Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010019.1 Corchorus capsularis cultivar CVL-1 contig10040, 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: 60402
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:189 original size:21 final size:21
Alignment explanation
Indices: 151--190 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
141 AAGTTGTTGA
** *
151 AACTTGAAACGGTTGGGTTCC
1 AACTTGAAACCCTGGGGTTCC
172 AACTTGAAACCCTGGGGTT
1 AACTTGAAACCCTGGGGTT
191 TCAAAATCGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (21 bp):
AACTTGAAACCCTGGGGTTCC
Found at i:258 original size:21 final size:21
Alignment explanation
Indices: 234--273 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
224 CTTGTAAAAG
*
234 CTTGAAATCTTGGGGTTTCAA
1 CTTGAAACCTTGGGGTTTCAA
255 CTTGAAACCTTGGGGTTTC
1 CTTGAAACCTTGGGGTTTC
274 TTTATCCTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (21 bp):
CTTGAAACCTTGGGGTTTCAA
Found at i:3246 original size:6 final size:6
Alignment explanation
Indices: 3237--3271 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
3227 ATAAAATAAA
3237 AAATAG AAATAG AAATATAG AAATAG AAATAG AAA
1 AAATAG AAATAG -AA-ATAG AAATAG AAATAG AAA
3272 ACAATTTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 19 0.70
7 4 0.15
8 4 0.15
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (6 bp):
AAATAG
Found at i:3258 original size:14 final size:14
Alignment explanation
Indices: 3226--3267 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
3216 GTTTCATATC
3226 TATA-AAATA-AAA
1 TATAGAAATAGAAA
*
3238 AATAGAAATAGAAA
1 TATAGAAATAGAAA
3252 TATAGAAATAGAAA
1 TATAGAAATAGAAA
3266 TA
1 TA
3268 GAAAACAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 3 0.12
13 5 0.19
14 18 0.69
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (14 bp):
TATAGAAATAGAAA
Found at i:3794 original size:32 final size:32
Alignment explanation
Indices: 3748--3859 Score: 109
Period size: 33 Copynumber: 3.4 Consensus size: 32
3738 TTTGGTCTAA
**
3748 CCGCCCCACCGGGGCGGCCTGCCGTGGCGAAG
1 CCGCCCCAGTGGGGCGGCCTGCCGTGGCGAAG
* **
3780 CCGCCCCAGTGGGGCGGCCTGCCCATGGTAAAG
1 CCGCCCCAGTGGGGCGGCCTG-CCGTGGCGAAG
* *
3813 CCGCCCCAGTGGGGAGGCTCCGCCGTGGCTG-AG
1 CCGCCCCAGTGGGGCGGC-CTGCCGTGGC-GAAG
* *
3846 CCGTCCTAGTGGGG
1 CCGCCCCAGTGGGG
3860 AGGCTCAGTG
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
32 19 0.29
33 44 0.68
34 2 0.03
ACGTcount: A:0.11, C:0.38, G:0.40, T:0.12
Consensus pattern (32 bp):
CCGCCCCAGTGGGGCGGCCTGCCGTGGCGAAG
Found at i:12597 original size:24 final size:23
Alignment explanation
Indices: 12569--12632 Score: 80
Period size: 24 Copynumber: 2.9 Consensus size: 23
12559 ATTTTTTTTC
*
12569 TCAATAGAATATATTCCTTTCTTT
1 TCAATAGAATATATTCCTTTC-CT
*
12593 TCAATAGAATATATTCCATTCCT
1 TCAATAGAATATATTCCTTTCCT
12616 T---TAGAATATATTCCTTT
1 TCAATAGAATATATTCCTTT
12633 GAATTCGATG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 15 0.41
