Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011661.1 Corchorus olitorius cultivar O-4 contig11694, 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: 1893
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Found at i:200 original size:101 final size:101
Alignment explanation
Indices: 1--191 Score: 278
Period size: 101 Copynumber: 1.9 Consensus size: 101
* * *
1 AAGACGATTCAAAAAGTCAATAATGGGCCCTAATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
1 AAGACGATTCAAAAAGTCAATAATGGGCCCGAATAGACACAAAATAACAAGTGTTCCAAATGAGC
* *
66 TAAAAAATTTACAGTGGACTAATCTCACCAAAATCG
66 TAAAAAATTCACAGTGGACGAATCTCACCAAAATCG
* *
102 AAGACGATTCAAAATG-GAACTAATGGGCCCCGAA-AGACACAAAATAACAAGTGTTCCAAATGA
1 AAGACGATTCAAAAAGTCAA-TAATGGG-CCCGAATAGACACAAAATAACAAGTGTTCCAAATGA
*
165 GCTAAAAACTTCACAGTGGACGAATCT
64 GCTAAAAAATTCACAGTGGACGAATCT
192 GTCTAAAATG
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
100 2 0.03
101 73 0.91
102 5 0.06
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.19
Consensus pattern (101 bp):
AAGACGATTCAAAAAGTCAATAATGGGCCCGAATAGACACAAAATAACAAGTGTTCCAAATGAGC
TAAAAAATTCACAGTGGACGAATCTCACCAAAATCG
Found at i:376 original size:154 final size:154
Alignment explanation
Indices: 96--662 Score: 902
Period size: 154 Copynumber: 3.7 Consensus size: 154
86 AATCTCACCA
** * * * *
96 AAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGAAAGACACAAAATAACAAGTGTTCCAA
1 AAATCGAAGACGATTCAAAATGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAA
* ** *
161 ATGAGCTAAAAACTTCACAGTGGACGAATCTGTCTAAAATGATTATAGTTAGGCCATAAACAATG
66 ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG
*
226 GAAAGTAAAGCATTGAGGTTTGCC
131 GAAAGAAAAGCATTGAGGTTTGCC
* * *
250 AAATCGAAGACGATTCAAAACGTCACTAATGGGCCTTGATAGGGCCAAAATAACAAGTGTTCCAA
1 AAATCGAAGACGATTCAAAATGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAA
* *
315 ATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTTTAGTTAGGCCATAAACAATG
66 ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG
*
380 GAAAGAAAAGCATTGAGGTATGCC
131 GAAAGAAAAGCATTGAGGTTTGCC
*
404 AAATCGAAGACGATTCAAAATGTCAGTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAA
1 AAATCGAAGACGATTCAAAATGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAA
*
469 ATGAGCTAAAAA-TGTTACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
66 ATGAGCTAAAAACT-TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
533 GGAAAGAAAAGCATTGAGGTTTGCC
130 GGAAAGAAAAGCATTGAGGTTTGCC
* * *
558 AAATCGAAGACGATTCAAAAAGTCAATAATGGGCCCTAATAGGCCCAAAATAACAAGTGTTCCAA
1 AAATCGAAGACGATTCAAAATGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAA
* *
623 ATGAGCTAAAAATTTTACAGTGGACTAATCTCACCAAAAT
66 ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
663 CGAAGACGAT
Statistics
Matches: 385, Mismatches: 26, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
153 1 0.00
154 383 0.99
155 1 0.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.22
Consensus pattern (154 bp):
AAATCGAAGACGATTCAAAATGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAA
ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG
GAAAGAAAAGCATTGAGGTTTGCC
Found at i:675 original size:101 final size:101
Alignment explanation
Indices: 558--763 Score: 317
