Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019153.1 Corchorus olitorius cultivar O-4 contig19186, 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: 60683
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:56 original size:16 final size:15
Alignment explanation
Indices: 37--70 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
27 AAAAAGAGGG
*
37 AAAAAGAAAAGGAAA
1 AAAAAGAAAAAGAAA
*
52 NAAAAGAAAAAGAAA
1 AAAAAGAAAAAGAAA
67 AAAA
1 AAAA
71 TTAAAGGTCG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAGAAA
Found at i:6240 original size:31 final size:31
Alignment explanation
Indices: 6199--6271 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
6189 GTTGACCAAT
*
6199 TTGAGACTAAATCTTTCAAATTTTGCTCAAA
1 TTGAGACTAAATCTTTCAAAATTTGCTCAAA
* * *
6230 TTGAGCCTAAATTTTTCAAAATTTGCTCAAT
1 TTGAGACTAAATCTTTCAAAATTTGCTCAAA
*
6261 TTGAGTCTAAA
1 TTGAGACTAAA
6272 AAATAATTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (31 bp):
TTGAGACTAAATCTTTCAAAATTTGCTCAAA
Found at i:8999 original size:21 final size:22
Alignment explanation
Indices: 8975--9095 Score: 113
Period size: 22 Copynumber: 5.5 Consensus size: 22
8965 AATTTTAAAA
* *
8975 GTTATCAAAA-TTCATTGTGTG
1 GTTATCAAAATTTTATAGTGTG
8996 GTTA-CTAAAATTTTATAGTGTG
1 GTTATC-AAAATTTTATAGTGTG
*
9018 GTTCTCAAAATTTTATAGTGTG
1 GTTATCAAAATTTTATAGTGTG
* *
9040 GTTACCAAAATTTCATAG-GTAG
1 GTTATCAAAATTTTATAGTGT-G
* * * *
9062 GATGTTAAAATTTTATAGTGTA
1 GTTATCAAAATTTTATAGTGTG
*
9084 GTTATCACAATT
1 GTTATCAAAATT
9096 CCATGGGATG
Statistics
Matches: 79, Mismatches: 16, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
20 1 0.01
21 10 0.13
22 65 0.82
23 3 0.04
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.42
Consensus pattern (22 bp):
GTTATCAAAATTTTATAGTGTG
Found at i:9136 original size:22 final size:22
Alignment explanation
Indices: 9108--9316 Score: 122
Period size: 22 Copynumber: 9.3 Consensus size: 22
9098 ATGGGATGTC
9108 ATCAAAATTTCATAAGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* *
9130 ATTAAAATAAAATTTCATAAGGATGTT
1 A-T----CAAAATTTCATAAGGAGGTT
9157 ATCAAAATTTCATAAGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* *
9179 ATCGAAA-TTCAT-GGGAAGGTT
1 ATCAAAATTTCATAAGG-AGGTT
* * * *
9200 GTCAAAATTTCACAGGGGGGTT
1 ATCAAAATTTCATAAGGAGGTT
**** *
9222 A-CTAAAATTTCATACTCTGATT
1 ATC-AAAATTTCATAAGGAGGTT
* * *
9244 ATCAAAATTTCATAGGGCGATT
1 ATCAAAATTTCATAAGGAGGTT
* *
9266 ATCGAAATCTT-ATATGGAGGTT
1 ATCAAAAT-TTCATAAGGAGGTT
* *
9288 ATTAAAATTTCAT-AGGAAGATT
1 ATCAAAATTTCATAAGG-AGGTT
9310 ATCAAAA
1 ATCAAAA
9317 CTCCATAGTG
Statistics
Matches: 144, Mismatches: 30, Indels: 26
0.72 0.15 0.13
Matches are distributed among these distances:
20 2 0.01
21 20 0.14
22 95 0.66
23 7 0.05
26 1 0.01
27 19 0.13
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (22 bp):
ATCAAAATTTCATAAGGAGGTT
Found at i:9415 original size:22 final size:22
Alignment explanation
Indices: 9364--9421 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
9354 GAGTGAGCTA
**
9364 ATCAAAATTTCA-AGTGTTGTT
1 ATCAAAATTTCATAGTGTAATT
*
9385 ACCAAAATTTCATAGTGTAATT
1 ATCAAAATTTCATAGTGTAATT
*
9407 ATCACAATTTCATAG
1 ATCAAAATTTCATAG
