Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011998.1 Corchorus capsularis cultivar CVL-1 contig12019, 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: 52379
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:2609 original size:14 final size:15
Alignment explanation
Indices: 2592--2625 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
2582 TTTCTTCTTC
2592 TTTTTTTTCC-CCCA
1 TTTTTTTTCCTCCCA
*
2606 TTTTTTTTCCTTCCA
1 TTTTTTTTCCTCCCA
2621 TTTTT
1 TTTTT
2626 GAAATTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.06, C:0.26, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTTTTTTCCTCCCA
Found at i:6762 original size:25 final size:24
Alignment explanation
Indices: 6728--6786 Score: 84
Period size: 25 Copynumber: 2.5 Consensus size: 24
6718 TTCAAGCCCT
*
6728 AAACTTCATTTCTAACAATTTCTTC
1 AAACTTCATTTCTAACAA-ATCTTC
*
6753 AAACTTCATTTTTAACAAATCTTC
1 AAACTTCATTTCTAACAAATCTTC
6777 AAA-TTCATTT
1 AAACTTCATTT
6787 TCCTTCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 7 0.22
24 8 0.25
25 17 0.53
ACGTcount: A:0.36, C:0.20, G:0.00, T:0.44
Consensus pattern (24 bp):
AAACTTCATTTCTAACAAATCTTC
Found at i:6825 original size:26 final size:26
Alignment explanation
Indices: 6796--6862 Score: 98
Period size: 26 Copynumber: 2.6 Consensus size: 26
6786 TTCCTTCATT
6796 TTAATCATAAACTAATTAAATAATAA
1 TTAATCATAAACTAATTAAATAATAA
* * *
6822 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATAATAA
*
6848 TTAAACATAAACTAA
1 TTAATCATAAACTAA
6863 GTAATTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.57, C:0.09, G:0.01, T:0.33
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATAATAA
Found at i:6837 original size:15 final size:15
Alignment explanation
Indices: 6796--6839 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
6786 TTCCTTCATT
*
6796 TTAATCATAAACTAA
1 TTAATAATAAACTAA
6811 TT-A-AAT-AA-TAA
1 TTAATAATAAACTAA
6822 TTAATAATAAACTAA
1 TTAATAATAAACTAA
6837 TTA
1 TTA
6840 GATACTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 8
0.73 0.03 0.24
Matches are distributed among these distances:
11 5 0.21
12 3 0.12
13 5 0.21
14 3 0.12
15 8 0.33
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAATAATAAACTAA
Found at i:6906 original size:33 final size:32
Alignment explanation
Indices: 6828--6906 Score: 76
Period size: 33 Copynumber: 2.4 Consensus size: 32
6818 ATAATTAATA
6828 ATAAACTAATTAGA-TACTAATTAAACATAAAC
1 ATAAACTAATTA-ATTACTAATTAAACATAAAC
*
6860 -T-AAGTAATTTTAATTAACTAATTAAA-ACTAAAC
1 ATAAACTAA--TTAATT-ACTAATTAAACA-TAAAC
6893 ATAAACTAATTAAT
1 ATAAACTAATTAAT
6907 ATTTTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
30 5 0.13
31 2 0.05
32 5 0.13
33 20 0.53
34 1 0.03
35 5 0.13
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (32 bp):
ATAAACTAATTAATTACTAATTAAACATAAAC
Found at i:6976 original size:32 final size:33
Alignment explanation
Indices: 6934--7039 Score: 126
Period size: 33 Copynumber: 3.2 Consensus size: 33
6924 AAAAAAAGGC
* ** *
6934 CGAGCAGCCCAGCTTGGGC-AACTTGTCCATGG
1 CGAGCCGCCCAGCTTGGGCGGCCTTGCCCATGG
6966 CGAGCCGCCCAAGC-TGGGCGGCCTTGCCCATGG
1 CGAGCCGCCC-AGCTTGGGCGGCCTTGCCCATGG
* * *
6999 GGAGCTGCCCAGTTTGGGCGGCCTTGCCCATGG
1 CGAGCCGCCCAGCTTGGGCGGCCTTGCCCATGG
7032 CGAGCCGC
