Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008147.1 Corchorus capsularis cultivar CVL-1 contig08168, 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: 24718
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:826 original size:39 final size:39
Alignment explanation
Indices: 782--859 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
772 AAAATCACGT
* *
782 TCATGCCGAAATGGTCAAAGAAGAAATGAGAAATGTGTC
1 TCATGCCGAAATGATCAAAGAAGAAAGGAGAAATGTGTC
*
821 TCATGCCGAAATGATCAAGGAAGAAAGGAGAAATGTGTC
1 TCATGCCGAAATGATCAAAGAAGAAAGGAGAAATGTGTC
860 GAACGACCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.41, C:0.13, G:0.27, T:0.19
Consensus pattern (39 bp):
TCATGCCGAAATGATCAAAGAAGAAAGGAGAAATGTGTC
Found at i:889 original size:57 final size:57
Alignment explanation
Indices: 821--983 Score: 272
Period size: 57 Copynumber: 2.9 Consensus size: 57
811 GAAATGTGTC
* *
821 TCATGCCGAAATGATCAAGGAAGAAAGGAGAAATGTGTCGAACGACCAAAATCACGT
1 TCATGCCGAAATGATCAAAGAAGAAAGGAGAAATGTGTCGAACGACCAAAATCACAT
878 TCATGCCGAAATGATCAAAGAAGAAAGGAGAAATGTGTCGAACGACCAAAATCACAT
1 TCATGCCGAAATGATCAAAGAAGAAAGGAGAAATGTGTCGAACGACCAAAATCACAT
* * * *
935 TCATGCCGAAATGGTTAAAGAAGAAAGGAGAAACGCGTCGAACGACCAA
1 TCATGCCGAAATGATCAAAGAAGAAAGGAGAAATGTGTCGAACGACCAA
984 GTTGCATCCA
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 100 1.00
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (57 bp):
TCATGCCGAAATGATCAAAGAAGAAAGGAGAAATGTGTCGAACGACCAAAATCACAT
Found at i:1682 original size:45 final size:45
Alignment explanation
Indices: 1593--1685 Score: 114
Period size: 45 Copynumber: 2.1 Consensus size: 45
1583 ATATCAATGG
* * ** **
1593 AAGTACAACAAATCAAATACTCTCGGTCAAAATGTGGCGTACGAC
1 AAGTACAACAAATCAAAGACTCACGGTCAAAAAATGGCACACGAC
* *
1638 AAGTTCAACAAATCAAAGACTCACGGTTAAAAAATGGCACACGAC
1 AAGTACAACAAATCAAAGACTCACGGTCAAAAAATGGCACACGAC
1683 AAG
1 AAG
1686 CGACAATATA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.17
Consensus pattern (45 bp):
AAGTACAACAAATCAAAGACTCACGGTCAAAAAATGGCACACGAC
Found at i:1824 original size:44 final size:45
Alignment explanation
Indices: 1764--1891 Score: 170
Period size: 44 Copynumber: 2.9 Consensus size: 45
1754 GGGAAGGAGG
*
1764 CAAACAAAAGACTCCCAATCACAAAGTGGCGTGCGACAAG-AAAA
1 CAAACAAAAGACTCCCAACCACAAAGTGGCGTGCGACAAGAAAAA
1808 CAAACAAAAGACTCCCAACCACAAAGTGGCGTGCGACAAGAAAAA
1 CAAACAAAAGACTCCCAACCACAAAGTGGCGTGCGACAAGAAAAA
* *** * *
1853 CAAA-AGAAAAACTATTAACCACAAAGTGGCATTCGACAA
1 CAAACA-AAAGACTCCCAACCACAAAGTGGCGTGCGACAA
1892 CATAGAAAGG
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
44 40 0.53
