Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009716.1 Corchorus capsularis cultivar CVL-1 contig09737, 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: 57961
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1089 original size:38 final size:39
Alignment explanation
Indices: 1017--1091 Score: 98
Period size: 38 Copynumber: 1.9 Consensus size: 39
1007 AATACAAAAG
* * **
1017 GAAAATGCCACATCCTTGATTGGAGATGGGAAGACAATT
1 GAAAATGCCACAGCCTTGATTGCAGATGAAAAGACAATT
*
1056 GAAAATGCCGCAGCCTT-ATTGCAGATGAAAAGACAA
1 GAAAATGCCACAGCCTTGATTGCAGATGAAAAGACAA
1092 ATACAAATGA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
38 16 0.52
39 15 0.48
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (39 bp):
GAAAATGCCACAGCCTTGATTGCAGATGAAAAGACAATT
Found at i:1103 original size:18 final size:18
Alignment explanation
Indices: 1083--1118 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1073 ATTGCAGATG
1083 AAAAGACAAATACAAATGA
1 AAAAGA-AAATACAAATGA
*
1102 AAAAGAAAATGCAAATG
1 AAAAGAAAATACAAATG
1119 CAAATGGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.67, C:0.08, G:0.14, T:0.11
Consensus pattern (18 bp):
AAAAGAAAATACAAATGA
Found at i:1563 original size:2 final size:2
Alignment explanation
Indices: 1552--1583 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1542 CATCCATGCC
1552 TA TA TA -A 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 TA TA T
1584 CTTTGATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2566 original size:49 final size:49
Alignment explanation
Indices: 2434--2991 Score: 734
Period size: 49 Copynumber: 11.4 Consensus size: 49
2424 GAAAAGGCAT
* * ** * * *
2434 TTTGGGAAATGGC-AGATAAGAATAAATACCTTCCGTCCGGGATGGGCGT
1 TTTGGGAAATAGCAAG-TAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
** *
2483 TTTGGGAAATAGCAAG-CGAAATAAATGGCTTCCGTCTGGGAAGGGCAC
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
2531 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCT--G--GGGCGC
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
*
2576 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTTTGGGAAGGGCGC
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
* * * * *
2625 TTTGGGAGATAGCAAGTAAAGATGAATGGCTTCCGTCTGAGAAGGGCGT
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
* *
2674 TTTGGGAAATAGCAAGCAAAAATAAATGGCTTCCGTCTGGGAATGGCGC
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
*
2723 TTTGGGAAATAGCAAGCAAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
1 TTTGGGAAATAGCAAG-TAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
* * *
2773 TTTGGGAGATAGCAAGTAAAGATGAATGGCTTCCGTCTGGGAAGGGCGC
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
* *
2822 TTTGGGAAATAACAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGACGC
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
* * * * *
2871 TTTGGGAGATAGCAAGTAAAGATGAATGGCTTCCTTCTGGGAAGGGCGT
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
* *
2920 TTTGGGAAATAGAAAGTAAAAAATAAATGGCTTCCGTCTGGGAAGGGCGT
1 TTTGGGAAATAGCAAGT-AAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
* *
2970 TTTAGGGGAA-AGCTAGTAAAAA
1 TTT-GGGAAATAGCAAGTAAAAA
2992 CTGAAAATTG
Statistics
Matches: 447, Mismatches: 53, Indels: 18
0.86 0.10 0.03
Matches are distributed among these distances:
45 42 0.09
47 2 0.00
48 39 0.09
49 274 0.61
50 85 0.19
51 5 0.01
ACGTcount: A:0.32, C:0.14, G:0.31, T:0.23
Consensus pattern (49 bp):
TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
Found at i:2803 original size:148 final size:146
Alignment explanation
Indices: 2434--2991 Score: 750
Period size: 148 Copynumber: 3.8 Consensus size: 146
2424 GAAAAGGCAT
