Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013143.1 Corchorus olitorius cultivar O-4 contig13176, 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: 76444
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:554 original size:21 final size:21
Alignment explanation
Indices: 530--600 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
520 CTTAGGCAAT
*
530 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
551 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
572 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
593 TCCAATGA
1 TCCAATGA
601 TCTCCTAGCA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 3 0.06
21 45 0.94
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:12594 original size:2 final size:2
Alignment explanation
Indices: 12589--12619 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12579 GCCCAAAAAA
12589 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
12620 ATTACCTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:13088 original size:12 final size:11
Alignment explanation
Indices: 13067--13096 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
13057 ACGTATATAG
13067 TTTTTTTGTTT
1 TTTTTTTGTTT
13078 TTTTGTTTGTTT
1 TTTT-TTTGTTT
13090 TTTTTTT
1 TTTTTTT
13097 TCAATCAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:15551 original size:42 final size:42
Alignment explanation
Indices: 15505--15599 Score: 145
Period size: 42 Copynumber: 2.3 Consensus size: 42
15495 ATAGATATAG
*
15505 ATTAAACAACATTTAAAGCATTCTATGTTTACTTTCACATTA
1 ATTAAACAACATTTAAAGCATTCTATATTTACTTTCACATTA
* ** *
15547 ATTAAACAACTTTTAATTCATTCTATATTTACTTTCACCTTA
1 ATTAAACAACATTTAAAGCATTCTATATTTACTTTCACATTA
15589 ATTAAACAACA
1 ATTAAACAACA
15600 AAAATACAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.39, C:0.18, G:0.02, T:0.41
Consensus pattern (42 bp):
ATTAAACAACATTTAAAGCATTCTATATTTACTTTCACATTA
Found at i:25739 original size:15 final size:15
Alignment explanation
Indices: 25719--25763 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
25709 TAAATGTGTC
*
25719 TCGTGTCGTGTCGTG
1 TCGTGTCGTGTCATG
25734 TCGTGTCGTGTCATG
1 TCGTGTCGTGTCATG
* *
25749 TTGTGTCATGTCATG
1 TCGTGTCGTGTCATG
25764 ACCTGAATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.07, C:0.18, G:0.33, T:0.42
Consensus pattern (15 bp):
TCGTGTCGTGTCATG
Found at i:25763 original size:5 final size:5
Alignment explanation
Indices: 25719--25760 Score: 57
Period size: 5 Copynumber: 8.4 Consensus size: 5
25709 TAAATGTGTC
* * *
25719 TCGTG TCGTG TCGTG TCGTG TCGTG TCATG TTGTG TCATG TC
1 TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG TC
25761 ATGACCTGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.05, C:0.19, G:0.33, T:0.43
Consensus pattern (5 bp):
TCGTG
