Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013422.1 Corchorus olitorius cultivar O-4 contig13455, 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: 43090
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:2072 original size:45 final size:45
Alignment explanation
Indices: 2004--2096 Score: 141
Period size: 45 Copynumber: 2.1 Consensus size: 45
1994 AATAACAATT
*
2004 AATATTAGCTTTATTTTGATGAATTATATAGAGATGGAGAAGTAG
1 AATATTAGCTTTATTTTGATGAATTACATAGAGATGGAGAAGTAG
* * * *
2049 AATATTAGTTTTATTTTGGTGAATTACCTAGAGATGGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACATAGAGATGGAGAAGTAG
2094 AAT
1 AAT
2097 TTATGTAATG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (45 bp):
AATATTAGCTTTATTTTGATGAATTACATAGAGATGGAGAAGTAG
Found at i:5806 original size:22 final size:21
Alignment explanation
Indices: 5762--5858 Score: 81
Period size: 22 Copynumber: 4.6 Consensus size: 21
5752 CATTGTTAGG
* *
5762 TTATCAAATTTTTTTATGG-AA
1 TTATCAAAATTTTATA-GGTAA
*
5783 TTTATCACAATTTTATAGGTAA
1 -TTATCAAAATTTTATAGGTAA
* *
5805 TTATCAAAATTTCATATGGTAG
1 TTATCAAAATTTTATA-GGTAA
* * *
5827 TTATCAAAATTTTAGA-GCAG
1 TTATCAAAATTTTATAGGTAA
5847 TTATCAAAATTT
1 TTATCAAAATTT
5859 CATAAAAATA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
20 15 0.23
21 16 0.25
22 33 0.52
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.44
Consensus pattern (21 bp):
TTATCAAAATTTTATAGGTAA
Found at i:5808 original size:21 final size:22
Alignment explanation
Indices: 5762--5840 Score: 90
Period size: 22 Copynumber: 3.6 Consensus size: 22
5752 CATTGTTAGG
* *
5762 TTATCAAATTTTTTTATGG-AA
1 TTATCAAAATTTTATATGGTAA
*
5783 TTTATCACAATTTTATA-GGTAA
1 -TTATCAAAATTTTATATGGTAA
* *
5805 TTATCAAAATTTCATATGGTAG
1 TTATCAAAATTTTATATGGTAA
5827 TTATCAAAATTTTA
1 TTATCAAAATTTTA
5841 GAGCAGTTAT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
21 16 0.33
22 32 0.67
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.47
Consensus pattern (22 bp):
TTATCAAAATTTTATATGGTAA
Found at i:7694 original size:19 final size:19
Alignment explanation
Indices: 7670--7706 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
7660 TCATAATACA
*
7670 TTAAACTATCAAATAGAAT
1 TTAAACAATCAAATAGAAT
*
7689 TTAAACAATGAAATAGAA
1 TTAAACAATCAAATAGAA
7707 AGACTTCAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.08, G:0.08, T:0.27
Consensus pattern (19 bp):
TTAAACAATCAAATAGAAT
Found at i:8183 original size:22 final size:22
Alignment explanation
Indices: 8151--8195 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
8141 GAGAGCATAG
*
8151 TTGATGTGCCCAAGGCTGATCA
1 TTGATGCGCCCAAGGCTGATCA
*
8173 TTGATGCGCCCAAGGCTTATCA
1 TTGATGCGCCCAAGGCTGATCA
8195 T
1 T
8196 GGACTTGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.29
Consensus pattern (22 bp):
TTGATGCGCCCAAGGCTGATCA
Found at i:19714 original size:58 final size:58
Alignment explanation
Indices: 19666--19835 Score: 229
Period size: 58 Copynumber: 2.9 Consensus size: 58
19656 ACATAATCAA
* ** *
19666 AATGCCCTTGGATGCACAAAAATGACCA-AATTGCCCCTGGACACGCAAAAATGACCAG
