Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022464.1 Corchorus olitorius cultivar O-4 contig22497, 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: 41340
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1203 original size:31 final size:31
Alignment explanation
Indices: 1165--1226 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
1155 GTTGTTTGAG
*
1165 AGGGACTAATATTTCCTCATATTACAAGTTT
1 AGGGACTAACATTTCCTCATATTACAAGTTT
*
1196 AGGGACTAACATTTCCTCATATTGCAAGTTT
1 AGGGACTAACATTTCCTCATATTACAAGTTT
1227 TTTTTTTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.37
Consensus pattern (31 bp):
AGGGACTAACATTTCCTCATATTACAAGTTT
Found at i:2398 original size:47 final size:47
Alignment explanation
Indices: 2306--2398 Score: 159
Period size: 47 Copynumber: 2.0 Consensus size: 47
2296 TTTACTCTTA
* *
2306 TAATATTGAATAGACTAGATTAAACAAAAGAGTTATATTATCCGTTT
1 TAATATTGAATAGACTAGATTAAACAAAAGAGTTATATAAACCGTTT
*
2353 TAATATTGAATCGACTAGATTAAACAAAAGAGTTATATAAACCGTT
1 TAATATTGAATAGACTAGATTAAACAAAAGAGTTATATAAACCGTT
2399 AAAACGGATA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (47 bp):
TAATATTGAATAGACTAGATTAAACAAAAGAGTTATATAAACCGTTT
Found at i:6808 original size:19 final size:19
Alignment explanation
Indices: 6766--6808 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
6756 ATAAGACTAA
**
6766 TCAAATTGTGACAATTTAC
1 TCAAATTGTGACAATCGAC
6785 TCAAATTGTGACAACTCGAC
1 TCAAATTGTGACAA-TCGAC
6805 -CAAA
1 TCAAA
6809 CACCATCTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.28
Consensus pattern (19 bp):
TCAAATTGTGACAATCGAC
Found at i:7600 original size:12 final size:12
Alignment explanation
Indices: 7569--7602 Score: 54
Period size: 10 Copynumber: 3.0 Consensus size: 12
7559 TGAATTCTGC
7569 AAAATTTGCTTG
1 AAAATTTGCTTG
7581 AAAA--TGCTTG
1 AAAATTTGCTTG
7591 AAAATTTGCTTG
1 AAAATTTGCTTG
7603 GAACATTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 10 0.50
12 10 0.50
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (12 bp):
AAAATTTGCTTG
Found at i:7738 original size:193 final size:197
Alignment explanation
Indices: 7376--7738 Score: 436
Period size: 204 Copynumber: 1.8 Consensus size: 197
7366 AGCCCGGACA
*
7376 TGAAAATGCTTGAAAATTGCTTGGAACATTACTAAAACTAAATTTGAACATTCATCTGGTCTTTA
1 TGAAAATGCTTGAAAATTGCTTGGAACATTACTAAAACAAAATTTGAACATTCATCTGGTCTTTA
* * **
7441 CTTACCATGCATCACCGTGTGACACTAACAAAGACTAATTGGGTTGACTGGTAATAATCCTTTAA
66 ATTACCATGCATCACC----GACAC-AACAAAGACCAATTGGAATGACTGGT-ATAATCCTTTAA
* ** * *
7506 TAAGAAAGCATTTTGAGTATGATCTTGCCTTTTTTTGGATTGGATTTCATGGTTGAATTCTGCAA
125 TAAGAAAGCATTTCGAGTACAATCCTGCCTTTCTTTGGATTGGATTTCATGGTTGAATTCTGCAA
7571 AATTTGCT
190 AATTTGCT
* * *
7579 TGAAAATGCTTGAAAATTTGCTTGGAACATTACTGAAACAAAATTTGATCATTTATCTGGTCTAC
1 TGAAAATGCTTGAAAA-TTGCTTGGAACATTACTAAAACAAAATTTGAACATTCATCTGGTCT--
7644 TTAATTACCATGCATCACC-AC-C-A-AAA-ACCAATAT-GAATGACTGGT-T-ATCCTTTAATA
63 TTAATTACCATGCATCACCGACACAACAAAGACCAAT-TGGAATGACTGGTATAATCCTTTAATA
* * *
7701 AGAACGCATTTCGGGTACAATCCTGGCTTTCTTTGGAT
127 AGAAAGCATTTCGAGTACAATCCTGCCTTTCTTTGGAT
7739 GAAATGAAAA
Statistics
Matches: 140, Mismatches: 16, Indels: 18
0.80 0.09 0.10
Matches are distributed among these distances:
193 41 0.29
194 1 0.01
196 14 0.10
197 4 0.03
198 1 0.01
200 1 0.01
201 2 0.01
203 16 0.11
204 42 0.30
206 18 0.13
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (197 bp):
TGAAAATGCTTGAAAATTGCTTGGAACATTACTAAAACAAAATTTGAACATTCATCTGGTCTTTA
ATTACCATGCATCACCGACACAACAAAGACCAATTGGAATGACTGGTATAATCCTTTAATAAGAA
AGCATTTCGAGTACAATCCTGCCTTTCTTTGGATTGGATTTCATGGTTGAATTCTGCAAAATTTG
CT
Found at i:14100 original size:33 final size:33
Alignment explanation
Indices: 14063--14130 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
14053 AGTTGGGCTG
* *
14063 CGTCGGCATATCGGCGGCGCCTCC-TGGGGGCGC
1 CGTCGGCATATCGACGCCGCC-CCGTGGGGGCGC
* *
14096 CGTCGGCATGTCGACGCCGCCCCGTTGGGGCGC
1 CGTCGGCATATCGACGCCGCCCCGTGGGGGCGC
14129 CG
1 CG
14131 CCGCCGGTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 2 0.07
33 28 0.93
ACGTcount: A:0.06, C:0.38, G:0.41, T:0.15
Consensus pattern (33 bp):
CGTCGGCATATCGACGCCGCCCCGTGGGGGCGC
Found at i:14565 original size:27 final size:27
Alignment explanation
Indices: 14527--14583 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
14517 AACGGGTAAA
*
14527 GAGGTTGAGGCTGCTCGGATGTATAGG
1 GAGGCTGAGGCTGCTCGGATGTATAGG
*
14554 GAGGCTGAGGCTGCTCGGATGTATATG
1 GAGGCTGAGGCTGCTCGGATGTATAGG
14581 GAG
1 GAG
14584 AGGGAGCCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.19, C:0.12, G:0.44, T:0.25
Consensus pattern (27 bp):
