Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014102.1 Corchorus olitorius cultivar O-4 contig14135, 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: 36969
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6313 original size:22 final size:22
Alignment explanation
Indices: 6284--6381 Score: 87
Period size: 22 Copynumber: 4.5 Consensus size: 22
6274 AAATTTAGAC
6284 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACCTTCATATGAAA
*
6305 TTTTGATAACC-ACACTATGAAA
1 TTTTGATAACCTTCA-TATGAAA
*
6327 TTTTGATAACCTCTC-CATGAAA
1 TTTTGATAACCT-TCATATGAAA
* * *
6349 TATT-AGTAACCTCCTTATGAAA
1 TTTTGA-TAACCTTCATATGAAA
*
6371 TTTTGTTAACC
1 TTTTGATAACC
6382 ACACTATGTA
Statistics
Matches: 62, Mismatches: 8, Indels: 13
0.75 0.10 0.16
Matches are distributed among these distances:
21 8 0.13
22 53 0.85
24 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (22 bp):
TTTTGATAACCTTCATATGAAA
Found at i:6389 original size:22 final size:22
Alignment explanation
Indices: 6298--6403 Score: 101
Period size: 22 Copynumber: 4.8 Consensus size: 22
6288 ATAACCTTCA
6298 TATGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCACAC
* *
6320 TATGAAATTTTGATAACCTCTC
1 TATGAAATTTTGATAACCACAC
* * *
6342 CATGAAATATT-AGTAACCTC-C
1 TATGAAATTTTGA-TAACCACAC
*
6363 TTATGAAATTTTGTTAACCACAC
1 -TATGAAATTTTGATAACCACAC
*
6386 TATGTAATTCTT-ATAACC
1 TATGAAATT-TTGATAACC
6404 TCGCTATGCC
Statistics
Matches: 69, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
21 2 0.03
22 64 0.93
23 3 0.04
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:6543 original size:22 final size:22
Alignment explanation
Indices: 6452--6668 Score: 135
Period size: 22 Copynumber: 9.8 Consensus size: 22
6442 CCTTTATATA
* *
6452 AAATTGTGATAACCAAACTATG
1 AAATTTTGATAACCACACTATG
** * *
6474 AAATTTCAATAACCTTC-CTAAG
1 AAATTTTGATAACC-ACACTATG
* *
6496 AAATTTTAATAA-CATGATCCTATG
1 AAATTTTGATAACCA-CA--CTATG
*
6520 AAATTTTGGTAACCACACTATG
1 AAATTTTGATAACCACACTATG
* *
6542 AAATTTTGATAACCTTC-CCATG
1 AAATTTTGATAACC-ACACTATG
6564 AAA-TTTGATAACTTC-CA-TATG
1 AAATTTTGATAAC--CACACTATG
* *
6585 AAATTTTGGTAACTACACTATG
1 AAATTTTGATAACCACACTATG
* *
6607 GAATTTTGATAACCTC-CTCATG
1 AAATTTTGATAACCACACT-ATG
* * *
6629 AAATTATAATAACCATC-TTATG
1 AAATTTTGATAACCA-CACTATG
6651 AAATTTTGATAACCACAC
1 AAATTTTGATAACCACAC
6669 AAAGACAAGA
Statistics
Matches: 148, Mismatches: 31, Indels: 32
0.70 0.15 0.15
Matches are distributed among these distances:
21 22 0.15
22 105 0.71
23 4 0.03
24 15 0.10
25 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.34
Consensus pattern (22 bp):
AAATTTTGATAACCACACTATG
Found at i:6612 original size:65 final size:66
Alignment explanation
Indices: 6438--6668 Score: 227
Period size: 65 Copynumber: 3.5 Consensus size: 66
6428 AATCTCTTTG
* * * * * * ** * *
6438 ATAACCTTTATATAAAATTGTGATAACCAAACTATGAAATTTCAATAACCTTCCT-AAGAAATTT