23 2 0.05
24 20 0.54
ACGTcount: A:0.31, C:0.17, G:0.05, T:0.47
Consensus pattern (23 bp):
TCAATAGAATATATTCCTTTCCT
Found at i:12692 original size:48 final size:49
Alignment explanation
Indices: 12618--12779 Score: 175
Period size: 57 Copynumber: 3.2 Consensus size: 49
12608 CCATTCCTTT
* * *
12618 AGAATATATTCCTTTGAATTCGATGTCATTGTCTGAC-AAAGAAGAAGA
1 AGAATATATTCGTTTGAATTCAATGTCATTGTATGACAAAAGAAGAAGA
*
12666 AGAATATATTCGTTTGAATTCAATGTCATTGTTTGACAAAAAAGAAGAAGAAGAAGA
1 AGAATATATTCGTTTGAATTCAATGTCATTGTATGAC-------AA-AAGAAGAAGA
* *
12723 AGAATATATTCGTTTGAATAT-AATGTCATTGTATGACAAAAAAAGCAGA
1 AGAATATATTCGTTTGAAT-TCAATGTCATTGTATGACAAAAGAAGAAGA
12772 AGAATATA
1 AGAATATA
12780 ATGTCATTCA
Statistics
Matches: 98, Mismatches: 6, Indels: 19
0.80 0.05 0.15
Matches are distributed among these distances:
48 34 0.35
49 16 0.16
50 2 0.02
56 1 0.01
57 44 0.45
58 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.30
Consensus pattern (49 bp):
AGAATATATTCGTTTGAATTCAATGTCATTGTATGACAAAAGAAGAAGA
Found at i:12741 original size:57 final size:58
Alignment explanation
Indices: 12656--12775 Score: 199
Period size: 57 Copynumber: 2.1 Consensus size: 58
12646 TTGTCTGACA
*
12656 AAGAAGAAGAAGAATATATTCGTTTGAAT-TCAATGTCATTGTTTGAC-AAAAAAGAAG
1 AAGAAGAAGAAGAATATATTCGTTTGAATAT-AATGTCATTGTATGACAAAAAAAGAAG
*
12713 AAGAAGAAGAAGAATATATTCGTTTGAATATAATGTCATTGTATGACAAAAAAAGCAG
1 AAGAAGAAGAAGAATATATTCGTTTGAATATAATGTCATTGTATGACAAAAAAAGAAG
12771 AAGAA
1 AAGAA
12776 TATAATGTCA
Statistics
Matches: 59, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
57 44 0.75
58 15 0.25
ACGTcount: A:0.48, C:0.07, G:0.19, T:0.26
Consensus pattern (58 bp):
AAGAAGAAGAAGAATATATTCGTTTGAATATAATGTCATTGTATGACAAAAAAAGAAG
Found at i:14417 original size:35 final size:36
Alignment explanation
Indices: 14338--14425 Score: 124
Period size: 37 Copynumber: 2.4 Consensus size: 36
14328 CTAGCATTAG
* *
14338 CATGTTTAGTTATTTTAATTGCCTACTAGTATTTTCT
1 CATGTTTAGTTGTTTTAATTGCCTACTACTA-TTTCT
**
14375 CATGTTTAGTTGTTTTAATTGTGTACTACTA-TTCT
1 CATGTTTAGTTGTTTTAATTGCCTACTACTATTTCT
14410 CATGTTTAGTTGTTTT
1 CATGTTTAGTTGTTTT
14426 TATAATTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
35 20 0.43
37 27 0.57
ACGTcount: A:0.19, C:0.11, G:0.14, T:0.56
Consensus pattern (36 bp):
CATGTTTAGTTGTTTTAATTGCCTACTACTATTTCT
Found at i:17711 original size:338 final size:332
Alignment explanation
Indices: 16906--17735 Score: 793
Period size: 338 Copynumber: 2.5 Consensus size: 332
16896 CCATGATGGT
* * * * * * * *
16906 AAAAATGATCCGAAAAA--TTTCCACAATTTTT-GTCAAAAATACTTACAAAATATATATAATTT
1 AAAAATGA-CCGAAAAATTTTTCCTCAATTTTTAG-CTAAAATAATCATAAAATACAGATAATTC
* * * * * * *
16968 AACACCAAAAAAATTGGAGCACTTTTCACG-TTATTAATATCGGTTTTCATATTTTTTCTGAATT
64 AACACCAAAAAGATTGAAGGAATTTTCACGCTT-CTAATATCGTTTTTCATATTTTTTCAGAATT
* * *
