Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011525.1 Corchorus capsularis cultivar CVL-1 contig11546, 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: 19987
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.30
Found at i:6790 original size:46 final size:47
Alignment explanation
Indices: 6725--6819 Score: 156
Period size: 46 Copynumber: 2.0 Consensus size: 47
6715 TACTATGCTC
* *
6725 AAAAAAACTTGGCCTAAAAAAGAAAGGGGTCGCAAAAAGA-AAAGAA
1 AAAAAAACTGGGCCTAAAAAAGAAAGAGGTCGCAAAAAGAGAAAGAA
*
6771 AAAAAAACTGGGCCTAAAAAAGAAAGAGGTCGCAAAAAGAGAAATAA
1 AAAAAAACTGGGCCTAAAAAAGAAAGAGGTCGCAAAAAGAGAAAGAA
6818 AA
1 AA
6820 TATAAGGAGG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
46 38 0.84
47 7 0.16
ACGTcount: A:0.60, C:0.11, G:0.21, T:0.08
Consensus pattern (47 bp):
AAAAAAACTGGGCCTAAAAAAGAAAGAGGTCGCAAAAAGAGAAAGAA
Found at i:7902 original size:34 final size:33
Alignment explanation
Indices: 7859--7992 Score: 144
Period size: 34 Copynumber: 3.9 Consensus size: 33
7849 GTTCGGTGAA
*
7859 TCAGATGACTCGGCGTAGCATCTTCAAAGTAGAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTA-AT
* *
7893 TCAGATGACTCAGTGTAGCATCTTCAAAAATTGAAAT
1 TCAGATGACTCGGTGTAGCATCTTC--AAA--GTAAT
* * *
7930 T-AGATGACTCGGTATAGCATCTTTAAAGTTTAAA
1 TCAGATGACTCGGTGTAGCATCTTCAAAG--TAAT
7964 TCAGATGACTCGGTGTAGCATCTTCAAAG
1 TCAGATGACTCGGTGTAGCATCTTCAAAG
7993 ATGAAATCAA
Statistics
Matches: 83, Mismatches: 10, Indels: 13
0.78 0.09 0.12
Matches are distributed among these distances:
32 1 0.01
34 29 0.35
35 25 0.30
36 23 0.28
37 3 0.04
38 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (33 bp):
TCAGATGACTCGGTGTAGCATCTTCAAAGTAAT
Found at i:7975 original size:35 final size:35
Alignment explanation
Indices: 7857--8001 Score: 184
Period size: 35 Copynumber: 4.1 Consensus size: 35
7847 CGGTTCGGTG
* *
7857 AATCAGATGACTCGGCGTAGCATCTTCAAAGTAG-
1 AATCAGATGACTCGGTGTAGCATCTTCAAAGTTGA
* * *
7891 ATTCAGATGACTCAGTGTAGCATCTTCAAAAATTGA
1 AATCAGATGACTCGGTGTAGCATCTTC-AAAGTTGA
* * * *
7927 AATTAGATGACTCGGTATAGCATCTTTAAAGTTTA
1 AATCAGATGACTCGGTGTAGCATCTTCAAAGTTGA
*
7962 AATCAGATGACTCGGTGTAGCATCTTCAAAGATGA
1 AATCAGATGACTCGGTGTAGCATCTTCAAAGTTGA
7997 AATCA
1 AATCA
8002 ACATCTTCAA
Statistics
Matches: 92, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
34 24 0.26
35 46 0.50
36 22 0.24
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (35 bp):
AATCAGATGACTCGGTGTAGCATCTTCAAAGTTGA
Found at i:8078 original size:127 final size:126
Alignment explanation
Indices: 7877--8114 Score: 291
Period size: 127 Copynumber: 1.9 Consensus size: 126
7867 CTCGGCGTAG
* * * * *
7877 CATCTTCAAAGTAGATTCAGATGACTCAGTGTAGCATCTTCAAAAATTGAAATTAGATGACTCGG
1 CATCTTCAAAGTAGATTCAAATGACTCAGTGTAGCATCCTCAAAAAGTGAAATCAGATGACCCGG
* * * * *
7942 TATAGCATCTTTAAAGTTTA-AATCAGATGACTCGGTGTAGCATCTTCAAAGATGAAATCAA
66 TACAACATCTTGAAAG-TTAGAATAAGATGACTCGGTGAAGCATCTTCAAAGATGAAATCAA
* * * *
8003 CATCTTCAAGGTTGGATTCAAATGACTCGGTGTAGCATCCTCAAAACGGTG-AATCAGATGACCC
1 CATCTTCAAAG-TAGATTCAAATGACTCAGTGTAGCATCCTCAAAA-AGTGAAATCAGATGACCC
* *
8067 GGTGCAACATCTTGAAAGTTAGATTAAGATGACTCGGTGAAGCATCTT
64 GGTACAACATCTTGAAAGTTAGAATAAGATGACTCGGTGAAGCATCTT
8115 TGAAGTGGGA
Statistics
Matches: 93, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
126 13 0.14
127 78 0.84
128 2 0.02
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29
Consensus pattern (126 bp):
CATCTTCAAAGTAGATTCAAATGACTCAGTGTAGCATCCTCAAAAAGTGAAATCAGATGACCCGG
