Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019124.1 Corchorus olitorius cultivar O-4 contig19157, 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: 73933
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:770 original size:2 final size:2
Alignment explanation
Indices: 763--787 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
753 AAAGCATCAT
763 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
788 TATATGCAAT
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:8357 original size:69 final size:71
Alignment explanation
Indices: 8250--8389 Score: 230
Period size: 69 Copynumber: 2.0 Consensus size: 71
8240 TTTTTTACCT
* * *
8250 TAGATTTGCATGTTTTCAAATAATTAAAAAATATATTTTTGTATCC-AAACACTTAAATATCCCT
1 TAGATTTACATGTTTGCAAACAATTAAAAAATATATTTTTGTATCCAAAACACTTAAATATCCCT
8314 TATATC
66 TATATC
8320 TAGATTTACATG-TTGCAAACAATTAAAAAATATATTTTTGTATCCGAAAACACTTAAATATCCC
1 TAGATTTACATGTTTGCAAACAATTAAAAAATATATTTTTGTATCC-AAAACACTTAAATATCCC
8384 TTATAT
65 TTATAT
8390 TTGTATCAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
69 31 0.48
70 11 0.17
71 23 0.35
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.39
Consensus pattern (71 bp):
TAGATTTACATGTTTGCAAACAATTAAAAAATATATTTTTGTATCCAAAACACTTAAATATCCCT
TATATC
Found at i:17507 original size:2 final size:2
Alignment explanation
Indices: 17500--17543 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
17490 CATGATCCTA
17500 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
17542 AT
1 AT
17544 TAATGTTATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19759 original size:19 final size:19
Alignment explanation
Indices: 19739--19775 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
19729 AATTAATTAT
19739 TTTA-ATATTAAATTTTTA
1 TTTATATATTAAATTTTTA
*
19757 TTTATATATTATATTTTTA
1 TTTATATATTAAATTTTTA
19776 CTTAAAAATT
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 (19 bp):
TTTATATATTAAATTTTTA
Found at i:19861 original size:15 final size:15
Alignment explanation
Indices: 19841--19870 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
19831 ATTTTTAACC
19841 TTATTTTACAATTAT
1 TTATTTTACAATTAT
19856 TTATTTTACAATTAT
1 TTATTTTACAATTAT
19871 ACAAGTTAAT
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:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATTTTACAATTAT
Found at i:26296 original size:23 final size:23
Alignment explanation
Indices: 26270--26315 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
26260 TATACAACTC
26270 AAAAAATTGATCCGAAATTTGGT
1 AAAAAATTGATCCGAAATTTGGT
26293 AAAAAATTGATCCGAAATTTGGT
1 AAAAAATTGATCCGAAATTTGGT
26316 TCCCTATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.30
Consensus pattern (23 bp):
AAAAAATTGATCCGAAATTTGGT
Found at i:26456 original size:37 final size:37
Alignment explanation
Indices: 26406--26478 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
26396 ACATCGGACA
* *
26406 ACTAGTTATGACACATCATGGGAGTAAATTCAGGTCG
1 ACTAGTTATGACACATAATGAGAGTAAATTCAGGTCG
26443 ACTAGTTATGACACATAATGAGAGTAAATTCAGGTC
1 ACTAGTTATGACACATAATGAGAGTAAATTCAGGTC
26479 AATTTTTTCG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (37 bp):
ACTAGTTATGACACATAATGAGAGTAAATTCAGGTCG
Found at i:26580 original size:2 final size:2
Alignment explanation