GAGGCTGAGGCTGCTCGGATGTATAGG
Found at i:14907 original size:21 final size:21
Alignment explanation
Indices: 14868--14907 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
14858 TTATGTGATA
**
14868 TTATAAATTGAAATGAATTAT
1 TTATAAATTGAAAAAAATTAT
14889 TTATAAATTGAAAAAAATT
1 TTATAAATTGAAAAAAATT
14908 TAATAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (21 bp):
TTATAAATTGAAAAAAATTAT
Found at i:16723 original size:20 final size:20
Alignment explanation
Indices: 16694--16731 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
16684 TATTTTGGGA
16694 TTTTTATGGATGTTTATGTC
1 TTTTTATGGATGTTTATGTC
* *
16714 TTTTTTTGGATTTTTATG
1 TTTTTATGGATGTTTATG
16732 GAATATACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.03, G:0.18, T:0.66
Consensus pattern (20 bp):
TTTTTATGGATGTTTATGTC
Found at i:16727 original size:10 final size:10
Alignment explanation
Indices: 16691--16733 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
16681 TTATATTTTG
16691 GGATTTTTAT
1 GGATTTTTAT
*
16701 GGATGTTTAT
1 GGATTTTTAT
** *
16711 GTCTTTTTTT
1 GGATTTTTAT
16721 GGATTTTTAT
1 GGATTTTTAT
16731 GGA
1 GGA
16734 ATATACTTAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.16, C:0.02, G:0.23, T:0.58
Consensus pattern (10 bp):
GGATTTTTAT
Found at i:17009 original size:32 final size:32
Alignment explanation
Indices: 16973--17037 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
16963 TATAAAATCA
16973 ATACTACCCCAGGACATTTTTTTGAGCCTCCC
1 ATACTACCCCAGGACATTTTTTTGAGCCTCCC
17005 ATACTACCCCAGGACATTTTTTTGAGCCTCCC
1 ATACTACCCCAGGACATTTTTTTGAGCCTCCC
17037 A
1 A
17038 ATCTTCTCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.23, C:0.34, G:0.12, T:0.31
Consensus pattern (32 bp):
ATACTACCCCAGGACATTTTTTTGAGCCTCCC
Found at i:20024 original size:33 final size:33
Alignment explanation
Indices: 19976--20064 Score: 97
Period size: 33 Copynumber: 2.7 Consensus size: 33
19966 TTTGGTCGGC
* * * * *
19976 GCCGCCCTAGCAGGGCGGCGTGGCTATGACCAT
1 GCCGCCCAAGGAGGGCGGCATGGCCAAGACCAT
* *
20009 GCCGCCCAAGGAGGGCGCCATGGCCAAGTCCAT
1 GCCGCCCAAGGAGGGCGGCATGGCCAAGACCAT
**
20042 GCCGCCCACCGAGGGCGGCATGG
1 GCCGCCCAAGGAGGGCGGCATGG
20065 ACATAGTAGG
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.17, C:0.36, G:0.37, T:0.10
Consensus pattern (33 bp):
GCCGCCCAAGGAGGGCGGCATGGCCAAGACCAT
Found at i:22778 original size:13 final size:13
Alignment explanation
Indices: 22760--22787 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
22750 CCAAAGGGTG
22760 TTTAACACACCTC
1 TTTAACACACCTC
22773 TTTAACACACCTC
1 TTTAACACACCTC
22786 TT
1 TT
22788 GAGATCTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.36, G:0.00, T:0.36
Consensus pattern (13 bp):
TTTAACACACCTC
Found at i:26589 original size:13 final size:13
Alignment explanation
Indices: 26571--26598 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
26561 TCAAAGGGTG
26571 TTTAACACACCTC
1 TTTAACACACCTC
26584 TTTAACACACCTC
1 TTTAACACACCTC
26597 TT
1 TT
26599 GAGATCTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.36, G:0.00, T:0.36
Consensus pattern (13 bp):
TTTAACACACCTC
Found at i:28858 original size:14 final size:14
Alignment explanation
Indices: 28839--28867 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28829 AGTTTTGGTT
28839 GAAATTAATTTCAG
1 GAAATTAATTTCAG
28853 GAAATTAATTTCAG
1 GAAATTAATTTCAG
28867 G
1 G
28868 CTACATACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.34
Consensus pattern (14 bp):
GAAATTAATTTCAG
Found at i:32275 original size:16 final size:16
Alignment explanation
Indices: 32250--32281 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
32240 ATTATAGAGT
*
32250 TTAGGGTTAATTTTAA
1 TTAGGATTAATTTTAA
32266 TTAGGATTAATTTTAA
1 TTAGGATTAATTTTAA
32282 AATCATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (16 bp):
TTAGGATTAATTTTAA
Found at i:32296 original size:26 final size:26
Alignment explanation
Indices: 32266--32342 Score: 111
Period size: 26 Copynumber: 3.0 Consensus size: 26
32256 TTAATTTTAA
32266 TTAGGATTAATTTTAAAATCATAATT
1 TTAGGATTAATTTTAAAATCATAATT
32292 TTAGGATTAATTTTAAAATCATAATT
1 TTAGGATTAATTTTAAAATCATAATT
*** *
32318 TTTTTA-AAATTTTAAAATCATAATT
1 TTAGGATTAATTTTAAAATCATAATT
32343 CTAAAATGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
25 18 0.38
26 29 0.62
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (26 bp):
TTAGGATTAATTTTAAAATCATAATT
Found at i:33661 original size:333 final size:331
Alignment explanation
Indices: 32988--34134 Score: 1132
Period size: 333 Copynumber: 3.5 Consensus size: 331
32978 TCATGATGGT
* * * *
