Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009654.1 Corchorus capsularis cultivar CVL-1 contig09675, 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: 38993
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:1735 original size:7 final size:7
Alignment explanation
Indices: 1723--1763 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
1713 ATACTGTATA
1723 ATACTAT
1 ATACTAT
1730 ATACTAT
1 ATACTAT
1737 ATACTAT
1 ATACTAT
1744 ATACTAT
1 ATACTAT
1751 ATACTAT
1 ATACTAT
1758 ATACTA
1 ATACTA
1764 CATTTAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (7 bp):
ATACTAT
Found at i:5726 original size:2 final size:2
Alignment explanation
Indices: 5714--5744 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5704 GACAATGTAT
*
5714 TA TA TA CA 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 T
5745 CATTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5998 original size:2 final size:2
Alignment explanation
Indices: 5991--6015 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5981 CTTCCAACCC
5991 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 T
6016 GTTATTGCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7996 original size:88 final size:87
Alignment explanation
Indices: 7877--8056 Score: 324
Period size: 88 Copynumber: 2.1 Consensus size: 87
7867 AATCTGCAAC
*
7877 AATACTCATAAATAAAATTGGGAGTCTATCAAAGATTACAAAATGTTCATTGTCTAAAACAGAGA
1 AATATTCATAAATAAAATTGGGAGTCTATCAAAGATTACAAAATGTTCATTGTCTAAAACAGAGA
*
7942 GCTCTCTTCGAAAATTTGCCAT
66 GCTCTCTTCAAAAATTTGCCAT
*
7964 AATATTCATAAATTAAATTAGGGAGTCTATCAAAGATTACAAAATGTTCATTGTCTAAAACAGAG
1 AATATTCATAAATAAAATT-GGGAGTCTATCAAAGATTACAAAATGTTCATTGTCTAAAACAGAG
8029 AGCTCTCTTCAAAAATTTGCCAT
65 AGCTCTCTTCAAAAATTTGCCAT
8052 AATAT
1 AATAT
8057 CAGCAGCCCA
Statistics
Matches: 89, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
87 17 0.19
88 72 0.81
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (87 bp):
AATATTCATAAATAAAATTGGGAGTCTATCAAAGATTACAAAATGTTCATTGTCTAAAACAGAGA
GCTCTCTTCAAAAATTTGCCAT
Found at i:17254 original size:20 final size:20
Alignment explanation
Indices: 17229--17299 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 20
17219 TTTATTTCTG
17229 GGTTTTTCCTAAAAGGATTA
1 GGTTTTTCCTAAAAGGATTA
** *
17249 GGTTTTACTTTTCCTACCAGTATTA
1 GG---T--TTTTCCTAAAAGGATTA
*
17274 GGATTTTCCTAAAAGGATTA
1 GGTTTTTCCTAAAAGGATTA
17294 GGTTTT
1 GGTTTT
17300 CCTTTTCCTA
Statistics
Matches: 38, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
20 21 0.55
23 1 0.03
25 16 0.42
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.44
Consensus pattern (20 bp):
GGTTTTTCCTAAAAGGATTA