Indices: 26573--26601 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
26563 TTATTACCAC
26573 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
26602 TTACAGCATA
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:29138 original size:2 final size:2
Alignment explanation
Indices: 29131--29168 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
29121 GTTAATTAAC
29131 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29169 CCCAATTTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30949 original size:20 final size:20
Alignment explanation
Indices: 30924--30963 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
30914 TTTGTCAGTT
* *
30924 TTCATTCACAGAAAAGAAAC
1 TTCATTCAAAAAAAAGAAAC
30944 TTCATTCAAAAAAAAGAAAC
1 TTCATTCAAAAAAAAGAAAC
30964 GAAGATTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.17, G:0.07, T:0.20
Consensus pattern (20 bp):
TTCATTCAAAAAAAAGAAAC
Found at i:37210 original size:31 final size:31
Alignment explanation
Indices: 37150--37211 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
37140 TTATTGAATG
* **
37150 AGATAACTTGTCATTTCTTTTTTTGAAGAAA
1 AGATAACTTGTCATTTATTTTGGTGAAGAAA
37181 AGATAACTTGTCATTTATTATTGGT-AAGAAA
1 AGATAACTTGTCATTTATT-TTGGTGAAGAAA
37212 TTAGTAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 24 0.89
32 3 0.11
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (31 bp):
AGATAACTTGTCATTTATTTTGGTGAAGAAA
Found at i:55791 original size:22 final size:23
Alignment explanation
Indices: 55738--55805 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 23
55728 ATCAATATTC
55738 ATAGTGTGGTTACTAGAATTTCT
1 ATAGTGTGGTTACTAGAATTTCT
* *
55761 A-A--GTGGTTATTATAATTT-T
1 ATAGTGTGGTTACTAGAATTTCT
* *
55780 ATAGTGTGGTTACAAAAATTTC-
1 ATAGTGTGGTTACTAGAATTTCT
55802 ATAG
1 ATAG
55806 GTTAGGATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
19 2 0.06
20 15 0.42
22 18 0.50
23 1 0.03
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (23 bp):
ATAGTGTGGTTACTAGAATTTCT
Found at i:55928 original size:22 final size:22
Alignment explanation
Indices: 55903--56029 Score: 125
Period size: 22 Copynumber: 5.8 Consensus size: 22
55893 TCACAGTGAT
*
55903 GTTATCAAAATTTTATATGGAG
1 GTTATCAAAATTTCATATGGAG
*
55925 GTTATCAAAATTTCATAAGGAG
1 GTTATCAAAATTTCATATGGAG
* *
55947 GCTATCAAAATTCCAT-TGGAAG
1 GTTATCAAAATTTCATATGG-AG
* *
55969 GTTATCAAAATTTCACAGGGAG
1 GTTATCAAAATTTCATATGGAG
* **
55991 GTTA-CTAAAATTTAATACT-CTG
1 GTTATC-AAAATTTCATA-TGGAG
56013 GTTATCAAAATTTCATA
1 GTTATCAAAATTTCATA
56030 GTGTGCTAAT
Statistics
Matches: 85, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
21 3 0.04
22 79 0.93
23 3 0.04
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.35
Consensus pattern (22 bp):
GTTATCAAAATTTCATATGGAG
Found at i:55938 original size:44 final size:44
Alignment explanation
Indices: 55794--56027 Score: 147
Period size: 44 Copynumber: 5.2 Consensus size: 44
55784 TGTGGTTACA
* * * * *
55794 AAAATTTCATAGGTTAGGATATCAAAATTTTATAATGTA-GTTATC
1 AAAATTTCACAGG-GAGGTTATCAAAATTTCAT-ATGGAGGTTATC
* * * * *
55839 ACAATTTCA-TGGGATGTTATCAAAATTTCATA-GGCAAGTTATTTAA
1 AAAATTTCACAGGGAGGTTATCAAAATTTCATATGG-AGGTTA--T-C
* * *
55885 ATTAAATTTCACAGTGATGTTATCAAAATTTTATATGGAGGTTATC
1 A--AAATTTCACAGGGAGGTTATCAAAATTTCATATGGAGGTTATC
* * * *
55931 AAAATTTCATAAGGAGGCTATCAAAATTCCAT-TGGAAGGTTATC