32988 AAAAATGACCCGAAAGAATTTTTTTCTCAAATTTTGGCAAAAATACTCATAATATATATATAATT
1 AAAAATTACCCGAAAG-A--TTTTCCTCAAATTTTGGCAAAAATACTCATAAAAAATATATAATT
* * * * * * *
33053 CAACATCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTGCTAAATT
63 TAACATCAAAAAGATTGAAGGATTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCAAATT
* * * * *
33118 AATTTTTAATTAAATCAAAATAAGATTCAGATACACGTTAAAAAAAATCCTTAAATACAATGTGA
128 AATTTCTAATTAAATCAAAACAAGATTCAGATACTCGTAAAAAAAAATCCTTAAATACAATGTGG
* * * * * *
33183 CTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAGTCTCGGCGCCAAAAGTTATGCAAAACA
193 CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACT
* * ** * * *
33248 GAGCCGTGGCCCCGGGGCGTGTTTTTAGCCAAAAATCGGGATGGTTTAGTACACGATTTCGGCTA
258 GAGCC-AGGCCCCAGAACGCGTTTTTAGCCAAAAACCGTGATGG-TTAGTACACGATTTCGGCTA
33313 AAATTTTGC--
321 AAATTTTGCAA
*** * *
33322 AAAAATTGATTTGAAAGATATTTCCTCAAATTTTGGCTAAAATACTCACAAAAAATATATAATTT
1 AAAAATT-ACCCGAAAGAT-TTTCCTCAAATTTTGGCAAAAATACTCATAAAAAATATATAATTT
* * * * * *
33387 GACATCAAAAAGATTGAAGGGTTTTTAACGCTTCTAATATAGTTTTTCCT-TTCTTTTCCGAATG
64 AACATCAAAAAGATTGAAGGATTTTTCACGCTTCTAATATCGTTTTTCCTATT-TTTTCCAAATT
* * ** * * *
33451 AATTTCTAATCAAATCGAGGCAATATTCAGATGCTCGTAAAAAAAAATCCTTAAATTCAATGTGG
128 AATTTCTAATTAAATCAAAACAAGATTCAGATACTCGTAAAAAAAAATCCTTAAATACAATGTGG
* *
33516 CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCACAAAAAATCATGCAAAACT
193 CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACT
* *
33581 GAGCCAGGCCCCAGAACGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACAATTTCGGCTAAA
258 GAGCCAGGCCCCAGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
33646 ATTTTGCAA
323 ATTTTGCAA
* * * * * *
33655 AAAAATTACCCGAAAGATTTTCATC--TTTTTAGCGAAAATACTCATAAAAGATATATAATTCAA
1 AAAAATTACCCGAAAGATTTTCCTCAAATTTTGGCAAAAATACTCATAAAAAATATATAATTTAA
* **
33718 GC--CAAAAAAATTGAAAGCTTTTTTCACGCTTCTAATATCGTTTTTCCTATTTTATTTCCAAAT
66 -CATCAAAAAGATTG-AAGGATTTTTCACGCTTCTAATATCGTTTTTCCTA-TTT-TTTCCAAAT
* ** *
33781 TAATTTCTGATTAAATCAAAACAAGATTTGGATACTCGTAAAAACAAATCCTTAAATACAATGTG
127 TAATTTCTAATTAAATCAAAACAAGATTCAGATACTCGTAAAAAAAAATCCTTAAATACAATGTG
* * *
33846 GCTGAGATTTGGTTAGATGAATATAGATATATTTTAAGGAGTCTTGCCGCCAAAAATCATTCAAA
192 GCTGAGATTTGGTTAGATGAATATAG--ATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAA
* * * * * * *
33911 ACTGACCCGGGCCCCTGAACACGTTTTTTTGTCAAAAAACCGTGATGG--A--AAACGATTTCGG
255 ACTGAGCCAGGCCCCAGAACGCG-TTTTTAG-CCAAAAACCGTGATGGTTAGTACACGATTTCGG
*
33972 CTAAAATTTTTC--
318 CTAAAATTTTGCAA
* * ** * * * *
33984 AAAAATTGACACGAAATATTATT-CTC-AATTTACAGCCAAAAGAATTATAAAAAATATATAATT
1 AAAAATT-ACCCGAAAGATT-TTCCTCAAATTT-TGGCAAAAATACTCATAAAAAATATATAATT
* * ** * *
34047 CAAC-GCGAAAAAGATTGAAGGGCTTCTCACGCTTTTAATATCG--TTT--T-TTTTTT-CAAAT
63 TAACATC-AAAAAGATTGAAGGATTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCAAAT
* * *
34105 TAATTTCTAATTGAATCGAAACATGATTCA
127 TAATTTCTAATTAAATCAAAACAAGATTCA
34135 AATGCTCGAG
Statistics
Matches: 676, Mismatches: 117, Indels: 50
0.80 0.14 0.06
Matches are distributed among these distances:
324 29 0.04
325 3 0.00
326 3 0.00
328 11 0.02
329 68 0.10
330 17 0.03
331 150 0.22
332 91 0.13
333 271 0.40
334 13 0.02
335 20 0.03
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (331 bp):
AAAAATTACCCGAAAGATTTTCCTCAAATTTTGGCAAAAATACTCATAAAAAATATATAATTTAA
CATCAAAAAGATTGAAGGATTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCAAATTAAT
TTCTAATTAAATCAAAACAAGATTCAGATACTCGTAAAAAAAAATCCTTAAATACAATGTGGCTG
AGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAG
CCAGGCCCCAGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATT
TTGCAA
Found at i:34700 original size:956 final size:966
Alignment explanation
Indices: 33297--37036 Score: 2351
Period size: 970 Copynumber: 3.9 Consensus size: 966
33287 GATGGTTTAG
** * * * *** * * * * *
33297 TACACGATTTCGGCTAAAATTTTGCAAAAATTGATTTGAAAGATATTTCCTCAAATTTTGGCTAA
1 TACACGATTTCAACTAATATTTCGCAAAAATTAACCAGAAATATTTTTCCTCAATTTTTGTCCAA
* * ** * * * * *
33362 AATACTCACAAAAAATATATAATTTGACAT-CAAAAAGATTGAAGG-GTTTTTAACGCTTCTAAT
66 AATACTCATAAAATATATATAATTCAAC-TCCAAAAAAATTGGAGGAATTTTCAA-GCTTTTAAT
* * * * * * * ** *
33425 ATAGTTTTTCCTTTCTTTTCCGAATGAATTTCTAATCAAATCGAGGCAATATTCAGATGCTCGTA
129 ATCGTCTTTCATAT-TTTTCTGAATTAATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTA
* *
33490 AAAAAAAATCCTTAAATTCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGT
193 AAAACAAATCCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAA-GAGT
* * ** * *
33555 CTTGGCACAAAAAATCATGCAAAACTGAGCCAGGCCCCAG-AACGCGTTTTTAGCCGAAAACCGT
