Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012055.1 Corchorus capsularis cultivar CVL-1 contig12076, 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: 104722
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5451 original size:31 final size:32
Alignment explanation
Indices: 5416--5483 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 32
5406 GCTATATTAT
*
5416 AAGACAACTTACCCTCTGAATTTCCAAATTC-
1 AAGACAACTTACCCTCTGAACTTCCAAATTCA
* * *
5447 AAGAC-AGTTAGCCTCTGGACTTCCAAATTCA
1 AAGACAACTTACCCTCTGAACTTCCAAATTCA
5478 AAGACA
1 AAGACA
5484 TTTGCCGCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 21 0.68
31 10 0.32
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.25
Consensus pattern (32 bp):
AAGACAACTTACCCTCTGAACTTCCAAATTCA
Found at i:6755 original size:29 final size:29
Alignment explanation
Indices: 6701--6758 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
6691 GTCAAACTAA
* * *
6701 TTGTATTTTTGACCTTTGTTCTTAAAAAT
1 TTGTACTTTTGACCTTTATTCATAAAAAT
6730 TTGTACTTTTGACCTTTAATT-ATAAAAAT
1 TTGTACTTTTGACCTTT-ATTCATAAAAAT
6759 ATATATATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 23 0.92
30 2 0.08
ACGTcount: A:0.29, C:0.10, G:0.09, T:0.52
Consensus pattern (29 bp):
TTGTACTTTTGACCTTTATTCATAAAAAT
Found at i:16190 original size:16 final size:16
Alignment explanation
Indices: 16169--16199 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
16159 ATGAATTTTA
16169 CAAAAAAAAAAAAAAT
1 CAAAAAAAAAAAAAAT
16185 CAAAAAAAAAAAAAA
1 CAAAAAAAAAAAAAA
16200 CAAGAAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.90, C:0.06, G:0.00, T:0.03
Consensus pattern (16 bp):
CAAAAAAAAAAAAAAT
Found at i:17340 original size:12 final size:11
Alignment explanation
Indices: 17323--17362 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
17313 TCATAACAAA
17323 TTTATAATTAAT
1 TTTATAATT-AT
17335 TTTATAATTAT
1 TTTATAATTAT
*
17346 TTGATAATTTAT
1 TTTATAA-TTAT
17358 TTTAT
1 TTTAT
17363 GTAGAAAGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 8 0.32
12 17 0.68
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (11 bp):
TTTATAATTAT
Found at i:22850 original size:37 final size:36
Alignment explanation
Indices: 22803--22876 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 36
22793 TAAATAAACT
* *
22803 ACTTATAAACTAAATAAAC-CACATCAACTAAACTCAC
1 ACTTACAAACTAAACAAACACAC-T-AACTAAACTCAC
* *
22840 ACTTACAAACTGAACAAACAGACTAACTAAACTCAC
1 ACTTACAAACTAAACAAACACACTAACTAAACTCAC
22876 A
1 A
22877 TTTTGTGAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 13 0.41
37 17 0.53
38 2 0.06
ACGTcount: A:0.51, C:0.27, G:0.03, T:0.19
Consensus pattern (36 bp):
ACTTACAAACTAAACAAACACACTAACTAAACTCAC
Found at i:26876 original size:1 final size:1
Alignment explanation
Indices: 26866--26909 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
26856 TTTTAGTAAC
* ** *
26866 TTTTTGTTTTTTGCTTTTTTTTTTTGTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
26910 CAGTTTTCAC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.02, G:0.07, T:0.91
Consensus pattern (1 bp):
T
Found at i:26883 original size:8 final size:7
Alignment explanation
Indices: 26866--26909 Score: 58
Period size: 6 Copynumber: 6.7 Consensus size: 7
26856 TTTTAGTAAC
26866 TTTTTGT
1 TTTTTGT
*
26873 TTTTTGC
1 TTTTTGT
26880 TTTTT-T
1 TTTTTGT
26886 TTTTTGT
1 TTTTTGT
26893 TTTTT-T
1 TTTTTGT
26899 TTTTT-T
1 TTTTTGT
26905 TTTTT
1 TTTTT
26910 CAGTTTTCAC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
6 17 0.50
7 17 0.50
ACGTcount: A:0.00, C:0.02, G:0.07, T:0.91
Consensus pattern (7 bp):
TTTTTGT
Found at i:26903 original size:13 final size:13