1 AAAATTTCACAGGGAGGTTATCAAAATTTCATATGG-AGGTTATC
* **
55975 AAAATTTCACAGGGAGGTTA-CTAAAATTTAATACT-CTGGTTATC
1 AAAATTTCACAGGGAGGTTATC-AAAATTTCATA-TGGAGGTTATC
56019 AAAATTTCA
1 AAAATTTCA
56028 TAGTGTGCTA
Statistics
Matches: 148, Mismatches: 28, Indels: 27
0.73 0.14 0.13
Matches are distributed among these distances:
41 1 0.01
42 2 0.01
43 23 0.16
44 75 0.51
45 9 0.06
46 3 0.02
47 1 0.01
48 7 0.05
49 25 0.17
50 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (44 bp):
AAAATTTCACAGGGAGGTTATCAAAATTTCATATGGAGGTTATC
Found at i:56121 original size:22 final size:21
Alignment explanation
Indices: 56068--56124 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 21
56058 TAGAGTGAGC
**
56068 TTATCAAAATTTCAAGTGTCG
1 TTATCAAAATTTCAAGTGTAA
*
56089 TTACCAAAATTTCATAGTGTAA
1 TTATCAAAATTTCA-AGTGTAA
*
56111 TTATCACAATTTCA
1 TTATCAAAATTTCA
56125 CAGAGGTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 13 0.43
22 17 0.57
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.39
Consensus pattern (21 bp):
TTATCAAAATTTCAAGTGTAA
Found at i:56162 original size:22 final size:22
Alignment explanation
Indices: 56111--56189 Score: 72
Period size: 22 Copynumber: 3.7 Consensus size: 22
56101 CATAGTGTAA
* *
56111 TTATCACAATTTCACA-G-AGG
1 TTATCAAAATTTCAGAGGAAGG
* *
56131 TTAACAAAATTTCATAGGAAGG
1 TTATCAAAATTTCAGAGGAAGG
* * * *
56153 TTATCGAAATTTTAGAGGGAGA
1 TTATCAAAATTTCAGAGGAAGG
56175 TTATCAAAATTTCAG
1 TTATCAAAATTTCAG
56190 TGTGGTTATA
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 13 0.28
21 1 0.02
22 32 0.70
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (22 bp):
TTATCAAAATTTCAGAGGAAGG
Found at i:56487 original size:22 final size:21
Alignment explanation
Indices: 56401--56650 Score: 186
Period size: 22 Copynumber: 11.6 Consensus size: 21
56391 GTGTAGTTAA
* *
56401 TTATCAAGATTTCATTGG-GAG
1 TTATCAAAATTTCATAGGAG-G
* * *
56422 TGATCAAAATTTAATA-GAGTTC
1 TTATCAAAATTTCATAGGAG--G
*
56444 TTATCAAAATTTCTTAGGAGG
1 TTATCAAAATTTCATAGGAGG
*
56465 TTAACAAAATTTCATAAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
* *
56487 TTATAAAAAATTCATAGGAAGG
1 TTATCAAAATTTCATAGG-AGG
* *
56509 TTATCAAAATTTCATGGGGTGG
1 TTATCAAAATTTCAT-AGGAGG
*
56531 TTTTCAAAATTTCAT--GAGG
1 TTATCAAAATTTCATAGGAGG
* *
56550 TTATTAAAATTTCAAATGGAGG
1 TTATCAAAATTTCATA-GGAGG
*
56572 TTATCAAAATTTTATAGGGAGG
1 TTATCAAAATTTCATA-GGAGG
* *
56594 TTTATAAAAATTTTATAGTGAGG
1 -TTATCAAAATTTCATAG-GAGG
* *
56617 TTATCACAATTTCAT-GGTATGT
1 TTATCAAAATTTCATAGG-A-GG
56639 TTATCAAAATTT
1 TTATCAAAATTT
56651 TGTAATGTGA
Statistics
Matches: 182, Mismatches: 34, Indels: 25
0.76 0.14 0.10
Matches are distributed among these distances:
19 15 0.08
20 2 0.01
21 31 0.17
22 110 0.60
23 24 0.13
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.38
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:56571 original size:85 final size:87
Alignment explanation
Indices: 56447--56606 Score: 209
Period size: 85 Copynumber: 1.9 Consensus size: 87
56437 AGAGTTCTTA
56447 TCAAAATTTCTTAGGAGGTTAACAAAATTTCATAAGGAGGTTATAAAAAATTCATAGGAAGG-TT
1 TCAAAATTTC-TAGGAGGTTAACAAAATTTCATAAGGAGGTTATAAAAAATTCATAGGAAGGTTT
*
56511 ATCAAAATTTCATGGGGTGGTTT
65 ATAAAAATTTCATGGGGTGGTTT
* ** * * * *
56534 TCAAAATTTC-ATGAGGTTATTAAAATTTCA-AATGGAGGTTATCAAAATTTTATAGGGAGGTTT
