Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018318.1 Corchorus olitorius cultivar O-4 contig18351, 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: 22752
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Found at i:365 original size:31 final size:31
Alignment explanation
Indices: 327--429 Score: 81
Period size: 31 Copynumber: 3.5 Consensus size: 31
317 TTGTACGACC
*
327 GAGGGATGCTCATTTTTCTTTTTACGCAAGT
1 GAGGGATGCCCATTTTTCTTTTTACGCAAGT
** * * *
358 GAGGGATGCCCATTGGGTCGTGTGAC-C----
1 GAGGGATGCCCATT-TTTCTTTTTACGCAAGT
* *
385 GAGGGATGCTCATTTTTCTTTTTGCGCAAGT
1 GAGGGATGCCCATTTTTCTTTTTACGCAAGT
*
416 GGGGGATGCCCATT
1 GAGGGATGCCCATT
430 GGGTCGTGTG
Statistics
Matches: 51, Mismatches: 15, Indels: 12
0.65 0.19 0.15
Matches are distributed among these distances:
26 5 0.10
27 14 0.27
31 26 0.51
32 6 0.12
ACGTcount: A:0.17, C:0.18, G:0.31, T:0.34
Consensus pattern (31 bp):
GAGGGATGCCCATTTTTCTTTTTACGCAAGT
Found at i:390 original size:58 final size:57
Alignment explanation
Indices: 323--510 Score: 245
Period size: 58 Copynumber: 3.2 Consensus size: 57
313 TAGGTTGTAC
*
323 GACCGAGGGATGCTCATTTTTCTTTTTACGCAAGTGAGGGATGCCCATTGGGTCGTGT
1 GACCGAGGGATGCTCATTTTTCTTTTT-CGCAAGTGGGGGATGCCCATTGGGTCGTGT
381 GACCGAGGGATGCTCATTTTTCTTTTTGCGCAAGTGGGGGATGCCCATTGGGTCGTGT
1 GACCGAGGGATGCTCATTTTTCTTTTT-CGCAAGTGGGGGATGCCCATTGGGTCGTGT
* * ****
439 GACCGAGGGATGTTCGA-TTTTCTTATT-GCATGAGTGGGGGATGCCCACCAAGTCGTGT
1 GACCGAGGGATGCTC-ATTTTTCTTTTTCGCA--AGTGGGGGATGCCCATTGGGTCGTGT
*
497 GACTGAGGGATGCT
1 GACCGAGGGATGCT
511 TGGTCGTTCT
Statistics
Matches: 117, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
56 3 0.03
58 113 0.97
59 1 0.01
ACGTcount: A:0.17, C:0.19, G:0.34, T:0.31
Consensus pattern (57 bp):
GACCGAGGGATGCTCATTTTTCTTTTTCGCAAGTGGGGGATGCCCATTGGGTCGTGT
Found at i:2091 original size:86 final size:86
Alignment explanation
Indices: 1946--2121 Score: 298
Period size: 86 Copynumber: 2.0 Consensus size: 86
1936 AGTTGGTTTT
** *
1946 TCCCATGTTTTCTCTTCCTAAGTAGTCTTGAGCTTGCCCCCCGAGTGGAGGTCTACCATGTGGTG
1 TCCCATGTTTGATCTTCCTAAATAGTCTTGAGCTTGCCCCCCGAGTGGAGGTCTACCATGTGGTG
*
2011 AGCGGTCATCGCTTGGTGGTC
66 AGCGGTAATCGCTTGGTGGTC
* *
2032 TCCCATGTTTGATCTTCCTAAATAGTCTTGAGCTTGCCCCCTGAGTGGAGGTTTACCATGTGGTG
1 TCCCATGTTTGATCTTCCTAAATAGTCTTGAGCTTGCCCCCCGAGTGGAGGTCTACCATGTGGTG
2097 AGCGGTAATCGCTTGGTGGTC
66 AGCGGTAATCGCTTGGTGGTC
2118 TCCC
1 TCCC
2122 GCCTTCCGTG
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
86 84 1.00
ACGTcount: A:0.14, C:0.26, G:0.27, T:0.33
Consensus pattern (86 bp):
TCCCATGTTTGATCTTCCTAAATAGTCTTGAGCTTGCCCCCCGAGTGGAGGTCTACCATGTGGTG
AGCGGTAATCGCTTGGTGGTC
Found at i:2228 original size:24 final size:24
Alignment explanation
Indices: 2183--2243 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
2173 GGCACGCTGT
* *
2183 CACTTCGGATGG-GGGTGTGCTCC
1 CACTTCCGATGGTGGGTGCGCTCC
**
2206 TGCTTCCGATGGTGGGTGCGCTCC
1 CACTTCCGATGGTGGGTGCGCTCC
*
2230 CACTTCTGATGGTG
1 CACTTCCGATGGTG
2244 AGCATTCAAC
