Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020752.1 Corchorus olitorius cultivar O-4 contig20785, 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: 53875
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1245 original size:42 final size:42
Alignment explanation
Indices: 1190--1277 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 42
1180 CTCATCAAAT
* * *
1190 CAAC-TTTTATTCATTCTATATTTATTTTTACCTTAATTAAA
1 CAACATTTAATTCATTCTATATTTACTTTCACCTTAATTAAA
*
1231 CAACATTTAATTCATTCTATGTTTACTTTCACCTTAATTAAA
1 CAACATTTAATTCATTCTATATTTACTTTCACCTTAATTAAA
1273 CAACA
1 CAACA
1278 AAAATACAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 4 0.10
42 38 0.90
ACGTcount: A:0.34, C:0.18, G:0.01, T:0.47
Consensus pattern (42 bp):
CAACATTTAATTCATTCTATATTTACTTTCACCTTAATTAAA
Found at i:1299 original size:45 final size:45
Alignment explanation
Indices: 1248--1339 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
1238 TAATTCATTC
1248 TATGTTTACTTTCACCTTAATTAAACAACAAAAATACAAAAATAA
1 TATGTTTACTTTCACCTTAATTAAACAACAAAAATACAAAAATAA
*
1293 TATGTTTACTTTTACCTTAATTAAACAACAAAAATACAAAAATAA
1 TATGTTTACTTTCACCTTAATTAAACAACAAAAATACAAAAATAA
1338 TA
1 TA
1340 GGAAATAAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.51, C:0.14, G:0.02, T:0.33
Consensus pattern (45 bp):
TATGTTTACTTTCACCTTAATTAAACAACAAAAATACAAAAATAA
Found at i:1662 original size:16 final size:16
Alignment explanation
Indices: 1641--1673 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1631 GGCCGTTTGT
1641 TACTTTCTAAAG-AGAG
1 TACTTTC-AAAGAAGAG
1657 TACTTTCAAAGAAGAG
1 TACTTTCAAAGAAGAG
1673 T
1 T
1674 GATTCCTAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (16 bp):
TACTTTCAAAGAAGAG
Found at i:2793 original size:15 final size:15
Alignment explanation
Indices: 2773--2801 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2763 GGTTTGTTCC
2773 GGCGGCGGCACAACT
1 GGCGGCGGCACAACT
2788 GGCGGCGGCACAAC
1 GGCGGCGGCACAAC
2802 CAAACCATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.34, G:0.41, T:0.03
Consensus pattern (15 bp):
GGCGGCGGCACAACT
Found at i:7467 original size:2 final size:2
Alignment explanation
Indices: 7456--7505 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
7446 AGTTTAGACT
* * *
7456 TA TA TA -A TA TA TA TA TA TA TA TA GA TA TA GA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
7497 GA TA TA TA T
1 TA TA TA TA T
7506 TCATTCGTCA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (2 bp):
TA
Found at i:7473 original size:6 final size:6
Alignment explanation
Indices: 7457--7502 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
7447 GTTTAGACTT
* *
7457 ATATA- ATATAT ATATAT ATATAG ATATAG ATATAG ATATAG ATATA
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATA
7503 TATTCATTCG
