Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009894.1 Corchorus capsularis cultivar CVL-1 contig09915, 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: 58048
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:248 original size:80 final size:81
Alignment explanation
Indices: 100--316 Score: 267
Period size: 80 Copynumber: 2.7 Consensus size: 81
90 AGTCCACAAT
* * * *
100 CTCTCTGCCTACTTACCATCTTT-CACCACCCAATATTCCTTATCATTCTAATACCCCACTACGG
1 CTCTCTGCCTACTTACCATCTTTGC-CCACCGAATATTCCTTATCATCCTAATACCCCACCACGA
164 TTTTAAAACCCTACCAC
65 TTTTAAAACCCTACCAC
* * *
181 CTCTCCGCCTACTTACCAT-TTTGCCCACCGAATATTCCTTATTATCCTGATACCCCACCACGAT
1 CTCTCTGCCTACTTACCATCTTTGCCCACCGAATATTCCTTATCATCCTAATACCCCACCACGAT
* * *
245 TTTAGAACTCTGCCAC
66 TTTAAAACCCTACCAC
* * * * * *
261 CTCTCTGCCTAATTACCATCTTCGTCCACTGAATAATCCTTATCATCATAATACCC
1 CTCTCTGCCTACTTACCATCTTTGCCCACCGAATATTCCTTATCATCCTAATACCC
317 TGCCACGGTT
Statistics
Matches: 115, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
80 67 0.58
81 48 0.42
ACGTcount: A:0.25, C:0.37, G:0.06, T:0.32
Consensus pattern (81 bp):
CTCTCTGCCTACTTACCATCTTTGCCCACCGAATATTCCTTATCATCCTAATACCCCACCACGAT
TTTAAAACCCTACCAC
Found at i:342 original size:81 final size:78
Alignment explanation
Indices: 100--342 Score: 231
Period size: 81 Copynumber: 3.0 Consensus size: 78
90 AGTCCACAAT
* *
100 CTCTCTGCCTACTTACCATCTTTC-ACCACCCAATATTCCTTATCATTCTAATACCCCACTACGG
1 CTCTCTGCCTACTTACCATC-TTCGACCACCGAATATTCCTTATCA-TCTAATACCCCACCACGG
164 TTTTAAAAC-CCTACCAC
64 TTTT-AAACTCC--CCAC
* * * * * *
181 CTCTCCGCCTACTTACCAT-TTTGCCCACCGAATATTCCTTATTATCCTGATACCCCACCACGAT
1 CTCTCTGCCTACTTACCATCTTCGACCACCGAATATTCCTTATCAT-CTAATACCCCACCACGGT
*
245 TTTAGAACTCTGCCAC
65 TTTA-AACTC-CCCAC
* * * * **
261 CTCTCTGCCTAATTACCATCTTCGTCCACTGAATAATCCTTATCATCATAATACCCTGCCACGGT
1 CTCTCTGCCTACTTACCATCTTCGACCACCGAATATTCCTTATCATC-TAATACCCCACCACGGT
326 TTTGAAACTACCCCAC
65 TTT-AAACT-CCCCAC
342 C
1 C
343 ACGGTTTTAA
Statistics
Matches: 132, Mismatches: 21, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
79 4 0.03
80 61 0.46
81 65 0.49
82 2 0.02
ACGTcount: A:0.25, C:0.37, G:0.07, T:0.31
Consensus pattern (78 bp):
CTCTCTGCCTACTTACCATCTTCGACCACCGAATATTCCTTATCATCTAATACCCCACCACGGTT
TTAAACTCCCCAC
Found at i:360 original size:19 final size:21
Alignment explanation
Indices: 319--362 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
309 TAATACCCTG
319 CCACGGTTTTGAAACTACCCCA
1 CCACGGTTTTGAAAC-ACCCCA
*
341 CCACGGTTTT-AAA-ACTCCA
1 CCACGGTTTTGAAACACCCCA
360 CCA
1 CCA
363 TCTCTCTGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 8 0.38
21 3 0.14
22 10 0.48
ACGTcount: A:0.30, C:0.36, G:0.11, T:0.23
Consensus pattern (21 bp):
CCACGGTTTTGAAACACCCCA
Found at i:416 original size:103 final size:103
Alignment explanation
Indices: 231--418 Score: 259
Period size: 103 Copynumber: 1.8 Consensus size: 103
221 ATTATCCTGA
* ** * *
231 TACCCCACCACGATTTTAGAACTCTGCCACCTCTCTGCCTAATTACCATCTTCGTCCACTGAATA
1 TACCCCACCACGATTTTAAAACTCCACCACCTCTCTGCCTAATTACAATCTTCGTCCACCGAATA
296 ATCCTTATCATCATAATACCCTGCCACGGTTTTGAAAC