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 9 0.30
24 21 0.70
ACGTcount: A:0.08, C:0.26, G:0.36, T:0.30
Consensus pattern (24 bp):
CACTTCCGATGGTGGGTGCGCTCC
Found at i:2523 original size:28 final size:28
Alignment explanation
Indices: 2491--2920 Score: 259
Period size: 28 Copynumber: 15.4 Consensus size: 28
2481 TTGTCTTCGA
2491 GAGCGTACTACCTCTTCGCGATCTTTGG
1 GAGCGTACTACCTCTTCGCGATCTTTGG
2519 GAGCGTACTACCTCTTCGCGATCTTTGG
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * * *
2547 GAGCGTACTACCTCTTTGTGATCCTTGA
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* *
2575 GAGCGTACTACCGCTTCGCGGT-TGTTGG
1 GAGCGTACTACCTCTTCGCGATCT-TTGG
* *
2603 GAGCGTACTACCGCTTCGCGCTCTTTGG
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * *
2631 GAGCGTACTACCGCTTCACGCTCTTTGG
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * * *
2659 GAGCGTACTACCACCTCGAGAGC-TTGG
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * * *
2686 AGGGCGTACTACCAT-TTCGTGAACTTTGA
1 -GAGCGTACTACC-TCTTCGCGATCTTTGG
* * * *
2715 G-GCGTACTACCACTTTGCGATCCTTGA
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * * * *
2742 GAGCATACTACCACCTCGGGAGC-TT-G
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * *
2768 GAGGGAATACTACCAT-TTCGCGAACTTTGA
1 GAGCG--TACTACC-TCTTCGCGATCTTTGG
* * * * *
2798 GAGCGTACTACCGCTTCACGCTTTTTGA
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * * * *
2826 TAGCGTACTACCACCTCGAGAGC-TTGG
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * * * *
2853 AGGGCGTACTACCGT-TCCGTGAACTTTGA
1 -GAGCGTACTACC-TCTTCGCGATCTTTGG
* * * * *
2882 G-GTGTACTACCACTTTGCGATCCTTGA
1 GAGCGTACTACCTCTTCGCGATCTTTGG
2909 GAGCGTACTACC
1 GAGCGTACTACC
2921 ACCTCGGGAG
Statistics
Matches: 311, Mismatches: 73, Indels: 36
0.74 0.17 0.09
Matches are distributed among these distances:
26 3 0.01
27 49 0.16
28 246 0.79
29 9 0.03
30 4 0.01
ACGTcount: A:0.19, C:0.27, G:0.26, T:0.28
Consensus pattern (28 bp):
GAGCGTACTACCTCTTCGCGATCTTTGG
Found at i:2558 original size:56 final size:56
Alignment explanation
Indices: 2491--2920 Score: 327
Period size: 56 Copynumber: 7.7 Consensus size: 56
2481 TTGTCTTCGA
* * * *
2491 GAGCGTACTACCTCTTCGCGATCTTTGGGAGCGTACTACCTCTTCGCGATCTTTGG
1 GAGCGTACTACCACTTCGCGATCCTTGAGAGCGTACTACCGCTTCGCGATCTTTGG
* * * *
2547 GAGCGTACTACCTCTTTGTGATCCTTGAGAGCGTACTACCGCTTCGCGGT-TGTTGG
1 GAGCGTACTACCACTTCGCGATCCTTGAGAGCGTACTACCGCTTCGCGATCT-TTGG
* * * * * *
2603 GAGCGTACTACCGCTTCGCGCTCTTTGGGAGCGTACTACCGCTTCACGCTCTTTGG
1 GAGCGTACTACCACTTCGCGATCCTTGAGAGCGTACTACCGCTTCGCGATCTTTGG
* * * * ** * * *
2659 GAGCGTACTACCACCTCGAGA-GCTTGGAGGGCGTACTACCATTTCGTGAACTTTGA
1 GAGCGTACTACCACTTCGCGATCCTT-GAGAGCGTACTACCGCTTCGCGATCTTTGG
* * * * * *
2715 G-GCGTACTACCACTTTGCGATCCTTGAGAGCATACTACCACCTCGGGAGC-TT-G
1 GAGCGTACTACCACTTCGCGATCCTTGAGAGCGTACTACCGCTTCGCGATCTTTGG
* * * * * * * *
2768 GAGGGAATACTACCATTTCGCGAACTTTGAGAGCGTACTACCGCTTCACGCTTTTTGA
1 GAGCG--TACTACCACTTCGCGATCCTTGAGAGCGTACTACCGCTTCGCGATCTTTGG
* * * * * * * *