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
5 5 0.13
6 34 0.87
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (6 bp):
ATATAG
Found at i:17457 original size:83 final size:81
Alignment explanation
Indices: 17320--17814 Score: 428
Period size: 83 Copynumber: 5.8 Consensus size: 81
17310 TAACTGCATG
** * *
17320 ATAAAAATT-CTCATTATACCTTTATTTAGATGCACCATTATACCTTGATGTATAATAGGAATGC
1 ATAAAAATTCCTCACCA-ACCTTTATTCAGATGCACCATTATACCTTGATGTATAATAGGAACGC
*
17384 CATCGCTTTTGCTACAA
65 CATCGTTTTTGCTACAA
* *
17401 ATAAAAATTCACGTCACCAACCTTTATTCAGATGCGCCATTATACCTTTATGTATAATAGGAACG
1 ATAAAAATTC-C-TCACCAACCTTTATTCAGATGCACCATTATACCTTGATGTATAATAGGAACG
17466 CCA-CTGTTATTGTGCCTTTAAGTGCATA
64 CCATC-GTT-TT-TG-C--T-A---CA-A
** * ** *
17494 AT-AAAATT-CTCATTATACCTTTGTTTGGATGCACCATTATACCTTGATGTATAATAGGAATGC
1 ATAAAAATTCCTCACCA-ACCTTTATTCAGATGCACCATTATACCTTGATGTATAATAGGAACGC
17557 CATCGTTTTTGCTACAA
65 CATCGTTTTTGCTACAA
* *
17574 ATAAAAATTCCTGTCACCAACCTTTATTCAGATGCGCCATTATACCTTTATGTATAATAGGAACG
1 ATAAAAATTCC--TCACCAACCTTTATTCAGATGCACCATTATACCTTGATGTATAATAGGAACG
17639 CCA-CTGTTATTGTGCCTTTAAGTGCATA
64 CCATC-GTT-TT-TG-C--T-A---CA-A
** * ** *
17667 AT-AAAATT-CTCATTATACCTTTGTTTGGATGCACCATTATACCTTGATGTATAATAGGAATGC
1 ATAAAAATTCCTCACCA-ACCTTTATTCAGATGCACCATTATACCTTGATGTATAATAGGAACGC
**
17730 CATCACTTTTGCTACAA
65 CATCGTTTTTGCTACAA
* * *
17747 ATAAAAATTCCCATCACCAACCTTTATTCAGATCCGCCATTATACCTTTATGTATAATAGGAACG
1 ATAAAAATT-CC-TCACCAACCTTTATTCAGATGCACCATTATACCTTGATGTATAATAGGAACG
17812 CCA
64 CCA
17815 CTGTTGTGCC
Statistics
Matches: 335, Mismatches: 42, Indels: 72
0.75 0.09 0.16
Matches are distributed among these distances:
80 6 0.02
81 25 0.07
82 3 0.01
83 137 0.41
84 18 0.05
85 6 0.02
86 2 0.01
87 2 0.01
88 6 0.02
89 14 0.04
90 91 0.27
91 3 0.01
92 16 0.05
93 6 0.02
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.35
Consensus pattern (81 bp):
ATAAAAATTCCTCACCAACCTTTATTCAGATGCACCATTATACCTTGATGTATAATAGGAACGCC
ATCGTTTTTGCTACAA
Found at i:17577 original size:173 final size:173
Alignment explanation
Indices: 17060--17819 Score: 1313
Period size: 173 Copynumber: 4.4 Consensus size: 173
17050 ACGCTTGAAT
* * * * *
17060 TTCCCATCACCGACCTTCATTCAAATGCGCCATTATACATTTATGTATAATAGGAACGCCACTGT
1 TTCCCGTCACCAACCTTTATTCAGATGCGCCATTATACCTTTATGTATAATAGGAACGCCACTGT
17125 TATTGTGCCTTTAACTGCATAATAAAATTTCTCATTATACCTTTATTTAGATGCACCATTATACC
66 TATTGTGCCTTTAACTGCATAATAAAA-TTCTCATTATACCTTTATTTAGATGCACCATTATACC
* *
17190 TTGATGTACAATAGGAATGCCATCACTTTTGCTACAAATAGAAA
130 TTGATGTATAATAGGAATGCCATCACTTTTGCTACAAATAAAAA
17234 TTCCCGTCACCAACCTTTATTCAGATGCGCCATTATACCTTTATGTATAATAGGAACGCCACTGT
1 TTCCCGTCACCAACCTTTATTCAGATGCGCCATTATACCTTTATGTATAATAGGAACGCCACTGT
*
17299 TATTGTGCCTTTAACTGCATGATAAAAATTCTCATTATACCTTTATTTAGATGCACCATTATACC