17032 AATTTCTAATTAAATCGAAACAAGATTGAAATGCACATAAAAACAAATCCTTAAATCCAATGTGG
128 AATTTCTAATTAAATCGAAACAAGATTCAAATGCTCATAAAAACAAATCCTTAAATCCAATGTAG
* * *
17097 TCGAAATTTGATTAGATGAATAAAGATATTTCAAGGAGTCTCAACGCCAAAAATCATGCAAAATA
193 TCGAAATTTGATTAGATGAATAAAGATATCTCAAAGAGTCTCAACGCCAAAAATCATACAAAATA
* * * *
17162 GAGCCGTGACCCCAAAACGCGTTTTTTAGCCAAAAATCATGAAGGTTAGTATACGATTTCGGCTA
258 GAGCCGGGACCCCAAAACGCGTTTTTAAGCCAAAAATCATGAAGATTAGTACACGATTTCGGCTA
17227 AAATTTTGCA
323 AAATTTTGCA
** * * * * * *
17237 AAAAATTTCCGAAAAATTTTTCGTCATTTTTTGGCTAAAATACTTATAAAATACAGATAATTTAA
1 AAAAATGACCGAAAAATTTTTCCTCAATTTTTAGCTAAAATAATCATAAAATACAGATAATTCAA
* *
17302 CACCAAAAAGATTGGAGGAATTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTCAGAATTAAT
66 CACCAAAAAGATTGAAGGAATTTTCACGCTTCTAATATCGTTTTTCATATTTTTTCAGAATTAAT
* * * * * *
17366 TTCTAATTAAATTGGAACAAGATTCAAATGCTCGTAAAAACAAGTTCTTAAATCCAATGTAGTTG
131 TTCTAATTAAATCGAAACAAGATTCAAATGCTCATAAAAACAAATCCTTAAATCCAATGTAGTCG
* * ** ***
17431 AGATTTTATAATTTATTAGATGAGTATGGATATCTCAAAGAGTCTTGGCGCCAAAAATCATACAA
196 A-A----AT--TTGATTAGATGAATAAAGATATCTCAAAGAGTCTCAACGCCAAAAATCATACAA
* * ** * * *
17496 AACT-TAGCCGGGACCGCGGAACGCG-TTTTAAGCCAAAAATCGTGATGATTATTACACGATTTC
254 AA-TAGAGCCGGGACCCCAAAACGCGTTTTTAAGCCAAAAATCATGAAGATTAGTACACGATTTC
* *
17559 -G-TAGAATTTTG-T
318 GGCTAAAATTTTGCA
* * * *
17571 AAAAATCGACTCG-AAAGTTATTTCCTCAATTTTTAGCTACAATAATCATAAAA-ATTATATAAT
1 AAAAAT-GAC-CGAAAAATT-TTTCCTCAATTTTTAGCTAAAATAATCATAAAATA-CAGATAAT
** ** * * *
17634 TCAATGCCAAAAAGATTGAAGGGCTTTTCATGCTTCTAATATCGTTTTTCGTATTATTTTCCGAA
62 TCAACACCAAAAAGATTGAAGGAATTTTCACGCTTCTAATATCGTTTTTCATATT-TTTTCAGAA
* * *
17699 TTAATCTCTAATTAAATCGAAACACGATTCACATGCT
126 TTAATTTCTAATTAAATCGAAACAAGATTCAAATGCT
17736 TGTTTTACAA
Statistics
Matches: 409, Mismatches: 72, Indels: 29
0.80 0.14 0.06
Matches are distributed among these distances:
330 8 0.02
331 77 0.19
332 81 0.20
333 3 0.01
334 6 0.01
335 16 0.04
336 82 0.20
337 33 0.08
338 102 0.25
339 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (332 bp):
AAAAATGACCGAAAAATTTTTCCTCAATTTTTAGCTAAAATAATCATAAAATACAGATAATTCAA
CACCAAAAAGATTGAAGGAATTTTCACGCTTCTAATATCGTTTTTCATATTTTTTCAGAATTAAT
TTCTAATTAAATCGAAACAAGATTCAAATGCTCATAAAAACAAATCCTTAAATCCAATGTAGTCG
AAATTTGATTAGATGAATAAAGATATCTCAAAGAGTCTCAACGCCAAAAATCATACAAAATAGAG
CCGGGACCCCAAAACGCGTTTTTAAGCCAAAAATCATGAAGATTAGTACACGATTTCGGCTAAAA
TTTTGCA
Found at i:17910 original size:2 final size:2
Alignment explanation
Indices: 17903--17929 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17893 TACTCATAGA
17903 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
17930 ATTCAACTCC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21386 original size:327 final size:328
Alignment explanation
Indices: 20617--21654 Score: 871
Period size: 327 Copynumber: 3.1 Consensus size: 328
20607 GTAAAAACAA
* * * * ** * **
20617 TGGCTGAGATTTGTTTTGATGAATATAGATATTTCGAGGAGTCTCGGTGCCAAAAATCATTCAAA