2826 TAGCGTACTACCACCTCGAGA-GCTTGGAGGGCGTACTACCG-TTCCGTGAACTTTGA
1 GAGCGTACTACCACTTCGCGATCCTT-GAGAGCGTACTACCGCTT-CGCGATCTTTGG
* *
2882 G-GTGTACTACCACTTTGCGATCCTTGAGAGCGTACTACC
1 GAGCGTACTACCACTTCGCGATCCTTGAGAGCGTACTACC
2921 ACCTCGGGAG
Statistics
Matches: 288, Mismatches: 74, Indels: 25
0.74 0.19 0.06
Matches are distributed among these distances:
53 1 0.00
54 4 0.01
55 70 0.24
56 207 0.72
57 3 0.01
58 3 0.01
ACGTcount: A:0.19, C:0.27, G:0.26, T:0.28
Consensus pattern (56 bp):
GAGCGTACTACCACTTCGCGATCCTTGAGAGCGTACTACCGCTTCGCGATCTTTGG
Found at i:2630 original size:84 final size:84
Alignment explanation
Indices: 2489--2920 Score: 286
Period size: 84 Copynumber: 5.2 Consensus size: 84
2479 TTTTGTCTTC
* *
2489 GAGAGCGTACTACCTCTTCGCGATCTTTGGGAGCGTACTACCTCTTCGCGATCTTTGGGAGCGTA
1 GAGAGCGTACTACCGCTTCGCGATCTTTGGGAGCGTACTACCGCTTCGCGATCTTTGGGAGCGTA
2554 CTACCTCTTTGTGATCCTT
66 CTACCTCTTTGTGATCCTT
* *
2573 GAGAGCGTACTACCGCTTCGCGGT-TGTTGGGAGCGTACTACCGCTTCGCGCTCTTTGGGAGCGT
1 GAGAGCGTACTACCGCTTCGCGATCT-TTGGGAGCGTACTACCGCTTCGCGATCTTTGGGAGCGT
* *** * *
2637 ACTACCGCTTCACGCTCTTT
65 ACTACCTCTTTGTGATCCTT
* * * * * * ** * * *
2657 GGGAGCGTACTACCACCTCGAGAGC-TTGGAGGGCGTACTACCATTTCGTGAACTTTGAG-GCGT
1 GAGAGCGTACTACCGCTTCGCGATCTTTGG-GAGCGTACTACCGCTTCGCGATCTTTGGGAGCGT
* *
2720 ACTACCACTTTGCGATCCTT
65 ACTACCTCTTTGTGATCCTT
* * * * * * ** * *
2740 GAGAGCATACTACCACCTCGGGAGC-TT-GGAGGGAATACTACCATTTCGCGAACTTTGAGAGCG
1 GAGAGCGTACTACCGCTTCGCGATCTTTGGGAGCG--TACTACCGCTTCGCGATCTTTGGGAGCG
* *** * **
2803 TACTACCGCTTCACGCTTTTT
64 TACTACCTCTTTGTGATCCTT
* * * * * * * * * *
2824 GATAGCGTACTACCACCTCGAGAGC-TTGGAGGGCGTACTACCG-TTCCGTGAACTTTGAG-GTG
1 GAGAGCGTACTACCGCTTCGCGATCTTTGG-GAGCGTACTACCGCTT-CGCGATCTTTGGGAGCG
* *
2886 TACTACCACTTTGCGATCCTT
64 TACTACCTCTTTGTGATCCTT
2907 GAGAGCGTACTACC
1 GAGAGCGTACTACC
2921 ACCTCGGGAG
Statistics
Matches: 284, Mismatches: 55, Indels: 19
0.79 0.15 0.05
Matches are distributed among these distances:
81 3 0.01
82 1 0.00
83 103 0.36
84 173 0.61
85 1 0.00
86 3 0.01
ACGTcount: A:0.19, C:0.27, G:0.26, T:0.28
Consensus pattern (84 bp):
GAGAGCGTACTACCGCTTCGCGATCTTTGGGAGCGTACTACCGCTTCGCGATCTTTGGGAGCGTA
CTACCTCTTTGTGATCCTT
Found at i:2744 original size:167 final size:165
Alignment explanation
Indices: 2484--2965 Score: 592
Period size: 167 Copynumber: 2.9 Consensus size: 165
2474 CGCATTTTTG
* * * * * * * * *
2484 TCTTCGAGAGCGTACTACCTCTTCGCGATCTTTGG-GAGCGTACTACCTCTTCGCGATCTTTGGG
1 TCTTTGAGAGCGTACTACCACCTCGAGAGC-TTGGAGGGCGTACTACCT-TTCGTGAACTTTGAG
* * * * *
2548 AGCGTACTACCTCTTTGTGATCCTTGAGAGCGTACTACCGCTTCGCGGTTG-TTGGGAGCG-TAC
64 -GCGTACTACCACTTTGCGATCCTTGAGAGCGTACTACCACCTCG-GG-AGCTT-GGAGCGATAC
* ** *
2611 TACCGCTTCGCGCTCTTTGGGAGCGTACTACCGCTTCACGC
125 TACCACTTCGCGAACTTTGAGAGCGTACTACCGCTTCACGC
*
2652 TCTTTGGGAGCGTACTACCACCTCGAGAGCTTGGAGGGCGTACTACCATTTCGTGAACTTTGAGG
1 TCTTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGCGTACTACC-TTTCGTGAACTTTGAGG
* *
2717 CGTACTACCACTTTGCGATCCTTGAGAGCATACTACCACCTCGGGAGCTTGGAGGGAATACTACC