1 AATGCCCTTAGATGTGCAAAAATGACCAGAA-AGCCCCTGGACACGCAAAAATGACCAG
* *
19724 AATGCCCTTAGATGTGCAAAAATGACCAGAAAGCCCCTGGGCATGCAAAAATGACCAG
1 AATGCCCTTAGATGTGCAAAAATGACCAGAAAGCCCCTGGACACGCAAAAATGACCAG
*
19782 AATGGCCTTAGATGTGCAAAAATGACCAGAAAGCCCCTAGGTA-A-GCAAAAATGA
1 AATGCCCTTAGATGTGCAAAAATGACCAGAAAGCCCCT-GG-ACACGCAAAAATGA
19836 TCAATTAAGA
Statistics
Matches: 101, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
58 96 0.95
59 5 0.05
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (58 bp):
AATGCCCTTAGATGTGCAAAAATGACCAGAAAGCCCCTGGACACGCAAAAATGACCAG
Found at i:19750 original size:29 final size:29
Alignment explanation
Indices: 19568--19817 Score: 189
Period size: 29 Copynumber: 8.6 Consensus size: 29
19558 AAATATAACT
* * *
19568 AAAATGACCAAAATGCCCATGGACGTGCA
1 AAAATGACCAGAATGCCCTTGGATGTGCA
* * * * * *
19597 AATATGACAAAAAGGCTCC-TGGATGCGTA
1 AAAATGACCAGAATGC-CCTTGGATGTGCA
* * *
19626 AATATGATCAAAATGCCCTTGGATGTGCA
1 AAAATGACCAGAATGCCCTTGGATGTGCA
* * * * **
19655 AACATAATCAAAATGCCCTTGGATGCACA
1 AAAATGACCAGAATGCCCTTGGATGTGCA
* ***
19684 AAAATGACCA-AATTGCCCCTGGACACGCA
1 AAAATGACCAGAA-TGCCCTTGGATGTGCA
*
19713 AAAATGACCAGAATGCCCTTAGATGTGCA
1 AAAATGACCAGAATGCCCTTGGATGTGCA
* * ***
19742 AAAATGACCAGAAAGCCCCTGGGCATGCA
1 AAAATGACCAGAATGCCCTTGGATGTGCA
* *
19771 AAAATGACCAGAATGGCCTTAGATGTGCA
1 AAAATGACCAGAATGCCCTTGGATGTGCA
*
19800 AAAATGACCAGAAAGCCC
1 AAAATGACCAGAATGCCC
19818 CTAGGTAAGC
Statistics
Matches: 175, Mismatches: 42, Indels: 8
0.78 0.19 0.04
Matches are distributed among these distances:
28 4 0.02
29 167 0.95
30 4 0.02
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (29 bp):
AAAATGACCAGAATGCCCTTGGATGTGCA
Found at i:19829 original size:29 final size:29
Alignment explanation
Indices: 19682--19835 Score: 148
Period size: 29 Copynumber: 5.3 Consensus size: 29
19672 CTTGGATGCA
* * * *
19682 CAAAAATGACCA-AATTGCCCCTGGACACG
1 CAAAAATGACCAGAA-AGCCCCTAGATATG
* * *
19711 CAAAAATGACCAGAATGCCCTTAGATGTG
1 CAAAAATGACCAGAAAGCCCCTAGATATG
* **
19740 CAAAAATGACCAGAAAGCCCCTGGGCATG
1 CAAAAATGACCAGAAAGCCCCTAGATATG
* * * *
19769 CAAAAATGACCAGAATGGCCTTAGATGTG
1 CAAAAATGACCAGAAAGCCCCTAGATATG
* *
19798 CAAAAATGACCAGAAAGCCCCTAGGTAAG
1 CAAAAATGACCAGAAAGCCCCTAGATATG
19827 CAAAAATGA
1 CAAAAATGA
19836 TCAATTAAGA
Statistics
Matches: 100, Mismatches: 24, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
29 98 0.98
30 2 0.02
ACGTcount: A:0.41, C:0.23, G:0.21, T:0.15
Consensus pattern (29 bp):
CAAAAATGACCAGAAAGCCCCTAGATATG
Found at i:20310 original size:59 final size:59
Alignment explanation
Indices: 20065--20639 Score: 888
Period size: 59 Copynumber: 9.7 Consensus size: 59
20055 TGGAATATAG
* * *
20065 ACTCTCAAACAGAGACCTCGACCAGGATTTT-AAAACAAGATGAGATTTTGAATTGAAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTG-AAA
* * *
20124 ACTCTCTAACAGAGACCTCGAACAAGATTTTTTTAAAGCAAGATAAGATTTTGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGA--TTTTAAAAACAAGATAAGATTTTGAATTGAAA
*