Period size: 101 Copynumber: 2.0 Consensus size: 101
548 GAGGTTTGCC
* * *
558 AAATCGAAGACGATTCAAAAAGTCAA-TAATGGG-CCCTAATAGGCCCAAAATAACAAGTGTTCC
1 AAATCGAAGACGATTCAAAAAG-CAACTAATGGGCCCCGAA-AGACACAAAATAACAAGTGTTCC
*
621 AAATGAGCTAAAAATTTTACAGTGGACTAATCTCACCA
64 AAATGAGCTAAAAACTTTACAGTGGACTAATCTCACCA
* *
659 AAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGAAAGACACAAAATAACAAGTGTTCCAA
1 AAATCGAAGACGATTCAAAAAGCAACTAATGGGCCCCGAAAGACACAAAATAACAAGTGTTCCAA
*
724 ATGAGTTAAAAACTTTACAGTGGACTAATCTCACCA
66 ATGAGCTAAAAACTTTACAGTGGACTAATCTCACCA
760 AAAT
1 AAAT
764 GATTATAGTT
Statistics
Matches: 96, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
100 2 0.02
101 89 0.93
102 5 0.05
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (101 bp):
AAATCGAAGACGATTCAAAAAGCAACTAATGGGCCCCGAAAGACACAAAATAACAAGTGTTCCAA
ATGAGCTAAAAACTTTACAGTGGACTAATCTCACCA
Found at i:765 original size:409 final size:407
Alignment explanation
Indices: 250--1069 Score: 1181
Period size: 409 Copynumber: 2.0 Consensus size: 407
240 GAGGTTTGCC
** ** * *
250 AAATCGAAGACGATTCAAAACGTCACTAATGGGCCTTGATAGGGCCAAAATAACAAGTGTTCCAA
1 AAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAAGACCAAAATAACAAGTGTTCCAA
* *
315 ATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTTTAGTTAGGCCATAAACAATG
66 ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG
* * ** * * *
380 GAAAGAAAAGCATTGA-GGTATGCCAAATCGAAGACGATTCAAAATGTCAGTAATGGGCCCTGAT
131 GAAAGAAAAGCATCGAGGGT-TGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAA
*
444 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAATGTT-ACAGTGGACTAATCTCACCAAAA
195 AGGCACAAAATAACAAGTGTTCCAAATGAGC-AAAAAT-TTCACAGTGGACTAATCTCA-CAAAA
*
508 TGATTATAGTTAGGCCATAAACAA-TGGAAA-GAAAAGCATTGAGGTTTGCCAAATCGAAGACGA
257 --A--ATAGTTAGGCCATAAACAACTGGAAACGAAAAGCATGGAGGTTTGCCAAATCGAAGACGA
* *
571 TTCAAAA-AGTCAA-TAATGGG-CCCTAATA-GGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
318 TTCAAAACA--AAACTAAAGGGACCCTAATACGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
* *
632 AAATTTTACAGTGGACTAATCTCACCA
381 AAACTTCACAGTGGACTAATCTCACCA
*
659 AAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGA-AAGACACAAAATAACAAGTGTTCCA
1 AAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAAGAC-CAAAATAACAAGTGTTCCA
* * *
723 AATGAGTTAAAAACTTTACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAACCAAT
65 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
*
788 GGAAAGAAAAGCATCGAGGGTTGGCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAA
130 GGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAA
* *
853 AGGCACAAAATAACAAGTGTTCGAAATGAGCAAAAATTTCACAGTGGACTAATCTCACTAAAAAT
195 AGGCACAAAATAACAAGTGTTCCAAATGAGCAAAAATTTCACAGTGGACTAATCTCACAAAAAAT
* *
918 AGTTAGGTCATAAACAACTGGAAACGAAAAGCGTGGAGGTTTGCCAAATCGAAGACGATTCAAAA
260 AGTTAGGCCATAAACAACTGGAAACGAAAAGCATGGAGGTTTGCCAAATCGAAGACGATTCAAAA
* *
983 CAAAACTAAAGGGACCCTGATACGGTCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
325 CAAAACTAAAGGGACCCTAATACGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
*
1048 AGTGGACTAATCTCACTA
390 AGTGGACTAATCTCACCA
1066 AAAT
1 AAAT
1070 GATTATAGTT
Statistics
Matches: 369, Mismatches: 33, Indels: 20
0.87 0.08 0.05
Matches are distributed among these distances:
403 18 0.05
404 8 0.02
405 45 0.12
406 8 0.02
407 66 0.18
408 26 0.07
409 195 0.53
410 3 0.01
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (407 bp):
AAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAAGACCAAAATAACAAGTGTTCCAA
ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG
GAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAA
GGCACAAAATAACAAGTGTTCCAAATGAGCAAAAATTTCACAGTGGACTAATCTCACAAAAAATA
GTTAGGCCATAAACAACTGGAAACGAAAAGCATGGAGGTTTGCCAAATCGAAGACGATTCAAAAC
AAAACTAAAGGGACCCTAATACGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
GTGGACTAATCTCACCA
Found at i:864 original size:255 final size:254
Alignment explanation
Indices: 404--915 Score: 796
Period size: 255 Copynumber: 2.0 Consensus size: 254
394 GAGGTATGCC
** * * * * *
404 AAATCGAAGACGATTCAAAATGTCAGTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAA
1 AAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGAAAGACACAAAATAACAAGTGTTCCAA
469 ATGAGCTAAAAATGTTACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG
66 ATGAGCTAAAAATGTTACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG
* * *
534 GAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAAGTCAATAATGGGCCCTAATA
131 GAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAAAGTCAATAATGGGCCCGAATA
* *
599 GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAATTTTACAGTGGACTAATCTCACCA
196 GGCACAAAATAACAAGTGTTCCAAATGAGC-AAAAATTTCACAGTGGACTAATCTCACCA
659 AAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGAAAGACACAAAATAACAAGTGTTCCAA
1 AAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGAAAGACACAAAATAACAAGTGTTCCAA
* *
724 ATGAGTTAAAAACT-TTACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAACCAAT
66 ATGAGCTAAAAA-TGTTACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
* * *
788 GGAAAGAAAAGCATCGAGGGTTGGCAAATCGAAGACGATTCAAAACG-GAACTAATGGGCCCCGA
130 GGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAAAGTCAA-TAATGGG-CCCGA
* *
852 A-AGGCACAAAATAACAAGTGTTCGAAATGAGCAAAAATTTCACAGTGGACTAATCTCACTA
193 ATAGGCACAAAATAACAAGTGTTCCAAATGAGCAAAAATTTCACAGTGGACTAATCTCACCA
913 AAA
1 AAA
916 ATAGTTAGGT
Statistics
Matches: 235, Mismatches: 19, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
254 32 0.14
255 197 0.84
256 6 0.03
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (254 bp):
AAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGAAAGACACAAAATAACAAGTGTTCCAA
ATGAGCTAAAAATGTTACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG
GAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAAAGTCAATAATGGGCCCGAATA
GGCACAAAATAACAAGTGTTCCAAATGAGCAAAAATTTCACAGTGGACTAATCTCACCA
Found at i:1054 original size:153 final size:151
Alignment explanation
Indices: 659--1893 Score: 1688
Period size: 153 Copynumber: 8.0 Consensus size: 151
649 AATCTCACCA
* *
659 AAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGAAAGACACAAAATAACAAGTGTTCCAA
1 AAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAA
* * * *
724 ATGAGTTAAAAACTTTACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAACCAATG
66 ATGAG-CAAAAACTTCACAGTGGACTAATCTCACTAAAA-GA-TATAGTTAGGCCATAAACAATG
*
789 GAAAGAAAAGCATCGAGGGTTGGC
128 GAAAGAAAAGCATCGAGGGTTGCC
*
813 AAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCGAA
1 AAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAA
* *
878 ATGAGCAAAAATTTCACAGTGGACTAATCTCACT-AAA-A-ATAGTTAGGTCATAAACAACTGGA
66 ATGAGCAAAAACTTCACAGTGGACTAATCTCACTAAAAGATATAGTTAGGCCATAAACAA-TGGA
* * *
940 AACGAAAAGCGTGGAGGTTTGCC
130 AA-GAAAAGCATCGAGGGTTGCC
** * * *
963 AAATCGAAGACGATTCAAAACAAAACTAAAGGGACCCTGATACGGTC-CAAAATAACAAGTGTTC
1 AAATCGAAGACGATTCAAAACGGAACTAATGGG-CCCCGA-AAGG-CACAAAATAACAAGTGTTC
1027 CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACA
63 CAAATGAGC-AAAAACTTCACAGTGGACTAATCTCACTAAAA-GA-TATAGTTAGGCCATAAACA
* * *
1092 ATGGAAAGAAAGGCATTGAGGATTGCC
125 ATGGAAAGAAAAGCATCGAGGGTTGCC
** * * * *
1119 AAATCGAAGACGATTCAAAACGTCACAAATGGGCCCCTGATAGGACCCAAAATAACAAGTGTTCG
1 AAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC-GAAAGG-CACAAAATAACAAGTGTTCC
1184 AAATGAGCAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTTAGGCCATAAACAA
64 AAATGAGCAAAAACTTCACAGTGGACTAATCTCACTAAAA-GA-TATAG-TTAGGCCATAAACAA
* ** *
1249 TGGAAAG-AAACCATTAAGGTTTGCC
126 TGGAAAGAAAAGCATCGAGGGTTGCC
** * * *
1274 AAATCGAAGACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAA
1 AAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAA
* *
1339 ACTGAGCTAAAAAACTTTACAGTTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
66 A-TGAGC--AAAAACTTCACAG-TGGACTAATCTCACTAAAA-GA-TATAGTTAGGCCATAAACA
*
1404 ATGGAAAGAAAAGCATCGAGGATTGCC
125 ATGGAAAGAAAAGCATCGAGGGTTGCC
*
1431 AAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAA
1 AAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAA
*
1496 ATGAGCAAAAACTTCACAGTGGAATAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGG
66 ATGAGCAAAAACTTCACAGTGGACTAATCTCACTAAAA-GA-TATAGTTAGGCCATAAACAATGG
1561 AAAGAAAAGCATCGAGGGTTGCC
129 AAAGAAAAGCATCGAGGGTTGCC
**
1584 AAATCGAAGACGATTCAAAACAAAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAA
1 AAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAA
* * * *
1649 ATGAACTAAAAACTTTACAGTGGACTAATCTCACCAAAAATGATTATAGTTAGGCCAGAAACAAT
66 ATGAGC-AAAAACTTCACAGTGGACTAATCTCA-CTAAAA-GA-TATAGTTAGGCCATAAACAAT
1714 GGAAAGAAAAGCATCGAGGGTTGCC
127 GGAAAGAAAAGCATCGAGGGTTGCC
* *
1739 AAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAATGGCACAAAATAACAAGTGTTCGAA
1 AAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAA
*
1804 ATGAGCGAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGG
66 ATGAGCAAAAACTTCACAGTGGACTAATCTCACTAAAA-GA-TATAGTTAGGCCATAAACAATGG
* * *
1869 AAAGAAAGGCATTGAGGTTTGCC
129 AAAGAAAAGCATCGAGGGTTGCC
1892 AA
1 AA
Statistics
Matches: 984, Mismatches: 76, Indels: 43
0.89 0.07 0.04
Matches are distributed among these distances:
148 17 0.02
149 6 0.01
150 47 0.05
151 5 0.01
152 31 0.03
153 263 0.27
154 141 0.14
155 216 0.22
156 133 0.14
157 107 0.11
158 18 0.02
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.20
Consensus pattern (151 bp):
AAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAA
ATGAGCAAAAACTTCACAGTGGACTAATCTCACTAAAAGATATAGTTAGGCCATAAACAATGGAA
AGAAAAGCATCGAGGGTTGCC
Found at i:1170 original size:563 final size:560
Alignment explanation
Indices: 1--1842 Score: 2045
Period size: 563 Copynumber: 3.2 Consensus size: 560
1 AAGACGATTCAAAAAGTCAATAATGGGCCCTAATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