1 TCAAAATTTCTAGGAGGTTAACAAAATTTCATAA-GGAGGTTATAAAAAATTCATAGGAAGGTTT
56597 ATAAAAATTT
65 ATAAAAATTT
56607 TATAGTGAGG
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
84 2 0.03
85 40 0.63
86 11 0.17
87 10 0.16
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.36
Consensus pattern (87 bp):
TCAAAATTTCTAGGAGGTTAACAAAATTTCATAAGGAGGTTATAAAAAATTCATAGGAAGGTTTA
TAAAAATTTCATGGGGTGGTTT
Found at i:56573 original size:63 final size:65
Alignment explanation
Indices: 56444--56620 Score: 184
Period size: 63 Copynumber: 2.7 Consensus size: 65
56434 AATAGAGTTC
* * *
56444 TTATCAAAATTTCTTA-GGAGG-TTAACAAAATTTCATAAGGAGGTTATAAAAAATTCATAGGAA
1 TTATCAAAATTTCATAGGGAGGTTTATCAAAATTTCAT-A-GAGGTTATAAAAAATTCAAAGGAA
56507 GG
64 GG
* * * *
56509 TTATCAAAATTTCATGGGGTGGTTT-TCAAAATTTCAT-GAGGTTATTAAAATTTCAAATGG-AG
1 TTATCAAAATTTCATAGGGAGGTTTATCAAAATTTCATAGAGGTTATAAAAAATTCAAA-GGAAG
56571 G
65 G
* * *
56572 TTATCAAAATTTTATAGGGAGGTTTATAAAAATTTTATAGTGAGGTTAT
1 TTATCAAAATTTCATAGGGAGGTTTATCAAAATTTCATA--GAGGTTAT
56621 CACAATTTCA
Statistics
Matches: 93, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
63 42 0.45
64 12 0.13
65 14 0.15
66 15 0.16
67 10 0.11
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.37
Consensus pattern (65 bp):
TTATCAAAATTTCATAGGGAGGTTTATCAAAATTTCATAGAGGTTATAAAAAATTCAAAGGAAGG
Found at i:56771 original size:22 final size:22
Alignment explanation
Indices: 56400--56765 Score: 93
Period size: 22 Copynumber: 16.7 Consensus size: 22
56390 GGTGTAGTTA
* * *
56400 ATTATCAAGATTTCATTGGGAG
1 ATTATCAAAATTTCATAGGGTG
* * * *
56422 -TGATCAAAATTTAATAGAGTT
1 ATTATCAAAATTTCATAGGGTG
* *
56443 CTTATCAAAATTTCTTAGGAG-G
1 ATTATCAAAATTTCATAGG-GTG
* * *
56465 -TTAACAAAATTTCATAAGGAG
1 ATTATCAAAATTTCATAGGGTG
* * * **
56486 GTTATAAAAAATTCATAGGAAG
1 ATTATCAAAATTTCATAGGGTG
* *
56508 GTTATCAAAATTTCATGGGGTG
1 ATTATCAAAATTTCATAGGGTG
* * *
56530 GTTTTCAAAATTTCAT-GAG-G
1 ATTATCAAAATTTCATAGGGTG
* * * *
56550 -TTATTAAAATTTCAAATGGAG
1 ATTATCAAAATTTCATAGGGTG
* * *
56571 GTTATCAAAATTTTATAGGGAGG
1 ATTATCAAAATTTCATAGGG-TG
* * * * *
56594 TTTATAAAAATTTTATAGTGAG
1 ATTATCAAAATTTCATAGGGTG
* * *
56616 GTTATCACAATTTCAT-GGTATG
1 ATTATCAAAATTTCATAGG-GTG
* ** **
56638 TTTATCAAAATTTTGTAATGTG
1 ATTATCAAAATTTCATAGGGTG
* * * * *
56660 ATTACCAATATTTTATCGGAATG
1 ATTATCAAAATTTCATAGG-GTG
* * **
56683 -TTCTCAAATTTTCATAATGTG
1 ATTATCAAAATTTCATAGGGTG
* * * * *
56704 CACTTACCCACATTTCATTGGG-A
1 -A-TTATCAAAATTTCATAGGGTG
*
56727 AGTTATCAAAATTTTATAGGGTG
1 A-TTATCAAAATTTCATAGGGTG
56750 ATTATCAAAATTTCAT
1 ATTATCAAAATTTCAT
56766 TAGGTGGTTA
Statistics
Matches: 240, Mismatches: 89, Indels: 30
0.67 0.25 0.08
Matches are distributed among these distances:
19 12 0.05
20 3 0.01
21 36 0.15
22 156 0.65
23 22 0.09
24 11 0.05
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.38
Consensus pattern (22 bp):
ATTATCAAAATTTCATAGGGTG
Found at i:56776 original size:22 final size:22
Alignment explanation
Indices: 56728--56781 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
56718 TCATTGGGAA
*
56728 GTTATCAAAATTTTATAGGGTG
1 GTTATCAAAATTTCATAGGGTG
*
56750 ATTATCAAAATTTCATTA-GGTG
1 GTTATCAAAATTTCA-TAGGGTG
*
56772 GTTATTAAAA
1 GTTATCAAAA
56782 AATTTATAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 25 0.93
23 2 0.07
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.41