45 35 0.47
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.10
Consensus pattern (45 bp):
CAAACAAAAGACTCCCAACCACAAAGTGGCGTGCGACAAGAAAAA
Found at i:1948 original size:58 final size:58
Alignment explanation
Indices: 1875--2056 Score: 287
Period size: 58 Copynumber: 3.1 Consensus size: 58
1865 TATTAACCAC
*
1875 AAAGTGGCATTCGACAACATAGAAAGGGAAGGAGACAAGTCAAAAATTCTCAATTGCA
1 AAAGTGGCATACGACAACATAGAAAGGGAAGGAGACAAGTCAAAAATTCTCAATTGCA
* *
1933 AAAGTGGCGTACGACAACTTAGAAAGGGAAGGAGACAAGTCAAAAATTCTCAATTGCA
1 AAAGTGGCATACGACAACATAGAAAGGGAAGGAGACAAGTCAAAAATTCTCAATTGCA
* *
1991 AAAGTGGCATATGACAACATAGAAAGGGAAGGAGACAA-ACAAAAAAATTCTCAATTGC-
1 AAAGTGGCATACGACAACATAGAAAGGGAAGGAGACAAGTC--AAAAATTCTCAATTGCA
2049 AAAGTGGC
1 AAAGTGGC
2057 GTGTGACAAC
Statistics
Matches: 115, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
57 1 0.01
58 98 0.85
59 16 0.14
ACGTcount: A:0.46, C:0.15, G:0.23, T:0.16
Consensus pattern (58 bp):
AAAGTGGCATACGACAACATAGAAAGGGAAGGAGACAAGTCAAAAATTCTCAATTGCA
Found at i:2541 original size:38 final size:38
Alignment explanation
Indices: 2499--2902 Score: 512
Period size: 38 Copynumber: 10.7 Consensus size: 38
2489 AACTGGCGCC
* *
2499 AAGCTGACAAAATGTGTCGACGGCCACATCGCTCGACG
1 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACG
* * *
2537 AAGCTGACGAAATGTGTCGACCGCCACATCACTCGA-G
1 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACG
* * *
2574 AAAGCTAACAAAATGTGTTGACCGCCACGTCGCTCGACA
1 -AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACG
* *
2613 AAGCTGACAAAATGTGCCGACCGCCACGTTTG-TCGACG
1 AAGCTGACAAAATGTGTCGACCGCCACG-TCGCTCGACG
*
2651 AAGCTGACAAAATGTGTCGACCGCCATGTCGCTCGAC-
1 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACG
* * *
2688 AAGCTGACAAAATGTGTCGACCGCCACATCACTCGACA
1 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACG
2726 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACG
1 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACG
* * *
2764 AAGTTGACAAACTGTGTCGACCGCCACGTTGCTCGAC-
1 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACG
* * *
2801 AAGCTGACAAAATGAGTCGACCGCCACATCGCTCGACA
1 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACG
* * ** *
2839 AAGTTGACCAAATGTGTCGACTACCACGTCGTTCGAC-
1 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACG
* *
2876 AAGCTGACTAAATGTGTCGACCACCAC
1 AAGCTGACAAAATGTGTCGACCGCCAC
2903 AGGCCACCTC
Statistics
Matches: 319, Mismatches: 41, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
37 93 0.29
38 224 0.70
39 2 0.01
ACGTcount: A:0.29, C:0.30, G:0.23, T:0.18
Consensus pattern (38 bp):
AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACG
Found at i:2730 original size:75 final size:75
Alignment explanation
Indices: 2498--2902 Score: 515
Period size: 75 Copynumber: 5.4 Consensus size: 75
2488 AAACTGGCGC
* * * *
2498 CAAGCTGACAAAATGTGTCGACGGCCACATCGCTCGACGAAGCTGACGAAATGTGTCGACCGCCA
1 CAAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACAAAGCTGACAAAATGTGTCGACCGCCA
*
2563 CATCACTCGA
66 CGTCACTCGA
* * * *
2573 GAAAGCTAACAAAATGTGTTGACCGCCACGTCGCTCGACAAAGCTGACAAAATGTGCCGACCGCC
1 -CAAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACAAAGCTGACAAAATGTGTCGACCGCC
***
2638 ACGTTTGTCGA
65 ACGTCACTCGA
*
2649 CGAAGCTGACAAAATGTGTCGACCGCCATGTCGCTCGAC-AAGCTGACAAAATGTGTCGACCGCC
1 C-AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACAAAGCTGACAAAATGTGTCGACCGCC
*
2713 ACATCACTCGA
65 ACGTCACTCGA
* * *
2724 CAAAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACGAAGTTGACAAACTGTGTCGACCGCC
1 C-AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACAAAGCTGACAAAATGTGTCGACCGCC
**
2789 ACGTTGCTCGA
65 ACGTCACTCGA
* * * * **
2800 CAAGCTGACAAAATGAGTCGACCGCCACATCGCTCGACAAAGTTGACCAAATGTGTCGACTACCA
1 CAAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACAAAGCTGACAAAATGTGTCGACCGCCA
**
2865 CGTCGTTCGA
66 CGTCACTCGA
* *
2875 CAAGCTGACTAAATGTGTCGACCACCAC
1 CAAGCTGACAAAATGTGTCGACCGCCAC
2903 AGGCCACCTC
Statistics
Matches: 287, Mismatches: 40, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
75 158 0.55
76 129 0.45
ACGTcount: A:0.29, C:0.30, G:0.23, T:0.18
Consensus pattern (75 bp):
CAAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACAAAGCTGACAAAATGTGTCGACCGCCA
CGTCACTCGA
Found at i:2747 original size:113 final size:113
Alignment explanation
Indices: 2499--2902 Score: 560
Period size: 113 Copynumber: 3.6 Consensus size: 113
2489 AACTGGCGCC
* * *
2499 AAGCTGACAAAATGTGTCGACGGCCACATCGCTCGACGAAGCTGACGAAATGTGTCGACCGCCAC
1 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACGAAGCTGACAAAATGTGTCGACCGCCAC
* * * * * *
2564 ATCACTCGAGAAAGCTAACAAAATGTGTTGACCGCCACGTCGCTCGACA
66 GTCGCTCGA-CAAGCTGACAAAATGTGTCGACCGCCACATCGCTCGACA
* *
2613 AAGCTGACAAAATGTGCCGACCGCCACGTTTG-TCGACGAAGCTGACAAAATGTGTCGACCGCCA
1 AAGCTGACAAAATGTGTCGACCGCCACG-TCGCTCGACGAAGCTGACAAAATGTGTCGACCGCCA
* *
2677 TGTCGCTCGACAAGCTGACAAAATGTGTCGACCGCCACATCACTCGACA
65 CGTCGCTCGACAAGCTGACAAAATGTGTCGACCGCCACATCGCTCGACA
* *
2726 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACGAAGTTGACAAACTGTGTCGACCGCCAC
1 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACGAAGCTGACAAAATGTGTCGACCGCCAC
* *
2791 GTTGCTCGACAAGCTGACAAAATGAGTCGACCGCCACATCGCTCGACA