Found at i:41406 original size:110 final size:110
Alignment explanation
Indices: 41272--41486 Score: 376
Period size: 110 Copynumber: 2.0 Consensus size: 110
41262 CTAGTTGATG
** * *
41272 ATATGAATTTATTATTGGTCTTTGATAATTGTGCATTCAAGAATTGGTGCTTTGTGGATTTAATT
1 ATATGAATCCATTATTGGTCTTTGATAATTATGCATTCAAGAATTGGTGCTTTGTGGATTTAAGT
41337 TTCCATAGAATTTCTAGTGCAAATAATGCTCAATCAGAATTCATA
66 TTCCATAGAATTTCTAGTGCAAATAATGCTCAATCAGAATTCATA
*
41382 ATATGAATCCATTATTGGTCTTTGATAATTATGCATTCAAGAATTGGTGCTTTGTGGATTTGAGT
1 ATATGAATCCATTATTGGTCTTTGATAATTATGCATTCAAGAATTGGTGCTTTGTGGATTTAAGT
*
41447 TTCCATAGAATTTCTAGTGCAAATAATGCTCATTCAGAAT
66 TTCCATAGAATTTCTAGTGCAAATAATGCTCAATCAGAAT
41487 GATAAGATGA
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
110 99 1.00
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (110 bp):
ATATGAATCCATTATTGGTCTTTGATAATTATGCATTCAAGAATTGGTGCTTTGTGGATTTAAGT
TTCCATAGAATTTCTAGTGCAAATAATGCTCAATCAGAATTCATA
Found at i:45472 original size:31 final size:31
Alignment explanation
Indices: 45424--45494 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
45414 TGCCCTTAAT
*
45424 TAAACTCTTAAACTTTTGTCTTTTTGCCCCC
1 TAAACTCTTAAACTTTTGTCATTTTGCCCCC
* * *
45455 TAAACTTTTACAA-TTTTGTCATTTTGTCTCC
1 TAAACTCTTA-AACTTTTGTCATTTTGCCCCC
45486 TAAATCTCT
1 TAAA-CTCT
45495 ATTTTTGATA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
31 28 0.85
32 5 0.15
ACGTcount: A:0.23, C:0.24, G:0.06, T:0.48
Consensus pattern (31 bp):
TAAACTCTTAAACTTTTGTCATTTTGCCCCC
Found at i:49814 original size:14 final size:14
Alignment explanation
Indices: 49795--49827 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
49785 CCCACCTACC
*
49795 AAATACAAAGTGAA
1 AAATACAAAGGGAA
49809 AAATACAAAGGGAA
1 AAATACAAAGGGAA
49823 AAATA
1 AAATA
49828 AAAAATTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.67, C:0.06, G:0.15, T:0.12
Consensus pattern (14 bp):
AAATACAAAGGGAA
Found at i:50131 original size:75 final size:75
Alignment explanation
Indices: 49954--50153 Score: 238
Period size: 75 Copynumber: 2.7 Consensus size: 75
49944 ACTAATAAAT
* * ** * * *
49954 TGAGAAAAAATCAAAACGGGGCGAAAAAAATCTCCAACATTAAAATTTGATGGGAGCTATCAGTA
1 TGAGAAAAGACCAAAACGGGGCGAAAAGGATCTCCAACGTTAAAAGTTGAAGGGAGCTATCAGTA
*
50019 AATTCCAGAG
66 AATTCCAAAG
* * * **
50029 TGAGAAAAGACCAAAACGTGGCGAAAAGGCTCTCCCACGTTAAAAGTTGAAGGGAGCTATTGGTA
1 TGAGAAAAGACCAAAACGGGGCGAAAAGGATCTCCAACGTTAAAAGTTGAAGGGAGCTATCAGTA
*
50094 AATTTCAAAG
66 AATTCCAAAG
* ** *
50104 TGAGAAAAGACCAAAACGGGGCGAAAAGGTTCTCTTATGTTAAAAGTTGA
1 TGAGAAAAGACCAAAACGGGGCGAAAAGGATCTCCAACGTTAAAAGTTGA
50154 TGAGAGCCTT
Statistics
Matches: 106, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
75 106 1.00
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.20
Consensus pattern (75 bp):