1 AAGACGATTCAAAAAGTCAATAATGGGCCCTAATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
66 TAAAAAATTTACAGTGGACTAATCTCACCAAAATCGAAGACGATTCAAAATGGAACTAATGGGCC
66 TAAAAAATTTACAGTGGACTAATCTCACCAAAATCGAAGACGATTCAAAATGGAACTAATGGGCC
** *
131 CCGAAAGACACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACGAATCTGTCT
131 CCGAAAGACACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACGAATCTCACC
* * *
196 AAAATGATTATAGTTAGGCCATAAACAATGGAAAGTAAAGCATTGAGGTTTGCCAAATCGAAGAC
196 AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGAC
** ** *
261 GATTCAAAACGTCACTAATGGGCCTTGATAGGGCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
261 GATTCAAAACGGAACTAATGGGCCCCGATAAGGCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
326 ACTTCACAGTGGACTAATCTCACTAAAATGATTTTAGTTAGGCCATAAACAATGGAAAGAAAAGC
326 ACTTCACAGTGGACTAATCTCACTAAAA-GA--TTAGTTAGGCCATAAACAATGGAAAGAAAAGC
* **** * *
391 ATTGAGGTATGCCAAATCGAAGACGATTCAAAATGTCAGTAATGGGCCCTGATAGGCCCAAAATA
388 ATGGAGGTATGCCAAATCGAAGACGATTCAAAACAAAACTAAAGGGCCCTGATAGGCCCAAAATA
*
456 ACAAGTGTTCCAAATGAGCTAAAAATGTTACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
453 ACAAGTGTTCCAAATGAGCTAAAAATGTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
*
521 GCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCG
518 GCCATAAACAATGGAAAGAAAAGCATTGAGGATTGCCAAATCG
564 AAGACGATTCAAAAAGTCAATAATGGGCCCTAATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
1 AAGACGATTCAAAAAGTCAATAATGGGCCCTAATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
*
629 TAAAAATTTTACAGTGGACTAATCTCACCAAAATCGAAGACGATTCAAAATGGAACTAATGGGCC
66 TAAAAAATTTACAGTGGACTAATCTCACCAAAATCGAAGACGATTCAAAATGGAACTAATGGGCC
* * *
694 CCGAAAGACACAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTTACAGTGGACTAATCTCACC
131 CCGAAAGACACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACGAATCTCACC
* *
759 AAAATGATTATAGTTAGGCCATAACCAATGGAAAGAAAAGCATCGAGGGTTGGCAAATCGAAGAC
196 AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGAC
*
824 GATTCAAAACGGAACTAATGGGCCCCGA-AAGGCACAAAATAACAAGTGTTCGAAATGAGC-AAA
261 GATTCAAAACGGAACTAATGGGCCCCGATAAGGC-CAAAATAACAAGTGTTCCAAATGAGCTAAA
* *
887 AATTTCACAGTGGACTAATCTCACTAAAA-A-TAGTTAGGTCATAAACAACTGGAAACGAAAAGC
325 AACTTCACAGTGGACTAATCTCACTAAAAGATTAGTTAGGCCATAAACAA-TGGAAA-GAAAAGC
* * *
950 GTGGAGGTTTGCCAAATCGAAGACGATTCAAAACAAAACTAAAGGGACCCTGATACGGTCCAAAA
388 ATGGAGGTATGCCAAATCGAAGACGATTCAAAACAAAACTAAAGGG-CCCTGATA-GGCCCAAAA
*
1015 TAACAAGTGTTCCAAATGAGCTAAAAACT-TCACAGTGGACTAATCTCACTAAAATGATTATAGT
451 TAACAAGTGTTCCAAATGAGCTAAAAA-TGTCACAGTGGACTAATCTCACCAAAATGATTATAGT
*
1079 TAGGCCATAAACAATGGAAAGAAAGGCATTGAGGATTGCCAAATCG
515 TAGGCCATAAACAATGGAAAGAAAAGCATTGAGGATTGCCAAATCG
* * *
1125 AAGACGATTCAAAACGTCACA-AATGGGCCCCTGATAGGACCCAAAATAACAAGTGTTCGAAATG
1 AAGACGATTCAAAAAGTCA-ATAATGGG-CCCTAATAGG-CCCAAAATAACAAGTGTTCCAAATG
* * * * *
1189 AGC-AAAAACTTCACAGTGGACTAATCTCACTAAAAT-GATTATAGTTTAGGCCA-TAAACAATG
63 AGCTAAAAAATTTACAGTGGACTAATCTCACCAAAATCG---A-AG---A--CGATTCAA-AAT-
* * ** **
1251 GAAAGAAACCATTAA-GGTTTGCCAAATCG-AAGACGATTCAAAACGTCACTAA-TGGGCCCTGA
117 G---G-AA-C--TAATGG---GCC---CCGAAAGAC-A--CAAAA--TAAC-AAGT-GTTCCAAA
** * ** * * * * *
1313 T-AGGCCCAAAA--TAACAAGTGTTCCAAACTGAGCTAAAAAACTTTACAGTTGGACTAATCTCA