1 CGAGCCGC
7040 TCAGTTGCCA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
32 16 0.26
33 46 0.74
ACGTcount: A:0.13, C:0.35, G:0.36, T:0.16
Consensus pattern (33 bp):
CGAGCCGCCCAGCTTGGGCGGCCTTGCCCATGG
Found at i:13947 original size:16 final size:16
Alignment explanation
Indices: 13926--13960 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
13916 CTCTGTCCCA
13926 TAATATAAGTCCATTT
1 TAATATAAGTCCATTT
13942 TAATATAAGTCCATTT
1 TAATATAAGTCCATTT
13958 TAA
1 TAA
13961 CCGTATCACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (16 bp):
TAATATAAGTCCATTT
Found at i:26275 original size:27 final size:27
Alignment explanation
Indices: 26245--26299 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
26235 TGCTTGAAAA
26245 TCCGAGTATTCCTTTCAATCTAGATAG
1 TCCGAGTATTCCTTTCAATCTAGATAG
26272 TCCGAGTATTCCTTTCAATCTAGATAG
1 TCCGAGTATTCCTTTCAATCTAGATAG
26299 T
1 T
26300 GTGGCAGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (27 bp):
TCCGAGTATTCCTTTCAATCTAGATAG
Found at i:26595 original size:5 final size:5
Alignment explanation
Indices: 26573--26611 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
26563 TTACTAGTAC
* *
26573 TATTA TTTTA TGTATA TATTA TATTA TATTA TATTA TAT
1 TATTA TATTA TAT-TA TATTA TATTA TATTA TATTA TAT
26612 ATTATTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
5 26 0.87
6 4 0.13
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (5 bp):
TATTA
Found at i:26619 original size:15 final size:15
Alignment explanation
Indices: 26573--26611 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
26563 TTACTAGTAC
* *
26573 TATTATTTTATGTATA
1 TATTATATTATAT-TA
26589 TATTATATTATATTA
1 TATTATATTATATTA
26604 TATTATAT
1 TATTATAT
26612 ATTATTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
TATTATATTATATTA
Found at i:37394 original size:2 final size:2
Alignment explanation
Indices: 37389--37415 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
37379 TATATATATA
37389 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
37416 ATACACATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:52147 original size:973 final size:954
Alignment explanation
Indices: 50126--52374 Score: 2732
Period size: 973 Copynumber: 2.3 Consensus size: 954
50116 TTTTTTTTCA
* * ** *
50126 AATTTTTTTTCATAATACTT-AGAAAAAATATATAATTAAAAGTCAAAAAAATCGAAGAGTTTTC
1 AATTTTTTTGCAAAATA-TTCAGAAAAAATATATAATTAAAACCCAAAAAAATTGAAGAGTTTTC
** * * *
50190 AAAGCATCAAATAT--TTTTTT-A--TTTTTTCCAATTTATTTCTAATTAAATCGAAATAAGATT
65 -TCGCTTCTAATATCGTTTTTTCATTTTTTTTCGAATTTATTTCTAATTAAATCGAAATAAGATT
** * * *
50250 CAGTTGCTTGTAAAA-AAATATCCTTAAATCC-TTTTCAACTGAGATTTGGTTAAATGAATATTG
129 CACATGCTCGTAAAAGAAA-ATCCTTAAATCCATTTT-AACTAAGATTTGGTTAAATGAATATAG
* ** * * * *
50313 ATATTTCAAGGAGTTTTTCT-GCAAAAAATCATGCAAAACTGAGTGGGTGTCCCGTAACATGTTT
192 ATATTTCAATGAGTTTTTCTGGC-AAAAATCATGCAAAACTGAGCCGGAG-CCC-CAAAACGTTT
* * * * * *
50377 TTAGCAAAAAAAACCATGATGGTTAGTATACGATTTCGGCTAAAAACTAAACCGAAATGTTTTTT
254 CTAGCAAAAAAAACCATGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGGAATATTTTTT
* * *
50442 CTCAATTTTCTTGCAAAATATTCAGAAAAAAATATATAATTCAATACCAAAAAGATTGACGGGCT
319 CTCAATTTTCTTGCAAAATATTCAGAAAAAAATATATAAATCAATACCAAAAAAATTGAAGGGCT
* * *