9422 AGGTTAACAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
21 11 0.35
22 20 0.65
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (22 bp):
ATCAAAATTTCATAGTGTAATT
Found at i:9600 original size:21 final size:22
Alignment explanation
Indices: 9585--9661 Score: 77
Period size: 21 Copynumber: 3.6 Consensus size: 22
9575 ATGAGTTCAT
9585 CAAAATTT-ATAGTGAGATTAA
1 CAAAATTTCATAGTGAGATTAA
* * * * **
9606 CAAAATTTGATAGGGTGGTTCT
1 CAAAATTTCATAGTGAGATTAA
*
9628 CAAAATTTTATAG-GAGATTAA
1 CAAAATTTCATAGTGAGATTAA
9649 CAAAATTTCATAG
1 CAAAATTTCATAG
9662 GTAAGTTATC
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 24 0.55
22 20 0.45
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAGTGAGATTAA
Found at i:9632 original size:43 final size:44
Alignment explanation
Indices: 9579--9900 Score: 160
Period size: 43 Copynumber: 7.5 Consensus size: 44
9569 TGACTAATGA
*
9579 GTTCATCAAAA-TTTATAGTGAGATTAACAAAATTTGATAGGGTG
1 GTTCATCAAAATTTTATAG-GAGATTAACAAAATTTCATAGGGTG
*
9623 GTTC-TCAAAATTTTATAGGAGATTAACAAAATTTCATA-GGTAA
1 GTTCATCAAAATTTTATAGGAGATTAACAAAATTTCATAGGGT-G
** * *
9666 GTT-ATCGTAATTTTAT-GGTGTAATTAATTATCAAAATTTCATTGGG-G
1 GTTCATCAAAATTTTATAGGAG--ATT-A--A-CAAAATTTCATAGGGTG
* *** * * *
9713 GTT-ATCAAAATTTAATAGTGTTCTTATCAAAATTTCGTA-GGAG
1 GTTCATCAAAATTTTATAG-GAGATTAACAAAATTTCATAGGGTG
* * *
9756 GTT-AACAAAA-TTT-TAGGAGGTTATAAAAAATTT-ATAGGGAT-
1 GTTCATCAAAATTTTATAGGAGATTA-ACAAAATTTCATAGGG-TG
* * * *
9797 GTTC-TCAAAATTTCATAAGATGGTTATCAAAATTTCAT-GAGGTG
1 GTTCATCAAAATTTTATAGGA-GATTAACAAAATTTCATAG-GGTG
* * * * * *
9841 GTT-TTCAAAATTTCAT--GAGGTTATCAAAATTTCAAAGGGAG
1 GTTCATCAAAATTTTATAGGAGATTAACAAAATTTCATAGGGTG
9882 GTT-ATCAAAATTTTATAGG
1 GTTCATCAAAATTTTATAGG
9901 GAGGTTTATA
Statistics
Matches: 218, Mismatches: 33, Indels: 55
0.71 0.11 0.18
Matches are distributed among these distances:
40 6 0.03
41 53 0.24
42 15 0.07
43 72 0.33
44 38 0.17
45 1 0.00
46 1 0.00
47 16 0.07
48 12 0.06
49 4 0.02
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (44 bp):
GTTCATCAAAATTTTATAGGAGATTAACAAAATTTCATAGGGTG
Found at i:9826 original size:22 final size:22
Alignment explanation
Indices: 9693--10090 Score: 133
Period size: 22 Copynumber: 18.5 Consensus size: 22
9683 GTGTAATTAA
* **
9693 TTATCAAAATTTCAT-TGGGGG
1 TTATCAAAATTTCATAAGATGG
* *
9714 TTATCAAAATTTAAT-AG-TGTTC
1 TTATCAAAATTTCATAAGATG--G
* *
9736 TTATCAAAATTTCGTAGGA-GG
1 TTATCAAAATTTCATAAGATGG
* *
9757 TTAACAAAATTT--TAGGA-GG
1 TTATCAAAATTTCATAAGATGG
* *
9776 TTATAAAAAATTT-ATAGGGAT-G
1 TTAT-CAAAATTTCATA-AGATGG
*
9798 TTCTCAAAATTTCATAAGATGG
1 TTATCAAAATTTCATAAGATGG
* *
9820 TTATCAAAATTTCATGAGGTGG
1 TTATCAAAATTTCATAAGATGG
*
9842 TTTTCAAAATTTCAT--GA-GG
1 TTATCAAAATTTCATAAGATGG
9861 TTATCAAAATTTCA-AAGGGA-GG
1 TTATCAAAATTTCATAA--GATGG
* *
9883 TTATCAAAATTTTATAGGGA-GG
1 TTATCAAAATTTCATA-AGATGG
*
9905 TTTATAAAAATTTCATAATGA-GG
1 -TTATCAAAATTTCATAA-GATGG
* * * *
9928 -CATCACAATTTTAT-GGTATGG
1 TTATCAAAATTTCATAAG-ATGG
* *
9949 CTATCAAAATTTCATAATG-TGA
1 TTATCAAAATTTCATAA-GATGG
* * * ** *
9971 TTACCAATATTTTATCGGAAGG
1 TTATCAAAATTTCATAAGATGG
*
9993 TTATCAAAATATCATAATG-TGCG
1 TTATCAAAATTTCATAA-GATG-G
* * * *
10016 CT-TC-ACATTTCAT-TGAGTGA
1 TTATCAAAATTTCATAAGA-TGG