TACAACATCTTGAAAGTTAGAATAAGATGACTCGGTGAAGCATCTTCAAAGATGAAATCAA
Found at i:8127 original size:35 final size:35
Alignment explanation
Indices: 8058--8127 Score: 81
Period size: 35 Copynumber: 2.0 Consensus size: 35
8048 ACGGTGAATC
*
8058 AGATGACCCGGTGCAACATCTTGAAAGTTAGATTA
1 AGATGACCCGGTGCAACATCTTGAAAGTGAGATTA
* *
8093 AGATGACTCGGTG-AAGCATCTTTG-AAGTGGGATTA
1 AGATGACCCGGTGCAA-CATC-TTGAAAGTGAGATTA
8128 GGTGAATCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
34 2 0.07
35 25 0.83
36 3 0.10
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.27
Consensus pattern (35 bp):
AGATGACCCGGTGCAACATCTTGAAAGTGAGATTA
Found at i:8413 original size:91 final size:89
Alignment explanation
Indices: 8202--8521 Score: 405
Period size: 91 Copynumber: 3.6 Consensus size: 89
8192 TTTGTTCATT
* * *
8202 ATTGGATTCGGTGAGCTCGGTGCAGTACATTCTCAAACAGTTAAGGGTGATCGGTG---CAAGTT
1 ATTGGATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGTTAAGGATGATCGGTGAATCAAGTT
8264 AGAGGCGGTGCCTTATTTCTTCAAG
66 -GAGGCGGTGCCTTATTTCTTCAAG
* * *
8289 ATTGGATTCGGTGAGCTCGGTGCAGCAGATTTTCAGACAGTTTAGGATGATTCGGTGAATCAAGT
1 ATTGGATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGTTAAGGATGA-TCGGTGAATCAAGT
*
8354 TGAGGCGGTGCCTTACTTCTTCAAG
65 TGAGGCGGTGCCTTATTTCTTCAAG
* * **
8379 ATTGGAATTCGATGAGCTCGGTGCAGCATATTTTCAAACAGTTCAAGGACAACTCGGTGAATCAA
1 ATTGG-ATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGTT-AAGGATGA-TCGGTGAATCAA
* *
8444 G-TGAACGCGGTGCATTATTTCTTCAAG
63 GTTG-AGGCGGTGCCTTATTTCTTCAAG
* * * *
8471 ATTGGATTCGGTGAGCTCGGTGTAGCACATTTTCAAAGACTTCAGGATGAT
1 ATTGGATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGTTAAGGATGAT
8522 TTGGTGGACC
Statistics
Matches: 201, Mismatches: 25, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
87 44 0.22
88 6 0.03
89 1 0.00
90 33 0.16
91 74 0.37
92 43 0.21
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (89 bp):
ATTGGATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGTTAAGGATGATCGGTGAATCAAGTT
GAGGCGGTGCCTTATTTCTTCAAG
Found at i:8558 original size:182 final size:177
Alignment explanation
Indices: 8202--8570 Score: 407
Period size: 182 Copynumber: 2.1 Consensus size: 177
8192 TTTGTTCATT
* * *** *
8202 ATTGGATTCGGTGAGCTCGGTGCAGTACATTCTCAAACAGTTAAGGGTGATCGGTGCAAGTTAGA
1 ATTGGATTCGATGAGCTCGGTGCAGCACATTCTCAAACAGTTAAGGACAATCGGTGCAAGTGAGA
* * * * * *
8267 GGCGGTGCCTTATTTCTTCAAGATTGGATTCGGTGAGCTCGGTGCAGCAGATTTTCAGACAGTTT
66 CGCGGTGCATTATTTCTTCAAGATTGGATTCGGTGAGCTCGGTGCAGCACATTTTCAAACACTTC
* ** * * **
8332 AGGATGATTCGGTGAATCAAGTTGAGGCGGTGCCTTACTTCTTCAAG
131 AGGATGATTCGGTGAACCAAGTCAAGGCAGCGCAATACTTCTTCAAG
* *
8379 ATTGGAATTCGATGAGCTCGGTGCAGCATATTTTCAAACAGTTCAAGGACAACTCGGTGAATCAA
1 ATTGG-ATTCGATGAGCTCGGTGCAGCACATTCTCAAACAGTT-AAGGACAA-TCGGTG---CAA
*
8444 GTGA-ACGCGGTGCATTATTTCTTCAAGATTGGATTCGGTGAGCTCGGTGTAGCACATTTTCAAA
60 GTGAGACGCGGTGCATTATTTCTTCAAGATTGGATTCGGTGAGCTCGGTGCAGCACATTTTCAAA
* * * ** * *
8508 GACTTCAGGATGATTTGGTGGACCAAGTCAATTCAGCGCAATATTTCTTCAAA
125 CACTTCAGGATGATTCGGTGAACCAAGTCAAGGCAGCGCAATACTTCTTCAAG
*
8561 ATTTGATTCG
1 ATTGGATTCG
8571 GTGGATCAAA
Statistics
Matches: 156, Mismatches: 30, Indels: 8
0.80 0.15 0.04
Matches are distributed among these distances:
177 5 0.03
178 33 0.21
179 5 0.03
180 6 0.04
181 5 0.03
182 96 0.62
183 6 0.04
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (177 bp):
ATTGGATTCGATGAGCTCGGTGCAGCACATTCTCAAACAGTTAAGGACAATCGGTGCAAGTGAGA