162 TGA-GCTAAAAACTTCAC-AGTGGACGAATCTCA-C--CAAAA---T-GA-TT------------
*
1375 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGATTGCCAAATCGAAG
205 -----------ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAG
*
1440 ACGATTCAAAACAGAACTAATGGGCCCCGA-AAGGCACAAAATAACAAGTGTTCCAAATGAGC-A
259 ACGATTCAAAACGGAACTAATGGGCCCCGATAAGGC-CAAAATAACAAGTGTTCCAAATGAGCTA
*
1503 AAAACTTCACAGTGGAATAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
323 AAAACTTCACAGTGGACTAATCTCACTAAAA-GA-T-TAGTTAGGCCATAAACAATGGAAAGAAA
* * * * *
1568 AGCATCGAGGGT-TGCCAAATCGAAGACGATTCAAAACAAAACTAATGGGCCCCGAAAGGCACAA
385 AGCATGGA-GGTATGCCAAATCGAAGACGATTCAAAACAAAACTAAAGGGCCCTGATAGGCCCAA
* *
1632 AATAACAAGTGTTCCAAATGAACTAAAAACT-TTACAGTGGACTAATCTCACCAAAAATGATTAT
449 AATAACAAGTGTTCCAAATGAGCTAAAAA-TGTCACAGTGGACTAATCTCACC-AAAATGATTAT
* * *
1696 AGTTAGGCCAGAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCG
512 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGATTGCCAAATCG
* * * * *
1745 AAGACGATTCAAAACG-GAACTAATGGGCCCCGAAT-GGCACAAAATAACAAGTGTTCGAAATGA
1 AAGACGATTCAAAAAGTCAA-TAATGGG-CCCTAATAGGCCCAAAATAACAAGTGTTCCAAATGA
* * * *
1808 GC-GAAAACTTCACAGTGGACTAATCTCACTAAAAT
64 GCTAAAAAATTTACAGTGGACTAATCTCACCAAAAT
1843 GATTATAGTT
Statistics
Matches: 1111, Mismatches: 86, Indels: 109
0.85 0.07 0.08
Matches are distributed among these distances:
557 17 0.02
558 6 0.01
559 44 0.04
560 9 0.01
561 137 0.12
562 76 0.07
563 324 0.29
564 1 0.00
565 2 0.00
568 1 0.00
569 3 0.00
570 5 0.00
571 1 0.00
574 1 0.00
575 2 0.00
576 1 0.00
577 2 0.00
578 3 0.00
580 3 0.00
582 5 0.00
583 3 0.00
585 5 0.00
586 3 0.00
587 15 0.01
588 13 0.01
590 4 0.00
593 1 0.00
594 1 0.00
595 2 0.00
618 201 0.18
619 57 0.05
620 91 0.08
621 46 0.04
622 9 0.01
623 17 0.02
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.20
Consensus pattern (560 bp):
AAGACGATTCAAAAAGTCAATAATGGGCCCTAATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
TAAAAAATTTACAGTGGACTAATCTCACCAAAATCGAAGACGATTCAAAATGGAACTAATGGGCC
CCGAAAGACACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACGAATCTCACC
AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGAC
GATTCAAAACGGAACTAATGGGCCCCGATAAGGCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
ACTTCACAGTGGACTAATCTCACTAAAAGATTAGTTAGGCCATAAACAATGGAAAGAAAAGCATG
GAGGTATGCCAAATCGAAGACGATTCAAAACAAAACTAAAGGGCCCTGATAGGCCCAAAATAACA
AGTGTTCCAAATGAGCTAAAAATGTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
ATAAACAATGGAAAGAAAAGCATTGAGGATTGCCAAATCG
Found at i:1800 original size:308 final size:307
Alignment explanation
Indices: 659--1893 Score: 1926
Period size: 308 Copynumber: 4.0 Consensus size: 307
649 AATCTCACCA
*** *
659 AAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGAAAGACACAAAATAACAAGTGTTCCAA
1 AAATCGAAGACGATTCAAAACAAAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAA
* *
724 ATGAGTTAAAAACTTTACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAACCAATG
66 ATGAGCTAAAAACTTTACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG
* *
789 GAAAGAAAAGCATCGAGGGTTGGCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAA
131 GAAAGAAAAGCATCGAGGATTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAA
*