* *
10036 TTATCAAAATTTCAT-GGGTGG
1 TTATCAAAATTTCATAAGATGG
* * *
10057 TCATCAAAATTTCATTAGGTGG
1 TTATCAAAATTTCATAAGATGG
*
10079 TTATTAAAATTT
1 TTATCAAAATTT
10091 GTATGATCCG
Statistics
Matches: 282, Mismatches: 64, Indels: 61
0.69 0.16 0.15
Matches are distributed among these distances:
19 27 0.10
20 11 0.04
21 78 0.28
22 141 0.50
23 24 0.09
24 1 0.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAAGATGG
Found at i:9868 original size:63 final size:63
Alignment explanation
Indices: 9693--9920 Score: 172
Period size: 63 Copynumber: 3.6 Consensus size: 63
9683 GTGTAATTAA
* * * **
9693 TTATCAAAATTTCATTGGG-GG-TTATCAAAATTTAAT-AGTGTTCTTATCAAAATTTCGTAGGA
1 TTATCAAAATTTCATAGGGAGGTTTATAAAAATTTCATGAG-G---TTATCAAAATTTCAAAGGA
9755 GG
62 GG
* * *
9757 TTAACAAAATTT--TA-GGAGG-TTATAAAAAATTT-ATAGGGATGTTCTCAAAATTTCATAA-G
1 TTATCAAAATTTCATAGGGAGGTTTAT-AAAAATTTCAT---GAGGTTATCAAAATTTCA-AAGG
9816 ATGG
61 A-GG
* *
9820 TTATCAAAATTTCAT-GAGGTGGTTT-TCAAAATTTCATGAGGTTATCAAAATTTCAAAGGGAGG
1 TTATCAAAATTTCATAG-GGAGGTTTATAAAAATTTCATGAGGTTATCAAAATTTCAAA-GGAGG
*
9883 TTATCAAAATTTTATAGGGAGGTTTATAAAAATTTCAT
1 TTATCAAAATTTCATAGGGAGGTTTATAAAAATTTCAT
9921 AATGAGGCAT
Statistics
Matches: 131, Mismatches: 15, Indels: 36
0.72 0.08 0.20
Matches are distributed among these distances:
61 2 0.02
62 25 0.19
63 60 0.46
64 25 0.19
65 9 0.07
66 8 0.06
67 2 0.02
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (63 bp):
TTATCAAAATTTCATAGGGAGGTTTATAAAAATTTCATGAGGTTATCAAAATTTCAAAGGAGG
Found at i:9893 original size:85 final size:84
Alignment explanation
Indices: 9693--9921 Score: 225
Period size: 85 Copynumber: 2.7 Consensus size: 84
9683 GTGTAATTAA
* * *
9693 TTATCAAAATTTCATTGGG-GGTTATCAAAATTTAAT-AG-TGTTCTTATCAAAATTTCGTAGGA
1 TTATCAAAATTTCATAGGGAGGTTATCAAAATTTAATAAGATG--GTTATCAAAATTTCATAGGA
*
9755 GGTTAACAAAATTTTAGGAGG
64 GGTTAACAAAATTTCAGGAGG
* * * * *
9776 TTATAAAAAATTT-ATAGGGATGTTCTCAAAATTTCATAAGATGGTTATCAAAATTTCATGAGGT
1 TTAT-CAAAATTTCATAGGGAGGTTATCAAAATTTAATAAGATGGTTATCAAAATTTCAT-AGGA
** *
9840 GGTTTTCAAAATTTCATGAGG
64 GGTTAACAAAATTTCAGGAGG
* * * *
9861 TTATCAAAATTTCAAAGGGAGGTTATCAAAATTTTATAGGGA-GGTTTATAAAAATTTCATA
1 TTATCAAAATTTCATAGGGAGGTTATCAAAATTTAATA-AGATGG-TTATCAAAATTTCATA
9922 ATGAGGCATC
Statistics
Matches: 119, Mismatches: 19, Indels: 14
0.78 0.12 0.09
Matches are distributed among these distances:
83 9 0.08
84 42 0.35
85 50 0.42
86 18 0.15
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (84 bp):
TTATCAAAATTTCATAGGGAGGTTATCAAAATTTAATAAGATGGTTATCAAAATTTCATAGGAGG
TTAACAAAATTTCAGGAGG
Found at i:9938 original size:44 final size:43
Alignment explanation
Indices: 9885--9967 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
9875 AAGGGAGGTT
*
9885 ATCAAAATTTTATAGGGA-GGTTTATAAAAATTTCATAATGAGGC
1 ATCAAAATTTTAT-GGGATGG-CTATAAAAATTTCATAATGAGGC
* * *
9929 ATCACAATTTTATGGTATGGCTATCAAAATTTCATAATG
1 ATCAAAATTTTATGGGATGGCTATAAAAATTTCATAATG
9968 TGATTACCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
43 20 0.59
44 14 0.41
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.36
Consensus pattern (43 bp):
ATCAAAATTTTATGGGATGGCTATAAAAATTTCATAATGAGGC
Found at i:9956 original size:107 final size:104