65 CGTACTACCACTTTGCGATCCTTGAGAGCGTACTACCACCTCGGGAGCTTGGAGCG-ATACTACC
*
2782 ATTTCGCGAACTTTGAGAGCGTACTACCGCTTCACGC
129 ACTTCGCGAACTTTGAGAGCGTACTACCGCTTCACGC
* * *
2819 TTTTTGATAGCGTACTACCACCTCGAGAGCTTGGAGGGCGTACTACCGTTCCGTGAACTTTGAGG
1 TCTTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGCGTACTACC-TTTCGTGAACTTTGAGG
* * *
2884 TGTACTACCACTTTGCGATCCTTGAGAGCGTACTACCACCTCGGGAGCTTGGTGGGAGTACTACC
65 CGTACTACCACTTTGCGATCCTTGAGAGCGTACTACCACCTCGGGAGCTTGGAGCGA-TACTACC
*
2949 ATTTCGCGAACTTTGAG
129 ACTTCGCGAACTTTGAG
2966 GCGCGTTCTA
Statistics
Matches: 278, Mismatches: 30, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
165 6 0.02
166 5 0.02
167 219 0.79
168 47 0.17
169 1 0.00
ACGTcount: A:0.19, C:0.27, G:0.26, T:0.28
Consensus pattern (165 bp):
TCTTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGCGTACTACCTTTCGTGAACTTTGAGGC
GTACTACCACTTTGCGATCCTTGAGAGCGTACTACCACCTCGGGAGCTTGGAGCGATACTACCAC
TTCGCGAACTTTGAGAGCGTACTACCGCTTCACGC
Found at i:2965 original size:56 final size:57
Alignment explanation
Indices: 2712--2965 Score: 168
Period size: 56 Copynumber: 4.5 Consensus size: 57
2702 TCGTGAACTT
* * * *
2712 TGAGGCGTACTACCACTTT-GCGATCCTTGAGAGCATACTACCACCTCGGGAGCTTGG
1 TGAGGAGTACTACCA-TTTCGCGAACTTTGAGAGCGTACTACCACCTCGGGAGCTTGG
* * * * **
2769 AG-GGAATACTACCATTTCGCGAACTTTGAGAGCGTACTACCGCTTC---ACGCTTTT
1 TGAGGAGTACTACCATTTCGCGAACTTTGAGAGCGTACTACCACCTCGGGA-GCTTGG
* * ** * * * * ** * *
2823 TGATAGCGTACTACCACCTCGAGAGCTTGGAGGGCGTACTACC-GTTCCGTGAACTT--
1 TGA-GGAGTACTACCATTTCGCGAACTTTGAGAGCGTACTACCACCT-CGGGAGCTTGG
* * *
2879 TGAGGTGTACTACCACTTT-GCGATCCTTGAGAGCGTACTACCACCTCGGGAGCTTGG
1 TGAGGAGTACTACCA-TTTCGCGAACTTTGAGAGCGTACTACCACCTCGGGAGCTTGG
2936 TG-GGAGTACTACCATTTCGCGAACTTTGAG
1 TGAGGAGTACTACCATTTCGCGAACTTTGAG
2966 GCGCGTTCTA
Statistics
Matches: 146, Mismatches: 38, Indels: 27
0.69 0.18 0.13
Matches are distributed among these distances:
53 1 0.01
54 5 0.03
55 43 0.29
56 90 0.62
57 3 0.02
58 3 0.02
59 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.27
Consensus pattern (57 bp):
TGAGGAGTACTACCATTTCGCGAACTTTGAGAGCGTACTACCACCTCGGGAGCTTGG
Found at i:3780 original size:31 final size:31
Alignment explanation
Indices: 3744--3844 Score: 79
Period size: 31 Copynumber: 3.4 Consensus size: 31
3734 GTACGACCGA
*
3744 GGGATGCTCATTTTTCTTTTTGCGCAAGTGG
1 GGGATGCCCATTTTTCTTTTTGCGCAAGTGG
** * * *
3775 GGGATGCCCATTGGGTC-GTGTGAC-C----GA
1 GGGATGCCCATT-TTTCTTTTTG-CGCAAGTGG
*
3802 GGGATGCTCATTTTTCTTTTTGCGCAAGTGG
1 GGGATGCCCATTTTTCTTTTTGCGCAAGTGG
3833 GGGATGCCCATT
1 GGGATGCCCATT
3845 GGGTCGTGTG
Statistics
Matches: 49, Mismatches: 13, Indels: 16
0.63 0.17 0.21
Matches are distributed among these distances:
26 3 0.06
27 16 0.33
31 27 0.55
32 3 0.06
ACGTcount: A:0.14, C:0.19, G:0.33, T:0.35
Consensus pattern (31 bp):
GGGATGCCCATTTTTCTTTTTGCGCAAGTGG
Found at i:3811 original size:58 final size:58
Alignment explanation
Indices: 3738--3985 Score: 302
Period size: 58 Copynumber: 4.3 Consensus size: 58