66 TATTGTGCCTTTAACTGCATAAT-AAAATTCTCATTATACCTTTATTTAGATGCACCATTATACC
*
17364 TTGATGTATAATAGGAATGCCATCGCTTTTGCTACAAATAAAAA
130 TTGATGTATAATAGGAATGCCATCACTTTTGCTACAAATAAAAA
*
17408 TTCACGTCACCAACCTTTATTCAGATGCGCCATTATACCTTTATGTATAATAGGAACGCCACTGT
1 TTCCCGTCACCAACCTTTATTCAGATGCGCCATTATACCTTTATGTATAATAGGAACGCCACTGT
* * *
17473 TATTGTGCCTTTAAGTGCATAATAAAATTCTCATTATACCTTTGTTTGGATGCACCATTATACCT
66 TATTGTGCCTTTAACTGCATAATAAAATTCTCATTATACCTTTATTTAGATGCACCATTATACCT
**
17538 TGATGTATAATAGGAATGCCATCGTTTTTGCTACAAATAAAAA
131 TGATGTATAATAGGAATGCCATCACTTTTGCTACAAATAAAAA
*
17581 TTCCTGTCACCAACCTTTATTCAGATGCGCCATTATACCTTTATGTATAATAGGAACGCCACTGT
1 TTCCCGTCACCAACCTTTATTCAGATGCGCCATTATACCTTTATGTATAATAGGAACGCCACTGT
* * *
17646 TATTGTGCCTTTAAGTGCATAATAAAATTCTCATTATACCTTTGTTTGGATGCACCATTATACCT
66 TATTGTGCCTTTAACTGCATAATAAAATTCTCATTATACCTTTATTTAGATGCACCATTATACCT
17711 TGATGTATAATAGGAATGCCATCACTTTTGCTACAAATAAAAA
131 TGATGTATAATAGGAATGCCATCACTTTTGCTACAAATAAAAA
* *
17754 TTCCCATCACCAACCTTTATTCAGATCCGCCATTATACCTTTATGTATAATAGGAACGCCACTGT
1 TTCCCGTCACCAACCTTTATTCAGATGCGCCATTATACCTTTATGTATAATAGGAACGCCACTGT
17819 T
66 T
17820 GTGCCCTTTA
Statistics
Matches: 563, Mismatches: 22, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
173 314 0.56
174 245 0.44
175 4 0.01
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (173 bp):
TTCCCGTCACCAACCTTTATTCAGATGCGCCATTATACCTTTATGTATAATAGGAACGCCACTGT
TATTGTGCCTTTAACTGCATAATAAAATTCTCATTATACCTTTATTTAGATGCACCATTATACCT
TGATGTATAATAGGAATGCCATCACTTTTGCTACAAATAAAAA
Found at i:25828 original size:12 final size:12
Alignment explanation
Indices: 25811--25835 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25801 TGTAAGTTTA
25811 GTTTATTTATTT
1 GTTTATTTATTT
25823 GTTTATTTATTT
1 GTTTATTTATTT
25835 G
1 G
25836 GTAGTTTAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.12, T:0.72
Consensus pattern (12 bp):
GTTTATTTATTT
Found at i:29804 original size:29 final size:29
Alignment explanation
Indices: 29748--29804 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
29738 ATTATTTTTA
*
29748 AATATATACTATGTAATATATAACATTAC
1 AATATATAATATGTAATATATAACATTAC
29777 AATATATAATATTGT-ATCATATAA-ATTA
1 AATATATAATA-TGTAAT-ATATAACATTA
29805 TATTTATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (29 bp):
AATATATAATATGTAATATATAACATTAC
Found at i:31877 original size:13 final size:13
Alignment explanation
Indices: 31861--31886 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31851 ATATTCTTAC
31861 ATAATGATATAAA
1 ATAATGATATAAA
31874 ATAATGATATAAA
1 ATAATGATATAAA
31887 TGGAAATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (13 bp):
ATAATGATATAAA
Found at i:32470 original size:21 final size:21
Alignment explanation
Indices: 32432--32471 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
