Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009966.1 Corchorus capsularis cultivar CVL-1 contig09987, 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: 21461
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36
Found at i:712 original size:3 final size:3
Alignment explanation
Indices: 704--731 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
694 ATGAAGTTCT
704 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
732 CGAGAGGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3617 original size:3 final size:3
Alignment explanation
Indices: 3604--3659 Score: 94
Period size: 3 Copynumber: 18.3 Consensus size: 3
3594 AAAAATATAT
*
3604 ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA TATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
3650 ATA ATA ATA A
1 ATA ATA ATA A
3660 GTTTTGCTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 47 0.94
4 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:5124 original size:2 final size:2
Alignment explanation
Indices: 5117--5155 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5107 GTGAATTATG
5117 TA TA TA TA 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 TA TA TA TA T
5156 CCAACAATTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6702 original size:89 final size:84
Alignment explanation
Indices: 6550--6792 Score: 287
Period size: 84 Copynumber: 2.8 Consensus size: 84
6540 TCAGGGTAAG
* * * *
6550 ATGTCCAAAATTTATTAAGCCATCATTTAAGCA-A-CCCATTTAAGTTATCTGATCAATGAAACT
1 ATGTCCAAAATTGATTAAGACATCATTTAAGCATATACCATTTAAGTTATCTGATCAATGGAACT
*
6613 TAAATTGAGAATTCAGGGGAAAA
66 TAAATTGAGAATGCA--GG--AA
* *
6636 ATGTCC-AACTTGATTAAG-CATCATTTAAGCATCTCATACCATTTAAGTTATTTGATCAATGGA
1 ATGTCCAAAATTGATTAAGACATCATTTAAGCA--T-ATACCATTTAAGTTATCTGATCAATGGA
* *
6699 ACTTAAATTGAGAGTGCATGAA
63 ACTTAAATTGAGAATGCAGGAA
* *
6721 ATGTCCAAAATTGATTAAGACATCATTTAAGCATATCCCATTTAAATTATCTGATCAATGGAACT
1 ATGTCCAAAATTGATTAAGACATCATTTAAGCATATACCATTTAAGTTATCTGATCAATGGAACT
6786 TGAAATT
66 T-AAATT
6793 TTATCAATGG
Statistics
Matches: 137, Mismatches: 12, Indels: 17
0.83 0.07 0.10
Matches are distributed among these distances:
84 42 0.31
85 24 0.18
86 17 0.12
87 14 0.10
88 1 0.01
89 39 0.28
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (84 bp):
ATGTCCAAAATTGATTAAGACATCATTTAAGCATATACCATTTAAGTTATCTGATCAATGGAACT
TAAATTGAGAATGCAGGAA
Found at i:8047 original size:96 final size:96
Alignment explanation
Indices: 7895--8186 Score: 424
Period size: 96 Copynumber: 3.0 Consensus size: 96
7885 ATATAAACAC
* * * * * * *
7895 ATGAATGAAATCTGTTTTTTCCTCGAAGGTTGGGTCTAATGGAAGGAACTCAAAACCCTTTTAAG
1 ATGAATGAAATCTG-TTCTTCCTCAAATGTCGGGTTTAGTGGAAGGAACTCGAAACCCTTTTAAG
*
7960 CAAGGTGTTTATGTATTTTGGTCCTTTTTAGTA
65 CAAGTTGTTTATGTATTTTGGTCC-TTTTAGTA
* * *
7993 ATGAATGGAATTTGTTCTTCCTCAAATGTCGGG-TTAGTGGAAGGAAGTCGAAACCCTTTTAAGC
1 ATGAATGAAATCTGTTCTTCCTCAAATGTCGGGTTTAGTGGAAGGAACTCGAAACCCTTTTAAGC
* *
8057 AAGTTGTTTATATATTTTGGTACTTTTAGTA
66 AAGTTGTTTATGTATTTTGGTCCTTTTAGTA
8088 ATGAATGAAATCTGTTCTTCCTCAAATGTCGGGTTTAGTGGAAGGAACTCGAAACCCTTTTAAGC
1 ATGAATGAAATCTGTTCTTCCTCAAATGTCGGGTTTAGTGGAAGGAACTCGAAACCCTTTTAAGC
* *
8153 AATTTGTTTATGCATTTTGGTCCTTTTAGTA
66 AAGTTGTTTATGTATTTTGGTCCTTTTAGTA
8184 ATG
1 ATG
8187 TCCAACACAA
Statistics