3728 TAGGTTGTAC
* * * **
3738 GACCGAGGGATGCTC-ATTTTTCTTTTTGCGCAAGTGGGGGATGCCCATTGGGTCGTGT
1 GACCGAGGGATGCTCGA-TTTTCTTATTGCACAAGTGGGGGATGCCCACTAAGTCGTGT
* * * **
3796 GACCGAGGGATGCTC-ATTTTTCTTTTTGCGCAAGTGGGGGATGCCCATTGGGTCGTGT
1 GACCGAGGGATGCTCGA-TTTTCTTATTGCACAAGTGGGGGATGCCCACTAAGTCGTGT
* **
3854 GACCGAGGGATGTTCGATTTTCTTATTGCATGAGTGGGGGATGCCCACTAAGTCGTGT
1 GACCGAGGGATGCTCGATTTTCTTATTGCACAAGTGGGGGATGCCCACTAAGTCGTGT
** * * *
3912 GACCGAGGGATGCTCGATTTTCTTATTGCATGAGTGGGGGTTCCCCACCAAGTCGTGT
1 GACCGAGGGATGCTCGATTTTCTTATTGCACAAGTGGGGGATGCCCACTAAGTCGTGT
3970 GACCGAGGGATGCTCG
1 GACCGAGGGATGCTCG
3986 GTCGTTCTTG
Statistics
Matches: 177, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
58 176 0.99
59 1 0.01
ACGTcount: A:0.16, C:0.20, G:0.34, T:0.30
Consensus pattern (58 bp):
GACCGAGGGATGCTCGATTTTCTTATTGCACAAGTGGGGGATGCCCACTAAGTCGTGT
Found at i:8264 original size:144 final size:146
Alignment explanation
Indices: 8001--8290 Score: 469
Period size: 144 Copynumber: 2.0 Consensus size: 146
7991 CAGTTTCCCA
* *
8001 TGTGAGGAATGAAGAAAAGTGTGACGAAATGAGAAGGCTGAGACAAGAAATGGAAGATGCAAATC
1 TGTGAGGAATGAAGAAAAG-GCGACGAAATGAGAAGGCTGAGACAAGAAATGGAAGATACAAATC
*
8066 TGCAAACTATGATTATGGAACAGACTTACTTAACCCTTTTCAAAAGTTTGGCAGAGGAATTTCAT
65 TGCAAACTATGATGATGGAACAGACTTACTTAACCCTTTTCAAAAGTTTGGCAGAGGAATTTCAT
* *
8131 ACTGAGATGCTTAACCG
130 ACCGAGATGATTAACCG
8148 TGTGAGGAATGAAGAAAA-GCG-CGAAATGAGAAGGCTGAGACAAGAAATGGAAGATACAAATCT
1 TGTGAGGAATGAAGAAAAGGCGACGAAATGAGAAGGCTGAGACAAGAAATGGAAGATACAAATCT
* * *
8211 GCAAGCTATGATGATGGAACAGA-TGTATTTAACCCTTTTCAGAAGTTTGGCAGAGGAATTTCAT
66 GCAAACTATGATGATGGAACAGACT-TACTTAACCCTTTTCAAAAGTTTGGCAGAGGAATTTCAT
8275 ACCGAGATGATTAACC
130 ACCGAGATGATTAACC
8291 ATCACCTGCA
Statistics
Matches: 134, Mismatches: 8, Indels: 5
0.91 0.05 0.03
Matches are distributed among these distances:
143 1 0.01
144 113 0.84
145 2 0.01
147 18 0.13
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.23
Consensus pattern (146 bp):
TGTGAGGAATGAAGAAAAGGCGACGAAATGAGAAGGCTGAGACAAGAAATGGAAGATACAAATCT
GCAAACTATGATGATGGAACAGACTTACTTAACCCTTTTCAAAAGTTTGGCAGAGGAATTTCATA
CCGAGATGATTAACCG
Found at i:20230 original size:332 final size:330
Alignment explanation
Indices: 19300--22486 Score: 2140
Period size: 332 Copynumber: 9.7 Consensus size: 330
19290 AAAGATGCCA
* * * * * *
19300 AAAAAGATTGGAGGACTTTTCATGATTTTAATATCGTTTTTCATATTTTTTTCTGAATTAATTTC
1 AAAAAGATTGAAAG-CTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCTGAATTAATTTC
* * * * * * *
19365 TAATTAAATCGAACCAAGATTCAGATGCACATAAAAACAAATCCTTAAATCCAATATGGCTGAAA
65 TAATTAAATCAAAACAAGATTCAGAAGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGA
* * * * *
19430 TTTGGTTAGATGAATAAAGATATTTCAAGGAGTCTCGGTGCCAAAAATCATGCAAAACAGA-GTC
130 TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGACCT-
* * * *
19494 GTGGCCCTGTAACGCGTTTTTAG-CCAAAAC--CCGTGATGGTTAGTACACGATTTCGGCTAAAA
194 G-GGCCCCGGAACGCGTTTTTAGCCCAAAACAACC---AT-GATAGTACACAATTTCGGCTAAAA
* * *