50507 TTTCAGGCTTTTAATATCGTTTTTCATTCTTTTCCGAATTAATTTTTAATTAAATCAAAACAAGA
384 TTTAACGCTTCTAATATCGTTTTTCATTCTTTTCCGAATTAATTTTTAATTAAATCAAAACAAGA
* * * * * *
50572 TTCAGCTCCTCGTAAAAACACATCTTTATATCCAATGTGGCTGAGATTTGGTTATATGAATATAG
449 TTCAGCTCCTCGTAAAAACAAATCCTTAAATCCAATGTGACTAAGATTTGGTTAGATGAATATAG
* * ** * *
50637 ATGTTTCAAGGAGTATTTATACGAAAAATTATGCAAAACTGAGTCGAGGCCCCAGAACGCGTTTT
514 ATATTTCAAGGAGTATTTATACGAAAAATCATGCAAAACTGAACCGAGACCCCAGAACGCATTTT
* * * *
50702 TAGACAAAAACAATGATGGTTAGTACCAGATTTCTGCTAAAAACTGACCCAAAAAGTATTTTCTC
579 TAGAAAAAAACAATGATGGTTAGTAACAGATTTCGGCTAAAAACTGACCCAAAAAGTATTCTCTC
* * *
50767 AATTTTTTGCCACAATACTCAGAAAATATATATAATTCAAAGCCAAAAAAATTGAAGGGTTTTTC
644 AATTTTTTGCCAAAATACTCAGAAAAAATATATAATTCAAACCCAAAAAAATTGAAGGGTTTTTC
* *
50832 ACGCTTCTAATATCATTTTTTTTCGAATTTATTTCTAATTAAATCGAAGCAAGATTCACATGCTC
709 ACGCTTCTAATATCATTTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAAATT-ACA---TC
50897 GTAAAAGGAAATCCTTAATCCATTTTGACTAAGATTTGGTTAGATGAATATAGATATTTCAATAA
770 GTAAAAGGAAATCCTTAATCCATTTTGACTAAGATTTGGTTAGATGAATATAGATATTTCAATAA
* * * *
50962 GTCTTTTTGGCAAAAATTATACAAAACTAAGCCGGAGCCCCAAAACGCGTTTCTTGCCAAAAAAA
835 GTCTTTTAGGCAAAAATCATACAAAACTAAGCCGGAACCCCAAAACGCGTTTCTAGCC-AAAAAA
* *
51027 ATCGTGATGCTTAGTACACGATTTCAGCTAAAAACTGACCCGAAATGCTTTTTCTC
899 ACCGTGATGCTTAGTACACGATTTCAGCTAAAAACTGACCCGAAATGCATTTTCTC
*
51083 AATTTTTTTGCAAAATATTCAGAAAAAATATATAATTTAAACCCAAAAAAATTGAAGAGTTTTTC
1 AATTTTTTTGCAAAATATTCAGAAAAAATATATAATTAAAACCCAAAAAAATTGAAGAG-TTTTC
*
51148 TCGCTTCTAATATCGTCTTTTTTTTTCATTTTTTTTCGAATTTATTTCTTATTAAATCGAAATAA
65 TCGCTTCTAATATCG-----TTTTTTCATTTTTTTTCGAATTTATTTCTAATTAAATCGAAATAA
* * *
51213 TATTCACATGCTCGTAAAAGGAAATCCTTAAATCCATTTTGACTAAGATTTGGTTAAATGAATAT
125 GATTCACATGCTCGTAAAAGAAAATCCTTAAATCCATTTTAACTAAGATTTGGTTAAATGAATAT
* * *
51278 GGATAATTCAATGAGTTTTTCTGGCAAAAATCAAGCAAAACTGAGCCGGAGCCTCCAAAAGCGTT
190 AGATATTTCAATGAGTTTTTCTGGCAAAAATCATGCAAAACTGAGCCGGAGCC-CCAAAA-CGTT
* *
51343 TCTAGCAAAAAAAAAAAACCATAATGGTTAGTACACGATTTCAGCTAAAAACTGACCCGGAATAT
253 TCTAGC----AAAAAAAACCATGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGGAATAT
51408 TTTTTCTCAATTCTT-TTGCAAAATATTCAG-AAAAAATATATAAATCAA-ACCCAAAAAAATTG
314 TTTTTCTCAATT-TTCTTGCAAAATATTCAGAAAAAAATATATAAATCAATA-CCAAAAAAATTG
* * * *
51470 AAGGGTTTTTAACGCTTCTAATATTGTTTTTTTCATTTTTTTTCCGAATTTATTTCTT-ATTAAA
377 AAGGGCTTTTAACGCTTCTAATATCG--TTTTTCA-TTCTTTTCCGAATTAATTT-TTAATTAAA
* * ** * *
51534 TCGAAACAAGATTCA-CATGCTCGTAAAAGGAAATCCTTAAATCCATTTTGACTAAGATTTGGTT
438 TCAAAACAAGATTCAGC-TCCTCGTAAAAACAAATCCTTAAATCCAATGTGACTAAGATTTGGTT
** * * * * *
51598 AGATGAATATAGATATTTCATTGAGTCTTTCTAGGAAAAATCATGCAGAATTGAACCG-GAACCC
502 AGATGAATATAGATATTTCAAGGAGTATTTATACGAAAAATCATGCAAAACTGAACCGAG-ACCC
**
51662 C-GAAACGCATTTTCTAGCAAAAAAACCGTGATGGTTAGTATAC-GATTTCGGCTAAAAACTGAC
566 CAG-AACGCATTTT-TAG-AAAAAAACAATGATGGTTAGTA-ACAGATTTCGGCTAAAAACTGAC
* * ** *
51725 CCGAAATGCT-TTCT-TCAATTTTTTG-CAAAATGTTCAGAAAAAATATATAATTCAAACCCCAA
627 CCAAAAAG-TATTCTCTCAATTTTTTGCCAAAATACTCAGAAAAAATATATAATTCAAACCCAAA
*
51787 AAAATTGAAGGGTTTTTCACGCTTCTAATGTCGTTTTTTTCATTTTTTTTTTCGAATTTATTTCT
691 AAAATTGAAGGGTTTTTCACGCTTCTAA---------TATCA--TTTTTTTTCGAATTTATTTCT
*
51852 TATTAAATCGAAACAAAATT-CA-CGTAAAAGGAAATCCTTAAATCCATTTTGACTAAGATTTGG