1 ATAACCATCATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACC-TCCTCATGAAATTA
6502 TA
65 TA
* *
6504 ATAACATGATCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCC-CATGAAAT
1 ATAAC--CATCATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACC-TCCTCATGAAAT
*
6568 T-TG
63 TATA
* * *
6571 ATAA-CTTCCATATGAAATTTTGGTAACTACACTATGGAATTTTGATAACCTCCTCATGAAATTA
1 ATAACCAT-CATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTCCTCATGAAATTA
6635 TA
65 TA
* *
6637 ATAACCATCTTATGAAATTTTGATAACCACAC
1 ATAACCATCATATGAAATTTTGGTAACCACAC
6669 AAAGACAAGA
Statistics
Matches: 136, Mismatches: 22, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
64 4 0.03
65 48 0.35
66 31 0.23
67 7 0.05
68 46 0.34
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (66 bp):
ATAACCATCATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTCCTCATGAAATTAT
A
Found at i:6863 original size:20 final size:20
Alignment explanation
Indices: 6825--6863 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
6815 TATTGATATT
6825 TAAAAAATTGAAATTAAAAG
1 TAAAAAATTGAAATTAAAAG
*
6845 TAAAATATT-AAATTCAAAA
1 TAAAAAATTGAAATT-AAAA
6864 AATAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TAAAAAATTGAAATTAAAAG
Found at i:7810 original size:26 final size:26
Alignment explanation
Indices: 7750--7811 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 26
7740 TTTAAATTTT
7750 TATTATTTTAATAATGGAATAATTAAAA
1 TATTA-TTTAATAATGGAAT-ATTAAAA
7778 TATTATTTAATAATGGCAAT-TTAAAA
1 TATTATTTAATAATGG-AATATTAAAA
7804 -ATATATTT
1 TAT-TATTT
7812 GAAAAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
25 2 0.06
26 11 0.34
27 11 0.34
28 8 0.25
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (26 bp):
TATTATTTAATAATGGAATATTAAAA
Found at i:12096 original size:2 final size:2
Alignment explanation
Indices: 12091--12141 Score: 52
Period size: 2 Copynumber: 25.5 Consensus size: 2
12081 CACACTACTA
* *
12091 AT AT AT ACT AT AT AT AT A- AT GCT AA AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT
12134 -T AT AT AT A
1 AT AT AT AT A
12142 AAAGTACGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
1 2 0.05
2 36 0.88
3 3 0.07
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:13690 original size:30 final size:30
Alignment explanation
Indices: 13594--13978 Score: 518
Period size: 30 Copynumber: 12.7 Consensus size: 30
13584 ACTAATATAT
* **
13594 ATTGACACTAGAAGTTGTCAATGGCCTTACA
1 ATTGACACCAGAAGTTGTC-ATGATCTTACA
**
13625 ATTGACACCAGAAGTTGTCAATGGCCTTACA
1 ATTGACACCAGAAGTTGTC-ATGATCTTACA
* *
13656 ATTGATACCAGAAGTTGTCATGATCTTGCA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
*
13686 ATTGACACCAGAAGTTGTCATGATCTTCCA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
*
13716 ATTGACACCAGAAGTTGTCATGATCTTCCA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
* * *
13746 ATTAACACCAAAAGTTGTCAATGGTCTTACA
1 ATTGACACCAGAAGTTGTC-ATGATCTTACA
* * * *