257 CTAGGCACCAAAAATCATGCAAAACTGAG-CAGGGTCCTGAAACGCGTTTTTAGCCAAAAACCGT
* *
33619 GATGGTTAGTACACAATTTCGGCTAAAATTTTGCAAAAAAATTACCCGAAAGATTTTCATCTTTT
321 GATGGTTAGTACACAATTTCAGCTAAAATTTTGCAAAAAAATAACCCGAAAGATTTTCATCTTTT
* *
33684 TAGCGAAAATACTCATAAAAGATATATAATTCAAGCCAAAAAAATTGAAAGCTTTTTTCACGCTT
386 TAGAGAAAATACTCAT-AAAGATATATAATTAAAGCCAAAAAAATTGAAAGC-TTTTTCACGCTT
* * * **
33749 CTAATATCGTTTTTCCTATTTTATTTCCAAATTAATTTCTGATTAAATCAAAACAAGATTTGGAT
449 CTAATATCGTTTTT-C-ATATT-TTTCCAAATTAA-ATCTAATTAAATCAAAACAAGATTCAGAT
* * *
33814 ACTCGTAAAAACAAATCCTTAAATACAATGTGGCTGAGATTTGGTTAGATGAATATAGATATATT
510 ACTCGTAAAAACAAATCCTTAAATACAATGTAGCTGAGATTTGATTAGATGAATA-AG-TATATC
* * * * * * *
33879 TTAAGGAG-TCTTGCCGCCAAAAATCATTCAAAACTGA-CCCGGGCCCCTGAACACGTTTTTTTG
573 TCAAAGAGTTCTAG-CGCCAAAAAACATGCAAAACTGAGCCCGGGCCCCAGAACACG-TTTTTAG
*
33942 TCAAAAAACCGTGATG-GA-AAACGATTTCGGCTAAAATTTT-TCAAAAATTGACACGAAA-TAT
636 -CAAAAAACCGTAATGAGATAAACGATTTCGGCTAAAATTTTGT-AAAAATTGACACGAAAGTAT
*
34003 TATTCTC-AATTTACAGCCAAAAGAATTATAAAAAATATATAATTCAACG-CGAAAAAGATTGAA
699 T-TCCTCAAATTTACA-CCAAAAGAATTATAAAAAATATATAATTCAACGTCG-AAAAGATTGAA
**
34066 GGGCTTCTCACGCTTT-TAATATC-G-TTT-T-TT-TTTT-CAAATTAATTTCTAATTGA-ATCG
761 GCACTTCTCACG-TTTCTAATATCGGTTTTCTATTATTTTCCAAATTAATTTCTAATT-ACATCG
*
34123 AAACATGATTCAAA-TG-CT-C-GA-GAAA-CCAA-A-T-A-TAGATAAATATAGATATTTCAA-
824 AAACATGATTCAAATTGTCTACAAACGAAATCCAAGAGTGATTAGATAAATATAGATATTTCAAT
** * * *
34177 GAAGT-TTTGCTACCAAAAATCATACAAAATTGACCCACGGCCCTAGAACGCGTTCTCAGCCAAA
889 G-AGTCTCGGC-ACCAAAAATCATACAAAACTGAACC-CGGCCCCAGAACGCGTTCTCAGCC-AA
34241 AAACC-G-T-GA-TAA-
950 AAACCGGTTCGACTAAC
** * * *
34253 TACACGATTTTGACTCAA-ATTTTGCAAAAATTAACCCGAAATATTTTTTTCTCAATTTTTAG-C
1 TACACGATTTCAACT-AATATTTCGCAAAAATTAACCAGAAATA-TTTTTCCTCAATTTTT-GTC
* * *
34316 CACAATACTCATAAAATATATATAATTC-AGTGCCAAAAAGATTGGAGGAATTTTCAAGCTTTTA
63 CAAAATACTCATAAAATATATATAATTCAACT-CCAAAAAAATTGGAGGAATTTTCAAGCTTTTA
* **
34380 ATATCGTCTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGAGACAGATGCTCGT
127 ATATCGTCTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGT
*
34445 AAAAACAAATCCTTAAATTCAATGTGGCTGAAATTTGATTAGATGAATATAGATATTTCAAGAAG
192 AAAAACAAATCCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAG-AG
* * * * * *
34510 TCTAGGCGCCAAATATCAAGCAAAACTAAGACGGGGTCCTGAAACGCGTTTTTAGCCAAAAACTG
256 TCTAGGCACCAAAAATCATGCAAAACTGAG-CAGGGTCCTGAAACGCGTTTTTAGCCAAAAACCG
** *
34575 TGATGGTTAGTACATGATTTCAGCTAAAATTTTGC-ACAAAATAACCCGTAAA-ATTTTCCA-CA
320 TGATGGTTAGTACACAATTTCAGCTAAAATTTTGCAAAAAAATAACCCG-AAAGATTTT-CATC-
* * * * * *
34637 ATTTTTGGATAAAATACTCAT-AATATATATAATTTAACAG-CAAAAATATTGGAGGAC-TTTTC
382 -TTTTTAGAGAAAATACTCATAAAGATATATAA-TTAA-AGCCAAAAAAATTGAAAG-CTTTTTC
* * ** *
34699 ACGCTTTTAATATTGTTTTTCATATTTTTCTGAATTAAATCTAATTAAATCGAAACAAGATTCAG
443 ACGCTTCTAATATCGTTTTTCATATTTTTCCAAATTAAATCTAATTAAATCAAAACAAGATTCAG
* * *
34764 ATGCTCGTAAAAACAAATTCTTAAATCCAATGTAGCTGAGATTTGATTAGATGAATAAGTATATC
508 ATACTCGTAAAAACAAATCCTTAAATACAATGTAGCTGAGATTTGATTAGATGAATAAGTATATC
* * * * * *
34829 TCAAAGAGTTCTAGCGCCAAAAAACATGCAAAACTTAGTCGGGGCCTCAGAACGCGTTTTTAGCC
573 TCAAAGAGTTCTAGCGCCAAAAAACATGCAAAACTGAGCCCGGGCCCCAGAACACGTTTTTAGCA
* * *
34894 AAAAATCGTAATGATTATTAAACGATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAAGTTATT
638 AAAAACCGTAATGA-GA-TAAACGATTTCGGCTAAAATTTTGTAAAAATTGACACGAAAG-TATT
* * * * * *
34959 TCCTCAAATTTTCACCACAATACTTATAAAAATTATATAATTCAACGTTGAAAAGATTGAAGCAC
700 TCCTCAAATTTACACCAAAAGAATTATAAAAAATATATAATTCAACGTCGAAAAGATTGAAGCAC
* * *
35024 TTTTCATGTTTCTAATATCGGTTTTCCTATTATTTTCCGAATTAATTTCTAATTACATCGAAACA
765 TTCTCACGTTTCTAATATCGGTTTT-CTATTATTTTCCAAATTAATTTCTAATTACATCGAAACA
* *
35089 TGATTCAAATGTTTGTTTTACAAACTCTTAAATCCAATGAGGCTGAGATTTTGTTAGATAAATAT
829 TGATTCAAA---TTG-TCTACAAA--C-GAAATCCAA-GA-G-T--GA-----TTAGATAAATAT
* * ** * * * *
35154 AGATATTTCAATGAGTCTCGGCGCCACAAATCATGTAACACTGAACCGGGCCCCGGAACGCGTTT
877 AGATATTTCAATGAGTCTCGGCACCAAAAATCATACAAAACTGAACCCGGCCCCAGAACGCGTTC
* *
35219 TTAGTCAAAAACCGTGATTTCGACTAAC
942 TCAGCCAAAAACCG-G--TTCGACTAAC
* * *
35247 GTACACGATTTCAACTAATATTTCGCAAAAATTGACTAGAAATATTTTTCCTCAATTTTTGTCTA
1 -TACACGATTTCAACTAATATTTCGCAAAAATTAACCAGAAATATTTTTCCTCAATTTTTGTCCA
* **
35312 AAATACTCATAAAATATATATAATTCAACTCCAAAAAAATTGGAGGACTTTTCTCGCTTTTAATA
65 AAATACTCATAAAATATATATAATTCAACTCCAAAAAAATTGGAGGAATTTTCAAGCTTTTAATA
* * * *
35377 TCGTTTTTCATATTTTTCTAAATTAATTTCTAATTGAATCCAAACAAAATTCAGATGCTCGTAAA
130 TCGTCTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAA
*
35442 AACAAATCCTTAAATGT-AATGTGGCTGAGATTTGATTAGATGGATATAGATATTTCAATGAGTC