* * ** * * *
2434 TTTGGGAAATGGC-AGATAAGAATAAATACCTTCCGTCCGGGATGGGCGTTTTGGGAAATAGCAA
1 TTTGGGAAATAGCAAG-TAAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAA
** *
2498 GCGAA-ATAAATGGCTTCCGTCTGGGAAGGGCACTTTGGGAAATAGCAAGTAAAAATAAATGGCT
65 GTAAAGATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATAAATGGCT
2562 TCCGTCT-GG--GGCGC
130 TCCGTCTGGGAAGGCGC
* *
2576 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTTTGGGAAGGGCGCTTTGGGAGATAGCAAG
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAG
* * * *
2641 TAAAGATGAATGGCTTCCGTCTGAGAAGGGCGTTTTGGGAAATAGCAAGCAAAAATAAATGGCTT
66 TAAAGATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATAAATGGCTT
2706 CCGTCTGGGAATGGCGC
131 CCGTCTGGGAA-GGCGC
* *
2723 TTTGGGAAATAGCAAGCAAAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGAGATAGCAA
1 TTTGGGAAATAGCAAG-TAAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAA
* *
2788 GTAAAGATGAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATAACAAGTAAAAATAAATGGCT
65 GTAAAGATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATAAATGGCT
2853 TCCGTCTGGGAAGGACGC
130 TCCGTCTGGGAAGG-CGC
* * * * * *
2871 TTTGGGAGATAGCAAGTAAAGATGAATGGCTTCCTTCTGGGAAGGGCGTTTTGGGAAATAGAAAG
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAG
* * * *
2936 TAAAAAATAAATGGCTTCCGTCTGGGAAGGGCGTTTTAGGGGAA-AGCTAGTAAAAA
66 T-AAAGATAAATGGCTTCCGTCTGGGAAGGGCGCTTT-GGGAAATAGCAAGTAAAAA
2992 CTGAAAATTG
Statistics
Matches: 370, Mismatches: 36, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
142 55 0.15
143 63 0.17
144 2 0.01
147 66 0.18
148 179 0.48
149 5 0.01
ACGTcount: A:0.32, C:0.14, G:0.31, T:0.23
Consensus pattern (146 bp):
TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAG
TAAAGATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATAAATGGCTT
CCGTCTGGGAAGGCGC
Found at i:6759 original size:22 final size:23
Alignment explanation
Indices: 6734--6784 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
6724 TTATTATATA
*
6734 TTCAC-CTTGGTTTTTTTGTCAT
1 TTCACTCTTGGTTCTTTTGTCAT
* *
6756 TTCACTTTTGGTTCTTTTGTTAT
1 TTCACTCTTGGTTCTTTTGTCAT
6779 TCTCAC
1 T-TCAC
6785 AAGCCTTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.21
23 15 0.62
24 4 0.17
ACGTcount: A:0.10, C:0.20, G:0.12, T:0.59
Consensus pattern (23 bp):
TTCACTCTTGGTTCTTTTGTCAT
Found at i:6767 original size:23 final size:24
Alignment explanation
Indices: 6740--6784 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
6730 TATATTCACC
*
6740 TTGGTTTTTTTGTCATT-TCACTT
1 TTGGTTCTTTTGTCATTCTCACTT
*
6763 TTGGTTCTTTTGTTATTCTCAC
1 TTGGTTCTTTTGTCATTCTCAC
6785 AAGCCTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.09, C:0.16, G:0.13, T:0.62
Consensus pattern (24 bp):
TTGGTTCTTTTGTCATTCTCACTT
Found at i:8051 original size:177 final size:178
Alignment explanation
Indices: 7795--8139 Score: 410
Period size: 177 Copynumber: 1.9 Consensus size: 178
7785 CCTATGACTA
* * * * * *
7795 CAACTTTCATGAAGGACTCGAAAACTAAATTTAATGTTTTAAGTATAAAAAATACTTCCGAAAAG
1 CAACTTTCATGAACGACTCGAAAACTAAATTTAATGTTTCAAATATAAAAAAGACTTCCAAAAAA
* * * * * *
7860 TTAGTTGTTTCGGTTAACGGGGATGG-GCGATCCACTTCATATTACT-TAACTTTTGCTCCATAC
66 ATAGTTGTTTCGGTTAACGGGAATGGACCG-TCCACTTAATATTA-TACAACTTTTGCTCCAGAC
** *
7923 GTCTTATTGAGGTGATTCAAGTGTCTCTCAAAAGGTTGTTTCATTATCTG
129 GTCCGATTGAGGTGATTCAAGTGTCTATCAAAAGGTTGTTTCATTATCTG
* * *
7973 CAACTTTTATTAACGACTCGAAAGCT-AATTTAATGTTTCAAATATAAAAAACGA-TTCCAAAAA
1 CAACTTTCATGAACGACTCGAAAACTAAATTTAATGTTTCAAATATAAAAAA-GACTTCCAAAAA
* * * * *
8036 AATATTTGTTTCGGTTAGCGGGAATGGACCGTCTACTTAATATTATACAAGTTTTGCTCCAGATG
65 AATAGTTGTTTCGGTTAACGGGAATGGACCGTCCACTTAATATTATACAACTTTTGCTCCAGACG
* *