20185 ACTCTCTAACAGAGACCTCGAACAGGATTTTTTAAAACCAA-ATAAGATTTTGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGA--TTTTAAAAACAAGATAAGATTTTGAATTGAAA
* *
20245 ACTCTCTAACAGAGACCTCGAAGAGGATTTTAAAAACAAGATAAGGTTTTGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAA
* * *
20304 ACTCTCTAATAGAGACCTCGAACAGGATTTTTAAAACCAGATAAGATTTTGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAA
20363 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAA
* * *
20422 ACTCTCTAAAATAGACCTCGAACAGGAATTTAAAAACAAGATAAGATTTTGAATTGAAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTG-AAA
** * *
20482 ACTCTCTAACAGAGGGCTCGAACAGGATTTT-GAAACAAGATGAGATTTTGAATTGAAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTG-AAA
20541 ACTCTCTAACAGAGACCTCGAACAGGATTTT-AAAACAAGATAAGATTTTGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAA
20599 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGA
20640 AAGGGAATTT
Statistics
Matches: 477, Mismatches: 33, Indels: 12
0.91 0.06 0.02
Matches are distributed among these distances:
58 45 0.09
59 291 0.61
60 74 0.16
61 45 0.09
62 22 0.05
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.26
Consensus pattern (59 bp):
ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAA
Found at i:21588 original size:36 final size:36
Alignment explanation
Indices: 21475--21588 Score: 158
Period size: 36 Copynumber: 3.1 Consensus size: 36
21465 TTATTTTCTT
* *
21475 TTTTTCTGACCTCTCTCTGTTTTAGG-CCTAGTTTTTC
1 TTTTTC-GACCTCTTTCTATTTTAGGTCC-AGTTTTTC
* *
21512 CTGTTCGACCTCTTTCTATTTTAGGTCCAGTTTTTC
1 TTTTTCGACCTCTTTCTATTTTAGGTCCAGTTTTTC
*
21548 TTTTTCGACCTCTTTCTATTTTAGGTCCAGTTTTTT
1 TTTTTCGACCTCTTTCTATTTTAGGTCCAGTTTTTC
21584 TTTTT
1 TTTTT
21589 TTTTTTTTAA
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
36 63 0.91
37 6 0.09
ACGTcount: A:0.10, C:0.22, G:0.12, T:0.56
Consensus pattern (36 bp):
TTTTTCGACCTCTTTCTATTTTAGGTCCAGTTTTTC
Found at i:36289 original size:21 final size:21
Alignment explanation
Indices: 36246--36289 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
36236 CCAATTTAGG
*
36246 TTTAGATTTAAATTTCTTGTT
1 TTTAGATTTAAATTTATTGTT
36267 TTTAGATTTAAGATTTATT-TT
1 TTTAGATTTAA-ATTTATTGTT
36288 TT
1 TT
36290 ATGTATCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.25, C:0.02, G:0.09, T:0.64
Consensus pattern (21 bp):
TTTAGATTTAAATTTATTGTT
Found at i:40967 original size:33 final size:34
Alignment explanation
Indices: 40898--40982 Score: 118
Period size: 33 Copynumber: 2.5 Consensus size: 34
40888 TTCAGTTCCA
* *
40898 GACCTCACACAGGTCTTTCTCAAGTTTTAATATC
1 GACCTCAGACAGGCCTTTCTCAAGTTTTAATATC
* *
40932 GACCTCAGACATGCCTTTCTC-AGTTTTAATTTC
1 GACCTCAGACAGGCCTTTCTCAAGTTTTAATATC
*
40965 GACCTCAGACAGGTCTTT
1 GACCTCAGACAGGCCTTT
40983 ATCTTTCAGT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
33 27 0.60
34 18 0.40
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.35
Consensus pattern (34 bp):
GACCTCAGACAGGCCTTTCTCAAGTTTTAATATC
Found at i:40997 original size:99 final size:96
Alignment explanation
Indices: 40864--41079 Score: 243
Period size: 99 Copynumber: 2.2 Consensus size: 96