Alignment explanation
Indices: 26866--26909 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
26856 TTTTAGTAAC
*
26866 TTTTTGTTTTTTG
1 TTTTTTTTTTTTG
*
26879 CTTTTTTTTTTTG
1 TTTTTTTTTTTTG
26892 TTTTTTTTTTTT-
1 TTTTTTTTTTTTG
26904 TTTTTT
1 TTTTTT
26910 CAGTTTTCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 6 0.21
13 22 0.79
ACGTcount: A:0.00, C:0.02, G:0.07, T:0.91
Consensus pattern (13 bp):
TTTTTTTTTTTTG
Found at i:26909 original size:20 final size:20
Alignment explanation
Indices: 26866--26908 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
26856 TTTTAGTAAC
26866 TTTTTGTTTTTTGCTTTTTT
1 TTTTTGTTTTTTGCTTTTTT
26886 TTTTTGTTTTTT--TTTTTT
1 TTTTTGTTTTTTGCTTTTTT
26904 TTTTT
1 TTTTT
26909 TCAGTTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 11 0.48
20 12 0.52
ACGTcount: A:0.00, C:0.02, G:0.07, T:0.91
Consensus pattern (20 bp):
TTTTTGTTTTTTGCTTTTTT
Found at i:28012 original size:19 final size:18
Alignment explanation
Indices: 27986--28022 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
27976 AATTAATTGT
27986 TTTAATATTAAATTTTTA
1 TTTAATATTAAATTTTTA
*
28004 TTTATATATTATATTTTTA
1 TTTA-ATATTAAATTTTTA
28023 CCTAGAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTAATATTAAATTTTTA
Found at i:30466 original size:25 final size:24
Alignment explanation
Indices: 30437--30495 Score: 75
Period size: 25 Copynumber: 2.5 Consensus size: 24
30427 ATCAAACCCT
*
30437 AAACTTCATTTCTAACAACTTCTTC
1 AAACTTCATTTCTAACAA-ATCTTC
* *
30462 AAACTTCATTTTTAAGAAATCTTC
1 AAACTTCATTTCTAACAAATCTTC
30486 AAA-TTCATTT
1 AAACTTCATTT
30496 TCCTTCATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 7 0.23
24 8 0.26
25 16 0.52
ACGTcount: A:0.36, C:0.20, G:0.02, T:0.42
Consensus pattern (24 bp):
AAACTTCATTTCTAACAAATCTTC
Found at i:30534 original size:26 final size:26
Alignment explanation
Indices: 30505--30572 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
30495 TTCCTTCATT
30505 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
30531 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
30557 TTAAACATAAATTAAT
1 TTAATCATAAACTAAT
30573 AAACTAAGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.54, C:0.09, G:0.01, T:0.35
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:30781 original size:12 final size:12
Alignment explanation
Indices: 30766--30797 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
30756 TTTCTCTCTT
30766 TTTTTTTCAAAA
1 TTTTTTTCAAAA
30778 TTTTTTTCAAAA
1 TTTTTTTCAAAA
30790 TATTTTTT
1 T-TTTTTT
30798 ACATCAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.68
13 6 0.32
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTTTTTCAAAA
Found at i:30967 original size:21 final size:22
Alignment explanation
Indices: 30936--30981 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
30926 AAAAATTATA
**
30936 AAAAGGGGGGGCGGTATTTAGC
1 AAAAGGGGGGGCGGTAAATAGC
30958 AAAA-GGGGGGCGGTAAATAGC
1 AAAAGGGGGGGCGGTAAATAGC
30979 AAA
1 AAA
30982 CCCCTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.37, C:0.09, G:0.41, T:0.13
Consensus pattern (22 bp):
AAAAGGGGGGGCGGTAAATAGC
Found at i:31406 original size:50 final size:50
Alignment explanation
Indices: 31339--31485 Score: 206
Period size: 50 Copynumber: 2.9 Consensus size: 50
31329 AAAAAAAATA
*
31339 TGATTATATTTATTAACCATATTATCCATATAATATTAGAGATAATTATGG
1 TGATTATATTTATTAACCATATTAACCATAT-ATATTAGAGATAATTATGG
*
31390 TGATTATA-CTATTAACCATATTAACCATATATATTAGAGATAATTATGG
1 TGATTATATTTATTAACCATATTAACCATATATATTAGAGATAATTATGG
* **** *
31439 TGATTATATTTATCAACCATATTAGTTTTATATATTAGAGAAAATTA