13777 ATTGACAACAAAAGTTGTCAAGTTCTTACA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
* * *
13807 ATTGACAACAGAAGTTGTCAAGTTCTTACA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
* *
13837 ATTGACACCAGAAGTTGTCAAGTTCTTACA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
*
13867 ATTGACACTAGAAGTTGTCATGATCTTACA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
13897 ATTGACACCAGAAGTTGTCATGATCTTACA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
*
13927 ATTGACACCAGAAGTTGTCAATGTTCTTACA
1 ATTGACACCAGAAGTTGTC-ATGATCTTACA
*
13958 ATTGACACCAAAAGTTGTCAT
1 ATTGACACCAGAAGTTGTCAT
13979 AATAAATTTC
Statistics
Matches: 329, Mismatches: 23, Indels: 5
0.92 0.06 0.01
Matches are distributed among these distances:
30 227 0.69
31 102 0.31
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (30 bp):
ATTGACACCAGAAGTTGTCATGATCTTACA
Found at i:13809 original size:121 final size:121
Alignment explanation
Indices: 13594--13978 Score: 547
Period size: 121 Copynumber: 3.2 Consensus size: 121
13584 ACTAATATAT
* ** *
13594 ATTGACACTAGAAGTTGTCAATGGCCTTACAATTGACACCAGAAGTTGTCAATGGCCTTACAATT
1 ATTGACACCAGAAGTTGTC-ATGATCTTACAATTGACACCAGAAGTTGTCAATGGTCTTACAATT
* * * *
13659 GATACCAGAAGTTGTCATGATCTTGCAATTGACACCAGAAGTTGTCATGATCTTCCA
65 GACACCAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTCATGTTCTTACA
* * *
13716 ATTGACACCAGAAGTTGTCATGATCTTCCAATTAACACCAAAAGTTGTCAATGGTCTTACAATTG
1 ATTGACACCAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTCAATGGTCTTACAATTG
* * * * * *
13781 ACAACAAAAGTTGTCAAGTTCTTACAATTGACAACAGAAGTTGTCAAGTTCTTACA
66 ACACCAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTCATGTTCTTACA
* * * *
13837 ATTGACACCAGAAGTTGTCAAGTTCTTACAATTGACACTAGAAGTTGTC-ATGATCTTACAATTG
1 ATTGACACCAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTCAATGGTCTTACAATTG
13901 ACACCAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTCAATGTTCTTACA
66 ACACCAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTC-ATGTTCTTACA
*
13958 ATTGACACCAAAAGTTGTCAT
1 ATTGACACCAGAAGTTGTCAT
13979 AATAAATTTC
Statistics
Matches: 230, Mismatches: 32, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
120 54 0.23
121 158 0.69
122 18 0.08
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (121 bp):
ATTGACACCAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTCAATGGTCTTACAATTG
ACACCAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTCATGTTCTTACA
Found at i:19628 original size:72 final size:72
Alignment explanation
Indices: 19539--19685 Score: 276
Period size: 72 Copynumber: 2.0 Consensus size: 72
19529 TTAACCATTC
* *
19539 TAAATTATCATTTATTCAATAAAATTTTTATTATTGTTATAATTTTATTAAATTTGCTAAACTTC
1 TAAATTATCATTGATTCAATAAAATTTTCATTATTGTTATAATTTTATTAAATTTGCTAAACTTC
19604 ATGAATA
66 ATGAATA
19611 TAAATTATCATTGATTCAATAAAATTTTCATTATTGTTATAATTTTATTAAATTTGCTAAACTTC
1 TAAATTATCATTGATTCAATAAAATTTTCATTATTGTTATAATTTTATTAAATTTGCTAAACTTC
19676 ATGAATA
66 ATGAATA