745 AATTAAATCGAAACAAAATTACATCGTAAAAGGAAATCCTT-AATCCATTTTGACTAAGATTTGG
* *
51915 TTAGATGAATATAGATATTTCAATGAGTCTTTCTAGG-AAAAATCATGA-AAAATTGAA-CCGGA
809 TTAGATGAATATAGATATTTCAATAAGTCTTT-TAGGCAAAAATCAT-ACAAAACT-AAGCCGGA
* * * *
51977 ACCCCGAAACGCGTTTTCTAGTC-AAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACT
871 ACCCCAAAACGCG-TTTCTAGCCAAAAAAACCGTGATGCTTAGTACACGATTTCAGCTAAAAACT
52041 GACCCGAAATGCATTTTCTC
935 GACCCGAAATGCATTTTCTC
* *
52061 AATTTTTTTTGGAAAATATTCAGAAAAAATATATAATTCAAACCCAAAAAAATTGAAGAGTTTTC
1 AA-TTTTTTTGCAAAATATTCAGAAAAAATATATAATTAAAACCCAAAAAAATTGAAGAGTTTTC
* * *
52126 TCGCTTTTAATATCGTTTTTTCATTTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAGATTA
65 TCGCTTCTAATATCGTTTTTTCATTTTTTTTCGAATTTATTTCTAATTAAATCGAAATAAGATTC
* * *
52191 ACATGCTCGTAAAAGAAAATCCTTAAATCGATTTTCACTAAGATTTGGTTAGATGAATATAGATA
130 ACATGCTCGTAAAAGAAAATCCTTAAATCCATTTTAACTAAGATTTGGTTAAATGAATATAGATA
* * * * *
52256 TTTCAATGAGTCTTTCTGGGAAAAATCATGCAAAATTGAGCCGGAGCCCCGAAACGAATTTCTTG
195 TTTCAATGAGTTTTTCTGGCAAAAATCATGCAAAACTGAGCCGGAGCCCCAAAACG--TTTCTAG
* ** *
52321 CCAAAAAAACTGTGATGGTTAGTACATGATTTCGGCTAAAAACTGACCCGGAAT
258 CAAAAAAAACCATGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGGAAT
52375 GCTTT
Statistics
Matches: 1112, Mismatches: 127, Indels: 94
0.83 0.10 0.07
Matches are distributed among these distances:
956 2 0.00
957 59 0.05
958 5 0.00
964 6 0.01
965 1 0.00
966 5 0.00
967 133 0.12
968 8 0.01
969 48 0.04
970 48 0.04
971 77 0.07
972 17 0.02
973 348 0.31
974 16 0.01
975 47 0.04
976 2 0.00
978 95 0.09
979 138 0.12
980 13 0.01
982 6 0.01
984 38 0.03
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (954 bp):
AATTTTTTTGCAAAATATTCAGAAAAAATATATAATTAAAACCCAAAAAAATTGAAGAGTTTTCT
CGCTTCTAATATCGTTTTTTCATTTTTTTTCGAATTTATTTCTAATTAAATCGAAATAAGATTCA
CATGCTCGTAAAAGAAAATCCTTAAATCCATTTTAACTAAGATTTGGTTAAATGAATATAGATAT
TTCAATGAGTTTTTCTGGCAAAAATCATGCAAAACTGAGCCGGAGCCCCAAAACGTTTCTAGCAA
AAAAAACCATGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGGAATATTTTTTCTCAATT
TTCTTGCAAAATATTCAGAAAAAAATATATAAATCAATACCAAAAAAATTGAAGGGCTTTTAACG
CTTCTAATATCGTTTTTCATTCTTTTCCGAATTAATTTTTAATTAAATCAAAACAAGATTCAGCT
CCTCGTAAAAACAAATCCTTAAATCCAATGTGACTAAGATTTGGTTAGATGAATATAGATATTTC
AAGGAGTATTTATACGAAAAATCATGCAAAACTGAACCGAGACCCCAGAACGCATTTTTAGAAAA
AAACAATGATGGTTAGTAACAGATTTCGGCTAAAAACTGACCCAAAAAGTATTCTCTCAATTTTT
TGCCAAAATACTCAGAAAAAATATATAATTCAAACCCAAAAAAATTGAAGGGTTTTTCACGCTTC
TAATATCATTTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAAATTACATCGTAAAAGGAAA
TCCTTAATCCATTTTGACTAAGATTTGGTTAGATGAATATAGATATTTCAATAAGTCTTTTAGGC
AAAAATCATACAAAACTAAGCCGGAACCCCAAAACGCGTTTCTAGCCAAAAAAACCGTGATGCTT
AGTACACGATTTCAGCTAAAAACTGACCCGAAATGCATTTTCTC
Found at i:52233 original size:643 final size:641
Alignment explanation
Indices: 50126--52379 Score: 2579
Period size: 643 Copynumber: 3.5 Consensus size: 641
50116 TTTTTTTTCA
* * * ** *
50126 AATTTTTTTTCATAATACTT-AGAAAAAATATATAATTAAAAGTCAAAAAAATCGAAGAGTTTTC
1 AATTTTTTTGCAAAATA-TTCAGAAAAAATATATAATTCAAACCCAAAAAAATTGAAGAGTTTTC
* * * * *
50190 AAAGCATCAAATATTTTTTT-A--TTTTTTCCAATTTATTTCTAATTAAATCGAAATAAGATTCA
65 -ACGCTTCTAATATTTTTTTCATTTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAGATTCA
** * * * *
50252 GTTGCTTGTAAAA-AAATATCCTTAAATCC-TTTTCAACTGAGATTTGGTTAAATGAATATTGAT
129 CATGCTCGTAAAAGAAA-ATCCTTAAATCCATTTTC-ACTAAGATTTGGTTAGATGAATATAGAT
* * * *** * * * *
50315 ATTTCAAGGAGTTTTTCTGCAAAAAATCATGCAAAACTGAGTGGGTGTCCCGTAA--CATGTTTT
192 ATTTCAATGAGTCTTTCTG-GAAAAATCATGCAAAACTGAACCGGAGCCCCGAAACGCAT-TTTC
* * * * *
50378 TAG-CAAAAAAAACCATGATGGTTAGTATACGATTTCGGCTAAAAACTAAACCGAAATGTTTTTT
255 TAGCCAAAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAATGCTTTTT
*
50442 CTCAATTTTCTTGCAAAATATTCAGAAAAAAATATATAATTCAATA--CCAAAAAGATTGACGGG
320 CTCAATTTT-TTGCAAAATATTCAG-AAAAAATATATAATTCAA-ACCCCAAAAA-ATTGAAGGG
* * * * * * *
50505 CTTTTCAGGCTTTTAATATCG--TTTTTCA--TTCTTTTCCGAATTAATTT-TTAATTAAATCAA
381 TTTTTCACGCTTCTAATATCGTTTTTTTCATTTTTTTTTTCGAATTTATTTCTT-ATTAAATCGA
* ** * * * * * * * *
50565 AACAAGATTCAGCTCCTCGTAAAAACACATCTTTATATCCAATGTGGCTGAGATTTGGTTATATG
445 AACAAAATTCA----C-CGTAAAAGGAAATCCTTAAATCCATTTTGACTAAGATTTGGTTAAATG
* * * * * *
50630 AATATAGATGTTTCAAGGAGTATTTATACGAAAAATTATGCAAAACTGAGTC-GAGGCCCCAGAA
505 AATATAGATATTTCAATGAGTATTTCTAGGAAAAATCATGCAAAACTGAGCCGGA-GCCCCA-AA
* * *
50694 CGCGTTTT-TAG-ACAAAAACAATGATGGTTAGTAC-CAGATTTCTGCTAAAAACTGACCCAAAA
568 CGCGTTTTCTAGCA-AAAAACCATGATGGTTAGTACAC-GATTTCAGCTAAAAACTGACCCGAAA
*
50756 AGTATTTTCTC
631 TGTATTTTCTC
* * * * *
50767 AA-TTTTTTGCCACAATACTCAGAAAATATATATAATTCAAAGCCAAAAAAATTGAAGGGTTTTT
1 AATTTTTTTG-CAAAATATTCAGAAAAAATATATAATTCAAACCCAAAAAAATTGAAGAG-TTTT
*
50831 CACGCTTCTAATA------TCATTTTTTTTCGAATTTATTTCTAATTAAATCGAAGCAAGATTCA
64 CACGCTTCTAATATTTTTTTCATTTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAGATTCA
* *
50890 CATGCTCGTAAAAGGAAATCCTT-AATCCATTTTGACTAAGATTTGGTTAGATGAATATAGATAT
129 CATGCTCGTAAAAGAAAATCCTTAAATCCATTTTCACTAAGATTTGGTTAGATGAATATAGATAT
* * * * * * *
50954 TTCAATAAGTCTTTTTGGCAAAAATTATACAAAACT-AAGCCGGAGCCCCAAAACGC-GTTTCTT
194 TTCAATGAGTCTTTCTGG-AAAAATCATGCAAAACTGAA-CCGGAGCCCCGAAACGCATTTTCTA
* * *
51017 GCCAAAAAAAATCGTGATGCTTAGTACACGATTTCAGCTAAAAACTGACCCGAAATGCTTTTTCT
257 GCCAAAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAATGCTTTTTCT
* * *
51082 CAATTTTTTTGCAAAATATTCAGAAAAAATATATAATTTAAACCCAAAAAAATTGAAGAGTTTTT
322 CAA-TTTTTTGCAAAATATTCAGAAAAAATATATAATTCAAACCCCAAAAAATTGAAGGGTTTTT
* * *
51147 CTCGCTTCTAATATCGTCTTTTTT-TTTCATTTTTTTTCGAATTTATTTCTTATTAAATCGAAAT
386 CACGCTTCTAATATCGT-TTTTTTCATT--TTTTTTTTCGAATTTATTTCTTATTAAATCGAAAC
*
51211 AATATTCACATGCTCGTAAAAGGAAATCCTTAAATCCATTTTGACTAAGATTTGGTTAAATGAAT
448 AAAATT--CA--C-CGTAAAAGGAAATCCTTAAATCCATTTTGACTAAGATTTGGTTAAATGAAT
* * * * *
51276 ATGGATAATTCAATGAGTTTTTCT-GGCAAAAATCAAGCAAAACTGAGCCGGAGCCTCCAAAAGC
508 ATAGATATTTCAATGAGTATTTCTAGG-AAAAATCATGCAAAACTGAGCCGGAGCC-CCAAACGC
* *
51340 G-TTTCTAGCAAAAAAAAAAAACCATAATGGTTAGTACACGATTTCAGCTAAAAACTGACCCGGA
571 GTTTTCTAGC------AAAAAACCATGATGGTTAGTACACGATTTCAGCTAAAAACTGACCCGAA
* *
51404 ATATTTTTTCTC
630 ATGTATTTTCTC
* * * *
51416 AATTCTTTTGCAAAATATTCAGAAAAAATATATAAATCAAACCCAAAAAAATTGAAGGGTTTTTA
1 AATTTTTTTGCAAAATATTCAGAAAAAATATATAATTCAAACCCAAAAAAATTGAAGAG-TTTTC
*
51481 ACGCTTCTAATATTGTTTTTTTCATTTTTTTTCCGAATTTATTTCTTATTAAATCGAAACAAGAT
65 ACGCTTCTAATA---TTTTTTTCATTTTTTTT-CGAATTTATTTCTAATTAAATCGAAACAAGAT
* *