TGAGAAAAGACCAAAACGGGGCGAAAAGGATCTCCAACGTTAAAAGTTGAAGGGAGCTATCAGTA
AATTCCAAAG
Found at i:50605 original size:2 final size:2
Alignment explanation
Indices: 50598--50655 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
50588 TATTCTCATA
50598 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
50640 TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC
50656 CAATTCGCTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:51815 original size:74 final size:74
Alignment explanation
Indices: 51727--52209 Score: 623
Period size: 74 Copynumber: 6.4 Consensus size: 74
51717 AAAACATTAA
* *
51727 ATCATTTTACATGCATGGTCAAACCCCAAAGGTTGATGGTCAAACCCCAAAATTCAATAGTCAAA
1 ATCATTGTACATGCATGGTCAAACCCCAAAGGATGATGGTCAAACCCCAAAATTCAATAGTCAAA
51792 CCACAAAAC
66 CCACAAAAC
51801 ATCATTGTACATGCATGGTCAAACCCCAAAGGATGATGGTCAAACCCCAAAATTCAATAGTCAAA
1 ATCATTGTACATGCATGGTCAAACCCCAAAGGATGATGGTCAAACCCCAAAATTCAATAGTCAAA
*
51866 CTACAAAAC
66 CCACAAAAC
* *
51875 ATTATTGTACATGCATGGTCAAACCCCAAAGGAT-ATTGGTCAAAGCCCAAAATTCAATAGTCAA
1 ATCATTGTACATGCATGGTCAAACCCCAAAGGATGA-TGGTCAAACCCCAAAATTCAATAGTCAA
*
51939 ACCACAAAAT
65 ACCACAAAAC
*
51949 ATCATTGTACATGCATGGTCAAACCCCAAAGGATGATGGTCAAACCCCAAATTTCAATAGTCAAA
1 ATCATTGTACATGCATGGTCAAACCCCAAAGGATGATGGTCAAACCCCAAAATTCAATAGTCAAA
52014 CCACAAAAC
66 CCACAAAAC
* * * *
52023 ATCATTGTACATGCATGGTCAAACCCCAAA--ATTCAATAGTCAAACCACAAAATATTATTATAC
1 ATCATTGTACATGCATGGTCAAACCCCAAAGGA-T-GATGGTCAAACCCCAAAAT-TCA--ATA-
* * * *
52086 ATGCATAGTCAAGCATTAA-
60 GT-CA-A-ACCA-CA-AAAC
* * * * *
52105 ATCATTCTGCATGCATGGTCAAATCCCAAAGGATGATGTTCAAATCCCAAAATTCAATAGTCAAA
1 ATCATTGTACATGCATGGTCAAACCCCAAAGGATGATGGTCAAACCCCAAAATTCAATAGTCAAA
*
52170 CCATAAAAC
66 CCACAAAAC
*
52179 ATCATTGTACATGCATGGTTAAACCCTCAAA
1 ATCATTGTACATGCATGGTCAAACCC-CAAA
52210 TTCAATAGTC
Statistics
Matches: 354, Mismatches: 38, Indels: 33
0.83 0.09 0.08
Matches are distributed among these distances:
72 1 0.00
73 4 0.01
74 275 0.78
75 9 0.03
76 1 0.00
77 5 0.01
78 2 0.01
79 5 0.01
80 1 0.00
81 4 0.01
82 43 0.12
83 3 0.01
84 1 0.00
ACGTcount: A:0.41, C:0.23, G:0.12, T:0.23
Consensus pattern (74 bp):
ATCATTGTACATGCATGGTCAAACCCCAAAGGATGATGGTCAAACCCCAAAATTCAATAGTCAAA
CCACAAAAC
Found at i:51944 original size:148 final size:147
Alignment explanation
Indices: 51625--52209 Score: 631
Period size: 148 Copynumber: 3.8 Consensus size: 147
51615 TTGTTCATGC
* ** * **
51625 ATAGTCAAACCACAAAAAAACATCATTGTACATGCATGATCAAACCATAAAGGATAATTTTCAAA
1 ATAGTCAAACCAC---AAAACATCATTGTACATGCATGGTCAAACCCCAAAGGATGATGGTCAAA
* ** *
51690 -CTCAAAAGTTTGATAGTCAAACCACAAAAAACATTAAATCATTTTACATGCATGGTCAAACCCC
63 CCCCAAAA-TTCAATAGTCAAACCAC--AAAAC-----ATCATTGTACATGCATGGTCAAACCCC
* *
51754 AAAGGTTGATGGTCAAACCCCAAAATTCA
120 AAAGGATCATGGTCAAA-CCCAAAATTCA
