Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011515.1 Corchorus capsularis cultivar CVL-1 contig11536, 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: 64938
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:19075 original size:16 final size:16
Alignment explanation
Indices: 19004--19076 Score: 51
Period size: 16 Copynumber: 4.6 Consensus size: 16
18994 AAAGTCAAAT
19004 ACCCGAACCTGAAAAA
1 ACCCGAACCTGAAAAA
*
19020 TCCCGAATCC-GAAAAA
1 ACCCGAA-CCTGAAAAA
*** *
19036 GTTC-AAACTCGAAAAA
1 ACCCGAACCT-GAAAAA
* *
19052 ATCAGAACCTGAAAAA
1 ACCCGAACCTGAAAAA
19068 ACCCGAACC
1 ACCCGAACC
19077 CGAATCCGAA
Statistics
Matches: 42, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
14 1 0.02
15 2 0.05
16 33 0.79
17 6 0.14
ACGTcount: A:0.48, C:0.29, G:0.12, T:0.11
Consensus pattern (16 bp):
ACCCGAACCTGAAAAA
Found at i:19272 original size:31 final size:32
Alignment explanation
Indices: 19227--19306 Score: 108
Period size: 32 Copynumber: 2.5 Consensus size: 32
19217 TTTGGCCAAA
* * * *
19227 ACCCAAACTGAACCC-AAACCGAATTAACCTG
1 ACCCAAATTCAACCCGAAACCAAACTAACCTG
*
19258 ACCCAAATTCAACCCGAACCCAAACTAACCTG
1 ACCCAAATTCAACCCGAAACCAAACTAACCTG
19290 ACCCAAATTCAACCCGA
1 ACCCAAATTCAACCCGA
19307 CCTAACTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
31 13 0.30
32 30 0.70
ACGTcount: A:0.41, C:0.39, G:0.07, T:0.12
Consensus pattern (32 bp):
ACCCAAATTCAACCCGAAACCAAACTAACCTG
Found at i:19308 original size:16 final size:15
Alignment explanation
Indices: 19248--19308 Score: 68
Period size: 16 Copynumber: 3.9 Consensus size: 15
19238 ACCCAAACCG
*
19248 AATTAACCTGACCCA
1 AATTAACCCGACCCA
19263 AATTCAACCCGAACCCA
1 AATT-AACCCG-ACCCA
* *
19280 AACTAACCTGACCCA
1 AATTAACCCGACCCA
19295 AATTCAACCCGACC
1 AATT-AACCCGACC
19309 TAACTTAAGC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
15 12 0.32
16 18 0.47
17 8 0.21
ACGTcount: A:0.39, C:0.39, G:0.07, T:0.15
Consensus pattern (15 bp):
AATTAACCCGACCCA
Found at i:24393 original size:16 final size:16
Alignment explanation
Indices: 24372--24444 Score: 65
Period size: 16 Copynumber: 4.6 Consensus size: 16
24362 CGGGCTCGGG
*
24372 CGGGTTTGGGTTTTTT
1 CGGGTTCGGGTTTTTT
***
24388 CGGGTTCGGGTTAAGT
1 CGGGTTCGGGTTTTTT
*
24404 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTTTTTT
* * * *
24420 CGGGCTCGGATTATGT
1 CGGGTTCGGGTTTTTT
24436 CGGGTTCGG
1 CGGGTTCGG
24445 TCTCTGGTAG
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.07, C:0.14, G:0.41, T:0.38
Consensus pattern (16 bp):
CGGGTTCGGGTTTTTT
Found at i:24420 original size:32 final size:32
Alignment explanation
Indices: 24372--24444 Score: 101
Period size: 32 Copynumber: 2.3 Consensus size: 32
24362 CGGGCTCGGG
* * * *
24372 CGGGTTTGGGTTTTTTCGGGTTCGGGTTAAGT
1 CGGGTTCGGGTATTTTCGGGCTCGGATTAAGT