CGCGGTGCATTATTTCTTCAAGATTGGATTCGGTGAGCTCGGTGCAGCACATTTTCAAACACTTC
AGGATGATTCGGTGAACCAAGTCAAGGCAGCGCAATACTTCTTCAAG
Found at i:9236 original size:14 final size:14
Alignment explanation
Indices: 9217--9250 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
9207 GCATATTAAC
9217 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
9231 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
*
9245 ATTAGT
1 TTTAGT
9251 ATCGTAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.50
Consensus pattern (14 bp):
TTTAGTCCATTTAG
Found at i:9427 original size:20 final size:20
Alignment explanation
Indices: 9389--9429 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
9379 ATAAATACAA
*
9389 GACATTTGATTTACGAATTG
1 GACATTTGATTTACAAATTG
*
9409 GACATTTGATTTGCAAATTG
1 GACATTTGATTTACAAATTG
9429 G
1 G
9430 TGCTTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (20 bp):
GACATTTGATTTACAAATTG
Found at i:11792 original size:2 final size:2
Alignment explanation
Indices: 11785--11813 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11775 TAGATTCTTG
11785 TA TA 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 TA TA T
11814 GTAATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12700 original size:48 final size:48
Alignment explanation
Indices: 12627--12880 Score: 366
Period size: 48 Copynumber: 5.3 Consensus size: 48
12617 TCGATTACCT
* **
12627 GTTTTGCCCTTCCCGGTCGGGAGGTGCTATCTTCAGTGTCAATTTCCA
1 GTTTTGCCCTTCCCGGTCGGAAGGTGCTATCTTCAGTGTTTATTTCCA
* * * * *
12675 GTTTTGCCCTTCCTGGTCGGAAGGTGCAATTTTCAGTGTTTCTTTCCT
1 GTTTTGCCCTTCCCGGTCGGAAGGTGCTATCTTCAGTGTTTATTTCCA
*
12723 GTTTTGCCCTTCCCGGTCGGAAGGTGCTAATTTTCAGTGTTTATTTCCA
1 GTTTTGCCCTTCCCGGTCGGAAGGTGCT-ATCTTCAGTGTTTATTTCCA
*
12772 GTTTTGCCCTTCCCGGTCGGAAGGTGC-AGTCTTCGGTGTTTATTTCCA
1 GTTTTGCCCTTCCCGGTCGGAAGGTGCTA-TCTTCAGTGTTTATTTCCA
* **
12820 ATTTTGCCCTTCCCGGTCGGAAGGTGCTATCTTCAGTGTCAATTTCCA
1 GTTTTGCCCTTCCCGGTCGGAAGGTGCTATCTTCAGTGTTTATTTCCA
12868 GTTTTGCCCTTCC
1 GTTTTGCCCTTCC
12881 TGTTTATTTC
Statistics
Matches: 184, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
47 1 0.01
48 137 0.74
49 46 0.25
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.39
Consensus pattern (48 bp):
GTTTTGCCCTTCCCGGTCGGAAGGTGCTATCTTCAGTGTTTATTTCCA
Found at i:12790 original size:97 final size:96
Alignment explanation
Indices: 12624--12880 Score: 406
Period size: 97 Copynumber: 2.7 Consensus size: 96
12614 ATGTCGATTA
* *
12624 CCTGTTTTGCCCTTCCCGGTCGGGAGGTGCTATCTTCAGTGTCAATTTCCAGTTTTGCCCTTCCT
1 CCTGTTTTGCCCTTCCCGGTCGGAAGGTGCTATCTTCAGTGTCAATTTCCAGTTTTGCCCTTCCC
* *
12689 GGTCGGAAGGTGCAATTTTCAGTGTTTCTTT
66 GGTCGGAAGGTGCAATCTTCAGTGTTTATTT
* **
12720 CCTGTTTTGCCCTTCCCGGTCGGAAGGTGCTAATTTTCAGTGTTTATTTCCAGTTTTGCCCTTCC
1 CCTGTTTTGCCCTTCCCGGTCGGAAGGTGCT-ATCTTCAGTGTCAATTTCCAGTTTTGCCCTTCC
* *
12785 CGGTCGGAAGGTGCAGTCTTCGGTGTTTATTT
65 CGGTCGGAAGGTGCAATCTTCAGTGTTTATTT
**
12817 CCAATTTTGCCCTTCCCGGTCGGAAGGTGCTATCTTCAGTGTCAATTTCCAGTTTTGCCCTTCC
1 CCTGTTTTGCCCTTCCCGGTCGGAAGGTGCTATCTTCAGTGTCAATTTCCAGTTTTGCCCTTCC
12881 TGTTTATTTC
Statistics
Matches: 146, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
96 60 0.41
97 86 0.59
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.39
Consensus pattern (96 bp):
CCTGTTTTGCCCTTCCCGGTCGGAAGGTGCTATCTTCAGTGTCAATTTCCAGTTTTGCCCTTCCC
GGTCGGAAGGTGCAATCTTCAGTGTTTATTT
Found at i:12938 original size:73 final size:73
Alignment explanation