8101 TCCGATTGAGGTGATTCAAGTTTCTATTAAAAGGTTGTT
130 TCCGATTGAGGTGATTCAAGTGTCTATCAAAAGGTTGTT
8140 GCATAATGTC
Statistics
Matches: 139, Mismatches: 25, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
176 1 0.01
177 113 0.81
178 25 0.18
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (178 bp):
CAACTTTCATGAACGACTCGAAAACTAAATTTAATGTTTCAAATATAAAAAAGACTTCCAAAAAA
ATAGTTGTTTCGGTTAACGGGAATGGACCGTCCACTTAATATTATACAACTTTTGCTCCAGACGT
CCGATTGAGGTGATTCAAGTGTCTATCAAAAGGTTGTTTCATTATCTG
Found at i:8766 original size:52 final size:52
Alignment explanation
Indices: 8650--8772 Score: 165
Period size: 52 Copynumber: 2.4 Consensus size: 52
8640 AAAAAGCTGC
* * *
8650 TTGAATGTTTTGAAAACGTGATGGGAATTTTCCCAATTTGAAAAGACCTAAA
1 TTGAATGTTTTGAAAACTTAATGGGAACTTTCCCAATTTGAAAAGACCTAAA
** * **
8702 TTGAACATTTTGAAAACTTAATGGGAACTTTCCCACTTTGAAAAGGGCTAAA
1 TTGAATGTTTTGAAAACTTAATGGGAACTTTCCCAATTTGAAAAGACCTAAA
*
8754 TTGAATGCTTTGAAAACTT
1 TTGAATGTTTTGAAAACTT
8773 TGAATGAAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 60 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (52 bp):
TTGAATGTTTTGAAAACTTAATGGGAACTTTCCCAATTTGAAAAGACCTAAA
Found at i:16526 original size:19 final size:19
Alignment explanation
Indices: 16497--16545 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
16487 CTACCTACCT
*
16497 AACAAATAAACAAACAAAT-
1 AACAAACAAAC-AACAAATA
*
16516 TACAAACAAACAACAAATA
1 AACAAACAAACAACAAATA
16535 AACAAACAAAC
1 AACAAACAAAC
16546 TCACATTCCG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 7 0.27
19 19 0.73
ACGTcount: A:0.71, C:0.20, G:0.00, T:0.08
Consensus pattern (19 bp):
AACAAACAAACAACAAATA
Found at i:24500 original size:6 final size:6
Alignment explanation
Indices: 24479--24520 Score: 59
Period size: 6 Copynumber: 6.8 Consensus size: 6
24469 ACCCTACGTA
24479 TATATC TATCTATC TATATC TATATC TATATC TATA-C TATAT
1 TATATC TA--TATC TATATC TATATC TATATC TATATC TATAT
24521 ATAAAAGTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 5 0.15
6 22 0.67
8 6 0.18
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATC
Found at i:25866 original size:47 final size:47
Alignment explanation
Indices: 25810--25904 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
25800 TTTAATATTT
25810 AATTCTTAAATTTATTTAATATATTTATTATTCGATTTTATTTTACA
1 AATTCTTAAATTTATTTAATATATTTATTATTCGATTTTATTTTACA
25857 AATTCTTAAATTTATTTAATATATTTATTATTCGATTTTATTTTACA
1 AATTCTTAAATTTATTTAATATATTTATTATTCGATTTTATTTTACA
25904 A
1 A
25905 TCCACCACTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (47 bp):
AATTCTTAAATTTATTTAATATATTTATTATTCGATTTTATTTTACA
Found at i:26377 original size:60 final size:61
Alignment explanation
Indices: 26281--26441 Score: 247
Period size: 60 Copynumber: 2.7 Consensus size: 61
26271 GCTAATTGCT
* * * *
26281 CAAATAAGGGCCTACCGTTTGTC-AAAATGCTTAAATAAGGGT-TCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACG-TTATCGAAAATGCTCAAATAAGGGTCCCGATCTTTTAATTTGGC
*
26341 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAA-GGTCCCGATCTTTTAGTTTGGC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGTCCCGATCTTTTAATTTGGC
26401 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGG
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGG
26442 CGTGATGTCA
Statistics
Matches: 93, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
59 7 0.08
60 84 0.90
61 2 0.02
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (61 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGTCCCGATCTTTTAATTTGGC
Found at i:26379 original size:31 final size:31
Alignment explanation
Indices: 26341--26442 Score: 95
Period size: 31 Copynumber: 3.4 Consensus size: 31