66 ATCCTTATCATCATAATACCCTGCCACGGTTTTGAAAC
* * * *
334 TACCCCACCACGGTTTTAAAACTCCACCATCTCTCTGCCTACTTACAATCTTCGTCCACCGGATA
1 TACCCCACCACGATTTTAAAACTCCACCACCTCTCTGCCTAATTACAATCTTCGTCCACCGAATA
* * * *
399 TTCCTTCTTATCCTAATACC
66 ATCCTTATCATCATAATACC
419 TCATTACGGT
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
103 72 1.00
ACGTcount: A:0.25, C:0.36, G:0.09, T:0.31
Consensus pattern (103 bp):
TACCCCACCACGATTTTAAAACTCCACCACCTCTCTGCCTAATTACAATCTTCGTCCACCGAATA
ATCCTTATCATCATAATACCCTGCCACGGTTTTGAAAC
Found at i:445 original size:103 final size:102
Alignment explanation
Indices: 235--445 Score: 228
Period size: 103 Copynumber: 2.0 Consensus size: 102
225 TCCTGATACC
* ** * *
235 CCACCACGATTTTAGAACTCTGCCACCTCTCTGCCTAATTACCATCTTCGTCCACTGAATAATCC
1 CCACCACGATTTTAAAACTCCACCACCTCTCTGCCTAATTACAATCTTCGTCCACCGAATAATCC
* *
300 TTATCATCATAATACCCTGCCACGGTTTTGAAACTACC
66 TTATCATCATAATACCCT-CCACGGTTTTAAAACTACA
* * * * *
338 CCACCACGGTTTTAAAACTCCACCATCTCTCTGCCTACTTACAATCTTCGTCCACCGGATATTCC
1 CCACCACGATTTTAAAACTCCACCACCTCTCTGCCTAATTACAATCTTCGTCCACCGAATAATCC
* * * *
403 TTCTTATCCTAATA-CCTCATTACGGTTTTAAAACT-CTA
66 TTATCATCATAATACCCTC--CACGGTTTTAAAACTAC-A
441 CCACC
1 CCACC
446 TCACTGCTAC
Statistics
Matches: 89, Mismatches: 16, Indels: 6
0.80 0.14 0.05
Matches are distributed among these distances:
101 1 0.01
102 4 0.04
103 84 0.94
ACGTcount: A:0.26, C:0.35, G:0.09, T:0.31
Consensus pattern (102 bp):
CCACCACGATTTTAAAACTCCACCACCTCTCTGCCTAATTACAATCTTCGTCCACCGAATAATCC
TTATCATCATAATACCCTCCACGGTTTTAAAACTACA
Found at i:944 original size:22 final size:23
Alignment explanation
Indices: 906--960 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
896 AAAACCCCCA
906 TATG-AATTGTTAGTAATCACAC
1 TATGAAATTGTTAGTAATCACAC
* * *
928 TCTGAAATTTTTA-TAATTACAC
1 TATGAAATTGTTAGTAATCACAC
950 TATGAAATTGT
1 TATGAAATTGT
961 GATACCGCTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 20 0.74
23 7 0.26
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (23 bp):
TATGAAATTGTTAGTAATCACAC
Found at i:998 original size:21 final size:24
Alignment explanation
Indices: 968--1032 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 24
958 TGTGATACCG
968 CTATGAAATTTTGATAATCT-TC-
1 CTATGAAATTTTGATAATCTATCT
990 CTAT-AAATTTTGATAATCTGATCT
1 CTATGAAATTTTGATAATCT-ATCT
*
1014 TTATGAAATTTTGATAATC
1 CTATGAAATTTTGATAATC
1033 ACTTTATGAG
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
21 15 0.39
22 4 0.11
23 2 0.05
24 3 0.08
25 14 0.37
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (24 bp):
CTATGAAATTTTGATAATCTATCT
Found at i:1040 original size:22 final size:22
Alignment explanation
Indices: 969--1051 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 22
959 GTGATACCGC
969 TATGAAATTTTGATAAT--CTT
1 TATGAAATTTTGATAATCACTT
989 CCTAT-AAATTTTGATAATCTGATCTT
1 --TATGAAATTTTGATAATC--A-CTT
1015 TATGAAATTTTGATAATCACTT
1 TATGAAATTTTGATAATCACTT
*
1037 TATGAGA-TTTGATAA
1 TATGAAATTTTGATAA
1052 CCTTCTATCA
Statistics
Matches: 54, Mismatches: 1, Indels: 13
0.79 0.01 0.19