Found at i:17273 original size:25 final size:25
Alignment explanation
Indices: 17245--17326 Score: 84
Period size: 25 Copynumber: 3.4 Consensus size: 25
17235 TCCTAAAAGG
17245 ATTAGGTTTTACTTTTCCTACCAGT
1 ATTAGGTTTTACTTTTCCTACCAGT
** *
17270 ATTAGG----A-TTTTCCTAAAAGG
1 ATTAGGTTTTACTTTTCCTACCAGT
*
17290 ATTAGGTTTTCCTTTTCCTACCAGT
1 ATTAGGTTTTACTTTTCCTACCAGT
17315 ATTAGGATTTTA
1 ATTAGG-TTTTA
17327 AATTAAGTGT
Statistics
Matches: 43, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
20 16 0.37
21 1 0.02
25 22 0.51
26 4 0.09
ACGTcount: A:0.24, C:0.16, G:0.15, T:0.45
Consensus pattern (25 bp):
ATTAGGTTTTACTTTTCCTACCAGT
Found at i:17283 original size:45 final size:45
Alignment explanation
Indices: 17232--17325 Score: 179
Period size: 45 Copynumber: 2.1 Consensus size: 45
17222 ATTTCTGGGT
17232 TTTTCCTAAAAGGATTAGGTTTTACTTTTCCTACCAGTATTAGGA
1 TTTTCCTAAAAGGATTAGGTTTTACTTTTCCTACCAGTATTAGGA
*
17277 TTTTCCTAAAAGGATTAGGTTTTCCTTTTCCTACCAGTATTAGGA
1 TTTTCCTAAAAGGATTAGGTTTTACTTTTCCTACCAGTATTAGGA
17322 TTTT
1 TTTT
17326 AAATTAAGTG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.24, C:0.16, G:0.15, T:0.45
Consensus pattern (45 bp):
TTTTCCTAAAAGGATTAGGTTTTACTTTTCCTACCAGTATTAGGA
Found at i:33423 original size:50 final size:50
Alignment explanation
Indices: 33348--33555 Score: 362
Period size: 50 Copynumber: 4.2 Consensus size: 50
33338 AAAATTTGAA
* *
33348 ACCGATGGGAGCTGACTCCCCGAACATGTAAAAGATTTAGTAATTAGGAG
1 ACCGATGGGAGCTGACTCCCCGAACATCTAAAAAATTTAGTAATTAGGAG
* *
33398 ACCGATGGGAGCTGACTCCCTGAACATCTAAAAAATTTAGTAATAAGGAG
1 ACCGATGGGAGCTGACTCCCCGAACATCTAAAAAATTTAGTAATTAGGAG
33448 ACCGATGGGAGCTGACTCCCCGAACATCTAAAAAATTTAGTAATTAGGAG
1 ACCGATGGGAGCTGACTCCCCGAACATCTAAAAAATTTAGTAATTAGGAG
* *
33498 ACCGATGGGAGCTGACTCCCCTAACATCTAAAAAATTTAGTAATTAGAAG
1 ACCGATGGGAGCTGACTCCCCGAACATCTAAAAAATTTAGTAATTAGGAG
33548 ACCGATGG
1 ACCGATGG
33556 ACATCTAAAA
Statistics
Matches: 150, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 150 1.00
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (50 bp):
ACCGATGGGAGCTGACTCCCCGAACATCTAAAAAATTTAGTAATTAGGAG
Found at i:33982 original size:224 final size:217
Alignment explanation
Indices: 33599--34001 Score: 626
Period size: 224 Copynumber: 1.8 Consensus size: 217
33589 AGATGCGGAA
* * *
33599 GATACAAGGCAGACATGGAGGGTACTTTGACTACATAGACAACAATCATAGTGATAGACACGGAA
1 GATACAAAGCAGACATGGAGGGTACTTTGACAACATAGACAACAATCATAGTGACAGACACGGAA
* *
33664 GATACAGTAAATGGCCAGCAGCTGCAAGTGAAGTAAGTTTATCATATTCTCAAATTTCCATTCTT
66 GATACAGTAAATGGCCAGCAGCTGCAAATGAAGTAAGTTTATAATATTCTCAAATTTCCATTCTT
* * *
33729 TACGATAAAATGTTTTATTTGTGAATATTCCATTGCATGTGGCTGATAAAATCTTTTCTTTTTTT
