Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012001.1 Corchorus olitorius cultivar O-4 contig12034, 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: 35905
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:1811 original size:27 final size:26
Alignment explanation
Indices: 1781--1839 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
1771 GCATAACAAG
*
1781 AAAATAATTTTTTTTTAATAAAAACGC
1 AAAA-AATTTTTTTTTAAGAAAAACGC
* *
1808 AAAAACTTTTTTTTTTAGAAAAACGC
1 AAAAAATTTTTTTTTAAGAAAAACGC
1834 AAAAAA
1 AAAAAA
1840 CACAAAACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 24 0.86
27 4 0.14
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (26 bp):
AAAAAATTTTTTTTTAAGAAAAACGC
Found at i:1840 original size:27 final size:26
Alignment explanation
Indices: 1788--1838 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
1778 AAGAAAATAA
*
1788 TTTTTTTTTAATAAAAACGCAAAAAC
1 TTTTTTTTTAAGAAAAACGCAAAAAC
*
1814 TTTTTTTTTTAGAAAAACGCAAAAA
1 TTTTTTTTTAAGAAAAACGCAAAAA
1839 ACACAAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (26 bp):
TTTTTTTTTAAGAAAAACGCAAAAAC
Found at i:1970 original size:33 final size:34
Alignment explanation
Indices: 1907--1978 Score: 87
Period size: 33 Copynumber: 2.1 Consensus size: 34
1897 AACAAACAAC
1907 AAAAATTTTTTTTTTTCAAATTAAAGACGCAAAG
1 AAAAATTTTTTTTTTTCAAATTAAAGACGCAAAG
* *
1941 AAAAATATATTTTTTTTT-GAA-TAAA-ACGCAGAG
1 AAAAAT-T-TTTTTTTTTCAAATTAAAGACGCAAAG
1974 AAAAA
1 AAAAA
1979 GAAAAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
33 12 0.35
34 10 0.29
35 3 0.09
36 9 0.26
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.35
Consensus pattern (34 bp):
AAAAATTTTTTTTTTTCAAATTAAAGACGCAAAG
Found at i:2318 original size:15 final size:16
Alignment explanation
Indices: 2290--2328 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
2280 GAGGTTGACA
*
2290 AAAAGCAATTAAAC-AG
1 AAAA-CAATGAAACTAG
2306 AAAACAATGAAACTAG
1 AAAACAATGAAACTAG
2322 AAAACAA
1 AAAACAA
2329 AGCAAAGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.67, C:0.13, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAACAATGAAACTAG
Found at i:8512 original size:96 final size:95
Alignment explanation
Indices: 8329--8514 Score: 257
Period size: 96 Copynumber: 1.9 Consensus size: 95
8319 TAAAGTTTAG
* *
8329 TACCTTTTTCTCCAACATCACTTTTTATCCATGGAAACATATTGGGAAACTTTAAATGTATAAAG
1 TACCTTTTTCTCCAACATCACTTTTTATCCATGGAAACATATTGAGAAACTGTAAATGTATAAAG
*
8394 TTCGGATACCCAGTACCAAAAAAAATTCAA
66 TTCGGATACCCACTACCAAAAAAAATTCAA
* ** * * *
8424 TACCTTTTTTTCCAACATCGTTCTTTTGTCCATTGAAACATATTTGAGAAACTGTAAATGTTTAA
1 TACCTTTTTCTCCAACATCACT-TTTTATCCATGGAAACATA-TTGAGAAACTGTAAATGTATAA
*
8489 AGTTCGG-TACCCACTTCCAAAAAAAA
64 AGTTCGGATACCCACTACCAAAAAAAA
8515 GGATAAAGTT
Statistics
Matches: 79, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
95 19 0.24
96 34 0.43
97 26 0.33
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.34
Consensus pattern (95 bp):
TACCTTTTTCTCCAACATCACTTTTTATCCATGGAAACATATTGAGAAACTGTAAATGTATAAAG