40854 TTTCGAAGCA
* * * *** * *
40864 TCGACCTCAGACAGCTCTCTCTCTTTCAGTTCCAGACCTCACACAGGTCTTTCTCAAGTTTTAAT
1 TCGACCTCAGACAGGTCTTTATCTTTCAGTTCCAGAAAACAAACAGGTCTTTCTC-AGTTTAAAT
* * * *
40929 ATCGACCTCAGACATGCCTTTCTCAGTTTTAATT
65 ATCGACCTCAAACAGGCCTTTATC--TTTCAATT
*
40963 TCGACCTCAGACAGGTCTTTATCTTTCAGTTCCAGAAAACAAACAGGTCTTTCTCAGTTTAAATC
1 TCGACCTCAGACAGGTCTTTATCTTTCAGTTCCAGAAAACAAACAGGTCTTTCTCAGTTTAAATA
* * *
41028 TTGACCTCAAACAGGTCTTTATCTTTCAGTT
66 TCGACCTCAAACAGGCCTTTATCTTTCAATT
*
41059 CCAGACCTCAGACAGGTCTTT
1 TC-GACCTCAGACAGGTCTTT
41080 CTCAAATTTT
Statistics
Matches: 99, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
96 7 0.07
97 18 0.18
98 26 0.26
99 48 0.48
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.34
Consensus pattern (96 bp):
TCGACCTCAGACAGGTCTTTATCTTTCAGTTCCAGAAAACAAACAGGTCTTTCTCAGTTTAAATA
TCGACCTCAAACAGGCCTTTATCTTTCAATT
Found at i:41034 original size:65 final size:65
Alignment explanation
Indices: 40946--41083 Score: 206
Period size: 65 Copynumber: 2.1 Consensus size: 65
40936 TCAGACATGC
* *
40946 CTTTCTCAGTTTTAATTTCGACCTCAGACAGGTCTTTATCTTTCAGTTCCAGAAAACAAACAGGT
1 CTTTCTCAGTTTAAATTTCGACCTCAAACAGGTCTTTATCTTTCAGTTCCAGAAAACAAACAGGT
*** *
41011 CTTTCTCAGTTTAAATCTT-GACCTCAAACAGGTCTTTATCTTTCAGTTCCAGACCTCAGACAGG
1 CTTTCTCAGTTTAAAT-TTCGACCTCAAACAGGTCTTTATCTTTCAGTTCCAGAAAACAAACAGG
41075 T
65 T
41076 CTTTCTCA
1 CTTTCTCA
41084 AATTTTAATA
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
65 64 0.97
66 2 0.03
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.36
Consensus pattern (65 bp):
CTTTCTCAGTTTAAATTTCGACCTCAAACAGGTCTTTATCTTTCAGTTCCAGAAAACAAACAGGT
Found at i:41044 original size:33 final size:33
Alignment explanation
Indices: 40898--41047 Score: 99
Period size: 33 Copynumber: 4.5 Consensus size: 33
40888 TTCAGTTCCA
* * * *
40898 GACCTCACACAGGTCTTTCTCAAGTTTTAATATC
1 GACCTCAAACAGGTCTTTCTC-AGTTTAAATCTT
* * * *
40932 GACCTCAGACATGCCTTTCTCAGTTTTAAT-TT
1 GACCTCAAACAGGTCTTTCTCAGTTTAAATCTT
* * ** **
40964 CGACCTCAGACAGGTCTTTATC--TTTCAGTTCCA
1 -GACCTCAAACAGGTCTTTCTCAGTTT-AAATCTT
***
40997 GAAAACAAACAGGTCTTTCTCAGTTTAAATCTT
1 GACCTCAAACAGGTCTTTCTCAGTTTAAATCTT
41030 GACCTCAAACAGGTCTTT
1 GACCTCAAACAGGTCTTT
41048 ATCTTTCAGT
Statistics
Matches: 87, Mismatches: 24, Indels: 11
0.71 0.20 0.09
Matches are distributed among these distances:
31 3 0.03
32 18 0.21
33 45 0.52
34 21 0.24
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (33 bp):
GACCTCAAACAGGTCTTTCTCAGTTTAAATCTT
Found at i:41074 original size:32 final size:33
Alignment explanation
Indices: 40866--41083 Score: 153
Period size: 32 Copynumber: 6.7 Consensus size: 33
40856 TCGAAGCATC
* * *
40866 GACCTCAGACAGCTCTCTCTC-TTTCAGTTCCA
1 GACCTCAGACAGGTCTTTCTCATTTCAATTCCA
* *
40898 GACCTCACACAGGTCTTTCTCAAGTTTTAATAT-C-
1 GACCTCAGACAGGTCTTTCTC-A-TTTCAAT-TCCA
* * * *
40932 GACCTCAGACATGCCTTTCTCAGTTTTAATTTC-
1 GACCTCAGACAGGTCTTTCTCA-TTTCAATTCCA
* *
40965 GACCTCAGACAGGTCTTTATC-TTTCAGTTCCA
1 GACCTCAGACAGGTCTTTCTCATTTCAATTCCA