Matches: 173, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
95 39 0.23
96 107 0.62
97 15 0.09
98 12 0.07
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (96 bp):
ATGAATGAAATCTGTTCTTCCTCAAATGTCGGGTTTAGTGGAAGGAACTCGAAACCCTTTTAAGC
AAGTTGTTTATGTATTTTGGTCCTTTTAGTA
Found at i:8694 original size:2 final size:2
Alignment explanation
Indices: 8687--8746 Score: 55
Period size: 2 Copynumber: 34.0 Consensus size: 2
8677 GTTTAATAAT
*
8687 TA TA TA TA T- TA T- TA TA TA TA TA -A T- TA TA TA TC TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8724 T- TA T- TA T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
8747 AATTTATAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
1 8 0.17
2 40 0.83
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:8702 original size:12 final size:12
Alignment explanation
Indices: 8685--8739 Score: 64
Period size: 12 Copynumber: 4.9 Consensus size: 12
8675 CCGTTTAATA
8685 ATTATATATATT
1 ATTATATATATT
*
8697 ATTATATATATA
1 ATTATATATATT
*
8709 ATTATATAT-CT
1 ATTATATATATT
8720 A--ATAT-TATT
1 ATTATATATATT
8729 ATTATATATAT
1 ATTATATATAT
8740 ATATATAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
8 1 0.03
9 6 0.17
11 5 0.14
12 23 0.66
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTATATATATT
Found at i:8725 original size:26 final size:25
Alignment explanation
Indices: 8682--8770 Score: 89
Period size: 26 Copynumber: 3.6 Consensus size: 25
8672 GAACCGTTTA
*
8682 ATAATTATATA-TATTATTATATAT
1 ATAATTATATATTAATATTATATAT
8706 ATAATTATATATCTAATATTAT-TATT
1 ATAATTATATAT-TAATATTATATA-T
*
8732 ATATATATATATATAAAT-TTATA-AT
1 ATA-AT-TATATATTAATATTATATAT
8757 -TAATTATATATTAA
1 ATAATTATATATTAA
8771 CTAAATGGTT
Statistics
Matches: 56, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
22 9 0.16
23 2 0.04
24 13 0.23
25 3 0.05
26 17 0.30
27 5 0.09
28 7 0.12
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (25 bp):
ATAATTATATATTAATATTATATAT
Found at i:8767 original size:32 final size:30
Alignment explanation
Indices: 8684--8767 Score: 91
Period size: 32 Copynumber: 2.7 Consensus size: 30
8674 ACCGTTTAAT
8684 AATTATATATATTATTATATATATAATTATA
1 AATT-TATATATTATTATATATATAATTATA
* *
8715 TATCTA-ATATTATTATTATATATATATATATA
1 AATTTATATATTATTA-TATATATA-AT-TATA
8747 AATTTATA-ATTAATTATATAT
1 AATTTATATATT-ATTATATAT
8768 TAACTAAATG
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
29 9 0.20
30 10 0.23
31 4 0.09
32 16 0.36
33 5 0.11
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (30 bp):
AATTTATATATTATTATATATATAATTATA
Found at i:16457 original size:45 final size:45
Alignment explanation
Indices: 16375--16460 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 45
16365 CGAAACTTGG
* **
16375 AGCACTTGGTAATCATGGAGCCAAAGCTCTCTTTGATCTCCTTCA
1 AGCACTTGGCAATCATGGAGCCAAAGCTCTCCGTGATCTCCTTCA
* * *
16420 AGCATTTGGCAATCATGGAGCCTAAGCTTTCCGTGATCTCC
1 AGCACTTGGCAATCATGGAGCCAAAGCTCTCCGTGATCTCC
16461 CTCACGTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (45 bp):
AGCACTTGGCAATCATGGAGCCAAAGCTCTCCGTGATCTCCTTCA
Found at i:17069 original size:34 final size:34
Alignment explanation
Indices: 16978--17193 Score: 368
Period size: 33 Copynumber: 6.5 Consensus size: 34
16968 AATGTGAGTG
*
16978 AAGGCAAGTTCAATG-TTGTTGGATGTGAGAATT