TTCGGATACCCACTACCAAAAAAAATTCAA
Found at i:9515 original size:234 final size:234
Alignment explanation
Indices: 9092--9566 Score: 636
Period size: 234 Copynumber: 2.0 Consensus size: 234
9082 GTTACTAAGC
* *
9092 CATTATTTAGATCTTACAATCAAATGAAGTTATGCCTTTTGAGAATAAAAATCAATAATTGTTTA
1 CATTATTTAGATCTTACAATCAAATGAAGTTATGCCTTCTGAGAATAAAAAACAATAATTGTTTA
* *
9157 TTGCATAAATAAAATATGATTCTGCTGTTTAGTTTGAAAAAAAAAGAAAAAAGAAAAATAATCAA
66 TTGCATAAATAAAATACGATTCTGCTGTTTAGTTTGAAAAAAAAAGAAAAAAGAAAAAAAATCAA
* ** * ** *
9222 TTTACAAGTTTCCGGATTATTCTCCTGGGTAGCTCATCATTTGGCTGCCACTACGACAACACCTC
131 TTTACAAGCTTCCAAAATATTCTCCTGGGTAGCTCATCATTTGGCCCCCACTACGACAACACCAC
* *
9287 ATGAAAGTTATCTACACAGAATTAAATGAG-AGTAAAAAT
196 ATCAAAGTTATCTACACAAAATTAAATGAGCA-TAAAAAT
*
9326 CATTATTTAGATCTTACAATCAGATGAAGTTATAG-CTTCTGAGAATAAAAAACAATAATTGTTT
1 CATTATTTAGATCTTACAATCAAATGAAGTTAT-GCCTTCTGAGAATAAAAAACAATAATTGTTT
* * *
9390 ATTGCATAAATAAAATACGA-TCTTGCTGTTTAGTTT-AAAAAAAAAGTAGAAGGAAAAAAAATC
65 ATTGCATAAATAAAATACGATTC-TGCTGTTTAGTTTGAAAAAAAAAGAAAAAAGAAAAAAAATC
** * ** *
9453 AATTTACCTGCTTCCAAAATACTT-TCGTGGGGTAGCTCATCATTTGGCCCCCGTTCCGACAACA
129 AATTTACAAGCTTCCAAAATA-TTCTCCT-GGGTAGCTCATCATTTGGCCCCCACTACGACAACA
* * *
9517 CCACATCAATGTTATCTTCATAAAATTAAATGAGCATAAAAAT
192 CCACATCAAAGTTATCTACACAAAATTAAATGAGCATAAAAAT
9560 CATTATT
1 CATTATT
9567 CATTTAGATA
Statistics
Matches: 210, Mismatches: 26, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
233 43 0.20
234 165 0.79
235 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (234 bp):
CATTATTTAGATCTTACAATCAAATGAAGTTATGCCTTCTGAGAATAAAAAACAATAATTGTTTA
TTGCATAAATAAAATACGATTCTGCTGTTTAGTTTGAAAAAAAAAGAAAAAAGAAAAAAAATCAA
TTTACAAGCTTCCAAAATATTCTCCTGGGTAGCTCATCATTTGGCCCCCACTACGACAACACCAC
ATCAAAGTTATCTACACAAAATTAAATGAGCATAAAAAT
Found at i:12843 original size:18 final size:18
Alignment explanation
Indices: 12795--12846 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
12785 CTTGTTTTAT
* *
12795 TTTGGGTCATGTGTGTGA
1 TTTGGGTCATGTTTGAGA
12813 TTTGGGTCATGTTTGAGA
1 TTTGGGTCATGTTTGAGA
12831 TTTGGGTCATGTTTGA
1 TTTGGGTCATGTTTGA
12847 TACCCTAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.13, C:0.06, G:0.35, T:0.46
Consensus pattern (18 bp):
TTTGGGTCATGTTTGAGA
Found at i:13492 original size:41 final size:41
Alignment explanation
Indices: 13416--13498 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 41
13406 TAAATTAAGT
* * * *
13416 TGTTTCATGTCAAATCCTATCTAATTTACTTAAACAGTTAA
1 TGTTTCATGTCAAATCCTAACTAATCTACTAAAACACTTAA
13457 TGTTTCATGTC-AATCCTAACTAATCTACTCAAAACACTTAA
1 TGTTTCATGTCAAATCCTAACTAATCTACT-AAAACACTTAA
13498 T
1 T
13499 TTTTTAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
40 16 0.43
41 21 0.57
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.39
Consensus pattern (41 bp):
TGTTTCATGTCAAATCCTAACTAATCTACTAAAACACTTAA
Found at i:14186 original size:12 final size:12
Alignment explanation
Indices: 14166--14200 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
14156 TGTTTGGTGT
14166 CAAGGAAAATAC