*** * * **
40997 GAAAACAAACAGGTCTTTCTCAGTTT-AAATCTT
1 GACCTCAGACAGGTCTTTCTCA-TTTCAATTCCA
* * *
41030 GACCTCAAACAGGTCTTTATC-TTTCAGTTCCA
1 GACCTCAGACAGGTCTTTCTCATTTCAATTCCA
41062 GACCTCAGACAGGTCTTTCTCA
1 GACCTCAGACAGGTCTTTCTCA
41084 AATTTTAATA
Statistics
Matches: 143, Mismatches: 33, Indels: 19
0.73 0.17 0.10
Matches are distributed among these distances:
31 10 0.07
32 57 0.40
33 48 0.34
34 21 0.15
35 6 0.04
36 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.34
Consensus pattern (33 bp):
GACCTCAGACAGGTCTTTCTCATTTCAATTCCA
Found at i:41107 original size:53 final size:52
Alignment explanation
Indices: 41044--41144 Score: 166
Period size: 53 Copynumber: 1.9 Consensus size: 52
41034 TCAAACAGGT
41044 CTTTATCTTTCAGTTCCAGACCTCAGACAGGTCTTTCTCAAATTTTAATAGGA
1 CTTTATCTTTCAGTTCCAGACCTCAGACAGGTCTTTCTC-AATTTTAATAGGA
* * *
41097 CTTTATCTTTCAGTTCCAGACCTTAGACATGTCTTTCTCAGTTTTAAT
1 CTTTATCTTTCAGTTCCAGACCTCAGACAGGTCTTTCTCAATTTTAAT
41145 TTTGACCTCA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 8 0.18
53 37 0.82
ACGTcount: A:0.24, C:0.23, G:0.12, T:0.42
Consensus pattern (52 bp):
CTTTATCTTTCAGTTCCAGACCTCAGACAGGTCTTTCTCAATTTTAATAGGA
Found at i:41465 original size:154 final size:153
Alignment explanation
Indices: 41158--43085 Score: 3045
Period size: 154 Copynumber: 12.5 Consensus size: 153
41148 GACCTCAGAC
* *
41158 AATGGTTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGAGGA
1 AATGATTATAGTTAGGCCATAAACAATGGAAAG-AAAGCATTGAGGGTTGCCAAATCGAAGACGA
* * *
41223 TTCAAAATGGAACTAAT--GCCCCGATAGGTCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAC
65 TTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAAC
41286 TTCACAGTGGACTAATCTCACCAA
130 TTCACAGTGGACTAATCTCACCAA
* *
41310 AATTATTATAGTTAGGCGATAAACAATGGAAAGAGAAGCATTGAGGGTTGCCAAATCGAAGACGA
1 AATGATTATAGTTAGGCCATAAACAATGGAAAGA-AAGCATTGAGGGTTGCCAAATCGAAGACGA
** *
41375 TTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAC
65 TTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAAC
41440 TTCACAGTGGACTAATCTCACCAA
130 TTCACAGTGGACTAATCTCACCAA
* * *
41464 AATGATTACAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGCGTTGCCAAATCGAAGACAA
1 AATGATTATAGTTAGGCCATAAACAATGGAAAG-AAAGCATTGAGGGTTGCCAAATCGAAGACGA
** * * *
41529 TTCAAAACGGAACTAATGGGCCCTAATAGGCAC-AAATAAAAAAGTGTTGCAAATTAGCTAAAAA
65 TTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAAT-AAAAAGTGTTCCAAATGAGCTAAAAA
*
41593 CTTCACACTGGACTAATCTCACCAA
129 CTTCACAGTGGACTAATCTCACCAA
* *
41618 AATGAATATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGATTGCCAAATCGAAGACGA
1 AATGATTATAGTTAGGCCATAAACAATGGAAAG-AAAGCATTGAGGGTTGCCAAATCGAAGACGA
* * * *
41683 TTCAAAACGGAACTAATGAGCCCCGATAGGCCTAAAATAAAAAGTGTTCCAATTTAGCTAAAAAC
65 TTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAAC
*
41748 TTCACAATGGACTAATCTCACCAA
130 TTCACAGTGGACTAATCTCACCAA
* * *
41772 AATTATTACAGTTAGGCCATAAACAATGGAAAGAGAAGCATTAAGGGTTGCCAAATCGAAGACGA
1 AATGATTATAGTTAGGCCATAAACAATGGAAAGA-AAGCATTGAGGGTTGCCAAATCGAAGACGA
* *
41837 TTCAAAACGGAACTAATGAGCCCCGATAGGCACAAAATAAAAAGTGTTCCAAATGAGCTAAAAAC