19683 TAA
1 TAA
19686 GTATTAAATC
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.48
Consensus pattern (72 bp):
TAAATTATCATTGATTCAATAAAATTTTCATTATTGTTATAATTTTATTAAATTTGCTAAACTTC
ATGAATA
Found at i:20924 original size:22 final size:22
Alignment explanation
Indices: 20899--20945 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
20889 TTTTTAGTTG
*
20899 AGTAAAACT-ATAAAAGTAAAAT
1 AGTAAAA-TGATAAAAATAAAAT
*
20921 AGTAAAATGGTAAAAATAAAAT
1 AGTAAAATGATAAAAATAAAAT
20943 AGT
1 AGT
20946 TATAAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23
Consensus pattern (22 bp):
AGTAAAATGATAAAAATAAAAT
Found at i:20950 original size:93 final size:93
Alignment explanation
Indices: 20837--21006 Score: 295
Period size: 93 Copynumber: 1.8 Consensus size: 93
20827 TAATAATATC
** *
20837 GTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGT
1 GTAAAAATAAAATAGGTATAAAAATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGACT
20902 AAAACTATAAAAGTAAAATAGTAAAATG
66 AAAACTATAAAAGTAAAATAGTAAAATG
*
20930 GTAAAAATAAAATAGTTATAAAAATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGACT
1 GTAAAAATAAAATAGGTATAAAAATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGACT
*
20995 AAAACTTTAAAA
66 AAAACTATAAAA
21007 ATTTAAACAA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.53, C:0.02, G:0.12, T:0.33
Consensus pattern (93 bp):
GTAAAAATAAAATAGGTATAAAAATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGACT
AAAACTATAAAAGTAAAATAGTAAAATG
Found at i:23084 original size:336 final size:331
Alignment explanation
Indices: 21477--25004 Score: 3283
Period size: 336 Copynumber: 10.6 Consensus size: 331
21467 GGTAAACATT
* * * *
21477 ACCCGAAAGATTTTTCCTCATTTTTTTAGC-AAAACTACTCAT-AAATATATATAATTAAACACC
1 ACCCGAAAG-TTTTTCCTCA-ATTTTTAGCTAAAA-TACTCATAAAAAATATATAATTCAACGCC
* * * *
21540 AAAATGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTCAGAATTAATTTC
63 AAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTTCTGAATTAATTTC
* * * **
21605 TAATTAAATCGAAACAAGATTCAGATGCACATAAAAACAAATCCTTGAATCCAATGTTCCTGAGA
127 TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGA
* * * * * **
21670 TTTGATTAGATGAATAAATATATTTCAAGGAGTTTCGACGTCAAAAATCATGCAAAAAACAGAGT
192 TTTGATTAGATGAATATAGATATTTCAAGGAGTTTCGGCGCCAAAAATCATGC--AAAACTGAAC
* * * * *
21735 TGTGGTCCTA-GAACGCGTTTTTACCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAT
255 CG-GGGCCCAGGAACGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAAT
*
21799 TTTGCAAAAATGG
319 TTTGCAAAAATTG
* * * **
21812 ACCCGAAAGATATTTCCTCAATTTTTGGTTAAAATACTCATAAAAAATATATAATTCAACATCAA
1 ACCCGAAAG-TTTTTCCTCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAACGCCAA
* * * ** *
21877 AAAGATTAAAGGGCTTTTAACGCTTCTAATATTATTTTTCCA-ATTTTTTCCGAATTAATTTCTA
65 AAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTT-CATATTTTTTCTGAATTAATTTCTA
* * * * *
21941 ATTAAATCGAAACAAGATTCAAATGCTCGCAAAAAAAAAAATCCTTAAATCTAATGTGTCTGAGA