1 CAAGGAAAATAC
* *
14178 TATGGAAAATAC
1 CAAGGAAAATAC
14190 CAAGGAAAATA
1 CAAGGAAAATA
14201 AAGCGAATGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.17, T:0.14
Consensus pattern (12 bp):
CAAGGAAAATAC
Found at i:16633 original size:54 final size:54
Alignment explanation
Indices: 16562--17395 Score: 1092
Period size: 54 Copynumber: 15.5 Consensus size: 54
16552 TAAGAAATAA
* * * *
16562 AGAGCAATTAAGCTAAAAGGTAAAAGAAAGAGTAATCAGTAATTTGCTTAAGTC
1 AGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAAGTC
* * *
16616 AGAGTAACTAAGCTAAAAACTAAAAG---GAGTAATCAGTAATTAGTTCAAGTC
1 AGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAAGTC
* * * **
16667 AGAGTAATTAAGCTAAAAAGTGAAAAAAAAAAAGAGTAATCAGCAATTTGCCTAAGTC
1 AGAGTAATTAAGCTAAAAAGT----AAAAGAAAGAGTAATCAGTAATTAGTTTAAGTC
* * *
16725 AGAGTAACTAA-CTTAAAAAGTAAAAGAAGGAGTAATCAGTAATTAGTTCAAGTC
1 AGAGTAATTAAGC-TAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAAGTC
* * *
16779 AGAGTAATTAAGCTAAAAACTAAAAGAATGAGTAATCAGTAATTAGTTTAATTC
1 AGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAAGTC
* * *
16833 AGAGTAATTAAGCTAAAAAATAAAAGAAAGAGTAATCAATAATTAGTTCAAGTC
1 AGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAAGTC
*
16887 AGAGTAATTAAGCTAAAAAGTAAAAG---GAGTAA-CTAGTAATTAGTTTAATTC
1 AGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATC-AGTAATTAGTTTAAGTC
* * * * * *
16938 AGAGTAATTAATCAAAAAAATAAAAGAAAGAGCAATCAATAATTAGTTTAATTC
1 AGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAAGTC
*
16992 AGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAATTC
1 AGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAAGTC
* * * * *
17046 AGAATGATTAAGCTAAAAGGTAAAAGAAAGAGTAATCAGTAATTTGTTTAAGTT
1 AGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAAGTC
* **
17100 AGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTTGCCTAAGTC
1 AGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAAGTC
* * *
17154 AGAGTAACTAAGCTAAAAAGTAAAAGAAGGAGTAATCAGTAATTAGTTCAAGTC
1 AGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAAGTC
*
17208 AGAGTAATTAAGCTAAAAAGTAAAAG-AAGCAGTAATCAGTAATTAGTTTAATTC
1 AGAGTAATTAAGCTAAAAAGTAAAAGAAAG-AGTAATCAGTAATTAGTTTAAGTC
* * *
17262 AGAGTAATTAAGCTAAAAAGTAAAAGAAAAAGTAATCAGTAATTAGTTAAATTC
1 AGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAAGTC
* ** * *
17316 AGAGTAATTAAGCTAAAAAGTAAAGGAAAGAGTAATCAAAAGATAAGTTTAATTC
1 AGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTA-ATTAGTTTAAGTC
17371 AGAGTAATTAAGCTAAAAAGTAAAA
1 AGAGTAATTAAGCTAAAAAGTAAAA
17396 TTGATAATAA
Statistics
Matches: 685, Mismatches: 78, Indels: 33
0.86 0.10 0.04
Matches are distributed among these distances:
50 1 0.00
51 84 0.12
53 2 0.00
54 516 0.75
55 43 0.06
57 1 0.00
58 38 0.06
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.25
Consensus pattern (54 bp):
AGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAAGTC
Found at i:16785 original size:26 final size:26
Alignment explanation
Indices: 16754--17323 Score: 96