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGGGTG
Found at i:56776 original size:44 final size:43
Alignment explanation
Indices: 56400--56792 Score: 175
Period size: 44 Copynumber: 9.0 Consensus size: 43
56390 GGTGTAGTTA
* * * * * *
56400 ATTATCAAGATTTCATTGG-GAGTGATCAAAATTTAATAGAGTT
1 ATTATCAAAATTTCATAGGAG-GTTATCAAAATTTTATAGGGTG
* * * * * *
56443 CTTATCAAAATTTCTTAGGAGGTTAACAAAATTTCATAAGGAG
1 ATTATCAAAATTTCATAGGAGGTTATCAAAATTTTATAGGGTG
* * * * *
56486 GTTATAAAAAATTCATAGGAAGGTTATCAAAATTTCATGGGGTG
1 ATTATCAAAATTTCATAGG-AGGTTATCAAAATTTTATAGGGTG
* * * * * * *
56530 GTTTTCAAAATTTCAT--GAGGTTATTAAAATTTCAAATGGAG
1 ATTATCAAAATTTCATAGGAGGTTATCAAAATTTTATAGGGTG
* * * * *
56571 GTTATCAAAATTTTATAGGGAGGTTTATAAAAATTTTATAGTGAG
1 ATTATCAAAATTTCATA-GGAGG-TTATCAAAATTTTATAGGGTG
* * * * **
56616 GTTATCACAATTTCAT-GGTATGTTTATCAAAATTTTGTAATGTG
1 ATTATCAAAATTTCATAGG-A-GGTTATCAAAATTTTATAGGGTG
* * * * * * **
56660 ATTACCAATATTTTATCGGAATGTTCTC-AAATTTTCATAATGTG
1 ATTATCAAAATTTCATAGG-AGGTTATCAAAATTTT-ATAGGGTG
* * * * *
56704 CACTTACCCACATTTCATTGGGAAGTTATCAAAATTTTATAGGGTG
1 -A-TTATCAAAATTTCA-TAGGAGGTTATCAAAATTTTATAGGGTG
* * *
56750 ATTATCAAAATTTCATTAGGTGGTTATTAAAAAATTTATAGGG
1 ATTATCAAAATTTCA-TAGGAGGTTA-TCAAAATTTTATAGGG
56793 AGTAGTGTAA
Statistics
Matches: 268, Mismatches: 67, Indels: 28
0.74 0.18 0.08
Matches are distributed among these distances:
41 33 0.12
42 1 0.00
43 54 0.20
44 97 0.36
45 50 0.19
46 23 0.09
47 10 0.04
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (43 bp):
ATTATCAAAATTTCATAGGAGGTTATCAAAATTTTATAGGGTG
Found at i:56814 original size:25 final size:22
Alignment explanation
Indices: 56786--56830 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 22
56776 TTAAAAAATT
56786 TATAGGGAGTAGTGTAACAAAATCC
1 TATAGGGA--AGT-TAACAAAATCC
*
56811 TATATGGAAGTTAACAAAAT
1 TATAGGGAAGTTAACAAAAT
56831 TTCGTATGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 9 0.47
23 3 0.16
25 7 0.37
ACGTcount: A:0.44, C:0.09, G:0.20, T:0.27
Consensus pattern (22 bp):
TATAGGGAAGTTAACAAAATCC
Found at i:56932 original size:20 final size:20
Alignment explanation
Indices: 56882--56940 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 20
56872 AACTTCAAAG
56882 TATA-ATTATCAAAATTTTA
1 TATAGATTATCAAAATTTTA
56901 TATAGAGGTTATCAAAATTTTA
1 TATAGA--TTATCAAAATTTTA
*
56923 TAGT-GATTATTAAAATTT
1 TA-TAGATTATCAAAATTT
56941 CATAAAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
19 4 0.11
20 12 0.34
22 18 0.51
23 1 0.03
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.46
Consensus pattern (20 bp):
TATAGATTATCAAAATTTTA
Found at i:63644 original size:13 final size:13
Alignment explanation
Indices: 63618--63653 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
63608 AAAAGCTTGG
63618 TTTTGAAGAAGTGC
1 TTTTGAA-AAGTGC
63632 TTTTGAAAAGTGC
1 TTTTGAAAAGTGC
*
63645 TTTTTAAAA
1 TTTTGAAAA
63654 TTGGGGTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (13 bp):
TTTTGAAAAGTGC
Found at i:66004 original size:5 final size:5
Alignment explanation
Indices: 65994--66019 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
65984 AAAAGTAAAC
65994 TCCTT TCCTT TCCTT TCCTT TCCTT T
1 TCCTT TCCTT TCCTT TCCTT TCCTT T
66020 GCTTCTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (5 bp):
TCCTT
Done.