Alignment explanation
Indices: 9737--9963 Score: 235
Period size: 107 Copynumber: 2.1 Consensus size: 104
9727 ATAGTGTTCT
* * * *
9737 TATCAAAATTTCGTAGGAGGTTAACAAAATTTTAGGAGGTTATAAAAAATTTATAGGGATGTTCT
1 TATCAAAATTTC--ATGAGGTTAACAAAATTTAAGGAGGTTATAAAAAATTTATAGGGAGGTTAT
* * * *
9802 CAAAATTTCATAAGATGGTTATCAAAATTTCATGAGGTGGT
64 AAAAATTTCATAAGATGGTCATCAAAATTTCATGAGATGGC
* * * *
9843 TTTCAAAATTTCATGAGGTTATCAAAATTTCAAAGGGAGGTTATCAAAATTTTATAGGGAGGTTT
1 TATCAAAATTTCATGAGGTTAACAAAATTT--AA-GGAGGTTATAAAAAATTTATAGGGAGG-TT
* *
9908 ATAAAAATTTCATAATGA-GG-CATCACAATTTTATG-GTATGGC
62 ATAAAAATTTCATAA-GATGGTCATCAAAATTTCATGAG-ATGGC
9950 TATCAAAATTTCAT
1 TATCAAAATTTCAT
9964 AATGTGATTA
Statistics
Matches: 100, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
104 16 0.16
106 13 0.13
107 52 0.52
108 17 0.17
109 2 0.02
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (104 bp):
TATCAAAATTTCATGAGGTTAACAAAATTTAAGGAGGTTATAAAAAATTTATAGGGAGGTTATAA
AAATTTCATAAGATGGTCATCAAAATTTCATGAGATGGC
Found at i:10207 original size:21 final size:20
Alignment explanation
Indices: 10176--10219 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 20
10166 TATCGTCATA
10176 AAAACTTTATAGTGTGATTATC
1 AAAACTTTATA--GTGATTATC
10198 AAAA-TTTATAGTGATTATC
1 AAAACTTTATAGTGATTATC
10217 AAA
1 AAA
10220 TTTCATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 12 0.55
21 6 0.27
22 4 0.18
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (20 bp):
AAAACTTTATAGTGATTATC
Found at i:12938 original size:20 final size:20
Alignment explanation
Indices: 12909--12947 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
12899 TATATACTAT
12909 CAAAAATCATAGGAAGGTTA
1 CAAAAATCATAGGAAGGTTA
*
12929 CAAAATTCATAGGAAGGTT
1 CAAAAATCATAGGAAGGTT
12948 TATTAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.23
Consensus pattern (20 bp):
CAAAAATCATAGGAAGGTTA
Found at i:13030 original size:43 final size:44
Alignment explanation
Indices: 12969--13068 Score: 112
Period size: 43 Copynumber: 2.3 Consensus size: 44
12959 CATTGTTAGG
* ** * * *
12969 TTATCAAAGTTTTTTATGGAATTTATTACAATTTTATAGG-TAA
1 TTATCAAAATTTCATATGGAAGTTATCACAATTTAATAGGATAA
* * *
13012 TTATCAAAATTTCATATGGCAGTTATCATAATTTAATAGGATAG
1 TTATCAAAATTTCATATGGAAGTTATCACAATTTAATAGGATAA
13056 TTATCAAAATTTC
1 TTATCAAAATTTC
13069 GTAAAGATAT
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 32 0.68
44 15 0.32
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (44 bp):
TTATCAAAATTTCATATGGAAGTTATCACAATTTAATAGGATAA
Found at i:13038 original size:22 final size:22
Alignment explanation
Indices: 13012--13068 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
13002 TTATAGGTAA
13012 TTATCAAAATTTCATATGG-CAG
1 TTATCAAAATTTCATA-GGACAG
* * *
13034 TTATCATAATTTAATAGGATAG
1 TTATCAAAATTTCATAGGACAG
13056 TTATCAAAATTTC
1 TTATCAAAATTTC
13069 GTAAAGATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 2 0.07
22 27 0.93
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGACAG
Found at i:14895 original size:51 final size:50
Alignment explanation
Indices: 14794--14899 Score: 135
Period size: 51 Copynumber: 2.1 Consensus size: 50
14784 GTTCTTCATA
* **