51546 TCACATGCTCGTAAAAGGAAATCCTTAAATCCATTTTGACTAAGATTTGGTTAGATGAATATAGA
126 TCACATGCTCGTAAAAGAAAATCCTTAAATCCATTTTCACTAAGATTTGGTTAGATGAATATAGA
* * * *
51611 TATTTCATTGAGTCTTTCTAGGAAAAATCATGCAGAATTGAACCGGAACCCCGAAACGCATTTTC
191 TATTTCAATGAGTCTTTCT-GGAAAAATCATGCAAAACTGAACCGGAGCCCCGAAACGCATTTTC
* *
51676 TAG-C-AAAAAAACCGTGATGGTTAGTATACGATTTCGGCTAAAAACTGACCCGAAATGCTTTCT
255 TAGCCAAAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAATGCTTTTT
*
51739 -TCAATTTTTTGCAAAATGTTCAGAAAAAATATATAATTCAAACCCCAAAAAATTGAAGGGTTTT
320 CTCAATTTTTTGCAAAATATTCAGAAAAAATATATAATTCAAACCCCAAAAAATTGAAGGGTTTT
*
51803 TCACGCTTCTAATGTCGTTTTTTTCATTTTTTTTTTCGAATTTATTTCTTATTAAATCGAAACAA
385 TCACGCTTCTAATATCGTTTTTTTCATTTTTTTTTTCGAATTTATTTCTTATTAAATCGAAACAA
*
51868 AATTCA-CGTAAAAGGAAATCCTTAAATCCATTTTGACTAAGATTTGGTTAGATGAATATAGATA
450 AATTCACCGTAAAAGGAAATCCTTAAATCCATTTTGACTAAGATTTGGTTAAATGAATATAGATA
* * * * *
51932 TTTCAATGAGTCTTTCTAGGAAAAATCATGAAAAATTGAACCGGAACCCCGAAACGCGTTTTCTA
515 TTTCAATGAGTATTTCTAGGAAAAATCATGCAAAACTGAGCCGGAGCCCC-AAACGCGTTTTCTA
* * *
51997 GTCAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAATGCATTTTCTC
579 G-CAAAAAACCATGATGGTTAGTACACGATTTCAGCTAAAAACTGACCCGAAATGTATTTTCTC
*
52061 AATTTTTTTTGGAAAATATTCAGAAAAAATATATAATTCAAACCCAAAAAAATTGAAGAGTTTTC
1 AA-TTTTTTTGCAAAATATTCAGAAAAAATATATAATTCAAACCCAAAAAAATTGAAGAGTTTTC
* * *
52126 TCGCTTTTAATATCGTTTTTTCATTTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAGATTA
65 ACGCTTCTAATAT--TTTTTTCATTTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAGATTC
*
52191 ACATGCTCGTAAAAGAAAATCCTTAAATCGATTTTCACTAAGATTTGGTTAGATGAATATAGATA
128 ACATGCTCGTAAAAGAAAATCCTTAAATCCATTTTCACTAAGATTTGGTTAGATGAATATAGATA
* * * *
52256 TTTCAATGAGTCTTTCTGGGAAAAATCATGCAAAATTGAGCCGGAGCCCCGAAACG-AATTTCTT
193 TTTCAATGAGTCTTTCT-GGAAAAATCATGCAAAACTGAACCGGAGCCCCGAAACGCATTTTCTA
* * *
52320 GCC-AAAAAAACTGTGATGGTTAGTACATGATTTCGGCTAAAAACTGACCCGGAATGCTTT
257 GCCAAAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAATGCTTT
Statistics
Matches: 1385, Mismatches: 166, Indels: 122
0.83 0.10 0.07
Matches are distributed among these distances:
635 1 0.00
636 3 0.00
637 114 0.08
638 137 0.10
639 7 0.01
640 12 0.01
641 51 0.04
642 17 0.01
643 323 0.23
644 23 0.02
645 72 0.05
646 53 0.04
648 2 0.00
649 213 0.15
650 17 0.01
651 1 0.00
653 2 0.00
655 39 0.03
656 6 0.00
657 74 0.05
658 15 0.01
659 110 0.08
660 83 0.06
661 10 0.01
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (641 bp):
AATTTTTTTGCAAAATATTCAGAAAAAATATATAATTCAAACCCAAAAAAATTGAAGAGTTTTCA
CGCTTCTAATATTTTTTTCATTTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAGATTCACA
TGCTCGTAAAAGAAAATCCTTAAATCCATTTTCACTAAGATTTGGTTAGATGAATATAGATATTT
CAATGAGTCTTTCTGGAAAAATCATGCAAAACTGAACCGGAGCCCCGAAACGCATTTTCTAGCCA
AAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAATGCTTTTTCTCAAT
TTTTTGCAAAATATTCAGAAAAAATATATAATTCAAACCCCAAAAAATTGAAGGGTTTTTCACGC
TTCTAATATCGTTTTTTTCATTTTTTTTTTCGAATTTATTTCTTATTAAATCGAAACAAAATTCA
CCGTAAAAGGAAATCCTTAAATCCATTTTGACTAAGATTTGGTTAAATGAATATAGATATTTCAA
TGAGTATTTCTAGGAAAAATCATGCAAAACTGAGCCGGAGCCCCAAACGCGTTTTCTAGCAAAAA
ACCATGATGGTTAGTACACGATTTCAGCTAAAAACTGACCCGAAATGTATTTTCTC
Found at i:52308 original size:324 final size:324
Alignment explanation