1 TGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCACCAAAAATAATGAAAA
* * * * * * * ***
20682 ACTGAACC--GGCCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGATTATTACATGATTTCAA
66 ACTGAGCCGGGGCC-CAGAAACACGCTTTTAGCCAAAAACCGTGATG--TAGTACACGATTTTTG
*** * * *
20745 CTAAAATTTTTCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTAGCCATAATACTCATAAAA
128 CTAAAATTTAAAAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCAT-AAA
* * * * *
20810 AATATATAATTCA-ACAAAAAAAATTGAACGGCTTTATACGCTTTTAATATCG-TTGTTCATATT
192 AATATATAATTCACACCAAAATAATTGAAAGACTTT-TACGCTTTTAATATTGATT-TTCATA--
* * *
20873 TTATTTCTGAACTAATTTCTAATTAAATCGAAATAAGA--TTCAGAT-ACTCGTAAAAACAAA-T
253 TT-TTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTTCAGATGA-TTGTAAAAACAAATT
* *
20934 CATTAAATGCAACG
316 C-TTAAATACAATG
* ** ** *
20948 TGGCTAAGATTTTATTTCATGAATATAGATATTTCAAGGAGTCTCGGCGTCAAATATAATGAAAA
1 TGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCACCAAAAATAATGAAAA
* * * *
21013 ACTGAGTCGGGGCCCCGAAACACGCTTTTGGCCAAAAACCGTGATG-AGTACTCGATTTTCT-CT
66 ACTGAGCCGGGGCCCAGAAACACGCTTTTAGCCAAAAACCGTGATGTAGTACACGATTTT-TGCT
* * *
21076 AAAATTTAAAAAAAAATGACCCGAAAAAT-TTTCCTCAATTTTTGGATAAAATACTCAT-AAAAT
130 AAAATTTAAAAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAT
* * *
21139 ATATAATTTATCTCCAAAATTATTGAAAGACTTTTCACGCTTTTAATATTGATTTTCATATTTTT
195 ATATAATTCA-CACCAAAATAATTGAAAGACTTTT-ACGCTTTTAATATTGATTTTCATATTTTT
21204 CTGAATTAATTTCTAATTAAATCGAAACAAGATTTTCAGATGATTGTAAAAACAAATTCTTAAAT
258 CTGAATTAATTTCTAATTAAATCGAAACAAGATTTTCAGATGATTGTAAAAACAAATTCTTAAAT
21269 ACAATG
323 ACAATG
* * * * * * *
21275 TGGCTCAGATTTGATTAGATGAATATGGATATCTT-AAGGAGTTTTGTCACCAAAAATATTGCAA
1 TGGCTAAGATTTGATTAGATGAATATAGATAT-TTCAAGGAGTCTCGGCACCAAAAATAATGAAA
* ** * ** * * *
21339 AACTGAGCCGTGGCTTAG-AACGCTTTTTTTAGCTAAAAACTGTGATGATTATTACACGATTTTT
65 AACTGAGCCGGGGCCCAGAAACAC-GCTTTTAGCCAAAAACCGTGATG--TAGTACACGATTTTT
* *** *
21403 GTTAAAATTTTGTAAAAATTGGCCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAA
127 GCTAAAATTTAAAAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCAT-AA
* * * **
21468 AATATATATAATTCAACGCCAAAATGATTG-AAGAGCTTTTGAC-ATTTCT-A-A-T-ATCCT-A
191 AA-ATATATAATTC-ACACCAAAATAATTGAAAGA-CTTTT-ACGCTTT-TAATATTGATTTTCA
**
21526 TA-TTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCTT-AGATTCAGATACTCGTAAAA
251 TATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATT-TTCAGA-T--GAT--T-GT-AAA
* *
21589 AACAAATCCTTAAATCCAATG
308 AACAAATTCTTAAATACAATG
* * *
21610 TGGCTGAGATTTGATTAGTTGAATATAGATATTTCAAGTAGTCTC
1 TGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTC
21655 AAAGTCAAAA
Statistics
Matches: 579, Mismatches: 95, Indels: 62
0.79 0.13 0.08
Matches are distributed among these distances:
325 33 0.06
326 20 0.03
327 109 0.19
328 105 0.18
329 44 0.08
330 38 0.07
331 92 0.16
332 29 0.05