1 AAGGCAAGTTCAATGTTTTTTGGATGTGAGAATT
17011 AAGGCAAGTTCAATG-TTTTTGGATGTGAGAATT
1 AAGGCAAGTTCAATGTTTTTTGGATGTGAGAATT
17044 AAGGCAAGTTCAATGTTTTTTGGATGTGAGAATT
1 AAGGCAAGTTCAATGTTTTTTGGATGTGAGAATT
*
17078 AAGGCAAGTTCAATGTTTTTTGGATTTGAGAATT
1 AAGGCAAGTTCAATGTTTTTTGGATGTGAGAATT
*
17112 AAGGCAAGTTCAATG-TTTTTGGAGGTGAGAATT
1 AAGGCAAGTTCAATGTTTTTTGGATGTGAGAATT
*
17145 AAGGCAAGTTCAATGTTTTTTGGATTTGAGAA-T
1 AAGGCAAGTTCAATGTTTTTTGGATGTGAGAATT
17178 AAGGCAAGTTCAATGT
1 AAGGCAAGTTCAATGT
17194 CAATTGGGAA
Statistics
Matches: 175, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
33 95 0.54
34 80 0.46
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.36
Consensus pattern (34 bp):
AAGGCAAGTTCAATGTTTTTTGGATGTGAGAATT
Found at i:17079 original size:67 final size:67
Alignment explanation
Indices: 16978--17193 Score: 382
Period size: 67 Copynumber: 3.2 Consensus size: 67
16968 AATGTGAGTG
* *
16978 AAGGCAAGTTCAATGTTGTTGGATGTGAGAATTAAGGCAAGTTCAATG-TTTTTGGATGTGAGAA
1 AAGGCAAGTTCAATGTTTTTGGATGTGAGAATTAAGGCAAGTTCAATGTTTTTTGGATTTGAGAA
17042 TT
66 TT
17044 AAGGCAAGTTCAATGTTTTTTGGATGTGAGAATTAAGGCAAGTTCAATGTTTTTTGGATTTGAGA
1 AAGGCAAGTTCAATG-TTTTTGGATGTGAGAATTAAGGCAAGTTCAATGTTTTTTGGATTTGAGA
17109 ATT
65 ATT
*
17112 AAGGCAAGTTCAATGTTTTTGGAGGTGAGAATTAAGGCAAGTTCAATGTTTTTTGGATTTGAGAA
1 AAGGCAAGTTCAATGTTTTTGGATGTGAGAATTAAGGCAAGTTCAATGTTTTTTGGATTTGAGAA
17177 -T
66 TT
17178 AAGGCAAGTTCAATGT
1 AAGGCAAGTTCAATGT
17194 CAATTGGGAA
Statistics
Matches: 145, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
66 32 0.22
67 81 0.56
68 32 0.22
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.36
Consensus pattern (67 bp):
AAGGCAAGTTCAATGTTTTTGGATGTGAGAATTAAGGCAAGTTCAATGTTTTTTGGATTTGAGAA
TT
Found at i:17419 original size:22 final size:22
Alignment explanation
Indices: 17391--17437 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
17381 GATTACTTGC
17391 GCTGGTCTCTTTTGAATGGTAA
1 GCTGGTCTCTTTTGAATGGTAA
17413 GCTGGTCTCTTTTGAATGGTAA
1 GCTGGTCTCTTTTGAATGGTAA
17435 GCT
1 GCT
17438 TTGATTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.17, C:0.15, G:0.28, T:0.40
Consensus pattern (22 bp):
GCTGGTCTCTTTTGAATGGTAA
Found at i:19154 original size:333 final size:332
Alignment explanation
Indices: 18354--21456 Score: 3708
Period size: 333 Copynumber: 9.4 Consensus size: 332
18344 AATCCTCTCT
* * * * * *
18354 CTAAAATTTTGCAAAAATTCACCC-AAAATTTTTTTTTTCTGAATTTTTGGCCACAACATTCATA
1 CTAAAATTTTGCAAAAATTGACCCGAAAA--ATATTTTCCTCAATTTTTGGCCACAACACTCATA
** * * * **
18418 AAATCTCTACAATTTAACACCAAAATTTTTGAAGAGTTTTTC-ACGCTTCTAATATTGTTTTTCT
64 AAAAATCTATAATTTAACACCAAAAATATTGAAGAGTTTTTCAAC-CTTCTAATA-TCATTTTCT
* * * * *
18482 TATTTTTTCTGAATTAATATTTAAATAAATGAAAATAAGAATCATAAGCTCGTAAAAAGAAATCC
127 TATTTTTTCTGAATTAATTTTTAATTAAATCAAAATAAGATTCAGAAGCTCGTAAAAAGAAATCC
* *
18547 TTAAATCCAAT-TAGACCGAGAATTGGTTAGATGAATATAGAT-ATTTCAAGTAGTCAT-GGCGC
192 TTAAATCCAATGT-GACTGAGAATTGGTTAGATGAATATAGATAATTT-AAGGAGTC-TCGGCGC
** * * * ** **
18609 CAAAAATTTTGCAAAATTGAGTCGGGGTCCTGTGATGCGTTTTTAGCCAAAAA-----AACG-TA
254 CAAAAATCATGCAAAATTGAGCCGGGGCCCCGAAATGCGTTTTTAGCCAAAAACCGTGATGGTTA
*
18668 --A-ATGATTTCAG
319 GTACATGATTTCGG
* * * *
18679 CTAAAATTTTGCAAAAATTGACCCAAAAAATTTTTTCTTGAATTTTTGGCCACAACACTCATAAA