26331 TTAATTTGGC
26341 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
* * * * ***
26372 CAAATAAGGTCCCGATC-TT-T-TAGTTTGGC-
1 CAAATAAGG-GCCTAACGTTATCGAAAAT-GCT
26401 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
26432 CAAATAAGGGC
1 CAAATAAGGGC
26443 GTGATGTCAG
Statistics
Matches: 51, Mismatches: 14, Indels: 12
0.66 0.18 0.16
Matches are distributed among these distances:
28 4 0.08
29 13 0.25
30 6 0.12
31 24 0.47
32 4 0.08
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.25
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCT
Found at i:26510 original size:31 final size:31
Alignment explanation
Indices: 26475--26639 Score: 130
Period size: 31 Copynumber: 5.5 Consensus size: 31
26465 GTGAGATAGA
*
26475 CCCTTATTTGAGCATTTTGGCAAACGTTAGG
1 CCCTTATTTGAGCATTTTGACAAACGTTAGG
** **
26506 CCCTTATTTG-GCCAAATT--CAAA-GATGGGG
1 CCCTTATTTGAG-CATTTTGACAAACG-TTAGG
* *
26535 CCCTTATTTGAGCATTTTGGCAAACGTTAAG
1 CCCTTATTTGAGCATTTTGACAAACGTTAGG
** * *
26566 CCCTTATTTG-GTCAAATTAAAAAATCG---GG
1 CCCTTATTTGAG-CATTTTGACAAA-CGTTAGG
*
26595 CCCTTATTTGAGCATTTTGACAAACGTTAGA
1 CCCTTATTTGAGCATTTTGACAAACGTTAGG
26626 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
26640 ATTAGCCCAA
Statistics
Matches: 102, Mismatches: 20, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
28 3 0.03
29 40 0.39
30 4 0.04
31 52 0.51
32 3 0.03
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (31 bp):
CCCTTATTTGAGCATTTTGACAAACGTTAGG
Found at i:26548 original size:60 final size:60
Alignment explanation
Indices: 26475--26635 Score: 259
Period size: 60 Copynumber: 2.7 Consensus size: 60
26465 GTGAGATAGA
* * *
26475 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGATGGGG
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAAATCGGG
* *
26535 CCCTTATTTGAGCATTTTGGCAAACGTTAAGCCCTTATTTGGTCAAATTAAAAAATCGGG
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAAATCGGG
* *
26595 CCCTTATTTGAGCATTTTGACAAACGTTAGACCCTTATTTG
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
26636 AGCAATTAGC
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 93 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAAATCGGG
Found at i:30332 original size:20 final size:20
Alignment explanation
Indices: 30307--30360 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
30297 GACAGTTTTT
30307 TGTTCAAATTCAACTAGAAC
1 TGTTCAAATTCAACTAGAAC
*
30327 TGTTCAAATTCAACTAGCAC
1 TGTTCAAATTCAACTAGAAC
30347 TAG--CAAATTCAACT
1 T-GTTCAAATTCAACT
30361 TACTCAAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 11 0.34
20 20 0.62
21 1 0.03
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (20 bp):
TGTTCAAATTCAACTAGAAC
Found at i:34301 original size:20 final size:20
Alignment explanation
Indices: 34276--34366 Score: 73
Period size: 20 Copynumber: 4.6 Consensus size: 20
34266 AGATATTTTT
*
34276 ATATAATGTATATATTTAAA
1 ATATAATATATATATTTAAA
* *
34296 ATATAATATATATGTTT-AT
1 ATATAATATATATATTTAAA
* *
34315 ATATAAATAAATAAAATTTAAA
1 ATAT-AATATAT-ATATTTAAA
*
34337 ATAT-AT-TATATA-TTATAT
1 ATATAATATATATATTTA-AA
34355 ATATAATATATA
1 ATATAATATATA
34367 AATAAATAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
17 3 0.05
18 7 0.13
19 9 0.16
20 27 0.49
21 4 0.07
22 5 0.09
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
ATATAATATATATATTTAAA
Found at i:35133 original size:20 final size:21
Alignment explanation
Indices: 35096--35135 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
35086 AACCCATTAA
*
35096 TTAAAGCGTGTCACTCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
*
35117 TTAAA-CGTGTTAATCGTGT
1 TTAAAGCGTGTCAATCGTGT
35136 ATTGACATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.38
