Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000186.1 Hibiscus syriacus cultivar Beakdansim tig00000329_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: 3152351
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 17 of 17
Found at i:3037334 original size:24 final size:24
Alignment explanation
Indices: 3037282--3037355 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
3037272 ATATATAATA
* *
3037282 ATATAAATATAAACTATATAGTTT
1 ATATATATATAAACTATATACTTT
3037306 ATATATATATAATAC-ATATAC--T
1 ATATATATATAA-ACTATATACTTT
* *
3037328 -T-TGTATATAAACTATATAGTTT
1 ATATATATATAAACTATATACTTT
3037350 ATATAT
1 ATATAT
3037356 GTTATATTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
19 2 0.05
20 13 0.33
21 1 0.03
22 2 0.05
23 1 0.03
24 18 0.46
25 2 0.05
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (24 bp):
ATATATATATAAACTATATACTTT
Found at i:3037345 original size:2 final size:2
Alignment explanation
Indices: 3036986--3037325 Score: 60
Period size: 2 Copynumber: 172.0 Consensus size: 2
3036976 TTTTTGAATT
* * * *
3036986 TA TA TA GTA TA AA T- TA TA TA AA TA TA AA CTA TA T- TA TA TA GA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * *
3037028 GTA TA AA TA TCA TC TA TA GTA TA TA -A TA TA TA AA TA TA AA CTA
1 -TA TA TA TA T-A TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA
**
3037071 TA GG T- TA TA TA -A TA TA TA TA TA TA TA -A TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
3037109 CA AA TA GTT TA TA TA TT TCA T- TA -A TA AA CTA TA TA TA TA -A
1 TA TA TA -TA TA TA TA TA T-A TA TA TA TA TA -TA TA TA TA TA TA
* * * * *
3037149 T- TCA TA TG TA AA T- TA TA TA GTT TA TA CA CA TA -A T- TCA TA
1 TA T-A TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA T-A TA
* * * *
3037188 TA TA -A TA -A TG TA AA CTA TA TA T- TA TA CA -A TA TA TA AA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
3037227 TCA AA TA TA GTA TA TA GTT TA TA TA TA AA T- TA TA GTT TA TA TA
1 T-A TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * *
3037270 TA -A TA TA TA -A TA -A TA TA AA TA TA AA CTA TA TA GTT 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
*
3037311 TA TA TA -A TA CA TA TA
1 TA TA TA TA TA TA TA TA
3037326 CTTTGTATAT
Statistics
Matches: 237, Mismatches: 59, Indels: 84
0.62 0.16 0.22
Matches are distributed among these distances:
1 23 0.10
2 191 0.81
3 23 0.10
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (2 bp):
TA
Found at i:3037354 original size:18 final size:18
Alignment explanation
Indices: 3037231--3037316 Score: 77
Period size: 18 Copynumber: 4.6 Consensus size: 18
3037221 TAAATATCAA
*
3037231 ATATAGTATATAGTTTAT
1 ATATAATATATAGTTTAT
3037249 ATATAA-ATTATAGTTTAT
1 ATATAATA-TATAGTTTAT
* *
3037267 ATATAATATATAATAATATAA
1 ATATAATATATAGT--T-TAT
3037288 ATATAAACTATATAGTTTAT
1 ATAT-AA-TATATAGTTTAT
3037308 ATAT-ATATA
1 ATATAATATA
3037317 ATACATATAC
Statistics
Matches: 56, Mismatches: 5, Indels: 15
0.74 0.07 0.20
Matches are distributed among these distances:
17 5 0.09
18 27 0.48
19 1 0.02
20 7 0.12
21 7 0.12
22 2 0.04
23 7 0.12
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (18 bp):
ATATAATATATAGTTTAT
Found at i:3038483 original size:18 final size:18
Alignment explanation
Indices: 3038460--3038504 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
3038450 CACGTAGACT
*
3038460 TTAACGGCTGTTAATCCA
1 TTAACGGATGTTAATCCA
*
3038478 TTAACGAATGTTAATCCA
1 TTAACGGATGTTAATCCA
3038496 TTAACGGAT
1 TTAACGGAT
3038505 TGATGATTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (18 bp):
TTAACGGATGTTAATCCA
Found at i:3041132 original size:6 final size:6
Alignment explanation
Indices: 3041121--3041147 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3041111 GACGGGGCTT
3041121 CTGAAC CTGAAC CTGAAC CTGAAC CTG
1 CTGAAC CTGAAC CTGAAC CTGAAC CTG
3041148 GCTGATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.33, G:0.19, T:0.19
Consensus pattern (6 bp):
CTGAAC
Found at i:3043541 original size:45 final size:44
Alignment explanation
Indices: 3043490--3043588 Score: 128
Period size: 44 Copynumber: 2.2 Consensus size: 44
3043480 GGCAAGATCT
*
3043490 GGGTCACATAGAATCAGCATCTCACAAGTACCCTAGG-TGAGGTCC
1 GGGTCACATAGAATCAGCACCTCA-AAGTACCCTAGGCT-AGGTCC
* * * *
3043535 GGGTCACATAGAATCAGCACCTTATAGTATCTTAGGCTAGGTCC
1 GGGTCACATAGAATCAGCACCTCAAAGTACCCTAGGCTAGGTCC
3043579 GGGTCACATA
1 GGGTCACATA
3043589 ACATCGGCAC
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
44 25 0.52
45 23 0.48
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.23
Consensus pattern (44 bp):
GGGTCACATAGAATCAGCACCTCAAAGTACCCTAGGCTAGGTCC
Found at i:3044672 original size:21 final size:21
Alignment explanation
Indices: 3044648--3044701 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
3044638 TCAAGGCTAC
*
3044648 AGTATCGATACTTCTCCTTAG
1 AGTATCAATACTTCTCCTTAG
3044669 AGTATCAATACTTCTCCTTAG
1 AGTATCAATACTTCTCCTTAG
3044690 AGTATCAATACT
1 AGTATCAATACT
3044702 CCTAACATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (21 bp):
AGTATCAATACTTCTCCTTAG
Found at i:3046267 original size:28 final size:28
Alignment explanation
Indices: 3046219--3046272 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
3046209 CATGAAGCTT
* *
3046219 GAAGAAGAAGATGAAAGAAGAAAATGGA
1 GAAGAAGAAGAGGAAAAAAGAAAATGGA
*
3046247 GAAGAAGAA-AGGAAGAAAAGAGAATG
1 GAAGAAGAAGAGGAA-AAAAGAAAATG
3046273 AGGAAAGTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.61, C:0.00, G:0.33, T:0.06
Consensus pattern (28 bp):
GAAGAAGAAGAGGAAAAAAGAAAATGGA
Found at i:3048159 original size:14 final size:14
Alignment explanation
Indices: 3048135--3048174 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
3048125 GGGACATTTA
*
3048135 AAATTAATAAAAAT
1 AAATGAATAAAAAT
*
3048149 AAGTGAAT-AAAAT
1 AAATGAATAAAAAT
3048162 AAATGAATAAAAA
1 AAATGAATAAAAA
3048175 ATAATAATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (14 bp):
AAATGAATAAAAAT
Found at i:3048804 original size:13 final size:13
Alignment explanation
Indices: 3048786--3048818 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
3048776 AGCATTGTGA
*
3048786 AAAGAAAATAATG
1 AAAGAAAATAAAG
3048799 AAAGAAAATAAAG
1 AAAGAAAATAAAG
3048812 AAAGAAA
1 AAAGAAA
3048819 GATGGAGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (13 bp):
AAAGAAAATAAAG
Found at i:3053253 original size:13 final size:13