Matches are distributed among these distances:
21 21 0.39
22 12 0.22
23 1 0.02
24 3 0.06
25 14 0.26
26 3 0.06
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.46
Consensus pattern (22 bp):
TATGAAATTTTGATAATCACTT
Found at i:1119 original size:22 final size:22
Alignment explanation
Indices: 969--1144 Score: 73
Period size: 21 Copynumber: 7.9 Consensus size: 22
959 GTGATACCGC
* *
969 TATGAAATTTTGATAATCTTCC
1 TATGAAATTTTGATAACCTTCA
* *
991 TAT-AAATTTTGATAATCTGATCTT
1 TATGAAATTTTGATAACCT--TC-A
1015 TATGAAATTTTGATAATCACTT--
1 TATGAAATTTTGATAA-C-CTTCA
*
1037 TATGAGA-TTTGATAACCTTC-
1 TATGAAATTTTGATAACCTTCA
* * *
1057 TAT-CAATTTTGGTACTCCTT-A
1 TATGAAATTTTGATA-ACCTTCA
*
1078 TGAAATTGACACTTTT-ATAACCTTCA
1 T---A-TGA-AATTTTGATAACCTTCA
*
1104 TATGAAATTTTGATAACC-ACA
1 TATGAAATTTTGATAACCTTCA
* *
1125 TTATAAAATTTTTATAACCT
1 -TATGAAATTTTGATAACCT
1145 CCTCATAATA
Statistics
Matches: 119, Mismatches: 15, Indels: 39
0.69 0.09 0.23
Matches are distributed among these distances:
19 4 0.03
20 10 0.08
21 35 0.29
22 34 0.29
23 3 0.03
24 4 0.03
25 18 0.15
26 4 0.03
27 7 0.06
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.44
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCA
Found at i:1227 original size:22 final size:21
Alignment explanation
Indices: 1090--1227 Score: 79
Period size: 22 Copynumber: 6.4 Consensus size: 21
1080 AAATTGACAC
*
1090 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TCCTATGAAA
* * *
1111 TTTTGATAACCACATTATAAAA
1 TTTTGATAACCTC-CTATGAAA
*
1133 TTTTTATAACCTCCTCAT--AA
1 TTTTGATAACCTCCT-ATGAAA
*
1153 TATT-AGTAACCTCCTAATGAAA
1 TTTTGA-TAACCTCCT-ATGAAA
* *
1175 TTTTGTTAACCACACTATGAAA
1 TTTTGATAACCTC-CTATGAAA
* *
1197 TCCTT-ATAACCTCGCTATGACA
1 T-TTTGATAACCTC-CTATGAAA
1219 TTTTGATAA
1 TTTTGATAA
1228 TCTCTTTGAT
Statistics
Matches: 90, Mismatches: 17, Indels: 19
0.71 0.13 0.15
Matches are distributed among these distances:
19 1 0.01
20 16 0.18
21 8 0.09
22 61 0.68
23 4 0.04
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.38
Consensus pattern (21 bp):
TTTTGATAACCTCCTATGAAA
Found at i:1324 original size:24 final size:22
Alignment explanation
Indices: 1263--1446 Score: 104
Period size: 22 Copynumber: 8.3 Consensus size: 22
1253 TTGTAATAAT
* *
1263 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
*
1285 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
* **
1307 TAACCTGATCCTATGAAATTTTGG
1 TAACC--AACCTATGAAATTTTAA
*
1331 TAACC-ACACTATGAAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
*** * **
1353 TAACTTTCATATGAAATTTTGG
1 TAACCAACCTATGAAATTTTAA
* **
1375 TAACC-ACACTATGGAATTTTGC
1 TAACCAAC-CTATGAAATTTTAA
* *
1397 TAACC-TCCTCATGAAATTATAA
1 TAACCAACCT-ATGAAATTTTAA
* * * *
1419 CAACCATCTTATGAAATTTTGA
1 TAACCAACCTATGAAATTTTAA
1441 TAACCA
1 TAACCA
1447 CATAGAGACA
Statistics
Matches: 127, Mismatches: 28, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
21 4 0.03
22 101 0.80
23 4 0.03
24 18 0.14
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:1411 original size:44 final size:44
Alignment explanation
Indices: 1270--1414 Score: 150