129 ATTAAATCGAAACAAGATTCAGATGCTCG--TAAAAACAAATCCTTAAATCCAATGTGGCTGAGA
* * * *
22006 TTTGGTTAGATGAATATAGATATTTAAAGGA--TT--GCACCAAAAATCATGCAATACTG-ACTC
192 TTTGATTAGATGAATATAGATATTTCAAGGAGTTTCGGCGCCAAAAATCATGCAAAACTGAAC-C
* * * *
22066 GGGTCCC-GGAACGCGTTTTTAGCCGAAAATCGTGATGGTTAGTACACGATTTCGGCTAAAATTT
256 GGGGCCCAGGAACGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTT
*
22130 TGGAAAAATTG
321 TGCAAAAATTG
* * * * * * * *
22141 ATCCGAAAGATTTTTCCTCGATTTCTAACGAAAATAATCATAAAAAACATATAATTCAATGCCAA
1 ACCCGAAAG-TTTTTCCTCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAACGCCAA
* *** * * *
22206 AAAAATTGAAATCCTTTTCCACGCTTTTAATATC-ATTTCCATA-TTTTTCTG-ATTAATTTCTT
65 AAAGATTGAAGGGCTTTT-CACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTA
** * * *
22268 ATTAAATTTAAACAAAATTCAGATGCTCGTAAAAACAAATCCTTCAATTCAATGTGGCTGAGATT
129 ATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATT
* * * *
22333 TGATTAGATAAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATTATGCAAAACT-AAGTCGG
194 TGATTAGATGAATATAGATATTTCAAGGAGTTTCGGCGCCAAAAATCATGCAAAACTGAA-CCGG
* * * * * * *
22397 GGCCCTGAAACGCGTTTTTAGCAAAAAAAATCGTGATGGTTACTACACGATTTCGGCTAAAACTT
258 GGCCCAGGAACGCGTTTTTAGC--CAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTT
22462 TGCAAAAAATT-
321 TGC-AAAAATTG
* * * *
22473 ACCCGAAAAATTATTCCGTCAATTTTTGGCTAAAATACTCAT--AATATATATAATTCAACGCCA
1 ACCCG-AAAGTTTTTCC-TCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAACGCCA
* * * * *
22536 AAAATATTGGAGGACTTTTCAAGCTTTTAATATTGTTTTTCATA-TTTTTCTGAATTAATTTCTA
64 AAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTA
* * * ***
22600 ATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATTTAAATGAGATT
129 ATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATT
* * * * * *
22665 TGATTAAATGAATATGGATATCTCAAAGAGTCTT-GGCGCCAAAAATCATGCAAAACTTAGCCGG
194 TGATTAGATGAATATAGATATTTCAAGGAGT-TTCGGCGCCAAAAATCATGCAAAACTGAACCGG
** * * * * *
22729 GGCCTTGGAAAGCGTTTTTAGCCAAAAAACCGTGATGATTATTATACGATTTCGATCGGTTAGAA
258 GGCCCAGGAACGCGTTTTTAGCC-AAAAACCGTGATGATTAGTACACGA-TT---TCGGCTAAAA
22794 TTTTGCAAAAATTG
318 TTTTGCAAAAATTG
* * * *
22808 ACTCGAAAGTTATTTCCTCAATTTTTAGCCACAATACTCATAAAAATTATATAATTCAACGCCAA
1 ACCCGAAAGTT-TTTCCTCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAACGCCAA
* * * * * *
22873 AAAGTTTGAAGGTCTTTTCATGCTTCTAATATCGTTTTTCCTATTATTTTCCGAATTAATTTCTA
65 AAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATT-TTTTCTGAATTAATTTCTA
* *** * *
22938 ATTAAATCGAAACATGATTCAGATGCTTC-T-TTTACAAATCCTTAAATCCAATTTGGCTGAAAT
129 ATTAAATCGAAACAAGATTCAGATGC-TCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGAT
* * * * * * * *
23001 TTGGTTAAATGAATGTAGATATTT-AAGGAGTTTCAGCG-CAAAAATTAATGCAACATTGAACCT
193 TTGATTAGATGAATATAGATATTTCAAGGAGTTTCGGCGCCAAAAA-TCATGCAAAACTGAACCG
* * * * *
23064 GGGCCCAGGAACGGGTTTTTAGCCAAAAACCGTGATTTCGACTAACGTACACGATATCGCCTAAT