32422 ACAAGAAAGA
*
32432 AAGAAAAACTAAATAACAATG
1 AAGAAAAAATAAATAACAATG
32453 AAGAAAAGAATAAA-AACAA
1 AAGAAAA-AATAAATAACAA
32472 GAGGAGAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.72, C:0.07, G:0.10, T:0.10
Consensus pattern (21 bp):
AAGAAAAAATAAATAACAATG
Found at i:38970 original size:37 final size:37
Alignment explanation
Indices: 38926--38996 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
38916 CTTGATCAAC
* *
38926 ATACATGTCTTTTCATATAGACATAACTTTATGATCA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
38963 ATACATGTCTTTCCAAATAGACATAACTTTATGA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGA
38997 ATAATTATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (37 bp):
ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
Found at i:40739 original size:26 final size:25
Alignment explanation
Indices: 40701--40752 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
40691 TTTCTTACAA
40701 AAATAATAGAAATAAACATTAGATAT
1 AAATAATAGAAATAAAC-TTAGATAT
* * * *
40727 AAATCATATAAATGAACTTATATAT
1 AAATAATAGAAATAAACTTAGATAT
40752 A
1 A
40753 TCTCATTGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (25 bp):
AAATAATAGAAATAAACTTAGATAT
Found at i:45828 original size:11 final size:11
Alignment explanation
Indices: 45809--45839 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
45799 ATAATGTCAA
*
45809 ATAGCAAATAT
1 ATAGGAAATAT
45820 ATAGGAAATAT
1 ATAGGAAATAT
45831 ATAGGAAAT
1 ATAGGAAAT
45840 GTTGCCGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.55, C:0.03, G:0.16, T:0.26
Consensus pattern (11 bp):
ATAGGAAATAT
Found at i:47570 original size:109 final size:109
Alignment explanation
Indices: 47379--47593 Score: 385
Period size: 109 Copynumber: 2.0 Consensus size: 109
47369 TAGTAATTTT
47379 GGTGCTTGTATTTTTCTGTAAATCCAATAGTTCATTGCACTTTGTATTGTATGGTATGTGTGCTT
1 GGTGCTTGTATTTTTCTGTAAATCCAATAGTTCATTGCACTTTGTATTGTATGGTATGTGTGCTT
*
47444 ATTTAATAGGTTTAATTGAATAAACAACACAATTAATAATAATA
66 ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
* * *
47488 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCATTTTGTATTGTTTGGTATGTGTGCTT
1 GGTGCTTGTATTTTTCTGTAAATCCAATAGTTCATTGCACTTTGTATTGTATGGTATGTGTGCTT
*
47553 ATTTAATAGGTTCAATTGAATAAACCACACAATTAATAATA
66 ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATA
47594 TATATATATA
Statistics
Matches: 101, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
109 101 1.00
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (109 bp):
GGTGCTTGTATTTTTCTGTAAATCCAATAGTTCATTGCACTTTGTATTGTATGGTATGTGTGCTT
ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
Found at i:48633 original size:11 final size:11
Alignment explanation
Indices: 48614--48644 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
48604 AAATTGAACC
*
48614 AAATCAAATTG