51783 ATAGTCAAACCACAAAACATCATTGTACATGCATGGTCAAACCCCAAAGGATGATGGTCAAACCC
1 ATAGTCAAACCACAAAACATCATTGTACATGCATGGTCAAACCCCAAAGGATGATGGTCAAACCC
* *
51848 CAAAATTCAATAGTCAAACTACAAAACATTATTGTACATGCATGGTCAAACCCCAAAGGAT-ATT
66 CAAAATTCAATAGTCAAACCACAAAACATCATTGTACATGCATGGTCAAACCCCAAAGGATCA-T
51912 GGTCAAAGCCCAAAATTCA
130 GGTCAAA-CCCAAAATTCA
*
51931 ATAGTCAAACCACAAAATATCATTGTACATGCATGGTCAAACCCCAAAGGATGATGGTCAAACCC
1 ATAGTCAAACCACAAAACATCATTGTACATGCATGGTCAAACCCCAAAGGATGATGGTCAAACCC
*
51996 CAAATTTCAATAGTCAAACCACAAAACATCATTGTACATGCATGGTCAAACCCCAAA--ATTCAA
66 CAAAATTCAATAGTCAAACCACAAAACATCATTGTACATGCATGGTCAAACCCCAAAGGA-TC-A
* *
52059 TAGTCAAACCACAAAATATTA
129 TGGTCAAACC-CAAAAT-TCA
* * * * * * * *
52080 TTATACATGCATAGTCAAGCATTAA-ATCATTCTGCATGCATGGTCAAATCCCAAAGGATGATGT
1 --ATA-GT-CA-A-ACCA-CA-AAACATCATTGTACATGCATGGTCAAACCCCAAAGGATGATGG
* * *
52144 TCAAATCCCAAAATTCAATAGTCAAACCATAAAACATCATTGTACATGCATGGTTAAACCCTCAA
58 TCAAACCCCAAAATTCAATAGTCAAACCACAAAACATCATTGTACATGCATGGTCAAACCC-CAA
52209 A
122 A
52210 TTCAATAGTC
Statistics
Matches: 379, Mismatches: 32, Indels: 33
0.85 0.07 0.07
Matches are distributed among these distances:
146 1 0.00
147 4 0.01
148 181 0.48
149 3 0.01
151 3 0.01
152 1 0.00
153 7 0.02
154 1 0.00
155 59 0.16
156 100 0.26
157 6 0.02
158 13 0.03
ACGTcount: A:0.43, C:0.23, G:0.12, T:0.23
Consensus pattern (147 bp):
ATAGTCAAACCACAAAACATCATTGTACATGCATGGTCAAACCCCAAAGGATGATGGTCAAACCC
CAAAATTCAATAGTCAAACCACAAAACATCATTGTACATGCATGGTCAAACCCCAAAGGATCATG
GTCAAACCCAAAATTCA
Found at i:52044 original size:53 final size:53
Alignment explanation
Indices: 51984--52262 Score: 232
Period size: 53 Copynumber: 5.3 Consensus size: 53
51974 CCAAAGGATG
*
51984 ATGGTCAAACCCCAAATTTCAATAGTCAAACCACAAAACATCATTGTACATGC
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACATCATTGTACATGC
* * *
52037 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAATATTATTATACATGC
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACATCATTGTACATGC
* * *** * **** * * ** *
52090 ATAGTCAAGCATTAAATCATTCTGCAT-G-C-ATGGTCAAATC-CCAAAG--GATG-
1 ATGGTCAAACCCCAAA--ATTC--AATAGTCAAACCACAAAACATCATTGTACATGC
* * *
52140 ATGTTCAAATCCCAAAATTCAATAGTCAAACCATAAAACATCATTGTACATGC
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACATCATTGTACATGC
* *
52193 ATGGTTAAACCCTC-AAATTCAATAGTCAAACCACAAAATATCATTGTACATGC
1 ATGGTCAAACCC-CAAAATTCAATAGTCAAACCACAAAACATCATTGTACATGC
*
52246 ATAGTCAAACCCCAAAA
1 ATGGTCAAACCCCAAAA
52263 GATGATGGTC
Statistics
Matches: 166, Mismatches: 47, Indels: 26
0.69 0.20 0.11
Matches are distributed among these distances:
46 2 0.01
47 1 0.01
48 5 0.03
49 5 0.03
50 12 0.07
51 3 0.02
52 4 0.02
53 120 0.72
54 6 0.04
55 5 0.03
56 1 0.01
57 2 0.01
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.24