257 GGGCCCAGGAACGCGTTTTTAGCCAAAAACCGTGA--T-GA-TTA-GTACACGATTTCGGCTAAA
*
23129 ATTTTGCAAAAATTA
317 ATTTTGCAAAAATTG
** * * ** *
23144 ACCAAAAATATTTTTTCTCAATTTTTATTTAAAATACT--TGAAAATATATATATAATTCAACTC
1 ACCCGAAA-GTTTTTCCTCAATTTTTAGCTAAAATACTCAT-AAAA-A-ATATATAATTCAACGC
* * * *
23207 AAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCATTTTTCATA-TTTTTCTGAATTAATTTC
62 CAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTC
* * * * * * *
23271 TAATTAAACCGAAACAAGATTCAGATGCACATAAAAACAAATCCTTAAATGCAATCTGGATGATA
127 TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGA
* * * *
23336 CTTGATTAGATGAATATAGATATTTCAAAGAGTCTCGACGCCAAAAATCATGCAAAACTGAACCG
192 TTTGATTAGATGAATATAGATATTTCAAGGAGTTTCGGCGCCAAAAATCATGCAAAACTGAACCG
* * * * * *
23401 GGGCACC-GAAATGCGTTTTTAGCAAAGAAAACCGTGATGGTTAGTACATGATTTCAGCTAAAAT
257 GGGC-CCAGGAACGCGTTTTTAGC-CA-AAAACCGTGATGATTAGTACACGATTTCGGCTAAAAT
23465 TTTGCAAAAAAATT-
319 TTTGC--AAAAATTG
* ** * * *
23479 ACCAGAAAAACTTTTCCTCAATTTTTAGCCACAAT-CTCATAAAAAAATATATAATTCAACGCTA
1 ACCCG-AAAGTTTTTCCTCAATTTTTAGCTAAAATACTCAT-AAAAAATATATAATTCAACGCCA
* * * ** *
23543 AAAAGATTTAAGGGCTTTTCGCGCTTCTAATATCGTTTTTTTTTATTTTTTTCCGAATTAATTTC
64 AAAAGATTGAAGGGCTTTTCACGCTTTTAATATCG-TTTTTCATA-TTTTTTCTGAATTAATTTC
* * ** *
23608 TAATTAAAACGAAACATGATTCAGATATTTGT---AA-AAA--C---AA--C-----GGCT--GA
127 TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGA
* * * * *
23655 TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGTGCCAAAAATCATTCAAAATTGAACC-
192 TTTGATTAGATGAATATAGATATTTCAAGGAGTTTCGGCGCCAAAAATCATGCAAAACTGAACCG
* * * * * *
23719 AGACCCCGGAACGCGTTTTTAGCC-AAAACCCTAATGATATTATTACACGATTTCGGCTAAAATT
257 GGGCCCAGGAACGCGTTTTTAGCCAAAAACCGTGATG--ATTAGTACACGATTTCGGCTAAAATT
*
23783 TTGTAAAAATTG
320 TTGCAAAAATTG
* * * * * * * * *
23795 ACCCGAAAAATATATCCTCAATTTTTATCCATAATACTTATAAAAACTATATAATTCAATGCCAA
1 ACCCG-AAAGTTTTTCCTCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAACGCCAA
* * * *
23860 AAATATTGAAGGGATTTTCATGCTTTTAATATCGTTTTTCATATGTTTTTCTAAATTAATTTCTA
65 AAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATAT-TTTTTCTGAATTAATTTCTA
* * * *
23925 ATTAAATCGAAACAAGATTTAGATGCTCGTAAAAA-AAATACTTAAATGCAATGTGGCTAAGATT
129 ATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATT
* * * * * *
23989 TTATCAGATGAATATAGATATTTCAAGGAGTGTCGGTGCCAAAAACCATGCAAAACTGAGCCGGG
194 TGATTAGATGAATATAGATATTTCAAGGAGTTTCGGCGCCAAAAATCATGCAAAACTGAACCGGG
* * * * *
24054 GCCCCGAAACACGTTTTTAGCCAAAAAAACGTGATGGATTAGTACACGATTTTGGCTAAAATTTT
259 GCCCAGGAACGCGTTTTTAGCC-AAAAACCGTGAT-GATTAGTACACGATTTCGGCTAAAATTTT
***
24119 GCACACAAAAAAAA
322 G----CAAAAATTG
* * * * **
24133 ACCCGAAAAATTTTTCC-CGAATTTTTGGATAAAATACTCATAAAATATATATAATTTGACGCCA
1 ACCCG-AAAGTTTTTCCTC-AATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAACGCCA
* * *
24197 AGAAGATTGGAGGGCTTTTCACGGTTTTAATATCGTTTTTCATA-TTTTTCTGAATTAATTTCTA
64 AAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTA
* * *
24261 ATTAAATCGAAACAAGATTCAAATGCTTGTAAAAACAAAT-CTTAAATCCAATGTGGCTAAGATT
129 ATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATT
* *** *
24325 TGATTAGATGAATAT-GCATATCTCAAGGAGTCTT-GGCATAAAAAATCATGCAAAACTGAGCCG
194 TGATTAGATGAATATAG-ATATTTCAAGGAGT-TTCGGCGCCAAAAATCATGCAAAACTGAACCG
** * * * * * *
24388 AGACCCCA--AACGCTTTTTTAGCCAGAAACTGTGATAATTATTACACGATTTCAGCTAAAATTT
257 -GGGCCCAGGAACGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTT
* *
24451 TGTAAAAATTA
321 TGCAAAAATTG
* * *
24462 ACCCGAAAGATATTTT-CTCAATTTTTGGCTAAAATACTCATAAAAACATATATAGTTCAACACC
1 ACCCGAAAG-T-TTTTCCTCAATTTTTAGCTAAAATACTCATAAAAA-ATATATAATTCAACGCC
* ** * ** *
24526 AAAAAGATTGAAGGGCTTTTGACG-TTTCTAATATAATTTTTCCTATTTTTTTCCAAATTAGTTT
63 AAAAAGATTGAAGGGCTTTTCACGCTTT-TAATATCGTTTTTCATA-TTTTTTCTGAATTAATTT
* * * *
24590 CTAATTAAATCGAAACAAAATTCAGATGCCCGTAAAAACATATCTTTAAATCCAATGTGGCTGAG
126 CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG
* * * * * *
24655 ATTTGATTAGATAAATATAGATATTTCAAGTAGTATCGGAGCCAAAAATCATGCAAAA-TTAAGT
191 ATTTGATTAGATGAATATAGATATTTCAAGGAGTTTCGGCGCCAAAAATCATGCAAAACTGAA-C
* * * *
24719 CGGGTCCTCA-GAACGCTTTTTTAGCCAAAAACTGATGATGGTTTGTTAGTACACGATTTCGGCT
255 CGGGGCC-CAGGAACGCGTTTTTAGCCAAAAACCG-TGAT-G---ATTAGTACACGATTTCGGCT
*
24783 AAAATTTTACAAAAATTG
314 AAAATTTTGCAAAAATTG
* * * * * *
24801 ACACAAAAGATTTCTCCTCAATTTTTGGTTAAAATATTCAT-AAAAATATATAATTCAACGCCAA
1 ACCCGAAAG-TTTTTCCTCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAACGCCAA
* * * * * *
24865 AAAGATTGGAGGGCTTTTTACTCTTTTAATATCGTATTTCTTATTTTTTCTAAATTAATTTCTAA
65 AAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAA
* *
24930 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTTGCTGAGATTT
130 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
*
24995 GGTTAGATGA
195 GATTAGATGA
25005 TGTAAAGTAT
Statistics
Matches: 2614, Mismatches: 460, Indels: 237
0.79 0.14 0.07
Matches are distributed among these distances:
314 1 0.00
315 66 0.03
316 78 0.03
317 31 0.01
318 21 0.01
319 58 0.02
320 1 0.00
321 3 0.00
323 2 0.00
325 57 0.02
326 1 0.00
327 36 0.01
328 14 0.01
329 204 0.08
330 103 0.04
331 69 0.03
332 315 0.12
333 148 0.06
334 225 0.09
335 222 0.08
336 474 0.18
337 244 0.09
338 156 0.06
339 79 0.03
340 6 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (331 bp):
ACCCGAAAGTTTTTCCTCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAA
AAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAAT
TAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTG
ATTAGATGAATATAGATATTTCAAGGAGTTTCGGCGCCAAAAATCATGCAAAACTGAACCGGGGC
CCAGGAACGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAA
AAATTG
Found at i:28996 original size:20 final size:20
Alignment explanation
Indices: 28971--29013 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
28961 CCCAAATTAC
*
28971 TATGTAATATATATATATAT
1 TATGTAATACATATATATAT
*