19556 TTTTGA-AAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATAT
254 TTTT-ACAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATA-
* ***
19620 ATATAATTCGATATC
317 A-ATAATTCAACGCC
* * * * * *
19635 AAAAAGATTGAAGGGTTTTTAACGCTTCTAATATTGCTTATTCCTATTTTTTTCCGAATTAATTT
1 AAAAAGATTGAA-AGCTTTTCACGCTTCTAATATCG-TTTTTCCTATTTTTTTCTGAATTAATTT
* * *
19700 CTAATTAAAT-AGAAACAATAAGATTCA-AATGCTCGTAAAAATAAATTCTTAAATCTAATGTGG
64 CTAATTAAATCA-AAAC---AAGATTCAGAA-GCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * * * *
19763 CTGAGATTTGGTTAGATGAATATAAATATTTCAAGGAGTCTTGACACAAAAAATCATACAAAACT
124 CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACT
* * * **** *
19828 GA-GTCGGGTCCCGGAACGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACAATTTCGGCT-A
189 GACCT-GGGCCCCGGAACGCGTTTTTAGCCCAAAACAACCAT-GATAGTACACAATTTCGGCTAA
* ** * *
19891 AATTTTACAAAAATTGACTCGAAAGATTTTTCCTC-ATTTTCTAGTGAAAACACTCATAAAAAAC
252 AATTTTACAAAAATTGACCCGAAAGATTTTTCCTCAATTTT-TAGCCAAAATACTCATAAAAAAT
19955 AAATAATTCAACGCC
316 AAATAATTCAACGCC
**
19970 AAAAA-AGTTGAAAGCTTTTTCACGCTTCTAATATCGTTTTTCCTATTTTATTTCAAAATTAATT
1 AAAAAGA-TTGAAAGC-TTTTCACGCTTCTAATATCGTTTTTCCTATTTT-TTTCTGAATTAATT
* * * * * * * *
20034 TCTGATTAAATCAAAACAAGATTTAGAAACTCGTACAAACAAATTCTTAAATACAATGCGACTGA
63 TCTAATTAAATCAAAACAAGATTCAGAAGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGA
*
20099 GATTTGGTTAGATGAATATATATA-TT-AAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGACC
128 GATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGACC
* * * ** * *
20162 TAGAGCCCCGGAATGCTTTTTTAGCAAAAAAACAACCAAGATGGTACACAATTTCGGCTAAAATT
193 T-GGGCCCCGGAACGCGTTTTTAGC-CCAAAACAACCATGATAGTACACAATTTCGGCTAAAATT
* * * * *
20227 TTACAAAAATTGATCCGAAATATTTTTTCTCAATTTTTAGCCACAATACTCATAAAAAATATATA
256 TTACAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATAAATA
*
20292 ATTCCACGCC
321 ATTCAACGCC
* * *
20302 AAAAAGATTGAAGGGCTTCTCACGCTTCTAATATCGTTTTTCCTATTTGTTTTC-AAATTAATTT
1 AAAAAGATTGAA-AGCTTTTCACGCTTCTAATATCGTTTTTCCTATTT-TTTTCTGAATTAATTT
** * *
20366 CTAATTAAATTGAAACATGATTCA-AATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAA
64 CTAATTAAATCAAAACAAGATTCAGAA-GCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGA
* * * *
20430 GATTTGGTTAGATGAATATAGATATTTCAAGGAATGTT-GCTACTAAAAATCATGCAAAACTGAC
128 GATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGC-GCCAAAAATCATGCAAAACTGA-
* ** * ** * * *
20494 CCGGGGCCCCAAAACGCGTTTTTA-ACCAAAA-AACTTTTATAGTACACGATTTCGGCTAATATT
191 CCTGGGCCCCGGAACGCGTTTTTAGCCCAAAACAACCATGATAGTACACAATTTCGGCTAAAATT
** * * * * * * * *
20557 TCCCAAAAATTGACCCAAAATATTTTTCCTCCATTTTTAGCCACAATACTTATAGAATATATATA
256 TTACAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATAAATA
** *
20622 ATGAAAAGCC
321 ATTCAACGCC
* * * * *
20632 AAAAATATTGGAGAA-CTCTTCACGCTTTTAATATCATTTTT--TATATTTTTCTGAATTAATTT
1 AAAAAGATT-GA-AAGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCTGAATTAATTT
* * * ** *
20694 CTAATTAAATC-GAACAAGATTCAGATGCTCGTAAAAACAAGTCCTTAAATTGAATGTGGCTAAG