1 TGATTATATTTATTAACCATATTAACCATATATATTAGAGATAATTA
31486 GATAATTATC
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
49 27 0.31
50 51 0.59
51 8 0.09
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (50 bp):
TGATTATATTTATTAACCATATTAACCATATATATTAGAGATAATTATGG
Found at i:35094 original size:21 final size:22
Alignment explanation
Indices: 35070--35117 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
35060 AGAGTCAAAA
35070 TTCTT-ACCCAAAAACTTCAAG
1 TTCTTCACCCAAAAACTTCAAG
*
35091 TTCTTCCACCCAAACACTTCAAG
1 TTCTT-CACCCAAAAACTTCAAG
35114 TTCT
1 TTCT
35118 GATAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 5 0.21
23 19 0.79
ACGTcount: A:0.31, C:0.33, G:0.04, T:0.31
Consensus pattern (22 bp):
TTCTTCACCCAAAAACTTCAAG
Found at i:35345 original size:14 final size:14
Alignment explanation
Indices: 35326--35356 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
35316 TAAAGTTTGG
35326 GATTTATTGTTAGA
1 GATTTATTGTTAGA
35340 GATTTATTGTTAGA
1 GATTTATTGTTAGA
35354 GAT
1 GAT
35357 CTCGAGTTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (14 bp):
GATTTATTGTTAGA
Found at i:58577 original size:2 final size:2
Alignment explanation
Indices: 58570--58594 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
58560 TTATTATTGT
58570 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 T
58595 TTGTTTAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:58841 original size:15 final size:15
Alignment explanation
Indices: 58821--58857 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
58811 AACTTCAAAT
*
58821 TAATTTTAAAATATA
1 TAATTTTAAAATAGA
*
58836 TAATTTTAAAATGGA
1 TAATTTTAAAATAGA
58851 TAATTTT
1 TAATTTT
58858 CCTTAATGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (15 bp):
TAATTTTAAAATAGA
Found at i:62573 original size:21 final size:19
Alignment explanation
Indices: 62533--62593 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 19
62523 AGTAATTAAA
*
62533 TATATAATATATAT-TTATT
1 TATA-AATATATTTATTATT
*
62552 TATAACTCATTATTTATTATT
1 TATAAAT-A-TATTTATTATT
62573 TA-AAATATATTTATTATT
1 TATAAATATATTTATTATT
62591 TAT
1 TAT
62594 TTATTAATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
18 15 0.43
19 6 0.17
20 7 0.20
21 7 0.20
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
TATAAATATATTTATTATT
Found at i:62588 original size:25 final size:25
Alignment explanation
Indices: 62560--62608 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
62550 TTTATAACTC
62560 ATTATTTA-TTATTTAAAATATATTT
1 ATTATTTATTTA-TTAAAATATATTT
*
62585 ATTATTTATTTATTAATATATATT
1 ATTATTTATTTATTAAAATATATT
62609 ATATCTAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
ATTATTTATTTATTAAAATATATTT
Found at i:63141 original size:29 final size:30
Alignment explanation
Indices: 63109--63175 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 30
63099 ATGCAATTTG
*
63109 GGATATAACCTTAC-AAATCAAGCAATTAA
1 GGATATAACCTTACAAAATCAAGCAAATAA
* *
63138 GGATATAACGTTACGAAAATCGAGCAAATAA
1 GGATATAACCTTAC-AAAATCAAGCAAATAA
63169 GGATATA
1 GGATATA
63176 GTCCGTTAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 13 0.39
31 20 0.61
ACGTcount: A:0.48, C:0.13, G:0.16, T:0.22
Consensus pattern (30 bp):
GGATATAACCTTACAAAATCAAGCAAATAA
Found at i:63329 original size:31 final size:31
Alignment explanation
Indices: 63294--63372 Score: 149
Period size: 31 Copynumber: 2.5 Consensus size: 31
63284 CCCTAACTGA
63294 TTATATCCTTAATTGCTCGAAATCGAAAACG
1 TTATATCCTTAATTGCTCGAAATCGAAAACG
63325 TTATATCCTTAATTGCTCGAAATCGAAAACG
1 TTATATCCTTAATTGCTCGAAATCGAAAACG
*
63356 TTATATTCTTAATTGCT
1 TTATATCCTTAATTGCT