14794 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
*
14844 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGT
14895 TTTTC
1 TTTTC
14900 ATTCAGAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
50 7 0.14
51 41 0.84
52 1 0.02
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.42
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
Found at i:15681 original size:22 final size:21
Alignment explanation
Indices: 15634--15681 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
15624 TTGCCCTTCT
*
15634 TCTCT-CTCCCCCACTAACTT
1 TCTCTCCTCCCCCACTAACTA
* *
15654 TTTCTCCTCCTCCCACTCACTA
1 TCTCTCCTCC-CCCACTAACTA
15676 TCTCTC
1 TCTCTC
15682 TTCATAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 4 0.18
21 4 0.18
22 14 0.64
ACGTcount: A:0.12, C:0.50, G:0.00, T:0.38
Consensus pattern (21 bp):
TCTCTCCTCCCCCACTAACTA
Found at i:17356 original size:29 final size:31
Alignment explanation
Indices: 17319--17386 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 31
17309 GGCATAAATC
* *
17319 TCAAATAAGGGGCTGAAC-TTT-AGAAAAGG
1 TCAAATAAGGGCCTCAACTTTTCAGAAAAGG
*
17348 TCAAATAAGGGCCTCAACTTTTCAGAAAGGG
1 TCAAATAAGGGCCTCAACTTTTCAGAAAAGG
17379 TCAAATAA
1 TCAAATAA
17387 ATCCATTCCG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 16 0.47
30 3 0.09
31 15 0.44
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (31 bp):
TCAAATAAGGGCCTCAACTTTTCAGAAAAGG
Found at i:17492 original size:15 final size:16
Alignment explanation
Indices: 17469--17508 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
17459 GTTAGGTCTA
*
17469 ATTTTTTTTC-ATTTT
1 ATTTATTTTCTATTTT
*
17484 ATTTCTTTTCTATTTT
1 ATTTATTTTCTATTTT
17500 ATTTATTTT
1 ATTTATTTT
17509 TCAGTTGCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (16 bp):
ATTTATTTTCTATTTT
Found at i:19788 original size:104 final size:97
Alignment explanation
Indices: 19569--19872 Score: 356
Period size: 104 Copynumber: 2.9 Consensus size: 97
19559 AACGCGCTCG
* *
19569 CTTTGGGTGTGGAAATTAAAGACCAGAGAAGACCAGGGCTTTCATTAGGCAATTGACTTGGATAT
1 CTTTGGGTGTGGAAATTAAAGA-C-TAGAAGGCCA-GGC-TT--TT-GGCAATTGACTTGGATAT
*
19634 GCAGCATGCTTTCTGCGAAAGATCTTGCTATTGTTGAACT
59 GCAGCGTGC-TTCTGCGAAAGATCTTGCTATTGTTGAACT
*
19674 CTTCGGGTGTGGAAATTAAAGACTAGAAGGCCAGGCTTTTGGCAATTGATGACTTGGATATGCAG
1 CTTTGGGTGTGGAAATTAAAGACTAGAAGGCCAGGCTTTTGGCAA-T--TGACTTGGATATGCAG
*
19739 CGTGCTTCTGCGAATGATCTTGCTATATATTGTTGAACT
63 CGTGCTTCTGCGAAAGATCTTGC----TATTGTTGAACT
* *
19778 CTTTGGGTGTGGAAATTAAAGACTAGAAAAGGTCGGGCTTTTGGCAATTGACTTGGATATGCAGC
1 CTTTGGGTGTGGAAATTAAAGACTAG--AAGGCCAGGCTTTTGGCAATTGACTTGGATATGCAGC
* *
19843 GTGCTTTCTTCGAAAGATATTGGCTATTGT
64 GTGC-TTCTGCGAAAGATCTT-GCTATTGT
19873 CAGTGACTTC
Statistics
Matches: 177, Mismatches: 11, Indels: 26
0.83 0.05 0.12
Matches are distributed among these distances:
98 5 0.03
99 3 0.02
100 17 0.10
101 28 0.16
102 3 0.02
103 29 0.16
104 51 0.29
105 24 0.14
106 17 0.10
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (97 bp):
CTTTGGGTGTGGAAATTAAAGACTAGAAGGCCAGGCTTTTGGCAATTGACTTGGATATGCAGCGT
GCTTCTGCGAAAGATCTTGCTATTGTTGAACT
Found at i:20070 original size:45 final size:45
Alignment explanation