Period size: 44 Copynumber: 3.2 Consensus size: 44
1260 AATTAACCAC
*** * * *
1270 CCTATGAAATTTCAATAACCA-ACCTAAGAAATTTTAATAACCTGAT
1 CCTATGAAATTTTGGTAACCACA-CTATGAAATTTTGATAA-CT-CT
*
1316 CCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACTTT
1 CCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACTCT
* * *
1360 CATATGAAATTTTGGTAACCACACTATGGAATTTTGCTAAC-CT
1 CCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACTCT
1403 CCTCATGAAATT
1 CCT-ATGAAATT
1415 ATAACAACCA
Statistics
Matches: 86, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
43 3 0.03
44 47 0.55
45 2 0.02
46 33 0.38
47 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (44 bp):
CCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACTCT
Found at i:1917 original size:31 final size:31
Alignment explanation
Indices: 1861--1921 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
1851 CAATTTAGAA
1861 ATATGTTTAAAAAAAAGATACAATTGGAAAT
1 ATATGTTTAAAAAAAAGATACAATTGGAAAT
* *
1892 ATAT-TTTAAAAATAAGGGTACAATTGGAAA
1 ATATGTTTAAAAA-AAAGATACAATTGGAAA
1922 ACATAAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 8 0.30
31 19 0.70
ACGTcount: A:0.52, C:0.03, G:0.15, T:0.30
Consensus pattern (31 bp):
ATATGTTTAAAAAAAAGATACAATTGGAAAT
Found at i:11208 original size:11 final size:12
Alignment explanation
Indices: 11186--11214 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
11176 TAGAACTTAG
11186 AAGATATAATTA
1 AAGATATAATTA
11198 AAGAT-TAATTA
1 AAGATATAATTA
11209 AAGATA
1 AAGATA
11215 AAAGGGTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.31
Consensus pattern (12 bp):
AAGATATAATTA
Found at i:11685 original size:2 final size:2
Alignment explanation
Indices: 11678--11743 Score: 64
Period size: 2 Copynumber: 32.5 Consensus size: 2
11668 GATATAAAAG
*
11678 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT ACT AGT AGT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T A-T A-T AT
* *
11720 AT A- AT AT AT AT AG AT AG AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
11744 CCTTCTTTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
1 2 0.04
2 46 0.85
3 6 0.11
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (2 bp):
AT
Found at i:13015 original size:36 final size:36
Alignment explanation
Indices: 12975--13044 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
12965 ATTTTTGGCC
12975 ATATACTCATAATCCTAAATTATGTGACAAAACCTT
1 ATATACTCATAATCCTAAATTATGTGACAAAACCTT
13011 ATATACTCATAATCCTAAATTATGTGACAAAACC
1 ATATACTCATAATCCTAAATTATGTGACAAAACC
13045 ATTTTTAGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.31
Consensus pattern (36 bp):
ATATACTCATAATCCTAAATTATGTGACAAAACCTT
Found at i:13492 original size:28 final size:29
Alignment explanation
Indices: 13447--13501 Score: 94
Period size: 28 Copynumber: 1.9 Consensus size: 29
13437 CATTAAGCTT
13447 AATATTATATATAAATATAAAGAAATATA
1 AATATTATATATAAATATAAAGAAATATA
*
13476 AATA-TATATATATATATAAAGAAATA
1 AATATTATATATAAATATAAAGAAATA
13502 AAAGAAACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (29 bp):
AATATTATATATAAATATAAAGAAATATA