1 CTAAAATTTTGCAAAAATTGACCCGAAAAATATTTTCCTCAATTTTTGGCCACAACACTCATAAA
* * *
18744 AACTCTATAATTTAACACAAAAAATATTGAAGAGTTTTTC-ACGCTTCTAATATCGTTTTTCTTA
66 AAATCTATAATTTAACACCAAAAATATTGAAGAGTTTTTCAAC-CTTCTAATATC-ATTTTCTTA
*
18808 TTTTTTATGAATTAATTTTTAATTAAATCAAAATAAGATTCAGAAGCTCGTAAAAAGAAATCCTT
129 TTTTTTCTGAATTAATTTTTAATTAAATCAAAATAAGATTCAGAAGCTCGTAAAAAGAAATCCTT
* * * *
18873 AAATCCAATGTGACTGATATTTGGTTAGATGAATATAGATAATTTAAGGACTCTCGGCGCCCAAA
194 AAATCCAATGTGACTGAGAATTGGTTAGATGAATATAGATAATTTAAGGAGTCTCGGCGCCAAAA
* * * * * *
18938 ATTATGCAAAATTAAGCCGGGGTCCCGAAACGCGTTGTTAGCCAAAAACCGTGATGGTTATTACA
259 ATCATGCAAAATTGAGCCGGGGCCCCGAAATGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACA
19003 TGATTTCGG
324 TGATTTCGG
* * * * *
19012 CTAAAATTTTGCGAAAATTGACTCAAAAAATATTTTCCTCAATTTTTGGCTACAACTCTCATAAA
1 CTAAAATTTTGCAAAAATTGACCCGAAAAATATTTTCCTCAATTTTTGGCCACAACACTCATAAA
* * * *
19077 AAATCTTTTATTTAAGACCAAAACTATTGAAGAGTTTTTCAACCTTCTAATATCATTTTCTTATT
66 AAATCTATAATTTAACACCAAAAATATTGAAGAGTTTTTCAACCTTCTAATATCATTTTCTTA-T
*
19142 TTTTTCTGAATTAATTTTTAATTAAATCAAAATAAGATTCAGAAGCTTGTAAAAAGAAATCCTTA
130 TTTTTCTGAATTAATTTTTAATTAAATCAAAATAAGATTCAGAAGCTCGTAAAAAGAAATCCTTA
* * * * * *
19207 AATCCAATGTGACCGAGAATTGGTTAGATGAATATAGATATTTTAAGTATTCTTGGTGCCAAAAA
195 AATCCAATGTGACTGAGAATTGGTTAGATGAATATAGATAATTTAAGGAGTCTCGGCGCCAAAAA
* * * * * * * *
19272 TCATACAAAATTGAGCCGGGACCCTGTAATGCGTTTTTATCTAAAAAACGTAATGGTTAGTACAT
260 TCATGCAAAATTGAGCCGGGGCCCCGAAATGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACAT
19337 GATTTCGG
325 GATTTCGG
** * * * *
19345 CTAAAATTTTGCAAAAATTGACCCGAAATTTTTTTTCCTGAA-TTTTGGCCACAACACTCATGAG
1 CTAAAATTTTGCAAAAATTGACCCGAAAAATATTTTCCTCAATTTTTGGCCACAACACTCATAAA
* * * *
19409 AACTCTATAGTTTAACACCAAAAATATTGAAGAGTTTCTC-ACGCTTCTAATATC--GTTCTTA-
66 AAATCTATAATTTAACACCAAAAATATTGAAGAGTTTTTCAAC-CTTCTAATATCATTTTCTTAT
* * * *
19470 TTTTTCTGAATTAATTTTTAATTAAATGAAAATAAGATTTAGAAACTCGTAAAAATAAATCCTTA
130 TTTTTCTGAATTAATTTTTAATTAAATCAAAATAAGATTCAGAAGCTCGTAAAAAGAAATCCTTA
* * * * * ** *
19535 AATCCAATATGACCGAGATTTGGTTAGATTAATATAGATGATACAAGGAGTATCGGCGCCAAAAA
195 AATCCAATGTGACTGAGAATTGGTTAGATGAATATAGATAATTTAAGGAGTCTCGGCGCCAAAAA
* * * * ** *
19600 TCATGCGAAATTGAGTCGAGGCCCCGAAACGCGTTTTTAGCCTCAAACCGTGATGGTTAATACAT
260 TCATGCAAAATTGAGCCGGGGCCCCGAAATGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACAT
* **
19665 TATTGAGG
325 GATTTCGG
* * *
19673 CTAAAATTTTGCAAAAATTAACCTGAAAAATATTTTTCTCAATTTTTGGCCACAACA--CATAAA
1 CTAAAATTTTGCAAAAATTGACCCGAAAAATATTTTCCTCAATTTTTGGCCACAACACTCATAAA
* * * *
19736 AATTATACAATTTAACACCAAAAATATTGAAGAGTTTTTCAA-GTATCTAATATCATTTTCTTAT
66 AAATCTATAATTTAACACCAAAAATATTGAAGAGTTTTTCAACCT-TCTAATATCATTTTCTTAT
* * * * *
19800 TTTTTTTGAATTAATTTGTAATTAAATCAAAATAAGATTTAGAAGCTCGTAAAAGGAAATACTTA
130 TTTTTCTGAATTAATTTTTAATTAAATCAAAATAAGATTCAGAAGCTCGTAAAAAGAAATCCTTA
* * * *
19865 AATCCAATGTGACTGA-AATTTGGTTAGATGAATATAGAT-ATTTCAAGGTGTCTTGGCACCAAG
195 AATCCAATGTGACTGAGAA-TTGGTTAGATGAATATAGATAATTT-AAGGAGTCTCGGCGCCAAA
** * * * *
19928 AATCACACAAGATTGAGCCGGGGCCCCGAAAAGCGTTTTTAACCAAAAACCATGATGG-T--T--
258 AATCATGCAAAATTGAGCCGGGGCCCCGAAATGCGTTTTTAGCCAAAAACCGTGATGGTTAGTAC
19988 ATGATTTCGG
323 ATGATTTCGG
* *
19998 CTAAAATTTTGCAAAAATTGACCCGAAAAATATTTTTCTCAATTTTT-GACACAACACTCATAAA