Period size: 26 Copynumber: 21.3 Consensus size: 26
16744 GTAAAAGAAG
*
16754 GAGTAATCAGTAATTAGTTCAAGTCA
1 GAGTAATCAGTAATTAGTTAAAGTCA
* ** * * *
16780 GAGTAATTAAGCTAAAAACTAAAAG-AA
1 GAGTAA-TCAG-TAATTAGTTAAAGTCA
* *
16807 TGAGTAATCAGTAATTAGTTTAATTCA
1 -GAGTAATCAGTAATTAGTTAAAGTCA
* ** * * **
16834 GAGTAATTAAGCTAAAAAATAAAAGAAA
1 GAGTAA-TCAG-TAATTAGTTAAAGTCA
* *
16862 GAGTAATCAATAATTAGTTCAAGTCA
1 GAGTAATCAGTAATTAGTTAAAGTCA
* ** *
16888 GAGTAATTAAGCTAAAAAGTAAAAG---
1 GAGTAA-TCAG-TAATTAGTTAAAGTCA
* *
16913 GAGTAA-CTAGTAATTAGTTTAATTCA
1 GAGTAATC-AGTAATTAGTTAAAGTCA
* * ** * * **
16939 GAGTAATTAATCAAAAAAATAAAAGAAA
1 GAGTAATCAGT--AATTAGTTAAAGTCA
* * * *
16967 GAGCAATCAATAATTAGTTTAATTCA
1 GAGTAATCAGTAATTAGTTAAAGTCA
* ** * **
16993 GAGTAATTAAGCTAAAAAGTAAAAGAAA
1 GAGTAA-TCAG-TAATTAGTTAAAGTCA
* *
17021 GAGTAATCAGTAATTAGTTTAATTCA
1 GAGTAATCAGTAATTAGTTAAAGTCA
* * * * * **
17047 GAATGATTAAGCTAA-AAGGTAAAAGAAA
1 GAGT-AATCAG-TAATTA-GTTAAAGTCA
* * *
17075 GAGTAATCAGTAATTTGTTTAAGTTA
1 GAGTAATCAGTAATTAGTTAAAGTCA
* ** * **
17101 GAGTAATTAAGCTAAAAAGTAAAAGAAA
1 GAGTAA-TCAG-TAATTAGTTAAAGTCA
* *
17129 GAGTAATCAGTAATTTGCCT-AAGTCA
1 GAGTAATCAGTAATTAG-TTAAAGTCA
* ** * *
17155 GAGTAACTAAGCTAAAAAGTAAAAG-AA
1 GAGTAA-TCAG-TAATTAGTTAAAGTCA
*
17182 GGAGTAATCAGTAATTAGTTCAAGTCA
1 -GAGTAATCAGTAATTAGTTAAAGTCA
* ** * *
17209 GAGTAATTAAGCTAAAAAGTAAAAG-AA
1 GAGTAA-TCAG-TAATTAGTTAAAGTCA
* *
17236 GCAGTAATCAGTAATTAGTTTAATTCA
1 G-AGTAATCAGTAATTAGTTAAAGTCA
* ** * **
17263 GAGTAATTAAGCTAAAAAGTAAAAGAAA
1 GAGTAA-TCAG-TAATTAGTTAAAGTCA
* *
17291 AAGTAATCAGTAATTAGTTAAATTCA
1 GAGTAATCAGTAATTAGTTAAAGTCA
17317 GAGTAAT
1 GAGTAAT
17324 TAAGCTAAAA
Statistics
Matches: 349, Mismatches: 160, Indels: 70
0.60 0.28 0.12
Matches are distributed among these distances:
23 8 0.02
24 2 0.01
25 6 0.02
26 139 0.40
27 59 0.17
28 135 0.39
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.27
Consensus pattern (26 bp):
GAGTAATCAGTAATTAGTTAAAGTCA
Found at i:17348 original size:28 final size:27
Alignment explanation
Indices: 17100--17351 Score: 83
Period size: 28 Copynumber: 9.3 Consensus size: 27
17090 TGTTTAAGTT
17100 AGAGTAATTAAGCTAAAAAGTAAAAGAA
1 AGAGTAATTAAGCTAAAAAGT-AAAGAA
* *** **
17128 AGAGTAA-TCAG-TAATTTGCCT-AAGTC
1 AGAGTAATTAAGCTAAAAAG--TAAAGAA
*
17154 AGAGTAACTAAGCTAAAAAGTAAAAGAA
1 AGAGTAATTAAGCTAAAAAGT-AAAGAA
* * ** * **
17182 GGAGTAA-TCAG-TAATTAGTTCAAGTC
1 AGAGTAATTAAGCTAAAAAG-TAAAGAA
17208 AGAGTAATTAAGCTAAAAAGTAAA-AGA
1 AGAGTAATTAAGCTAAAAAGTAAAGA-A
* ** * ***
17235 AGCAGTAA-TCAG-TAATTAGTTTAATTC
1 AG-AGTAATTAAGCTAAAAAG-TAAAGAA
17262 AGAGTAATTAAGCTAAAAAGTAAAAGAA
1 AGAGTAATTAAGCTAAAAAGT-AAAGAA
* * ** ***
17290 AAAGTAA-TCAG-TAATTAGTTAAATTC
1 AGAGTAATTAAGCTAAAAAG-TAAAGAA
17316 AGAGTAATTAAGCTAAAAAGTAAAGGAA
1 AGAGTAATTAAGCTAAAAAGTAAA-GAA
17344 AGAGTAAT
1 AGAGTAAT
17352 CAAAAGATAA
Statistics
Matches: 151, Mismatches: 53, Indels: 40
0.62 0.22 0.16
Matches are distributed among these distances:
26 53 0.35
27 41 0.27
28 57 0.38
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.24