64 CTAATTAAATCAAAACAAGATTCAGAAGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG
* * * *
20758 ATTTGATTAGATAAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTAAGTC
129 ATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGA-CC
* ** * * * * ** ***
20823 GGGGTTCCGAAACGCGTTTTTAGCCAAAAAAAAACTGTGATGATTAGTACATGATTTTAACTAAA
193 TGGGCCCCGGAACGCGTTTTTAGCC-CAAAACAAC---CATGA-TAGTACACAATTTCGGCTAAA
** * * * * *
20888 ATTTTGTAAAAAGTGACCCAAAAAATTTTTCTGTCAATTTTT-GCCATAAATACTCATAAAATAT
253 ATTTTACAAAAATTGACCCGAAAGATTTTTC-CTCAATTTTTAGCCA-AAATACTCATAAAAAAT
* * *
20952 ATATAATTTAACACC
316 AAATAATTCAACGCC
* *** * * *
20967 AAAAGGATTGGGGGACTTTTCACGCTTTTAATATCGTGTTT-C-ATATTTTTCTGAATTAATTTC
1 AAAAAGATTGAAAG-CTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCTGAATTAATTTC
* * * * **
21030 TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAATCAAATTCTTAAATCCAATGTAGAATGAG
65 TAATTAAATCAAAACAAGATTCAGAAGCTCGTAAAAACAAATCCTTAAATCCAATGT-GGCTGAG
** * * * * * ** *
21095 ATTTAATTAGATGAATATGGATATGTCAAAGATTTTTTACGCCAAAAATCATGCAAAACTTAGCC
129 ATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGA-CC
* ** * * * *
21160 GGGGCCTTGAAACGCCG----T-G------------ATGATTATTACACGATTTCGCCTAAAATT
193 TGGGCCCCGGAACG-CGTTTTTAGCCCAAAACAACCATGA-TAGTACACAATTTCGGCTAAAATT
* * * * * * *
21208 TTACAAAAAAT-A-CC-AAAAATTTTTTTCTCAATTTTTAGCTAAAATACTCATGAAATATATAT
256 TTACAAAAATTGACCCGAAAGA-TTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATAAAT
* * *
21270 AATTTTAA-ACT
320 AA-TTCAACGCC
* * * * * * * * * *
21281 AAAAAGATTGGAGGACGTTTCACGATTTTCATATCGTTTTTCATA-ATTTTTCTAAATTAATTTT
1 AAAAAGATTGAAAG-CTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCTGAATTAATTTC
* * * * * * * *
21345 TAATTTAATCGAAATAAGATTTAGATGCTCGTAAAAACAAATCCTCAAATGCAATGTGTCTGAGA
65 TAATTAAATCAAAACAAGATTCAGAAGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGA
* ** * * * * *
21410 TTTGATTAGATGAATACGGATATCTCAAGTAGTCTTAGCGCCAAAAATCATGCAAAACTAACCCA
130 TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGA-CCT
** * * **** * *
21475 GGGCCTTGGAACGCATTTTTAGCCAAAAACTGTGATGATTATTACACGATTTCGGCTAAAATTTT
194 GGGCCCCGGAACGCGTTTTTAGCCCAAAACAACCATGA-TAGTACACAATTTCGGCTAAAATTTT
** * * * * * * *
21540 GTAAAAAATGACCGGAAATATATTTCCTCAATTTTTTTGCTAAATTA-TCAT-AAAAATAATATA
258 ACAAAAATTGACCCGAAAGATTTTTCCTCAA-TTTTTAGCCAAAATACTCATAAAAAATAA-ATA
*
21603 ATTCTACGCC
321 ATTCAACGCC
* * * * * * * * * *
21613 AAAAATATTGAAGGAATTTTTATGCTTCTAATTTAGTTTTTCCTACTATTTTC-GAATTAGTTTC
1 AAAAAGATTGAAAG-CTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCTGAATTAATTTC
* * * * * * * *
21677 TAATTAAAACGAAAGAAGATTTAGATGCTCGTAAAAACAATTCCTTAAATACAATGTGACTGAGA
65 TAATTAAATCAAAACAAGATTCAGAAGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGA
* * * * * * * *
21742 TTTGATTAGTTTAATATAAATAGTTCAAGGAGTCTTGGCGCCAAAAATCATGCAATATTGACCCG
130 TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGA-CCT
* * * ** * * * *
21807 GGGTCCTGGAACGCGTTTTTAG-CCAAAAAAAAAAGTGAT-GTTGCACGATTTCGACTAATATTT