63373 TGTTTTGTAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (31 bp):
TTATATCCTTAATTGCTCGAAATCGAAAACG
Found at i:63423 original size:31 final size:31
Alignment explanation
Indices: 63294--63435 Score: 126
Period size: 31 Copynumber: 4.6 Consensus size: 31
63284 CCCTAACTGA
* * *
63294 TTATATCCTTAATTGCTCGAAATCGAAAACG
1 TTATATCCTTAATTGCTTGCAATAGAAAACG
* * *
63325 TTATATCCTTAATTGCTCGAAATCGAAAACG
1 TTATATCCTTAATTGCTTGCAATAGAAAACG
* ** * * *
63356 TTATATTCTTAATTGCTTG-TTTTG-TAACT
1 TTATATCCTTAATTGCTTGCAATAGAAAACG
* **
63385 TTATATCCTTAATTGTTTGCGGTAGAAAACG
1 TTATATCCTTAATTGCTTGCAATAGAAAACG
*
63416 TTATATCCTAAATTGCTTGC
1 TTATATCCTTAATTGCTTGC
63436 TTATCATCTA
Statistics
Matches: 93, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
29 20 0.22
30 4 0.04
31 69 0.74
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (31 bp):
TTATATCCTTAATTGCTTGCAATAGAAAACG
Found at i:64346 original size:3 final size:3
Alignment explanation
Indices: 64338--64386 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
64328 GAAATTAGGG
*
64338 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
64386 T
1 T
64387 GAAAATACGG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:64469 original size:31 final size:30
Alignment explanation
Indices: 64428--64564 Score: 132
Period size: 31 Copynumber: 4.5 Consensus size: 30
64418 GTCAAATACT
* *** *
64428 CAATTTAGGATATAACGTTTGTTGCTGCAAG
1 CAATTAAGGATATAACGTTT-TCAATTCAAG
* **
64459 CAATTAAGGATATAACG-TTACAAAACAAG
1 CAATTAAGGATATAACGTTTTCAATTCAAG
* *
64488 CAATTAAGGATATAACGTTTTTTAATTCGAG
1 CAATTAAGGATATAACG-TTTTCAATTCAAG
* *
64519 CAATTAAGGATATAACATTTTCGATTTCAAG
1 CAATTAAGGATATAACGTTTTC-AATTCAAG
64550 CAATTAAGGATATAA
1 CAATTAAGGATATAA
64565 TCAGTTAGGG
Statistics
Matches: 87, Mismatches: 16, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
29 21 0.24
30 6 0.07
31 60 0.69
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (30 bp):
CAATTAAGGATATAACGTTTTCAATTCAAG
Found at i:64722 original size:31 final size:29
Alignment explanation
Indices: 64687--64749 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
64677 ACGGACTATG
* *
64687 TCCTTATTTGCTCGATTTTCGTAACGTTATA
1 TCCTTAATTGCT-GATTTT-ATAACGTTATA
*
64718 TCCTTAATTGCTTATTTTATAACGTTATA
1 TCCTTAATTGCTGATTTTATAACGTTATA
64747 TCC
1 TCC
64750 CAAATTGCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 13 0.45
30 5 0.17
31 11 0.38
ACGTcount: A:0.22, C:0.19, G:0.10, T:0.49
Consensus pattern (29 bp):
TCCTTAATTGCTGATTTTATAACGTTATA
Found at i:64935 original size:41 final size:41
Alignment explanation
Indices: 64870--64952 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
64860 TTTCTTATTT
* *
64870 GGCCAATAGCTTCACCACTTCAAAATATAAATTGATTTTTA
1 GGCCAATAGCTTCACCACTACAAAAAATAAATTGATTTTTA
**
64911 GGCCAATAGCTTCAGTACTACAAAAAATAAATTGATTTTTA
1 GGCCAATAGCTTCACCACTACAAAAAATAAATTGATTTTTA
64952 G
1 G
64953 ATTTAGTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.33
Consensus pattern (41 bp):
GGCCAATAGCTTCACCACTACAAAAAATAAATTGATTTTTA
Found at i:65357 original size:32 final size:32
Alignment explanation
Indices: 65313--65391 Score: 122
Period size: 32 Copynumber: 2.5 Consensus size: 32
65303 AGCCACGCGG
*
65313 AGCCTCCCCACTAGGACAGCTCTGCCACGGCT
1 AGCCGCCCCACTAGGACAGCTCTGCCACGGCT
* **
65345 AGCCGCCTCACTAGGATGGCTCTGCCACGGCT
1 AGCCGCCCCACTAGGACAGCTCTGCCACGGCT
65377 AGCCGCCCCACTAGG
1 AGCCGCCCCACTAGG
65392 GCGGCAAGGC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.18, C:0.42, G:0.25, T:0.15
Consensus pattern (32 bp):
AGCCGCCCCACTAGGACAGCTCTGCCACGGCT
Found at i:65497 original size:33 final size:33
Alignment explanation