*
24404 CGGGTTCGGGTATTTTCGGGCTCGGATTATGT
1 CGGGTTCGGGTATTTTCGGGCTCGGATTAAGT
24436 CGGGTTCGG
1 CGGGTTCGG
24445 TCTCTGGTAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.07, C:0.14, G:0.41, T:0.38
Consensus pattern (32 bp):
CGGGTTCGGGTATTTTCGGGCTCGGATTAAGT
Found at i:33818 original size:19 final size:18
Alignment explanation
Indices: 33791--33826 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
33781 GGTGGCTAGG
*
33791 GTTTTAAGAAGAAGAAGAA
1 GTTTGAAGAAGAA-AAGAA
33810 GTTTGAAGAAGAAAAGA
1 GTTTGAAGAAGAAAAGA
33827 CATACGAGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.53, C:0.00, G:0.28, T:0.19
Consensus pattern (18 bp):
GTTTGAAGAAGAAAAGAA
Found at i:41724 original size:7 final size:7
Alignment explanation
Indices: 41707--41737 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
41697 CTATAGGCGA
41707 TTAGTAAT
1 TTAG-AAT
41715 TTAGAAT
1 TTAGAAT
41722 TTAGAAT
1 TTAGAAT
41729 TTAGAAT
1 TTAGAAT
41736 TT
1 TT
41738 TGTCTTCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.83
8 4 0.17
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (7 bp):
TTAGAAT
Found at i:42351 original size:22 final size:22
Alignment explanation
Indices: 42324--42959 Score: 365
Period size: 22 Copynumber: 29.4 Consensus size: 22
42314 AATTAAATTC
42324 AAAGAGTAAAATAGTAATCAGT
1 AAAGAGTAAAATAGTAATCAGT
42346 AAAGAGT--AATAGTAATCA-T
1 AAAGAGTAAAATAGTAATCAGT
* * *
42365 TAAGAAGT--AATGGTAAACAGT
1 AAAG-AGTAAAATAGTAATCAGT
*
42386 AAACAGTAAAA-AGGTAATCAGT
1 AAAGAGTAAAATA-GTAATCAGT
* * **
42408 AAAGGGTAAAATGGTAATTTGT
1 AAAGAGTAAAATAGTAATCAGT
* *
42430 AAAGGGTAAAATGGTAATCAGT
1 AAAGAGTAAAATAGTAATCAGT
42452 AAAGAGT-AAA-AGTAATCGGCAGT
1 AAAGAGTAAAATAGTAAT---CAGT
* *
42475 AAAAAGTAAAATACTAATCAGT
1 AAAGAGTAAAATAGTAATCAGT
*
42497 -AAGAGTAAAATAGTAATAAGT
1 AAAGAGTAAAATAGTAATCAGT
* * *
42518 AAAAAGTAAAATGGTGATCAGT
1 AAAGAGTAAAATAGTAATCAGT
* * **
42540 AAGAAAG-AAAA-AGGAAGAAG-
1 AA-AGAGTAAAATAGTAATCAGT
* * * *
42560 AAGAAAGTAAAATGGTAGTCAAT
1 AA-AGAGTAAAATAGTAATCAGT
* *
42583 AAAAAGTAAAATGGTAATCAGT
1 AAAGAGTAAAATAGTAATCAGT
42605 AAAGAGT--AATAGTAATCGGCAGT
1 AAAGAGTAAAATAGTAAT---CAGT
*
42628 AAAAAGTAAAATAGTAATCAGT
1 AAAGAGTAAAATAGTAATCAGT
42650 -AAGAGTAAAATAGTAATCAGT
1 AAAGAGTAAAATAGTAATCAGT
*
42671 -AAGAGTAAAATGGTAATCAGT
1 AAAGAGTAAAATAGTAATCAGT
* * **
42692 AAGAAAG-AAAA-AGGAAGAAG-
1 AA-AGAGTAAAATAGTAATCAGT
* *
42712 AAGAAAGTAAAAGA-TAATCAGT
1 AA-AGAGTAAAATAGTAATCAGT
* * *
42734 AAAGGGCAAAATGGTAATCAGT
1 AAAGAGTAAAATAGTAATCAGT
* * *
42756 AAAAAGTAAGAGAGTAATCAGT
1 AAAGAGTAAAATAGTAATCAGT
* **
42778 AAAGA--AAAATGGTAAAGAGT
1 AAAGAGTAAAATAGTAATCAGT
* *
42798 TAAGAGTAAAGAAAAGAGTAATCAGT
1 AAAGAGT----AAAATAGTAATCAGT
* *
42824 -AAGAAGT--AATGGTAGTCAGT
1 AAAG-AGTAAAATAGTAATCAGT
* *