Indices: 12808--12953 Score: 222
Period size: 73 Copynumber: 2.0 Consensus size: 73
12798 CAGTCTTCGG
12808 TGTTTATTTCCAATTTTGCCCTTCCCGGTCGGAAGGTGCTATCTTCAGTGTCAATTTCCAGTTTT
1 TGTTTATTTCCAATTTTGCCCTTCCCGGTCGGAAGGTGCTATCTTCAGTGTCAATTTCCAGTTTT
12873 GCCCTTCC
66 GCCCTTCC
* * * ** *
12881 TGTTTATTTCCAGTTTTGCCCTTCCTGGTCGGAAGGTGC-AGTCTTCGGTGTTTATTTCCTGTTT
1 TGTTTATTTCCAATTTTGCCCTTCCCGGTCGGAAGGTGCTA-TCTTCAGTGTCAATTTCCAGTTT
12945 TGCCCTTCC
65 TGCCCTTCC
12954 CGGTCGGAAG
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
72 1 0.02
73 65 0.98
ACGTcount: A:0.11, C:0.26, G:0.20, T:0.43
Consensus pattern (73 bp):
TGTTTATTTCCAATTTTGCCCTTCCCGGTCGGAAGGTGCTATCTTCAGTGTCAATTTCCAGTTTT
GCCCTTCC
Found at i:12971 original size:23 final size:23
Alignment explanation
Indices: 12945--12991 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
12935 TTTCCTGTTT
*
12945 TGCCCTTCCCGGTCGGAAGGTGC
1 TGCCCTTCCCGATCGGAAGGTGC
*
12968 TGCCCTTCTCGATCGGAAGGTGC
1 TGCCCTTCCCGATCGGAAGGTGC
12991 T
1 T
12992 ATTTTCAGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.11, C:0.32, G:0.32, T:0.26
Consensus pattern (23 bp):
TGCCCTTCCCGATCGGAAGGTGC
Found at i:13056 original size:48 final size:48
Alignment explanation
Indices: 12968--13228 Score: 264
Period size: 48 Copynumber: 5.5 Consensus size: 48
12958 CGGAAGGTGC
* *
12968 TGCCCTTCTCGATCGGAAGGTGCTA-TTTTCAGTGTCTATTTCCAATTT
1 TGCCCTTCCCGGTCGGAAGGTGC-AGTTTTCAGTGTCTATTTCCAATTT
** * * * **
13016 TGCCCTTCCCAATCGGAAGGTGCAGTCTTCGGTGGT-TATTTGCTTTTT
1 TGCCCTTCCCGGTCGGAAGGTGCAGTTTTCAGT-GTCTATTTCCAATTT
* * *
13064 TGCCCTTGCCGGTCGGAAGGCGCTA-TTTTCAGTGTCTATTTCCAGTTT
1 TGCCCTTCCCGGTCGGAAGGTGC-AGTTTTCAGTGTCTATTTCCAATTT
* * *
13112 TGCCCTTCCCGGTCAGAAGGTGCCGTCTTCAGTGTCTATTTCCAGA---
1 TGCCCTTCCCGGTCGGAAGGTGCAGTTTTCAGTGTCTATTTCCA-ATTT
* * * *
13158 TGCTCTTCCCGGTCGAAAGGTGCAGTTTTCAGTGTTTATTTCCAGTTT
1 TGCCCTTCCCGGTCGGAAGGTGCAGTTTTCAGTGTCTATTTCCAATTT
*
13206 TGCCCTCCCCGGTCGGAAGGTGC
1 TGCCCTTCCCGGTCGGAAGGTGC
13229 TATATTTGTC
Statistics
Matches: 172, Mismatches: 32, Indels: 18
0.77 0.14 0.08
Matches are distributed among these distances:
46 38 0.22
47 3 0.02
48 128 0.74
49 3 0.02
ACGTcount: A:0.14, C:0.26, G:0.24, T:0.36
Consensus pattern (48 bp):
TGCCCTTCCCGGTCGGAAGGTGCAGTTTTCAGTGTCTATTTCCAATTT
Found at i:13132 original size:96 final size:94
Alignment explanation
Indices: 12968--13228 Score: 310
Period size: 96 Copynumber: 2.8 Consensus size: 94
12958 CGGAAGGTGC
* * * **
12968 TGCCCTTCTCGATCGGAAGGTGCTATTTTCAGTGTCTATTTCCAATTTTGCCCTTCCCAATCGGA
1 TGCCCTTCCCGGTCGGAAGGTGCTATTTTCAGTGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGA
* ****
13033 AGGTGCAGTCTTCGGTGGT-TATTTGCTTTTT
66 AGGTGCAGTCTTCAGT-GTCTATTT-C-CAGA
* * *
13064 TGCCCTTGCCGGTCGGAAGGCGCTATTTTCAGTGTCTATTTCCAGTTTTGCCCTTCCCGGTCAGA
1 TGCCCTTCCCGGTCGGAAGGTGCTATTTTCAGTGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGA
*
13129 AGGTGCCGTCTTCAGTGTCTATTTCCAGA
66 AGGTGCAGTCTTCAGTGTCTATTTCCAGA
* * * *
13158 TGCTCTTCCCGGTCGAAAGGTGC-AGTTTTCAGTGTTTATTTCCAGTTTTGCCCTCCCCGGTCGG
1 TGCCCTTCCCGGTCGGAAGGTGCTA-TTTTCAGTGTCTATTTCCAGTTTTGCCCTTCCCGGTCGG
13222 AAGGTGC
65 AAGGTGC
13229 TATATTTGTC
Statistics
Matches: 142, Mismatches: 21, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
93 1 0.01
94 62 0.44
95 3 0.02
96 76 0.54
ACGTcount: A:0.14, C:0.26, G:0.24, T:0.36
Consensus pattern (94 bp):
TGCCCTTCCCGGTCGGAAGGTGCTATTTTCAGTGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGA
AGGTGCAGTCTTCAGTGTCTATTTCCAGA
Found at i:17056 original size:19 final size:20
Alignment explanation
Indices: 17001--17057 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 20
16991 TGATAGAAGA
* *
17001 AAATTAAGAGGAGTAAATAT
1 AAATTAAGAGAAGTAAATAG
* * * *
17021 TAATTAGGGGAAATAAA-AG
1 AAATTAAGAGAAGTAAATAG
17040 AAATTAAGAGAAGTAAAT
1 AAATTAAGAGAAGTAAAT
17058 CTTAATTCAG
Statistics
Matches: 26, Mismatches: 10, Indels: 2
0.68 0.26 0.05
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.23
Consensus pattern (20 bp):
AAATTAAGAGAAGTAAATAG
Found at i:17277 original size:35 final size:35
Alignment explanation
Indices: 17240--17423 Score: 212
Period size: 35 Copynumber: 5.2 Consensus size: 35
17230 AGAGAGAGAG
* * *
17240 AGACTGGCTAAATTTCAAGGAAATTAAGTATGAAG
1 AGACTGGCTTAATTTCAAGGAAATTAAGTAAGAAA
* *
17275 AGACTGGCTAAATTTCAAGGGAATTAAGT-AGAAA
1 AGACTGGCTTAATTTCAAGGAAATTAAGTAAGAAA
* * *
17309 AGACTGGTTTAAGTTCAAGGAAATTAAGTAAAAAA
1 AGACTGGCTTAATTTCAAGGAAATTAAGTAAGAAA
*
17344 AGACTGGCTTAATTTCAAGAAGGGAAATTAGGTAAAGAAA
1 AGACTGGCTTAATTTC---AA-GGAAATTAAGT-AAGAAA
*
17384 AGATTGGCTTAATTTCAAGGAAATTAAGT-A-AAA
1 AGACTGGCTTAATTTCAAGGAAATTAAGTAAGAAA
17417 AGACTGG
1 AGACTGG
17424 ATCAGTTTTA
Statistics
Matches: 128, Mismatches: 15, Indels: 14
0.82 0.10 0.09
Matches are distributed among these distances:
33 9 0.07
34 29 0.23
35 46 0.36
36 10 0.08
37 2 0.02
38 2 0.02
39 10 0.08
40 20 0.16
ACGTcount: A:0.45, C:0.08, G:0.23, T:0.25
Consensus pattern (35 bp):
AGACTGGCTTAATTTCAAGGAAATTAAGTAAGAAA
Found at i:17351 original size:69 final size:72
Alignment explanation
Indices: 17240--17417 Score: 218
Period size: 69 Copynumber: 2.5 Consensus size: 72
17230 AGAGAGAGAG
* * ** *
17240 AGACTGGCTAAATTTCAAGGAAATTAAGTATGAAGAGACTGGCTAAATTTC-AAGGG-AATTAAG
1 AGACTGGCTTAAGTTCAAGGAAATTAAGTAAAAAAAGACTGGCTAAATTTCAAAGGGAAATTAAG
17303 T-AGAAA
66 TAAGAAA
* *
17309 AGACTGGTTTAAGTTCAAGGAAATTAAGTAAAAAAAGACTGGCTTAATTTCAAGAAGGGAAATTA
1 AGACTGGCTTAAGTTCAAGGAAATTAAGTAAAAAAAGACTGGCTAAATTTC-A-AAGGGAAATTA
*
17374 GGTAAAGAAA
64 AGT-AAGAAA
* *
17384 AGATTGGCTTAATTTCAAGGAAATTAAGTAAAAA
1 AGACTGGCTTAAGTTCAAGGAAATTAAGTAAAAA
17418 GACTGGATCA
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
69 44 0.48
72 5 0.05
73 7 0.08
75 36 0.39
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.25
Consensus pattern (72 bp):
AGACTGGCTTAAGTTCAAGGAAATTAAGTAAAAAAAGACTGGCTAAATTTCAAAGGGAAATTAAG
TAAGAAA
Found at i:17563 original size:35 final size:35
Alignment explanation
Indices: 17519--17793 Score: 442
Period size: 35 Copynumber: 7.8 Consensus size: 35
17509 AATTCAGGGT
17519 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAG
1 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAG
*
17554 AATTAAGTAAATTAGTAAAGACTTAATTTCACAAG
1 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAG
* **
17589 AATTAAGCAAAATTATAAAAGACTTAATTTCACAAG
1 AATTAAG-TAAATTAGCAAAGACTTAATTTCACAAG
*
17625 AATTAAGTAAATTAGTAAAGACTTAATTTCACAAG
1 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAG
17660 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAG
1 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAG
*
17695 AATTAAGCAAATTAGCAAAGACTTAATTTCACAAG
1 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAG
*
17730 AATTAAGCAAAATTAGCAAAGACTTAATTTCACAAG
1 AATTAAG-TAAATTAGCAAAGACTTAATTTCACAAG
* *
17766 AATTAAGTAAAGTCAGCAAAGATTTAAT
1 AATTAAGTAAA-TTAGCAAAGACTTAAT