131 TACAATAAAATGTTTTATTTGTGAATATTCCACTGCATGTGGCTAATAAAATCTTTTCTTTTTTT
33794 CTCCCAGGTAGTTCTTGTGGCT
196 CTCCCAGGTAGTTCTTGTGGCT
*
33816 GATACAAAGCAGACATGGAGGGTACTTTGACAACATAGACAACAATCGTAGTGACAGACACGGAA
1 GATACAAAGCAGACATGGAGGGTACTTTGACAACATAGACAACAATCATAGTGACAGACAC----
* * *
33881 GTGGAAGATGCAGTAAATGGCCATCAGCTGCAAATGAAAGTAAGTTTATAATATTCTTAAATTTC
62 --GGAAGATACAGTAAATGGCCAGCAGCTGCAAATG-AAGTAAGTTTATAATATTCTCAAATTTC
*
33946 CATTCTTTGCAATAAAATGTTTTATTTGTGAATATTCCACTGCATGTGGCTAATAA
124 CATTCTTTACAATAAAATGTTTTATTTGTGAATATTCCACTGCATGTGGCTAATAA
34002 TTTTTTTTCC
Statistics
Matches: 166, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
217 57 0.34
223 31 0.19
224 78 0.47
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (217 bp):
GATACAAAGCAGACATGGAGGGTACTTTGACAACATAGACAACAATCATAGTGACAGACACGGAA
GATACAGTAAATGGCCAGCAGCTGCAAATGAAGTAAGTTTATAATATTCTCAAATTTCCATTCTT
TACAATAAAATGTTTTATTTGTGAATATTCCACTGCATGTGGCTAATAAAATCTTTTCTTTTTTT
CTCCCAGGTAGTTCTTGTGGCT
Found at i:35189 original size:42 final size:40
Alignment explanation
Indices: 35102--35190 Score: 106
Period size: 42 Copynumber: 2.2 Consensus size: 40
35092 GCTATATTTT
* *
35102 TGACAAATTAGGCCTGAATAATTTAATTGGGACATAATTC
1 TGACGAATTAGGCCTGAATAATTTAATCGGGACATAATTC
* * * *
35142 AGACGAATTAGGCCTGAAAATAATTTTATCGGGCCATAGTTC
1 TGACGAATTAGGCCTG--AATAATTTAATCGGGACATAATTC
35184 TGACGAA
1 TGACGAA
35191 CTATACCTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 14 0.35
42 26 0.65
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (40 bp):
TGACGAATTAGGCCTGAATAATTTAATCGGGACATAATTC
Found at i:36429 original size:48 final size:48
Alignment explanation
Indices: 36320--36429 Score: 112
Period size: 48 Copynumber: 2.3 Consensus size: 48
36310 CCAAAAGATG
* * * *
36320 AAGGCCAACCATCACGACTTTTGGAAGCAAAAATTGGCCGAAATTACA
1 AAGGCTAACCATCACCACTTTTGGAAGCAAAAATTCGCCGAAAATACA
** ** * * *
36368 AAGGCTATTCATCACCACTTTTGGGGGCCAAAATTCGCTGAAAATCCA
1 AAGGCTAACCATCACCACTTTTGGAAGCAAAAATTCGCCGAAAATACA
*
36416 AAGGTTAACCATCA
1 AAGGCTAACCATCA
36430 AGACATCCGG
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (48 bp):
AAGGCTAACCATCACCACTTTTGGAAGCAAAAATTCGCCGAAAATACA
Found at i:36826 original size:48 final size:48
Alignment explanation
Indices: 36616--36826 Score: 126
Period size: 48 Copynumber: 4.5 Consensus size: 48
36606 TTGGGGACCG
* * * * * *
36616 AAATTGGCCG-GAAGTCCAAATGCTAATCATCACCACTTTTGGAGGCCA
1 AAATTGGCCGAAAAG-CCAAAGGCTAACCATCACGACTTTCGAAGGCCA
* * * * * * *
36664 AAATTGACTGAAAAGCTAATGGCTAACCATCATGACTTTC-AAGGGCT
1 AAATTGGCCGAAAAGCCAAAGGCTAACCATCACGACTTTCGAAGGCCA
* * ** * * * *
36711 AAAGT-G-TGAAAATTCAAAGGTTAACCATCAGGATTTTCGAGGGCCA