42844 AAAAAGT--AATGGTAATCAGT
1 AAAGAGTAAAATAGTAATCAGT
* * * *
42864 AAAAAGTAAAATGGTAATTAGA
1 AAAGAGTAAAATAGTAATCAGT
*
42886 AAAGAGTAAAATGGTAATCAGT
1 AAAGAGTAAAATAGTAATCAGT
* * **
42908 AAAAAGTAAAAGAGTAAAAAGT
1 AAAGAGTAAAATAGTAATCAGT
* * **
42930 AAAGA-AAAAATGGTAAAGAGT
1 AAAGAGTAAAATAGTAATCAGT
42951 AAAGAGTAA
1 AAAGAGTAA
42960 TCAACAAGGA
Statistics
Matches: 482, Mismatches: 94, Indels: 76
0.74 0.14 0.12
Matches are distributed among these distances:
19 4 0.01
20 99 0.21
21 110 0.23
22 206 0.43
23 29 0.06
24 3 0.01
25 17 0.04
26 14 0.03
ACGTcount: A:0.54, C:0.04, G:0.22, T:0.20
Consensus pattern (22 bp):
AAAGAGTAAAATAGTAATCAGT
Found at i:42603 original size:153 final size:151
Alignment explanation
Indices: 42435--42774 Score: 536
Period size: 153 Copynumber: 2.2 Consensus size: 151
42425 TTTGTAAAGG
42435 GTAAAATGGTAATCAGTAAAGAGTAAAAGTAATCGGCAGTAAAAAGTAAAATACTAATCAGTAAG
1 GTAAAATGGTAATCAGTAAAGAGTAAAAGTAATCGGCAGTAAAAAGTAAAATACTAATCAGTAAG
*
42500 AGTAAAATAGTAATAAGTAAAAAGTAAAATGGTGATCAGTAAGAAAGAAAAAGGAAGAAGAAGAA
66 AGTAAAATAGTAATAAGT-AAAAGTAAAATGGTAATCAGTAAGAAAGAAAAAGGAAGAAGAAGAA
* *
42565 AGTAAAATGGTAGTCAATAAAAA
130 AGTAAAA-GATAATCAATAAAAA
* *
42588 GTAAAATGGTAATCAGTAAAGAGTAATAGTAATCGGCAGTAAAAAGTAAAATAGTAATCAGTAAG
1 GTAAAATGGTAATCAGTAAAGAGTAAAAGTAATCGGCAGTAAAAAGTAAAATACTAATCAGTAAG
* *
42653 AGTAAAATAGTAATCAGTAAGAGTAAAATGGTAATCAGTAAGAAAGAAAAAGGAAGAAGAAGAAA
66 AGTAAAATAGTAATAAGTAAAAGTAAAATGGTAATCAGTAAGAAAGAAAAAGGAAGAAGAAGAAA
* **
42718 GTAAAAGATAATCAGTAAAGG
131 GTAAAAGATAATCAATAAAAA
* *
42739 GCAAAATGGTAATCAGTAAAAAGTAAGAGAGTAATC
1 GTAAAATGGTAATCAGTAAAGAGTAA-A-AGTAATC
42775 AGTAAAGAAA
Statistics
Matches: 172, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
151 34 0.20
152 51 0.30
153 87 0.51
ACGTcount: A:0.54, C:0.05, G:0.22, T:0.19
Consensus pattern (151 bp):
GTAAAATGGTAATCAGTAAAGAGTAAAAGTAATCGGCAGTAAAAAGTAAAATACTAATCAGTAAG
AGTAAAATAGTAATAAGTAAAAGTAAAATGGTAATCAGTAAGAAAGAAAAAGGAAGAAGAAGAAA
GTAAAAGATAATCAATAAAAA
Found at i:42835 original size:152 final size:156
Alignment explanation
Indices: 42353--42959 Score: 535
Period size: 153 Copynumber: 4.0 Consensus size: 156
42343 AGTAAAGAGT
* * * ** **
42353 AATAGTAATCATTAAGAAGT-AATGGTAAACAGTAA-ACAGTAAAAAGGTAATCAGTAA-AGGGT
1 AATAGTAATCAGTAAGAAGTAAATGGTAATCAGTAAGAAAG-AAAAAGG-AAGAAG-AAGAAAGT
** * * ** *
42415 AAAATGGTAATTTGTAAAGGGTAAAATGGTAATCAGTAAAGAGTAAA-AGTAATC-G-GCAGTAA
63 AAAATGGTAATCAGTAAAGAGTAAAATGGTAATCAGTAAAAAGTAAAGAGTAATCAGTAAAGAAA
*
42477 AAA--GTAAA-A-TACTAATCAGTAAGAGTAA
128 AAATGGTAAAGAGT--TAA-GAGTAAGAGTAA
* * *
42505 AATAGTAATAAGTAAAAAGTAAAATGGTGATCAGTAAGAAAGAAAAAGGAAGAAGAAGAAAGTAA
1 AATAGTAATCAGTAAGAAGT-AAATGGTAATCAGTAAGAAAGAAAAAGGAAGAAGAAGAAAGTAA
* * * * * ** *
42570 AATGGTAGTCAATAAAAAGTAAAATGGTAATCAGTAAAGAGT-AATAGTAATC-G-GCAGTAAAA