1 CTAAAATTTTGCAAAAATTGACCCGAAAAATATTTTCCTCAATTTTTGGCCACAACACTCATAAA
* * * * *
20062 AAATCTATAATTCACCACCAGAAATATTGAAGAGTTTTTCAAACTTCGAATATCATTTTCTTATT
66 AAATCTATAATTTAACACCAAAAATATTGAAGAGTTTTTCAACCTTCTAATATCATTTTCTTATT
* * *
20127 TTTTCTGAATTAATTTTTAATTAAATCGAAATAAGATTTAGAAGCTCGTAAAAAGAAATCCATAA
131 TTTTCTGAATTAATTTTTAATTAAATCAAAATAAGATTCAGAAGCTCGTAAAAAGAAATCCTTAA
* * * * * *
20192 AT-TAATGTTACTGAGAATTGGTTATATGAATATAGATAATTCAAGGAGTCTCGGCACCAAAAGT
196 ATCCAATGTGACTGAGAATTGGTTAGATGAATATAGATAATTTAAGGAGTCTCGGCGCCAAAAAT
* * * *
20256 CATGCAAAATTGAGCCAGGGCCCCGAAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACATA
261 CATGCAAAATTGAGCCGGGGCCCCGAAATGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACATG
20321 ATTTCGG
326 ATTTCGG
* * *
20328 ATAAAATTTTGCAAAATTTGACCCGAAAAATATTTTCCTCAATTTTTTGCCACAACACTCATAAA
1 CTAAAATTTTGCAAAAATTGACCCGAAAAATATTTTCCTCAATTTTTGGCCACAACACTCATAAA
* *
20393 ATATCTATAATTTAACACCAAAAATATCGAAGAGTTTTTCAACCTTCTAATATCATTTTCTTATT
66 AAATCTATAATTTAACACCAAAAATATTGAAGAGTTTTTCAACCTTCTAATATCATTTTCTTA-T
* * *
20458 TTTTTTTGAATTAATTCTTAATTAAATCGAAATAAGATTCAGAAGCTCGTAAAAAGAAATCCTTA
130 TTTTTCTGAATTAATTTTTAATTAAATCAAAATAAGATTCAGAAGCTCGTAAAAAGAAATCCTTA
* * * *
20523 AATCCAATGTGACTGAGAATTGGTTAGATGAATATCGATAATTGAAGGTGTCTCGTCGCCAAAAA
195 AATCCAATGTGACTGAGAATTGGTTAGATGAATATAGATAATTTAAGGAGTCTCGGCGCCAAAAA
* * * * ** *
20588 TCATGCAAAATTTAGTC-GGGCACTGAAATGCGTTTTTAGCCAAAAATTGTGA-GAGTAACGTAC
260 TCATGCAAAATTGAGCCGGGGCCCCGAAATGCGTTTTTAGCCAAAAACCGTGATG-GTTA-GTAC
20651 ATGATTTCGG
323 ATGATTTCGG
*** * * *
20661 CTAAAATTTTGCAAAAATTGACAAAAAAAATTTTTTTCTAAATTTTTGGCCACAACACTCATAAA
1 CTAAAATTTTGCAAAAATTGACCCGAAAAATATTTTCCTCAATTTTTGGCCACAACACTCATAAA
* * **
20726 AACTCTATAATCTAACACCAAAAATATTGAAGAGTTTTTCAAGTTTCTAATATCATTTTCTTATT
66 AAATCTATAATTTAACACCAAAAATATTGAAGAGTTTTTCAACCTTCTAATATCATTTTCTTATT
* * * *
20791 TTTTCTGAATTAATTTTTAATTAAATCGAAATAAGATTCAAAAGTTCGTGAAAAGAAATCCTTAA
131 TTTTCTGAATTAATTTTTAATTAAATCAAAATAAGATTCAGAAGCTCGTAAAAAGAAATCCTTAA
* * *
20856 ATCCAATGTTACTGAGAATTGGTTAGATGAATATAGATAATTCAAGGAGTCACGGCGCCAAAAAT
196 ATCCAATGTGACTGAGAATTGGTTAGATGAATATAGATAATTTAAGGAGTCTCGGCGCCAAAAAT
* * * *
20921 CATGAAAAATTGAGCCGGAGCCCCGAAATGCGTTTTTAGCCTAAAACCGTTATGGTTAGTACATG
261 CATGCAAAATTGAGCCGGGGCCCCGAAATGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACATG
20986 ATTTCGG
326 ATTTCGG
* * * * *
20993 GTAAAATTTTGCAAAAATTGACCCTAAAAATATTTTCCTGAATTTTTGGCCACAACACTCTTGAA
1 CTAAAATTTTGCAAAAATTGACCCGAAAAATATTTTCCTCAATTTTTGGCCACAACACTCATAAA
* * **
21058 AACTCTATAATTTAGCACCAAAAATATTGAAGAGTTTTTC-ACGCTTCTAATATTGTTTTTCTTA
66 AAATCTATAATTTAACACCAAAAATATTGAAGAGTTTTTCAAC-CTTCTAATA-TCATTTTCTTA
* * * * *
21122 TTTTTTTCTGAA--AATTTTTAATGAAATGAAAATAAGATTAAGAAGCTCGTAAAAGGAAATCAT
129 -TTTTTTCTGAATTAATTTTTAATTAAATCAAAATAAGATTCAGAAGCTCGTAAAAAGAAATCCT
* * * * * *
21185 TAAATCCAATGTAACTGAGAATTGGCTAGATGAATATAGATATTTTAAGGTGTCTTGGCGTC-AA
193 TAAATCCAATGTGACTGAGAATTGGTTAGATGAATATAGATAATTTAAGGAGTCTCGGCGCCAAA
* * * * * * *
21249 AATCATGCAAAATTGAGCCGAGACCCTGTAATGCGTTTTTAGCAAAAAAAAACGTGATGGTTATT
258 AATCATGCAAAATTGAGCCGGGGCCCCGAAATGCGTTTTTAGC--CAAAAACCGTGATGGTTAGT
*
21314 ATATGATTTCGG
321 ACATGATTTCGG
* * * * **
21326 CTAAAATTTTGTAAAAATTGATCCGAAGAATTTTTTATTCAATTTTTGGCCACAACACTCATAAA