Found at i:22773 original size:3 final size:3
Alignment explanation
Indices: 22765--22816 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
22755 AATGCATATC
22765 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
22812 ATA AT
1 ATA AT
22817 CACCATTTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:26277 original size:30 final size:30
Alignment explanation
Indices: 26243--26306 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
26233 CTTCATACTT
26243 TTATGCTTTATGCTATTTAGTCCTTTACAA
1 TTATGCTTTATGCTATTTAGTCCTTTACAA
26273 TTATGCTTTATGCTATTTAGTCCTTTACAA
1 TTATGCTTTATGCTATTTAGTCCTTTACAA
26303 TTAT
1 TTAT
26307 AGGTTGGACG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.23, C:0.16, G:0.09, T:0.52
Consensus pattern (30 bp):
TTATGCTTTATGCTATTTAGTCCTTTACAA
Found at i:40313 original size:41 final size:41
Alignment explanation
Indices: 40256--40333 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
40246 AGAATAACGT
**
40256 TAACGTGTTGTATTTTGATGACAATTTAAGAAAAATGAAGA
1 TAACGTGCCGTATTTTGATGACAATTTAAGAAAAATGAAGA
* *
40297 TAACGTGCCGTATTTTGATGACGATTTCAGAAAAATG
1 TAACGTGCCGTATTTTGATGACAATTTAAGAAAAATG
40334 CAATTTTTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (41 bp):
TAACGTGCCGTATTTTGATGACAATTTAAGAAAAATGAAGA
Found at i:40478 original size:33 final size:33
Alignment explanation
Indices: 40390--40486 Score: 92
Period size: 33 Copynumber: 2.9 Consensus size: 33
40380 GGGCGGCTTA
* *
40390 CCGTGGC-GAAGCCGCCCCAGTAGGG-AGTCTCCG
1 CCGTGGCTGAA-CCTCCCCAGTGGGGAAG-CTCCG
* *
40423 CCGTGGTTGAGCCTCCCCAGTGGGGAAGCTCCG
1 CCGTGGCTGAACCTCCCCAGTGGGGAAGCTCCG
* *
40456 CCGTGGCTGAACCGT-CCTAGTGGGGAGGCTC
1 CCGTGGCTGAACC-TCCCCAGTGGGGAAGCTC
40487 AGTGTAAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
33 48 0.91
34 5 0.09
ACGTcount: A:0.13, C:0.33, G:0.37, T:0.16
Consensus pattern (33 bp):
CCGTGGCTGAACCTCCCCAGTGGGGAAGCTCCG
Found at i:40781 original size:71 final size:71
Alignment explanation
Indices: 40645--40795 Score: 180
Period size: 71 Copynumber: 2.1 Consensus size: 71
40635 GTCACCGTCC
* * * *
40645 ATTGATTCATTTGACTATTCAAGTCTAGATTAGTCGTCGTCTATTGATTCATTTGACTGTTTGAT
1 ATTGATTCATTTGACTATTCAACTCTAGATTAGTCGTCGTCCATTGATTCATTTGACTATATGAT
40710 AT-GCAT
66 ATAG-AT
** * * *
40716 ATTGATTCATTTGACTATTTGACTCTAGATTAGTTGTCGTCCATTGATTTATTTG-GTCATATGA
1 ATTGATTCATTTGACTATTCAACTCTAGATTAGTCGTCGTCCATTGATTCATTTGACT-ATATGA
40780 TATAGAT
65 TATAGAT
*
40787 ATGGATTCA
1 ATTGATTCA
40796 ACTCGATTCG
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
70 1 0.01
71 66 0.97
72 1 0.01
ACGTcount: A:0.25, C:0.13, G:0.17, T:0.45
Consensus pattern (71 bp):
ATTGATTCATTTGACTATTCAACTCTAGATTAGTCGTCGTCCATTGATTCATTTGACTATATGAT
ATAGAT
Found at i:40940 original size:47 final size:48
Alignment explanation
Indices: 40784--40951 Score: 161
Period size: 47 Copynumber: 3.5 Consensus size: 48
40774 ATATGATATA
* *
40784 GATATGGATTCAACTCGATTCGACTCTAGATATTGCCCATTTGACTGTTT
1 GATATGGATTCAACTCGATTCGACT-T-TATATTGTCCATTTGACTGTTT
* * * * *
40834 GATATGGA-TCAACTTGATTCGAC--TCTA--GTTCACTCTAGA-TGATATA