1 AAATTGGCCGAAAAGCCAAAGGCTAACCATCACGACTTTCGAAGGCCA
* * ** * *
36757 AGAA-TGACCGAGAAGTTAAAGGCTGATCATCACGACTTTCGAAGGCCA
1 A-AATTGGCCGAAAAGCCAAAGGCTAACCATCACGACTTTCGAAGGCCA
36805 AAATTGGCCGAAAAGCCAAAGG
1 AAATTGGCCGAAAAGCCAAAGG
36827 TTGTTAGTAC
Statistics
Matches: 117, Mismatches: 40, Indels: 12
0.69 0.24 0.07
Matches are distributed among these distances:
45 25 0.21
46 6 0.05
47 12 0.10
48 71 0.61
49 3 0.03
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (48 bp):
AAATTGGCCGAAAAGCCAAAGGCTAACCATCACGACTTTCGAAGGCCA
Found at i:37716 original size:333 final size:331
Alignment explanation
Indices: 36829--38992 Score: 2213
Period size: 333 Copynumber: 6.5 Consensus size: 331
36819 GCCAAAGGTT
* ** * *
36829 GTTAGTACACGATTTCAGCTAAAATTTTGC-AAAATTG-ACTTGAAAGATTTTTCCTTAATGTTT
1 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAAC-TGTTAGATTTTTCC-TCATTTTT
** * * * * *
36892 T-GTTAGAATACTCATAAAGAGTATATAATTCAACGACAAAAAAGATTGAAGGGCTTTTCATGCT
64 TAGCCACAATACTCATAAAGAATATATAATTCAACG-CCAAAAAGATTGAAGGGTTTTTCACGCT
* * * * * * *
36956 TCAAATAATGGTTTTT-C---TTTTTC-AAATTAACTGCTGATTAAATCGAAACAAGATTCAAAT
128 TCTAAT-ATCGTTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAATCTAAACAAGATTCAAAT
* ** * * * *
37016 GCTCGT-AAAACAAATCCTTTAATCCAATGTGGTTGACATTTGGTTAGATTAATACAGATATTAC
192 GCTCGTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTAGATGAATATAGATATTTC
* * * * * * * * *
37080 GA-GTC-A-TGGCGCCAAAAATCATGCAAAATTGAGGCAGCGCCATGAAACACGTTTTTAACCAA
257 AAGGACTATTGGCGCCAAAAATCATGCAAAATTGAGTCGGGGCC-CGGAACGCGTTTTTAGCCAA
*
37142 AAATTGT-AT-
321 AAACTGTGATG
* * * * * * * *
37151 -CT--TACACGATTTTGCCTAAAATTTTGCAAGAATTGACCCGTAAGATTTTTCCTCAATTTTTA
1 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAACTGTTAGATTTTTCCTCATTTTTTA
** * * * * * *
37213 GTGAAAATACTCATAAAAAATGTATAATTCAACGCCAAAAAGATTGAAGGATTTTTCACGTTTCA
66 GCCACAATACTCATAAAGAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACGCTTCT
* * ** * * *
37278 AATATCGTTTTCCCTATTTTTTCTGTATTAATTTCTGTTTAAATCTAAACATGATCCATATGCTC
131 AATATCGTTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAATCTAAACAAGATTCAAATGCTC
* * * * * *
37343 GTAAAAATAAATTCTTAAACCCAAGGT-AGCTGAAATTTGGTTAGGT-AAGTATAGATATTTCAA
196 GTAAAAACAAATCCTTAAATCCAATGTGA-CTGAGATTTGGTTAGATGAA-TATAGATATTTCAA
* *
37406 GGACTATTGGCGCTAAAAATCATGCAAAATTGAGTCGGGGCCTCGGAACGTGTTTTTAGCCAAAA
259 GGACTATTGGCGCCAAAAATCATGCAAAATTGAGTCGGGGCC-CGGAACGCGTTTTTAGCCAAAA
37471 ACTGTGATG
323 ACTGTGATG
*
37480 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCCTCATTTTTTA
1 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAACTGTTAGATTTTTCCTCATTTTTTA