1 CTAAAATTTTGCAAAAATTGACCCGAAAAATATTTTCCTCAATTTTTGGCCACAACACTCATAAA
* * ** *
21391 AAATCTATAATTTAACGCCAAAAATATTGAAGAGTTTTCCAAGATTCTAATATCGTTTTTCTTAT
66 AAATCTATAATTTAACACCAAAAATATTGAAGAGTTTTTCAACCTTCTAATATC-ATTTTCTTAT
21456 T
130 T
21457 CTTTA
Statistics
Matches: 2387, Mismatches: 342, Indels: 91
0.85 0.12 0.03
Matches are distributed among these distances:
323 2 0.00
324 245 0.10
325 174 0.07
326 133 0.06
327 50 0.02
328 205 0.09
329 26 0.01
330 213 0.09
331 115 0.05
332 517 0.22
333 692 0.29
334 15 0.01
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (332 bp):
CTAAAATTTTGCAAAAATTGACCCGAAAAATATTTTCCTCAATTTTTGGCCACAACACTCATAAA
AAATCTATAATTTAACACCAAAAATATTGAAGAGTTTTTCAACCTTCTAATATCATTTTCTTATT
TTTTCTGAATTAATTTTTAATTAAATCAAAATAAGATTCAGAAGCTCGTAAAAAGAAATCCTTAA
ATCCAATGTGACTGAGAATTGGTTAGATGAATATAGATAATTTAAGGAGTCTCGGCGCCAAAAAT
CATGCAAAATTGAGCCGGGGCCCCGAAATGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACATG
ATTTCGG
Found at i:20992 original size:665 final size:661
Alignment explanation
Indices: 18354--21456 Score: 3814
Period size: 665 Copynumber: 4.7 Consensus size: 661
18344 AATCCTCTCT
* * * * * *
18354 CTAAAATTTTGCAAAAATTCACCC-AAAATTTTTTTTTTCTGAATTTTTGGCCACAACATTCATA
1 CTAAAATTTTGCAAAAATTGACCCGAAAA--ATATTTTCCTCAATTTTTGGCCACAACACTCATA
* * * * **
18418 AAATCTCTACAATTTAACACCAAAATTTTTGAAGAGTTTTTC-ACGCTTCTAATATTGTTTTTCT
64 AAA-ATCTATAATTTAACACCAAAAATATTGAAGAGTTTTTCAAC-CTTCTAATA-TCATTTTCT
* * *
18482 TA-TTTTTTCTGAATTAATATTTAAATAAAT-GAAAATAAGAATCATAAGCTCGTAAAAAGAAAT
126 TATTTTTTTCTGAATTAAT-TTTAATTAAATCG-AAATAAGATTCAGAAGCTCGTAAAAAGAAAT
* *
18545 CCTTAAATCCAAT-TAGACCGAGAATTGGTTAGATGAATATAGATATTTCAA-GTAGTCATGGCG
189 CCTTAAATCCAATGT-GACTGAGAATTGGTTAGATGAATATAGATATTTCAAGGT-GTCTTGGCG
** * * * *
18608 CCAAAAATTTTGCAAAATTGAGTCGGGGTCCTGTGATGCGTTTTTAGCCAAAAAA----A-CGT-
252 CCAAAAATCATGCAAAATTGAG-CCGGGCCCTGTAATGCGTTTTTAGCCAAAAAACGTGATGGTA
* *
18667 A--A-ATGATTTCAGCTAAAATTTTGCAAAAATTGACCCAAAAAA-TTTTTTCTTGAATTTTTGG
316 AGTACATGATTTCGGCTAAAATTTTGCAAAAATTGA-CCAAAAAATTTTTTTC-TCAATTTTTGG
* *
18728 CCACAACACTCATAAAAACTCTATAATTTAACACAAAAAATATTGAAGAGTTTTTCACGCTTCTA
379 CCACAACACTCATAAAAACTCTATAATTTAACACCAAAAATATTGAAGAGTTTTTCAAGCTTCTA
* * * *
18793 ATATCGTTTTTCTTATTTTTTATGAATTAATTTTTAATTAAATCAAAATAAGATTCAGAAGCTCG
444 ATATC-ATTTTCTTATTTTTTCTGAATTAATTTTTAATTAAATCGAAATAAGATTCAAAAGCTCG
* * *
18858 TAAAAAGAAATCCTTAAATCCAATGTGACTGATATTTGGTTAGATGAATATAGATAATTTAAGGA
508 TAAAAAGAAATCCTTAAATCCAATGTGACTGAGAATTGGTTAGATGAATATAGATAATTCAAGGA
* * * * * * * *
18923 CTCTCGGCGCCCAAAATTATGCAAAATTAAGCCGGGGTCCCGAAACGCGTTGTTAGCCAAAAACC
573 GTCACGGCGCCAAAAATCATGCAAAATTGAGCCGGAGCCCCGAAACGCGTTTTTAGCCAAAAACC
*
18988 GTGATGGTTATTACATGATTTCGG
638 GTGATGGTTAGTACATGATTTCGG
* * * * *
19012 CTAAAATTTTGCGAAAATTGACTCAAAAAATATTTTCCTCAATTTTTGGCTACAACTCTCATAAA
1 CTAAAATTTTGCAAAAATTGACCCGAAAAATATTTTCCTCAATTTTTGGCCACAACACTCAT-AA
* * * *
19077 AAATCTTTTATTTAAGACCAAAACTATTGAAGAGTTTTTCAACCTTCTAATATCATTTTCTTATT
65 AAATCTATAATTTAACACCAAAAATATTGAAGAGTTTTTCAACCTTCTAATATCATTTTCTTATT
* *
19142 TTTTTCTGAATTAATTTTTAATTAAATCAAAATAAGATTCAGAAGCTTGTAAAAAGAAATCCTTA
130 TTTTTCTGAATTAA-TTTTAATTAAATCGAAATAAGATTCAGAAGCTCGTAAAAAGAAATCCTTA
* * * *