333 16 0.03
334 34 0.06
335 59 0.10
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (328 bp):
TGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCACCAAAAATAATGAAAA
ACTGAGCCGGGGCCCAGAAACACGCTTTTAGCCAAAAACCGTGATGTAGTACACGATTTTTGCTA
AAATTTAAAAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAATA
TATAATTCACACCAAAATAATTGAAAGACTTTTACGCTTTTAATATTGATTTTCATATTTTTCTG
AATTAATTTCTAATTAAATCGAAACAAGATTTTCAGATGATTGTAAAAACAAATTCTTAAATACA
ATG
Found at i:24670 original size:15 final size:16
Alignment explanation
Indices: 24652--24681 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
24642 ATAAATAATA
24652 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
24667 ATATTATAATCTAAA
1 ATATTATAATCTAAA
24682 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:24954 original size:36 final size:34
Alignment explanation
Indices: 24913--24979 Score: 107
Period size: 36 Copynumber: 1.9 Consensus size: 34
24903 TAGTAAGATA
24913 GTAAGATATATATATATATATATATATATATGTCAC
1 GTAAGATATATATATATAT-TATA-ATATATGTCAC
*
24949 GTAAGATATATATATATATTATAATTTATGT
1 GTAAGATATATATATATATTATAATATATGT
24980 TTTATACATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 7 0.23
35 4 0.13
36 19 0.63
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (34 bp):
GTAAGATATATATATATATTATAATATATGTCAC
Found at i:24963 original size:2 final size:2
Alignment explanation
Indices: 24918--24943 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
24908 AGATAGTAAG
24918 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
24944 GTCACGTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27781 original size:26 final size:27
Alignment explanation
Indices: 27730--27784 Score: 94
Period size: 26 Copynumber: 2.1 Consensus size: 27
27720 TACAAATCCA
27730 ATGTAAACTCAATTGGCAAATTGGGTC
1 ATGTAAACTCAATTGGCAAATTGGGTC
*
27757 ATGTAAACTTAATT-GCAAATTGGGTC
1 ATGTAAACTCAATTGGCAAATTGGGTC
27783 AT
1 AT
27785 CGGAGTTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.33
Consensus pattern (27 bp):
ATGTAAACTCAATTGGCAAATTGGGTC
Found at i:28714 original size:11 final size:11
Alignment explanation
Indices: 28700--28737 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
28690 ATTCATAACA
28700 AATTTATAATT
1 AATTTATAATT
28711 AATTTATAATT
1 AATTTATAATT
28722 -ATTTGATAATT
1 AATTT-ATAATT
*
28733 TATTT
1 AATTT
28738 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:31411 original size:19 final size:19
Alignment explanation
Indices: 31387--31426 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
31377 AAACAACAAC
31387 AACAACAACAGCCACCACA
1 AACAACAACAGCCACCACA
31406 AACAACAACAGCCACCACA
1 AACAACAACAGCCACCACA
31425 AA
1 AA
31427 TCCACAATAG
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:0.55, C:0.40, G:0.05, T:0.00
Consensus pattern (19 bp):
AACAACAACAGCCACCACA
Found at i:31411 original size:22 final size:20
Alignment explanation