* * * * *
37545 GGCACAATACTAATAAGGAATATATAATTCAATGCCAAAAAGATTGAAGGGTTTTTTCACGCATC
66 GCCACAATACTCATAAAGAATATATAATTCAACGCCAAAAAGATTGAAGGG-TTTTTCACGCTTC
* *
37610 TAATATCGTTTTTCCTATTTTTTCTGAATTAATTTATAATTAAATCTAAACAAGATTTAAATGCT
130 TAATATCGTTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAATCTAAACAAGATTCAAATGCT
* * * * *
37675 CGTAAAAACAAATCCTCAAATCCATTGTGATTGAGATTTGGTAAGATTAATATAGATATTTCAAG
195 CGTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAG
* ** * * * *
37740 GATTCATAT--CGCCAAAAATCATGCAAAACGGAGCCGGTGTCCCGGAACCCATTTTTAGCCAAA
260 GACT-AT-TGGCGCCAAAAATCATGCAAAATTGAGTCGG-GGCCCGGAACGCGTTTTTAGCC-AA
37803 AAACTGTGATG
321 AAACTGTGATG
* *
37814 GTTAGTACACGATTTCGGCTAAAATTTTGCGAAAATTG-ACT-TATCAGATTTTTCCTCAATTTT
1 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAACTGT-T-AGATTTTTCCTCATTTTT
* * * *
37877 TAGCCACAATACTCATAAAAAAATATATATTTCAACGCCAAAAACATTGAAGGGTATTTT-ATGC
64 TAGCCACAATACTCAT-AAAGAATATATAATTCAACGCCAAAAAGATTGAAGGGT-TTTTCACGC
* * *
37941 TTCTAATATCG-TTTTCCT-TTATTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGA
127 TTCTAATATCGTTTTTCCTATT-TTTTCTGAATTAATTTCTAATTAAATCTAAACAAGATTCAAA
* * * *
38004 TGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCAGAGATTTGGTTAGATGAATTTAGAAATTT
191 TGCTCGTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTAGATGAATATAGATATTT
* * * * * *
38069 TAAGGAGTCTTGGCACCAAAAATCATGCAAAATTGAGTCGGGGCCCCGGAATGCGTTTTCAGCCA
256 CAAGGACTATTGGCGCCAAAAATCATGCAAAATTGAGTCGGGG-CCCGGAACGCGTTTTTAGCCA
38134 AAAACTGTGATG
320 AAAACTGTGATG
* * *
38146 GTTAGTACACGATTTAGACTAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCCTCATTTTTTA
1 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAACTGTTAGATTTTTCCTCATTTTTTA
* * ** * *
38211 GCCACAATAGTAATATGGAATATATATGATTCAATGCCAAAAAGATTGAAGGGTTTTTCACGCAT
66 GCCACAATACTCATAAAGAATATATA--ATTCAACGCCAAAAAGATTGAAGGGTTTTTCACGCTT
* * *
38276 CTAATATCGTTTTCCCTATTTTTTCTGAATTAATTTATAATTAAATCTAAACAAGATTTAAATGC
129 CTAATATCGTTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAATCTAAACAAGATTCAAATGC
* * * * * *
38341 TCGTAAAAACAAATCCTTAAATCCATTTTGATTGAGATTTCGTAAGATCAATATAGATATTTCAA
194 TCGTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAA
* * ** * * * * *
38406 GGATTCTTAACGCCAAAAATCATGCAAAATGGAGCCGGTGCCCTGGAACCCATTTTTAGCCAAAA
259 GGACTATTGGCGCCAAAAATCATGCAAAATTGAGTCGGGGCCC-GGAACGCGTTTTTAGCC-AAA
38471 AACTGTGAT-
322 AACTGTGATG
* *** * *
38480 G---GTACACGATTTCGGCTAAAATTTTGCAAACATTG-ACCCATCGAATTTTTCCTCAATTTTT
1 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAACTGTTAG-ATTTTTCCTCATTTTTT
* * * *
38541 AGCCACAATACTCATAAAAAAATATATATTTCAACGCCAAAAAGATTGAAGGGTTTTTTATGCTT