Consensus pattern (53 bp):
ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACATCATTGTACATGC
Found at i:52162 original size:156 final size:156
Alignment explanation
Indices: 51949--52253 Score: 504
Period size: 156 Copynumber: 2.0 Consensus size: 156
51939 ACCACAAAAT
* *
51949 ATCATTGTACATGCATGGTCAAACCCCAAAGGATGATGGTCAAACCCCAAATTTCAATAGTCAAA
1 ATCATTCTACATGCATGGTCAAACCCCAAAGGATGATGGTCAAACCCCAAAATTCAATAGTCAAA
52014 CCACAAAACATCATTGTACATGCATGGTCAAACCC-CAAAATTCAATAGTCAAACCACAAAATAT
66 CCACAAAACATCATTGTACATGCATGGTCAAACCCTC-AAATTCAATAGTCAAACCACAAAATAT
*
52078 TATTATACATGCATAGTCAAGCATTAA
130 CATTATACATGCATAGTCAAGCATTAA
* * * *
52105 ATCATTCTGCATGCATGGTCAAATCCCAAAGGATGATGTTCAAATCCCAAAATTCAATAGTCAAA
1 ATCATTCTACATGCATGGTCAAACCCCAAAGGATGATGGTCAAACCCCAAAATTCAATAGTCAAA
* *
52170 CCATAAAACATCATTGTACATGCATGGTTAAACCCTCAAATTCAATAGTCAAACCACAAAATATC
66 CCACAAAACATCATTGTACATGCATGGTCAAACCCTCAAATTCAATAGTCAAACCACAAAATATC
*
52235 ATTGTACATGCATAGTCAA
131 ATTATACATGCATAGTCAA
52254 ACCCCAAAAG
Statistics
Matches: 138, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
156 137 0.99
157 1 0.01
ACGTcount: A:0.41, C:0.23, G:0.11, T:0.25
Consensus pattern (156 bp):
ATCATTCTACATGCATGGTCAAACCCCAAAGGATGATGGTCAAACCCCAAAATTCAATAGTCAAA
CCACAAAACATCATTGTACATGCATGGTCAAACCCTCAAATTCAATAGTCAAACCACAAAATATC
ATTATACATGCATAGTCAAGCATTAA
Found at i:52267 original size:127 final size:130
Alignment explanation
Indices: 52105--52398 Score: 326
Period size: 127 Copynumber: 2.2 Consensus size: 130
52095 CAAGCATTAA
* * * * * * *
52105 ATCATTCTGCATGCATGGTCAAATCCCAAAGGATGATGTTCAAATCCCAAAATTCAATAGTCAAA
1 ATCATTGTACATGCATAGTCAAACCCCAAAAGATGATGGTCAAACCCCAAAATTCAATAGTCAAA
* * * *
52170 CCA-TAAAAC-ATCATTGTACATGCATGGTTAAACCCTC-AAATTCAATAGTCAAACCACAAAAT
66 CCACAAAAACAATCATTGTACATGCACGGTCAAACCCCCAAAATT-AATAGTCAAACCACAAAAT
52232 -
130 C
* *
52232 ATCATTGTACATGCATAGTCAAACCCCAAAAGATGATGGTCAAACCCCAAAGTTCGATAGTCAAA
1 ATCATTGTACATGCATAGTCAAACCCCAAAAGATGATGGTCAAACCCCAAAATTCAATAGTCAAA
* * *
52297 CCACGAAAAACATATCATTGTATATGCACGGTCAAACCCCCAAAAATTGATAGTCAAACCATAAA
66 CCAC-AAAAACA-ATCATTGTACATGCACGGTCAAACCCCC-AAAATTAATAGTCAAACCACAAA
52362 ATGC
128 AT-C
* * *
52366 ATTTTATTGTATATGCATAGTCAAACCACAAAA
1 A--TCATTGTACATGCATAGTCAAACCCCAAAA
52399 AATCATTGTA
Statistics
Matches: 138, Mismatches: 19, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
127 59 0.43
129 5 0.04
131 24 0.17
132 17 0.12
133 5 0.04
134 1 0.01
136 27 0.20
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.24
Consensus pattern (130 bp):
ATCATTGTACATGCATAGTCAAACCCCAAAAGATGATGGTCAAACCCCAAAATTCAATAGTCAAA
CCACAAAAACAATCATTGTACATGCACGGTCAAACCCCCAAAATTAATAGTCAAACCACAAAATC
Found at i:52292 original size:74 final size:77