19207 AATCCAATGTGACCGAGAATTGGTTAGATGAATATAGATATTTTAA-GTATTCTTGGTGCCAAAA
194 AATCCAATGTGACTGAGAATTGGTTAGATGAATATAGATATTTCAAGGT-GTCTTGGCGCCAAAA
* * * * *
19271 ATCATACAAAATTGAGCCGGGACCCTGTAATGCGTTTTTATCTAAAAAACGTAATGGTTAGTACA
258 ATCATGCAAAATTGAGCCGGG-CCCTGTAATGCGTTTTTAGCCAAAAAACGTGATGGTAAGTACA
** * *
19336 TGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATTTTTTTTCCTGAA-TTTTGGCCACAAC
322 TGATTTCGGCTAAAATTTTGCAAAAATTGACCAAAAAATTTTTTT-CTCAATTTTTGGCCACAAC
* * * * *
19400 ACTCATGAGAACTCTATAGTTTAACACCAAAAATATTGAAGAGTTTCTCACGCTTCTAATATC--
386 ACTCATAAAAACTCTATAATTTAACACCAAAAATATTGAAGAGTTTTTCAAGCTTCTAATATCAT
* *
19463 GTTCTTA-TTTTTCTGAATTAATTTTTAATTAAAT-GAAAATAAGATTTAGAAA-CTCGTAAAAA
451 TTTCTTATTTTTTCTGAATTAATTTTTAATTAAATCG-AAATAAGATTCA-AAAGCTCGTAAAAA
* * * * * * *
19525 TAAATCCTTAAATCCAATATGACCGAGATTTGGTTAGATTAATATAGATGATACAAGGAGT-ATC
514 GAAATCCTTAAATCCAATGTGACTGAGAATTGGTTAGATGAATATAGATAATTCAAGGAGTCA-C
* * **
19589 GGCGCCAAAAATCATGCGAAATTGAGTC-GAGGCCCCGAAACGCGTTTTTAGCCTCAAACCGTGA
578 GGCGCCAAAAATCATGCAAAATTGAGCCGGA-GCCCCGAAACGCGTTTTTAGCCAAAAACCGTGA
* * **
19653 TGGTTAATACATTATTGAGG
642 TGGTTAGTACATGATTTCGG
* * *
19673 CTAAAATTTTGCAAAAATTAACCTGAAAAATATTTTTCTCAATTTTTGGCCACAACA--CATAAA
1 CTAAAATTTTGCAAAAATTGACCCGAAAAATATTTTCCTCAATTTTTGGCCACAACACTCATAAA
*
19736 AAT-TATACAATTTAACACCAAAAATATTGAAGAGTTTTTCAA-GTATCTAATATCATTTTCTTA
66 AATCTAT--AATTTAACACCAAAAATATTGAAGAGTTTTTCAACCT-TCTAATATCATTTTCTTA
* * * *
19799 TTTTTTT-TGAATTAATTTGTAATTAAATCAAAATAAGATTTAGAAGCTCGTAAAAGGAAATACT
128 TTTTTTTCTGAATTAATTT-TAATTAAATCGAAATAAGATTCAGAAGCTCGTAAAAAGAAATCCT
*
19863 TAAATCCAATGTGACTGA-AATTTGGTTAGATGAATATAGATATTTCAAGGTGTCTTGGCACCAA
192 TAAATCCAATGTGACTGAGAA-TTGGTTAGATGAATATAGATATTTCAAGGTGTCTTGGCGCCAA
* ** * * * * * * *
19927 GAATCACACAAGATTGAGCCGGGGCCCCGAAAAGCGTTTTTAACCAAAAACCATGATGGT---T-
256 AAATCATGCAAAATTGAGCC-GGGCCCTGTAATGCGTTTTTAGCCAAAAAACGTGATGGTAAGTA
* * *
19988 -ATGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATATTTTTCTCAATTTTT-GACACA
320 CATGATTTCGGCTAAAATTTTGCAAAAATTGA-CCAAAAAATTTTTTTCTCAATTTTTGGCCACA
* * * * * *
20051 ACACTCATAAAAAATCTATAATTCACCACCAGAAATATTGAAGAGTTTTTCAAACTTCGAATATC
384 ACACTCATAAAAACTCTATAATTTAACACCAAAAATATTGAAGAGTTTTTCAAGCTTCTAATATC
* *
20116 ATTTTCTTATTTTTTCTGAATTAATTTTTAATTAAATCGAAATAAGATTTAGAAGCTCGTAAAAA
449 ATTTTCTTATTTTTTCTGAATTAATTTTTAATTAAATCGAAATAAGATTCAAAAGCTCGTAAAAA
* * * * *
20181 GAAATCCATAAAT-TAATGTTACTGAGAATTGGTTATATGAATATAGATAATTCAAGGAGTCTCG
514 GAAATCCTTAAATCCAATGTGACTGAGAATTGGTTAGATGAATATAGATAATTCAAGGAGTCACG
* * *
20245 GCACCAAAAGTCATGCAAAATTGAGCCAGG-GCCCCGAAACGCGTTTTTAGCAAAAAACCGTGAT
579 GCGCCAAAAATCATGCAAAATTGAGCC-GGAGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGAT
*
20309 GGTTAGTACATAATTTCGG
643 GGTTAGTACATGATTTCGG
* * *
20328 ATAAAATTTTGCAAAATTTGACCCGAAAAATATTTTCCTCAATTTTTTGCCACAACACTCATAAA
1 CTAAAATTTTGCAAAAATTGACCCGAAAAATATTTTCCTCAATTTTTGGCCACAACACTCATAAA
*
20393 ATATCTATAATTTAACACCAAAAATATCGAAGAGTTTTTCAACCTTCTAATATCATTTTCTTATT
66 A-ATCTATAATTTAACACCAAAAATATTGAAGAGTTTTTCAACCTTCTAATATCATTTTCTTATT
*
20458 TTTTTTTGAATTAATTCTTAATTAAATCGAAATAAGATTCAGAAGCTCGTAAAAAGAAATCCTTA
130 TTTTTCTGAATTAATT-TTAATTAAATCGAAATAAGATTCAGAAGCTCGTAAAAAGAAATCCTTA
* * * * *
20523 AATCCAATGTGACTGAGAATTGGTTAGATGAATATCGATAATTGAAGGTGTCTCGTCGCCAAAAA