Indices: 20006--20096 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
19996 TTACACTTAT
20006 AGAACTAAGTTACAGACTACGTACCCCTACTCCTAAAGGATGGAA
1 AGAACTAAGTTACAGACTACGTACCCCTACTCCTAAAGGATGGAA
*
20051 AGAACTAAGTTACAGACTACGTACCCGTACTCCTAAAGGATGGAA
1 AGAACTAAGTTACAGACTACGTACCCCTACTCCTAAAGGATGGAA
20096 A
1 A
20097 CTATGGTGTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (45 bp):
AGAACTAAGTTACAGACTACGTACCCCTACTCCTAAAGGATGGAA
Found at i:23624 original size:11 final size:10
Alignment explanation
Indices: 23594--23626 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
23584 TTCCCCTTCT
23594 TTTTTTATT-
1 TTTTTTATTG
23603 TTTTTTATTG
1 TTTTTTATTG
23613 TTTTTTACTTG
1 TTTTTTA-TTG
23624 TTT
1 TTT
23627 GCAGACTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.41
10 7 0.32
11 6 0.27
ACGTcount: A:0.09, C:0.03, G:0.06, T:0.82
Consensus pattern (10 bp):
TTTTTTATTG
Found at i:24648 original size:81 final size:81
Alignment explanation
Indices: 24499--24885 Score: 602
Period size: 81 Copynumber: 4.8 Consensus size: 81
24489 TTCAAACAAT
* * * ** * *
24499 TCATTACGGGATGTTCGTCCTCTTTATTAG-T-TA--GGGACACCTGTTTTAGATGTTCAGCCGT
1 TCATTAGGGGACGTTCGTCCTCTTTTTTAGTTATACGGGGACACC-AATTTAGGTGTTCAACCGT
*
24560 TGGTAGAGGGAAACGTC
65 TGATAGAGGGAAACGTC
** * *
24577 TCATTAGGGGACGTTTATCCTCTTTATTAGTTATACGGGGACACCAGTTTAGGTGTTCAACCGTT
1 TCATTAGGGGACGTTCGTCCTCTTTTTTAGTTATACGGGGACACCAATTTAGGTGTTCAACCGTT
* *
24642 GATAGAGGAAAATGTC
66 GATAGAGGGAAACGTC
*
24658 TCATTAGGGGACGTTCGTCCTCTTTTTTAGTTATACGGGGACAACAATTTAGGTGTTCAACCGTT
1 TCATTAGGGGACGTTCGTCCTCTTTTTTAGTTATACGGGGACACCAATTTAGGTGTTCAACCGTT
24723 GATAGAGGGAAACGTC
66 GATAGAGGGAAACGTC
24739 TCATTAGGGGACGTTCGTCCTCTTTTTTAGTTATACGGGGACACCAATTTAGGTGTTCAACCGTT
1 TCATTAGGGGACGTTCGTCCTCTTTTTTAGTTATACGGGGACACCAATTTAGGTGTTCAACCGTT
24804 GATAGAGGGAAACGTC
66 GATAGAGGGAAACGTC
24820 TCATTAGGGGACGTTCGTCCTCTTTTTTAGTTATACGGGGACACCAATTTAGGTGTTCAACCGTT
1 TCATTAGGGGACGTTCGTCCTCTTTTTTAGTTATACGGGGACACCAATTTAGGTGTTCAACCGTT
24885 G
66 G
24886 TTAGTGTATT
Statistics
Matches: 286, Mismatches: 19, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
78 26 0.09
79 1 0.00
80 2 0.01
81 249 0.87
82 8 0.03
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (81 bp):
TCATTAGGGGACGTTCGTCCTCTTTTTTAGTTATACGGGGACACCAATTTAGGTGTTCAACCGTT
GATAGAGGGAAACGTC
Found at i:25193 original size:29 final size:30
Alignment explanation
Indices: 25146--25206 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
25136 GAAGTTCGTG
* *
25146 TTTGAAGACTCATTGAAGACTTATTTGAAGA
1 TTTGAAGAC-CATTGAAGAATTATTTCAAGA
25177 TTTGAAGA-CATTGAAGAATTATTTCAAGA
1 TTTGAAGACCATTGAAGAATTATTTCAAGA
25206 T
1 T
25207 CGGCCAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 20 0.71
31 8 0.29
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (30 bp):
TTTGAAGACCATTGAAGAATTATTTCAAGA
Found at i:27207 original size:13 final size:13
Alignment explanation
Indices: 27185--27217 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
27175 CTACTAACAA
27185 TTTTTCTTTTGAG
1 TTTTTCTTTTGAG
*
27198 TTTTTTTTTTGAG
1 TTTTTCTTTTGAG
27211 TTTTTCT
1 TTTTTCT
27218 AGGAAGCTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.06, C:0.06, G:0.12, T:0.76
Consensus pattern (13 bp):