1 AAATGAAATTG
48625 AAATGAAATTG
1 AAATGAAATTG
48636 AAATGAAAT
1 AAATGAAAT
48645 GCAATTCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.58, C:0.03, G:0.13, T:0.26
Consensus pattern (11 bp):
AAATGAAATTG
Found at i:52090 original size:324 final size:322
Alignment explanation
Indices: 51485--52308 Score: 924
Period size: 322 Copynumber: 2.5 Consensus size: 322
51475 ATTTTTTTGT
* * * * * *
51485 TTTTGCATGATTTTTGGCATAAATACTCCTTGAAATATCTATACTCATCGAACAAAATCCCAGCC
1 TTTTGCATGATTTTTGGC-GAAATACT-CTTGAAATATCTATATTTATCAAACCAAATCTCAGCC
* * * * * *
51550 ACGTTCGATTTAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAAAAATAAA
64 ACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* ** * * * *
51615 TTCGGAAAAAA-ATGGAAAGACAATATTAGAAGCGTGAAAAGCCCGTCAATTTTTTTGGCGTTGA
129 TTCGGAAAAAATAT-GAAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGCGTTGA
** * ***
51679 ATTATATATTTTTTCTGAGAATTGTGGCAAAAAAATGAGAAAAAACTTTTCCGATCAGTTTTTAG
193 ATTATATATTTTTTCAAAGAATTGTGGCAAAAAAATCAGAAAAAAAAATTCCGATCAGTTTTTAG
* *
51744 CCGAAATCGTGTACTAACCATCACAGTTTTTGG-CTAGAAACGCG-TTCCCGAGCCCCGACTCAA
258 CCGAAATCGTGTACTAACCATCACAGTATTTGGCCTAAAAACGCGTTTCCCGAGCCCCGACTCAA
* * *
51807 TTTTGCATGATTTTTGGCGCAAAGACTACTTAAAATATCTATATTTATCAAACCAAATGTCAGCC
1 TTTTGCATGATTTTTGGCG-AAATACT-CTTGAAATATCTATATTTATCAAACCAAATCTCAGCC
* * * * *
51872 ACAAT-GGTTATAAGGATTTGTTTTTATGAGCATCTAAATCTTGTTTCGGTTTAATTAGAAATTA
64 ACATTAGATT-TAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* *
51936 ATTCAGAAAAAATATTGTAAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGTGTT
128 ATTCGGAAAAAATA-TG-AAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGCGTT
* * * *
52001 GAATTATATATTTTTTCAAAGTATTGTGGCAAAAAATTCAGAAAAAAAAATTCGGGTCAGTTTTT
191 GAATTATATATTTTTTCAAAGAATTGTGGCAAAAAAATCAGAAAAAAAAATTCCGATCAGTTTTT
** * ** * *
52066 AGCCGAAAATCGTGTACT-ACCATCATGGTATTTGGCCTAAAAACGTGTTTCGGGGGCCCCGGCT
256 AGCCG-AAATCGTGTACTAACCATCACAGTATTTGGCCTAAAAACGCGTTTCCCGAGCCCCGACT
**
52130 CCG
320 CAA
* *
52133 TTTTGCATGATTTTTGGCAGAAATACTCATTGAAATATCTATAATCATCTAATCAATCTCAAGCT
1 TTTTGCATGATTTTTGGC-GAAATACTC-TTGAAATATCTAT-AT--T-T-ATCAAAC-CAA-AT
* *
52198 CTCAGCCACATTAGATTTAAGGATATGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAG
57 CTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG
* *
52263 AAA-TAGATTCGGAAAAAATA-GAAAAATGATATTTAAAGCGAGAAAA
122 AAATTA-ATTCGGAAAAAATATGAAAAATGATATTAAAAGCGTGAAAA
52309 ATATTTCAAT
Statistics
Matches: 418, Mismatches: 65, Indels: 30
0.81 0.13 0.06
Matches are distributed among these distances:
321 3 0.01
322 115 0.28
323 2 0.00
324 114 0.27
325 22 0.05
326 49 0.12
327 3 0.01
329 1 0.00
330 24 0.06
331 7 0.02
332 5 0.01
333 70 0.17
334 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (322 bp):