Alignment explanation
Indices: 3053235--3053288 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
3053225 AAAATTAATG
*
3053235 AAAATAAATGAAT
1 AAAATAAATAAAT
3053248 AAAATAAATAAAT
1 AAAATAAATAAAT
* *
3053261 AAAAAATAATAATGAG
1 AAAATA-AATAA--AT
3053277 AAAATAAATAAA
1 AAAATAAATAAA
3053289 GTAGAAGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
13 18 0.53
14 5 0.15
15 5 0.15
16 6 0.18
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:3060824 original size:16 final size:17
Alignment explanation
Indices: 3060803--3060835 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
3060793 ATGGTACATT
3060803 CATATCTGTGTC-CAAA
1 CATATCTGTGTCTCAAA
3060819 CATATCTGTGTCTCAAA
1 CATATCTGTGTCTCAAA
3060836 TACATTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.33
Consensus pattern (17 bp):
CATATCTGTGTCTCAAA
Found at i:3062650 original size:93 final size:93
Alignment explanation
Indices: 3062540--3062716 Score: 291
Period size: 93 Copynumber: 1.9 Consensus size: 93
3062530 ATATTGTGGT
* * *
3062540 ATTGACACGTGTCTTTATATGATTGGAAGATTAAATATATTGAATTAATTTAAAATTATAACCAT
1 ATTGACACGTATATTTATATGATTAGAAGATTAAATATATTGAATTAATTTAAAATTATAACCAT
*
3062605 TTTGATAGATTGTGTAAGTAATCAGGAC
66 TTTGATAGATTATGTAAGTAATCAGGAC
* * *
3062633 ATTGACACGTATATTTATATGATTAGAAGATTAGATATATTGAATTAATTTAAAATTATGATCAT
1 ATTGACACGTATATTTATATGATTAGAAGATTAAATATATTGAATTAATTTAAAATTATAACCAT
3062698 TTTGATAGATTATGTAAGT
66 TTTGATAGATTATGTAAGT
3062717 TTTTTTAAAG
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 77 1.00
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.41
Consensus pattern (93 bp):
ATTGACACGTATATTTATATGATTAGAAGATTAAATATATTGAATTAATTTAAAATTATAACCAT
TTTGATAGATTATGTAAGTAATCAGGAC
Found at i:3065273 original size:24 final size:24
Alignment explanation
Indices: 3065244--3065323 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 24
3065234 TAGTTTAGGG
3065244 TTAGGGTTTTTATGTTTAACTGGT
1 TTAGGGTTTTTATGTTTAACTGGT
* *
3065268 TTAGGGTTATTTA-GAATAAAGC-GGT
1 TTAGGGTT-TTTATG-TTTAA-CTGGT
* * *
3065293 TTA-GTTTTTTTTGTTTAAATGGT
1 TTAGGGTTTTTATGTTTAACTGGT
3065316 TTAGGGTT
1 TTAGGGTT
3065324 AGATTAAAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
23 12 0.29
24 16 0.38
25 13 0.31
26 1 0.02
ACGTcount: A:0.21, C:0.03, G:0.25, T:0.51
Consensus pattern (24 bp):
TTAGGGTTTTTATGTTTAACTGGT
Found at i:3069781 original size:18 final size:19
Alignment explanation
Indices: 3069744--3069784 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3069734 AAGATTTAAT
*
3069744 TAAATAAAATAGATAATAA
1 TAAATAAAAGAGATAATAA
*
3069763 TAAATAAAAGGGA-AATAA
1 TAAATAAAAGAGATAATAA
3069781 TAAA
1 TAAA
3069785 ATAATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.22
Consensus pattern (19 bp):
TAAATAAAAGAGATAATAA
Found at i:3069840 original size:4 final size:4
Alignment explanation
Indices: 3069825--3069853 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
3069815 TTTAAAGAAG
3069825 AATA AA-A AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AA
3069854 ATAACTGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AATA
Found at i:3070504 original size:12 final size:13
Alignment explanation
Indices: 3070485--3070515 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
3070475 CTAAAATACC
3070485 TATAAAATAATAT
1 TATAAAATAATAT
3070498 T-TAAAATAATAT
1 TATAAAATAATAT
3070510 TATAAA
1 TATAAA
3070516 TCCTAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TATAAAATAATAT
Found at i:3070605 original size:76 final size:71
Alignment explanation
Indices: 3070441--3070630 Score: 220
Period size: 76 Copynumber: 2.6 Consensus size: 71
3070431 TAAAACATCT
* * * * *
3070441 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTATAAAATAATATTTAAAAT
1 TAAAACCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTACAAAATAAAATTAAAAAT
*
3070505 AATATTA
65 AATATCA
*
3070512 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCT---ACAAA-ATAAAAT-TAA
*
3070577 AAATAATATCC
61 AAATAATATCA
* **
3070588 TAAAACTTAATTAAAATACTAAAACCTATTTAATGTAAAATAC
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATAC
3070631 AAAGAAAAAA
Statistics
Matches: 103, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
70 5 0.05
71 38 0.37
74 4 0.04
75 6 0.06
76 50 0.49
ACGTcount: A:0.56, C:0.13, G:0.01, T:0.31
Consensus pattern (71 bp):
TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTACAAAATAAAATTAAAAATA
ATATCA
Found at i:3070654 original size:76 final size:76
Alignment explanation
Indices: 3070441--3070654 Score: 217
Period size: 76 Copynumber: 2.9 Consensus size: 76
3070431 TAAAACATCT
* * * *
3070441 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACC---TATAAA-ATAATATTT-
1 TAAAACCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCAAAAAAAAAGATAATATTTA
*
3070500 AAAATAATATTA
65 AAAATAATATCA
* * * * *
3070512 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCAAAAAAAAAGATAATATTTAA
*
3070577 AAATAATATCC
66 AAATAATATCA
* ** * *
3070588 TAAAACTTAATTAAAATACTAAAACCTATTTAATGTAAAATA-CAAAGAAAAAATATAATGTTTA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCAAA-AAAAAAGATAATATTTA
3070652 AAA
65 AAA
3070655 TATTATTCTA
Statistics
Matches: 119, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
70 5 0.04
71 37 0.31
74 4 0.03
75 10 0.08
76 63 0.53
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (76 bp):
TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCAAAAAAAAAGATAATATTTAA
AAATAATATCA
Found at i:3073884 original size:26 final size:26
Alignment explanation
Indices: 3073848--3073900 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
3073838 AATCAAGTTT
*
3073848 TGAAATTACTCCCTCTTACTTTAACA
1 TGAAATTACTCCCCCTTACTTTAACA
3073874 TGAAATTACTCCCCCTTACTTTAACA
1 TGAAATTACTCCCCCTTACTTTAACA
3073900 T
1 T
3073901 TACTTTAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.30, C:0.28, G:0.04, T:0.38
Consensus pattern (26 bp):
TGAAATTACTCCCCCTTACTTTAACA
Found at i:3073905 original size:11 final size:11
Alignment explanation
Indices: 3073889--3073952 Score: 55
Period size: 11 Copynumber: 6.0 Consensus size: 11
3073879 TTACTCCCCC
3073889 TTACTTTAACA
1 TTACTTTAACA
3073900 TTACTTTAAC-
1 TTACTTTAACA
3073910 --ACTTTAACA
1 TTACTTTAACA
** *
3073919 CTTA-TTCTTCCC
1 -TTACTT-TAACA
3073931 TTACTTTAACA
1 TTACTTTAACA
3073942 TTACTTTAACA
1 TTACTTTAACA
3073953 CTTTAACACT