1 GATATGGATTCAACTCGATTCGACTTTATATTGTCCA-T-TTGACTG-T-TT
40880 GATATGGATTCAACTCGATTCGACTTTATATTGTCCATTTGACTGTTT
1 GATATGGATTCAACTCGATTCGACTTTATATTGTCCATTTGACTGTTT
*
40928 GATATGGA-TCAACTTGATTCGACT
1 GATATGGATTCAACTCGATTCGACT
40952 CTGGTCCACT
Statistics
Matches: 95, Mismatches: 13, Indels: 23
0.73 0.10 0.18
Matches are distributed among these distances:
43 3 0.03
44 3 0.03
45 6 0.06
46 9 0.09
47 29 0.31
48 9 0.09
49 21 0.22
50 11 0.12
51 4 0.04
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (48 bp):
GATATGGATTCAACTCGATTCGACTTTATATTGTCCATTTGACTGTTT
Found at i:40940 original size:94 final size:96
Alignment explanation
Indices: 40776--40964 Score: 328
Period size: 94 Copynumber: 2.0 Consensus size: 96
40766 ATTTGGTCAT
40776 ATGATATAGATATGGATTCAACTCGATTCGACTCTAGATATTGCCCATTTGACTGTTTGATATGG
1 ATGATATAGATATGGATTCAACTCGATTCGACTCTAGATATTGCCCATTTGACTGTTTGATATGG
*
40841 ATCAACTTGATTCGACTCTAGTTCACTCTAG
66 ATCAACTTGATTCGACTCTAGTCCACTCTAG
* *
40872 ATGATATAGATATGGATTCAACTCGATTCGACT-T-TATATTGTCCATTTGACTGTTTGATATGG
1 ATGATATAGATATGGATTCAACTCGATTCGACTCTAGATATTGCCCATTTGACTGTTTGATATGG
*
40935 ATCAACTTGATTCGACTCTGGTCCACTCTA
66 ATCAACTTGATTCGACTCTAGTCCACTCTA
40965 AATTAATCAC
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
94 55 0.62
95 1 0.01
96 33 0.37
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (96 bp):
ATGATATAGATATGGATTCAACTCGATTCGACTCTAGATATTGCCCATTTGACTGTTTGATATGG
ATCAACTTGATTCGACTCTAGTCCACTCTAG
Found at i:48130 original size:3 final size:3
Alignment explanation
Indices: 48122--48154 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
48112 CTCTGAAAAT
48122 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
48155 GAGGTTCATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:51862 original size:24 final size:24
Alignment explanation
Indices: 51832--51877 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
51822 CTTATTCTAA
51832 TAATTAAAGTTTAACCTGAATTTC
1 TAATTAAAGTTTAACCTGAATTTC
51856 TAATTAAAGTTTAACCTGAATT
1 TAATTAAAGTTTAACCTGAATT
51878 AATTCTGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (24 bp):
TAATTAAAGTTTAACCTGAATTTC
Found at i:53981 original size:22 final size:21
Alignment explanation
Indices: 53952--53996 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
53942 TTTAATAAAA
* *
53952 AAGGAAACAATGTGTGCAAAC
1 AAGGAAACAAGGTGTACAAAC
53973 AAGGTAAACAAGGTGTACAAAC
1 AAGG-AAACAAGGTGTACAAAC
53995 AA
1 AA
53997 CCATTGAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.51, C:0.13, G:0.22, T:0.13
Consensus pattern (21 bp):
AAGGAAACAAGGTGTACAAAC
Found at i:57996 original size:22 final size:23
Alignment explanation
Indices: 57958--58003 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
57948 ATTTATATGG
*
57958 CCCATAACTTACTTTTA-CTAAA
1 CCCATAACTAACTTTTATCTAAA
57980 CCCATAACTAA-TCTTTATCTAAA
1 CCCATAACTAACT-TTTATCTAAA
58003 C
1 C
58004 TATAAAATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 1 0.05
22 14 0.67
23 6 0.29
ACGTcount: A:0.37, C:0.28, G:0.00, T:0.35
Consensus pattern (23 bp):
CCCATAACTAACTTTTATCTAAA
Done.