65 AATGGTAATCAGTAAAGAGTAAAATGGTAATCAGTAAAAAGTAAAGAGTAATCAGTAAAGAAAAA
* *
42632 A--GTAAAATAG-TAATCAGTAAGAGTAA
130 ATGGT-AAAGAGTTAA-GAGTAAGAGTAA
42658 AATAGTAATCAGTAAG-AGTAAAATGGTAATCAGTAAGAAAGAAAAAGGAAGAAGAAGAAAGTAA
1 AATAGTAATCAGTAAGAAGT-AAATGGTAATCAGTAAGAAAGAAAAAGGAAGAAGAAGAAAGTAA
* * *
42722 AA-GATAATCAGTAAAGGGCAAAATGGTAATCAGTAAAAAGTAAGAGAGTAATCAGTAAAG-AAA
65 AATGGTAATCAGTAAAGAGTAAAATGGTAATCAGTAAAAAGTAA-AGAGTAATCAGTAAAGAAAA
42785 AATGGTAAAGAGTTAAGAGTAA-AG-AA
129 AATGGTAAAGAGTTAAGAGTAAGAGTAA
* * * * **
42811 AAGAGTAATCAGTAAGAAGT-AATGGTAGTCAGTAA-AAAG-TAATGGTAATCAGTAA-AAAGTA
1 AATAGTAATCAGTAAGAAGTAAATGGTAATCAGTAAGAAAGAAAAAGG-AAGAAG-AAGAAAGTA
* * **
42872 AAATGGTAATTAGAAAAGAGTAAAATGGTAATCAGTAAAAAGTAAAAGAGTAAAAAGTAAAGAAA
64 AAATGGTAATCAGTAAAGAGTAAAATGGTAATCAGTAAAAAGT-AAAGAGTAATCAGTAAAGAAA
*
42937 AAATGGTAAAGAGTAAAGAGTAA
128 AAATGGTAAAGAGTTAAGAGTAA
42960 TCAACAAGGA
Statistics
Matches: 389, Mismatches: 45, Indels: 41
0.82 0.09 0.09
Matches are distributed among these distances:
150 4 0.01
151 49 0.13
152 135 0.35
153 146 0.38
154 34 0.09
155 16 0.04
156 5 0.01
ACGTcount: A:0.54, C:0.04, G:0.22, T:0.20
Consensus pattern (156 bp):
AATAGTAATCAGTAAGAAGTAAATGGTAATCAGTAAGAAAGAAAAAGGAAGAAGAAGAAAGTAAA
ATGGTAATCAGTAAAGAGTAAAATGGTAATCAGTAAAAAGTAAAGAGTAATCAGTAAAGAAAAAA
TGGTAAAGAGTTAAGAGTAAGAGTAA
Found at i:42852 original size:46 final size:43
Alignment explanation
Indices: 42563--42910 Score: 185
Period size: 42 Copynumber: 8.1 Consensus size: 43
42553 GAAGAAGAAG
* * *
42563 AAAGTAAAATGGTAGTCAATAAAAAGTAAA-ATG-GTAATCAGT
1 AAAGAAAAATGGTAATCAGTAAAAAGTAAAGA-GAGTAATCAGT
** * *
42605 AAAGAGTAATAGTAATCGGCAGTAAAAAGTAAA-ATAGTAATCAGT
1 AAAGAAAAATGGTAAT---CAGTAAAAAGTAAAGAGAGTAATCAGT
* * *
42650 AAGAGTAAAATAGTAATCAGT-AAGAGTAAA-ATG-GTAATCAGT
1 AA-AGAAAAATGGTAATCAGTAAAAAGTAAAGA-GAGTAATCAGT
**
42692 AAGAAAGAAAAA-GG-AAGAAG-AAGAAAGTAAA-AGA-TAATCAGT
1 ---AAAGAAAAATGGTAATCAGTAA-AAAGTAAAGAGAGTAATCAGT
*
42734 AAAGGGCAAAATGGTAATCAGTAAAAAGT-AAGAGAGTAATCAGT
1 AAA--GAAAAATGGTAATCAGTAAAAAGTAAAGAGAGTAATCAGT
** * *
42778 AAAGAAAAATGGTAAAGAGTTAAGAGTAAAGAAAAGAGTAATCAGT
1 AAAGAAAAATGGTAATCAGTAAAAAGTAAAG---AGAGTAATCAGT
* * *
42824 -AAGAAGTAATGGTAGTCAGTAAAAAGT-AA-TG-GTAATCAGT
1 AAAGAA-AAATGGTAATCAGTAAAAAGTAAAGAGAGTAATCAGT
* *
42864 AAAAAGTAAAATGGTAATTAG-AAAAGAGTAAA-ATG-GTAATCAGT
1 --AAAGAAAAATGGTAATCAGTAAAA-AGTAAAGA-GAGTAATCAGT
42908 AAA
1 AAA
42911 AAGTAAAAGA
Statistics
Matches: 239, Mismatches: 37, Indels: 60
0.71 0.11 0.18
Matches are distributed among these distances:
39 3 0.01
40 9 0.04
41 10 0.04
42 82 0.34
43 34 0.14
44 29 0.12
45 34 0.14
46 38 0.16
ACGTcount: A:0.53, C:0.04, G:0.22, T:0.20
Consensus pattern (43 bp):
AAAGAAAAATGGTAATCAGTAAAAAGTAAAGAGAGTAATCAGT