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
8 8 0.20
11 28 0.68
12 5 0.12
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.45
Consensus pattern (11 bp):
TTACTTTAACA
Found at i:3073915 original size:19 final size:19
Alignment explanation
Indices: 3073891--3073960 Score: 77
Period size: 19 Copynumber: 3.5 Consensus size: 19
3073881 ACTCCCCCTT
3073891 ACTTTAACATTACTTTAAC
1 ACTTTAACATTACTTTAAC
* **
3073910 ACTTTAACACTTATTCTTCCC
1 ACTTTAACA-TTACT-TTAAC
3073931 TTACTTTAACATTACTTTAAC
1 --ACTTTAACATTACTTTAAC
3073952 ACTTTAACA
1 ACTTTAACA
3073961 CTTATTCTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
19 18 0.44
20 4 0.10
21 6 0.15
22 4 0.10
23 9 0.22
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.43
Consensus pattern (19 bp):
ACTTTAACATTACTTTAAC
Found at i:3073936 original size:42 final size:42
Alignment explanation
Indices: 3073886--3073970 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
3073876 AAATTACTCC
3073886 CCCTTACTTTAACATTACTTTAACACTTTAACACTTATTCTT
1 CCCTTACTTTAACATTACTTTAACACTTTAACACTTATTCTT
3073928 CCCTTACTTTAACATTACTTTAACACTTTAACACTTATTCTT
1 CCCTTACTTTAACATTACTTTAACACTTTAACACTTATTCTT
3073970 C
1 C
3073971 TCCCCCTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.28, C:0.27, G:0.00, T:0.45
Consensus pattern (42 bp):
CCCTTACTTTAACATTACTTTAACACTTTAACACTTATTCTT
Found at i:3087543 original size:18 final size:19
Alignment explanation
Indices: 3087506--3087546 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3087496 GAGATTTAAT
*
3087506 TAAATAAAATAGATAATAA
1 TAAATAAAAGAGATAATAA
*
3087525 TAAATAAAAGGGA-AATAA
1 TAAATAAAAGAGATAATAA
3087543 TAAA
1 TAAA
3087547 ATAATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.22
Consensus pattern (19 bp):
TAAATAAAAGAGATAATAA
Found at i:3088284 original size:69 final size:75
Alignment explanation
Indices: 3088204--3088390 Score: 233
Period size: 76 Copynumber: 2.6 Consensus size: 75
3088194 TAAAACATCT
* * * *
3088204 TAAATCATAATTAAAACACTAAAA-CTATTTAAACTAAAATA-T-ATA-AAA-ATAATAT-TTAA
1 TAAATCATAATTAAAATACTAAAACCTATTTAAACTAAAATACTAAAACAAAGATAAAATATAAA
*
3088263 AATAATATTC
66 AATAATATCC
*
3088273 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAATCATAATTAAAATACTAAAACCTATTTAAACTAAAATA-CTAAAACAAAGATAAAATATAA
3088338 AAATAATATCC
65 AAATAATATCC
* * **
3088349 TAAAACTTAATTAAAATACTAAAACCTATTTAATGTAAAATA
1 TAAATCATAATTAAAATACTAAAACCTATTTAAACTAAAATA
3088391 AAAAGATAAA
Statistics
Matches: 101, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
69 22 0.22
70 17 0.17
72 1 0.01
73 2 0.02
74 3 0.03
75 6 0.06
76 50 0.50
ACGTcount: A:0.57, C:0.11, G:0.01, T:0.30
Consensus pattern (75 bp):
TAAATCATAATTAAAATACTAAAACCTATTTAAACTAAAATACTAAAACAAAGATAAAATATAAA
AATAATATCC
Found at i:3089275 original size:21 final size:20
Alignment explanation
Indices: 3089221--3089297 Score: 55
Period size: 20 Copynumber: 3.8 Consensus size: 20
3089211 TCTTTGGCTC
* * * *
3089221 AAAGGGTCGATCACTTAGCA
1 AAAGGATCGATCCCTTTGAA
* * *
3089241 AAAGGATTGTTCCCTTTGACC
1 AAAGGATCGATCCCTTTGA-A
* *
3089262 AAATGATCGATCCCCTTGAA
1 AAAGGATCGATCCCTTTGAA
*
3089282 AAAGGATCGATTCCTT
1 AAAGGATCGATCCCTT
3089298 GGACAATAGT
Statistics
Matches: 41, Mismatches: 15, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.27
Consensus pattern (20 bp):
AAAGGATCGATCCCTTTGAA
Found at i:3090254 original size:20 final size:21
Alignment explanation
Indices: 3090229--3090274 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
3090219 AGGTGGTTTA
*
3090229 TTCTGGTGGAGATG-AGGTTC
1 TTCTGGTGAAGATGAAGGTTC
3090249 TTCTGGTGAAGATGAAGGTTC
1 TTCTGGTGAAGATGAAGGTTC
*
3090270 CTCTG
1 TTCTG
3090275 TCAATCCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.17, C:0.13, G:0.35, T:0.35
Consensus pattern (21 bp):
TTCTGGTGAAGATGAAGGTTC
Found at i:3091715 original size:26 final size:25
Alignment explanation
Indices: 3091643--3091722 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 25
3091633 TAATCTAATT
* * *
3091643 CTAAACCATTTAAACAAAAAAAAACC
1 CTAAA-CATTTTAACATACAAAAACC
3091669 CTAAACTATTTT-AC-T-CTAAAAACC
1 CTAAAC-ATTTTAACATAC-AAAAACC
*
3091693 CTAAATCATTTTAACATACAAAAAAC
1 CTAAA-CATTTTAACATACAAAAACC
3091719 CTAA
1 CTAA
3091723 CCTTAAACCA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
24 17 0.39
25 6 0.14
26 20 0.45
27 1 0.02
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.25
Consensus pattern (25 bp):
CTAAACATTTTAACATACAAAAACC
Found at i:3092187 original size:2 final size:2
Alignment explanation
Indices: 3092180--3092215 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3092170 AATTTTTGTA
3092180 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
3092216 TAAATATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3094392 original size:2 final size:2
Alignment explanation
Indices: 3094387--3094417 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3094377 TCTCTCTCTT
3094387 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3094418 TAAATTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3108282 original size:13 final size:16
Alignment explanation
Indices: 3108248--3108279 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
3108238 ATTTGCAATG
3108248 TTTATTCGATACAAAT
1 TTTATTCGATACAAAT
3108264 TTTATT-GA-ACAAAT
1 TTTATTCGATACAAAT
3108278 TT
1 TT
3108280 ATTTTCTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 2 0.12
16 6 0.38
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (16 bp):
TTTATTCGATACAAAT
Found at i:3109127 original size:23 final size:23
Alignment explanation
Indices: 3109080--3109133 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
3109070 TAAATAAAAG
3109080 TTATTCAAAGATAATTTAATAATT
1 TTATT-AAAGATAATTTAATAATT
*
3109104 TTATTAAAGTATCATTTAAT-ATT
1 TTATTAAAG-ATAATTTAATAATT
3109127 TTATTAA
1 TTATTAA
3109134 TACAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 14 0.50
24 14 0.50
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (23 bp):
TTATTAAAGATAATTTAATAATT
Found at i:3110326 original size:17 final size:17
Alignment explanation
Indices: 3110306--3110368 Score: 69
Period size: 17 Copynumber: 3.7 Consensus size: 17
3110296 TCTAAGTTAT
3110306 TTTATT-TTATTATTTTC
1 TTTATTATTATT-TTTTC
3110323 TTTAATTATTATTTTTTC
1 TTT-ATTATTATTTTTTC
*
3110341 TTTCTTCA-TATTTTTTC
1 TTTATT-ATTATTTTTTC
3110358 TTTATT-TTATT
1 TTTATTATTATT
3110369 GCTTTTAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