TTTTGCATGATTTTTGGCGAAATACTCTTGAAATATCTATATTTATCAAACCAAATCTCAGCCAC
ATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT
CGGAAAAAATATGAAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGCGTTGAATT
ATATATTTTTTCAAAGAATTGTGGCAAAAAAATCAGAAAAAAAAATTCCGATCAGTTTTTAGCCG
AAATCGTGTACTAACCATCACAGTATTTGGCCTAAAAACGCGTTTCCCGAGCCCCGACTCAA
Found at i:53604 original size:885 final size:881
Alignment explanation
Indices: 51253--53875 Score: 4391
Period size: 885 Copynumber: 3.0 Consensus size: 881
51243 ACGCGTTTCG
*
51253 TGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAATCTCAGGCTCTCAGCC
1 TGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAATCAATCTCAGGCTCTCAGCC
* * * *
51318 GCTTTTAGACTTAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATAG
66 AC-ATTAGATTTAAGGATATGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATAG
*
51383 ATTCGGAAAAAAATAGAAAAATGATAATTAAAGCGAGAAAAATATTTCAATTTTTTTTTTGCGTT
130 ATTCGGAAAAAAA-AGAAAAATGATATTTAAAGCGAGAAAAATATTTCAA--TTTTTTTTGCGTT
* *
51448 GAATTGTGTATTTTTTGCCGAATATATATTTTTTTGTTTTTGCATGATTTTTGGCATAAATACTC
192 GAATTGTGTATTTTTTGCC---TAT-T-TTTTTTTGTTTTTGCATGATTTTTGACGTAAATACTC
* * *
51513 CTTGAAATATCTATACTCATCGAACAAAATCCCAGCCACGTTCGATTTAAGTATTTGTTTTTACG
252 CTGGAAATATCTATATTCATCGAACAAAATTCCAGCCACGTTCGATTTAAGTATTTGTTTTTACG
* * *
51578 AGCATCTGAATCTTGTTTCAATTTAATTAAAAATAAATTCGGAAAAAAATGGAAAGACAATATTA
317 AGCATCTGAATCTTGTTTCAATTTAATTAAAAATTAATTC-GAAAAAAATGGAAAAACGATATTA
* *
51643 GAAGCGTGAAAAGCCCGTCAATTTTTTTGGCGTTGAATTATATAT-TTTTTCTGAGAATTGTGGC
381 GAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATATTTTTCTGAGTATTGTGGC
** * *
51707 AAAAAAATGAGAAAAAACTTTTCCGATCAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTT
446 AAAAATTTGAG-AAAAACTTTTCCGATTAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTT
*
51772 TTTGGCTAGAAACGCGTTCCCGAGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGACTACT
510 TTTGGCTGGAAACGCGTTCCCGAGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGACTACT
* *
51837 TAAAATATCTATATTTATCAAACCAAATGTCAGCCACAATGGTTATAAGGATTTGTTTTTATGAG
575 TGAAATATCTATATTTATCAAACCAAATGTCAGCCACAATGGTTATAAGGATTTGTTTTTACGAG
*
51902 CATCTAAATCTTGTTTCGGTTTAATTAGAAATTAATTCAGAAAAAATATTGTAAAAATGATATTA
640 CATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATTGTAAAAATGATATTA
* **
51967 AAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTGAATTATATATTTTTTCAAAGTATTGTGGCA
705 AAAGCGTGAAAAGACCATCAACCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCA
*
52032 AAAAATTCAG--AAAAAAAAATTCGGGTCAGTTTTTAGCCGAAAATCGTGTACT-ACCATCATGG
770 AAAAATTCAGAAAAAAAAAAATTCGGGTCAGTTTTTAGCTGAAAATCGTGTACTAACCATCATGG
* * * *
52094 TATTTGGCCT-AAAAACGTGTTTCGGGGGCCCCGGCTCCGTTTTGCA
835 TATTTGGGCTAAAAAACGCGTTTCGGGGGACCCGGCTCAGTTTTGCA
* * * *
52140 TGATTTTTGGCAGAAATACTCATTGAAATATCTATAATCATCTAATCAATCTCAAGCTCTCAGCC