TTTTTCTTTTGAG
Found at i:29118 original size:12 final size:13
Alignment explanation
Indices: 29096--29125 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
29086 ATTAAAAATT
29096 AAAATCAATCAAG
1 AAAATCAATCAAG
29109 AAAA-CAATCAAG
1 AAAATCAATCAAG
29121 AAAAT
1 AAAAT
29126 TAAAGAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13
Consensus pattern (13 bp):
AAAATCAATCAAG
Found at i:30437 original size:18 final size:19
Alignment explanation
Indices: 30416--30456 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
30406 CTCTTGAAAT
*
30416 AAATCTTCAA-TGGTCTTC
1 AAATCTCCAATTGGTCTTC
*
30434 AAATCTCCAATTTGTCTTC
1 AAATCTCCAATTGGTCTTC
30453 AAAT
1 AAAT
30457 GGTCTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (19 bp):
AAATCTCCAATTGGTCTTC
Found at i:33961 original size:29 final size:30
Alignment explanation
Indices: 33914--33973 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
33904 GAAGTTCGTG
* *
33914 TTTGAAGACTCATTGAAGACTTATTTGAAGA
1 TTTGAAGAC-CATTGAAGAATTATTTCAAGA
33945 TTTGAAGA-CATTGAAGAATTATTTCAAGA
1 TTTGAAGACCATTGAAGAATTATTTCAAGA
33974 GGAAAGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 19 0.70
31 8 0.30
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.35
Consensus pattern (30 bp):
TTTGAAGACCATTGAAGAATTATTTCAAGA
Found at i:40742 original size:18 final size:18
Alignment explanation
Indices: 40719--40754 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
40709 TCGAGTGGTG
40719 GAGCAGTTCTTAAAGCAA
1 GAGCAGTTCTTAAAGCAA
40737 GAGCAGTTCTTAAAGCAA
1 GAGCAGTTCTTAAAGCAA
40755 TTTTCAGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (18 bp):
GAGCAGTTCTTAAAGCAA
Found at i:42276 original size:14 final size:14
Alignment explanation
Indices: 42257--42297 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 14
42247 TTTCTCCTTG
*
42257 TTTTAACATGTTCA
1 TTTTAACATGTCCA
42271 TTTTAACTTATGTCCA
1 TTTTAAC--ATGTCCA
42287 TTTTAACATGT
1 TTTTAACATGT
42298 ATGCCTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 11 0.46
16 13 0.54
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.51
Consensus pattern (14 bp):
TTTTAACATGTCCA
Found at i:52023 original size:21 final size:20
Alignment explanation
Indices: 51999--52109 Score: 82
Period size: 21 Copynumber: 5.3 Consensus size: 20
51989 AGGATTCATG
51999 TTTTGGTGTGAAGATGTCACA
1 TTTTGGTGT-AAGATGTCACA
* * *
52020 TTTTGGGGTAA-AGGTGACA
1 TTTTGGTGTAAGATGTCACA
*
52039 TATTTGGTGGTAAAGATGCCACA
1 T-TTTGGT-GT-AAGATGTCACA
* **
52062 TTTTGGGGTAA-ATGGGACA
1 TTTTGGTGTAAGATGTCACA
52081 TGTTTGGGTGTAAAGATGTCACA
1 T-TTT-GGTGT-AAGATGTCACA
52104 TTTTGG
1 TTTTGG
52110 GATAAAGGTG
Statistics
Matches: 69, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
19 14 0.20
20 12 0.17
21 18 0.26
22 12 0.17
23 13 0.19
ACGTcount: A:0.25, C:0.08, G:0.32, T:0.35
Consensus pattern (20 bp):
TTTTGGTGTAAGATGTCACA
Found at i:52062 original size:42 final size:41
Alignment explanation
Indices: 52000--52182 Score: 199
Period size: 42 Copynumber: 4.4 Consensus size: 41
51990 GGATTCATGT
* * *
52000 TTTGGTGTGAAGATGTCACATTTTGGGGTAAA-GGTGACATA
1 TTTGGGGTAAAGATGCCACATTTTGGGGTAAATGG-GACATA
*
52041 TTTGGTGGTAAAGATGCCACATTTTGGGGTAAATGGGACATG