66 GTCGCTCGACAAGCTGACAAAATGTGTCGACCGCCACATCGCTCGACA
* * ** * * *
2839 AAGTTGACCAAATGTGTCGACTACCACGTCGTTCGAC-AAGCTGACTAAATGTGTCGACCACCAC
1 AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACGAAGCTGACAAAATGTGTCGACCGCCAC
2903 AGGCCACCTC
Statistics
Matches: 258, Mismatches: 30, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
112 25 0.10
113 168 0.65
114 63 0.24
115 2 0.01
ACGTcount: A:0.29, C:0.30, G:0.23, T:0.18
Consensus pattern (113 bp):
AAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACGAAGCTGACAAAATGTGTCGACCGCCAC
GTCGCTCGACAAGCTGACAAAATGTGTCGACCGCCACATCGCTCGACA
Found at i:3480 original size:23 final size:23
Alignment explanation
Indices: 3450--3508 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
3440 TGCTTGGCGC
*
3450 CCGACCACTTCCAAGCCTAGTGA
1 CCGACCACTTCCAAGCCAAGTGA
*
3473 CCGACCACTTCCAGGCCAAGTGA
1 CCGACCACTTCCAAGCCAAGTGA
3496 CCGACCACTTCCA
1 CCGACCACTTCCA
3509 TGCTCGGCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.25, C:0.42, G:0.17, T:0.15
Consensus pattern (23 bp):
CCGACCACTTCCAAGCCAAGTGA
Found at i:3590 original size:23 final size:23
Alignment explanation
Indices: 3558--3636 Score: 86
Period size: 23 Copynumber: 3.4 Consensus size: 23
3548 TGCTTGGCGC
* *
3558 CCGACAACTTCCAAGCCTAGCGA
1 CCGACCACTTCCAAGCCCAGCGA
* *
3581 CCGACCACTTCCAGGCCCAGTGA
1 CCGACCACTTCCAAGCCCAGCGA
* * *
3604 CCGACCACTTCCATGCTCGGCGA
1 CCGACCACTTCCAAGCCCAGCGA
*
3627 TCGACCACTT
1 CCGACCACTT
3637 AGGACCACAA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.23, C:0.42, G:0.19, T:0.16
Consensus pattern (23 bp):
CCGACCACTTCCAAGCCCAGCGA
Found at i:3615 original size:108 final size:108
Alignment explanation
Indices: 3426--3637 Score: 370
Period size: 108 Copynumber: 2.0 Consensus size: 108
3416 GGCAATTGTT
* * *
3426 GAGCATGGCGCAATTGCTTGGCGCCCGACCACTTCCAAGCCTAGTGACCGACCACTTCCAGGCCA
1 GAGCATGGCACAATTGCTTGGCGCCCGACAACTTCCAAGCCTAGCGACCGACCACTTCCAGGCCA
3491 AGTGACCGACCACTTCCATGCTCGGCGATCAACCACTTAAGAC
66 AGTGACCGACCACTTCCATGCTCGGCGATCAACCACTTAAGAC
* *
3534 GAGCATGGCATAATTGCTTGGCGCCCGACAACTTCCAAGCCTAGCGACCGACCACTTCCAGGCCC
1 GAGCATGGCACAATTGCTTGGCGCCCGACAACTTCCAAGCCTAGCGACCGACCACTTCCAGGCCA
*
3599 AGTGACCGACCACTTCCATGCTCGGCGATCGACCACTTA
66 AGTGACCGACCACTTCCATGCTCGGCGATCAACCACTTA
3638 GGACCACAAG
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
108 98 1.00
ACGTcount: A:0.24, C:0.36, G:0.22, T:0.18
Consensus pattern (108 bp):
GAGCATGGCACAATTGCTTGGCGCCCGACAACTTCCAAGCCTAGCGACCGACCACTTCCAGGCCA
AGTGACCGACCACTTCCATGCTCGGCGATCAACCACTTAAGAC
Found at i:3707 original size:13 final size:14