17794 CCAAAGATGA
Statistics
Matches: 224, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
35 144 0.64
36 80 0.36
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.28
Consensus pattern (35 bp):
AATTAAGTAAATTAGCAAAGACTTAATTTCACAAG
Found at i:17633 original size:106 final size:105
Alignment explanation
Indices: 17519--17793 Score: 460
Period size: 106 Copynumber: 2.6 Consensus size: 105
17509 AATTCAGGGT
*
17519 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAATTAGTAAAGACTTAATTTC
1 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAATTAGCAAAGACTTAATTTC
*
17584 ACAAGAATTAAGCAAAATTATAAAAGACTTAATTTCACAAG
66 ACAAGAATTAAGC-AAATTAGAAAAGACTTAATTTCACAAG
*
17625 AATTAAGTAAATTAGTAAAGACTTAATTTCACAAGAATTAAGTAAATTAGCAAAGACTTAATTTC
1 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAATTAGCAAAGACTTAATTTC
*
17690 ACAAGAATTAAGCAAATTAGCAAAGACTTAATTTCACAAG
66 ACAAGAATTAAGCAAATTAGAAAAGACTTAATTTCACAAG
* * *
17730 AATTAAGCAAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAAGTCAGCAAAGATTTAAT
1 AATTAAG-TAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAA-TTAGCAAAGACTTAAT
17794 CCAAAGATGA
Statistics
Matches: 159, Mismatches: 8, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
105 32 0.20
106 113 0.71
107 14 0.09
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.28
Consensus pattern (105 bp):
AATTAAGTAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAATTAGCAAAGACTTAATTTC
ACAAGAATTAAGCAAATTAGAAAAGACTTAATTTCACAAG
Found at i:17680 original size:20 final size:20
Alignment explanation
Indices: 17622--17720 Score: 51
Period size: 20 Copynumber: 5.5 Consensus size: 20
17612 TTAATTTCAC
*
17622 AAGAATTAAGTAAATTAGTA
1 AAGAATTAAGTAAATTAGCA
*
17642 AAGACTTAA-T---TT--CA
1 AAGAATTAAGTAAATTAGCA
17656 CAAGAATTAAGTAAATTAGCA
1 -AAGAATTAAGTAAATTAGCA
*
17677 AAGACTTAA-T---TT--CA
1 AAGAATTAAGTAAATTAGCA
*
17691 CAAGAATTAAGCAAATTAGCA
1 -AAGAATTAAGTAAATTAGCA
*
17712 AAGACTTAA
1 AAGAATTAA
17721 TTTCACAAGA
Statistics
Matches: 58, Mismatches: 7, Indels: 28
0.62 0.08 0.30
Matches are distributed among these distances:
14 3 0.05
15 16 0.28
16 5 0.09
19 6 0.10
20 24 0.41
21 4 0.07
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.27
Consensus pattern (20 bp):
AAGAATTAAGTAAATTAGCA
Found at i:17680 original size:141 final size:141
Alignment explanation
Indices: 17519--17776 Score: 480
Period size: 141 Copynumber: 1.8 Consensus size: 141
17509 AATTCAGGGT
* *
17519 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAATTAGTAAAGACTTAATTTC
1 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAGAATTAAGCAAATTAGCAAAGACTTAATTTC
*
17584 ACAAGAATTAAGCAAAATTATAAAAGACTTAATTTCACAAGAATTAAGTAAATTAGTAAAGACTT
66 ACAAGAATTAAGCAAAATTAGAAAAGACTTAATTTCACAAGAATTAAGTAAATTAGTAAAGACTT
17649 AATTTCACAAG
131 AATTTCACAAG
17660 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAGAATTAAGCAAATTAGCAAAGACTTAATTTC
1 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAGAATTAAGCAAATTAGCAAAGACTTAATTTC
*
17725 ACAAGAATTAAGCAAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAA
66 ACAAGAATTAAGCAAAATTAGAAAAGACTTAATTTCACAAGAATTAAGTAAA
17777 GTCAGCAAAG
Statistics
Matches: 113, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
141 113 1.00
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.28
Consensus pattern (141 bp):
AATTAAGTAAATTAGCAAAGACTTAATTTCACAAGAATTAAGCAAATTAGCAAAGACTTAATTTC
ACAAGAATTAAGCAAAATTAGAAAAGACTTAATTTCACAAGAATTAAGTAAATTAGTAAAGACTT