Consensus pattern (21 bp):
TTAAAGCGTGTCAATCGTGTC
Found at i:35655 original size:206 final size:206
Alignment explanation
Indices: 35301--35714 Score: 828
Period size: 206 Copynumber: 2.0 Consensus size: 206
35291 AATTGAGCTA
35301 AATCTCATCAATTCAAACAAAATGAATAGAAAAACTTAATGAGAATGGATAATACTAATGGAATT
1 AATCTCATCAATTCAAACAAAATGAATAGAAAAACTTAATGAGAATGGATAATACTAATGGAATT
35366 AAATTAATATCATATATTCTTAGTAATTATATTATAAGTACTAATTAAGTACAAGAAACATGCTA
66 AAATTAATATCATATATTCTTAGTAATTATATTATAAGTACTAATTAAGTACAAGAAACATGCTA
35431 GTAAATAAATTATATATAATTTTCTCTCATTTATCTCAAAATTTAGATTTTAAAATTCATAATAA
131 GTAAATAAATTATATATAATTTTCTCTCATTTATCTCAAAATTTAGATTTTAAAATTCATAATAA
35496 GATGAAATCTC
196 GATGAAATCTC
35507 AATCTCATCAATTCAAACAAAATGAATAGAAAAACTTAATGAGAATGGATAATACTAATGGAATT
1 AATCTCATCAATTCAAACAAAATGAATAGAAAAACTTAATGAGAATGGATAATACTAATGGAATT
35572 AAATTAATATCATATATTCTTAGTAATTATATTATAAGTACTAATTAAGTACAAGAAACATGCTA
66 AAATTAATATCATATATTCTTAGTAATTATATTATAAGTACTAATTAAGTACAAGAAACATGCTA
35637 GTAAATAAATTATATATAATTTTCTCTCATTTATCTCAAAATTTAGATTTTAAAATTCATAATAA
131 GTAAATAAATTATATATAATTTTCTCTCATTTATCTCAAAATTTAGATTTTAAAATTCATAATAA
35702 GATGAAATCTC
196 GATGAAATCTC
35713 AA
1 AA
35715 ACTCGAACTA
Statistics
Matches: 208, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
206 208 1.00
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.35
Consensus pattern (206 bp):
AATCTCATCAATTCAAACAAAATGAATAGAAAAACTTAATGAGAATGGATAATACTAATGGAATT
AAATTAATATCATATATTCTTAGTAATTATATTATAAGTACTAATTAAGTACAAGAAACATGCTA
GTAAATAAATTATATATAATTTTCTCTCATTTATCTCAAAATTTAGATTTTAAAATTCATAATAA
GATGAAATCTC
Found at i:38134 original size:3 final size:3
Alignment explanation
Indices: 38128--38192 Score: 53
Period size: 3 Copynumber: 22.0 Consensus size: 3
38118 AGAAGACCTC
* * * * *
38128 CTT CTT CAT C-T CATT CT- CTT CTT CTT CCT CTT CCT CTT CCT CTC
1 CTT CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
38172 CCT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT
38193 TCTTTCGCTT
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
2 4 0.08
3 42 0.88
4 2 0.04
ACGTcount: A:0.03, C:0.42, G:0.00, T:0.55
Consensus pattern (3 bp):
CTT
Found at i:38192 original size:6 final size:6
Alignment explanation
Indices: 38143--38190 Score: 60
Period size: 6 Copynumber: 8.0 Consensus size: 6
38133 TCATCTCATT
* * * *
38143 CTCTTC TTCTTC CTCTTC CTCTTC CTCTCC CTCTTC TTCTTC TTCTTC
1 CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC
38191 TTTCTTTCGC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (6 bp):
CTCTTC
Found at i:43801 original size:10 final size:10
Alignment explanation
Indices: 43788--43812 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
43778 AAAGTGGAGA
43788 AATTTTGCAG
1 AATTTTGCAG
43798 AATTTTGCAG
1 AATTTTGCAG
43808 AATTT
1 AATTT
43813 CAGAGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (10 bp):
AATTTTGCAG
Found at i:44151 original size:31 final size:31
Alignment explanation
Indices: 44127--44202 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
44117 TAAATCTTTT
44127 ATTTTAG-GAGGGTCAA-AGTGATAAAACTTCA
1 ATTTTAGTG-GGGTCAATA-TGATAAAACTTCA
44158 ATTTTAGTGGGGTCAATATGATAAAACTTCA
1 ATTTTAGTGGGGTCAATATGATAAAACTTCA
44189 ATTTTAGTGGGGTC
1 ATTTTAGTGGGGTC
44203 GATTGGTAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
31 41 0.95
32 2 0.05
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.34
Consensus pattern (31 bp):
ATTTTAGTGGGGTCAATATGATAAAACTTCA
Found at i:45068 original size:25 final size:25
Alignment explanation
Indices: 45040--45091 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
45030 ATAACATGCG
*