194 GGGCCCCGGAACGCGTTTTTAGCCCAAAACAACCA-TGATAG-TACACAATTTCGGCTAAAATTT
* * * * * * * * * *
21870 TGCAAAAAATGACGCGAAATACTTTT-CTCAAATTTTAGTCACAATACACAT-AAAAATATATAA
257 TACAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATAAATAA
21933 TTCAACGCC
322 TTCAACGCC
* * * * * * *
21942 AAAAAGATTGAAGGGCTTTTCATGCTTCTGATACCATTTTTCCTA--TTTTTCCGAATTAATTTA
1 AAAAAGATTGAA-AGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCTGAATTAATTTC
* * * *
22005 TAATTAAA-AAGAAACATGGTTCA-AATGCT--T----A-TAA-----AAA--CAA--TGGCTGA
65 TAATTAAATCA-AAACAAGATTCAGAA-GCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGA
* * * * * * **
22052 GATTTGGTTAGATGAATATAGACATTTCCAGGAGTCTCGACGCCAAAAATCAT-TAAATCTGAAA
128 GATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGACC
* * * ** * * *
22116 TGGGCCTCAGAACGCGTTTTTAG-CCAAAACCCATGATGATTATTACACGATTCCGGCTAAAATT
193 TGGGCCCCGGAACGCGTTTTTAGCCCAAAA-CAACCATGA-TAGTACACAATTTCGGCTAAAATT
* * * * * * *
22180 TTACAAAAATTGACCCGATAGATATTTCCT-AAATTTTATCCATAATATTCATAAAAAATATATA
256 TTACAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATAAATA
*
22244 ATTCAATGCC
321 ATTCAACGCC
* * * * * *
22254 AAAAAGATTGAAGGACTTGTGACGCTTTTAATATCGTTTTTCATATTTTTTTCTAAATTAATTTC
1 AAAAAGATTGAAAG-CTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCTGAATTAATTTC
* * * * * * *
22319 TAATTAAATCGAAACATGATTCAGATGCCCGTTAAAACAAAAAAAAAAATACTTAAAATGCAATG
65 TAATTAAATCAAAACAAGATTCAGAAGCTCG-T-------AAAAACAAATCCTT-AAATCCAATG
* * * *
22384 TGGCTAAGATTT-ATTAGATGAATATAGTTATTTCAAGGAGT-TTCGGTGCCAAAAATCATGCAA
121 TGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTT-GGCGCCAAAAATCATGCAA
* * *
22447 AACTGAACTGGTGCCCCGAAACGCGTTTTTAGCCAAAAAC
185 AACTGACCTGG-GCCCCGGAACGCGTTTTTAGCCCAAAAC
22487 CGTGATGGTT
Statistics
Matches: 2284, Mismatches: 444, Indels: 243
0.77 0.15 0.08
Matches are distributed among these distances:
310 27 0.01
311 64 0.03
312 106 0.05
313 1 0.00
314 183 0.08
315 83 0.04
316 5 0.00
317 34 0.01
318 1 0.00
321 1 0.00
322 1 0.00
326 1 0.00
327 128 0.06
328 56 0.02
329 61 0.03
330 207 0.09
331 185 0.08
332 371 0.16
333 80 0.04
334 64 0.03
335 186 0.08
336 88 0.04
337 123 0.05
338 81 0.04
339 124 0.05
340 18 0.01
341 5 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (330 bp):
AAAAAGATTGAAAGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCTGAATTAATTTCT
AATTAAATCAAAACAAGATTCAGAAGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGAT
TTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGACCTGG
GCCCCGGAACGCGTTTTTAGCCCAAAACAACCATGATAGTACACAATTTCGGCTAAAATTTTACA
AAAATTGACCCGAAAGATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATAAATAATTCA
ACGCC
Found at i:22582 original size:2 final size:2
Alignment explanation
Indices: 22575--22601 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
22565 AATACTCCTA
22575 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
22602 ATTTAACGGC
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
Done.