1 TGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAATCAATCTCAGGCTCTCAGCC
52205 ACATTAGATTTAAGGATATGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATAGA
66 ACATTAGATTTAAGGATATGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATAGA
* *
52270 TTCGGAAAAAATAGAAAAATGATATTTAAAGCGAGAAAAATATTTCAATTTTTTTTGCTTTGAAT
131 TTCGGAAAAAAAAGAAAAATGATATTTAAAGCGAGAAAAATATTTCAATTTTTTTTGCGTTGAAT
* *
52335 TGTGTATTTTTTGCCTAATTTTTTTTGTTTTTGCATGCTTTTTGACGTAAATACTCCTGGAAATA
196 TGTGTATTTTTTGCCTATTTTTTTTTGTTTTTGCATGATTTTTGACGTAAATACTCCTGGAAATA
* *
52400 TCTATATTCATCGAACAAAA-TCTCAGCCACGTTCGATTTGAGTATTTGGTTTTACGAGCATCTG
261 TCTATATTCATCGAACAAAATTC-CAGCCACGTTCGATTTAAGTATTTGTTTTTACGAGCATCTG
*
52464 AATCTTGTTTCAATTTAATTAAAAATTAATTCGGAAAAAATGGAAAAACGATATTAGAAGCGTGA
325 AATCTTGTTTCAATTTAATTAAAAATTAATTCGAAAAAAATGGAAAAACGATATTAGAAGCGTGA
52529 AAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATA-TTTTCTGAGTATTGTGGCAAAAATTTG
390 AAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATATTTTTCTGAGTATTGTGGCAAAAATTTG
* * *
52593 AGAAAAACTTTTTCCGATTAGTTTTTAGCCGAAATCTTGTACTAACCATTACGGTTTTTGGTTGG
455 AGAAAAAC-TTTTCCGATTAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTGG
*
52658 AAACGCGTTCCCGAGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATC
519 AAACGCGTTCCCGAGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGACTACTTGAAATATC
** * *
52723 TATATTTATCAAACCAAATGTCAGCCACGTTGGATAGAAGGATTTGTTTTTACGAGCATCTAAAT
584 TATATTTATCAAACCAAATGTCAGCCACAATGGTTATAAGGATTTGTTTTTACGAGCATCTAAAT
* * *
52788 CTTGTTTCGATTTAGTTAGAAATTAATTTAGAAAAAATTTTGTAAAAATGATATTAAAAGCGTGA
649 CTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATTGTAAAAATGATATTAAAAGCGTGA
52853 AAAGACCATCAACCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCA
714 AAAGACCATCAACCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCA
52918 GAAAAAAAAAAAATTCGGGTCAGTTTTTAGCTGAAAATCGTGTACTAACCATCATGGTATTTGGG
779 G-AAAAAAAAAAATTCGGGTCAGTTTTTAGCTGAAAATCGTGTACTAACCATCATGGTATTTGGG
52983 CTAAAAAACGCGTTTCGGGGGACCCGGCTCAGTTTTGCA
843 CTAAAAAACGCGTTTCGGGGGACCCGGCTCAGTTTTGCA
*
53022 TGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATGTAATCAATCTCAGGCTCTCAGCC
1 TGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAATCAATCTCAGGCTCTCAGCC
53087 ACATTAGATTTAAGGATATGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATAGA
66 ACATTAGATTTAAGGATATGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATAGA
*
53152 TTCGGAAAAAAGAAGAAAAAATGATATTTAAAGCGAGAAAAAAATTTC-ATTTTTTTTGCGTTGA
131 TTCGGAAAAAA-AAG-AAAAATGATATTTAAAGCGAGAAAAATATTTCAATTTTTTTTGCGTTGA
* * *
53216 ATTGTGTAATTTTTGCCTCATTTTTTTTTGTTTTTCCATGATTTTTGACGTAAATACTTCTGGAA
194 ATTGTGTATTTTTTGCCT-ATTTTTTTTTGTTTTTGCATGATTTTTGACGTAAATACTCCTGGAA
*