1 TTTGG-GGTAAAGATGCCACATTTTGGGGTAAATGGGACATA
* * ***
52083 TTTGGGTGTAAAGATGTCACATTTTGGGATAAA-GGTGGTGTA
1 TTTGGG-GTAAAGATGCCACATTTTGGGGTAAATGG-GACATA
* *
52125 TTTGAAGGTAAAGATACCACATTTTGGGGTAAATGGGACATA
1 TTTG-GGGTAAAGATGCCACATTTTGGGGTAAATGGGACATA
52167 TTTGGGTGTAAAGATG
1 TTTGGG-GTAAAGATG
52183 TGTTGTTGGT
Statistics
Matches: 116, Mismatches: 19, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
41 9 0.08
42 102 0.88
43 5 0.04
ACGTcount: A:0.28, C:0.07, G:0.32, T:0.33
Consensus pattern (41 bp):
TTTGGGGTAAAGATGCCACATTTTGGGGTAAATGGGACATA
Found at i:52091 original size:84 final size:84
Alignment explanation
Indices: 51995--52183 Score: 288
Period size: 84 Copynumber: 2.2 Consensus size: 84
51985 GCAGAGGATT
* * * ** *
51995 CATGTTTTGGTGTGAAGATGTCACATTTTGGGGTAAAGGTGACATATTTGGTGGTAAAGATGCCA
1 CATGTTTGGGTGTAAAGATGTCACATTTTGGGATAAAGGTGACATATTTGAAGGTAAAGATACCA
52060 CATTTTGGGGTAAATGGGA
66 CATTTTGGGGTAAATGGGA
***
52079 CATGTTTGGGTGTAAAGATGTCACATTTTGGGATAAAGGTGGTGTATTTGAAGGTAAAGATACCA
1 CATGTTTGGGTGTAAAGATGTCACATTTTGGGATAAAGGTGACATATTTGAAGGTAAAGATACCA
52144 CATTTTGGGGTAAATGGGA
66 CATTTTGGGGTAAATGGGA
*
52163 CATATTTGGGTGTAAAGATGT
1 CATGTTTGGGTGTAAAGATGT
52184 GTTGTTGGTG
Statistics
Matches: 95, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
84 95 1.00
ACGTcount: A:0.28, C:0.07, G:0.31, T:0.33
Consensus pattern (84 bp):
CATGTTTGGGTGTAAAGATGTCACATTTTGGGATAAAGGTGACATATTTGAAGGTAAAGATACCA
CATTTTGGGGTAAATGGGA
Found at i:55264 original size:18 final size:20
Alignment explanation
Indices: 55241--55293 Score: 65
Period size: 18 Copynumber: 2.7 Consensus size: 20
55231 ACTTTAACTT
55241 TTATGTAGTGTTAT-TA-TG
1 TTATGTAGTGTTATGTAGTG
*
55259 TTATGTAGAGTTATGTAGTG
1 TTATGTAGTGTTATGTAGTG
*
55279 TTATATAGATGTTAT
1 TTATGTAG-TGTTAT
55294 AGAATAGTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 13 0.45
19 2 0.07
20 9 0.31
21 5 0.17
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (20 bp):
TTATGTAGTGTTATGTAGTG
Found at i:55271 original size:10 final size:10
Alignment explanation
Indices: 55241--55293 Score: 65
Period size: 10 Copynumber: 5.4 Consensus size: 10
55231 ACTTTAACTT
55241 TTATGTAGTG
1 TTATGTAGTG
55251 TTAT-TA-TG
1 TTATGTAGTG
*
55259 TTATGTAGAG
1 TTATGTAGTG
55269 TTATGTAGTG
1 TTATGTAGTG
*
55279 TTATATAGATG
1 TTATGTAG-TG
55290 TTAT
1 TTAT
55294 AGAATAGTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
8 6 0.16
9 4 0.11
10 21 0.57
11 6 0.16
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (10 bp):
TTATGTAGTG
Found at i:57741 original size:76 final size:76
Alignment explanation
Indices: 57604--57755 Score: 175
Period size: 76 Copynumber: 2.0 Consensus size: 76
57594 ACAAGGACCC
** *
57604 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGTTTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
57669 GGGCAGTGTCA
66 GGGCAGTGTCA
* * * **
57680 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
*
57742 GATGGGCTGTGTCA
63 GATGGGCAGTGTCA
57756 TAGCTCATCA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
75 4 0.06
76 54 0.84
77 6 0.09
ACGTcount: A:0.17, C:0.29, G:0.29, T:0.25
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Done.