65 AGCCACAATACTCAT-AAAGAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACGCTT
* * * *
38606 CTAATATCGTTTTTCCT-TTATTTTCCGAATTAATATCTAATTAAATCGAAACAAGATTCAGATG
129 CTAATATCGTTTTTCCTATT-TTTTCTGAATTAATTTCTAATTAAATCTAAACAAGATTCAAATG
* * * * *
38670 CTCGTAAAAACAAATCCTTAAATCCCATGTGGCAGAGATTTGGTTAGATGAACT-TTGATATTTT
193 CTCGTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTAGATGAA-TATAGATATTTC
* * * ** *
38734 AAGGAGTCTTGGCACCAAAAATCATGCAAAATTGCTTCGGGGCCCCGGAATGCGTTTTCT-GCCA
257 AAGGACTATTGGCGCCAAAAATCATGCAAAATTGAGTCGGGG-CCCGGAACGCGTTTT-TAGCCA
*
38798 AAAACCGTGATGG
320 AAAACTGTGAT-G
* *
38811 TTAGTTAGTACACGATTTCGGTTAAAATTTTGCAAAAATTGAACTGTTTGATTTTT-CTCATTTT
1 ---GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAACTGTTAGATTTTTCCTCATTTT
* ** ** * * **
38875 TTAGCCACAATACTAATATGGAATATATATGATTCAATTCC-AAAATATTGAAAGGCCTTTCACG
63 TTAGCCACAATACTCATAAAGAATATATA--ATTCAACGCCAAAAAGATTGAAGGGTTTTTCACG
* *
38939 CATCTAATATCGTTTTTCCTATTTTTTCTGAATTAATTTATAATTAAATCTAAA
126 CTTCTAATATCGTTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAATCTAAA
38993 T
Statistics
Matches: 1521, Mismatches: 260, Indels: 108
0.81 0.14 0.06
Matches are distributed among these distances:
318 7 0.00
319 58 0.04
320 47 0.03
321 2 0.00
322 6 0.00
323 36 0.02
324 44 0.03
325 2 0.00
326 1 0.00
327 52 0.03
328 2 0.00
329 13 0.01
330 187 0.12
331 75 0.05
332 190 0.12
333 351 0.23
334 251 0.17
335 60 0.04
336 86 0.06
337 47 0.03
338 4 0.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (331 bp):
GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAACTGTTAGATTTTTCCTCATTTTTTA
GCCACAATACTCATAAAGAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACGCTTCT
AATATCGTTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAATCTAAACAAGATTCAAATGCTC
GTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGG
ACTATTGGCGCCAAAAATCATGCAAAATTGAGTCGGGGCCCGGAACGCGTTTTTAGCCAAAAACT
GTGATG
Found at i:38465 original size:667 final size:663
Alignment explanation
Indices: 36992--38992 Score: 2870
Period size: 666 Copynumber: 3.0 Consensus size: 663
36982 TTAACTGCTG
* * * * * *
36992 ATTAAATCGAAACAAGATTCAAATGCTCGT-AAAACAAATCCTTTAATCCAATGTGGTTGACATT
1 ATTAAATCTAAACAAGATTTAAATGCTCGTAAAAACAAATCCTTAAATCCATTGTGATTGAGATT
* * * * ** * * * *
37056 TGGTTAGATTAATACAGATA-TT--ACGAGTCATGGCGCCAAAAATCATGCAAAATTGAGGCAGC
66 TGGTAAGATTAATATAGATATTTCAAGGATTCATAACGCCAAAAATCATGCAAAATGGAGCCGGT
* * * * * * * * *
37118 GCCATGAAACACGTTTTTAACC-AAAAATTGT-ATCT-TACACGATTTTGCCTAAAATTTTGCAA
131 GCCCTGGAACCCATTTTTAGCCAAAAAACTGTGATGTGTACACGATTTCGGCTAAAATTTTGCAA
* * ** * * *