45040 TGCGCTGAGCAAACGAGTC-TGTGCT
1 TGCGCTGAGAAAACGAG-CATGTGCT
* *
45065 TGCGTTTAGAAAACGAGCATGTGCT
1 TGCGCTGAGAAAACGAGCATGTGCT
45090 TG
1 TG
45092 TGTTTGGAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (25 bp):
TGCGCTGAGAAAACGAGCATGTGCT
Found at i:45648 original size:18 final size:18
Alignment explanation
Indices: 45621--45661 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
45611 AATTAATTGT
45621 TTTAATATTA-ATTTTTA
1 TTTAATATTATATTTTTA
45638 TTTATATATTATATTTTTA
1 TTTA-ATATTATATTTTTA
*
45657 CTTAA
1 TTTAA
45662 AAATTAGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 7 0.33
19 10 0.48
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTAATATTATATTTTTA
Found at i:48098 original size:16 final size:18
Alignment explanation
Indices: 48066--48100 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
48056 GGTTCTTCCG
48066 ATGAACTAGAGAAACAGA
1 ATGAACTAGAGAAACAGA
48084 ATGAAC-AGA-AAACAGA
1 ATGAACTAGAGAAACAGA
48100 A
1 A
48101 GAAAAAGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.60, C:0.11, G:0.20, T:0.09
Consensus pattern (18 bp):
ATGAACTAGAGAAACAGA
Found at i:52082 original size:11 final size:11
Alignment explanation
Indices: 52066--52090 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
52056 TGGATTGTGG
52066 GATTGTAATGA
1 GATTGTAATGA
52077 GATTGTAATGA
1 GATTGTAATGA
52088 GAT
1 GAT
52091 GCGTTTCGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.28, T:0.36
Consensus pattern (11 bp):
GATTGTAATGA
Found at i:56077 original size:21 final size:21
Alignment explanation
Indices: 56053--56098 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
56043 AATGAAACCC
56053 AAAACAA-A-AAAAAAGGAAGAA
1 AAAACAAGATAAAAAA--AAGAA
56074 AAAACAAGATAAAAAAAAGAA
1 AAAACAAGATAAAAAAAAGAA
56095 AAAA
1 AAAA
56099 GAACAGAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 16 0.70
22 1 0.04
23 6 0.26
ACGTcount: A:0.83, C:0.04, G:0.11, T:0.02
Consensus pattern (21 bp):
AAAACAAGATAAAAAAAAGAA
Found at i:57804 original size:31 final size:31
Alignment explanation
Indices: 57761--57925 Score: 148
Period size: 31 Copynumber: 5.5 Consensus size: 31
57751 ATTGGCTAAT
*
57761 TGCTTAAATAAGGGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
* * * **
57792 TGCTCAAATAAGGGTCTGATC-TTT--TAATT
1 TGCTCAAATAAGGGCCT-AACGTTTGCCAAAA
57821 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGCCAAAA
* * **
57852 TGCTCAAATAAGGGCCCCATC-TTTG--AATT
1 TGCTCAAATAAGGG-CCTAACGTTTGCCAAAA
57881 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGCCAAAA
57912 TGCTCAAATAAGGG
1 TGCTCAAATAAGGG
57926 TCTGTCTCAC
Statistics
Matches: 103, Mismatches: 19, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
28 6 0.06
29 35 0.34
30 8 0.08
31 48 0.47
32 6 0.06
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.27
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
Found at i:57859 original size:60 final size:60
Alignment explanation
Indices: 57766--57929 Score: 292
Period size: 60 Copynumber: 2.7 Consensus size: 60
57756 CTAATTGCTT
*
57766 AAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGCC
1 AAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTGAATTTGGCC
* **
57826 AAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGGCC
1 AAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTGAATTTGGCC
57886 AAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTG
1 AAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTG
57930 TCTCACGCAT
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 97 1.00
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (60 bp):
AAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTGAATTTGGCC
Done.