Alignment explanation
Indices: 3677--3739 Score: 66
Period size: 13 Copynumber: 4.8 Consensus size: 14
3667 GCCAGCTGGC
3677 ACTCCACACGT--G
1 ACTCCACACGTACG
3689 ACCTCCA-ACGTACG
1 A-CTCCACACGTACG
3703 ACTCCACACGT--G
1 ACTCCACACGTACG
3715 ACCTCCA-ACGTACG
1 A-CTCCACACGTACG
3729 ACTCCACACGT
1 ACTCCACACGT
3740 GACCACCAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
12 11 0.26
13 20 0.47
14 12 0.28
ACGTcount: A:0.27, C:0.43, G:0.14, T:0.16
Consensus pattern (14 bp):
ACTCCACACGTACG
Found at i:3713 original size:26 final size:26
Alignment explanation
Indices: 3677--3768 Score: 150
Period size: 26 Copynumber: 3.5 Consensus size: 26
3667 GCCAGCTGGC
3677 ACTCCACACGTGACCTCCAACGTACG
1 ACTCCACACGTGACCTCCAACGTACG
3703 ACTCCACACGTGACCTCCAACGTACG
1 ACTCCACACGTGACCTCCAACGTACG
* *
3729 ACTCCACACGTGACCACCAACGGAC-
1 ACTCCACACGTGACCTCCAACGTACG
3754 ACCTCCACACGTGAC
1 A-CTCCACACGTGAC
3769 ATCGTGCGTG
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
25 1 0.02
26 62 0.98
ACGTcount: A:0.28, C:0.43, G:0.15, T:0.13
Consensus pattern (26 bp):
ACTCCACACGTGACCTCCAACGTACG
Found at i:6242 original size:24 final size:24
Alignment explanation
Indices: 6215--6261 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
6205 ATTAAACATC
6215 TCAACATATTGAGAGATATTTTAT
1 TCAACATATTGAGAGATATTTTAT
*
6239 TCAACATATTGAGAGTTATTTTA
1 TCAACATATTGAGAGATATTTTA
6262 ACTATCTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.43
Consensus pattern (24 bp):
TCAACATATTGAGAGATATTTTAT
Found at i:6727 original size:122 final size:129
Alignment explanation
Indices: 6504--6774 Score: 425
Period size: 122 Copynumber: 2.1 Consensus size: 129
6494 TTTTATAGAA
* *
6504 CTTTC-TTCATATTTTTCTTCTCATCGTTCATAACCTTTCTTCATTTTACAGAATATTCTTCTTC
1 CTTTCATTGATATTTTTCATCTCATCGTTCATAACCTTTCTTCATTTTACAGAATATTCTTCTTC
*
6568 ATCTTTTTCTTTCCTTCTCTTGCTTGGCTTTTTGGTCATGCAAGGACTGATGAAATGTGTTTGAT
66 ATC-TTTTC-TTCCTTCTCTTGCTTGGCTTTTTGGTCATGCAAGGACTGATGAAATGCGTTTGAT
6633 T
129 T
6634 CTTTCATTGATATTTTTCATCTCATCGTTCATAACCTTTCTTCATTTTACAG-A-A-TCTTCTTC
1 CTTTCATTGATATTTTTCATCTCATCGTTCATAACCTTTCTTCATTTTACAGAATATTCTTCTTC
6696 ATC-TTTC-T-C-TCTCTTGCTTGGCTTTTTGGTCATGCAAGGACTGATGAAATGCGTTTGATT
66 ATCTTTTCTTCCTTCTCTTGCTTGGCTTTTTGGTCATGCAAGGACTGATGAAATGCGTTTGATT
6756 CTTTCATTGAT-TGTTTTCA
1 CTTTCATTGATAT-TTTTCA
6775 GATCGCTTCA
Statistics
Matches: 136, Mismatches: 3, Indels: 12
0.90 0.02 0.08
Matches are distributed among these distances:
121 1 0.01
122 67 0.49
123 1 0.01
124 1 0.01
126 4 0.03
128 11 0.08
129 1 0.01
130 6 0.04
131 44 0.32
ACGTcount: A:0.18, C:0.21, G:0.12, T:0.49