Indices: 50117--52379 Score: 2578
Period size: 324 Copynumber: 7.0 Consensus size: 324
50107 TGAAAGGTTT
* * * * ** *
50117 TTTTTTTCAAATTTTTTTTCATAATACTT-AGAAAAAATATATAATTAAAAGTCAAAAAAATCGA
1 TTTTTCTC-AATTTTTTTGCAAAATA-TTCAGAAAAAATATATAATTCAAACCCAAAAAAATTGA
* * * * *
50181 AGAG-TTTTCAAAGCATCAAATAT--TTTTTT-A--TTTTTTCCAATTTATTTCTAATTAAATCG
64 AGGGTTTTTC-ACGCTTCTAATATCGTTTTTTCATTTTTTTTCGAATTTATTTCTAATTAAATCG
* ** * * * * *
50240 AAATAAGATTCAGTTGCTTGTAAAA-AAATATCCTTAAATCC-TTTTCAACTGAGATTTGGTTAA
128 AAACAAGATTCACATGCTCGTAAAAGGAA-ATCCTTAAATCCATTTT-GACTAAGATTTGGTTAG
* * * ** ** * * *
50303 ATGAATATTGATATTTCAAGGAGTTTTTCTGCAAAAAATCATGCAAAACTGAGTGGGTGTCCCGT
191 ATGAATATAGATATTTCAATGAGTCTTTCTGGGAAAAATCATGCAAAACTGAGCCGGAGCCCCGA
** * * * *
50368 AACATGTTTT-TAGCAAAAAAAACCATGATGGTTAGTATACGATTTCGGCTAAAAACTAAACCGA
256 AACGCGTTTTCTAGC-AAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGA
*
50432 AATGT
320 AATGC
* *
50437 TTTTTCTCAATTTTCTTGCAAAATATTCAGAAAAAAATATATAATTCAATA-CCAAAAAGATTGA
1 TTTTTCTCAATTTTTTTGCAAAATATTCAG-AAAAAATATATAATTCAA-ACCCAAAAAAATTGA
* * * * * * * * *
50501 CGGGCTTTTCAGGCTTTTAATATCG-TTTTTCATTCTTTTCCGAATTAATTTTTAATTAAATCAA
64 AGGGTTTTTCACGCTTCTAATATCGTTTTTTCATTTTTTTTCGAATTTATTTCTAATTAAATCGA
* ** * * * * * * * *
50565 AACAAGATTCAGC-TCCTCGTAAAAACACATCTTTATATCCAATGTGGCTGAGATTTGGTTATAT
129 AACAAGATTCA-CATGCTCGTAAAAGGAAATCCTTAAATCCATTTTGACTAAGATTTGGTTAGAT
* * * * ** * *
50629 GAATATAGATGTTTCAAGGAGTATTTATACGAAAAATTATGCAAAACTGAGTC-GAGGCCCC-AG
193 GAATATAGATATTTCAATGAGTCTTTCTGGGAAAAATCATGCAAAACTGAGCCGGA-GCCCCGA-
* ** * *
50692 AACGCGTTTT-TAG-ACAAAAACAATGATGGTTAGTAC-CAGATTTCTGCTAAAAACTGACCCAA
256 AACGCGTTTTCTAGCAAAAAAACCGTGATGGTTAGTACAC-GATTTCGGCTAAAAACTGACCCGA
*
50754 AAAG-
320 AATGC
* * * *
50758 TATTTTCTCAA-TTTTTTGCCACAATACTCAGAAAATATATATAATTCAAAGCCAAAAAAATTGA
1 T-TTTTCTCAATTTTTTTG-CAAAATATTCAGAAAAAATATATAATTCAAACCCAAAAAAATTGA
50822 AGGGTTTTTCACGCTTCTAATA--------TCATTTTTTTTCGAATTTATTTCTAATTAAATCGA
64 AGGGTTTTTCACGCTTCTAATATCGTTTTTTCATTTTTTTTCGAATTTATTTCTAATTAAATCGA
*
50879 AGCAAGATTCACATGCTCGTAAAAGGAAATCCTT-AATCCATTTTGACTAAGATTTGGTTAGATG
129 AACAAGATTCACATGCTCGTAAAAGGAAATCCTTAAATCCATTTTGACTAAGATTTGGTTAGATG
* * * * * * *
50943 AATATAGATATTTCAATAAGTCTTTTTGGCAAAAATTATACAAAACTAAGCCGGAGCCCCAAAAC
194 AATATAGATATTTCAATGAGTCTTTCTGGGAAAAATCATGCAAAACTGAGCCGGAGCCCCGAAAC
* * * *
51008 GCG-TTTCTTGCCAAAAAAAATCGTGATGCTTAGTACACGATTTCAGCTAAAAACTGACCCGAAA
259 GCGTTTTCTAG-C-AAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAA
51072 TGC
322 TGC
*
51075 TTTTTCTCAATTTTTTTGCAAAATATTCAGAAAAAATATATAATTTAAACCCAAAAAAATTGAAG
1 TTTTTCTCAATTTTTTTGCAAAATATTCAGAAAAAATATATAATTCAAACCCAAAAAAATTGAAG
* * *
51140 AGTTTTTCTCGCTTCTAATATCGTCTTTTTTTTTCATTTTTTTTCGAATTTATTTCTTATTAAAT
66 GGTTTTTCACGCTTCTAATATCG-----TTTTTTCATTTTTTTTCGAATTTATTTCTAATTAAAT
* * *
51205 CGAAATAATATTCACATGCTCGTAAAAGGAAATCCTTAAATCCATTTTGACTAAGATTTGGTTAA
126 CGAAACAAGATTCACATGCTCGTAAAAGGAAATCCTTAAATCCATTTTGACTAAGATTTGGTTAG
* * * * *
51270 ATGAATATGGATAATTCAATGAGTTTTTCTGGCAAAAATCAAGCAAAACTGAGCCGGAGCCTCC-
191 ATGAATATAGATATTTCAATGAGTCTTTCTGGGAAAAATCATGCAAAACTGAGCCGGAGCC-CCG
* * * *
51334 AAAAGCG-TTTCTAGCAAAAAAAAAAAACCATAATGGTTAGTACACGATTTCAGCTAAAAACTGA