Alignment explanation
Indices: 52193--52356 Score: 203
Period size: 74 Copynumber: 2.1 Consensus size: 77
52183 TTGTACATGC
* *
52193 ATGGTTAAACCCTCAAATTCAATAGTCAAACCAC-AAA-ATATCATTGTACATGCATAGTCAAA-
1 ATGGTCAAACCCTCAAATTCAATAGTCAAACCACAAAACATATCATTGTACATGCACAGTCAAAC
52255 CCCCAAAAGA-TG
66 CCCCAAAA-ATTG
* * *
52267 ATGGTCAAACCC-CAAAGTTCGATAGTCAAACCACGAAAAACATATCATTGTATATGCACGGTCA
1 ATGGTCAAACCCTCAAA-TTCAATAGTCAAACCAC--AAAACATATCATTGTACATGCACAGTCA
52331 AACCCCCAAAAATTG
63 AACCCCCAAAAATTG
*
52346 ATAGTCAAACC
1 ATGGTCAAACC
52357 ATAAAATGCA
Statistics
Matches: 77, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
73 4 0.05
74 27 0.35
77 3 0.04
78 23 0.30
79 20 0.26
ACGTcount: A:0.42, C:0.24, G:0.12, T:0.21
Consensus pattern (77 bp):
ATGGTCAAACCCTCAAATTCAATAGTCAAACCACAAAACATATCATTGTACATGCACAGTCAAAC
CCCCAAAAATTG
Found at i:52294 original size:21 final size:21
Alignment explanation
Indices: 52246--52298 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
52236 TTGTACATGC
52246 ATAGTCAAACCCCAAAAGATG
1 ATAGTCAAACCCCAAAAGATG
* *
52267 ATGGTCAAACCCC-AAAGTTCG
1 ATAGTCAAACCCCAAAAGAT-G
52288 ATAGTCAAACC
1 ATAGTCAAACC
52299 ACGAAAAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 5 0.18
21 23 0.82
ACGTcount: A:0.42, C:0.26, G:0.15, T:0.17
Consensus pattern (21 bp):
ATAGTCAAACCCCAAAAGATG
Found at i:52375 original size:58 final size:59
Alignment explanation
Indices: 52269--52401 Score: 148
Period size: 58 Copynumber: 2.3 Consensus size: 59
52259 AAAAGATGAT
*
52269 GGTCAAA-CCCC-AAAGTTCGATAGTCAAACCACGAAAAACATATCATTGTATATGCAC
1 GGTCAAACCCCCAAAAATTCGATAGTCAAACCACGAAAAACATATCATTGTATATGCAC
* * * * *
52326 GGTCAAACCCCCAAAAATT-GATAGTCAAACCA-TAAAATGCATTTTATTGTATATGCAT
1 GGTCAAACCCCCAAAAATTCGATAGTCAAACCACGAAAA-ACATATCATTGTATATGCAC
* * *
52384 AGTCAAACCACAAAAAAT
1 GGTCAAACCCCCAAAAAT
52402 CATTGTACAT
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
57 11 0.17
58 48 0.75
59 5 0.08
ACGTcount: A:0.43, C:0.22, G:0.12, T:0.23
Consensus pattern (59 bp):
GGTCAAACCCCCAAAAATTCGATAGTCAAACCACGAAAAACATATCATTGTATATGCAC
Found at i:52446 original size:89 final size:92
Alignment explanation
Indices: 52288--52486 Score: 255
Period size: 89 Copynumber: 2.2 Consensus size: 92
52278 CCAAAGTTCG
*
52288 ATAGTCAAACCACGAAAAACATATCATTGTATATGCACGGTCAAACCCCCAAAAATTGATAGTCA
1 ATAGTCAAACCAC--AAAACATATCATTGTACATGCACGGTCAAACCCCCAAAAATTGATAGTCA
* *
52353 AACCATAAAATGCATTTTATTGTATATGC
64 AACCACAAAAAGCATTTTATTGTATATGC
** *
52382 ATAGTCAAACCACAAAA-A-ATCATTGTACATGCATTGTCAAA-TCCC-AAAATTCGATAGTCAA
1 ATAGTCAAACCACAAAACATATCATTGTACATGCACGGTCAAACCCCCAAAAATT-GATAGTCAA
*
52443 ACCACAAAAAGCATTTTATTGTATGTGC
65 ACCACAAAAAGCATTTTATTGTATATGC
*
52471 AT-GATCAAACCCCAAA
1 ATAG-TCAAACCACAAA
52487 TTTTGATGAT
Statistics