Found at i:42923 original size:15 final size:15
Alignment explanation
Indices: 42861--42932 Score: 60
Period size: 15 Copynumber: 4.9 Consensus size: 15
42851 AATGGTAATC
42861 AGTAAAAAGTAAAATG
1 AGTAAAAAGTAAAA-G
**
42877 -GTAATTAG-AAAAG
1 AGTAAAAAGTAAAAG
* **
42890 AGTAAAATGGT-AATC
1 AGTAAAA-AGTAAAAG
42905 AGTAAAAAGTAAAAG
1 AGTAAAAAGTAAAAG
42920 AGTAAAAAGTAAA
1 AGTAAAAAGTAAA
42933 GAAAAAATGG
Statistics
Matches: 42, Mismatches: 10, Indels: 9
0.69 0.16 0.15
Matches are distributed among these distances:
13 1 0.02
14 10 0.24
15 31 0.74
ACGTcount: A:0.60, C:0.01, G:0.19, T:0.19
Consensus pattern (15 bp):
AGTAAAAAGTAAAAG
Found at i:42933 original size:14 final size:14
Alignment explanation
Indices: 42886--42959 Score: 62
Period size: 15 Copynumber: 5.1 Consensus size: 14
42876 GGTAATTAGA
*
42886 AAAGAGTAAAATGGT
1 AAAGAGTAAAA-AGT
**
42901 AATCAGTAAAAAGT
1 AAAGAGTAAAAAGT
42915 AAAAGAGTAAAAAGT
1 -AAAGAGTAAAAAGT
42930 AAAGA--AAAAATGGT
1 AAAGAGTAAAAA--GT
*
42944 AAAGAGTAAAGAGT
1 AAAGAGTAAAAAGT
42958 AA
1 AA
42960 TCAACAAGGA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
12 5 0.10
14 18 0.38
15 21 0.44
16 4 0.08
ACGTcount: A:0.61, C:0.01, G:0.22, T:0.16
Consensus pattern (14 bp):
AAAGAGTAAAAAGT
Found at i:42954 original size:7 final size:7
Alignment explanation
Indices: 42905--43028 Score: 56
Period size: 7 Copynumber: 17.7 Consensus size: 7
42895 AATGGTAATC
*
42905 AGTAAAA
1 AGTAAAG
42912 AGTAAAAG
1 AGT-AAAG
*
42920 AGTAAAA
1 AGTAAAG
42927 AGTAAAG
1 AGTAAAG
**
42934 AAAAAATG
1 AGTAAA-G
42942 -GTAAAG
1 AGTAAAG
42948 AGTAAAG
1 AGTAAAG
**
42955 AGTAATC
1 AGTAAAG
** *
42962 AACAAGG
1 AGTAAAG
*
42969 AGGAAATG
1 AGTAAA-G
42977 -GTAAAG
1 AGTAAAG
*
42983 AGTAATG
1 AGTAAAG
**
42990 AGTAATC
1 AGTAAAG
42997 AGTAAAG
1 AGTAAAG
* *
43004 AATAATG
1 AGTAAAG
43011 -GTAAAG
1 AGTAAAG
*
43017 ACTAAAG
1 AGTAAAG
43024 AGTAA
1 AGTAA
43029 TCAGTAAAGG
Statistics
Matches: 84, Mismatches: 27, Indels: 12
0.68 0.22 0.10
Matches are distributed among these distances:
6 6 0.07
7 70 0.83
8 8 0.10
ACGTcount: A:0.56, C:0.03, G:0.23, T:0.17
Consensus pattern (7 bp):
AGTAAAG
Found at i:43023 original size:69 final size:67
Alignment explanation
Indices: 42906--43080 Score: 185
Period size: 69 Copynumber: 2.5 Consensus size: 67
42896 ATGGTAATCA
* ** * *
42906 GTAAAAAGTAAAAGAGTAAAAAGTAAAGAAAAAATGGTAAAGAGTAAAGAGTAATCA-ACAAGGA
1 GTAAAAAGT-AAATAGTAATCAGTAAAG-AATAATGGTAAAGACTAAAGAGTAATCAGA-AAGGA
42970 GGAAATG
63 --AAATG
*
42977 GTAAAGAGT-AATGAGTAATCAGTAAAGAATAATGGTAAAGACTAAAGAGTAATCAGTAAAGGAA
1 GTAAAAAGTAAAT-AGTAATCAGTAAAGAATAATGGTAAAGACTAAAGAGTAATCAG-AAAGGAA
43041 AATG
64 AATG
*
43045 GTAAAAAGTAAAATATTAATCAGTAAA-AAGTAATGG
1 GTAAAAAGT-AAATAGTAATCAGTAAAGAA-TAATGG
43081 CAATCAGTAA
Statistics