16 4 0.10
17 19 0.47
18 12 0.30
19 5 0.12
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTATTATTATTTTTTC
Found at i:3114531 original size:106 final size:106
Alignment explanation
Indices: 3114372--3114613 Score: 387
Period size: 106 Copynumber: 2.3 Consensus size: 106
3114362 ACGAAAGGGC
* * *
3114372 TTCCCAATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCAAGACAACACAAGCT
1 TTCCCAATTTCAAAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACAAGCT
* * *
3114437 CAACTTCACAGTGAAGGGGCGGCTGACTGTCAATAAATAAT
66 CAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAAT
3114478 TTCCCAATTTCAAAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACAAGCT
1 TTCCCAATTTCAAAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACAAGCT
*
3114543 CAACTTTACAGCGAAGGGGCGGCTGACTGTCAACAAACAAT
66 CAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAAT
* *
3114584 TTCCCAGTTCCAGAA-CCAATTTCAACTTCA
1 TTCCCAATTTCA-AAGCCAATTTCAACTTCA
3114614 TGACGGAGGA
Statistics
Matches: 126, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
106 124 0.98
107 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (106 bp):
TTCCCAATTTCAAAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACAAGCT
CAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAAT
Found at i:3115293 original size:85 final size:84
Alignment explanation
Indices: 3115098--3115346 Score: 243
Period size: 84 Copynumber: 3.0 Consensus size: 84
3115088 TCGTGCTCAA
* * * ** * * * * * *
3115098 CAAATACCTTCGAGTTCGACTACGCTCAGCTC-CTGGCATATCATTTACAGCATAACTCAAGGCT
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATTATTTGCAGCATAACTTAAGTCG
* *
3115162 AGAAGAGTTATCTGTC-AC
66 AGAAGGGTTATCTGCCAAC
* * *
3115180 CAAAGACCTTCAAGATCGATTACACTCAGCTTCAAGGGCACATTATTTGCAGCATAACTTAAGTC
1 CAAAGACCTTCGAGTTCGATTACACTCAGC-TCAAAGGCACATTATTTGCAGCATAACTTAAGTC
3115245 GAGAAGGGTTATCTGCCAAC
65 GAGAAGGGTTATCTGCCAAC
* ** ** * *
3115265 CGAAGACCTTCGAGTTCGATTACACTCAGCTCAAATACACATCT-TTTGCAATATAGCTTAAATC
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT-TATTTGCAGCATAACTTAAGTC
*
3115329 GAGAAGGGCTATCTGCCA
65 GAGAAGGGTTATCTGCCA
3115347 CAAAAAAACT
Statistics
Matches: 137, Mismatches: 26, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
82 25 0.18
83 2 0.01
84 80 0.58
85 30 0.22
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (84 bp):
CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATTATTTGCAGCATAACTTAAGTCG
AGAAGGGTTATCTGCCAAC
Found at i:3115363 original size:84 final size:84
Alignment explanation
Indices: 3115195--3115380 Score: 196
Period size: 84 Copynumber: 2.2 Consensus size: 84
3115185 ACCTTCAAGA
* * * * *
3115195 TCGATTACACTCAGCTTCAAGGGCACATTATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG
1 TCGATTACACTCAGC-TCAAAGACACATTATTTGCAACATAACTTAAATCGAGAAGGGCTATCTG
** * * *
3115260 CCAACCGAAGACCTTCGAGT
65 CCAACAAAAAAACTACGAGT
* * *
3115280 TCGATTACACTCAGCTCAAATACACATCT-TTTGCAATATAGCTTAAATCGAGAAGGGCTATCTG
1 TCGATTACACTCAGCTCAAAGACACAT-TATTTGCAACATAACTTAAATCGAGAAGGGCTATCTG
3115344 CC-ACAAAAAAACTGACGAGT
65 CCAACAAAAAAACT-ACGAGT
* *
3115364 TCGATTTCATTCAGCTC
1 TCGATTACACTCAGCTC
3115381 GATGACAGCG
Statistics
Matches: 84, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
83 7 0.08
84 61 0.73
85 16 0.19
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.27
Consensus pattern (84 bp):
TCGATTACACTCAGCTCAAAGACACATTATTTGCAACATAACTTAAATCGAGAAGGGCTATCTGC
CAACAAAAAAACTACGAGT
Found at i:3116746 original size:5 final size:5
Alignment explanation
Indices: 3116736--3116760 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3116726 ATCCTCTAAG
3116736 TTATT TTATT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT
3116761 ATTTTCTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:3116764 original size:13 final size:13
Alignment explanation
Indices: 3116736--3116784 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
3116726 ATCCTCTAAG
3116736 TTATTTTATTTTATT
1 TTATTTTA--TTATT
3116751 TTATTTTATTATT
1 TTATTTTATTATT
* *
3116764 TTCTTTAATTATT
1 TTATTTTATTATT
3116777 ATTATTTT
1 -TTATTTT
3116785 CTTTCTTCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 16 0.55
14 5 0.17
15 8 0.28
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (13 bp):
TTATTTTATTATT
Found at i:3116780 original size:19 final size:19
Alignment explanation
Indices: 3116736--3116788 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 19
3116726 ATCCTCTAAG
* *
3116736 TTATT-TTATTTTATTTTA
1 TTATTATTATTTTCTTTAA
3116754 TT-TTATTATTTTCTTTAA
1 TTATTATTATTTTCTTTAA
3116772 TTATTATTATTTTCTTT
1 TTATTATTATTTTCTTT
3116789 CTTCATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 2 0.06
18 15 0.48
19 14 0.45
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (19 bp):
TTATTATTATTTTCTTTAA
Found at i:3116887 original size:4 final size:4
Alignment explanation
Indices: 3116880--3116942 Score: 65
Period size: 4 Copynumber: 15.5 Consensus size: 4
3116870 TTTTTATTAC
* * **
3116880 TTAT TTATT TTAT ATAT TTAT TTATT TTAT TTAC TTA- ACAT TTAT TTAT
1 TTAT TTA-T TTAT TTAT TTAT TTA-T TTAT TTAT TTAT TTAT TTAT TTAT
3116929 TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TT
3116943 GTCTAACATC
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
3 1 0.02
4 40 0.82
5 8 0.16
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (4 bp):
TTAT
Found at i:3116890 original size:17 final size:16
Alignment explanation
Indices: 3116871--3116916 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
3116861 TTTTCCTTTT
3116871 TTTTATTACTTATTTA
1 TTTTATTACTTATTTA
*
3116887 TTTTATATATTTATTTA
1 TTTTAT-TACTTATTTA
3116904 TTTTATTTACTTA
1 TTTTA-TTACTTA
3116917 ACATTTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 6 0.23
17 19 0.73
18 1 0.04
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTATTACTTATTTA
Found at i:3121051 original size:106 final size:106
Alignment explanation
Indices: 3120892--3121153 Score: 445
Period size: 106 Copynumber: 2.5 Consensus size: 106
3120882 ACGAAGGGGC
3120892 TTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCT
1 TTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCT
* *
3120957 CAACTTCACAGCGAAGGGGCGGCTGACTGTCAATAAATAAT
66 CAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAAT
*
3120998 TTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGCT
1 TTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCT
3121063 CAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAAT
66 CAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAAT
* * * *
3121104 TTCCCAGTTCCAGAACCAATTTCAACTTCAC-GACGGAGGATATTGGACTC
1 TTCCCAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
3121154 GAAGCATATA
Statistics
Matches: 148, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
105 1 0.01
106 147 0.99
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (106 bp):
TTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCT
CAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAAT
Found at i:3121815 original size:85 final size:84
Alignment explanation
Indices: 3121618--3121871 Score: 255
Period size: 84 Copynumber: 3.0 Consensus size: 84
3121608 TCGTGCTCAA
* * * ** * * * * * *
3121618 CAAATACCTTCGAGTTTGACTACGCTCAGCTC-CTGGCATATCATTTACAGCATAACTCAAGGCT
1 CAAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACATTATTTGCAGCATAACTTAAGTCG
* *
3121682 AGAAGAGTTATCTGTC-AC
66 AGAAGGGTTATCTGCCAAC
* * *
3121700 CAAAGACCTTCAAGTTCGATTACACTCAGCTTCAAGGGCACATTATTTGCAGCATAACTTAAGTC
1 CAAAGACCTTCGAGTTTGATTACACTCAGC-TCAAAGGCACATTATTTGCAGCATAACTTAAGTC
3121765 GAGAAGGGTTATCTGCCAAC
65 GAGAAGGGTTATCTGCCAAC
* ** * * *
3121785 CGAAGACCTTCGAGTTTGATTACACTCAGCTCAAATACACATCT-TTTGCAGTATAGCTTAAATC
1 CAAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACAT-TATTTGCAGCATAACTTAAGTC
*
3121849 GAGAAGGGCTATCTGCC-AC
65 GAGAAGGGTTATCTGCCAAC
3121868 CAAA
1 CAAA
3121872 AAACTGACGA
Statistics
Matches: 142, Mismatches: 26, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
82 25 0.18
83 7 0.05
84 80 0.56
85 30 0.21
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (84 bp):
CAAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACATTATTTGCAGCATAACTTAAGTCG
AGAAGGGTTATCTGCCAAC
Found at i:3121883 original size:84 final size:85
Alignment explanation
Indices: 3121712--3121889 Score: 209
Period size: 84 Copynumber: 2.1 Consensus size: 85
3121702 AAGACCTTCA
* * * *
3121712 AGTTCGATTACACTCAGCTTCAAGGGCACATTATTTGCAGCATAACTTAAGTCGAGAAGGGTTAT
1 AGTTCGATTACACTCAGCTTCAAAGACACATTATTTGCAGCATAACTTAAATCGAGAAGGGCTAT
* * * *
3121777 CTGCCAACCGAAGACCTTCG
66 CTGCCAACCAAAAAACTACG
* * * *
3121797 AGTTTGATTACACTCAGC-TCAAATACACATCT-TTTGCAGTATAGCTTAAATCGAGAAGGGCTA
1 AGTTCGATTACACTCAGCTTCAAAGACACAT-TATTTGCAGCATAACTTAAATCGAGAAGGGCTA
3121860 TCTGCC-ACCAAAAAACTGACG
65 TCTGCCAACCAAAAAACT-ACG
3121881 AGTTCGATT
1 AGTTCGATT
3121890 TCATTCAGTT
Statistics
Matches: 78, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
83 8 0.10
84 52 0.67
85 18 0.23
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.27
Consensus pattern (85 bp):
AGTTCGATTACACTCAGCTTCAAAGACACATTATTTGCAGCATAACTTAAATCGAGAAGGGCTAT
CTGCCAACCAAAAAACTACG
Found at i:3123407 original size:17 final size:15
Alignment explanation
Indices: 3123386--3123433 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 15
3123376 TATTTTTTCC
3123386 TTTTTTATTACTTAT
1 TTTTTTATTACTTAT
*
3123401 TTATTTTATATATTTAT
1 TT-TTTTAT-TACTTAT
3123418 TTCTTTTATTTACTTA
1 TT-TTTTA-TTACTTA
3123434 ACATTTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 2 0.07
16 6 0.22
17 18 0.67
18 1 0.04
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTTATTACTTAT
Found at i:3123427 original size:13 final size:13
Alignment explanation
Indices: 3123397--3123455 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
3123387 TTTTTATTAC
3123397 TTATTTATTTTAT
1 TTATTTATTTTAT
*
3123410 ATATTTATTTCT-T
1 TTATTTATTT-TAT
**
3123423 TTATTTACTTAACAT
1 TTATTTA-TT-TTAT
3123438 TTATTTA-TTTAT
1 TTATTTATTTTAT
3123450 TTATTT
1 TTATTT
3123456 GTCTAACATC
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
12 8 0.22
13 17 0.47
14 3 0.08
15 8 0.22
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.69
Consensus pattern (13 bp):
TTATTTATTTTAT
Found at i:3125230 original size:64 final size:64
Alignment explanation
Indices: 3125133--3125267 Score: 200
Period size: 64 Copynumber: 2.1 Consensus size: 64
3125123 ACATAATGTA
* ** *
3125133 ATAA-GTAGAGTTTTTATAATAAAATAGGTATTTAACCGGAAATATTATTAAGTACAATAACAT
1 ATAAGGTAGAGTTTATATAATAAAATAGACATTTAACCGGAAATATTATCAAGTACAATAACAT
* *
3125196 ATAAGGTAGTGTTTATATAATAAAATAGACATTTAACCGGAAATATTATCAAGTACAATAATAT
1 ATAAGGTAGAGTTTATATAATAAAATAGACATTTAACCGGAAATATTATCAAGTACAATAACAT
*
3125260 ATTAGGTA
1 ATAAGGTA
3125268 ACACTTATAT
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
63 4 0.06
64 60 0.94
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.34
Consensus pattern (64 bp):
ATAAGGTAGAGTTTATATAATAAAATAGACATTTAACCGGAAATATTATCAAGTACAATAACAT
Found at i:3125730 original size:199 final size:199
Alignment explanation
Indices: 3125295--3126017 Score: 860
Period size: 199 Copynumber: 3.6 Consensus size: 199
3125285 TATGTAGCGC
* * *
3125295 TTATATTGACATATTTTCTAAGTAAACC-GATATATTTATACC-GGTAACATTGTAAATTTACCT
1 TTATGTTGACCTATTTTCTAATTAAACCAG-TATATTTATACCGGGT-ACATTGTAAATTTACCT
* * *
3125358 ATTACATTATAATTATCGGTTTCGATATTTTTTGGATCGATACAATTT--TAAATGTATCGACAC
64 ATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATAC-TTTTAATAAATGTATCGACAC
* * * *
3125421 TTTATGCTTGTACCTCG-TTGGACATTCATTCTGTAA-AAAAGTATCGACACAAACTTAAAAAGT
128 TTTATGCGTGCACCTCGTTTGGACATTCATTCTG-AACAAAAATATCGACACAAA-TTAACAAGT
3125484 GTCGATACA
191 GTCGATACA
* * * *
3125493 TTAT-TTAGACCTATTTTCTCATAAAACTATTATATTTATACCGGGTACATTGTAAATTTACCTA
1 TTATGTT-GACCTATTTTCTAATTAAACCAGTATATTTATACCGGGTACATTGTAAATTTACCTA
* * *
3125557 TCACATTGTAATTATCGGTTTCGATGTTTTTGGGATCGACACTTTTAATAAATGTATCGACACTT
65 TTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTT
* **
3125622 TATGCGTGCACC-CGTTTGG-CATTCATTAT-AGACAAAATATATTAACACAAATTTAACAAGTG
130 TATGCGTGCACCTCGTTTGGACATTCATTCTGA-ACAAAA-ATATCGACACAAA-TTAACAAGTG
*
3125684 TCGATACT
192 TCGATACA
* * ** * ** *
3125692 TTATGATGACCTATTTTCTCATTAAACTGGTATATTTATACTGATTACATTGTAAATTTACATAT
1 TTATGTTGACCTATTTTCTAATTAAACCAGTATATTTATACCGGGTACATTGTAAATTTACCTAT
* * * * *
3125757 TACATTATAATTATCGGTTTCGATGTTATTGGGATCAATACTTTTAATAATTGTATCGATAATTT
66 TACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTT
* *
3125822 ATGCGTGCACCTCGTTTGGACATTCATTCTGAACAATAAGTATCGACACAAATTACACAAGTGTA
131 ATGCGTGCACCTCGTTTGGACATTCATTCTGAACAA-AAATATCGACACAAATTA-ACAAGTGTC
3125887 GATACA
194 GATACA
* * * *