65 TTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAAC
41902 TTCACAGTGGACTAATCTCACCAA
130 TTCACAGTGGACTAATCTCACCAA
41926 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAGCATTGAGGGTTGCCAAATCGAAGACGAT
1 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAGCATTGAGGGTTGCCAAATCGAAGACGAT
**
41991 TCAAAACGGAACTAATGGGCCCCGATAGATCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACT
66 TCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACT
*
42056 TCACAGTGCACTAATCTCACCAA
131 TCACAGTGGACTAATCTCACCAA
42079 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAGCATTGAGGGTTGCCAAATCGAAGACGAT
1 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAGCATTGAGGGTTGCCAAATCGAAGACGAT
**
42144 TCAAAACGGAACTAATGGGCCCCGATAGATCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACT
66 TCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACT
* *
42209 TCAAAGTGCACTAATCTCACCAA
131 TCACAGTGGACTAATCTCACCAA
42232 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAGCATTGAGGGTTGCCAAATCGAAGACGAT
1 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAGCATTGAGGGTTGCCAAATCGAAGACGAT
* * * *
42297 TCAAAACGGAACTAATGGTCCCCGATAGGCACAAAATAAAAAGTGTTTCAAATTAGCTAAAAACT
66 TCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACT
*
42362 TCACAGTGGACTAATCTCAACAA
131 TCACAGTGGACTAATCTCACCAA
* * *
42385 AATGATTATAGTTAGGCTATAAACAATGGAAAGAAAGCATTGAGGGTTGCCAAATCGATGATGAT
1 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAGCATTGAGGGTTGCCAAATCGAAGACGAT
** * * *
42450 TCAAAACGTCACTAATGGGCCCCGATTGGCCCAAAATAAAAAGTGTTGCGAATGAGCTAAAAACT
66 TCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACT
*
42515 TCACAGAGGACTAATCTCACCAA
131 TCACAGTGGACTAATCTCACCAA
* * * *
42538 AATGATTACACTTATGCCAAAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGA
1 AATGATTATAGTTAGGCCATAAACAATGGAAAG-AAAGCATTGAGGGTTGCCAAATCGAAGACGA
* * * *
42603 TACAAAACGGAACTAATGGGCCCCGATAGGCACAAAATAAAAAGTGTTACAAATTAGCTAAAAAC
65 TTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAAC
42668 TTCACAGTGGACTAATCTCACCAA
130 TTCACAGTGGACTAATCTCACCAA
* *
42692 AATTATTATAGTTAGGCCATAAACAATGGAAAGAAAGCATTGAGGGTTGCCAAATCCAAGACGAT
1 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAGCATTGAGGGTTGCCAAATCGAAGACGAT
** * * * *
42757 TCAAAACGTCACTAATGGGCCCCGATAGGCCTAAAATAAAAAGTGTTCTAATTTAGCTAAAAACT
66 TCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACT
** *
42822 TCACAACGGACTAATTTCACCAA
131 TCACAGTGGACTAATCTCACCAA
*
42845 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATAT-AGGGTTGCTAAATCGAAGACG
1 AATGATTATAGTTAGGCCATAAACAATGGAAAG-AAAGCAT-TGAGGGTTGCCAAATCGAAGACG
* *
42909 ATTCAAAACGGAACTAATGGGCCCCGATAGGCACAAAATAAAAAGTGTTCCAAATTAGCTAAAAA
64 ATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAA
42974 CTTCACAGTGGACTAATCTCACCAA
129 CTTCACAGTGGACTAATCTCACCAA
*
42999 AATGATTATAGTTAGGCCATAAACAATGGAAATAAAGCATTGAGGGTTGCCAAATCGAAGACGAC
1 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAGCATTGAGGGTTGCCAAATCGAAGACGA-
43064 TTACGAAAACGGAACTAATGGG
