACTCTGCAACGACCTTCACTAGGCTAGGAACACTAGTTGGTGTCATGAGCTTGTACTATCG
* * *
629448 GATGACTCTGCAACGACCTTCACTAGGCTAGGAACACTAATTGGTGTCATGAGCTTGTATTATCG
1 GACGACTCTGCAACGACCTTCACTAGGCTAGGAACACTAGTTGGTGTCATGAGCTTGTACTATCG
* * *
629513 GACGA-TCTGCAATGACCTTCACTAGGCTAGGAACACTAGTAGTTGTCATGAGC-TGATACTATC
1 GACGACTCTGCAACGACCTTCACTAGGCTAGGAACACTAGTTGGTGTCATGAGCTTG-TACTATC
629576 G
65 G
*
629577 GACGATTCTGCAACGACCTTCACTAGGCTAGGAACAC
1 GACGACTCTGCAACGACCTTCACTAGGCTAGGAACAC
629614 AATCATGATT
Statistics
Matches: 216, Mismatches: 13, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
63 2 0.01
64 56 0.26
65 158 0.73
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (65 bp):
GACGACTCTGCAACGACCTTCACTAGGCTAGGAACACTAGTTGGTGTCATGAGCTTGTACTATCG
Found at i:629578 original size:129 final size:130
Alignment explanation
Indices: 629318--629613 Score: 470
Period size: 129 Copynumber: 2.3 Consensus size: 130
629308 TTGGTGTCAT
* * * *
629318 GACGATTCTGCAATGATCTTCACTAGGCTAGGAACACTAGTTGGTGTCATGAGCTTGTACTATCG
1 GACGACTCTGCAACGACCTTCACTAGGCTAGGAACACTAATTGGTGTCATGAGCTTGTACTATCG
* *
629383 GATGACTCTGCAACGACCTTCACTAGGCTAGGAACACTAGTTGGTGTCATGAGCTTGTACTATCG
66 GACGACTCTGCAACGACCTTCACTAGGCTAGGAACACTAGTAGGTGTCATGAGCTTGTACTATCG
* *
629448 GATGACTCTGCAACGACCTTCACTAGGCTAGGAACACTAATTGGTGTCATGAGCTTGTATTATCG
1 GACGACTCTGCAACGACCTTCACTAGGCTAGGAACACTAATTGGTGTCATGAGCTTGTACTATCG
* *
629513 GACGA-TCTGCAATGACCTTCACTAGGCTAGGAACACTAGTAGTTGTCATGAGC-TGATACTATC
66 GACGACTCTGCAACGACCTTCACTAGGCTAGGAACACTAGTAGGTGTCATGAGCTTG-TACTATC
629576 G
130 G
*
629577 GACGATTCTGCAACGACCTTCACTAGGCTAGGAACAC
1 GACGACTCTGCAACGACCTTCACTAGGCTAGGAACAC
629614 AATCATGATT
Statistics
Matches: 153, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
128 2 0.01
129 88 0.58
130 63 0.41
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (130 bp):
GACGACTCTGCAACGACCTTCACTAGGCTAGGAACACTAATTGGTGTCATGAGCTTGTACTATCG
GACGACTCTGCAACGACCTTCACTAGGCTAGGAACACTAGTAGGTGTCATGAGCTTGTACTATCG
Found at i:629993 original size:31 final size:31
Alignment explanation
Indices: 629955--630037 Score: 130
Period size: 31 Copynumber: 2.7 Consensus size: 31
629945 TAACGCGGTT
*
629955 AGTACCTAAACTATAAGTTTTGATCCATTTC
1 AGTACCTAAACTATAAATTTTGATCCATTTC
629986 AGTACCTAAACTATAAATTTTGATCCATTTC
1 AGTACCTAAACTATAAATTTTGATCCATTTC
* * *
630017 AGTATCTAAACTTTCAATTTT
1 AGTACCTAAACTATAAATTTT
630038 TTCAAAATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.41
Consensus pattern (31 bp):
AGTACCTAAACTATAAATTTTGATCCATTTC
Found at i:631822 original size:21 final size:21
Alignment explanation
Indices: 631798--631841 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
631788 ATATCTTCAT
*
631798 CTTATACTATTAAAAATTATA
1 CTTATAATATTAAAAATTATA
**
631819 CTTATAATATTAAATTTTATA
1 CTTATAATATTAAAAATTATA
631840 CT
1 CT
631842 ATAGCTAATA
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:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (21 bp):
CTTATAATATTAAAAATTATA
Done.