195 AACAAATCCTTAAAT-TCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAA-GAGTC
* * * * *
35506 TCGACACCAAAAATCATGCAATACTGAGCTGGGTCCTCGAAACACGTTTTTAG-CAAAAGACCGT
258 TAGGCACCAAAAATCATGCAAAACTGAGCAGGGTCCT-GAAACGCGTTTTTAGCCAAAA-ACCGT
** * * * * *
35570 GAT-G--ACCCAAAAAATTT-A-C-ACCAATTTTGGC--TATAAT-A--C---------TCA---
321 GATGGTTA-GTACACAATTTCAGCTA-AAATTTT-GCAAAAAAATAACCCGAAAGATTTTCATCT
* * * * * *
35612 ---T-GA-AAAATA-T-ATATATATATATATAATTTAATA-ACAAAAATACTGGAGGAC-TTTTC
383 TTTTAGAGAAAATACTCATA-A-AGATATATAA-TTAA-AGCCAAAAAAATTGAAAG-CTTTTTC
* * * * *
35668 ACGCTTTTCATATCGTTTTTCATATTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCA
443 ACGCTTCTAATATCGTTTTTCATATTTTTCCAAATTAA-ATCTAATTAAATCAAAACAAGATTCA
** * * * *
35733 GATGTTCGTAAAAACAAATACTTAAATGCAATGTGGCTGA-ACTTTGATTAGATGAAT-ATTAAT
507 GATACTCGTAAAAACAAATCCTTAAATACAATGTAGCTGAGA-TTTGATTAGATGAATAAGT-AT
* * * * ** *
35796 ATCTCAAGGAG-TCTTGGCGTCAAAAATCATGCAAAACTGA-CCCGGGGCCCTGGAACGCGTTTT
570 ATCTCAAAGAGTTC-TAGCGCCAAAAAACATGCAAAACTGAGCCC-GGGCCCCAGAACACGTTTT
* * * * * * *
35859 TAGCCAAAAACCGTGATGATTATTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAG
633 TAGCAAAAAACCGTAATGA-GA-TAAACGATTTCGGCTAAAATTTTGTAAAAATTGACACGAAAG
* * *** * * * * *
35924 ATATTTCCTTAATTTTTGGCTAAAATAATCAT--AAAA-A-A-AATTCAACGTCAAAAATATTGA
696 -TATTTCCTCAAATTTACACCAAAAGAATTATAAAAAATATATAATTCAACGTCGAAAAGATTGA
* * * * * * * *
35984 AGGATTTTTTATGCTTCTAATATCGTTTTTCCTACTT-TTTT-CAAATTAGTTTCTAATTA-ACT
760 AGCACTTCTCACGTTTCTAATATCGGTTTT-CTA-TTATTTTCCAAATTAATTTCTAATTACA-T
* * * * *
36046 C-AAACAAGATTTAGA-TGCTCGTAAAAACAAATCATTAAATCCAATGTGGCTGAGATTTTATTA
822 CGAAACATGATTCAAATTG-TC-T----ACAAA-C--GAAATCCAA-------GAG---TGATTA
* * * * * * ** ** ***
36109 GATGAATATAGATATCTCAAGGAGTCTTGACGCCAAAAATCATGTAAAACTGACACGGGGTTTC-
868 GATAAATATAGATATTTCAATGAGTCTCGGCACCAAAAATCATACAAAACTGA-ACCCGGCCCCA
* * * * * * **
36173 GAACACGTTTTGAGCAAAAAAAAAACTG-T-GA-T-GG
932 GAACGCGTTCTCAGC---CAAAAACCGGTTCGACTAAC
* * * ** *
36207 TACACGATTTCAGCTAATATTTTGTAAAAATTGGCCCGAAATAATTTTTCCTCAATTTTTAGT-C
1 TACACGATTTCAACTAATATTTCGCAAAAATTAACCAGAAAT-ATTTTTCCTCAATTTTT-GTCC
* * * * * *** * *
36271 ACAATACTCATAAAAAACATATAATTCAACACCAAAAAGATT-GAGGGGCTTTCACGTTTTTAAT
64 AAAATACTCATAAAATATATATAATTCAACTCCAAAAAAATTGGAGGAATTTTCAAGCTTTTAAT
* * ** ** *
36335 ATCGTTTTTCCTATGTTTTTCCAAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTTGT
129 ATCGTCTTT-C-ATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGT
* *
36400 ----A-AAA--C-------CAA--TGGCTGAGATTTGGTTAGATGAATATAGGTATTTCAAGGAG
192 AAAAACAAATCCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAA-GAG
* * *** * * * * * *
36449 TCTCGACGTAAAAAATCATGCAAAACTGAATC-GGGCCCCGTAATGCGTTTTTAGCCAAAAACGG
256 TCTAGGCACCAAAAATCATGCAAAACTG-AGCAGGGTCCTGAAACGCGTTTTTAGCCAAAAACCG
* * * * * * * *
36513 TGATGATTATTACACGATTTCAGCTAAAATTTTGC-AAAAACTGATCCGAAAGATATCTCCTCAA
320 TGATGGTTAGTACACAATTTCAGCTAAAATTTTGCAAAAAAATAACCCGAAAGAT-TTTCATC--
** * * * * * * *
36577 TTTTTAGCCACAATACTCATAAAAAATAAATAATTTAACGCCAAAAAGATTGAAGGGC-TTTTGA
382 TTTTTAGAGAAAATACTCAT-AAAGATATATAA-TTAAAGCCAAAAAAATTGAA-AGCTTTTTCA
* * * * * *
36641 CGCTTCTAATGTC-TTTTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAGACAAGATTCAG
444 CGCTTCTAATATCGTTTTTCATATTTTTCCAAATTAA-ATCTAATTAAATCAAAACAAGATTCAG
* * * *
36705 ATGCACGTAAAAACAAATCCTTAAATCCAATGT-GGTGAGATTTGATTAGATGAATATAG-ATAT
508 ATACTCGTAAAAACAAATCCTTAAATACAATGTAGCTGAGATTTGATTAGATGAATA-AGTATAT
* * * * * * *
36768 TTC-AAGTAG-TCTAGAAGCCAAAAATCATGCAAAATTGAG-CCGGGTCCCGGAACGCGTTTTT-
572 CTCAAAG-AGTTCTAG-CGCCAAAAAACATGCAAAACTGAGCCCGGGCCCCAGAACACGTTTTTA
* ** * * * *
36829 GCCAAAAATTGTGATTTTTAGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACACGAA
635 GCAAAAAACCGT-A--ATGAG--A-TAAACGATTTCGGCTAAAATTTTGTAAAAATTGACACGAA
* * * *** * * * ** * * *
36894 AGATTTTTCCTTAATTTTTGGCTAAAATACTCCT-AAAAATATATAATTCAACGCCAAAAATATT
694 AG-TATTTCCTCAAATTTACACCAAAAGAATTATAAAAAATATATAATTCAACGTCGAAAAGATT
* ** * * ** *
36958 GGAGGGCTTTTCACGCTTT-TAATATC-GTATTTCTTATT-TTTTCTAAATTAATTTCTGTTTAA
758 GAAGCACTTCTCACG-TTTCTAATATCGGT-TTTC-TATTATTTTCCAAATTAATTTCTAATTAC
37020 ATCGAAACGA-GATTCAA
820 ATCGAAAC-ATGATTCAA
37037 GATTCAGATG
Statistics
Matches: 2264, Mismatches: 344, Indels: 331
0.77 0.12 0.11
Matches are distributed among these distances:
944 19 0.01
945 71 0.03
946 8 0.00
947 6 0.00
948 10 0.00
949 14 0.01
950 37 0.02
951 21 0.01
952 74 0.03
953 50 0.02
954 65 0.03
955 16 0.01
956 221 0.10
957 145 0.06
958 28 0.01
959 67 0.03
960 61 0.03
961 85 0.04
962 2 0.00
963 15 0.01
964 94 0.04
965 60 0.03
966 6 0.00