28991 TATGTAATACATATCTATAT
1 TATGTAATACATATATATAT
29011 TAT
1 TAT
29014 TTCTAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.49
Consensus pattern (20 bp):
TATGTAATACATATATATAT
Found at i:30019 original size:19 final size:18
Alignment explanation
Indices: 29944--30030 Score: 61
Period size: 17 Copynumber: 4.7 Consensus size: 18
29934 CCGACCGACT
*
29944 AAATATATAATATAATTTTAA
1 AAATAT-TAATAT-A-TTTAG
* *
29965 AAATATT-ATATATATAT
1 AAATATTAATATATTTAG
* *
29982 ATATATTAATA-ATTCAG
1 AAATATTAATATATTTAG
29999 AAATATTAATATTATTTAG
1 AAATATTAATA-TATTTAG
* *
30018 AAAAATAAATATA
1 AAATATTAATATA
30031 GCCTACAATA
Statistics
Matches: 53, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
17 22 0.42
18 6 0.11
19 18 0.34
20 1 0.02
21 6 0.11
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.41
Consensus pattern (18 bp):
AAATATTAATATATTTAG
Found at i:32813 original size:19 final size:19
Alignment explanation
Indices: 32789--32828 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
32779 TAGGAAAATC
32789 TTGACTTTGAGACACGCTT
1 TTGACTTTGAGACACGCTT
32808 TTGACTTTGAGACACGCTT
1 TTGACTTTGAGACACGCTT
32827 TT
1 TT
32829 CTTACCTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (19 bp):
TTGACTTTGAGACACGCTT
Found at i:33138 original size:20 final size:20
Alignment explanation
Indices: 33113--33150 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
33103 TACTCACATC
33113 AAGTTGGTGACGATTCAAAA
1 AAGTTGGTGACGATTCAAAA
*
33133 AAGTTGGTGATGATTCAA
1 AAGTTGGTGACGATTCAA
33151 CTTATGACAT
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:0.37, C:0.08, G:0.26, T:0.29
Consensus pattern (20 bp):
AAGTTGGTGACGATTCAAAA
Found at i:35610 original size:60 final size:60
Alignment explanation
Indices: 35525--35664 Score: 158
Period size: 63 Copynumber: 2.3 Consensus size: 60
35515 ATCGTTTGCA
* * * *
35525 AAAATGCTTAAATAAGTGCTCAAAG-AAAAAAAATGCTTAAATCAGGGCCCAACGTTTACG
1 AAAATGCTCAAATAAGTGCTCAAAGAAAAAAAAATGCTCAAATAAGGGCCAAACGTTTA-G
* * *
35585 AAAATGCTCAAATAAGT-ATCCAAAGAAAAAAAAAAATGCTCAAATAAGGGTCAAACTTTTAG
1 AAAATGCTCAAATAAGTGCT-CAAAG--AAAAAAAAATGCTCAAATAAGGGCCAAACGTTTAG
35647 AAAATTGCTCAAATAAGT
1 AAAA-TGCTCAAATAAGT
35665 CTATGCCATC
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
59 1 0.01
60 21 0.31
62 5 0.07
63 41 0.60
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.22
Consensus pattern (60 bp):
AAAATGCTCAAATAAGTGCTCAAAGAAAAAAAAATGCTCAAATAAGGGCCAAACGTTTAG
Found at i:35709 original size:22 final size:22
Alignment explanation
Indices: 35684--35735 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
35674 CACTGTGTGG
35684 TTATCAAAATTCCATAAT-AAGA
1 TTATCAAAATTCCAT-ATGAAGA
* *
35706 TTATCAAAATTTCATATGGAGA
1 TTATCAAAATTCCATATGAAGA
35728 TTATCAAA
1 TTATCAAA
35736 TTTTCATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 2 0.07
22 25 0.93
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTCCATATGAAGA
Done.