Consensus pattern (129 bp):
CTTTCATTGATATTTTTCATCTCATCGTTCATAACCTTTCTTCATTTTACAGAATATTCTTCTTC
ATCTTTTCTTCCTTCTCTTGCTTGGCTTTTTGGTCATGCAAGGACTGATGAAATGCGTTTGATT
Found at i:8843 original size:140 final size:140
Alignment explanation
Indices: 8588--8866 Score: 495
Period size: 140 Copynumber: 2.0 Consensus size: 140
8578 TCCTCTCTCT
* *
8588 GAAACGCCACATTAGTTTTGGGTTCTGTTAATTTATTTTATTGACCTTAGGAGTGTATGTTCCTA
1 GAAACGCCACATTAGTTTTGAGTTCTGTCAATTTATTTTATTGACCTTAGGAGTGTATGTTCCTA
*
8653 GGATTTTGATTGCTTAGAATAATGGTTTAGGGTAATTGTCGTCCATGGGGTGCGCTCCCTTTGAT
66 GGATTTTGATTGCTTAGAATAATGGTTTAGGGTAATTGTCGTCCAGGGGGTGCGCTCCCTTTGAT
8718 CAAACACTTC
131 CAAACACTTC
*
8728 GAAACGCCACATTAGTTTTGAGTTTTGTCAATTTATTTTATTGACCTTAGGAGTGTATGTTCCTA
1 GAAACGCCACATTAGTTTTGAGTTCTGTCAATTTATTTTATTGACCTTAGGAGTGTATGTTCCTA
* *
8793 GGATTTTGATTGCTTAGAATAATGGTTTAGGGTAATTTTCTTCCAGGGGGTGCGCTCCCTTTGAT
66 GGATTTTGATTGCTTAGAATAATGGTTTAGGGTAATTGTCGTCCAGGGGGTGCGCTCCCTTTGAT
*
8858 CACACACTT
131 CAAACACTT
8867 TCTTTTTTCT
Statistics
Matches: 132, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 132 1.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (140 bp):
GAAACGCCACATTAGTTTTGAGTTCTGTCAATTTATTTTATTGACCTTAGGAGTGTATGTTCCTA
GGATTTTGATTGCTTAGAATAATGGTTTAGGGTAATTGTCGTCCAGGGGGTGCGCTCCCTTTGAT
CAAACACTTC
Found at i:18930 original size:30 final size:26
Alignment explanation
Indices: 18894--18960 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 26
18884 TTTTTGTTCC
*
18894 AACTAACCATTATATTTTGGCCAAAAAGAA
1 AACTAACCATTATATGTT-GCC--AAA-AA
18924 AACTAACCA--ATATGTTGCCAAAAA
1 AACTAACCATTATATGTTGCCAAAAA
18948 AACTAACCATTAT
1 AACTAACCATTAT
18961 GAATATGAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
24 11 0.32
25 3 0.09
26 2 0.06
27 3 0.09
28 6 0.18
30 9 0.26
ACGTcount: A:0.48, C:0.19, G:0.07, T:0.25
Consensus pattern (26 bp):
AACTAACCATTATATGTTGCCAAAAA
Found at i:19761 original size:63 final size:63
Alignment explanation
Indices: 19662--19782 Score: 158
Period size: 63 Copynumber: 1.9 Consensus size: 63
19652 CAGGTAACAT
**
19662 GTTTTTCTTCTTCTTGTTTCAATCTTTCAATTTTCTGGATTTTTTGCTCT-TTGTTTTCCAGAC
1 GTTTTTCTTCTTCTTGTTTCAATCTTTCAATTTTCTGGAGATTTTGCTCTGTT-TTTTCCAGAC
* *
19725 GTTTTTCTTCTTGC-TGATTT-TATCTTTCAGTTTTCTGGAGATTTTGCTCTGTTTTTTC
1 GTTTTTCTTCTT-CTTG-TTTCAATCTTTCAATTTTCTGGAGATTTTGCTCTGTTTTTTC
19783 TTTCCTGCTT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
63 45 0.88
64 6 0.12
ACGTcount: A:0.10, C:0.17, G:0.13, T:0.60
Consensus pattern (63 bp):
GTTTTTCTTCTTCTTGTTTCAATCTTTCAATTTTCTGGAGATTTTGCTCTGTTTTTTCCAGAC
Done.