967 9 0.00
968 21 0.01
969 106 0.05
970 265 0.12
971 85 0.04
972 111 0.05
973 12 0.01
974 6 0.00
975 9 0.00
976 58 0.03
977 14 0.01
978 2 0.00
979 1 0.00
982 1 0.00
986 7 0.00
987 19 0.01
988 44 0.02
989 6 0.00
990 11 0.00
991 5 0.00
992 8 0.00
993 18 0.01
994 233 0.10
995 38 0.02
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (966 bp):
TACACGATTTCAACTAATATTTCGCAAAAATTAACCAGAAATATTTTTCCTCAATTTTTGTCCAA
AATACTCATAAAATATATATAATTCAACTCCAAAAAAATTGGAGGAATTTTCAAGCTTTTAATAT
CGTCTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAA
ACAAATCCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGAGTCTAG
GCACCAAAAATCATGCAAAACTGAGCAGGGTCCTGAAACGCGTTTTTAGCCAAAAACCGTGATGG
TTAGTACACAATTTCAGCTAAAATTTTGCAAAAAAATAACCCGAAAGATTTTCATCTTTTTAGAG
AAAATACTCATAAAGATATATAATTAAAGCCAAAAAAATTGAAAGCTTTTTCACGCTTCTAATAT
CGTTTTTCATATTTTTCCAAATTAAATCTAATTAAATCAAAACAAGATTCAGATACTCGTAAAAA
CAAATCCTTAAATACAATGTAGCTGAGATTTGATTAGATGAATAAGTATATCTCAAAGAGTTCTA
GCGCCAAAAAACATGCAAAACTGAGCCCGGGCCCCAGAACACGTTTTTAGCAAAAAACCGTAATG
AGATAAACGATTTCGGCTAAAATTTTGTAAAAATTGACACGAAAGTATTTCCTCAAATTTACACC
AAAAGAATTATAAAAAATATATAATTCAACGTCGAAAAGATTGAAGCACTTCTCACGTTTCTAAT
ATCGGTTTTCTATTATTTTCCAAATTAATTTCTAATTACATCGAAACATGATTCAAATTGTCTAC
AAACGAAATCCAAGAGTGATTAGATAAATATAGATATTTCAATGAGTCTCGGCACCAAAAATCAT
ACAAAACTGAACCCGGCCCCAGAACGCGTTCTCAGCCAAAAACCGGTTCGACTAAC
Found at i:35662 original size:303 final size:303
Alignment explanation
Indices: 35325--35877 Score: 801
Period size: 303 Copynumber: 1.8 Consensus size: 303
35315 TACTCATAAA
* * *
35325 ATATATATAATTCAACTCCAAAAAAATTGGAGGACTTTTCTCGCTTTTAATATCGTTTTTCATAT
1 ATATATATAATTCAACTACAAAAAAACTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATAT
* *
35390 TTTTCTAAATTAATTTCTAATTGAATCCAAACAAAATTCAGATGCTCGTAAAAACAAATCCTTAA
66 TTTTCTAAATTAATTTCTAATTAAATCCAAACAAAATTCAGATGCTCGTAAAAACAAATACTTAA
* * * *
35455 ATGTAATGTGGCTGAGA-TTTGATTAGATGGATA-TAGATATTTCAATGAGTCTCGACACCAAAA
131 ATGCAATGTGGCTGA-ACTTTGATTAGATGAATATTA-ATATCTCAAGGAGTCTCGACACCAAAA
* * * *
35518 ATCATGCAATACTGA-GCTGGGTCCTCGAAACACGTTTTTAG-CAAAAGACCGTGATGACCCAAA
194 ATCATGCAAAACTGACCCGGGGCCCT-GAAACACGTTTTTAGCCAAAA-ACCGTGATGACCCAAA
35581 AAATTTACACCAATTTTGGCTATAATACTCATGAAAAATATATATAT
257 AAATTTACACCAATTTTGGCTATAATACTCATGAAAAATATATATAT
* * *
35628 ATATATATAATTTAA-TAACAAAAATACTGGAGGACTTTTCACGCTTTTCATATCGTTTTTCATA
1 ATATATATAATTCAACT-ACAAAAAAACTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATA
* * *
35692 TTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGTTCGTAAAAACAAATACTTA
65 TTTTTCTAAATTAATTTCTAATTAAATCCAAACAAAATTCAGATGCTCGTAAAAACAAATACTTA
* * **
35757 AATGCAATGTGGCTGAACTTTGATTAGATGAATATTAATATCTCAAGGAGTCTTGGCGTCAAAAA
130 AATGCAATGTGGCTGAACTTTGATTAGATGAATATTAATATCTCAAGGAGTCTCGACACCAAAAA
* *
35822 TCATGCAAAACTGACCCGGGGCCCTGGAACGCGTTTTTAGCCAAAAACCGTGATGA
195 TCATGCAAAACTGACCCGGGGCCCTGAAACACGTTTTTAGCCAAAAACCGTGATGA
35878 TTATTACACG
Statistics
Matches: 220, Mismatches: 25, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
302 2 0.01
303 204 0.93
304 14 0.06
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (303 bp):
ATATATATAATTCAACTACAAAAAAACTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATAT
TTTTCTAAATTAATTTCTAATTAAATCCAAACAAAATTCAGATGCTCGTAAAAACAAATACTTAA
ATGCAATGTGGCTGAACTTTGATTAGATGAATATTAATATCTCAAGGAGTCTCGACACCAAAAAT
CATGCAAAACTGACCCGGGGCCCTGAAACACGTTTTTAGCCAAAAACCGTGATGACCCAAAAAAT
TTACACCAATTTTGGCTATAATACTCATGAAAAATATATATAT
Found at i:36266 original size:326 final size:327
Alignment explanation
Indices: 35662--37097 Score: 1392
Period size: 326 Copynumber: 4.4 Consensus size: 327
35652 TACTGGAGGA
* * *
35662 CTTTTCACGCTTTTCATATCGTTTTTCATA-TTTTTCTAAATTAATTTCTAATTAAATCGAAACA
1 CTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTC-AAATTAATTTCTAATTAAATCGAAACA
* *
35726 AGATTCAGATGTTCGTAAAAACAAATACTTAAATGCAATGTGGCTGA-ACTTTGATTAGATGAAT
65 AGATTCAGATGCTCGTAAAAACAAATA-TTAAATCCAATGTGGCTGAGA-TTTGATTAGATGAAT
* * * *
35790 ATTA-ATATCTCAAGGAGTCTTGGCGTCAAAAATCATGCAAAACTGACCCGGGGCCCTGGAACGC
128 A-TAGATATCTCAAGGAGTCTTGACGCCAAAAATCATGCAAAACTGACAC-GGGCCC-CGAACGC
* * * *
35854 GTTTTTAGC-CAAAAACCGTGATGATTATTACACGATTTCAGCTAAAATTTTGCAAAAATTGACC
190 GTTTTGAGCAAAAAAAAC-TGATGATTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACC
* * * * *
35918 CGAAAGATATTTCCTTAATTTTTGGCTAAAATAATCAT-AAAA-A-A-AATTCAACGTCAAAAAT
254 CGAAAGATATTTCCTCAATTTTTAGCTAAAATACTCATAAAAACATATAATTCAACGCCAAAAAG
*
35979 ATTGAAGGA
319 ATTGAAGGG
* * * * *
35988 TTTTTTATGCTTCTAATATCGTTTTTCCTACTTTTTTCAAATTAGTTTCTAATTAACTC-AAACA