Matches: 90, Mismatches: 8, Indels: 14
0.80 0.07 0.12
Matches are distributed among these distances:
68 15 0.17
69 46 0.51
70 20 0.22
71 9 0.10
ACGTcount: A:0.55, C:0.03, G:0.22, T:0.19
Consensus pattern (67 bp):
GTAAAAAGTAAATAGTAATCAGTAAAGAATAATGGTAAAGACTAAAGAGTAATCAGAAAGGAAAA
TG
Found at i:43071 original size:35 final size:34
Alignment explanation
Indices: 42906--43071 Score: 167
Period size: 35 Copynumber: 4.8 Consensus size: 34
42896 ATGGTAATCA
* ** *
42906 GTAAAAAGTAAAAGAGTAAAAAGTAAAGAAAAAATG
1 GTAAAGAGT-AAAGAGTAATCAGTAAAG-GAAAATG
42942 GTAAAGAGTAAAGAGTAATCA--ACAAGGAGGAAATG
1 GTAAAGAGTAAAGAGTAATCAGTA-AAGGA--AAATG
*
42977 GTAAAGAGTAATGAGTAATCAGTAAA-GAATAATG
1 GTAAAGAGTAAAGAGTAATCAGTAAAGGAA-AATG
*
43011 GTAAAGACTAAAGAGTAATCAGTAAAGGAAAATG
1 GTAAAGAGTAAAGAGTAATCAGTAAAGGAAAATG
* * *
43045 GTAAAAAGTAAAATATTAATCAGTAAA
1 GTAAAGAGT-AAAGAGTAATCAGTAAA
43072 AAGTAATGGC
Statistics
Matches: 111, Mismatches: 11, Indels: 17
0.80 0.08 0.12
Matches are distributed among these distances:
33 3 0.03
34 42 0.38
35 55 0.50
36 10 0.09
37 1 0.01
ACGTcount: A:0.56, C:0.04, G:0.22, T:0.19
Consensus pattern (34 bp):
GTAAAGAGTAAAGAGTAATCAGTAAAGGAAAATG
Found at i:43158 original size:21 final size:21
Alignment explanation
Indices: 43095--43161 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 21
43085 CAGTAAAGAA
*
43095 TAAAATGGTAATTAGTAATCAG
1 TAAAATAGTAA-TAGTAATCAG
* *
43117 T-AAAGAGTAA-AGAATATTCAG
1 TAAAATAGTAATAG--TAATCAG
43138 TAAAATAGTAATAGTAATCAG
1 TAAAATAGTAATAGTAATCAG
43159 TAA
1 TAA
43162 TTCAGTAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
19 2 0.06
21 23 0.64
22 9 0.25
23 2 0.06
ACGTcount: A:0.51, C:0.04, G:0.16, T:0.28
Consensus pattern (21 bp):
TAAAATAGTAATAGTAATCAG
Found at i:45275 original size:2 final size:2
Alignment explanation
Indices: 45268--45295 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
45258 GGGCTAAATC
45268 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
45296 TCTAAGTCAT
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:47074 original size:70 final size:70
Alignment explanation
Indices: 46961--47096 Score: 236
Period size: 70 Copynumber: 1.9 Consensus size: 70
46951 GCTTTCGTTA
46961 CTTTAGCACTTTTAGTAGGGACGTTATGTATTGCTTTGAAATGTTATATTTTCCTTGTAATGTTA
1 CTTTAGCACTTTTAGTAGGGACGTTATGTATTGCTTTGAAATGTTATATTTTCCTTGTAATGTTA
47026 TGTTC
66 TGTTC
* * * *
47031 CTTTATCACTTTTAGTGGGGACTTTATGTATTGCTTTGGAATGTTATATTTTCCTTGTAATGTTA
1 CTTTAGCACTTTTAGTAGGGACGTTATGTATTGCTTTGAAATGTTATATTTTCCTTGTAATGTTA
47096 T
66 T
47097 ATTTATGGAC
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 62 1.00
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.50
Consensus pattern (70 bp):
CTTTAGCACTTTTAGTAGGGACGTTATGTATTGCTTTGAAATGTTATATTTTCCTTGTAATGTTA