854 GGCACAAAATAACAAGTGTTCGAAATGAGCAAAAATTTCACAGTGGACTAATCTCACT-AAA--A
196 GGCACAAAATAACAAGTGTTCGAAATGAGCAAAAACTTCACAGTGGACTAATCTCACTAAAATGA
* * *
916 --ATAGTTAGGTCATAAACAACTGGAAACGAAAAGCGTGGAGGTTTGCC
261 TTATAGTTAGGCCATAAACAA-TGGAAA-GAAAAGCATTGAGGTTTGCC
* * *
963 AAATCGAAGACGATTCAAAACAAAACTAAAGGGACCCTGATACGGTC-CAAAATAACAAGTGTTC
1 AAATCGAAGACGATTCAAAACAAAACTAATGGG-CCCCGA-AAGG-CACAAAATAACAAGTGTTC
* *
1027 CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACA
63 CAAATGAGCTAAAAACTTTACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
* * ** *
1092 ATGGAAAGAAAGGCATTGAGGATTGCCAAATCGAAGACGATTCAAAACGTCACAAATGGGCCCCT
128 ATGGAAAGAAAAGCATCGAGGATTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC-
* *
1157 GATAGGACCCAAAATAACAAGTGTTCGAAATGAGCAAAAACTTCACAGTGGACTAATCTCACTAA
192 GAAAGG-CACAAAATAACAAGTGTTCGAAATGAGCAAAAACTTCACAGTGGACTAATCTCACTAA
* *
1222 AATGATTATAGTTTAGGCCATAAACAATGGAAAG-AAACCATTAAGGTTTGCC
256 AATGATTATAG-TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCC
*** * * *
1274 AAATCGAAGACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAA
1 AAATCGAAGACGATTCAAAACAAAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAA
1339 ACTGAGCTAAAAAACTTTACAGTTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
66 A-TGAGCT-AAAAACTTTACAG-TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
*
1404 ATGGAAAGAAAAGCATCGAGGATTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCG
128 ATGGAAAGAAAAGCATCGAGGATTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCG
* *
1469 AAAGGCACAAAATAACAAGTGTTCCAAATGAGCAAAAACTTCACAGTGGAATAATCTCACTAAAA
193 AAAGGCACAAAATAACAAGTGTTCGAAATGAGCAAAAACTTCACAGTGGACTAATCTCACTAAAA
* *
1534 TGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCC
258 TGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCC
1584 AAATCGAAGACGATTCAAAACAAAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAA
1 AAATCGAAGACGATTCAAAACAAAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAA
* *
1649 ATGAACTAAAAACTTTACAGTGGACTAATCTCACCAAAAATGATTATAGTTAGGCCAGAAACAAT
66 ATGAGCTAAAAACTTTACAGTGGACTAATCTCACC-AAAATGATTATAGTTAGGCCATAAACAAT
*
1714 GGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAA
130 GGAAAGAAAAGCATCGAGGATTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAA
* *
1779 TGGCACAAAATAACAAGTGTTCGAAATGAGCGAAAACTTCACAGTGGACTAATCTCACTAAAATG
195 AGGCACAAAATAACAAGTGTTCGAAATGAGCAAAAACTTCACAGTGGACTAATCTCACTAAAATG
*
1844 ATTATAGTTAGGCCATAAACAATGGAAAGAAAGGCATTGAGGTTTGCC
260 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCC
1892 AA
1 AA
Statistics
Matches: 849, Mismatches: 65, Indels: 30
0.90 0.07 0.03
Matches are distributed among these distances:
304 29 0.03
305 5 0.01
306 137 0.16
307 21 0.02
308 267 0.31
309 53 0.06
310 152 0.18
311 61 0.07
312 100 0.12
313 10 0.01
314 14 0.02
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.20
Consensus pattern (307 bp):
AAATCGAAGACGATTCAAAACAAAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAA
ATGAGCTAAAAACTTTACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG
GAAAGAAAAGCATCGAGGATTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAA
GGCACAAAATAACAAGTGTTCGAAATGAGCAAAAACTTCACAGTGGACTAATCTCACTAAAATGA
TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCC
Done.