37180 GAATTGACCCGTAAGATTTTTCCTCAATTTTTAGTGAAAATACTCAT-AAAAAATGTATAATTCA
196 -AATTGACCCATCAGATTTTTCCTCAATTTTTAGCCACAATACTCATAAAAAAATATATATTTCA
* * * * * *
37244 ACGCCAAAAAGATTGAAGGATTTTTCACGTTTCAAATATCGTTTTCCCTATT-TTTTCTGTATTA
260 ACGCCAAAAAGATTGAAGGGTTTTT-ATGCTTCTAATATCGTTTT-CCT-TTATTTTCCGAATTA
** * * * * * * * * *
37308 ATTTCTGTTTAAATCTAAACATGATCCATATGCTCGTAAAAATAAATTCTTAAACCCAAGGTAGC
322 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
* * * * * * * * * *
37373 TGAAATTTGGTTAGGT-AAGTATAGATATTTCAAGGACTATTGGCGCTAAAAATCATGCAAAATT
387 AGAGATTTGGTTAGATGAACTTTAGATATTTTAAGGAGTCTTGGCACCAAAAATCATGCAAAATT
* * * *
37437 GAGTCGGGGCCTCGGAACGTGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAA
452 GAGTCGGGGCCCCGGAATGCGTTTTCAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAA
* *
37502 AATTTTGCAAAAATTGAACTGTTTGATTTTTCCTCATTTTTTAGGCACAATACTAATAAGGAATA
517 AATTTTGCAAAAATTGAACTGTTTGATTTTTCCTCATTTTTTAGCCACAATACTAATATGGAATA
37567 TATA--ATTCAATGCCAAAAAGATTGAAGGGTTTTTTCACGCATCTAATATCGTTTTTCCTATTT
582 TATATGATTCAATGCCAAAAAGATTGAAGGG-TTTTTCACGCATCTAATATCGTTTTTCCTATTT
37630 TTTCTGAATTAATTTATA
646 TTTCTGAATTAATTTATA
*
37648 ATTAAATCTAAACAAGATTTAAATGCTCGTAAAAACAAATCCTCAAATCCATTGTGATTGAGATT
1 ATTAAATCTAAACAAGATTTAAATGCTCGTAAAAACAAATCCTTAAATCCATTGTGATTGAGATT
* *
37713 TGGTAAGATTAATATAGATATTTCAAGGATTCATATCGCCAAAAATCATGCAAAACGGAGCCGGT
66 TGGTAAGATTAATATAGATATTTCAAGGATTCATAACGCCAAAAATCATGCAAAATGGAGCCGGT
37778 GTCCC-GGAACCCATTTTTAGCCAAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTT
131 G-CCCTGGAACCCATTTTTAGCCAAAAAACTGTGAT-G-T-GTACACGATTTCGGCTAAAATTTT
**
37842 GCGAAAATTGACTTATCAGATTTTTCCTCAATTTTTAGCCACAATACTCATAAAAAAATATATAT
192 GC-AAAATTGACCCATCAGATTTTTCCTCAATTTTTAGCCACAATACTCATAAAAAAATATATAT
*
37907 TTCAACGCCAAAAACATTGAAGGGTATTTTATGCTTCTAATATCGTTTTCCTTTATTTTCCGAAT
256 TTCAACGCCAAAAAGATTGAAGGGT-TTTTATGCTTCTAATATCGTTTTCCTTTATTTTCCGAAT
37972 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
320 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
*
38037 GCAGAGATTTGGTTAGATGAA-TTTAGAAATTTTAAGGAGTCTTGGCACCAAAAATCATGCAAAA
385 GCAGAGATTTGGTTAGATGAACTTTAGATATTTTAAGGAGTCTTGGCACCAAAAATCATGCAAAA
* *
38101 TTGAGTCGGGGCCCCGGAATGCGTTTTCAGCCAAAAACTGTGATGGTTAGTACACGATTTAGACT
450 TTGAGTCGGGGCCCCGGAATGCGTTTTCAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCT
*
38166 AAAATTTTGCAAAAATTGAACTGTTTGATTTTTCCTCATTTTTTAGCCACAATAGTAATATGGAA
515 AAAATTTTGCAAAAATTGAACTGTTTGATTTTTCCTCATTTTTTAGCCACAATACTAATATGGAA
*
38231 TATATATGATTCAATGCCAAAAAGATTGAAGGGTTTTTCACGCATCTAATATCGTTTTCCCTATT
580 TATATATGATTCAATGCCAAAAAGATTGAAGGGTTTTTCACGCATCTAATATCGTTTTTCCTATT
38296 TTTTCTGAATTAATTTATA