Indices: 65455--65572 Score: 123
Period size: 33 Copynumber: 3.6 Consensus size: 33
65445 TAGTATCGGT
* *
65455 GCCGCCCCAGGGGGGCGGTCTATCCATGGTAGG
1 GCCGCCCCAGGGGGGCGGCCTAGCCATGGTAGG
* * *
65488 GCCGCCCCAGGGAGGCGGCCTGGCCATGGTAGT
1 GCCGCCCCAGGGGGGCGGCCTAGCCATGGTAGG
* * *
65521 GCCGCCCCAGGAGGGCGGCTTGGCCATGGCTCA--
1 GCCGCCCCAGGGGGGCGGCCTAGCCATGG-T-AGG
*
65554 GCCGCCCCAGGGGGACGGC
1 GCCGCCCCAGGGGGGCGGC
65573 ACCGGTGGGG
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
33 71 0.97
34 1 0.01
35 1 0.01
ACGTcount: A:0.12, C:0.35, G:0.42, T:0.11
Consensus pattern (33 bp):
GCCGCCCCAGGGGGGCGGCCTAGCCATGGTAGG
Found at i:65738 original size:33 final size:32
Alignment explanation
Indices: 65639--65781 Score: 106
Period size: 32 Copynumber: 4.6 Consensus size: 32
65629 AAAAATGCCG
* *
65639 AGCCGCCCCA-TCGGGGCGGCCTGTCGTGGCGA
1 AGCCGCCCCAGT-GGGGCGGCCTGCCATGGCGA
* *
65671 AGCCGCCCCA-TCGGGAC-G---GCC--GGCTA
1 AGCCGCCCCAGT-GGGGCGGCCTGCCATGGCGA
*
65697 AGCCGCCCCAGTGGGGCGGCCTGCCCATGGTGA
1 AGCCGCCCCAGTGGGGCGGCCTG-CCATGGCGA
* *
65730 AGCCGCCCCA-TGAGGGCGGCTTGCTATGGCGA
1 AGCCGCCCCAGTG-GGGCGGCCTGCCATGGCGA
* *
65762 AGCCTCCCAAGTGGGGCGGC
1 AGCCGCCCCAGTGGGGCGGC
65782 TTCGCCACGG
Statistics
Matches: 90, Mismatches: 11, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
26 18 0.20
27 2 0.02
28 2 0.02
30 1 0.01
31 3 0.03
32 40 0.44
33 24 0.27
ACGTcount: A:0.13, C:0.36, G:0.38, T:0.12
Consensus pattern (32 bp):
AGCCGCCCCAGTGGGGCGGCCTGCCATGGCGA
Found at i:65779 original size:32 final size:33
Alignment explanation
Indices: 65696--65783 Score: 108
Period size: 32 Copynumber: 2.7 Consensus size: 33
65686 ACGGCCGGCT
* *
65696 AAGCCGCCCCAGTGGGGCGGCCTGCCCATGGTG
1 AAGCCGCCCCAGTGGGGCGGCTTGCCCATGGCG
*
65729 AAGCCGCCCCA-TGAGGGCGGCTTG-CTATGGCG
1 AAGCCGCCCCAGTG-GGGCGGCTTGCCCATGGCG
* *
65761 AAGCCTCCCAAGTGGGGCGGCTT
1 AAGCCGCCCCAGTGGGGCGGCTT
65784 CGCCACGGTA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
32 26 0.54
33 22 0.46
ACGTcount: A:0.15, C:0.33, G:0.38, T:0.15
Consensus pattern (33 bp):
AAGCCGCCCCAGTGGGGCGGCTTGCCCATGGCG
Found at i:66122 original size:27 final size:26
Alignment explanation
Indices: 66092--66142 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
66082 TTATAATTGG
*
66092 ATTTTTGGTGAAAAAACAAGTGTTTCC
1 ATTTTAGGT-AAAAAACAAGTGTTTCC
*
66119 ATTTTAGGTATAAAACAAGTGTTT
1 ATTTTAGGTAAAAAACAAGTGTTT
66143 TTTAAAGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (26 bp):
ATTTTAGGTAAAAAACAAGTGTTTCC
Found at i:67097 original size:11 final size:11
Alignment explanation
Indices: 67054--67091 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
67044 TTCCTATATA
*
67054 AAATAAATTAT
1 AAATTAATTAT
67065 CAAA-TAATTAT
1 -AAATTAATTAT
67076 AAATTAATTAT
1 AAATTAATTAT
67087 AAATT
1 AAATT
67092 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:67262 original size:18 final size:18
Alignment explanation
Indices: 67239--67277 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
67229 TATCCCCTTA
*
67239 TATTTATGGTGATGTATC
1 TATTTATGGCGATGTATC
67257 TATTTATGGCGATGTATC
1 TATTTATGGCGATGTATC
67275 TAT
1 TAT
67278 GTGCCTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.08, G:0.21, T:0.49
Consensus pattern (18 bp):
TATTTATGGCGATGTATC
Found at i:67385 original size:16 final size:16
Alignment explanation
Indices: 67364--67394 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
67354 TTTTTCTCCA
67364 TATTCTATTGTCTTTC
1 TATTCTATTGTCTTTC
*
67380 TATTCTGTTGTCTTT
1 TATTCTATTGTCTTT
67395 TTCATACTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.16, G:0.10, T:0.65
Consensus pattern (16 bp):
TATTCTATTGTCTTTC