Matches: 95, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
88 7 0.07
89 50 0.53
90 20 0.21
91 1 0.01
92 4 0.04
94 13 0.14
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (92 bp):
ATAGTCAAACCACAAAACATATCATTGTACATGCACGGTCAAACCCCCAAAAATTGATAGTCAAA
CCACAAAAAGCATTTTATTGTATATGC
Found at i:52495 original size:21 final size:21
Alignment explanation
Indices: 52471--52514 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
52461 TTGTATGTGC
52471 ATGATCAAACCCCAAATTTTG
1 ATGATCAAACCCCAAATTTTG
*
52492 ATGATTAAACCCCAAATTTTG
1 ATGATCAAACCCCAAATTTTG
52513 AT
1 AT
52515 AGTCAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (21 bp):
ATGATCAAACCCCAAATTTTG
Found at i:53581 original size:24 final size:25
Alignment explanation
Indices: 53554--53602 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
53544 AAATAAGAAG
53554 TTTGTCCAAAATA-TATATAAATAA
1 TTTGTCCAAAATATTATATAAATAA
*
53578 TTTGTCCAAAATATTATATATATAA
1 TTTGTCCAAAATATTATATAAATAA
53603 ATAGCTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (25 bp):
TTTGTCCAAAATATTATATAAATAA
Found at i:53738 original size:72 final size:72
Alignment explanation
Indices: 53658--53801 Score: 245
Period size: 72 Copynumber: 2.0 Consensus size: 72
53648 CACAAGCAGG
53658 GGAGAGAAGATCAGGTGACGGAAAAACATGGATAAAAAAATTAATTTGACATGTG-GCATGCAAT
1 GGAGAGAAGATCAGGTGACGGAAAAACATGGATAAAAAAATTAATTTGACATGTGAG-ATGCAAT
53722 TATAGGAC
65 TATAGGAC
* **
53730 GGAGAGAAGATCAGGTGAGGGAAAAACATGGATACGAAAATTAATTTGACATGTGAGATGCAATT
1 GGAGAGAAGATCAGGTGACGGAAAAACATGGATAAAAAAATTAATTTGACATGTGAGATGCAATT
53795 ATAGGAC
66 ATAGGAC
53802 CACATCACCC
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
72 67 0.99
73 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.28, T:0.21
Consensus pattern (72 bp):
GGAGAGAAGATCAGGTGACGGAAAAACATGGATAAAAAAATTAATTTGACATGTGAGATGCAATT
ATAGGAC
Found at i:61404 original size:2 final size:2
Alignment explanation
Indices: 61397--61437 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
61387 TATTAACCTC
*
61397 TA TA TA TA TA TA TA TA TA TA CA CTA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA T
61438 TAAGTAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.94
3 1 0.03
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:67878 original size:41 final size:41
Alignment explanation
Indices: 67821--67908 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 41
67811 CAGAAAAAGC
**
67821 CATACATTAAGGTTCATATAACAGGTAATATAGTTCTTAAA
1 CATACATTAAGGTTCATATAACAGGTAATATAGTTCCAAAA
* ** *
67862 CATACATTAAGTTTCATATGTCAGGTGATATAGTTCCAAAA
1 CATACATTAAGGTTCATATAACAGGTAATATAGTTCCAAAA
67903 CATACA
1 CATACA
67909 CGAGTAAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (41 bp):
CATACATTAAGGTTCATATAACAGGTAATATAGTTCCAAAA
Done.