65 TT-C-AAAACGGAACTAATGGG
43086 GGCCC
Statistics
Matches: 1639, Mismatches: 123, Indels: 24
0.92 0.07 0.01
Matches are distributed among these distances:
151 1 0.00
152 74 0.05
153 750 0.46
154 790 0.48
155 7 0.00
156 17 0.01
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (153 bp):
AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAGCATTGAGGGTTGCCAAATCGAAGACGAT
TCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACT
TCACAGTGGACTAATCTCACCAA
Found at i:42723 original size:307 final size:307
Alignment explanation
Indices: 41158--43085 Score: 3080
Period size: 307 Copynumber: 6.3 Consensus size: 307
41148 GACCTCAGAC
* *
41158 AATGGTTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGAGGA
1 AATGATTATAGTTAGGCCATAAACAATGGAAAG-AAAGCATTGAGGGTTGCCAAATCGAAGACGA
* * *
41223 TTCAAAATGGAACTAAT--GCCCCGATAGGTCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAC
65 TTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAAC
* * *
41286 TTCACAGTGGACTAATCTCACCAAAATTATTATAGTTAGGCGATAAACAATGGAAAGAGAAGCAT
130 TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT
** * *
41351 TGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAAC
195 TGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCACAAAATAAA
*
41416 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
260 AAGTGTTCCAAATTAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
* * *
41464 AATGATTACAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGCGTTGCCAAATCGAAGACAA
1 AATGATTATAGTTAGGCCATAAACAATGGAAAG-AAAGCATTGAGGGTTGCCAAATCGAAGACGA
** * * *
41529 TTCAAAACGGAACTAATGGGCCCTAATAGGCAC-AAATAAAAAAGTGTTGCAAATTAGCTAAAAA
65 TTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAAT-AAAAAGTGTTCCAAATGAGCTAAAAA
* *
41593 CTTCACACTGGACTAATCTCACCAAAATGAATATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
129 CTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
* *
41658 TTGAGGATTGCCAAATCGAAGACGATTCAAAACGGAACTAATGAGCCCCGATAGGC-CTAAAATA
194 TTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCAC-AAAATA
* *
41722 AAAAGTGTTCCAATTTAGCTAAAAACTTCACAATGGACTAATCTCACCAA
258 AAAAGTGTTCCAAATTAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
* * *
41772 AATTATTACAGTTAGGCCATAAACAATGGAAAGAGAAGCATTAAGGGTTGCCAAATCGAAGACGA
1 AATGATTATAGTTAGGCCATAAACAATGGAAAGA-AAGCATTGAGGGTTGCCAAATCGAAGACGA
* *
41837 TTCAAAACGGAACTAATGAGCCCCGATAGGCACAAAATAAAAAGTGTTCCAAATGAGCTAAAAAC
65 TTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAAC
41902 TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG-AAAGCAT
130 TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT
*
41966 TGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGATC-CAAAATAA
195 TGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAG-GCACAAAATAA
* *
42030 AAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGCACTAATCTCACCAA
259 AAAGTGTTCCAAATTAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
42079 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAGCATTGAGGGTTGCCAAATCGAAGACGAT