Indices: 31382--31426 Score: 74
Period size: 19 Copynumber: 2.2 Consensus size: 20
31372 AAGCCAAACA
31382 ACAACAACAACAACAGCCACC
1 ACAA-AACAACAACAGCCACC
31403 AC-AAACAACAACAGCCACC
1 ACAAAACAACAACAGCCACC
31422 ACAAA
1 ACAAA
31427 TCCACAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 18 0.78
20 3 0.13
21 2 0.09
ACGTcount: A:0.56, C:0.40, G:0.04, T:0.00
Consensus pattern (20 bp):
ACAAAACAACAACAGCCACC
Found at i:33131 original size:30 final size:30
Alignment explanation
Indices: 33088--33442 Score: 422
Period size: 30 Copynumber: 11.7 Consensus size: 30
33078 ATAAATCTCC
* *
33088 ATTGAAACCAGAAGTTGTCATAATCTTGCA
1 ATTGACACCAGAAGTTGTCATGATCTTGCA
* *
33118 ATTGACACGAGAAGTTGTCATGATTTTGCA
1 ATTGACACCAGAAGTTGTCATGATCTTGCA
* *
33148 ATTGACACGAGAAGTTGTCATAATCTTGCA
1 ATTGACACCAGAAGTTGTCATGATCTTGCA
* * * *
33178 ATTGAGACGAGAAGTTGTCAATGGTCTTACA
1 ATTGACACCAGAAGTTGTC-ATGATCTTGCA
*
33209 ATTGACACCAGAAGTTGTCAATGATTTTGCA
1 ATTGACACCAGAAGTTGTC-ATGATCTTGCA
*
33240 ATTGACACCATAAGTTGTCATGATCTTGCA
1 ATTGACACCAGAAGTTGTCATGATCTTGCA
* * * *
33270 ATTGACACCAGAAGATGTCATAGTTTTATTCA
1 ATTGACACCAGAAGTTGTCAT-GATCT-TGCA
* * *
33302 TTTGACACCATAAGTTGTCATGATCTTACA
1 ATTGACACCAGAAGTTGTCATGATCTTGCA
* * * *
33332 ATTGAGACGAGAAGTTGTCAATGGTCTTACA
1 ATTGACACCAGAAGTTGTC-ATGATCTTGCA
*
33363 ATTGACACCAGAAGTTGTCATGATCTTACA
1 ATTGACACCAGAAGTTGTCATGATCTTGCA
* *
33393 AATGACACCAAAAGTTGTCATGATCTTGCA
1 ATTGACACCAGAAGTTGTCATGATCTTGCA
*
33423 ATTGACACCAGAAGATGTCA
1 ATTGACACCAGAAGTTGTCA
33443 CCAGAAGATG
Statistics
Matches: 279, Mismatches: 42, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
30 173 0.62
31 85 0.30
32 21 0.08
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (30 bp):
ATTGACACCAGAAGTTGTCATGATCTTGCA
Found at i:33446 original size:13 final size:13
Alignment explanation
Indices: 33428--33455 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
33418 TTGCAATTGA
33428 CACCAGAAGATGT
1 CACCAGAAGATGT
33441 CACCAGAAGATGT
1 CACCAGAAGATGT
33454 CA
1 CA
33456 TGATCTTGCA
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:0.39, C:0.25, G:0.21, T:0.14
Consensus pattern (13 bp):
CACCAGAAGATGT
Found at i:33459 original size:43 final size:43
Alignment explanation
Indices: 33398--33485 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
33388 TTACAAATGA
*
33398 CACCAAAAGTTGTCATGATCTTGCAATTGACACCAGAAGATGT
1 CACCAAAAGATGTCATGATCTTGCAATTGACACCAGAAGATGT
*
33441 CACCAGAAGATGTCATGATCTTGCAATTGACACCAGAAGATGT
1 CACCAAAAGATGTCATGATCTTGCAATTGACACCAGAAGATGT
33484 CA
1 CA
33486 TGATCTTGCA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (43 bp):
CACCAAAAGATGTCATGATCTTGCAATTGACACCAGAAGATGT
Found at i:33477 original size:30 final size:30
Alignment explanation
Indices: 33441--33639 Score: 308
Period size: 30 Copynumber: 6.6 Consensus size: 30
33431 CAGAAGATGT
33441 CACCAGAAGATGTCATGATCTTGCAATTGA
1 CACCAGAAGATGTCATGATCTTGCAATTGA