3125893 TTATGTTGACTTATTTTCTAATT-AACCAGTATATTTATACCGGTTACATTATTAATTTACCTAT
1 TTATGTTGACCTATTTTCTAATTAAACCAGTATATTTATACCGGGTACATTGTAAATTTACCTAT
* * *
3125957 TACATTTTAATTATTGGTTTCGATTTTTTTGGG-TCGATACTTTTAGA-AAATGTATCGACAC
66 TACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTA-ATAAATGTATCGACAC
3126018 ATATTTAGGT
Statistics
Matches: 448, Mismatches: 61, Indels: 31
0.83 0.11 0.06
Matches are distributed among these distances:
196 1 0.00
197 6 0.01
198 102 0.23
199 205 0.46
200 75 0.17
201 56 0.12
202 3 0.01
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (199 bp):
TTATGTTGACCTATTTTCTAATTAAACCAGTATATTTATACCGGGTACATTGTAAATTTACCTAT
TACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTT
ATGCGTGCACCTCGTTTGGACATTCATTCTGAACAAAAATATCGACACAAATTAACAAGTGTCGA
TACA
Found at i:3130987 original size:200 final size:200
Alignment explanation
Indices: 3130118--3131284 Score: 1516
Period size: 200 Copynumber: 5.8 Consensus size: 200
3130108 TGCGTTATTT
* * * *
3130118 AAAAGTATCGACACAAAGTT-AAAAGTGCCGATACAT-TATGTAGACCTATTTTCTCATAAAACA
1 AAAAGTATCGACACAAAATTCAAAAGTGTCGATACATGT-TGTAGACCTATTCTCTCATAAAACC
* * **
3130181 GGTATAGTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATAAGTTTCGATGTTT
65 GGTATATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
* * * * *
3130246 TTGGGATCGACACTTTTTAAAAATGTATCGACACTTTATGGGTACACCCTTTTGGGCTTTGATTC
130 TTGGGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTACACCATTTTGGGCATTCATTC
*
3130311 -TGAACC
195 TTG-ACA
* * * * * *
3130317 AAAAGTATCGACATAAATTTCACAAGTGTCGATACATGTTGTAAACTTATTCTCTCATAAAATCG
1 AAAAGTATCGACACAAAATTCAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCG
3130382 GTATATTTATACCGGTTACATTGA-AAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
66 GTATATTTATACCGGTTACATT-ACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
* * *
3130446 TTGGGGTCGATACTTTTTAAAAAATGTATCGACACTTTATGCGTGCAACCCTTTT-GGCATTCAT
130 TTGGGATCGATACTTTTT-AAAAATGTATCGACACTTTATGCGTAC-ACCATTTTGGGCATTCAT
3130510 T-TTGGACA
193 TCTT-GACA
* *
3130518 AAAAGTATCGACAC-AGATTCCACAAGTGTCGATACAT-TATGTAGACCTATTCTCTCATAAAAC
1 AAAAGTATCGACACAAAATT-CAAAAGTGTCGATACATGT-TGTAGACCTATTCTCTCATAAAAC
* ** ** * *
3130581 CGGTATAGTTATAATGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATATT
64 CGGTATATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTT
* *
3130646 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCA-TTTGGGCATTCATT
129 TTTGGGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTACACCATTTTGGGCATTCATT
3130710 CTTGACA
194 CTTGACA
* * *
3130717 AAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCTTAAAATCG
1 AAAAGTATCGACACAAAATTCAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCG
*
3130782 GTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTT
66 GTATATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTT
* * * *
3130847 TGGGATCGATACTTTTTATAAATGTATCGATAATTTATGCGTTCACCATTTTGGGCATTCATTCT
131 TGGGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTACACCATTTTGGGCATTCATTCT
3130912 TGACA
196 TGACA
* *
3130917 AAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACATATTCTCTCATAAAACCG
1 AAAAGTATCGACACAAAATTCAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCG
* * *
3130982 GTATATTTATGCCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTTGATGTTTT
66 GTATATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTT
* * * * *
3131047 TGGGATCGACACTTTTTTAAAATGTATCGACACTTTATGGGTACACC-TGTTTAGCCATTTC-TT
131 TGGGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTACACCAT-TTTGGGCA-TTCATT
*
3131110 CTGGAC-
194 CTTGACA
* * * *
3131116 AAAAGTATCGACAC-AAATTCCACAAGTGTCGATACATGTTTTAGACATATTCTCTCA-AACAAT
1 AAAAGTATCGACACAAAATT-CAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAA-AAC
** ** * * * *
3131179 CGGTATATTTATATTGGTTACATTGTAAATTTACCTATTACATTATAATTTTCGGTTTTGATGTT
64 CGGTATATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTT
* * *
3131244 TTTAGGATCGATAATTTTTAAAAATGTATTGACACTTTATG
129 TTTGGGATCGATACTTTTTAAAAATGTATCGACACTTTATG
3131285 TAATTTTTGG
Statistics
Matches: 865, Mismatches: 84, Indels: 38
0.88 0.09 0.04
Matches are distributed among these distances:
198 10 0.01
199 334 0.39
200 344 0.40
201 168 0.19
202 9 0.01
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (200 bp):
AAAAGTATCGACACAAAATTCAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCG
GTATATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTT
TGGGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTACACCATTTTGGGCATTCATTCT
TGACA
Found at i:3131054 original size:399 final size:395
Alignment explanation
Indices: 3130118--3131284 Score: 1576
Period size: 399 Copynumber: 2.9 Consensus size: 395
3130108 TGCGTTATTT
* * * *
3130118 AAAAGTATCGACACAAAGTTAAAAGTGCCGATACATTATGTAGACCTATTTTCTCATAAAACAGG
1 AAAAGTATCGACACAAAATTAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGG
**
3130183 TATAGTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATAAGTTTCGATGTTTTT
66 TATAGTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTT
* * * *
3130248 GGGATCGACACTTTTTAAAAATGTATCGACACTTTATGGGTACACCCTTTTGGGCTTTGATTC-T
131 GGGATCGACACTTTTTATAAATGTATCGACACTTTATGGGTACA-CCATTTGGGCATTCATTCTT
* * * *
3130312 GAACCAAAAGTATCGACATAAATTTCACAAGTGTCGATACATGTTGTAAACTTATTCTCTCATAA
195 G-A-CAAAAGTATCGACACAAAATTCACAAGTGTCGATACATGTTGTAGACATATTCTCTC-TAA
3130377 AATCGGTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGAT
257 AATCGGTATATTTATACCGGTTACATT-AAAAATTACCTATTACATTATAATTATGGGTTTCGAT
* * *
3130442 GTTTTTGGGGTCGATACTTTTTAAAAAATGTATCGACACTTTATGCGTGCAACCCTTTTGGCATT
321 GTTTTTGGGATCGATACTTTTT-AAAAATGTATCGACAATTTATGCGTGCAACCATTTTGGCATT
3130507 CATTTTGGACA
385 CATTTTGGACA
* *
3130518 AAAAGTATCGACAC-AGATTCCACAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
1 AAAAGTATCGACACAAAATT--AAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
** * ** * *
3130582 GGTATAGTTATAATGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATATTT
64 GGTATAGTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
* * *
3130647 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCATTTGGGCATTCATTCT
129 TTGGGATCGACACTTTTTATAAATGTATCGACACTTTATGGGTACACCATTTGGGCATTCATTCT
* * *
3130712 TGACAAAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCTTAA
194 TGAC-AAAAGTATCGACACAAAATTCACAAGTGTCGATACATGTTGTAGACATATTCTCTC-TAA
*