1 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAGCATTGAGGGTTGCCAAATCGAAGACGAT
**
42144 TCAAAACGGAACTAATGGGCCCCGATAGATCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACT
66 TCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACT
* *
42209 TCAAAGTGCACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG-AAAGCATT
131 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT
*
42273 GAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGTCCCCGATAGGCACAAAATAAAA
196 GAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCACAAAATAAAA
* *
42338 AGTGTTTCAAATTAGCTAAAAACTTCACAGTGGACTAATCTCAACAA
261 AGTGTTCCAAATTAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
* * *
42385 AATGATTATAGTTAGGCTATAAACAATGGAAAGAAAGCATTGAGGGTTGCCAAATCGATGATGAT
1 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAGCATTGAGGGTTGCCAAATCGAAGACGAT
** * * *
42450 TCAAAACGTCACTAATGGGCCCCGATTGGCCCAAAATAAAAAGTGTTGCGAATGAGCTAAAAACT
66 TCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACT
* * * * *
42515 TCACAGAGGACTAATCTCACCAAAATGATTACACTTATGCCAAAAACAATGGAAAGAAAAGCATT
131 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT
*
42580 GAGGGTTGCCAAATCGAAGACGATACAAAACGGAACTAATGGGCCCCGATAGGCACAAAATAAAA
196 GAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCACAAAATAAAA
*
42645 AGTGTTACAAATTAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
261 AGTGTTCCAAATTAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
* *
42692 AATTATTATAGTTAGGCCATAAACAATGGAAAGAAAGCATTGAGGGTTGCCAAATCCAAGACGAT
1 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAGCATTGAGGGTTGCCAAATCGAAGACGAT
** * * * *
42757 TCAAAACGTCACTAATGGGCCCCGATAGGCCTAAAATAAAAAGTGTTCTAATTTAGCTAAAAACT
66 TCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACT
** *
42822 TCACAACGGACTAATTTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATA
131 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT-
*
42887 T-AGGGTTGCTAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCACAAAATAAA
195 TGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCACAAAATAAA
42951 AAGTGTTCCAAATTAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
260 AAGTGTTCCAAATTAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
*
42999 AATGATTATAGTTAGGCCATAAACAATGGAAATAAAGCATTGAGGGTTGCCAAATCGAAGACGAC
1 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAGCATTGAGGGTTGCCAAATCGAAGACGA-
43064 TTACGAAAACGGAACTAATGGG
65 TT-C-AAAACGGAACTAATGGG
43086 GGCCC
Statistics
Matches: 1502, Mismatches: 107, Indels: 22
0.92 0.07 0.01
Matches are distributed among these distances:
305 1 0.00
306 502 0.33
307 608 0.40
308 371 0.25
309 5 0.00
310 15 0.01
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (307 bp):
AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAGCATTGAGGGTTGCCAAATCGAAGACGAT
TCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACT
TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT
GAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCACAAAATAAAA
AGTGTTCCAAATTAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
Done.