TGTTC
Found at i:49293 original size:18 final size:18
Alignment explanation
Indices: 49270--49306 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
49260 TATTTACTTC
49270 TATAATTATTATCTTAAT
1 TATAATTATTATCTTAAT
49288 TATAATTATTATCTTAAT
1 TATAATTATTATCTTAAT
49306 T
1 T
49307 TTATTTTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (18 bp):
TATAATTATTATCTTAAT
Found at i:49311 original size:32 final size:32
Alignment explanation
Indices: 49275--49335 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
49265 ACTTCTATAA
* * *
49275 TTATTATCTTAATTATAATTATTATCTTAATT
1 TTATTATCTCAAATAAAATTATTATCTTAATT
* *
49307 TTATTTTGTCAAATAAAATTATTATCTTA
1 TTATTATCTCAAATAAAATTATTATCTTA
49336 GTTTGCTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.56
Consensus pattern (32 bp):
TTATTATCTCAAATAAAATTATTATCTTAATT
Found at i:49976 original size:24 final size:26
Alignment explanation
Indices: 49923--49976 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 26
49913 TATAAACTTT
* *
49923 AAATATTTTAATAATGTCTAAATTAT
1 AAATATTTTAATAATGTCTAAAATAA
49949 AAATA-TTT-ATATATGT-TAAAATAA
1 AAATATTTTAATA-ATGTCTAAAATAA
49973 AAAT
1 AAAT
49977 TTAACACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 13 0.52
25 7 0.28
26 5 0.20
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.43
Consensus pattern (26 bp):
AAATATTTTAATAATGTCTAAAATAA
Found at i:50133 original size:21 final size:21
Alignment explanation
Indices: 50109--50157 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
50099 CGCTGATTAC
* *
50109 AATCTCATTTGTACAGTATCT
1 AATCTCATCTGTACAGTAACT
50130 AATCTCATCTGTACAGTAACT
1 AATCTCATCTGTACAGTAACT
50151 AATCTCA
1 AATCTCA
50158 CCATCTCAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (21 bp):
AATCTCATCTGTACAGTAACT
Found at i:53948 original size:37 final size:37
Alignment explanation
Indices: 53787--53949 Score: 166
Period size: 37 Copynumber: 4.4 Consensus size: 37
53777 CAGTGCTTTA
* * * *
53787 TAAGGAGAGCTTTGCAGTAAAGAGGGTACTGCCACAG
1 TAAGGAGAGCTCTGCAGTAAAGAGGGTGCTACCGCAG
* * *
53824 TAAGGAGAGCTCTAC-GATGAAGAGGGTGCTGCCGCAG
1 TAAGGAGAGCTCTGCAG-TAAAGAGGGTGCTACCGCAG
*** *
53861 TAAGGAGAGCTCTATGGTAAAGAGGGTGCTATCGCAG
1 TAAGGAGAGCTCTGCAGTAAAGAGGGTGCTACCGCAG
* * * **
53898 CAAGAAGAGCTCTGCAGTAAATAGGGTGCTACCGTGG
1 TAAGGAGAGCTCTGCAGTAAAGAGGGTGCTACCGCAG
53935 TAAGGAGAGCTCTGC
1 TAAGGAGAGCTCTGC
53950 GATGAAGAGT
Statistics
Matches: 104, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
36 1 0.01
37 102 0.98
38 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.34, T:0.19
Consensus pattern (37 bp):
TAAGGAGAGCTCTGCAGTAAAGAGGGTGCTACCGCAG
Found at i:56083 original size:35 final size:33
Alignment explanation
Indices: 56044--56116 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