AATTTCACAAG
Found at i:17858 original size:141 final size:139
Alignment explanation
Indices: 17519--17835 Score: 422
Period size: 141 Copynumber: 2.2 Consensus size: 139
17509 AATTCAGGGT
* * *
17519 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAATTAGTAAAGACTTAATTTC
1 AATTAAGTAAACTAGCAAAGACTCAATTTCACAAGAATTAAGCAAA-TAG-AAAGACTTAATTTC
* * *
17584 ACAAGAATTAAGCAAAATTATAAAAGACTTAATTTCACAAGAATTAAGTAAATTAGTAAAGACTT
64 ACAAGAATTAAGCAAAATTAGAAAAGACTTAATTTCACAAGAATTAAGTAAATCAGCAAAGACTT
*
17649 AATTTCACAAG
129 AATTCCACAAG
* *
17660 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAGAATTAAGCAAATTAGCAAAGACTTAATTTC
1 AATTAAGTAAACTAGCAAAGACTCAATTTCACAAGAATTAAGCAAA-TAG-AAAGACTTAATTTC
* *
17725 ACAAGAATTAAGCAAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAAGTCAGCAAAGATT
64 ACAAGAATTAAGCAAAATTAGAAAAGACTTAATTTCACAAGAATTAAGTAAA-TCAGCAAAGACT
17790 TAA-TCCA-AAG
128 TAATTCCACAAG
*
17800 ATGATTAAGTAAGACTAGACAAAGGGCTCAATTTCA
1 A--ATTAAGTAA-ACTAG-CAAA-GACTCAATTTCA
17836 AGGAAATTAG
Statistics
Matches: 159, Mismatches: 11, Indels: 8
0.89 0.06 0.04
Matches are distributed among these distances:
140 4 0.03
141 116 0.73
142 21 0.13
143 4 0.03
144 4 0.03
145 10 0.06
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.27
Consensus pattern (139 bp):
AATTAAGTAAACTAGCAAAGACTCAATTTCACAAGAATTAAGCAAATAGAAAGACTTAATTTCAC
AAGAATTAAGCAAAATTAGAAAAGACTTAATTTCACAAGAATTAAGTAAATCAGCAAAGACTTAA
TTCCACAAG
Found at i:17865 original size:11 final size:11
Alignment explanation
Indices: 17849--17911 Score: 108
Period size: 11 Copynumber: 5.7 Consensus size: 11
17839 AAATTAGGCA
17849 AAAGAAGACTG
1 AAAGAAGACTG
17860 AAAGAAGACTG
1 AAAGAAGACTG
*
17871 GAAGAAGACTG
1 AAAGAAGACTG
*
17882 AAAAAAGACTG
1 AAAGAAGACTG
17893 AAAGAAGACTG
1 AAAGAAGACTG
17904 AAAGAAGA
1 AAAGAAGA
17912 TTGACTTAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 48 1.00
ACGTcount: A:0.57, C:0.08, G:0.27, T:0.08
Consensus pattern (11 bp):
AAAGAAGACTG
Found at i:18014 original size:36 final size:35
Alignment explanation
Indices: 17927--18163 Score: 291
Period size: 36 Copynumber: 6.6 Consensus size: 35
17917 TTAATTAGGT
* * *
17927 AGAAGAAGACTGACTTAATTTCAAGGAAATTAAGTAA
1 AGAAG-AGACTG-CTTAGTTTCAAGGAAACTAGGTAA
17964 A-AA-AGACTGACTTAGTTTCAAGGAAACTAGGTAA
1 AGAAGAGACTG-CTTAGTTTCAAGGAAACTAGGTAA
17998 AGAAGAGACTAGCTTAGTTTCAAGGAAACTAGGTAA
1 AGAAGAGACT-GCTTAGTTTCAAGGAAACTAGGTAA
18034 AGAAGAGACTGGCTTAGTTTCAAGGAAACTAGGTAA
1 AGAAGAGACT-GCTTAGTTTCAAGGAAACTAGGTAA
18070 AGAAGAGACTGACTTAGTTTCAAGGAAACTAGGTAA
1 AGAAGAGACTG-CTTAGTTTCAAGGAAACTAGGTAA
* * * * **
18106 AGAAAAGACTGGTTTAGTTTCAAAGAAATTAAATAA
1 AGAAGAGACT-GCTTAGTTTCAAGGAAACTAGGTAA
*
18142 AGAA-AGACTGGCTTAATTTCAA
1 AGAAGAGACT-GCTTAGTTTCAA
18164 AGAAGGAAAT
Statistics
Matches: 183, Mismatches: 12, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
34 29 0.16
35 19 0.10
36 132 0.72
37 3 0.02
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (35 bp):
AGAAGAGACTGCTTAGTTTCAAGGAAACTAGGTAA
Found at i:18060 original size:72 final size:71
Alignment explanation
Indices: 17927--18202 Score: 324
Period size: 72 Copynumber: 3.8 Consensus size: 71
17917 TTAATTAGGT
* * *
17927 AGAAGAAGACTGACTTAATTTCAAGGAAATTAAGTAAA-AAAGACTGACTTAGTTTCAAGGAAAC
1 AGAAG-AGACTGACTTAATTTCAAGGAAACTAGGTAAAGAAAGACTGGCTTAGTTTCAAGGAAAC
17991 TAGGTAA
65 TAGGTAA
*
17998 AGAAGAGACT-AGCTTAGTTTCAAGGAAACTAGGTAAAGAAGAGACTGGCTTAGTTTCAAGGAAA