194 AATCCAATGTGACTGAGAATTGGTTAGATGAATATAGATATTTCAAGGTGTCTTGGCGCCAAAAA
* * * * **
20588 TCATGCAAAATTTAGTCGGGCACTGAAATGCGTTTTTAGCCAAAAATTGTGA-GAGTAACGTACA
259 TCATGCAAAATTGAGCCGGGCCCTGTAATGCGTTTTTAGCCAAAAAACGTGATG-GTAA-GTACA
* *
20652 TGATTTCGGCTAAAATTTTGCAAAAATTGACAAAAAAAATTTTTTTCTAAATTTTTGGCCACAAC
322 TGATTTCGGCTAAAATTTTGCAAAAATTGAC-CAAAAAATTTTTTTCTCAATTTTTGGCCACAAC
* *
20717 ACTCATAAAAACTCTATAATCTAACACCAAAAATATTGAAGAGTTTTTCAAGTTTCTAATATCAT
386 ACTCATAAAAACTCTATAATTTAACACCAAAAATATTGAAGAGTTTTTCAAGCTTCTAATATCAT
* *
20782 TTTCTTATTTTTTCTGAATTAATTTTTAATTAAATCGAAATAAGATTCAAAAGTTCGTGAAAAGA
451 TTTCTTATTTTTTCTGAATTAATTTTTAATTAAATCGAAATAAGATTCAAAAGCTCGTAAAAAGA
*
20847 AATCCTTAAATCCAATGTTACTGAGAATTGGTTAGATGAATATAGATAATTCAAGGAGTCACGGC
516 AATCCTTAAATCCAATGTGACTGAGAATTGGTTAGATGAATATAGATAATTCAAGGAGTCACGGC
* * * *
20912 GCCAAAAATCATGAAAAATTGAGCCGGAGCCCCGAAATGCGTTTTTAGCCTAAAACCGTTATGGT
581 GCCAAAAATCATGCAAAATTGAGCCGGAGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGT
20977 TAGTACATGATTTCGG
646 TAGTACATGATTTCGG
* * * *
20993 GTAAAATTTTGCAAAAATTGACCCTAAAAATATTTTCCTGAATTTTTGGCCACAACACTCTTGAA
1 CTAAAATTTTGCAAAAATTGACCCGAAAAATATTTTCCTCAATTTTTGGCCACAACACTCAT-AA
* * **
21058 AACTCTATAATTTAGCACCAAAAATATTGAAGAGTTTTTC-ACGCTTCTAATATTGTTTTTCTTA
65 AAATCTATAATTTAACACCAAAAATATTGAAGAGTTTTTCAAC-CTTCTAATA-TCATTTTCTTA
* * * *
21122 TTTTTTTCTGAA--AATTTTTAATGAAAT-GAAAATAAGATTAAGAAGCTCGTAAAAGGAAATCA
128 TTTTTTTCTGAATTAA-TTTTAATTAAATCG-AAATAAGATTCAGAAGCTCGTAAAAAGAAATCC
* * * *
21184 TTAAATCCAATGTAACTGAGAATTGGCTAGATGAATATAGATATTTTAAGGTGTCTTGGCGTC-A
191 TTAAATCCAATGTGACTGAGAATTGGTTAGATGAATATAGATATTTCAAGGTGTCTTGGCGCCAA
* * * *
21248 AAATCATGCAAAATTGAGCCGAGACCCTGTAATGCGTTTTTAGCAAAAAAAAACGTGATGGTTAT
256 AAATCATGCAAAATTGAGCCG-GGCCCTGTAATGCGTTTTTAGC--CAAAAAACGTGATGGTAAG
* * * *
21313 TATATGATTTCGGCTAAAATTTTGTAAAAATTGATCCGAAGAATTTTTTAT-TCAATTTTTGGCC
318 TACATGATTTCGGCTAAAATTTTGCAAAAATTGA-CCAAAAAATTTTTT-TCTCAATTTTTGGCC
* * * *
21377 ACAACACTCATAAAAAATCTATAATTTAACGCCAAAAATATTGAAGAGTTTTCCAAGATTCTAAT
381 ACAACACTCATAAAAACTCTATAATTTAACACCAAAAATATTGAAGAGTTTTTCAAGCTTCTAAT
*
21442 ATCGTTTTTCTTATT
446 ATC-ATTTTCTTATT
21457 CTTTA
Statistics
Matches: 2118, Mismatches: 256, Indels: 134
0.84 0.10 0.05
Matches are distributed among these distances:
653 94 0.04
654 15 0.01
655 169 0.08
656 74 0.03
657 322 0.15
658 306 0.14
659 74 0.03
660 1 0.00
661 219 0.10
662 11 0.01
663 73 0.03
664 254 0.12
665 416 0.20
666 88 0.04
667 2 0.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (661 bp):
CTAAAATTTTGCAAAAATTGACCCGAAAAATATTTTCCTCAATTTTTGGCCACAACACTCATAAA
AATCTATAATTTAACACCAAAAATATTGAAGAGTTTTTCAACCTTCTAATATCATTTTCTTATTT
TTTTCTGAATTAATTTTAATTAAATCGAAATAAGATTCAGAAGCTCGTAAAAAGAAATCCTTAAA
TCCAATGTGACTGAGAATTGGTTAGATGAATATAGATATTTCAAGGTGTCTTGGCGCCAAAAATC
ATGCAAAATTGAGCCGGGCCCTGTAATGCGTTTTTAGCCAAAAAACGTGATGGTAAGTACATGAT
TTCGGCTAAAATTTTGCAAAAATTGACCAAAAAATTTTTTTCTCAATTTTTGGCCACAACACTCA
TAAAAACTCTATAATTTAACACCAAAAATATTGAAGAGTTTTTCAAGCTTCTAATATCATTTTCT
TATTTTTTCTGAATTAATTTTTAATTAAATCGAAATAAGATTCAAAAGCTCGTAAAAAGAAATCC
TTAAATCCAATGTGACTGAGAATTGGTTAGATGAATATAGATAATTCAAGGAGTCACGGCGCCAA
AAATCATGCAAAATTGAGCCGGAGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTA
CATGATTTCGG
Done.