Found at i:69278 original size:16 final size:16
Alignment explanation
Indices: 69256--69309 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
69246 TTTTTAAATG
*
69256 AAAAATTAAGTAATTA
1 AAAAATTAAGCAATTA
* ** *
69272 AATAATTTTGGAATTA
1 AAAAATTAAGCAATTA
69288 AAAAATTAAGCAATTA
1 AAAAATTAAGCAATTA
69304 AAAAAT
1 AAAAAT
69310 AAAAAATAGG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.31
Consensus pattern (16 bp):
AAAAATTAAGCAATTA
Found at i:70239 original size:36 final size:35
Alignment explanation
Indices: 70199--70277 Score: 108
Period size: 33 Copynumber: 2.3 Consensus size: 35
70189 GCATAATGTA
*
70199 GATGATCTTGTTGAACTACCAGTACTCACACACAAT
1 GATGATCTT-TTCAACTACCAGTACTCACACACAAT
**
70235 GATGATC--TTCAACTACCAGTGTTCACACACAAT
1 GATGATCTTTTCAACTACCAGTACTCACACACAAT
70268 GATGATCTTT
1 GATGATCTTT
70278 AACTACTAGC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
33 30 0.79
35 1 0.03
36 7 0.18
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (35 bp):
GATGATCTTTTCAACTACCAGTACTCACACACAAT
Found at i:70249 original size:33 final size:33
Alignment explanation
Indices: 70212--70283 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
70202 GATCTTGTTG
70212 AACTACCAGTACTCACACACAATGATGATCTTC
1 AACTACCAGTACTCACACACAATGATGATCTTC
** *
70245 AACTACCAGTGTTCACACACAATGATGATCTTT
1 AACTACCAGTACTCACACACAATGATGATCTTC
70278 AACTAC
1 AACTAC
70284 TAGCAGCTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.36, C:0.28, G:0.10, T:0.26
Consensus pattern (33 bp):
AACTACCAGTACTCACACACAATGATGATCTTC
Found at i:70325 original size:18 final size:18
Alignment explanation
Indices: 70302--70343 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
70292 GAAGAGAATG
70302 ATGATCAAGTGGCTGGTA
1 ATGATCAAGTGGCTGGTA
* *
70320 ATGATCAATTGGTTGGTA
1 ATGATCAAGTGGCTGGTA
70338 ATGATC
1 ATGATC
70344 CAATGCTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.33
Consensus pattern (18 bp):
ATGATCAAGTGGCTGGTA
Found at i:70353 original size:18 final size:18
Alignment explanation
Indices: 70302--70358 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
70292 GAAGAGAATG
*
70302 ATGATCAAGTGGC-TGGTA
1 ATGATCAA-TTGCTTGGTA
*
70320 ATGATCAATTGGTTGGTA
1 ATGATCAATTGCTTGGTA
70338 ATGATCCAA-TGCTTGGTA
1 ATGAT-CAATTGCTTGGTA
70356 ATG
1 ATG
70359 TGGGTGTGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
17 2 0.06
18 29 0.85
19 3 0.09
ACGTcount: A:0.28, C:0.11, G:0.28, T:0.33
Consensus pattern (18 bp):
ATGATCAATTGCTTGGTA
Found at i:70481 original size:27 final size:27
Alignment explanation
Indices: 70450--70510 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
70440 GTTTAGGAGA
* *
70450 GGAAGAAGTAGGTGGTGAGGTTCAAAT
1 GGAAGAAGTAGGCGCTGAGGTTCAAAT
70477 GGAAGAAGTAGGCGCTGAGGTTCAAAT
1 GGAAGAAGTAGGCGCTGAGGTTCAAAT
*
70504 AGAAGAA
1 GGAAGAA
70511 CCTGTTGGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.38, C:0.07, G:0.38, T:0.18
Consensus pattern (27 bp):
GGAAGAAGTAGGCGCTGAGGTTCAAAT
Found at i:74750 original size:29 final size:30
Alignment explanation
Indices: 74675--74751 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 30
74665 TTTGACACCG
**
74675 AGTGCAAACCCACACTCAAATACAATCCCA
1 AGTGCAAACCCACACTTGAATACAATCCCA
74705 AGTGCAAACCCACACTTGAAT-CAA-CCCA
1 AGTGCAAACCCACACTTGAATACAATCCCA
*
74733 AGTGCATAACCCGCACTTG
1 AGTGCA-AACCCACACTTG
74752 TAAAAACACA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 10 0.23
29 14 0.33
30 19 0.44
ACGTcount: A:0.38, C:0.35, G:0.12, T:0.16
Consensus pattern (30 bp):
AGTGCAAACCCACACTTGAATACAATCCCA
Found at i:76915 original size:18 final size:18
Alignment explanation