3130777 AATCGGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGAT
257 AATCGGTATATTTATACCGGTTACATTA-AAAATTACCTATTACATTATAATTATGGGTTTCGAT
* * *
3130842 GTTTTTGGGATCGATACTTTTTATAAATGTATCGATAATTTATGCGTTC-ACCATTTTGGGCATT
321 GTTTTTGGGATCGATACTTTTTAAAAATGTATCGACAATTTATGCGTGCAACCATTTT-GGCATT
3130906 CATTCTT-GACA
385 CATT-TTGGACA
*
3130917 AAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGT-TGTAGACATATTCTCTCATAAAACC
1 AAAAGTATCGACACAAAATT-AAAAGTGTCGATACAT-TATGTAGACCTATTCTCTCATAAAACC
* * *
3130981 GGTATATTTATGCCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTTGATGTTT
64 GGTATAGTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
* * *
3131046 TTGGGATCGACACTTTTT-TAAAATGTATCGACACTTTATGGGTACACCTGTTTAGCCATTTC-T
129 TTGGGATCGACACTTTTTAT-AAATGTATCGACACTTTATGGGTACACC-ATTTGGGCA-TTCAT
* * *
3131109 TCTGGACAAAAGTATCGACAC-AAATTCCACAAGTGTCGATACATGTTTTAGACATATTCTCTCA
191 TCTTGACAAAAGTATCGACACAAAATT-CACAAGTGTCGATACATGTTGTAGACATATTCTCTCT
** * * * * *
3131173 AACAATCGGTATATTTATATTGGTTACATTGTAAATTTACCTATTACATTATAATTTTCGGTTTT
255 AA-AATCGGTATATTTATACCGGTTACATT-AAAAATTACCTATTACATTATAATTATGGGTTTC
* * * *
3131238 GATGTTTTTAGGATCGATAATTTTTAAAAATGTATTGACACTTTATG
318 GATGTTTTTGGGATCGATACTTTTTAAAAATGTATCGACAATTTATG
3131285 TAATTTTTGG
Statistics
Matches: 676, Mismatches: 76, Indels: 31
0.86 0.10 0.04
Matches are distributed among these distances:
398 15 0.02
399 333 0.49
400 186 0.28
401 142 0.21
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (395 bp):
AAAAGTATCGACACAAAATTAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGG
TATAGTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTT
GGGATCGACACTTTTTATAAATGTATCGACACTTTATGGGTACACCATTTGGGCATTCATTCTTG
ACAAAAGTATCGACACAAAATTCACAAGTGTCGATACATGTTGTAGACATATTCTCTCTAAAATC
GGTATATTTATACCGGTTACATTAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTT
TGGGATCGATACTTTTTAAAAATGTATCGACAATTTATGCGTGCAACCATTTTGGCATTCATTTT
GGACA
Found at i:3133218 original size:200 final size:197
Alignment explanation
Indices: 3132726--3133882 Score: 1317
Period size: 200 Copynumber: 5.8 Consensus size: 197
3132716 ATTTAAAATG
* ** * * * *
3132726 GTATCGACATAAATTTAACAATTGTCGATACTTTATG-ATGACCTATTTTCTCATAAAACTGGTA
1 GTATCGACACAAATTCCACAAGTGTCGATACATTATGTA-GACCTATTCTCTCATAAAACCGGTA
* * * *
3132790 TAGTTATACTAGTTATATTACAAAATTACCTATTATATTATAATTATGTGTTTCGATGTTTTTGG
65 TAGTTATAC-CGTTACATTA-AAAATTACCTATTATATTATAATTATGGGTTTCGATGTTTCTGG
* * * * *
3132855 GATCGACATTTTTTAAAAATATATCGACACTTTATGGGTGCACCCTTTTTGGGCTTTGATTCTGG
128 GATCGATACTTTTTATAAATATATCGACACTTTATGGGTGCACCC-TTTTGGGCATTCATTCTGG
*
3132920 ACCAAAC
192 A-CAAAA
* *
3132927 GTATCGATACAAATTCCACAAGTGTCGATACATGT-TGTAGACCTATTCTCTCATAAAATCGGTA
1 GTATCGACACAAATTCCACAAGTGTCGATACAT-TATGTAGACCTATTCTCTCATAAAACCGGTA
* *
3132991 TATTTATACCGATTACATTGAAAAATTACCTATTATATTATAATTATGGGTTTCGATGTGTCTGG
65 TAGTTATACCG-TTACATT-AAAAATTACCTATTATATTATAATTATGGGTTTCGATGTTTCTGG
* * * * * *
3133056 GATTGATACTTTTTATAAATGTATCGACACTTTATGTGTACACCCTTTGGGGCATTCCTTCTGGA
128 GATCGATACTTTTTATAAATATATCGACACTTTATGGGTGCACCCTTTTGGGCATTCATTCTGGA
3133121 CAAATA
193 CAAA-A
* * * * *
3133127 GTATCAACACAAATTACATAAGTGTCGATACATTATGTAGATCTATTTTCTCATAAAACCGGTAT
1 GTATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTAT
* * * * *
3133192 AGTTATACCAGTTATATTACAAAATTACATATTACATTATAATTATGGGTTTCGATGTTTTTAGG
66 AGTTATACC-GTTACATTA-AAAATTACCTATTATATTATAATTATGGGTTTCGATGTTTCTGGG
* * * * * *
3133257 ATCGACACTTTTTAAAAATATATCAACACTTTATAGGTGCACCCTTTTGGGCTTTGATTCTGGAC
129 ATCGATACTTTTTATAAATATATCGACACTTTATGGGTGCACCCTTTTGGGCATTCATTCTGGA-
3133322 CAAAA
193 CAAAA
* * * *
3133327 GTATCGACACAAATTCCACGAGTGTCGATACATGT-TGTACACCTATTCTTTCATAACACCGGTA
1 GTATCGACACAAATTCCACAAGTGTCGATACAT-TATGTAGACCTATTCTCTCATAAAACCGGTA
* * * *
3133391 TATTTATATCGGTTACATTGAAAAATTACCTGTTATATTATAATTATGGGTTTCGATGTGTCTGG
65 TAGTTATA-CCGTTACATT-AAAAATTACCTATTATATTATAATTATGGGTTTCGATGTTTCTGG
* *
3133456 GATCGATACTTTTTATAAATGTATCGACACTTTATGGGTGCACCCTTTTGGGCATTCCTTCTGGA
128 GATCGATACTTTTTATAAATATATCGACACTTTATGGGTGCACCCTTTTGGGCATTCATTCTGGA
*
3133521 AAAATA
193 CAAA-A
* *
3133527 GTATCGACACAAATTCCAGAAGTGTCGATAAATTATGTAGACCTATTCTCTCATAAAACCGGTAT
1 GTATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTAT
* * * *
3133592 AGTTATACCGGTTACATTGTAAATTTACC-----TATTA-CATTATGAGTTTCGATGTTTCTGGG
66 AGTTATACC-GTTACATT-AAAAATTACCTATTATATTATAATTATGGGTTTCGATGTTTCTGGG
* * * * * * *
3133651 ATCGATACTTTTTTCTAAATGTTTCGACACAATTTATGTGTTCATCATTTTGGGCATTCATTCTG
129 ATCGATAC-TTTTTATAAATATATCGACAC--TTTATGGGTGCACCCTTTTGGGCATTCATTCTG
3133716 GACAAAAA
191 GAC-AAAA
* * * * *
3133724 GTATCGACACAAAATT-AAAAAGTGTCGATACATTATGTAGACCTATTCTCACAAAAAATCGGTA
1 GTATCGACAC-AAATTCCACAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTA
* * * * * *
3133788 TATTTATACTCGTTATATTAAAAAATTACTTATTACATTATAATTATTGGTTTCGATGTTTTTGG
65 TAGTTATAC-CGTTACATT-AAAAATTACCTATTATATTATAATTATGGGTTTCGATGTTTCTGG
3133853 GATCGATACTTTTTATAAATATATCGACAC
128 GATCGATACTTTTTATAAATATATCGACAC
3133883 ATATGCTTAC
Statistics
Matches: 808, Mismatches: 121, Indels: 53
0.82 0.12 0.05
Matches are distributed among these distances:
194 30 0.04
195 24 0.03
197 105 0.13
198 9 0.01
199 11 0.01
200 423 0.52
201 152 0.19
202 25 0.03
203 29 0.04
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (197 bp):
GTATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTAT
AGTTATACCGTTACATTAAAAATTACCTATTATATTATAATTATGGGTTTCGATGTTTCTGGGAT
CGATACTTTTTATAAATATATCGACACTTTATGGGTGCACCCTTTTGGGCATTCATTCTGGACAA
AA
Found at i:3133489 original size:400 final size:399
Alignment explanation
Indices: 3132748--3133882 Score: 1552
Period size: 400 Copynumber: 2.8 Consensus size: 399
3132738 ATTTAACAAT
* * *
3132748 TGTCGATACTTTATG-ATGACCTATTTTCTCATAAAACTGGTATAGTTATACTAGTTATATTACA
1 TGTCGATACATTATGTA-GACCTATTTTCTCATAAAACCGGTATAGTTATACCAGTTATATTACA
* * *
3132812 AAATTACCTATTATATTATAATTATGTGTTTCGATGTTTTTGGGATCGACATTTTTTAAAAATAT
65 AAATTACCTATTACATTATAATTATGAGTTTCGATGTTTTTGGGATCGACACTTTTTAAAAATAT
* * *
3132877 ATCGACACTTTATGGGTGCACCCTTTTTGGGCTTTGATTCTGGACCAAACGTATCGATACAAATT
130 ATCAACACTTTAT-GGTGCACCC-TTTTGGGCTTTGATTCTGGACCAAAAGTATCGACACAAATT
* *
3132942 CCACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAATCGGTATATTTATACCGATTAC
193 CCACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAATCGGTATATTTATATCGGTTAC
*