255 AAACGCGTTTTCTAGC-----AAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGA
* **
51398 CCCGGAATAT
315 CCCGAAATGC
* *
51408 TTTTTCTCAATTCTTTTGCAAAATATTCAGAAAAAATATATAAATCAAACCCAAAAAAATTGAAG
1 TTTTTCTCAATTTTTTTGCAAAATATTCAGAAAAAATATATAATTCAAACCCAAAAAAATTGAAG
* * *
51473 GGTTTTTAACGCTTCTAATATTGTTTTTTTCATTTTTTTTCCGAATTTATTTCTTATTAAATCGA
66 GGTTTTTCACGCTTCTAATATCG-TTTTTTCATTTTTTTT-CGAATTTATTTCTAATTAAATCGA
51538 AACAAGATTCACATGCTCGTAAAAGGAAATCCTTAAATCCATTTTGACTAAGATTTGGTTAGATG
129 AACAAGATTCACATGCTCGTAAAAGGAAATCCTTAAATCCATTTTGACTAAGATTTGGTTAGATG
* * * * * *
51603 AATATAGATATTTCATTGAGTCTTTCTAGGAAAAATCATGCAGAATTGAACCGGAACCCCGAAAC
194 AATATAGATATTTCAATGAGTCTTTCTGGGAAAAATCATGCAAAACTGAGCCGGAGCCCCGAAAC
* *
51668 GCATTTTCTAGCAAAAAAACCGTGATGGTTAGTATACGATTTCGGCTAAAAACTGACCCGAAATG
259 GCGTTTTCTAGCAAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAATG
51733 C
324 C
* * *
51734 TTTCT-TCAA-TTTTTTGCAAAATGTTCAGAAAAAATATATAATTCAAACCCCAAAAAATTGAAG
1 TTTTTCTCAATTTTTTTGCAAAATATTCAGAAAAAATATATAATTCAAACCCAAAAAAATTGAAG
* *
51797 GGTTTTTCACGCTTCTAATGTCGTTTTTTTCATTTTTTTTTTCGAATTTATTTCTTATTAAATCG
66 GGTTTTTCACGCTTCTAATATCG-TTTTTTCA--TTTTTTTTCGAATTTATTTCTAATTAAATCG
*
51862 AAACAAAATT--CA----CGTAAAAGGAAATCCTTAAATCCATTTTGACTAAGATTTGGTTAGAT
128 AAACAAGATTCACATGCTCGTAAAAGGAAATCCTTAAATCCATTTTGACTAAGATTTGGTTAGAT
* * * * *
51921 GAATATAGATATTTCAATGAGTCTTTCTAGGAAAAATCATGAAAAATTGAACCGGAACCCCGAAA
193 GAATATAGATATTTCAATGAGTCTTTCTGGGAAAAATCATGCAAAACTGAGCCGGAGCCCCGAAA
51986 CGCGTTTTCTAGTC-AAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAA
258 CGCGTTTTCTAG-CAAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAA
52050 TGC
322 TGC
* *
52053 ATTTTCTCAATTTTTTTTGGAAAATATTCAGAAAAAATATATAATTCAAACCCAAAAAAATTGAA
1 TTTTTCTCAA-TTTTTTTGCAAAATATTCAGAAAAAATATATAATTCAAACCCAAAAAAATTGAA
* * *
52118 GAG-TTTTCTCGCTTTTAATATCGTTTTTTCATTTTTTTTCGAATTTATTTCTAATTAAATCGAA
65 GGGTTTTTCACGCTTCTAATATCGTTTTTTCATTTTTTTTCGAATTTATTTCTAATTAAATCGAA
* * * *
52182 ACAAGATTAACATGCTCGTAAAAGAAAATCCTTAAATCGATTTTCACTAAGATTTGGTTAGATGA
130 ACAAGATTCACATGCTCGTAAAAGGAAATCCTTAAATCCATTTTGACTAAGATTTGGTTAGATGA
*
52247 ATATAGATATTTCAATGAGTCTTTCTGGGAAAAATCATGCAAAATTGAGCCGGAGCCCCGAAACG
195 ATATAGATATTTCAATGAGTCTTTCTGGGAAAAATCATGCAAAACTGAGCCGGAGCCCCGAAACG
** * * * *
52312 -AATTTCTTGCCAAAAAAACTGTGATGGTTAGTACATGATTTCGGCTAAAAACTGACCCGGAATG
260 CGTTTTCTAG-CAAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAATG
52376 C
324 C
52377 TTT
1 TTT
Statistics
Matches: 1680, Mismatches: 200, Indels: 122
0.84 0.10 0.06
Matches are distributed among these distances:
312 3 0.00
313 79 0.05
314 59 0.04
316 112 0.07
317 9 0.01
318 41 0.02
319 191 0.11
320 61 0.04
321 83 0.05
322 115 0.07
323 10 0.01
324 367 0.22
325 39 0.02
326 59 0.04
329 85 0.05
330 228 0.14
331 10 0.01
333 129 0.08
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.35
Consensus pattern (324 bp):
TTTTTCTCAATTTTTTTGCAAAATATTCAGAAAAAATATATAATTCAAACCCAAAAAAATTGAAG
GGTTTTTCACGCTTCTAATATCGTTTTTTCATTTTTTTTCGAATTTATTTCTAATTAAATCGAAA
CAAGATTCACATGCTCGTAAAAGGAAATCCTTAAATCCATTTTGACTAAGATTTGGTTAGATGAA
TATAGATATTTCAATGAGTCTTTCTGGGAAAAATCATGCAAAACTGAGCCGGAGCCCCGAAACGC
GTTTTCTAGCAAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAATGC
Done.