Indices: 76892--76926 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
76882 CAATGCCTTT
*
76892 ATCTTTTTTCTTCTGTTC
1 ATCTTTCTTCTTCTGTTC
76910 ATCTTTCTTCTTCTGTT
1 ATCTTTCTTCTTCTGTT
76927 GCTCACCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.23, G:0.06, T:0.66
Consensus pattern (18 bp):
ATCTTTCTTCTTCTGTTC
Found at i:81242 original size:23 final size:23
Alignment explanation
Indices: 81136--81353 Score: 167
Period size: 22 Copynumber: 9.6 Consensus size: 23
81126 TAAAGCAAAA
* *
81136 CAACATCTTGAACCA-CAAAACAA
1 CAACATTTTGAA-CATCAAAACAG
** *
81159 CAACA-TGAGAAAATCAAAACAG
1 CAACATTTTGAACATCAAAACAG
* *
81181 CAACATTTTGGAAAAGCAAAACAG
1 CAACATTTT-GAACATCAAAACAG
* ** *
81205 CAATA-TGAGAACATCAAAACAA
1 CAACATTTTGAACATCAAAACAG
81227 CAACATTTTGAACATCAAAACAG
1 CAACATTTTGAACATCAAAACAG
*** *
81250 CAACA-CGAGAACATCAAAACAA
1 CAACATTTTGAACATCAAAACAG
81272 CAACATTTTGAACATCAAAACAG
1 CAACATTTTGAACATCAAAACAG
* * *
81295 CCACATTATCAACA-CAAAACAG
1 CAACATTTTGAACATCAAAACAG
* * * *
81317 CCACATTATCAACAACAAAACAG
1 CAACATTTTGAACATCAAAACAG
* *
81340 CACCATTTTCAACA
1 CAACATTTTGAACA
81354 ATAAAAAAAC
Statistics
Matches: 157, Mismatches: 32, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
21 1 0.01
22 70 0.45
23 69 0.44
24 17 0.11
ACGTcount: A:0.52, C:0.25, G:0.08, T:0.15
Consensus pattern (23 bp):
CAACATTTTGAACATCAAAACAG
Found at i:81261 original size:45 final size:45
Alignment explanation
Indices: 81134--81341 Score: 231
Period size: 45 Copynumber: 4.6 Consensus size: 45
81124 AATAAAGCAA
* * *
81134 AACAACATCTTGAACCA-CAAAACAACAACATGAGAAAATCAAAAC
1 AACAACATTTTGAA-CATCAAAACAGCAACATGAGAACATCAAAAC
* * * *
81179 AGCAACATTTTGGAAAAGCAAAACAGCAATATGAGAACATCAAAAC
1 AACAACATTTT-GAACATCAAAACAGCAACATGAGAACATCAAAAC
*
81225 AACAACATTTTGAACATCAAAACAGCAACACGAGAACATCAAAAC
1 AACAACATTTTGAACATCAAAACAGCAACATGAGAACATCAAAAC
* * *
81270 AACAACATTTTGAACATCAAAACAGCCACATTATCAACA-CAAAAC
1 AACAACATTTTGAACATCAAAACAGCAACATGA-GAACATCAAAAC
* * * * *
81315 AGCCACATTATCAACAACAAAACAGCA
1 AACAACATTTTGAACATCAAAACAGCA
81342 CCATTTTCAA
Statistics
Matches: 139, Mismatches: 21, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
45 97 0.70
46 42 0.30
ACGTcount: A:0.53, C:0.24, G:0.09, T:0.14
Consensus pattern (45 bp):
AACAACATTTTGAACATCAAAACAGCAACATGAGAACATCAAAAC
Found at i:81315 original size:22 final size:23
Alignment explanation
Indices: 81214--81353 Score: 124
Period size: 23 Copynumber: 6.2 Consensus size: 23
81204 GCAATATGAG
* * * *
81214 AACATCAAAACAACAACATTTTG
1 AACATCAAAACAGCCACATTATC
* ** *
81237 AACATCAAAACAGCAACACGA-G
1 AACATCAAAACAGCCACATTATC
* * * *
81259 AACATCAAAACAACAACATTTTG
1 AACATCAAAACAGCCACATTATC
81282 AACATCAAAACAGCCACATTATC
1 AACATCAAAACAGCCACATTATC
81305 AACA-CAAAACAGCCACATTATC
1 AACATCAAAACAGCCACATTATC
* *
81327 AACAACAAAACAG-CACCATTTTC
1 AACATCAAAACAGCCA-CATTATC
81350 AACA
1 AACA
81354 ATAAAAAAAC
Statistics
Matches: 101, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
22 42 0.42
23 59 0.58
ACGTcount: A:0.51, C:0.27, G:0.06, T:0.16
Consensus pattern (23 bp):
AACATCAAAACAGCCACATTATC
Found at i:81336 original size:68 final size:68
Alignment explanation
Indices: 81213--81353 Score: 158
Period size: 68 Copynumber: 2.1 Consensus size: 68
81203 AGCAATATGA
* * * *
81213 GAACATCAAAACAACAACATTTTGAACATCAAAACAGCAACACGAGAACATCAAAACAACAACAT
1 GAACATCAAAACAACAACATTATCAACATCAAAACAGCAACACGACAACAACAAAACAACAACAT
81278 TTT
66 TTT
* * * ** * *
81281 GAACATCAAAACAGCCACATTATCAACA-CAAAACAGCCACATTATCAACAACAAAACAGCACCA
1 GAACATCAAAACAACAACATTATCAACATCAAAACAGCAACACGA-CAACAACAAAACAACAACA
81345 TTTT
65 TTTT
*
81349 CAACA
1 GAACA