3133007 ATTGAAAAATTACCTATTATATTATAATTATGGGTTTCGATGTGTCTGGGATTGATACTTTTTAT
258 ATTGAAAAATTACCTATTATATTATAATTATGGGTTTCGATGTGTCTGGGATCGATACTTTTTAT
* *
3133072 AAATGTATCGACACTTTATGTGTACACCCTTTGGGGCATTCCTTCTGGACAAATAGTATCAACAC
323 AAATGTATCGACACTTTATGGGTACACCCTTTGGGGCATTCCTTCTGGAAAAATAGTATCAACAC
*
3133137 AAATTACATAAG
388 AAATTACAGAAG
*
3133149 TGTCGATACATTATGTAGATCTATTTTCTCATAAAACCGGTATAGTTATACCAGTTATATTACAA
1 TGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATAGTTATACCAGTTATATTACAA
* * *
3133214 AATTACATATTACATTATAATTATGGGTTTCGATGTTTTTAGGATCGACACTTTTTAAAAATATA
66 AATTACCTATTACATTATAATTATGAGTTTCGATGTTTTTGGGATCGACACTTTTTAAAAATATA
3133279 TCAACACTTTATAGGTGCACCCTTTTGGGCTTTGATTCTGGACCAAAAGTATCGACACAAATTCC
131 TCAACACTTTAT-GGTGCACCCTTTTGGGCTTTGATTCTGGACCAAAAGTATCGACACAAATTCC
* * * * *
3133344 ACGAGTGTCGATACATGTTGTACACCTATTCTTTCATAACACCGGTATATTTATATCGGTTACAT
195 ACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAATCGGTATATTTATATCGGTTACAT
*
3133409 TGAAAAATTACCTGTTATATTATAATTATGGGTTTCGATGTGTCTGGGATCGATACTTTTTATAA
260 TGAAAAATTACCTATTATATTATAATTATGGGTTTCGATGTGTCTGGGATCGATACTTTTTATAA
* * *
3133474 ATGTATCGACACTTTATGGGTGCACCCTTTTGGGCATTCCTTCTGGAAAAATAGTATCGACACAA
325 ATGTATCGACACTTTATGGGTACACCCTTTGGGGCATTCCTTCTGGAAAAATAGTATCAACACAA
*
3133539 ATTCCAGAAG
390 ATTACAGAAG
* * * * **
3133549 TGTCGATAAATTATGTAGACCTATTCTCTCATAAAACCGGTATAGTTATACCGGTTACATTGTAA
1 TGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATAGTTATACCAGTTATATTACAA
* * * ** *
3133614 ATTTACCTATTAC------ATTATGAGTTTCGATGTTTCTGGGATCGATACTTTTTTCTAAATGT
66 AATTACCTATTACATTATAATTATGAGTTTCGATGTTTTTGGGATCGACAC-TTTTTAAAAATAT
* * * * * * * *
3133673 TTCGACACAATTTATGTGTTCATCATTTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAAA
130 ATC-A-ACACTTTATG-GTGCACCCTTTTGGGCTTTGATTCTGGACCAAAAGTATCGACAC-AAA
* * * *
3133738 TT-AAAAAGTGTCGATACAT-TATGTAGACCTATTCTCACAAAAAATCGGTATATTTATACTC-G
191 TTCCACAAGTGTCGATACATGT-TGTAGACCTATTCTCTCATAAAATCGGTATATTTATA-TCGG
* * * * * * *
3133800 TTATATTAAAAAATTACTTATTACATTATAATTATTGGTTTCGATGTTTTTGGGATCGATACTTT
254 TTACATTGAAAAATTACCTATTATATTATAATTATGGGTTTCGATGTGTCTGGGATCGATACTTT
*
3133865 TTATAAATATATCGACAC
319 TTATAAATGTATCGACAC
3133883 ATATGCTTAC
Statistics
Matches: 655, Mismatches: 71, Indels: 20
0.88 0.10 0.03
Matches are distributed among these distances:
394 28 0.04
395 12 0.02
396 3 0.00
397 166 0.25
398 7 0.01
400 299 0.46
401 139 0.21
402 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (399 bp):
TGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATAGTTATACCAGTTATATTACAA
AATTACCTATTACATTATAATTATGAGTTTCGATGTTTTTGGGATCGACACTTTTTAAAAATATA
TCAACACTTTATGGTGCACCCTTTTGGGCTTTGATTCTGGACCAAAAGTATCGACACAAATTCCA
CAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAATCGGTATATTTATATCGGTTACATT
GAAAAATTACCTATTATATTATAATTATGGGTTTCGATGTGTCTGGGATCGATACTTTTTATAAA
TGTATCGACACTTTATGGGTACACCCTTTGGGGCATTCCTTCTGGAAAAATAGTATCAACACAAA
TTACAGAAG
Found at i:3136139 original size:21 final size:21
Alignment explanation
Indices: 3136114--3136157 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
3136104 CCCTTTATGC
3136114 CTCTCAAGTGTCTCTTCGACT
1 CTCTCAAGTGTCTCTTCGACT
*
3136135 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTCTCTTCGACT
3136156 CT
1 CT
3136158 TGATTGTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.34, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTCTCTTCGACT
Found at i:3138577 original size:182 final size:182
Alignment explanation
Indices: 3138343--3138834 Score: 797
Period size: 182 Copynumber: 2.7 Consensus size: 182
3138333 TACGTGTACT
* * *
3138343 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACTGTTTTTATCATTTCGAGATCG
1 TATTAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCGATTTTATCATTTCGAGATCG
* * * *
3138408 GTTTTGTCATATTGTTACCTGTTATATCGTTGTAGATCGATACATTTGTATAAAGTATCGATACT
66 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACT
*
3138473 TTATA-AGCGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCGATACTTA
131 TTATAGA-CGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCAATACTTA
*
3138525 TATTAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCGGTTTTATCATTTCGAGATCG
1 TATTAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCGATTTTATCATTTCGAGATCG
3138590 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACT
3138655 TTATAGACGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCAATACTTA
131 TTATAGACGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCAATACTTA
* * * * * * * *
3138707 TATTAAAGTATCAACACTTTAAATATATCTGGTAGTGCTTTACCAATTTTGTCTTTTCGTGACCG
1 TATTAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCGATTTTATCATTTCGAGATCG
* *
3138772 GTTTTGTCATATTTTTACCTGTTATATTGATGTGGATCGATACATTTTTATAAAGTATCGACA
66 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACA
3138835 TAAACCGACA
Statistics
Matches: 290, Mismatches: 19, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
182 289 1.00
183 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (182 bp):
TATTAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCGATTTTATCATTTCGAGATCG
GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACT
TTATAGACGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCAATACTTA
Found at i:3140048 original size:2 final size:2
Alignment explanation
Indices: 3140041--3140074 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3140031 GACCGTACCC
3140041 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
3140075 TAATAGTATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3142008 original size:17 final size:17
Alignment explanation
Indices: 3141986--3142020 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3141976 CACGTGAGGA
*
3141986 TTATTTTTCTTTTTATT
1 TTATTTATCTTTTTATT
3142003 TTATTTATCTTTTTATT
1 TTATTTATCTTTTTATT
3142020 T
1 T
3142021 ACTGTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.80
Consensus pattern (17 bp):
TTATTTATCTTTTTATT
Found at i:3148323 original size:20 final size:19
Alignment explanation
Indices: 3148295--3148332 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3148285 TAACTTTTTC
3148295 TTTTATCTTTCATTATTAAT
1 TTTTATCTTTCATT-TTAAT
*
3148315 TTTTCTCTTTCATTTTAA
1 TTTTATCTTTCATTTTAA
3148333 CTTTACCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.21, C:0.13, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTATCTTTCATTTTAAT
Done.