53281 ATATCTAGATTCATCGAACAAAATTCCAGCCACGTTCGATTTAAGTATTTGTTTTTACGAGCATC
258 ATATCTATATTCATCGAACAAAATTCCAGCCACGTTCGATTTAAGTATTTGTTTTTACGAGCATC
* *
53346 TGAATCTTGTTTCAATTTAATCAAAAATTAATTCAGAAAAAAATTGAAAAACGATATTAGAAGCG
323 TGAATCTTGTTTCAATTTAATTAAAAATTAATTC-GAAAAAAATGGAAAAACGATATTAGAAGCG
* *
53411 TGAAAAGCCCGTCAATCTTTTTGGAGTTGAATTATATATATTTTTCTGAGTATTGTGGCTAAAAT
387 TGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATATTTTTCTGAGTATTGTGGCAAAAAT
53476 TTGAGAAAAACTTTTCCGATTAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCT
452 TTGAGAAAAACTTTTCCGATTAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCT
53541 GGAAACGCGTTCCCGAGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGACTACTTGAAATA
517 GGAAACGCGTTCCCGAGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGACTACTTGAAATA
* *
53606 TCTATATTCATCAAACCAAATGTCAGCCACAATGGTTATAAGGATTTGTTTTTACGAGTATCTAA
582 TCTATATTTATCAAACCAAATGTCAGCCACAATGGTTATAAGGATTTGTTTTTACGAGCATCTAA
*
53671 ATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATTGTAAAAATGATATTAAACGCGT
647 ATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATTGTAAAAATGATATTAAAAGCGT
53736 GAAAAGACCATCAACCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATT
712 GAAAAGACCATCAACCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATT
*
53801 CA-TAAAAAAAAAATTACGGGTCAGTTTTTAGCTGAAAATCGTGTACTAACCATCATGGTATTTG
777 CAGAAAAAAAAAAATT-CGGGTCAGTTTTTAGCTGAAAATCGTGTACTAACCATCATGGTATTT-
53865 GGGCTAAAAAA
840 GGGCTAAAAAA
Statistics
Matches: 1630, Mismatches: 90, Indels: 34
0.93 0.05 0.02
Matches are distributed among these distances:
876 6 0.00
877 389 0.24
878 131 0.08
879 1 0.00
880 43 0.03
881 19 0.01
882 169 0.10
883 77 0.05
884 212 0.13
885 417 0.26
886 105 0.06
887 61 0.04
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (881 bp):
TGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAATCAATCTCAGGCTCTCAGCC
ACATTAGATTTAAGGATATGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATAGA
TTCGGAAAAAAAAGAAAAATGATATTTAAAGCGAGAAAAATATTTCAATTTTTTTTGCGTTGAAT
TGTGTATTTTTTGCCTATTTTTTTTTGTTTTTGCATGATTTTTGACGTAAATACTCCTGGAAATA
TCTATATTCATCGAACAAAATTCCAGCCACGTTCGATTTAAGTATTTGTTTTTACGAGCATCTGA
ATCTTGTTTCAATTTAATTAAAAATTAATTCGAAAAAAATGGAAAAACGATATTAGAAGCGTGAA
AAGCCCGTCAATCTTTTTGGCGTTGAATTATATATATTTTTCTGAGTATTGTGGCAAAAATTTGA
GAAAAACTTTTCCGATTAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTGGAA
ACGCGTTCCCGAGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGACTACTTGAAATATCTA
TATTTATCAAACCAAATGTCAGCCACAATGGTTATAAGGATTTGTTTTTACGAGCATCTAAATCT
TGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATTGTAAAAATGATATTAAAAGCGTGAAA
AGACCATCAACCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGA
AAAAAAAAAATTCGGGTCAGTTTTTAGCTGAAAATCGTGTACTAACCATCATGGTATTTGGGCTA
AAAAACGCGTTTCGGGGGACCCGGCTCAGTTTTGCA
Done.