81354 ATAAAAAAAC
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
67 13 0.22
68 47 0.78
ACGTcount: A:0.51, C:0.27, G:0.06, T:0.16
Consensus pattern (68 bp):
GAACATCAAAACAACAACATTATCAACATCAAAACAGCAACACGACAACAACAAAACAACAACAT
TTT
Found at i:84119 original size:15 final size:15
Alignment explanation
Indices: 84099--84128 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
84089 ATGTAGCACT
84099 CTTCAAGAGAAACAA
1 CTTCAAGAGAAACAA
84114 CTTCAAGAGAAACAA
1 CTTCAAGAGAAACAA
84129 TATCGCACTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.20, G:0.13, T:0.13
Consensus pattern (15 bp):
CTTCAAGAGAAACAA
Found at i:84972 original size:2 final size:2
Alignment explanation
Indices: 84965--84992 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
84955 TTCAGAATCC
84965 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
84993 GCGTGTCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:85148 original size:42 final size:43
Alignment explanation
Indices: 85069--85150 Score: 105
Period size: 42 Copynumber: 1.9 Consensus size: 43
85059 CTTAAACATA
* *
85069 TTAATCGTGTCGTTGACACGATTATGACCCGAAACACGATAATC
1 TTAATCGTGTCG-CGACACGATTATGACACGAAACACGATAATC
*
85113 TTAATCGTGTC-CGACACGATT-TCGACACGAGACACGAT
1 TTAATCGTGTCGCGACACGATTAT-GACACGAAACACGAT
85151 TAGCCAAACA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 1 0.03
42 22 0.65
44 11 0.32
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (43 bp):
TTAATCGTGTCGCGACACGATTATGACACGAAACACGATAATC
Found at i:87321 original size:21 final size:22
Alignment explanation
Indices: 87274--87321 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
87264 GTTCCAGCCA
**
87274 TCATTG-CCTTCTTCTTTTTCT
1 TCATTGTCCTTCTTCTGATTCT
87295 TC-TTGTCCTTCTTCTGATTC-
1 TCATTGTCCTTCTTCTGATTCT
87315 TCATTGT
1 TCATTGT
87322 TGTTCAATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.06, C:0.27, G:0.08, T:0.58
Consensus pattern (22 bp):
TCATTGTCCTTCTTCTGATTCT
Found at i:92247 original size:17 final size:18
Alignment explanation
Indices: 92225--92260 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
92215 TAACACAAAT
92225 CACATAC-TTCACATACC
1 CACATACTTTCACATACC
92242 CACATACTTTTCACATACC
1 CACATAC-TTTCACATACC
92261 TTCATAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
19 10 0.59
ACGTcount: A:0.33, C:0.39, G:0.00, T:0.28
Consensus pattern (18 bp):
CACATACTTTCACATACC
Found at i:93066 original size:15 final size:15
Alignment explanation
Indices: 93046--93076 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
93036 TTGTTTTTAG
*
93046 TTTAATTGCTTTCTT
1 TTTAATTGATTTCTT
93061 TTTAATTGATTTCTT
1 TTTAATTGATTTCTT
93076 T
1 T
93077 AAATCCCCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.10, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTAATTGATTTCTT
Found at i:94485 original size:17 final size:17
Alignment explanation
Indices: 94465--94505 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
94455 AGGCTACAAA
94465 AGGAATCATGCTGCAAC
1 AGGAATCATGCTGCAAC
*
94482 AGGAATCATGCTGCAGC
1 AGGAATCATGCTGCAAC
94499 AGGAATC
1 AGGAATC
94506 GCGCGGCTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.34, C:0.22, G:0.27, T:0.17
Consensus pattern (17 bp):
AGGAATCATGCTGCAAC
Found at i:94696 original size:14 final size:12
Alignment explanation
Indices: 94664--94693 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
94654 GTCTGACAAA
94664 ACAACAAAAAAC
1 ACAACAAAAAAC
94676 ACAACAAAAAAC
1 ACAACAAAAAAC
94688 ACAACA
1 ACAACA
94694 CAAGGAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.73, C:0.27, G:0.00, T:0.00
Consensus pattern (12 bp):
ACAACAAAAAAC
Done.