1 AGAAGAGACTGA-CTTAATTTCAAGGAAACTAGGTAAAGAA-AGACTGGCTTAGTTTCAAGGAAA
18062 CTAGGTAA
64 CTAGGTAA
* * * *
18070 AGAAGAGACTGACTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGTTTAGTTTCAAAGAAAT
1 AGAAGAGACTGACTTAATTTCAAGGAAACTAGGTAAAG-AAAGACTGGCTTAGTTTCAAGGAAAC
**
18135 TAAATAA
65 TAGGTAA
* * * * *
18142 AGAA-AGACTGGCTTAATTTCAAAGAAGGAAATTAAGTAAAGAAAGACTGGCCTAATTTCAA
1 AGAAGAGACTGACTTAATTTC----AAGGAAACTAGGTAAAGAAAGACTGGCTTAGTTTCAA
18203 AGAAGGAGAT
Statistics
Matches: 180, Mismatches: 16, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
69 1 0.01
70 27 0.15
71 21 0.12
72 96 0.53
73 3 0.02
74 17 0.09
75 15 0.08
ACGTcount: A:0.45, C:0.10, G:0.22, T:0.24
Consensus pattern (71 bp):
AGAAGAGACTGACTTAATTTCAAGGAAACTAGGTAAAGAAAGACTGGCTTAGTTTCAAGGAAACT
AGGTAA
Found at i:18096 original size:108 final size:106
Alignment explanation
Indices: 17927--18190 Score: 341
Period size: 108 Copynumber: 2.4 Consensus size: 106
17917 TTAATTAGGT
* *
17927 AGAAGAAGACTGACTTAATTTCAAGGAAATTAAGTAAAAAAGACTGACTTAGTTTCAAGGAAACT
1 AGAAG-AGACTGGCTTAATTTCAAGGAAACTAAGTAAAAAAGACTGACTTAGTTTCAAGGAAACT
* * **
17992 AGGTAAAGAAGAGACTAGCTTAGTTTCAAGGAAACTAGGTAA
65 AGGTAAAGAAAAGACTAGCTTAGTTTCAAAGAAACTAAATAA
* *
18034 AGAAGAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAGAGACTGACTTAGTTTCAAGGAAAC
1 AGAAGAGACTGGCTTAATTTCAAGGAAACTAAGTAAA-AA-AGACTGACTTAGTTTCAAGGAAAC
* * *
18099 TAGGTAAAGAAAAGACTGGTTTAGTTTCAAAGAAATTAAATAA
64 TAGGTAAAGAAAAGACTAGCTTAGTTTCAAAGAAACTAAATAA
*
18142 AGAA-AGACTGGCTTAATTTCAAAGAAGGAAATTAAGTAAAGAAAGACTG
1 AGAAGAGACTGGCTTAATTTC----AAGGAAACTAAGTAAA-AAAGACTG
18191 GCCTAATTTC
Statistics
Matches: 137, Mismatches: 14, Indels: 9
0.86 0.09 0.06
Matches are distributed among these distances:
106 28 0.20
107 22 0.16
108 64 0.47
110 6 0.04
111 17 0.12
ACGTcount: A:0.45, C:0.09, G:0.22, T:0.23
Consensus pattern (106 bp):
AGAAGAGACTGGCTTAATTTCAAGGAAACTAAGTAAAAAAGACTGACTTAGTTTCAAGGAAACTA
GGTAAAGAAAAGACTAGCTTAGTTTCAAAGAAACTAAATAA
Found at i:18262 original size:32 final size:32
Alignment explanation
Indices: 18224--18326 Score: 109
Period size: 32 Copynumber: 3.1 Consensus size: 32
18214 AAGTGGAGTC
18224 AATAAAAGGCTTAATTCAGGGTAATTAAGTAG
1 AATAAAAGGCTTAATTCAGGGTAATTAAGTAG
** **
18256 AATAAAAAACTTAATTCAGAATAATTAAGTAGGG
1 AATAAAAGGCTTAATTCAGGGTAATTAAGTA--G
*
18290 TCAAT-AAAGAGCTTAATTCAGGGTAATTAAGTGG
1 --AATAAAAG-GCTTAATTCAGGGTAATTAAGTAG
18324 AAT
1 AAT
18327 TAATAAAGAA
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
32 30 0.53
34 2 0.04
35 3 0.05
36 22 0.39
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.28
Consensus pattern (32 bp):
AATAAAAGGCTTAATTCAGGGTAATTAAGTAG
Found at i:18334 original size:36 final size:35
Alignment explanation
Indices: 18211--18342 Score: 137
Period size: 36 Copynumber: 3.8 Consensus size: 35
18201 AAAGAAGGAG
*
18211 ATTAAGTGGAGTCAATAAAAGGCTTAATTCAGGGTA
1 ATTAAGTGGAATCAATAAAA-GCTTAATTCAGGGTA
* **
18247 ATTAAGTAGAAT-AA-AAAA-CTTAATTCAGAATA
1 ATTAAGTGGAATCAATAAAAGCTTAATTCAGGGTA
*
18279 ATTAAGTAGG-GTCAATAAAGAGCTTAATTCAGGGTA
1 ATTAAGT-GGAATCAATAAA-AGCTTAATTCAGGGTA
* *
18315 ATTAAGTGGAATTAATAAAGAACTTAAT
1 ATTAAGTGGAATCAATAAA-AGCTTAAT
18343 AAAAACAAGA
Statistics
Matches: 79, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
32 20 0.25
33 3 0.04
34 7 0.09
35 5 0.06
36 44 0.56
ACGTcount: A:0.45, C:0.07, G:0.19, T:0.29
Consensus pattern (35 bp):
ATTAAGTGGAATCAATAAAAGCTTAATTCAGGGTA
Done.