Consensus pattern (27 bp):
AGAGTAATTAAGCTAAAAAGTAAAGAA
Found at i:19545 original size:38 final size:38
Alignment explanation
Indices: 19498--19637 Score: 149
Period size: 38 Copynumber: 3.7 Consensus size: 38
19488 TAGATAACAG
*
19498 TTAACCCCCTGAGGCACGAGTCCACTCTTACCTTCAGT
1 TTAACCCCCTGAGGCACGAGTCCACTCTTACCATCAGT
* * * *
19536 TTAACCCCCTGAGGTACGGGTCCGCTCTTACCAAACAGT
1 TTAACCCCCTGAGGCACGAGTCCACTCTTACC-ATCAGT
* * *
19575 TGAA-CCCCTGAGGCAC-AGCACCACTCTTACCATCAAT
1 TTAACCCCCTGAGGCACGAG-TCCACTCTTACCATCAGT
* * *
19612 TTAACCCGCTGAGGTACGGGTCCACT
1 TTAACCCCCTGAGGCACGAGTCCACT
19638 ATGCACAGCC
Statistics
Matches: 81, Mismatches: 17, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
37 8 0.10
38 65 0.80
39 8 0.10
ACGTcount: A:0.24, C:0.35, G:0.19, T:0.23
Consensus pattern (38 bp):
TTAACCCCCTGAGGCACGAGTCCACTCTTACCATCAGT
Found at i:19624 original size:76 final size:76
Alignment explanation
Indices: 19493--19634 Score: 216
Period size: 76 Copynumber: 1.9 Consensus size: 76
19483 GAGTCTAGAT
* * *
19493 AACAGTTAACCCCCTGAGGCACGAGTCCACTCTTACCTTCAGTTTAACCCCCTGAGGTACGGGTC
1 AACAGTTAACCCCCTGAGGCACGAGACCACTCTTACCATCAATTTAACCCCCTGAGGTACGGGTC
19558 CGCTCTTACCA
66 CGCTCTTACCA
*
19569 AACAGTTGAA-CCCCTGAGGCAC-AGCACCACTCTTACCATCAATTTAACCCGCTGAGGTACGGG
1 AACAGTT-AACCCCCTGAGGCACGAG-ACCACTCTTACCATCAATTTAACCCCCTGAGGTACGGG
19632 TCC
64 TCC
19635 ACTATGCACA
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
75 2 0.03
76 56 0.93
77 2 0.03
ACGTcount: A:0.25, C:0.35, G:0.19, T:0.22
Consensus pattern (76 bp):
AACAGTTAACCCCCTGAGGCACGAGACCACTCTTACCATCAATTTAACCCCCTGAGGTACGGGTC
CGCTCTTACCA
Found at i:30342 original size:29 final size:30
Alignment explanation
Indices: 30310--30367 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
30300 ATGTATTTAA
*
30310 ACTCTGTTAATTTCGGAT-GATGTGCTAAG
1 ACTCTGTTAATTTCGGATGGATGTACTAAG
* *
30339 ACTCTTTTAGTTTCGGATGGATGTACTAA
1 ACTCTGTTAATTTCGGATGGATGTACTAA
30368 AAGTTCAGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.40
Consensus pattern (30 bp):
ACTCTGTTAATTTCGGATGGATGTACTAAG
Found at i:30982 original size:21 final size:21
Alignment explanation
Indices: 30958--31012 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
30948 AGAATTAGTG
* *
30958 CGCCGAGATGAAGAGGCGAAA
1 CGCCGAGAAGAAGAGGCAAAA
30979 CGCCGAGAAGAAGAGGCAAAA
1 CGCCGAGAAGAAGAGGCAAAA
31000 CGCCGAGAAGAAG
1 CGCCGAGAAGAAG
31013 CCACGAATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.42, C:0.20, G:0.36, T:0.02
Consensus pattern (21 bp):
CGCCGAGAAGAAGAGGCAAAA
Found at i:31152 original size:21 final size:21
Alignment explanation
Indices: 31126--31188 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
31116 AATGCCTGAA
**
31126 GCAAGCTTAGATTTGACTGGG
1 GCAAGCTTAGGGTTGACTGGG
31147 GCAAGCTTAGGGTTGACTGGG
1 GCAAGCTTAGGGTTGACTGGG
*
31168 GCAAGCTCAGGGTTGACTGGG
1 GCAAGCTTAGGGTTGACTGGG
31189 ACGGTGACTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.21, C:0.16, G:0.40, T:0.24
Consensus pattern (21 bp):
GCAAGCTTAGGGTTGACTGGG
Done.