1 CTTTTCACGCTTCTAATATCGTTTTTCCTA-TTTTTTCAAATTAATTTCTAATTAAATCGAAACA
* *
36052 AGATTTAGATGCTCGTAAAAACAAATCATTAAATCCAATGTGGCTGAGATTTTATTAGATGAATA
65 AGATTCAGATGCTCGTAAAAACAAAT-ATTAAATCCAATGTGGCTGAGATTTGATTAGATGAATA
* *** *
36117 TAGATATCTCAAGGAGTCTTGACGCCAAAAATCATGTAAAACTGACACGGGGTTTCGAACACGTT
129 TAGATATCTCAAGGAGTCTTGACGCCAAAAATCATGCAAAACTGACAC-GGGCCCCGAACGCGTT
* * * *
36182 TTGAGCAAAAAAAAAACTG-TGA-TGGTACACGATTTCAGCTAATATTTTGTAAAAATTGGCCCG
193 TTGAGC--AAAAAAAACTGATGATTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCG
* * * *
36245 AAATAATTTTTCCTCAATTTTTAG-TCACAATACTCATAAAAAACATATAATTCAACACCAAAAA
256 AAA-GATATTTCCTCAATTTTTAGCT-AAAATACTCAT-AAAAACATATAATTCAACGCCAAAAA
*
36309 GATTGAGGGG
318 GATTGAAGGG
* *
36319 C-TTTCACGTTTTTAATATCGTTTTTCCTATGTTTTTCCAAATTAATTTCTAATTAAATCGAAAC
1 CTTTTCACGCTTCTAATATCGTTTTTCCTAT-TTTTT-CAAATTAATTTCTAATTAAATCGAAAC
* * *
36383 ATGATTCAGATGCT--T--------GTA--AAA-CCAA--TGGCTGAGATTTGGTTAGATGAATA
64 AAGATTCAGATGCTCGTAAAAACAAATATTAAATCCAATGTGGCTGAGATTTGATTAGATGAATA
* * * ** *
36433 TAGGTATTTCAAGGAGTCTCGACGTAAAAAATCATGCAAAACTGA-ATCGGGCCCCGTAATGCGT
129 TAGATATCTCAAGGAGTCTTGACGCCAAAAATCATGCAAAACTGACA-CGGGCCCCG-AACGCGT
* * *** * * *
36497 TTTTAGCCAAAAACGGTGATGATTATTACACGATTTCAGCTAAAATTTTGCAAAAACTGATCCGA
192 TTTGAGCAAAAAAAACTGATGATTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGA
* * * *
36562 AAGATATCTCCTCAATTTTTAGCCACAATACTCATAAAAA-ATAAATAATTTAACGCCAAAAAGA
257 AAGATATTTCCTCAATTTTTAGCTAAAATACTCATAAAAACAT--ATAATTCAACGCCAAAAAGA
36626 TTGAAGGG
320 TTGAAGGG
* * * * *
36634 CTTTTGACGCTTCTAATGTC-TTTTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAGACAA
1 CTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCAAATTAATTTCTAATTAAATCGAAACAA
* *
36698 GATTCAGATGCACGTAAAAACAAATCCTTAAATCCAATGTGG-TGAGATTTGATTAGATGAATAT
66 GATTCAGATGCTCGTAAAAACAAAT-ATTAAATCCAATGTGGCTGAGATTTGATTAGATGAATAT
* * * * * *
36762 AGATATTTCAAGTAGTCTAGAAGCCAAAAATCATGCAAAATTGAGC-CGGGTCCCGGAACGCGTT
130 AGATATCTCAAGGAGTCTTGACGCCAAAAATCATGCAAAACTGA-CACGGG-CCCCGAACGCGTT
* * *** * * *
36826 TT-TGCCAAAAATTGTGATTTTTAGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACA
193 TTGAGCAAAAAAAACTGA---TGA-TTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACC
* * * * * *
36890 CGAAAGATTTTTCCTTAATTTTTGGCTAAAATACTCCTAAAAATATATAATTCAACGCCAAAAAT
254 CGAAAGATATTTCCTCAATTTTTAGCTAAAATACTCATAAAAACATATAATTCAACGCCAAAAAG
*
36955 ATTGGAGGG
319 ATTGAAGGG
* * * **
36964 CTTTTCACGCTTTTAATATCGTATTTCTTATTTTTTCTAAATTAATTTCTGTTTAAATCGAAACG
1 CTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTC-AAATTAATTTCTAATTAAATCG--A--
* * * * *
37029 AGATTCAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATTCAATATTGCTGAGATTTGGTTAG
61 A-A--CAAGATTCAGATGCTCGTAAAAACAAA-TATTAAATCCAATGTGGCTGAGATTTGATTAG
37094 ATGA
122 ATGA
37098 TGTAAAGTAT
Statistics
Matches: 912, Mismatches: 137, Indels: 108
0.79 0.12 0.09
Matches are distributed among these distances:
313 39 0.04
314 16 0.02
315 74 0.08
316 125 0.14
318 4 0.00
319 3 0.00
321 1 0.00
322 1 0.00
323 1 0.00
325 55 0.06
326 162 0.18
327 39 0.04
328 87 0.10
329 9 0.01
330 75 0.08
331 125 0.14
332 37 0.04
334 1 0.00
337 1 0.00
339 39 0.04
340 18 0.02
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Consensus pattern (327 bp):
CTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCAAATTAATTTCTAATTAAATCGAAACAA
GATTCAGATGCTCGTAAAAACAAATATTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATA
GATATCTCAAGGAGTCTTGACGCCAAAAATCATGCAAAACTGACACGGGCCCCGAACGCGTTTTG
AGCAAAAAAAACTGATGATTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAGA
TATTTCCTCAATTTTTAGCTAAAATACTCATAAAAACATATAATTCAACGCCAAAAAGATTGAAG
GG
Found at i:36465 original size:316 final size:313
Alignment explanation
Indices: 35766--37035 Score: 918
Period size: 316 Copynumber: 3.9 Consensus size: 313
35756 AAATGCAATG
* *
35766 TGGCTGA-ACTTTGATTAGATGAATATTA-ATATCTCAAGGAGTCTTGGCGTC-AAAAATCATGC
1 TGGCTGAGA-TTTGATTAGATGAATA-TAGATATCTCAAGGAGTCTCGACG-CAAAAAATCATGC
** * * * * * * *
35828 AAAACTGACCCGGGGCCCTGGAACGCGTTTTTAGC-CAAAAACCGTGATGATTATTACACGATTT
63 AAAACTGAATC-GGGCCCCGTAACACGTTTTGAGCAAAAAAAAC-TGATGATTAGTACACGATTT
* * * * * * * *
35892 CAGCTAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCTTAATTTTTGGCTAAAATAATCAT-
126 CAGCTAAAATTTTGCAAAAACTGACCCGAAAAATATCTCCTCAATTTTTAGCCACAATACTCATA
** * ** * *
35956 --AAA-AAA-AATTCAACGTCAAAAATATTGAAGGATTTTTTATGCTTCTAATATCGTTTTTCCT
191 AAAAACAAATAATTCAACACCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATC-TTTTTCCT
* * * * *
36017 ACTTTTTTCAAATTAGTTTCTAATTAACTC-AAACAAGATTTAGATGCTCGTAAAAACAAATCAT