33471 CACCAGAAGATGTCATGATCTTGCAATTGA
1 CACCAGAAGATGTCATGATCTTGCAATTGA
*
33501 CACCAGAAGTTGTCATGATCTTGCAATTGA
1 CACCAGAAGATGTCATGATCTTGCAATTGA
33531 CACCAGAAGATGTCATGATCTTGCAATTGA
1 CACCAGAAGATGTCATGATCTTGCAATTGA
* * **
33561 CACCAGAAGATGTCATTATCCTATAATTGA
1 CACCAGAAGATGTCATGATCTTGCAATTGA
* * * *
33591 CACCAGAAGTTGTCGTGATCCTACAATTGA
1 CACCAGAAGATGTCATGATCTTGCAATTGA
*
33621 CACCAGAAGTTGTCATGAT
1 CACCAGAAGATGTCATGAT
33640 TTTACCTTTC
Statistics
Matches: 158, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 158 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (30 bp):
CACCAGAAGATGTCATGATCTTGCAATTGA
Found at i:33487 original size:73 final size:73
Alignment explanation
Indices: 33368--33515 Score: 242
Period size: 73 Copynumber: 2.0 Consensus size: 73
33358 TTACAATTGA
* *
33368 CACCAGAAGTTGTCATGATCTTACAAATGACACCAAAAGTTGTCATGATCTTGCAATTGACACCA
1 CACCAGAAGATGTCATGATCTTACAAATGACACCAAAAGATGTCATGATCTTGCAATTGACACCA
33433 GAAGATGT
66 GAAGATGT
* * *
33441 CACCAGAAGATGTCATGATCTTGCAATTGACACCAGAAGATGTCATGATCTTGCAATTGACACCA
1 CACCAGAAGATGTCATGATCTTACAAATGACACCAAAAGATGTCATGATCTTGCAATTGACACCA
*
33506 GAAGTTGT
66 GAAGATGT
33514 CA
1 CA
33516 TGATCTTGCA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (73 bp):
CACCAGAAGATGTCATGATCTTACAAATGACACCAAAAGATGTCATGATCTTGCAATTGACACCA
GAAGATGT
Found at i:52623 original size:15 final size:15
Alignment explanation
Indices: 52603--52633 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
52593 AAGAGATGAT
52603 TGAAGAAATTAACCC
1 TGAAGAAATTAACCC
52618 TGAAGAAATTAACCC
1 TGAAGAAATTAACCC
52633 T
1 T
52634 TGAACATAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (15 bp):
TGAAGAAATTAACCC
Found at i:53059 original size:95 final size:95
Alignment explanation
Indices: 52895--53085 Score: 328
Period size: 95 Copynumber: 2.0 Consensus size: 95
52885 TGAAGTTACT
* *
52895 TTGCGACAGTTGCAGGTCTGCATCAAAAGTAGAGGAAAACTCCCACAACAGAAAACTTGAAGATT
1 TTGCGACAGTTGCAGGTCTGCATCAAAAGTAGAGGAAAACTACCACAACAGAAAACTTGAAGATA
* *
52960 AGGCAGCGACATCAGGCACTAAAAAGGTCA
66 AGGCAGCGACATCAGACACTAAAAAAGTCA
**
52990 TTGCGACAGTTGCAGGTCTGCATCAAAAGTAGAGGAAAACTACCACAATGGAAAACTTGAAGATA
1 TTGCGACAGTTGCAGGTCTGCATCAAAAGTAGAGGAAAACTACCACAACAGAAAACTTGAAGATA
53055 AGGCAGCGACATCAGACACTAAAAAAGTCA
66 AGGCAGCGACATCAGACACTAAAAAAGTCA
53085 T
1 T
53086 CTAATGAACT
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
95 90 1.00
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.17
Consensus pattern (95 bp):
TTGCGACAGTTGCAGGTCTGCATCAAAAGTAGAGGAAAACTACCACAACAGAAAACTTGAAGATA
AGGCAGCGACATCAGACACTAAAAAAGTCA
Found at i:54849 original size:2 final size:2
Alignment explanation
Indices: 54842--54869 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
54832 CAGTGAGGTA
54842 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54870 CTAATAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.