645 TTTTCTGAATTAATTTATA
*
38315 ATTAAATCTAAACAAGATTTAAATGCTCGTAAAAACAAATCCTTAAATCCATTTTGATTGAGATT
1 ATTAAATCTAAACAAGATTTAAATGCTCGTAAAAACAAATCCTTAAATCCATTGTGATTGAGATT
* * *
38380 TCGTAAGATCAATATAGATATTTCAAGGATTCTTAACGCCAAAAATCATGCAAAATGGAGCCGGT
66 TGGTAAGATTAATATAGATATTTCAAGGATTCATAACGCCAAAAATCATGCAAAATGGAGCCGGT
38445 GCCCTGGAACCCATTTTTAGCCAAAAAACTGTGATG-GTACACGATTTCGGCTAAAATTTTGCAA
131 GCCCTGGAACCCATTTTTAGCCAAAAAACTGTGATGTGTACACGATTTCGGCTAAAATTTTGCAA
38509 ACATTGACCCATC-GAATTTTTCCTCAATTTTTAGCCACAATACTCATAAAAAAATATATATTTC
196 A-ATTGACCCATCAG-ATTTTTCCTCAATTTTTAGCCACAATACTCATAAAAAAATATATATTTC
38573 AACGCCAAAAAGATTGAAGGGTTTTTTATGCTTCTAATATCGTTTTTCCTTTATTTTCCGAATTA
259 AACGCCAAAAAGATTGAAGGG-TTTTTATGCTTCTAATATCG-TTTTCCTTTATTTTCCGAATTA
* *
38638 ATATCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCCATGTGGC
322 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
38703 AGAGATTTGGTTAGATGAACTTT-GATATTTTAAGGAGTCTTGGCACCAAAAATCATGCAAAATT
387 AGAGATTTGGTTAGATGAACTTTAGATATTTTAAGGAGTCTTGGCACCAAAAATCATGCAAAATT
** * *
38767 GCTTCGGGGCCCCGGAATGCGTTTTCTGCCAAAAACCGTGATGGTTAGTTAGTACACGATTTCGG
452 GAGTCGGGGCCCCGGAATGCGTTTTCAGCCAAAAACTGTGAT-G---GTTAGTACACGATTTCGG
*
38832 TTAAAATTTTGCAAAAATTGAACTGTTTGATTTTT-CTCATTTTTTAGCCACAATACTAATATGG
513 CTAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCCTCATTTTTTAGCCACAATACTAATATGG
* * * **
38896 AATATATATGATTCAATTCC-AAAATATTGAAAGGCCTTTCACGCATCTAATATCGTTTTTCCTA
578 AATATATATGATTCAATGCCAAAAAGATTGAAGGGTTTTTCACGCATCTAATATCGTTTTTCCTA
38960 TTTTTTCTGAATTAATTTATA
643 TTTTTTCTGAATTAATTTATA
38981 ATTAAATCTAAA
1 ATTAAATCTAAA
38993 T
Statistics
Matches: 1216, Mismatches: 101, Indels: 46
0.89 0.07 0.03
Matches are distributed among these distances:
656 28 0.02
657 47 0.04
658 2 0.00
660 45 0.04
661 10 0.01
662 6 0.00
663 123 0.10
664 184 0.15
665 6 0.00
666 381 0.31
667 305 0.25
668 79 0.06
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (663 bp):
ATTAAATCTAAACAAGATTTAAATGCTCGTAAAAACAAATCCTTAAATCCATTGTGATTGAGATT
TGGTAAGATTAATATAGATATTTCAAGGATTCATAACGCCAAAAATCATGCAAAATGGAGCCGGT
GCCCTGGAACCCATTTTTAGCCAAAAAACTGTGATGTGTACACGATTTCGGCTAAAATTTTGCAA
AATTGACCCATCAGATTTTTCCTCAATTTTTAGCCACAATACTCATAAAAAAATATATATTTCAA
CGCCAAAAAGATTGAAGGGTTTTTATGCTTCTAATATCGTTTTCCTTTATTTTCCGAATTAATTT
CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCAGAG
ATTTGGTTAGATGAACTTTAGATATTTTAAGGAGTCTTGGCACCAAAAATCATGCAAAATTGAGT
CGGGGCCCCGGAATGCGTTTTCAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATT
TTGCAAAAATTGAACTGTTTGATTTTTCCTCATTTTTTAGCCACAATACTAATATGGAATATATA
TGATTCAATGCCAAAAAGATTGAAGGGTTTTTCACGCATCTAATATCGTTTTTCCTATTTTTTCT
GAATTAATTTATA
Done.