255 A-TTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCT--T--------GT-A-
36081 TAAATCCAA
307 -AAA-CCAA
* * * *
36090 TGTGGCTGAGATTTTATTAGATGAATATAGATATCTCAAGGAGTCTTGACGCCAAAAATCATGTA
1 --TGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTCGACGCAAAAAATCATGCA
*** *
36155 AAACTGACA-CGGGGTTTCG-AACACGTTTTGAGCAAAAAAAAAACTG-TGA-TGGTACACGATT
64 AAACTGA-ATC-GGGCCCCGTAACACGTTTTGAGC--AAAAAAAACTGATGATTAGTACACGATT
* * * * * * *
36216 TCAGCTAATATTTTGTAAAAATTGGCCCGAAATAATTTTTCCTCAATTTTTAGTCACAATACTCA
125 TCAGCTAAAATTTTGCAAAAACTGACCCGAAA-AATATCTCCTCAATTTTTAGCCACAATACTCA
* * * *
36281 TAAAAAACATATAATTCAACACCAAAAAGATTGAGGGGC-TTTCACGTTTTTAATATCGTTTTTC
189 TAAAAAACAAATAATTCAACACCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATC-TTTTTC
*
36345 CTATGTTTTTCCAAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTTGTAAAACCAA
253 CTA--TTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAACCAA
* * * *
36408 TGGCTGAGATTTGGTTAGATGAATATAGGTATTTCAAGGAGTCTCGACGTAAAAAATCATGCAAA
1 TGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTCGACGCAAAAAATCATGCAAA
** * * *** *
36473 ACTGAATCGGGCCCCGTAATGCGTTTTTAGCCAAAAACGGTGATGATTATTACACGATTTCAGCT
66 ACTGAATCGGGCCCCGTAACACGTTTTGAGCAAAAAAAACTGATGATTAGTACACGATTTCAGCT
* *
36538 AAAATTTTGCAAAAACTGATCCGAAAGATATCTCCTCAATTTTTAGCCACAATACTCATAAAAAA
131 AAAATTTTGCAAAAACTGACCCGAAAAATATCTCCTCAATTTTTAGCCACAATACTCATAAAAAA
* * * * *
36603 TAAATAATTTAACGCCAAAAAGATTGAAGGGCTTTTGACGCTTCTAATGTCTTTTTCCTATTTTT
196 CAAATAATTCAACACCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCTTTTTCCTATTTTT
* * * *
36668 CCGAATTAATTTCTAATTAAATCGAGACAAGATTCAGATGCACGTAAAAACAAATCCTTAAATCC
261 CCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATG--C-T---------T--GTAAAACC
36733 AA
312 AA
* * * * * *
36735 TGTGGTGAGATTTGATTAGATGAATATAGATATTTCAAGTAGTCTAGAAGCCAAAAATCATGCAA
1 TG-GCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTCGACGCAAAAAATCATGCAA
* ** * * * * * *** *
36800 AATTGAGCCGGGTCCCGGAACGCGTTTT-TGCCAAAAATTGTGATTTTTAGTTAGTACACGATTT
65 AACTGAATCGGGCCCCGTAACACGTTTTGAGCAAAAAAAACTGA---TGA-TTAGTACACGATTT
* * * * * * * * * * *
36864 CGGCTAAAATTTTGCAAAAATTGACACGAAAGATTTTTCCTTAATTTTTGGCTAAAATACTCCT-
126 CAGCTAAAATTTTGCAAAAACTGACCCGAAAAATATCTCCTCAATTTTTAGCCACAATACTCATA
* * * * * * * *
36928 AAAAATATATAATTCAACGCCAAAAATATTGGAGGGCTTTTCACGCTTTTAATATCGTATTTCTT
191 AAAAACAAATAATTCAACACCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATC-TTTTTCCT
* ** *
36993 ATTTTTTCTAAATTAATTTCTGTTTAAATCGAAACGAGATTCA
255 A-TTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCA
37036 AGATTCAGAT
Statistics
Matches: 772, Mismatches: 131, Indels: 76
0.79 0.13 0.08
Matches are distributed among these distances:
313 42 0.05
314 7 0.01
315 81 0.10
316 126 0.16
318 4 0.01
319 3 0.00
321 1 0.00
322 1 0.00
325 55 0.07
326 94 0.12
327 25 0.03
328 82 0.11
329 3 0.00
330 78 0.10
331 119 0.15
332 51 0.07
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (313 bp):
TGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTCGACGCAAAAAATCATGCAAA
ACTGAATCGGGCCCCGTAACACGTTTTGAGCAAAAAAAACTGATGATTAGTACACGATTTCAGCT
AAAATTTTGCAAAAACTGACCCGAAAAATATCTCCTCAATTTTTAGCCACAATACTCATAAAAAA
CAAATAATTCAACACCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCTTTTTCCTATTTTT
CCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAACCAA
Found at i:37434 original size:21 final size:22
Alignment explanation
Indices: 37392--37434 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
37382 CATAATTAAT
* *
37392 AAAAAGTTGAATCATCTCAAAA
1 AAAAAGTTAAATCATCTAAAAA
*
37414 AAAAAGTTAAATGA-CTAAAAA
1 AAAAAGTTAAATCATCTAAAAA
37435 GAATACTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.21
Consensus pattern (22 bp):
AAAAAGTTAAATCATCTAAAAA
Found at i:39081 original size:21 final size:21
Alignment explanation
Indices: 39029--39088 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
39019 GTGAATATTA
* *
39029 ATCAATATTTGGTGTAATGAT
1 ATCATTATTAGGTGTAATGAT
* *
39050 -TC-TTTTTAGGTGTAATGGT
1 ATCATTATTAGGTGTAATGAT
39069 ATCATTATTAGGTGTAATGA
1 ATCATTATTAGGTGTAATGA
39089 AAAATCAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
19 13 0.42
20 4 0.13
21 14 0.45
ACGTcount: A:0.28, C:0.05, G:0.22, T:0.45
Consensus pattern (21 bp):
ATCATTATTAGGTGTAATGAT
Found at i:39665 original size:1 final size:1
Alignment explanation
Indices: 39659--39686 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
39649 CTTCTTCGGG
39659 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
39687 GCTTATAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.