56034 TGGAGGAGCA
*
56044 TGGAGATGGAAGCACTAATGACCGGCCACGCGACT
1 TGGAGATGGAAG-AC-AATCACCGGCCACGCGACT
*** *
56079 TGGAGATGTCCGACCATCACCGGCCACGCGACT
1 TGGAGATGGAAGACAATCACCGGCCACGCGACT
56112 TGGAG
1 TGGAG
56117 TTGCCCGGCC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
33 22 0.67
34 2 0.06
35 9 0.27
ACGTcount: A:0.25, C:0.29, G:0.32, T:0.15
Consensus pattern (33 bp):
TGGAGATGGAAGACAATCACCGGCCACGCGACT
Found at i:56104 original size:33 final size:33
Alignment explanation
Indices: 56064--56143 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
56054 AGCACTAATG
*
56064 ACCGGCCACGCGACTTGGAGATGTCCGACCATC
1 ACCGGCCACGCGACTTGGAGATGCCCGACCATC
* *
56097 ACCGGCCACGCGACTTGGAGTTGCCCGGCCATC
1 ACCGGCCACGCGACTTGGAGATGCCCGACCATC
*
56130 ACCGGCCATGCGAC
1 ACCGGCCACGCGAC
56144 AAGGACATGC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.19, C:0.39, G:0.29, T:0.14
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGATGCCCGACCATC
Found at i:63008 original size:10 final size:10
Alignment explanation
Indices: 62993--63028 Score: 72
Period size: 10 Copynumber: 3.6 Consensus size: 10
62983 AGTTGCTGCC
62993 AAATTCCAGA
1 AAATTCCAGA
63003 AAATTCCAGA
1 AAATTCCAGA
63013 AAATTCCAGA
1 AAATTCCAGA
63023 AAATTC
1 AAATTC
63029 TAGAGTCCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.22
Consensus pattern (10 bp):
AAATTCCAGA
Found at i:63982 original size:6 final size:6
Alignment explanation
Indices: 63971--63997 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
63961 TTAATTCTGC
63971 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
63998 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:64336 original size:26 final size:27
Alignment explanation
Indices: 64307--64369 Score: 76
Period size: 25 Copynumber: 2.4 Consensus size: 27
64297 CCGTTTTTTC
64307 TAAAAAAAAAAAAAG-GTTTGCGACGA
1 TAAAAAAAAAAAAAGTGTTTGCGACGA
** * *
64333 T-AAAAAAAAAATTGTTTTTGCGTCGA
1 TAAAAAAAAAAAAAGTGTTTGCGACGA
64359 TAAAAAAAAAA
1 TAAAAAAAAAA
64370 GTTTTTTCCG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 11 0.35
26 11 0.35
27 9 0.29
ACGTcount: A:0.57, C:0.06, G:0.14, T:0.22
Consensus pattern (27 bp):
TAAAAAAAAAAAAAGTGTTTGCGACGA
Found at i:64373 original size:24 final size:24
Alignment explanation
Indices: 64311--64375 Score: 87
Period size: 26 Copynumber: 2.7 Consensus size: 24
64301 TTTTTCTAAA
*
64311 AAAAAAAAAAG-GTTTGCGACGAT
1 AAAAAAAAAAGTTTTTGCGACGAT
*
64334 AAAAAAAAAATTGTTTTTGCGTCGAT
1 AAAAAAAAAA--GTTTTTGCGACGAT
64360 AAAAAAAAAAGTTTTT
1 AAAAAAAAAAGTTTTT
64376 TCCGTTTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
23 10 0.27
24 6 0.16
25 1 0.03
26 20 0.54
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.28
Consensus pattern (24 bp):
AAAAAAAAAAGTTTTTGCGACGAT
Done.